Exploring the inhibitory potential of novel piperidine-derivatives against main protease (Mpro) of SARS-CoV-2: A hybrid approach consisting of molecular docking, MD simulations and MMPBSA analysis

Amina Rafique; Shabbir Muhammad; Javed Iqbal; Abdullah G Al-Sehemi; Mohammad Y Alshahrani; Khurshid Ayub; Mazhar Amjad Gilani

doi:10.1016/j.molliq.2023.121904

Exploring the inhibitory potential of novel piperidine-derivatives against main protease (M^pro) of SARS-CoV-2: A hybrid approach consisting of molecular docking, MD simulations and MMPBSA analysis

J Mol Liq. 2023 Jul 15:382:121904. doi: 10.1016/j.molliq.2023.121904. Epub 2023 Apr 26.

Authors

Amina Rafique¹, Shabbir Muhammad², Javed Iqbal¹, Abdullah G Al-Sehemi², Mohammad Y Alshahrani³, Khurshid Ayub⁴, Mazhar Amjad Gilani⁵

Affiliations

¹ Department of Chemistry, University of Agriculture, Faisalabad 38000, Pakistan.
² Department of Chemistry, College of Science, King Khalid University, P.O. Box 9004, Abha 61413, Saudi Arabia.
³ Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, King Khalid University, P.O. Box 61413, Abha 9088, Saudi Arabia.
⁴ Department of Chemistry, COMSATS University Islamabad, Abbottabad Campus, Abbottabad, KPK 22060, Pakistan.
⁵ Department of Chemistry, COMSATS University Islamabad, Lahore Campus, Lahore, Pakistan.

Abstract

In the current study, a hybrid computational approach consisting of different computational methods to explore the molecular electronic structures, bioactivity and therapeutic potential of piperidine compounds against SARS-CoV-2. The quantum chemical methods are used to study electronic structures of designed derivatives, molecular docking methods are used to see the most potential docking interactions for main protease (M^Pro) of SARS-CoV-2 while molecular dynamic and MMPBSA analyses are performed in bulk water solvation process to mimic real protein like aqueous environment and effectiveness of docked complexes. We designed and optimized piperidine derivatives from experimentally known precursor using quantum chemical methods. The UV-Visible, IR, molecular orbitals, molecular electrostatic plots, and global chemical reactivity descriptors are carried out which illustrate that the designed compounds are kinetically stable and reactive. The results of MD simulations and binding free energy revealed that all the complex systems possess adequate dynamic stability, and flexibility based on their RMSD, RMSF, radius of gyration, and hydrogen bond analysis. The computed net binding free energy ${(Δ G}_{b i n d}$ ) as calculated by MMPBSA method for the complexes showed the values of -4.29 kcal.mol^-1 for P1, -5.52 kcal.mol^-1 for P2, -6.12 kcal.mol^-1 for P3, -6.35 kcal.mol^-1 for P4, -5.19 kcal.mol^-1 for P5, 3.09 kcal.mol^-1 for P6, -6.78 kcal.mol^-1 for P7, and -6.29 kcal.mol^-1 for P8.The ADMET analysis further confirmed that none of among the designed ligands violates the Lipinski rule of five (RO5). The current comprehensive investigation predicts that all our designed compounds are recommended as prospective therapeutic drugs against M^pro of SARS-CoV-2 and it provokes the scientific community to further perform their in-vitro analysis.

Keywords: COVID-19 (6LU7); Molecular docking; Molecular dynamics; Piperidine inhibitors; Quantum computational methods; SARS-CoV-2.