Active site-specific quantum tunneling of hACE2 receptor to assess its complexing poses with selective bioactive compounds in co-suppressing SARS-CoV-2 influx and subsequent cardiac injury

Tanzina Sharmin Nipun; Tanzila Ismail Ema; Md Abdur Rashid Mia; Md Saddam Hossen; Farzana Alam Arshe; Shahlaa Zernaz Ahmed; Afsana Masud; Fatiha Faheem Taheya; Arysha Alif Khan; Fauzia Haque; Salauddin Al Azad; Md Al Hasibuzzaman; Mohammad Tanbir; Samin Anis; Sharmin Akter; Sabrina Jahan Mily; Dipta Dey

doi:10.5455/javar.2021.h544

Active site-specific quantum tunneling of hACE2 receptor to assess its complexing poses with selective bioactive compounds in co-suppressing SARS-CoV-2 influx and subsequent cardiac injury

J Adv Vet Anim Res. 2021 Sep 29;8(4):540-556. doi: 10.5455/javar.2021.h544. eCollection 2021 Dec.

Authors

Tanzina Sharmin Nipun¹, Tanzila Ismail Ema², Md Abdur Rashid Mia³, Md Saddam Hossen⁴, Farzana Alam Arshe², Shahlaa Zernaz Ahmed², Afsana Masud², Fatiha Faheem Taheya², Arysha Alif Khan², Fauzia Haque², Salauddin Al Azad⁵, Md Al Hasibuzzaman⁶, Mohammad Tanbir², Samin Anis⁷, Sharmin Akter⁸, Sabrina Jahan Mily⁹, Dipta Dey¹⁰

Affiliations

¹ Department of Pharmaceutical Chemistry, Faculty of Pharmacy, International Islamic University Malaysia, Kuantan, Malaysia.
² Department of Biochemistry and Microbiology, North South University, Dhaka, Bangladesh.
³ Department of Pharmaceutical Technology, Faculty of Pharmacy, International Islamic University Malaysia, Kuantan, Malaysia.
⁴ Microbiology Major, Faculty of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, PR China.
⁵ Fermentation Engineering Major, School of Biotechnology, Jiangnan University, Wuxi, PR China.
⁶ School of Medicine, Ningbo University, Ningbo City, PR China.
⁷ Chattogram Maa-O-Shishu Hospital Medical College, University of Chittagong, Chattogram, Bangladesh.
⁸ Department of Genetics and Plant Breeding, Bangabandhu Sheikh Mujibur Rahman Agricultural University, Gazipur, Bangladesh.
⁹ Ministry of Health, People's Republic of Bangladesh, Dhaka, Bangladesh.
¹⁰ Department of Biochemistry and Molecular Biology, Bangabandhu Sheikh Mujibur Rahman Science and Technology University, Gopalgonj, Bangladesh.

Abstract

Objective: This research aims to study the target specificity of selective bioactive compounds in complexing with the human angiotensin-converting enzyme (hACE2) receptor to impede the severe acute respiratory syndrome coronavirus 2 influx mechanism resulting in cardiac injury and depending on the receptor's active site properties and quantum tunneling.

Materials and methods: A library of 120 phytochemical ligands was prepared, from which 5 were selected considering their absorption, distribution, metabolism, and excretion (ADMET) and quantitative structure-activity relationship (QSAR) profiles. The protein active sites and belonging quantum tunnels were defined to conduct supramolecular docking of the aforementioned ligands. The hydrogen bond formation and hydrophobic interactions between the ligand-receptor complexes were studied following the molecular docking steps. A comprehensive molecular dynamic simulation (MDS) was conducted for each of the ligand-receptor complexes to figure out the values - root mean square deviation (RMSD) (Å), root mean square fluctuation (RMSF) (Å), H-bonds, Cα, solvent accessible surface area (SASA) (Å²), molecular surface area (MolSA) (Å²), Rg (nm), and polar surface area (PSA) (Å). Finally, computational programming and algorithms were used to interpret the dynamic simulation outputs into their graphical quantitative forms.

Results: ADMET and QSAR profiles revealed that the most active candidates from the library to be used were apigenin, isovitexin, piperolactam A, and quercetin as test ligands, whereas serpentine as the control. Based on the binding affinities of supramolecular docking and the parameters of molecular dynamic simulation, the strength of the test ligands can be classified as isovitexin > quercetin > piperolactam A > apigenin when complexed with the hACE2 receptor. Surprisingly, serpentine showed lower affinity (-8.6 kcal/mol) than that of isovitexin (-9.9 kcal/mol) and quercetin (-8.9 kcal/mol). The MDS analysis revealed all ligands except isovitexin having a value lower than 2.5 Ǻ. All the test ligands exhibited acceptable fluctuation ranges of RMSD (Å), RMSF (Å), H-bonds, Cα, SASA (Å²), MolSA (Å²), Rg (nm), and PSA (Å) values.

Conclusion: Considering each of the parameters of molecular optimization, docking, and dynamic simulation interventions, all of the test ligands can be suggested as potential targeted drugs in blocking the hACE2 receptor.

Keywords: SARS-CoV-2; cardiac injury; drug design; hACE2 receptor; molecular dynamic; quantum tunneling; simulation; supramolecular docking.