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Vieira RV, Peiter GC, de Melo FF, Zarpelon-Schutz AC, Teixeira KN. In silico prospective analysis of the medicinal plants activity on the CagA oncoprotein from Helicobacter pylori. World J Clin Oncol 2024; 15:653-663. [PMID: 38835850 PMCID: PMC11145963 DOI: 10.5306/wjco.v15.i5.653] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Revised: 04/01/2024] [Accepted: 04/18/2024] [Indexed: 05/21/2024] Open
Abstract
BACKGROUND Colonization with Helicobacter pylori (H. pylori) has a strong correlation with gastric cancer, and the virulence factor CagA is implicated in carcinogenesis. Studies have been conducted using medicinal plants with the aim of eliminating the pathogen; however, the possibility of blocking H. pylori-induced cell differentiation to prevent the onset and/or progression of tumors has not been addressed. This type of study is expensive and time-consuming, requiring in vitro and/or in vivo tests, which can be solved using bioinformatics. Therefore, prospective computational analyses were conducted to assess the feasibility of interaction between phenolic compounds from medicinal plants and the CagA oncoprotein. AIM To perform a computational prospecting of the interactions between phenolic compounds from medicinal plants and the CagA oncoprotein of H. pylori. METHODS In this in silico study, the structures of the phenolic compounds (ligands) kaempferol, myricetin, quercetin, ponciretin (flavonoids), and chlorogenic acid (phenolic acid) were selected from the PubChem database. These phenolic compounds were chosen based on previous studies that suggested medicinal plants as non-drug treatments to eliminate H. pylori infection. The three-dimensional structure model of the CagA oncoprotein of H. pylori (receptor) was obtained through molecular modeling using computational tools from the I-Tasser platform, employing the threading methodology. The primary sequence of CagA was sourced from GenBank (BAK52797.1). A screening was conducted to identify binding sites in the structure of the CagA oncoprotein that could potentially interact with the ligands, utilizing the GRaSP online platform. Both the ligands and receptor were prepared for molecular docking using AutoDock Tools 4 (ADT) software, and the simulations were carried out using a combination of ADT and AutoDock Vina v.1.2.0 software. Two sets of simulations were performed: One involving the central region of CagA with phenolic compounds, and another involving the carboxy-terminus region of CagA with phenolic compounds. The receptor-ligand complexes were then analyzed using PyMol and BIOVIA Discovery Studio software. RESULTS The structure model obtained for the CagA oncoprotein exhibited high quality (C-score = 0.09) and was validated using parameters from the MolProbity platform. The GRaSP online platform identified 24 residues (phenylalanine and leucine) as potential binding sites on the CagA oncoprotein. Molecular docking simulations were conducted with the three-dimensional model of the CagA oncoprotein. No complexes were observed in the simulations between the carboxy-terminus region of CagA and the phenolic compounds; however, all phenolic compounds interacted with the central region of the oncoprotein. Phenolic compounds and CagA exhibited significant affinity energy (-7.9 to -9.1 kcal/mol): CagA/kaempferol formed 28 chemical bonds, CagA/myricetin formed 18 chemical bonds, CagA/quercetin formed 16 chemical bonds, CagA/ponciretin formed 13 chemical bonds, and CagA/chlorogenic acid formed 17 chemical bonds. Although none of the phenolic compounds directly bound to the amino acid residues of the K-Xn-R-X-R membrane binding motif, all of them bound to residues, mostly positively or negatively charged, located near this region. CONCLUSION In silico, the tested phenolic compounds formed stable complexes with CagA. Therefore, they could be tested in vitro and/or in vivo to validate the findings, and to assess interference in CagA/cellular target interactions and in the oncogenic differentiation of gastric cells.
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Affiliation(s)
| | | | - Fabrício Freire de Melo
- Universidade Federal da Bahia, Instituto Multidisciplinar em Saúde-Campus Anísio Teixeira, Vitória da Conquista 45029-094, Brazil
| | - Ana Carla Zarpelon-Schutz
- Universidade Federal do Paraná, Campus Toledo, Toledo 85919-899, Brazil
- Universidade Federal do Paraná-Setor Palotina, Programa de Pós-graduação em Biotecnologia, Palotina 85950-000, Brazil
| | - Kádima Nayara Teixeira
- Universidade Federal do Paraná, Campus Toledo, Toledo 85919-899, Brazil
- Universidade Federal do Paraná-Setor Palotina, Programa de Pós-graduação em Biotecnologia, Palotina 85950-000, Brazil
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2
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Utgés JS, MacGowan SA, Ives CM, Barton GJ. Classification of likely functional class for ligand binding sites identified from fragment screening. Commun Biol 2024; 7:320. [PMID: 38480979 PMCID: PMC10937669 DOI: 10.1038/s42003-024-05970-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Accepted: 02/23/2024] [Indexed: 03/17/2024] Open
Abstract
Fragment screening is used to identify binding sites and leads in drug discovery, but it is often unclear which binding sites are functionally important. Here, data from 37 experiments, and 1309 protein structures binding to 1601 ligands were analysed. A method to group ligands by binding sites is introduced and sites clustered according to profiles of relative solvent accessibility. This identified 293 unique ligand binding sites, grouped into four clusters (C1-4). C1 includes larger, buried, conserved, and population missense-depleted sites, enriched in known functional sites. C4 comprises smaller, accessible, divergent, missense-enriched sites, depleted in functional sites. A site in C1 is 28 times more likely to be functional than one in C4. Seventeen sites, which to the best of our knowledge are novel, in 13 proteins are identified as likely to be functionally important with examples from human tenascin and 5-aminolevulinate synthase highlighted. A multi-layer perceptron, and K-nearest neighbours model are presented to predict cluster labels for ligand binding sites with an accuracy of 96% and 100%, respectively, so allowing functional classification of sites for proteins not in this set. Our findings will be of interest to those studying protein-ligand interactions and developing new drugs or function modulators.
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Affiliation(s)
- Javier S Utgés
- Division of Computational Biology, School of Life Sciences, University of Dundee, Dundee, Scotland, UK
| | - Stuart A MacGowan
- Division of Computational Biology, School of Life Sciences, University of Dundee, Dundee, Scotland, UK
| | - Callum M Ives
- Division of Computational Biology, School of Life Sciences, University of Dundee, Dundee, Scotland, UK
- Department of Chemistry and Hamilton Institute, Maynooth University, Maynooth, Ireland
| | - Geoffrey J Barton
- Division of Computational Biology, School of Life Sciences, University of Dundee, Dundee, Scotland, UK.
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3
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Nunes de Andrade Medeiros SR, Conrado Bezerra I, José da Silva A, Leal Pedroza LA, Gomes Martins RM, Moniz AMH, Gonçalves Reis de Melo AC, Souza Paiva W, Gubert P, Alves de Melo Filho A. In Vitro and In Silico Antioxidant Activity and Molecular Characterization of Bauhinia ungulata L. Essential Oil. Chem Biodivers 2024; 21:e202301536. [PMID: 38090811 DOI: 10.1002/cbdv.202301536] [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: 09/29/2023] [Accepted: 12/10/2023] [Indexed: 01/23/2024]
Abstract
Bauhinia ungulata is an antioxidant medicinal plant that has been manipuled in Brazil to lower glycemic index as well is for alternative treatment for diabetes. Therefore, the present hearch has aimed to investigates the antioxidant effects of the essential oil of Bauhinia ungulata L. (EOBU) collected in Amazon region better specified in Boa Vista, Roraima, Brazil, located in the Amazon region. Gas chromatography had been used to characterize the components, and antioxidant assays such as DPPH, TAC, reducing power, Fe2+ chelation, and total phenols had also been performed. The major constituents had molecularly anchored with the human catalase (CAT) enzyme, and maltol has showed as a positive control. Among the 25 revealed components, the main ones have been α-bisabolol (27.2 %), β-Caryophyllene (12.5 %) and Epi-γ-eudesmol (13.6 %). The EOBU has comproved a TAC value of 618.79 mg of ascorbic acid equivalent, free radical scavenging capacity (DPPH) around 53.7 % and 65.27 %, Fe2+ chelation capacity of 161±6 and 126.7±39.6, for 0.1 mg.mL-1 and 0.5 mg.mL-1 , respectively. The power around the EOBU has appeared percentages equals to 28.66 %, 44.6 %, and 77.03 % in the concentrations tested. As well as, 96.5 % of total phenols. The compounds α-bisabolol (-5.7±0.4 Kcal.mol-1 ) and β-caryophyllene (-6.1±0.5 Kcal.mol-1 ) have showed good interaction with CAT compared to Maltol (-4.4±0.4 Kcal.mol-1 ). The present work has demonstrated that EOBU functions as a potent antioxidant, capable of scavenging free radicals and reducing oxidative stress damage.
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Affiliation(s)
- Sandra Regina Nunes de Andrade Medeiros
- Biodiversity and Biotechnology of the Legal Amazon, PPG Bionorte, Federal University of Roraima (UFRR), Boa Vista, RR, Brazil
- Keizo Asami Institute, Federal University of Pernambuco (UFPE), Recife, PE, Brazil
| | | | - Artur José da Silva
- Keizo Asami Institute, Federal University of Pernambuco (UFPE), Recife, PE, Brazil
| | | | - Regildo Max Gomes Martins
- Biotechnology Multi-institutional Program, PPGBIOTEC, Federal University of Amazonas (UFAM), Manaus, Amazonas, Brazil
| | - Ana Maria Henrique Moniz
- Biodiversity and Biotechnology of the Legal Amazon, PPG Bionorte, Federal University of Roraima (UFRR), Boa Vista, RR, Brazil
| | - Ana Cristina Gonçalves Reis de Melo
- Environmental Chemistry Laboratory, Center for Research and Graduate Studies in Science and Technology, Federal University of Roraima (UFRR), Boa Vista, RR, Brazil
| | - Weslley Souza Paiva
- Post-Graduate Program in Biochemistry and Molecular Biology, Federal University of Rio Grande do Norte, Natal, Brazil
| | - Priscila Gubert
- Keizo Asami Institute, Federal University of Pernambuco (UFPE), Recife, PE, Brazil
- Post-Graduate Program in Biology Applied in Health, Federal University of Pernambuco, Recife, PE, Brazil
| | - Antonio Alves de Melo Filho
- Biodiversity and Biotechnology of the Legal Amazon, PPG Bionorte, Federal University of Roraima (UFRR), Boa Vista, RR, Brazil
- Environmental Chemistry Laboratory, Center for Research and Graduate Studies in Science and Technology, Federal University of Roraima (UFRR), Boa Vista, RR, Brazil
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4
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Eguida M, Rognan D. Estimating the Similarity between Protein Pockets. Int J Mol Sci 2022; 23:12462. [PMID: 36293316 PMCID: PMC9604425 DOI: 10.3390/ijms232012462] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Revised: 10/15/2022] [Accepted: 10/16/2022] [Indexed: 10/28/2023] Open
Abstract
With the exponential increase in publicly available protein structures, the comparison of protein binding sites naturally emerged as a scientific topic to explain observations or generate hypotheses for ligand design, notably to predict ligand selectivity for on- and off-targets, explain polypharmacology, and design target-focused libraries. The current review summarizes the state-of-the-art computational methods applied to pocket detection and comparison as well as structural druggability estimates. The major strengths and weaknesses of current pocket descriptors, alignment methods, and similarity search algorithms are presented. Lastly, an exhaustive survey of both retrospective and prospective applications in diverse medicinal chemistry scenarios illustrates the capability of the existing methods and the hurdle that still needs to be overcome for more accurate predictions.
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Affiliation(s)
| | - Didier Rognan
- Laboratoire d’Innovation Thérapeutique, UMR7200 CNRS-Université de Strasbourg, 67400 Illkirch, France
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5
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Paiva VDA, Gomes IDS, Monteiro CR, Mendonça MV, Martins PM, Santana CA, Gonçalves-Almeida V, Izidoro SC, Melo-Minardi RCD, Silveira SDA. Protein structural bioinformatics: An overview. Comput Biol Med 2022; 147:105695. [DOI: 10.1016/j.compbiomed.2022.105695] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Revised: 06/01/2022] [Accepted: 06/02/2022] [Indexed: 11/27/2022]
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Santana CA, Izidoro SC, de Melo-Minardi RC, Tyzack JD, Ribeiro AJM, Pires DEV, Thornton JM, de A Silveira S. GRaSP-web: a machine learning strategy to predict binding sites based on residue neighborhood graphs. Nucleic Acids Res 2022; 50:W392-W397. [PMID: 35524575 PMCID: PMC9252730 DOI: 10.1093/nar/gkac323] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Revised: 04/14/2022] [Accepted: 04/22/2022] [Indexed: 11/14/2022] Open
Abstract
Proteins are essential macromolecules for the maintenance of living systems. Many of them perform their function by interacting with other molecules in regions called binding sites. The identification and characterization of these regions are of fundamental importance to determine protein function, being a fundamental step in processes such as drug design and discovery. However, identifying such binding regions is not trivial due to the drawbacks of experimental methods, which are costly and time-consuming. Here we propose GRaSP-web, a web server that uses GRaSP (Graph-based Residue neighborhood Strategy to Predict binding sites), a residue-centric method based on graphs that uses machine learning to predict putative ligand binding site residues. The method outperformed 6 state-of-the-art residue-centric methods (MCC of 0.61). Also, GRaSP-web is scalable as it takes 10-20 seconds to predict binding sites for a protein complex (the state-of-the-art residue-centric method takes 2-5h on the average). It proved to be consistent in predicting binding sites for bound/unbound structures (MCC 0.61 for both) and for a large dataset of multi-chain proteins (4500 entries, MCC 0.61). GRaSPWeb is freely available at https://grasp.ufv.br.
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Affiliation(s)
- Charles A Santana
- Department of Biochemistry and Immunology, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, Brazil.,Department of Computer Science, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, Brazil
| | - Sandro C Izidoro
- Institute of Technological Sciences (ICT), Advanced Campus at Itabira, Universidade Federal de Itajubá, Itabira 35903-087, Brazil
| | - Raquel C de Melo-Minardi
- Department of Biochemistry and Immunology, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, Brazil.,Department of Computer Science, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, Brazil
| | - Jonathan D Tyzack
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - António J M Ribeiro
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Douglas E V Pires
- School of Computing and Information Systems, University of Melbourne, Parkville 3052, Australia
| | - Janet M Thornton
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Sabrina de A Silveira
- Department of Computer Science, Universidade Federal de Viçosa, Viçosa 36570-900, Brazil
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7
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Gomes IDS, Santana CA, Marcolino LS, de Lima LHF, de Melo-Minardi RC, Dias RS, de Paula SO, Silveira SDA. Computational prediction of potential inhibitors for SARS-COV-2 main protease based on machine learning, docking, MM-PBSA calculations, and metadynamics. PLoS One 2022; 17:e0267471. [PMID: 35452494 PMCID: PMC9032443 DOI: 10.1371/journal.pone.0267471] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Accepted: 04/06/2022] [Indexed: 11/23/2022] Open
Abstract
The development of new drugs is a very complex and time-consuming process, and for this reason, researchers have been resorting heavily to drug repurposing techniques as an alternative for the treatment of various diseases. This approach is especially interesting when it comes to emerging diseases with high rates of infection, because the lack of a quickly cure brings many human losses until the mitigation of the epidemic, as is the case of COVID-19. In this work, we combine an in-house developed machine learning strategy with docking, MM-PBSA calculations, and metadynamics to detect potential inhibitors for SARS-COV-2 main protease among FDA approved compounds. To assess the ability of our machine learning strategy to retrieve potential compounds we calculated the Enrichment Factor of compound datasets for three well known protein targets: HIV-1 reverse transcriptase (PDB 4B3P), 5-HT2A serotonin receptor (PDB 6A94), and H1 histamine receptor (PDB 3RZE). The Enrichment Factor for each target was, respectively, 102.5, 12.4, 10.6, which are considered significant values. Regarding the identification of molecules that can potentially inhibit the main protease of SARS-COV-2, compounds output by the machine learning step went through a docking experiment against SARS-COV-2 Mpro. The best scored poses were the input for MM-PBSA calculations and metadynamics using CHARMM and AMBER force fields to predict the binding energy for each complex. Our work points out six molecules, highlighting the strong interaction obtained for Mpro-mirabegron complex. Among these six, to the best of our knowledge, ambenonium has not yet been described in the literature as a candidate inhibitor for the SARS-COV-2 main protease in its active pocket.
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Affiliation(s)
- Isabela de Souza Gomes
- Department of Computer Science, Universidade Federal de Viçosa, Viçosa, Minas Gerais, Brazil
| | - Charles Abreu Santana
- Department of Biochemistry and Immunology, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
- Department of Computer Science, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | | | - Leonardo Henrique França de Lima
- Department of Exact and Biological Sciences, Universidade Federal de São João del-Rei, Sete Lagoas Campus, Sete Lagoas, Minas Gerais, Brazil
| | - Raquel Cardoso de Melo-Minardi
- Department of Biochemistry and Immunology, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
- Department of Computer Science, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Roberto Sousa Dias
- Department of General Biology, Universidade Federal de Viçosa, Viçosa, Minas Gerais, Brazil
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8
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McGreig JE, Uri H, Antczak M, Sternberg MJE, Michaelis M, Wass MN. 3DLigandSite: structure-based prediction of protein-ligand binding sites. Nucleic Acids Res 2022; 50:W13-W20. [PMID: 35412635 PMCID: PMC9252821 DOI: 10.1093/nar/gkac250] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Revised: 03/13/2022] [Accepted: 04/03/2022] [Indexed: 01/13/2023] Open
Abstract
3DLigandSite is a web tool for the prediction of ligand-binding sites in proteins. Here, we report a significant update since the first release of 3DLigandSite in 2010. The overall methodology remains the same, with candidate binding sites in proteins inferred using known binding sites in related protein structures as templates. However, the initial structural modelling step now uses the newly available structures from the AlphaFold database or alternatively Phyre2 when AlphaFold structures are not available. Further, a sequence-based search using HHSearch has been introduced to identify template structures with bound ligands that are used to infer the ligand-binding residues in the query protein. Finally, we introduced a machine learning element as the final prediction step, which improves the accuracy of predictions and provides a confidence score for each residue predicted to be part of a binding site. Validation of 3DLigandSite on a set of 6416 binding sites obtained 92% recall at 75% precision for non-metal binding sites and 52% recall at 75% precision for metal binding sites. 3DLigandSite is available at https://www.wass-michaelislab.org/3dligandsite. Users submit either a protein sequence or structure. Results are displayed in multiple formats including an interactive Mol* molecular visualization of the protein and the predicted binding sites.
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Affiliation(s)
- Jake E McGreig
- School of Biosciences, Division of Natural Sciences, University of Kent, Canterbury, Kent CT2 7NJ, UK
| | - Hannah Uri
- School of Biosciences, Division of Natural Sciences, University of Kent, Canterbury, Kent CT2 7NJ, UK
| | - Magdalena Antczak
- School of Biosciences, Division of Natural Sciences, University of Kent, Canterbury, Kent CT2 7NJ, UK
| | - Michael J E Sternberg
- Centre for Integrative Systems Biology and Bioinformatics, Department of Life Sciences, Imperial College London, London SW7 2AZ, UK
| | - Martin Michaelis
- School of Biosciences, Division of Natural Sciences, University of Kent, Canterbury, Kent CT2 7NJ, UK
| | - Mark N Wass
- School of Biosciences, Division of Natural Sciences, University of Kent, Canterbury, Kent CT2 7NJ, UK
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9
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Rauer C, Sen N, Waman VP, Abbasian M, Orengo CA. Computational approaches to predict protein functional families and functional sites. Curr Opin Struct Biol 2021; 70:108-122. [PMID: 34225010 DOI: 10.1016/j.sbi.2021.05.012] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Revised: 05/13/2021] [Accepted: 05/25/2021] [Indexed: 01/06/2023]
Abstract
Understanding the mechanisms of protein function is indispensable for many biological applications, such as protein engineering and drug design. However, experimental annotations are sparse, and therefore, theoretical strategies are needed to fill the gap. Here, we present the latest developments in building functional subclassifications of protein superfamilies and using evolutionary conservation to detect functional determinants, for example, catalytic-, binding- and specificity-determining residues important for delineating the functional families. We also briefly review other features exploited for functional site detection and new machine learning strategies for combining multiple features.
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Affiliation(s)
- Clemens Rauer
- Institute of Structural and Molecular Biology, University College London, London, WC1E 6BT, UK
| | - Neeladri Sen
- Institute of Structural and Molecular Biology, University College London, London, WC1E 6BT, UK
| | - Vaishali P Waman
- Institute of Structural and Molecular Biology, University College London, London, WC1E 6BT, UK
| | - Mahnaz Abbasian
- Institute of Structural and Molecular Biology, University College London, London, WC1E 6BT, UK
| | - Christine A Orengo
- Institute of Structural and Molecular Biology, University College London, London, WC1E 6BT, UK.
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