Cargando…

Discovery of small molecule PLpro inhibitor against COVID-19 using structure-based virtual screening, molecular dynamics simulation, and molecular mechanics/Generalized Born surface area (MM/GBSA) calculation

COVID-19 is spreading in a global pandemic that is endangering human life and health. Therefore, there is an urgent need to target COVID-19 to find effective treatments for this emerging acute respiratory infection. Viral Papain-Like cysteine protease (PLpro), similar to papain and the cysteine deub...

Descripción completa

Detalles Bibliográficos
Autores principales:	Pang, Jie, Gao, Shan, Sun, Zengxian, Yang, Guangsheng
Formato:	Online Artículo Texto
Lenguaje:	English
Publicado:	Springer US 2020
Materias:	Original Research
Acceso en línea:	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7578240/ https://www.ncbi.nlm.nih.gov/pubmed/33106741 http://dx.doi.org/10.1007/s11224-020-01665-y

Ejemplares similares

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)

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)

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

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

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)

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)

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

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)

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)

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)

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)

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)

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

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)

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)

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)

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)

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)

Exploring potential SARS-CoV-2 Mpro non-covalent inhibitors through docking, pharmacophore profile matching, molecular dynamic simulation, and MM-GBSA
por: Shi, Yunfan, et al.
Publicado: (2023)

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)

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

Insights into the Interaction Mechanisms of the Proviral Integration Site of Moloney Murine Leukemia Virus (Pim) Kinases with Pan-Pim Inhibitors PIM447 and AZD1208: A Molecular Dynamics Simulation and MM/GBSA Calculation Study
por: Chen, Qingqing, et al.
Publicado: (2019)

Repurposing the antibacterial drugs for inhibition of SARS-CoV2-PLpro using molecular docking, MD simulation and binding energy calculation
por: Patel, Rohit, et al.
Publicado: (2021)

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)

In-silico molecular modelling, MM/GBSA binding free energy and molecular dynamics simulation study of novel pyrido fused imidazo[4,5-c]quinolines as potential anti-tumor agents
por: Dasmahapatra, Upala, et al.
Publicado: (2022)

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)

Interactions between DC-SIGN and the envelope protein from Dengue and Zika viruses: a structural perspective based on molecular dynamics and MM/GBSA analyses
por: Menechino, Bruno Stein Barbosa, et al.
Publicado: (2023)

Seq12, Seq12m, and Seq13m, peptide analogues of the spike glycoprotein shows antiviral properties against SARS-CoV-2: An in silico study through molecular docking, molecular dynamics simulation, and MM-PB/GBSA calculations
por: Dutta, Kunal, et al.
Publicado: (2021)

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

An Effective MM/GBSA Protocol for Absolute Binding Free Energy Calculations: A Case Study on SARS-CoV-2 Spike Protein and the Human ACE2 Receptor †
por: Forouzesh, Negin, et al.
Publicado: (2021)

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

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)

Ligand-Based Virtual Screening, Molecular Docking, Molecular Dynamics, and MM-PBSA Calculations towards the Identification of Potential Novel Ricin Inhibitors
por: Botelho, Fernanda D., et al.
Publicado: (2020)

Identification of Novel Potential β-N-Acetyl-D-Hexosaminidase Inhibitors by Virtual Screening, Molecular Dynamics Simulation and MM-PBSA Calculations
por: Liu, Jianling, et al.
Publicado: (2012)

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)

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)

Pharmacotherapeutic Potential of Natural Products to Target the SARS-CoV-2 PLpro Using Molecular Screening and Simulation Approaches
por: Sayaf, Abrar Mohammad, 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)

Tomatidine and Patchouli Alcohol as Inhibitors of SARS-CoV-2 Enzymes (3CLpro, PLpro and NSP15) by Molecular Docking and Molecular Dynamics Simulations
por: Zrieq, Rafat, et al.
Publicado: (2021)

Cannot write session to /tmp/vufind_sessions/sess_43kkl12orc22rb4kp2bfsd3vgn