Synthesis, molecular docking, and binding Gibbs free energy calculation of β-nitrostyrene derivatives: Potential inhibitors of SARS-CoV-2 3CL protease

Jia, Zejun; Lan, Xiao-Wei; Lü, Kui; Meng, Xuan; Jing, Wen-Jie; Jia, Shiru; Zhao, Kai; Dai, Yujie

doi:10.1016/j.molstruc.2023.135409

Cited by 9 publications

(1 citation statement)

References 68 publications

(32 reference statements)

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“…Among the various computational tools used for investigating inhibitor−protein binding, MD simulations [40][41][42][43][44][45][46], Gaussian accelerated molecular dynamics (GaMD) simulations [47][48][49] and binding free energy predictions [50][51][52][53][54] have been popular methods. Furthermore, conventional MD (cMD) and GaMD simulations were applied to successfully explore inhibitor-induced conformational changes [55][56][57][58][59].…”

Section: Introductionmentioning

confidence: 99%

Binding Mechanism of Inhibitors to BRD4 and BRD9 Decoded by Multiple Independent Molecular Dynamics Simulations and Deep Learning

Wang,

Yang,

Zhao

et al. 2024

Molecules

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Bromodomain 4 and 9 (BRD4 and BRD9) have been regarded as important targets of drug designs in regard to the treatment of multiple diseases. In our current study, molecular dynamics (MD) simulations, deep learning (DL) and binding free energy calculations are integrated to probe the binding modes of three inhibitors (H1B, JQ1 and TVU) to BRD4 and BRD9. The MD trajectory-based DL successfully identify significant functional function domains, such as BC-loop and ZA-loop. The information from the post-processing analysis of MD simulations indicates that inhibitor binding highly influences the structural flexibility and dynamic behavior of BRD4 and BRD9. The results of the MM-GBSA calculations not only suggest that the binding ability of H1B, JQ1 and TVU to BRD9 are stronger than to BRD4, but they also verify that van der Walls interactions are the primary forces responsible for inhibitor binding. The hot spots of BRD4 and BRD9 revealed by residue-based free energy estimation provide target sites of drug design in regard to BRD4 and BRD9. This work is anticipated to provide useful theoretical aids for the development of selective inhibitors over BRD family members.

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Section: Introductionmentioning

confidence: 99%

Binding Mechanism of Inhibitors to BRD4 and BRD9 Decoded by Multiple Independent Molecular Dynamics Simulations and Deep Learning

Wang,

Yang,

Zhao

et al. 2024

Molecules

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Kinetic Studies on Ruthenium(III) Chloride‐Catalyzed Oxidation of Benzyl and Homobenzyl Alcohols Using Cerium(IV) Sulfate under Acidic Medium

Yadav,

Srivastav,

Singh

et al. 2024

ChemistrySelect

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This study investigates the kinetics of oxidative conversion of benzyl and homobenzyl alcohols to carbonyls using cerium(IV) sulfate in the presence of ruthenium(III) complex under mild acidic conditions. The results revealed that the low concentration of both alcohols and cerium(IV) ions drives the reaction to a first‐order kinetics, whereas a higher concentration induces zero‐order kinetics. In addition, the kinetics of the reaction were altered by the additives of hydrogen ions, cerium(III) ions, and chloride ions. We hope this study will be helpful in understanding the reaction kinetics of the oxidation of primary alcohols.

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Potential anticancer agents of Curcuma aeruginosa-based kombucha: In vitro and in silico study

Hartati,

Kurnia,

Nafisah

et al. 2024

Food Chemistry Advances

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Synthesis, molecular docking, and binding Gibbs free energy calculation of β-nitrostyrene derivatives: Potential inhibitors of SARS-CoV-2 3CL protease

Cited by 9 publications

References 68 publications

Binding Mechanism of Inhibitors to BRD4 and BRD9 Decoded by Multiple Independent Molecular Dynamics Simulations and Deep Learning

Binding Mechanism of Inhibitors to BRD4 and BRD9 Decoded by Multiple Independent Molecular Dynamics Simulations and Deep Learning

Kinetic Studies on Ruthenium(III) Chloride‐Catalyzed Oxidation of Benzyl and Homobenzyl Alcohols Using Cerium(IV) Sulfate under Acidic Medium

Potential anticancer agents of Curcuma aeruginosa-based kombucha: In vitro and in silico study

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