SCI What can Big Data do for Chemistry 2017 MedChemica
•Télécharger en tant que PPTX, PDF•
1 j'aime•874 vues
This document discusses how advanced analytics and big data techniques can be applied in the chemistry industry. It provides examples of how matched molecular pair analysis has been used to extract statistically valid structure-activity relationships from large datasets and summarize them in the form of transformation rules. These rules have helped suggest new molecules, explore structure-activity relationships, identify exceptional structure-property relationships, and enable the rapid optimization of drug candidates. The document argues that combining data from multiple sources yields more comprehensive rules and that interfaces must be designed with the intended users in mind.
Recommandé
Recommandé
Contenu connexe
Tendances
Tendances (9)
Similaire à SCI What can Big Data do for Chemistry 2017 MedChemica
Similaire à SCI What can Big Data do for Chemistry 2017 MedChemica (20)
Dernier
Dernier (20)
SCI What can Big Data do for Chemistry 2017 MedChemica
- 1. MedChemica What have we done? What could we do with Advanced Analytics in the Chemistry Industry? Ed Griffen MedChemica Ltd
- 2. MedChemica Big Data – Focus on Benefits not Features From the Gartner IT Glossary: What is Big Data? Big Data is high-volume, high-velocity and/or high-variety information assets that demand cost-effective, innovative forms of information processing that enable enhanced insight, decision making, and process automation. 2 Features Benefits
- 3. MedChemica Where is Big Data proving most Successful? • Customer analysis • Targeted advertising • Language translation 3 • What do these have in common? • Underlying theoretical model insufficiently accurate or unknown • Very, very large data sets • Straightforward statistical methods • Most users are unskilled and not interested in mechanics
- 4. MedChemica What are the classes of chemical problem? 4 ‘Potency’ Properties Production Patents • Lead finding • Potency improvement • Pharmacokinetics • Solubility • Off target toxicity • First successful route • ‘Best” route • Freedom to Operate Product Size Duration of action Safety margin Speed Cost Commercial Position Common to all • Pharmaceuticals • Agrochemicals • Flavors and Fragrances • Consumer products • Materials science • Underlying theoretical model insufficiently accurate or unknown • Very, very large data sets • Straightforward statistical methods • Most users are unskilled and not interested in mechanics
- 5. MedChemica ‘Big Data’ analysis for Chemistry Making and testing compounds is expensive! • No new compounds to make • No new testing to do • Exploit the compounds and data you’ve already paid for • Accelerate all new projects • Augment the skills and experience of your chemists • Mythbusting… All very cost effective
- 6. MedChemica Help the HiPPOs – or they’ll crush you 6 1. McAfee & Brynjolfsson “Big Data: The Management Revolution”, Harvard Business Review October 2012 “Companies often make most of their important decisions by relying on “HiPPO”—the highest- paid person’s opinion.”1 Chemistry HiPPs: • experts in pattern recognition • judged on their ability to make the best decisions with partial data • highly trained • time poor • delivery focused • gatekeepers to the adoption of new approaches
- 7. MedChemica Making a real textbook of Medicinal Chemistry MMPA MMPA MMPA Combine and Extract Rules Multiple Pharma ADMET data >437000 rules Better Project decisions Increased Medicinal Chemistry learning Kramer, Robb, Ting, Zheng, Griffen, et al: J. Med. Chem 2017 http://pubs.acs.org/doi/10.1021/acs.jmedchem.7b00935 ‘Potency’ Properties Production Patents • Lead finding • Potency improvement • Pharmacokinetics • Solubility • Off target toxicity • First successful route • ‘Best” route • Freedom to Operate
- 8. MedChemica Making the complicated simple: HOT-Fit Learning from the development of clinical decision support software Algorithms Technology Data Speed Benefits Human System Use User Satisfaction Organization Structure Environment E.Kilsdonk, L.W.Peute, M.W.M.Jaspers, Factors Influencing Implementation Success of Guideline-based Clinical Decision Support Systems: a systematic review and gaps analysis, International Journal of Medical Informatics http://dx.doi.org/10.1016/j.ijmedinf.2016.12.001
- 9. MedChemica Chemistry Knowledge extraction methods Remember: your HiPPO needs to understand 9 substructures Physical chemistry descriptors(Hansch, Taft, Fujita, Abraham) Atomic, pair, triplet descriptors Indices Counts & descriptive statistics MMPA (M)LR Free Wilson PLS Trees / Forests SVM Bayesian NN Deep Learning Dark Black Descriptors Method It’s a summit – but what else is out there?
- 10. MedChemica • Matched Molecular Pairs – Molecules that differ only by a particular, well-defined structural transformation Griffen, E. et al. J. Med. Chem. 2011, 54(22), pp.7739-7750. Advanced MMPA with MCPairs • Transformation with environment capture – MMPs can be recorded as transformations from A B Δ Data A- B 1 2 2 3 3 3 4 4 4 12 23 3 34 4 4 A B Environment is key - must be captured in the chemical encoding
- 11. MMPA: Environment really matters HMe: • Median Dlog(Solubility) • 225 different environments 2.5log 1.5log HMe: • Median Dlog(Clint) Human microsomal clearance • 278 different environments MedChemica
- 12. MedChemica Matched Molecular Pair methods matter If you don’t use both you’ll miss 12-56% of the pairs 2 Methods: Maximum Common SubStructure(MCSS) Fragment and Index(FI) Warner, Sheridan Hussein & Rea Strengths: Ring replacement linker and core swaps Macrocycle ring pairs 12 EGF D1 Cav3.2 fF+I fMCSS 0.1 0.9 0.1 0.9 0.1 0.9 0.1 0.9 0.1 0.9 0.1 0.9 Leach et al J.Chem. Inf. Model. 2017 http://dx.doi.org/10.1021/acs.jcim.7b00335
- 13. MedChemica Identify and group matching SMIRKS Calc ulate statistical parameters for eac h unique SMIRKS(n, median, sd, se, n_up/ n_down) Is n ≥ 6? Not enough data: ignore transformation Is the | median| ≤ 0.05 and the interc entile range (10-90%) ≤ 0.3? Perform two-tailed binomial test on the transformation to determine the signific anc e of the up/ down frequenc y transformation is c lassified as ‘neutral’ Transformation c lassified as ‘NED’ (No Effec t Determined) Transformation c lassified as ‘increase’ or ‘ decrease’ depending on whic h direc tion the property is c hanging passfail yesno yesno Rule selection 0 +ve-ve Median data difference Neutral IncreaseDecrease NED • No assumption of normal distribution • Manage ‘censored’ = qualified / out-of-range data
- 14. MedChemica Making the complicated simple: HOT-Fit Algorithms Technology Human Organization Data Speed System Use User Satisfaction Structure Environment Benefits
- 15. MedChemica Where to get data? • Public data is unrepresentative • Censored by publication bias • Pharma data – can’t share structures due to IP. • Use chemical transformations to encode knowledge from matched molecular pair (MMP) analysis now sharable Novartis: Kramer, C.; Kalliokoski, T. et al The Experimental Uncertainty of Heterogeneous Public Ki Data J. Med. Chem 2012, 55, 5165 If project data really looked like that, there would be no problem in the Pharma industry.
- 16. MedChemica Data Sources Roche Database AZ Data MMP finder AZ Database MMP finder MMP finder Roche Data Genentech Data Grand Rule Database Grand Rule Database Grand Rule Database Grand Rule Database AZ Exploitation Roche Exploitation Genentech Exploitation >500 million pairs MedChemica Aggregation Individual company firewall Genentech Database 0.5 million rules
- 17. MedChemica Merge Pharma 1 100k rules Pharma 2 92k rules Pharma 3 37k rules 5.8k rules in common (pre-merge) ~ 2% New Rules 88k ~26% of total Combining data yields brand new rules Gains: 300 - 900% Merging knowledge – GRDv1
- 18. MedChemica Knowledge Extracted Numbers of statistically valid transforms Grouped Datasets Number of Rules logD7.4 153449 Merged solubility 46655 In vitro microsomal clearance: Human, rat, mouse, cyno, dog 88423 In vitro hepatocyte clearance : Human, rat, mouse, cyno, dog 26627 MCDK permeability A-B / B – A efflux 1852 Cytochrome P450 inhibition: 2C9, 2D6 , 3A4 , 2C19 , 1A2 40605 Cardiac ion channels NaV 1.5, hERG ion channel inhibition 15636 Glutathione Stability 116 plasma protein or albumin binding Human, rat, mouse, cyno, dog 64622 Grand Rule Database v3
- 19. MedChemica Single company vs merged Comparison between Roche-only and GRD rules for human microsomal clearance. Overall R2 is 0.76 and RMSE 0.11.
- 20. MedChemica Chemists use logD as a benchmark: • Standard to use lipophilicity as a design surrogate • Provides a context for changes • Key multi-objective design issues are centered round conflicting logD correlations: • Solubility & metabolic stabilitypotency & permeability • Particularly useful to look at chemical transformations that ‘ break the dogma’ of logD correlation
- 21. MedChemica Solubility : logD – trends & exceptions >=20 examples per rule, n=13,453 R2 = 0.66, slope = -0.57, intercept = 0. Magenta line: line of slope -1, intercept 0, dark blue line linear best fit, pale blue density ellipse contains 99% and the mid blue ellipse contains 50% of the transformations.
- 22. MedChemica Exceptional Solubility transformations Transformation median ΔlogD ±std (nPairs) median ΔlogSol ±std (nPairs) Comment 0.00 ± 0.67 (91) 0.73 ± 0.72 (87) DlogD == Solubility -0.10 ±0.83 (83) 0.65 ± 0.96 (69) 0.07 ± 0.50 (108) 0.52 ± 0.77 (80) -0.10 ± 0.54 (208) 0.40 ± 0.78 (115) -0.59 ± 0.49 (82) 0.03 ± 0.72 (98) DlogD Solubility ==
- 23. MedChemica Clearance : logD – trends & exceptions >=20 examples per rule, n=11,572 R2 = 0.40, slope 0.23, intercept = 0. Magenta line: line of slope 1, intercept 0, dark blue line linear best fit, pale blue density ellipse contains 99% and the mid blue ellipse contains 50% of the transformations.
- 24. MedChemica Exceptional HLM transformations Transformation median ΔlogD ±std (nPairs) HLM median Δlog(Clint) ±std (nPairs) Comment 0.35±0.45 (15) -0.34±0.71 (13) DlogD Clint 0.70±0.74 (117) -0.32±0.51 (53) 0.73±0.61 (26) -0.23±0.36 (18) 0.00±0.11 (19) -0.59±0.38 (14) DlogD == Clint -0.69±0.42 (8) 0.76±0.59 (7) DlogD Clint
- 25. MedChemica Making the complicated simple: HOT-Fit Algorithms Technology Human Organization Data Speed System Use User Satisfaction Structure Environment Benefits
- 26. MedChemica MMPA: Engineering challenges • Quick to implement on a small scale • Always becomes an n2 problem…. • ‘Challenging’ at enterprise scales 100,000+ - Cheminformatics ‘gotchas’ • Tautomers, charge states • Unusual aromatic systems • Highly symmetric molecules • Capturing and coding environments accurately - Structure and data integrity - Assay ontologies - Database schema optimized for cluster I/O Speed at scale essential – time poor users
- 27. MedChemica Interface Design depends on the User 27 • > 2 x 1012 searches / year • Totally unskilled users • Simple consistent interface • Rocket scientists ? Meet your HiPPO where they’re skilled • Intuitive ( = fast & familiar) • Summary data + option to drill into the detail • Web browsers • Excel
- 28. MedChemica Exploiting Knowledge for Compound Optimization Measured Data rule finder Rule Database Compounds from Rules Problem molecule New molecule suggestions rule finder MCPairs= “..it’s like asking 150 of your peers for ideas in just a few seconds” – AZ Principal Scientist
- 29. MedChemica Exploiting Knowledge for Compound Optimization https://www.youtube.com/watch?v=nQxXddJDTfc
- 30. MedChemica More examples of Success 30 Thompson; M.J. et al J. Med. Chem., 2015, 58 (23), pp 9309–9333 DOI: 10.1021/acs.jmedchem.5b01312
- 31. MedChemica “Me-Betters” on a Massive scale Enumerator System 1162 Marketed Drugs Wealth of Follow-on opportunities Grand Rule Database v3 Improve solubility & metabolism = lower dose = uid from bid/tid Safer, better compliance ~425 improvement suggestions / drug
- 33. MedChemica • MMP based clustering • QSAR from MMPA • Matched molecular series •Interface design is key There is so much more… ?
- 34. MedChemica What can we do with Advanced Analytics? Accelerate Chemistry by using: • right algorithms that our users understand • as much data as possible • fast, “user appropriate” interfaces deliver better products into development faster. 34
- 35. MedChemica Collaborators and Users - experience
Notes de l'éditeur
- Lot’s of people come forward with ideas to ‘revolutionise drug discovery’, but being more data driven is surprisingly cheap compared to most of them. Eg ‘new modalities’ like therapeutic RNAs or chimeric antigen receptors, r even large ring macrocycles.
- We may be at the summit but who can tell? And what is around us? Alternatively we may want to have a completely clear view and potential cliffs and valleys, but by the time you get there, so much has been published that compounds are probabaly in the clinic if not to market – but of course there may still be opportunities