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Knight IS, Mailhot O, Tang KG, Irwin JJ. DockOpt: A Tool for Automatic Optimization of Docking Models. J Chem Inf Model 2024; 64:1004-1016. [PMID: 38206771 PMCID: PMC10865354 DOI: 10.1021/acs.jcim.3c01406] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2023] [Revised: 12/17/2023] [Accepted: 12/26/2023] [Indexed: 01/13/2024]
Abstract
Molecular docking is a widely used technique for leveraging protein structure for ligand discovery, but it remains difficult to utilize due to limitations that have not been adequately addressed. Despite some progress toward automation, docking still requires expert guidance, hindering its adoption by a broader range of investigators. To make docking more accessible, we developed a new utility called DockOpt, which automates the creation, evaluation, and optimization of docking models prior to their deployment in large-scale prospective screens. DockOpt outperforms our previous automated pipeline across all 43 targets in the DUDE-Z benchmark data set, and the generated models for 84% of targets demonstrate sufficient enrichment to warrant their use in prospective screens, with normalized LogAUC values of at least 15%. DockOpt is available as part of the Python package Pydock3 included in the UCSF DOCK 3.8 distribution, which is available for free to academic researchers at https://dock.compbio.ucsf.edu and free for everyone upon registration at https://tldr.docking.org.
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Affiliation(s)
- Ian S. Knight
- Department of Pharmaceutical Chemistry, UCSF, 1700 Fourth Street, San Francisco, California 94158-2330, United States
| | - Olivier Mailhot
- Department of Pharmaceutical Chemistry, UCSF, 1700 Fourth Street, San Francisco, California 94158-2330, United States
| | - Khanh G. Tang
- Department of Pharmaceutical Chemistry, UCSF, 1700 Fourth Street, San Francisco, California 94158-2330, United States
| | - John J. Irwin
- Department of Pharmaceutical Chemistry, UCSF, 1700 Fourth Street, San Francisco, California 94158-2330, United States
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Chakrabarti M, Tan YS, Balius TE. Considerations Around Structure-Based Drug Discovery for KRAS Using DOCK. Methods Mol Biol 2024; 2797:67-90. [PMID: 38570453 DOI: 10.1007/978-1-0716-3822-4_6] [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] [Indexed: 04/05/2024]
Abstract
Molecular docking is a popular computational tool in drug discovery. Leveraging structural information, docking software predicts binding poses of small molecules to cavities on the surfaces of proteins. Virtual screening for ligand discovery is a useful application of docking software. In this chapter, using the enigmatic KRAS protein as an example system, we endeavor to teach the reader about best practices for performing molecular docking with UCSF DOCK. We discuss methods for virtual screening and docking molecules on KRAS. We present the following six points to optimize our docking setup for prosecuting a virtual screen: protein structure choice, pocket selection, optimization of the scoring function, modification of sampling spheres and sampling procedures, choosing an appropriate portion of chemical space to dock, and the choice of which top scoring molecules to pick for purchase.
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Affiliation(s)
- Mayukh Chakrabarti
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Y Stanley Tan
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Trent E Balius
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA.
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Bitencourt-Ferreira G, Villarreal MA, Quiroga R, Biziukova N, Poroikov V, Tarasova O, de Azevedo Junior WF. Exploring Scoring Function Space: Developing Computational Models for Drug Discovery. Curr Med Chem 2024; 31:2361-2377. [PMID: 36944627 DOI: 10.2174/0929867330666230321103731] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Revised: 12/15/2022] [Accepted: 12/29/2022] [Indexed: 03/23/2023]
Abstract
BACKGROUND The idea of scoring function space established a systems-level approach to address the development of models to predict the affinity of drug molecules by those interested in drug discovery. OBJECTIVE Our goal here is to review the concept of scoring function space and how to explore it to develop machine learning models to address protein-ligand binding affinity. METHODS We searched the articles available in PubMed related to the scoring function space. We also utilized crystallographic structures found in the protein data bank (PDB) to represent the protein space. RESULTS The application of systems-level approaches to address receptor-drug interactions allows us to have a holistic view of the process of drug discovery. The scoring function space adds flexibility to the process since it makes it possible to see drug discovery as a relationship involving mathematical spaces. CONCLUSION The application of the concept of scoring function space has provided us with an integrated view of drug discovery methods. This concept is useful during drug discovery, where we see the process as a computational search of the scoring function space to find an adequate model to predict receptor-drug binding affinity.
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Affiliation(s)
| | - Marcos A Villarreal
- CONICET-Departamento de Matemática y Física, Instituto de Investigaciones en Fisicoquímica de Córdoba (INFIQC), Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, Ciudad Universitaria, Córdoba, Argentina
| | - Rodrigo Quiroga
- CONICET-Departamento de Matemática y Física, Instituto de Investigaciones en Fisicoquímica de Córdoba (INFIQC), Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, Ciudad Universitaria, Córdoba, Argentina
| | - Nadezhda Biziukova
- Institute of Biomedical Chemistry, Pogodinskaya Str., 10/8, Moscow, 119121, Russia
| | - Vladimir Poroikov
- Institute of Biomedical Chemistry, Pogodinskaya Str., 10/8, Moscow, 119121, Russia
| | - Olga Tarasova
- Institute of Biomedical Chemistry, Pogodinskaya Str., 10/8, Moscow, 119121, Russia
| | - Walter F de Azevedo Junior
- Pontifical Catholic University of Rio Grande do Sul - PUCRS, Porto Alegre-RS, Brazil
- Specialization Program in Bioinformatics, The Pontifical Catholic University of Rio Grande do Sul (PUCRS), Av. Ipiranga, 6681 Porto Alegre / RS 90619-900, Brazil
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Wolf B, Blaschke CRK, Mungaray S, Weselman BT, Stefanenko M, Fedoriuk M, Bai H, Rodgers J, Palygin O, Drake RR, Nowling TK. Metabolic Markers and Association of Biological Sex in Lupus Nephritis. Int J Mol Sci 2023; 24:16490. [PMID: 38003679 PMCID: PMC10671813 DOI: 10.3390/ijms242216490] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Revised: 11/08/2023] [Accepted: 11/10/2023] [Indexed: 11/26/2023] Open
Abstract
Lupus nephritis (LN) is a serious complication for many patients who develop systemic lupus erythematosus, which primarily afflicts women. Our studies to identify biomarkers and the pathogenic mechanisms underlying LN will provide a better understanding of disease progression and sex bias, and lead to identification of additional potential therapeutic targets. The glycosphingolipid lactosylceramide (LacCer) and N-linked glycosylated proteins (N-glycans) were measured in urine and serum collected from LN and healthy control (HC) subjects (10 females and 10 males in each group). The sera from the LN and HC subjects were used to stimulate cytokine secretion and intracellular Ca2+ flux in female- and male-derived primary human renal mesangial cells (hRMCs). Significant differences were observed in the urine of LN patients compared to HCs. All major LacCers species were significantly elevated and differences between LN and HC were more pronounced in males. 72 individual N-glycans were altered in LN compared to HC and three N-glycans were significantly different between the sexes. In hRMCs, Ca2+ flux, but not cytokine secretion, was higher in response to LN sera compared to HC sera. Ca2+ flux, cytokine secretion, and glycosphingolipid levels were significantly higher in female-derived compared to male-derived hRMCs. Relative abundance of some LacCers and hexosylceramides were higher in female-derived compared to male-derived hRMCs. Urine LacCers and N-glycome could serve as definitive LN biomarkers and likely reflect renal disease activity. Despite higher sensitivity of female hRMCs, males may experience greater increases in LacCers, which may underscore worse disease in males. Elevated glycosphingolipid metabolism may poise renal cells to be more sensitive to external stimuli.
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Affiliation(s)
- Bethany Wolf
- Department of Public Health Sciences, Medical University of South Carolina, 135 Cannon Street, Suite 303 MSC 835, Charleston, SC 29425, USA;
| | - Calvin R. K. Blaschke
- Department of Cell and Molecular Pharmacology and Experimental Therapeutics, Medical University of South Carolina, 173 Ashley Avenue Basic Science Building 358, Charleston, SC 29425, USA (B.T.W.); (H.B.); (R.R.D.)
| | - Sandy Mungaray
- Division of Rheumatology, Department of Medicine, Medical University of South Carolina, 171 Ashley Avenue, Charleston, SC 29425, USA; (S.M.); (J.R.)
| | - Bryan T. Weselman
- Department of Cell and Molecular Pharmacology and Experimental Therapeutics, Medical University of South Carolina, 173 Ashley Avenue Basic Science Building 358, Charleston, SC 29425, USA (B.T.W.); (H.B.); (R.R.D.)
| | - Mariia Stefanenko
- Division of Nephrology, Department of Medicine, Medical University of South Carolina, Clinical Sciences Building, 96 Jonathan Lucas Street, Charleston, SC 29425, USA; (M.S.); (M.F.); (O.P.)
| | - Mykhailo Fedoriuk
- Division of Nephrology, Department of Medicine, Medical University of South Carolina, Clinical Sciences Building, 96 Jonathan Lucas Street, Charleston, SC 29425, USA; (M.S.); (M.F.); (O.P.)
| | - Hongxia Bai
- Department of Cell and Molecular Pharmacology and Experimental Therapeutics, Medical University of South Carolina, 173 Ashley Avenue Basic Science Building 358, Charleston, SC 29425, USA (B.T.W.); (H.B.); (R.R.D.)
| | - Jessalyn Rodgers
- Division of Rheumatology, Department of Medicine, Medical University of South Carolina, 171 Ashley Avenue, Charleston, SC 29425, USA; (S.M.); (J.R.)
| | - Oleg Palygin
- Division of Nephrology, Department of Medicine, Medical University of South Carolina, Clinical Sciences Building, 96 Jonathan Lucas Street, Charleston, SC 29425, USA; (M.S.); (M.F.); (O.P.)
| | - Richard R. Drake
- Department of Cell and Molecular Pharmacology and Experimental Therapeutics, Medical University of South Carolina, 173 Ashley Avenue Basic Science Building 358, Charleston, SC 29425, USA (B.T.W.); (H.B.); (R.R.D.)
| | - Tamara K. Nowling
- Division of Rheumatology, Department of Medicine, Medical University of South Carolina, 171 Ashley Avenue, Charleston, SC 29425, USA; (S.M.); (J.R.)
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