| Literature DB >> 35502159 |
Yuan Xu1, Mahmood Al-Mualm2, Ermias Mergia Terefe3, Maksuda Ilyasovna Shamsutdinova4, Maria Jade Catalan Opulencia5, Fahad Alsaikhan6, Abduladheem Turki Jalil7, Ali Thaeer Hammid8, Ayesheh Enayati9, Hassan Mirzaei9, Vahid Khori9, Ali Jabbari9, Aref Salehi9, Alireza Soltani10, Abdullah Mohamed11.
Abstract
In the novel SARS-CoV-2 (COVID-19) as a global emergency event, the main reason of the cardiac injury from COVID-19 is angiotensin-converting enzyme 2 (ACE2) targeting in SARS-CoV-2 infection. The inhibition of ACE2 induces an increase in the angiotensin II (Ang II) and the angiotensin II receptor type 1 (AT1R) leading to impaired cardiac function or cardiac inflammatory responses. The ethyl acetate fraction of Potentilla reptans L. root can rescue heart dysfunction, oxidative stress, cardiac arrhythmias and apoptosis. Therefore, isolated components of P. reptans evaluated to identify natural anti-SARS-CoV-2 agents via molecular docking. In silico molecular docking study were carried out using the Auto Dock software on the isolated compounds of Potentilla reptans root. The protein targets of selective ACE and others obtained from Protein Data Bank (PDB). The best binding pose between amino acid residues involved in active site of the targets and compounds was discovered via molecular docking. Furthermore, ADMET properties of the compounds were evaluated. The triterpenoids of P. reptans showed more ACE inhibitory potential than catechin in both domains. They were selective on the nACE domain, especially compound 5. Also, the compound 5 & 6 had the highest binding affinity toward active site of nACE, cACE, AT1R, ACE2, and TNF-α receptors. Meanwhile, compound 3 showed more activity to inhibit TXA2. Drug likeness and ADMET analysis showed that the compounds passed the criteria of drug likeness and Lipinski rules. The current study depicted that P. reptans root showed cardioprotective effect in COVID-19 infection and manipulation of angiotensin II-induced side effects.Entities:
Keywords: ADMET; Angiotensin II; COVID-19; Molecular docking simulation; Potentilla reptans
Year: 2022 PMID: 35502159 PMCID: PMC9044627 DOI: 10.1016/j.arabjc.2022.103942
Source DB: PubMed Journal: Arab J Chem ISSN: 1878-5352 Impact factor: 6.212
Fig. 1Structures of isolated compounds from P. reptans root.
Molecular docking simulation results for the compounds and receptors.
| Compound | Binding Energy (kcal/mol) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Captopril | −7.6 | −7.0 | −7.1 | −7.4 | −7.3 | −7.1 | −7.1 | −7.2 | −7.6 | −7.4 | −7.3 | −7.4 |
| Catechin | −7.3 | −7.2 | −7.4 | −7.7 | −7.5 | −7.6 | −7.3 | −7.3 | −7.8 | −7.8 | −7.5 | −7.5 |
| 1 | −7.6 | −7.8 | −8.2 | −8.7 | −8.8 | −8.3 | −7.7 | −7.7 | −8.7 | −7.3 | −8.0 | −7.9 |
| 2 | −7.8 | −7.6 | −7.9 | −9.5 | −9.5 | −9.1 | −7.9 | −7.8 | −9.8 | −7.1 | −8.3 | −8.1 |
| 3 | −8.1 | −8.7 | −8.6 | −9.2 | −9.4 | −9.2 | −8.1 | −8.0 | −9.4 | −7.7 | −9.2 | −8.2 |
| 4 | −8.0 | −8.5 | −8.8 | −9.0 | −9.7 | −9.7 | −8.6 | −8.2 | −9.7 | −7.5 | −8.9 | −8.5 |
| 5 | −8.2 | −8.3 | −8.9 | −9.6 | −10.4 | −9.8 | −8.4 | −9.4 | −9.9 | −8.3 | −8.1 | −8.3 |
| 6 | −7.7 | −9.3 | −9.6 | −10.2 | −9.6 | −9.6 | −9.1 | −8.6 | −9.5 | −6.3 | −8.8 | −8.6 |
Fig. 2Presentation of 2D model of interactions between compound 5 (A-B) and compound 6 (C-E) on selective ACE domains. A) Compound 5 and nACE (PDB ID:6F9V); B) Compound 5 and nACE (PDB ID:6EN5); C) Compound 6 and cACE (PDB ID: 6F9T); D) Compound 6 and cACE (PDB ID: 6F9U); E) Compound 6 and cACE (PDB ID: 2OC2).
Fig. 3Presentation of 2D model of interactions between A) compound 5 and AT1R (PDB ID: 4ZUD); B) compound 6 and (AT1R) (PDB ID: 4YAY); C) compound 5 and (ACE2) (PDB ID: 1R4L).
Fig. 4Presentation of 2D model of interactions between A) compound 6 and (TNF-α) (PDB ID: 2AZ5); B) compound 3 and (TXA2) (PDB ID: 6IIU).
Drug-likeness properties of compounds.
| – | >-4 | <=5 | <=10 | <=5 | <=10 | 40–130 | <140 | |
| 650 | −3.71 | 3.2 | 10 | 7 | 4 | 171 | 177 | |
| 650 | −3.86 | 2.43 | 10 | 7 | 4 | 171 | 177 | |
| 648 | −3.76 | 3.26 | 10 | 6 | 4 | 170 | 173 | |
| 650 | −3.89 | 3.22 | 10 | 7 | 4 | 171 | 177 | |
| 696 | −3.61 | 2.06 | 12 | 8 | 6 | 178 | 206 | |
| 858 | −3.08 | 1.29 | 17 | 11 | 9 | 209 | 285 | |
| 290 | −2.73 | 1.34 | 6 | 5 | 1 | 74 | 110 | |
| 217 | −0.06 | 0.27 | 4 | 1 | 4 | 60 | 57 |
HBA: Number of hydrogen bonds acceptors; HBD: Number of hydrogen bond donors; Log S: Logarithm of water solubility; C Log P: Calculated logarithm of compound partition coefficient between n-octanol and water; MR: Molecular refractivity; MW: molecular weight; NRB: Number of rotatable bonds; TPSA: Topological polar surface area.
ADMET (absorption, distribution, metabolism, excretion and toxicity) profile of compounds.
| – | – | – | No | No | No | No | No | No | No | – | |
| No | Yes | No | Yes | No | No | No | No | No | No | 3.1 | |
| No | Yes | No | Yes | No | No | No | No | No | No | 3.1 | |
| No | Yes | No | Yes | No | No | No | No | No | No | 3.2 | |
| No | Yes | No | Yes | No | No | No | No | No | No | 3.5 | |
| No | Yes | No | Yes | No | No | No | No | No | No | 3.0 | |
| No | No | No | Yes | No | No | No | No | No | No | 3.3 | |
| No | Yes | No | No | No | No | No | No | No | No | 2.0 | |
| Yes | Yes | No | No | Yes | No | No | No | No | No | 1.8 |
AOC: Acute oral toxicity; BBB: Blood Brain Barrier; CIG: Carcinogens; HIA: Human Intestinal Absorption; HPT: Hepatotoxicity; P-GI: P-glycoprotein inhibitor. Caco2: A model of the intestinal epithelial barrier; AMES: To assess the mutagenic potential of chemical compounds.