1
|
Sohrab SS, Alsaqaf F, Hassan AM, Tolah AM, Bajrai LH, Azhar EI. Genomic Diversity and Recombination Analysis of the Spike Protein Gene from Selected Human Coronaviruses. Biology (Basel) 2024; 13:282. [PMID: 38666894 PMCID: PMC11048170 DOI: 10.3390/biology13040282] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2024] [Revised: 04/17/2024] [Accepted: 04/19/2024] [Indexed: 04/28/2024]
Abstract
Human coronaviruses (HCoVs) are seriously associated with respiratory diseases in humans and animals. The first human pathogenic SARS-CoV emerged in 2002-2003. The second was MERS-CoV, reported from Jeddah, the Kingdom of Saudi Arabia, in 2012, and the third one was SARS-CoV-2, identified from Wuhan City, China, in late December 2019. The HCoV-Spike (S) gene has the highest mutation/insertion/deletion rate and has been the most utilized target for vaccine/antiviral development. In this manuscript, we discuss the genetic diversity, phylogenetic relationships, and recombination patterns of selected HCoVs with emphasis on the S protein gene of MERS-CoV and SARS-CoV-2 to elucidate the possible emergence of new variants/strains of coronavirus in the near future. The findings showed that MERS-CoV and SARS-CoV-2 have significant sequence identity with the selected HCoVs. The phylogenetic tree analysis formed a separate cluster for each HCoV. The recombination pattern analysis showed that the HCoV-NL63-Japan was a probable recombinant. The HCoV-NL63-USA was identified as a major parent while the HCoV-NL63-Netherland was identified as a minor parent. The recombination breakpoints start in the viral genome at the 142 nucleotide position and end at the 1082 nucleotide position with a 99% CI and Bonferroni-corrected p-value of 0.05. The findings of this study provide insightful information about HCoV-S gene diversity, recombination, and evolutionary patterns. Based on these data, it can be concluded that the possible emergence of new strains/variants of HCoV is imminent.
Collapse
Affiliation(s)
- Sayed Sartaj Sohrab
- Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, P.O. Box 80216, Jeddah 21589, Saudi Arabia; (F.A.); (A.M.H.); (A.M.T.); (L.H.B.)
- Department of Medical Laboratory Sciences, Faculty of Applied Medical Sciences, King Abdulaziz University, P.O. Box 80216, Jeddah 21589, Saudi Arabia
| | - Fatima Alsaqaf
- Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, P.O. Box 80216, Jeddah 21589, Saudi Arabia; (F.A.); (A.M.H.); (A.M.T.); (L.H.B.)
| | - Ahmed Mohamed Hassan
- Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, P.O. Box 80216, Jeddah 21589, Saudi Arabia; (F.A.); (A.M.H.); (A.M.T.); (L.H.B.)
| | - Ahmed Majdi Tolah
- Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, P.O. Box 80216, Jeddah 21589, Saudi Arabia; (F.A.); (A.M.H.); (A.M.T.); (L.H.B.)
- Department of Medical Laboratory Sciences, Faculty of Applied Medical Science, King Abdulaziz University, P.O. Box 21911, Rabigh 344, Saudi Arabia
| | - Leena Hussein Bajrai
- Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, P.O. Box 80216, Jeddah 21589, Saudi Arabia; (F.A.); (A.M.H.); (A.M.T.); (L.H.B.)
- Biochemistry Department, Faculty of Sciences, King Abdulaziz University, P.O. Box 80216, Jeddah 21589, Saudi Arabia
| | - Esam Ibraheem Azhar
- Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, P.O. Box 80216, Jeddah 21589, Saudi Arabia; (F.A.); (A.M.H.); (A.M.T.); (L.H.B.)
- Department of Medical Laboratory Sciences, Faculty of Applied Medical Sciences, King Abdulaziz University, P.O. Box 80216, Jeddah 21589, Saudi Arabia
| |
Collapse
|
2
|
Bajrai LH, Almalki AA, Sahoo AK, Dwivedi VD, Azhar EI. Exploring plant-derived small molecules as inhibitors of Marburg virus RNA binding protein activity. J Biomol Struct Dyn 2024:1-11. [PMID: 38270432 DOI: 10.1080/07391102.2024.2306500] [Citation(s) in RCA: 0] [Impact Index Per Article: 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: 11/08/2023] [Accepted: 01/10/2024] [Indexed: 01/26/2024]
Abstract
The search for antiviral medications is greatly influenced by the hunt for potent inhibitors of viral proteins. To find possible inhibitors of the RNA binding activity of the Marburg virus VP35 protein, we used a thorough in silico drug discovery approach in this investigation. A comprehensive virtual screening process, followed by a detailed MMGBSA analysis, led to the discovery of four potential inhibitory compounds viz. Kudzuisoflavone A, Miquelianin, Rutin, and Protopseudohypericin. They were identified from an extensive library of phytomolecules derived from three medicinal plants: Adiantum capillus-veneris, Hypericum perforatum, and Pueraria montana. In molecular dynamics (MD) simulations, all these compounds showed steady binding to the target protein and favourable interactions. Notably, the free binding energies of all the selected compounds were better than the myricetin, a well-known blocker of the VP35 protein of the Ebola virus. Overall, this investigation offers insightful information about the molecular interactions and binding dynamics of the identified inhibitors' binding to the VP35 protein of the Marburg virus. The findings highlight the potential of three particular medicinal plants as sources of key chemicals for the creation of brand-new Marburg virus antiviral drugs. More experimental validation and optimization of the identified inhibitors are necessary in order to transform these findings into effective medicines for treating Marburg virus infections.Communicated by Ramaswamy H. Sarma.
Collapse
Affiliation(s)
- Leena Hussein Bajrai
- Special Infectious Agents Unit-BSL3, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
- Biochemistry Department, Faculty of Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Abdulrahman Abdullah Almalki
- Clinical Laboratory Department, King Abdulaziz University Hospital, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Amaresh Kumar Sahoo
- Department of Applied Sciences, Indian Institute of Information Technology Allahabad, Allahabad, India
| | - Vivek Dhar Dwivedi
- Center for Global Health Research, Saveetha Institute of Medical and Technical Sciences, Saveetha Medical College and Hospitals, Saveetha University, Chennai, India
- Bioinformatics Research Division, Quanta Calculus, Greater Noida, India
| | - Esam Ibraheem Azhar
- Special Infectious Agents Unit-BSL3, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
- Department of Medical Laboratory Sciences, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| |
Collapse
|
3
|
Bajrai LH, El-Kafrawy SA, Hassan AM, Tolah AM, Alnahas RS, Sohrab SS, Rehan M, Azhar EI. In vitro screening of anti-viral and virucidal effects against SARS-CoV-2 by Hypericum perforatum and Echinacea. Sci Rep 2022; 12:21723. [PMID: 36522420 PMCID: PMC9754313 DOI: 10.1038/s41598-022-26157-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Accepted: 12/12/2022] [Indexed: 12/23/2022] Open
Abstract
Hypericum perforatum and Echinacea are reported to have antiviral activities against several viral infections. In this study, H. perforatum (St. John's Wort) and Echinacea were tested in vitro using Vero E6 cells for their anti-viral effects against the newly identified Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) through its infectious cycle from 0 to 48 h post infection. The hypericin of H. perforatum and the different parts (roots, seeds, aerial) of two types of Echinacea species (Echinacea purpurea and Echinacea angustifolia) were tested for their anti-viral activities to measure the inhibition of viral load using quantitative real-time polymerase chain reaction (qRT-PCR) on cell culture assay. Interestingly, the H. perforatum-Echinacea mixture (1:1 ratio) of H. perforatum and Echinacea was tested as well on SARS-CoV-2 and showed crucial anti-viral activity competing H. perforatum then Echinacea effects as anti-viral treatment. Therefore, the results H. perforatum and Echinacea species, applied in this study showed significant anti-viral and virucidal effects in the following order of potency: H. perforatum, H. perforatum-Echinacea mixture, and Echinacea on SARS-CoV-2 infectious cycle. Additionally, molecular simulation analysis of the compounds with essential proteins (Mpro and RdRp) of the SARS-CoV-2 revealed the most potent bioactive compounds such as Echinacin, Echinacoside, Cyanin, Cyanidin 3-(6''-alonylglucoside, Quercetin-3-O-glucuronide, Proanthocyanidins, Rutin, Kaempferol-3-O-rutinoside, and Quercetin-3-O-xyloside. Thus, based on the outcome of this study, it is demanding the setup of clinical trial with specific therapeutic protocol.
Collapse
Affiliation(s)
- Leena Hussein Bajrai
- Special Infectious Agents Unit-BSL3, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia.
- Biochemistry Department, Faculty of Sciences, King Abdulaziz University, Jeddah, Saudi Arabia.
| | - Sherif Ali El-Kafrawy
- Special Infectious Agents Unit-BSL3, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
- Department of Medical Laboratory Sciences, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Ahmed Mohamed Hassan
- Special Infectious Agents Unit-BSL3, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Ahmed Majdi Tolah
- Special Infectious Agents Unit-BSL3, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
- Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, King Abdulaziz University, Rabig, Saudi Arabia
| | - Rabie Saleh Alnahas
- Special Infectious Agents Unit-BSL3, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Sayed Sartaj Sohrab
- Special Infectious Agents Unit-BSL3, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
- Department of Medical Laboratory Sciences, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Mohd Rehan
- Department of Medical Laboratory Sciences, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
- King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Esam Ibraheem Azhar
- Special Infectious Agents Unit-BSL3, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia.
- Department of Medical Laboratory Sciences, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, Saudi Arabia.
| |
Collapse
|
4
|
Bajrai LH, Khateb AM, Alawi MM, Felemban HR, Sindi AA, Dwivedi VD, Azhar EI. Glycosylated Flavonoid Compounds as Potent CYP121 Inhibitors of Mycobacterium tuberculosis. Biomolecules 2022; 12:1356. [PMID: 36291570 PMCID: PMC9599785 DOI: 10.3390/biom12101356] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Revised: 09/10/2022] [Accepted: 09/14/2022] [Indexed: 07/30/2023] Open
Abstract
Due to the concerning rise in the number of multiple- and prolonged-drug-resistant (MDR and XDR) Mycobacterium tuberculosis (Mtb) strains, unprecedented demand has been created to design and develop novel therapeutic drugs with higher efficacy and safety. In this study, with a focused view on implementing an in silico drug design pipeline, a diverse set of glycosylated flavonoids were screened against the Mtb cytochrome-P450 enzyme 121 (CYP121), which is established as an approved drug target for the treatment of Mtb infection. A total of 148 glycosylated flavonoids were screened using structure-based virtual screening against the crystallized ligand, i.e., the L44 inhibitor, binding pocket in the Mtb CYP121 protein. Following this, only the top six compounds with the highest binding scores (kcal/mol) were considered for further intermolecular interaction and dynamic stability using 100 ns classical molecular dynamics simulation. These results suggested a considerable number of hydrogen and hydrophobic interactions and thermodynamic stability in comparison to the reference complex, i.e., the CYP121-L44 inhibitor. Furthermore, binding free energy via the MMGBSA method conducted on the last 10 ns interval of MD simulation trajectories revealed the substantial affinity of glycosylated compounds with Mtb CYP121 protein against reference complex. Notably, both the docked poses and residual energy decomposition via the MMGBSA method demonstrated the essential role of active residues in the interactions with glycosylated compounds by comparison with the reference complex. Collectively, this study demonstrates the viability of these screened glycosylated flavonoids as potential inhibitors of Mtb CYP121 for further experimental validation to develop a therapy for the treatment of drug-resistant Mtb strains.
Collapse
Affiliation(s)
- Leena Hussein Bajrai
- Special Infectious Agents Unit-BSL3, King Fahd Medical Research Center, King Abdulaziz University, Jeddah 21362, Saudi Arabia
- Biochemistry Department, Faculty of Sciences, King Abdulaziz University, Jeddah 21362, Saudi Arabia
| | - Aiah M. Khateb
- Special Infectious Agents Unit-BSL3, King Fahd Medical Research Center, King Abdulaziz University, Jeddah 21362, Saudi Arabia
- Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, Taibah University, Madinah 42353, Saudi Arabia
| | - Maha M. Alawi
- Special Infectious Agents Unit-BSL3, King Fahd Medical Research Center, King Abdulaziz University, Jeddah 21362, Saudi Arabia
- Department of Medical Microbiology and Parasitology, Faculty of Medicine, King Abdulaziz University, Jeddah 21589, Saudi Arabia
- Infection Control & Environmental Health Unit, King Abdulaziz University Hospital, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Hashim R. Felemban
- Special Infectious Agents Unit-BSL3, King Fahd Medical Research Center, King Abdulaziz University, Jeddah 21362, Saudi Arabia
- Medical Laboratory Sciences Department, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah 21362, Saudi Arabia
| | - Anees A. Sindi
- Special Infectious Agents Unit-BSL3, King Fahd Medical Research Center, King Abdulaziz University, Jeddah 21362, Saudi Arabia
- Department of Anesthesia and Critical Care, Faculty of Medicine, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Vivek Dhar Dwivedi
- Bioinformatics Research Division, Quanta Calculus Pvt. Ltd., Greater Noida 201310, India
- Institute of Advanced Materials, IAAM, 59053 Ulrika, Sweden
| | - Esam Ibraheem Azhar
- Special Infectious Agents Unit-BSL3, King Fahd Medical Research Center, King Abdulaziz University, Jeddah 21362, Saudi Arabia
- Medical Laboratory Sciences Department, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah 21362, Saudi Arabia
| |
Collapse
|
5
|
Khouja HI, Ashankyty IM, Bajrai LH, Kumar PKP, Kamal MA, Firoz A, Mobashir M. Multi-staged gene expression profiling reveals potential genes and the critical pathways in kidney cancer. Sci Rep 2022; 12:7240. [PMID: 35508649 PMCID: PMC9065671 DOI: 10.1038/s41598-022-11143-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Accepted: 10/11/2021] [Indexed: 02/05/2023] Open
Abstract
Cancer is among the highly complex disease and renal cell carcinoma is the sixth-leading cause of cancer death. In order to understand complex diseases such as cancer, diabetes and kidney diseases, high-throughput data are generated at large scale and it has helped in the research and diagnostic advancement. However, to unravel the meaningful information from such large datasets for comprehensive and minute understanding of cell phenotypes and disease pathophysiology remains a trivial challenge and also the molecular events leading to disease onset and progression are not well understood. With this goal, we have collected gene expression datasets from publicly available dataset which are for two different stages (I and II) for renal cell carcinoma and furthermore, the TCGA and cBioPortal database have been utilized for clinical relevance understanding. In this work, we have applied computational approach to unravel the differentially expressed genes, their networks for the enriched pathways. Based on our results, we conclude that among the most dominantly altered pathways for renal cell carcinoma, are PI3K-Akt, Foxo, endocytosis, MAPK, Tight junction, cytokine-cytokine receptor interaction pathways and the major source of alteration for these pathways are MAP3K13, CHAF1A, FDX1, ARHGAP26, ITGBL1, C10orf118, MTO1, LAMP2, STAMBP, DLC1, NSMAF, YY1, TPGS2, SCARB2, PRSS23, SYNJ1, CNPPD1, PPP2R5E. In terms of clinical significance, there are large number of differentially expressed genes which appears to be playing critical roles in survival.
Collapse
Affiliation(s)
- Hamed Ishaq Khouja
- Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, Saudi Arabia.
| | - Ibraheem Mohammed Ashankyty
- Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Leena Hussein Bajrai
- Special Infectious Agents Unit-BSL3, King Fahad Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
- Biochemistry Department, Sciences College, King Abdulaziz University, Jeddah, Saudi Arabia
| | - P K Praveen Kumar
- Department of Biotechnology, Sri Venkateswara College of Engineering, Sriperumbudur, 602105, India
| | - Mohammad Amjad Kamal
- West China School of Nursing/Institutes for Systems Genetics, Frontiers Science Center for Disease-Related Molecular Network, West China Hospital, Sichuan University, Chengdu, 610041, Sichuan, China
- King Fahd Medical Research Center, King Abdulaziz University, P. O. Box 80216, Jeddah, 21589, Saudi Arabia
- Enzymoics, Novel Global Community Educational Foundation, 7 Peterlee Place, Hebersham, NSW, 2770, Australia
| | - Ahmad Firoz
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah, Kingdom of Saudi Arabia
| | - Mohammad Mobashir
- SciLifeLab, Department of Oncology and Pathology, Karolinska Institutet, Box 1031, 171 21, Stockholm, Sweden.
| |
Collapse
|
6
|
Bajrai LH, Sohrab SS, Mobashir M, Kamal MA, Rizvi MA, Azhar EI. Understanding the role of potential pathways and its components including hypoxia and immune system in case of oral cancer. Sci Rep 2021; 11:19576. [PMID: 34599215 PMCID: PMC8486818 DOI: 10.1038/s41598-021-98031-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Accepted: 09/02/2021] [Indexed: 02/08/2023] Open
Abstract
There are a few biological functions or phenomenon which are universally associated with majority of the cancers and hypoxia and immune systems are among them. Hypoxia often occurs in most of the cancers which helps the cells in adapting different responses with respect to the normal cells which may be the activation of signaling pathways which regulate proliferation, angiogenesis, and cell death. Similar to it, immune signaling pathways are known to play critical roles in cancers. Moreover, there are a number of genes which are known to be associated with these hypoxia and immune system and appear to direct affect the tumor growth and propagations. Cancer is among the leading cause of death and oral cancer is the tenth-leading cause due to cancer death. In this study, we were mainly interested to understand the impact of alteration in the expression of hypoxia and immune system-related genes and their contribution to head and neck squamous cell carcinoma. Moreover, we have collected the genes associated with hypoxia and immune system from the literatures. In this work, we have performed meta-analysis of the gene and microRNA expression and mutational datasets obtained from public database for different grades of tumor in case of oral cancer. Based on our results, we conclude that the critical pathways which dominantly enriched are associated with metabolism, cell cycle, immune system and based on the survival analysis of the hypoxic genes, we observe that the potential genes associated with head and neck squamous cell carcinoma and its progression are STC2, PGK1, P4HA1, HK1, SPIB, ANXA5, SERPINE1, HGF, PFKM, TGFB1, L1CAM, ELK4, EHF, and CDK2.
Collapse
Affiliation(s)
- Leena Hussein Bajrai
- Special Infectious Agents Unit, King Fahd Medical Research Centre, King Abdulaziz University, Jeddah, Saudi Arabia.,Biochemistry Department, Faculty of Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Sayed Sartaj Sohrab
- Special Infectious Agents Unit, King Fahd Medical Research Centre, King Abdulaziz University, Jeddah, Saudi Arabia.,Medical Laboratory Sciences Department, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Mohammad Mobashir
- Department of Microbiology, Tumor and Cell Biology (MTC) Karolinska Institute, Novels väg 16, Solna, 17165, Stockholm, Sweden. .,The Genome Biology Lab, Department of Biosciences, Jamia Millia Islamia, New Delhi, 110025, India. .,SciLifeLab, Department of Oncology and Pathology, Karolinska Institutet, P. O. Box 1031, 17121, Stockholm, Sweden.
| | - Mohammad Amjad Kamal
- West China School of Nursing / Institutes for Systems Genetics, Frontiers Science Center for Disease-Related Molecular Network, West China Hospital, Sichuan University, Chengdu, 610041, Sichuan, China.,King Fahd Medical Research Center, King Abdulaziz University, P. O. Box 80216, Jeddah, 21589, Saudi Arabia.,Enzymoics, Novel Global Community Educational Foundation, 7 Peterlee Place, Hebersham, NSW, 2770, Australia
| | - Moshahid Alam Rizvi
- The Genome Biology Lab, Department of Biosciences, Jamia Millia Islamia, New Delhi, 110025, India
| | - Esam Ibraheem Azhar
- Special Infectious Agents Unit, King Fahd Medical Research Centre, King Abdulaziz University, Jeddah, Saudi Arabia. .,Medical Laboratory Sciences Department, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, Saudi Arabia.
| |
Collapse
|
7
|
Bharadwaj S, El-Kafrawy SA, Alandijany TA, Bajrai LH, Shah AA, Dubey A, Sahoo AK, Yadava U, Kamal MA, Azhar EI, Kang SG, Dwivedi VD. Structure-Based Identification of Natural Products as SARS-CoV-2 M pro Antagonist from Echinacea angustifolia Using Computational Approaches. Viruses 2021; 13:305. [PMID: 33672054 PMCID: PMC7919488 DOI: 10.3390/v13020305] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Revised: 02/05/2021] [Accepted: 02/10/2021] [Indexed: 12/14/2022] Open
Abstract
Coronavirus disease-19 (COVID-19) pandemic, caused by the novel SARS-CoV-2 virus, continues to be a global threat. The number of cases and deaths will remain escalating due to the lack of effective therapeutic agents. Several studies have established the importance of the viral main protease (Mpro) in the replication of SARS-CoV-2 which makes it an attractive target for antiviral drug development, including pharmaceutical repurposing and other medicinal chemistry approaches. Identification of natural products with considerable inhibitory potential against SARS-CoV-2 could be beneficial as a rapid and potent alternative with drug-likeness by comparison to de novo antiviral drug discovery approaches. Thereof, we carried out the structure-based screening of natural products from Echinacea-angustifolia, commonly used to prevent cold and other microbial respiratory infections, targeting SARS-CoV-2 Mpro. Four natural products namely, Echinacoside, Quercetagetin 7-glucoside, Levan N, Inulin from chicory, and 1,3-Dicaffeoylquinic acid, revealed significant docking energy (>-10 kcal/mol) in the SARS-CoV-2 Mpro catalytic pocket via substantial intermolecular contacts formation against co-crystallized ligand (<-4 kcal/mol). Furthermore, the docked poses of SARS-CoV-2 Mpro with selected natural products showed conformational stability through molecular dynamics. Exploring the end-point net binding energy exhibited substantial contribution of Coulomb and van der Waals interactions to the stability of respective docked conformations. These results advocated the natural products from Echinacea angustifolia for further experimental studies with an elevated probability to discover the potent SARS-CoV-2 Mpro antagonist with higher affinity and drug-likeness.
Collapse
Affiliation(s)
- Shiv Bharadwaj
- Department of Biotechnology, Institute of Biotechnology, College of Life and Applied Sciences, Yeungnam University, 280 Daehak-Ro, Gyeongsan, Gyeongbuk 38541, Korea;
| | - Sherif Aly El-Kafrawy
- Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, 21589 Jeddah, Saudi Arabia; (S.A.E.-K.); (T.A.A.); (L.H.B.); (M.A.K.)
- Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Thamir A. Alandijany
- Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, 21589 Jeddah, Saudi Arabia; (S.A.E.-K.); (T.A.A.); (L.H.B.); (M.A.K.)
- Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Leena Hussein Bajrai
- Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, 21589 Jeddah, Saudi Arabia; (S.A.E.-K.); (T.A.A.); (L.H.B.); (M.A.K.)
- Biochemistry Department, Faculty of Sciences, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Altaf Ahmad Shah
- Department of Biosciences, Integral University, Lucknow 226026, India;
| | - Amit Dubey
- Computational Chemistry and Drug Discovery Division, Quanta Calculus Pvt. Ltd., Kushinagar 274203, India;
| | - Amaresh Kumar Sahoo
- Department of Applied Sciences, Indian Institute of Information Technology Allahabad, Allahabad 211015, Uttar Pradesh, India;
| | - Umesh Yadava
- Department of Physics, Deen Dayal Upadhyay Gorakhpur University, Gorakhpur 273009, India;
| | - Mohammad Amjad Kamal
- Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, 21589 Jeddah, Saudi Arabia; (S.A.E.-K.); (T.A.A.); (L.H.B.); (M.A.K.)
- Enzymoics, 7 Peterlee Place, Novel Global Community Educational Foundation, Hebersham, NSW 2770, Australia
| | - Esam Ibraheem Azhar
- Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, 21589 Jeddah, Saudi Arabia; (S.A.E.-K.); (T.A.A.); (L.H.B.); (M.A.K.)
- Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Sang Gu Kang
- Department of Biotechnology, Institute of Biotechnology, College of Life and Applied Sciences, Yeungnam University, 280 Daehak-Ro, Gyeongsan, Gyeongbuk 38541, Korea;
| | - Vivek Dhar Dwivedi
- Centre for Bioinformatics, Computational and Systems Biology, Pathfinder Research and Training Foundation, Greater Noida 201308, India
| |
Collapse
|
8
|
Bharadwaj S, Azhar EI, Kamal MA, Bajrai LH, Dubey A, Jha K, Yadava U, Kang SG, Dwivedi VD. SARS-CoV-2 M pro inhibitors: identification of anti-SARS-CoV-2 M pro compounds from FDA approved drugs. J Biomol Struct Dyn 2020; 40:2769-2784. [PMID: 33150855 PMCID: PMC7651494 DOI: 10.1080/07391102.2020.1842807] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Recent outbreak of COVID-19 pandemic caused by severe acute respiratory syndrome-Coronavirus-2 (SARS-CoV-2) has raised serious global concern for public health. The viral main 3-chymotrypsin-like cysteine protease (Mpro), known to control coronavirus replication and essential for viral life cycle, has been established as an essential drug discovery target for SARS-CoV-2. Herein, we employed computationally screening of Druglib database containing FDA approved drugs against active pocket of SARS-CoV-2 Mpro using MTiopen screen web server, yields a total of 1051 FDA approved drugs with docking energy >-7 kcal/mol. The top 10 screened potential compounds against SARS-CoV-2 Mpro were then studied by re-docking, binding affinity, intermolecular interaction, and complex stability via 100 ns all atoms molecular dynamics (MD) simulation followed by post-simulation analysis, including end point binding free energy, essential dynamics, and residual correlation analysis against native crystal structure ligand N3 inhibitor. Based on comparative molecular simulation and interaction profiling of the screened drugs with SARS-CoV-2 Mpro revealed R428 (-10.5 kcal/mol), Teniposide (-9.8 kcal/mol), VS-5584 (-9.4 kcal/mol), and Setileuton (-8.5 kcal/mol) with stronger stability and affinity than other drugs and N3 inhibitor; and hence, these drugs are advocated for further validation using in vitro enzyme inhibition and in vivo studies against SARS-CoV-2 infection.Communicated by Ramaswamy H. Sarma.
Collapse
Affiliation(s)
- Shiv Bharadwaj
- Department of Biotechnology, Institute of Biotechnology, College of Life and Applied Sciences, Yeungnam University, Gyeongsan, Republic of Korea
| | - Esam Ibraheem Azhar
- Medical Laboratory Sciences Department, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, Saudi Arabia.,Special Infectious Agents Unit, King Fahd Medical Research Centre, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Mohammad Amjad Kamal
- King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia.,Enzymoics, Novel Global Community Educational Foundation, Hebersham, Australia
| | - Leena Hussein Bajrai
- Special Infectious Agents Unit, King Fahd Medical Research Centre, King Abdulaziz University, Jeddah, Saudi Arabia.,Biochemistry Department, Faculty of Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Amit Dubey
- Department of Biochemistry, University of Allahabad, Prayagraj, India
| | - Kanupriya Jha
- Center for Bioinformatics, Computational and System Biology, Pathfinder Research and Training Foundation, Greater Noida, India
| | - Umesh Yadava
- Department of Physics, Deen Dayal Upadhyaya Gorakhpur University, Gorakhpur, India
| | - Sang Gu Kang
- Department of Biotechnology, Institute of Biotechnology, College of Life and Applied Sciences, Yeungnam University, Gyeongsan, Republic of Korea
| | - Vivek Dhar Dwivedi
- Center for Bioinformatics, Computational and System Biology, Pathfinder Research and Training Foundation, Greater Noida, India
| |
Collapse
|
9
|
Bajrai LH, Azhar EI, Yasir M, Jardot P, Barrassi L, Raoult D, La Scola B, Pagnier I. Legionella saoudiensis sp. nov., isolated from a sewage water sample. Int J Syst Evol Microbiol 2016; 66:4367-4371. [DOI: 10.1099/ijsem.0.001357] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Leena Hussein Bajrai
- Department of Biochemistry, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
- Unité des Rickettsies, URMITE UMR CNRS 7278 IRD 198 INSERM U1095, Facultés de Médecine et de Pharmacie, IHU Méditerranée Infection, Aix-Marseille Université, 27 Boulevard Jean Moulin, 13385 Marseille Cedex 05, France
| | - Esam Ibraheem Azhar
- Department of Medical Laboratory Technology, Special Infectious Agents Unit, King Fahd Medical Research Center, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Muhammad Yasir
- Department of Medical Laboratory Technology, Special Infectious Agents Unit, King Fahd Medical Research Center, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Priscilla Jardot
- Unité des Rickettsies, URMITE UMR CNRS 7278 IRD 198 INSERM U1095, Facultés de Médecine et de Pharmacie, IHU Méditerranée Infection, Aix-Marseille Université, 27 Boulevard Jean Moulin, 13385 Marseille Cedex 05, France
| | - Lina Barrassi
- Unité des Rickettsies, URMITE UMR CNRS 7278 IRD 198 INSERM U1095, Facultés de Médecine et de Pharmacie, IHU Méditerranée Infection, Aix-Marseille Université, 27 Boulevard Jean Moulin, 13385 Marseille Cedex 05, France
| | - Didier Raoult
- Unité des Rickettsies, URMITE UMR CNRS 7278 IRD 198 INSERM U1095, Facultés de Médecine et de Pharmacie, IHU Méditerranée Infection, Aix-Marseille Université, 27 Boulevard Jean Moulin, 13385 Marseille Cedex 05, France
| | - Bernard La Scola
- Unité des Rickettsies, URMITE UMR CNRS 7278 IRD 198 INSERM U1095, Facultés de Médecine et de Pharmacie, IHU Méditerranée Infection, Aix-Marseille Université, 27 Boulevard Jean Moulin, 13385 Marseille Cedex 05, France
| | - Isabelle Pagnier
- Unité des Rickettsies, URMITE UMR CNRS 7278 IRD 198 INSERM U1095, Facultés de Médecine et de Pharmacie, IHU Méditerranée Infection, Aix-Marseille Université, 27 Boulevard Jean Moulin, 13385 Marseille Cedex 05, France
| |
Collapse
|