Virtual screening and molecular dynamics simulation study of approved drugs as a binder to the linoleic acid binding site on spike protein of SARS-CoV-2 and double mutant (E484Q and L452R)

• Published in: Indian journal of pharmacology 2022-11, Vol.54 (6), p.431-442
• Main Authors: Prajapat, Manisha, Sarma, Phulen, Shekhar, Nishant, Chauhan, Arushi, Kaur, Gurjeet, Bhattacharyya, Anusuya, Avti, Pramod, Choudhary, Gajendra, Bansal, Seema, Sharma, Saurabh, Kaur, Hardeep, Kumar, Subodh, Mann, Harvinder, Raja, Anupam, Singh, Ashutosh, Singh, Rahul, Sharma, Amit, Prakash, Ajay, Medhi, Bikash
• Format: Article
• Language: English
• Subjects: Analysis; Antiviral Agents - chemistry; Antiviral Agents - pharmacology; Binding Sites; Drugs; FDA approval; Health aspects; Ligands; Linoleic Acid; Linoleic acids; Molecular dynamics; Molecular Dynamics Simulation; Original; Physiological aspects; Protein binding; Proteins; SARS-CoV-2 - drug effects; SARS-CoV-2 - genetics; Severe acute respiratory syndrome coronavirus 2; Simulation; Spike Glycoprotein, Coronavirus - genetics; Viral proteins
• ISSN: 0253-7613; 1998-3751
• DOI: 10.4103/ijp.ijp_111_22

INTRODUCTION: Binding of linoleic acid (LA) to the spike trimer stabilizes it in closed conformation hindering its binding to angiotensin-converting enzyme-2, thus decreasing infectivity. In the current study, we tend to repurpose Food and Drug Administration-approved drugs as binder to the LA binding pocket in wild and double mutant spike protein. MATERIALS AND METHODS: Approved drugs from DrugBank database (n = 2456) were prepared using Ligprep module of Schrodinger. Crystal structure of LA bound to spike trimer was retrieved (PDB: 6ZB4) and prepared using protein preparation wizard and grid was generated. A virtual screening was performed. With the help of molecular dynamics (MD) studies interaction profile of screened drugs were further evaluated. The selected hits were further evaluated for binding to the double mutant form of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2). RESULTS AND DISCUSSION: Following virtual screening, a total of 26 molecules were shortlisted, which were further evaluated using 1ns MD simulation study. Four ligands showing better root mean square deviation (RMSD), RMSD to LA with interaction profile similar to LA were further evaluated using 100 ns MD simulation studies. A total of 2 hits were identified, which performed better than LA (selexipag and pralatrexate). Both these ligands were also found to bind to LA binding site of the double mutant form (E484Q and L452R); however, the binding affinity of pralatrexate was found to be better. CONCLUSION: We have identified 2 ligands (selexipag and pralatrexate) as possible stable binders to the LA binding site in spike trimer (wild and mutant form). Among them, pralatrexate has shown in vitro activity against SARS-CoV-2, validating our study results.