Site-directed mutagenesis (P61G) of copper, zinc superoxide dismutase enhances its kinetic properties and tolerance to inactivation by H2O2

Kumar, Sachin; Bhardwaj, Vijay Kumar; Kaachra, Anish; Guleria, Shweta; Kumar, Arun; Purohit, Rituraj; Kumar, Sanjay

doi:10.1016/j.plaphy.2021.09.041

Cited by 8 publications

(7 citation statements)

References 40 publications

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“…Molecular docking is a key strategy to predict the protein–ligand affinity. Molecular docking generates the receptor–ligand poses and ranks them based on their interaction energy 40–42 . The DS software was used for the analysis of the interaction energy and binding poses between DENV‐2 C and DSPD molecules along with the standard inhibitor ST‐148.…”

Section: Resultsmentioning

confidence: 99%

“…Molecular docking generates the receptor-ligand poses and ranks them based on their interaction energy. [40][41][42] The DS software was used for the analysis of the interaction energy and binding poses between DENV-2 C and DSPD molecules along with the standard inhibitor ST-148. We obtained a low CDOCKER interaction energy for DSPD-DENV-2 C complexes ranging from −50.21 to −55.60 kcal/mol (Table S1).…”

Section: Interaction Of Selected Molecules With Denv-2 C Proteinmentioning

confidence: 99%

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Identification of acridinedione scaffolds as potential inhibitor of DENV‐2 C protein: An in silico strategy to combat dengue

Kumar

Bhardwaj

Singh

et al. 2022

J of Cellular Biochemistry

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Dengue is a prominent viral disease transmitted by mosquitoes to humans that affects mainly tropical and subtropical countries worldwide. The global spread of dengue virus (DENV) is mainly occurred by Aedes aegypti and Aedes albopictus mosquitoes. The dengue virus serotypes-2 (DENV-2) is a widely prevalent serotype of DENV, that causes the hemorrhagic fever and bleeding in the mucosa, which can be fatal. In the life cycle of DENV-2, a structural capsid (DENV-2 C) protein forms the nucleocapsid assembly and bind to the viral progeny RNA. For DENV-2 maturation, the nucleocapsid is a vital component. We used virtual ligand screening to filter out the best in-house synthesized acridinedione analogs (DSPD molecules) that could efficiently bind to DENV-2 C protein. The molecular docking and dynamics simulations studies were performed to analyze the effect of DSPD molecules on DENV-2 C protein after binding. Our findings showed that DSPD molecules strongly interacted with DENV-2 C protein, as evident from molecular interactions and several time-dependent molecular dynamics-driven analyses. Moreover, this study was also supported by the thermodynamic binding free energy and steered molecular dynamics simulations. Therefore, we intend to suggest that the DSPD3 molecule could be used as a potential therapeutic molecule against dengue complications as compared to the cocrystallized inhibitor ST-148. However, further studies are required to demonstrate the ability of DSPD3 to induce DENV-2 C tetramer formation.

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Section: Resultsmentioning

confidence: 99%

Section: Interaction Of Selected Molecules With Denv-2 C Proteinmentioning

confidence: 99%

Identification of acridinedione scaffolds as potential inhibitor of DENV‐2 C protein: An in silico strategy to combat dengue

Kumar

Bhardwaj

Singh

et al. 2022

J of Cellular Biochemistry

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“…[335] A combination of HotSpot Wizard and CUPSAT identified residues for site-directed mutagenesis and resulted in a mutant with improved kinetics and increased H 2 O 2 tolerance in a mechanism elucidated via MD simulations. [336] A strategy for the potential cure of genetic diseases is gene editing -a technology that in recent years made a leap toward reality by the discovery of sequence-programmable nucleases. To cleave their target DNA, a guide RNA and two catalytic magnesium ions are required by the prototypical Cas9.…”

Section: Examplesmentioning

confidence: 99%

Curse and Blessing of Non‐Proteinogenic Parts in Computational Enzyme Engineering

Korbeld

Fürst

2023

ChemBioChem

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Enzyme engineering aims to improve or install a new function in biocatalysts for applications ranging from chemical synthesis to biomedicine. For decades, computational techniques have been developed to predict the effect of protein changes and design new enzymes. However, these techniques may have been optimized to deal with proteins composed of the standard amino acid alphabet, while the function of many enzymes relies on non‐proteogenic parts like cofactors, nucleic acids, and post‐translational modifications. Enzyme systems containing such molecules might be handled or modeled improperly by computational tools, and thus be unsuitable, or require additional tweaking, parameterization, or preparation. In this review, we give an overview of common and recent tools and workflows available to computational enzyme engineers. We highlight the various pitfalls that come with including non‐proteogenic compounds in computations and outline potential ways to address common issues. Finally, we showcase successful examples from the literature that computationally engineered such enzymes.

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“…In in silico drug design, molecular docking is the most efficient method for estimating the binding energy and interaction styles of ligands with known three-dimensional protein structures. [36][37][38] In this article, 17 BCH molecules (Fig. 1) were docked with the BRD3-BD2 protein to analyze interactions and rank the molecules based on binding energy by comparing with the reference inhibitors (JQ-1 and LY294002).…”

Section: Interaction Profiles Of Selected Molecules With Brd3-bd2 Pro...mentioning

confidence: 99%

Evaluation of plant-derived semi-synthetic molecules against BRD3-BD2 protein: a computational strategy to combat breast cancer

Kumar

Bhardwaj

Singh

et al. 2022

Mol. Syst. Des. Eng.

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Site-directed mutagenesis (P61G) of copper, zinc superoxide dismutase enhances its kinetic properties and tolerance to inactivation by H2O2

Cited by 8 publications

References 40 publications

Identification of acridinedione scaffolds as potential inhibitor of DENV‐2 C protein: An in silico strategy to combat dengue

Identification of acridinedione scaffolds as potential inhibitor of DENV‐2 C protein: An in silico strategy to combat dengue

Curse and Blessing of Non‐Proteinogenic Parts in Computational Enzyme Engineering

Evaluation of plant-derived semi-synthetic molecules against BRD3-BD2 protein: a computational strategy to combat breast cancer

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