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- Title
Molecular Dynamic Simulation Search for Possible Amphiphilic Drug Discovery for Covid-19.
- Authors
Daood, Umer; Gopinath, Divya; Pichika, Malikarjuna Rao; Mak, Kit-Kay; Seow, Liang Lin
- Abstract
To determine whether quaternary ammonium (k21) binds to Severe Acute Respiratory Syndrome–Coronavirus 2 (SARS-CoV-2) spike protein via computational molecular docking simulations, the crystal structure of the SARS-CoV-2 spike receptor-binding domain complexed with ACE-2 (PDB ID: 6LZG) was downloaded from RCSB PD and prepared using Schrodinger 2019-4. The entry of SARS-CoV-2 inside humans is through lung tissues with a pH of 7.38–7.42. A two-dimensional structure of k-21 was drawn using the 2D-sketcher of Maestro 12.2 and trimmed of C18 alkyl chains from all four arms with the assumption that the core moiety k-21 was without C18. The immunogenic potential of k21/QA was conducted using the C-ImmSim server for a position-specific scoring matrix analyzing the human host immune system response. Therapeutic probability was shown using prediction models with negative and positive control drugs. Negative scores show that the binding of a quaternary ammonium compound with the spike protein's binding site is favorable. The drug molecule has a large Root Mean Square Deviation fluctuation due to the less complex geometry of the drug molecule, which is suggestive of a profound impact on the regular geometry of a viral protein. There is high concentration of Immunoglobulin M/Immunoglobulin G, which is concomitant of virus reduction. The proposed drug formulation based on quaternary ammonium to characterize affinity to the SARS-CoV-2 spike protein using simulation and computational immunological methods has shown promising findings.
- Subjects
COVID-19; DYNAMIC simulation; VIRAL proteins; IMMUNOGLOBULIN M; QUATERNARY ammonium compounds; SARS-CoV-2
- Publication
Molecules, 2021, Vol 26, Issue 8, p2214
- ISSN
1420-3049
- Publication type
Article
- DOI
10.3390/molecules26082214