PEPTIDOMIMETICS

What do we understand by this!!!! Protein Protein interactions are important and central to biology and provide one mechanism to convert genomic information into regulated biological response

Ramachandran Plot

What are the important protein peptide interactions Binding of peptide ligands to proteases Binding of peptides hormones to peptide receptors Recruitment of protein to effect signal transduction In addition peptides also act as neurotransmitters, neuromodulators, hormones, autocrine and paracrine factors.

Use of proteins as drugs is difficult? 1. Poor pharmacokinetic profile. 2. Easily proteolysed. 3. Poorly transported. 4. Rapidly excreted.

Formulations of these drugs have tried to address some of the problems.

For these reasons, peptide portions have been replaced by non-peptide structures resulting in -peptidomimetics.

New class of drugs belonging to this area have emerged.

I local topography about an amide bondamide bond isosteres II a small non-peptide molecule binds to the receptor.morpholine Mimicking the secondary structure of peptides has become one of the most tools for rational drug design. III-posses novel templates which appear unrelated to original peptides but contains an essential group positioned above the novel non-peptide scaffold to serve as topographical mimic IV- GRAB

Hughes in 1970s showed that two different chemical structures have similar agonist property. Opiod natural product.morphine was found to resemble N-terminal structure of Endogenous opioid peptides ..enkephelins and beta endorphin

The similarity between the morphine phenol system and the N-terminal tyrosine residue in the peptide opioids implied that these units reacts with opioid receptors in a similar manner to elicite comparable response

Pyrrolinones constrain the peptide like side chain into an extended beta Structure topography that fits into the active sites of most peptidases Pyrrolinones are resistant to normal proteolyses They retain atom to atom correspondence to parent peptide They accomplish two aspects: ..Replace amide bond with metabolically stable units ..Affect conformational constraint on peptides or on peptide replacement

Pyrrolinones constrain the peptide like side chain into an extended beta structure topography that fits the active site of most peptidases.

Cyclic lactams stabilse beta and gamma turns in linear peptides

TRANSITION STATE ANALOGUE INHIBITORS

Pauling

Thorsett et.al., Synthesised bicyclic lactams of ACE

DISCOVERY OF NOVEL NON-PEPTIDE PEPTIDOMIMETICS

GROUP REPLACEMENT ASSISTED BINDING

STRUCTURE BASED DRUG DESIGN

SBDD by use of structural biology is the most logical approach in DD pardigm Great utility for the design of enzyme inhibitors, tight binding receptor ligands and Novel proteins

ATTACHMENT: Retrovirus: RNA, capsid, membrane Host: gp120 (x4) gp41 ENTRY, REVERSE TRANSCRIPTION

INTEGRATION

TRANCRIPTION

Translation

Protease

Assembly, Budding

HIV Protease
Strong structural and weak sequence homology to mammalian acid proteases (e.g. pepsin) Essential to the life cycle of the HIV virus

The aspartyl endoprotease encoded by HIV-P catalyses essential events in the maturation of infective virus particle, cleavage of polyprotein precursor to yield active products. HIV P is a symmetrical homodimer of identical 99 residue monomers, structurally and mechanistically similar to pseudosymmetric pepsin family of proteases of which renin is a member As protease was in minute quantities, it had to be overproduced in more by DNA Recombinant technique. One of the first structures was determined with material synthesized nonbiologically Through peptide synthesis.

The active site of the enzyme is C2 symmetric in the absence of substrates or inhibitors and contains two essential aspartic acid residues Asp25 and Asp25 The entrance to the active site is partly occluded by flaps constructed of two Beta strands (residues 43 49 and 52 -58) from each monomer connected by a Turn. In the absence of substrate or inhibitor, flaps seem to be rather flexible. On binding of inhibitors and presumably of substrates, the residues within the Flaps undergo movements up to several angstroms to interact with the bound ligand

 Water Binding Hypothesized

To Note about Architecture of Protease

Symmetric dimer (pepsin is monomer) Asp 25 at base of pocket in a rigid network of h bonds Hydrophobic, flaps at top, Ile 50 at tip holds a water molecule

Complementary Pockets
Peptide or inhibitor: P4-P3-P2-P1-P1-P2-P3-P4 Cut at P1-P1 bond Pockets Subsites on Enzyme: S4-S3-S2-S1-S1-S2-S3-S4 S1,S1,P1,P1,S2,S2,P2,P2 hydrophobic 3 and 4 ill defined

Binding Features
Extended conformation, Backbone-backbone amide hydrogen bonds between peptide and enzyme structural bound water near P1 Catalytic bound water molecule near asp

Peptidomimetic
DMP 323 Cyclic (less flexible) Top: Urea fragment, carbonyl replaces structural water molecule Middle: Aromatic rings fill S1 S1 S2 S2 Bottom: hydroxyl groups interact with aspartic acids Nearly C2 symmetric Nanomolar binding

 Mechanical analogy: lever : fulcrum and bar

Residues in the active site of HIV protease. C2 axis that relates the residue of the two monomers. Carboxylates Asp 25 and Asp 25 are the catalytic group.

Active site bound with saquanir

A tightly bound water is observed in the structures of most HIV-P inhibitor Complexes accepting H bonds from the backbone amides of both flap residues Ile 50 and Ile 50 and donating to carbonyls of the bound inhibitors. This is called as the flap water The active site contains some hydrophobic site also apart from water molecules.

Indinavir

Ritonavir

Saquinavir