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Alves Silva JC, Barden Grillo I, A Urquiza-Carvalho G, Bruno Rocha G. Exploring the electronic structure of knotted proteins: the case of two ornithine transcarbamylase family. J Mol Model 2024; 30:265. [PMID: 39008190 DOI: 10.1007/s00894-024-06009-9] [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: 01/31/2024] [Accepted: 06/06/2024] [Indexed: 07/16/2024]
Abstract
CONTEXT Geometrical knots are rare structural arrangements in proteins in which the polypeptide chain ties itself into a knot, which is very intriguing due to the uncertainty of their impact on the protein properties. Presently, classical molecular dynamics is the most employed technique in the few studies found on this topic, so any information on how the presence of knots affects the reactivity and electronic properties of proteins is even scarcer. Using the electronic structure methods and quantum chemical descriptors analysis, we found that the same amino-acid residues in the knot core have statistically larger values for the unknotted protein, for both hard-hard and soft-soft interaction descriptors. In addition, we present a computationally feasible protocol, where we show it is possible to separate the contribution of the geometrical knot to the reactivity and other electronic structure properties. METHODS In order to investigate these systems, we used PRIMoRDiA, a new software developed by our research group, to explore the electronic structure of biological macromolecules. We evaluated several local quantum chemical descriptors to unveil relevant patterns potentially originating from the presence of the geometrical knot in two proteins, belonging to the ornithine transcarbamylase family. We compared several sampled structures from these two enzymes that are highly similar in both tertiary structure and function, but one of them has a knot whereas the other does not. The sampling was carried out through molecular dynamics simulations using ff14SB force field along 50 ns, and the semiempirical convergence was performed with PM7 Hamiltonian.
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Affiliation(s)
- José Cícero Alves Silva
- Department of Chemistry, Federal University of Paraíba, Cid. Universitária, João Pessoa, 58051-900, Paraíba, Brazil
| | - Igor Barden Grillo
- Department of Chemistry, Federal University of Paraíba, Cid. Universitária, João Pessoa, 58051-900, Paraíba, Brazil
| | - Gabriel A Urquiza-Carvalho
- Department of Chemistry, Federal University of Pernambuco, Cid. Universitária, Recife, 50670-901, Pernambuco, Brazil
| | - Gerd Bruno Rocha
- Department of Chemistry, Federal University of Paraíba, Cid. Universitária, João Pessoa, 58051-900, Paraíba, Brazil.
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Geerlings P. From Density Functional Theory to Conceptual Density Functional Theory and Biosystems. Pharmaceuticals (Basel) 2022; 15:ph15091112. [PMID: 36145333 PMCID: PMC9505550 DOI: 10.3390/ph15091112] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Revised: 08/26/2022] [Accepted: 08/27/2022] [Indexed: 12/03/2022] Open
Abstract
The position of conceptual density functional theory (CDFT) in the history of density functional theory (DFT) is sketched followed by a chronological report on the introduction of the various DFT descriptors such as the electronegativity, hardness, softness, Fukui function, local version of softness and hardness, dual descriptor, linear response function, and softness kernel. Through a perturbational approach they can all be characterized as response functions, reflecting the intrinsic reactivity of an atom or molecule upon perturbation by a different system, including recent extensions by external fields. Derived descriptors such as the electrophilicity or generalized philicity, derived from the nature of the energy vs. N behavior, complete this picture. These descriptors can be used as such or in the context of principles such as Sanderson’s electronegativity equalization principle, Pearson’s hard and soft acids and bases principle, the maximum hardness, and more recently, the minimum electrophilicity principle. CDFT has known an ever-growing use in various subdisciplines of chemistry: from organic to inorganic chemistry, from polymer to materials chemistry, and from catalysis to nanotechnology. The increasing size of the systems under study has been coped with thanks to methodological evolutions but also through the impressive evolution in software and hardware. In this flow, biosystems entered the application portfolio in the past twenty years with studies varying (among others) from enzymatic catalysis to biological activity and/or the toxicity of organic molecules and to computational peptidology. On the basis of this evolution, one can expect that “the best is yet to come”.
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Affiliation(s)
- Paul Geerlings
- Research Group of General Chemistry (ALGC), Faculty of Science and Bio-Engineering Science, Vrije Universiteit Brussel (VUB), Pleinlaan 2, B-1050 Brussels, Belgium
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Kaya Y, Erçağ A, Serdaroğlu G, Kaya S, Grillo IB, Rocha GB. Synthesis, spectroscopic characterization, DFT calculations, and molecular docking studies of new unsymmetric bishydrazone derivatives. J Mol Struct 2021. [DOI: 10.1016/j.molstruc.2021.131224] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Yañez O, Báez-Grez R, Inostroza D, Pino-Rios R, Rabanal-León WA, Contreras-García J, Cardenas C, Tiznado W. Kick-Fukui: A Fukui Function-Guided Method for Molecular Structure Prediction. J Chem Inf Model 2021; 61:3955-3963. [PMID: 34378935 DOI: 10.1021/acs.jcim.1c00605] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Here, we introduce a hybrid method, named Kick-Fukui, to explore the potential energy surface (PES) of clusters and molecules using the Coulombic integral between the Fukui functions in the first screening of the best individuals. In the process, small stable molecules or clusters whose combination has the stoichiometry of the explored species are used as assembly units. First, a small set of candidates has been selected from a large and stochastically generated (Kick) population according to the maximum value of the Coulombic integral between the Fukui functions of both fragments. Subsequently, these few candidates are optimized using a gradient method and density functional theory (DFT) calculations. The performance of the program has been evaluated to explore the PES of various systems, including atomic and molecular clusters. In most cases studied, the global minimum (GM) has been identified with a low computational cost. The strategy does not allow to identify the GM of some silicon clusters; however, it predicts local minima very close in energy to the GM that could be used as the initial population of evolutionary algorithms.
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Affiliation(s)
- Osvaldo Yañez
- Center of New Drugs for Hypertension (CENDHY), 8380494 Santiago, Chile.,Department of Pharmaceutical Science and Technology, School of Chemical and Pharmaceutical Sciences, Universidad de Chile, 8380494 Santiago, Chile.,Computational and Theoretical Chemistry Group, Departamento de Ciencias Químicas, Facultad de Ciencias Exactas, Universidad Andres Bello, República 498, 8370035 Santiago, Chile
| | - Rodrigo Báez-Grez
- Computational and Theoretical Chemistry Group, Departamento de Ciencias Químicas, Facultad de Ciencias Exactas, Universidad Andres Bello, República 498, 8370035 Santiago, Chile
| | - Diego Inostroza
- Computational and Theoretical Chemistry Group, Departamento de Ciencias Químicas, Facultad de Ciencias Exactas, Universidad Andres Bello, República 498, 8370035 Santiago, Chile.,Universidad Andres Bello, Programa de Doctorado en Fisicoquímica Molecular, Facultad de Ciencias Exactas, 8370035 Santiago, Chile
| | - Ricardo Pino-Rios
- Laboratorio de Química Teórica, Facultad de Química y Biología, Universidad de Santiago de Chile (USACH), 8320000 Santiago, Chile
| | - Walter A Rabanal-León
- Departamento de Química Analítica e Inorgánica, Facultad de Ciencias Químicas, Universidad de Concepción, Edmundo Larenas 129, Casilla 160-C, 4070371 Concepción, Chile
| | - Julia Contreras-García
- Sorbonne Universités and CNRS, Laboratoire de Chimie Théorique (LCT), 75005 Paris, France
| | - Carlos Cardenas
- Departamento de Física, Facultad de Ciencias, Universidad de Chile, Casilla 635, Santiago 7790681, Chile.,Centro para el Desarrollo de la Nanociencias y Nanotecnologia, CEDENNA, Avenida Ecuador 3493, 9170124 Santiago, Chile
| | - William Tiznado
- Computational and Theoretical Chemistry Group, Departamento de Ciencias Químicas, Facultad de Ciencias Exactas, Universidad Andres Bello, República 498, 8370035 Santiago, Chile
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Rocha REO, Chaves EJF, Fischer PHC, Costa LSC, Grillo IB, da Cruz LEG, Guedes FC, da Silveira CH, Scotti MT, Camargo AD, Machado KS, Werhli AV, Ferreira RS, Rocha GB, de Lima LHF. A higher flexibility at the SARS-CoV-2 main protease active site compared to SARS-CoV and its potentialities for new inhibitor virtual screening targeting multi-conformers. J Biomol Struct Dyn 2021; 40:9214-9234. [PMID: 33970798 PMCID: PMC8127201 DOI: 10.1080/07391102.2021.1924271] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Accepted: 04/26/2021] [Indexed: 12/14/2022]
Abstract
The main-protease (Mpro) catalyzes a crucial step for the SARS-CoV-2 life cycle. The recent SARS-CoV-2 presents the main protease (MCoV2pro) with 12 mutations compared to SARS-CoV (MCoV1pro). Recent studies point out that these subtle differences lead to mobility variances at the active site loops with functional implications. We use metadynamics simulations and a sort of computational analysis to probe the dynamic, pharmacophoric and catalytic environment differences between the monomers of both enzymes. So, we verify how much intrinsic distinctions are preserved in the functional dimer of MCoV2pro, as well as its implications for ligand accessibility and optimized drug screening. We find a significantly higher accessibility to open binding conformers in the MCoV2pro monomer compared to MCoV1pro. A higher hydration propensity for the MCoV2pro S2 loop with the A46S substitution seems to exercise a key role. Quantum calculations suggest that the wider conformations for MCoV2pro are less catalytically active in the monomer. However, the statistics for contacts involving the N-finger suggest higher maintenance of this activity at the dimer. Docking analyses suggest that the ability to vary the active site width can be important to improve the access of the ligand to the active site in different ways. So, we carry out a multiconformational virtual screening with different ligand bases. The results point to the importance of taking into account the protein conformational multiplicity for new promissors anti MCoV2pro ligands. We hope these results will be useful in prospecting, repurposing and/or designing new anti SARS-CoV-2 drugs.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Rafael E. O. Rocha
- Laboratory of Molecular Modeling and Drug Design, Department of Biochemistry and Imunology, Institute of Biological Sciences, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
- Laboratory of Structural Biology, Department of Molecular Biology, Universität Salzburg, Salzburg, Austria
| | - Elton J. F. Chaves
- Laboratory of Computational and Quantum Chemistry, Department of Chemistry, Universidade Federal da Paraíba, João Pessoa, Brazil
| | - Pedro H. C. Fischer
- Laboratory of Molecular Modeling and Bioinformatics, Department of Exact and Biological Sciences, Universidade Federal de São João Del Rei, Sete Lagoas, Brazil
| | - Leon S. C. Costa
- Comp. Modeling Coordination, Laboratório Nacional de Computação Científica, Petrópolis, Brazil
| | - Igor Barden Grillo
- Laboratory of Computational and Quantum Chemistry, Department of Chemistry, Universidade Federal da Paraíba, João Pessoa, Brazil
| | - Luiz E. G. da Cruz
- Laboratory of Computational and Quantum Chemistry, Department of Chemistry, Universidade Federal da Paraíba, João Pessoa, Brazil
| | - Fabiana C. Guedes
- Structural Bioinformatic Laboratory, Institute of Technological Sciences, Universidade Federal de Itajubá, Itabira, Brazil
| | - Carlos H. da Silveira
- Structural Bioinformatic Laboratory, Institute of Technological Sciences, Universidade Federal de Itajubá, Itabira, Brazil
| | - Marcus T. Scotti
- Graduate Program in Natural and Synthetic Bioactive Products; Universidade Federal da Paraíba, João Pessoa, Brazil
| | - Alex D. Camargo
- Computational Biology Laboratory, Center for computational sciences, Universidade Federal do Rio Grande, Rio Grande, Brazil
| | - Karina S. Machado
- Computational Biology Laboratory, Center for computational sciences, Universidade Federal do Rio Grande, Rio Grande, Brazil
| | - Adriano V. Werhli
- Computational Biology Laboratory, Center for computational sciences, Universidade Federal do Rio Grande, Rio Grande, Brazil
| | - Rafaela S. Ferreira
- Laboratory of Molecular Modeling and Drug Design, Department of Biochemistry and Imunology, Institute of Biological Sciences, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Gerd B. Rocha
- Laboratory of Computational and Quantum Chemistry, Department of Chemistry, Universidade Federal da Paraíba, João Pessoa, Brazil
| | - Leonardo H. F. de Lima
- Laboratory of Molecular Modeling and Bioinformatics, Department of Exact and Biological Sciences, Universidade Federal de São João Del Rei, Sete Lagoas, Brazil
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Rocha-Santos A, Chaves EJ, Grillo IB, de Freitas AS, Araújo DAM, Rocha GB. Thermochemical and Quantum Descriptor Calculations for Gaining Insight into Ricin Toxin A (RTA) Inhibitors. ACS OMEGA 2021; 6:8764-8777. [PMID: 33842748 PMCID: PMC8027999 DOI: 10.1021/acsomega.0c02588] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Accepted: 12/30/2020] [Indexed: 05/03/2023]
Abstract
In this work, we performed a study to assess the interactions between the ricin toxin A (RTA) subunit of ricin and some of its inhibitors using modern semiempirical quantum chemistry and ONIOM quantum mechanics/molecular mechanics (QM/MM) methods. Two approaches were followed (calculation of binding enthalpies, ΔH bind, and reactivity quantum chemical descriptors) and compared with the respective half-maximal inhibitory concentration (IC50) experimental data, to gain insight into RTA inhibitors and verify which quantum chemical method would better describe RTA-ligand interactions. The geometries for all RTA-ligand complexes were obtained after running classical molecular dynamics simulations in aqueous media. We found that single-point energy calculations of ΔH bind with the PM6-DH+, PM6-D3H4, and PM7 semiempirical methods and ONIOM QM/MM presented a good correlation with the IC50 data. We also observed, however, that the correlation decreased significantly when we calculated ΔH bind after full-atom geometry optimization with all semiempirical methods. Based on the results from reactivity descriptors calculations for the cases studied, we noted that both types of interactions, molecular overlap and electrostatic interactions, play significant roles in the overall affinity of these ligands for the RTA binding pocket.
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Affiliation(s)
- Acassio Rocha-Santos
- Department
of Chemistry, Federal University of Paraíba, Cidade Universitária, João Pessoa, PB 58051-900, Brazil
| | - Elton José
Ferreira Chaves
- Department
of Biotechnology, Federal University of
Paraíba, Cidade Universitária, João Pessoa, PB 58051-900, Brazil
| | - Igor Barden Grillo
- Department
of Chemistry, Federal University of Paraíba, Cidade Universitária, João Pessoa, PB 58051-900, Brazil
| | - Amanara Souza de Freitas
- Department
of Chemical Engineering, Federal University
of Paraíba, Cidade Universitária, João Pessoa, PB 58051-900, Brazil
| | | | - Gerd Bruno Rocha
- Department
of Chemistry, Federal University of Paraíba, Cidade Universitária, João Pessoa, PB 58051-900, Brazil
- . Phone/Fax: +55-83-3216-7437
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Grillo IB, Urquiza-Carvalho GA, Rocha GB. PRIMoRDiA: A Software to Explore Reactivity and Electronic Structure in Large Biomolecules. J Chem Inf Model 2020; 60:5885-5890. [PMID: 33186016 DOI: 10.1021/acs.jcim.0c00655] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Plenty of enzymes with structural data do not have their mechanism of catalysis elucidated. Reactivity descriptors, theoretical quantities generated from resolved electronic structure, provide a way to predict and rationalize chemical processes of such systems. In this Application Note, we present PRIMoRDiA (PRIMoRDiA Macromolecular Reactivity Descriptors Access), a software built to calculate the reactivity descriptors of large biosystems by employing an efficient and accurate treatment of the large output files produced by quantum chemistry packages. Here, we show the general implementation details and the software main features. Calculated descriptors were applied for a set of enzymatic systems in order to show their relevance for biological studies and the software potential for use in large scale. Also, we test PRIMoRDiA to aid in the interaction depiction between the SARS-CoV-2 main protease and a potential inhibitor.
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Affiliation(s)
- Igor Barden Grillo
- Department of Chemistry, Federal University of Paraíba, João Pessoa - PB 58051-900, Brazil
| | | | - Gerd Bruno Rocha
- Department of Chemistry, Federal University of Paraíba, João Pessoa - PB 58051-900, Brazil
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Theoretical characterization of the shikimate 5-dehydrogenase reaction from Mycobacterium tuberculosis by hybrid QC/MM simulations and quantum chemical descriptors. J Mol Model 2020; 26:297. [PMID: 33030705 DOI: 10.1007/s00894-020-04536-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Accepted: 09/07/2020] [Indexed: 11/27/2022]
Abstract
In this study, we have investigated the enzyme shikimate 5-dehydrogenase from the causative agent of tuberculosis, Mycobacterium tuberculosis. We have employed a mixture of computational techniques, including molecular dynamics, hybrid quantum chemical/molecular mechanical potentials, relaxed surface scans, quantum chemical descriptors and free-energy simulations, to elucidate the enzyme's reaction pathway. Overall, we find a two-step mechanism, with a single transition state, that proceeds by an energetically uphill hydride transfer, followed by an energetically downhill proton transfer. Our mechanism and calculated free energy barrier for the reaction, 64.9 kJ mol- 1, are in good agreement with those predicted from experiment. An analysis of quantum chemical descriptors along the reaction pathway indicated a possibly important, yet currently unreported, role of the active site threonine residue, Thr65.
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