ROC-guided virtual screening, molecular dynamics simulation, and bioactivity validation assessment Z195914464 as a 3CL Mpro inhibitor DOI

Xiongpiao Wei,

Min Li,

Yuanbiao Tu

et al.

Biophysical Chemistry, Journal Year: 2024, Volume and Issue: 317, P. 107357 - 107357

Published: Nov. 23, 2024

Language: Английский

Natural compounds inhibit Monkeypox virus methyltransferase VP39 in silico studies DOI
Quynh Mai Thai, Hường Thị Thu Phùng,

Ngoc Quynh Anh Pham

et al.

Journal of Biomolecular Structure and Dynamics, Journal Year: 2024, Volume and Issue: unknown, P. 1 - 9

Published: Feb. 28, 2024

VP39, an essential 2′-O-RNA methyltransferase enzyme discovered in Monkeypox virus (MPXV), plays a vital role viral RNA replication and transcription. Inhibition of the may prevent replication. In this context, using combination molecular docking dynamics (MDs) simulations, inhibitory ability NCI Diversity Set VII natural compounds to VP39 protein was investigated. It should be noted that computed binding free energy ligand via linear interaction (LIE) approaches are good agreement with corresponding experiments coefficients R=0.72 0.75, respectively. NSC 319990, 196515 376254 were demonstrated can inhibit MPVX similar affinity compared available inhibitor sinefungin. Moreover, nine residues involving Gln39, Gly68, Gly72, Asp95, Arg97, Val116, Asp138, Arg140 Asn156 argued they play important process inhibitors VP39.

Language: Английский

Citations

8
Alchemical approach performance in calculating the ligand-binding free energy DOI Creative Commons

Sơn Tùng Ngô,

Quynh Mai Thai, Trung Hai Nguyen

et al.

RSC Advances, Journal Year: 2024, Volume and Issue: 14(21), P. 14875 - 14885

Published: Jan. 1, 2024

FEP calculation performance depends on the considered targets.

Language: Английский

Citations

6
MedChemExpress compounds prevent neuraminidase N1 via physics- and knowledge-based methods DOI Creative Commons
Quynh Mai Thai, Trung Hai Nguyen, Hường Thị Thu Phùng

et al.

RSC Advances, Journal Year: 2024, Volume and Issue: 14(27), P. 18950 - 18956

Published: Jan. 1, 2024

MedChemExpress compounds prevent neuraminidase N1 via physics- and knowledge-based methods.

Language: Английский

Citations

5
Estimating AChE inhibitors from MCE database by machine learning and atomistic calculations DOI
Quynh Mai Thai, Trung Hai Nguyen, George Binh Lenon

et al.

Journal of Molecular Graphics and Modelling, Journal Year: 2024, Volume and Issue: 134, P. 108906 - 108906

Published: Nov. 14, 2024

Language: Английский

Citations

5
Key insights into recent advances and challenges in COVID-19 management DOI Creative Commons

Prakash Monika,

Anushka A. Poola,

Prithvi S. Prabhu

et al.

Deleted Journal, Journal Year: 2025, Volume and Issue: 22(1)

Published: Jan. 15, 2025

SARS-CoV-2 infection, commonly called COVID-19, has taken a jump from being rarely talked about to becoming household name. Making it history as the 5th global pandemic, this public health crisis millions of lives all over world. Right identification patient zero, pandemic unfolded in waves triggering domino effect that impacted aspects life. Global efforts have been underway combat and minimize its repercussions, resulting development efficient vaccines drugs treat disease control spread infection. However, making benefits these available everyone walking path towards end remains challenge. Keeping view, review intends present summary sequential recent advancements field diagnostics treatment, challenges continue remain overcoming crisis. It can be understood task controlling managing impact such massive goes well beyond boundaries what present-day technology medicine care offer. A collaborative integrative approach between academic, scientific, social, economic factors, along with close supervision reinforcement current safety protocols, help ensure better management strategy progression COVID-19.

Language: Английский

Citations

0
Upgrading nirmatrelvir to inhibit SARS-CoV-2 Mpro via DeepFrag and free energy calculations DOI Creative Commons
Nguyễn Minh Tâm, Trung Hai Nguyen, Phạm Minh Quân

et al.

Journal of Molecular Graphics and Modelling, Journal Year: 2023, Volume and Issue: 124, P. 108535 - 108535

Published: June 1, 2023

Language: Английский

Citations

9
Machine learning combines atomistic simulations to predict SARS-CoV-2 Mpro inhibitors from natural compounds DOI Open Access
Trung Hai Nguyen, Quynh Mai Thai, Phạm Minh Quân

et al.

Molecular Diversity, Journal Year: 2023, Volume and Issue: 28(2), P. 553 - 561

Published: Feb. 24, 2023

Language: Английский

Citations

8
QMrebind: incorporating quantum mechanical force field reparameterization at the ligand binding site for improved drug-target kinetics through milestoning simulations DOI Creative Commons
Anupam Anand Ojha, Lane Votapka, Rommie E. Amaro

et al.

Chemical Science, Journal Year: 2023, Volume and Issue: 14(45), P. 13159 - 13175

Published: Jan. 1, 2023

Graphical representation of the partition phase-space receptor (grey)-ligand (yellow) complex into MD region (further partitioned Voronoi cells) and BD region.

Language: Английский

Citations

7
Exploring the covalent inhibition mechanisms of inhibitors with two different warheads acting on SARS-CoV-2 Mpro by QM/MM simulations DOI
Xiaoyue Yang,

Mengguo Chen,

Fanru Yuan

et al.

Computational and Theoretical Chemistry, Journal Year: 2024, Volume and Issue: 1242, P. 114979 - 114979

Published: Nov. 5, 2024

Language: Английский

Citations

0
ROC-guided virtual screening, molecular dynamics simulation, and bioactivity validation assessment Z195914464 as a 3CL Mpro inhibitor DOI

Xiongpiao Wei,

Min Li,

Yuanbiao Tu

et al.

Biophysical Chemistry, Journal Year: 2024, Volume and Issue: 317, P. 107357 - 107357

Published: Nov. 23, 2024

Language: Английский

Citations

0