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Islam MR, Biswas S, Amena U, Rahman M, Islam S, Islam MA, Saleh MA, Hassan HM, Al‐Emam A, Zaki MEA. Modified oxymatrine as novel therapeutic inhibitors against Monkeypox and Marburg virus through computational drug design approaches. J Cell Mol Med 2024; 28:e70116. [PMID: 39340487 PMCID: PMC11437895 DOI: 10.1111/jcmm.70116] [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: 03/21/2024] [Revised: 08/06/2024] [Accepted: 09/17/2024] [Indexed: 09/30/2024] Open
Abstract
Global impact of viral diseases specially Monkeypox (mpox) and Marburg virus, emphasizing the urgent need for effective drug interventions. Oxymatrine is an alkaloid which has been selected and modified using various functional groups to enhance its efficacy. The modifications were evaluated using various computatioanal analysis such as pass prediction, molecular docking, ADMET, and molecular dynamic simulation. Mpox and Marburg virus were chosen as target diseases based on their maximum pass prediction spectrum against viral disease. After that, molecular docking, dynamic simulation, DFT, calculation and ADMET prediction were determined. The main objective of this study was to enhance the efficacy of oxymatrine derivatives through functional group modifications and computational analyses to develop effective drug candidates against mpox and Marburg viruses. The calculated binding affinities indicated strong interactions against both mpox virus and Marburg virus. After that, the molecular dynamic simulation was conducted at 100 ns, which confirmed the stability of the binding interactions between the modified oxymatrine derivatives and target proteins. Then, the modified oxymatrine derivatives conducted theoretical ADMET profiling, which demonstrated their potential for effective drug development. Moreover, HOMO-LUMO calculation was performed to understand the chemical reactivity and physicochemical properties of compounds. This computational analysis indicated that modified oxymatrine derivatives for the treatment of mpox and Marburg virus suggested effective drug candidates based on their binding affinity, drug-like properties, stability and chemical reactivity. However, further experimental validation is necessary to confirm their clinical value and efficacy as therapeutic candidates.
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Affiliation(s)
- Md. Rezaul Islam
- Department of Pharmacy, Faculty of Allied Health SciencesDaffodil International UniversityAshuliaDhakaBangladesh
| | - Suvro Biswas
- Department of Genetic Engineering and BiotechnologyUniversity of RajshahiRajshahiBangladesh
| | - Ummy Amena
- Department of Pharmacy, Faculty of Life & Earth SciencesJagannath UniversityDhakaBangladesh
| | - Miadur Rahman
- Department of Pharmaceutical SciencesNorth South UniversityDhakaBangladesh
| | - Shirmin Islam
- Department of Genetic Engineering and BiotechnologyUniversity of RajshahiRajshahiBangladesh
| | - Md. Ariful Islam
- Department of Genetic Engineering and BiotechnologyUniversity of RajshahiRajshahiBangladesh
| | - Md. Abu Saleh
- Department of Genetic Engineering and BiotechnologyUniversity of RajshahiRajshahiBangladesh
| | - Hesham M. Hassan
- Department of Pathology, College of MedicineKing Khalid UniversityAsirSaudi Arabia
| | - Ahmed Al‐Emam
- Department of Pathology, College of MedicineKing Khalid UniversityAsirSaudi Arabia
| | - Magdi E. A. Zaki
- Department of Chemistry, College of ScienceImam Mohammad Ibn Saud Islamic University RiyadhRiyadhSaudi Arabia
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Mahendran TR, Cynthia B, Thevendran R, Maheswaran S. Prospects of Innovative Therapeutics in Combating the COVID-19 Pandemic. Mol Biotechnol 2024:10.1007/s12033-024-01240-4. [PMID: 39085563 DOI: 10.1007/s12033-024-01240-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2024] [Accepted: 07/03/2024] [Indexed: 08/02/2024]
Abstract
The sudden global crisis of COVID-19, driven by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), demands swift containment measures due to its rapid spread and numerous problematic mutations, which complicate the establishment of herd immunity. With escalating fatalities across various nations no foreseeable end in sight, there is a pressing need to create swiftly deployable, rapid, cost-effective detection, and treatment methods. While various steps are taken to mitigate the transmission and severity of the disease, vaccination is proven throughout mankind history as the best method to acquire immunity and circumvent the spread of infectious diseases. Nonetheless, relying solely on vaccination might not be adequate to match the relentless viral mutations observed in emerging variants of SARS-CoV-2, including alterations to their RBD domain, acquisition of escape mutations, and potential resistance to antibody binding. Beyond the immune system activation achieved through vaccination, it is crucial to develop new medications or treatment methods to either impede the infection or enhance existing treatment modalities. This review emphasizes innovative treatment strategies that aim to directly disrupt the virus's ability to replicate and spread, which could play a role in ending the SARS-CoV-2 pandemic.
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Affiliation(s)
- Thamby Rajah Mahendran
- School of Biological Sciences, Universiti Sains Malaysia, 11800, Minden, Penang, Malaysia
| | - Binsin Cynthia
- School of Biological Sciences, Universiti Sains Malaysia, 11800, Minden, Penang, Malaysia
| | - Ramesh Thevendran
- Centre of Excellence for Nanobiotechnology & Nanomedicine (CoExNano), Faculty of Applied Sciences, AIMST University, 08100, Bedong, Kedah, Malaysia
- Faculty of Applied Sciences, AIMST University, 08100, Bedong, Kedah, Malaysia
| | - Solayappan Maheswaran
- Centre of Excellence for Nanobiotechnology & Nanomedicine (CoExNano), Faculty of Applied Sciences, AIMST University, 08100, Bedong, Kedah, Malaysia.
- Faculty of Applied Sciences, AIMST University, 08100, Bedong, Kedah, Malaysia.
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3
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Inniss NL, Rzhetskaya M, Ling-Hu T, Lorenzo-Redondo R, Bachta KE, Satchell KJF, Hultquist JF. Activity and inhibition of the SARS-CoV-2 Omicron nsp13 R392C variant using RNA duplex unwinding assays. SLAS DISCOVERY : ADVANCING LIFE SCIENCES R & D 2024; 29:100145. [PMID: 38301954 PMCID: PMC11160173 DOI: 10.1016/j.slasd.2024.01.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/03/2024] [Accepted: 01/29/2024] [Indexed: 02/03/2024]
Abstract
SARS-CoV-2 nsp13 helicase is an essential enzyme for viral replication and a promising target for antiviral drug development. This study compares the double-stranded RNA (dsRNA) unwinding activity of nsp13 and the Omicron nsp13R392C variant, which is predominant in currently circulating lineages. Using in vitro gel- and fluorescence-based assays, we found that both nsp13 and nsp13R392C have dsRNA unwinding activity with equivalent kinetics. Furthermore, the R392C mutation had no effect on the efficiency of the nsp13-specific helicase inhibitor SSYA10-001. We additionally confirmed the activity of several other helicase inhibitors against nsp13, including punicalagin that inhibited dsRNA unwinding at nanomolar concentrations. Overall, this study reveals the utility of using dsRNA unwinding assays to screen small molecules for antiviral activity against nsp13 and the Omicron nsp13R392C variant. Continual monitoring of newly emergent variants will be essential for considering resistance profiles of lead compounds as they are advanced towards next-generation therapeutic development.
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Affiliation(s)
- Nicole L Inniss
- Department of Microbiology-Immunology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611 USA; Center for Structural Biology of Infectious Diseases, Northwestern University Feinberg School of Medicine, Chicago, IL 60611 USA
| | - Margarita Rzhetskaya
- Department of Microbiology-Immunology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611 USA; Department of Medicine, Division of Infectious Diseases, Northwestern University Feinberg School of Medicine, Chicago, IL 60611 USA; Center for Pathogen Genomics and Microbial Evolution, Havey Institute for Global Health, Northwestern University Feinberg School of Medicine, Chicago, IL 60611 USA
| | - Ted Ling-Hu
- Department of Microbiology-Immunology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611 USA; Department of Medicine, Division of Infectious Diseases, Northwestern University Feinberg School of Medicine, Chicago, IL 60611 USA; Center for Pathogen Genomics and Microbial Evolution, Havey Institute for Global Health, Northwestern University Feinberg School of Medicine, Chicago, IL 60611 USA
| | - Ramon Lorenzo-Redondo
- Department of Medicine, Division of Infectious Diseases, Northwestern University Feinberg School of Medicine, Chicago, IL 60611 USA; Center for Pathogen Genomics and Microbial Evolution, Havey Institute for Global Health, Northwestern University Feinberg School of Medicine, Chicago, IL 60611 USA
| | - Kelly E Bachta
- Department of Medicine, Division of Infectious Diseases, Northwestern University Feinberg School of Medicine, Chicago, IL 60611 USA; Center for Pathogen Genomics and Microbial Evolution, Havey Institute for Global Health, Northwestern University Feinberg School of Medicine, Chicago, IL 60611 USA
| | - Karla J F Satchell
- Department of Microbiology-Immunology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611 USA; Center for Structural Biology of Infectious Diseases, Northwestern University Feinberg School of Medicine, Chicago, IL 60611 USA; Center for Pathogen Genomics and Microbial Evolution, Havey Institute for Global Health, Northwestern University Feinberg School of Medicine, Chicago, IL 60611 USA.
| | - Judd F Hultquist
- Department of Microbiology-Immunology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611 USA; Department of Medicine, Division of Infectious Diseases, Northwestern University Feinberg School of Medicine, Chicago, IL 60611 USA; Center for Pathogen Genomics and Microbial Evolution, Havey Institute for Global Health, Northwestern University Feinberg School of Medicine, Chicago, IL 60611 USA.
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4
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Alipour Z, Zarezadeh S, Ghotbi-Ravandi AA. The Potential of Anti-coronavirus Plant Secondary Metabolites in COVID-19 Drug Discovery as an Alternative to Repurposed Drugs: A Review. PLANTA MEDICA 2024; 90:172-203. [PMID: 37956978 DOI: 10.1055/a-2209-6357] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2023]
Abstract
In early 2020, a global pandemic was announced due to the emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), known to cause COVID-19. Despite worldwide efforts, there are only limited options regarding antiviral drug treatments for COVID-19. Although vaccines are now available, issues such as declining efficacy against different SARS-CoV-2 variants and the aging of vaccine-induced immunity highlight the importance of finding more antiviral drugs as a second line of defense against the disease. Drug repurposing has been used to rapidly find COVID-19 therapeutic options. Due to the lack of clinical evidence for the therapeutic benefits and certain serious side effects of repurposed antivirals, the search for an antiviral drug against SARS-CoV-2 with fewer side effects continues. In recent years, numerous studies have included antiviral chemicals from a variety of plant species. A better knowledge of the possible antiviral natural products and their mechanism against SARS-CoV-2 will help to develop stronger and more targeted direct-acting antiviral agents. The aim of the present study was to compile the current data on potential plant metabolites that can be investigated in COVID-19 drug discovery and development. This review represents a collection of plant secondary metabolites and their mode of action against SARS-CoV and SARS-CoV-2.
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Affiliation(s)
- Zahra Alipour
- Department of Plant Sciences and Biotechnology, Faculty of Life Sciences and Biotechnology, Shahid Beheshti University, Tehran, Iran
| | - Somayeh Zarezadeh
- Department of Plant Sciences and Biotechnology, Faculty of Life Sciences and Biotechnology, Shahid Beheshti University, Tehran, Iran
| | - Ali Akbar Ghotbi-Ravandi
- Department of Plant Sciences and Biotechnology, Faculty of Life Sciences and Biotechnology, Shahid Beheshti University, Tehran, Iran
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5
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Biswas S, Mita MA, Afrose S, Hasan MR, Shimu MSS, Zaman S, Saleh MA. An in silico approach to develop potential therapies against Middle East Respiratory Syndrome Coronavirus (MERS-CoV). Heliyon 2024; 10:e25837. [PMID: 38379969 PMCID: PMC10877303 DOI: 10.1016/j.heliyon.2024.e25837] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Revised: 02/02/2024] [Accepted: 02/02/2024] [Indexed: 02/22/2024] Open
Abstract
A deadly respiratory disease Middle East Respiratory Syndrome (MERS) is caused by a perilous virus known as MERS-CoV, which has a severe impact on human health. Currently, there is no approved vaccine, prophylaxis, or antiviral therapeutics for preventing MERS-CoV infection. Due to its inexorable and integral role in the maturation and replication of the MERS-CoV virus, the 3C-like protease is unavoidly a viable therapeutic target. In this study, 2369 phytoconstituents were enlisted from Japanese medicinal plants, and these compounds were screened against 3C-like protease to identify feasible inhibitors. The best three compounds were identified as Kihadanin B, Robustaflavone, and 3-beta-O- (trans-p-Coumaroyl) maslinic acid, with binding energies of -9.8, -9.4, and -9.2 kcal/mol, respectively. The top three potential candidates interacted with several active site residues in the targeted protein, including Cys145, Met168, Glu169, Ala171, and Gln192. The best three compounds were assessed by in silico technique to determine their drug-likeness properties, and they exhibited the least harmful features and the greatest drug-like qualities. Various descriptors, such as solvent-accessible surface area, root-mean-square fluctuation, root-mean-square deviation, hydrogen bond, and radius of gyration, validated the stability and firmness of the protein-ligand complexes throughout the 100ns molecular dynamics simulation. Moreover, the top three compounds exhibited better binding energy along with better stability and firmness than the inhibitor (Nafamostat), which was further confirmed by the binding free energy calculation. Therefore, this computational investigation could aid in the development of efficient therapeutics for life-threatening MERS-CoV infections.
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Affiliation(s)
- Suvro Biswas
- Microbiology Laboratory, Department of Genetic Engineering and Biotechnology, University of Rajshahi, Rajshahi, 6205, Bangladesh
| | - Mohasana Akter Mita
- Department of Genetic Engineering and Biotechnology, University of Rajshahi, Rajshahi, 6205, Bangladesh
| | - Shamima Afrose
- Department of Genetic Engineering and Biotechnology, University of Rajshahi, Rajshahi, 6205, Bangladesh
| | - Md. Robiul Hasan
- Department of Genetic Engineering and Biotechnology, University of Rajshahi, Rajshahi, 6205, Bangladesh
| | | | - Shahriar Zaman
- Microbiology Laboratory, Department of Genetic Engineering and Biotechnology, University of Rajshahi, Rajshahi, 6205, Bangladesh
| | - Md. Abu Saleh
- Microbiology Laboratory, Department of Genetic Engineering and Biotechnology, University of Rajshahi, Rajshahi, 6205, Bangladesh
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Liu J, Mu D, Xu J, Liu Y, Zhang G, Tang Y, Wang D, Wang F, Liang D, Hou Y. Inhibition of TLR4 Signaling by Isorhapontigenin Targeting of the AHR Alleviates Cerebral Ischemia/Reperfusion Injury. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023; 71:13270-13283. [PMID: 37624928 DOI: 10.1021/acs.jafc.3c00152] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/27/2023]
Abstract
Ischemic stroke is a major risk factor in human health, yet there are no drugs to cure cerebral ischemia/reperfusion injury (CIRI). Inflammation plays a fundamental role in the consequences of CIRI. Isorhapontigenin (ISOR) exhibits great anti-inflammatory activity; however, it is unclear whether ISOR can treat ischemic stroke through an anti-inflammation effect. Here, middle cerebral artery occlusion/reperfusion (MCAO/R) was used to investigate the effects of ISOR on CIRI. The in vitro activity was measured in BV-2 cells exposed to oxygen-glucose deprivation/reperfusion. As measured by neurological scores, brain water content, and infarction, neurological dysfunction was improved in the ISOR group. The neuronal death and microglial activation in the ipsilateral cortex were reduced by ISOR. TLR4 signaling was significantly inhibited by ISOR in vivo and in vitro. By reverse molecular docking, cellular thermal shift, and drug affinity-responsive target stability assays, an aryl hydrocarbon receptor (AHR) was found to be a target of ISOR. Furthermore, AHR knockdown blocked the effect of ISOR on TLR4 signaling, suggesting that ISOR may regulate TLR4-mediated inflammation through AHR, thereby protecting neurons from CIRI. This study demonstrated that ISOR is a promising drug candidate for the treatment of ischemic stroke and provided a theoretical basis for the development of the medicinal value of ISOR-derived foods, such as grapes.
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Affiliation(s)
- Jingyu Liu
- Key Laboratory of Bioresource Research and Development of Liaoning Province, College of Life and Health Sciences, Northeastern University, Shenyang 110167, China
- National Frontiers Science Center for Industrial Intelligence and Systems Optimization, Key Laboratory of Data Analytics and Optimization for Smart Industry, Ministry of Education, Northeastern University, Shenyang 110167, China
| | - Danyang Mu
- Key Laboratory of Bioresource Research and Development of Liaoning Province, College of Life and Health Sciences, Northeastern University, Shenyang 110167, China
- National Frontiers Science Center for Industrial Intelligence and Systems Optimization, Key Laboratory of Data Analytics and Optimization for Smart Industry, Ministry of Education, Northeastern University, Shenyang 110167, China
| | - Jikai Xu
- Key Laboratory of Bioresource Research and Development of Liaoning Province, College of Life and Health Sciences, Northeastern University, Shenyang 110167, China
- National Frontiers Science Center for Industrial Intelligence and Systems Optimization, Key Laboratory of Data Analytics and Optimization for Smart Industry, Ministry of Education, Northeastern University, Shenyang 110167, China
| | - Yueyang Liu
- Department of Pharmacology, Shenyang Pharmaceutical University, Shenyang 110016, China
| | - Guijie Zhang
- College of Pharmacy, Guilin Medical University, Guilin 541004, China
| | - Yue Tang
- Key Laboratory of Bioresource Research and Development of Liaoning Province, College of Life and Health Sciences, Northeastern University, Shenyang 110167, China
| | - Dequan Wang
- Key Laboratory of Bioresource Research and Development of Liaoning Province, College of Life and Health Sciences, Northeastern University, Shenyang 110167, China
| | - Feng Wang
- Key Laboratory of Bioresource Research and Development of Liaoning Province, College of Life and Health Sciences, Northeastern University, Shenyang 110167, China
| | - Dong Liang
- State Key Laboratory for Chemistry and Molecular Engineering of Medicinal Resources, School of Chemistry and Pharmaceutical Sciences, Guangxi Normal University, Guilin 541004, China
| | - Yue Hou
- Key Laboratory of Bioresource Research and Development of Liaoning Province, College of Life and Health Sciences, Northeastern University, Shenyang 110167, China
- National Frontiers Science Center for Industrial Intelligence and Systems Optimization, Key Laboratory of Data Analytics and Optimization for Smart Industry, Ministry of Education, Northeastern University, Shenyang 110167, China
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Li Z, Yang B, Ding Y, Meng J, Hu J, Zhou X, Liu L, Wu Z, Yang S. Insights into a class of natural eugenol and its optimized derivatives as potential tobacco mosaic virus helicase inhibitors by structure-based virtual screening. Int J Biol Macromol 2023; 248:125892. [PMID: 37473893 DOI: 10.1016/j.ijbiomac.2023.125892] [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: 02/15/2023] [Revised: 06/13/2023] [Accepted: 07/17/2023] [Indexed: 07/22/2023]
Abstract
Plant diseases caused by malignant and refractory phytopathogenic viruses have considerably restricted crop yields and quality. To date, drug design targeting functional proteins or enzymes of viruses is an efficient and viable strategy to guide the development of new pesticides. Herein, a series of novel eugenol derivatives targeting the tobacco mosaic virus (TMV) helicase have been designed using structure-based virtual screening (SBVS). Structure-activity relationship indicated that 2 t displayed the most powerful bonding capability (Kd = 0.2 μM) along with brilliant TMV helicase ATPase inhibitory potency (IC50 = 141.9 μM) and applausive anti-TMV capability (EC50 = 315.7 μg/mL), ostentatiously outperforming that of commercial Acyclovir (Kd = 23.0 μM, IC50 = 183.7 μM) and Ribavirin (EC50 = 624.3 μg/mL). Molecular dynamics simulations and docking suggested ligand 2 t was stable and bound in the active pocket of the TMV helicase by multiple interactions. Given these superior properties, eugenol-based derivatives could be considered as the novel potential plant viral helicase inhibitors. Furthermore, this effective and feasible SBVS strategy established a valuable screening platform for helicase-targeted drug development.
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Affiliation(s)
- Zhenxing Li
- National Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for R&D of Fine Chemicals of Guizhou University, Guiyang 550025, China
| | - Binxin Yang
- National Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for R&D of Fine Chemicals of Guizhou University, Guiyang 550025, China
| | - Yue Ding
- National Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for R&D of Fine Chemicals of Guizhou University, Guiyang 550025, China
| | - Jiao Meng
- National Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for R&D of Fine Chemicals of Guizhou University, Guiyang 550025, China
| | - Jinhong Hu
- National Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for R&D of Fine Chemicals of Guizhou University, Guiyang 550025, China
| | - Xiang Zhou
- National Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for R&D of Fine Chemicals of Guizhou University, Guiyang 550025, China
| | - Liwei Liu
- National Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for R&D of Fine Chemicals of Guizhou University, Guiyang 550025, China
| | - Zhibing Wu
- National Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for R&D of Fine Chemicals of Guizhou University, Guiyang 550025, China
| | - Song Yang
- National Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for R&D of Fine Chemicals of Guizhou University, Guiyang 550025, China.
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Raman K, Rajagopal K, Ramesh B, Nallasivan PK, Raja MKMM, Jupudi S, Byran G, Khan SL, Bin Emran T. Drug target of natural products and COVID-19: how far has science progressed? Ann Med Surg (Lond) 2023; 85:2731-2742. [PMID: 37363478 PMCID: PMC10289732 DOI: 10.1097/ms9.0000000000000703] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Accepted: 04/10/2023] [Indexed: 06/28/2023] Open
Abstract
The new coronavirus [severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)] that caused a viral disease with a high risk of mortality (coronavirus disease 2019) was found toward the end of 2019. This was a significant acute respiratory syndrome. In a brief period, this virus spread throughout the entire planet, causing tremendous loss of life and economic damage. The process of developing new treatments takes time, and there are presently no recognized specific treatments to treat this infection. The most promising participants, who subsequently developed into prospective leads, were dropped from the clinical research in their latter phases. Medication that has previously acquired permission may only be repurposed for use for various medical reasons following a thorough investigation for safety and effectiveness. Because there are now no effective treatments available, natural products are being used haphazardly as antiviral medications and immunity boosters. The fundamental statement that most natural compounds have powerful antiviral action does not apply to SARS-CoV-2. Middle East respiratory syndrome coronavirus and severe acute respiratory syndrome coronavirus infections are inhibited by natural treatments. According to an in silico study, the virus' nonstructural proteins, including PLpro, Mpro, and RdRp, as well as structural proteins like the spike (S) protein, have been shown to have a strong affinity for several natural products and to be inhibited by them. The virus also suggests that it is a valid candidate for therapeutic research since it utilizes the intracellular angiotensin-converting enzyme 2 receptor of the host cell. In this study, interesting targets for SARS-CoV-2 medication development are explored, as well as the antiviral properties of some well-known natural compounds.
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Affiliation(s)
- Kannan Raman
- Department of Pharmaceutical Chemistry, JSS College of Pharmacy (JSS Academy of Higher Education & Research), Ooty, The Nilgiris, Tamil Nadu India
| | - Kalirajan Rajagopal
- Department of Pharmaceutical Chemistry, JSS College of Pharmacy (JSS Academy of Higher Education & Research), Ooty, The Nilgiris, Tamil Nadu India
| | - B. Ramesh
- Kakatiya Government College, Hanumakonda, Telangana India
| | - P. Kumar Nallasivan
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Karpagam Academy of Higher Education, Coimbatore India
| | - M. K. Mohan M. Raja
- Parul Institute of Pharmacy and Research, Parul University, Vadodara, Gujarat India
| | - Srikanth Jupudi
- Department of Pharmaceutical Chemistry, JSS College of Pharmacy (JSS Academy of Higher Education & Research), Ooty, The Nilgiris, Tamil Nadu India
| | - Gowramma Byran
- Department of Pharmaceutical Chemistry, JSS College of Pharmacy (JSS Academy of Higher Education & Research), Ooty, The Nilgiris, Tamil Nadu India
| | - Sharuk L. Khan
- Department of Pharmaceutical Chemistry, N.B.S. Institute of Pharmacy, Ausa, Maharashtra, India
| | - Talha Bin Emran
- Department of Pharmacy, BGC Trust University Bangladesh, Chittagong, Bangladesh
- Department of Pharmacy, Faculty of Allied Health Sciences, Daffodil International University, Dhaka, Bangladesh
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In Silico Analysis of Ferroptosis-Related Genes and Its Implication in Drug Prediction against Fluorosis. Int J Mol Sci 2023; 24:ijms24044221. [PMID: 36835629 PMCID: PMC9961266 DOI: 10.3390/ijms24044221] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Revised: 02/10/2023] [Accepted: 02/13/2023] [Indexed: 02/22/2023] Open
Abstract
Fluorosis is a serious global public health problem. Interestingly, so far, there is no specific drug treatment for the treatment of fluorosis. In this paper, the potential mechanisms of 35 ferroptosis-related genes in U87 glial cells exposed to fluoride were explored by bioinformatics methods. Significantly, these genes are involved in oxidative stress, ferroptosis, and decanoate CoA ligase activity. Ten pivotal genes were found by the Maximal Clique Centrality (MCC) algorithm. Furthermore, according to the Connectivity Map (CMap) and the Comparative Toxicogenomics Database (CTD), 10 possible drugs for fluorosis were predicted and screened, and a drug target ferroptosis-related gene network was constructed. Molecular docking was used to study the interaction between small molecule compounds and target proteins. Molecular dynamics (MD) simulation results show that the structure of the Celestrol-HMOX1 composite is stable and the docking effect is the best. In general, Celastrol and LDN-193189 may target ferroptosis-related genes to alleviate the symptoms of fluorosis, which may be effective candidate drugs for the treatment of fluorosis.
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Mahmud ML, Islam S, Biswas S, Mortuza MG, Paul GK, Uddin MS, Akhtar-E-Ekram M, Saleh MA, Zaman S, Syed A, Elgorban AM, Zaghloul NSS. Klebsiella pneumoniae Volatile Organic Compounds (VOCs) Protect Artemia salina from Fish Pathogen Aeromonas sp.: A Combined In Vitro, In Vivo, and In Silico Approach. Microorganisms 2023; 11:microorganisms11010172. [PMID: 36677466 PMCID: PMC9862385 DOI: 10.3390/microorganisms11010172] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Revised: 11/24/2022] [Accepted: 11/26/2022] [Indexed: 01/12/2023] Open
Abstract
Antibiotic resistance is an alarming threat all over the world, and the biofilm formation efficacy of bacteria is making the situation worse. The antagonistic efficacy of Klebsiella pneumoniae against one of the known fish pathogens, Aeromonas sp., is examined in this study. Moreover, Aeromonas sp.'s biofilm formation ability and in vivo pathogenicity on Artemia salina are also justified here. Firstly, six selected bacterial strains were used to obtain antimicrobial compounds against this pathogenic strain. Among those, Klebsiella pneumoniae, another pathogenic bacterium, surprisingly demonstrated remarkable antagonistic activity against Aeromonas sp. in both in vitro and in vivo assays. The biofilm distrusting potentiality of Klebsiella pneumoniae's cell-free supernatants (CFSs) was likewise found to be around 56%. Furthermore, the volatile compounds of Klebsiella pneumoniae were identified by GC-MS in order to explore compounds with antibacterial efficacy against Aeromonas sp. through an in silico study, where 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase (MTAN) (PDB: 5B7P) was chosen as a target protein for its unique characteristics and pathogenicity. Several volatile compounds, such as oxime- methoxy-phenyl-, fluoren-9-ol, 3,6-dimethoxy-9-(2-phenylethynyl)-, and 2H-indol-2-one, 1,3-dihydro- showed a strong binding affinity, with free energy of -6.7, -7.1, and -6.4 Kcal/mol, respectively, in complexes with the protein MTAN. Moreover, the root-mean-square deviation, solvent-accessible surface area, radius of gyration, root-mean-square fluctuations, and hydrogen bonds were used to ensure the binding stability of the docked complexes in the atomistic simulation. Thus, Klebsiella pneumoniae and its potential compounds can be employed as an alternative to antibiotics for aquaculture, demonstrating their effectiveness in suppressing Aeromonas sp.
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Affiliation(s)
- Md. Liton Mahmud
- Microbiology Laboratory, Department of Genetic Engineering and Biotechnology, University of Rajshahi, Rajshahi 6205, Bangladesh
| | - Shirmin Islam
- Microbiology Laboratory, Department of Genetic Engineering and Biotechnology, University of Rajshahi, Rajshahi 6205, Bangladesh
| | - Suvro Biswas
- Microbiology Laboratory, Department of Genetic Engineering and Biotechnology, University of Rajshahi, Rajshahi 6205, Bangladesh
| | - Md. Golam Mortuza
- Department of Science and Humanities, Bangladesh Army International University of Science and Technology, Cumilla 3500, Bangladesh
| | - Gobindo Kumar Paul
- Microbiology Laboratory, Department of Genetic Engineering and Biotechnology, University of Rajshahi, Rajshahi 6205, Bangladesh
- Bangladesh Reference Institute for Chemical Measurements (BRICM), Bangladesh Council of Scientific and Industrial Research (BCSIR), Dhaka 1205, Bangladesh
| | - Md. Salah Uddin
- Microbiology Laboratory, Department of Genetic Engineering and Biotechnology, University of Rajshahi, Rajshahi 6205, Bangladesh
| | - Md. Akhtar-E-Ekram
- Microbiology Laboratory, Department of Genetic Engineering and Biotechnology, University of Rajshahi, Rajshahi 6205, Bangladesh
| | - Md. Abu Saleh
- Microbiology Laboratory, Department of Genetic Engineering and Biotechnology, University of Rajshahi, Rajshahi 6205, Bangladesh
- Correspondence: (M.A.S.); (S.Z.)
| | - Shahriar Zaman
- Microbiology Laboratory, Department of Genetic Engineering and Biotechnology, University of Rajshahi, Rajshahi 6205, Bangladesh
- Correspondence: (M.A.S.); (S.Z.)
| | - Asad Syed
- Department of Botany and Microbiology, College of Science, King Saud University, P.O. Box 2455, Riyadh 11451, Saudi Arabia
| | - Abdallah M. Elgorban
- Department of Botany and Microbiology, College of Science, King Saud University, P.O. Box 2455, Riyadh 11451, Saudi Arabia
| | - Nouf S. S. Zaghloul
- Bristol Centre for Functional Nanomaterials, HH Wills Physics Laboratory, Tyndall Avenue, University of Bristol, Bristol BS8 1FD, UK
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11
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Singh MP, Singh N, Mishra D, Ehsan S, Chaturvedi VK, Chaudhary A, Singh V, Vamanu E. Computational Approaches to Designing Antiviral Drugs against COVID-19: A Comprehensive Review. Curr Pharm Des 2023; 29:2601-2617. [PMID: 37916490 DOI: 10.2174/0113816128259795231023193419] [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: 05/18/2023] [Accepted: 09/21/2023] [Indexed: 11/03/2023]
Abstract
The global impact of the COVID-19 pandemic caused by SARS-CoV-2 necessitates innovative strategies for the rapid development of effective treatments. Computational methodologies, such as molecular modelling, molecular dynamics simulations, and artificial intelligence, have emerged as indispensable tools in the drug discovery process. This review aimed to provide a comprehensive overview of these computational approaches and their application in the design of antiviral agents for COVID-19. Starting with an examination of ligand-based and structure-based drug discovery, the review has delved into the intricate ways through which molecular modelling can accelerate the identification of potential therapies. Additionally, the investigation extends to phytochemicals sourced from nature, which have shown promise as potential antiviral agents. Noteworthy compounds, including gallic acid, naringin, hesperidin, Tinospora cordifolia, curcumin, nimbin, azadironic acid, nimbionone, nimbionol, and nimocinol, have exhibited high affinity for COVID-19 Mpro and favourable binding energy profiles compared to current drugs. Although these compounds hold potential, their further validation through in vitro and in vivo experimentation is imperative. Throughout this exploration, the review has emphasized the pivotal role of computational biologists, bioinformaticians, and biotechnologists in driving rapid advancements in clinical research and therapeutic development. By combining state-of-the-art computational techniques with insights from structural and molecular biology, the search for potent antiviral agents has been accelerated. The collaboration between these disciplines holds immense promise in addressing the transmissibility and virulence of SARS-CoV-2.
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Affiliation(s)
- Mohan P Singh
- Centre of Biotechnology, University of Allahabad, Prayagraj 211002, India
| | - Nidhi Singh
- Centre of Bioinformatics, University of Allahabad, Prayagraj 211002, India
| | - Divya Mishra
- Centre of Bioinformatics, University of Allahabad, Prayagraj 211002, India
| | - Saba Ehsan
- Centre of Biotechnology, University of Allahabad, Prayagraj 211002, India
| | - Vivek K Chaturvedi
- Department of Gastroenterology, Institute of Medical Sciences, Banaras Hindu University, Varanasi 221005, India
| | - Anupriya Chaudhary
- Centre of Biotechnology, University of Allahabad, Prayagraj 211002, India
| | - Veer Singh
- Department of Biochemistry, Rajendra Memorial Research Institute of Medical Sciences, Patna 800007, India
| | - Emanuel Vamanu
- Faculty of Biotechnology, University of Agricultural Sciences and Veterinary Medicine of Bucharest, Bucharest 011464, Romania
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12
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Adegbola PI, Fadahunsi OS, Ogunjinmi OE, Adegbola AE, Ojeniyi FD, Adesanya A, Olagoke E, Adisa AD, Ehigie AF, Adetutu A, Semire B. Potential inhibitory properties of structurally modified quercetin/isohamnetin glucosides against SARS-CoV-2 Mpro; molecular docking and dynamics simulation strategies. INFORMATICS IN MEDICINE UNLOCKED 2023; 37:101167. [PMID: 36686560 PMCID: PMC9837157 DOI: 10.1016/j.imu.2023.101167] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Revised: 01/05/2023] [Accepted: 01/08/2023] [Indexed: 01/15/2023] Open
Abstract
Concerned organizations and individuals are fully engaged in seeking appropriate measures towards managing Severe Acute Respiratory Syndrome Coronavirus 2 (SAR-CoV-2) infection because of the unprecedented economic and health impact. SAR-CoV-2 Main protease (SARS-CoV-2 Mpro) is unique to the survival and viability of the virus. Therefore, inhibition of Mpro can block the viral propagation. Thirty (30) derivatives were built by changing the glucosides in the Meta and para position of quercetin and isohamnetin. Molecular docking analysis was used for the screening of the compounds. Dynamics simulation was performed to assess the stability of the best pose docked complex. Molecular mechanics binding free energy calculation was done by Molecular Mechanics/Poisson-Boltzmann Surface Area (MMPBSA). Overall analysis showed that the compounds are allosteric inhibitors of SARS-CoV-2 Mpro. Dynamic simulation analysis established the stability of Mpro-ISM-1, Mpro-ISD-3, Mpro-IST-2, Mpro-QM-2, and Mpro-QD-6 complexes with a maximum of 7 hydrogen bonds involved in their interaction. The MMPBSA binding free energies for ISM-1, ISD-3, IST-2, QM-2, and QD-6 were -92.47 ± 9.06, -222.27 ± 32.5, 180.72 ± 47.92, 156.46 ± 49.88 and -93.52 ± 48.75 kcal/mol respectively. All the compounds showed good pharmacokinetic properties, while only ISM-1 inhibits hERG and might be cardio-toxic. Observations in this study established that the glucoside position indeed influenced the affinity for SARS-CoV-2 Mpro. The study also suggested the potentials of ISD-3, QM-2 and QD-6 as potent inhibitors of the main protease, further experimental and clinical studies are however necessary to validate and establish the need for further drug development processes. Therefore, future studies will be on the chemical synthesis of the compounds and investigation of the in-vitro inhibition of SARS-CoV-2.
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Affiliation(s)
- Peter Ifeoluwa Adegbola
- Department of Biochemistry, Faculty of Basic Medical Sciences, Ladoke Akintola University of Technology, Ogbomoso, Nigeria
| | - Olumide Samuel Fadahunsi
- Department of Biochemistry, Faculty of Basic Medical Sciences, Ladoke Akintola University of Technology, Ogbomoso, Nigeria
| | - Oluwasayo Esther Ogunjinmi
- Department of Industrial Chemistry, Faculty of Natural and Applied Sciences, First Technical University, Ibadan, Nigeria
| | - Aanuoluwa Eunice Adegbola
- Department of Pure and Applied Chemistry, Faculty of Pure and Applied Sciences, Ladoke Akintola University of Technology, Ogbomoso, Nigeria
| | - Fiyinfoluwa Demilade Ojeniyi
- Department of Biochemistry, Faculty of Basic Medical Sciences, Ladoke Akintola University of Technology, Ogbomoso, Nigeria
| | - Adetayo Adesanya
- Department of Biochemistry, Faculty of Basic Medical Sciences, Ladoke Akintola University of Technology, Ogbomoso, Nigeria
| | - Emmanuel Olagoke
- Department of Biochemistry, Faculty of Basic Medical Sciences, Ladoke Akintola University of Technology, Ogbomoso, Nigeria
| | - Ayobami Damilare Adisa
- Department of Biochemistry, Faculty of Basic Medical Sciences, Ladoke Akintola University of Technology, Ogbomoso, Nigeria
| | - Adeola Folasade Ehigie
- Department of Biochemistry, Faculty of Basic Medical Sciences, Ladoke Akintola University of Technology, Ogbomoso, Nigeria,Corresponding author
| | - Adewale Adetutu
- Department of Biochemistry, Faculty of Basic Medical Sciences, Ladoke Akintola University of Technology, Ogbomoso, Nigeria,Corresponding author
| | - Banjo Semire
- Department of Pure and Applied Chemistry, Faculty of Pure and Applied Sciences, Ladoke Akintola University of Technology, Ogbomoso, Nigeria,Corresponding author
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13
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Kundu P, Debnath SL, Ahad MF, Devnath HS, Saha L, Karmakar UK, Sadhu SK. Exploration of In Vivo and In Vitro Biological Effects of Sonneratia caseolaris (L.) Fruits Supported by Molecular Docking and ADMET Study. BIOMED RESEARCH INTERNATIONAL 2023; 2023:4522446. [PMID: 37096224 PMCID: PMC10122579 DOI: 10.1155/2023/4522446] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/17/2022] [Revised: 02/06/2023] [Accepted: 02/18/2023] [Indexed: 04/26/2023]
Abstract
Sonneratia caseolaris (L.) is a common mangrove plant which has significant medicinal value in traditional medicine. Ethanol extract from the fruits of S. caseolaris (SCE) was used in this project to explore its different pharmacological effects considering its traditional usage. In the castor oil-induced diarrheal method, SCE significantly lengthened the latency of the first defecation period up to 95.8 and 119.4 min as well as lowering stool count by 43.3% and 64.4% at the doses of 250 and 500 mg/kg, respectively. In evaluating the neuropharmacological effect using the open-field model, a significant central nervous system (CNS) depressant nature was observed after a reduction in the no. of squares crossed by mice at various time intervals. In evaluating the blood coagulation effect, SCE significantly reduced blood clotting time at 5.86, 5.52, and 5.01 min at 25, 50, and 100 mg/ml doses, respectively. In the assessment of the anthelmintic effect, SCE significantly killed Paramphistomum cervi (P. cervi) where the death times of the nematodes were 40.3, 36.8, and 29.9 min at 12.5, 25, and 50 mg/ml doses, respectively. The extract showed a very poor cytotoxic effect in brine shrimp lethality bioassay. In molecular docking analysis, maslinic acid, oleanolic acid, luteolin, luteolin 7-O-β-glucoside, myricetin, ellagic acid, and R-nyasol showed the best binding affinities with the selected proteins which might be the credible reasons for eliciting pharmacological responses. Among these seven compounds, only luteolin 7-O-β-glucoside had two violations in Lipinski's rule of five.
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Affiliation(s)
- Pritam Kundu
- Pharmacy Discipline, Life Science School, Khulna University, Khulna 9208, Bangladesh
| | - Shovan Lal Debnath
- Pharmacy Discipline, Life Science School, Khulna University, Khulna 9208, Bangladesh
| | - Md. Faisal Ahad
- Pharmacy Discipline, Life Science School, Khulna University, Khulna 9208, Bangladesh
| | - Hiron Saraj Devnath
- Pharmacy Discipline, Life Science School, Khulna University, Khulna 9208, Bangladesh
| | - Lopa Saha
- Pharmacy Discipline, Life Science School, Khulna University, Khulna 9208, Bangladesh
| | - Utpal Kumar Karmakar
- Pharmacy Discipline, Life Science School, Khulna University, Khulna 9208, Bangladesh
| | - Samir Kumar Sadhu
- Pharmacy Discipline, Life Science School, Khulna University, Khulna 9208, Bangladesh
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14
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Sun Y, Zhao B, Wang Y, Chen Z, Zhang H, Qu L, Zhao Y, Song J. Optimization of potential non-covalent inhibitors for the SARS-CoV-2 main protease inspected by a descriptor of the subpocket occupancy. Phys Chem Chem Phys 2022; 24:29940-29951. [PMID: 36468652 DOI: 10.1039/d2cp03681a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
The main protease is regarded as an essential drug target for treating Coronavirus Disease 2019. In the present study, 13 marketed drugs were investigated to explore the possible binding mechanism, utilizing molecular docking, molecular dynamics simulation, and MM-PB(GB)SA binding energy calculations. Our results suggest that fusidic acid, polydatin, SEN-1269, AZD6482, and UNC-2327 have high binding affinities of more than 23 kcal mol-1. A descriptor was defined for the energetic occupancy of the subpocket, and it was found that S4 had a low occupancy of less than 10% on average. The molecular optimization of ADZ6482 via reinforcement learning algorithms was carried out to screen out three lead compounds, in which slight structural changes give more considerable binding energies and an occupancy of the S4 subpocket of up to 43%. The energetic occupancy could be a useful descriptor for evaluating the local binding affinity for drug design.
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Affiliation(s)
- Yujia Sun
- Green Catalysis Center, and College of Chemistry, Zhengzhou University, No. 100 Science Avenue, Zhengzhou, Henan, 450001, P. R. China.
| | - Bodi Zhao
- Green Catalysis Center, and College of Chemistry, Zhengzhou University, No. 100 Science Avenue, Zhengzhou, Henan, 450001, P. R. China.
| | - Yuqi Wang
- Green Catalysis Center, and College of Chemistry, Zhengzhou University, No. 100 Science Avenue, Zhengzhou, Henan, 450001, P. R. China.
| | - Zitong Chen
- Green Catalysis Center, and College of Chemistry, Zhengzhou University, No. 100 Science Avenue, Zhengzhou, Henan, 450001, P. R. China.
| | - Huaiyu Zhang
- Institute of Computational Quantum Chemistry, College of Chemistry and Materials Science, Hebei Normal University, Shijiazhuang, Hebei, 050024, P. R. China
| | - Lingbo Qu
- Green Catalysis Center, and College of Chemistry, Zhengzhou University, No. 100 Science Avenue, Zhengzhou, Henan, 450001, P. R. China.
| | - Yuan Zhao
- The Key Laboratory of Natural Medicine and Immuno - Engineering, Henan University, Kaifeng, Henan, 475000, P. R. China
| | - Jinshuai Song
- Green Catalysis Center, and College of Chemistry, Zhengzhou University, No. 100 Science Avenue, Zhengzhou, Henan, 450001, P. R. China.
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15
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Paul GK, Mahmud S, Dutta AK, Sarkar S, Laboni AA, Hossain MS, Nagata A, Karmaker P, Razu MH, Kazi T, Uddin MS, Zaman S, Islam MS, Khan M, Saleh MA. Volatile compounds of Bacillus pseudomycoides induce growth and drought tolerance in wheat (Triticum aestivum L.). Sci Rep 2022; 12:19137. [PMID: 36352019 PMCID: PMC9646913 DOI: 10.1038/s41598-022-22354-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Accepted: 10/13/2022] [Indexed: 11/11/2022] Open
Abstract
The plant growth-boosting biofilm-forming bacteria Bacillus pseudomycoides is able to promote growth and drought stress tolerance in wheat by suppressing the MYB gene, which synthesizes Myb protein (TaMpc1-D4) through secreted volatile compounds. In the present study, Triticum aestivum seeds were inoculated with five distinct bacterial strains. The growth, germination rate, root-shoot length, RWC, and chlorophyll content of seedlings were investigated. Furthermore, the levels of soluble sugars, proteins, H2O2, NO, cell death, and antioxidant enzymes (CAT, SOD, POD, and APX) were observed throughout the growth stage. All of the results showed that B. pseudomycoides had a substantially higher ability to form biofilm and promote these traits than the other strains. In terms of molecular gene expression, B. pseudomycoides inoculation strongly expressed the Dreb1 gene by silencing the expression of MYB gene through secreted volatile compounds. For identifying the specific volatile compound that silenced the MYB gene, molecular docking with Myb protein was performed. Out of 45 volatile compounds found, 2,6-ditert-butylcyclohexa-2,5-diene-1,4-dione and 3,5-ditert-butylphenol had a binding free energy of - 6.2 and - 6.5, Kcal/mol, respectively, which predicted that these compounds could suppress this protein's expression. In molecular dynamics simulations, the RMSD, SASA, Rg, RMSF, and hydrogen bonding values found assured the docked complexes' binding stability. These findings suggest that these targeted compounds may be suppressing Myb protein expression as well as the expression of Dreb1 and other drought response genes in wheat. More research (field trial) into plant growth and drought stress is needed to support the findings of this study.
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Affiliation(s)
- Gobindo Kumar Paul
- grid.412656.20000 0004 0451 7306Microbiology Laboratory, Department of Genetic Engineering and Biotechnology, University of Rajshahi, Rajshahi, 6205 Bangladesh ,Bangladesh Reference Institute for Chemical Measurements (BRiCM), Dhaka, Bangladesh
| | - Shafi Mahmud
- grid.1001.00000 0001 2180 7477Division of Genome Sciences and Cancer, The John Curtin School of Medical Research, and The Shine-Dalgarno Centre for RNA Innovation, The Australian National University, Canberra, ACT 2601 Australia
| | - Amit Kumar Dutta
- grid.412656.20000 0004 0451 7306Department of Microbiology, University of Rajshahi, Rajshahi, 6205 Bangladesh
| | - Swagotom Sarkar
- Bangladesh Reference Institute for Chemical Measurements (BRiCM), Dhaka, Bangladesh
| | - Aysha Akter Laboni
- Bangladesh Reference Institute for Chemical Measurements (BRiCM), Dhaka, Bangladesh
| | - Md. Shamim Hossain
- grid.411762.70000 0004 0454 7011Department of Biotechnology and Genetic Engineering, Islamic University, Kushtia, 7003 Bangladesh
| | - Abir Nagata
- grid.136593.b0000 0004 0373 3971Department of Regenerative Dermatology, Graduate School of Medicine, Osaka University, Suita, 565-0871 Japan
| | - Pranab Karmaker
- Bangladesh Reference Institute for Chemical Measurements (BRiCM), Dhaka, Bangladesh
| | - Mamudul Hasan Razu
- Bangladesh Reference Institute for Chemical Measurements (BRiCM), Dhaka, Bangladesh
| | - Taheruzzaman Kazi
- grid.136593.b0000 0004 0373 3971Department of Regenerative Dermatology, Graduate School of Medicine, Osaka University, Suita, 565-0871 Japan
| | - Md. Salah Uddin
- grid.412656.20000 0004 0451 7306Microbiology Laboratory, Department of Genetic Engineering and Biotechnology, University of Rajshahi, Rajshahi, 6205 Bangladesh
| | - Shahriar Zaman
- grid.412656.20000 0004 0451 7306Microbiology Laboratory, Department of Genetic Engineering and Biotechnology, University of Rajshahi, Rajshahi, 6205 Bangladesh
| | - Md Sayeedul Islam
- grid.136593.b0000 0004 0373 3971Department of Biological Sciences, Graduate School of Science, Osaka University, Machikaneyama-Cho 1-1, Toyonaka, Osaka 560-0043 Japan
| | - Mala Khan
- Bangladesh Reference Institute for Chemical Measurements (BRiCM), Dhaka, Bangladesh
| | - Md. Abu Saleh
- grid.412656.20000 0004 0451 7306Microbiology Laboratory, Department of Genetic Engineering and Biotechnology, University of Rajshahi, Rajshahi, 6205 Bangladesh
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16
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Plant Molecular Pharming and Plant-Derived Compounds towards Generation of Vaccines and Therapeutics against Coronaviruses. Vaccines (Basel) 2022; 10:vaccines10111805. [DOI: 10.3390/vaccines10111805] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Revised: 10/14/2022] [Accepted: 10/19/2022] [Indexed: 11/17/2022] Open
Abstract
The current century has witnessed infections of pandemic proportions caused by Coronaviruses (CoV) including severe acute respiratory syndrome-related CoV (SARS-CoV), Middle East respiratory syndrome-related CoV (MERS-CoV) and the recently identified SARS-CoV2. Significantly, the SARS-CoV2 outbreak, declared a pandemic in early 2020, has wreaked devastation and imposed intense pressure on medical establishments world-wide in a short time period by spreading at a rapid pace, resulting in high morbidity and mortality. Therefore, there is a compelling need to combat and contain the CoV infections. The current review addresses the unique features of the molecular virology of major Coronaviruses that may be tractable towards antiviral targeting and design of novel preventative and therapeutic intervention strategies. Plant-derived vaccines, in particular oral vaccines, afford safer, effectual and low-cost avenues to develop antivirals and fast response vaccines, requiring minimal infrastructure and trained personnel for vaccine administration in developing countries. This review article discusses recent developments in the generation of plant-based vaccines, therapeutic/drug molecules, monoclonal antibodies and phytochemicals to preclude and combat infections caused by SARS-CoV, MERS-CoV and SARS-CoV-2 viruses. Efficacious plant-derived antivirals could contribute significantly to combating emerging and re-emerging pathogenic CoV infections and help stem the tide of any future pandemics.
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17
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Fadahunsi OS, Olorunnisola OS, Adegbola PI, Subair TI, Elegbeleye OE. Angiotensin converting enzyme inhibitors from medicinal plants: a molecular docking and dynamic simulation approach. In Silico Pharmacol 2022; 10:20. [PMID: 36245815 PMCID: PMC9561457 DOI: 10.1007/s40203-022-00135-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Accepted: 09/20/2022] [Indexed: 02/02/2023] Open
Abstract
Angiotensin converting enzyme (ACE) is a key enzyme and mediator in the aetiology of high blood pressure (HBP) and hypertension. As one of the leading cause of untimely death worldwide, there is a lot of research and studies on the management and treatment of hypertension. The usage of medicinal plants in the management of hypertension as alternative to synthetic allopathic drugs is a common practice in folkloric and traditional medicine. Therefore, this study was aimed to investigate the ACE inhibitory activity of some medicinal plants which are commonly used in the treatment of HBP in southwestern part of Nigeria using extensive in-silico approach. Compounds identified in the plants through GC-MS technique, together with Lisinopril were docked against ACE protein. It was observed that only 40 of the compounds had binding affinity ≥ - 6.8 kcal/mol which was demonstrated by the standard drug (lisinopril). Interaction between the compounds and ACE was via conventional hydrogen, carbon hydrogen, alkyl, pi-alkyl, pi-carbon, and Van Der Wall bonds among others. Most of these compounds exhibited drug like properties, without violating majority of the physicochemical descriptors and Lipinski rule of 5. The ADMET evaluation revealed that only 2 compounds (cyclopentadecanone and oxacycloheptadecan-2-one) which were identified in Bacopa florinbunda plant were predicted non-toxic and thus were subjected to molecular dynamics and simulation with ACE. From the molecular dynamics and mechanics analysis, both cyclopentadecanone and oxacycloheptadecan-2-one showed high stability and inhibitory potentials when bound to ACE. Oxacycloheptadecan-2-one was more stable than lisinopril and cyclopentadecanone in the ligand-ACE complex; we therefore suggested its experimental and clinical validation as drug candidates for the treatment of hypertension. Supplementary Information The online version contains supplementary material available at 10.1007/s40203-022-00135-z.
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Affiliation(s)
- Olumide Samuel Fadahunsi
- Department of Biochemistry, Faculty of Basic Medical Sciences, Ladoke Akintola University of Technology, Ogbomoso, Oyo Nigeria
| | - Olubukola Sinbad Olorunnisola
- Department of Biochemistry, Faculty of Basic Medical Sciences, Ladoke Akintola University of Technology, Ogbomoso, Oyo Nigeria
| | - Peter Ifeoluwa Adegbola
- Department of Biochemistry, Faculty of Basic Medical Sciences, Ladoke Akintola University of Technology, Ogbomoso, Oyo Nigeria
- Molecular Bio-Computation and Drug Design Laboratory, School of Health Sciences, University of KwaZulu-Natal, Westville Campus, Durban, 4001 South Africa
| | - Temitayo I. Subair
- Molecular Bio-Computation and Drug Design Laboratory, School of Health Sciences, University of KwaZulu-Natal, Westville Campus, Durban, 4001 South Africa
| | - Oluwabamise Emmanuel Elegbeleye
- Department of Biochemistry, Faculty of Basic Medical Sciences, Ladoke Akintola University of Technology, Ogbomoso, Oyo Nigeria
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18
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Mousavi S, Zare S, Mirzaei M, Feizi A. Novel Drug Design for Treatment of COVID-19: A Systematic Review of Preclinical Studies. THE CANADIAN JOURNAL OF INFECTIOUS DISEASES & MEDICAL MICROBIOLOGY = JOURNAL CANADIEN DES MALADIES INFECTIEUSES ET DE LA MICROBIOLOGIE MEDICALE 2022; 2022:2044282. [PMID: 36199815 PMCID: PMC9527439 DOI: 10.1155/2022/2044282] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/19/2022] [Revised: 05/23/2022] [Accepted: 08/03/2022] [Indexed: 11/27/2022]
Abstract
Background Since the beginning of the novel coronavirus (SARS-CoV-2) disease outbreak, there has been an increasing interest in discovering potential therapeutic agents for this disease. In this regard, we conducted a systematic review through an overview of drug development (in silico, in vitro, and in vivo) for treating COVID-19. Methods A systematic search was carried out in major databases including PubMed, Web of Science, Scopus, EMBASE, and Google Scholar from December 2019 to March 2021. A combination of the following terms was used: coronavirus, COVID-19, SARS-CoV-2, drug design, drug development, In silico, In vitro, and In vivo. A narrative synthesis was performed as a qualitative method for the data synthesis of each outcome measure. Results A total of 2168 articles were identified through searching databases. Finally, 315 studies (266 in silico, 34 in vitro, and 15 in vivo) were included. In studies with in silico approach, 98 article study repurposed drug and 91 studies evaluated herbal medicine on COVID-19. Among 260 drugs repurposed by the computational method, the best results were observed with saquinavir (n = 9), ritonavir (n = 8), and lopinavir (n = 6). Main protease (n = 154) following spike glycoprotein (n = 62) and other nonstructural protein of virus (n = 45) was among the most studied targets. Doxycycline, chlorpromazine, azithromycin, heparin, bepridil, and glycyrrhizic acid showed both in silico and in vitro inhibitory effects against SARS-CoV-2. Conclusion The preclinical studies of novel drug design for COVID-19 focused on main protease and spike glycoprotein as targets for antiviral development. From evaluated structures, saquinavir, ritonavir, eucalyptus, Tinospora cordifolia, aloe, green tea, curcumin, pyrazole, and triazole derivatives in in silico studies and doxycycline, chlorpromazine, and heparin from in vitro and human monoclonal antibodies from in vivo studies showed promised results regarding efficacy. It seems that due to the nature of COVID-19 disease, finding some drugs with multitarget antiviral actions and anti-inflammatory potential is valuable and some herbal medicines have this potential.
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Affiliation(s)
- Sarah Mousavi
- Department of Clinical Pharmacy and Pharmacy Practice, School of Pharmacy and Pharmaceutical Sciences, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Shima Zare
- School of Pharmacy and Pharmaceutical Sciences, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Mahmoud Mirzaei
- Child Growth and Development Research Center, Research Institute for Primordial Prevention of Non-Communicable Disease, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Awat Feizi
- Department of Epidemiology and Biostatistics, School of Health, Isfahan University of Medical Sciences, Isfahan, Iran
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19
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Garg P, Vanamamalai VK, Jali I, Sharma S. In silico prediction of the animal susceptibility and virtual screening of natural compounds against SARS-CoV-2: Molecular dynamics simulation based analysis. Front Genet 2022; 13:906955. [PMID: 36110222 PMCID: PMC9468858 DOI: 10.3389/fgene.2022.906955] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Accepted: 08/03/2022] [Indexed: 11/17/2022] Open
Abstract
COVID-19 is an infectious disease caused by the SARS-CoV-2 virus. It has six open reading frames (orf1ab, orf3a, orf6, orf7a, orf8, and orf10), a spike protein, a membrane protein, an envelope small membrane protein, and a nucleocapsid protein, out of which, orf1ab is the largest ORF coding different important non-structural proteins. In this study, an effort was made to evaluate the susceptibility of different animals against SARS-CoV-2 by analyzing the interactions of Spike and ACE2 proteins of the animals and propose a list of potential natural compounds binding to orf1ab of SARS-CoV-2. Here, we analyzed structural interactions between spike proteins of SARS-CoV-2 and the ACE2 receptor of 16 different hosts. A simulation for 50 ns was performed on these complexes. Based on post-simulation analysis, Chelonia mydas was found to have a more stable complex, while Bubalus bubalis, Aquila chrysaetos chrysaetos, Crocodylus porosus, and Loxodonta africana were found to have the least stable complexes with more fluctuations than all other organisms. Apart from that, we performed domain assignment of orf1ab of SARS-CoV-2 and identified 14 distinct domains. Out of these, Domain 3 (DNA/RNA polymerases) was selected as a target, as it showed no similarities with host proteomes and was validated in silico. Then, the top 10 molecules were selected from the virtual screening of ∼1.8 lakh molecules from the ZINC database, based on binding energy, and validated for ADME and toxicological properties. Three molecules were selected and analyzed further. The structural analysis showed that these molecules were residing within the pocket of the receptor. Finally, a simulation for 200 ns was performed on complexes with three selected molecules. Based on post-simulation analysis (RMSD, RMSF, Rg, SASA, and energies), the molecule ZINC000103666966 was found as the most suitable inhibitory compound against Domain 3. As this is an in silico prediction, further experimental studies could unravel the potential of the proposed molecule against SARS-CoV-2.
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Kobir ME, Ahmed A, Roni MAH, Chakma U, Amin MR, Chandro A, Kumer A. Anti-lung cancer drug discovery approaches by polysaccharides: an in silico study, quantum calculation and molecular dynamics study. J Biomol Struct Dyn 2022:1-17. [DOI: 10.1080/07391102.2022.2110156] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/15/2022]
Affiliation(s)
- Md. Eleas Kobir
- Department of Pharmacy, Atish Dipankar University of Science & Technology, Uttara, Bangladesh
| | - Asif Ahmed
- Department of Biochemistry and Molecular Biology, Jahangirnagar University, Savar, Bangladesh
| | - Md. Abul Hasan Roni
- Department of Science and Humanities, Bangladesh Army International University of Science and Technology, Cumilla, Bangladesh
| | - Unesco Chakma
- Department of Electrical and Electronics Engineering, European University of Bangladesh, Gabtoli, Bangladesh
- Laboratory of Computational Research for Drug Design and Material Science, Department of Chemistry, European University of Bangladesh, Dhaka, Bangladesh
| | - Md. Ruhul Amin
- Department of Pharmacy, Atish Dipankar University of Science & Technology, Uttara, Bangladesh
| | - Akhel Chandro
- Faculty of Animal Science and Veterinary Medicine, Department of Poultry Science, Sher-e-Bangla Agricultural University, Dhaka, Bangladesh
| | - Ajoy Kumer
- Laboratory of Computational Research for Drug Design and Material Science, Department of Chemistry, European University of Bangladesh, Dhaka, Bangladesh
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Fu Y, Saxu R, Ahmad Ridwan K, Zhao C, Kong X, Rong Y, Zheng W, Yu P, Teng Y. Selenium substituted axitinib reduces axitinib side effects and maintains its anti-renal tumor activity. RSC Adv 2022; 12:21821-21826. [PMID: 36043080 PMCID: PMC9358677 DOI: 10.1039/d2ra01882a] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Accepted: 07/21/2022] [Indexed: 11/21/2022] Open
Abstract
Axitinib is a potent vascular endothelial growth factor receptor (VEGFR) inhibitor, which has a strong inhibitory effect on the three isoforms of VEGFR 1-3. Having strong therapeutic efficacy, its broad use is limited by its side effects such as hypertension, proteinuria, cardiovascular damage, and liver and kidney dysfunction. Selenium compounds are broadly reported to have a good protective effect on cardiovascular disease, inflammation, infection, and immune function. In this study, a selenium substitute of axitinib was synthesized, and its anti-renal cell carcinoma activity and side effects were investigated. The results of the study indicated that Se-axitinib had potent antitumor activity on renal cell carcinoma (RCC), alleviated vascular hyperpermeability, and also alleviated axitinib-related side effects including hypertension, liver dysfunction and kidney dysfunction significantly. Therefore, we suggest that Se-axitinib could be a solution to the severe side effects of VEGFR inhibitors and provide evidence to improve the outcome of RCC treatment.
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Affiliation(s)
- Ying Fu
- China International Science and Technology Cooperation Base of Food Nutrition/Safety and Medicinal Chemistry, College of Bioengineering, Tianjin University of Science and Technology Tianjin 300457 China
| | - Rengui Saxu
- China International Science and Technology Cooperation Base of Food Nutrition/Safety and Medicinal Chemistry, College of Bioengineering, Tianjin University of Science and Technology Tianjin 300457 China
| | - Kadir Ahmad Ridwan
- China International Science and Technology Cooperation Base of Food Nutrition/Safety and Medicinal Chemistry, College of Bioengineering, Tianjin University of Science and Technology Tianjin 300457 China
| | - Cai Zhao
- China International Science and Technology Cooperation Base of Food Nutrition/Safety and Medicinal Chemistry, College of Bioengineering, Tianjin University of Science and Technology Tianjin 300457 China
| | - Xiangshun Kong
- China International Science and Technology Cooperation Base of Food Nutrition/Safety and Medicinal Chemistry, College of Bioengineering, Tianjin University of Science and Technology Tianjin 300457 China
| | - Yao Rong
- China International Science and Technology Cooperation Base of Food Nutrition/Safety and Medicinal Chemistry, College of Bioengineering, Tianjin University of Science and Technology Tianjin 300457 China
| | - Weida Zheng
- Medical College, Yanbian University No.977 Gongyuan Road Yanji City Jilin Province 133002 P. R. China
| | - Peng Yu
- China International Science and Technology Cooperation Base of Food Nutrition/Safety and Medicinal Chemistry, College of Bioengineering, Tianjin University of Science and Technology Tianjin 300457 China
| | - Yuou Teng
- China International Science and Technology Cooperation Base of Food Nutrition/Safety and Medicinal Chemistry, College of Bioengineering, Tianjin University of Science and Technology Tianjin 300457 China
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22
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Role of natural products towards the SARS-CoV-2: A critical review. Ann Med Surg (Lond) 2022; 80:104062. [PMID: 35814035 PMCID: PMC9249430 DOI: 10.1016/j.amsu.2022.104062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2022] [Revised: 06/11/2022] [Accepted: 06/22/2022] [Indexed: 11/23/2022] Open
Abstract
Despite the fact that various therapeutic compounds are being investigated, there is still a scarcity of effective and reliable therapeutic regimens to treat COVID-19. Ever since the COVID-19 pandemic, a diversity of traditional herbal treatments has been investigated to cure infected people, either alone or in conjunction with mainstream pharmaceuticals, with encouraging outcomes. In this article, we look at the latest research on the usage of natural products to alleviate the severity of COVID-19. To determine the activity of the natural products, act against SARS-CoV-2 to various targets like Mpro, ACE-II, papain-like, chymotrypsin-like proteases, and some antiviral targets. The processes underlying this preventative or therapeutic action are also examined. We used PubMed, Scopus, Google Scholar, and the WHO site to perform our review. The anti-SARS-CoV-2 impacts of various herbal extracts and purified compounds may be mediated via direct prevention of viral replication or entrance. Interestingly, certain items might avert SARS-CoV-2 from infecting human cells by blocking the ACE-2 protein or the serine protease TMPRRS2. Natural products have also been stated to suppress proteins intricate in the virus life cycle, like papain-like and chymotrypsin-like proteases. To conclude, natural products can be used alone or in combination as remedies or treatments for COVID-19. In addition, their compositions may provide insight into the development of effective and reliable antiviral drugs. The COVID-19 pandemic caused by a novel coronavirus SARS-CoV-2, resulted in thousands of deaths across the world. Globally, numerous studies and researchers have recently started fighting this virus. In this article, we look at the latest research on the usage of natural products to alleviate the severity of COVID-19. The anti-SARS-CoV-2 impacts of various herbal extracts and purified compounds may be mediated via direct prevention of viral replication or entrance.
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Rani I, Kalsi A, Kaur G, Sharma P, Gupta S, Gautam RK, Chopra H, Bibi S, Ahmad SU, Singh I, Dhawan M, Emran TB. Modern drug discovery applications for the identification of novel candidates for COVID-19 infections. Ann Med Surg (Lond) 2022; 80:104125. [PMID: 35845863 PMCID: PMC9273307 DOI: 10.1016/j.amsu.2022.104125] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Revised: 07/05/2022] [Accepted: 07/06/2022] [Indexed: 11/23/2022] Open
Abstract
In early December 2019, a large pneumonia epidemic occurred in Wuhan, China. The World Health Organization is concerned about the outbreak of another coronavirus with the powerful, rapid, and contagious transmission. Anyone with minor symptoms like fever and cough or travel history to contaminated places might be suspected of having COVID-19. COVID-19 therapy focuses on treating the disease's symptoms. So far, no such therapeutic molecule has been shown effective in treating this condition. So the treatment is mostly supportive and plasma. Globally, numerous studies and researchers have recently started fighting this virus. Vaccines and chemical compounds are also being investigated against infection. COVID-19 was successfully diagnosed using RNA detection and very sensitive RT-PCR (reverse transcription-polymerase chain reaction). The evolution of particular vaccinations is required to reduce illness severity and spread. Numerous computational analyses and molecular docking have predicted various target compounds that might stop this condition. This paper examines the main characteristics of coronavirus and the computational analyses necessary to avoid infection.
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Affiliation(s)
- Isha Rani
- MM College of Pharmacy, Maharishi Markandeshwar (Deemed to be University), Mullana, Haryana, India
| | - Avjit Kalsi
- MM School of Pharmacy, MM University, Sadopur, Ambala, Haryana, India
| | - Gagandeep Kaur
- Chitkara School of Pharmacy, Chitkara University-Baddi, Himachal Pradesh, India
| | - Pankaj Sharma
- Apotex Research Pvt. Ltd, Bangalore, Karnataka, India
| | - Sumeet Gupta
- MM College of Pharmacy, Maharishi Markandeshwar (Deemed to be University), Mullana, Haryana, India
| | - Rupesh K. Gautam
- MM School of Pharmacy, MM University, Sadopur, Ambala, Haryana, India
| | - Hitesh Chopra
- Department of Pharmaceutics, Chitkara College of Pharmacy, Chitkara University, Punjab, India
| | - Shabana Bibi
- Yunnan Herbal Laboratory, College of Ecology and Environmental Sciences, Yunnan University, Kunming, 650091, Yunnan, China
- The International Joint Research Center for Sustainable Utilization of Cordyceps Bioresources in China and Southeast Asia, Yunnan University, Kunming, 650091, Yunnan, China
| | - Syed Umair Ahmad
- Department of Bioinformatics, Hazara University, Mansehra, Pakistan
| | - Inderbir Singh
- Department of Pharmaceutics, Chitkara College of Pharmacy, Chitkara University, Punjab, India
| | - Manish Dhawan
- Department of Microbiology, Punjab Agricultural University, Ludhiana, 141004, Punjab, India
- Trafford College, Altrincham, Manchester, WA14 5PQ, UK
| | - Talha Bin Emran
- Department of Pharmacy, BGC Trust University Bangladesh, Chittagong, 4381, Bangladesh
- Department of Pharmacy, Faculty of Allied Health Sciences, Daffodil International University, Dhaka, 1207, Bangladesh
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Antonopoulou I, Sapountzaki E, Rova U, Christakopoulos P. The Inhibitory Potential of Ferulic Acid Derivatives against the SARS-CoV-2 Main Protease: Molecular Docking, Molecular Dynamics, and ADMET Evaluation. Biomedicines 2022; 10:biomedicines10081787. [PMID: 35892687 PMCID: PMC9329733 DOI: 10.3390/biomedicines10081787] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Revised: 07/19/2022] [Accepted: 07/21/2022] [Indexed: 11/16/2022] Open
Abstract
The main protease (Mpro) of SARS-CoV-2 is an appealing target for the development of antiviral compounds, due to its critical role in the viral life cycle and its high conservation among different coronaviruses and the continuously emerging mutants of SARS-CoV-2. Ferulic acid (FA) is a phytochemical with several health benefits that is abundant in plant biomass and has been used as a basis for the enzymatic or chemical synthesis of derivatives with improved properties, including antiviral activity against a range of viruses. This study tested 54 reported FA derivatives for their inhibitory potential against Mpro by in silico simulations. Molecular docking was performed using Autodock Vina, resulting in comparable or better binding affinities for 14 compounds compared to the known inhibitors N3 and GC376. ADMET analysis showed limited bioavailability but significantly improved the solubility for the enzymatically synthesized hits while better bioavailability and druglikeness properties but higher toxicity were observed for the chemically synthesized ones. MD simulations confirmed the stability of the complexes of the most promising compounds with Mpro, highlighting FA rutinoside and compound e27 as the best candidates from each derivative category.
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25
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Gao K, Wang R, Chen J, Cheng L, Frishcosy J, Huzumi Y, Qiu Y, Schluckbier T, Wei X, Wei GW. Methodology-Centered Review of Molecular Modeling, Simulation, and Prediction of SARS-CoV-2. Chem Rev 2022; 122:11287-11368. [PMID: 35594413 PMCID: PMC9159519 DOI: 10.1021/acs.chemrev.1c00965] [Citation(s) in RCA: 33] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Despite tremendous efforts in the past two years, our understanding of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), virus-host interactions, immune response, virulence, transmission, and evolution is still very limited. This limitation calls for further in-depth investigation. Computational studies have become an indispensable component in combating coronavirus disease 2019 (COVID-19) due to their low cost, their efficiency, and the fact that they are free from safety and ethical constraints. Additionally, the mechanism that governs the global evolution and transmission of SARS-CoV-2 cannot be revealed from individual experiments and was discovered by integrating genotyping of massive viral sequences, biophysical modeling of protein-protein interactions, deep mutational data, deep learning, and advanced mathematics. There exists a tsunami of literature on the molecular modeling, simulations, and predictions of SARS-CoV-2 and related developments of drugs, vaccines, antibodies, and diagnostics. To provide readers with a quick update about this literature, we present a comprehensive and systematic methodology-centered review. Aspects such as molecular biophysics, bioinformatics, cheminformatics, machine learning, and mathematics are discussed. This review will be beneficial to researchers who are looking for ways to contribute to SARS-CoV-2 studies and those who are interested in the status of the field.
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Affiliation(s)
- Kaifu Gao
- Department
of Mathematics, Michigan State University, East Lansing, Michigan 48824, United States
| | - Rui Wang
- Department
of Mathematics, Michigan State University, East Lansing, Michigan 48824, United States
| | - Jiahui Chen
- Department
of Mathematics, Michigan State University, East Lansing, Michigan 48824, United States
| | - Limei Cheng
- Clinical
Pharmacology and Pharmacometrics, Bristol
Myers Squibb, Princeton, New Jersey 08536, United States
| | - Jaclyn Frishcosy
- Department
of Mathematics, Michigan State University, East Lansing, Michigan 48824, United States
| | - Yuta Huzumi
- Department
of Mathematics, Michigan State University, East Lansing, Michigan 48824, United States
| | - Yuchi Qiu
- Department
of Mathematics, Michigan State University, East Lansing, Michigan 48824, United States
| | - Tom Schluckbier
- Department
of Mathematics, Michigan State University, East Lansing, Michigan 48824, United States
| | - Xiaoqi Wei
- Department
of Mathematics, Michigan State University, East Lansing, Michigan 48824, United States
| | - Guo-Wei Wei
- Department
of Mathematics, Michigan State University, East Lansing, Michigan 48824, United States
- Department
of Electrical and Computer Engineering, Michigan State University, East Lansing, Michigan 48824, United States
- Department
of Biochemistry and Molecular Biology, Michigan
State University, East Lansing, Michigan 48824, United States
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Chakrabartty I, Khan M, Mahanta S, Chopra H, Dhawan M, Choudhary OP, Bibi S, Mohanta YK, Emran TB. Comparative overview of emerging RNA viruses: Epidemiology, pathogenesis, diagnosis and current treatment. Ann Med Surg (Lond) 2022; 79:103985. [PMID: 35721786 PMCID: PMC9188442 DOI: 10.1016/j.amsu.2022.103985] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2022] [Revised: 06/07/2022] [Accepted: 06/08/2022] [Indexed: 02/06/2023] Open
Abstract
From many decades, emerging infections have threatened humanity. The pandemics caused by different CoVs have already claimed and will continue to claim millions of lives. The SARS, Ebola, MERS epidemics and the most recent emergence of COVID-19 pandemic have threatened populations across borders. Since a highly pathogenic CoV has been evolved into the human population in the twenty-first century known as SARS, scientific advancements and innovative methods to tackle these viruses have increased in order to improve response preparedness towards the unpredictable threat posed by these rapidly emerging pathogens. Recently published review articles on SARS-CoV-2 have mainly focused on its pathogenesis, epidemiology and available treatments. However, in this review, we have done a systematic comparison of all three CoVs i.e., SARS, MERS and SARS-CoV-2 along with Ebola and Zika in terms of their epidemiology, virology, clinical features and current treatment strategies. This review focuses on important emerging RNA viruses starting from Zika, Ebola and the CoVs which include SARS, MERS and SARS-CoV-2. Each of these viruses has been elaborated on the basis of their epidemiology, virulence, transmission and treatment. However, special attention has been given to SARS-CoV-2 and the disease caused by it i.e., COVID-19 due to current havoc caused worldwide. At the end, insights into the current understanding of the lessons learned from previous epidemics to combat emerging CoVs have been described. The travel-related viral spread, the unprecedented nosocomial outbreaks and the high case-fatality rates associated with these highly transmissible and pathogenic viruses highlight the need for new prophylactic and therapeutic actions which include but are not limited to clinical indicators, contact tracing, and laboratory investigations as important factors that need to be taken into account in order to arrive at the final conclusion. Recently published review articles on SARS-CoV-2 have mainly focused on its pathogenesis, epidemiology and available treatments. The pandemics caused by different CoVs have already claimed and will continue to claim millions of lives. This review focuses on important emerging RNA viruses starting from Zika, Ebola and the CoVs which include SARS, MERS and SARS-CoV-2. Globally, numerous studies and researchers have recently started fighting this virus.
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Affiliation(s)
- Ishani Chakrabartty
- Department of Applied Biology, School of Biological Sciences, University of Science and Technology Meghalaya (USTM), 9th Mile, Techno City, Baridua, Ri-Bhoi 793101, Meghalaya, India
| | - Maryam Khan
- Department of Biochemistry, Faculty of Life Sciences, Aligarh Muslim University, Aligarh, 202002, U.P, India
| | - Saurov Mahanta
- National Institute of Electronics and Information Technology (NIELIT), Guwahati Centre Guwahati, 781008, Assam, India
| | - Hitesh Chopra
- Chitkara College of Pharmacy, Chitkara University, Rajpura, Punjab, India
| | - Manish Dhawan
- Department of Microbiology, Punjab Agricultural University, Ludhiana, 141004, Punjab, India.,Trafford College, Altrincham, Manchester, WA14 5PQ, UK
| | - Om Prakash Choudhary
- Department of Veterinary Anatomy and Histology, College of Veterinary Sciences and Animal Husbandry, Central Agricultural University (I), Selesih, Aizawl, India
| | - Shabana Bibi
- Department of Biosciences, Shifa Tameer-e-Millat University, Islamabad, Pakistan.,Yunnan Herbal Laboratory, College of Ecology and Environmental Sciences, Yunnan University, Kunming, 650091, China
| | - Yugal Kishore Mohanta
- Department of Applied Biology, School of Biological Sciences, University of Science and Technology Meghalaya (USTM), 9th Mile, Techno City, Baridua, Ri-Bhoi 793101, Meghalaya, India
| | - Talha Bin Emran
- Department of Pharmacy, BGC Trust University Bangladesh, Chittagong, 4381, Bangladesh.,Department of Pharmacy, Faculty of Allied Health Sciences, Daffodil International University, Dhaka, 1207, Bangladesh
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Understanding the omicron variant (B.1.1.529) of SARS-CoV-2: Mutational impacts, concerns, and the possible solutions. Ann Med Surg (Lond) 2022; 78:103737. [PMID: 35571678 PMCID: PMC9078452 DOI: 10.1016/j.amsu.2022.103737] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Revised: 04/28/2022] [Accepted: 05/03/2022] [Indexed: 01/18/2023] Open
Abstract
Despite many nations' best efforts to contain the so-called COVID-19 pandemic, the emergence of the SARS-CoV-2 Omicron strain (B.1.1.529) has been identified as a serious concern. After more than two years of COVID-19 pandemic and more than a year of worldwide vaccination efforts, the globe will not be free of COVID-19 variants such as Delta and Omicron variants. According to current statistics, the Omicron variant has more than 30 mutations when contrasted to other VOCs such as Alpha (B.1.1.7), Beta (B.1.351), and Delta (B.1.617.2). High numbers of changes, particularly in the spike protein (S-Protein), raise worries about the virus's capacity to resist pre-existing immunity acquired by vaccination or spontaneous infection and antibody-based therapy. The Omicron variant raised international concerns, resuming travel bans and coming up with many questions about its severity, transmissibility, testing, detection, and vaccines efficiency against it. Additionally, inadequate health care infrastructures and many immunocompromised individuals increase the infection susceptibility. The current status of low vaccination rates will play a significant role in omicron spreading and create a fertile ground for producing new variants. As a result, this article emphasizes the mutational changes and their consequences. In addition, the potential preventing measures have been examined in detail. In South Africa, WHO designated the first cases of the SARS-CoV-2 Omicron variant (B.1.1.529). This variation is notable for having an extremely high number of spike protein mutations. Omicron has about 50 mutations, particularly 32 spike protein mutations. Omicron considers the most common variant in South Africa as an alternative to Delta.
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28
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In vitro antioxidant and cytotoxicity activities and in silico anticancer property of methanolic leaf extract of Leucas indica. INFORMATICS IN MEDICINE UNLOCKED 2022. [DOI: 10.1016/j.imu.2022.100963] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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Dracorhodin Perchlorate Regulates the Expression of Inflammatory Cytokines through the TLR4 Pathway and Improves Skin Wound Healing in Diabetic Rats. EVIDENCE-BASED COMPLEMENTARY AND ALTERNATIVE MEDICINE 2022; 2022:9050686. [PMID: 35463063 PMCID: PMC9023164 DOI: 10.1155/2022/9050686] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/17/2021] [Revised: 03/10/2022] [Accepted: 03/21/2022] [Indexed: 12/23/2022]
Abstract
Background Dragon's blood is a natural medicine with hemostatic and blood-activating effects and is used to promote wound healing. Dracorhodin perchlorate (DP) is a stable form of dracarhod and is used as a substitute for cochinchinenin. DP promotes the proliferation of rat fibroblasts and promotes wound healing in rats. Methods DP ointment (0.2 mg/mL) was applied to the skin wounds of nondiabetic and diabetic rats, and the skin of the wound was collected. Wound healing rate, H&E staining, Masson staining, TLR4 pathway, related inflammatory factors, nitric oxide synthase, and so forth were detected. Results DP treatment alleviated the prolonged inflammatory cell infiltration time and the increase in the TLR4 pathway and inflammatory factors caused by diabetes. DP also promoted wound healing by increasing eNOS protein expression and NO content in the later stage of wound healing. Conclusion DP promotes wound healing in diabetic rats by regulating the TLR4 pathway and related inflammatory factors. Therefore, adjuvant treatment of DP can be developed for diabetic wound healing.
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Abas AH, Marfuah S, Idroes R, Kusumawaty D, Fatimawali, Park MN, Siyadatpanah A, Alhumaydhi FA, Mahmud S, Tallei TE, Emran TB, Kim B. Can the SARS-CoV-2 Omicron Variant Confer Natural Immunity against COVID-19? Molecules 2022; 27:2221. [PMID: 35408618 PMCID: PMC9000495 DOI: 10.3390/molecules27072221] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Revised: 03/23/2022] [Accepted: 03/24/2022] [Indexed: 02/06/2023] Open
Abstract
The coronavirus disease 2019 (COVID-19) pandemic is still ongoing, with no signs of abatement in sight. The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which is the causative agent of this pandemic and has claimed over 5 million lives, is still mutating, resulting in numerous variants. One of the newest variants is Omicron, which shows an increase in its transmissibility, but also reportedly reduces hospitalization rates and shows milder symptoms, such as in those who have been vaccinated. As a result, many believe that Omicron provides a natural vaccination, which is the first step toward ending the COVID-19 pandemic. Based on published research and scientific evidence, we review and discuss how the end of this pandemic is predicted to occur as a result of Omicron variants being surpassed in the community. In light of the findings of our research, we believe that it is most likely true that the Omicron variant is a natural way of vaccinating the masses and slowing the spread of this deadly pandemic. While the mutation that causes the Omicron variant is encouraging, subsequent mutations do not guarantee that the disease it causes will be less severe. As the virus continues to evolve, humans must constantly adapt by increasing their immunity through vaccination.
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Affiliation(s)
- Abdul Hawil Abas
- Department of Biology, Faculty of Mathematics and Natural Sciences, Sam Ratulangi University, Manado 95115, North Sulawesi, Indonesia; (A.H.A.); (S.M.)
| | - Siti Marfuah
- Department of Biology, Faculty of Mathematics and Natural Sciences, Sam Ratulangi University, Manado 95115, North Sulawesi, Indonesia; (A.H.A.); (S.M.)
| | - Rinaldi Idroes
- Department of Pharmacy, Faculty of Mathematics and Natural Sciences, Universitas Syiah Kuala, Kopelma Darussalam, Banda Aceh 23111, Aceh, Indonesia;
| | - Diah Kusumawaty
- Department of Biology, Faculty of Mathematics and Natural Sciences Education, Universitas Pendidikan Indonesia, Bandung 40154, West Java, Indonesia;
| | - Fatimawali
- Pharmacy Study Program, Faculty of Mathematics and Natural Sciences, Sam Ratulangi University, Manado 95115, North Sulawesi, Indonesia;
| | - Moon Nyeo Park
- College of Korean Medicine, Kyung Hee University, Hoegidong Dongdaemungu, Seoul 05253, Korea;
| | - Abolghasem Siyadatpanah
- Ferdows School of Paramedical and Health, Birjand University of Medical Sciences, Birjand 97178-53577, Iran;
| | - Fahad A. Alhumaydhi
- Department of Medical Laboratories, College of Applied Medical Sciences, Qassim University, Buraydah 52571, Saudi Arabia;
| | - Shafi Mahmud
- Department of Genome Science, John Curtin School of Medical Research, Australian National University, Canberra, ACT 0200, Australia;
| | - Trina Ekawati Tallei
- Department of Biology, Faculty of Mathematics and Natural Sciences, Sam Ratulangi University, Manado 95115, North Sulawesi, Indonesia; (A.H.A.); (S.M.)
| | - Talha Bin Emran
- Department of Pharmacy, BGC Trust University Bangladesh, Chittagong 4381, Bangladesh
| | - Bonglee Kim
- College of Korean Medicine, Kyung Hee University, Hoegidong Dongdaemungu, Seoul 05253, Korea;
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Hajdrik P, Pályi B, Kis Z, Kovács N, Veres DS, Szigeti K, Budán F, Hegedüs I, Kovács T, Bergmann R, Máthé D. In Vitro Determination of Inhibitory Effects of Humic Substances Complexing Zn and Se on SARS-CoV-2 Virus Replication. Foods 2022; 11:694. [PMID: 35267328 PMCID: PMC8909382 DOI: 10.3390/foods11050694] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Revised: 02/22/2022] [Accepted: 02/23/2022] [Indexed: 02/06/2023] Open
Abstract
(1) Background: Humic substances are well-known human nutritional supplement materials and they play an important performance-enhancing role as animal feed additives. For decades, ingredients of humic substances have been proven to carry potent antiviral effects against different viruses. (2) Methods: Here, the antiviral activity of a humic substance containing ascorbic acid, Se- and Zn2+ ions intended as a nutritional supplement material was investigated against SARS-CoV-2 virus B1.1.7 Variant of Concern ("Alpha Variant") in a VeroE6 cell line. (3) Results: This combination has a significant in vitro antiviral effect at a very low concentration range of its intended active ingredients. (4) Conclusions: Even picomolar concentration ranges of humic substances, Vitamin C and Zn/Se ions in the given composition, were enough to achieve 50% viral replication inhibition in the applied SARS-CoV-2 virus inhibition test.
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Affiliation(s)
- Polett Hajdrik
- Department of Biophysics and Radiation Biology, Semmelweis University, Üllői út 26., H-1085 Budapest, Hungary; (P.H.); (N.K.); (D.S.V.); (K.S.); (I.H.); (R.B.)
| | - Bernadett Pályi
- National Biosafety Laboratory, National Public Health Center, Albert Flórián út 2-6, H-1097 Budapest, Hungary; (B.P.); (Z.K.)
| | - Zoltán Kis
- National Biosafety Laboratory, National Public Health Center, Albert Flórián út 2-6, H-1097 Budapest, Hungary; (B.P.); (Z.K.)
- Department of Microbiology, Semmelweis University, Üllői út 26., H-1085 Budapest, Hungary
| | - Noémi Kovács
- Department of Biophysics and Radiation Biology, Semmelweis University, Üllői út 26., H-1085 Budapest, Hungary; (P.H.); (N.K.); (D.S.V.); (K.S.); (I.H.); (R.B.)
- CROmed Translational Research Ltd., Tűzoltó u. 37-47, H-1094 Budapest, Hungary
| | - Dániel Sándor Veres
- Department of Biophysics and Radiation Biology, Semmelweis University, Üllői út 26., H-1085 Budapest, Hungary; (P.H.); (N.K.); (D.S.V.); (K.S.); (I.H.); (R.B.)
| | - Krisztián Szigeti
- Department of Biophysics and Radiation Biology, Semmelweis University, Üllői út 26., H-1085 Budapest, Hungary; (P.H.); (N.K.); (D.S.V.); (K.S.); (I.H.); (R.B.)
| | - Ferenc Budán
- Institute of Transdisciplinary Discoveries, Medical School, University of Pécs, Ifjúság útja 11, H-7624 Pécs, Hungary;
- Institute of Physiology, Medical School, University of Pécs, Szigeti út 12, H-7624 Pécs, Hungary
| | - Imre Hegedüs
- Department of Biophysics and Radiation Biology, Semmelweis University, Üllői út 26., H-1085 Budapest, Hungary; (P.H.); (N.K.); (D.S.V.); (K.S.); (I.H.); (R.B.)
| | - Tibor Kovács
- Institute of Radiochemistry and Radioecology, University of Pannonia, Egyetem u. 10., H-8200 Veszprem, Hungary;
| | - Ralf Bergmann
- Department of Biophysics and Radiation Biology, Semmelweis University, Üllői út 26., H-1085 Budapest, Hungary; (P.H.); (N.K.); (D.S.V.); (K.S.); (I.H.); (R.B.)
- Helmholtz-Zentrum Dresden Rossendorf, Bautzner Landstraße 400, 01328 Dresden, Germany
| | - Domokos Máthé
- Department of Biophysics and Radiation Biology, Semmelweis University, Üllői út 26., H-1085 Budapest, Hungary; (P.H.); (N.K.); (D.S.V.); (K.S.); (I.H.); (R.B.)
- CROmed Translational Research Ltd., Tűzoltó u. 37-47, H-1094 Budapest, Hungary
- Hungarian Centre of Excellence for Molecular Medicine, In Vivo Imaging Advanced Core Facility, Semmelweis University Site, Római Blvd. 21, H-6723 Szeged, Hungary
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Li SG, Yang KS, Blankenship LR, Cho CCD, Xu S, Wang H, Liu WR. An Enhanced Hybrid Screening Approach to Identify Potent Inhibitors for the SARS-CoV-2 Main Protease From the NCI Compound Library. Front Chem 2022; 10:816576. [PMID: 35252116 PMCID: PMC8892251 DOI: 10.3389/fchem.2022.816576] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Accepted: 01/28/2022] [Indexed: 12/20/2022] Open
Abstract
The emergence and rapid spread of SARS-CoV-2, the pathogen of COVID-19, have caused a worldwide public health crisis. The SARS-CoV-2 main protease (Mpro) is an essential enzyme for the virus and therefore an appealing target for the development of antivirals to treat COVID-19 patients. Recently, many in silico screenings have been performed against the main protease to discover novel hits. However, the actual hit rate of virtual screening is often low, and most of the predicted compounds are false positive hits. In this study, we developed a refined virtual screening strategy that incorporated molecular docking and post-docking filtering based on parameters including molecular weight and surface area, aiming to achieve predictions with fewer false positive hits. We applied this strategy to the NCI library containing 284,176 compounds against Mpro. In vitro potency analyses validated several potent inhibitors and thus confirmed the feasibility of our virtual screening strategy. Overall, The study resulted in several potent hit Mpro inhibitors, in which two inhibitors have IC50 values below 1 μM, that are worth being further optimized and explored. Meanwhile, the refined virtual screen strategy is also applicable to improve general in silico screening hit rates and is useful to accelerate drug discovery for treating COVID-19 and other viral infections.
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Affiliation(s)
- Shuhua G. Li
- Texas A&M Drug Discovery Laboratory, Department of Chemistry, Texas A&M University, College Station, TX, United States
| | - Kai S. Yang
- Texas A&M Drug Discovery Laboratory, Department of Chemistry, Texas A&M University, College Station, TX, United States
| | - Lauren R. Blankenship
- Texas A&M Drug Discovery Laboratory, Department of Chemistry, Texas A&M University, College Station, TX, United States
| | - Chia-Chuan D. Cho
- Texas A&M Drug Discovery Laboratory, Department of Chemistry, Texas A&M University, College Station, TX, United States
| | - Shiqing Xu
- Texas A&M Drug Discovery Laboratory, Department of Chemistry, Texas A&M University, College Station, TX, United States
- *Correspondence: Shiqing Xu, ; Hongbin Wang, ; Wenshe Ray Liu,
| | - Hongbin Wang
- Center for Biomedical Informatics, College of Medicine, Texas A&M University, Houston, TX, United States
- *Correspondence: Shiqing Xu, ; Hongbin Wang, ; Wenshe Ray Liu,
| | - Wenshe Ray Liu
- Texas A&M Drug Discovery Laboratory, Department of Chemistry, Texas A&M University, College Station, TX, United States
- Institute of Biosciences and Technology and Department of Translational Medical Sciences, College of Medicine, Texas A&M University, Houston, TX, United States
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX, United States
- Department of Molecular and Cellular Medicine, College of Medicine, Texas A&M University, College Station, TX, United States
- *Correspondence: Shiqing Xu, ; Hongbin Wang, ; Wenshe Ray Liu,
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Network Pharmacology- and Molecular Docking-Based Identification of Potential Phytocompounds from Argyreia capitiformis in the Treatment of Inflammation. EVIDENCE-BASED COMPLEMENTARY AND ALTERNATIVE MEDICINE 2022; 2022:8037488. [PMID: 35140801 PMCID: PMC8820870 DOI: 10.1155/2022/8037488] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/18/2021] [Revised: 01/03/2022] [Accepted: 01/15/2022] [Indexed: 12/16/2022]
Abstract
The methanolic extract of Argyreia capitiformis stem was examined for anti-inflammatory activities following network pharmacology analysis and molecular docking study. Based on gas chromatography-mass spectrometry (GC-MS) analysis, 49 compounds were identified from the methanolic extract of A. capitiformis stem. A network pharmacology analysis was conducted against the identified compounds, and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis and Gene Ontology analysis of biological processes and molecular functions were performed. Six proteins (IL1R1, IRAK4, MYD88, TIRAP, TLR4, and TRAF6) were identified from the KEGG pathway analysis and subjected to molecular docking study. Additionally, six best ligand efficiency compounds and positive control (aspirin) from each protein were evaluated for their stability using the molecular dynamics simulation study. Our study suggested that IL1R1, IRAK4, MYD88, TIRAP, TLR4, and TRAF6 proteins may be targeted by compounds in the methanolic extract of A. capitiformis stem to provide anti-inflammatory effects.
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Kumar Paul G, Mahmud S, Aldahish AA, Afroze M, Biswas S, Briti Ray Gupta S, Hasan Razu M, Zaman S, Salah Uddin M, Nahari MH, Merae Alshahrani M, Abdul Rahman Alshahrani M, Khan M, Abu Saleh M. Computational screening and biochemical analysis of Pistacia integerrima and Pandanus odorifer plants to find effective inhibitors against Receptor-Binding domain (RBD) of the spike protein of SARS-Cov-2. ARAB J CHEM 2022; 15:103600. [PMID: 34909068 PMCID: PMC8632739 DOI: 10.1016/j.arabjc.2021.103600] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2021] [Accepted: 11/25/2021] [Indexed: 01/25/2023] Open
Abstract
Although World Health Organization-approved emergency vaccines are available in many countries, the mortality rate from COVID-19 remains high due to the fourth or fifth wave and the delta variant of the coronavirus. Thus, an effective mechanistic investigation in treating this disease is urgently needed. In this work, we extracted phytochemicals from two mangrove plants, Pistacia integerrima and Pandanus odorifer, assessing their potential actions against the receptor-binding domain (RBD) of the spike protein of SARS-CoV-2. The antioxidant activities of Pistacia integerrima leaves and fruits were 142.10 and 97.13 µg/mL, respectively, whereas Pandanus odorifer leaves and fruits were 112.50 and 292.71 µg/mL, respectively. Furthermore, leaf extracts from both plants had lower cytotoxicity against Artemia salina than fruit extracts. Gas chromatography-mass spectrometry analysis revealed a total of 145 potential phytochemicals from these extracts. Three phytochemicals, 28-demethyl-beta-amyrone, 24-Noroleana-3,12-diene, and stigmasterol, displayed binding free energy values of - 8.3, -7.5, and - 8.1 Kcal/mol, respectively, in complexes with the spike protein of SARS-CoV-2. The root-mean-square deviation, solvent-accessible surface area, radius of gyration, root-mean-square fluctuations, and hydrogen bonds were used to ensure the binding stability of the docked complexes in the atomistic simulation. Thus, wet-lab validations are necessary to support these findings.
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Affiliation(s)
- Gobindo Kumar Paul
- Microbiology Laboratory, Department of Genetic Engineering and Biotechnology, University of Rajshahi, Rajshahi 6205, Bangladesh
| | - Shafi Mahmud
- Microbiology Laboratory, Department of Genetic Engineering and Biotechnology, University of Rajshahi, Rajshahi 6205, Bangladesh
| | - Afaf A Aldahish
- Department of Pharmacology and Toxicology, College of Pharmacy, King Khalid University, Abha 62529, Asir, Saudi Arabia
| | - Mirola Afroze
- Bangladesh Reference Institute for Chemical Measurements, BRiCM, Bangladesh Council of Scientific and Industrial Research, Dhanmondi, Dhaka 1205, Bangladesh
| | - Suvro Biswas
- Microbiology Laboratory, Department of Genetic Engineering and Biotechnology, University of Rajshahi, Rajshahi 6205, Bangladesh
| | - Swagota Briti Ray Gupta
- Microbiology Laboratory, Department of Genetic Engineering and Biotechnology, University of Rajshahi, Rajshahi 6205, Bangladesh
| | - Mahmudul Hasan Razu
- Bangladesh Reference Institute for Chemical Measurements, BRiCM, Bangladesh Council of Scientific and Industrial Research, Dhanmondi, Dhaka 1205, Bangladesh
| | - Shahriar Zaman
- Microbiology Laboratory, Department of Genetic Engineering and Biotechnology, University of Rajshahi, Rajshahi 6205, Bangladesh
| | - Md Salah Uddin
- Microbiology Laboratory, Department of Genetic Engineering and Biotechnology, University of Rajshahi, Rajshahi 6205, Bangladesh
| | - Mohammed H Nahari
- Department of Clinical Laboratory Sciences, Faculty of Applied Medical Sciences, Najran University, PO Box 1988, Najran 61441, Saudi Arabia
| | - Mohammed Merae Alshahrani
- Department of Clinical Laboratory Sciences, Faculty of Applied Medical Sciences, Najran University, PO Box 1988, Najran 61441, Saudi Arabia
| | - Mohammed Abdul Rahman Alshahrani
- Department of Clinical Laboratory Sciences, Faculty of Applied Medical Sciences, Najran University, PO Box 1988, Najran 61441, Saudi Arabia
| | - Mala Khan
- Bangladesh Reference Institute for Chemical Measurements, BRiCM, Bangladesh Council of Scientific and Industrial Research, Dhanmondi, Dhaka 1205, Bangladesh
| | - Md Abu Saleh
- Microbiology Laboratory, Department of Genetic Engineering and Biotechnology, University of Rajshahi, Rajshahi 6205, Bangladesh
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Effect of a Nutritional Support System to Increase Survival and Reduce Mortality in Patients with COVID-19 in Stage III and Comorbidities: A Blinded Randomized Controlled Clinical Trial. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2022; 19:ijerph19031172. [PMID: 35162195 PMCID: PMC8835093 DOI: 10.3390/ijerph19031172] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/13/2021] [Revised: 12/20/2021] [Accepted: 12/31/2021] [Indexed: 02/08/2023]
Abstract
The COVID-19 evolution depends on immunological capacity. The global hospital mortality rate is 15–20%, but in México it is 46%. There are several therapeutic protocols, however, integral nutrition is not considered. In this study, a Nutritional Support System (NSS) was employed to increase survival and reduce mortality in patients with stage III COVID-19. A randomized, blinded, controlled clinical trial was performed. Eighty patients (aged 30 to 75 years, both sexes) were assigned to (1) “Control Group” (CG) hospital diet and medical treatment or (2) “Intervention Group” (IG) hospital diet, medical treatment, and the NSS (vitamins, minerals, fiber, omega-3, amino acids, B-complex, and probiotics). IG significantly increased survival and reduced mortality compared to CG (p = 0.027). IG decreased progression to Mechanical Ventilation Assistance (MVA) by 10%, reduced the intubation period by 15 days, and increased survival in intubated patients by 38% compared to CG. IG showed improvement compared to CG in decrease in supplemental oxygen (p = 0.014), the qSOFA test (p = 0.040), constipation (p = 0.014), the PHQ-9 test (p = 0.003), and in the follow-up, saturation with oxygen (p = 0.030). The NSS increases survival and decreases mortality in patients with stage III COVID-19.
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Exploring the Immune-Boosting Functions of Vitamins and Minerals as Nutritional Food Bioactive Compounds: A Comprehensive Review. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27020555. [PMID: 35056870 PMCID: PMC8779769 DOI: 10.3390/molecules27020555] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/11/2021] [Revised: 01/04/2022] [Accepted: 01/10/2022] [Indexed: 02/06/2023]
Abstract
Food components have long been recognized to play a fundamental role in the growth and development of the human body, conferring protective functionalities against foreign matter that can be severe public health problems. Micronutrients such as vitamins and minerals are essential to the human body, and individuals must meet their daily requirements through dietary sources. Micronutrients act as immunomodulators and protect the host immune response, thus preventing immune evasion by pathogenic organisms. Several experimental investigations have been undertaken to appraise the immunomodulatory functions of vitamins and minerals. Based on these experimental findings, this review describes the immune-boosting functionalities of micronutrients and the mechanisms of action through which these functions are mediated. Deficiencies of vitamins and minerals in plasma concentrations can lead to a reduction in the performance of the immune system functioning, representing a key contributor to unfavorable immunological states. This review provides a descriptive overview of the characteristics of the immune system and the utilization of micronutrients (vitamins and minerals) in preventative strategies designed to reduce morbidity and mortality among patients suffering from immune invasions or autoimmune disorders.
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Arwansyah A, Arif AR, Ramli I, Hasrianti H, Kurniawan I, Ambarsari L, Sumaryada TI, Taiyeb M. Investigation of Active Compounds of
Brucea Javanica
In Treating Hypertension Using A Network Pharmacology‐Based Analysis Combined with Homology Modeling, Molecular Docking and Molecular Dynamics Simulation. ChemistrySelect 2022. [DOI: 10.1002/slct.202102801] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Arwansyah Arwansyah
- Department of Chemistry Faculty of Science Universitas Cokroaminoto Palopo 91921- Palopo Indonesia
| | - Abdur Rahman Arif
- Department of Chemistry Faculty of Mathematics and Natural Sciences Hasanuddin University 90245 -Makassar Indonesia
| | - Irwan Ramli
- Department of Physics Faculty of Science Universitas Cokroaminoto Palopo 91921- Palopo Indonesia
| | - Hasrianti Hasrianti
- Department of Biology Faculty of Science Universitas Cokroaminoto Palopo 91921- Palopo Indonesia
| | - Isman Kurniawan
- School of Computing Telkom University 40257- Bandung Indonesia
- Research Center of Human Centric Engineering Telkom University 40257-Bandung Indonesia
| | - Laksmi Ambarsari
- Department of Biochemistry Faculty of Mathematics and Natural Sciences Bogor Agricultural University 16680 -Bogor Indonesia
| | - Tony Ibnu Sumaryada
- Department of Physics Faculty of Mathematics and Natural Sciences Bogor Agricultural University 16680- Bogor Indonesia
| | - Mushawwir Taiyeb
- Department of Biology Faculty of Mathematics and Natural Sciences Makassar State University 90222- Makassar Indonesia
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Tallei TE, Fatimawali, Adam AA, Elseehy MM, El-Shehawi AM, Mahmoud EA, Tania AD, Niode NJ, Kusumawaty D, Rahimah S, Effendi Y, Idroes R, Celik I, Hossain MJ, Emran TB. Fruit Bromelain-Derived Peptide Potentially Restrains the Attachment of SARS-CoV-2 Variants to hACE2: A Pharmacoinformatics Approach. Molecules 2022; 27:260. [PMID: 35011492 PMCID: PMC8746556 DOI: 10.3390/molecules27010260] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2021] [Revised: 12/09/2021] [Accepted: 12/10/2021] [Indexed: 12/14/2022] Open
Abstract
Before entering the cell, the SARS-CoV-2 spike glycoprotein receptor-binding domain (RBD) binds to the human angiotensin-converting enzyme 2 (hACE2) receptor. Hence, this RBD is a critical target for the development of antiviral agents. Recent studies have discovered that SARS-CoV-2 variants with mutations in the RBD have spread globally. The purpose of this in silico study was to determine the potential of a fruit bromelain-derived peptide. DYGAVNEVK. to inhibit the entry of various SARS-CoV-2 variants into human cells by targeting the hACE binding site within the RBD. Molecular docking analysis revealed that DYGAVNEVK interacts with several critical RBD binding residues responsible for the adhesion of the RBD to hACE2. Moreover, 100 ns MD simulations revealed stable interactions between DYGAVNEVK and RBD variants derived from the trajectory of root-mean-square deviation (RMSD), radius of gyration (Rg), and root-mean-square fluctuation (RMSF) analysis, as well as free binding energy calculations. Overall, our computational results indicate that DYGAVNEVK warrants further investigation as a candidate for preventing SARS-CoV-2 due to its interaction with the RBD of SARS-CoV-2 variants.
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Affiliation(s)
- Trina Ekawati Tallei
- Department of Biology, Faculty of Mathematics and Natural Sciences, Sam Ratulangi University, Manado 95115, Indonesia
- The University Centre of Excellence for Biotechnology and Conservation of Wallacea, Institute for Research and Community Services, Sam Ratulangi University, Manado 95115, Indonesia; (F.); (N.J.N.)
| | - Fatimawali
- The University Centre of Excellence for Biotechnology and Conservation of Wallacea, Institute for Research and Community Services, Sam Ratulangi University, Manado 95115, Indonesia; (F.); (N.J.N.)
- Pharmacy Study Program, Faculty of Mathematics and Natural Sciences, Sam Ratulangi University, Manado 95115, Indonesia;
| | - Ahmad Akroman Adam
- Dentistry Study Program, Faculty of Medicine, Sam Ratulangi University, Manado 95115, Indonesia;
| | - Mona M. Elseehy
- Department of Genetics, Faculty of Agriculture, University of Alexandria, Alexandria 21545, Egypt;
| | - Ahmed M. El-Shehawi
- Department of Biotechnology, College of Science, Taif University, P.O. Box 11099, Taif 21944, Saudi Arabia;
| | - Eman A. Mahmoud
- Department of Food Industries, Faculty of Agriculture, Damietta University, Damietta 34511, Egypt;
| | - Adinda Dwi Tania
- Pharmacy Study Program, Faculty of Mathematics and Natural Sciences, Sam Ratulangi University, Manado 95115, Indonesia;
| | - Nurdjannah Jane Niode
- The University Centre of Excellence for Biotechnology and Conservation of Wallacea, Institute for Research and Community Services, Sam Ratulangi University, Manado 95115, Indonesia; (F.); (N.J.N.)
- Department of Dermatology and Venereology, Faculty of Medicine, University of Sam Ratulangi, RD Kandou Hospital, Manado 95163, Indonesia
| | - Diah Kusumawaty
- Department of Biology, Faculty of Mathematics and Natural Sciences Education, Universitas Pendidikan Indonesia, Bandung 40154, Indonesia;
| | - Souvia Rahimah
- Food Technology Study Program, Department of Food Industrial Technology, Faculty of Agroindustrial Technology, Universitas Padjadjaran, Jatinangor 45363, Indonesia;
| | - Yunus Effendi
- Department of Biology, Faculty of Science and Technology, Al-Azhar Indonesia University, Jakarta 12110, Indonesia;
| | - Rinaldi Idroes
- Department of Pharmacy, Faculty of Mathematics and Natural Sciences, Universitas Syiah Kuala, Kopelma Darussalam, Banda Aceh 23111, Indonesia;
| | - Ismail Celik
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Erciyes University, Kayseri 38039, Turkey;
| | - Md. Jamal Hossain
- Department of Pharmacy, State University of Bangladesh, 77 Satmasjid Road, Dhanmondi, Dhaka 1205, Bangladesh;
| | - Talha Bin Emran
- Department of Pharmacy, BGC Trust University Bangladesh, Chittagong 4381, Bangladesh
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Tallei TE, Kepel BJ, Alorabi M, El-Shehawi AM, Bodhi W, Tumilaar SG, Celik I, Mostafa-Hedeab G, Mohamed AAR, Emran TB. Appraisal of Bioactive Compounds of Betel Fruit as Antimalarial Agents by Targeting Plasmepsin 1 and 2: A Computational Approach. Pharmaceuticals (Basel) 2021; 14:ph14121285. [PMID: 34959685 PMCID: PMC8707617 DOI: 10.3390/ph14121285] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Revised: 12/01/2021] [Accepted: 12/03/2021] [Indexed: 11/16/2022] Open
Abstract
In many countries, the fruit of betel (Piper betle Linn) is traditionally used as medicine for treating malaria. It is a fatal disease, and existing medications are rapidly losing potency, necessitating the development of innovative pharmaceutics. The current study attempted to determine the compounds in the n-hexane fraction of betel fruit extract and investigate the potential inhibition of bioactive compounds against aspartic protease plasmepsin 1 (PDB ID: 3QS1) and plasmepsin 2 (PDB ID: 1LEE) of Plasmodium falciparum using a computational approach. The ethanol extract was fractionated into n-hexane and further analyzed using gas chromatography-mass spectrometry (GC-MS) to obtain information regarding the compounds contained in betel fruit. Each compound's potential antimalarial activity was evaluated using AutoDock Vina and compared to artemisinin, an antimalarial drug. Molecular dynamics simulations (MDSs) were performed to evaluate the stability of the interaction between the ligand and receptors. Results detected 20 probable compounds in the n-hexane extract of betel fruit based on GC-MS analysis. The docking study revealed that androstan-17-one,3-ethyl-3-hydroxy-, (5 alpha)- has the highest binding affinity for plasmepsin 1 and plasmepsin 2. The compound exhibits a similar interaction with artemisinin at the active site of the receptors. The compound does not violate Lipinski's rules of five. It belongs to class 5 toxicity with an LD50 of 3000 mg/kg. MDS results showed stable interactions between the compound and the receptors. Our study concluded that androstan-17-one,3-ethyl-3-hydroxy-, (5 alpha)- from betel fruit has the potential to be further investigated as a potential inhibitor of the aspartic protease plasmepsin 1 and plasmepsin 2 of Plasmodium falciparum.
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Affiliation(s)
- Trina Ekawati Tallei
- The University Center of Excellence for Biotechnology and Conservation of Wallacea, Institute for Research and Community Services, Sam Ratulangi University, Manado 95115, Indonesia
- Department of Biology, Faculty of Mathematics and Natural Sciences, Sam Ratulangi University, Manado 95115, Indonesia
- Correspondence: (F.); (T.E.T.); (T.B.E.); Tel.: +62-812-4408-855 (F.); +62-811-4314-880 (T.E.T.); +880-01819-942214 (T.B.E.)
| | - Billy Johnson Kepel
- Department of Chemistry, Faculty of Medicine, Sam Ratulangi University, Manado 95115, Indonesia; (B.J.K.); (W.B.)
| | - Mohammed Alorabi
- Department of Biotechnology, College of Science, Taif University, Taif 21944, Saudi Arabia; (M.A.); (A.M.E.-S.)
| | - Ahmed M. El-Shehawi
- Department of Biotechnology, College of Science, Taif University, Taif 21944, Saudi Arabia; (M.A.); (A.M.E.-S.)
| | - Widdhi Bodhi
- Department of Chemistry, Faculty of Medicine, Sam Ratulangi University, Manado 95115, Indonesia; (B.J.K.); (W.B.)
| | - Sefren Geiner Tumilaar
- Pharmacy Study Program, Faculty of Mathematics and Natural Sciences, Sam Ratulangi University, Manado 95115, Indonesia;
| | - Ismail Celik
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Erciyes University, Kayseri 38039, Turkey;
| | - Gomaa Mostafa-Hedeab
- Pharmacology Department, Health Sciences Research Unit, Medical College, Jouf University, Sakaka 72446, Saudi Arabia;
- Pharmacology Department, Faculty of Medicine, Beni-Suef University, Beni Suef 62521, Egypt
| | | | - Talha Bin Emran
- Department of Pharmacy, BGC Trust University Bangladesh, Chittagong 4381, Bangladesh
- Correspondence: (F.); (T.E.T.); (T.B.E.); Tel.: +62-812-4408-855 (F.); +62-811-4314-880 (T.E.T.); +880-01819-942214 (T.B.E.)
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Sami SA, Marma KKS, Mahmud S, Khan MAN, Albogami S, El-Shehawi AM, Rakib A, Chakraborty A, Mohiuddin M, Dhama K, Uddin MMN, Hossain MK, Tallei TE, Emran TB. Designing of a Multi-epitope Vaccine against the Structural Proteins of Marburg Virus Exploiting the Immunoinformatics Approach. ACS OMEGA 2021; 6:32043-32071. [PMID: 34870027 PMCID: PMC8638006 DOI: 10.1021/acsomega.1c04817] [Citation(s) in RCA: 46] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Accepted: 11/10/2021] [Indexed: 05/08/2023]
Abstract
Marburg virus disease (MVD) caused by the Marburg virus (MARV) generally appears with flu-like symptoms and leads to severe hemorrhagic fever. It spreads via direct contact with infected individuals or animals. Despite being considered to be less threatening in terms of appearances and the number of infected patients, the high fatality rate of this pathogenic virus is a major concern. Until now, no vaccine has been developed to combat this deadly virus. Therefore, vaccination for this virus is necessary to reduce its mortality. Our current investigation focuses on the design and formulation of a multi-epitope vaccine based on the structural proteins of MARV employing immunoinformatics approaches. The screening of potential T-cell and B-cell epitopes from the seven structural proteins of MARV was carried out through specific selection parameters. Afterward, we compiled the shortlisted epitopes by attaching them to an appropriate adjuvant and linkers. Population coverage analysis, conservancy analysis, and MHC cluster analysis of the shortlisted epitopes were satisfactory. Importantly, physicochemical characteristics, human homology assessment, and structure validation of the vaccine construct delineated convenient outcomes. We implemented disulfide bond engineering to stabilize the tertiary or quaternary interactions. Furthermore, stability and physical movements of the vaccine protein were explored using normal-mode analysis. The immune simulation study of the vaccine complexes also exhibited significant results. Additionally, the protein-protein docking and molecular dynamics simulation of the final construct exhibited a higher affinity toward toll-like receptor-4 (TLR4). From simulation trajectories, multiple descriptors, namely, root mean square deviations (rmsd), radius of gyration (Rg), root mean square fluctuations (RMSF), solvent-accessible surface area (SASA), and hydrogen bonds, have been taken into account to demonstrate the inflexible and rigid nature of receptor molecules and the constructed vaccine. Inclusively, our findings suggested the vaccine constructs' ability to regulate promising immune responses against MARV pathogenesis.
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Affiliation(s)
- Saad Ahmed Sami
- Department of Pharmacy,
Faculty of Biological Sciences, University
of Chittagong, Chittagong 4331, Bangladesh
| | - Kay Kay Shain Marma
- Department of Pharmacy,
Faculty of Biological Sciences, University
of Chittagong, Chittagong 4331, Bangladesh
| | - Shafi Mahmud
- Microbiology
Laboratory, Bioinformatics Division, Department of Genetic Engineering
and Biotechnology, University of Rajshahi, Rajshahi 6205, Bangladesh
| | - Md. Asif Nadim Khan
- Department of Biochemistry and Molecular
Biology, Faculty of Biological Sciences, University of Chittagong, Chittagong 4331, Bangladesh
| | - Sarah Albogami
- Department
of Biotechnology, College of Science, Taif
University, P.O. Box 11099, Taif 21944, Saudi Arabia
| | - Ahmed M. El-Shehawi
- Department
of Biotechnology, College of Science, Taif
University, P.O. Box 11099, Taif 21944, Saudi Arabia
| | - Ahmed Rakib
- Department of Pharmacy,
Faculty of Biological Sciences, University
of Chittagong, Chittagong 4331, Bangladesh
| | - Agnila Chakraborty
- Department of Pharmacy,
Faculty of Biological Sciences, University
of Chittagong, Chittagong 4331, Bangladesh
| | - Mostafah Mohiuddin
- Department of Pharmacy,
Faculty of Biological Sciences, University
of Chittagong, Chittagong 4331, Bangladesh
| | - Kuldeep Dhama
- Division of Pathology, ICAR-Indian Veterinary
Research Institute, Izatnagar, Bareilly, Uttar Pradesh 243122, India
| | - Mir Muhammad Nasir Uddin
- Department of Pharmacy,
Faculty of Biological Sciences, University
of Chittagong, Chittagong 4331, Bangladesh
| | - Mohammed Kamrul Hossain
- Department of Pharmacy,
Faculty of Biological Sciences, University
of Chittagong, Chittagong 4331, Bangladesh
| | - Trina Ekawati Tallei
- Department of Biology,
Faculty of Mathematics and Natural Sciences, Sam Ratulangi University, Manado, North Sulawesi 95115, Indonesia
| | - Talha Bin Emran
- Department of Pharmacy, BGC Trust University Bangladesh, Chittagong 4381, Bangladesh
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Islam F, Bibi S, Meem AFK, Islam MM, Rahaman MS, Bepary S, Rahman MM, Rahman MM, Elzaki A, Kajoak S, Osman H, ElSamani M, Khandaker MU, Idris AM, Emran TB. Natural Bioactive Molecules: An Alternative Approach to the Treatment and Control of COVID-19. Int J Mol Sci 2021; 22:12638. [PMID: 34884440 PMCID: PMC8658031 DOI: 10.3390/ijms222312638] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Revised: 11/11/2021] [Accepted: 11/19/2021] [Indexed: 02/07/2023] Open
Abstract
Several coronaviruses (CoVs) have been associated with serious health hazards in recent decades, resulting in the deaths of thousands around the globe. The recent coronavirus pandemic has emphasized the importance of discovering novel and effective antiviral medicines as quickly as possible to prevent more loss of human lives. Positive-sense RNA viruses with group spikes protruding from their surfaces and an abnormally large RNA genome enclose CoVs. CoVs have already been related to a range of respiratory infectious diseases possibly fatal to humans, such as MERS, SARS, and the current COVID-19 outbreak. As a result, effective prevention, treatment, and medications against human coronavirus (HCoV) is urgently needed. In recent years, many natural substances have been discovered with a variety of biological significance, including antiviral properties. Throughout this work, we reviewed a wide range of natural substances that interrupt the life cycles for MERS and SARS, as well as their potential application in the treatment of COVID-19.
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Affiliation(s)
- Fahadul Islam
- Department of Pharmacy, Daffodil International University, Dhaka 1207, Bangladesh; (F.I.); (A.F.K.M.); (M.M.I.); (M.S.R.); (S.B.); (M.M.R.); (M.M.R.)
| | - Shabana Bibi
- Yunnan Herbal Laboratory, College of Ecology and Environmental Sciences, Yunnan University, Kunming 650091, China;
- International Joint Research Center for Sustainable Utilization of Cordyceps Bioresources in China and Southeast Asia, Yunnan University, Kunming 650091, China
| | - Atkia Farzana Khan Meem
- Department of Pharmacy, Daffodil International University, Dhaka 1207, Bangladesh; (F.I.); (A.F.K.M.); (M.M.I.); (M.S.R.); (S.B.); (M.M.R.); (M.M.R.)
| | - Md. Mohaimenul Islam
- Department of Pharmacy, Daffodil International University, Dhaka 1207, Bangladesh; (F.I.); (A.F.K.M.); (M.M.I.); (M.S.R.); (S.B.); (M.M.R.); (M.M.R.)
| | - Md. Saidur Rahaman
- Department of Pharmacy, Daffodil International University, Dhaka 1207, Bangladesh; (F.I.); (A.F.K.M.); (M.M.I.); (M.S.R.); (S.B.); (M.M.R.); (M.M.R.)
| | - Sristy Bepary
- Department of Pharmacy, Daffodil International University, Dhaka 1207, Bangladesh; (F.I.); (A.F.K.M.); (M.M.I.); (M.S.R.); (S.B.); (M.M.R.); (M.M.R.)
| | - Md. Mizanur Rahman
- Department of Pharmacy, Daffodil International University, Dhaka 1207, Bangladesh; (F.I.); (A.F.K.M.); (M.M.I.); (M.S.R.); (S.B.); (M.M.R.); (M.M.R.)
| | - Md. Mominur Rahman
- Department of Pharmacy, Daffodil International University, Dhaka 1207, Bangladesh; (F.I.); (A.F.K.M.); (M.M.I.); (M.S.R.); (S.B.); (M.M.R.); (M.M.R.)
| | - Amin Elzaki
- Department of Radiological Sciences, College of Applied Medical Sciences, Taif University, Taif 21944, Saudi Arabia; (A.E.); (S.K.); (H.O.); (M.E.)
| | - Samih Kajoak
- Department of Radiological Sciences, College of Applied Medical Sciences, Taif University, Taif 21944, Saudi Arabia; (A.E.); (S.K.); (H.O.); (M.E.)
| | - Hamid Osman
- Department of Radiological Sciences, College of Applied Medical Sciences, Taif University, Taif 21944, Saudi Arabia; (A.E.); (S.K.); (H.O.); (M.E.)
| | - Mohamed ElSamani
- Department of Radiological Sciences, College of Applied Medical Sciences, Taif University, Taif 21944, Saudi Arabia; (A.E.); (S.K.); (H.O.); (M.E.)
| | - Mayeen Uddin Khandaker
- Centre for Applied Physics and Radiation Technologies, School of Engineering and Technology, Sunway University, Bandar Sunway 47500, Selangor, Malaysia;
| | - Abubakr M. Idris
- Department of Chemistry, College of Science, King Khalid University, Abha 62529, Saudi Arabia;
- Research Center for Advanced Materials Science (RCAMS), King Khalid University, Abha 62529, Saudi Arabia
| | - Talha Bin Emran
- Department of Pharmacy, BGC Trust University Bangladesh, Chittagong 4381, Bangladesh
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42
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Paul GK, Mahmud S, Hasan MM, Zaman S, Uddin MS, Saleh MA. Biochemical and in silico study of leaf and bark extracts from Aphanamixis polystachya against common pathogenic bacteria. Saudi J Biol Sci 2021; 28:6592-6605. [PMID: 34764775 PMCID: PMC8568816 DOI: 10.1016/j.sjbs.2021.07.032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Revised: 06/29/2021] [Accepted: 07/08/2021] [Indexed: 11/16/2022] Open
Abstract
Aphanamixis polystachya may be a natural, renewable resource against antibiotic-resistant bacterial infections. The antibacterial activity of A. polystachya leaf and bark extracts was investigated against three antibiotic-resistant bacterial species and one fungus. Methanolic leaf extract showed only limited antibacterial activity but both methanolic and aqueous bark extract showed high antimicrobial activity. In an antioxidant activity test, leaf and bark extracts exhibited 50% free radical scavenging at a concentration of 107.14 ± 3.14 μg/mL and 97.13 ± 3.05 μg/mL, respectively, indicating that bark extracts offer more antioxidative activity than leaf extracts. Bark extracts also showed lower toxicity than leaf extracts. This suggests that bark extracts may offer greater development potential than leaf extracts. The molecular dynamics were also investigated through the simulated exploration of multiple potential interactions to understand the interaction dynamics (root-mean-square deviation, solvent-accessible surface area, radius of gyration, and the hydrogen bonding of chosen compounds to protein targets) and possible mechanisms of inhibition. This molecular modeling of compounds derived from A. polystachya revealed that inhibition may occur by binding to the active sites of the target proteins of the tested bacterial strains. A. polystachya bark extract may be used as a natural source of drugs to control antibiotic-resistant bacteria.
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Affiliation(s)
| | | | - Md. Mehedi Hasan
- Microbiology Laboratory, Department of Genetic Engineering and Biotechnology, University of Rajshahi, Rajshahi 6205, Bangladesh
| | - Shahriar Zaman
- Microbiology Laboratory, Department of Genetic Engineering and Biotechnology, University of Rajshahi, Rajshahi 6205, Bangladesh
| | - Md. Salah Uddin
- Microbiology Laboratory, Department of Genetic Engineering and Biotechnology, University of Rajshahi, Rajshahi 6205, Bangladesh
| | - Md. Abu Saleh
- Microbiology Laboratory, Department of Genetic Engineering and Biotechnology, University of Rajshahi, Rajshahi 6205, Bangladesh
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43
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Sarker MT, Hasan AQF, Rafi MO, Hossain MJ, El-Mageed HRA, Elsapagh RM, Capasso R, Emran TB. A Comprehensive Overview of the Newly Emerged COVID-19 Pandemic: Features, Origin, Genomics, Epidemiology, Treatment, and Prevention. BIOLOGICS 2021; 1:357-383. [DOI: 10.3390/biologics1030021] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/01/2023]
Abstract
The coronavirus disease 2019 (COVID-19), a life-threatening pandemic caused by severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), has resulted in massive destruction and is still continuously adding to its death toll. The advent of this global outbreak has not yet been confirmed; however, investigation for suitable prophylaxis against this lethal virus is being carried out by experts all around the globe. The SARS-CoV-2 belongs to the Coronaviridae superfamily, like the other previously occurring human coronavirus variants. To better understand a new virus variant, such as the SARS-CoV-2 delta variant, it is vital to investigate previous virus strains, including their genomic composition and functionality. Our study aimed at addressing the basic overview of the virus’ profile that may provide the scientific community with evidence-based insights into COVID-19. Therefore, this study accomplished a comprehensive literature review that includes the virus’ origin, classification, structure, life cycle, genome, mutation, epidemiology, and subsequent essential factors associated with host–virus interaction. Moreover, we summarized the considerable diagnostic measures, treatment options, including multiple therapeutic approaches, and prevention, as well as future directions that may reduce the impact and misery caused by this devastating pandemic. The observations and data provided here have been screened and accumulated through extensive literature study, hence this study will help the scientific community properly understand this new virus and provide further leads for therapeutic interventions.
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44
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Mousavi SS, Karami A, Haghighi TM, Tumilaar SG, Fatimawali, Idroes R, Mahmud S, Celik I, Ağagündüz D, Tallei TE, Emran TB, Capasso R. In Silico Evaluation of Iranian Medicinal Plant Phytoconstituents as Inhibitors against Main Protease and the Receptor-Binding Domain of SARS-CoV-2. Molecules 2021; 26:5724. [PMID: 34577194 PMCID: PMC8470205 DOI: 10.3390/molecules26185724] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2021] [Revised: 08/22/2021] [Accepted: 09/01/2021] [Indexed: 12/22/2022] Open
Abstract
The novel coronavirus disease 2019 (COVID-19) is caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which initially appeared in Wuhan, China, in December 2019. Elderly individuals and those with comorbid conditions may be more vulnerable to this disease. Consequently, several research laboratories continue to focus on developing drugs to treat this infection because this disease has developed into a global pandemic with an extremely limited number of specific treatments available. Natural herbal remedies have long been used to treat illnesses in a variety of cultures. Modern medicine has achieved success due to the effectiveness of traditional medicines, which are derived from medicinal plants. The objective of this study was to determine whether components of natural origin from Iranian medicinal plants have an antiviral effect that can prevent humans from this coronavirus infection using the most reliable molecular docking method; in our case, we focused on the main protease (Mpro) and a receptor-binding domain (RBD). The results of molecular docking showed that among 169 molecules of natural origin from common Iranian medicinal plants, 20 molecules (chelidimerine, rutin, fumariline, catechin gallate, adlumidine, astragalin, somniferine, etc.) can be proposed as inhibitors against this coronavirus based on the binding free energy and type of interactions between these molecules and the studied proteins. Moreover, a molecular dynamics simulation study revealed that the chelidimerine-Mpro and somniferine-RBD complexes were stable for up to 50 ns below 0.5 nm. Our results provide valuable insights into this mechanism, which sheds light on future structure-based designs of high-potency inhibitors for SARS-CoV-2.
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Affiliation(s)
- Seyyed Sasan Mousavi
- Department of Horticultural Science, School of Agriculture, Shiraz University, Shiraz 71441, Iran; (S.S.M.); (A.K.); (T.M.H.)
| | - Akbar Karami
- Department of Horticultural Science, School of Agriculture, Shiraz University, Shiraz 71441, Iran; (S.S.M.); (A.K.); (T.M.H.)
| | - Tahereh Movahhed Haghighi
- Department of Horticultural Science, School of Agriculture, Shiraz University, Shiraz 71441, Iran; (S.S.M.); (A.K.); (T.M.H.)
| | - Sefren Geiner Tumilaar
- Pharmacy Study Program, Faculty of Mathematics and Natural Sciences, Sam Ratulangi University, Manado 95115, Indonesia; (S.G.T.); (F.)
| | - Fatimawali
- Pharmacy Study Program, Faculty of Mathematics and Natural Sciences, Sam Ratulangi University, Manado 95115, Indonesia; (S.G.T.); (F.)
- The University Center of Excellence for Biotechnology and Conservation of Wallacea, Sam Ratulangi University, Manado 95115, Indonesia
| | - Rinaldi Idroes
- Department of Pharmacy, Faculty of Mathematics and Natural Sciences, Universitas Syiah Kuala, Kopelma Darussalam, Banda Aceh 23111, Indonesia;
| | - Shafi Mahmud
- Microbiology Laboratory, Department of Genetic Engineering and Biotechnology, University of Rajshahi, Rajshahi 6205, Bangladesh;
| | - Ismail Celik
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Erciyes University, Kayseri 38039, Turkey;
| | - Duygu Ağagündüz
- Department of Nutrition and Dietetics, Faculty of Health Sciences, Gazi University, Emek, Ankara 06490, Turkey;
| | - Trina Ekawati Tallei
- The University Center of Excellence for Biotechnology and Conservation of Wallacea, Sam Ratulangi University, Manado 95115, Indonesia
- Department of Biology, Faculty of Mathematics and Natural Sciences, Sam Ratulangi University, Manado 95115, Indonesia
| | - Talha Bin Emran
- Department of Pharmacy, BGC Trust University Bangladesh, Chittagong 4381, Bangladesh
| | - Raffaele Capasso
- Department of Agricultural Sciences, University of Naples Federico II, Portici, 80055 Naples, Italy
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45
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Interactions of the Receptor Binding Domain of SARS-CoV-2 Variants with hACE2: Insights from Molecular Docking Analysis and Molecular Dynamic Simulation. BIOLOGY 2021; 10:biology10090880. [PMID: 34571756 PMCID: PMC8470537 DOI: 10.3390/biology10090880] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Revised: 08/28/2021] [Accepted: 09/02/2021] [Indexed: 12/23/2022]
Abstract
Since the beginning of the coronavirus 19 (COVID-19) pandemic in late 2019, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been evolving through the acquisition of genomic mutations, leading to the emergence of multiple variants of concern (VOCs) and variants of interest (VOIs). Currently, four VOCs (Alpha, Beta, Delta, and Gamma) and seven VOIs (Epsilon, Zeta, Eta, Theta, Iota, Kappa, and Lambda) of SARS-CoV-2 have been identified in worldwide circulation. Here, we investigated the interactions of the receptor-binding domain (RBD) of five SARS-CoV-2 variants with the human angiotensin-converting enzyme 2 (hACE2) receptor in host cells, to determine the extent of molecular divergence and the impact of mutation, using protein-protein docking and dynamics simulation approaches. Along with the wild-type (WT) SARS-CoV-2, this study included the Brazilian (BR/lineage P.1/Gamma), Indian (IN/lineage B.1.617/Delta), South African (SA/lineage B.1.351/Beta), United Kingdom (UK/lineage B.1.1.7/Alpha), and United States (US/lineage B.1.429/Epsilon) variants. The protein-protein docking and dynamics simulation studies revealed that these point mutations considerably affected the structural behavior of the spike (S) protein compared to the WT, which also affected the binding of RBD with hACE2 at the respective sites. Additional experimental studies are required to determine whether these effects have an influence on drug-S protein binding and its potential therapeutic effect.
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Mahmud S, Biswas S, Kumar Paul G, Mita MA, Afrose S, Robiul Hasan M, Sharmin Sultana Shimu M, Uddin MAR, Salah Uddin M, Zaman S, Kaderi Kibria KM, Arif Khan M, Bin Emran T, Abu Saleh M. Antiviral peptides against the main protease of SARS-CoV-2: A molecular docking and dynamics study. ARAB J CHEM 2021; 14:103315. [PMID: 34909064 PMCID: PMC8277949 DOI: 10.1016/j.arabjc.2021.103315] [Citation(s) in RCA: 43] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Accepted: 07/04/2021] [Indexed: 01/08/2023] Open
Abstract
The recent coronavirus outbreak has changed the world's economy and health sectors due to the high mortality and transmission rates. Because the development of new effective vaccines or treatments against the virus can take time, an urgent need exists for the rapid development and design of new drug candidates to combat this pathogen. Here, we obtained antiviral peptides obtained from the data repository of antimicrobial peptides (DRAMP) and screened their predicted tertiary structures for the ability to inhibit the main protease of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) using multiple combinatorial docking programs, including PatchDock, FireDock, and ClusPro. The four best peptides, DRAMP00877, DRAMP02333, DRAMP02669, and DRAMP03804, had binding energies of -1125.3, -1084.5, -1005.2, and -924.2 Kcal/mol, respectively, as determined using ClusPro, and binding energies of -55.37, -50.96, -49.25, -54.81 Kcal/mol, respectively, as determined using FireDock, which were better binding energy values than observed for other peptide molecules. These peptides were found to bind with the active cavity of the SARS-CoV-2 main protease; at Glu166, Cys145, Asn142, Phe140, and Met165, in addition to the substrate-binding sites, Domain 2 and Domain 3, whereas fewer interactions were observed with Domain 1. The docking studies were further confirmed by a molecular dynamics simulation study, in which several descriptors, including the root-mean-square difference (RMSD), root-mean-square fluctuation (RMSF), solvent-accessible surface area (SASA), radius of gyration (Rg), and hydrogen bond formation, confirmed the stable nature of the peptide-main protease complexes. Toxicity and allergenicity studies confirmed the non-allergenic nature of the peptides. This present study suggests that these identified antiviral peptide molecules might inhibit the main protease of SARS-CoV-2, although further wet-lab experiments remain necessary to verify these findings.
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Affiliation(s)
- Shafi Mahmud
- Microbiology Laboratory, Department of Genetic Engineering and Biotechnology, University of Rajshahi, Rajshahi 6205, Bangladesh
| | - Suvro Biswas
- Department of Genetic Engineering and Biotechnology, University of Rajshahi, Rajshahi 6205, Bangladesh
| | - Gobindo Kumar Paul
- Microbiology Laboratory, Department of Genetic Engineering and Biotechnology, University of Rajshahi, Rajshahi 6205, Bangladesh
| | - Mohasana Akter Mita
- Department of Genetic Engineering and Biotechnology, University of Rajshahi, Rajshahi 6205, Bangladesh
| | - Shamima Afrose
- Department of Genetic Engineering and Biotechnology, University of Rajshahi, Rajshahi 6205, Bangladesh
| | - Md Robiul Hasan
- Department of Genetic Engineering and Biotechnology, University of Rajshahi, Rajshahi 6205, Bangladesh
| | - Mst Sharmin Sultana Shimu
- Department of Genetic Engineering and Biotechnology, University of Rajshahi, Rajshahi 6205, Bangladesh
| | - Mohammad Abu Raihan Uddin
- Department of Biochemistry and Biotechnology, University of Science and Technology Chittagong, Bangladesh
| | - Md Salah Uddin
- Microbiology Laboratory, Department of Genetic Engineering and Biotechnology, University of Rajshahi, Rajshahi 6205, Bangladesh
| | - Shahriar Zaman
- Microbiology Laboratory, Department of Genetic Engineering and Biotechnology, University of Rajshahi, Rajshahi 6205, Bangladesh
| | - K M Kaderi Kibria
- Department of Biotechnology and Genetic Engineering, Faculty of Life Sciences, Mawlana Bhashani Science and Technology University, Tangail 1902, Bangladesh
| | - Md Arif Khan
- Department of Biotechnology and Genetic Engineering, University of Development Alternative, Dhaka, Bangladesh
| | - Talha Bin Emran
- Department of Pharmacy, BGC Trust University, Chittagong 4381, Bangladesh
| | - Md Abu Saleh
- Microbiology Laboratory, Department of Genetic Engineering and Biotechnology, University of Rajshahi, Rajshahi 6205, Bangladesh
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47
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Yan F, Gao F. An overview of potential inhibitors targeting non-structural proteins 3 (PL pro and Mac1) and 5 (3CL pro/M pro) of SARS-CoV-2. Comput Struct Biotechnol J 2021; 19:4868-4883. [PMID: 34457214 PMCID: PMC8382591 DOI: 10.1016/j.csbj.2021.08.036] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2021] [Revised: 08/02/2021] [Accepted: 08/21/2021] [Indexed: 12/11/2022] Open
Abstract
There is an urgent need to develop effective treatments for coronavirus disease 2019 (COVID-19), which is caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The rapid spread of SARS-CoV-2 has resulted in a global pandemic that has not only affected the daily lives of individuals but also had a significant impact on the global economy and public health. Although extensive research has been conducted to identify inhibitors targeting SARS-CoV-2, there are still no effective treatment strategies to combat COVID-19. SARS-CoV-2 comprises two important proteolytic enzymes, namely, the papain-like proteinase, located within non-structural protein 3 (nsp3), and nsp5, both of which cleave large replicase polypeptides into multiple fragments that are required for viral replication. Moreover, a domain within nsp3, known as the macrodomain (Mac1), also plays an important role in viral replication. Inhibition of their functions should be able to significantly interfere with the replication cycle of the virus, and therefore these key proteins may serve as potential therapeutic targets. The functions of the above viral targets and their corresponding inhibitors have been summarized in the current review. This review provides comprehensive updates of nsp3 and nsp5 inhibitor development and would help advance the discovery of novel anti-viral therapeutics against SARS-CoV-2.
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Affiliation(s)
- Fangfang Yan
- Department of Physics, School of Science, Tianjin University, Tianjin 300072, China
| | - Feng Gao
- Department of Physics, School of Science, Tianjin University, Tianjin 300072, China
- Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin 300072, China
- SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin 300072, China
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48
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Dutta M, Tareq AM, Rakib A, Mahmud S, Sami SA, Mallick J, Islam MN, Majumder M, Uddin MZ, Alsubaie A, Almalki ASA, Khandaker MU, Bradley D, Rana MS, Emran TB. Phytochemicals from Leucas zeylanica Targeting Main Protease of SARS-CoV-2: Chemical Profiles, Molecular Docking, and Molecular Dynamics Simulations. BIOLOGY 2021; 10:789. [PMID: 34440024 PMCID: PMC8389631 DOI: 10.3390/biology10080789] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Revised: 08/05/2021] [Accepted: 08/15/2021] [Indexed: 02/07/2023]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), a contemporary coronavirus, has impacted global economic activity and has a high transmission rate. As a result of the virus's severe medical effects, developing effective vaccinations is vital. Plant-derived metabolites have been discovered as potential SARS-CoV-2 inhibitors. The SARS-CoV-2 main protease (Mpro) is a target for therapeutic research because of its highly conserved protein sequence. Gas chromatography-mass spectrometry (GC-MS) and molecular docking were used to screen 34 compounds identified from Leucas zeylanica for potential inhibitory activity against the SARS-CoV-2 Mpro. In addition, prime molecular mechanics-generalized Born surface area (MM-GBSA) was used to screen the compound dataset using a molecular dynamics simulation. From molecular docking analysis, 26 compounds were capable of interaction with the SARS-CoV-2 Mpro, while three compounds, namely 11-oxa-dispiro[4.0.4.1]undecan-1-ol (-5.755 kcal/mol), azetidin-2-one 3,3-dimethyl-4-(1-aminoethyl) (-5.39 kcal/mol), and lorazepam, 2TMS derivative (-5.246 kcal/mol), exhibited the highest docking scores. These three ligands were assessed by MM-GBSA, which revealed that they bind with the necessary Mpro amino acids in the catalytic groove to cause protein inhibition, including Ser144, Cys145, and His41. The molecular dynamics simulation confirmed the complex rigidity and stability of the docked ligand-Mpro complexes based on the analysis of mean radical variations, root-mean-square fluctuations, solvent-accessible surface area, radius of gyration, and hydrogen bond formation. The study of the postmolecular dynamics confirmation also confirmed that lorazepam, 11-oxa-dispiro[4.0.4.1]undecan-1-ol, and azetidin-2-one-3, 3-dimethyl-4-(1-aminoethyl) interact with similar Mpro binding pockets. The results of our computerized drug design approach may assist in the fight against SARS-CoV-2.
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Affiliation(s)
- Mycal Dutta
- Department of Pharmacy, BGC Trust University Bangladesh, Chittagong 4381, Bangladesh; (M.D.); (J.M.); (M.Z.U.)
- Department of Pharmacy, Jahangirnagar University, Savar, Dhaka 1342, Bangladesh
| | - Abu Montakim Tareq
- Department of Pharmacy, International Islamic University Chittagong, Chittagong 4318, Bangladesh; (A.M.T.); (M.N.I.)
| | - Ahmed Rakib
- Department of Pharmacy, Faculty of Biological Sciences, University of Chittagong, Chittagong 4331, Bangladesh; (A.R.); (S.A.S.)
| | - Shafi Mahmud
- Microbiology Laboratory, Department of Genetic Engineering and Biotechnology, University of Rajshahi, Rajshahi 6205, Bangladesh;
| | - Saad Ahmed Sami
- Department of Pharmacy, Faculty of Biological Sciences, University of Chittagong, Chittagong 4331, Bangladesh; (A.R.); (S.A.S.)
| | - Jewel Mallick
- Department of Pharmacy, BGC Trust University Bangladesh, Chittagong 4381, Bangladesh; (M.D.); (J.M.); (M.Z.U.)
- Department of Pharmacy, Jahangirnagar University, Savar, Dhaka 1342, Bangladesh
| | - Mohammad Nazmul Islam
- Department of Pharmacy, International Islamic University Chittagong, Chittagong 4318, Bangladesh; (A.M.T.); (M.N.I.)
| | - Mohuya Majumder
- Drug Discovery, GUSTO A Research Group, Chittagong 4203, Bangladesh;
| | - Md. Zia Uddin
- Department of Pharmacy, BGC Trust University Bangladesh, Chittagong 4381, Bangladesh; (M.D.); (J.M.); (M.Z.U.)
- Department of Pharmacy, Jahangirnagar University, Savar, Dhaka 1342, Bangladesh
| | - Abdullah Alsubaie
- Department of Physics, College of Khurma, Taif University, Taif 21944, Saudi Arabia;
| | | | - Mayeen Uddin Khandaker
- Centre for Applied Physics and Radiation Technologies, School of Engineering and Technology, Sunway University, Bandar Sunway 47500, Malaysia; (M.U.K.); (D.A.B.)
| | - D.A. Bradley
- Centre for Applied Physics and Radiation Technologies, School of Engineering and Technology, Sunway University, Bandar Sunway 47500, Malaysia; (M.U.K.); (D.A.B.)
- Department of Physics, University of Surrey, Guilford GU2 7XH, UK
| | - Md. Sohel Rana
- Department of Pharmacy, Jahangirnagar University, Savar, Dhaka 1342, Bangladesh
| | - Talha Bin Emran
- Department of Pharmacy, BGC Trust University Bangladesh, Chittagong 4381, Bangladesh; (M.D.); (J.M.); (M.Z.U.)
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49
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Mahmud S, Biswas S, Paul GK, Mita MA, Promi MM, Afrose S, Hasan MR, Zaman S, Uddin MS, Dhama K, Emran TB, Saleh MA, Simal-Gandara J. Plant-Based Phytochemical Screening by Targeting Main Protease of SARS-CoV-2 to Design Effective Potent Inhibitors. BIOLOGY 2021; 10:589. [PMID: 34206970 PMCID: PMC8301192 DOI: 10.3390/biology10070589] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Revised: 06/18/2021] [Accepted: 06/22/2021] [Indexed: 02/07/2023]
Abstract
Currently, a worldwide pandemic has been declared in response to the spread of coronavirus disease 2019 (COVID-19), a fatal and fast-spreading viral infection caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The low availability of efficient vaccines and treatment options has resulted in a high mortality rate, bringing the world economy to its knees. Thus, mechanistic investigations of drugs capable of counteracting this disease are in high demand. The main protease (Mpro) expressed by SARS-CoV-2 has been targeted for the development of potential drug candidates due to the crucial role played by Mpro in viral replication and transcription. We generated a phytochemical library containing 1672 phytochemicals derived from 56 plants, which have been reported as having antiviral, antibacterial, and antifungal activity. A molecular docking program was used to screen the top three candidate compounds: epicatechin-3-O-gallate, psi-taraxasterol, and catechin gallate, which had respective binding affinities of -8.4, -8.5, and -8.8 kcal/mol. Several active sites in the targeted protein, including Cys145, His41, Met49, Glu66, and Met165, were found to interact with the top three candidate compounds. The multiple simulation profile, root-mean-square deviation, root-mean-square fluctuation, radius of gyration, and solvent-accessible surface area values supported the inflexible nature of the docked protein-compound complexes. The toxicity and carcinogenicity profiles were assessed, which showed that epicatechin-3-O-gallate, psi-taraxasterol, and catechin gallate had favorable pharmacological properties with no adverse effects. These findings suggest that these compounds could be developed as part of an effective drug development pathway to treat COVID-19.
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Affiliation(s)
- Shafi Mahmud
- Microbiology Laboratory, Department of Genetic Engineering and Biotechnology, University of Rajshahi, Rajshahi 6205, Bangladesh; (S.M.); (G.K.P.); (S.Z.); (M.S.U.)
| | - Suvro Biswas
- Department of Genetic Engineering and Biotechnology, University of Rajshahi, Rajshahi 6205, Bangladesh; (S.B.); (M.A.M.); (M.M.P.); (S.A.); (M.R.H.)
| | - Gobindo Kumar Paul
- Microbiology Laboratory, Department of Genetic Engineering and Biotechnology, University of Rajshahi, Rajshahi 6205, Bangladesh; (S.M.); (G.K.P.); (S.Z.); (M.S.U.)
| | - Mohasana Akter Mita
- Department of Genetic Engineering and Biotechnology, University of Rajshahi, Rajshahi 6205, Bangladesh; (S.B.); (M.A.M.); (M.M.P.); (S.A.); (M.R.H.)
| | - Maria Meha Promi
- Department of Genetic Engineering and Biotechnology, University of Rajshahi, Rajshahi 6205, Bangladesh; (S.B.); (M.A.M.); (M.M.P.); (S.A.); (M.R.H.)
| | - Shamima Afrose
- Department of Genetic Engineering and Biotechnology, University of Rajshahi, Rajshahi 6205, Bangladesh; (S.B.); (M.A.M.); (M.M.P.); (S.A.); (M.R.H.)
| | - Md. Robiul Hasan
- Department of Genetic Engineering and Biotechnology, University of Rajshahi, Rajshahi 6205, Bangladesh; (S.B.); (M.A.M.); (M.M.P.); (S.A.); (M.R.H.)
| | - Shahriar Zaman
- Microbiology Laboratory, Department of Genetic Engineering and Biotechnology, University of Rajshahi, Rajshahi 6205, Bangladesh; (S.M.); (G.K.P.); (S.Z.); (M.S.U.)
| | - Md. Salah Uddin
- Microbiology Laboratory, Department of Genetic Engineering and Biotechnology, University of Rajshahi, Rajshahi 6205, Bangladesh; (S.M.); (G.K.P.); (S.Z.); (M.S.U.)
| | - Kuldeep Dhama
- Division of Pathology, Indian Veterinary Research Institute, Izatnagar, Bareilly 243122, UP, India;
| | - Talha Bin Emran
- Department of Pharmacy, BGC Trust University Bangladesh, Chittagong 4381, Bangladesh
| | - Md. Abu Saleh
- Microbiology Laboratory, Department of Genetic Engineering and Biotechnology, University of Rajshahi, Rajshahi 6205, Bangladesh; (S.M.); (G.K.P.); (S.Z.); (M.S.U.)
| | - Jesus Simal-Gandara
- Nutrition and Bromatology Group, Department of Analytical and Food Chemistry, Faculty of Food Science and Technology, University of Vigo–Ourense Campus, E32004 Ourense, Spain
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50
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Obaidullah AJ, Alanazi MM, Alsaif NA, Albassam H, Almehizia AA, Alqahtani AM, Mahmud S, Sami SA, Emran TB. Immunoinformatics-guided design of a multi-epitope vaccine based on the structural proteins of severe acute respiratory syndrome coronavirus 2. RSC Adv 2021; 11:18103-18121. [PMID: 35480208 PMCID: PMC9033181 DOI: 10.1039/d1ra02885e] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Accepted: 05/12/2021] [Indexed: 12/14/2022] Open
Abstract
Coronavirus disease 2019 (COVID-19) is caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), resulting in a contagious respiratory tract infection that has become a global burden since the end of 2019. Notably, fewer patients infected with SARS-CoV-2 progress from acute disease onset to death compared with the progression rate associated with two other coronaviruses, SARS-CoV and Middle East respiratory syndrome coronavirus (MERS-CoV). Several research organizations and pharmaceutical industries have attempted to develop successful vaccine candidates for the prevention of COVID-19. However, increasing evidence indicates that the SARS-CoV-2 genome undergoes frequent mutation; thus, an adequate analysis of the viral strain remains necessary to construct effective vaccines. The current study attempted to design a multi-epitope vaccine by utilizing an approach based on the SARS-CoV-2 structural proteins. We predicted the antigenic T- and B-lymphocyte responses to four structural proteins after screening all structural proteins according to specific characteristics. The predicted epitopes were combined using suitable adjuvants and linkers, and a secondary structure profile indicated that the vaccine shared similar properties with the native protein. Importantly, the molecular docking analysis and molecular dynamics simulations revealed that the constructed vaccine possessed a high affinity for toll-like receptor 4 (TLR4). In addition, multiple descriptors were obtained from the simulation trajectories, including the root-mean-square deviation (RMSD), root-mean-square fluctuation (RMSF), solvent-accessible surface area (SASA), and radius of gyration (R g), demonstrating the rigid nature and inflexibility of the vaccine and receptor molecules. In addition, codon optimization, based on Escherichia coli K12, was used to determine the GC content and the codon adaptation index (CAI) value, which further followed for the incorporation into the cloning vector pET28+(a). Collectively, these findings suggested that the constructed vaccine could be used to modulate the immune reaction against SARS-CoV-2.
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Affiliation(s)
- Ahmad J Obaidullah
- Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University P.O. Box 2457 Riyadh 11451 Saudi Arabia
| | - Mohammed M Alanazi
- Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University P.O. Box 2457 Riyadh 11451 Saudi Arabia
| | - Nawaf A Alsaif
- Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University P.O. Box 2457 Riyadh 11451 Saudi Arabia
| | - Hussam Albassam
- Department of Pharmacology and Toxicology, College of Pharmacy, King Saud University P.O. Box 2457 Riyadh 11451 Saudi Arabia
| | - Abdulrahman A Almehizia
- Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University P.O. Box 2457 Riyadh 11451 Saudi Arabia
| | - Ali M Alqahtani
- Department of Pharmacology, College of Pharmacy, King Khalid University Abha 62529 Saudi Arabia
| | - Shafi Mahmud
- Microbiology Laboratory, Bioinformatics Division, Department of Genetic Engineering and Biotechnology, University of Rajshahi Rajshahi 6205 Bangladesh
| | - Saad Ahmed Sami
- Department of Pharmacy, Faculty of Biological Sciences, University of Chittagong Chittagong 4331 Bangladesh
| | - Talha Bin Emran
- Department of Pharmacy, BGC Trust University Bangladesh Chittagong 4381 Bangladesh
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