Virtual screening in drug discovery

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1 Virtual screening in drug discovery Pavel Polishchuk Institute of Molecular and Translational Medicine Palacky University

2 Drug development workflow Vistoli G., et al., Drug Discovery Today, 2008, 13,

3 The challenge Chemical space Biological space ~10 36 drug-like compounds (1) ~ human proteins {2} Drug discovery (1) Polishchuk, P. G.; Madzhidov, T. I.; Varnek, A., J Comput Aided Mol Des 2013, 27, (2) 3

4 Vastness of chemical space real datasets ~ 110 M compounds ~ 75 M compounds Commercial ~ 88 M compounds Free virtually enumerated dataset GDB B compounds = 1.66x10 11 estimated size of drug-like chemical space compounds 4

5 Screening High-throughput screening up to 10 6 of compounds can be tested expensive not all targets are suitable for HTS Virtual screening up to 10 9 of compounds can be tested 5

6 Virtual screening methods 3D structure of target unknown known Ligand-based Structure-based actives known actives and inactives known 1 or more actives few or more actives Similarity search Pharmacophore search Machine learning (QSAR) Docking capacity: ~ 10 9 ~ 10 7 ~ 10 7 ~ 10 6 complexity increases 6

7 Similarity search 3D structure of target unknown known Ligand-based Structure-based actives known actives and inactives known 1 or more actives few or more actives Similarity search Pharmacophore search Machine learning (QSAR) Docking capacity: ~ 10 9 ~ 10 7 ~ 10 7 ~ 10 6 complexity increases 7

8 Similarity principle Similar compounds have similar properties morphine codeine Rank and select similar compounds reference compound decrease similarity 8

9 Are they similar? morphine codeine S-thalidomide R-thalidomide tirofibane tirofibane ethyl ester eptifibatide

10 Similarity search Structure representation structural keys fingerprints Similarity measure Tanimoto Dice Euclidian morphine codeine Tanimoto Dice MACCS Atom pairs Morgan (ECFP4-like) Morgan (FCFP4-like) calculated with RDKit Similarity search output depends on descriptors and similarity measure selected 10

11 Similarity search: example agonists of CCR compounds 100 FCFP4 compounds IC 50 = 17 μm purchased & tested IC 50 = 5.8 μm IC 50 = 14.1 μm Kellenberger, E., et al., Identification of nonpeptide CCR5 receptor agonists by structure-based virtual screening. Journal of Medicinal Chemistry 2007, 50,

12 Similarity search: conclusion + Little information is required to start searching + Different chemotypes can be retrieved + Ultra fast screening + Scaffold hopping - Hits will share common substructures with reference structures that may reduce their patentability - Results depend on chosen descriptors and similarity measure - Chemical similarity is not always followed by biological one 12

13 Pharmacophore search 3D structure of target unknown known Ligand-based Structure-based actives known actives and inactives known 1 or more actives few or more actives Similarity search Pharmacophore search Machine learning (QSAR) Docking capacity: ~ 10 9 ~ 10 7 ~ 10 7 ~ 10 6 complexity increases 13

14 Pharmacophore definition A pharmacophore is the ensemble of steric and electronic features that is necessary to ensure the optimal supramolecular interaction with a specific biological target structure and to trigger (or block) its biological response. Annu. Rep. Med. Chem. 1998, 33,

15 Early pharmacophore hypotheses 6.7 Å 6.9 Å 2.3 Å 2.4 Å π π interaction ionic interaction π π interaction X ionic interaction A H-bond B H-bond (R)-(-) Epinephrine (Adrenalin) (S)-(+) Epinephrine 15

16 Atom- and pharmacophore-based alignment Methotrexate Dihydrofolate Hydrogen bonding patterns Atom-based alignment Pharmacophore alignment 16

17 Feature-based pharmacophore models Features: Electrostatic interactions, H-bonding, aromatic interactions, hydrophobic regions, coordination to metal ions... Pharmacophore features H-bond donor H-bond acceptor Positive ionizable Negative ionizable Hydrophobic Aromatic ring 17

18 Feature-based pharmacophores (LigandScout) PDB code: 2VDM H-bonds formed by the ligand Hydrophobic interaction Pharmacophore features H-bond donor H-bond acceptor Positive ionizable Negative ionizable Hydrophobic 18

19 Typical ligand-based pharmacophore modeling workflow Clean structures of ligands Generate conformers Assign pharmacophore features Find common pharmacophores Score pharmacophore hypotheses Validation of pharmacophore models 19

20 Shared consensus pharmacophore (LigandScout) 2IVV 2IVU RET Kinase Inhibitors 20

21 Pharmacophore examples Shared model on 83 antagonists of fibrinogen receptor Pharmacophore models obtained for clusters of compounds Precision: 0.72 Recall: 0.77 Precision: 0.77 Recall: 0.27 Precision: 0.67 Recall: 0.29 Precision: 0.90 Recall: 0.04 Polishchuk, P. G. et al., Journal of Medicinal Chemistry 2015, 58,

22 Pharmacophore example Ala scan NMR Urotensin II - ETPDc[CFWKYCV] potent vasoconstrictor IC 50 = 400 nm 500 hits Flohr S. et al., J. Med. Chem., 2002, 45 (9), pp

23 Pharmacophores: conclusion + Universal representation of binding pattern + Qualitative output + Very fast screening + Scaffold hopping - Structure-based models can be very specific - Ligand-based models depend on conformational sampling 23

24 Machine learning (QSAR) 3D structure of target unknown known Ligand-based Structure-based actives known actives and inactives known 1 or more actives few or more actives Similarity search Pharmacophore search Machine learning (QSAR) Docking capacity: ~ 10 9 ~ 10 7 ~ 10 7 ~ 10 6 complexity increases 24

25 Modeling of compounds properties Activity = F(structure) X 1 X 2 X 3 X 4 X 5 X 6 X N Activity = M(E(structure)) M mapping function E encoding function 25

26 QSAR modeling workflow Structure Descriptors (features) End-point values Model X 1 X 2 X 3 X 4 X 5 X 6 X N Y Encoding (represent structure with numerical features) Mapping (machine learning) 26

27 Overall QSAR workflow Input data Preprocessing Feature engineering Model training Model validation Interpretation x ' i x i j x z j Bioassays Databases Data normalization & curation Feature extraction Feature selection Feature combination Classification Regression Clustering Cross-validation Bootstrap Test set Applicability Domain OECD principles for the validation, for regulatory purposes, of (Q)SAR models 1) a defined endpoint 2) an unambiguous algorithm 3) a defined domain of applicability 4) appropriate measures of goodness-of fit, robustness and predictivity 5) a mechanistic interpretation, if possible 27

28 QSAR model building plant growth inhibition activity of phenoxyacetic acids Hansch equation 1/C = 4.08π 2.14π σ π = logp X logp H σ - Hammet constant Free-Wilson models Inhibition activity of compounds against Staphylococcus aureus R is H or CH 3 ; X is Br, Cl, NO 2 and Y is NO 2, NH 2, NHC(=O)CH 3 Act = 75R H 112R CH3 + 84X Cl 16X Br 26X NO Y NH2 + 18Y NHC(=O)CH3 218Y NO2

29 QSAR: example Antimalarial activity 7 hits, EC 50 < 2μM EC 50 = 95 nm Zhang L. et al., J. Chem. Inf. Model., 2013, 53 (2), pp

30 QSAR: conclusion + Qualitative and quantitative output + May work for compounds having different mechanisms of action + Fast screening - Very demanding to the quality of input data - Applicability limited by the training set structures - Hard to encode stereochemistry 30

31 Molecular docking 3D structure of target unknown known Ligand-based Structure-based actives known actives and inactives known 1 or more actives few or more actives Similarity search Pharmacophore search Machine learning (QSAR) Docking capacity: ~ 10 9 ~ 10 7 ~ 10 7 ~ 10 6 complexity increases 31

32 Docking is an in silico tool which predicts Bioorganic & Medicinal Chemistry, 20 (12), 2012, Pose a possible relative orientation of a ligand and a receptor as well as conformation of a ligand and a receptor when they are form complex Score the strength of binding of the ligand and the receptor.

33 Why docking is a hard task Complex 3D jigsaw puzzle Conformational flexibility many degrees of freedom Mutual adaptation ( induced fit ) Solvation in aqueous media Complexity of thermodynamic contribution No easy route to evaluation of ΔG Simplification and heuristic approaches are necessary At its simplest level, this is a problem of subtraction of large numbers, inaccurately calculated, to arrive at a small number. (Leach A.R., Shoichet B.K., Peishoff C.E.. J. Med. Chem. 2006, 49, ) 33

34 Sampling and scoring Protein-ligand docking software consists of two main components which work together: 1. Search algorithm (sampling) - generates a large number of poses of a molecule in the binding site. 2. Scoring function - calculates a score or binding affinity for a particular pose 34

35 Search algorithms (sampling) Ligand Rigid Receptor Rigid Fast & Simple Flexible Rigid Flexible Flexible Slow & Complex 35

36 Classes of scoring function Forcefield-based Based on terms from molecular mechanics forcefields GoldScore, DOCK, AutoDock Empirical Parameterised against experimental binding affinities ChemScore, PLP, Glide SP/XP Knowledge-based potentials Based on statistical analysis of observed pairwise distributions PMF, DrugScore, ASP 36

37 Docking quality assessment Energy reproducibility HIV-1 protease Test set size = 800 molecules r < 0.55 R. Wang J. Chem. Inf. Comput. Sci., 2004, 44 (6), pp

38 Docking quality assessment Antagonists of α IIb β 3 Activity, pic 50 PLANTS S4MPLE Krysko, A.A., et al., Bioorganic & Medicinal Chemistry Letters, 2016, 26,

39 Validation Self-docking reproducibility of a pose Docking of a set of ligands with known affinity reproducibility of affinity 39

40 Molecular docking: example β 2 -adrenoreceptor ligands ZINC compounds DOCK diversity selection 500 compounds 25 compounds K i < 4μM 6 hits binding mode comparing to carazolol (X-ray ligand) K i = 9 nm Kolb, P. et al., PNAS of the United States of America, 2009, 106,

41 Molecular docking: conclusion + Relatively fast + Determine binding poses & energy + Good in ranking ligands for virtual screening - Low accuracy of binding energy estimation - Require knowledge about binding site 41

42 Consensus virtual screening 2D Pharmacophore QSAR (ISIDA, SIRMS) 3D Pharmacophore (LigandScout) Field-similarity (Cresset) Docking (MOE, PLANTS, FlexX) Shape-similarity (ROCS) 42

43 Virtual screening BioinfoDB (curated ZINC) ~ compounds 2D pharmacophore model 16Å bonds (C sp3 C sp3 ) 210 compounds 3D pharmacophore (ligand-based) QSAR models 0 compounds 0 compounds No hits commercial libraries contain just a few number of zwitterionic compounds Polishchuk, P. G. et al., Journal of Medicinal Chemistry 2015, 58,

44 Virtual screening of focused library 3D pharmacophore models ensemble QSAR 6930 (24066 stereisomers) 2064 Docking Shape- and field-based ADME/Tox, PASS, synthetic feasibility Polishchuk, P. G. et al., Journal of Medicinal Chemistry 2015, 58,

45 Biological activity of synthesized compounds Affinity for αiibβ3 Anti-aggregation Tirofiban Polishchuk, P. G. et al., Journal of Medicinal Chemistry 2015, 58,

46 Examples of CADD contribution to drug development Aliskiren Target Indication Role of CADD Renin Hypertension Structure-based optimization of the size of the hydrophobic group filling the large S1-S3 cavity. The methoxyalkoxy sidechain of the inhibitor is essential for strong binding Nilotinib Abl-kinase Chronic myeloid leukemia Replacement of imatinib N-methyl piperazine by a methylindole that optimally fits a subpocket of the kinase inactive structure Rilpivirine HIV reverse transcriptase AIDS Adaptation to the allosteric nonnucleoside binding site and targeting of the conserved Trp299 Rognan D., Pharmacology & Therapeutics 2017, 174,

47 PhD topic Computationally guided de novo design of compounds with desired properties Development of a platform for multi-objective optimization of compound properties (ADME, activity, selectivity, etc) based on computational models (QSAR, pharmacophore, docking, etc) Input structure(s) to be optimized QSAR model(s), docking Estimation of atoms/fragments contributions based on QSAR models, docking Transformation of structural motifs with negative influence on the target property Pharmacophore model(s), etc Property prediction Decision module: Is compound satisfy optimal criteria (profile)? Yes Selection, synthesis and testing No

48 Thank you for your attention 48