1
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Zabolotna Y, Volochnyuk DM, Ryabukhin SV, Horvath D, Gavrilenko KS, Marcou G, Moroz YS, Oksiuta O, Varnek A. A Close-up Look at the Chemical Space of Commercially Available Building Blocks for Medicinal Chemistry. J Chem Inf Model 2021; 62:2171-2185. [PMID: 34928600 DOI: 10.1021/acs.jcim.1c00811] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The ability to efficiently synthesize desired compounds can be a limiting factor for chemical space exploration in drug discovery. This ability is conditioned not only by the existence of well-studied synthetic protocols but also by the availability of corresponding reagents, so-called building blocks (BBs). In this work, we present a detailed analysis of the chemical space of 400 000 purchasable BBs. The chemical space was defined by corresponding synthons─fragments contributed to the final molecules upon reaction. They allow an analysis of BB physicochemical properties and diversity, unbiased by the leaving and protective groups in actual reagents. The main classes of BBs were analyzed in terms of their availability, rule-of-two-defined quality, and diversity. Available BBs were eventually compared to a reference set of biologically relevant synthons derived from ChEMBL fragmentation, in order to illustrate how well they cover the actual medicinal chemistry needs. This was performed on a newly constructed universal generative topographic map of synthon chemical space that enables visualization of both libraries and analysis of their overlapped and library-specific regions.
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Affiliation(s)
- Yuliana Zabolotna
- University of Strasbourg, Laboratoire de Chemoinformatique, 4, rue B. Pascal, Strasbourg 67081, France
| | - Dmitriy M Volochnyuk
- Institute of Organic Chemistry, National Academy of Sciences of Ukraine, Murmanska Street 5, Kyiv 02660, Ukraine.,Enamine Ltd., 78 Chervonotkatska str., 02660 Kiev, Ukraine
| | - Sergey V Ryabukhin
- The Institute of High Technologies, Kyiv National Taras Shevchenko University, 64 Volodymyrska Street, Kyiv 01601, Ukraine.,Enamine Ltd., 78 Chervonotkatska str., 02660 Kiev, Ukraine
| | - Dragos Horvath
- University of Strasbourg, Laboratoire de Chemoinformatique, 4, rue B. Pascal, Strasbourg 67081, France
| | - Konstantin S Gavrilenko
- Research-And-Education ChemBioCenter, National Taras Shevchenko University of Kyiv, Chervonotkatska str., 61, 03022 Kiev, Ukraine.,Enamine Ltd., 78 Chervonotkatska str., 02660 Kiev, Ukraine
| | - Gilles Marcou
- University of Strasbourg, Laboratoire de Chemoinformatique, 4, rue B. Pascal, Strasbourg 67081, France
| | - Yurii S Moroz
- Research-And-Education ChemBioCenter, National Taras Shevchenko University of Kyiv, Chervonotkatska str., 61, 03022 Kiev, Ukraine.,Chemspace, Chervonotkatska Street 78, 02094 Kyiv, Ukraine
| | - Oleksandr Oksiuta
- Institute of Organic Chemistry, National Academy of Sciences of Ukraine, Murmanska Street 5, Kyiv 02660, Ukraine.,Chemspace, Chervonotkatska Street 78, 02094 Kyiv, Ukraine
| | - Alexandre Varnek
- University of Strasbourg, Laboratoire de Chemoinformatique, 4, rue B. Pascal, Strasbourg 67081, France.,Institute for Chemical Reaction Design and Discovery (WPI-ICReDD), Hokkaido University, Kita 21 Nishi 10, Kita-ku, 001-0021 Sapporo, Japan
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2
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Wang Y, Haight I, Gupta R, Vasudevan A. What is in Our Kit? An Analysis of Building Blocks Used in Medicinal Chemistry Parallel Libraries. J Med Chem 2021; 64:17115-17122. [PMID: 34807604 DOI: 10.1021/acs.jmedchem.1c01139] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Building blocks are the molecular foundations for drug molecule design. The building block is one of the determining factors of final compound qualities in any given medicinal chemistry campaign. Herein, we describe our analysis of the building blocks used in parallel library synthesis at AbbVie. The results gave insights into the synthetic tractability and accessibilities of building blocks used in medicinal chemistry. Furthermore, our analysis showed that opportunities still exist for the identification and future incorporation of underrepresented building blocks, even for commonly used reactions, to obtain intellectual and competitive advantages in drug discovery.
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Affiliation(s)
- Ying Wang
- AbbVie Inc., 1 North Waukegan Road, North Chicago, Illinois 60064, United States
| | - Isabella Haight
- AbbVie Inc., 1 North Waukegan Road, North Chicago, Illinois 60064, United States
| | - Rishi Gupta
- AbbVie Inc., 1 North Waukegan Road, North Chicago, Illinois 60064, United States
| | - Anil Vasudevan
- AbbVie Inc., 1 North Waukegan Road, North Chicago, Illinois 60064, United States
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3
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Dombrowski AW, Aguirre AL, Shrestha A, Sarris KA, Wang Y. The Chosen Few: Parallel Library Reaction Methodologies for Drug Discovery. J Org Chem 2021; 87:1880-1897. [PMID: 34780177 DOI: 10.1021/acs.joc.1c01427] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Parallel library synthesis is an important tool for drug discovery because it enables the synthesis of closely related analogues in parallel via robust and general synthetic transformations. In this perspective, we analyzed the synthetic methodologies used in >5000 parallel libraries representing 15 prevalent synthetic transformations. The library data set contains complex substrates and diverse arrays of building blocks used over the last 14 years at AbbVie. The library synthetic methodologies that have demonstrated robustness and generality with proven success are described along with their substrate scopes. The evolution of the synthetic methodologies for library synthesis over the past decade is discussed. We also highlight that the combination of parallel library synthesis with high-throughput experimentation will continue to facilitate the discovery of library-amenable synthetic methodologies in drug discovery.
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Affiliation(s)
- Amanda W Dombrowski
- Advanced Chemistry Technologies Group, AbbVie, Inc., North Chicago, Illinois 60064, United States
| | - Ana L Aguirre
- Advanced Chemistry Technologies Group, AbbVie, Inc., North Chicago, Illinois 60064, United States
| | - Anurupa Shrestha
- Advanced Chemistry Technologies Group, AbbVie, Inc., North Chicago, Illinois 60064, United States
| | - Kathy A Sarris
- Advanced Chemistry Technologies Group, AbbVie, Inc., North Chicago, Illinois 60064, United States
| | - Ying Wang
- Advanced Chemistry Technologies Group, AbbVie, Inc., North Chicago, Illinois 60064, United States
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4
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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: 14] [Impact Index Per Article: 3.5] [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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5
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Ghanakota P, Bos PH, Konze KD, Staker J, Marques G, Marshall K, Leswing K, Abel R, Bhat S. Combining Cloud-Based Free-Energy Calculations, Synthetically Aware Enumerations, and Goal-Directed Generative Machine Learning for Rapid Large-Scale Chemical Exploration and Optimization. J Chem Inf Model 2020; 60:4311-4325. [PMID: 32484669 DOI: 10.1021/acs.jcim.0c00120] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Affiliation(s)
- Phani Ghanakota
- Schrödinger, Inc., 120 West 45th Street, 17th floor, New York, New York 10036, United States
| | - Pieter H. Bos
- Schrödinger, Inc., 120 West 45th Street, 17th floor, New York, New York 10036, United States
| | - Kyle D. Konze
- Schrödinger, Inc., 120 West 45th Street, 17th floor, New York, New York 10036, United States
| | - Joshua Staker
- Schrödinger, Inc., 120 West 45th Street, 17th floor, New York, New York 10036, United States
| | - Gabriel Marques
- Schrödinger, Inc., 120 West 45th Street, 17th floor, New York, New York 10036, United States
| | - Kyle Marshall
- Schrödinger, Inc., 120 West 45th Street, 17th floor, New York, New York 10036, United States
| | - Karl Leswing
- Schrödinger, Inc., 120 West 45th Street, 17th floor, New York, New York 10036, United States
| | - Robert Abel
- Schrödinger, Inc., 120 West 45th Street, 17th floor, New York, New York 10036, United States
| | - Sathesh Bhat
- Schrödinger, Inc., 120 West 45th Street, 17th floor, New York, New York 10036, United States
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6
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Foscato M, Venkatraman V, Jensen VR. DENOPTIM: Software for Computational de Novo Design of Organic and Inorganic Molecules. J Chem Inf Model 2019; 59:4077-4082. [DOI: 10.1021/acs.jcim.9b00516] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- Marco Foscato
- Department of Chemistry, University of Bergen, Allégaten 41, N-5007 Bergen, Norway
| | - Vishwesh Venkatraman
- Department of Chemistry, Norwegian University of Science and Technology, N-7491 Trondheim, Norway
| | - Vidar R. Jensen
- Department of Chemistry, University of Bergen, Allégaten 41, N-5007 Bergen, Norway
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7
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Sommer K, Flachsenberg F, Rarey M. NAOMInext – Synthetically feasible fragment growing in a structure-based design context. Eur J Med Chem 2019; 163:747-762. [DOI: 10.1016/j.ejmech.2018.11.075] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2018] [Revised: 11/27/2018] [Accepted: 11/30/2018] [Indexed: 12/31/2022]
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8
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van Hilten N, Chevillard F, Kolb P. Virtual Compound Libraries in Computer-Assisted Drug Discovery. J Chem Inf Model 2019; 59:644-651. [PMID: 30624918 DOI: 10.1021/acs.jcim.8b00737] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
The use of virtual compound libraries in computer-assisted drug discovery has gained in popularity and has already lead to numerous successes. Here, we examine key static and dynamic virtual library concepts that have been developed over the past decade. To facilitate the search for new drugs in the vastness of chemical space, there are still several hurdles to overcome, including the current difficulties in screening and parsing efficiency and the need for more reliable vendors and accurate synthesis prediction tools. These challenges should be tackled by both the developers of virtual libraries and by their users, in order for the exploration of chemical space to live up to its potential.
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Affiliation(s)
- Niek van Hilten
- Department of Pharmaceutical Chemistry , Philipps-University Marburg , Marbacher Weg 6 , 35032 Marburg , Germany
| | - Florent Chevillard
- Department of Pharmaceutical Chemistry , Philipps-University Marburg , Marbacher Weg 6 , 35032 Marburg , Germany
| | - Peter Kolb
- Department of Pharmaceutical Chemistry , Philipps-University Marburg , Marbacher Weg 6 , 35032 Marburg , Germany
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9
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Batiste L, Unzue A, Dolbois A, Hassler F, Wang X, Deerain N, Zhu J, Spiliotopoulos D, Nevado C, Caflisch A. Chemical Space Expansion of Bromodomain Ligands Guided by in Silico Virtual Couplings (AutoCouple). ACS CENTRAL SCIENCE 2018; 4:180-188. [PMID: 29532017 PMCID: PMC5833004 DOI: 10.1021/acscentsci.7b00401] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2017] [Indexed: 10/24/2023]
Abstract
Expanding the chemical space and simultaneously ensuring synthetic accessibility is of upmost importance, not only for the discovery of effective binders for novel protein classes but, more importantly, for the development of compounds against hard-to-drug proteins. Here, we present AutoCouple, a de novo approach to computational ligand design focused on the diversity-oriented generation of chemical entities via virtual couplings. In a benchmark application, chemically diverse compounds with low-nanomolar potency for the CBP bromodomain and high selectivity against the BRD4(1) bromodomain were achieved by the synthesis of about 50 derivatives of the original fragment. The binding mode was confirmed by X-ray crystallography, target engagement in cells was demonstrated, and antiproliferative activity was showcased in three cancer cell lines. These results reveal AutoCouple as a useful in silico coupling method to expand the chemical space in hit optimization campaigns resulting in potent, selective, and cell permeable bromodomain ligands.
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Affiliation(s)
- Laurent Batiste
- Department
of Biochemistry, University of Zurich, Winterthurerstrasse 190, CH-8057, Zürich, Switzerland
| | - Andrea Unzue
- Department
of Chemistry, University of Zurich, Winterthurerstrasse 190, CH-8057, Zürich, Switzerland
| | - Aymeric Dolbois
- Department
of Chemistry, University of Zurich, Winterthurerstrasse 190, CH-8057, Zürich, Switzerland
| | - Fabrice Hassler
- Department
of Chemistry, University of Zurich, Winterthurerstrasse 190, CH-8057, Zürich, Switzerland
| | - Xuan Wang
- Department
of Biochemistry, University of Zurich, Winterthurerstrasse 190, CH-8057, Zürich, Switzerland
- Department
of Chemistry, University of Zurich, Winterthurerstrasse 190, CH-8057, Zürich, Switzerland
| | - Nicholas Deerain
- Department
of Biochemistry, University of Zurich, Winterthurerstrasse 190, CH-8057, Zürich, Switzerland
| | - Jian Zhu
- Department
of Biochemistry, University of Zurich, Winterthurerstrasse 190, CH-8057, Zürich, Switzerland
| | - Dimitrios Spiliotopoulos
- Department
of Biochemistry, University of Zurich, Winterthurerstrasse 190, CH-8057, Zürich, Switzerland
| | - Cristina Nevado
- Department
of Chemistry, University of Zurich, Winterthurerstrasse 190, CH-8057, Zürich, Switzerland
| | - Amedeo Caflisch
- Department
of Biochemistry, University of Zurich, Winterthurerstrasse 190, CH-8057, Zürich, Switzerland
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10
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Chevillard F, Rimmer H, Betti C, Pardon E, Ballet S, van Hilten N, Steyaert J, Diederich WE, Kolb P. Binding-Site Compatible Fragment Growing Applied to the Design of β 2-Adrenergic Receptor Ligands. J Med Chem 2018; 61:1118-1129. [PMID: 29364664 DOI: 10.1021/acs.jmedchem.7b01558] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Fragment-based drug discovery is intimately linked to fragment extension approaches that can be accelerated using software for de novo design. Although computers allow for the facile generation of millions of suggestions, synthetic feasibility is however often neglected. In this study we computationally extended, chemically synthesized, and experimentally assayed new ligands for the β2-adrenergic receptor (β2AR) by growing fragment-sized ligands. In order to address the synthetic tractability issue, our in silico workflow aims at derivatized products based on robust organic reactions. The study started from the predicted binding modes of five fragments. We suggested a total of eight diverse extensions that were easily synthesized, and further assays showed that four products had an improved affinity (up to 40-fold) compared to their respective initial fragment. The described workflow, which we call "growing via merging" and for which the key tools are available online, can improve early fragment-based drug discovery projects, making it a useful creative tool for medicinal chemists during structure-activity relationship (SAR) studies.
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Affiliation(s)
- Florent Chevillard
- Department of Pharmaceutical Chemistry, Philipps-University Marburg , Marbacher Weg 6, 35032 Marburg, Germany
| | - Helena Rimmer
- Department of Pharmaceutical Chemistry and Center for Tumor Biology and Immunology, Philipps-University Marburg , Hans-Meerwein-Straße 3, 35032 Marburg, Germany
| | - Cecilia Betti
- Research Group of Organic Chemistry, Departments of Chemistry and Bio-Engineering Sciences, Vrije Universiteit Brussel , Pleinlaan 2, 1050 Brussels, Belgium
| | - Els Pardon
- VIB-VUB Center for Structural Biology, VIB , 1050 Brussels, Belgium.,Structural Biology Brussels, Vrije Universiteit Brussel , 1050 Brussels, Belgium
| | - Steven Ballet
- Research Group of Organic Chemistry, Departments of Chemistry and Bio-Engineering Sciences, Vrije Universiteit Brussel , Pleinlaan 2, 1050 Brussels, Belgium
| | - Niek van Hilten
- Department of Pharmaceutical Chemistry, Philipps-University Marburg , Marbacher Weg 6, 35032 Marburg, Germany
| | - Jan Steyaert
- VIB-VUB Center for Structural Biology, VIB , 1050 Brussels, Belgium.,Structural Biology Brussels, Vrije Universiteit Brussel , 1050 Brussels, Belgium
| | - Wibke E Diederich
- Department of Pharmaceutical Chemistry and Center for Tumor Biology and Immunology, Philipps-University Marburg , Hans-Meerwein-Straße 3, 35032 Marburg, Germany
| | - Peter Kolb
- Department of Pharmaceutical Chemistry, Philipps-University Marburg , Marbacher Weg 6, 35032 Marburg, Germany
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11
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Pottel J, Moitessier N. Customizable Generation of Synthetically Accessible, Local Chemical Subspaces. J Chem Inf Model 2017; 57:454-467. [DOI: 10.1021/acs.jcim.6b00648] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Joshua Pottel
- Department of Chemistry, McGill University, 801
Sherbrooke Street W., Montréal, Québec, Canada H3A 0B8
| | - Nicolas Moitessier
- Department of Chemistry, McGill University, 801
Sherbrooke Street W., Montréal, Québec, Canada H3A 0B8
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12
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Taylor RD, MacCoss M, Lawson ADG. Combining Molecular Scaffolds from FDA Approved Drugs: Application to Drug Discovery. J Med Chem 2016; 60:1638-1647. [DOI: 10.1021/acs.jmedchem.6b01367] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Affiliation(s)
| | - Malcolm MacCoss
- Bohicket Pharma Consulting LLC, 2556 Seabrook Island Road, Seabrook Island, South Carolina 29455, United States
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13
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14
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Friedrich L, Rodrigues T, Neuhaus CS, Schneider P, Schneider G. From Complex Natural Products to Simple Synthetic Mimetics by Computational De Novo Design. Angew Chem Int Ed Engl 2016; 55:6789-92. [DOI: 10.1002/anie.201601941] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2016] [Revised: 04/03/2016] [Indexed: 11/08/2022]
Affiliation(s)
- Lukas Friedrich
- Department of Chemistry and Applied Biosciences; Swiss Federal Institute of Technology (ETH); Vladimir-Prelog-Weg 4 8093 Zurich Switzerland
| | - Tiago Rodrigues
- Department of Chemistry and Applied Biosciences; Swiss Federal Institute of Technology (ETH); Vladimir-Prelog-Weg 4 8093 Zurich Switzerland
| | - Claudia S. Neuhaus
- Department of Chemistry and Applied Biosciences; Swiss Federal Institute of Technology (ETH); Vladimir-Prelog-Weg 4 8093 Zurich Switzerland
| | - Petra Schneider
- Department of Chemistry and Applied Biosciences; Swiss Federal Institute of Technology (ETH); Vladimir-Prelog-Weg 4 8093 Zurich Switzerland
- inSili.com GmbH; Segantinisteig 3 8049 Zurich Switzerland
| | - Gisbert Schneider
- Department of Chemistry and Applied Biosciences; Swiss Federal Institute of Technology (ETH); Vladimir-Prelog-Weg 4 8093 Zurich Switzerland
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15
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Friedrich L, Rodrigues T, Neuhaus CS, Schneider P, Schneider G. Von komplexen Naturstoffen zu synthetisch leicht zugänglichen Mimetika mithilfe von computergestütztem De-novo-Design. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201601941] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Lukas Friedrich
- Department für Chemie und Angewandte Biowissenschaften; Eidgenössische Technische Hochschule; Vladimir-Prelog-Weg 4 8093 Zürich Schweiz
| | - Tiago Rodrigues
- Department für Chemie und Angewandte Biowissenschaften; Eidgenössische Technische Hochschule; Vladimir-Prelog-Weg 4 8093 Zürich Schweiz
| | - Claudia S. Neuhaus
- Department für Chemie und Angewandte Biowissenschaften; Eidgenössische Technische Hochschule; Vladimir-Prelog-Weg 4 8093 Zürich Schweiz
| | - Petra Schneider
- Department für Chemie und Angewandte Biowissenschaften; Eidgenössische Technische Hochschule; Vladimir-Prelog-Weg 4 8093 Zürich Schweiz
- inSili.com GmbH; Segantinisteig 3 8049 Zürich Schweiz
| | - Gisbert Schneider
- Department für Chemie und Angewandte Biowissenschaften; Eidgenössische Technische Hochschule; Vladimir-Prelog-Weg 4 8093 Zürich Schweiz
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16
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Masek BB, Baker DS, Dorfman RJ, DuBrucq K, Francis VC, Nagy S, Richey BL, Soltanshahi F. Multistep Reaction Based De Novo Drug Design: Generating Synthetically Feasible Design Ideas. J Chem Inf Model 2016; 56:605-20. [PMID: 27031173 DOI: 10.1021/acs.jcim.5b00697] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We describe a "multistep reaction driven" evolutionary algorithm approach to de novo molecular design. Structures generated by the approach include a proposed synthesis path intended to aid the chemist in assessing the synthetic feasibility of the ideas that are generated. The methodology is independent of how the design ideas are scored, allowing multicriteria drug design to address multiple issues including activity at one or more pharmacological targets, selectivity, physical and ADME properties, and off target liabilities; the methods are compatible with common computer-aided drug discovery "scoring" methodologies such as 2D- and 3D-ligand similarity, docking, desirability functions based on physiochemical properties, and/or predictions from 2D/3D QSAR or machine learning models and combinations thereof to be used to guide design. We have performed experiments to assess the extent to which known drug space can be covered by our approach. Using a library of 88 generic reactions and a database of ∼20 000 reactants, we find that our methods can identify "close" analogs for ∼50% of the known small molecule drugs with molecular weight less than 300. To assess the quality of the in silico generated synthetic pathways, synthesis chemists were asked to rate the viability of synthesis pathways: both "real" and in silico generated. In silico reaction schemes generated by our methods were rated as very plausible with scores similar to known literature synthesis schemes.
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Affiliation(s)
- Brian B Masek
- Certara , 210 N. Tucker Blvd, Suite 350, Saint Louis, Missouri 63101, United States
| | - David S Baker
- Certara , 210 N. Tucker Blvd, Suite 350, Saint Louis, Missouri 63101, United States
| | - Roman J Dorfman
- Certara , 210 N. Tucker Blvd, Suite 350, Saint Louis, Missouri 63101, United States
| | - Karen DuBrucq
- Certara , 210 N. Tucker Blvd, Suite 350, Saint Louis, Missouri 63101, United States
| | - Victoria C Francis
- Certara , 210 N. Tucker Blvd, Suite 350, Saint Louis, Missouri 63101, United States
| | - Stephan Nagy
- Certara , 210 N. Tucker Blvd, Suite 350, Saint Louis, Missouri 63101, United States
| | - Bree L Richey
- Certara , 210 N. Tucker Blvd, Suite 350, Saint Louis, Missouri 63101, United States
| | - Farhad Soltanshahi
- Certara , 210 N. Tucker Blvd, Suite 350, Saint Louis, Missouri 63101, United States
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17
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Abstract
Computational medicinal chemistry offers viable strategies for finding, characterizing, and optimizing innovative pharmacologically active compounds. Technological advances in both computer hardware and software as well as biological chemistry have enabled a renaissance of computer-assisted "de novo" design of molecules with desired pharmacological properties. Here, we present our current perspective on the concept of automated molecule generation by highlighting chemocentric methods that may capture druglike chemical space, consider ligand promiscuity for hit and lead finding, and provide fresh ideas for the rational design of customized screening of compound libraries.
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Affiliation(s)
- Petra Schneider
- Department of Chemistry and Applied Biosciences, Institute of Pharmaceutical Sciences, Swiss Federal Institute of Technology (ETH) , Vladimir-Prelog-Weg 4, 8093 Zürich, Switzerland.,inSili.com LLC , Segantinisteig 3, 8049 Zürich, Switzerland
| | - Gisbert Schneider
- Department of Chemistry and Applied Biosciences, Institute of Pharmaceutical Sciences, Swiss Federal Institute of Technology (ETH) , Vladimir-Prelog-Weg 4, 8093 Zürich, Switzerland
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18
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Prathipati P, Mizuguchi K. Integration of Ligand and Structure Based Approaches for CSAR-2014. J Chem Inf Model 2015; 56:974-87. [PMID: 26492437 DOI: 10.1021/acs.jcim.5b00477] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
The prediction of binding poses and affinities is an area of active interest in computer-aided drug design (CADD). Given the documented limitations with either ligand or structure based approaches, we employed an integrated approach and developed a rapid protocol for binding mode and affinity predictions. This workflow was applied to the three protein targets of Community Structure-Activity Resource-2014 (CSAR-2014) exercise: Factor Xa (FXa), Spleen Tyrosine Kinase (SYK), and tRNA (guanine-N(1))-methyltransferase (TrmD). Our docking and scoring workflow incorporates compound clustering and ligand and protein structure based pharmacophore modeling, followed by local docking, minimization, and scoring. While the former part of the protocol ensures high-quality ligand alignments and mapping, the subsequent minimization and scoring provides the predicted binding modes and affinities. We made blind predictions of docking pose for 1, 5, and 14 ligands docked into 1, 2, and 12 crystal structures of FXa, SYK, and TrmD, respectively. The resulting 174 poses were compared with cocrystallized structures (1, 5, and 14 complexes) made available at the end of CSAR. Our predicted poses were related to the experimentally determined structures with a mean root-mean-square deviation value of 3.4 Å. Further, we were able to classify high and low affinity ligands with the area under the curve values of 0.47, 0.60, and 0.69 for FXa, SYK, and TrmD, respectively, indicating the validity of our approach in at least two of the three systems. Detailed critical analysis of the results and CSAR methodology ranking procedures suggested that a straightforward application of our workflow has limitations, as some of the performance measures do not reflect the actual utility of pose and affinity predictions in the biological context of individual systems.
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Affiliation(s)
- Philip Prathipati
- National Institutes of Biomedical Innovation, Health and Nutrition , 7-6-8 Saito-Asagi, Ibaraki City, Osaka 567-0085, Japan
| | - Kenji Mizuguchi
- National Institutes of Biomedical Innovation, Health and Nutrition , 7-6-8 Saito-Asagi, Ibaraki City, Osaka 567-0085, Japan
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19
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Chevillard F, Kolb P. SCUBIDOO: A Large yet Screenable and Easily Searchable Database of Computationally Created Chemical Compounds Optimized toward High Likelihood of Synthetic Tractability. J Chem Inf Model 2015; 55:1824-35. [PMID: 26282054 DOI: 10.1021/acs.jcim.5b00203] [Citation(s) in RCA: 64] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
De novo drug design is widely assisted by computational approaches that enable the generation of a tremendous amount of new virtual molecules within a short time frame. While the novelty of the computationally generated compounds can easily be assessed, such approaches often neglect the synthetic feasibility of the molecules, thus creating a potential hurdle that can be a barrier to further investigation. Therefore, we have developed SCUBIDOO, a freely accessible database concept that currently holds 21 million virtual products originating from a small library of building blocks and a collection of robust organic reactions. This large data set was reduced to three representative and computationally tractable samples denoted as S, M, and L, containing 9994, 99,977, and 999,794 products, respectively. These small sets are useful as starting points for ligand identification and optimization projects. The generated products come with synthesis instructions and alerts of possible side reactions, and we show that they exhibit drug-like properties while still extending into unexplored quadrants of chemical space, thus suggesting novelty. We show multiple examples that demonstrate how SCUBIDOO can facilitate the search around initial hits. This database might be a useful idea generator for early ligand discovery projects since it allows a focus on those molecules that are likely to be synthetically feasible and can therefore be studied further. Together with its modular building block construction principle, this database is also suitable for structure-activity relationship studies or fragment-growing strategies.
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Affiliation(s)
- F Chevillard
- Department of Pharmaceutical Chemistry, Philipps-University Marburg , 35032 Marburg, Germany
| | - P Kolb
- Department of Pharmaceutical Chemistry, Philipps-University Marburg , 35032 Marburg, Germany
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20
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Kubyshkin V, Kheylik Y, Mykhailiuk PK. Synthesis and studies on gem-fluorinated 2-azabicyclo[n.1.0]alkanes. J Fluor Chem 2015. [DOI: 10.1016/j.jfluchem.2015.03.008] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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21
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Goldberg FW, Kettle JG, Kogej T, Perry MW, Tomkinson NP. Designing novel building blocks is an overlooked strategy to improve compound quality. Drug Discov Today 2015; 20:11-7. [DOI: 10.1016/j.drudis.2014.09.023] [Citation(s) in RCA: 146] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2014] [Revised: 07/28/2014] [Accepted: 09/26/2014] [Indexed: 12/19/2022]
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22
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Foscato M, Occhipinti G, Venkatraman V, Alsberg BK, Jensen VR. Automated Design of Realistic Organometallic Molecules from Fragments. J Chem Inf Model 2014; 54:767-80. [DOI: 10.1021/ci4007497] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Marco Foscato
- Department
of Chemistry, University of Bergen, Allégaten 41, N-5007 Bergen, Norway
| | - Giovanni Occhipinti
- Department
of Chemistry, University of Bergen, Allégaten 41, N-5007 Bergen, Norway
| | - Vishwesh Venkatraman
- Department
of Chemistry, Norwegian University of Science and Technology, N-7491 Trondheim, Norway
| | - Bjørn K. Alsberg
- Department
of Chemistry, Norwegian University of Science and Technology, N-7491 Trondheim, Norway
| | - Vidar R. Jensen
- Department
of Chemistry, University of Bergen, Allégaten 41, N-5007 Bergen, Norway
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23
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Peng Z. Very large virtual compound spaces: construction, storage and utility in drug discovery. DRUG DISCOVERY TODAY. TECHNOLOGIES 2013; 10:e387-e394. [PMID: 24050135 DOI: 10.1016/j.ddtec.2013.01.004] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Recent activities in the construction, storage and exploration of very large virtual compound spaces are reviewed by this report. As expected, the systematic exploration of compound spaces at the highest resolution (individual atoms and bonds) is intrinsically intractable. By contrast, by staying within a finite number of reactions and a finite number of reactants or fragments, several virtual compound spaces have been constructed in a combinatorial fashion with sizes ranging from 10(11)11 to 10(20)20 compounds. Multiple search methods have been developed to perform searches (e.g. similarity, exact and substructure) into those compound spaces without the need for full enumeration. The up-front investment spent on synthetic feasibility during the construction of some of those virtual compound spaces enables a wider adoption by medicinal chemists to design and synthesize important compounds for drug discovery. Recent activities in the area of exploring virtual compound spaces via the evolutionary approach based on Genetic Algorithm also suggests a positive shift of focus from method development to workflow, integration and ease of use, all of which are required for this approach to be widely adopted by medicinal chemists.
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Hähnke V, Rupp M, Hartmann AK, Schneider G. Pharmacophore Alignment Search Tool (PhAST): Significance Assessment of Chemical Similarity. Mol Inform 2013; 32:625-46. [PMID: 27481770 DOI: 10.1002/minf.201300021] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2013] [Accepted: 04/19/2013] [Indexed: 11/06/2022]
Abstract
Previously, we proposed a ligand-based virtual screening technique (PhAST) based on global alignment of linearized interaction patterns. Here, we applied techniques developed for similarity assessment in local sequence alignments to our method resulting in p-values for chemical similarity. We compared two sampling strategies, a simple sampling strategy and a Markov Chain Monte Carlo (MCMC) method, and investigated the similarity of sampled distributions to Gaussian, Gumbel, modified Gumbel, and Gamma distributions. The Gumbel distribution with a Gaussian correction term was identified as the most similar to the observed empirical distributions. These techniques were applied in retrospective screenings on a drug-like dataset. Obtained p-values were adjusted to the size of the screening library with four different methods. Evaluation of E-value thresholds corroborated the Bonferroni correction as a preferred means to identify significant chemical similarity with PhAST. An online version of PhAST with significance estimation is available at http://modlab-cadd.ethz.ch/.
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Affiliation(s)
- Volker Hähnke
- Eidgenössische Technische Hochschule (ETH), Department of Chemistry and Applied Biosciences, Institute of Pharmaceutical Sciences, Wolfgang-Pauli-Str. 10, 8093 Zürich, Switzerland phone: +1 (202)436-5989.
| | - Matthias Rupp
- Eidgenössische Technische Hochschule (ETH), Department of Chemistry and Applied Biosciences, Institute of Pharmaceutical Sciences, Wolfgang-Pauli-Str. 10, 8093 Zürich, Switzerland phone: +1 (202)436-5989
| | - Alexander K Hartmann
- Universität Oldenburg, Computational Theoretical Physics, Institut für Physik, Carl-von-Ossietzky Strasse 9-11, 26111 Oldenburg, Germany
| | - Gisbert Schneider
- Eidgenössische Technische Hochschule (ETH), Department of Chemistry and Applied Biosciences, Institute of Pharmaceutical Sciences, Wolfgang-Pauli-Str. 10, 8093 Zürich, Switzerland phone: +1 (202)436-5989
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25
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Evers A, Hessler G, Wang LH, Werrel S, Monecke P, Matter H. CROSS: An Efficient Workflow for Reaction-Driven Rescaffolding and Side-Chain Optimization Using Robust Chemical Reactions and Available Reagents. J Med Chem 2013; 56:4656-70. [DOI: 10.1021/jm400404v] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Andreas Evers
- Struct., Design & Informatics, R&D LGCR, Sanofi-Aventis Deutschland GmbH, Industriepark Höchst, 65926 Frankfurt am Main, Germany
| | - Gerhard Hessler
- Struct., Design & Informatics, R&D LGCR, Sanofi-Aventis Deutschland GmbH, Industriepark Höchst, 65926 Frankfurt am Main, Germany
| | - Li-hsing Wang
- F2S IAIS PnS, Sanofi-Aventis
Deutschland GmbH, Industriepark Höchst, 65926 Frankfurt am
Main, Germany
| | - Simon Werrel
- Struct., Design & Informatics, R&D LGCR, Sanofi-Aventis Deutschland GmbH, Industriepark Höchst, 65926 Frankfurt am Main, Germany
| | - Peter Monecke
- Chemistry, R&D LGCR, Sanofi-Aventis Deutschland GmbH, Industriepark Höchst, 65926 Frankfurt am Main, Germany
| | - Hans Matter
- Struct., Design & Informatics, R&D LGCR, Sanofi-Aventis Deutschland GmbH, Industriepark Höchst, 65926 Frankfurt am Main, Germany
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26
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Spänkuch B, Keppner S, Lange L, Rodrigues T, Zettl H, Koch CP, Reutlinger M, Hartenfeller M, Schneider P, Schneider G. Drugs by numbers: reaction-driven de novo design of potent and selective anticancer leads. Angew Chem Int Ed Engl 2013; 52:4676-81. [PMID: 23166089 DOI: 10.1002/anie.201206897] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2012] [Indexed: 11/07/2022]
Abstract
A potent and selective inhibitor of the anticancer target Polo-like kinase 1 was found by computer-based molecular design. This type II kinase inhibitor was synthesized as suggested by the design software DOGS and exhibited significant antiproliferative effects against HeLa cells without affecting nontransformed cells. The study provides a proof-of-concept for reaction-based de novo design as a leading tool for drug discovery.
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Affiliation(s)
- Birgit Spänkuch
- Universitätsfrauenklinik, Molekulare Onkologie und Gynäkologie, Eberhard Karls Universität, Calwerstrasse 7, 72076 Tübingen, Germany
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27
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Yu MJ. Druggable chemical space and enumerative combinatorics. J Cheminform 2013; 5:19. [PMID: 23594604 PMCID: PMC3641967 DOI: 10.1186/1758-2946-5-19] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2013] [Accepted: 04/07/2013] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND There is a growing body of literature describing the properties of marketed drugs, the concept of drug-likeness and the vastness of chemical space. In that context, enumerative combinatorics with simple atomic components may be useful in the conception and design of structurally novel compounds for expanding and enhancing high-throughput screening (HTS) libraries. RESULTS A random combination of mono- and diatomic carbon, hydrogen, nitrogen, and oxygen containing components in the absence of molecular weight constraints but with the ability to form rings affords virtual compounds that fall in bulk physicochemical space typically associated with drugs, but whose ring assemblies fall in new or under-represented areas of chemical shape space. When compared against compounds in the ChEMBL_14, MDDR, Drug Bank and Dictionary of Natural Products, the percentage of virtual compounds with a Tanimoto index of 1.0 (ECFP_4) was found to be as high as 0.21. Depending on therapeutic target, this value may be in range of what might be expected from an experimental HTS campaign in terms of a true hit rate. CONCLUSION Virtual compounds derived through enumerative combinatorics of simple atomic components have drug-like properties with ring assemblies that fall in new or under-represented areas of shape space. Structures derived in this manner could provide the starting point or inspiration for the design of structurally novel scaffolds in an unbiased fashion.
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Affiliation(s)
- Melvin J Yu
- Eisai Inc,, 4 Corporate, Dr, Andover, MA, 01810, USA.
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28
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Significance estimation for sequence-based chemical similarity searching (PhAST) and application to AuroraA kinase inhibitors. Future Med Chem 2013; 4:1897-906. [PMID: 23088272 DOI: 10.4155/fmc.12.148] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Chemical similarity searching allows the retrieval of preferred screening molecules from a compound database. Candidates are ranked according to their similarity to a reference compound (query). Assessing the statistical significance of chemical similarity scores helps prioritizing significant hits, and identifying cases where the database does not contain any promising compounds. METHOD Our text-based similarity measure, Pharmacophore Alignment Search Tool (PhAST), employs pair-wise sequence alignment. We adapted the concept of E-values as significance estimates and employed a sampling technique that incorporates the principle of importance sampling in a Markov chain Monte Carlo simulation to generate distributions of random alignment scores. These distributions were used to compute significance estimates for similarity scores in a preliminary prospective virtual screen for inhibitors of Aurora A kinase. CONCLUSION Assessing the significance of compound similarity computed with PhAST allows for a statistically motivated identification of candidate screening compounds. Inhibitors of Aurora A kinase were retrieved from a large compound library.
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Rodrigues T, Roudnicky F, Koch CP, Kudoh T, Reker D, Detmar M, Schneider G. De novo design and optimization of Aurora A kinase inhibitors. Chem Sci 2013. [DOI: 10.1039/c2sc21842a] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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30
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Rabal O, Oyarzabal J. Biologically Relevant Chemical Space Navigator: From Patent and Structure–Activity Relationship Analysis to Library Acquisition and Design. J Chem Inf Model 2012; 52:3123-37. [DOI: 10.1021/ci3004539] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Obdulia Rabal
- Small Molecule Discovery Platform,
Center for Applied Medical Research (CIMA), University of Navarra, Avda. Pio XII 55, E-31008 Pamplona, Spain
| | - Julen Oyarzabal
- Small Molecule Discovery Platform,
Center for Applied Medical Research (CIMA), University of Navarra, Avda. Pio XII 55, E-31008 Pamplona, Spain
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31
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Spänkuch B, Keppner S, Lange L, Rodrigues T, Zettl H, Koch CP, Reutlinger M, Hartenfeller M, Schneider P, Schneider G. Wirkstoffe nach Zahlen: reaktionsbasierter De-novo-Entwurf von potenten und selektiven Leitstrukturen für die Krebsforschung. Angew Chem Int Ed Engl 2012. [DOI: 10.1002/ange.201206897] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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