Inhibitors of the peptidoglycan biosynthesis enzymes MurA-F

M Hrast, I Sosič, R Šink, S Gobec - Bioorganic chemistry, 2014‏ - Elsevier
The widespread emergence of resistant bacterial strains is becoming a serious threat to
public health. This thus signifies the need for the development of new antibacterial agents …

Mur ligase inhibitors as anti-bacterials: a comprehensive review

JN Sangshetti, SS Joshi, RH Patil… - Current …, 2017‏ - ingentaconnect.com
Exploring a new target for antibacterial drug discovery has gained much attention because
of the emergence of Multidrug Resistance (MDR) strains of bacteria. To overcome this …

Identification mechanism of BACE1 on inhibitors probed by using multiple separate molecular dynamics simulations and comparative calculations of binding free …

Y Wang, F Yang, D Yan, Y Zeng, B Wei, J Chen, W He - Molecules, 2023‏ - mdpi.com
β-amyloid cleaving enzyme 1 (BACE1) is regarded as an important target of drug design
toward the treatment of Alzheimer's disease (AD). In this study, three separate molecular …

[HTML][HTML] Insights into the Interaction Mechanisms of Peptide and Non-Peptide Inhibitors with MDM2 Using Gaussian-Accelerated Molecular Dynamics Simulations and …

W Yang, J Wang, L Zhao, J Chen - Molecules, 2024‏ - mdpi.com
Inhibiting MDM2-p53 interaction is considered an efficient mode of cancer treatment. In our
current study, Gaussian-accelerated molecular dynamics (GaMD), deep learning (DL), and …

A challenging system: free energy prediction for factor Xa

HG Wallnoefer, KR Liedl, T Fox - Journal of Computational …, 2011‏ - Wiley Online Library
Factor Xa (fXa) is a promising target for antithrombotic drugs. Recently, we presented a
molecular dynamics study on fXa, which highlighted the need for a careful system setup to …

Prediction of potency of protease inhibitors using free energy simulations with polarizable quantum mechanics-based ligand charges and a hybrid water model

D Das, Y Koh, Y Tojo, AK Ghosh… - Journal of Chemical …, 2009‏ - ACS Publications
Reliable and robust prediction of the binding affinity for drug molecules continues to be a
daunting challenge. We simulated the binding interactions and free energy of binding of …

Molecular docking, molecular dynamics simulations, and free energy calculation insights into the binding mechanism between vs-4718 and focal adhesion kinase

M Shi, T Chen, S Wei, C Zhao, X Zhang, X Li… - ACS …, 2022‏ - ACS Publications
Focal adhesion kinase (FAK) is a 125 kDa nonreceptor tyrosine kinase that plays an
important role in many carcinomas. Thus, the targeting of FAK by small molecules is …

Theoretical studies on the susceptibility of oseltamivir against variants of 2009 A/H1N1 influenza neuraminidase

L Li, Y Li, L Zhang, T Hou - Journal of chemical information and …, 2012‏ - ACS Publications
The outbreak and high speed global spread of the new strain of influenza A/H1N1 virus in
2009 posed a serious threat to global health. It is more likely that drug-resistant influenza …

In silico discovery of 2-amino-4-(2, 4-dihydroxyphenyl) thiazoles as novel inhibitors of DNA gyrase B

M Brvar, A Perdih, M Oblak, LP Mašič… - Bioorganic & Medicinal …, 2010‏ - Elsevier
Cyclothialidines are a class of bacterial DNA gyrase B (GyrB) subunit inhibitors, targeting its
ATP-binding site. Starting from the available structural information on cyclothialidine …

[HTML][HTML] Unveiling Allosteric Regulation and Binding Mechanism of BRD9 through Molecular Dynamics Simulations and Markov Modeling

B Wang, J Wang, W Yang, L Zhao, B Wei, J Chen - Molecules, 2024‏ - mdpi.com
Bromodomain-containing protein 9 (BRD9) is a key player in chromatin remodeling and
gene expression regulation, and it is closely associated with the development of various …