Structure-Based Bioactive Phytochemical Design from Ayurvedic Formulations Towards Spike and Mpro Druggable Targets of SARS-CoV-2

The present COVID-19 global crisis invoked different disciplines of the biomedical research community to address the contagious human to human viral transmission and infection severity. Traditional or de novo drug discovery approach is a very time consuming process and will conflict with the urgency to discover new anti-viral drugs for combating the present global pandemic. Modern anti-viral drugs are not very effective and show resistance with serious adverse effects. Thus, identifying bioactive natural ingredients (phytochemical) from different medicinal plants or Ayurvedic formulations provides an effective alternative therapy for SARS-CoV-2 viral infections. We performed structure-based phytochemical design studies involving bioactive phytochemicals from medicinal plants towards two key druggable targets, spike glycoprotein and main protease (Mpro) of SARS-CoV-2. Phyllaemblicin class of phytocompounds showed better binding affinity towards both these SARS-CoV-2 targets and its binding mode revealed interactions with critical amino acid residues at its active sites. Also, we have successfully shown that the SARS-CoV-2 spike glycoprotein interaction towards human ACE2 receptor as its port of human cellular entry was blocked due to conformational variations in ACE2 receptor recognition by the binding of the phytocompound, Phyllaemblicin C at the ACE2 binding domain of spike protein. Our study shows that the Phyllaemblicin class of phytochemicals can be a potential dual inhibitor of spike and Mpro proteins of SARS-CoV-2 and could be promising for the treatment of COVID-19. </p

Understanding the Structure–Function Relationship of Lysozyme Resistance in Staphylococcus aureus by Peptidoglycan O‑Acetylation Using Molecular Docking, Dynamics, and Lysis Assay

Lysozyme is an important component of the host innate defense system. It cleaves the β-1,4 glycosidic bonds between <i>N</i>-acetylmuramic acid and <i>N</i>-acetylglucosamine of bacterial peptidoglycan and induce bacterial lysis. Staphylococcus aureus (S. aureus), an opportunistic commensal pathogen, is highly resistant to lysozyme, because of the O-acetylation of peptidoglycan by <i>O</i>-acetyl transferase (<i>oatA</i>). To understand the structure–function relationship of lysozyme resistance in S. aureus by peptidoglycan O-acetylation, we adapted an integrated approach to (i) understand the effect of lysozyme on the growth of S. aureus parental and the <i>oatA</i> mutant strain, (ii) study the lysozyme induced lysis of exponentially grown and stationary phase of both the S. aureus parental and <i>oatA</i> mutant strain, (iii) investigate the dynamic interaction mechanism between normal (de-O-acetylated) and O-acetylated peptidoglycan substrate in complex with lysozyme using molecular docking and molecular dynamics simulations, and (iv) quantify lysozyme resistance of S. aureus parental and the <i>oatA</i> mutant in different human biological fluids. The results indicated for the first time that the active site cleft of lysozyme binding with O-acetylated peptidoglycan in S. aureus was sterically hindered and the structural stability was higher for the lysozyme in complex with normal peptidoglycan. This could have conferred reduced survival of the S. aureus <i>oatA</i> mutant in different human biological fluids. Consistent with this computational analysis, the experimental data confirmed decrease in the growth, lysozyme induced lysis, and lysozyme resistance, due to peptidoglycan O<i>-</i>acetylation in S. aureus