A review targeting the infection by CHIKV using computational and experimental approaches

Kumar, Durgesh; Kumari, Kamlesh; Chandra, Ramesh; Jain, Pallavi; Vodwal, Lata; Gambhir, Geetu; Singh, Prashant

doi:10.1080/07391102.2021.1904004

Cited by 4 publications

(5 citation statements)

References 122 publications

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“…Many tools for performing molecular docking are available; some of the widely accepted tools are MolDock, iGemdock, ParDock, GOLD, LeDock, etc. In this work, ParDock was used for finding the binding between the molecules and protease [42,43]. It comprises protein-ligand docking techniques based on best fitting of the ligand in the cavity of the protein or receptor.…”

Section: Molecular Dockingmentioning

confidence: 99%

In Silico Evaluation of Binding of 2-Deoxy-D-Glucose with Mpro of nCoV to Combat COVID-19

et al. 2022

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COVID-19 has threatened the existence of humanity andthis infection occurs due to SARS-CoV-2 or novel coronavirus, was first reported in Wuhan, China. Therefore, there is a need to find a promising drug to cure the people suffering from the infection. The second wave of this viral infection was shaking the world in the first half of 2021. Drugs Controllers of India has allowed the emergency use of 2-deoxy-D-glucose (2DG) in 2021 for patients suffering from this viral infection. The potentiality of 2-deoxy-D-glucose to intervene in D-glucose metabolism exists and energy deprivation is an effective parameter to inhibit cancer cell development. Once 2DG arrives in the cells, it becomes phosphorylated to 2-deoxy-D-glucose-6-phosphate (2-DG6P), a charged molecule expressively captured inside the cells. On the other hand, 2DG lacks the ability to convert into fructose-6-phosphate, resulting in a hampering of the activity of both glucose-6-phosphate isomerase and hexokinase, and finally causing cell death. Hence, the potential and effectiveness of 2DG with the main protease (Mpro) of novel coronavirus (nCoV) should be investigated using the molecular docking and molecular dynamics (MD) simulations. The ability of 2DG to inhibit the Mpro of nCoV is compared with 2-deoxyglucose (2DAG), an acyclic molecule, and 2-deoxy-D-ribose (2DR). The binding energy of the molecules with the Mpro of nCoV is calculated using molecular docking and superimposed analysis data is obtained. The binding energy of 2DG, 2DR and 2DAG was −2.40, −2.22 and −2.88 kcal/mol respectively. Although the molecular docking does not provide reliable information, therefore, the binding affinity can be confirmed by molecular dynamics simulations. Various trajectories such as Rg, RMSD, RMSF, and hydrogen bonds are obtained from the molecular dynamics (MD) simulations. 2DG was found to be a better inhibitor than the 2DAG and 2DR based on the results obtained from the MD simulations at 300 K. Furthermore, temperature-dependent MD simulations of the Mpro of nCoV with promising 2DG was performed at 295, 310 and 315 K, and the effective binding with the Mpro of nCoV occurred at 295 K. With the use of DFT calculations, optimized geometry and localization of electron density of the frontier molecular orbitals were calculated.

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Section: Molecular Dockingmentioning

confidence: 99%

In Silico Evaluation of Binding of 2-Deoxy-D-Glucose with Mpro of nCoV to Combat COVID-19

et al. 2022

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“…It also serves the purposes of machine learning and research and development, in addition to optimization. It is analogous to biology for the formation of chromosomes, with variables such as selection, crossover, and mutation constituting genetic processes that may initially be applied to a random population [28][29][30][31]. GA aspires to produce solutions for future generations.…”

Section: Research Gaps and Motivationsmentioning

confidence: 99%

“…, and P is the probability that a randomly considered candidate in a set of candidates of T as above mentioned (30):…”

mentioning

confidence: 99%

GA-GDEMATEL: A Novel Approach to Optimize Recruitment and Personnel Selection Problems

Nguyen

2022

Mathematical Problems in Engineering

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The complexity of human resource management (HRM) requires an integrated method of subjective and objective evaluation rather than intuitive decisions such as multicriteria decision-making (MCDM). This study proposes a hybrid Genetic Algorithm and Decision-Making Trial and Evaluation Laboratory (GA-GDEMATEL)-based grey theory systems approach to solve personnel selection problems in a real-case study from a Vietnamese agriculture manufacturing and services corporation. First, the GDEMATEL approach is deployed to investigate the causal relationship between the proposed criteria and determine the subjective weights of recruitment criteria. Second, the GA model utilizes selection, crossover, and mutation with a new objective function of Minimizing Distance to Ideal Solution (MDIS) to find the optimal solution for robust recruitment based on GDEMATEL weights. Notably, the GA-GDEMATEL could be exploited effectively in a short time to optimize personnel selection in “deep and wide” aspects. Moreover, the study’s findings on recruiting evaluation and selection problems provide a support model and new research perspectives to the literature and help managers achieve the best solution by dealing with qualitative and quantitative criteria more effectively.

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“…A rapid onset of disease with no pro-dermal phase, following an incubation period of 2-4 days. [1][2][3] CHIKV enters into the target cells via endocytosis. Upon endocytosis, endosomes undergo conformational change in acidic environments in viral envelope and exposes E1 peptide, mediating virus-host cell membrane fusion.…”

Section: Introductionmentioning

confidence: 99%

“…Similarly, nsp3 plays important role during replication of CHIKV genome. [2,12,13] Molecular dynamics (MD) simulations is a time-saving, computational approach to perform molecular docking and provides the energy for complex formation between the receptor and a small molecule.…”

Section: Introductionmentioning

confidence: 99%

Impact of Temperature on Structural Changes in nsp2 and nsp3 of CHIKV: Molecular Dynamics Simulations

Kumar

Meena

Kumar

et al. 2022

Preprint

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Authors have considered non-structural protease-2 (nsp2) and non-structural protease-3 (nsp3) of CHIKV for the investigation as they are involved in the replication of the virus and increases the infections in the human. CHIKV protease (nsp2), has a catalytic dyad (Cys1013/His1083) that processes viral polyproteins. Further, it has also been suggested that the catalytic dyad is interchangeable to a serine (proximal) and hence making called non-papain-like cysteine protease. Similarly, nsp3 plays important role during replication of CHIKV genome. In this work, we have investigated the effect of temperature on the structural stability of nsp2 and nsp3 of CHIKV. Although, we did not get any regular patter for change in the RMSD and RMSF for the nsp3 of CHIKV and observed that RMSD for nsp3 of CHIKV is acceptable at all the temperature (300, 325 and 350 K) but the minimum RMSD values are obtained at 325 K. Similarly, no regular pattern is observed for RMSF trajectories of nsp3 of CHIKV at different temperature and minimum fluctuations in the position of amino-acids at 325 K. Further, the RMSD and RMSF trajectories for nsp2 of CHIKV are investigated and observed a regular pattern in the RMSD and RMSF trajectories generated from MD simulations on increasing the temperature. In this, RMSD values are minimum at 300 K while the fluctuation in the position of amino-acids are maximum.

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A review targeting the infection by CHIKV using computational and experimental approaches

Cited by 4 publications

References 122 publications

In Silico Evaluation of Binding of 2-Deoxy-D-Glucose with Mpro of nCoV to Combat COVID-19

In Silico Evaluation of Binding of 2-Deoxy-D-Glucose with Mpro of nCoV to Combat COVID-19

GA-GDEMATEL: A Novel Approach to Optimize Recruitment and Personnel Selection Problems

Impact of Temperature on Structural Changes in nsp2 and nsp3 of CHIKV: Molecular Dynamics Simulations

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