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Wolk O, Goldblum A. Predicting the Likelihood of Molecules to Act as Modulators of Protein-Protein Interactions. J Chem Inf Model 2023; 63:126-137. [PMID: 36512704 DOI: 10.1021/acs.jcim.2c00920] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Targeting protein-protein interactions (PPIs) by small molecule modulators (iPPIs) is an attractive strategy for drug therapy, and some iPPIs have already been introduced into the clinic. Blocking PPIs is however considered to be a more difficult task than inhibiting enzymes or antagonizing receptor activity. In this paper, we examine whether it is possible to predict the likelihood of molecules to act as iPPIs. Using our in-house iterative stochastic elimination (ISE) algorithm, we constructed two classification models that successfully distinguish between iPPIs from the iPPI-DB database and decoy molecules from either the Enamine HTS collection (ISE 1) or the ZINC database (ISE 2). External test sets of iPPIs taken from the TIMBAL database and decoys from Enamine HTS or ZINC were screened by the models: the area under the curve for the receiver operating characteristic curve was 0.85-0.89, and the Enrichment Factor increased from an initial 1 to as much as 66 for ISE 1 and 57 for ISE 2. Screening of the Enamine HTS and ZINC data sets through both models results in a library of ∼1.3 million molecules that pass either one of the models. This library is enriched with iPPI candidates that are structurally different from known iPPIs, and thus, it is useful for target-specific screenings and should accelerate the discovery of iPPI drug candidates. The entire library is available in Table S6.
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Affiliation(s)
- Omri Wolk
- Molecular Modeling Laboratory, Institute for Drug Research, The Hebrew University of Jerusalem, Jerusalem 91120, Israel
| | - Amiram Goldblum
- Molecular Modeling Laboratory, Institute for Drug Research, The Hebrew University of Jerusalem, Jerusalem 91120, Israel
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Stepanenko N, Wolk O, Bianchi E, Wright GJ, Schachter-Safrai N, Makedonski K, Ouro A, Ben-Meir A, Buganim Y, Goldblum A. In silico Docking Analysis for Blocking JUNO-IZUMO1 Interaction Identifies Two Small Molecules that Block in vitro Fertilization. Front Cell Dev Biol 2022; 10:824629. [PMID: 35478965 PMCID: PMC9037035 DOI: 10.3389/fcell.2022.824629] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Accepted: 02/28/2022] [Indexed: 11/23/2022] Open
Abstract
Combined hormone drugs are the basis for orally administered contraception. However, they are associated with severe side effects that are even more impactful for women in developing countries, where resources are limited. The risk of side effects may be reduced by non-hormonal small molecules which specifically target proteins involved in fertilization. In this study, we present a virtual docking experiment directed to discover molecules that target the crucial fertilization interactions of JUNO (oocyte) and IZUMO1 (sperm). We docked 913,000 molecules to two crystal structures of JUNO and ranked them on the basis of energy-related criteria. Of the 32 tested candidates, two molecules (i.e., Z786028994 and Z1290281203) demonstrated fertilization inhibitory effect in both an in vitro fertilization (IVF) assay in mice and an in vitro penetration of human sperm into hamster oocytes. Despite this clear effect on fertilization, these two molecules did not show JUNO–IZUMO1 interaction blocking activity as assessed by AVidity-based EXtracellular Interaction Screening (AVEXIS). Therefore, further research is required to determine the mechanism of action of these two fertilization inhibitors.
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Affiliation(s)
- Nataliia Stepanenko
- Department of Developmental Biology and Cancer Research, Faculty of Medicine, The Institute for Medical Research Israel-Canada, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Omri Wolk
- Laboratory of Molecular Modeling and Drug Discovery, Faculty of Medicine, School of Pharmacy, The Institute for Drug Research, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Enrica Bianchi
- Department of Biology, Hull York Medical School, York Biomedical Research Institute, University of York, York, United Kingdom
| | - Gavin James Wright
- Department of Biology, Hull York Medical School, York Biomedical Research Institute, University of York, York, United Kingdom
| | - Natali Schachter-Safrai
- Infertility and IVF Unit, Department of Obstetrics and Gynecology, Hadassah Ein-Kerem Medical Center and Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Kiril Makedonski
- Department of Developmental Biology and Cancer Research, Faculty of Medicine, The Institute for Medical Research Israel-Canada, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Alberto Ouro
- Department of Developmental Biology and Cancer Research, Faculty of Medicine, The Institute for Medical Research Israel-Canada, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Assaf Ben-Meir
- Infertility and IVF Unit, Department of Obstetrics and Gynecology, Hadassah Ein-Kerem Medical Center and Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Yosef Buganim
- Department of Developmental Biology and Cancer Research, Faculty of Medicine, The Institute for Medical Research Israel-Canada, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Amiram Goldblum
- Laboratory of Molecular Modeling and Drug Discovery, Faculty of Medicine, School of Pharmacy, The Institute for Drug Research, Hebrew University of Jerusalem, Jerusalem, Israel
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Alonso‐Gil S. MonteCarbo: A software to generate and dock multifunctionalized ring molecules. J Comput Chem 2021; 42:1526-1534. [PMID: 33982793 PMCID: PMC8359999 DOI: 10.1002/jcc.26559] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2021] [Revised: 04/25/2021] [Accepted: 04/28/2021] [Indexed: 02/01/2023]
Abstract
MonteCarbo is an open-source software to construct simple 5-, 6-, and 7-membered ring multifunctionalized monosaccharides and nucleobases and dock them into the active site of carbohydrate-active enzymes. The core bash script executes simple orders to generate the Z-matrix of the neutral molecule of interest. After that, a Fortran90 code based on a pseudo-random number generator (Monte Carlo method) is executed to assign dihedral angles to the different rotamers present in the structure (ring and rotating functional groups). The program also has a generalized internal coordinates (GIC) implementation of the Cremer and Pople puckering coordinates ring. Once the structures are generated and optimized, a second code is ready to execute in serial the docking of multiple conformers in the active site of a wide family of enzymes.
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Affiliation(s)
- Santiago Alonso‐Gil
- Department of Structural and Computational Biology, Max F. Perutz LaboratoriesUniversity of ViennaViennaAustria
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Fischer A, Smieško M, Sellner M, Lill MA. Decision Making in Structure-Based Drug Discovery: Visual Inspection of Docking Results. J Med Chem 2021; 64:2489-2500. [PMID: 33617246 DOI: 10.1021/acs.jmedchem.0c02227] [Citation(s) in RCA: 85] [Impact Index Per Article: 28.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Molecular docking is a computational method widely used in drug discovery. Due to the inherent inaccuracies of molecular docking, visual inspection of binding modes is a crucial routine in the decision making process of computational medicinal chemists. Despite its apparent importance for medicinal chemistry projects, guidelines for the visual docking pose assessment have been hardly discussed in the literature. Here, we review the medicinal chemistry literature with the aim of identifying consistent principles for visual inspection, highlighting cases of its successful application, and discussing its limitations. In this context, we conducted a survey reaching experts in both academia and the pharmaceutical industry, which also included a challenge to distinguish native from incorrect poses. We were able to collect 93 expert opinions that offer valuable insights into visually supported decision-making processes. This perspective shall motivate discussions among experienced computational medicinal chemists and guide young scientists new to the field to stratify their compounds.
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Affiliation(s)
- André Fischer
- Computational Pharmacy, Department of Pharmaceutical Sciences, University of Basel, Klingelbergstrasse 61, 4056 Basel, Switzerland
| | - Martin Smieško
- Computational Pharmacy, Department of Pharmaceutical Sciences, University of Basel, Klingelbergstrasse 61, 4056 Basel, Switzerland
| | - Manuel Sellner
- Computational Pharmacy, Department of Pharmaceutical Sciences, University of Basel, Klingelbergstrasse 61, 4056 Basel, Switzerland
| | - Markus A Lill
- Computational Pharmacy, Department of Pharmaceutical Sciences, University of Basel, Klingelbergstrasse 61, 4056 Basel, Switzerland
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