Cargando…

Exploring potential SARS-CoV-2 Mpro non-covalent inhibitors through docking, pharmacophore profile matching, molecular dynamic simulation, and MM-GBSA

CONTEXT: In the replication of SARS-CoV-2, the main protease (Mpro/3CLpro) is significant. It is conserved in a number of novel coronavirus variations, and no known human proteases share its cleavage sites. Therefore, 3CLpro is an ideal target. In the report, we screened five potential inhibitors (1...

Descripción completa

Detalles Bibliográficos
Autores principales:	Shi, Yunfan, Dong, Liting, Ju, Zhuang, Li, Qiufu, Cui, Yanru, Liu, Yiran, He, Jiaoyu, Ding, Xianping
Formato:	Online Artículo Texto
Lenguaje:	English
Publicado:	Springer Berlin Heidelberg 2023
Materias:	Original Paper
Acceso en línea:	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10100623/ https://www.ncbi.nlm.nih.gov/pubmed/37055578 http://dx.doi.org/10.1007/s00894-023-05534-3

Ejemplares similares

Study of the Differential Activity of Thrombin Inhibitors Using Docking, QSAR, Molecular Dynamics, and MM-GBSA
por: Mena-Ulecia, Karel, et al.
Publicado: (2015)

A Comprehensive Docking and MM/GBSA Rescoring Study of Ligand Recognition upon Binding Antithrombin
por: Zhang, Xiaohua, et al.
Publicado: (2017)

The MM/PBSA and MM/GBSA methods to estimate ligand-binding affinities
por: Genheden, Samuel, et al.
Publicado: (2015)

Effect of nelfinavir stereoisomers on coronavirus main protease: Molecular docking, molecular dynamics simulation and MM/GBSA study
por: Sargolzaei, Mohsen
Publicado: (2021)

HawkDock: a web server to predict and analyze the protein–protein complex based on computational docking and MM/GBSA
por: Weng, Gaoqi, et al.
Publicado: (2019)

Binding-affinity predictions of HSP90 in the D3R Grand Challenge 2015 with docking, MM/GBSA, QM/MM, and free-energy simulations
por: Misini Ignjatović, Majda, et al.
Publicado: (2016)

The polymorphism analysis and epitope predicted of Alphapapillomavirus 9 E6 in Sichuan, China
por: He, Jiaoyu, et al.
Publicado: (2022)

The genetic variability, phylogeny and functional significance of E6, E7 and LCR in human papillomavirus type 52 isolates in Sichuan, China
por: Song, Zhilin, et al.
Publicado: (2021)

Targeting SARS-CoV-2 main protease by teicoplanin: A mechanistic insight by docking, MM/GBSA and molecular dynamics simulation
por: Azam, Faizul, et al.
Publicado: (2021)

Modeling Peptide Nucleic Acid Binding Enthalpies Using MM-GBSA
por: Goodman, Jack, et al.
Publicado: (2022)

Identification of potential human pancreatic α-amylase inhibitors from natural products by molecular docking, MM/GBSA calculations, MD simulations, and ADMET analysis
por: Basnet, Santosh, et al.
Publicado: (2023)

Identification of natural inhibitors against angiotensin I converting enzyme for cardiac safety using induced fit docking and MM-GBSA studies
por: Vijayakumar, Balakrishnan, et al.
Publicado: (2014)

Predicting mutations deleterious to function in beta-lactamase TEM1 using MM-GBSA
por: Negron, Christopher, et al.
Publicado: (2019)

Protease inhibition, in vitro antibacterial and IFD/MM-GBSA studies of ciprofloxacin-based acetanilides
por: Akhtar, Rabia, et al.
Publicado: (2023)

Discovery of anti-MERS-CoV small covalent inhibitors through pharmacophore modeling, covalent docking and molecular dynamics simulation
por: Alamri, Mubarak A., et al.
Publicado: (2021)

From Myricetin to the Discovery of Novel Natural Human ENPP1 Inhibitors: A Virtual Screening, Molecular Docking, Molecular Dynamics Simulation, and MM/GBSA Study
por: Song, Shaohan, et al.
Publicado: (2022)

Assessing the performance of MM/PBSA and MM/GBSA methods. 8. Predicting binding free energies and poses of protein–RNA complexes
por: Chen, Fu, et al.
Publicado: (2018)

Genetic variability of human papillomavirus type 39 based on E6, E7 and L1 genes in Southwest China
por: He, Jiaoyu, et al.
Publicado: (2021)

Molecular docking of substituted pteridinones and pyrimidines to the ATP-binding site of the N-terminal domain of RSK2 and associated MM/GBSA and molecular field datasets
por: Casalvieri, Kimberly A., et al.
Publicado: (2020)

Insight into the LFA-1/SARS-CoV-2 Orf7a Complex by Protein–Protein Docking, Molecular Dynamics, and MM-GBSA Calculations
por: Ongaro, Alberto, et al.
Publicado: (2021)

Investigation of nonsynonymous mutations in the spike protein of SARS-CoV-2 and its interaction with the ACE2 receptor by molecular docking and MM/GBSA approach
por: Aljindan, Reem Y., et al.
Publicado: (2021)

A chromosome-level genome assembly of Artocarpus nanchuanensis (Moraceae), an extremely endangered fruit tree
por: He, Jiaoyu, et al.
Publicado: (2022)

Probing Origin of Binding Difference of inhibitors to MDM2 and MDMX by Polarizable Molecular Dynamics Simulation and QM/MM-GBSA Calculation
por: Chen, Jianzhong, et al.
Publicado: (2015)

Drug repurposing against main protease and RNA-dependent RNA polymerase of SARS-CoV-2 using molecular docking, MM-GBSA calculations and molecular dynamics
por: Mohammed, Ahmed O., et al.
Publicado: (2022)

Prediction of potential inhibitors of the dimeric SARS-CoV2 main proteinase through the MM/GBSA approach
por: Bello, Martiniano
Publicado: (2020)

Study of the Affinity between the Protein Kinase PKA and Peptide Substrates Derived from Kemptide Using Molecular Dynamics Simulations and MM/GBSA
por: Mena-Ulecia, Karel, et al.
Publicado: (2014)

Identification of saquinavir as a potent inhibitor of dimeric SARS-CoV2 main protease through MM/GBSA
por: Bello, Martiniano, et al.
Publicado: (2020)

PharmDock: a pharmacophore-based docking program
por: Hu, Bingjie, et al.
Publicado: (2014)

Multi-target potential of Indian phytochemicals against SARS-CoV-2: A docking, molecular dynamics and MM-GBSA approach extended to Omicron B.1.1.529.
por: Roshni, Jency, et al.
Publicado: (2022)

Molecular dynamics simulations and MM-GBSA reveal novel guanosine derivatives against SARS-CoV-2 RNA dependent RNA polymerase
por: Elfiky, Abdo A., et al.
Publicado: (2022)

Pharmacophore-Based Similarity Scoring for DOCK
por: Jiang, Lingling, et al.
Publicado: (2014)

MM/GBSA prediction of relative binding affinities of carbonic anhydrase inhibitors: effect of atomic charges and comparison with Autodock4(Zn)
por: Taylor, Mackenzie, et al.
Publicado: (2023)

Search for the Pharmacophore of Histone Deacetylase Inhibitors Using Pharmacophore Query and Docking Study
por: Haji Agha Bozorgi, Atefeh, et al.
Publicado: (2014)

Using Chou’s 5-steps rule to study pharmacophore-based virtual screening of SARS-CoV-2 Mpro inhibitors
por: Pundir, Hemlata, et al.
Publicado: (2020)

Deciphering Selectivity Mechanism of BRD9 and TAF1(2) toward Inhibitors Based on Multiple Short Molecular Dynamics Simulations and MM-GBSA Calculations
por: Wang, Lifei, et al.
Publicado: (2023)

Exploring Covalent Docking Mechanisms of Boron-Based Inhibitors to Class A, C and D β-Lactamases Using Time-dependent Hybrid QM/MM Simulations
por: Charzewski, Łukasz, et al.
Publicado: (2021)

Binding Selectivity of Inhibitors toward Bromodomains BAZ2A and BAZ2B Uncovered by Multiple Short Molecular Dynamics Simulations and MM-GBSA Calculations
por: Wang, Lifei, et al.
Publicado: (2021)

Discovery of a Selective 6-Hydroxy-1, 4-Diazepan-2-one Containing Butyrylcholinesterase Inhibitor by Virtual Screening and MM-GBSA Rescoring
por: Zhou, You, et al.
Publicado: (2020)

Marine-Derived Compounds for CDK5 Inhibition in Cancer: Integrating Multi-Stage Virtual Screening, MM/GBSA Analysis and Molecular Dynamics Investigations
por: Shoaib, Tagyedeen H., et al.
Publicado: (2023)

CovalentDock Cloud: a web server for automated covalent docking
por: Ouyang, Xuchang, et al.
Publicado: (2013)

Cannot write session to /tmp/vufind_sessions/sess_4eap98co1s8934hh3189damkuv