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Zhang X, Shen C, Wang T, Deng Y, Kang Y, Li D, Hou T, Pan P. ML-PLIC: a web platform for characterizing protein-ligand interactions and developing machine learning-based scoring functions. Brief Bioinform 2023; 24:bbad295. [PMID: 37738401 DOI: 10.1093/bib/bbad295] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Revised: 07/17/2023] [Accepted: 07/31/2023] [Indexed: 09/24/2023] Open
Abstract
Cracking the entangling code of protein-ligand interaction (PLI) is of great importance to structure-based drug design and discovery. Different physical and biochemical representations can be used to describe PLI such as energy terms and interaction fingerprints, which can be analyzed by machine learning (ML) algorithms to create ML-based scoring functions (MLSFs). Here, we propose the ML-based PLI capturer (ML-PLIC), a web platform that automatically characterizes PLI and generates MLSFs to identify the potential binders of a specific protein target through virtual screening (VS). ML-PLIC comprises five modules, including Docking for ligand docking, Descriptors for PLI generation, Modeling for MLSF training, Screening for VS and Pipeline for the integration of the aforementioned functions. We validated the MLSFs constructed by ML-PLIC in three benchmark datasets (Directory of Useful Decoys-Enhanced, Active as Decoys and TocoDecoy), demonstrating accuracy outperforming traditional docking tools and competitive performance to the deep learning-based SF, and provided a case study of the Serine/threonine-protein kinase WEE1 in which MLSFs were developed by using the ML-based VS pipeline in ML-PLIC. Underpinning the latest version of ML-PLIC is a powerful platform that incorporates physical and biological knowledge about PLI, leveraging PLI characterization and MLSF generation into the design of structure-based VS pipeline. The ML-PLIC web platform is now freely available at http://cadd.zju.edu.cn/plic/.
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Affiliation(s)
- Xujun Zhang
- Innovation Institute for Artificial Intelligence in Medicine of Zhejiang University, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, Zhejiang, China
| | - Chao Shen
- Innovation Institute for Artificial Intelligence in Medicine of Zhejiang University, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, Zhejiang, China
- Hangzhou Carbonsilicon AI Technology Co., Ltd, Hangzhou 310018, Zhejiang, China
| | - Tianyue Wang
- Innovation Institute for Artificial Intelligence in Medicine of Zhejiang University, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, Zhejiang, China
| | - Yafeng Deng
- Hangzhou Carbonsilicon AI Technology Co., Ltd, Hangzhou 310018, Zhejiang, China
| | - Yu Kang
- Innovation Institute for Artificial Intelligence in Medicine of Zhejiang University, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, Zhejiang, China
| | - Dan Li
- Innovation Institute for Artificial Intelligence in Medicine of Zhejiang University, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, Zhejiang, China
| | - Tingjun Hou
- Innovation Institute for Artificial Intelligence in Medicine of Zhejiang University, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, Zhejiang, China
| | - Peichen Pan
- Innovation Institute for Artificial Intelligence in Medicine of Zhejiang University, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, Zhejiang, China
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2
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Ren Q, Huang PY, Liu Y, Liao WK, Zhou ZX, Zhao CS. SYNTHESIS, CRYSTAL STRUCTURE, AND DFT STUDY OF 4-(2-CHLOROBENZYL)-1-(5-NITRO-2-(PYRROLIDIN-1-YL)PHENYL)- [1,2,4]TRIAZOLO[4,3-a]QUINAZOLIN-5(4H)-ONE. J STRUCT CHEM+ 2021. [DOI: 10.1134/s0022476621090171] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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3
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The Application of In Silico Methods on Umami Taste Receptor. Handb Exp Pharmacol 2021; 275:137-154. [PMID: 34247277 DOI: 10.1007/164_2021_515] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
The umami taste receptor is a heterodimer composed of two members of the T1R taste receptor family: T1R1 (taste receptor type 1 member 1) and T1R3 (taste receptor type 1 member 3). Taste receptor T1R1-T1R3 can be activated, or modulated, by binding to several natural ligands, such as L-glutamate, inosine-5'-monophosphate (IMP), and guanosine-5'-monophosphate (GMP). Because no structure of the umami taste receptor has been solved until now, in silico techniques, such as homology modelling, molecular docking, and molecular dynamics (MD) simulations, are used to generate a 3D structure model of this receptor and to understand its molecular mechanisms. The purpose of this chapter is to highlight how computational methods can provide a better deciphering of the mechanisms of action of umami ligands in activating the umami taste receptors leading to advancements in the taste research field.
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Sivakumar KC, Haixiao J, Naman CB, Sajeevan TP. Prospects of multitarget drug designing strategies by linking molecular docking and molecular dynamics to explore the protein-ligand recognition process. Drug Dev Res 2020; 81:685-699. [PMID: 32329098 DOI: 10.1002/ddr.21673] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2019] [Revised: 03/24/2020] [Accepted: 04/06/2020] [Indexed: 12/14/2022]
Abstract
The designing of drugs that can simultaneously affect different protein targets is one novel and promising way to treat complex diseases. Multitarget drugs act on multiple protein receptors each implicated in the same disease state, and may be considered to be more beneficial than conventional drug therapies. For example, these drugs can have improved therapeutic potency due to synergistic effects on multiple targets, as well as improved safety and resistance profiles due to the combined regulation of potential primary therapeutic targets and compensatory elements and lower dosage typically required. This review analyzes in-silico methods that facilitate multitarget drug design that facilitate the discovery and development of novel therapeutic agents. Here presented is a summary of the progress in structure-based drug discovery techniques that study the process of molecular recognition of targets and ligands, moving from static molecular docking to improved molecular dynamics approaches in multitarget drug design, and the advantages and limitations of each.
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Affiliation(s)
- Krishnankutty Chandrika Sivakumar
- National Centre for Aquatic Animal Health, Cochin University of Science and Technology, Kochi, India.,Bioinformatics Facility, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram, India
| | - Jin Haixiao
- Li Dak Sum Marine Biopharmaceutical Research Center, Department of Marine Pharmacy, College of Food and Pharmaceutical Sciences, Ningbo University, Ningbo, China
| | - C Benjamin Naman
- Li Dak Sum Marine Biopharmaceutical Research Center, Department of Marine Pharmacy, College of Food and Pharmaceutical Sciences, Ningbo University, Ningbo, China.,Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, California, USA
| | - T P Sajeevan
- National Centre for Aquatic Animal Health, Cochin University of Science and Technology, Kochi, India
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5
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Machine Learning to Identify Flexibility Signatures of Class A GPCR Inhibition. Biomolecules 2020; 10:biom10030454. [PMID: 32183371 PMCID: PMC7175283 DOI: 10.3390/biom10030454] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Revised: 03/11/2020] [Accepted: 03/11/2020] [Indexed: 01/06/2023] Open
Abstract
We show that machine learning can pinpoint features distinguishing inactive from active states in proteins, in particular identifying key ligand binding site flexibility transitions in GPCRs that are triggered by biologically active ligands. Our analysis was performed on the helical segments and loops in 18 inactive and 9 active class A G protein-coupled receptors (GPCRs). These three-dimensional (3D) structures were determined in complex with ligands. However, considering the flexible versus rigid state identified by graph-theoretic ProFlex rigidity analysis for each helix and loop segment with the ligand removed, followed by feature selection and k-nearest neighbor classification, was sufficient to identify four segments surrounding the ligand binding site whose flexibility/rigidity accurately predicts whether a GPCR is in an active or inactive state. GPCRs bound to inhibitors were similar in their pattern of flexible versus rigid regions, whereas agonist-bound GPCRs were more flexible and diverse. This new ligand-proximal flexibility signature of GPCR activity was identified without knowledge of the ligand binding mode or previously defined switch regions, while being adjacent to the known transmission switch. Following this proof of concept, the ProFlex flexibility analysis coupled with pattern recognition and activity classification may be useful for predicting whether newly designed ligands behave as activators or inhibitors in protein families in general, based on the pattern of flexibility they induce in the protein.
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6
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Da C, Zhang D, Stashko M, Vasileiadi E, Parker R, Minson KA, Huey MG, Huelse JM, Hunter D, Gilbert TSK, Norris-Drouin J, Miley M, Herring LE, Graves LM, DeRyckere D, Earp HS, Graham D, Frye SV, Wang X, Kireev D. Data-Driven Construction of Antitumor Agents with Controlled Polypharmacology. J Am Chem Soc 2019; 141:15700-15709. [PMID: 31497954 PMCID: PMC6894422 DOI: 10.1021/jacs.9b08660] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Controlling which particular members of a large protein family are targeted by a drug is key to achieving a desired therapeutic response. In this study, we report a rational data-driven strategy for achieving restricted polypharmacology in the design of antitumor agents selectively targeting the TYRO3, AXL, and MERTK (TAM) family tyrosine kinases. Our computational approach, based on the concept of fragments in structural environments (FRASE), distills relevant chemical information from structural and chemogenomic databases to assemble a three-dimensional inhibitor structure directly in the protein pocket. Target engagement by the inhibitors designed led to disruption of oncogenic phenotypes as demonstrated in enzymatic assays and in a panel of cancer cell lines, including acute lymphoblastic and myeloid leukemia (ALL/AML) and nonsmall cell lung cancer (NSCLC). Structural rationale underlying the approach was corroborated by X-ray crystallography. The lead compound demonstrated potent target inhibition in a pharmacodynamic study in leukemic mice.
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Affiliation(s)
- Chenxiao Da
- Center for Integrative Chemical Biology and Drug Discovery, Division of Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, 27599-7363
| | - Dehui Zhang
- Center for Integrative Chemical Biology and Drug Discovery, Division of Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, 27599-7363
| | - Michael Stashko
- Center for Integrative Chemical Biology and Drug Discovery, Division of Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, 27599-7363
| | - Eleana Vasileiadi
- Aflac Cancer and Blood Disorders Center, Children’s Healthcare of Atlanta, and Department of Pediatrics, Emory University, Atlanta, GA 30322
| | - Rebecca Parker
- Aflac Cancer and Blood Disorders Center, Children’s Healthcare of Atlanta, and Department of Pediatrics, Emory University, Atlanta, GA 30322
| | - Katherine A. Minson
- Aflac Cancer and Blood Disorders Center, Children’s Healthcare of Atlanta, and Department of Pediatrics, Emory University, Atlanta, GA 30322
| | - Madeline G. Huey
- Aflac Cancer and Blood Disorders Center, Children’s Healthcare of Atlanta, and Department of Pediatrics, Emory University, Atlanta, GA 30322
| | - Justus M. Huelse
- Aflac Cancer and Blood Disorders Center, Children’s Healthcare of Atlanta, and Department of Pediatrics, Emory University, Atlanta, GA 30322
| | - Debra Hunter
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
- Lineberger Comprehensive Cancer Center, Department of Medicine, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Thomas S. K. Gilbert
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Jacqueline Norris-Drouin
- Center for Integrative Chemical Biology and Drug Discovery, Division of Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, 27599-7363
| | - Michael Miley
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Laura E. Herring
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Lee M. Graves
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Deborah DeRyckere
- Aflac Cancer and Blood Disorders Center, Children’s Healthcare of Atlanta, and Department of Pediatrics, Emory University, Atlanta, GA 30322
| | - H. Shelton Earp
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
- Lineberger Comprehensive Cancer Center, Department of Medicine, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Douglas Graham
- Aflac Cancer and Blood Disorders Center, Children’s Healthcare of Atlanta, and Department of Pediatrics, Emory University, Atlanta, GA 30322
| | - Stephen V. Frye
- Center for Integrative Chemical Biology and Drug Discovery, Division of Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, 27599-7363
- Lineberger Comprehensive Cancer Center, Department of Medicine, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Xiaodong Wang
- Center for Integrative Chemical Biology and Drug Discovery, Division of Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, 27599-7363
| | - Dmitri Kireev
- Center for Integrative Chemical Biology and Drug Discovery, Division of Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, 27599-7363
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7
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Sehgal SA, Hammad MA, Tahir RA, Akram HN, Ahmad F. Current Therapeutic Molecules and Targets in Neurodegenerative Diseases Based on in silico Drug Design. Curr Neuropharmacol 2018; 16:649-663. [PMID: 29542412 PMCID: PMC6080102 DOI: 10.2174/1570159x16666180315142137] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2017] [Revised: 01/01/2018] [Accepted: 03/02/2018] [Indexed: 12/20/2022] Open
Abstract
Abstract: Background As the number of elderly persons increases, neurodegenerative diseases are becoming ubiquitous. There is currently a great need for knowledge concerning management of old-age neurodegenerative diseases; the most important of which are: Alzheimer’s disease, Parkinson’s disease, Amyotrophic Lateral Sclerosis, and Huntington’s disease. Objective To summarize the potential of computationally predicted molecules and targets against neurodegenerative diseases. Method Review of literature published since 1997 against neurodegenerative diseases, utilizing as keywords: in silico, Alzheimer’s disease, Parkinson’s disease, Amyotrophic Lateral Sclerosis ALS, and Huntington’s disease was conducted. Results and Conclusion Due to the costs associated with experimentation and current ethical law, performing experiments directly on living organisms has become much more difficult. In this scenario, in silico techniques have been successful and have become powerful tools in the search to cure disease. Researchers use the Computer Aided Drug Design pipeline which: 1) generates 3-dimensional structures of target proteins through homology modeling 2) achieves stabilization through molecular dynamics simulation, and 3) exploits molecular docking through large compound libraries. Next generation sequencing is continually producing enormous amounts of raw sequence data while neuroimaging is producing a multitude of raw image data. To solve such pressing problems, these new tools and algorithms are required. This review elaborates precise in silico tools and techniques for drug targets, active molecules, and molecular docking studies, together with future prospects and challenges concerning possible breakthroughs in Alzheimer’s, Parkinson’s, Amyotrophic Lateral Sclerosis, and Huntington’s disease.
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Affiliation(s)
- Sheikh Arslan Sehgal
- State Key Laboratory of Biomembrane and Membrane Biotechnology, Institute of Zoology, Chinese Academy of Sciences; Beijing, China.,Department of Biosciences, COMSATS Institute of Information Technology, Sahiwal, Pakistan.,University of Chinese Academy of Sciences, Beijing, China
| | - Mirza A Hammad
- University of Chinese Academy of Sciences, Beijing, China.,National Laboratory of Biomacromolecules, Institute of Biophysics; Chinese Academy of Sciences; Beijing, China
| | - Rana Adnan Tahir
- Department of Biosciences, COMSATS Institute of Information Technology, Sahiwal, Pakistan.,Beijing Key Laboratory of Separation and Analysis in Biomedical and Pharmaceuticals, Department of Biomedical Engineering, School of Life Sciences, Beijing Institute of Technology, China
| | - Hafiza Nisha Akram
- Department of Environmental Sciences, Quaid-e-Azam University Islamabad, Pakistan
| | - Faheem Ahmad
- Department of Biosciences, COMSATS Institute of Information Technology, Islamabad, Pakistan
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8
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Raschka S, Wolf AJ, Bemister-Buffington J, Kuhn LA. Protein–ligand interfaces are polarized: discovery of a strong trend for intermolecular hydrogen bonds to favor donors on the protein side with implications for predicting and designing ligand complexes. J Comput Aided Mol Des 2018; 32:511-528. [DOI: 10.1007/s10822-018-0105-2] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2017] [Accepted: 02/05/2018] [Indexed: 10/18/2022]
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9
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Enabling the hypothesis-driven prioritization of ligand candidates in big databases: Screenlamp and its application to GPCR inhibitor discovery for invasive species control. J Comput Aided Mol Des 2018; 32:415-433. [DOI: 10.1007/s10822-018-0100-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2017] [Accepted: 01/17/2018] [Indexed: 01/20/2023]
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10
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Raschka S, Scott AM, Huertas M, Li W, Kuhn LA. Automated Inference of Chemical Discriminants of Biological Activity. Methods Mol Biol 2018; 1762:307-338. [PMID: 29594779 DOI: 10.1007/978-1-4939-7756-7_16] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Ligand-based virtual screening has become a standard technique for the efficient discovery of bioactive small molecules. Following assays to determine the activity of compounds selected by virtual screening, or other approaches in which dozens to thousands of molecules have been tested, machine learning techniques make it straightforward to discover the patterns of chemical groups that correlate with the desired biological activity. Defining the chemical features that generate activity can be used to guide the selection of molecules for subsequent rounds of screening and assaying, as well as help design new, more active molecules for organic synthesis.The quantitative structure-activity relationship machine learning protocols we describe here, using decision trees, random forests, and sequential feature selection, take as input the chemical structure of a single, known active small molecule (e.g., an inhibitor, agonist, or substrate) for comparison with the structure of each tested molecule. Knowledge of the atomic structure of the protein target and its interactions with the active compound are not required. These protocols can be modified and applied to any data set that consists of a series of measured structural, chemical, or other features for each tested molecule, along with the experimentally measured value of the response variable you would like to predict or optimize for your project, for instance, inhibitory activity in a biological assay or ΔGbinding. To illustrate the use of different machine learning algorithms, we step through the analysis of a dataset of inhibitor candidates from virtual screening that were tested recently for their ability to inhibit GPCR-mediated signaling in a vertebrate.
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Affiliation(s)
- Sebastian Raschka
- Department of Biochemistry and Molecular Biology , Michigan State University, East Lansing, MI, USA
| | - Anne M Scott
- Department of Fisheries and Wildlife, Michigan State University, East Lansing, MI, USA
| | - Mar Huertas
- Department of Fisheries and Wildlife, Michigan State University, East Lansing, MI, USA
- Department of Biology, Texas State University, San Marcos, TX, USA
| | - Weiming Li
- Department of Fisheries and Wildlife, Michigan State University, East Lansing, MI, USA
| | - Leslie A Kuhn
- Department of Biochemistry and Molecular Biology , Michigan State University, East Lansing, MI, USA.
- Department of Fisheries and Wildlife, Michigan State University, East Lansing, MI, USA.
- Department of Computer Science and Engineering, Michigan State University, East Lansing, MI, USA.
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11
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Identification of Binding Mode and Prospective Structural Features of Novel Nef Protein Inhibitors as Potential Anti-HIV Drugs. Cell Biochem Biophys 2016; 75:49-64. [DOI: 10.1007/s12013-016-0774-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2016] [Accepted: 11/28/2016] [Indexed: 12/16/2022]
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12
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Incorporation of side chain flexibility into protein binding pockets using MTflex. Bioorg Med Chem 2016; 24:4978-4987. [DOI: 10.1016/j.bmc.2016.08.030] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2016] [Revised: 08/16/2016] [Accepted: 08/18/2016] [Indexed: 01/15/2023]
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13
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Cele FN, Ramesh M, Soliman ME. Per-residue energy decomposition pharmacophore model to enhance virtual screening in drug discovery: a study for identification of reverse transcriptase inhibitors as potential anti-HIV agents. DRUG DESIGN DEVELOPMENT AND THERAPY 2016; 10:1365-77. [PMID: 27114700 PMCID: PMC4833373 DOI: 10.2147/dddt.s95533] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
A novel virtual screening approach is implemented herein, which is a further improvement of our previously published "target-bound pharmacophore modeling approach". The generated pharmacophore library is based only on highly contributing amino acid residues, instead of arbitrary pharmacophores, which are most commonly used in the conventional approaches in literature. Highly contributing amino acid residues were distinguished based on free binding energy contributions obtained from calculation from molecular dynamic (MD) simulations. To the best of our knowledge; this is the first attempt in the literature using such an approach; previous approaches have relied on the docking score to generate energy-based pharmacophore models. However, docking scores are reportedly unreliable. Thus, we present a model for a per-residue energy decomposition, constructed from MD simulation ensembles generating a more trustworthy pharmacophore model, which can be applied in drug discovery workflow. This work is aimed at introducing a more rational approach to the field of drug design, rather than comparing the validity of this approach against those previously reported. We recommend additional computational and experimental work to further validate this approach. This approach was used to screen for potential reverse transcriptase inhibitors using the pharmacophoric features of compound GSK952. The complex was subjected to docking, thereafter, MD simulation confirmed the stability of the system. Experimentally determined inhibitors with known HIV-reverse transcriptase inhibitory activity were used to validate the protocol. Two potential hits (ZINC46849657 and ZINC54359621) showed a significant potential with regard to free binding energy. Reported results obtained from this work confirm that this new approach is favorable in the future of the drug design industry.
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Affiliation(s)
- Favourite N Cele
- Molecular Modelling and Drug Design Research Group, School of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Muthusamy Ramesh
- Molecular Modelling and Drug Design Research Group, School of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Mahmoud Es Soliman
- Molecular Modelling and Drug Design Research Group, School of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
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14
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Glaab E. Building a virtual ligand screening pipeline using free software: a survey. Brief Bioinform 2016; 17:352-66. [PMID: 26094053 PMCID: PMC4793892 DOI: 10.1093/bib/bbv037] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2015] [Revised: 05/20/2015] [Indexed: 12/17/2022] Open
Abstract
Virtual screening, the search for bioactive compounds via computational methods, provides a wide range of opportunities to speed up drug development and reduce the associated risks and costs. While virtual screening is already a standard practice in pharmaceutical companies, its applications in preclinical academic research still remain under-exploited, in spite of an increasing availability of dedicated free databases and software tools. In this survey, an overview of recent developments in this field is presented, focusing on free software and data repositories for screening as alternatives to their commercial counterparts, and outlining how available resources can be interlinked into a comprehensive virtual screening pipeline using typical academic computing facilities. Finally, to facilitate the set-up of corresponding pipelines, a downloadable software system is provided, using platform virtualization to integrate pre-installed screening tools and scripts for reproducible application across different operating systems.
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15
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Ratnayake ND, Liu N, Kuhn LA, Walker KD. Ring-Substituted α-Arylalanines for Probing Substituent Effects on the Isomerization Reaction Catalyzed by an Aminomutase. ACS Catal 2014. [DOI: 10.1021/cs500474s] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Nishanka Dilini Ratnayake
- Department of Chemistry, ‡Department of Biochemistry and Molecular Biology, and §Computer Science & Engineering, Michigan State University, East Lansing, Michigan 48824, United States
| | - Nan Liu
- Department of Chemistry, ‡Department of Biochemistry and Molecular Biology, and §Computer Science & Engineering, Michigan State University, East Lansing, Michigan 48824, United States
| | - Leslie A. Kuhn
- Department of Chemistry, ‡Department of Biochemistry and Molecular Biology, and §Computer Science & Engineering, Michigan State University, East Lansing, Michigan 48824, United States
| | - Kevin D. Walker
- Department of Chemistry, ‡Department of Biochemistry and Molecular Biology, and §Computer Science & Engineering, Michigan State University, East Lansing, Michigan 48824, United States
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16
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Malisi C, Schumann M, Toussaint NC, Kageyama J, Kohlbacher O, Höcker B. Binding pocket optimization by computational protein design. PLoS One 2012; 7:e52505. [PMID: 23300688 PMCID: PMC3531388 DOI: 10.1371/journal.pone.0052505] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2012] [Accepted: 11/14/2012] [Indexed: 01/19/2023] Open
Abstract
Engineering specific interactions between proteins and small molecules is extremely useful for biological studies, as these interactions are essential for molecular recognition. Furthermore, many biotechnological applications are made possible by such an engineering approach, ranging from biosensors to the design of custom enzyme catalysts. Here, we present a novel method for the computational design of protein-small ligand binding named PocketOptimizer. The program can be used to modify protein binding pocket residues to improve or establish binding of a small molecule. It is a modular pipeline based on a number of customizable molecular modeling tools to predict mutations that alter the affinity of a target protein to its ligand. At its heart it uses a receptor-ligand scoring function to estimate the binding free energy between protein and ligand. We compiled a benchmark set that we used to systematically assess the performance of our method. It consists of proteins for which mutational variants with different binding affinities for their ligands and experimentally determined structures exist. Within this test set PocketOptimizer correctly predicts the mutant with the higher affinity in about 69% of the cases. A detailed analysis of the results reveals that the strengths of PocketOptimizer lie in the correct introduction of stabilizing hydrogen bonds to the ligand, as well as in the improved geometric complemetarity between ligand and binding pocket. Apart from the novel method for binding pocket design we also introduce a much needed benchmark data set for the comparison of affinities of mutant binding pockets, and that we use to asses programs for in silico design of ligand binding.
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Affiliation(s)
- Christoph Malisi
- Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Marcel Schumann
- Center for Bioinformatics, Quantitative Biology Center, and Department of Computer Science, University of Tübingen, Tübingen, Germany
| | - Nora C. Toussaint
- Center for Bioinformatics, Quantitative Biology Center, and Department of Computer Science, University of Tübingen, Tübingen, Germany
| | - Jorge Kageyama
- Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Oliver Kohlbacher
- Center for Bioinformatics, Quantitative Biology Center, and Department of Computer Science, University of Tübingen, Tübingen, Germany
| | - Birte Höcker
- Max Planck Institute for Developmental Biology, Tübingen, Germany
- * E-mail:
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Andersson CD, Karlberg T, Ekblad T, Lindgren AEG, Thorsell AG, Spjut S, Uciechowska U, Niemiec MS, Wittung-Stafshede P, Weigelt J, Elofsson M, Schüler H, Linusson A. Discovery of Ligands for ADP-Ribosyltransferases via Docking-Based Virtual Screening. J Med Chem 2012; 55:7706-18. [DOI: 10.1021/jm300746d] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
| | - Tobias Karlberg
- Department of Medical Biochemistry
and Biophysics, Karolinska Institutet, SE-17177 Stockholm, Sweden
| | - Torun Ekblad
- Department of Medical Biochemistry
and Biophysics, Karolinska Institutet, SE-17177 Stockholm, Sweden
| | | | - Ann-Gerd Thorsell
- Department of Medical Biochemistry
and Biophysics, Karolinska Institutet, SE-17177 Stockholm, Sweden
| | - Sara Spjut
- Department of Chemistry, Umeå
University, SE-90187 Umeå, Sweden
| | | | | | | | - Johan Weigelt
- Department of Medical Biochemistry
and Biophysics, Karolinska Institutet, SE-17177 Stockholm, Sweden
| | - Mikael Elofsson
- Department of Chemistry, Umeå
University, SE-90187 Umeå, Sweden
| | - Herwig Schüler
- Department of Medical Biochemistry
and Biophysics, Karolinska Institutet, SE-17177 Stockholm, Sweden
| | - Anna Linusson
- Department of Chemistry, Umeå
University, SE-90187 Umeå, Sweden
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18
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Saranya N, Selvaraj S. An alphabetic code based atomic level molecular similarity search in databases. Bioinformation 2012; 8:498-503. [PMID: 22829718 PMCID: PMC3398777 DOI: 10.6026/97320630008498] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2012] [Accepted: 05/27/2012] [Indexed: 11/23/2022] Open
Abstract
Atomic level molecular similarity and diversity studies have gained considerable importance through their wide application in Bioinformatics and Chemo-informatics for drug design. The availability of large volumes of data on chemical compounds requires new methodologies for efficient and effective searching of its archives in less time with optimal computational power. We describe an alphabetic algorithm for similarity searching based on atom-atom bonding preference for ligands. We represented 170 cyclindependent kinase 2 inhibitors using strings of pre-defined alphabets for searching using known protein sequence alignment tools. Thus, a common pattern was extracted using this set of compounds for database searching to retrieve similar active compounds. Area under the receiver operating characteristic (ROC) curve was used for the discrimination of similar and dissimilar compounds in the databases. An average retrieval rate of about 60% is obtained in cross-validation using the home-grown dataset and the directory of useful decoys (DUD, formally known as the ZINC database) data. This will help in the effective retrieval of similar compounds using database search.
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Affiliation(s)
- Nallusamy Saranya
- Department of Bioinformatics, School of Life Sciences, Bharathidasan University, Tiruchirapalli – 620024, Tamilnadu, India
| | - Samuel Selvaraj
- Department of Bioinformatics, School of Life Sciences, Bharathidasan University, Tiruchirapalli – 620024, Tamilnadu, India
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19
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Biesiada J, Porollo A, Velayutham P, Kouril M, Meller J. Survey of public domain software for docking simulations and virtual screening. Hum Genomics 2012; 5:497-505. [PMID: 21807604 PMCID: PMC3525969 DOI: 10.1186/1479-7364-5-5-497] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Progress in functional genomics and structural studies on biological macromolecules are generating a growing number of potential targets for therapeutics, adding to the importance of computational approaches for small molecule docking and virtual screening of candidate compounds. In this review, recent improvements in several public domain packages that are widely used in the context of drug development, including DOCK, AutoDock, AutoDock Vina and Screening for Ligands by Induced-fit Docking Efficiently (SLIDE) are surveyed. The authors also survey methods for the analysis and visualisation of docking simulations, as an important step in the overall assessment of the results. In order to illustrate the performance and limitations of current docking programs, the authors used the National Center for Toxicological Research (NCTR) oestrogen receptor benchmark set of 232 oestrogenic compounds with experimentally measured strength of binding to oestrogen receptor alpha. The methods tested here yielded a correlation coefficient of up to 0.6 between the predicted and observed binding affinities for active compounds in this benchmark.
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Affiliation(s)
- Jacek Biesiada
- Biomedical Informatics, Children's Hospital Research Foundation, Cincinnati, OH 45229, USA
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20
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Biesiada J, Porollo A, Meller J. On setting up and assessing docking simulations for virtual screening. Methods Mol Biol 2012; 928:1-16. [PMID: 22956129 DOI: 10.1007/978-1-62703-008-3_1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Small molecule docking and virtual screening of candidate compounds have become an integral part of drug discovery pipelines, complementing and streamlining experimental efforts in that regard. In this chapter, we describe specific software packages and protocols that can be used to efficiently set up a computational screening using a library of compounds and a docking program. We also discuss consensus- and clustering-based approaches that can be used to assess the results, and potentially re-rank the hits. While docking programs share many common features, they may require tailored implementation of virtual screening pipelines for specific computing platforms. Here, we primarily focus on solutions for several public domain packages that are widely used in the context of drug development.
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Affiliation(s)
- Jacek Biesiada
- Biomedical Informatics, Children's Hospital Research Foundation, Cincinnati, OH, USA
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21
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Sotriffer C, Matter H. The Challenge of Affinity Prediction: Scoring Functions for Structure-Based Virtual Screening. METHODS AND PRINCIPLES IN MEDICINAL CHEMISTRY 2011. [DOI: 10.1002/9783527633326.ch7] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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22
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Stark JL, Powers R. Application of NMR and molecular docking in structure-based drug discovery. Top Curr Chem (Cham) 2011; 326:1-34. [PMID: 21915777 DOI: 10.1007/128_2011_213] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Drug discovery is a complex and costly endeavor, where few drugs that reach the clinical testing phase make it to market. High-throughput screening (HTS) is the primary method used by the pharmaceutical industry to identify initial lead compounds. Unfortunately, HTS has a high failure rate and is not particularly efficient at identifying viable drug leads. These shortcomings have encouraged the development of alternative methods to drive the drug discovery process. Specifically, nuclear magnetic resonance (NMR) spectroscopy and molecular docking are routinely being employed as important components of drug discovery research. Molecular docking provides an extremely rapid way to evaluate likely binders from a large chemical library with minimal cost. NMR ligand-affinity screens can directly detect a protein-ligand interaction, can measure a corresponding dissociation constant, and can reliably identify the ligand binding site and generate a co-structure. Furthermore, NMR ligand affinity screens and molecular docking are perfectly complementary techniques, where the combination of the two has the potential to improve the efficiency and success rate of drug discovery. This review will highlight the use of NMR ligand affinity screens and molecular docking in drug discovery and describe recent examples where the two techniques were combined to identify new and effective therapeutic drugs.
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Affiliation(s)
- Jaime L Stark
- Department of Chemistry, University of Nebraska, Lincoln, NE 68588-0304, USA
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23
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Yuriev E, Agostino M, Ramsland PA. Challenges and advances in computational docking: 2009 in review. J Mol Recognit 2010; 24:149-64. [DOI: 10.1002/jmr.1077] [Citation(s) in RCA: 223] [Impact Index Per Article: 15.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2010] [Revised: 07/20/2010] [Accepted: 07/21/2010] [Indexed: 12/12/2022]
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