tetano
Editor, Senior Moderator
J Adv Vet Anim Res
. 2021 Sep 29;8(4):540-556.
doi: 10.5455/javar.2021.h544. eCollection 2021 Dec.
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[SUP] 1 [/SUP], Tanzila Ismail Ema[SUP] 2 [/SUP], Md Abdur Rashid Mia[SUP] 3 [/SUP], Md Saddam Hossen[SUP] 4 [/SUP], Farzana Alam Arshe[SUP] 2 [/SUP], Shahlaa Zernaz Ahmed[SUP] 2 [/SUP], Afsana Masud[SUP] 2 [/SUP], Fatiha Faheem Taheya[SUP] 2 [/SUP], Arysha Alif Khan[SUP] 2 [/SUP], Fauzia Haque[SUP] 2 [/SUP], Salauddin Al Azad[SUP] 5 [/SUP], Md Al Hasibuzzaman[SUP] 6 [/SUP], Mohammad Tanbir[SUP] 2 [/SUP], Samin Anis[SUP] 7 [/SUP], Sharmin Akter[SUP] 8 [/SUP], Sabrina Jahan Mily[SUP] 9 [/SUP], Dipta Dey[SUP] 10 [/SUP]
Affiliations
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) (Å[SUP]2[/SUP]), molecular surface area (MolSA) (Å[SUP]2[/SUP]), 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 (Å[SUP]2[/SUP]), MolSA (Å[SUP]2[/SUP]), 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.
. 2021 Sep 29;8(4):540-556.
doi: 10.5455/javar.2021.h544. eCollection 2021 Dec.
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[SUP] 1 [/SUP], Tanzila Ismail Ema[SUP] 2 [/SUP], Md Abdur Rashid Mia[SUP] 3 [/SUP], Md Saddam Hossen[SUP] 4 [/SUP], Farzana Alam Arshe[SUP] 2 [/SUP], Shahlaa Zernaz Ahmed[SUP] 2 [/SUP], Afsana Masud[SUP] 2 [/SUP], Fatiha Faheem Taheya[SUP] 2 [/SUP], Arysha Alif Khan[SUP] 2 [/SUP], Fauzia Haque[SUP] 2 [/SUP], Salauddin Al Azad[SUP] 5 [/SUP], Md Al Hasibuzzaman[SUP] 6 [/SUP], Mohammad Tanbir[SUP] 2 [/SUP], Samin Anis[SUP] 7 [/SUP], Sharmin Akter[SUP] 8 [/SUP], Sabrina Jahan Mily[SUP] 9 [/SUP], Dipta Dey[SUP] 10 [/SUP]
Affiliations
- PMID: 35106293
- PMCID: PMC8757663
- DOI: 10.5455/javar.2021.h544
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) (Å[SUP]2[/SUP]), molecular surface area (MolSA) (Å[SUP]2[/SUP]), 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 (Å[SUP]2[/SUP]), MolSA (Å[SUP]2[/SUP]), 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.