Molecular dynamics study of some non-hydrogen-bonding base pair DNA strands

Tiwari, Rakesh; Ojha, Rajendra Prasad; Tiwari, Gargi; Pandey, Vishnudatt; Mall, Vijaysree

doi:10.1063/1.5033174

Cited by 1 publication

(2 citation statements)

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“…Smaller conformational deviation results in the lower RMSF values. RMSD and RMSF stabilities were found to be critical in referring strong binding affinities by several research groups 72,73 . RMSF analysis of MD trajectories revealed regions with enhanced flexibility in all proteins‐peptide investigated.…”

Section: Resultsmentioning

confidence: 96%

“…RMSD and RMSF stabilities were found to be critical in referring strong binding affinities by several research groups. 72 , 73 RMSF analysis of MD trajectories revealed regions with enhanced flexibility in all proteins‐peptide investigated. Figure 2E displayed that the amino acid residues SER1 to ARG4 of Mpro and other Mpro‐peptide complexes exhibited higher RMSF values ranging from an average of 4.4 to 1.4 Å.…”

Section: Resultsmentioning

confidence: 98%

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Large scale peptide screening against main protease of SARS CoV‐2

et al. 2022

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The COVID‐19 pandemic has been a public health emergency, with deadly forms constantly emerging around the world, highlighting the dire need for highly effective antiviral therapeutics. Peptide therapeutics show significant potential for this viral disease due to their efficiency, safety, and specificity. Here, two thousand seven hundred eight antibacterial peptides were screened computationally targeting the Main protease (Mpro) of SARS CoV‐2. Six top‐ranked peptides according to their binding scores, binding pose were investigated by molecular dynamics to explore the interaction and binding behavior of peptide‐Mpro complexes. The structural and energetic characteristics of Mpro‐DRAMP01760 and Mpro‐DRAMP01808 complexes fluctuated less during a 250 ns MD simulation. In addition, three peptides (DRAMP01760, DRAMP01808, and DRAMP01342) bind strongly to Mpro protein, according to the free energy landscape and principal component analysis. Peptide helicity and secondary structure analysis are in agreement with our findings. Interaction analysis of protein‐peptide complexes demonstrated that Mpro's residue CYS145, HIS41, PRO168, GLU166, GLN189, ASN142, MET49, and THR26 play significant contributions in peptide‐protein attachment. Binding free energy analysis (MM‐PBSA) demonstrated the energy profile of interacting residues of Mpro in peptide‐Mpro complexes. To summarize, the peptides DRAMP01808 and DRAMP01760 may be highly Mpro specific, resulting disruption in a viral replication and transcription. The results of this research are expected to assist future research toward the development of antiviral peptide‐based therapeutics for Covid‐19 treatment.

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Section: Resultsmentioning

confidence: 96%

Section: Resultsmentioning

confidence: 98%