Structural Bioinformatics in Drug Discovery Melissa Passino

Structural Bioinformatics What is SBI? “Structural bioinformatics is a subset of bioinformatics concerned with the use of biological structures – proteins, DNA, RNA, ligands etc. and complexes thereof to further our understanding of biological systems.” http://biology.sdsc.edu/strucb.html

SBI in Drug Design and Discovery SBI can be used to examine: drug targets (usually proteins) binding of ligands ↓ “rational” drug design (benefits = saved time and $$$)

Traditional Methods of Drug Discovery natural (plant-derived) treatment for illness/ailments ↓ isolation of active compound (small, organic)

manipulation of structure to get better drug synthesis of compound ↓ manipulation of structure to get better drug (greater efficacy, fewer side effects) Aspirin

Modern Methods of Drug Discovery NEW and IMPROVED! What’s different? Drug discovery process begins with a disease (rather than a treatment) Use disease model to pinpoint relevant genetic/biological components (i.e. possible drug targets)

discovery of a “lead” molecule Modern Drug Discovery disease → genetic/biological target ↓ discovery of a “lead” molecule - design assay to measure function of target - use assay to look for modulators of target’s function high throughput screen (HTS) - to identify “hits” (compounds with binding in low nM to low μM range)

Modern Drug Discovery small molecule hits ↓ manipulate structure to increase potency i.e. decrease Ki to low nM affinity *optimization of lead molecule into candidate drug* fulfillment of required pharmacological properties: potency, absorption, bioavailability, metabolism, safety clinical trials

Interesting facts... Over 90% of drugs entering clinical trials fail to make it to market The average cost to bring a new drug to market is estimated at $770 million

Impact of Structural Bioinformatics on Drug Discovery Fig 1 & 2 Fauman et al. Speeds up key steps in DD process by combining aspects of bioinformatics, structural biology, and structure-based drug design

Identifying Targets: The “Druggable Genome”

human genome polysaccharides nucleic acids proteins lipids Problems with toxicity, specificity, and difficulty in creating potent inhibitors eliminate the first 3 categories...

proteins with binding site human genome polysaccharides nucleic acids proteins lipids proteins with binding site “druggable genome” = subset of genes which express proteins capable of binding small drug-like molecules

Relating druggable targets to disease... Analysis of pharm industry reveals: Over 400 proteins used as drug targets Sequence analysis of these proteins shows that most targets fall within a few major gene families (GPCRs, kinases, proteases and peptidases) Fig. 3, Fauman et al.

Is this a “druggable” target? Assessing Target Druggability Once a target is defined for your disease of interest, SBI can help answer the question: Is this a “druggable” target? Does it have sequence/domains similar to known targets? Does the target have a site where a drug can bind, and with appropriate affinity?

Other roles for SBI in drug discovery Binding pocket modeling Lead identification Similarity with known proteins or ligands Chemical library design / combinatorial chemistry Virtual screening *Lead optimization* Binding ADMET

SBI in cancer therapy: MMPIs

Used to treat “major” cancers: lung, GI, prostate Inability to control metastasis is the leading cause of death in patients with cancer (Zucker et al. Oncogene. 2000, 19, 6642-6650.) Matrix metalloproteinase inhibitors (MMPIs) are a newer class of cancer therapeutics can prevent metastasis (but not cytotoxic); may also play role in blocking tumor angiogenesis (growth inhibition) Used to treat “major” cancers: lung, GI, prostate

What is an MMP? Family of over 20 structurally related proteinases Principal substrates: protein components of extracellular matrix (collagen, fibronectin, laminin, proteoglycan core protein) Functions: Breakdown of connective tissue; tissue remodeling Role in cancer: Increased levels/activity of MMPs in area surrounding tumor

Brown PD. Breast Cancer Res Treat 1998, 52, 125-136.

Whittaker et al. Chem. Rev. 1999, 99, 2735-2776

Whittaker et al. Chem. Rev. 1999, 99, 2735-2776 MMP-1,3,8 MMP-2 MMP-7 MMP-10 to 13,19,20 MMP-9 Whittaker et al. Chem. Rev. 1999, 99, 2735-2776 MMP-14 to 17

Whittaker et al. Chem. Rev. 1999, 99, 2735-2776 MMP catalysis “metallo” in MMP = zinc → catalytic domain contains 2 zinc atoms Whittaker et al. Chem. Rev. 1999, 99, 2735-2776

Brown PD. Breast Cancer Res Treat 1998, 52, 125-136. Peptidic inhibitors Structure based design based on natural substrate collagen zinc binding group Poor Ki values, not very selective (inhibit other MPs) Brown PD. Breast Cancer Res Treat 1998, 52, 125-136.

Peptidic hydroxamate inhibitors Specificity for MMPs over other MPs Better binding (low nM Ki) But poor oral bioavailability

A (not very) long time ago, in a town (not too) far away… …lived a company named Agouron… …and this company had a dream, a dream to design a nonpeptidic hydroxamate inhibitor of MMPs…

...so they made some special crystals… used x-ray crystallography/3D structure of recombinant human MMPs bound to various inhibitors ↓ to determine key a.a. residues, ligand substituents needed for binding Gelatinase A http://www.rcsb.org/pdb/

…and used the magic of structural bioinformatics to design many, many nonpeptidic hydroxylates. oral bioavailabity anti-metastasis anti-growth Ki repeat…

Results… AG3340 “Prinomastat” Good oral bioavailability Selective for specific MMPs may implicate their roles in certain cancers

Prinomastat Evidence showing prevention of lung cancer metastasis in rat and mice models Clinical trials → non small cell lung cancer → hormone refractory prostate cancer …stopped at Phase 3 (Aug 2000) because did not show effects against late stage metastasis

Morals of the story… SBI can be used as basis for lead discovery and optimization MMPs are good targets for chemotherapy to help control metastasis… …but MMPIs must be combined with other cytotoxic drugs to get maximum benefits, and used at earliest stage possible