In silico analysis and identification of novel inhibitor for new H1N1 swine influenza virus

Dammalli, Manjunath; Chandramohan, Vivek; Biradar, Mahantesh Iranna; Nagaraju, Navya; Gangadharappa, Bhavya

doi:10.1016/s2222-1808(14)60694-0

Cited by 16 publications

(5 citation statements)

References 22 publications

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“…They are RNA infections with a sectioned genome that is involved single abandoned RNA portions. These eight fragments encode eleven proteins in which two are surface glycoproteins, hemagglutinin (HA) and neuraminidase (NA) (Dammalli et al 2014). HA ties with sialic corrosive identi ed on the outside of the focused-on host cell to start infection disease and sialic corrosive was pull out from infection by NA.…”

Section: Molecular Docking Study Of H1n1mentioning

confidence: 99%

WITHDRAWN: Molecular docking used as an advanced tool to determine novel compounds on emerging infectious diseases: A systematic review

Gouthami

Veeraraghavan²,

Rahdar³

et al. 2022

Progress in Biophysics and Molecular Biology

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Section: Molecular Docking Study Of H1n1mentioning

confidence: 99%

WITHDRAWN: Molecular docking used as an advanced tool to determine novel compounds on emerging infectious diseases: A systematic review

Gouthami

Veeraraghavan²,

Rahdar³

et al. 2022

Progress in Biophysics and Molecular Biology

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“…The original amino acid residues were replaced with mutant variants (N130D, N130S and N216K) 22 . The mutated structures were optimized using CHARMm force fields 23 . They were subjected to a standard dynamics cascade with a convergence energy of 0.001 kcal/mol 24 .…”

Section: Methodsmentioning

confidence: 99%

Prediction of deleterious single nucleotide polymorphisms and their effect on the sequence and structure of the human CCND1 gene

Yoganarasimha

Chandramohan

Murthy

et al. 2017

Journal of Taibah University Medical Sciences

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Objective The CCND1 gene expresses a protein, G1/S-specific cyclin, that regulates the G1/S transition in the cell cycle and also inhibits retinoblastoma (RB) proteins. Overexpression or rearrangements of this gene can result in various tumours. This study aimed to identify possible deleterious non-synonymous single nucleotide polymorphisms (SNP's) of CCND1 using computational methods. Methods SNPs in the human CCND1 gene were retrieved from dbSNP. These SNPs were screened by the Sorting Intolerant From Tolerant (SIFT) algorithm and the PredictSNP classification. Mutants with deleterious SNPs were built using Discovery Studio 3.5, and dynamics studies were performed on native and mutant varieties. Results In Homo sapiens , 1194 SNPs were found, of which 94 were missense and 2 were nonsense SNPs. Three SNPs were found to be deleterious. Molecular dynamics and trajectory analysis showed that there was a significant deviation of the root mean square deviation (RMSD) values in the N216K mutant from the values of the native protein. Conclusion Based on this study, we propose that the SNP with SNP ID rs112525097 (NM_053056.2:c.648C>G) might cause aberrations in CCND1 , which might lead to a change in the function of the G1/S-specific cyclin protein. This, in turn, may lead to the development of acute myeloid leukaemia (AML).

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“…For molecular docking studies, a flexible docking approach was employed using the LeadIT [ 31 ] software in which wild NS3 protease and mutants R155K and D168A were considered as receptor proteins. The docking results for receptor-ligand complex comprised intermolecular interaction energies, namely, hydrogen bonding and hydrophobic and electrostatic interaction.…”

Section: Methodsmentioning

confidence: 99%

Evaluating Andrographolide as a Potent Inhibitor of NS3-4A Protease and Its Drug-Resistant Mutants UsingIn SilicoApproaches

Chandramohan¹,

Kaphle²,

Chekuri³

et al. 2015

Advances in Virology

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Current combination therapy of PEG-INF and ribavirin against the Hepatitis C Virus (HCV) genotype-1 infections is ineffective in maintaining sustained viral response in 50% of the infection cases. New compounds in the form of protease inhibitors can complement the combination therapy. Asunaprevir is new to the drug regiment as the NS3-4A protease inhibitor, but it is susceptible to two mutations, namely, R155K and D168A in the protein. Thus, in our study, we sought to evaluate Andrographolide, a labdane-diterpenoid from the Andrographis paniculata plant as an effective compound for inhibiting the NS3-4A protease as well as its concomitant drug-resistant mutants by using molecular docking and dynamic simulations. Our study shows that Andrographolide has best docking scores of −15.0862, −15.2322, and −13.9072 compared to those of Asunaprevir −3.7159, −2.6431, and −5.4149 with wild-type R155K and D168A mutants, respectively. Also, as shown in the MD simulations, the compound was good in binding the target proteins and maintains strong bonds causing very less to negligible perturbation in the protein backbone structures. Our results validate the susceptibility of Asunaprevir to protein variants as seen from our docking studies and trajectory period analysis. Therefore, from our study, we hope to add one more option in the drug regiment to tackle drug resistance in HCV infections.

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In silico analysis and identification of novel inhibitor for new H1N1 swine influenza virus

Cited by 16 publications

References 22 publications

WITHDRAWN: Molecular docking used as an advanced tool to determine novel compounds on emerging infectious diseases: A systematic review

WITHDRAWN: Molecular docking used as an advanced tool to determine novel compounds on emerging infectious diseases: A systematic review

Prediction of deleterious single nucleotide polymorphisms and their effect on the sequence and structure of the human CCND1 gene

Evaluating Andrographolide as a Potent Inhibitor of NS3-4A Protease and Its Drug-Resistant Mutants UsingIn SilicoApproaches

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