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Santos TMR, Tavares CA, Pereira AF, da Cunha EFF, Ramalho TC. Evaluation of autophagy inhibition to combat cancer: (vanadium complex)-protein interactions, parameterization, and validation of a new force field. J Mol Model 2023; 29:123. [PMID: 36995564 PMCID: PMC10061415 DOI: 10.1007/s00894-023-05530-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Accepted: 03/23/2023] [Indexed: 03/31/2023]
Abstract
Autophagy has drawn attention from the scientific community, mainly because of its significant advantages over chemotherapeutic processes. One of these advantages is its direct action on cancer cells, avoiding possible side effects, unlike chemotherapy, which reaches tumor cells and affects healthy cells in the body, leading to a great loss in the quality of life of patients. In this way, it is known that vanadium complex (VC) [VO(oda)(phen)] has proven inhibition effect on autophagy process in pancreatic cancer cells. Keeping that in mind, molecular dynamics (MD) simulations can be considered excellent strategies to investigate the interaction of metal complexes and their biological targets. However, simulations of this type are strongly dependent on the appropriate choice of force field (FF). Therefore, this work proposes the development of AMBER FF parameters for VC, having a minimum energy structure as a starting point, obtained through DFT calculations with B3LYP/def2-TZVP level of theory plus ECP for the vanadium atom. An MD simulation in vacuum was performed to validate the developed FF. From the structural analyses, satisfying values of VC bond lengths and angles were obtained, where a good agreement with the experimental data and the quantum reference was found. The RMSD analysis showed an average of only 0.3%. Finally, we performed docking and MD (120 ns) simulations with explicit solvent between VC and PI3K. Overall, our findings encourage new parameterizations of metal complexes with significant biological applications, as well as allow to contribute to the elucidation of the complex process of autophagy.
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Affiliation(s)
- Taináh M R Santos
- Laboratory of Molecular Modelling, Department of Chemistry, Federal University of Lavras, /MG, Lavras, 37200-000, Brazil.
| | - Camila A Tavares
- Laboratory of Molecular Modelling, Department of Chemistry, Federal University of Lavras, /MG, Lavras, 37200-000, Brazil
| | - Ander F Pereira
- Institute of Chemistry, University of Campinas, /SP, Campinas, 13083-970, Brazil
| | - Elaine F F da Cunha
- Laboratory of Molecular Modelling, Department of Chemistry, Federal University of Lavras, /MG, Lavras, 37200-000, Brazil
| | - Teodorico C Ramalho
- Laboratory of Molecular Modelling, Department of Chemistry, Federal University of Lavras, /MG, Lavras, 37200-000, Brazil.
- Department of Chemistry, Faculty of Science, University of Hradec Kralove, Hradec Kralove, Czech Republic.
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Application of Nanomaterials in the Prevention, Detection, and Treatment of Methicillin-Resistant Staphylococcus aureus (MRSA). Pharmaceutics 2022; 14:pharmaceutics14040805. [PMID: 35456638 PMCID: PMC9030647 DOI: 10.3390/pharmaceutics14040805] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2022] [Revised: 04/01/2022] [Accepted: 04/04/2022] [Indexed: 01/27/2023] Open
Abstract
Due to differences in geographic surveillance systems, chemical sanitization practices, and antibiotic stewardship (AS) implementation employed during the COVID-19 pandemic, many experts have expressed concerns regarding a future surge in global antimicrobial resistance (AMR). A potential beneficiary of these differences is the Gram-positive bacteria MRSA. MRSA is a bacterial pathogen with a high potential for mutational resistance, allowing it to engage various AMR mechanisms circumventing conventional antibiotic therapies and the host’s immune response. Coupled with a lack of novel FDA-approved antibiotics reaching the clinic, the onus is on researchers to develop alternative treatment tools to mitigate against an increase in pathogenic resistance. Mitigation strategies can take the form of synthetic or biomimetic nanomaterials/vesicles employed in vaccines, rapid diagnostics, antibiotic delivery, and nanotherapeutics. This review seeks to discuss the current potential of the aforementioned nanomaterials in detecting and treating MRSA.
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