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Ullah A, Ullah S, Halim SA, Waqas M, Ali B, Ataya FS, El-Sabbagh NM, Batiha GES, Avula SK, Csuk R, Khan A, Al-Harrasi A. Identification of new pharmacophore against SARS-CoV-2 spike protein by multi-fold computational and biochemical techniques. Sci Rep 2024; 14:3590. [PMID: 38351259 PMCID: PMC10864406 DOI: 10.1038/s41598-024-53911-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2023] [Accepted: 02/06/2024] [Indexed: 02/16/2024] Open
Abstract
COVID-19 appeared as a highly contagious disease after its outbreak in December 2019 by the virus, named SARS-CoV-2. The threat, which originated in Wuhan, China, swiftly became an international emergency. Among different genomic products, spike protein of virus plays a crucial role in the initiation of the infection by binding to the human lung cells, therefore, SARS-CoV-2's spike protein is a promising therapeutic target. Using a combination of a structure-based virtual screening and biochemical assay, this study seeks possible therapeutic candidates that specifically target the viral spike protein. A database of ~ 850 naturally derived compounds was screened against SARS-CoV-2 spike protein to find natural inhibitors. Using virtual screening and inhibitory experiments, we identified acetyl 11-keto-boswellic acid (AKBA) as a promising molecule for spike protein, which encouraged us to scan the rest of AKBA derivatives in our in-house database via 2D-similarity searching. Later 19 compounds with > 85% similarity with AKBA were selected and docked with receptor binding domain (RBD) of spike protein. Those hits declared significant interactions at the RBD interface, best possess and excellent drug-likeness and pharmacokinetics properties with high gastrointestinal absorption (GIA) without toxicity and allergenicity. Our in-silico observations were eventually validated by in vitro bioassay, interestingly, 10 compounds (A3, A4, C3, C6A, C6B, C6C, C6E, C6H, C6I, and C6J) displayed significant inhibitory ability with good percent inhibition (range: > 72-90). The compounds C3 (90.00%), C6E (91.00%), C6C (87.20%), and C6D (86.23%) demonstrated excellent anti-SARS CoV-2 spike protein activities. The docking interaction of high percent inhibition of inhibitor compounds C3 and C6E was confirmed by MD Simulation. In the molecular dynamics simulation, we observed the stable dynamics of spike protein inhibitor complexes and the influence of inhibitor binding on the protein's conformational arrangements. The binding free energy ΔGTOTAL of C3 (-38.0 ± 0.08 kcal/mol) and C6E (-41.98 ± 0.08 kcal/mol) respectively indicate a strong binding affinity to Spike protein active pocket. These findings demonstrate that these molecules particularly inhibit the function of spike protein and, therefore have the potential to be evaluated as drug candidates against SARS-CoV-2.
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Affiliation(s)
- Atta Ullah
- Natural and Medical Sciences Research Center, University of Nizwa, Birkat-Ul-Mouz, P.O Box 33, Postal Code 616, Nizwa, Sultanate of Oman
| | - Saeed Ullah
- Natural and Medical Sciences Research Center, University of Nizwa, Birkat-Ul-Mouz, P.O Box 33, Postal Code 616, Nizwa, Sultanate of Oman
| | - Sobia Ahsan Halim
- Natural and Medical Sciences Research Center, University of Nizwa, Birkat-Ul-Mouz, P.O Box 33, Postal Code 616, Nizwa, Sultanate of Oman
| | - Muhammad Waqas
- Natural and Medical Sciences Research Center, University of Nizwa, Birkat-Ul-Mouz, P.O Box 33, Postal Code 616, Nizwa, Sultanate of Oman
| | - Basharat Ali
- Sulaiman Bin Abdullah Aba Al-Khail-Centre for Interdisciplinary Research in Basic Sciences (SA-CIRBS), International Islamic University, Islamabad, Pakistan
| | - Farid S Ataya
- Department of Biochemistry, College of Science, King Saud University, PO Box 2455, 11451, Riyadh, Saudi Arabia
| | - Nasser M El-Sabbagh
- Department of Veterinary Pharmacology, Faculty of Veterinary Medicine, Alexandria University, Edfina, Egypt
| | - Gaber El-Saber Batiha
- Department of Pharmacology and Therapeutics, Faculty of Veterinary Medicine, Damanhour University, Damanhour, 22511, AlBeheira, Egypt
| | - Satya Kumar Avula
- Natural and Medical Sciences Research Center, University of Nizwa, Birkat-Ul-Mouz, P.O Box 33, Postal Code 616, Nizwa, Sultanate of Oman
| | - Rene Csuk
- Organic Chemistry, Martin-Luther-University Halle-Wittenberg, Kurt-Mothes-Str. 2, 06120, Halle (Saale), Germany
| | - Ajmal Khan
- Natural and Medical Sciences Research Center, University of Nizwa, Birkat-Ul-Mouz, P.O Box 33, Postal Code 616, Nizwa, Sultanate of Oman.
| | - Ahmed Al-Harrasi
- Natural and Medical Sciences Research Center, University of Nizwa, Birkat-Ul-Mouz, P.O Box 33, Postal Code 616, Nizwa, Sultanate of Oman.
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Huang F, Chen C. Investigation of Bucillamine as anti-COVID-19 drug: DFT study, molecular docking, molecular dynamic simulation and ADMET analysis. J Biomol Struct Dyn 2024; 42:34-42. [PMID: 36995042 DOI: 10.1080/07391102.2023.2192791] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Accepted: 03/10/2023] [Indexed: 03/31/2023]
Abstract
The novel coronavirus disease-2019 (COVID-19), caused by SARS-CoV-2, is a global health pandemic beginning in early December 2019 in Wuhan, Hubei province, China. The effective drug target among coronaviruses is the SARS-CoV-2 main protease (Mpro), because of its crucial role in processing viral polyproteins translated from the viral RNA. In this study, the bioactivity of the selected thiol drug named Bucillamine (BUC) was evaluated as a potential drug for COVID-19 treatment by using computational modeling strategies. First, the molecular electrostatic potential density (ESP) calculation was performed to estimate the chemically active atoms of BUC. Additionally, BUC was docked to the Mpro (PDB: 6LU7) to evaluate the protein-ligand binding affinities. Besides, the estimated ESP results by density functional theory (DFT) were used to illustrate the molecular docking findings. Moreover, the frontier orbitals analysis was calculated to determine the charge transfer between the Mpro and BUC. Then, the stability of protein-ligand complex was subjected to the molecular dynamic simulations. Finally, an in silico study was performed to predict drug-likeness and absorption, distribution, metabolism, excretion and toxicity profiles (ADMET) of BUC. These results propose that BUC can be a potential drug candidate against the COVID-19 disease progression.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Fengwen Huang
- Key Laboratory of Neuroscience, Department of Biomedical Science, City University of HongKong, Hong Kong, China
- Shenzhen Key Laboratory of Marine Bioresources and Ecology, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, China
| | - Chen Chen
- Shenzhen Key Laboratory of Marine Bioresources and Ecology, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, China
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Gomaa AA, Abdel-Wadood YA, Gomaa MA. Glycyrrhizin and boswellic acids, the golden nutraceuticals: multitargeting for treatment of mild-moderate COVID-19 and prevention of post-COVID cognitive impairment. Inflammopharmacology 2022; 30:1977-1992. [PMID: 36136251 PMCID: PMC9493173 DOI: 10.1007/s10787-022-01062-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Accepted: 08/18/2022] [Indexed: 12/04/2022]
Abstract
Breakthrough infections have been reported in fully vaccinated persons. Furthermore, rebound symptoms have been reported following the new FDA granted emergency use to combat SARS-CoV-2. Glycyrrhizin (GR) and boswellic acids (BAs) combination has been shown to have highly successful actions against COVID-19 in our recent clinical trial. However, the study is limited by the small sample size, and therefore, the aim of this article is to comprehensively evaluate recent evidence on the efficacy of GR and BAs in preventing the development of COVID-19 in patients with mild and moderate infections and in preventing post-COVID-19 cognitive impairment, which is the most important symptom after recovery from Covid-19 disease. We have reviewed and discussed information published since the outbreak of the COVID-19 pandemic until July 2022 on preclinical (in vivo, in vivo and bioinformatics) and clinical studies related to the antiviral, anti-inflammatory and immunomodulatory activity of Gr and BAs. Sixteen studies were performed to determine the efficacy of GR against SARS-CoV-2. Ten studies were used primarily for in vitro and in vivo assays and six used molecular docking studies. However, the antiviral activity of BAs against SARS-CoV-2 was determined in only five studies using molecular modeling and bioinformatics. All these studies confirmed that GR n and BAs have strong antiviral activity and can be used as a therapeutic agent for COVID-19 and as a protective agent against SARS-CoV-2. They may act by inhibiting the main protease SARS-CoV-2 (Mpro) responsible for replication and blocking spike protein-mediated cell entry. Only seven rigorously designed clinical trials regarding the usefulness of GR, BAs or their combinations in the treatment of COVID-19 have been published as of July 2022. Although there is no clinical study regarding the treatment of cognitive impairment after COVID-19 that has been published so far, several preclinical and clinical studies have demonstrated the potential effect of GR and BAs in the prevention and treatment of cognitive impairment by inhibiting the activity of several molecules that activate inflammatory signaling pathway. In conclusion, the findings of our study documented the beneficial use of GR and BAs to treat SARS-CoV-2 and its variants and prevent post-COVID cognitive impairment. However, it warrants further studies with a larger randomized sample size to ensure that the studies have sufficient evidence of benefits against COVID-19 and post-COVID-19 symptoms.
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Affiliation(s)
- Adel A Gomaa
- Department of Pharmacology, Faculty of Medicine, Assiut University, Assiut, Egypt.
| | | | - Mohamed A Gomaa
- Department of Plastic Surgery, Faculty Medicine, Assiut University, Assiut, Egypt
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