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Qiu X, Zhang Q, Li Z, Zhang J, Liu H. Revealing the Interaction Mechanism between Mycobacterium tuberculosis GyrB and Novobiocin, SPR719 through Binding Thermodynamics and Dissociation Kinetics Analysis. Int J Mol Sci 2024; 25:3764. [PMID: 38612573 PMCID: PMC11011931 DOI: 10.3390/ijms25073764] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2024] [Revised: 03/22/2024] [Accepted: 03/24/2024] [Indexed: 04/14/2024] Open
Abstract
With the rapid emergence of drug-resistant strains of Mycobacterium tuberculosis (Mtb), various levels of resistance against existing anti-tuberculosis (TB) drugs have developed. Consequently, the identification of new anti-TB targets and drugs is critically urgent. DNA gyrase subunit B (GyrB) has been identified as a potential anti-TB target, with novobiocin and SPR719 proposed as inhibitors targeting GyrB. Therefore, elucidating the molecular interactions between GyrB and its inhibitors is crucial for the discovery and design of efficient GyrB inhibitors for combating multidrug-resistant TB. In this study, we revealed the detailed binding mechanisms and dissociation processes of the representative inhibitors, novobiocin and SPR719, with GyrB using classical molecular dynamics (MD) simulations, tau-random acceleration molecular dynamics (τ-RAMD) simulations, and steered molecular dynamics (SMD) simulations. Our simulation results demonstrate that both electrostatic and van der Waals interactions contribute favorably to the inhibitors' binding to GyrB, with Asn52, Asp79, Arg82, Lys108, Tyr114, and Arg141 being key residues for the inhibitors' attachment to GyrB. The τ-RAMD simulations indicate that the inhibitors primarily dissociate from the ATP channel. The SMD simulation results reveal that both inhibitors follow a similar dissociation mechanism, requiring the overcoming of hydrophobic interactions and hydrogen bonding interactions formed with the ATP active site. The binding and dissociation mechanisms of GyrB with inhibitors novobiocin and SPR719 obtained in our work will provide new insights for the development of promising GyrB inhibitors.
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Affiliation(s)
- Xiaofei Qiu
- School of Pharmacy, Lanzhou University, Lanzhou 730000, China; (X.Q.); (Z.L.); (J.Z.)
| | - Qianqian Zhang
- Faculty of Applied Science, Macao Polytechnic University, Macao SAR, China;
| | - Zhaoguo Li
- School of Pharmacy, Lanzhou University, Lanzhou 730000, China; (X.Q.); (Z.L.); (J.Z.)
| | - Juan Zhang
- School of Pharmacy, Lanzhou University, Lanzhou 730000, China; (X.Q.); (Z.L.); (J.Z.)
| | - Huanxiang Liu
- Faculty of Applied Science, Macao Polytechnic University, Macao SAR, China;
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Benny S, Rajappan Krishnendu P, Kumar S, Bhaskar V, Manisha DS, Abdelgawad MA, Ghoneim MM, Naguib IA, Pappachen LK, Mary Zachariah S, Mathew B, Tp A. A computational investigation of thymidylate synthase inhibitors through a combined approach of 3D-QSAR and pharmacophore modelling. J Biomol Struct Dyn 2023:1-20. [PMID: 37870113 DOI: 10.1080/07391102.2023.2270752] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Accepted: 08/03/2023] [Indexed: 10/24/2023]
Abstract
Thymidylate synthase (TS) is a crucial target of cancer drug discovery and is mainly involved in the De novo synthesis of the DNA precursor thymine. In the present study, to generate reliable models and identify a few promising molecules, we combined QSAR modelling with the pharmacophore hypothesis-generating technique. Input molecules were clustered on their similarity, and a cluster of 74 molecules with a pyrimidine moiety was chosen as the set for 3D-QSAR and pharmacophore modelling. Atom-based and field-based 3D-QSAR models were generated and statistically validated with R2 > 0.90 and Q2 > 0.75. The common pharmacophore hypothesis(CPH) generation identified the best six-point model ADHRRR. Using these best models, a library of FDA-approved drugs was screened for activity and filtered via molecular docking, ADME profiling, and molecular dynamics simulations. The top ten promising TS-inhibiting candidates were identified, and their chemical features profitable for TS inhibitors were explored.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Sonu Benny
- Department of Pharmaceutical Chemistry, Amrita School of Pharmacy, Amrita Vishwa Vidyapeetham, AIMS Health Sciences Campus, Kochi, Kerala, India
| | - Prayaga Rajappan Krishnendu
- Department of Pharmaceutical Chemistry, Amrita School of Pharmacy, Amrita Vishwa Vidyapeetham, AIMS Health Sciences Campus, Kochi, Kerala, India
| | - Sunil Kumar
- Department of Pharmaceutical Chemistry, Amrita School of Pharmacy, Amrita Vishwa Vidyapeetham, AIMS Health Sciences Campus, Kochi, Kerala, India
| | - Vaishnav Bhaskar
- Department of Pharmaceutical Chemistry, Amrita School of Pharmacy, Amrita Vishwa Vidyapeetham, AIMS Health Sciences Campus, Kochi, Kerala, India
| | - Deepthi S Manisha
- Department of Pharmaceutical Chemistry, Amrita School of Pharmacy, Amrita Vishwa Vidyapeetham, AIMS Health Sciences Campus, Kochi, Kerala, India
| | - Mohamed A Abdelgawad
- Department of pharmaceutical chemistry, College of Pharmacy, Jouf University, Sakaka, Saudi Arabia
- Department of Pharmaceutical Organic Chemistry, Faculty of Pharmacy, Beni-Suef University, Beni-Suef, Egypt
| | - Mohammed M Ghoneim
- Department of Pharmacy Practice, College of Pharmacy, AlMaarefa University, Saudi Arabia
| | - Ibrahim A Naguib
- Department of Pharmaceutical Chemistry, College of Pharmacy, Taif University, Taif, Saudi Arabia
| | - Leena K Pappachen
- Department of Pharmaceutical Chemistry, Amrita School of Pharmacy, Amrita Vishwa Vidyapeetham, AIMS Health Sciences Campus, Kochi, Kerala, India
| | - Subin Mary Zachariah
- Department of Pharmaceutical Chemistry, Amrita School of Pharmacy, Amrita Vishwa Vidyapeetham, AIMS Health Sciences Campus, Kochi, Kerala, India
| | - Bijo Mathew
- Department of Pharmaceutical Chemistry, Amrita School of Pharmacy, Amrita Vishwa Vidyapeetham, AIMS Health Sciences Campus, Kochi, Kerala, India
| | - Aneesh Tp
- Department of Pharmaceutical Chemistry, Amrita School of Pharmacy, Amrita Vishwa Vidyapeetham, AIMS Health Sciences Campus, Kochi, Kerala, India
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Albino SL, da Silva Moura WC, dos Reis MML, Sousa GLS, da Silva PR, de Oliveira MGC, Borges TKDS, Albuquerque LFF, de Almeida SMV, de Lima MDCA, Kuckelhaus SAS, Nascimento IJDS, Junior FJBM, da Silva TG, de Moura RO. ACW-02 an Acridine Triazolidine Derivative Presents Antileishmanial Activity Mediated by DNA Interaction and Immunomodulation. Pharmaceuticals (Basel) 2023; 16:204. [PMID: 37259353 PMCID: PMC9967605 DOI: 10.3390/ph16020204] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2022] [Revised: 01/26/2023] [Accepted: 01/27/2023] [Indexed: 03/11/2024] Open
Abstract
The present study proposed the synthesis of a novel acridine derivative not yet described in the literature, chemical characterization by NMR, MS, and IR, followed by investigations of its antileishmanial potential. In vitro assays were performed to assess its antileishmanial activity against L. amazonensis strains and cytotoxicity against macrophages through MTT assay and annexin V-FITC/PI, and the ability to perform an immunomodulatory action using CBA. To investigate possible molecular targets, its interaction with DNA in vitro and in silico targets were evaluated. As results, the compound showed good antileishmanial activity, with IC50 of 6.57 (amastigotes) and 94.97 (promastigotes) µg mL-1, associated with non-cytotoxicity to macrophages (CC50 > 256.00 µg mL-1). When assessed by flow cytometry, 99.8% of macrophages remained viable. The compound induced an antileishmanial effect in infected macrophages and altered TNF-α, IL-10 and IL-6 expression, suggesting a slight immunomodulatory activity. DNA assay showed an interaction with the minor grooves due to the hyperchromic effect of 47.53% and Kb 1.17 × 106 M-1, and was sustained by docking studies. Molecular dynamics simulations and MM-PBSA calculations propose cysteine protease B as a possible target. Therefore, this study demonstrates that the new compound is a promising molecule and contributes as a model for future works.
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Affiliation(s)
- Sonaly Lima Albino
- Programa de Pós Graduação em Inovação Terapêutica, Universidade Federal de Pernambuco, Recife 50670-901, Brazil
- Laboratório de Desenvolvimento e Síntese de Fármacos, Departamento de Farmácia, Universidade Estadual da Paraíba, Campina Grande 58429-500, Brazil
- Programa de Pós Graduação em Ciências Farmacêuticas, Universidade Estadual da Paraíba, Campina Grande 58429-500, Brazil
| | - Willian Charles da Silva Moura
- Laboratório de Desenvolvimento e Síntese de Fármacos, Departamento de Farmácia, Universidade Estadual da Paraíba, Campina Grande 58429-500, Brazil
- Programa de Pós Graduação em Ciências Farmacêuticas, Universidade Estadual da Paraíba, Campina Grande 58429-500, Brazil
| | - Malu Maria Lucas dos Reis
- Laboratório de Desenvolvimento e Síntese de Fármacos, Departamento de Farmácia, Universidade Estadual da Paraíba, Campina Grande 58429-500, Brazil
| | - Gleyton Leonel Silva Sousa
- Laboratório de Desenvolvimento e Síntese de Fármacos, Departamento de Farmácia, Universidade Estadual da Paraíba, Campina Grande 58429-500, Brazil
- Programa de Pós Graduação em Química, Universidade Federal Rural do Rio de Janeiro, Seropédica 23890-000, Brazil
| | - Pablo Rayff da Silva
- Programa de Pós Graduação em Produtos Naturais, Sintéticos e Bioativos, Universidade Federal da Paraiba, João Pessoa 58051-900, Brazil
| | | | - Tatiana Karla dos Santos Borges
- Laboratório de Imunologia Celular, Área de Patologia, Faculdade de Medicina, Campus Darcy Ribeiro, Brasília 70910-900, Brazil
| | - Lucas Fraga Friaça Albuquerque
- Laboratório de Imunologia Celular, Área de Patologia, Faculdade de Medicina, Campus Darcy Ribeiro, Brasília 70910-900, Brazil
| | | | - Maria do Carmo Alves de Lima
- Laboratório de Química e Inovação Terapêutica, Departamento de Antibióticos, Universidade Federal de Pernambuco, Recife 50670-901, Brazil
| | - Selma Aparecida Souza Kuckelhaus
- Área de Morfologia, Faculdade de Medicina—UnB, Universidade de Brasília, Campus Darcy Ribeiro/Asa Norte, Brasília 70910-900, Brazil
| | - Igor José dos Santos Nascimento
- Laboratório de Desenvolvimento e Síntese de Fármacos, Departamento de Farmácia, Universidade Estadual da Paraíba, Campina Grande 58429-500, Brazil
- Programa de Pós Graduação em Ciências Farmacêuticas, Universidade Estadual da Paraíba, Campina Grande 58429-500, Brazil
| | | | | | - Ricardo Olímpio de Moura
- Laboratório de Desenvolvimento e Síntese de Fármacos, Departamento de Farmácia, Universidade Estadual da Paraíba, Campina Grande 58429-500, Brazil
- Programa de Pós Graduação em Ciências Farmacêuticas, Universidade Estadual da Paraíba, Campina Grande 58429-500, Brazil
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Dos Santos Nascimento IJ, da Silva Rodrigues ÉE, da Silva MF, de Araújo-Júnior JX, de Moura RO. Advances in Computational Methods to Discover New NS2B-NS3 Inhibitors Useful Against Dengue and Zika Viruses. Curr Top Med Chem 2022; 22:2435-2462. [PMID: 36415099 DOI: 10.2174/1568026623666221122121330] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Revised: 09/20/2022] [Accepted: 09/27/2022] [Indexed: 11/24/2022]
Abstract
The Flaviviridae virus family consists of the genera Hepacivirus, Pestivirus, and Flavivirus, with approximately 70 viral types that use arthropods as vectors. Among these diseases, dengue (DENV) and zika virus (ZIKV) serotypes stand out, responsible for thousands of deaths worldwide. Due to the significant increase in cases, the World Health Organization (WHO) declared DENV a potential threat for 2019 due to being transmitted by infected travelers. Furthermore, ZIKV also has a high rate of transmissibility, highlighted in the outbreak in 2015, generating consequences such as Guillain-Barré syndrome and microcephaly. According to clinical outcomes, those infected with DENV can be asymptomatic, and in other cases, it can be lethal. On the other hand, ZIKV has severe neurological symptoms in newborn babies and adults. More serious symptoms include microcephaly, brain calcifications, intrauterine growth restriction, and fetal death. Despite these worrying data, no drug or vaccine is approved to treat these diseases. In the drug discovery process, one of the targets explored against these diseases is the NS2B-NS3 complex, which presents the catalytic triad His51, Asp75, and Ser135, with the function of cleaving polyproteins, with specificity for basic amino acid residues, Lys- Arg, Arg-Arg, Arg-Lys or Gln-Arg. Since NS3 is highly conserved in all DENV serotypes and plays a vital role in viral replication, this complex is an excellent drug target. In recent years, computer-aided drug discovery (CADD) is increasingly essential in drug discovery campaigns, making the process faster and more cost-effective, mainly explained by discovering new drugs against DENV and ZIKV. Finally, the main advances in computational methods applied to discover new compounds against these diseases will be presented here. In fact, molecular dynamics simulations and virtual screening is the most explored approach, providing several hit and lead compounds that can be used in further optimizations. In addition, fragment-based drug design and quantum chemistry/molecular mechanics (QM/MM) provides new insights for developing anti-DENV/ZIKV drugs. We hope that this review offers further helpful information for researchers worldwide and stimulates the use of computational methods to find a promising drug for treating DENV and ZIKV.
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Affiliation(s)
- Igor José Dos Santos Nascimento
- Department of Pharmacy, Estácio of Alagoas College, Maceió, Brazil.,Department of Pharmacy, Cesmac University Center, Maceió, Brazil.,Department of Pharmacy, Drug Development and Synthesis Laboratory, State University of Paraíba, Campina Grande, Brazil
| | | | - Manuele Figueiredo da Silva
- Laboratory of Medicinal Chemistry, Pharmaceutical Sciences Institute, Federal University of Alagoas, Maceió, Brazil
| | - João Xavier de Araújo-Júnior
- Laboratory of Medicinal Chemistry, Pharmaceutical Sciences Institute, Federal University of Alagoas, Maceió, Brazil
| | - Ricardo Olimpio de Moura
- Department of Pharmacy, Drug Development and Synthesis Laboratory, State University of Paraíba, Campina Grande, Brazil
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