1
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Xiong J, Cui R, Li Z, Zhang W, Zhang R, Fu Z, Liu X, Li Z, Chen K, Zheng M. Transfer learning enhanced graph neural network for aldehyde oxidase metabolism prediction and its experimental application. Acta Pharm Sin B 2024; 14:623-634. [PMID: 38322350 PMCID: PMC10840476 DOI: 10.1016/j.apsb.2023.10.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2023] [Revised: 09/07/2023] [Accepted: 10/11/2023] [Indexed: 02/08/2024] Open
Abstract
Aldehyde oxidase (AOX) is a molybdoenzyme that is primarily expressed in the liver and is involved in the metabolism of drugs and other xenobiotics. AOX-mediated metabolism can result in unexpected outcomes, such as the production of toxic metabolites and high metabolic clearance, which can lead to the clinical failure of novel therapeutic agents. Computational models can assist medicinal chemists in rapidly evaluating the AOX metabolic risk of compounds during the early phases of drug discovery and provide valuable clues for manipulating AOX-mediated metabolism liability. In this study, we developed a novel graph neural network called AOMP for predicting AOX-mediated metabolism. AOMP integrated the tasks of metabolic substrate/non-substrate classification and metabolic site prediction, while utilizing transfer learning from 13C nuclear magnetic resonance data to enhance its performance on both tasks. AOMP significantly outperformed the benchmark methods in both cross-validation and external testing. Using AOMP, we systematically assessed the AOX-mediated metabolism of common fragments in kinase inhibitors and successfully identified four new scaffolds with AOX metabolism liability, which were validated through in vitro experiments. Furthermore, for the convenience of the community, we established the first online service for AOX metabolism prediction based on AOMP, which is freely available at https://aomp.alphama.com.cn.
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Affiliation(s)
- Jiacheng Xiong
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Rongrong Cui
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhaojun Li
- College of Computer and Information Engineering, Dezhou University, Dezhou 253023, China
- AI Department, Suzhou Alphama Biotechnology Co., Ltd., Suzhou 215000, China
| | - Wei Zhang
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Runze Zhang
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zunyun Fu
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiaohong Liu
- AI Department, Suzhou Alphama Biotechnology Co., Ltd., Suzhou 215000, China
| | - Zhenghao Li
- Shanghai Institute for Advanced Immunochemical Studies, and School of Life Science and Technology, ShanghaiTech University, Shanghai 200031, China
| | - Kaixian Chen
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Mingyue Zheng
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- State Key Laboratory of Pharmaceutical Biotechnology, Nanjing University, Nanjing 210023, China
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2
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Zhao Z, Bourne PE. How Ligands Interact with the Kinase Hinge. ACS Med Chem Lett 2023; 14:1503-1508. [PMID: 37974950 PMCID: PMC10641887 DOI: 10.1021/acsmedchemlett.3c00212] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Accepted: 10/03/2023] [Indexed: 11/19/2023] Open
Abstract
ATP-competitive kinase inhibitors form hydrogen bond interactions with the kinase hinge region at the adenine binding site. Thus, it is crucial to explore hinge-ligand recognition as part of a rational drug design strategy. Here, harnessing known ligand-bound kinase structures and experimental assay resources, we first created a kinase structure-assay database (KSAD) containing 2705 nM ligand-bound kinase complexes. Then, using KSAD, we systematically investigate hinge-ligand binding patterns using interaction fingerprints, thereby delineating 15 different hydrogen-bond interaction modes. We believe these results will be valuable for de novo drug design and/or scaffold hopping of kinase-targeted drugs.
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Affiliation(s)
- Zheng Zhao
- School of Data Science and Department
of Biomedical Engineering, University of
Virginia, Charlottesville, Virginia 22904, United States
| | - Philip E. Bourne
- School of Data Science and Department
of Biomedical Engineering, University of
Virginia, Charlottesville, Virginia 22904, United States
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3
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Mazzucato R, Roberti M, Capelli AM, Rancati F, Biagetti M, Fiorelli C, Bruno P, Ronchi P, Bertolini S, Corsi M, Pala D. Application of an "inhalation by design" approach to the identification and in-vitro evaluation of novel purine based PI3Kδ inhibitors. Eur J Med Chem 2023; 254:115331. [PMID: 37094451 DOI: 10.1016/j.ejmech.2023.115331] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Revised: 03/29/2023] [Accepted: 03/29/2023] [Indexed: 04/26/2023]
Abstract
PI3Kδ is a lipid kinase which plays a key role in airway inflammatory conditions. Accordingly, the inhibition of PI3Kδ can be considered a valuable strategy for the treatment of chronic respiratory diseases such as Asthma and Chronic obstructive pulmonary disease (COPD). In this work, we describe our efforts to identify new PI3Kδ inhibitors following an "inhalation by design" strategy. Starting from the identification of a purine scaffold, we carried out a preliminary SAR expansion which led to the identification of a new hit characterized by a high enzymatic potency and moderate PI3Kδ selectivity. A subsequent optimization led to novel purine based derivatives with favorable in vitro ADME profiles, which might represent promising starting points for future development of new inhaled drug candidates.
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Affiliation(s)
- Roberta Mazzucato
- Chemistry Research and Drug Design Department, Chiesi Farmaceutici S.p.A, Nuovo Centro Ricerche, Largo Belloli 11/a, 43122, Parma, Italy.
| | - Marinella Roberti
- Department of Pharmacy and Biotechnology, University of Bologna, 40126, Bologna, Italy
| | - Anna Maria Capelli
- Corporate Drug Development, Chiesi Farmaceutici S.p.A, Nuovo Centro Ricerche, Largo Belloli 11/a, 43122, Parma, Italy
| | - Fabio Rancati
- Chemistry Research and Drug Design Department, Chiesi Farmaceutici S.p.A, Nuovo Centro Ricerche, Largo Belloli 11/a, 43122, Parma, Italy
| | - Matteo Biagetti
- Pipeline Innovation Department, Chiesi Farmaceutici S.p.A, Nuovo Centro Ricerche, Largo Belloli 11/a, 43122, Parma, Italy
| | - Claudio Fiorelli
- Chemistry Research and Drug Design Department, Chiesi Farmaceutici S.p.A, Nuovo Centro Ricerche, Largo Belloli 11/a, 43122, Parma, Italy
| | - Paolo Bruno
- Chemistry Research and Drug Design Department, Chiesi Farmaceutici S.p.A, Nuovo Centro Ricerche, Largo Belloli 11/a, 43122, Parma, Italy
| | - Paolo Ronchi
- Chemistry Research and Drug Design Department, Chiesi Farmaceutici S.p.A, Nuovo Centro Ricerche, Largo Belloli 11/a, 43122, Parma, Italy
| | - Serena Bertolini
- Experimental Pharmacology and Translational Science, Chiesi Farmaceutici S.p.A, Nuovo Centro Ricerche, Largo Belloli 11/a, 43122, Parma, Italy
| | - Mauro Corsi
- In Vitro Biology Department, Aptuit, an Evotec Company, Via A. Fleming 4, 37135, Verona, Italy
| | - Daniele Pala
- Chemistry Research and Drug Design Department, Chiesi Farmaceutici S.p.A, Nuovo Centro Ricerche, Largo Belloli 11/a, 43122, Parma, Italy.
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4
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Dai X, Xu Y, Qiu H, Qian X, Lin M, Luo L, Zhao Y, Huang D, Zhang Y, Chen Y, Liu H, Jiang Y. KID: A Kinase-Focused Interaction Database and Its Application in the Construction of Kinase-Focused Molecule Databases. J Chem Inf Model 2022; 62:6022-6034. [PMID: 36447388 DOI: 10.1021/acs.jcim.2c00908] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
Abstract
Protein kinases are important drug targets for the treatment of several diseases. The interaction between kinases and ligands is vital in the process of small-molecule kinase inhibitor (SMKI) design. In this study, we propose a method to extract fragments and amino acid residues from crystal structures for kinase-ligand interactions. In addition, core fragments that interact with the important hinge region of kinases were extracted along with their decorations. Based on the superimposed structural data of kinases from the kinase-ligand interaction fingerprint and structure database, we obtained two libraries, namely, a hinge-unfocused fragment-amino acid pair library (FAP Lib) that contains 6672 pairs of fragments and corresponding amino-acids, and a hinge-focused hinge binder library (HB Lib) of 3560 pairs of hinge-binding scaffolds with their corresponding decorations. These two libraries constitute a kinase-focused interaction database (KID). In depth analysis was conducted on KID to explore important characteristics of fragments in the design of SMKIs. With KID, we built two kinase-focused molecule databases, one called Recomb_DB, which contains 1,72,346 molecules generated through fragment recombination based on the FAP Lib, and another called RsdHB_DB, which contains 93,030 molecules generated based on our HB Lib using molecular generation methods. Compared with five databases both commercial and non-commercial, these two databases both ranked top 3 in scaffold diversity, top 4 in molecule fingerprint diversity, and are more focused on the chemical space of kinase inhibitors. Hence, KID presents a useful addition to existing databases for the exploration of novel SMKIs.
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Affiliation(s)
- Xiaowen Dai
- Laboratory of Molecular Design and Drug Discovery, School of Science, China Pharmaceutical University, 639 Longmian Avenue, Nanjing 211198, China
| | - Yuan Xu
- Laboratory of Molecular Design and Drug Discovery, School of Science, China Pharmaceutical University, 639 Longmian Avenue, Nanjing 211198, China
| | - Haodi Qiu
- Laboratory of Molecular Design and Drug Discovery, School of Science, China Pharmaceutical University, 639 Longmian Avenue, Nanjing 211198, China
| | - Xu Qian
- Laboratory of Molecular Design and Drug Discovery, School of Science, China Pharmaceutical University, 639 Longmian Avenue, Nanjing 211198, China
| | - Mingde Lin
- Laboratory of Molecular Design and Drug Discovery, School of Science, China Pharmaceutical University, 639 Longmian Avenue, Nanjing 211198, China
| | - Lin Luo
- Laboratory of Molecular Design and Drug Discovery, School of Science, China Pharmaceutical University, 639 Longmian Avenue, Nanjing 211198, China
| | - Yang Zhao
- Laboratory of Molecular Design and Drug Discovery, School of Science, China Pharmaceutical University, 639 Longmian Avenue, Nanjing 211198, China
| | - Dingfang Huang
- Laboratory of Molecular Design and Drug Discovery, School of Science, China Pharmaceutical University, 639 Longmian Avenue, Nanjing 211198, China
| | - Yanmin Zhang
- Laboratory of Molecular Design and Drug Discovery, School of Science, China Pharmaceutical University, 639 Longmian Avenue, Nanjing 211198, China
| | - Yadong Chen
- Laboratory of Molecular Design and Drug Discovery, School of Science, China Pharmaceutical University, 639 Longmian Avenue, Nanjing 211198, China
| | - Haichun Liu
- Laboratory of Molecular Design and Drug Discovery, School of Science, China Pharmaceutical University, 639 Longmian Avenue, Nanjing 211198, China
| | - Yulei Jiang
- Laboratory of Molecular Design and Drug Discovery, School of Science, China Pharmaceutical University, 639 Longmian Avenue, Nanjing 211198, China
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5
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Hu L, Yang Y, Zheng S, Xu J, Ran T, Chen H. Kinase Inhibitor Scaffold Hopping with Deep Learning Approaches. J Chem Inf Model 2021; 61:4900-4912. [PMID: 34586824 DOI: 10.1021/acs.jcim.1c00608] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The protein kinase family contains many promising drug targets. Many kinase inhibitors target the ATP-binding pocket, leading to approved drugs in past decades. Scaffold hopping is an effective approach for drug design. The kinase ATP-binding pocket is highly conserved, crossing the whole kinase family. This provides an opportunity to develop a scaffold hopping approach to explore diversified scaffolds among various kinase inhibitors. In this work, we report the SyntaLinker-Hybrid scheme for kinase inhibitor scaffold hopping. With this scheme, we replace molecular fragments bound at the conserved kinase hinge region with deep generative models. Thus, we are able to generate new kinase-inhibitor-like structures hybridizing the privileged fragments against the hinge region. We demonstrate that this scheme allows generation of kinase-inhibitor-like molecules with novel scaffolds, while retaining the binding features of existing kinase inhibitors. This work can be employed in lead identification against kinase targets.
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Affiliation(s)
- Lizhao Hu
- School of Biotechnology and Health Sciences, Wuyi University, Jiangmen 529020, China.,Research Center for Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-Sen University, 132 East Circle at University City, Guangzhou 510006, China
| | - Yuyao Yang
- Center of Cell Lineage and Atlas, Bioland Laboratory (Guangzhou Regenerative Medicine and Health-Guangdong Laboratory), Guangzhou 510530, China.,Research Center for Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-Sen University, 132 East Circle at University City, Guangzhou 510006, China
| | - Shuangjia Zheng
- School of Data and Computer Science, Sun Yat-sen University, Guangzhou 510006, China
| | - Jun Xu
- School of Biotechnology and Health Sciences, Wuyi University, Jiangmen 529020, China.,Research Center for Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-Sen University, 132 East Circle at University City, Guangzhou 510006, China
| | - Ting Ran
- Center of Cell Lineage and Atlas, Bioland Laboratory (Guangzhou Regenerative Medicine and Health-Guangdong Laboratory), Guangzhou 510530, China
| | - Hongming Chen
- Center of Cell Lineage and Atlas, Bioland Laboratory (Guangzhou Regenerative Medicine and Health-Guangdong Laboratory), Guangzhou 510530, China
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6
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Kalogirou AS, East MP, Laitinen T, Torrice CD, Maffuid KA, Drewry DH, Koutentis PA, Johnson GL, Crona DJ, Asquith CRM. Synthesis and Evaluation of Novel 1,2,6-Thiadiazinone Kinase Inhibitors as Potent Inhibitors of Solid Tumors. Molecules 2021; 26:molecules26195911. [PMID: 34641454 PMCID: PMC8513058 DOI: 10.3390/molecules26195911] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Revised: 09/22/2021] [Accepted: 09/24/2021] [Indexed: 11/16/2022] Open
Abstract
A focused series of substituted 4H-1,2,6-thiadiazin-4-ones was designed and synthesized to probe the anti-cancer properties of this scaffold. Insights from previous kinase inhibitor programs were used to carefully select several different substitution patterns. Compounds were tested on bladder, prostate, pancreatic, breast, chordoma, and lung cancer cell lines with an additional skin fibroblast cell line as a toxicity control. This resulted in the identification of several low single digit micro molar compounds with promising therapeutic windows, particularly for bladder and prostate cancer. A number of key structural features of the 4H-1,2,6-thiadiazin-4-one scaffold are discussed that show promising scope for future improvement.
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Affiliation(s)
- Andreas S. Kalogirou
- Department of Life Sciences, School of Sciences, European University Cyprus, 6 Diogenis Str., Engomi, P.O. Box 22006, Nicosia 1516, Cyprus
- Department of Chemistry, University of Cyprus, P.O. Box 20537, Nicosia 1678, Cyprus;
- Correspondence: (A.S.K.); (C.R.M.A.); Tel.: +357-22-559655 (A.S.K.); +1-919-491-3177 (C.R.M.A.)
| | - Michael P. East
- Department of Pharmacology, School of Medicine, University of North Carolina, Chapel Hill, NC 27599, USA; (M.P.E.); (G.L.J.)
| | - Tuomo Laitinen
- School of Pharmacy, Faculty of Health Sciences, University of Eastern Finland, 70211 Kuopio, Finland;
| | - Chad D. Torrice
- Division of Pharmacotherapy and Experimental Therapeutics, Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, NC 27599, USA; (C.D.T.); (K.A.M.); (D.J.C.)
| | - Kaitlyn A. Maffuid
- Division of Pharmacotherapy and Experimental Therapeutics, Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, NC 27599, USA; (C.D.T.); (K.A.M.); (D.J.C.)
| | - David H. Drewry
- Structural Genomics Consortium, Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, NC 27599, USA;
- Lineberger Comprehensive Cancer Center, School of Medicine, University of North Carolina, Chapel Hill, NC 27599, USA
| | | | - Gary L. Johnson
- Department of Pharmacology, School of Medicine, University of North Carolina, Chapel Hill, NC 27599, USA; (M.P.E.); (G.L.J.)
- Lineberger Comprehensive Cancer Center, School of Medicine, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Daniel J. Crona
- Division of Pharmacotherapy and Experimental Therapeutics, Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, NC 27599, USA; (C.D.T.); (K.A.M.); (D.J.C.)
- Lineberger Comprehensive Cancer Center, School of Medicine, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Christopher R. M. Asquith
- Department of Pharmacology, School of Medicine, University of North Carolina, Chapel Hill, NC 27599, USA; (M.P.E.); (G.L.J.)
- Correspondence: (A.S.K.); (C.R.M.A.); Tel.: +357-22-559655 (A.S.K.); +1-919-491-3177 (C.R.M.A.)
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7
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Oebbeke M, Siefker C, Wagner B, Heine A, Klebe G. Fragment‐Bindung an die Kinase‐Scharnier‐Region: Wenn Ladungsverteilung und lokale p
K
a
‐Verschiebungen etablierte Bioisosterie‐Konzepte fehlleiten. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202011295] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Matthias Oebbeke
- Philipps Universität Marburg Institut für Pharmazeutische Chemie Marbacher Weg 6 35032 Marburg Deutschland
| | - Christof Siefker
- Philipps Universität Marburg Institut für Pharmazeutische Chemie Marbacher Weg 6 35032 Marburg Deutschland
| | - Björn Wagner
- Roche Innovation Center Grenzacherstr. 124 4070 Basel Schweiz
| | - Andreas Heine
- Philipps Universität Marburg Institut für Pharmazeutische Chemie Marbacher Weg 6 35032 Marburg Deutschland
| | - Gerhard Klebe
- Philipps Universität Marburg Institut für Pharmazeutische Chemie Marbacher Weg 6 35032 Marburg Deutschland
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8
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Oebbeke M, Siefker C, Wagner B, Heine A, Klebe G. Fragment Binding to Kinase Hinge: If Charge Distribution and Local pK a Shifts Mislead Popular Bioisosterism Concepts. Angew Chem Int Ed Engl 2021; 60:252-258. [PMID: 33021032 PMCID: PMC7821265 DOI: 10.1002/anie.202011295] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Indexed: 12/25/2022]
Abstract
Medicinal‐chemistry optimization follows strategies replacing functional groups and attaching larger substituents at a promising lead scaffold. Well‐established bioisosterism rules are considered, however, it is difficult to estimate whether the introduced modifications really match the required properties at a binding site. The electron density distribution and pKa values are modulated influencing protonation states and bioavailability. Considering the adjacent H‐bond donor/acceptor pattern of the hinge binding motif in a kinase, we studied by crystallography a set of fragments to map the required interaction pattern. Unexpectedly, benzoic acid and benzamidine, decorated with the correct substituents, are totally bioisosteric just as carboxamide and phenolic OH. A mono‐dentate pyridine nitrogen out‐performs bi‐dentate functionalities. The importance of correctly designing pKa values of attached functional groups by additional substituents at the parent scaffold is rendered prominent.
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Affiliation(s)
- Matthias Oebbeke
- Philipps Universität Marburg, Institut für Pharmazeutische Chemie, Marbacher Weg 6, 35032, Marburg, Germany
| | - Christof Siefker
- Philipps Universität Marburg, Institut für Pharmazeutische Chemie, Marbacher Weg 6, 35032, Marburg, Germany
| | - Björn Wagner
- Roche Innovation Center, Grenzacherstr. 124, 4070, Basel, Switzerland
| | - Andreas Heine
- Philipps Universität Marburg, Institut für Pharmazeutische Chemie, Marbacher Weg 6, 35032, Marburg, Germany
| | - Gerhard Klebe
- Philipps Universität Marburg, Institut für Pharmazeutische Chemie, Marbacher Weg 6, 35032, Marburg, Germany
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9
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Sydow D, Schmiel P, Mortier J, Volkamer A. KinFragLib: Exploring the Kinase Inhibitor Space Using Subpocket-Focused Fragmentation and Recombination. J Chem Inf Model 2020; 60:6081-6094. [PMID: 33155465 DOI: 10.1021/acs.jcim.0c00839] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Protein kinases play a crucial role in many cell signaling processes, making them one of the most important families of drug targets. In this context, fragment-based drug design strategies have been successfully applied to develop novel kinase inhibitors. These strategies usually follow a knowledge-driven approach to optimize a focused set of fragments to a potent kinase inhibitor. Alternatively, KinFragLib explores and extends the chemical space of kinase inhibitors using data-driven fragmentation and recombination. The method builds on available structural kinome data from the KLIFS database for over 2500 kinase DFG-in structures cocrystallized with noncovalent kinase ligands. The computational fragmentation method splits the ligands into fragments with respect to their 3D proximity to six predefined functionally relevant subpocket centers. The resulting fragment library consists of six subpocket pools with over 7000 fragments, available at https://github.com/volkamerlab/KinFragLib. KinFragLib offers two main applications: on the one hand, in-depth analyses of the chemical space of known kinase inhibitors, subpocket characteristics, and connections, and on the other hand, subpocket-informed recombination of fragments to generate potential novel inhibitors. The latter showed that recombining only a subset of 624 representative fragments generated 6.7 million molecules. This combinatorial library contains, besides some known kinase inhibitors, more than 99% novel chemical matter compared to ChEMBL and 63% molecules compliant with Lipinski's rule of five.
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Affiliation(s)
- Dominique Sydow
- In Silico Toxicology and Structural Bioinformatics, Institute of Physiology, Charité-Universitätsmedizin Berlin, Charitéplatz 1, 10117 Berlin, Germany
| | - Paula Schmiel
- In Silico Toxicology and Structural Bioinformatics, Institute of Physiology, Charité-Universitätsmedizin Berlin, Charitéplatz 1, 10117 Berlin, Germany
| | - Jérémie Mortier
- Digital Technologies, Computational Molecular Design, Bayer AG, 13342 Berlin, Germany
| | - Andrea Volkamer
- In Silico Toxicology and Structural Bioinformatics, Institute of Physiology, Charité-Universitätsmedizin Berlin, Charitéplatz 1, 10117 Berlin, Germany
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10
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Yang Y, Zhang Y, Hua Y, Chen X, Fan Y, Wang Y, Liang L, Deng C, Lu T, Chen Y, Liu H. In Silico Design and Analysis of a Kinase-Focused Combinatorial Library Considering Diversity and Quality. J Chem Inf Model 2020; 60:92-107. [PMID: 31886658 DOI: 10.1021/acs.jcim.9b00841] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
A structurally diverse, high-quality, and kinase-focused database plays a critical role in finding hits or leads in kinase drug discovery. Here, we propose a workflow for designing a virtual kinase-focused combinatorial library using existing structures. Based on the analysis of known protein kinase inhibitors (PKIs), detailed fragment optimization, fragment selection, fragment linking, and a molecular filtering scheme were defined. Quick recognition of core fragments that can possibly form dual hydrogen bonds with the hinge region of the ATP-pocket was proposed. Furthermore, three diversity and four quality metrics were chosen for compound library analysis, which can be applied to databases with over 30 million structures. Compared with 13 commercial libraries, our protocol demonstrates a special advantage in terms of good skeleton diversity, acceptable fingerprint diversity, balanced scaffold distribution, and high quality, which can work well not only on existing PKIs, but also on four chosen commercial libraries. Overall, the strategy can greatly facilitate the expansion of a desirable chemical space for kinase drug discovery.
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Affiliation(s)
- Yan Yang
- Laboratory of Molecular Design and Drug Discovery, School of Science , China Pharmaceutical University , 639 Longmian Avenue , Nanjing 211198 , China
| | - Yanmin Zhang
- Laboratory of Molecular Design and Drug Discovery, School of Science , China Pharmaceutical University , 639 Longmian Avenue , Nanjing 211198 , China
| | - Yi Hua
- Laboratory of Molecular Design and Drug Discovery, School of Science , China Pharmaceutical University , 639 Longmian Avenue , Nanjing 211198 , China
| | - Xingye Chen
- Laboratory of Molecular Design and Drug Discovery, School of Science , China Pharmaceutical University , 639 Longmian Avenue , Nanjing 211198 , China
| | - Yuanrong Fan
- Laboratory of Molecular Design and Drug Discovery, School of Science , China Pharmaceutical University , 639 Longmian Avenue , Nanjing 211198 , China
| | - Yuchen Wang
- Laboratory of Molecular Design and Drug Discovery, School of Science , China Pharmaceutical University , 639 Longmian Avenue , Nanjing 211198 , China
| | - Li Liang
- Laboratory of Molecular Design and Drug Discovery, School of Science , China Pharmaceutical University , 639 Longmian Avenue , Nanjing 211198 , China
| | - Chenglong Deng
- Laboratory of Molecular Design and Drug Discovery, School of Science , China Pharmaceutical University , 639 Longmian Avenue , Nanjing 211198 , China
| | - Tao Lu
- Laboratory of Molecular Design and Drug Discovery, School of Science , China Pharmaceutical University , 639 Longmian Avenue , Nanjing 211198 , China.,State Key Laboratory of Natural Medicines , China Pharmaceutical University , 24 Tongjiaxiang , Nanjing 210009 , China
| | - Yadong Chen
- Laboratory of Molecular Design and Drug Discovery, School of Science , China Pharmaceutical University , 639 Longmian Avenue , Nanjing 211198 , China
| | - Haichun Liu
- Laboratory of Molecular Design and Drug Discovery, School of Science , China Pharmaceutical University , 639 Longmian Avenue , Nanjing 211198 , China
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11
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Lightfoot HL, Goldberg FW, Sedelmeier J. Evolution of Small Molecule Kinase Drugs. ACS Med Chem Lett 2019; 10:153-160. [PMID: 30783496 DOI: 10.1021/acsmedchemlett.8b00445] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2018] [Accepted: 12/17/2018] [Indexed: 12/14/2022] Open
Abstract
The development of small molecule kinase drugs is a rapidly evolving field and represents one of the most important research areas within oncology. This innovation letter provides an overview and analysis of approved kinase drugs according to their WHO registration (INN) dates, primary biological targets, and selectivity and structural similarities, which are also depicted in an associated poster. It also discusses new trends in kinase drug discovery programs such as new kinase targets, novel mechanisms of action, and diverse indications.
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Affiliation(s)
- Helen L. Lightfoot
- IMED Biotech Unit,Discovery Sciences, AstraZeneca, Alderley Park SK10 4TG, U.K
| | - Frederick W. Goldberg
- Oncology, IMED Biotech Unit, Medicinal Chemistry, AstraZeneca, Cambridge CB4 0WG, U.K
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Kooistra AJ, Vass M, McGuire R, Leurs R, de Esch IJP, Vriend G, Verhoeven S, de Graaf C. 3D-e-Chem: Structural Cheminformatics Workflows for Computer-Aided Drug Discovery. ChemMedChem 2018; 13:614-626. [PMID: 29337438 PMCID: PMC5900740 DOI: 10.1002/cmdc.201700754] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2017] [Revised: 01/11/2018] [Indexed: 01/06/2023]
Abstract
eScience technologies are needed to process the information available in many heterogeneous types of protein-ligand interaction data and to capture these data into models that enable the design of efficacious and safe medicines. Here we present scientific KNIME tools and workflows that enable the integration of chemical, pharmacological, and structural information for: i) structure-based bioactivity data mapping, ii) structure-based identification of scaffold replacement strategies for ligand design, iii) ligand-based target prediction, iv) protein sequence-based binding site identification and ligand repurposing, and v) structure-based pharmacophore comparison for ligand repurposing across protein families. The modular setup of the workflows and the use of well-established standards allows the re-use of these protocols and facilitates the design of customized computer-aided drug discovery workflows.
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Affiliation(s)
- Albert J. Kooistra
- Centre for Molecular and Biomolecular Informatics (CMBI)Radboud University Medical Center (RadboudUMC)NijmegenThe Netherlands
- Division of Medicinal Chemistry, Faculty of Science, Amsterdam Institute for Molecules, Medicines and Systems (AIMMS)Vrije Universiteit AmsterdamAmsterdamThe Netherlands
| | - Márton Vass
- Division of Medicinal Chemistry, Faculty of Science, Amsterdam Institute for Molecules, Medicines and Systems (AIMMS)Vrije Universiteit AmsterdamAmsterdamThe Netherlands
| | - Ross McGuire
- Centre for Molecular and Biomolecular Informatics (CMBI)Radboud University Medical Center (RadboudUMC)NijmegenThe Netherlands
- BioAxis Research, Pivot ParkOssThe Netherlands
| | - Rob Leurs
- Division of Medicinal Chemistry, Faculty of Science, Amsterdam Institute for Molecules, Medicines and Systems (AIMMS)Vrije Universiteit AmsterdamAmsterdamThe Netherlands
| | - Iwan J. P. de Esch
- Division of Medicinal Chemistry, Faculty of Science, Amsterdam Institute for Molecules, Medicines and Systems (AIMMS)Vrije Universiteit AmsterdamAmsterdamThe Netherlands
| | - Gert Vriend
- Centre for Molecular and Biomolecular Informatics (CMBI)Radboud University Medical Center (RadboudUMC)NijmegenThe Netherlands
| | | | - Chris de Graaf
- Division of Medicinal Chemistry, Faculty of Science, Amsterdam Institute for Molecules, Medicines and Systems (AIMMS)Vrije Universiteit AmsterdamAmsterdamThe Netherlands
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