Journal: Biochemistry and Biophysics Reports

Article Title: In silico studies to understand the interactions of flavonoid inhibitor with nsp12-RNA dependent RNA polymerase of SARS-CoV-2 and its homologs

doi: 10.1016/j.bbrep.2025.101975

Figure Lengend Snippet: Structure complex of SARS-CoV-2 RdRp enzyme with HHF318 (A) HHF318 at the NTP binding site of SARS-CoV-2 RdRp enzyme with RNA (mesh rendering) and Magnesium (blue sphere), (B) Structure of HHF318: 3,3′,4′,5,5′,8-Hexahydroxyflavone.

Article Snippet: Graphs showing parameters of Molecular Dynamics simulation of RdRp complexes with HHF318 molecule. ( A ) Temperature; ( B ) Pressure; ( C ) Volume; ( D ) Total energy; ( E ) Ligand RMSD; ( F ) Protein RMSD; ( G ) Potential energy.

Techniques: Binding Assay

Journal: Biochemistry and Biophysics Reports

Article Title: In silico studies to understand the interactions of flavonoid inhibitor with nsp12-RNA dependent RNA polymerase of SARS-CoV-2 and its homologs

doi: 10.1016/j.bbrep.2025.101975

Figure Lengend Snippet: Graphs showing parameters of Molecular Dynamics simulation of RdRp complexes with HHF318 molecule. ( A ) Temperature; ( B ) Pressure; ( C ) Volume; ( D ) Total energy; ( E ) Ligand RMSD; ( F ) Protein RMSD; ( G ) Potential energy. Plots for SARS-CoV-2 , SARS-CoV-1 , MERS-CoV , and Bat-CoV are shown in green, cyan, pink and yellow, respectively. Post MD free energy landscapes of RdRp-HHF318 complexes ( H ) SARS-CoV-2 RdRp-HHF318, ( I ) SARS-CoV-1 RdRp-HHF318, ( J ) MERS-CoV RdRp-HHF318, and ( K ) Bat-CoV RdRp-HHF318. Lowest energy and highest energy conformations are shown by dark blue and red, respectively. The white Asterix indicates the representative structure used for analysis.

Article Snippet: Graphs showing parameters of Molecular Dynamics simulation of RdRp complexes with HHF318 molecule. ( A ) Temperature; ( B ) Pressure; ( C ) Volume; ( D ) Total energy; ( E ) Ligand RMSD; ( F ) Protein RMSD; ( G ) Potential energy.

Techniques:

Journal: Biochemistry and Biophysics Reports

Article Title: In silico studies to understand the interactions of flavonoid inhibitor with nsp12-RNA dependent RNA polymerase of SARS-CoV-2 and its homologs

doi: 10.1016/j.bbrep.2025.101975

Figure Lengend Snippet: HHF318 interactions with the RdRp enzymes ( A ) line and stick diagram showing interactions of HHF318 with SARS-CoV-2 RdRp, ( B ) line and stick diagram showing interactions of HHF318 with SARS-CoV-1 RdRp, ( C ) line and stick diagram showing interactions of HHF318 with MERS-CoV RdRp and ( D ) line and stick diagram showing interactions of HHF318 with Bat-CoV RdRp. Hydrogen bonds are shown as red dotted lines, Magnesium coordination bonds are shown as red-blue lines and hydrophobic interactions are shown as black dotted lines.

Article Snippet: Graphs showing parameters of Molecular Dynamics simulation of RdRp complexes with HHF318 molecule. ( A ) Temperature; ( B ) Pressure; ( C ) Volume; ( D ) Total energy; ( E ) Ligand RMSD; ( F ) Protein RMSD; ( G ) Potential energy.

Techniques:

Journal: Biochemistry and Biophysics Reports

Article Title: In silico studies to understand the interactions of flavonoid inhibitor with nsp12-RNA dependent RNA polymerase of SARS-CoV-2 and its homologs

doi: 10.1016/j.bbrep.2025.101975

Figure Lengend Snippet: Superimposed Cryo-EM structure of SARS-CoV-2 RdRp with ATP (orange) and SARS-CoV-2 RdRp with HHF318 (white) at the NTP binding site. RNA is shown as orange cartoon and magnesium is shown as blue sphere.

Article Snippet: Graphs showing parameters of Molecular Dynamics simulation of RdRp complexes with HHF318 molecule. ( A ) Temperature; ( B ) Pressure; ( C ) Volume; ( D ) Total energy; ( E ) Ligand RMSD; ( F ) Protein RMSD; ( G ) Potential energy.

Techniques: Cryo-EM Sample Prep, Binding Assay

Journal: Biochemistry and Biophysics Reports

Article Title: In silico studies to understand the interactions of flavonoid inhibitor with nsp12-RNA dependent RNA polymerase of SARS-CoV-2 and its homologs

doi: 10.1016/j.bbrep.2025.101975

Figure Lengend Snippet: Physico-chemical and pharmacokinetic properties of HHF318.

Article Snippet: Graphs showing parameters of Molecular Dynamics simulation of RdRp complexes with HHF318 molecule. ( A ) Temperature; ( B ) Pressure; ( C ) Volume; ( D ) Total energy; ( E ) Ligand RMSD; ( F ) Protein RMSD; ( G ) Potential energy.

Techniques: Molecular Weight, Solubility

Journal: Biochemistry and Biophysics Reports

Article Title: In silico studies to understand the interactions of flavonoid inhibitor with nsp12-RNA dependent RNA polymerase of SARS-CoV-2 and its homologs

doi: 10.1016/j.bbrep.2025.101975

Figure Lengend Snippet: Docked complexes of HHF318 with ATP binding human proteins. ( A ) DNA-Ligase-HHF318, ( B ) Pi3K–HHF318, ( C ) Hexokinase-HHF318. Dissociation constants (Kd) are indicated below each of the three complexes.

Article Snippet: Graphs showing parameters of Molecular Dynamics simulation of RdRp complexes with HHF318 molecule. ( A ) Temperature; ( B ) Pressure; ( C ) Volume; ( D ) Total energy; ( E ) Ligand RMSD; ( F ) Protein RMSD; ( G ) Potential energy.

Techniques: Binding Assay