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Hönig SMN, Lemmen C, Rarey M. Small molecule superposition: A comprehensive overview on pose scoring of the latest methods. WIRES COMPUTATIONAL MOLECULAR SCIENCE 2022. [DOI: 10.1002/wcms.1640] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Sophia M. N. Hönig
- ZBH ‐ Center for Bioinformatics Universität Hamburg Hamburg Germany
- BioSolveIT Sankt Augustin Germany
| | | | - Matthias Rarey
- ZBH ‐ Center for Bioinformatics Universität Hamburg Hamburg Germany
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QSAR-Based Computational Approaches to Accelerate the Discovery of Sigma-2 Receptor (S2R) Ligands as Therapeutic Drugs. Molecules 2021; 26:molecules26175270. [PMID: 34500703 PMCID: PMC8434483 DOI: 10.3390/molecules26175270] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Revised: 08/05/2021] [Accepted: 08/16/2021] [Indexed: 11/16/2022] Open
Abstract
S2R overexpression is associated with various forms of cancer as well as both neuropsychiatric disorders (e.g., schizophrenia) and neurodegenerative diseases (Alzheimer’s disease: AD). In the present study, three ligand-based methods (QSAR modeling, pharmacophore mapping, and shape-based screening) were implemented to select putative S2R ligands from the DrugBank library comprising 2000+ entries. Four separate optimization algorithms (i.e., stepwise regression, Lasso, genetic algorithm (GA), and a customized extension of GA called GreedGene) were adapted to select descriptors for the QSAR models. The subsequent biological evaluation of selected compounds revealed that three FDA-approved drugs for unrelated therapeutic indications exhibited sub-1 uM binding affinity for S2R. In particular, the antidepressant drug nefazodone elicited a S2R binding affinity Ki = 140 nM. A total of 159 unique S2R ligands were retrieved from 16 publications for model building, validation, and testing. To our best knowledge, the present report represents the first case to develop comprehensive QSAR models sourced by pooling and curating a large assemblage of structurally diverse S2R ligands, which should prove useful for identifying new drug leads and predicting their S2R binding affinity prior to the resource-demanding tasks of chemical synthesis and biological evaluation.
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Singh N, Chaput L, Villoutreix BO. Virtual screening web servers: designing chemical probes and drug candidates in the cyberspace. Brief Bioinform 2020; 22:1790-1818. [PMID: 32187356 PMCID: PMC7986591 DOI: 10.1093/bib/bbaa034] [Citation(s) in RCA: 55] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The interplay between life sciences and advancing technology drives a continuous cycle of chemical data growth; these data are most often stored in open or partially open databases. In parallel, many different types of algorithms are being developed to manipulate these chemical objects and associated bioactivity data. Virtual screening methods are among the most popular computational approaches in pharmaceutical research. Today, user-friendly web-based tools are available to help scientists perform virtual screening experiments. This article provides an overview of internet resources enabling and supporting chemical biology and early drug discovery with a main emphasis on web servers dedicated to virtual ligand screening and small-molecule docking. This survey first introduces some key concepts and then presents recent and easily accessible virtual screening and related target-fishing tools as well as briefly discusses case studies enabled by some of these web services. Notwithstanding further improvements, already available web-based tools not only contribute to the design of bioactive molecules and assist drug repositioning but also help to generate new ideas and explore different hypotheses in a timely fashion while contributing to teaching in the field of drug development.
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Affiliation(s)
- Natesh Singh
- Univ. Lille, Inserm, Institut Pasteur de Lille, U1177 Drugs and Molecules for Living Systems, F-59000 Lille, France
| | - Ludovic Chaput
- Univ. Lille, Inserm, Institut Pasteur de Lille, U1177 Drugs and Molecules for Living Systems, F-59000 Lille, France
| | - Bruno O Villoutreix
- Univ. Lille, Inserm, Institut Pasteur de Lille, U1177 Drugs and Molecules for Living Systems, F-59000 Lille, France
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Fehlmann T, Hutter MC. Conservation and Relevance of Pharmacophore Point Types. J Chem Inf Model 2019; 59:1314-1323. [PMID: 30807146 DOI: 10.1021/acs.jcim.8b00757] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Pharmacophore models in general use a variety of features for distinct chemical characteristics, such as hydrogen-bond properties, lipohilicity, and ionizability. Usually, features have to match onto their identical type. To clarify if this stringent one-to-one assignment is justified, we investigated a set of 581 unique ligands from the BindingDB with known orientation inside the respective binding pockets and conducted a statistical analysis of the likelihood of observed exchanges in between the pharmacophore features, respectively their degree of conservation. To find out if certain features are obsolete, we derived a ranking to determine the most relevant ones. We found that the most conserved one-to-one feature is the negative ionizable (acids), followed by hydrogen-bond donor, positive ionizable (basic nitrogens), hydrogen-bond acceptor, aromatic, nonaromatic π-systems, and other lipophilic characteristics. The most likely exchanges were found between carboxylate groups and hydrogen-bond acceptors and likewise between basic nitrogens and hydrogen-bond donors, which reflects the characteristics of Lewis acids and bases. Exchanges between hydrogen-bond donors and hydrogen-bond acceptors are hardly more likely than by chance. The kind of target (e.g., kinase, phosphatase, protease, phosphodiesterase, nuclear receptor, metal-containing, or transmembrane protein) did not show substantial influence on the degree of conservation. The relevance of the actual pharmacophore features was found to be strongly dependent on the applied ranking scheme. Mutual information ranks all hydrophobic features as least important, whereas the aromatic feature is put into second place by using a geometric series. Both ranking schemes see the negative ionizable feature of higher significance than the positively ionizable feature.
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Affiliation(s)
- Tobias Fehlmann
- Center for Bioinformatics , Saarland University , Campus E2.1 , 66123 Saarbruecken , Germany
| | - Michael C Hutter
- Center for Bioinformatics , Saarland University , Campus E2.1 , 66123 Saarbruecken , Germany
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A review of ligand-based virtual screening web tools and screening algorithms in large molecular databases in the age of big data. Future Med Chem 2018; 10:2641-2658. [PMID: 30499744 DOI: 10.4155/fmc-2018-0076] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Virtual screening has become a widely used technique for helping in drug discovery processes. The key to this success is its ability to aid in the identification of novel bioactive compounds by screening large molecular databases. Several web servers have emerged in the last few years supplying platforms to guide users in screening publicly accessible chemical databases in a reasonable time. In this review, we discuss a representative set of online virtual screening servers and their underlying similarity algorithms. Other related topics, such as molecular representation or freely accessible databases are also treated. The most relevant contributions to this review arise from critical discussions concerning the pros and cons of servers and algorithms, and the challenges that future works must solve in a virtual screening framework.
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Kang JS, Zhang AL, Faheem M, Zhang CJ, Ai N, Buynak JD, Welsh WJ, Oelschlaeger P. Virtual Screening and Experimental Testing of B1 Metallo-β-lactamase Inhibitors. J Chem Inf Model 2018; 58:1902-1914. [PMID: 30107123 DOI: 10.1021/acs.jcim.8b00133] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The global rise of metallo-β-lactamases (MBLs) is problematic due to their ability to inactivate most β-lactam antibiotics. MBL inhibitors that could be coadministered with and restore the efficacy of β-lactams are highly sought after. In this study, we employ virtual screening of candidate MBL inhibitors without thiols or carboxylates to avoid off-target effects using the Avalanche software package, followed by experimental validation of the selected compounds. As target enzymes, we chose the clinically relevant B1 MBLs NDM-1, IMP-1, and VIM-2. Among 32 compounds selected from an approximately 1.5 million compound library, 6 exhibited IC50 values less than 40 μM against NDM-1 and/or IMP-1. The most potent inhibitors of NDM-1, IMP-1, and VIM-2 had IC50 values of 19 ± 2, 14 ± 1, and 50 ± 20 μM, respectively. While chemically diverse, the most potent inhibitors all contain combinations of hydroxyl, ketone, ester, amide, or sulfonyl groups. Docking studies suggest that these electron-dense moieties are involved in Zn(II) coordination and interaction with protein residues. These novel scaffolds could serve as the basis for further development of MBL inhibitors. A procedure for renaming NDM-1 residues to conform to the class B β-lactamase (BBL) numbering scheme is also included.
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Affiliation(s)
- Joon S Kang
- Department of Pharmaceutical Sciences, College of Pharmacy , Western University of Health Sciences , Pomona , California 91766-1854 , United States.,Department of Biological Sciences , California State Polytechnic University , Pomona , California 91768-2557 , United States
| | - Antonia L Zhang
- Department of Pharmaceutical Sciences, College of Pharmacy , Western University of Health Sciences , Pomona , California 91766-1854 , United States
| | - Mohammad Faheem
- Department of Pharmaceutical Sciences, College of Pharmacy , Western University of Health Sciences , Pomona , California 91766-1854 , United States
| | - Charles J Zhang
- Department of Pharmaceutical Sciences, College of Pharmacy , Western University of Health Sciences , Pomona , California 91766-1854 , United States
| | - Ni Ai
- Pharmaceutical Informatics Institute, School of Pharmaceutical Sciences , Zhejiang University , Zhejiang 31005 , People's Republic of China
| | - John D Buynak
- Department of Chemistry , Southern Methodist University , Dallas , Texas 75275-0314 , United States
| | - William J Welsh
- Department of Pharmacology, Robert Wood Johnson Medical School, Rutgers, and Division of Chem Informatics, Biomedical Informatics Shared Resource, Rutgers-Cancer Institute of New Jersey , The State University of New Jersey , Piscataway , New Jersey 08854-8021 , United States
| | - Peter Oelschlaeger
- Department of Pharmaceutical Sciences, College of Pharmacy , Western University of Health Sciences , Pomona , California 91766-1854 , United States
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MolAlign: an algorithm for aligning multiple small molecules. J Comput Aided Mol Des 2017; 31:523-546. [DOI: 10.1007/s10822-017-0023-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2017] [Accepted: 05/08/2017] [Indexed: 12/13/2022]
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Kimani SG, Kumar S, Bansal N, Singh K, Kholodovych V, Comollo T, Peng Y, Kotenko SV, Sarafianos SG, Bertino JR, Welsh WJ, Birge RB. Small molecule inhibitors block Gas6-inducible TAM activation and tumorigenicity. Sci Rep 2017; 7:43908. [PMID: 28272423 PMCID: PMC5341070 DOI: 10.1038/srep43908] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2016] [Accepted: 01/31/2017] [Indexed: 12/13/2022] Open
Abstract
TAM receptors (Tyro-3, Axl, and Mertk) are a family of three homologous type I receptor tyrosine kinases that are implicated in several human malignancies. Overexpression of TAMs and their major ligand Growth arrest-specific factor 6 (Gas6) is associated with more aggressive staging of cancers, poorer predicted patient survival, acquired drug resistance and metastasis. Here we describe small molecule inhibitors (RU-301 and RU-302) that target the extracellular domain of Axl at the interface of the Ig-1 ectodomain of Axl and the Lg-1 of Gas6. These inhibitors effectively block Gas6-inducible Axl receptor activation with low micromolar IC50s in cell-based reporter assays, inhibit Gas6-inducible motility in Axl-expressing cell lines, and suppress H1299 lung cancer tumor growth in a mouse xenograft NOD-SCIDγ model. Furthermore, using homology models and biochemical verifications, we show that RU301 and 302 also inhibit Gas6 inducible activation of Mertk and Tyro3 suggesting they can act as pan-TAM inhibitors that block the interface between the TAM Ig1 ectodomain and the Gas6 Lg domain. Together, these observations establish that small molecules that bind to the interface between TAM Ig1 domain and Gas6 Lg1 domain can inhibit TAM activation, and support the further development of small molecule Gas6-TAM interaction inhibitors as a novel class of cancer therapeutics.
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Affiliation(s)
- Stanley G Kimani
- Rutgers University, New Jersey Medical School, Department of Microbiology, Biochemistry and Molecular Genetics, Cancer Center, 205 South Orange Ave, Newark, NJ 07103, USA
| | - Sushil Kumar
- Rutgers University, New Jersey Medical School, Department of Microbiology, Biochemistry and Molecular Genetics, Cancer Center, 205 South Orange Ave, Newark, NJ 07103, USA
| | - Nitu Bansal
- Rutgers University, Cancer Institute of New Jersey, 195 Little Albany Street, New Brunswick, NJ 08903, USA
| | - Kamalendra Singh
- Department of Molecular Microbiology and Immunology, and Department of Biochemistry, Bond Life Sciences Center, University of Missouri, Columbia, MO 65211, USA
| | - Vladyslav Kholodovych
- Rutgers University, Office of Advanced Research Computing, 96 Frelinghuysen Road, Piscataway, NJ 08854, USA.,Rutgers University, Robert Wood Johnson Medical Center, Department of Pharmacology, 675 Hoes Lane, Piscataway, NJ 08854, USA
| | - Thomas Comollo
- Rutgers University, New Jersey Medical School, Department of Microbiology, Biochemistry and Molecular Genetics, Cancer Center, 205 South Orange Ave, Newark, NJ 07103, USA
| | - Youyi Peng
- Rutgers University, Cancer Institute of New Jersey, 195 Little Albany Street, New Brunswick, NJ 08903, USA
| | - Sergei V Kotenko
- Rutgers University, New Jersey Medical School, Department of Microbiology, Biochemistry and Molecular Genetics, Cancer Center, 205 South Orange Ave, Newark, NJ 07103, USA
| | - Stefan G Sarafianos
- Department of Molecular Microbiology and Immunology, and Department of Biochemistry, Bond Life Sciences Center, University of Missouri, Columbia, MO 65211, USA
| | - Joseph R Bertino
- Rutgers University, Cancer Institute of New Jersey, 195 Little Albany Street, New Brunswick, NJ 08903, USA
| | - William J Welsh
- Rutgers University, Cancer Institute of New Jersey, 195 Little Albany Street, New Brunswick, NJ 08903, USA.,Rutgers University, Robert Wood Johnson Medical Center, Department of Pharmacology, 675 Hoes Lane, Piscataway, NJ 08854, USA
| | - Raymond B Birge
- Rutgers University, New Jersey Medical School, Department of Microbiology, Biochemistry and Molecular Genetics, Cancer Center, 205 South Orange Ave, Newark, NJ 07103, USA
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Abstract
Drug discovery is a multidisciplinary and multivariate optimization endeavor. As such, in silico screening tools have gained considerable importance to archive, analyze and exploit the vast and ever-increasing amount of experimental data generated throughout the process. The current review will focus on the computer-aided prediction of the numerous properties that need to be controlled during the discovery of a preliminary hit and its promotion to a viable clinical candidate. It does not pretend to the almost impossible task of an exhaustive report but will highlight a few key points that need to be collectively addressed both by chemists and biologists to fuel the drug discovery pipeline with innovative and safe drug candidates.
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Affiliation(s)
- Didier Rognan
- Laboratoire d'Innovation Thérapeutique, UMR 7200 CNRS-Université de Strasbourg, 74 route du Rhin, 67400 Illkirch, France.
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