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Higgins WT, Vibhute S, Bennett C, Lindert S. Discovery of Nanomolar Inhibitors for Human Dihydroorotate Dehydrogenase Using Structure-Based Drug Discovery Methods. J Chem Inf Model 2024; 64:435-448. [PMID: 38175956 DOI: 10.1021/acs.jcim.3c01358] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2024]
Abstract
We used a structure-based drug discovery approach to identify novel inhibitors of human dihydroorotate dehydrogenase (DHODH), which is a therapeutic target for treating cancer and autoimmune and inflammatory diseases. In the case of acute myeloid leukemia, no previously discovered DHODH inhibitors have yet succeeded in this clinical application. Thus, there remains a strong need for new inhibitors that could be used as alternatives to the current standard-of-care. Our goal was to identify novel inhibitors of DHODH. We implemented prefiltering steps to omit PAINS and Lipinski violators at the earliest stages of this project. This enriched compounds in the data set that had a higher potential of favorable oral druggability. Guided by Glide SP docking scores, we found 20 structurally unique compounds from the ChemBridge EXPRESS-pick library that inhibited DHODH with IC50, DHODH values between 91 nM and 2.7 μM. Ten of these compounds reduced MOLM-13 cell viability with IC50, MOLM-13 values between 2.3 and 50.6 μM. Compound 16 (IC50, DHODH = 91 nM) inhibited DHODH more potently than the known DHODH inhibitor, teriflunomide (IC50, DHODH = 130 nM), during biochemical characterizations and presented a promising scaffold for future hit-to-lead optimization efforts. Compound 17 (IC50, MOLM-13 = 2.3 μM) was most successful at reducing survival in MOLM-13 cell lines compared with our other hits. The discovered compounds represent excellent starting points for the development and optimization of novel DHODH inhibitors.
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Affiliation(s)
- William T Higgins
- Department of Chemistry and Biochemistry, Ohio State University, Columbus, Ohio 43210, United States
| | - Sandip Vibhute
- Medicinal Chemistry Shared Resource, Comprehensive Cancer Center, Ohio State University, Columbus, Ohio 43210, United States
| | - Chad Bennett
- Medicinal Chemistry Shared Resource, Comprehensive Cancer Center, Ohio State University, Columbus, Ohio 43210, United States
- Drug Development Institute, Ohio State University, Columbus, Ohio 43210, United States
| | - Steffen Lindert
- Department of Chemistry and Biochemistry, Ohio State University, Columbus, Ohio 43210, United States
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2
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Huang CH, Lin ST. MARS Plus: An Improved Molecular Design Tool for Complex Compounds Involving Ionic, Stereo, and Cis-Trans Isomeric Structures. J Chem Inf Model 2023; 63:7711-7728. [PMID: 38100117 DOI: 10.1021/acs.jcim.3c01745] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2023]
Abstract
MARS (Molecular Assembling and Representation Suite) (Hsu et al. J. Chem. Inf. Model. 2019, 59, 3703-3713) is a toolbox for the molecular design of organic molecules. MARS uses integer arrays to represent the elements and connectivity between elements of a molecule. It provides a collection of operations to manipulate the elemental composition and connectivity of a molecule (or a pair of molecules), enabling the creation of novel chemical compounds. In this work, the original MARS is extended to handle complex molecular structures, including geometric (cis-trans) isomers, stereo isomers, cyclic compounds, and ionic species. The extended version of MARS, referred to as MARS+, has a more comprehensive coverage of the chemical space and therefore can explore molecules with a greater chemical and physical diversity. Compared to other molecular design tools, MARS+ is designed to perform all possible manipulations on a given molecule or a pair of molecules. Molecular structure manipulation can be conducted in either a controlled or a random fashion. Furthermore, every structure manipulation has a counterpart so that the operation can be reversed. Nearly any possible chemical structure can be generated with MARS+ via a combination of molecular operations. The capabilities of MARS+ are examined by the design of new ionic liquids (ILs). The results show that MARS+ is a useful tool for computer-aided molecular design (CAMD) and molecular structure enumeration.
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Affiliation(s)
- Chen-Hsuan Huang
- Department of Chemical Engineering, National Taiwan University, Taipei 10617, Taiwan
| | - Shiang-Tai Lin
- Department of Chemical Engineering, National Taiwan University, Taipei 10617, Taiwan
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3
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Fromer JC, Coley CW. Computer-aided multi-objective optimization in small molecule discovery. PATTERNS (NEW YORK, N.Y.) 2023; 4:100678. [PMID: 36873904 PMCID: PMC9982302 DOI: 10.1016/j.patter.2023.100678] [Citation(s) in RCA: 25] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/12/2023]
Abstract
Molecular discovery is a multi-objective optimization problem that requires identifying a molecule or set of molecules that balance multiple, often competing, properties. Multi-objective molecular design is commonly addressed by combining properties of interest into a single objective function using scalarization, which imposes assumptions about relative importance and uncovers little about the trade-offs between objectives. In contrast to scalarization, Pareto optimization does not require knowledge of relative importance and reveals the trade-offs between objectives. However, it introduces additional considerations in algorithm design. In this review, we describe pool-based and de novo generative approaches to multi-objective molecular discovery with a focus on Pareto optimization algorithms. We show how pool-based molecular discovery is a relatively direct extension of multi-objective Bayesian optimization and how the plethora of different generative models extend from single-objective to multi-objective optimization in similar ways using non-dominated sorting in the reward function (reinforcement learning) or to select molecules for retraining (distribution learning) or propagation (genetic algorithms). Finally, we discuss some remaining challenges and opportunities in the field, emphasizing the opportunity to adopt Bayesian optimization techniques into multi-objective de novo design.
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Affiliation(s)
- Jenna C Fromer
- Department of Chemical Engineering, MIT, Cambridge, MA 02139, USA
| | - Connor W Coley
- Department of Chemical Engineering, MIT, Cambridge, MA 02139, USA.,Department of Electrical Engineering and Computer Science, MIT, Cambridge, MA 02139, USA
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4
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Chalmers G. Introducing ligand GA, a genetic algorithm molecular tool for automated protein inhibitor design. Sci Rep 2022; 12:20877. [PMID: 36463310 PMCID: PMC9719503 DOI: 10.1038/s41598-022-22281-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Accepted: 10/12/2022] [Indexed: 12/07/2022] Open
Abstract
Ligand GA is introduced in this work and approaches the problem of finding small molecules inhibiting protein functions by using the protein site to find close to optimal or optimal small molecule binders. Genetic algorithms (GA) are an effective means for approximating or solving computationally hard mathematics problems with large search spaces such as this one. The algorithm is designed to include constraints on the generated molecules from ADME restriction, localization in a binding site, specified hydrogen bond requirements, toxicity prevention from multiple proteins, sub-structure restrictions, and database inclusion. This algorithm and work is in the context of computational modeling, ligand design and docking to protein sites.
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Affiliation(s)
- Gordon Chalmers
- grid.213876.90000 0004 1936 738XComplex Carbohydrate Research Center, University of Georgia, Athens, GA 30602 USA
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5
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Prentis LE, Singleton CD, Bickel JD, Allen WJ, Rizzo RC. A molecular evolution algorithm for ligand design in DOCK. J Comput Chem 2022; 43:1942-1963. [PMID: 36073674 PMCID: PMC9623574 DOI: 10.1002/jcc.26993] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Revised: 06/13/2022] [Accepted: 08/03/2022] [Indexed: 01/11/2023]
Abstract
As a complement to virtual screening, de novo design of small molecules is an alternative approach for identifying potential drug candidates. Here, we present a new 3D genetic algorithm to evolve molecules through breeding, mutation, fitness pressure, and selection. The method, termed DOCK_GA, builds upon and leverages powerful sampling, scoring, and searching routines previously implemented into DOCK6. Three primary experiments were used during development: Single-molecule evolution evaluated three selection methods (elitism, tournament, and roulette), in four clinically relevant systems, in terms of mutation type and crossover success, chemical properties, ensemble diversity, and fitness convergence, among others. Large scale benchmarking assessed performance across 651 different protein-ligand systems. Ensemble-based evolution demonstrated using multiple inhibitors simultaneously to seed growth in a SARS-CoV-2 target. Key takeaways include: (1) The algorithm is robust as demonstrated by the successful evolution of molecules across a large diverse dataset. (2) Users have flexibility with regards to parent input, selection method, fitness function, and molecular descriptors. (3) The program is straightforward to run and only requires a single executable and input file at run-time. (4) The elitism selection method yields more tightly clustered molecules in terms of 2D/3D similarity, with more favorable fitness, followed by tournament and roulette.
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Affiliation(s)
- Lauren E. Prentis
- Department of Biochemistry & Cell BiologyStony Brook UniversityStony BrookNew YorkUSA
| | | | - John D. Bickel
- Department of ChemistryStony Brook UniversityStony BrookNew YorkUSA
| | - William J. Allen
- Department of Applied Mathematics & StatisticsStony Brook UniversityStony BrookNew YorkUSA
| | - Robert C. Rizzo
- Department of Applied Mathematics & StatisticsStony Brook UniversityStony BrookNew YorkUSA,Institute of Chemical Biology & Drug DiscoveryStony Brook UniversityStony BrookNew YorkUSA,Laufer Center for Physical & Quantitative BiologyStony Brook UniversityStony BrookNew YorkUSA
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6
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da Costa APL, Silva JRA, de Molfetta FA. Computational discovery of sulfonamide derivatives as potential inhibitors of the cruzain enzyme from T. cruzi by molecular docking, molecular dynamics and MM/GBSA approaches. MOLECULAR SIMULATION 2022. [DOI: 10.1080/08927022.2022.2120625] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
Affiliation(s)
- Ana Paula Lima da Costa
- Laboratório de Modelagem Molecular, Instituto de Ciências Exatas e Naturais, Universidade Federal do Pará, Belém, Brazil
| | - José Rogério A. Silva
- Laboratório de Planejamento e Desenvolvimento de Fármacos, Instituto de Ciências Exatas e Naturais, Universidade Federal do Pará, Belém, Brazil
| | - Fábio Alberto de Molfetta
- Laboratório de Modelagem Molecular, Instituto de Ciências Exatas e Naturais, Universidade Federal do Pará, Belém, Brazil
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7
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Urbina F, Lowden CT, Culberson JC, Ekins S. MegaSyn: Integrating Generative Molecular Design, Automated Analog Designer, and Synthetic Viability Prediction. ACS OMEGA 2022; 7:18699-18713. [PMID: 35694522 PMCID: PMC9178760 DOI: 10.1021/acsomega.2c01404] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Accepted: 05/11/2022] [Indexed: 05/04/2023]
Abstract
Generative machine learning models have become widely adopted in drug discovery and other fields to produce new molecules and explore molecular space, with the goal of discovering novel compounds with optimized properties. These generative models are frequently combined with transfer learning or scoring of the physicochemical properties to steer generative design, yet often, they are not capable of addressing a wide variety of potential problems, as well as converge into similar molecular space when combined with a scoring function for the desired properties. In addition, these generated compounds may not be synthetically feasible, reducing their capabilities and limiting their usefulness in real-world scenarios. Here, we introduce a suite of automated tools called MegaSyn representing three components: a new hill-climb algorithm, which makes use of SMILES-based recurrent neural network (RNN) generative models, analog generation software, and retrosynthetic analysis coupled with fragment analysis to score molecules for their synthetic feasibility. We show that by deconstructing the targeted molecules and focusing on substructures, combined with an ensemble of generative models, MegaSyn generally performs well for the specific tasks of generating new scaffolds as well as targeted analogs, which are likely synthesizable and druglike. We now describe the development, benchmarking, and testing of this suite of tools and propose how they might be used to optimize molecules or prioritize promising lead compounds using these RNN examples provided by multiple test case examples.
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Affiliation(s)
- Fabio Urbina
- Collaborations
Pharmaceuticals, Inc., 840 Main Campus Drive, Lab 3510, Raleigh, North Carolina 27606, United States
| | - Christopher T. Lowden
- Workflow
Informatics Corporation, 9316 Bramden Court, Wake Forest, North Carolina 27587, United States
| | - J. Christopher Culberson
- Workflow
Informatics Corporation, 9316 Bramden Court, Wake Forest, North Carolina 27587, United States
| | - Sean Ekins
- Collaborations
Pharmaceuticals, Inc., 840 Main Campus Drive, Lab 3510, Raleigh, North Carolina 27606, United States
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8
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Wang ZZ, Wang MS, Wang F, Shi XX, Huang W, Hao GF, Yang GF. Exploring the kinase-inhibitor fragment interaction space facilitates the discovery of kinase inhibitor overcoming resistance by mutations. Brief Bioinform 2022; 23:6596988. [PMID: 35649390 DOI: 10.1093/bib/bbac203] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Revised: 04/07/2022] [Accepted: 05/03/2022] [Indexed: 11/13/2022] Open
Abstract
Protein kinases play crucial roles in many cellular signaling processes, making them become important targets for drug discovery. But drug resistance mediated by mutation puts a barrier to the therapeutic effect of kinase inhibitors. Fragment-based drug discovery has been successfully applied to overcome such resistance. However, the complicate kinase-inhibitor fragment interaction and fragment-to-lead process seriously limit the efficiency of kinase inhibitor discovery against resistance caused by mutation. Here, we constructed a comprehensive web platform KinaFrag for the fragment-based kinase inhibitor discovery to overcome resistance. The kinase-inhibitor fragment space was investigated from 7783 crystal kinase-inhibitor fragment complexes, and the structural requirements of kinase subpockets were analyzed. The core fragment-based virtual screening workflow towards specific subpockets was developed to generate new kinase inhibitors. A series of tropomyosin receptor kinase (TRK) inhibitors were designed, and the most potent compound YT9 exhibits up to 70-fold activity improvement than marketed drugs larotrectinib and selitrectinib against G595R, G667C and F589L mutations of TRKA. YT9 shows promising antiproliferative against tumor cells in vitro and effectively inhibits tumor growth in vivo for wild type TRK and TRK mutants. Our results illustrate the great potential of KinaFrag in the kinase inhibitor discovery to combat resistance mediated by mutation. KinaFrag is freely available at http://chemyang.ccnu.edu.cn/ccb/database/KinaFrag/.
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Affiliation(s)
- Zhi-Zheng Wang
- Key Laboratory of Pesticide & Chemical Biology, Ministry of Education, International Joint Research Center for Intelligent Biosensor Technology and Health, College of Chemistry, Central China Normal University, Wuhan, 430079, P. R. China
| | - Ming-Shu Wang
- Key Laboratory of Pesticide & Chemical Biology, Ministry of Education, International Joint Research Center for Intelligent Biosensor Technology and Health, College of Chemistry, Central China Normal University, Wuhan, 430079, P. R. China
| | - Fan Wang
- Key Laboratory of Pesticide & Chemical Biology, Ministry of Education, International Joint Research Center for Intelligent Biosensor Technology and Health, College of Chemistry, Central China Normal University, Wuhan, 430079, P. R. China
| | - Xing-Xing Shi
- Key Laboratory of Pesticide & Chemical Biology, Ministry of Education, International Joint Research Center for Intelligent Biosensor Technology and Health, College of Chemistry, Central China Normal University, Wuhan, 430079, P. R. China
| | - Wei Huang
- Key Laboratory of Pesticide & Chemical Biology, Ministry of Education, International Joint Research Center for Intelligent Biosensor Technology and Health, College of Chemistry, Central China Normal University, Wuhan, 430079, P. R. China
| | - Ge-Fei Hao
- Key Laboratory of Pesticide & Chemical Biology, Ministry of Education, International Joint Research Center for Intelligent Biosensor Technology and Health, College of Chemistry, Central China Normal University, Wuhan, 430079, P. R. China
| | - Guang-Fu Yang
- Key Laboratory of Pesticide & Chemical Biology, Ministry of Education, International Joint Research Center for Intelligent Biosensor Technology and Health, College of Chemistry, Central China Normal University, Wuhan, 430079, P. R. China
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9
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10
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Green H, Durrant JD. DeepFrag: An Open-Source Browser App for Deep-Learning Lead Optimization. J Chem Inf Model 2021; 61:2523-2529. [PMID: 34029094 PMCID: PMC8243318 DOI: 10.1021/acs.jcim.1c00103] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2021] [Indexed: 11/28/2022]
Abstract
Lead optimization, a critical step in early stage drug discovery, involves making chemical modifications to a small-molecule ligand to improve properties such as binding affinity. We recently developed DeepFrag, a deep-learning model capable of recommending such modifications. Though a powerful hypothesis-generating tool, DeepFrag is currently implemented in Python and so requires a certain degree of computational expertise. To encourage broader adoption, we have created the DeepFrag browser app, which provides a user-friendly graphical user interface that runs the DeepFrag model in users' web browsers. The browser app does not require users to upload their molecular structures to a third-party server, nor does it require the separate installation of any third-party software. We are hopeful that the app will be a useful tool for both researchers and students. It can be accessed free of charge, without registration, at http://durrantlab.com/deepfrag. The source code is also available at http://git.durrantlab.com/jdurrant/deepfrag-app, released under the terms of the open-source Apache License, Version 2.0.
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Affiliation(s)
- Harrison Green
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Jacob D. Durrant
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
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11
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Lumley JA, Desai P, Wang J, Cahya S, Zhang H. The Derivation of a Matched Molecular Pairs Based ADME/Tox Knowledge Base for Compound Optimization. J Chem Inf Model 2020; 60:4757-4771. [PMID: 32975944 DOI: 10.1021/acs.jcim.0c00583] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Matched Molecular Pairs (MMP) analysis is a well-established technique for Structure Activity and Property Analysis (SAR and SPR). Summarizing multiple MMPs that describe the same structural change into a single chemical transform can be a powerful tool for prediction (termed Transform from here on). This is particularly useful in the area of Absorption, Distribution, Metabolism, and Elimination (ADME) analysis that is less influenced by 3D structural binding effects. The creation of a knowledge database containing many of these Transforms across typical ADME assays promises to be a powerful approach to aid multidimensional optimization. We present a detailed workflow for the derivation of such a database. We include details of an MMP fragmentation algorithm with associated statistical summarization methods for the derivation of Transforms. This is made freely available as part of the LillyMol software package. We describe the application of this method to several ADME/Tox (Toxicity) assay data sets and highlight multiple cases where the impact of traditional medicinal chemistry Transforms is contradicted by MMP data. We also describe the internal software interface used by medicinal chemists to aid the design of new compounds via automated suggestion. This approach utilizes the matched pairs database to "suggest" improved compounds in an automated design scenario. A nonvisual script-based version of the automated suggestions code with an associated set of described chemical Transforms is also made freely available along with this paper and as part of the LillyMol software package. Finally, we contrast this knowledge database against a larger database of all MMPs derived from a 2 million compound diversity set and a subset of MMPs seen in historical discovery projects. The comparison against all transforms in the diversity collection highlights the very low coverage of the transform database as compared to all possible transforms involving 15 atom fragments. The comparison against a smaller subset of Transforms seen on internal Medicinal Chemistry projects shows better coverage of the transform database for a small set of common medicinal chemistry strategies. Within the context of all possible transforms available to a medicinal chemistry project team, the challenge remains to move beyond mere idea generation from past projects toward high quality prediction for novel ADME/Tox modulating Transforms.
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Affiliation(s)
- James A Lumley
- Data Science and Engineering, Lilly Research Laboratories, Eli Lilly and Company, Erl Wood Manor, Windlesham, Surrey GU20 6PH, United Kingdom
| | - Prashant Desai
- Computational ADME, ADME-Toxicology-PKPD, Lilly Research Laboratories, Eli Lilly and Company, Indianapolis, Indiana 46285, United States
| | - Jibo Wang
- Discovery Chemistry Research Technologies, Lilly Research Laboratories, Eli Lilly and Company, Indianapolis, Indiana 46285, United States
| | - Suntara Cahya
- Discovery Statistics, Lilly Biotechnology Center, Eli Lilly and Company, San Diego, California 92121, United States
| | - Hongzhou Zhang
- Data Science and Engineering, Lilly Research Laboratories, Eli Lilly and Company, Indianapolis, Indiana 46285, United States
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12
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Chaudhari R, Fong LW, Tan Z, Huang B, Zhang S. An up-to-date overview of computational polypharmacology in modern drug discovery. Expert Opin Drug Discov 2020; 15:1025-1044. [PMID: 32452701 PMCID: PMC7415563 DOI: 10.1080/17460441.2020.1767063] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Accepted: 05/06/2020] [Indexed: 12/30/2022]
Abstract
INTRODUCTION In recent years, computational polypharmacology has gained significant attention to study the promiscuous nature of drugs. Despite tremendous challenges, community-wide efforts have led to a variety of novel approaches for predicting drug polypharmacology. In particular, some rapid advances using machine learning and artificial intelligence have been reported with great success. AREAS COVERED In this article, the authors provide a comprehensive update on the current state-of-the-art polypharmacology approaches and their applications, focusing on those reports published after our 2017 review article. The authors particularly discuss some novel, groundbreaking concepts, and methods that have been developed recently and applied to drug polypharmacology studies. EXPERT OPINION Polypharmacology is evolving and novel concepts are being introduced to counter the current challenges in the field. However, major hurdles remain including incompleteness of high-quality experimental data, lack of in vitro and in vivo assays to characterize multi-targeting agents, shortage of robust computational methods, and challenges to identify the best target combinations and design effective multi-targeting agents. Fortunately, numerous national/international efforts including multi-omics and artificial intelligence initiatives as well as most recent collaborations on addressing the COVID-19 pandemic have shown significant promise to propel the field of polypharmacology forward.
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Affiliation(s)
- Rajan Chaudhari
- Intelligent Molecular Discovery Laboratory, Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, Texas 77030, United States
| | - Long Wolf Fong
- Intelligent Molecular Discovery Laboratory, Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, Texas 77030, United States
- MD Anderson UTHealth Graduate School of Biomedical Sciences, 6767 Bertner Avenue, Houston, Texas 77030, United States
| | - Zhi Tan
- Intelligent Molecular Discovery Laboratory, Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, Texas 77030, United States
| | - Beibei Huang
- Intelligent Molecular Discovery Laboratory, Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, Texas 77030, United States
| | - Shuxing Zhang
- Intelligent Molecular Discovery Laboratory, Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, Texas 77030, United States
- MD Anderson UTHealth Graduate School of Biomedical Sciences, 6767 Bertner Avenue, Houston, Texas 77030, United States
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Spiegel JO, Durrant JD. AutoGrow4: an open-source genetic algorithm for de novo drug design and lead optimization. J Cheminform 2020; 12:25. [PMID: 33431021 PMCID: PMC7165399 DOI: 10.1186/s13321-020-00429-4] [Citation(s) in RCA: 49] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Accepted: 03/31/2020] [Indexed: 02/06/2023] Open
Abstract
We here present AutoGrow4, an open-source program for semi-automated computer-aided drug discovery. AutoGrow4 uses a genetic algorithm to evolve predicted ligands on demand and so is not limited to a virtual library of pre-enumerated compounds. It is a useful tool for generating entirely novel drug-like molecules and for optimizing preexisting ligands. By leveraging recent computational and cheminformatics advancements, AutoGrow4 is faster, more stable, and more modular than previous versions. It implements new docking-program compatibility, chemical filters, multithreading options, and selection methods to support a wide range of user needs. To illustrate both de novo design and lead optimization, we here apply AutoGrow4 to the catalytic domain of poly(ADP-ribose) polymerase 1 (PARP-1), a well characterized DNA-damage-recognition protein. AutoGrow4 produces drug-like compounds with better predicted binding affinities than FDA-approved PARP-1 inhibitors (positive controls). The predicted binding modes of the AutoGrow4 compounds mimic those of the known inhibitors, even when AutoGrow4 is seeded with random small molecules. AutoGrow4 is available under the terms of the Apache License, Version 2.0. A copy can be downloaded free of charge from http://durrantlab.com/autogrow4.
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Affiliation(s)
- Jacob O. Spiegel
- Department of Biological Sciences, University of Pittsburgh, 4200 Fifth Ave, Pittsburgh, PA 15260 USA
| | - Jacob D. Durrant
- Department of Biological Sciences, University of Pittsburgh, 4200 Fifth Ave, Pittsburgh, PA 15260 USA
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14
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Perez C, Soler D, Soliva R, Guallar V. FragPELE: Dynamic Ligand Growing within a Binding Site. A Novel Tool for Hit-To-Lead Drug Design. J Chem Inf Model 2020; 60:1728-1736. [PMID: 32027130 DOI: 10.1021/acs.jcim.9b00938] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The early stages of drug discovery rely on hit-to-lead programs, where initial hits undergo partial optimization to improve binding affinities for their biological target. This is an expensive and time-consuming process, requiring multiple iterations of trial and error designs, an ideal scenario for applying computer simulation. However, most state-of-the-art modeling techniques fail to provide a fast and reliable answer to the Induced-Fit protein-ligand problem. To aid in this matter, we present FragPELE, a new tool for in silico hit-to-lead drug design, capable of growing a fragment from a bound core while exploring the protein-ligand conformational space. We tested the ability of FragPELE to predict crystallographic data, even in cases where cryptic sub-pockets open because of the presence of particular R-groups. Additionally, we evaluated the potential of the software on growing and scoring five congeneric series from the 2015 FEP+ dataset, comparing them to FEP+, SP and Induced-Fit Glide, and MMGBSA simulations. Results show that FragPELE could be useful not only for finding new cavities and novel binding modes in cases where standard docking tools cannot but also to rank ligand activities in a reasonable amount of time and with acceptable precision.
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Affiliation(s)
- Carles Perez
- Life Sciences Department, Barcelona Supercomputing Center (BSC), Barcelona 08034, Spain
| | - Daniel Soler
- Nostrum Biodiscovery, Carrer Jordi Girona 29, Nexus II D128, 08034 Barcelona, Spain
| | - Robert Soliva
- Nostrum Biodiscovery, Carrer Jordi Girona 29, Nexus II D128, 08034 Barcelona, Spain
| | - Victor Guallar
- Life Sciences Department, Barcelona Supercomputing Center (BSC), Barcelona 08034, Spain.,ICREA: Institució Catalana de Recerca i Estudis Avançats, Passeig Lluís Companys 23, 08010 Barcelona, Spain
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15
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de Souza Neto LR, Moreira-Filho JT, Neves BJ, Maidana RLBR, Guimarães ACR, Furnham N, Andrade CH, Silva FP. In silico Strategies to Support Fragment-to-Lead Optimization in Drug Discovery. Front Chem 2020; 8:93. [PMID: 32133344 PMCID: PMC7040036 DOI: 10.3389/fchem.2020.00093] [Citation(s) in RCA: 100] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2019] [Accepted: 01/30/2020] [Indexed: 12/16/2022] Open
Abstract
Fragment-based drug (or lead) discovery (FBDD or FBLD) has developed in the last two decades to become a successful key technology in the pharmaceutical industry for early stage drug discovery and development. The FBDD strategy consists of screening low molecular weight compounds against macromolecular targets (usually proteins) of clinical relevance. These small molecular fragments can bind at one or more sites on the target and act as starting points for the development of lead compounds. In developing the fragments attractive features that can translate into compounds with favorable physical, pharmacokinetics and toxicity (ADMET-absorption, distribution, metabolism, excretion, and toxicity) properties can be integrated. Structure-enabled fragment screening campaigns use a combination of screening by a range of biophysical techniques, such as differential scanning fluorimetry, surface plasmon resonance, and thermophoresis, followed by structural characterization of fragment binding using NMR or X-ray crystallography. Structural characterization is also used in subsequent analysis for growing fragments of selected screening hits. The latest iteration of the FBDD workflow employs a high-throughput methodology of massively parallel screening by X-ray crystallography of individually soaked fragments. In this review we will outline the FBDD strategies and explore a variety of in silico approaches to support the follow-up fragment-to-lead optimization of either: growing, linking, and merging. These fragment expansion strategies include hot spot analysis, druggability prediction, SAR (structure-activity relationships) by catalog methods, application of machine learning/deep learning models for virtual screening and several de novo design methods for proposing synthesizable new compounds. Finally, we will highlight recent case studies in fragment-based drug discovery where in silico methods have successfully contributed to the development of lead compounds.
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Affiliation(s)
- Lauro Ribeiro de Souza Neto
- LaBECFar – Laboratório de Bioquímica Experimental e Computacional de Fármacos, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
| | - José Teófilo Moreira-Filho
- LabMol – Laboratory for Molecular Modeling and Drug Design, Faculdade de Farmácia, Universidade Federal de Goiás, Goiânia, Brazil
| | - Bruno Junior Neves
- LabMol – Laboratory for Molecular Modeling and Drug Design, Faculdade de Farmácia, Universidade Federal de Goiás, Goiânia, Brazil
- Laboratory of Cheminformatics, Centro Universitário de Anápolis – UniEVANGÉLICA, Anápolis, Brazil
| | - Rocío Lucía Beatriz Riveros Maidana
- LaBECFar – Laboratório de Bioquímica Experimental e Computacional de Fármacos, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
- Laboratório de Genômica Funcional e Bioinformática, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
| | - Ana Carolina Ramos Guimarães
- Laboratório de Genômica Funcional e Bioinformática, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
| | - Nicholas Furnham
- Department of Infection Biology, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Carolina Horta Andrade
- LabMol – Laboratory for Molecular Modeling and Drug Design, Faculdade de Farmácia, Universidade Federal de Goiás, Goiânia, Brazil
| | - Floriano Paes Silva
- LaBECFar – Laboratório de Bioquímica Experimental e Computacional de Fármacos, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
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16
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Click chemistry in silico, docking, quantum chemical calculations, and molecular dynamics simulations to identify novel 1,2,4-triazole-based compounds as potential aromatase inhibitors. SN APPLIED SCIENCES 2019. [DOI: 10.1007/s42452-019-1051-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022] Open
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17
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Diharce J, Cueto M, Beltramo M, Aucagne V, Bonnet P. In Silico Peptide Ligation: Iterative Residue Docking and Linking as a New Approach to Predict Protein-Peptide Interactions. Molecules 2019; 24:E1351. [PMID: 30959812 PMCID: PMC6480567 DOI: 10.3390/molecules24071351] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2019] [Revised: 04/02/2019] [Accepted: 04/03/2019] [Indexed: 11/16/2022] Open
Abstract
Peptide⁻protein interactions are corner-stones of living functions involved in essential mechanisms, such as cell signaling. Given the difficulty of obtaining direct experimental structural biology data, prediction of those interactions is of crucial interest for the rational development of new drugs, notably to fight diseases, such as cancer or Alzheimer's disease. Because of the high flexibility of natural unconstrained linear peptides, prediction of their binding mode in a protein cavity remains challenging. Several theoretical approaches have been developed in the last decade to address this issue. Nevertheless, improvements are needed, such as the conformation prediction of peptide side-chains, which are dependent on peptide length and flexibility. Here, we present a novel in silico method, Iterative Residue Docking and Linking (IRDL), to efficiently predict peptide⁻protein interactions. In order to reduce the conformational space, this innovative method splits peptides into several short segments. Then, it uses the performance of intramolecular covalent docking to rebuild, sequentially, the complete peptide in the active site of its protein target. Once the peptide is constructed, a rescoring step is applied in order to correctly rank all IRDL solutions. Applied on a set of 11 crystallized peptide⁻protein complexes, the IRDL method shows promising results, since it is able to retrieve experimental binding conformations with a Root Mean Square Deviation (RMSD) below 2 Å in the top five ranked solutions. For some complexes, IRDL method outperforms two other docking protocols evaluated in this study. Hence, IRDL is a new tool that could be used in drug design projects to predict peptide⁻protein interactions.
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Affiliation(s)
- Julien Diharce
- Institut de Chimie Organique et Analytique (ICOA), UMR CNRS-Université d'Orléans 7311, Université d'Orléans BP 6759, 45067, Orléans CEDEX 2, France.
| | - Mickaël Cueto
- Institut de Chimie Organique et Analytique (ICOA), UMR CNRS-Université d'Orléans 7311, Université d'Orléans BP 6759, 45067, Orléans CEDEX 2, France.
| | - Massimiliano Beltramo
- UMR Physiologie de la Reproduction et des Comportements (INRA, UMR85; CNRS, UMR7247; Universitéde Tours; IFCE), F-37380 Nouzilly, France.
| | - Vincent Aucagne
- Centre de Biophysique Moléculaire (CNRS UPR4301), Rue Charles Sadron, F-45071 Orléans cedex 2, France.
| | - Pascal Bonnet
- Institut de Chimie Organique et Analytique (ICOA), UMR CNRS-Université d'Orléans 7311, Université d'Orléans BP 6759, 45067, Orléans CEDEX 2, France.
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18
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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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19
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Hoffer L, Muller C, Roche P, Morelli X. Chemistry-driven Hit-to-lead Optimization Guided by Structure-based Approaches. Mol Inform 2018; 37:e1800059. [PMID: 30051601 DOI: 10.1002/minf.201800059] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2018] [Accepted: 06/24/2018] [Indexed: 12/17/2022]
Abstract
For several decades, hit identification for drug discovery has been facilitated by developments in both fragment-based and high-throughput screening technologies. However, a major bottleneck in drug discovery projects continues to be the optimization of primary hits from screening campaigns in order to derive lead compounds. Computational chemistry or molecular modeling can play an important role during this hit-to-lead (H2L) stage by both suggesting putative optimizations and decreasing the number of compounds to be experimentally synthesized and evaluated. However, it is also crucial to consider the feasibility of organically synthesizing these virtually designed compounds. Furthermore, the generated molecules should have reasonable physicochemical properties and be medicinally relevant. This review focuses on chemistry-driven and structure-based computational methods that can be used to tackle the difficult problem of H2L optimization, with emphasis being placed on the strategy developed in our laboratory.
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Affiliation(s)
- Laurent Hoffer
- CNRS, Inserm, Institut Paoli-Calmettes, Aix-Marseille Univ, CRCM, Marseille, France
| | | | - Philippe Roche
- CNRS, Inserm, Institut Paoli-Calmettes, Aix-Marseille Univ, CRCM, Marseille, France
| | - Xavier Morelli
- CNRS, Inserm, Institut Paoli-Calmettes, Aix-Marseille Univ, CRCM, Marseille, France.,Institut Paoli-Calmettes, IPC Drug Discovery, Marseille, France
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20
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Daeyaert F, Deem MW. In silico design of chiral dimers to direct the synthesis of a chiral zeolite. Mol Phys 2018. [DOI: 10.1080/00268976.2018.1492747] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Affiliation(s)
- Frits Daeyaert
- Department of Bioengineering, Rice University, Houston, TX, USA
| | - Michael W. Deem
- Department of Bioengineering, Rice University, Houston, TX, USA
- Department of Physics & Astronomy, Rice University, Houston, TX, USA
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21
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Allen WJ, Fochtman BC, Balius TE, Rizzo RC. Customizable de novo design strategies for DOCK: Application to HIVgp41 and other therapeutic targets. J Comput Chem 2017; 38:2641-2663. [PMID: 28940386 DOI: 10.1002/jcc.25052] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2017] [Accepted: 08/03/2017] [Indexed: 12/12/2022]
Abstract
De novo design can be used to explore vast areas of chemical space in computational lead discovery. As a complement to virtual screening, from-scratch construction of molecules is not limited to compounds in pre-existing vendor catalogs. Here, we present an iterative fragment growth method, integrated into the program DOCK, in which new molecules are built using rules for allowable connections based on known molecules. The method leverages DOCK's advanced scoring and pruning approaches and users can define very specific criteria in terms of properties or features to customize growth toward a particular region of chemical space. The code was validated using three increasingly difficult classes of calculations: (1) Rebuilding known X-ray ligands taken from 663 complexes using only their component parts (focused libraries), (2) construction of new ligands in 57 drug target sites using a library derived from ∼13M drug-like compounds (generic libraries), and (3) application to a challenging protein-protein interface on the viral drug target HIVgp41. The computational testing confirms that the de novo DOCK routines are robust and working as envisioned, and the compelling results highlight the potential utility for designing new molecules against a wide variety of important protein targets. © 2017 Wiley Periodicals, Inc.
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Affiliation(s)
- William J Allen
- Department of Applied Mathematics and Statistics, Stony Brook University, Stony Brook, New York, 11794
| | - Brian C Fochtman
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, New York, 11794
| | - Trent E Balius
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, California, 94158
| | - Robert C Rizzo
- Department of Applied Mathematics and Statistics, Stony Brook University, Stony Brook, New York, 11794.,Institute of Chemical Biology and Drug Discovery, Stony Brook University, Stony Brook, New York, 11794.,Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, New York, 11794
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22
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Ropp P, Friedman A, Durrant JD. Scoria: a Python module for manipulating 3D molecular data. J Cheminform 2017; 9:52. [PMID: 29086076 PMCID: PMC5603467 DOI: 10.1186/s13321-017-0237-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2017] [Accepted: 09/04/2017] [Indexed: 01/19/2023] Open
Abstract
Third-party packages have transformed the Python programming language into a powerful computational-biology tool. Package installation is easy for experienced users, but novices sometimes struggle with dependencies and compilers. This presents a barrier that can hinder the otherwise broad adoption of new tools. We present Scoria, a Python package for manipulating three-dimensional molecular data. Unlike similar packages, Scoria requires no dependencies, compilation, or system-wide installation. One can incorporate the Scoria source code directly into their own programs. But Scoria is not designed to compete with other similar packages. Rather, it complements them. Our package leverages others (e.g. NumPy, SciPy), if present, to speed and extend its own functionality. To show its utility, we use Scoria to analyze a molecular dynamics trajectory. Our FootPrint script colors the atoms of one chain by the frequency of their contacts with a second chain. We are hopeful that Scoria will be a useful tool for the computational-biology community. A copy is available for download free of charge (Apache License 2.0) at http://durrantlab.com/scoria/.. ![]()
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Affiliation(s)
- Patrick Ropp
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, 15260, USA
| | - Aaron Friedman
- Biomedical Sciences Graduate Program, University of California San Diego, La Jolla, CA, 92093, USA
| | - Jacob D Durrant
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, 15260, USA.
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23
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Chaudhari R, Tan Z, Huang B, Zhang S. Computational polypharmacology: a new paradigm for drug discovery. Expert Opin Drug Discov 2017; 12:279-291. [PMID: 28067061 PMCID: PMC7241838 DOI: 10.1080/17460441.2017.1280024] [Citation(s) in RCA: 62] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
INTRODUCTION Over the past couple of years, the cost of drug development has sharply increased along with the high rate of clinical trial failures. Such increase in expenses is partially due to the inability of the "one drug - one target" approach to predict drug side effects and toxicities. To tackle this issue, an alternative approach, known as polypharmacology, is being adopted to study small molecule interactions with multiple targets. Apart from developing more potent and effective drugs, this approach allows for studies of off-target activities and the facilitation of drug repositioning. Although exhaustive polypharmacology studies in-vitro or in-vivo are not practical, computational methods of predicting unknown targets or side effects are being developed. Areas covered: This article describes various computational approaches that have been developed to study polypharmacology profiles of small molecules. It also provides a brief description of the algorithms used in these state-of-the-art methods. Expert opinion: Recent success in computational prediction of multi-targeting drugs has established polypharmacology as a promising alternative approach to tackle some of the daunting complications in drug discovery. This will not only help discover more effective agents, but also present tremendous opportunities to study novel target pharmacology and facilitate drug repositioning efforts in the pharmaceutical industry.
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Affiliation(s)
- Rajan Chaudhari
- Integrated Molecular Discovery Laboratory, Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX 77030
| | - Zhi Tan
- Integrated Molecular Discovery Laboratory, Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX 77030
- The University of Texas Graduate School of Biomedical Sciences, Houston, TX 77030
| | - Beibei Huang
- Integrated Molecular Discovery Laboratory, Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX 77030
| | - Shuxing Zhang
- Integrated Molecular Discovery Laboratory, Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX 77030
- The University of Texas Graduate School of Biomedical Sciences, Houston, TX 77030
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24
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Andrianov AM, Kashyn IA, Tuzikov AV. Computational identification of novel entry inhibitor scaffolds mimicking primary receptor CD4 of HIV-1 gp120. J Mol Model 2017; 23:18. [DOI: 10.1007/s00894-016-3189-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2016] [Accepted: 12/15/2016] [Indexed: 11/24/2022]
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25
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Leelananda SP, Lindert S. Computational methods in drug discovery. Beilstein J Org Chem 2016; 12:2694-2718. [PMID: 28144341 PMCID: PMC5238551 DOI: 10.3762/bjoc.12.267] [Citation(s) in RCA: 285] [Impact Index Per Article: 35.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2016] [Accepted: 11/22/2016] [Indexed: 12/11/2022] Open
Abstract
The process for drug discovery and development is challenging, time consuming and expensive. Computer-aided drug discovery (CADD) tools can act as a virtual shortcut, assisting in the expedition of this long process and potentially reducing the cost of research and development. Today CADD has become an effective and indispensable tool in therapeutic development. The human genome project has made available a substantial amount of sequence data that can be used in various drug discovery projects. Additionally, increasing knowledge of biological structures, as well as increasing computer power have made it possible to use computational methods effectively in various phases of the drug discovery and development pipeline. The importance of in silico tools is greater than ever before and has advanced pharmaceutical research. Here we present an overview of computational methods used in different facets of drug discovery and highlight some of the recent successes. In this review, both structure-based and ligand-based drug discovery methods are discussed. Advances in virtual high-throughput screening, protein structure prediction methods, protein-ligand docking, pharmacophore modeling and QSAR techniques are reviewed.
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Affiliation(s)
- Sumudu P Leelananda
- Department of Chemistry and Biochemistry, Ohio State University, Columbus, OH 43210, USA
| | - Steffen Lindert
- Department of Chemistry and Biochemistry, Ohio State University, Columbus, OH 43210, USA
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26
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Pannuzzo G, Graziano ACE, Pannuzzo M, Masman MF, Avola R, Cardile V. Zoledronate derivatives as potential inhibitors of uridine diphosphate-galactose ceramide galactosyltransferase 8: A combined molecular docking and dynamic study. J Neurosci Res 2016; 94:1318-1326. [DOI: 10.1002/jnr.23761] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/29/2023]
Affiliation(s)
- Giovanna Pannuzzo
- Department of Biomedical and Biotechnological Sciences, Section of Physiology; University of Catania; Catania Italy
| | | | - Martina Pannuzzo
- Department of Computational Biology; Universität Erlangen-Nürnberg; Erlangen Germany
| | - Marcelo Fabricio Masman
- Department of Biocatalysis and Biotransformation, Groningen Biomolecular Sciences and Biotechnology Institute; University of Groningen; Groningen The Netherlands
| | - Rosanna Avola
- Department of Biomedical and Biotechnological Sciences, Section of Physiology; University of Catania; Catania Italy
| | - Venera Cardile
- Department of Biomedical and Biotechnological Sciences, Section of Physiology; University of Catania; Catania Italy
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27
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Abstract
The success of molecular modeling and computational chemistry efforts are, by definition, dependent on quality software applications. Open source software development provides many advantages to users of modeling applications, not the least of which is that the software is free and completely extendable. In this review we categorize, enumerate, and describe available open source software packages for molecular modeling and computational chemistry. An updated online version of this catalog can be found at https://opensourcemolecularmodeling.github.io.
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28
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Daeyaert F, Deem MW. A Pareto Algorithm for Efficient De Novo Design of Multi-functional Molecules. Mol Inform 2016; 36. [PMID: 28124835 DOI: 10.1002/minf.201600044] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2016] [Accepted: 07/06/2016] [Indexed: 12/19/2022]
Abstract
We have introduced a Pareto sorting algorithm into Synopsis, a de novo design program that generates synthesizable molecules with desirable properties. We give a detailed description of the algorithm and illustrate its working in 2 different de novo design settings: the design of putative dual and selective FGFR and VEGFR inhibitors, and the successful design of organic structure determining agents (OSDAs) for the synthesis of zeolites. We show that the introduction of Pareto sorting not only enables the simultaneous optimization of multiple properties but also greatly improves the performance of the algorithm to generate molecules with hard-to-meet constraints. This in turn allows us to suggest approaches to address the problem of false positive hits in de novo structure based drug design by introducing structural and physicochemical constraints in the designed molecules, and by forcing essential interactions between these molecules and their target receptor.
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Affiliation(s)
- Frits Daeyaert
- FD Computing, Stijn Streuvelsstraat 64, 2340, Beerse, Belgium.,Department of Bioengineering, Rice University, 6100 Main Street, Houston, TX, USA
| | - Micheal W Deem
- Department of Bioengineering, Rice University, 6100 Main Street, Houston, TX, USA
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29
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Anuwongcharoen N, Shoombuatong W, Tantimongcolwat T, Prachayasittikul V, Nantasenamat C. Exploring the chemical space of influenza neuraminidase inhibitors. PeerJ 2016; 4:e1958. [PMID: 27114890 PMCID: PMC4841240 DOI: 10.7717/peerj.1958] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2015] [Accepted: 03/31/2016] [Indexed: 12/01/2022] Open
Abstract
The fight against the emergence of mutant influenza strains has led to the screening of an increasing number of compounds for inhibitory activity against influenza neuraminidase. This study explores the chemical space of neuraminidase inhibitors (NAIs), which provides an opportunity to obtain further molecular insights regarding the underlying basis of their bioactivity. In particular, a large set of 347 and 175 NAIs against influenza A and B, respectively, was compiled from the literature. Molecular and quantum chemical descriptors were obtained from low-energy conformational structures geometrically optimized at the PM6 level. The bioactivities of NAIs were classified as active or inactive according to their half maximum inhibitory concentration (IC50) value in which IC50 < 1µM and ≥ 10µM were defined as active and inactive compounds, respectively. Interpretable decision rules were derived from a quantitative structure–activity relationship (QSAR) model established using a set of substructure descriptors via decision tree analysis. Univariate analysis, feature importance analysis from decision tree modeling and molecular scaffold analysis were performed on both data sets for discriminating important structural features amongst active and inactive NAIs. Good predictive performance was achieved as deduced from accuracy and Matthews correlation coefficient values in excess of 81% and 0.58, respectively, for both influenza A and B NAIs. Furthermore, molecular docking was employed to investigate the binding modes and their moiety preferences of active NAIs against both influenza A and B neuraminidases. Moreover, novel NAIs with robust binding fitness towards influenza A and B neuraminidase were generated via combinatorial library enumeration and their binding fitness was on par or better than FDA-approved drugs. The results from this study are anticipated to be beneficial for guiding the rational drug design of novel NAIs for treating influenza infections.
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Affiliation(s)
- Nuttapat Anuwongcharoen
- Center of Data Mining and Biomedical Informatics, Faculty of Medical Technology, Mahidol University, Bangkok, Thailand; Department of Clinical Microbiology and Applied Technology, Faculty of Medical Technology, Mahidol University, Bangkok, Thailand
| | - Watshara Shoombuatong
- Center of Data Mining and Biomedical Informatics, Faculty of Medical Technology, Mahidol University , Bangkok , Thailand
| | - Tanawut Tantimongcolwat
- Center for Research and Innovation, Faculty of Medical Technology, Mahidol University , Bangkok , Thailand
| | - Virapong Prachayasittikul
- Department of Clinical Microbiology and Applied Technology, Faculty of Medical Technology, Mahidol University , Bangkok , Thailand
| | - Chanin Nantasenamat
- Center of Data Mining and Biomedical Informatics, Faculty of Medical Technology, Mahidol University , Bangkok , Thailand
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30
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Prakash P, Sayyed-Ahmad A, Gorfe AA. pMD-Membrane: A Method for Ligand Binding Site Identification in Membrane-Bound Proteins. PLoS Comput Biol 2015; 11:e1004469. [PMID: 26506102 PMCID: PMC4623977 DOI: 10.1371/journal.pcbi.1004469] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2015] [Accepted: 07/27/2015] [Indexed: 12/22/2022] Open
Abstract
Probe-based or mixed solvent molecular dynamics simulation is a useful approach for the identification and characterization of druggable sites in drug targets. However, thus far the method has been applied only to soluble proteins. A major reason for this is the potential effect of the probe molecules on membrane structure. We have developed a technique to overcome this limitation that entails modification of force field parameters to reduce a few pairwise non-bonded interactions between selected atoms of the probe molecules and bilayer lipids. We used the resulting technique, termed pMD-membrane, to identify allosteric ligand binding sites on the G12D and G13D oncogenic mutants of the K-Ras protein bound to a negatively charged lipid bilayer. In addition, we show that differences in probe occupancy can be used to quantify changes in the accessibility of druggable sites due to conformational changes induced by membrane binding or mutation.
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Affiliation(s)
- Priyanka Prakash
- University of Texas Health Science Center at Houston, Department of Integrative Biology and Pharmacology, Houston, Texas, United States of America
| | - Abdallah Sayyed-Ahmad
- University of Texas Health Science Center at Houston, Department of Integrative Biology and Pharmacology, Houston, Texas, United States of America
| | - Alemayehu A. Gorfe
- University of Texas Health Science Center at Houston, Department of Integrative Biology and Pharmacology, Houston, Texas, United States of America
- * E-mail:
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31
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Chéron N, Jasty N, Shakhnovich EI. OpenGrowth: An Automated and Rational Algorithm for Finding New Protein Ligands. J Med Chem 2015; 59:4171-88. [DOI: 10.1021/acs.jmedchem.5b00886] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Nicolas Chéron
- Department of Chemistry and
Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, United States
| | - Naveen Jasty
- Department of Chemistry and
Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, United States
| | - Eugene I. Shakhnovich
- Department of Chemistry and
Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, United States
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32
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Wasko MJ, Pellegrene KA, Madura JD, Surratt CK. A Role for Fragment-Based Drug Design in Developing Novel Lead Compounds for Central Nervous System Targets. Front Neurol 2015; 6:197. [PMID: 26441817 PMCID: PMC4566055 DOI: 10.3389/fneur.2015.00197] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2015] [Accepted: 08/24/2015] [Indexed: 01/12/2023] Open
Abstract
Hundreds of millions of U.S. dollars are invested in the research and development of a single drug. Lead compound development is an area ripe for new design strategies. Therapeutic lead candidates have been traditionally found using high-throughput in vitro pharmacological screening, a costly method for assaying thousands of compounds. This approach has recently been augmented by virtual screening (VS), which employs computer models of the target protein to narrow the search for possible leads. A variant of VS is fragment-based drug design (FBDD), an emerging in silico lead discovery method that introduces low-molecular weight fragments, rather than intact compounds, into the binding pocket of the receptor model. These fragments serve as starting points for “growing” the lead candidate. Current efforts in virtual FBDD within central nervous system (CNS) targets are reviewed, as is a recent rule-based optimization strategy in which new molecules are generated within a 3D receptor-binding pocket using the fragment as a scaffold. This process not only places special emphasis on creating synthesizable molecules but also exposes computational questions worth addressing. Fragment-based methods provide a viable, relatively low-cost alternative for therapeutic lead discovery and optimization that can be applied to CNS targets to augment current design strategies.
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Affiliation(s)
- Michael J Wasko
- Mylan School of Pharmacy, Graduate School of Pharmaceutical Sciences, Duquesne University , Pittsburgh, PA , USA
| | - Kendy A Pellegrene
- Mylan School of Pharmacy, Graduate School of Pharmaceutical Sciences, Duquesne University , Pittsburgh, PA , USA
| | - Jeffry D Madura
- Department of Chemistry and Biochemistry, Center for Computational Sciences, Bayer School of Natural and Environmental Sciences, Duquesne University , Pittsburgh, PA , USA
| | - Christopher K Surratt
- Mylan School of Pharmacy, Graduate School of Pharmaceutical Sciences, Duquesne University , Pittsburgh, PA , USA
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Andrianov AM, Kashyn IA, Tuzikov AV. Computational discovery of novel HIV-1 entry inhibitors based on potent and broad neutralizing antibody VRC01. J Mol Graph Model 2015; 61:262-71. [DOI: 10.1016/j.jmgm.2015.08.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2015] [Revised: 08/05/2015] [Accepted: 08/05/2015] [Indexed: 10/23/2022]
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Rentzsch R, Renard BY. Docking small peptides remains a great challenge: an assessment using AutoDock Vina. Brief Bioinform 2015; 16:1045-56. [PMID: 25900849 DOI: 10.1093/bib/bbv008] [Citation(s) in RCA: 92] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2014] [Indexed: 02/03/2023] Open
Abstract
There is a growing interest in the mechanisms and the prediction of how flexible peptides bind proteins, often in a highly selective and conserved manner. While both existing small-molecule docking methods and custom protocols can be used, even short peptides make difficult targets owing to their high torsional flexibility. Any benchmarking should therefore start with those. We compiled a meta-data set of 47 complexes with peptides up to five residues, based on 11 related studies from the past decade. Although their highly varying strategies and constraints preclude direct, quantitative comparisons, we still provide a comprehensive overview of the reported results, using a simple yet stringent measure: the quality of the top-scoring peptide pose. Using the entire data set, this is augmented by our own benchmark of AutoDock Vina, a freely available, fast and widely used docking tool. It particularly addresses non-expert users and was therefore implemented in a highly integrated manner. Guidelines addressing important issues such as the amount of sampling required for result reproducibility are so far lacking. Using peptide docking as an example, this is the first study to address these issues in detail. Finally, to encourage further, standardized benchmarking efforts, the compiled data set is made available in an accessible, transparent and extendable manner.
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Nantasenamat C, Prachayasittikul V. Maximizing computational tools for successful drug discovery. Expert Opin Drug Discov 2015; 10:321-9. [PMID: 25693813 DOI: 10.1517/17460441.2015.1016497] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Drug discovery is an iterative cycle of identifying promising hits followed by lead optimization via bioisosteric replacements. In the search for compounds affording good bioactivity, equal importance should also be placed on achieving those with favorable pharmacokinetic properties. Thus, the balance and realization of both key properties is an intricate problem that requires great caution. In this editorial, the authors explore the available computational tools in the context of the extant of big data that has borne out via advents of the Omics revolution. As such, the selection of appropriate computational tools for analyzing the vast number of chemical libraries, target proteins and interactomes is the first step toward maximizing the chance for success. However, in order to realize this, it is also necessary to have a solid foundation on the big concepts of drug discovery as well as knowing which tools are available in order to give drug discovery scientists the best opportunity.
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Affiliation(s)
- Chanin Nantasenamat
- Mahidol University, Center of Data Mining and Biomedical Informatics, Faculty of Medical Technology , 10700 Bangkok , Thailand
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Abstract
Fragment-based drug design has proved itself as a powerful technique for increasing the sampling and diversity of chemical space and enabling the design of novel leads and compounds. Computational techniques for identifying fragments, binding sites and particularly for linking, growing, and evolving fragments play a significant role in the process. Information from ADME studies and clustering property information in the form of toxicophores and chemotypes can play a significant role in aiding the design of novel, selective fragments with good activity profiles.
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Affiliation(s)
- Rachelle J Bienstock
- Independent Researcher and Consultant, 300 Pitch Pine Lane, Chapel Hill, NC, 27514, USA,
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Cook I, Wang T, Falany CN, Leyh TS. High accuracy in silico sulfotransferase models. J Biol Chem 2013; 288:34494-501. [PMID: 24129576 PMCID: PMC3843064 DOI: 10.1074/jbc.m113.510974] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2013] [Revised: 10/06/2013] [Indexed: 12/29/2022] Open
Abstract
Predicting enzymatic behavior in silico is an integral part of our efforts to understand biology. Hundreds of millions of compounds lie in targeted in silico libraries waiting for their metabolic potential to be discovered. In silico "enzymes" capable of accurately determining whether compounds can inhibit or react is often the missing piece in this endeavor. This problem has now been solved for the cytosolic sulfotransferases (SULTs). SULTs regulate the bioactivities of thousands of compounds--endogenous metabolites, drugs and other xenobiotics--by transferring the sulfuryl moiety (SO3) from 3'-phosphoadenosine 5'-phosphosulfate to the hydroxyls and primary amines of these acceptors. SULT1A1 and 2A1 catalyze the majority of sulfation that occurs during human Phase II metabolism. Here, recent insights into the structure and dynamics of SULT binding and reactivity are incorporated into in silico models of 1A1 and 2A1 that are used to identify substrates and inhibitors in a structurally diverse set of 1,455 high value compounds: the FDA-approved small molecule drugs. The SULT1A1 models predict 76 substrates. Of these, 53 were known substrates. Of the remaining 23, 21 were tested, and all were sulfated. The SULT2A1 models predict 22 substrates, 14 of which are known substrates. Of the remaining 8, 4 were tested, and all are substrates. The models proved to be 100% accurate in identifying substrates and made no false predictions at Kd thresholds of 100 μM. In total, 23 "new" drug substrates were identified, and new linkages to drug inhibitors are predicted. It now appears to be possible to accurately predict Phase II sulfonation in silico.
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Affiliation(s)
- Ian Cook
- From the Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, New York 10461-1926 and
| | - Ting Wang
- From the Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, New York 10461-1926 and
| | - Charles N. Falany
- the Department of Pharmacology and Toxicology, University of Alabama School of Medicine at Birmingham, Birmingham, Alabama 35294-0019
| | - Thomas S. Leyh
- From the Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, New York 10461-1926 and
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