LIBRARY DESIGN FOR COLLABORATIVE DRUG DISCOVERY: EXPANDING DRUGGABLE CHEMOGENOMIC SPACE
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1 5 th Embassy in Tokyo LIBRARY DESIGN FOR COLLABORATIVE DRUG DISCOVERY: EXPANDING DRUGGABLE CHEMOGENOMIC SPACE Kazuyoshi Ikeda, Ph.D. Keio University
2 SELF-INTRODUCTION Keio University, Faculty of Pharmacy ( 慶應義塾大学薬学部生命機能物理学研究室 ) Bio/Chemo-informatics in-silico drug discovery Library design (a part of AMED project) Structural Biology (NMR, Prof.Osawa) Onarimon ( 御成門 ), Tokyo Near Zouzyougi Temple ( 増上寺 )
3 TODAY S TOPICS Ø Background: Comparison of Compound Libraries Ø Library Design Informatics Using Drug Discovery Data and Virtual Compounds Ø Collaborative Drug Discovery May Expand Druggable Chemical Space
4 CHEMICAL SPACE IS VAST Reymond JL. & Awale M., ACS Chem Neurosci. (2012) 19;3: Number of stars in our galaxy: Estimated size of small molecule chemical space: >10 12
5 IMPACT OF OPEN SCREENING DATA Drug Discovery Data Resources #Activities and Compounds by Year HTS or Screening Literature in ChEMBL ü >50% from non-literature data ü HTS data is rapidly increasing by open drug discovery projects
6 SIZE OF PUBLIC CHEMICAL DATABASES GDB Billion organic small compounds PubChem - 96M HTS screening cmpds incl. inactivies SureChem - 16 Million patent compounds ChEMBL (ver24) -1.8 Million bioactive compounds BindingDB -65K binding molecules to structures DrugBank -10K approved drugs
7 LIMITED BIOACTIVE SPACE ALogP Small Drugs vs Natural Products Ro5 Ro5 PPI Inhibitors Ro4 Beyond Ro5 MW ü 85% of approved small molecule drugs within Lipinski s Ro5 space MW ü Only half of PPI Inhibitors are within Ro5. ü Rule of 4 covers over 90% of those.
8 Mapping Virtual Rings on Patent Compounds NIH-MLSMR Library 489 ChEMBL Unpatented Bioactive Compounds 931 (45 Rings) VEHICLe (virtual exploratory heterocyclic SureChem (Patent) 2,072 library) 24,807 Rings
9 Library Design Protocol Using Patent & Virtual Cmpds -DATA EXTRACTIONü Mechanism of Action ü Target Information ü Activity Type & Value -3D-SAR Modelingü 3D-Alignment -Focused-Library Generationü Scaffold Hopping based on Electrostatic similarity. patent/bioactive virtual ü 3D-QSAR Model Predicition
10 Phosphodiesterase 5A inhibitor (VIAGRA) with Patent & Bioactive 1. SILDENAFIL 3. VERDENAFIL Sildenafil Electrostatic Surface New Structures ü Starting from Sildenafil, various scaffolds are generated by the similarity of electrostatic interaction surfaces. ü a library of compounds with the similar bioactivity is designed. Possible Promising Structures
11 A Protein Try-Kinase (B-RAF) with Virtual Structural Alert Filter B-RAF in complex with Dabrafenib (5csw) 3D SAR Prediction Druglikeness Novel Structure Library
12 COLLABORATIVE DRUG DISCOVERY
13 LIBRARY SHARING B/W ASTRAZENECA-BAYER Big pharma screening collections: More of the same or unique libraries? the AstraZeneca- Bayer Pharma AG case (2013) ü Most compounds between AZ and BYR with similarity of less than 0.7.
14 LILLY S OPEN INNOVATION PROGRAM Max_Tanimoto < 0.9 or 0.85 Lilly collects compounds which didn t exist in their library from >300 external collaborators via secure informatics system. Total over 50K compounds tested including hits/leads for different targets. Open Innovation Drug Discovery (OIDD): A Potential Path to Novel Therapeutic Chemical Space., Alvim-Gaston M, et al. Current Topics in Medicinal Chemistry 2014 vol: 14 pp:
15 CHEMICAL SPACE COMPLEMENT ü Their original library was complemented with unique compounds that fill the gaps (disk-like).
16 CONTEST-BASED IN SILICO SCREENING
17 CONCEPT OF IPAB-CONTEST A non-profit organization, IPAB (Initiative for PArallel Bioinformatics) and Tokyo Institute of Technology ( 東工大 ) organizes an open CADD contest. N-lobe Gate Keeper Gly loop Hing Region P-loop Activation Segegment (DFG motif) Catalytic Loop 10 teams joined to predict inhibitors for a Tyr Kinase (cyes) using different computational methods applied. Assays were performed to confirm the submitted compound s activities later. C-lobe
18 IPAB CONTEST RESULT chiba et al. scientific reports (2016, 2017)
19 SUMMARIES Ø The understanding of the chemical space is important for designing efficient compound libraries. Ø A library design informatics approach using drug discovery data and virtual compounds generates a drug-like focused library with novel structures. Ø Collaborative drug discovery and informatics method may contribute to expand druggable chemical space.
20 ACKNOWLEDGEMENT Keio University Prof. Masanori Osawa Dr. Yugo Shimizu Special Thanks to Ikegami-san & Marcus
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