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Patel H, Ihlenfeldt WD, Judson PN, Moroz YS, Pevzner Y, Peach ML, Delannée V, Tarasova NI, Nicklaus MC. SAVI, in silico generation of billions of easily synthesizable compounds through expert-system type rules. Sci Data 2020; 7:384. [PMID: 33177514 PMCID: PMC7658252 DOI: 10.1038/s41597-020-00727-4] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Accepted: 10/16/2020] [Indexed: 01/08/2023] Open
Abstract
We have made available a database of over 1 billion compounds predicted to be easily synthesizable, called Synthetically Accessible Virtual Inventory (SAVI). They have been created by a set of transforms based on an adaptation and extension of the CHMTRN/PATRAN programming languages describing chemical synthesis expert knowledge, which originally stem from the LHASA project. The chemoinformatics toolkit CACTVS was used to apply a total of 53 transforms to about 150,000 readily available building blocks (enamine.net). Only single-step, two-reactant syntheses were calculated for this database even though the technology can execute multi-step reactions. The possibility to incorporate scoring systems in CHMTRN allowed us to subdivide the database of 1.75 billion compounds in sets according to their predicted synthesizability, with the most-synthesizable class comprising 1.09 billion synthetic products. Properties calculated for all SAVI products show that the database should be well-suited for drug discovery. It is being made publicly available for free download from https://doi.org/10.35115/37n9-5738.
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Affiliation(s)
- Hitesh Patel
- Computer-Aided Drug Design Group, Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD, 21702, USA
| | | | - Philip N Judson
- Heather Lea, Bland Hill, Norwood, Harrogate, HG3 1TE, England
| | - Yurii S Moroz
- Enamine Ltd, 78 Chervonotkatska Street, Suite 1, Kyiv, 02094, Ukraine and Chemspace LLC, 85 Chervonotkatska Street, Suite 1, Kyiv, 02094, Ukraine
| | - Yuri Pevzner
- Computer-Aided Drug Design Group, Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD, 21702, USA
- AbbVie, Inc., North Chicago, IL, 60064, USA
| | - Megan L Peach
- Basic Science Program, Frederick National Laboratory for Cancer Research, Frederick, MD, 21702, USA
| | - Victorien Delannée
- Computer-Aided Drug Design Group, Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD, 21702, USA
| | - Nadya I Tarasova
- Synthetic Biologics and Drug Discovery Group, Laboratory of Cancer Immunometabolism, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD, 21702, USA
| | - Marc C Nicklaus
- Computer-Aided Drug Design Group, Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD, 21702, USA.
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[Special Issue for Honor Award dedicating to Prof Kimito Funatsu]Fast Evaluation of Potential Synthesis Routes Using Transition State Database(TSDB). JOURNAL OF COMPUTER AIDED CHEMISTRY 2019. [DOI: 10.2751/jcac.20.50] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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[Special Issue for Honor Award dedicating to Prof Kimito Funatsu](Mini-review)Meanings of the Honor Award for Prof Kimito Funatsu. JOURNAL OF COMPUTER AIDED CHEMISTRY 2019. [DOI: 10.2751/jcac.20.23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Mitra RN, Show K, Barman D, Sarkar S, Maiti DK. NHC-Catalyzed Dual Stetter Reaction: A Mild Cascade Annulation for the Syntheses of Naphthoquinones, Isoflavanones, and Sugar-Based Chiral Analogues. J Org Chem 2018; 84:42-52. [PMID: 30562016 DOI: 10.1021/acs.joc.8b01503] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Rajendra N. Mitra
- Department of Chemistry, University of Calcutta, University College of Science, 92, A. P. C. Road, Kolkata, West Bengal 700009, India
| | - Krishanu Show
- Department of Chemistry, University of Calcutta, University College of Science, 92, A. P. C. Road, Kolkata, West Bengal 700009, India
| | - Debabrata Barman
- Department of Chemistry, University of Calcutta, University College of Science, 92, A. P. C. Road, Kolkata, West Bengal 700009, India
| | - Satinath Sarkar
- Department of Chemistry, University of Calcutta, University College of Science, 92, A. P. C. Road, Kolkata, West Bengal 700009, India
| | - Dilip K. Maiti
- Department of Chemistry, University of Calcutta, University College of Science, 92, A. P. C. Road, Kolkata, West Bengal 700009, India
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Goto A, Sanada S, Lei L, Hori K. Theoretical and Experimental Studies on Elementary Reactions in Living Radical Polymerization via Organic Amine Catalysis. Macromolecules 2016. [DOI: 10.1021/acs.macromol.6b00230] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Affiliation(s)
- Atsushi Goto
- Division
of Chemistry and Biological Chemistry, School of Physical and Mathematical
Sciences, Nanyang Technological University, 21 Nanyang Link, 637371 Singapore
| | - Shohei Sanada
- Graduate
School of Science and Engineering, Yamaguchi University, 2-16-1 Tokiwadai, Ube, Yamaguchi 755-8611, Japan
| | - Lin Lei
- Key
Laboratory of Synthetic and Natural Functional Molecule Chemistry
of Ministry of Education, College of Chemistry and Materials Science, Northwest University, Xi’an, Shaanxi 710069, China
| | - Kenji Hori
- Graduate
School of Science and Engineering, Yamaguchi University, 2-16-1 Tokiwadai, Ube, Yamaguchi 755-8611, Japan
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Yamamoto H, Yamaguchi T, Yoshimura K, Sumimoto M, Hori K. Towards in silico Synthetic Route Development. Computer Aided Organic Synthesis Developments of Target Compounds. J SYN ORG CHEM JPN 2012. [DOI: 10.5059/yukigoseikyokaishi.70.722] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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