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Farias AB, Cortés-Avalos D, Ibarra JA, Perez-Rueda E. The interaction of InvF-RNAP is mediated by the chaperone SicA in Salmonella sp: an in silico prediction. PeerJ 2024; 12:e17069. [PMID: 38549779 PMCID: PMC10977090 DOI: 10.7717/peerj.17069] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Accepted: 02/18/2024] [Indexed: 04/02/2024] Open
Abstract
In this work we carried out an in silico analysis to understand the interaction between InvF-SicA and RNAP in the bacterium Salmonella Typhimurium strain LT2. Structural analysis of InvF allowed the identification of three possible potential cavities for interaction with SicA. This interaction could occur with the structural motif known as tetratricopeptide repeat (TPR) 1 and 2 in the two cavities located in the interface of the InvF and α-CTD of RNAP. Indeed, molecular dynamics simulations showed that SicA stabilizes the Helix-turn-Helix DNA-binding motifs, i.e., maintaining their proper conformation, mainly in the DNA Binding Domain (DBD). Finally, to evaluate the role of amino acids that contribute to protein-protein affinity, an alanine scanning mutagenesis approach, indicated that R177 and R181, located in the DBD motif, caused the greatest changes in binding affinity with α-CTD, suggesting a central role in the stabilization of the complex. However, it seems that the N-terminal region also plays a key role in the protein-protein interaction, especially the amino acid R40, since we observed conformational flexibility in this region allowing it to interact with interface residues. We consider that this analysis opens the possibility to validate experimentally the amino acids involved in protein-protein interactions and explore other regulatory complexes where chaperones are involved.
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Affiliation(s)
- André B. Farias
- Instituto de Investigaciones en Matemáticas Aplicadas y en Sistemas, Unidad Académica del Estado de Yucatán, Universidad Nacional Autónoma de México, Mérida, Yucatán, Mexico
- Laboratório Nacional de Computação Científica—LNCC, Petrópolis, Rio de Janeiro, Brazil
| | - Daniel Cortés-Avalos
- Laboratorio de Genética Microbiana, Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Universidad Nacional Autónoma de México, Ciudad de México, Ciudad de México, México
| | - J. Antonio Ibarra
- Laboratorio de Genética Microbiana, Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Universidad Nacional Autónoma de México, Ciudad de México, Ciudad de México, México
| | - Ernesto Perez-Rueda
- Instituto de Investigaciones en Matemáticas Aplicadas y en Sistemas, Unidad Académica del Estado de Yucatán, Universidad Nacional Autónoma de México, Mérida, Yucatán, Mexico
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Santos D, Gomes HF, Ribeiro L, Farias AB, Romeiro NC, da Fonseca RN, Nepomuceno-Silva JL, Moraes J. Inhibition of Aedes aegypti DNA topoisomerase II by etoposide: Impact on survival and morphology of larvae and pupae. Comp Biochem Physiol C Toxicol Pharmacol 2021; 247:109066. [PMID: 33930525 DOI: 10.1016/j.cbpc.2021.109066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Revised: 04/18/2021] [Accepted: 04/21/2021] [Indexed: 10/01/2022]
Abstract
DNA topoisomerase II enzymes maintain DNA stability during vital processes, such as genome replication, transcription and chromosomal segregation during mitosis and meiosis. In the present work, we analyzed functional aspects of the DNA topoisomerase II (AeTopII) enzyme of the mosquito Aedes aegypti. Here, we show that AeTopII mRNA is expressed at all stages of mosquito development. By in situ hybridization, we found that the AeTopII mRNA is concentrated along the ovarian follicular cells as well as in the region of the follicles. The observed expression profiles likely reflect increased topoisomerase II cellular requirements due to the intense ovarian growth and egg production following blood feeding in Ae. aegypti females. The drug etoposide, a classic inhibitor of topoisomerase II, was used for in vivo testing with 2nd stage larvae, in order to investigate the functional importance of this enzyme in Ae. aegypti survival and development. Inhibition of topoisomerase II activity with etoposide concentrations ranging from 10 to 200 μM did not leads to the immediate death of larvae. However, after 10 days of observation, etoposide treatments resulted in 30-40% decrease in survival, in a dose dependent manner, with persisting larvae and pupae presenting incomplete development, as well as morphological abnormalities. Also, approximately 50% of the treated larvae did not reach the pupal stage. Thus, we conclude that AeTopII is a vital enzyme in the development of Ae. aegypti and its sensitivity to inhibitors should be explored for potential chemical agents to be used in vector control.
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Affiliation(s)
- Daniele Santos
- Laboratório Integrado de Bioquímica Hatisaburo Masuda, NUPEM, Instituto de Biodiversidade e Sustentabilidade, Universidade Federal do Rio de Janeiro, Avenida São José Barreto, N° 764, Bairro, São José do Barreto, Macaé, RJ CEP: 27.965-045, Brazil
| | - Helga F Gomes
- Laboratório Integrado de Bioquímica Hatisaburo Masuda, NUPEM, Instituto de Biodiversidade e Sustentabilidade, Universidade Federal do Rio de Janeiro, Avenida São José Barreto, N° 764, Bairro, São José do Barreto, Macaé, RJ CEP: 27.965-045, Brazil
| | - Lupis Ribeiro
- Laboratório Integrado Ciências Morfofuncionais, NUPEM, Instituto de Biodiversidade e Sustentabilidade, Universidade Federal do Rio de Janeiro, Avenida São José Barreto, N° 764, Bairro, São José do Barreto, Macaé, RJ CEP: 27.965-045, Brazil
| | - André B Farias
- Instituto de Química, Universidade Federal do Rio de Janeiro, Rio de Janeiro CEP: 21941-909, Brazil; Laboratório Integrado de Computação Científica, Universidade Federal do Rio de Janeiro, Campus Macaé Professor Aloísio Teixeira, Avenida Aluízio da Silva Gomes, 50, CEP 27930-560, Granja dos Cavaleiros, Macaé, RJ, Brazil
| | - Nelilma C Romeiro
- Laboratório Integrado de Computação Científica, Universidade Federal do Rio de Janeiro, Campus Macaé Professor Aloísio Teixeira, Avenida Aluízio da Silva Gomes, 50, CEP 27930-560, Granja dos Cavaleiros, Macaé, RJ, Brazil
| | - Rodrigo Nunes da Fonseca
- Laboratório Integrado Ciências Morfofuncionais, NUPEM, Instituto de Biodiversidade e Sustentabilidade, Universidade Federal do Rio de Janeiro, Avenida São José Barreto, N° 764, Bairro, São José do Barreto, Macaé, RJ CEP: 27.965-045, Brazil
| | - José L Nepomuceno-Silva
- Laboratório Integrado de Bioquímica Hatisaburo Masuda, NUPEM, Instituto de Biodiversidade e Sustentabilidade, Universidade Federal do Rio de Janeiro, Avenida São José Barreto, N° 764, Bairro, São José do Barreto, Macaé, RJ CEP: 27.965-045, Brazil
| | - Jorge Moraes
- Laboratório Integrado de Bioquímica Hatisaburo Masuda, NUPEM, Instituto de Biodiversidade e Sustentabilidade, Universidade Federal do Rio de Janeiro, Avenida São José Barreto, N° 764, Bairro, São José do Barreto, Macaé, RJ CEP: 27.965-045, Brazil.
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Abstract
Non-structural protein 9 (Nsp9) plays a key role in viral replication of coronavirus and represents a promising target for anti-SARS-CoV-2 strategies.
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Affiliation(s)
- André B. Farias
- Instituto de Química
- Universidade Federal do Rio de Janeiro
- Rio de Janeiro
- Brazil
| | - Graziâni Candiotto
- Instituto de Química
- Universidade Federal do Rio de Janeiro
- Rio de Janeiro
- Brazil
| | | | - Laura Goracci
- Department of Chemistry
- Biology and Biotechnology
- University of Perugia
- Perugia
- Italy
| | - Gabriele Cruciani
- Department of Chemistry
- Biology and Biotechnology
- University of Perugia
- Perugia
- Italy
| | - Edson R. A. Oliveira
- Department of Microbiology and Immunology
- University of Illinois at Chicago
- Chicago
- USA
| | - Bruno A. C. Horta
- Instituto de Química
- Universidade Federal do Rio de Janeiro
- Rio de Janeiro
- Brazil
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Crizanto de Lima E, Castelo-Branco FS, Maquiaveli CC, Farias AB, Rennó MN, Boechat N, Silva ER. Phenylhydrazides as inhibitors of Leishmania amazonensis arginase and antileishmanial activity. Bioorg Med Chem 2019; 27:3853-3859. [PMID: 31311700 DOI: 10.1016/j.bmc.2019.07.022] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2019] [Revised: 07/03/2019] [Accepted: 07/10/2019] [Indexed: 01/20/2023]
Abstract
Searching for new substances with antileishmanial activity, we synthesized and evaluated a series of α,α-difluorohydrazide and α,α-difluoramides against Leishmania amazonensis arginase (LaArg). Four α,α-difluorohydrazide derivatives showed activity against LaArg with Ki in the range of 1.3-26 μM. The study of the kinetics of LaArg inhibition showed that these substances might act via different inhibitory mechanisms or even by a combination of these. The compounds were tested against L. amazonensis promastigotes and the best result was obtained to the compound 4 (EC50 of 12.7 ± 0.3 μM). In addition, in order to obtain further insight into the binding mode of such compounds, molecular docking studies were performed to obtain additional validation of experimental results. Considering these results, it is possible to conclude that α,α-difluorohydrazide derivatives are a promising scaffold in the development of new substances against the etiological agent of leishmaniasis by targeting LaArg.
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Affiliation(s)
- Evanoel Crizanto de Lima
- Laboratório de Catálise e Síntese de Substâncias Bioativas, Universidade Federal do Rio de Janeiro Campus Macaé Professor Aloísio Teixeira, Estrada do Imburo s/n - Ajuda de Baixo, Macaé, RJ CEP 27979-000, Brazil
| | - Frederico S Castelo-Branco
- Departamento de Sintese de Fármacos, Instituto de Tecnologia em Fármacos, Farmanguinhos - FIOCRUZ, Rio de Janeiro, RJ 21041-250, Brazil
| | - Claudia C Maquiaveli
- Universidade de São Paulo Faculdade de Zootecnia e Engenharia de Alimentos, Departamento de Medicina Veterinária, Laboratório de Farmacologia e Bioquímica (LFBq), Av. Duque de Caxias Norte, 225, Pirassununga, SP 13635-900, Brazil
| | - André B Farias
- Instituto de Biodiversidade e Sustentabilidade NUPEM/UFRJ, Universidade Federal do Rio de Janeiro, Campus Macaé Professor Aloísio Teixeira, Av. São José do Barreto, 764, Macaé, RJ 27965-045, Brazil
| | - Magdalena N Rennó
- Instituto de Biodiversidade e Sustentabilidade NUPEM/UFRJ, Universidade Federal do Rio de Janeiro, Campus Macaé Professor Aloísio Teixeira, Av. São José do Barreto, 764, Macaé, RJ 27965-045, Brazil
| | - Nubia Boechat
- Departamento de Sintese de Fármacos, Instituto de Tecnologia em Fármacos, Farmanguinhos - FIOCRUZ, Rio de Janeiro, RJ 21041-250, Brazil.
| | - Edson R Silva
- Universidade de São Paulo Faculdade de Zootecnia e Engenharia de Alimentos, Departamento de Medicina Veterinária, Laboratório de Farmacologia e Bioquímica (LFBq), Av. Duque de Caxias Norte, 225, Pirassununga, SP 13635-900, Brazil.
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