DPRE1 Inhibitor Reference 07-28-2016 230748

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1. N-methylation of a bactericidal compound as a resistance mechanism in Mycobacterium tuberculosis

By Warrier, Thulasi; Kapilashrami, Kanishk; Argyrou, Argyrides; Ioerger, Thomas R.; Little, David; Murphy, Kenan C.;
Nandakumar, Madhumitha; Park, Suna; Gold, Ben; Mi, Jianjie; et al
From Proceedings of the National Academy of Sciences of the United States of America (2016), Ahead of Print.
Language: English, Database: CAPLUS, DOI:10.1073/pnas.1606590113
The rising incidence of antimicrobial resistance (AMR) makes it imperative to understand the underlying mechanisms.
Mycobacterium tuberculosis (Mtb) is the single leading cause of death from a bacterial pathogen and estd. to be the
leading cause of death from AMR. A pyrido-benzimidazole, 14, was reported to have potent bactericidal activity against
Mtb. Here, we isolated multiple Mtb clones resistant to 14. Each had mutations in the putative DNA-binding and
dimerization domains of rv2887, a gene encoding a transcriptional repressor of the MarR family. The mutations in
Rv2887 led to markedly increased expression of rv0560c. We characterized Rv0560c as an S-adenosyl-L-methioninedependent methyltransferase that N-methylates 14, abolishing its mycobactericidal activity. An Mtb strain lacking
rv0560c became resistant to 14 by mutating decaprenylphosphoryl--d-ribose 2-oxidase (DprE1), an essential enzyme in
arabinogalactan synthesis; 14 proved to be a nanomolar inhibitor of DprE1, and methylation of 14 by Rv0560c abrogated
this activity. Thus, 14 joins a growing list of DprE1 inhibitors that are potently mycobactericidal. Bacterial methylation of
an antibacterial agent, 14, catalyzed by Rv0560c of Mtb, is a previously unreported mechanism of AMR.
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Copyright 2016 American Chemical Society (ACS). All Rights Reserved.
2. Synthesis and Antitubercular Activity of New Benzo[b]thiophenes

By Mahajan, Pravin S.; Nikam, Mukesh D.; Nawale, Laxman U.; Khedkar, Vijay M.; Sarkar, Dhiman; Gill, Charansingh
H.
From ACS Medicinal Chemistry Letters (2016), Ahead of Print. Language: English, Database: CAPLUS,
DOI:10.1021/acsmedchemlett.6b00077
In vitro and ex vivo efficacies of four series of
benzo[b]thiophene-2-carboxylic acid derivs. were studied
against Mycobacterium tuberculosis H37Ra (MTB).
Benzo[b]thiophenes were also tested in vitro against multidrug
resistant Mycobacterium tuberculosis H37Ra (MDR-MTB), and
7b was found to be highly active against A- and D-MDRMTB/MTB (MIC ranges 2.73-22.86 g/mL). The activity of all
benzo[b]thiophenes against M. bovis BCG (BCG) was also
assessed grown under aerobic and under conditions of oxygen
depletion. Compds. 8c and 8g showed significant activity with
MICs of 0.60 and 0.61 g/mL against dormant BCG. The low
cytotoxicity and high selectivity index data against human
cancer cell lines, HeLa, Panc-1, and THP-1 indicate the
potential importance of the development of benzo[b]thiophenebased 1,3-diketones and flavones as lead candidates to treat
mycobacterial infections. Mol. docking studies into the active
site of DprE1 (Decaprenylphosphoryl--D-ribose-2'-epimerase)
enzyme revealed a similar binding mode to native ligand in the
crystal structure thereby helping to understand the ligandprotein interactions and establish a structural basis for inhibition
of MTB. In summary, its good activity in in vitro and ex vivo
model, as well as its activity against multidrug-resistant M.
tuberculosis H37Ra in a potentially latent state, makes 7b an
attractive drug candidate for the therapy of tuberculosis.
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3. Molecular docking studies of chalcone derivatives with decaprenylphosphoryl-d-ribose oxidase (DprE1) as

target protein
By Prasath, M.; Srinivasan, T.; Balaji, R. Arun; Revathy, R.
From Journal of Chemical and Pharmaceutical Research (2015), 7(11), 894-901. Language: English, Database:
CAPLUS
In Structure Based Drug Designing (SBDD), mol. docking is routinely used for understanding drug receptor interaction.
In this communication, three chalcone derivs. were synthesized and the entire three chalcone moieties were
characterized using singe crystal X-ray diffraction and reported. Chalcone deriv. possesses good anti-tubercular activity,
so it was docked against Decaprenylphosphoryl-d-ribose Oxidase (DprE1) as target protein. The in silico studies show
that the three chalcone compds. having min. binding energy and have good affinity toward the active pocket, thus, they
may be considered as good inhibitor of DprE1.
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4. Synthesis and docking studies of pyrazine-thiazolidinone hybrid scaffold targeting dormant tuberculosis
By Chitre, T. S.; Asgaonkar, K. D.; Miniyar, P. B.; Dharme, A. B.; Arkile, M. A.; Yeware, A.; Sarkar, D.; Khedkar, V. M.;
Jha, P. C.
From Bioorganic & Medicinal Chemistry Letters (2016), 26(9), 2224-2228. Language: English, Database: CAPLUS,
DOI:10.1016/j.bmcl.2016.03.055
The persistence of Mycobacterium tuberculosis (MTB) in dormant stage assists the pathogen to develop resistance
against current antimycobactrial drugs. To address this issue, the authors report herein the synthesis of N-(4-oxo-2substituted-thiazolidin-3-yl)pyrazine-2-carbohydrazide derivs. designed by following the mol. hybridization approach
using pyrazine and thiazolidinone scaffolds. The compds. were evaluated against MTB H37Ra and Mycobacterium bovis
BCG in dormancy model. Most of the compds. had IC50 values in 0.3-1 g/mL range. The active compds. were further
tested for antiproliferative activity against THP-1, Panc-1, A549, and MCF-7 cell lines using MTT assay and exhibited no
significant cytotoxicity. The authors also report mol. docking studies using active analogs and MTB decaprenylphosphoryl--D-ribose-2'-epimerase (DprE1) to rationalize the biol. activity and to provide an insight into the
probable mechanism of action and binding mode of hybridized structures. The results obtained validate the use of mol.
hybridization approach and also suggest that reported compds. can provide a novel pharmacophore to synthesize lead
compds. against dormant MTB.
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5. Development of 3,5-Dinitrobenzylsulfanyl-1,3,4-oxadiazoles and Thiadiazoles as Selective Antitubercular

Agents Active Against Replicating and Nonreplicating Mycobacterium tuberculosis
By Karabanovich, Galina; Zemanova, Julia; Smutny, Tomas; Szekely, Rita; Sarkan, Michal; Centarova, Ivana; Vocat,
Anthony; Pavkova, Ivona; Conka, Patrik; Nemecek, Jan; et al
From Journal of Medicinal Chemistry (2016), 59(6), 2362-2380. Language: English, Database: CAPLUS,
DOI:10.1021/acs.jmedchem.5b00608
Herein, we report the discovery and structure-activity
relationships of 5-substituted-2-[(3,5-dinitrobenzyl)sulfanyl]1,3,4-oxadiazoles and 1,3,4-thiadiazoles as a new class of
antituberculosis agents. The majority of these compds.
exhibited outstanding in vitro activity against Mycobacterium
tuberculosis CNCTC My 331/88 and six multidrug-resistant clin.
isolated strains of M. tuberculosis, with min. inhibitory concn.
values as low as 0.03 M (0.011-0.026 g/mL). The
investigated compds. had a highly selective antimycobacterial
effect because they showed no activity against the other
bacteria or fungi tested in this study. Furthermore, the
investigated compds. exhibited low in vitro toxicities in four
proliferating mammalian cell lines and in isolated primary
human hepatocytes. Several in vitro genotoxicity assays
indicated that the selected compds. have no mutagenic activity.
The oxadiazole and thiadiazole derivs. with the most favorable
activity/toxicity profiles also showed potency comparable to that
of rifampicin against the nonreplicating streptomycin-starved M.
tuberculosis 18b-Lux strain, and therefore, these derivs., are of
particular interest.
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6. Nitroarenes as Antitubercular Agents: Stereoelectronic Modulation to Mitigate Mutagenicity

By Landge, Sudhir; Ramachandran, Vasanthi; Kumar, Anupriya; Neres, Joao; Murugan, Kannan; Sadler, Claire;
Fellows, Mick D.; Humnabadkar, Vaishali; Vachaspati, Prakash; Raichurkar, Anandkumar; et al
From ChemMedChem (2016), 11(3), 331-339. Language: English, Database: CAPLUS, DOI:10.1002/cmdc.201500462
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Nitroarenes are less preferred in drug discovery due to their potential to be mutagenic. However, several nitroarenes
were shown to be promising antitubercular agents with specific modes of action, namely, nitroimidazoles and
benzothiazinones. The nitro group in these compds. is activated through different mechanisms, both enzymic and nonenzymic, in mycobacteria prior to binding to the target of interest. From a whole-cell screening program, the authors
identified a novel lead nitrobenzothiazole (BT) series that acts by inhibition of decaprenylphosphoryl--D-ribose 2'epimerase (DprE1) of Mycobacterium tuberculosis (Mtb). The lead was found to be mutagenic to start with. The authors'
efforts to mitigate mutagenicity resulted in the identification of 6-methyl-7-nitro-5-(trifluoromethyl)-1,3-benzothiazoles
(cBTs), a novel class of antitubercular agents that are non-mutagenic and exhibit an improved safety profile. The Me
group ortho to the nitro group decreases the electron affinity of the series, and is hence responsible for the nonmutagenic nature of these compds. Addnl., the co-crystal structure of cBT in complex with Mtb DprE1 established the
mode of binding. This investigation led to a new non-mutagenic antitubercular agent and demonstrates that the
mutagenic nature of nitroarenes can be solved by modulation of stereoelectronic properties.
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7. Design, Syntheses, and Anti-TB Activity of 1,3-Benzothiazinone Azide and Click Chemistry Products Inspired
by BTZ043
By Tiwari, Rohit; Miller, Patricia A.; Chiarelli, Laurent R.; Mori, Giorgia; Sarkan, Michal; Centarova, Ivana; Cho,
Sanghyun; Mikusova, Katarina; Franzblau, Scott G.; Oliver, Allen G.; et al
From ACS Medicinal Chemistry Letters (2016), 7(3), 266-270. Language: English, Database: CAPLUS,
DOI:10.1021/acsmedchemlett.5b00424
Electron deficient nitroarom. compds. such as BTZ043 and its
closest congener, PBTZ169, and related agents are a
promising new class of anti-TB compds. Herein we report the
design and syntheses of 1,3-benzothiazinone azide (BTZ-N3, I)
and related click chem. products based on the mol. mode of
activation of BTZ043. Our computational docking studies
indicate that BTZ-N3 binds in the essentially same pocket as
that of BTZ043. Detailed biochem. studies with cell envelope
enzyme fractions of Mycobacterium smegmatis combined with
our model biochem. reactivity studies with nucleophiles
indicated that, in contrast to BTZ043, the azide analog may
have a different mode of activation for anti-TB activity.
Subsequent enzymic studies with recombinant DprE1 from Mtb
followed by MIC detn. in NTB1 strain of Mtb (harboring
Cys387Ser mutation in DprE1 and is BTZ043 resistant)
unequivocally indicated that BTZ-N3 is an effective reversible
and noncovalent inhibitor of DprE1.
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8. Discovery of benzothiazoles as antimycobacterial agents: Synthesis, structure-activity relationships and

binding studies with Mycobacterium tuberculosis decaprenylphosphoryl--D-ribose 2'-oxidase
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By Landge, Sudhir; Mullick, Amrita B.; Nagalapur, Kavitha; Neres, Joao; Subbulakshmi, Venkita; Murugan, Kannan;
Ghosh, Anirban; Sadler, Claire; Fellows, Mick D.; Humnabadkar, Vaishali; et al
From Bioorganic & Medicinal Chemistry (2015), 23(24), 7694-7710. Language: English, Database: CAPLUS,
DOI:10.1016/j.bmc.2015.11.017
We report the discovery of benzothiazoles, a novel anti-mycobacterial series, identified from a whole cell based
screening campaign. Benzothiazoles exert their bactericidal activity against Mycobacterium tuberculosis (Mtb) through
potent inhibition of decaprenylphosphoryl--D-ribose 2'-oxidase (DprE1), the key enzyme involved in arabinogalactan
synthesis. Specific target linkage and mode of binding were established using co-crystn. and protein mass spectrometry
studies. Most importantly, the current study provides insights on the utilization of systematic medicinal chem.
approaches to mitigate safety liabilities while improving potency during progression from an initial genotoxic hit, the
benzothiazole N-oxides (BTOs) to the lead-like AMES neg., crowded benzothiazoles (cBTs). These findings offer
opportunities for development of safe clin. candidates against tuberculosis. The design strategy adopted could find
potential application in discovery of safe drugs in other therapy areas too.
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9. Structure, dynamics, and interaction of Mycobacterium tuberculosis (Mtb) DprE1 and DprE2 examined by
molecular modeling, simulation, and electrostatic studies
By Bhutani, Isha; Loharch, Saurabh; Gupta, Pawan; Madathil, Rethi; Parkesh, Raman
From PLoS One (2015), 10(3), e0119771/1-e0119771/31. Language: English, Database: CAPLUS,
DOI:10.1371/journal.pone.0119771
The enzymes decaprenylphosphoryl--D-ribose oxidase (DprE1) and decaprenylphosphoryl--D-ribose-2-epimerase
(DprE2) catalyze epimerization of decaprenylphosporyl ribose (DPR) todecaprenylphosporyl arabinose (DPA) and are
crit. for the survival of Mtb. Crystal structures of DprE1 so far reported display significant disordered regions and no
structural information is known for DprE2. The authors used homol. modeling, protein threading, mol. docking and
dynamics studies to study the structural and dynamic features of Mtb DprE1 and DprE2 and DprE1-DprE2 complex. A
three-dimensional model for DprE2 was generated using the threading approach coupled with ab initio modeling. A 50
ns simulation of DprE1 and DprE2 revealed the overall stability of the structures. Principal Component Anal. (PCA)
demonstrated the convergence of sampling in both DprE1 and DprE2. In DprE1, residues in the 269-330 area showed
considerable fluctuation in agreement with the regions of disorder obsd. in the reported crystal structures. In DprE2,
large fluctuations were detected in residues 95-113, 146-157, and 197-226. The study combined docking and MD
simulation studies to map and characterize the key residues involved in DprE1-DprE2 interaction. A 60 ns MD simulation
for DprE1-DprE2 complex was also performed. Anal. of data revealed that the docked complex is stabilized by Hbonding, hydrophobic and ionic interactions. The key residues of DprE1 involved in DprE1-DprE2 interactions belong to
the disordered region. The authors also examd. the docked complex of DprE1-BTZ043 to study the binding pocket of
DprE1 and its interactions with the inhibitor BTZ043. In summary, the authors hypothesize that DprE1-DprE2 interaction
is crucial for the synthesis of DPA and DprE1-DprE2 complex may be a new therapeutic target amenable to pharmacol.
validation. The findings have important implications in tuberculosis (TB) drug discovery and will facilitate drug
development efforts against TB.
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10. Design and synthesis of 11-substituted bile acid derivatives as potential anti-tuberculosis agents
By Pore, Vandana S.; Divse, Jaisingh M.; Charolkar, Chaitanya R.; Nawale, Laxman U.; Khedkar, Vijay M.; Sarkar,
Dhiman
DOI:10.1016/j.bmcl.2015.08.006
We have synthesized a series of novel 11-triazolyl bile acid derivs. In addn., we also have synthesized N-alkyl and Nacyl derivs. of C-11 amino bile acid esters. All the compds. were evaluated for the inhibitory activity against
Mycobacterium tuberculosis H37Ra (MTB) at 30 g/mL level. Four lead compds. were further confirmed from their dose
dependent effect against MTB. These compds. were found to be active against Dormant and active stage MTB under
both in vitro as well as within THP1 host macrophages. The most promising compd. I showed strong antitubercular
activities against MTB under in vitro and ex vivo (IC90 value of 3 g/mL) conditions and almost insignificant cytotoxicity
up to 100 g/mL against THP-1, A549 and PANC-1 human cancer cell lines. Inactivity of all these compds. against Gram
pos. and Gram neg. bacteria indicates their specificity. Mol. docking studies of these compds. into the active site of
DprE1 enzyme revealed a similar binding mode to native ligands in the crystal structure thereby helping to establish a
structural basis of inhibition of MTB. The synthesized compds. were analyzed for ADME properties and showed potential
to develop good oral drug candidates. Our results clearly indicate the identification of some novel, selective and specific
inhibitors against MTB that can be explored further for potential antitubercular drug.
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11. Whole Cell Target Engagement Identifies Novel Inhibitors of Mycobacterium tuberculosis
Decaprenylphosphoryl--D-ribose Oxidase
By Batt, Sarah M.; Cacho Izquierdo, Monica; Castro Pichel, Julia; Stubbs, Christopher J.; Vela-Glez Del Peral, Laura;
Perez-Herran, Esther; Dhar, Neeraj; Mouzon, Bernadette; Rees, Mike; Hutchinson, Jonathan P.; et al
From ACS Infectious Diseases (2015), 1(12), 615-626. Language: English, Database: CAPLUS,
DOI:10.1021/acsinfecdis.5b00065
We have targeted the Mycobacterium tuberculosis
decaprenylphosphoryl--D-ribose oxidase (Mt-DprE1) for
potential chemotherapeutic intervention of tuberculosis. A
multicopy suppression strategy that overexpressed Mt-DprE1 in
M. bovis BCG was used to profile the publically available
GlaxoSmithKline antimycobacterial compd. set, and one
compd. (GSK710) was identified that showed an 8-fold higher
min. inhibitory concn. relative to the control strain. Analogs of
GSK710 show a clear relationship between whole cell potency
and in vitro activity using an enzymic assay employing
recombinant Mt-DprE1, with binding affinity measured by
fluorescence quenching of the flavin cofactor of the enzyme.
M. bovis BCG spontaneous resistant mutants to GSK710 and a
closely related analog were isolated and sequencing of ten
such mutants revealed a single point mutation at two sites,
E221Q or G248S within DprE1, providing further evidence that
DprE1 is the main target of these compds. Finally, time-lapse
microscopy expts. showed that exposure of M. tuberculosis to a
compd. of this series arrests bacterial growth rapidly followed
by a slower cytolysis phase.
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12. The 8-pyrrole-benzothiazinones are noncovalent inhibitors of DprE1 from Mycobacterium tuberculosis
By Makarov, Vadim; Neres, Joao; Hartkoorn, Ruben C.; Ryabova, Olga B.; Kazakova, Elena; Sarkan, Michal; Huszar,
Stanislav; Piton, Jeremie; Kolly, Gaelle S.; Vocat, Anthony; et al
From Antimicrobial Agents and Chemotherapy (2015), 59(8), 4446-4452. Language: English, Database: CAPLUS,
DOI:10.1128/AAC.00778-15
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8-Nitro-benzothiazinones (BTZs), such as BTZ043 and PBTZ169, inhibit decaprenylphosphoryl--d-ribose 2'-oxidase

(DprE1) and display nanomolar bactericidal activity against Mycobacterium tuberculosis in vitro. Structure-activity
relationship (SAR) studies revealed the 8-nitro group of the BTZ scaffold to be crucial for the mechanism of action, which
involves formation of a semimercaptal bond with Cys387 in the active site of DprE1. To date, substitution of the 8-nitro
group has led to extensive loss of antimycobacterial activity. Here, we report the synthesis and characterization of the
pyrrole-benzothiazinones PyrBTZ01 and PyrBTZ02, non-nitro-benzothiazinones that retain significant antimycobacterial
activity, with MICs of 0.16 g/mL against M. tuberculosis. These compds. inhibit DprE1 with 50% inhibitory concn. (IC50)
values of <8 M and present favorable in vitro absorption-distribution-metab.-excretion/toxicity (ADME/T) and in vivo
pharmacokinetic profiles. The most promising compd., PyrBTZ01, did not show efficacy in a mouse model of acute
tuberculosis, suggesting that BTZ-mediated killing through DprE1 inhibition requires a combination of both covalent bond
formation and compd. potency.
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13. DprE1 Is a Vulnerable Tuberculosis Drug Target Due to Its Cell Wall Localization
By Brecik, Miroslav; Centarova, Ivana; Mukherjee, Raju; Kolly, Gaelle S.; Huszar, Stanislav; Bobovska, Adela;
Kilacskova, Emoke; Mokosova, Veronika; Svetlikova, Zuzana; Sarkan, Michal; et al
From ACS Chemical Biology (2015), 10(7), 1631-1636. Language: English, Database: CAPLUS,
DOI:10.1021/acschembio.5b00237
The flavo-enzyme DprE1 catalyzes a key epimerization step in
the decaprenyl-phosphoryl D-arabinose (DPA) pathway, which
is essential for mycobacterial cell wall biogenesis and targeted
by several new tuberculosis drug candidates. Here, using
differential radiolabeling with DPA precursors and high-resoln.
fluorescence microscopy, we disclose the unexpected
extracytoplasmic localization of DprE1 and periplasmic
synthesis of DPA. Collectively, this explains the vulnerability of
DprE1 and the remarkable potency of the best inhibitors.
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14. Development of selective DprE1 inhibitors: Design, synthesis, crystal structure and antitubercular activity of
benzothiazolylpyrimidine-5-carboxamides
By Chikhale, Rupesh; Menghani, Sunil; Babu, Ramavath; Bansode, Ratnadeep; Bhargavi, G.; Karodia, Nazira;
Rajasekharan, M. V.; Paradkar, Anant; Khedekar, Pramod
From European Journal of Medicinal Chemistry (2015), 96, 30-46. Language: English, Database: CAPLUS,
DOI:10.1016/j.ejmech.2015.04.011
Decaprenylphosphoryl-b-D-ribose 20-epimerase (DprE1) is a potential drug target for development of antitubercular
agents. Structure based drug discovery approach yielded twenty novel derivs. of benzothiazolylpyrimidine-5carboxamides which were synthesized by three component one pot reaction involving benzothiazolyl oxobutanamide,
thiourea and substituted arom. benzaldehydes. These derivs. were evaluated for antitubercular activity to det. MIC. Log
P of these compds. is 2.0-3.0 making them suitable for oral dosing. DprE1 selectivity and pharmacokinetic studies were
carried out for these compds. of which N-(benzo[d]thiazol-2-yl)-1,2,3,4-tetrahydro-6-methyl-4-phenyl-2-thioxopyrimidine5-carboxamide and N-(benzo[d]thiazol-2-yl)-4-(4-(dimethylamino)phenyl)1,2,3,4-tetrahydro-6-methyl-2-thioxopyrimidine5-carboxamide are highly selective and bioavailability is >52% by oral dose. Crystal structure of N-(benzo[d]thiazol-2-yl)1,2,3,4-tetrahydro-6-methyl-4-phenyl-2-thioxopyrimidine-5-carboxamide was studied and mol. packing was detd., it
exhibited a triclinic crystal lattice arrangement having hydrogen bonded dimeric arrangement. Drug receptor interactions
were studied which exhibited docking in the active site of receptor with hydrogen bonding, hydrophobic interactions, vdW
interactions with amino acid residues such as Cys387, Asn385, Lys418, Tyr314, Gln334 and Lys367 resp. 3D QSAR
anal. was carried out by kNN-MFA method to det. and develop theor. model, best suitable model is based on Simulated
Annealing k-Neariest Neighbor Mol. Field Anal. (SA kNN-MFA). The model provided with hydrophobic descriptors in pos.
side indicating the need of bulky groups, steric and electroneg. descriptors in neg. coordinates hints with contribution by
the electroneg. substitutions as favorable and desirable moieties for enhancing the activity. The q2, q2_se and Pred_r2se
are 0.5000, 0.6404 and 1.0094, resp. A pharmacophore model was generated which suggested for necessity of arom.,
aliph. carbon center and hydrogen bond donor for development of newer DprE1 selective inhibitors.
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15. Synthesis and antitubercular evaluation of 4-carbonyl piperazine substituted 1,3-benzothiazin-4-one

derivatives
By Peng, Cui-Ting; Gao, Chao; Wang, Ning-Yu; You, Xin-Yu; Zhang, Li-Dan; Zhu, Yong-Xia; Ying, Xv; Zuo, WeiQiong; Ran, Kai; Deng, Hong-Xia; et al
DOI:10.1016/j.bmcl.2015.02.061
A new series of 4-carbonyl piperazine substituted 1,3-benzothiazin-4-one derivs. was synthesized and evaluated for antimycobacterial activity against Mycobacterium tuberculosis H37Ra as well as their druggability. The results showed that
most of these derivs., esp. the compds. with simple alkyl side chains, exhibited good antitubercular activities and
favorable aq. solubilities with no obvious cytotoxicity. It suggested that the 4-carbonyl piperazine substituents in
benzothiazinone scaffold were well tolerated, in which the compd. I, with an antitubercular activity of MIC 0.008 M,
exhibited an excellent aq. soly. of 104 g/mL, which was 100-fold better than the potent DprE1 inhibitor Comp.1
(BTZ038), also more sol. than PBTZ169.
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16. Computer-aided Identification of Novel DprE1 Inhibitors as Potential Anti-TB Lead Compounds: A Hybrid
Virtual-screening and Molecular Dynamics Approach
By Maharaj, Yushir; Bhakat, Soumendranath; Soliman, Mahmoud E. S.
From Letters in Drug Design & Discovery (2015), 12(4), 302-313. Language: English, Database: CAPLUS,
DOI:10.2174/1570180811666141001005536
By means of a combined computational protocol involving hybrid ligand/receptor-based virtual screening, mol. dynamics
simulations and per-residue energy contribution, two compds. were suggested as possible potential TB inhibitors. Using
docking calcns., which were validated by mol. dynamics simulations, binding free energy calcns. indicated that the
suggested compds. showed better binding affinity with DprE1 when compared to CT319, a known DprE1 inhibitor.
Results showed that compds. retrieved from both pharmacophore and shape-similarity libraries pose crucial hydrogen
bond interactions with compd. A and compd. B. While compd. B formed a hydrogen bond interaction with Lys418,
compd. A formed a stable hydrogen bond interaction with Leu317. Furthermore, both compds. exhibited apparent
stability during mol. dynamics simulations with neither system exceeding an RMSD of 2.5 A. MM/GBSA based binding
free energy profile of both top ranked compds. further validated the docking result as both of these hits showed a better
binding free energy profile when compared with CT319. Also, the hydrogen bond interactions between crucial residues
and the top two ligands were well stabilized during the simulation time. However, while further exptl. investigations are
required, the results obtained from this study could serve as a roadmap to assist medicinal and biol. chemists in the
process of design and development of potential anti-TB drugs.
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17. Preparation of azaindole compounds that target DprE1 for treatment of Mycobacterium infections
By Naik, Maruti N.; Peer Mohamed, Shahul Hameed; Shandil, Radha K.; Shinde, Vikas Narayan; Shirude, Pravin S.;
Chatterji, Monalisa
From PCT Int. Appl. (2015), WO 2015009525 A1 20150122, Language: English, Database: CAPLUS
The invention provides compds. of formula I (wherein R1 is H,
F, Br, OMe and Me; R2 and R3 are independently H or Me; X is
N or (un)substituted CH; R5 is H, F, CF3, and CN; Y is N or
(un)substituted CH; Z is N or (un)substituted CH; R8 is H, F, Me
and OMe; n is 1 or 2; R9 is F, cyclopropyl, OMe, etc.) and
methods of treating a Mycobacterium infection or tuberculosis,
or inhibiting DprE1 (decaprenylphosphoryl--D-ribose 2'epimerase 1) with the same. Synthetic procedures for prepg. I
are exemplified. Example compd. II, prepd. by reacting III and
2-fluoroethanamine, had an MIC of 12.5 M against
Mycobacterium tuberculosis (Mtb). In general, the compds. of
the invention were cidal for Mtb and M. smegmatis and retained
MIC for drug sensitive and single drug resistant clin. isolates of
Mtb. Drug resistance, drug metab., pharmacokinetics,
cytotoxicity, and drug interaction potential of the compds. were
also studied.
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18. 2-Carboxyquinoxalines Kill Mycobacterium tuberculosis through Noncovalent Inhibition of DprE1

By Neres, Joao; Hartkoorn, Ruben C.; Chiarelli, Laurent R.; Gadupudi, Ramakrishna; Pasca, Maria Rosalia; Mori,
Giorgia; Venturelli, Alberto; Savina, Svetlana; Makarov, Vadim; Kolly, Gaelle S.; et al
From ACS Chemical Biology (2015), 10(3), 705-714. Language: English, Database: CAPLUS, DOI:10.1021/cb5007163
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Phenotypic screening of a quinoxaline library against

replicating Mycobacterium tuberculosis led to the identification
of lead compd. Ty38c (3-((4-methoxybenzyl)amino)-6(trifluoromethyl)quinoxaline-2-carboxylic acid). With an MIC99
and MBC of 3.1 M, Ty38c is bactericidal and active against
intracellular bacteria. To investigate its mechanism of action,
we isolated mutants resistant to Ty38c and sequenced their
genomes. Mutations were found in rv3405c, coding for the
transcriptional repressor of the divergently expressed rv3406
gene. Biochem. studies clearly showed that Rv3406
decarboxylates Ty38c into its inactive keto metabolite. The
actual target was then identified by isolating Ty38c-resistant
mutants of an M. tuberculosis strain lacking rv3406. Here,
mutations were found in dprE1, encoding the
decaprenylphosphoryl-D-ribose oxidase DprE1, essential for
biogenesis of the mycobacterial cell wall. Genetics, biochem.
validation, and X-ray crystallog. revealed Ty38c to be a
noncovalent, noncompetitive DprE1 inhibitor. Structure-activity
relationship studies generated a family of DprE1 inhibitors with
a range of IC50's and bactericidal activity. Co-crystal structures
of DprE1 in complex with eight different quinoxaline analogs
provided a high-resoln. interaction map of the active site of this
extremely vulnerable target in M. tuberculosis.
~7 Citings
19. 1,4-azaindole, a potential drug candidate for treatment of tuberculosis

By Chatterji, Monalisa; Shandil, Radha; Manjunatha, M. R.; Solapure, Suresh; Ramachandran, Vasanthi; Kumar,
Naveen; Saralaya, Ramanatha; Panduga, Vijender; Reddy, Jitendar; Prabhakar, K. R.; et al
From Antimicrobial Agents and Chemotherapy (2014), 58(9), 5325-5331, 8 pp.. Language: English, Database:
CAPLUS, DOI:10.1128/AAC.03233-14
New therapeutic strategies against multidrug-resistant (MDR) and extensively drug-resistant (XDR) Mycobacterium
tuberculosis are urgently required to combat the global tuberculosis (TB) threat. Toward this end, we previously reported
the identification of 1,4-azaindoles, a promising class of compds. with potent antitubercular activity through noncovalent
inhibition of decaprenylphosphoryl--d-ribose 2'-epimerase (DprE1). Further, this series was optimized to improve its
physicochem. properties and pharmacokinetics in mice. Here, we describe the short-listing of a potential clin. candidate,
compd. 2, that has potent cellular activity, drug-like properties, efficacy in mouse and rat chronic TB infection models,
and minimal in vitro safety risks. We also demonstrate that the compds., including compd. 2, have no antagonistic
activity with other anti-TB drugs. Moreover, compd. 2 shows synergy with PA824 and TMC207 in vitro, and the synergy
effect is translated in vivo with TMC207. The series is predicted to have a low clearance in humans, and the predicted
human dose for compd. 2 is 1 g/day. Altogether, our data suggest that a 1,4-azaindole (compd. 2) is a promising
candidate for the development of a novel anti-TB drug.
~2 Citings
20. DprE1 - from the Discovery to the Promising Tuberculosis Drug Target
By Mikusova, Katarina; Makarov, Vadim; Neres, Joao
From Current Pharmaceutical Design (2014), 20(27), 4379-4403. Language: English, Database: CAPLUS,
DOI:10.2174/138161282027140630122724
A review. Several groups working in the field of the development of new antituberculosis drugs have recently reported
active compds. targeting mycobacterial enzyme DprE1. Along with its counterpart, DprE2, it catalyzes a unique
epimerization reaction resulting in the synthesis of decaprenylphosphoryl arabinose, the single donor of arabinosyl
residues for the build-up of arabinans, fundamental components of the mycobacterial cell wall. This review presents the
historical background leading to the discovery of DprE1, focusing on the biochem. and structural characterization of this
important emerging target and introducing the mols. acting on DprE1 including the development of the most successful
series - the benzothiazinones, currently in late pre-clin. development, which turned to be suicide inhibitors of DprE1.
~7 Citings
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21. 2-Phenylindole and arylsulfonamide: novel scaffolds bactericidal against Mycobacterium tuberculosis
By Naik, Maruti; Ghorpade, Sandeep; Jena, Lalit Kumar; Gorai, Gopinath; Narayan, Ashwini; Guptha, Supreeth;
Sharma, Sreevalli; Dinesh, Neela; Kaur, Parvinder; Nandishaiah, Radha; et al
From ACS Medicinal Chemistry Letters (2014), 5(9), 1005-1009. Language: English, Database: CAPLUS,
DOI:10.1021/ml5001933
A cellular activity-based screen on Mycobacterium tuberculosis
(Mtb) H37Rv using a focused library from the AstraZeneca
corporate collection led to the identification of 2-phenylindoles
and arylsulfonamides, novel antimycobacterial scaffolds. Both
the series were bactericidal in vitro and in an intracellular
macrophage infection model, active against drug sensitive and
drug resistant Mtb clin. isolates, and specific to mycobacteria.
The scaffolds showed promising structure-activity relationships;
compds. with submicromolar cellular potency were identified
during the hit to lead exploration. Furthermore, compds. from
both scaffolds were tested for inhibition of known target
enzymes or pathways of antimycobacterial drugs ,including
InhA, RNA polymerase, DprE1, topoisomerases, protein
synthesis, and oxidative-phosphorylation. The compds. did not
inhibit any of the targets, suggesting the potential of a possible
novel mode of action(s). Hence, both scaffolds provide the
opportunity to be developed further as leads and tool compds.
to uncover novel mechanisms for tuberculosis drug discovery.
~8 Citings
22. Lead Optimization of 1,4-Azaindoles as Antimycobacterial Agents

By Shirude, Pravin S.; Shandil, Radha K.; Manjunatha, M. R.; Sadler, Claire; Panda, Manoranjan; Panduga, Vijender;
Reddy, Jitendar; Saralaya, Ramanatha; Nanduri, Robert; Ambady, Anisha; et al
DOI:10.1021/jm500571f
In a previous report, we described the discovery of 1,4azaindoles, a chem. series with excellent in vitro and in vivo
antimycobacterial potency through noncovalent inhibition of
decaprenylphosphoryl--D-ribose-2'-epimerase (DprE1).
Nevertheless, high mouse metabolic turnover and
phosphodiesterase 6 (PDE6) off-target activity limited its
advancement. Herein, we report lead optimization of this
series, culminating in potent, metabolically stable compds. that
have a robust pharmacokinetic profile without any PDE6
liability. Furthermore, we demonstrate efficacy for 1,4azaindoles in a rat chronic TB infection model. We believe that
compds. from the 1,4-azaindole series are suitable for in vivo
combination and safety studies.
~11 Citings
23. 4-Aminoquinolone Piperidine Amides: Noncovalent Inhibitors of DprE1 with Long Residence Time and
Potent Antimycobacterial Activity
By Naik, Maruti; Humnabadkar, Vaishali; Tantry, Subramanyam J.; Panda, Manoranjan; Narayan, Ashwini; Guptha,
Supreeth; Panduga, Vijender; Manjrekar, Praveena; Jena, Lalit kumar; Koushik, Krishna; et al
DOI:10.1021/jm5005978
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4-Aminoquinolone piperidine amides (AQs) were identified as a

novel scaffold starting from a whole cell screen, with potent
cidality on Mycobacterium tuberculosis (Mtb). Evaluation of the
min. inhibitory concns., followed by whole genome sequencing
of mutants raised against AQs, identified
decaprenylphosphoryl--D-ribose 2'-epimerase (DprE1) as the
primary target responsible for the antitubercular activity. Mass
spectrometry and enzyme kinetic studies indicated that AQs
are noncovalent, reversible inhibitors of DprE1 with slow on
rates and long residence times of 100 min on the enzyme. In
general, AQs have excellent leadlike properties and good in
vitro secondary pharmacol. profile. Although the scaffold
started off as a single active compd. with moderate potency
from the whole cell screen, structure-activity relationship
optimization of the scaffold led to compds. with potent DprE1
inhibition (IC50 < 10 nM) along with potent cellular activity (MIC
= 60 nM) against Mtb.
~11 Citings
24. Discovery of Pyrazolopyridones as a Novel Class of Noncovalent DprE1 Inhibitor with Potent AntiMycobacterial Activity
By Panda, Manoranjan; Ramachandran, Sreekanth; Ramachandran, Vasanthi; Shirude, Pravin S.; Humnabadkar,
Vaishali; Nagalapur, Kavitha; Sharma, Sreevalli; Kaur, Parvinder; Guptha, Supreeth; Narayan, Ashwini; et al
DOI:10.1021/jm5002937
A novel pyrazolopyridone class of inhibitors was identified from
whole cell screening against Mycobacterium tuberculosis (Mtb).
The series exhibits excellent bactericidality in vitro, resulting in
a 4 log redn. in colony forming units following compd.
exposure. The significant modulation of min. inhibitory concn.
(MIC) against a Mtb strain overexpressing the Rv3790 gene
suggested the target of pyrazolopyridones to be
decaprenylphosphoryl--D-ribose-2'-epimerase (DprE1).
Genetic mapping of resistance mutation coupled with potent
enzyme inhibition activity confirmed the mol. target. Detailed
biochem. characterization revealed the series to be a
noncovalent inhibitor of DprE1. Docking studies at the active
site suggest that the series can be further diversified to improve
the physicochem. properties without compromising the
antimycobacterial activity. The pyrazolopyridone class of
inhibitors offers an attractive non-nitro lead series targeting the
essential and vulnerable DprE1 enzyme for the discovery of
novel antimycobacterial agents to treat both drug susceptible
and drug resistant strains of Mtb.
~14 Citings
25. Sulfur rich 2-mercaptobenzothiazole and 1,2,3-triazole conjugates as novel antitubercular agents
By Mir, Fauzia; Shafi, Syed; Zaman, M. S.; Kalia, Nitin Pal; Rajput, Vikrant S.; Mulakayala, Chaitanya; Mulakayala,
Naveen; Khan, Inshad A.; Alam, M. S.
From European Journal of Medicinal Chemistry (2014), 76, 274-283. Language: English, Database: CAPLUS,
DOI:10.1016/j.ejmech.2014.02.017
A series of benzo-fused heterocyclic derivs. such as amide conjugates of 2-(benzo[d]thiazol-2-ylthio)acetic acid with
arom./aliph./cyclic secondary amines, e.g. I [R1 = Ph, 2-ClC6H4, 3-O2NC6H4, etc.], and 1,2,3-triazole conjugates of 2mercaptobenzothiazoles and amide conjugates of indole-3-glyoxalic acid with cyclic secondary amines II [R2 = piperidin1-yl, piperazin-1-yl, morpholin-1-yl, etc.] have been synthesized and were screened for their antitubercular activity
against Mycobacterium tuberculosis H37Rv strain by broth microdilution assay method. Several compds. inhibited the
growth of the H37Rv strain at concns. of 8 g/mL. These compds. have been further identified as bactericidal and are
completely killing the microbes at 32-64 g/mL concns. Mol. docking studies of the active compds. reveal that these
compds. are targeting DprE1 and may act as DprE1 inhibitors.
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~15 Citings
26. Towards a new combination therapy for tuberculosis with next generation benzothiazinones
By Makarov, Vadim; Lechartier, Benoit; Zhang, Ming; Neres, Joao; van der Sar, Astrid M.; Raadsen, Susanne A.;
Hartkoorn, Ruben C.; Ryabova, Olga B.; Vocat, Anthony; Decosterd, Laurent A.; et al
From EMBO Molecular Medicine (2014), 6(3), 372-383. Language: English, Database: CAPLUS,
DOI:10.1002/emmm.201303575
The benzothiazinone lead compd., BTZ043, kills Mycobacterium tuberculosis by inhibiting the essential flavo-enzyme
DprE1, decaprenylphosphoryl-beta-D-ribose 2-epimerase. Here, we synthesized a new series of piperazine-contg.
benzothiazinones (PBTZ) and show that, like BTZ043, the preclin. candidate PBTZ169 binds covalently to DprE1. The
crystal structure of the DprE1-PBTZ169 complex reveals formation of a semimercaptal adduct with Cys387 in the active
site and explains the irreversible inactivation of the enzyme. Compared to BTZ043, PBTZ169 has improved potency,
safety and efficacy in zebrafish and mouse models of tuberculosis (TB). When combined with other TB drugs, PBTZ169
showed additive activity against M. tuberculosis in vitro except with bedaquiline (BDQ) where synergy was obsd. A new
regimen comprising PBTZ169, BDQ and pyrazinamide was found to be more efficacious than the std. three drug
treatment in a murine model of chronic disease. PBTZ169 is thus an attractive drug candidate to treat TB in humans.
~36 Citings
27. A large scale virtual screen of DprE1

By Wilsey, Claire; Gurka, Jessica; Toth, David; Franco, Jimmy
From Computational Biology and Chemistry (2013), 47, 121-125. Language: English, Database: CAPLUS,
DOI:10.1016/j.compbiolchem.2013.08.006
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Tuberculosis continues to plague the world with the World Health Organization estg. that about one third of the world's
population is infected. Due to the emergence of MDR and XDR strains of TB, the need for novel therapeutics has
become increasing urgent. Herein the authors report the results of a virtual screen of 4.1 million compds. against a
promising drug target, DrpE1. The virtual compds. were obtained from the Zinc docking site and screened using the mol.
docking program, AutoDock Vina. The computational hits have led to the identification of several promising lead
compds.
~2 Citings
28. Azaindoles: Noncovalent DprE1 Inhibitors from Scaffold Morphing Efforts, Kill Mycobacterium tuberculosis
and Are Efficacious in Vivo
By Shirude, Pravin S.; Shandil, Radha; Sadler, Claire; Naik, Maruti; Hosagrahara, Vinayak; Hameed, Shahul; Shinde,
Vikas; Bathula, Chandramohan; Humnabadkar, Vaishali; Kumar, Naveen; et al
DOI:10.1021/jm401382v
We report 1,4-azaindoles as a new inhibitor class that kills
Mycobacterium tuberculosis in vitro and demonstrates efficacy
in mouse tuberculosis models. The series emerged from
scaffold morphing efforts and was demonstrated to
noncovalently inhibit decaprenylphosphoryl--d-ribose2'epimerase (DprE1). With "drug-like" properties and no
expectation of pre-existing resistance in the clinic, this chem.
class has the potential to be developed as a therapy for drugsensitive and drug-resistant tuberculosis.
~31 Citings
29. Synthesis and characterization of an anti-tubercular Benzothiazinone derivative

By Sweis, Wesley; Bond, Michael; Richter, Adrian; Imming, Peter; Osei-Agyekum, Nadia
From Abstracts, 44th Western Regional Meeting of the American Chemical Society, Santa Clara, CA, United States,
October 3-6 (2013), WRM-218. Language: English, Database: CAPLUS
Benzothiazinones are among the small group compds. that have activity against mycobacteria. BTZs are suicide
substrate inhibitors of DprE1 and DprE2 enzymes. These enzymes lead to the prodn. of mycolic acids that are essential
to the mycobacterial cell wall. Analyzing the interaction of BTZ in the binding pocket, it is apparent that the R-group on
the 2nd ring of BTZs is unspecific and can be changed to grant higher lipophilicity and possibly higher activity. A novel
synthesis was devised to increase the lipophilicity and see what other effects may take place. The compd. to introduce
the R-group was synthesized using benzoyl chloride and yielded thiomorpholine-4-carbothioamide. In BTZ synthesis the
starting compd. was AR-96, which is 2-chloro-3-nitro-5-(trifluoromethyl)benzoic acid. It was reacted with the
thiomorpholine-4-carbothioamide to yield the final BTZ SB-2. Both the SB-1 and SB-2 compds. were confirmed by
1HNMR and ESI mass spectrums. Soly. and MICs will be taken and then will be compared to other BTZs.
~0 Citings
30. The DprE1 enzyme, one of the most vulnerable targets of Mycobacterium tuberculosis
By Riccardi, Giovanna; Pasca, Maria Rosalia; Chiarelli, Laurent Roberto; Manina, Giulia; Mattevi, Andrea; Binda,
Claudia
From Applied Microbiology and Biotechnology (2013), 97(20), 8841-8848. Language: English, Database: CAPLUS,
DOI:10.1007/s00253-013-5218-x
A review. The re-emergence of tuberculosis (TB) in recent years led the World Health Organization (WHO) to launch the
Stop TB Strategy program. In addn. to repurposing existing drugs and exploring novel mol. combinations, an essential
step to face the burden of TB will be to develop new drugs by identifying vulnerable bacterial targets. Recent studies
have focused on decaprenylphosphoryl-D-ribose oxidase (DprE1) of M. tuberculosis, an essential enzyme involved in cell
wall metab., for which new promising mols. have proved efficacy as antitubercular agents. Here, the authors summarize
the state of the art concerning DprE1 in terms of structure, enzymic activity, and inhibitors. This enzyme is emerging as
one of the most vulnerable targets in M. tuberculosis.
~12 Citings
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31. Identification of novel DprE1 inhibitors for the treatment of tuberculosis

By Franco, Jimmy; Laverty, Daniel; Daniels, Dave; Wilsey, Claire; Golijanin, Petar; Gurka, Jessica
From Abstracts of Papers, 245th ACS National Meeting & Exposition, New Orleans, LA, United States, April 7-11, 2013
(2013), MEDI-161. Language: English, Database: CAPLUS
Mycobacterium tuberculosis (M. Tb) is the leading cause of mortality due to a bacterial pathogen. The CDC ests. that
about one third of the world's population is infected with M. It is anticipated that there will be more cases of TB this year
than any other point in history. Insufficient progress has been made in the treatment of TB in the last fifty years, which
has allowed for the appearance of multidrug resistant strains (MDR-TB) and extensively drug-resistant strains (XDR-TB).
One target that recently has shown promise is DprE1, an essential protein for viability. DprE1 is essential for the
conversion of decaprenylphosphoryl--D-ribose (DPR) to decaprenylphosphoryl--Darabinofuranose (DPA),which is an
essential component of the cell wall. DprE1 is highly conserved within mycobacteria and the lack of an alternative
pathway makes DrpE1 a lucrative drug target.
Our approach to target DprE1 is two fold. The first method utilizes
an activated Cys residue in the active site of DprE1. We have used the recently solved structure of DprE1 to construct a
new class of electrophilic inhibitors that can covalently bind to DprE1. The feasibility of these compds. has been
validated by a Kirby-Bauer disk diffusion assay. The second method uses a traditional class of non-covalent inhibitors.
Using AutoDock Vina we have conducted a large virtual screen using a large library of small mols. obtained from the Zinc
Database. The top computational hits were subsequently visually screened using PyMOL. The top hits from the visual
inspection were then empirically evaluated using a Kirby-Bauer disk diffusion assay. Using this method we have been
able to identify several promising new inhibitors.
~0 Citings
32. Thiolates Chemically Induce Redox Activation of BTZ043 and Related Potent Nitroaromatic Anti-Tuberculosis
Agents
By Tiwari, Rohit; Moraski, Garrett C.; Krchnak, Viktor; Miller, Patricia A.; Colon-Martinez, Mariangelli; Herrero, Eliza;
Oliver, Allen G.; Miller, Marvin J.
From Journal of the American Chemical Society (2013), 135(9), 3539-3549. Language: English, Database: CAPLUS,
DOI:10.1021/ja311058q
The development of multidrug resistant (MDR) and extensively
drug resistant (XDR) forms of tuberculosis (TB) has stimulated
research efforts globally to expand the new drug pipeline.
Nitroarom. compds., including 1,3-benzothiazin-4-ones (BTZs)
and related agents, are a promising new class for the treatment
of TB. Research has shown that the nitroso intermediates of
BTZs that are generated in vivo cause suicide inhibition of
decaprenylphosphoryl--d-ribose 2' oxidase (DprE1), which is
responsible for cell wall arabinogalactan biosynthesis. We
have designed and synthesized novel anti-TB agents inspired
from BTZs and other nitroarom. compds. Computational
studies indicated that the unsubstituted arom. carbons of
BTZ043 and related nitroarom. compds. are the most electrondeficient and might be prone to nucleophilic attack. Our chem.
studies on BTZ043 and the addnl. nitroarom. compds.
synthesized by us and others confirmed the postulated
reactivity. The results indicate that nucleophiles such as
thiolates, cyanide, and hydride induce nonenzymic redn. of the
nitro groups present in these compds. to the corresponding
nitroso intermediates by addn. at the unsubstituted electrondeficient arom. carbon present in these compds. Furthermore,
we demonstrate here that these compds. are good candidates
for the classical von Richter reaction. These chem. studies
offer an alternate hypothesis for the mechanism of action of
nitroarom. anti-TB agents, in that the cysteine thiol(ate) or a
hydride source at the active site of DprE1 may trigger the redn.
of the nitro groups in a manner similar to the von Richter
reaction to the nitroso intermediates, to initiate the inhibition of
DprE1.
~17 Citings
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33. In vitro combination studies of benzothiazinone lead compound BTZ043 against Mycobacterium tuberculosis
By Lechartier, Benoit; Hartkoorn, Ruben C.; Cole, Stewart T.
From Antimicrobial Agents and Chemotherapy (2012), 56(11), 5790-5793. Language: English, Database: CAPLUS,
DOI:10.1128/AAC.01476-12
Benzothiazinones (BTZ) are a new class of drug candidates to combat tuberculosis that inhibit decaprenylphosphoribose epimerase (DprE1), an essential enzyme involved in arabinan biosynthesis. Using the checkerboard
method and cell viability assays, the authors have studied the interaction profiles of BTZ043, the current lead compd.,
with several antituberculosis drugs or drug candidates against Mycobacterium tuberculosis strain H37Rv, namely,
rifampin, isoniazid, ethambutol, TMC207, PA-824, moxifloxacin, meropenem with or without clavulanate, and SQ-109.
No antagonism was found between BTZ043 and the tested compds., and most of the interactions were purely additive.
Data from two different approaches clearly indicate that BTZ043 acts synergistically with TMC207, with a fractional
inhibitory concn. index of 0.5. TMC207 at a quarter of the MIC (20 ng/mL) used in combination with BTZ043 (1/4 MIC,
0.375 ng/mL) had a stronger bactericidal effect on M. tuberculosis than TMC207 alone at a concn. of 80 ng/mL. This
synergy was not obsd. when the combination was tested on a BTZ-resistant M. tuberculosis mutant, suggesting that
DprE1 inhibition is the basis for the interaction. This finding excludes the possibility of synergy occurring through an offtarget mechanism. We therefore hypothesize that sub-MICs of BTZ043 weaken the bacterial cell wall and allow
improved penetration of TMC207 to its target. Synergy between two new antimycobacterial compds., such as TMC207
and BTZ043, with novel targets, offers an attractive foundation for a new tuberculosis regimen.
~29 Citings
34. Structural basis for benzothiazinone-mediated killing of Mycobacterium tuberculosis

By Neres, Joao; Pojer, Florence; Molteni, Elisabetta; Chiarelli, Laurent R.; Dhar, Neeraj; Boy-Rottger, Stefanie; Buroni,
Silvia; Fullam, Elizabeth; Degiacomi, Giulia; Lucarelli, Anna Paola; et al
From Science Translational Medicine (2012), 4(150), 121, 11 pp.. Language: English, Database: CAPLUS,
DOI:10.1126/scitranslmed.3004395
The benzothiazinone BTZ043 is a tuberculosis drug candidate with nanomolar whole-cell activity. BTZ043 targets the
DprE1 catalytic component of the essential enzyme decaprenylphosphoryl--D-ribofuranose-2'-epimerase, thus blocking
biosynthesis of arabinans, vital components of mycobacterial cell walls. Crystal structures of DprE1, in its native form
and in a complex with BTZ043, reveal formation of a semimercaptal adduct between the drug and an active-site cysteine,
as well as contacts to a neighboring catalytic lysine residue. Kinetic studies confirm that BTZ043 is a mechanism-based,
covalent inhibitor. This explains the exquisite potency of BTZ043, which, when fluorescently labeled, localizes DprE1 at
the poles of growing bacteria. Menaquinone can reoxidize the FAD cofactor in DprE1 and may be the natural electron
acceptor for this reaction in the mycobacterium. The authors' structural and kinetic anal. provides both insight into a crit.
epimerization reaction and a platform for structure-based design of improved inhibitors.
~10 Citings
35. Structural basis of inhibition of Mycobacterium tuberculosis DprE1 by benzothiazinone inhibitors

By Batt, Sarah M.; Jabeen, Talat; Bhowruth, Veemal; Quill, Lee; Lund, Peter A.; Eggeling, Lothar; Alderwick, Luke J.;
Futterer, Klaus; Besra, Gurdyal S.
From Proceedings of the National Academy of Sciences of the United States of America (2012), 109(28), 1135411359, S11354/1-S11354/10. Language: English, Database: CAPLUS, DOI:10.1073/pnas.1205735109
Resistance against currently used antitubercular therapeutics increasingly undermines efforts to contain the worldwide
tuberculosis (TB) epidemic. Recently, benzothiazinone (BTZ) inhibitors have shown nanomolar potency against both
drug-susceptible and multidrug-resistant strains of the tubercle bacillus. However, their proposed mode of action is
lacking structural evidence. The authors report here the crystal structure of the BTZ target, FAD-contg. oxidoreductase
Mycobacterium tuberculosis DprE1, which is essential for viability. Different crystal forms of ligand-free DprEl reveal
considerable levels of structural flexibility of two surface loops that seem to govern accessibility of the active site.
Structures of complexes with the BTZ-derived nitroso deriv. CT325 reveal the mode of inhibitor binding, which includes a
covalent link to conserved Cys387, and reveal a trifluoromethyl group as a second key determinant of interaction with the
enzyme. The authors found that a noncovalent complex was formed between DprE1 and CT319, which is structurally
identical to CT325 except for an inert nitro group replacing the reactive nitroso group. This demonstrates that binding of
BTZ-class inhibitors to DprE1 is not strictly dependent on formation of the covalent link to Cys387. On the basis of the
structural and activity data, the authors propose that the complex of DrpE1 bound to CT325 is a representative of the
BTZ-target complex. These results mark a significant step forward in the characterization of a key TB drug target.
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~42 Citings
36. Antituberculars which target decaprenylphosphoryl--D-ribofuranose 2'-oxidase DprE1: state of art

[Retraction of document cited in CA157:656839]
By Buroni, Silvia; Pasca, Maria Rosalia; Jesus Lopes Ribeiro, Ana Luisa; Degiacomi, Giulia; Molteni, Elisabetta;
Riccardi, Giovanna
From Applied Microbiology and Biotechnology (2012), 95(5), 1369. Language: English, Database: CAPLUS,
DOI:10.1007/s00253-012-4217-7
A review. This article has been retracted by agreement between the Editor-in-Chief, publisher, and authors due to
copyright issues.
~0 Citings

By Batt, Sarah M.; Jabeen, Talat; Bhowruth, Veemal; Quill, Lee; Lund, Peter A.; Eggeling, Lothar; Alderwick, Luke J.;
Futterer, Klaus; Besra, Gurdyal S.
From Proceedings of the National Academy of Sciences of the United States of America, Early Edition (2012), (June
25 2012), 1-6, 6 pp.. Language: English, Database: CAPLUS, DOI:10.1073/pnas.1205735109
lacking structural evidence. We report here the crystal structure of the BTZ target, FAD-contg. oxidoreductase
Mycobacterium tuberculosis DprE1, which is essential for viability. Different crystal forms of ligand-free DprE1 reveal
Structures of complexes with the BTZ-derived nitroso deriv. CT325 reveal the mode of inhibitor binding, which includes a
covalent link to conserved Cys387, and reveal a trifluoromethyl group as a second key determinant of interaction with the
enzyme. Surprisingly, we find that a noncovalent complex was formed between DprE1 and CT319, which is structurally
identical to CT325 except for an inert nitro group replacing the reactive nitroso group. This demonstrates that binding of
BTZ-class inhibitors to DprE1 is not strictly dependent on formation of the covalent link to Cys387. On the basis of the
structural and activity data, we propose that the complex of DrpE1 bound to CT325 is a representative of the BTZ-target
complex. These results mark a significant step forward in the characterization of a key TB drug target.
~0 Citings
38. Identification of Novel Inhibitors of M. tuberculosis Growth Using Whole Cell Based High-Throughput
Screening
By Stanley, Sarah A.; Schmidt Grant, Sarah; Kawate, Tomohiko; Iwase, Noriaki; Shimizu, Motohisa; Wivagg, Carl;
Silvis, Melanie; Kazyanskaya, Edward; Aquadro, John; Golas, Aaron; et al
From ACS Chemical Biology (2012), 7(8), 1377-1384. Language: English, Database: CAPLUS,
DOI:10.1021/cb300151m
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Despite the urgent need for new antitubercular drugs, few are
on the horizon. To combat the problem of emerging drug
resistance, structurally unique chem. entities that inhibit new
targets will be required. Here, we describe our investigations
using whole cell screening of a diverse collection of small mols.
as a methodol. for identifying novel inhibitors that target new
pathways for Mycobacterium tuberculosis drug discovery. We
find that conducting primary screens using model
mycobacterial species may limit the potential for identifying new
inhibitors with efficacy against M. tuberculosis. In addn., we
confirm the importance of developing in vitro assay conditions
that are reflective of in vivo biol. for maximizing the proportion
of hits from whole cell screening that are likely to have activity
in vivo. Finally, we describe the identification and
characterization of two novel inhibitors that target steps in M.
tuberculosis cell wall biosynthesis. The first is a novel
benzimidazole, I, that targets mycobacterial membrane protein
large 3 (MmpL3), a proposed transporter for cell wall mycolic
acids. The second is a nitro-triazole, II, that inhibits
decaprenylphosphoryl--d-ribose 2'-epimerase (DprE1), an
epimerase required for cell wall biosynthesis. These proteins
are both among the small no. of new targets that have been
identified by forward chem. genetics using resistance
generation coupled with genome sequencing. This suggests
that methodologies currently employed for screening and target
identification may lead to a bias in target discovery and that
alternative methods should be explored.
~73 Citings
39. Antituberculars which target decaprenylphosphoryl--D-ribofuranose 2'-oxidase DprE1: state of art

By Buroni, Silvia; Pasca, Maria Rosalia; de Jesus Lopes Ribeiro, Ana Luisa; Degiacomi, Giulia; Molteni, Elisabetta;
Riccardi, Giovanna
From Applied Microbiology and Biotechnology (2012), 94(4), 907-916. Language: English, Database: CAPLUS,
DOI:10.1007/s00253-012-4013-4
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A review. Multidrug resistance is a major barrier in the battle against tuberculosis and still a leading cause of death
worldwide. In order to fight this pathogen, two routes are practicable: vaccination or drug treatment. Vaccination against
Mycobacterium tuberculosis with the current vaccine Mycobacterium bovis Bacillus Calmette-Guerin is partially
successful, being its efficacy variable. A few new tuberculosis vaccines are now in various phases of clin. trials. The
emergence of multidrug-resistant strains of M. tuberculosis gave the impulse to discover new effective antitubercular
drugs, a few of which are in clin. development. Here, the authors focus on three different classes of very promising
antitubercular drugs recently discovered (benzothiazinones, dinitrobenzamides, and benzoquinoxalines) that share the
same cellular target: a subunit of the heteromeric decaprenylphosphoryl--d-ribose 2'-epimerase, encoded by the dprE1
(or Rv3790) gene. This enzyme is involved in the biosynthesis of d-arabinose which is crucial for the synthesis of the
mycobacterial cell wall and essential for the pathogen's survival.
~1 Citing
40. Benzothiazinones Are Suicide Inhibitors of Mycobacterial Decaprenylphosphoryl--D-ribofuranose 2'Oxidase DprE1

By Trefzer, Claudia; Skovierova, Henrieta; Buroni, Silvia; Bobovska, Adela; Nenci, Simone; Molteni, Elisabetta; Pojer,
Florence; Pasca, Maria R.; Makarov, Vadim; Cole, Stewart T.; et al
From Journal of the American Chemical Society (2012), 134(2), 912-915. Language: English, Database: CAPLUS,
DOI:10.1021/ja211042r
Benzothiazinones (BTZs) are antituberculosis drug candidates
with nanomolar bactericidal activity against tubercle bacilli.
Here we demonstrate that BTZs are suicide substrates of the
FAD-dependent decaprenylphosphoryl--D-ribofuranose 2'oxidase DprE1, an enzyme involved in cell-wall biogenesis.
BTZs are reduced by DprE1 to an electrophile, which then
reacts in a near-quant. manner with an active-site cysteine of
DprE1, thus providing a rationale for the extraordinary potency
of BTZs. Mutant DprE1 enzymes from BTZ-resistant strains
reduce BTZs to inert metabolites while avoiding covalent
inactivation. Our results explain the basis for drug sensitivity
and resistance to an exceptionally potent class of
antituberculosis agents.
~47 Citings
41. New tuberculosis drugs on the horizon

By Cole, Stewart T.; Riccardi, Giovanna
From Current Opinion in Microbiology (2011), 14(5), 570-576. Language: English, Database: CAPLUS,
DOI:10.1016/j.mib.2011.07.022
A review. Tuberculosis (TB) remains a major global health concern whose control has been exacerbated by HIV and the
emergence of multidrug-resistant (MDR-TB) and extensively drug-resistant (XDR-TB) strains of Mycobacterium
tuberculosis. The demand for new and faster acting TB drugs is thus greater than ever. In the past decade intensive
efforts have been made to discover new leads for TB drug development using both target-based and cell-based
approaches. Here, we describe the most promising anti-tubercular drug candidates that are in clin. development and
introduce some nitro-arom. compds. that inhibit a new target, DprE1, an essential enzyme involved in a crucial step in
mycobacterial cell wall biosynthesis.
~39 Citings
42. Benzothiazinones: Prodrugs That Covalently Modify the Decaprenylphosphoryl--D-ribose 2'-epimerase

DprE1 of Mycobacterium tuberculosis
By Trefzer, Claudia; Rengifo-Gonzalez, Monica; Hinner, Marlon J.; Schneider, Patricia; Makarov, Vadim; Cole, Stewart
T.; Johnsson, Kai
From Journal of the American Chemical Society (2010), 132(39), 13663-13665. Language: English, Database:
CAPLUS, DOI:10.1021/ja106357w
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Benzothiazinones (BTZs) form a new class of potent

antimycobacterial agents. Although the target of BTZs has
been identified as decaprenylphosphoryl--D-ribose 2'epimerase (DprE1), their detailed mechanism of action remains
obscure. Here we demonstrate that BTZs are activated in the
bacterium by redn. of an essential nitro group to a nitroso
deriv., which then specifically reacts with a cysteine residue in
the active site of DprE1.
~62 Citings
43. High content screening identifies decaprenyl-phosphoribose 2' epimerase as a target for intracellular
antimycobacterial inhibitors
By Christophe, Thierry; Jackson, Mary; Jeon, Hee Kyoung; Fenistein, Denis; Contreras-Dominguez, Monica; Kim,
Jaeseung; Genovesio, Auguste; Carralot, Jean-Philippe; Ewann, Fanny; Kim, Eun Hye; et al
From PLoS Pathogens (2009), 5(10), No pp. given. Language: English, Database: CAPLUS,
DOI:10.1371/journal.ppat.1000645
A crit. feature of Mycobacterium tuberculosis, the causative agent of human tuberculosis (TB), is its ability to survive and
multiply within macrophages, making these host cells an ideal niche for persisting microbes. Killing the intracellular
tubercle bacilli is a key requirement for efficient tuberculosis treatment, yet identifying potent inhibitors has been
hampered by labor-intensive techniques and lack of validated targets. Here, we present the development of a
phenotypic cell-based assay that uses automated confocal fluorescence microscopy for high throughput screening of
chems. that interfere with the replication of M. tuberculosis within macrophages. Screening a library of 57,000 small
mols. led to the identification of 135 active compds. with potent intracellular anti-mycobacterial efficacy and no host cell
toxicity. Among these, the dinitrobenzamide derivs. (DNB) showed high activity against M. tuberculosis, including
extensively drug resistant (XDR) strains. More importantly, we demonstrate that incubation of M. tuberculosis with DNB
inhibited the formation of both lipoarabinomannan and arabinogalactan, attributable to the inhibition of decaprenylphospho-arabinose synthesis catalyzed by the decaprenyl-phosphoribose 2' epimerase DprE1/DprE2. Inhibition of this
new target will likely contribute to new therapeutic solns. against emerging XDR-TB. Beyond validating the high
throughput/content screening approach, our results open new avenues for finding the next generation of antimicrobials.
~13 Citings
44. N-methylation of a bactericidal compound as a resistance mechanism in Mycobacterium tuberculosis

By Warrier Thulasi; Little David; Nandakumar Madhumitha; Park Suna; Gold Ben; Mi Jianjie; Zhang Tuo; Burns-Huang
Kristin; Roberts Julia; Ling Yan; et al
From Proceedings of the National Academy of Sciences of the United States of America (2016), , Language: English,
Database: MEDLINE
The rising incidence of antimicrobial resistance (AMR) makes it imperative to understand the underlying mechanisms.
Mycobacterium tuberculosis (Mtb) is the single leading cause of death from a bacterial pathogen and estimated to be
the leading cause of death from AMR. A pyrido-benzimidazole, 14, was reported to have potent bactericidal activity
against Mtb. Here, we isolated multiple Mtb clones resistant to 14. Each had mutations in the putative DNA-binding
and dimerization domains of rv2887, a gene encoding a transcriptional repressor of the MarR family. The mutations in
Rv2887 led to markedly increased expression of rv0560c. We characterized Rv0560c as an S-adenosyl-L-methioninedependent methyltransferase that N-methylates 14, abolishing its mycobactericidal activity. An Mtb strain lacking
rv0560c became resistant to 14 by mutating decaprenylphosphoryl--d-ribose 2-oxidase (DprE1), an essential enzyme
in arabinogalactan synthesis; 14 proved to be a nanomolar inhibitor of DprE1, and methylation of 14 by Rv0560c
abrogated this activity. Thus, 14 joins a growing list of DprE1 inhibitors that are potently mycobactericidal. Bacterial
methylation of an antibacterial agent, 14, catalyzed by Rv0560c of Mtb, is a previously unreported mechanism of AMR.
~0 Citings
Copyright 2016 U.S. National Library of Medicine.
45. Benzothiazinethione is a potent preclinical candidate for the treatment of drug-resistant tuberculosis
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By Gao Chao; Peng Cuiting; Shi Yaojie; You Xinyu; Ran Kai; Xiong Lu; Ye Ting-Hong; Zhang Lidan; Wang Ningyu;
Zhu Yongxia; et al
From Scientific reports (2016), 629717, Language: English, Database: MEDLINE
New chemotherapeutic compounds are needed to combat multidrug-resistant Mycobacterium tuberculosis (Mtb), which
remains a serious public-health challenge. Decaprenylphosphoryl--D-ribose 2'-epimerase (DprE1 enzyme) has been
characterized as an attractive therapeutic target to address this urgent demand. Herein, we have identified a new
class of DprE1 inhibitors benzothiazinethiones as antitubercular agents. Benzothiazinethione analogue SKLB-TB1001
exhibited excellent activity against Mtb in the Microplate Alamar blue assay and intracellular model, meanwhile SKLBTB1001 was also highly potent against multi-drug resistant extensively and drug resistant clinical isolates. Importantly,
no antagonism interaction was found with any two-drug combinations tested in the present study and the combination
of SKLB-TB1001 with rifampicin (RMP) was proved to be synergistic. Furthermore, benzothiazinethione showed
superb in vivo antitubercular efficacy in an acute Mtb infection mouse model, significantly better than that of BTZ043.
These data combined with the bioavailability and safety profiles of benzothiazinethione indicates SKLB-TB1001 is a
promising preclinical candidate for the treatment of drug-resistant tuberculosis.
~0 Citings
46. Design, Syntheses, and Anti-TB Activity of 1,3-Benzothiazinone Azide and Click Chemistry Products Inspired
by BTZ043
By Tiwari Rohit; Miller Patricia A; Oliver Allen G; Miller Marvin J; Chiarelli Laurent R; Mori Giorgia; Sarkan Michal;
Centarova Ivana; Mikusova Katarina; Cho Sanghyun; et al
From ACS medicinal chemistry letters (2016), 7(3), 266-70, Language: English, Database: MEDLINE
Electron deficient nitroaromatic compounds such as BTZ043 and its closest congener, PBTZ169, and related agents
are a promising new class of anti-TB compounds. Herein we report the design and syntheses of 1,3-benzothiazinone
azide (BTZ-N3) and related click chemistry products based on the molecular mode of activation of BTZ043. Our
computational docking studies indicate that BTZ-N3 binds in the essentially same pocket as that of BTZ043. Detailed
biochemical studies with cell envelope enzyme fractions of Mycobacterium smegmatis combined with our model
biochemical reactivity studies with nucleophiles indicated that, in contrast to BTZ043, the azide analogue may have a
different mode of activation for anti-TB activity. Subsequent enzymatic studies with recombinant DprE1 from Mtb
followed by MIC determination in NTB1 strain of Mtb (harboring Cys387Ser mutation in DprE1 and is BTZ043 resistant)
unequivocally indicated that BTZ-N3 is an effective reversible and noncovalent inhibitor of DprE1.
~0 Citings
47. Nitroarenes as Antitubercular Agents: Stereoelectronic Modulation to Mitigate Mutagenicity

By Landge Sudhir; Ramachandran Vasanthi; Kumar Anupriya; Murugan Kannan; Humnabadkar Vaishali; Vachaspati
Prakash; Raichurkar Anandkumar; Sharma Sreevalli; Ravishankar Sudha; Guptha Supreeth; et al
From ChemMedChem (2016), 11(3), 331-9, Language: English, Database: MEDLINE
Nitroarenes are less preferred in drug discovery due to their potential to be mutagenic. However, several nitroarenes
were shown to be promising antitubercular agents with specific modes of action, namely, nitroimidazoles and
benzothiazinones. The nitro group in these compounds is activated through different mechanisms, both enzymatic and
non-enzymatic, in mycobacteria prior to binding to the target of interest. From a whole-cell screening program, we
identified a novel lead nitrobenzothiazole (BT) series that acts by inhibition of decaprenylphosphoryl--d-ribose 2'epimerase (DprE1) of Mycobacterium tuberculosis (Mtb). The lead was found to be mutagenic to start with. Our
efforts to mitigate mutagenicity resulted in the identification of 6-methyl-7-nitro-5-(trifluoromethyl)-1,3-benzothiazoles
(cBTs), a novel class of antitubercular agents that are non-mutagenic and exhibit an improved safety profile. The
methyl group ortho to the nitro group decreases the electron affinity of the series, and is hence responsible for the nonmutagenic nature of these compounds. Additionally, the co-crystal structure of cBT in complex with Mtb DprE1
established the mode of binding. This investigation led to a new non-mutagenic antitubercular agent and demonstrates
that the mutagenic nature of nitroarenes can be solved by modulation of stereoelectronic properties.
~0 Citings
48. Discovery of benzothiazoles as antimycobacterial agents: Synthesis, structure-activity relationships and

binding studies with Mycobacterium tuberculosis decaprenylphosphoryl--D-ribose 2'-oxidase
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By Landge Sudhir; Mullick Amrita B; Nagalapur Kavitha; Subbulakshmi Venkita; Murugan Kannan; Ghosh Anirban;
Humnabadkar Vaishali; Mahadevaswamy Jyothi; Vachaspati Prakash; Sharma Sreevalli; et al
From Bioorganic & medicinal chemistry (2015), 23(24), 7694-710, Language: English, Database: MEDLINE
We report the discovery of benzothiazoles, a novel anti-mycobacterial series, identified from a whole cell based
screening campaign. Benzothiazoles exert their bactericidal activity against Mycobacterium tuberculosis (Mtb) through
potent inhibition of decaprenylphosphoryl--d-ribose 2'-oxidase (DprE1), the key enzyme involved in arabinogalactan
synthesis. Specific target linkage and mode of binding were established using co-crystallization and protein mass
spectrometry studies. Most importantly, the current study provides insights on the utilization of systematic medicinal
chemistry approaches to mitigate safety liabilities while improving potency during progression from an initial genotoxic
hit, the benzothiazole N-oxides (BTOs) to the lead-like AMES negative, crowded benzothiazoles (cBTs). These
findings offer opportunities for development of safe clinical candidates against tuberculosis. The design strategy
adopted could find potential application in discovery of safe drugs in other therapy areas too.
~0 Citings
49. In Vivo Activity of the Benzothiazinones PBTZ169 and BTZ043 against Nocardia brasiliensis
By Gonzalez-Martinez Norma Alejandra; De Osio-Cortez Alexandra; Ocampo-Candiani Jorge; Vera-Cabrera Lucio;
Lozano-Garza Hector Gerardo; Castro-Garza Jorge; Vargas-Villarreal Javier; Cavazos-Rocha Norma; Makarov Vadim;
Cole Stewart T
From PLoS neglected tropical diseases (2015), 9(10), e0004022, Language: English, Database: MEDLINE
BACKGROUND: Mycetoma is a neglected, chronic, and deforming infectious disease caused by fungi and
actinomycetes. In Mexico, N. brasiliensis is the predominant etiologic agent. Therapeutic alternatives are necessary
because the current drug regimens have several disadvantages. Benzothiazinones (BTZ) are a new class of
candidate drugs that inhibit decaprenyl-phosphoribose-epimerase (DprE1), an essential enzyme involved in the cell
wall biosynthesis of Corynebacterineae. METHODOLOGY/PRINCIPAL FINDINGS: In this study, the in vitro activity of
the next generation BTZ, PBTZ169, was tested against thirty Nocardia brasiliensis isolates. The MIC50 and MIC90
values for PBTZ169 were 0.0075 and 0.03 g/mL, respectively. Because Nocardia is a potential intracellular
bacterium, a THP-1 macrophage monolayer was infected with N. brasiliensis HUJEG-1 and then treated with
PBTZ169, resulting in a decrease in the number of colony-forming units (CFUs) at a concentration of 0.25X the in vitro
value. The in vivo activity was evaluated after infecting female BALB/c mice in the right hind food-pad. After 6 weeks,
treatment was initiated with PBTZ169 and its activity was compared with the first generation compound, BTZ043. Both
BTZ compounds were administered at 100 mg/kg twice daily by gavage, and sulfamethoxazole/trimethoprim (SXT), at
100 mg/kg sulfamethoxazole, was used as a positive control. After 22 weeks of therapy, only PBTZ169 and SXT
displayed statistically significant activity. CONCLUSION: These results indicate that DprE1 inhibitors may be useful
for treating infections of Nocardia and may therefore be active against other actinomycetoma agents. We must test
combinations of these compounds with other antimicrobial agents, such as linezolid, tedizolid or SXT, that have good
to excellent in vivo activity, as well as new DprE1 inhibitors that can achieve higher plasma levels.
~0 Citings
50. The 8-Pyrrole-Benzothiazinones Are Noncovalent Inhibitors of DprE1 from Mycobacterium tuberculosis
By Makarov Vadim; Ryabova Olga B; Kazakova Elena; Neres Joao; Hartkoorn Ruben C; Piton Jeremie; Kolly Gaelle S;
Vocat Anthony; Conroy Trent M; Cole Stewart T; et al
From Antimicrobial agents and chemotherapy (2015), 59(8), 4446-52, Language: English, Database: MEDLINE
8-Nitro-benzothiazinones (BTZs), such as BTZ043 and PBTZ169, inhibit decaprenylphosphoryl--d-ribose 2'-oxidase
(DprE1) and display nanomolar bactericidal activity against Mycobacterium tuberculosis in vitro. Structure-activity
relationship (SAR) studies revealed the 8-nitro group of the BTZ scaffold to be crucial for the mechanism of action,
which involves formation of a semimercaptal bond with Cys387 in the active site of DprE1. To date, substitution of the
8-nitro group has led to extensive loss of antimycobacterial activity. Here, we report the synthesis and characterization
of the pyrrole-benzothiazinones PyrBTZ01 and PyrBTZ02, non-nitro-benzothiazinones that retain significant
antimycobacterial activity, with MICs of 0.16 g/ml against M. tuberculosis. These compounds inhibit DprE1 with 50%
inhibitory concentration (IC50) values of <8 M and present favorable in vitro absorption-distribution-metabolismexcretion/toxicity (ADME/T) and in vivo pharmacokinetic profiles. The most promising compound, PyrBTZ01, did not
show efficacy in a mouse model of acute tuberculosis, suggesting that BTZ-mediated killing through DprE1 inhibition
requires a combination of both covalent bond formation and compound potency.
~0 Citings
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51. DprE1 Is a Vulnerable Tuberculosis Drug Target Due to Its Cell Wall Localization
By Brecik Miroslav; Centarova Ivana; Huszar Stanislav; Bobovska Adela; Kilacskova Emoke; Mokosova Veronika;
Svetlikova Zuzana; Sarkan Michal; Kordulakova Jana; Mikusova Katarina; et al
From ACS chemical biology (2015), 10(7), 1631-6, Language: English, Database: MEDLINE
The flavo-enzyme DprE1 catalyzes a key epimerization step in the decaprenyl-phosphoryl d-arabinose (DPA) pathway,
which is essential for mycobacterial cell wall biogenesis and targeted by several new tuberculosis drug candidates.
Here, using differential radiolabeling with DPA precursors and high-resolution fluorescence microscopy, we disclose
the unexpected extracytoplasmic localization of DprE1 and periplasmic synthesis of DPA. Collectively, this explains
the vulnerability of DprE1 and the remarkable potency of the best inhibitors.
~1 Citing
52. Development of selective DprE1 inhibitors: Design, synthesis, crystal structure and antitubercular activity of
benzothiazolylpyrimidine-5-carboxamides
By Chikhale Rupesh; Menghani Sunil; Babu Ramavath; Bhargavi G; Rajasekharan M V; Bansode Ratnadeep; Karodia
Nazira; Paradkar Anant; Khedekar Pramod
From European journal of medicinal chemistry (2015), 9630-46, Language: English, Database: MEDLINE
Decaprenylphosphoryl-b-D-ribose 20-epimerase (DprE1) is a potential drug target for development of antitubercular
agents. Structure based drug discovery approach yielded twenty novel derivatives of benzothiazolylpyrimidine-5carboxamides (7a-t) which were synthesised by three component one pot reaction involving benzothiazolyl
oxobutanamide, thiourea and substituted aromatic benzaldehydes. These derivatives were evaluated for
antitubercular activity to determine MIC and compound 7a, 7e, 7f and 7o were found to be potentially active against
Mycobacterium tuberculosis (H37Rv). Log P of these compounds was found to be between 2.0 and 3.0 making them
suitable for oral dosing. DprE1 selectivity and pharmacokinetic studies were carried out for these compounds of which
7a and 7o were found to be highly selective and bioavailability was found to be above 52% by oral dose. Crystal
structure of 7a was studied and molecular packing was determined, it exhibited a triclinic crystal lattice arrangement
having hydrogen bonded dimeric arrangement. Drug receptor interactions were studied which exhibited docking in the
active site of receptor with hydrogen bonding, hydrophobic interactions, vdW interactions with amino acid residues
such as Cys387, Asn385, Lys418, Tyr314, Gln334 and Lys367 respectively. 3D QSAR analysis was carried out by
kNN-MFA method to determine and develop theoretical model, best suitable model was found to be based on
Simulated Annealing k-Neariest Neighbour Molecular Field Analysis (SA kNN-MFA). The model provided with
hydrophobic descriptors in positive side indicating the need of bulky groups, steric and electronegative descriptors in
negative coordinates hints with contribution by the electronegative substitutions as favourable and desirable moieties
for enhancing the activity. The q(2), q(2)_se and Pred_r(2)se were found to be 0.5000, 0.6404 and 1.0094
respectively. A pharmacophore model was generated which suggested for necessity of aromatic, aliphatic carbon
centre and hydrogen bond donor for development of newer DprE1 selective inhibitors.
~0 Citings
53. Structure, dynamics, and interaction of Mycobacterium tuberculosis (Mtb) DprE1 and DprE2 examined by
molecular modeling, simulation, and electrostatic studies
By Bhutani Isha; Loharch Saurabh; Gupta Pawan; Madathil Rethi; Parkesh Raman
From PloS one (2015), 10(3), e0119771, Language: English, Database: MEDLINE
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The enzymes decaprenylphosphoryl--D-ribose oxidase (DprE1) and decaprenylphosphoryl--D-ribose-2-epimerase

(DprE2) catalyze epimerization of decaprenylphosporyl ribose (DPR) todecaprenylphosporyl arabinose (DPA) and are
critical for the survival of Mtb. Crystal structures of DprE1 so far reported display significant disordered regions and no
structural information is known for DprE2. We used homology modeling, protein threading, molecular docking and
dynamics studies to investigate the structural and dynamic features of Mtb DprE1 and DprE2 and DprE1-DprE2
complex. A three-dimensional model for DprE2 was generated using the threading approach coupled with ab initio
modeling. A 50 ns simulation of DprE1 and DprE2 revealed the overall stability of the structures. Principal Component
Analysis (PCA) demonstrated the convergence of sampling in both DprE1 and DprE2. In DprE1, residues in the 269330 area showed considerable fluctuation in agreement with the regions of disorder observed in the reported crystal
structures. In DprE2, large fluctuations were detected in residues 95-113, 146-157, and 197-226. The study combined
docking and MD simulation studies to map and characterize the key residues involved in DprE1-DprE2 interaction. A
60 ns MD simulation for DprE1-DprE2 complex was also performed. Analysis of data revealed that the docked
complex is stabilized by H-bonding, hydrophobic and ionic interactions. The key residues of DprE1 involved in DprE1DprE2 interactions belong to the disordered region. We also examined the docked complex of DprE1-BTZ043 to
investigate the binding pocket of DprE1 and its interactions with the inhibitor BTZ043. In summary, we hypothesize
that DprE1-DprE2 interaction is crucial for the synthesis of DPA and DprE1-DprE2 complex may be a new therapeutic
target amenable to pharmacological validation. The findings have important implications in tuberculosis (TB) drug
discovery and will facilitate drug development efforts against TB.
~0 Citings
54. Synthesis and antitubercular evaluation of 4-carbonyl piperazine substituted 1,3-benzothiazin-4-one

derivatives
By Peng Cui-Ting; Gao Chao; Wang Ning-Yu; Zhu Yong-Xia; Xv Ying; Zuo Wei-Qiong; Ran Kai; Deng Hong-Xia; Lei
Qian; Xiao Kun-Jie; et al
From Bioorganic & medicinal chemistry letters (2015), 25(7), 1373-6, Language: English, Database: MEDLINE
Tuberculosis (TB) remains a major human health problem. New therapeutic antitubercular agents are urgent needed
to control the global tuberculosis pandemic. We synthesized a new series of 4-carbonyl piperazine substituted 1,3benzothiazin-4-one derivatives and evaluated their anti-mycobacterial activities against Mycobacterium tuberculosis
H37Ra as well as their druggabilities. The results showed that most of these derivatives, especially the compounds
with simple alkyl side chains, exhibited good antitubercular activities and favorable aqueous solubilities with no obvious
cytotoxicity. It suggested that the 4-carbonyl piperazine substituents in benzothiazinone scaffold were well tolerated, in
which the compound 8h, with an antitubercular activity of MIC 0.008 M, exhibited an excellent aqueous solubility of
104 g/mL, which was 100-fold better than the potent DprE1 inhibitor Comp.1 (BTZ038), also more soluble than
PBTZ169.
~1 Citing
55. 2-Carboxyquinoxalines kill mycobacterium tuberculosis through noncovalent inhibition of DprE1

By Neres Joao; Hartkoorn Ruben C; Chiarelli Laurent R; Pasca Maria Rosalia; Mori Giorgia; Savina Svetlana; Makarov
Vadim; Kolly Gaelle S; Molteni Elisabetta; Binda Claudia; et al
Phenotypic screening of a quinoxaline library against replicating Mycobacterium tuberculosis led to the identification of
lead compound Ty38c (3-((4-methoxybenzyl)amino)-6-(trifluoromethyl)quinoxaline-2-carboxylic acid). With an MIC99
and MBC of 3.1 M, Ty38c is bactericidal and active against intracellular bacteria. To investigate its mechanism of
action, we isolated mutants resistant to Ty38c and sequenced their genomes. Mutations were found in rv3405c,
coding for the transcriptional repressor of the divergently expressed rv3406 gene. Biochemical studies clearly showed
that Rv3406 decarboxylates Ty38c into its inactive keto metabolite. The actual target was then identified by isolating
Ty38c-resistant mutants of an M. tuberculosis strain lacking rv3406. Here, mutations were found in dprE1, encoding
the decaprenylphosphoryl-d-ribose oxidase DprE1, essential for biogenesis of the mycobacterial cell wall. Genetics,
biochemical validation, and X-ray crystallography revealed Ty38c to be a noncovalent, noncompetitive DprE1 inhibitor.
Structure-activity relationship studies generated a family of DprE1 inhibitors with a range of IC50's and bactericidal
activity. Co-crystal structures of DprE1 in complex with eight different quinoxaline analogs provided a high-resolution
interaction map of the active site of this extremely vulnerable target in M. tuberculosis.
~2 Citings
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56. 2-Phenylindole and Arylsulphonamide: Novel Scaffolds Bactericidal against Mycobacterium tuberculosis
By Naik Maruti; Ghorpade Sandeep; Jena Lalit Kumar; Gorai Gopinath; Narayan Ashwini; Guptha Supreeth; Sharma
Sreevalli; Dinesh Neela; Kaur Parvinder; Nandishaiah Radha; et al
From ACS medicinal chemistry letters (2014), 5(9), 1005-9, Language: English, Database: MEDLINE
A cellular activity-based screen on Mycobacterium tuberculosis (Mtb) H37Rv using a focused library from the
AstraZeneca corporate collection led to the identification of 2-phenylindoles and arylsulphonamides, novel
antimycobacterial scaffolds. Both the series were bactericidal in vitro and in an intracellular macrophage infection
model, active against drug sensitive and drug resistant Mtb clinical isolates, and specific to mycobacteria. The
scaffolds showed promising structure-activity relationships; compounds with submicromolar cellular potency were
identified during the hit to lead exploration. Furthermore, compounds from both scaffolds were tested for inhibition of
known target enzymes or pathways of antimycobacterial drugs including InhA, RNA polymerase, DprE1,
topoisomerases, protein synthesis, and oxidative-phosphorylation. Compounds did not inhibit any of the targets
suggesting the potential of a possible novel mode of action(s). Hence, both scaffolds provide the opportunity to be
developed further as leads and tool compounds to uncover novel mechanisms for tuberculosis drug discovery.
~0 Citings
57. 1,4-azaindole, a potential drug candidate for treatment of tuberculosis

By Chatterji Monalisa; Ramachandran Vasanthi; Sharma Sreevalli; Narayanan Shridhar; Shandil Radha; Solapure
Suresh; Kumar Naveen; Saralaya Ramanatha; Panduga Vijender; Reddy Jitendar; et al
New therapeutic strategies against multidrug-resistant (MDR) and extensively drug-resistant (XDR) Mycobacterium
tuberculosis are urgently required to combat the global tuberculosis (TB) threat. Toward this end, we previously
reported the identification of 1,4-azaindoles, a promising class of compounds with potent antitubercular activity through
noncovalent inhibition of decaprenylphosphoryl--D-ribose 2'-epimerase (DprE1). Further, this series was optimized to
improve its physicochemical properties and pharmacokinetics in mice. Here, we describe the short-listing of a potential
clinical candidate, compound 2, that has potent cellular activity, drug-like properties, efficacy in mouse and rat chronic
TB infection models, and minimal in vitro safety risks. We also demonstrate that the compounds, including compound
2, have no antagonistic activity with other anti-TB drugs. Moreover, compound 2 shows synergy with PA824 and
TMC207 in vitro, and the synergy effect is translated in vivo with TMC207. The series is predicted to have a low
clearance in humans, and the predicted human dose for compound 2 is 1 g/day. Altogether, our data suggest that a
1,4-azaindole (compound 2) is a promising candidate for the development of a novel anti-TB drug.
~1 Citing
58. Lead optimization of 1,4-azaindoles as antimycobacterial agents

By Shirude Pravin S; Shandil Radha K; Manjunatha M R; Sadler Claire; Panda Manoranjan; Panduga Vijender; Reddy
Jitendar; Saralaya Ramanatha; Nanduri Robert; Ambady Anisha; et al
From Journal of medicinal chemistry (2014), 57(13), 5728-37, Language: English, Database: MEDLINE
In a previous report, we described the discovery of 1,4-azaindoles, a chemical series with excellent in vitro and in vivo
antimycobacterial potency through noncovalent inhibition of decaprenylphosphoryl--d-ribose-2'-epimerase (DprE1).
Nevertheless, high mouse metabolic turnover and phosphodiesterase 6 (PDE6) off-target activity limited its
advancement. Herein, we report lead optimization of this series, culminating in potent, metabolically stable compounds
that have a robust pharmacokinetic profile without any PDE6 liability. Furthermore, we demonstrate efficacy for 1,4azaindoles in a rat chronic TB infection model. We believe that compounds from the 1,4-azaindole series are suitable
for in vivo combination and safety studies.
~1 Citing
59. 4-aminoquinolone piperidine amides: noncovalent inhibitors of DprE1 with long residence time and potent
antimycobacterial activity
By Naik Maruti; Humnabadkar Vaishali; Tantry Subramanyam J; Panda Manoranjan; Narayan Ashwini; Guptha
Supreeth; Panduga Vijender; Manjrekar Praveena; Jena Lalit Kumar; Koushik Krishna; et al
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4-Aminoquinolone piperidine amides (AQs) were identified as a novel scaffold starting from a whole cell screen, with
potent cidality on Mycobacterium tuberculosis (Mtb). Evaluation of the minimum inhibitory concentrations, followed by
whole genome sequencing of mutants raised against AQs, identified decaprenylphosphoryl--d-ribose 2'-epimerase
(DprE1) as the primary target responsible for the antitubercular activity. Mass spectrometry and enzyme kinetic
studies indicated that AQs are noncovalent, reversible inhibitors of DprE1 with slow on rates and long residence times
of 100 min on the enzyme. In general, AQs have excellent leadlike properties and good in vitro secondary
pharmacology profile. Although the scaffold started off as a single active compound with moderate potency from the
whole cell screen, structure-activity relationship optimization of the scaffold led to compounds with potent DprE1
inhibition (IC50 < 10 nM) along with potent cellular activity (MIC = 60 nM) against Mtb.
~2 Citings
60. Discovery of pyrazolopyridones as a novel class of noncovalent DprE1 inhibitor with potent antimycobacterial activity
By Panda Manoranjan; Ramachandran Sreekanth; Ramachandran Vasanthi; Shirude Pravin S; Humnabadkar Vaishali;
Nagalapur Kavitha; Sharma Sreevalli; Kaur Parvinder; Guptha Supreeth; Narayan Ashwini; et al
A novel pyrazolopyridone class of inhibitors was identified from whole cell screening against Mycobacterium
tuberculosis (Mtb). The series exhibits excellent bactericidality in vitro, resulting in a 4 log reduction in colony forming
units following compound exposure. The significant modulation of minimum inhibitory concentration (MIC) against a
Mtb strain overexpressing the Rv3790 gene suggested the target of pyrazolopyridones to be decaprenylphosphoryl-D-ribose-2'-epimerase (DprE1). Genetic mapping of resistance mutation coupled with potent enzyme inhibition activity
confirmed the molecular target. Detailed biochemical characterization revealed the series to be a noncovalent inhibitor
of DprE1. Docking studies at the active site suggest that the series can be further diversified to improve the
physicochemical properties without compromising the antimycobacterial activity. The pyrazolopyridone class of
inhibitors offers an attractive non-nitro lead series targeting the essential and vulnerable DprE1 enzyme for the
discovery of novel antimycobacterial agents to treat both drug susceptible and drug resistant strains of Mtb.
~2 Citings
61. Sulfur rich 2-mercaptobenzothiazole and 1,2,3-triazole conjugates as novel antitubercular agents
By Mir Fauzia; Alam M S; Shafi Syed; Zaman M S; Kalia Nitin Pal; Rajput Vikrant S; Mulakayala Chaitanya;
Mulakayala Naveen; Khan Inshad A
From European journal of medicinal chemistry (2014), 76274-83, Language: English, Database: MEDLINE
A series of benzfused heterocyclic derivatives such as amide conjugates of 2-(benzo[d]thiazol-2-ylthio)acetic acid with
aromatic/aliphatic/cyclic secondary amines (5a-5o & 8a-8m); 1,2,3-triazole conjugates of 2-mercaptobenzothiazoles
and amide conjugates of indole-3-glyoxalic acid with cyclic secondary amines (14a-14g) have been synthesized and
were screened for their antitubercular activity against Mycobacterium tuberculosis H37Rv strain by broth microdilution
assay method. Compounds 8b, 8f, 8g and 8l inhibited the growth of the H37Rv strain at concentrations of 8 g/mL.
These compounds (8b, 8f, 8g and 8l) have been further identified as bactericidal and are completely killing the
microbes at 32-64 g/mL concentrations. Molecular docking studies of the active compounds reveal that these
compounds are targeting DprE1 and may act as DprE1 inhibitors.
~0 Citings
62. Towards a new combination therapy for tuberculosis with next generation benzothiazinones
By Makarov Vadim; Lechartier Benoit; Zhang Ming; Neres Joao; van der Sar Astrid M; Raadsen Susanne A; Hartkoorn
Ruben C; Ryabova Olga B; Vocat Anthony; Decosterd Laurent A; et al
From EMBO molecular medicine (2014), 6(3), 372-83, Language: English, Database: MEDLINE
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The benzothiazinone lead compound, BTZ043, kills Mycobacterium tuberculosis by inhibiting the essential flavoenzyme DprE1, decaprenylphosphoryl-beta-D-ribose 2-epimerase. Here, we synthesized a new series of piperazinecontaining benzothiazinones (PBTZ) and show that, like BTZ043, the preclinical candidate PBTZ169 binds covalently
to DprE1. The crystal structure of the DprE1-PBTZ169 complex reveals formation of a semimercaptal adduct with
Cys387 in the active site and explains the irreversible inactivation of the enzyme. Compared to BTZ043, PBTZ169 has
improved potency, safety and efficacy in zebrafish and mouse models of tuberculosis (TB). When combined with other
TB drugs, PBTZ169 showed additive activity against M. tuberculosis in vitro except with bedaquiline (BDQ) where
synergy was observed. A new regimen comprising PBTZ169, BDQ and pyrazinamide was found to be more
efficacious than the standard three drug treatment in a murine model of chronic disease. PBTZ169 is thus an attractive
drug candidate to treat TB in humans.
~11 Citings
63. DprE1--from the discovery to the promising tuberculosis drug target

By Mikusova Katarina; Makarov Vadim; Neres Joao
From Current pharmaceutical design (2014), 20(27), 4379-403, Language: English, Database: MEDLINE
Several groups working in the field of the development of new antituberculosis drugs have recently reported active
compounds targeting mycobacterial enzyme DprE1. Along with its counterpart, DprE2, it catalyses a unique
epimerization reaction resulting in the synthesis of decaprenylphosphoryl arabinose, the single donor of arabinosyl
residues for the build-up of arabinans, fundamental components of the mycobacterial cell wall. This review presents
the historical background leading to the discovery of DprE1, focusing on the biochemical and structural
characterization of this important emerging target and introducing the molecules acting on DprE1 including the
development of the most successful series--the benzothiazinones, currently in late pre-clinical development, which
turned to be suicide inhibitors of DprE1.
~1 Citing
64. Azaindoles: noncovalent DprE1 inhibitors from scaffold morphing efforts, kill Mycobacterium tuberculosis
and are efficacious in vivo
By Shirude Pravin S; Shandil Radha; Sadler Claire; Naik Maruti; Hosagrahara Vinayak; Hameed Shahul; Shinde Vikas;
Bathula Chandramohan; Humnabadkar Vaishali; Kumar Naveen; et al
We report 1,4-azaindoles as a new inhibitor class that kills Mycobacterium tuberculosis in vitro and demonstrates
efficacy in mouse tuberculosis models. The series emerged from scaffold morphing efforts and was demonstrated to
noncovalently inhibit decaprenylphosphoryl--D-ribose2'-epimerase (DprE1). With "drug-like" properties and no
expectation of pre-existing resistance in the clinic, this chemical class has the potential to be developed as a therapy
for drug-sensitive and drug-resistant tuberculosis.
~5 Citings
65. The DprE1 enzyme, one of the most vulnerable targets of Mycobacterium tuberculosis
By Riccardi Giovanna; Pasca Maria Rosalia; Chiarelli Laurent Roberto; Manina Giulia; Mattevi Andrea; Binda Claudia
From Applied microbiology and biotechnology (2013), 97(20), 8841-8, Language: English, Database: MEDLINE
The re-emergence of tuberculosis in recent years led the World Health Organization (WHO) to launch the Stop TB
Strategy program. Beside repurposing the existing drugs and exploring novel molecular combinations, an essential
step to face the burden of tuberculosis will be to develop new drugs by identifying vulnerable bacterial targets. Recent
studies have focused on decaprenylphosphoryl-D-ribose oxidase (DprE1) of Mycobacterium tuberculosis, an essential
enzyme involved in cell wall metabolism, for which new promising molecules have proved efficacy as antitubercular
agents. This review summarizes the state of the art concerning DprE1 in terms of structure, enzymatic activity and
inhibitors. This enzyme is emerging as one of the most vulnerable target in M. tuberculosis.
~0 Citings
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66. Thiolates chemically induce redox activation of BTZ043 and related potent nitroaromatic anti-tuberculosis
agents
By Tiwari Rohit; Moraski Garrett C; Krchnak Viktor; Miller Patricia A; Colon-Martinez Mariangelli; Herrero Eliza; Oliver
Allen G; Miller Marvin J
From Journal of the American Chemical Society (2013), 135(9), 3539-49, Language: English, Database: MEDLINE
The development of multidrug resistant (MDR) and extensively drug resistant (XDR) forms of tuberculosis (TB) has
stimulated research efforts globally to expand the new drug pipeline. Nitroaromatic compounds, including 1,3benzothiazin-4-ones (BTZs) and related agents, are a promising new class for the treatment of TB. Research has
shown that the nitroso intermediates of BTZs that are generated in vivo cause suicide inhibition of
decaprenylphosphoryl--D-ribose 2' oxidase (DprE1), which is responsible for cell wall arabinogalactan biosynthesis.
We have designed and synthesized novel anti-TB agents inspired from BTZs and other nitroaromatic compounds.
Computational studies indicated that the unsubstituted aromatic carbons of BTZ043 and related nitroaromatic
compounds are the most electron-deficient and might be prone to nucleophilic attack. Our chemical studies on
BTZ043 and the additional nitroaromatic compounds synthesized by us and others confirmed the postulated reactivity.
The results indicate that nucleophiles such as thiolates, cyanide, and hydride induce nonenzymatic reduction of the
nitro groups present in these compounds to the corresponding nitroso intermediates by addition at the unsubstituted
electron-deficient aromatic carbon present in these compounds. Furthermore, we demonstrate here that these
compounds are good candidates for the classical von Richter reaction. These chemical studies offer an alternate
hypothesis for the mechanism of action of nitroaromatic anti-TB agents, in that the cysteine thiol(ate) or a hydride
source at the active site of DprE1 may trigger the reduction of the nitro groups in a manner similar to the von Richter
reaction to the nitroso intermediates, to initiate the inhibition of DprE1.
~4 Citings
67. In vitro combination studies of benzothiazinone lead compound BTZ043 against Mycobacterium tuberculosis
By Lechartier Benoit; Hartkoorn Ruben C; Cole Stewart T
Benzothiazinones (BTZ) are a new class of drug candidates to combat tuberculosis that inhibit decaprenylphosphoribose epimerase (DprE1), an essential enzyme involved in arabinan biosynthesis. Using the checkerboard
method and cell viability assays, we have studied the interaction profiles of BTZ043, the current lead compound, with
several antituberculosis drugs or drug candidates against Mycobacterium tuberculosis strain H37Rv, namely, rifampin,
isoniazid, ethambutol, TMC207, PA-824, moxifloxacin, meropenem with or without clavulanate, and SQ-109. No
antagonism was found between BTZ043 and the tested compounds, and most of the interactions were purely additive.
Data from two different approaches clearly indicate that BTZ043 acts synergistically with TMC207, with a fractional
inhibitory concentration index of 0.5. TMC207 at a quarter of the MIC (20 ng/ml) used in combination with BTZ043 (1/4
MIC, 0.375 ng/ml) had a stronger bactericidal effect on M. tuberculosis than TMC207 alone at a concentration of 80
ng/ml. This synergy was not observed when the combination was tested on a BTZ-resistant M. tuberculosis mutant,
suggesting that DprE1 inhibition is the basis for the interaction. This finding excludes the possibility of synergy
occurring through an off-target mechanism. We therefore hypothesize that sub-MICs of BTZ043 weaken the bacterial
cell wall and allow improved penetration of TMC207 to its target. Synergy between two new antimycobacterial
compounds, such as TMC207 and BTZ043, with novel targets, offers an attractive foundation for a new tuberculosis
regimen.
~9 Citings

By Batt Sarah M; Jabeen Talat; Bhowruth Veemal; Quill Lee; Lund Peter A; Eggeling Lothar; Alderwick Luke J; Futterer
Klaus; Besra Gurdyal S
From Proceedings of the National Academy of Sciences of the United States of America (2012), 109(28), 11354-9,
Language: English, Database: MEDLINE
SciFinder
Page 28
lacking structural evidence. We report here the crystal structure of the BTZ target, FAD-containing oxidoreductase
Mycobacterium tuberculosis DprE1, which is essential for viability. Different crystal forms of ligand-free DprE1 reveal
Structures of complexes with the BTZ-derived nitroso derivative CT325 reveal the mode of inhibitor binding, which
includes a covalent link to conserved Cys387, and reveal a trifluoromethyl group as a second key determinant of
interaction with the enzyme. Surprisingly, we find that a noncovalent complex was formed between DprE1 and CT319,
which is structurally identical to CT325 except for an inert nitro group replacing the reactive nitroso group. This
demonstrates that binding of BTZ-class inhibitors to DprE1 is not strictly dependent on formation of the covalent link to
Cys387. On the basis of the structural and activity data, we propose that the complex of DrpE1 bound to CT325 is a
representative of the BTZ-target complex. These results mark a significant step forward in the characterization of a
key TB drug target.
~13 Citings
69. Identification of novel inhibitors of M. tuberculosis growth using whole cell based high-throughput screening
By Stanley Sarah A; Grant Sarah Schmidt; Kawate Tomohiko; Iwase Noriaki; Shimizu Motohisa; Wivagg Carl; Silvis
Melanie; Kazyanskaya Edward; Aquadro John; Golas Aaron; et al
Despite the urgent need for new antitubercular drugs, few are on the horizon. To combat the problem of emerging
drug resistance, structurally unique chemical entities that inhibit new targets will be required. Here we describe our
investigations using whole cell screening of a diverse collection of small molecules as a methodology for identifying
novel inhibitors that target new pathways for Mycobacterium tuberculosis drug discovery. We find that conducting
primary screens using model mycobacterial species may limit the potential for identifying new inhibitors with efficacy
against M. tuberculosis. In addition, we confirm the importance of developing in vitro assay conditions that are
reflective of in vivo biology for maximizing the proportion of hits from whole cell screening that are likely to have activity
in vivo. Finally, we describe the identification and characterization of two novel inhibitors that target steps in M.
tuberculosis cell wall biosynthesis. The first is a novel benzimidazole that targets mycobacterial membrane protein
large 3 (MmpL3), a proposed transporter for cell wall mycolic acids. The second is a nitro-triazole that inhibits
decaprenylphosphoryl--D-ribose 2'-epimerase (DprE1), an epimerase required for cell wall biosynthesis. These
proteins are both among the small number of new targets that have been identified by forward chemical genetics using
resistance generation coupled with genome sequencing. This suggests that methodologies currently employed for
screening and target identification may lead to a bias in target discovery and that alternative methods should be
explored.
~32 Citings
70. Benzothiazinones are suicide inhibitors of mycobacterial decaprenylphosphoryl--D-ribofuranose 2'-oxidase

DprE1
By Trefzer Claudia; Skovierova Henrieta; Buroni Silvia; Bobovska Adela; Nenci Simone; Molteni Elisabetta; Pojer
Florence; Pasca Maria R; Makarov Vadim; Cole Stewart T; et al
From Journal of the American Chemical Society (2012), 134(2), 912-5, Language: English, Database: MEDLINE
Benzothiazinones (BTZs) are antituberculosis drug candidates with nanomolar bactericidal activity against tubercle
bacilli. Here we demonstrate that BTZs are suicide substrates of the FAD-dependent decaprenylphosphoryl--Dribofuranose 2'-oxidase DprE1, an enzyme involved in cell-wall biogenesis. BTZs are reduced by DprE1 to an
electrophile, which then reacts in a near-quantitative manner with an active-site cysteine of DprE1, thus providing a
rationale for the extraordinary potency of BTZs. Mutant DprE1 enzymes from BTZ-resistant strains reduce BTZs to
inert metabolites while avoiding covalent inactivation. Our results explain the basis for drug sensitivity and resistance
to an exceptionally potent class of antituberculosis agents.
~16 Citings
71. New tuberculosis drugs on the horizon
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By Cole Stewart T; Riccardi Giovanna

From Current opinion in microbiology (2011), 14(5), 570-6, Language: English, Database: MEDLINE
Tuberculosis (TB) remains a major global health concern whose control has been exacerbated by HIV and the
emergence of multidrug-resistant (MDR-TB) and extensively drug-resistant (XDR-TB) strains of Mycobacterium
tuberculosis. The demand for new and faster acting TB drugs is thus greater than ever. In the past decade intensive
efforts have been made to discover new leads for TB drug development using both target-based and cell-based
approaches. Here, we describe the most promising anti-tubercular drug candidates that are in clinical development
and introduce some nitro-aromatic compounds that inhibit a new target, DprE1, an essential enzyme involved in a
crucial step in mycobacterial cell wall biosynthesis.
~11 Citings
72. High content screening identifies decaprenyl-phosphoribose 2' epimerase as a target for intracellular
antimycobacterial inhibitors
By Christophe Thierry; Jackson Mary; Jeon Hee Kyoung; Fenistein Denis; Contreras-Dominguez Monica; Kim
Jaeseung; Genovesio Auguste; Carralot Jean-Philippe; Ewann Fanny; Kim Eun Hye; et al
From PLoS pathogens (2009), 5(10), e1000645, Language: English, Database: MEDLINE
A critical feature of Mycobacterium tuberculosis, the causative agent of human tuberculosis (TB), is its ability to survive
and multiply within macrophages, making these host cells an ideal niche for persisting microbes. Killing the
intracellular tubercle bacilli is a key requirement for efficient tuberculosis treatment, yet identifying potent inhibitors has
been hampered by labor-intensive techniques and lack of validated targets. Here, we present the development of a
phenotypic cell-based assay that uses automated confocal fluorescence microscopy for high throughput screening of
chemicals that interfere with the replication of M. tuberculosis within macrophages. Screening a library of 57,000 small
molecules led to the identification of 135 active compounds with potent intracellular anti-mycobacterial efficacy and no
host cell toxicity. Among these, the dinitrobenzamide derivatives (DNB) showed high activity against M. tuberculosis,
including extensively drug resistant (XDR) strains. More importantly, we demonstrate that incubation of M. tuberculosis
with DNB inhibited the formation of both lipoarabinomannan and arabinogalactan, attributable to the inhibition of
decaprenyl-phospho-arabinose synthesis catalyzed by the decaprenyl-phosphoribose 2' epimerase DprE1/DprE2.
Inhibition of this new target will likely contribute to new therapeutic solutions against emerging XDR-TB. Beyond
validating the high throughput/content screening approach, our results open new avenues for finding the next
generation of antimicrobials.
~37 Citings

DPRE1 Inhibitor Reference 07-28-2016 230748

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1. N-methylation of a bactericidal compound as a resistance mechanism in Mycobacterium tuberculosis

2. Synthesis and Antitubercular Activity of New Benzo[b]thiophenes

3. Molecular docking studies of chalcone derivatives with decaprenylphosphoryl-d-ribose oxidase (DprE1) as

5. Development of 3,5-Dinitrobenzylsulfanyl-1,3,4-oxadiazoles and Thiadiazoles as Selective Antitubercular

6. Nitroarenes as Antitubercular Agents: Stereoelectronic Modulation to Mitigate Mutagenicity

8. Discovery of benzothiazoles as antimycobacterial agents: Synthesis, structure-activity relationships and

8-Nitro-benzothiazinones (BTZs), such as BTZ043 and PBTZ169, inhibit decaprenylphosphoryl--d-ribose 2'-oxidase

Copyright 2016 American Chemical Society (ACS). All Rights Reserved.

15. Synthesis and antitubercular evaluation of 4-carbonyl piperazine substituted 1,3-benzothiazin-4-one

18. 2-Carboxyquinoxalines Kill Mycobacterium tuberculosis through Noncovalent Inhibition of DprE1

Phenotypic screening of a quinoxaline library against

19. 1,4-azaindole, a potential drug candidate for treatment of tuberculosis

22. Lead Optimization of 1,4-Azaindoles as Antimycobacterial Agents

4-Aminoquinolone piperidine amides (AQs) were identified as a

27. A large scale virtual screen of DprE1

29. Synthesis and characterization of an anti-tubercular Benzothiazinone derivative

Copyright 2016 American Chemical Society (ACS). All Rights Reserved.

31. Identification of novel DprE1 inhibitors for the treatment of tuberculosis

Copyright 2016 American Chemical Society (ACS). All Rights Reserved.

34. Structural basis for benzothiazinone-mediated killing of Mycobacterium tuberculosis

35. Structural basis of inhibition of Mycobacterium tuberculosis DprE1 by benzothiazinone inhibitors

36. Antituberculars which target decaprenylphosphoryl--D-ribofuranose 2'-oxidase DprE1: state of art

37. Structural basis of inhibition of Mycobacterium tuberculosis DprE1 by benzothiazinone inhibitors

39. Antituberculars which target decaprenylphosphoryl--D-ribofuranose 2'-oxidase DprE1: state of art

40. Benzothiazinones Are Suicide Inhibitors of Mycobacterial Decaprenylphosphoryl--D-ribofuranose 2'Oxidase DprE1

41. New tuberculosis drugs on the horizon

42. Benzothiazinones: Prodrugs That Covalently Modify the Decaprenylphosphoryl--D-ribose 2'-epimerase

Benzothiazinones (BTZs) form a new class of potent

44. N-methylation of a bactericidal compound as a resistance mechanism in Mycobacterium tuberculosis

47. Nitroarenes as Antitubercular Agents: Stereoelectronic Modulation to Mitigate Mutagenicity

48. Discovery of benzothiazoles as antimycobacterial agents: Synthesis, structure-activity relationships and

Copyright 2016 U.S. National Library of Medicine.

The enzymes decaprenylphosphoryl--D-ribose oxidase (DprE1) and decaprenylphosphoryl--D-ribose-2-epimerase

54. Synthesis and antitubercular evaluation of 4-carbonyl piperazine substituted 1,3-benzothiazin-4-one

55. 2-Carboxyquinoxalines kill mycobacterium tuberculosis through noncovalent inhibition of DprE1

57. 1,4-azaindole, a potential drug candidate for treatment of tuberculosis

58. Lead optimization of 1,4-azaindoles as antimycobacterial agents

63. DprE1--from the discovery to the promising tuberculosis drug target

Copyright 2016 U.S. National Library of Medicine.

68. Structural basis of inhibition of Mycobacterium tuberculosis DprE1 by benzothiazinone inhibitors

70. Benzothiazinones are suicide inhibitors of mycobacterial decaprenylphosphoryl--D-ribofuranose 2'-oxidase

71. New tuberculosis drugs on the horizon

By Cole Stewart T; Riccardi Giovanna

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