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LITERATURE REVIEW
LITERATURE REVIEW
It has been nearly 40 years since the quantitative structure-activity relationship
(QSAR) paradigm first found its way into the practice of agro chemistry,
pharmaceutical chemistry, toxicology, and eventually most facets of chemistry. Its
attributed to the strength of its initial postulate that activity was a function of
structure. It is described by electronic attributes, hydrophobicity, and steric
properties.
computational techniques that have ensued to describe and refine the many
variables and approaches. The overall goals of QSAR retain their original essence
and remain focused on the predictive ability of the approach and its receptiveness
to mechanistic interpretation.
It is well recognized that QSAR is one of the best tools for in silico (using siliconbased computer technologies to perform simulations, modeling and experiments)
drug design. There is a dedicated quest for robust QSAR models. Origin of QSAR
is from the field of toxicology (1).It was noted by Cros in 1863 that toxicity of
substances is governed by their properties, which in turn are determined by their
chemical structure. This showed interrelationship exists between structure,
properties, and toxicity (2).
74
Structure Activity Relationships (SAR) studies have been published since 1868,
when Crum-Brown & Fraser stipulated the idea that the physiological action of a
substance in a certain biological system is a function of its chemical constitution
.Meyer and Overton suggested that the narcotic (depressant) action of a group of
(3)
(7)
75
(10)
(12)
common probe atom, similarity indices are calculated at regularly spaced grid
points for the pre aligned molecules. Later on, Chris L. Waller & Steven D. Wyrick
76
(13)
77
1996 afterward in 1997 Pourmorad, Shaifee et al. gave the synthesis and calcium
channel antagonist activity of 4- imidazolyl -1,4 dihydropyridine .they concluded
the symmetrical esters showed that increasing the length of methylene chain of
ester more than 3 units decrease calcium channel antagonist activity (18).
Quantitative structure activity relationship study is based on structure/ activity as
well as required large or small datasets. So, in 1997 A new Genetic Algorithm
(GA) strategies for variable selection of QSAR study had been reported by
Hasegawa, Miyashita et al. In these study they use GA based PLS analysis and
found high internal predictivity for small set of datasets. The GAPLS (GA-based
PLS) program is written in FORTRAN language and is running on VAX
workstation (19).
After the development of 3D QSAR a new method 4D QSAR introduced by
Christian D. P. Klein and A. J. Hopfinger in 1998
provided the set of conformation of datasets, which were analyzed using Partial
least regression in combination with the genetic function approximation algorithm
to construct QSAR model (20).
78
for the
80
et al. gave the synthesis and Evaluation of a New Class of Nifedipine Analogs with
T-Type Calcium Channel Blocking Activity (29).
Kharkar Prashant et al. in 2002 for developing Three-Dimensional Quantitative
Structure-Activity Relationship of 1, 4-Dihydropyridines as Antitubercular Agents
.In 2002 Victor E. Kuzmin et al. used 4D QSAR approach for the molecular
(30)
structure of macro cyclic pyridinophanes for anticancer and antiviral activity. This
novel 4D QSAR approach is based on simplex representation of molecular
structure with PLS regression for developing QSAR models (31).In 2002 by Zefirov,
Palyulin et al. gave a new Fragmental approach, this was employed through
fragmental descriptors for QSPR/QSAR .They are applicable for modeling of a
wide range of properties and biological activities very often providing good
predictive models and interpretable results
(32)
gave a novel methods for predicting logP, pKa, and logD values using data sets
(592 molecules for logP and 1029 for pKa) containing a wide range of molecular
structures. logP (based on polarizability and atom charge) and pKa (based on a
novel tree structured fingerprint) (33).Sheridan in 2002 enhance the use of biological
activity for large data sets , in these order he written a method that extracts one-toone replacements of chemical groups in pairs of drug-like molecules with the same
biological activity .they also counts the frequency of the replacements in a large
collection of such molecules (34).
81
(35)
Zefirov et al. in 2003 through the derivation of new HB descriptors for hydrogen
bonding and fluid phase equilibria. These descriptors also functions in ligand
docking and in Absorption, Distribution, Metabolism, Excretion (ADME)
evaluations (36).In 2003 Golbraikh and Tropsha et al. has reported that topological
chirality descriptors can be successfully used to generate 2D QSAR models for
data sets containing stereo isomers. In these QSAR study descriptors obtained
using Molconn-Z program, predictive ability of a model obtained using MATLAB,
RS configurations for chiral atoms were assigned using a SYBYL Programming
Language (SPL) script (37).In 2003 Hansch and Hoek-man et al. explained
the
model for 12 pairs of enzyme inhibitors (39). In 2003 Alberto and Goobi describes
Directed Sphere Exclusion (DISE), a modification of the Sphere Exclusion
algorithm, which retains all positive properties of the Sphere Exclusion algorithm
but generates a more even distribution of the selected compounds in the chemical
space (40).In 2003 Herve et al. describe a Probe feature selection method that can
be applied directly to models that are linear with respect to their parameters, and
indirectly to others. It is independent of the target machine. This method is very
useful for those who cannot expert in statics (41). Bleck-mann and Miler et al. in
2003 investigated the relation between the structure of epothilones (a new class of
anti-tumor agents) and their potential to influence the tubulin-microtubule
equilibrium (42).
Du and Chou et al. in 2004 reported a 2D QSAR study to Liver alcohol
Dehydrogenase (LADH) of molecular family and pyrazole derivatives. They used
quantum chemical and structure-based technique heuristic molecular lipophilicity
potential (HMLP) in the liver alcohol dehydrogenase (LADH) for pyrazole
derivatives
(43)
(50)
pyridines and developed a new 3D QSAR approach using partial least component
analysis for potent and selective inhibitors of A1 adenosine receptors method (51).
Dervarics et al. in 2006 introduced a newly devised chirality -sensitive flexibility
(CSF) descriptor, which is based on the distance between a pharmacophore point
and a plane defined by three pharmacophore points. These descriptors are used for
3+3D QSAR (52).In 2005 Gramatica et al. they compare different molecular
descriptors in the development of new statistically validated QSAR models to
predict the aquatic toxicity of chemicals in Pimephales promelas (Fathead
Minnow).they applied multiple linear regression based on theoretical descriptor.
For QSAR modeling, descriptors were selected by the Genetic Algorithm-Variable
Subset Selection procedure. They verified the effectiveness of Genetic Algorithms
as a fast and efficient procedure to select (not by chance)significant variables to
manage complex systems (53).Hammeteja et al. In 2005 evaluated three different
factor selection procedures including Eigen value ranking, correlation ranking, and
85
Nazneen Khan et al. in 2006 investigated the relationship between the various
physiochemical parameters and antibacterial activity of N-alkyl derivatives of
imidazole that may be helpful in development of potent antibacterial agent using
both 2D and 3D QSAR approaches. Stepwise Multi Linear Regression (MLR) was
used to obtain QSAR equation from calculated descriptors (58).In 2006 Tingjun Houa
et al. gave a brief review on many physiochemical descriptors .among all these
descriptors authors discussed about one of descriptor known as Abraham
descriptor. They concluded that Abraham Descriptor is the simplest way of
calculating the hydrogen bonding capacity is to count the number of hydrogen
bond donor and acceptor atoms or to count the number of lone pairs of electrons on
certain kinds of atoms
(59)
prediction models for aliphatic carboxylic acids and alcohols using MLR with
empirical atomic inductive descriptors. They demonstrated that pKa has captured
the substitutents inductive effect on the acidic center. Therefore it can also be used
for QSAR/QSPR studies of reactivity in organic compounds (60).Later on, In 2006
Abraham and Ibrahim et al. had investigated gas to olive oil partition coefficient
through linear free energy equation for 218 compounds. The linear free energy
Equation shows that olive oil is not very polar as a solvent but is reasonably basic,
although with a weaker hydrogen bond base than ethyl acetate or acetone, and has
no hydrogen bond acidity (61).
87
In 2007 Gupta et al. developed a QSAR equation using De novo, Hansch approach
and Fujita-ban analysis for estrogen analogues
(62)
reported the development of a QSAR equation relating the ligand binding activity
of various literature reported aryl piperazines acting as agonists at the 5-HT 1A
receptor to their 2D descriptors. Significant equation was generated using MOE
2004.03 and validated subsequently using leave one out and test set prediction
methods. The equation revealed the importance of combination of electronic and
lipophilic parameters in explaining the observed variance
(63)
(65)
activity-relationship
analysis.
Semi-empirical
quantum
chemical
calculation was used to find the optimum 3-D geometry of the molecules. For
88
(66)
(67)
effects of the structural features of some 4, 5-dichloroimidazolyl-1, 4dihydropyridine on their calcium channel antagonist activity, using molecular
modeling and Quantitative Structure Activity-Relationship analysis. They used
both symmetrical and asymmetrical dihydropyridine derivatives (68).
In 2008 A.S.Narute et al. performed Quantitative structure activity relationship
study on a series of (substituted 1,2 dihydro)4-thoazolidinones and 2-azetidinones
bearing benzo -thiophene nucleus with anti-tubercular activity.QSAR study has
been carried out using a combination of various physiochemical descriptors
.In
(69)
2008 further studies were conducted by the same author comparing QSAR models
obtained through different chemometric methods, including factor analysis-based
multiple linear regression (FA-MLR), principal component regression (PCR) and
partial least squares combined with genetic algorithm for variable selection (GA89
(71)
and Muratov et al. in 2009 developed a random forest statistical approach for
Tetrahymena pyriformis through various 2D descriptors .They explained that the
Principle Linear Regression (PLS), K-Nearest Neighbor (KNN), Random Forest
(RF) is insignificantly gave better results rather than any separate model
. In
(76)
computational methods, tools and databases used for organizing and extracting
biological meaning from antimicrobial research. They also mentioned that the
QSAR modeling is one of the most broadly used chemo informatics approach. This
is widely used as a tool for antimicrobial drug discovery (82).
In 2011 Mukesh Sharma et al. A 2D QSAR studies were conducted with a series
of angiotensin 2 antagonist .The physiochemical and alignment independent
descriptors were found to have an important role governing the change in
antihypertensive activity
(83)
(85)
92
(87)
1,4 dihyro
(90)
pyridine apart from CVS activities also exhibit other pharmacological activities
such as antitubercular activity (91),antibacterial activity (92),anti-inflammatory activity
, anticonvulsant activity
(93)
(94)
(96)
(97)
.In 2011
Al-Said and Ghorab et al. observed the anti-breast cancer activity of some novel
1,2-dihydropyridine, thiophene and thiazole derivatives
activity, some new
(98).
Surendra Kumar et al. in 2011 and their activity screened against HepG2(liver),
Hepa (cervical) ,MCF-7 breast cancer cells
93
(99)
(102)
94
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95
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97
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and.
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101
QSAR
study
on
benzenesulfonamide
dissociation
constant
pKa:
QSAR
analysis
of
2,4-diaminopyrido[2,3-d]pyrimidines
and2,4-
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84.
Application
of
different
chemometric
tools
in
QSAR
study
of
Synthesis
and
anti-inflammatory
activity
of
1,4-dihyropyridines
109
Synthesis
and
antimicrobial
evaluation
of
new
1,4
-dihydro-4-
110
111