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da Costa APL, Cardoso FJB, Molfetta FAD. An in silico molecular modeling approach of halolactone derivatives as potential inhibitors for human immunodeficiency virus type-1 reverse transcriptase enzyme. J Biomol Struct Dyn 2023; 41:1715-1729. [PMID: 34996334 DOI: 10.1080/07391102.2021.2024256] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Acquired Immune Deficiency Syndrome (AIDS) is an infectious disease caused by Human Immunodeficiency Virus (HIV) infection and its replication requires the Reverse Transcriptase (RT) enzyme. RT plays a key role in the HIV life cycle, making it one of the most important targets for designing new drugs. Thus, in order to increase therapeutic options against AIDS, halolactone derivatives (D-halolactone) that have been showed as potential non-nucleoside inhibitors of the RT enzyme were studied. In the present work, a series of D-halolactone were investigated by molecular modeling studies, combining Three-dimensional Quantitative Structure-Activity Relationship (3 D-QSAR), molecular docking and Molecular Dynamics (MD) techniques, to understand the molecular characteristics that promote biological activity. The internal and external validation parameters indicated that the 3 D-QSAR model has good predictive capacity and statistical significance. Contour maps provided useful information on the structural characteristics of compounds for anti-HIV-1 activity. The docking results showed that D-halolactone present good complementarity by the RT allosteric site. In MD simulations it was observed that the formation of enzyme-ligand complexes were favorable, and from the free energy decomposition it was found that Leu100, Val106, Tyr181, Try188, and Trp229 are key residues for stabilization in the enzymatic site. Thus, the results showed that the proposed models can be used to design promising HIV-1 RT inhibitors. Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Ana Paula Lima da Costa
- Laboratório de Modelagem Molecular, Instituto de Ciências Exatas e Naturais, Universidade Federal do Pará, Belém, Pará, Brazil
| | - Fábio José Bonfim Cardoso
- Laboratório de Modelagem Molecular, Instituto de Ciências Exatas e Naturais, Universidade Federal do Pará, Belém, Pará, Brazil
| | - Fábio Alberto de Molfetta
- Laboratório de Modelagem Molecular, Instituto de Ciências Exatas e Naturais, Universidade Federal do Pará, Belém, Pará, Brazil
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Li Y, Liu S, Wang J, Rui X, Tian H, Li C, Guo C. In Silico Studies of Piperidine Derivatives as Protein Kinase B Inhibitors
through 3D-QSAR, Molecular Docking and Molecular Dynamics Simulation. LETT DRUG DES DISCOV 2022. [DOI: 10.2174/1570180818666211207105516] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Background:
Protein kinase B (Akt) is a serine/threonine-protein kinase that drives the diverse
physiological process. Akt is a promising therapeutic target, which involves cancer cell growth, survival,
proliferation and metabolism.
Objective:
The study aims to design highly active Akt inhibitors, and to elucidate the structural requirements
for their biological activity, we analyzed the key binding features and summarized the structural
determinants for their bioactivities.
Methods:
A series of piperidine derivatives have been investigated employing three-dimensional quantitative
structure-activity relationship (3D-QSAR), molecular docking and molecular dynamics simulation.
Results:
The statistics of the comparative molecular field analysis (CoMFA) model (Q2=0.631, R2=0.951)
and the comparative molecular similarity index analysis (CoMSIA) model (Q2=0.663, R2=0.966) indicated
that our 3D-QSAR model was accurate and reliable. Besides, the stability of receptor-ligand interactions
under physiological conditions was then evaluated by molecular dynamics simulation, in agreement
with the molecular docking results.
Conclusion:
Our study provided valuable insights for the discovery of potent Akt inhibitors.
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Affiliation(s)
- Yaxin Li
- Department of Pharmacy, Hebei North University, Zhangjiakou 075000, P.R. China
- Hebei Key Laboratory of Neuropharmacology,
Hebei North University, Zhangjiakou 075000, P.R. China
| | - Sisi Liu
- Department of Pharmacy, Hebei North University, Zhangjiakou 075000, P.R. China
- Hebei Key Laboratory of Neuropharmacology,
Hebei North University, Zhangjiakou 075000, P.R. China
| | - Jin Wang
- Department of Pharmacy, Hebei North University, Zhangjiakou 075000, P.R. China
- Hebei Key Laboratory of Neuropharmacology,
Hebei North University, Zhangjiakou 075000, P.R. China
| | - Xue Rui
- Department of Pharmacy, Hebei North University, Zhangjiakou 075000, P.R. China
| | - Haobo Tian
- Department of Pharmacy, Hebei North University, Zhangjiakou 075000, P.R. China
| | - Chenshuo Li
- Department of Pharmacy, Hebei North University, Zhangjiakou 075000, P.R. China
| | - Chunyan Guo
- Department of Pharmacy, Hebei North University, Zhangjiakou 075000, P.R. China
- Hebei Key Laboratory of Neuropharmacology,
Hebei North University, Zhangjiakou 075000, P.R. China
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