Conformetrix A new dimension in drug discovery Conformetrix © All rights reserved. Conformetrix Ltd Background technology and its application to drug discovery Barrie Martin, MedChem ELRIG Drug Discovery September 2012 Manchester

Conformetrix © All rights reserved. Key Facts  Spin-out from the University of Manchester, 2008  Bionow start-up of the year, 2008  VC investor – Aquarius Equity Partners  Series A funding to start preclinical research, 2011  Bionow emerging technology of the year, 2011  First strategic collaboration signed 2012 (AstraZeneca)

Conformetrix © All rights reserved. What we do Proprietary data analysis Standard NMR experimentation Ensemble of ligand conformations occupied in solution

Conformetrix © All rights reserved. What we explore Bi-modal Population: 50: 50 Bi-modal Population: 50: 50 Uni-modal angle: -77 ° libration: 25° Uni-modal angle: -77 ° libration: 25° Tri-modal 47: 47: 6 Tri-modal 47: 47: 6 The complete conformational space the molecule naturally inhabits… …which comprises librations about mode conformations

Conformetrix © All rights reserved. Example 1: Carazolol   2 -Adrenergic receptor antagonist.  6 Rotatable bonds.  ~10 6 possible conformations.  Co-crystal available 2007.

Conformetrix © All rights reserved. Carazolol Ensemble of all conformations explored in solution 3 conformations account for 42% of the population

Conformetrix © All rights reserved. Carazolol 3 conformations account for 42% of the population

Conformetrix © All rights reserved. Carazolol  Bioactive conformation (grey) overlayed onto one of the three preferred solution conformations.  Superimposable within the error of the crystal.

Conformetrix © All rights reserved. Conformetrix structure and co-crystal. Computational chemistry and co-crystal Conformetrix structure determined within 2 weeks Carazolol

Conformetrix © All rights reserved. Example 2: Lisinopril  Angiotensin converting enzyme inhibitor  11 Rotatable bonds  ~10 11 possible conformations

Conformetrix © All rights reserved. Occupancy Conformation index 45% of the occupancy In 1 of 9 conformations 9 idealised conformations of Lisinopril. Lisinopril

Conformetrix © All rights reserved. Ile Pro His Lisinopril Conformetrix structure vs. bioactive conformation Conventional NMRMolecular ModellingFree ligand X-ray

Conformetrix © All rights reserved. Example 3: Angiotensin(1-7)  Peptide/ligand overlay on key pharmacophore points  Solution structures of endogenous ligands can act as the template for drug design and library enrichment

Conformetrix © All rights reserved. Broad applicability Lisinopril Carazolol Hyaluronan TRH Losartan AngiotensinII Tocinoic acid Amikacin

Conformetrix © All rights reserved. Predictive of bioactive conformation Lisinopril Streptomycin Amikacin Carazolol Hyaluronan (HA) Ivermectin

Conformetrix © All rights reserved. Potential applications in drug design

Conformetrix © All rights reserved. Virtual screening a) Pharmacophore model b) Single compound c) Natural ligand

Conformetrix © All rights reserved. Target 1: TRHR Thyrotropin-releasing hormone TRH - Tripeptide

Conformetrix © All rights reserved. Thyrotropin-releasing hormone TRH - Tripeptide 4 modes Multi-modal for dynamic binding or receptor sub-types? Target 1: TRHR

Conformetrix © All rights reserved. 12 selected for assay VS 3.6m Whole molecule used as pharmacophore model for in silico screen Target 1: TRHR

Conformetrix © All rights reserved. C4X_1_03 First Non-Peptidic TRHR agonist Target 1: TRHR Overlay of structures highlights similar range of motions and next steps for Med Chem.

Conformetrix © All rights reserved. Target 2: GPCR  Type A GPCR  No structural data on target  >340 ligand patents  5 clinical-stage compounds  Conformetrix solved structures for 6 published compounds  Virtual screening, de novo design, scaffold hopping and isostere replacement used to identify novel chemistries  6 novel active frameworks identified in First Design Sets  Potencies down to 35nM

Conformetrix © All rights reserved. Target 2: isostere replacement Molecule 1 Clinical Candidate Very potent 5nM Very flexible: 9 degrees of freedom Lipophile Amide Lipophile SCA Scaffold One major shape in solution 80% occupancy Several conformational features identified that confer the 3D shape Conformetrix Can a Conformetrix structure be used for design in the same way as co-crystal structure?

Conformetrix © All rights reserved. Lipophile SCA Scaffold Redesign Opportunity to Cyclise Conformational Lock Lipophile Amide Scaffold Redesign35nM Cyclisation100nM Indicates that we have been able to discover the bioactive conformation Analogous to drug design with X-ray co-crystallography But, this is a GPCR target with no structural information available Two novel series of potent compounds identified in first design set Target 2: isostere replacement

Conformetrix © All rights reserved. 1000nM140nMInactive  140nM published candidate compound generated by introduction of a small chiral group  The improved potency of molecule 2 over the parent compound and the inactive enantiomer was explained by enhanced lipophilic interaction Target 2: an unexpected ‘lock’ Molecule 2

Conformetrix © All rights reserved.  Conformations demonstrate that the alkyl group acts as a conformational ‘lock’  Provides an alternative explanation for the SAR 1000nM140nMInactive Target 2: an unexpected ‘lock’

Conformetrix © All rights reserved. The two molecules position key interactive groups (amide & lipophile) in the same relative orientations in solution Molecule 1 Molecule 2 Conformational Lock Lipophile Amide Target 2: scaffold hopping 140nM 5nM Overlay of solution conformers

Conformetrix © All rights reserved. Conformational Lock Lipophile Conformational analysis used to: identify surprising conformational features; identify overlapping pharmacophore points; generate novel scaffolds and IP. Molecule 1 & 2 hybrid 200nM Target 2: scaffold hopping

Conformetrix © All rights reserved. Molecule 3; EC 50 = 5nM 70% occupancy in one of two conformations Molecule 4; EC 50 = 10nM ScaffoldHBAScaffold HBA Scaffold HBA ScaffoldHBA 51% occupancy in one of two conformations. Target 3: using consensus overlays

Conformetrix © All rights reserved. Surprisingly, Molecule 3 is more flexible than Molecule 4 in solution The two ligands have a consensus area in their ensembles This area is equivalent to one of the most occupied conformations of both molecules Target 3: using consensus overlays

Conformetrix © All rights reserved. Repeated with a third scaffold Target 3: using consensus overlays

Conformetrix © All rights reserved. The most populated conformation is found in this region in every case A high resolution pharmacophore model has been used to design two novel series of agonists for this target Potencies approx. 100nM Target 3: using consensus overlays

Conformetrix © All rights reserved. Technology summary  Conformetrix technology has shown that flexible molecules exist in solution in a limited number of conformations.  Of these idealised conformations, one always closely resembles the bioactive conformation.  Conformational analysis can be used to identify common pharmacophore features, conformational ‘locks’ and unfavourable conformations to direct de novo design, scaffold hopping and virtual screening.  Early evidence from pre-clinical projects has shown that Conformetrix’s approach can be used to identify potent, novel chemistries against valuable targets

Conformetrix © All rights reserved. Conformetrix Board  Clive Dix (Chairman)  Sam Williams (CEO)  Charles Blundell (CSO)  Andrew Almond (CTO)  Harry Finch  Duncan Peyton  Alex Stevenson NMR Spectroscopy  Charles Blundell  Martin Watson  Wojtek Augustyniak  Jonathon Byrne  Jan-Christoph Westermann Medicinal Chemistry  Barrie Martin  Thorsten Nowak Technology Development  Andrew Almond  Michael Denison