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El-Hosari DG, Hussein WM, Elgendy MO, Elgendy SO, Ibrahim ARN, Fahmy AM, Hassan A, Mokhtar FA, Hussein MF, Abdelrahim MEA, Haggag EG. Galangal-Cinnamon Spice Mixture Blocks the Coronavirus Infection Pathway through Inhibition of SARS-CoV-2 M Pro, Three HCoV-229E Targets; Quantum-Chemical Calculations Support In Vitro Evaluation. Pharmaceuticals (Basel) 2023; 16:1378. [PMID: 37895849 PMCID: PMC10610207 DOI: 10.3390/ph16101378] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Revised: 09/17/2023] [Accepted: 09/19/2023] [Indexed: 10/29/2023] Open
Abstract
Natural products such as domestic herbal drugs which are easily accessible and cost-effective can be used as a complementary treatment in mild and moderate COVID-19 cases. This study aimed to detect and describe the efficiency of phenolics detected in the galangal-cinnamon mixture in the inhibition of SARS-CoV-2's different protein targets. The potential antiviral effect of galangal-cinnamon aqueous extract (GCAE) against Low Pathogenic HCoV-229E was assessed using cytopathic effect inhibition assay and the crystal violet method. Low Pathogenic HCoV-229E was used as it is safer for in vitro laboratory experimentation and due to the conformation and the binding pockets similarity between HCoV-229E and SARS-CoV-2 MPro. The GCAE showed a significant antiviral effect against HCoV-229E (IC50 15.083 µg/mL). Twelve phenolic compounds were detected in the extract with ellagic, cinnamic, and gallic acids being the major identified phenolic acids, while rutin was the major identified flavonoid glycoside. Quantum-chemical calculations were made to find molecular properties using the DFT/B3LYP method with 6-311++G(2d,2p) basis set. Quantum-chemical values such as EHOMO, ELUMO, energy gap, ionization potential, chemical hardness, softness, and electronegativity values were calculated and discussed. Phenolic compounds detected by HPLC-DAD-UV in the GCAE were docked into the active site of 3 HCoV-229E targets (PDB IDs. 2ZU2, 6U7G, 7VN9, and 6WTT) to find the potential inhibitors that block the Coronavirus infection pathways from quantum and docking data for these compounds. There are good adaptations between the theoretical and experimental results showing that rutin has the highest activity against Low Pathogenic HCoV-229E in the GCAE extract.
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Affiliation(s)
- Doaa G. El-Hosari
- Pharmacognosy Department, Faculty of Pharmacy, Helwan University, Cairo 11795, Egypt; (W.M.H.); (E.G.H.)
| | - Wesam M. Hussein
- Pharmacognosy Department, Faculty of Pharmacy, Helwan University, Cairo 11795, Egypt; (W.M.H.); (E.G.H.)
| | - Marwa O. Elgendy
- Department of Clinical Pharmacy, Beni-Suef University Hospitals, Faculty of Medicine, Beni-Suef University, Beni-Suef 62521, Egypt
- Department of Clinical Pharmacy, Faculty of Pharmacy, Nahda University (NUB), Beni-Suef 62513, Egypt
| | - Sara O. Elgendy
- Clinical and Chemical Pathology Department, Faculty of Medicine, Beni-Suef University, Beni-Suef 62521, Egypt;
| | - Ahmed R. N. Ibrahim
- Department of Clinical Pharmacy, College of Pharmacy, King Khalid University, Abha 61421, Saudi Arabia;
| | - Alzhraa M. Fahmy
- Tropical Medicine and Infectious Diseases Department, Faculty of Medicine, Beni-Suef University, Beni-Suef 62521, Egypt;
| | - Afnan Hassan
- Biomedical Sciences Program, University of Science and Technology, Zewail City of Science and Technology, Cairo 12578, Egypt;
| | - Fatma Alzahraa Mokhtar
- Department of Pharmacognosy, Faculty of Pharmacy, El Saleheya El Gadida University, El Saleheya El Gadida 44813, Egypt;
| | - Modather F. Hussein
- Chemistry Department, Collage of Science, Jouf University, P.O. Box 2014, Sakaka 72388, Saudi Arabia;
- Chemistry Department, Faculty of Science, Al-Azhar University, Asyut Branch, Assiut 71524, Egypt
| | - Mohamed E. A. Abdelrahim
- Clinical Pharmacy Department, Faculty of Pharmacy, Beni-Suef University, Beni-Suef 62521, Egypt;
| | - Eman G. Haggag
- Pharmacognosy Department, Faculty of Pharmacy, Helwan University, Cairo 11795, Egypt; (W.M.H.); (E.G.H.)
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Abstract
An intermediate electrostatic field is introduced to improve the accuracy of fragment-based quantum-chemical computational methods by including long-range polarizations of biomolecules. The point charge distribution of the intermediate field is generated by a charge sensitivity analysis that is parameterized for five different population analyses, namely, atoms-in-molecules, Hirshfeld, Mulliken, natural orbital, and Voronoi population analysis. Two model systems are chosen to demonstrate the performance of the generalized elongation method (ELG) combined with the intermediate electrostatic field. The calculations are performed for the STO-3G, 6-31G, and 6-31G(d) basis sets and compared with reference Hartree-Fock calculations. It is shown that the error in the total energy is reduced by one order of magnitude, independently of the population analyses used. This demonstrates the importance of long-range polarization in electronic-structure calculations by fragmentation techniques.
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Affiliation(s)
- Kai Liu
- Department of Material Sciences, Faculty of Engineering Sciences, Kyushu University, 6-1 Kasuga Park, Fukuoka 816-8580 (Japan)
| | - Jacek Korchowiec
- K. Gumiński Department of Theoretical Chemistry, Faculty of Chemistry, Jagiellonian University, R. Ingardena 3, 30-060 Kraków (Poland)
| | - Yuriko Aoki
- Department of Material Sciences, Faculty of Engineering Sciences, Kyushu University, 6-1 Kasuga Park, Fukuoka 816-8580 (Japan). .,Japan Science and Technology Agency, CREST, 4-1-8 Hon-chou, Kawaguchi, Saitama, 332-0012 (Japan).
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