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da Silva TU, Pougy KDC, Albuquerque MG, Lima CHDS, Machado SDP. Molecular dynamics simulations of aqueous systems of inhibitor candidates for adenosine-5’-phosphosufate reductase. J Biomol Struct Dyn 2022; 41:2466-2477. [PMID: 35100944 DOI: 10.1080/07391102.2022.2033137] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
Molecular dynamics (MD) simulations were used to evaluate some chelating agents as potential candidates to inhibitors for dissimilatory adenosine-5'-phosphosulfate reductase (APSrAB). Molecular docking methods were used to evaluate the best binding modes of these molecules to the enzyme at two binding sites: of the substrate (enzyme active site) by mean the redocking protocol of substrate; and of one of the [Fe4S4]2+ groups by mean of the clusterization protocol. The best docking poses were selected by criteria such as low energy and RMSD (redocking) and the cluster with the higher number of similar poses (clusterization), which were submitted to MD simulations. RMSD, RDF, and hydrogen bonds results revelated that all ligands left the cube site, while in the active site, some ligands remained in their docking region, pointing to the enzyme active site as the best target for the selected ligands. The binding energy results of ligands hydroxamic acid (HXA) and catechol (CAT) showed that they bonded favorably to the enzyme and key residues of the active site contributed significantly to the protein-ligand bind, indicating HAX and CAT may compete with the substrate for interactions with these residues and displaying potential as candidates for experimental studies about APSrAB inhibitors.Communicated by Ramaswamy H. Sarma.
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Uelisson da Silva T, Tomaz da Silva E, de Carvalho Pougy K, Henrique da Silva Lima C, de Paula Machado S. Molecular modeling of indazole-3-carboxylic acid and its metal complexes (Zn, Ni, Co, Fe and Mn) as NO synthase inhibitors: DFT calculations, docking studies and molecular dynamics simulations. INORG CHEM COMMUN 2022. [DOI: 10.1016/j.inoche.2021.109120] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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Dos Santos ES, de Azevedo Santos Ferreira J, Dos Santos JN, Chinalia FA, Matos JL, Coqueiro G, Ramos-de-Souza E, de Almeida PF. Screening and testing potential inhibitors of sulphide gas production by sulphate-reducing bacteria. J Mol Model 2021; 27:189. [PMID: 34046767 DOI: 10.1007/s00894-021-04801-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Accepted: 05/17/2021] [Indexed: 11/28/2022]
Abstract
Sulphate-reducing bacteria are commonly associated with biological causes of oil well souring. Biosulphetogenesis can directly affect oil quality and storage due to the accumulation of sulphides. In addition, these microorganisms can create bio-incrustation that can clog pipes. Sulphite reductase (SIR) is the enzyme responsible for converting ion sulphite into sulphide and several substances may interfere or control such activity. This interference can hinder growth of the sulphate-reducing bacteria and, consequently, it reduces sulphide accumulation in situ. This work focuses on molecular modelling techniques along with in vitro experiments in order to investigate the potential of two essential oils and one vegetable oil as main inhibitors of sulphite reductase activity. Docking simulation identified several substances present in Rosmarinus officinalis, Tea tree and Neem extractable oils as potential inhibitors of SIR. Substances present in Neem vegetable oil are the most potent inhibitors, followed by Rosmarinus officinalis and Tea tree essential oils. The Neem oil mixture showed a superior effectiveness in intracellular SIR inhibitory effects.
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Affiliation(s)
- Elias Silva Dos Santos
- Instituto de Física, Universidade Federal da Bahia, Rua Barão de Geremoabo s/n - Ondina, Salvador, BA, 40.300-000, Brazil.
| | - Joalene de Azevedo Santos Ferreira
- Instituto de Ciências da Saúde, Universidade Federal da Bahia, Av. Reitor Miguel Calmon, s/n - Vale do Canela, Salvador, BA, 40.231-300, Brazil
| | - Jacson Nunes Dos Santos
- Instituto de Ciências da Saúde, Universidade Federal da Bahia, Av. Reitor Miguel Calmon, s/n - Vale do Canela, Salvador, BA, 40.231-300, Brazil
| | - Fábio Alexandre Chinalia
- Instituto de Ciências da Saúde, Universidade Federal da Bahia, Av. Reitor Miguel Calmon, s/n - Vale do Canela, Salvador, BA, 40.231-300, Brazil
| | - Josilene Lima Matos
- Instituto de Ciências da Saúde, Universidade Federal da Bahia, Av. Reitor Miguel Calmon, s/n - Vale do Canela, Salvador, BA, 40.231-300, Brazil
| | - Gustavo Coqueiro
- Instituto de Ciências da Saúde, Universidade Federal da Bahia, Av. Reitor Miguel Calmon, s/n - Vale do Canela, Salvador, BA, 40.231-300, Brazil
| | - Elias Ramos-de-Souza
- Instituto Federal de Educação, Ciência e Tecnologia da Bahia, Rua Emídio dos Santos, s/n, Barbalho, Salvador, BA, 40.301-015, Brazil
| | - Paulo Fernando de Almeida
- Instituto de Ciências da Saúde, Universidade Federal da Bahia, Av. Reitor Miguel Calmon, s/n - Vale do Canela, Salvador, BA, 40.231-300, Brazil
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da Silva TU, Pougy KDC, Albuquerque MG, da Silva Lima CH, Machado SDP. Development of parameters compatible with the CHARMM36 force field for [Fe 4S 4] 2+ clusters and molecular dynamics simulations of adenosine-5'-phosphosulfate reductase in GROMACS 2019. J Biomol Struct Dyn 2020; 40:3481-3491. [PMID: 33183173 DOI: 10.1080/07391102.2020.1847687] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
DFT calculations were used to obtain parameters compatible with the CHARMM36 force field for iron-sulfur clusters (Fe-S) of the type [Fe4S4]2+ that are coordinated to dissimilatory adenosine-5'-phosphosulfate reductase (APSrAB). Classical molecular dynamics (MD) simulations were performed on two APSrAB systems to validate the parameters and verify the stability of the studied systems. The time analysis of the parameters inserted into the force field was in reasonable agreement with the experimental X-ray diffraction data. The analysis of the time evolution of the studied systems indicated that these systems and, in particular, the clusters in their respective cavities had a good stability and were in agreement with what was observed in previous works. The parameters obtained provide the basis for the study of APSrAB as well as other systems that contain [Fe4S4]2+ through the CHARMM36 force field.
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