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Ahmed Atto Al-Shuaeeb R, Abd El-Mageed HR, Ahmed S, Mohamed HS, Hamza ZS, Rafi MO, Ahmad I, Patel H. In silico investigation and potential therapeutic approaches of isoquinoline alkaloids for neurodegenerative diseases: computer-aided drug design perspective. J Biomol Struct Dyn 2023; 41:14484-14496. [PMID: 37184133 DOI: 10.1080/07391102.2023.2212778] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2022] [Accepted: 02/13/2023] [Indexed: 05/16/2023]
Abstract
Microtubule affinity regulating kinase (MARK4) has been proposed as a potential therapeutic target for diabetes, cancer, and neurological diseases. We used a variety of computational studies techniques to examine the binding affinity and MARK4 inhibitory potential of several isoquinoline alkaloids. MARK4 has been associated with tau protein phosphorylation and, consequently, Alzheimer's disease. The three molecules with the highest binding affinities inside the 5ES1 receptor, according to molecular docking experiments, are isoliensinine, liensinine, and methylcorypalline. Isoliensinine had the highest drug score and drug likeness, coming in at 1.17, while Liensinine and Methylcorypalline came in at 1.15 and 1.07, respectively. The thesis claims that three compounds have a better chance than the others of being identified as therapeutic leads. The bulk of the compounds under investigation didn't break any of Lipinski's five rules, especially methylcorypalline, which did and is probably orally active. The majority of the compounds under investigation, particularly Isoliensinine, Liensinine, and Methylcorypalline, show the potential to exhibit drug-like behaviour, which is strongly confirmed by ADMET characteristics estimates. The chemicals Isoliensinine, Liensinine, and Methylcorypalline, especially Methylcorypalline, form the most stable combination with the 5ES1, according to a 100 ns molecular dynamics simulation of these compounds docked inside 5ES1 complexes. Methylcorypalline has a higher binding affinity inside 5ES1, according to additional MM/GBSA experiments using MD trajectories. Overall, research supports the use of the drug development tool methylcolipalin for its ability to inhibit MARK4, which may have implications for the treatment of neurodegenerative diseases.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
| | - H R Abd El-Mageed
- Micro-analysis and Environmental Research and Community Services Center, Faculty of Science, Beni-Suef University, Beni-Suef, Egypt
| | - Shimaa Ahmed
- Department of chemistry, Faculty of Science, Beni-Suef University, Beni-Suef, Egypt
| | - Hussein S Mohamed
- Chemistry of Medicinal and Aromatic Plants Department, Research Institute of Medicinal and Aromatic Plants (RIMAP), Beni-Suef University, Beni-Suef, Egypt
| | - Zeinab S Hamza
- Chemistry of Medicinal and Aromatic Plants Department, Research Institute of Medicinal and Aromatic Plants (RIMAP), Beni-Suef University, Beni-Suef, Egypt
| | - Md Oliullah Rafi
- Department of Genetic Engineering and Biotechnology, Jashore University of Science and Technology, Jashore, Bangladesh
| | - Iqrar Ahmad
- Division of Computer Aided Drug Design, Department of Pharmaceutical Chemistry, R. C. Patel Institute of Pharmaceutical Education and Research, Shirpur, India
| | - Harun Patel
- Division of Computer Aided Drug Design, Department of Pharmaceutical Chemistry, R. C. Patel Institute of Pharmaceutical Education and Research, Shirpur, India
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Al-Shuaeeb RAA, Abd El-Mageed HR, Ahmed SA, Mohamed HS, Hamza ZS, Rafi MO, Rahman MS. Identification of potent COVID-19 main protease inhibitors by loading of favipiravir on Mg 12O 12 and Zn 12O 12 nanoclusters: an in silico strategy for COVID-19 treatment. J Biomol Struct Dyn 2023; 41:11437-11449. [PMID: 36591698 DOI: 10.1080/07391102.2022.2162967] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Accepted: 12/18/2022] [Indexed: 01/03/2023]
Abstract
Pandemic new severe acute respiratory syndrome coronavirus (SARS-CoV-2) virus has increased throughout the world. There is no effective treatment against this virus until now. Since its appearance in Wuhan, China in December 2019, SARS-CoV-2 becomes the largest challenge the world is opposite today, including the discovery of an antiviral drug for this virus. Several viral proteins have been prioritized as SARS-CoV-2 antiviral drug targets, among them the papain-like protease (PLpro) and the main protease (Mpro). Inhibition of these proteases would target viral replication, viral maturation and suppression of host innate immune responses. Potential candidates have been identified to show inhibitory effects against Mpro, both in biochemical assays and viral replication in cells. There are different molecules such as lopinavir and favipiravir considerably inhibit the activity of Mpro in vitro. Different studies have shown that structurally improved favipiravir and other similar compounds can inhibit SARS-CoV-2 main protease. In this work, we study the interactions between favipiravir with Mg12O12 and Zn12O12 nanoclusters by density functional theory (DFT) and quantum mechanics atoms in molecules (QMAIM) methods to summarize the ability to load favipiravir onto Mg12O12 and Zn12O12 nanoclusters. Favipiravir-Mg12O12 and favipiravir-Zn12O12 lowest structures complexes were chosen to dock inside the SARS-CoV-2 main protease by molecular docking study. The molecular docking analysis revealed that the binding affinity of Mg12O12 and Zn12O12 nanoclusters inside the Mpro receptor is larger than that of favipiravir. Also, the loading of favipiravir on the surface of Mg12O12 and Zn12O12 nanoclusters increased the binding affinity against the Mpro receptor. Subsequently, 100 ns molecular dynamics simulation of the favipiravir-Mg12O12, and favipiravir-Zn12O12 docked inside the Mpro complexes established that favipiravir-Mg12O12, forms the most stable complex with the Mpro. Further molecular mechanics Poisson Boltzmann surface area (MMPBSA) analyses using the MD trajectories also demonstrated the higher binding affinity of favipiravir-Mg12O12 inside the Mpro. In summary, this study demonstrates a new way to characterize leads for novel anti-viral drugs against SARS-CoV-2, by improving the drug ability of favipiravir via loading it on Mg12O12 and Zn12O12 nanoclusters.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
| | - H R Abd El-Mageed
- Micro-analysis and Environmental Research and Community Services Center, Faculty of Science, Beni-Suef University, Beni-Suef City, Egypt
| | - Shimaa A Ahmed
- Department of Chemistry, Faculty of Science, Beni-Suef University, Beni-Suef, Egypt
| | - Hussein S Mohamed
- Chemistry of Medicinal and Aromatic Plants Department, Research institute of medicinal and aromatic plants (RIMAP), Beni-Suef University, Beni-Suef, Egypt
| | - Zeinab S Hamza
- Chemistry of Medicinal and Aromatic Plants Department, Research institute of medicinal and aromatic plants (RIMAP), Beni-Suef University, Beni-Suef, Egypt
| | - Md Oliullah Rafi
- Department of Genetic Engineering and Biotechnology, Jashore University of Science and Technology, Jessore Sadar Upazila, Bangladesh
| | - Md Shahedur Rahman
- Department of Genetic Engineering and Biotechnology, Jashore University of Science and Technology, Jessore Sadar Upazila, Bangladesh
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Rafi MO, Al-Khafaji K, Mandal SM, Meghla NS, Biswas PK, Rahman MS. A subunit vaccine against pneumonia: targeting S treptococcus pneumoniae and Klebsiella pneumoniae. Netw Model Anal Health Inform Bioinform 2023; 12:21. [PMID: 37096010 PMCID: PMC10115389 DOI: 10.1007/s13721-023-00416-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/24/2022] [Revised: 03/25/2023] [Accepted: 04/09/2023] [Indexed: 04/26/2023]
Abstract
Community-acquired pneumonia is primarily caused by Streptococcus pneumoniae and Klebsiella pneumoniae, two pathogens that have high morbidity and mortality rates. This is largely due to bacterial resistance development against current antibiotics and the lack of effective vaccines. The objective of this work was to develop an immunogenic multi-epitope subunit vaccine capable of eliciting a robust immune response against S. pneumoniae and K. pneumoniae. The targeted proteins were the pneumococcal surface proteins (PspA and PspC) and choline-binding protein (CbpA) of S. pneumoniae and the outer membrane proteins (OmpA and OmpW) of K. pneumoniae. Different computational approaches and various immune filters were employed for designing a vaccine. The immunogenicity and safety of the vaccine were evaluated by utilizing many physicochemical and antigenic profiles. To improve structural stability, disulfide engineering was applied to a portion of the vaccine structure with high mobility. Molecular docking was performed to examine the binding affinities and biological interactions at the atomic level between the vaccine and Toll-like receptors (TLR2 and 4). Further, the dynamic stabilities of the vaccine and TLRs complexes were investigated by molecular dynamics simulations. While the immune response induction capability of the vaccine was assessed by the immune simulation study. Vaccine translation and expression efficiency was determined through an in silico cloning experiment utilizing the pET28a(+) plasmid vector. The obtained results revealed that the designed vaccine is structurally stable and able to generate an effective immune response to combat pneumococcal infection. Supplementary Information The online version contains supplementary material available at 10.1007/s13721-023-00416-3.
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Affiliation(s)
- Md. Oliullah Rafi
- Bioinformatics and Microbial Biotechnology Laboratory, Department of Genetic Engineering and Biotechnology, Jashore University of Science and Technology, Jashore, 7408 Bangladesh
- Department of Genetic Engineering and Biotechnology, Jashore University of Science and Technology, Jashore, 7408 Bangladesh
| | | | - Santi M. Mandal
- Central Research Facility, Indian Institute of Technology Kharagpur, Kharagpur, 721302 India
| | - Nigar Sultana Meghla
- Department of Microbiology, Jashore University of Science and Technology, Jashore, 7408 Bangladesh
| | - Polash Kumar Biswas
- Department of Stem Cell and Regenerative Biotechnology, Incurable Disease Animal Model & Stem Cell Institute (IDASI), Konkuk University, 120 Neungdong-ro, Gwangjin-gu, Seoul, 05029 South Korea
| | - Md. Shahedur Rahman
- Bioinformatics and Microbial Biotechnology Laboratory, Department of Genetic Engineering and Biotechnology, Jashore University of Science and Technology, Jashore, 7408 Bangladesh
- Department of Genetic Engineering and Biotechnology, Jashore University of Science and Technology, Jashore, 7408 Bangladesh
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Hossain MJ, Ahmmed F, Khan MR, Rashid PT, Hossain S, Rafi MO, Islam MR, Mitra S, Emran TB, Islam F, Alam M, Sarker MMR, Naina Mohamed I. Impact of Prolonged COVID-19 Lockdown on Body Mass Index, Eating Habits, and Physical Activity of University Students in Bangladesh: A Web-Based Cross-Sectional Study. Front Nutr 2022; 9:873105. [PMID: 35669065 PMCID: PMC9165530 DOI: 10.3389/fnut.2022.873105] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Accepted: 04/11/2022] [Indexed: 12/20/2022] Open
Abstract
Objectives This current study aims to assess the prevalence and factors associated with body mass index (BMI), dietary patterns, and the extent of physical activities among university students following the prolonged coronavirus disease 2019 (COVID-19) lockdown in Bangladesh. Methods A cross-sectional web-based survey was conducted between July 10 to August 10, 2021, through a pre-designed Google Form to collect the data from Bangladeshi university students (age: ≥18 years). Informed consent was electronically obtained from each participant, and a simple snowball technique was employed during the sampling. Frequency and percentage distribution, paired t-test, chi-square [χ2] test, and multinomial and binary logistic regression analyses were consecutively applied to analyze the collected data. Results Among the total participants (n = 1,602), 45.1% were female and 55.6% were 22–25 years' age group students. The BMI (mean ± standard deviation, SD) during the COVID-19 lockdown was 23.52 ± 7.68 kg/m2, which was 22.77 ± 4.11 kg/m2 during the pre-lockdown period (mean difference = 0.753; p < 0.001). The multinomial logistic regression analysis found a significant impact of gender [male vs. female: adjusted relative risk ratio (RRR) = 1.448; 95% confidence interval (CI) = 1.022, 2.053; p = 0.037], age (years) (<22 vs. >25: RRR =0.389, 95% CI = 0.213,0.710; p = 0.002, and 22–25 vs. >25: RRR = 0.473, 95% CI = 0.290, 0.772; p = 0.003), monthly family income (BDT) (<25,000 vs. >50,000: RRR = 0.525, 95% CI = 0.334,0.826; p = 0.005), university type (public vs. private: RRR = 0.540, 95% CI = 0.369, 0.791; p = 0.002), eating larger meals/snacks (increased vs. unchanged: RRR = 2.401, 95% CI = 1.597, 3.610; p < 0.001 and decreased vs. unchanged: RRR = 1.893, 95% CI = 1.218, 2.942; p = 0.005), and verbally or physically abuse (yes vs. no: RRR = 1.438, 95% CI = 0.977, 2.116; p = 0.066) on obesity during COVID-19 pandemic. Besides, the female students and those who have constant eating habits, were more likely to be underweight. Additionally, the binary logistic regression analysis found that the students from private universities [others vs. private: adjusted odds ratio (AOR) = 0.461, 95% CI = 0.313, 0.680; p < 0.001], urban areas (urban vs. rural: AOR = 1.451, 95% CI = 1.165, 1.806; p = 0.001), wealthier families (<25,000 BDT vs. >50,000 BDT: AOR = 0.727, 95% CI = 0.540, 0.979; p = 0.036), and who were taking larger meals/snacks (increased vs. unchanged: AOR = 2.806, 95% CI = 2.190, 3.596; p < 0.001) and had conflicts/arguments with others (no vs. yes: AOR = 0.524, 95% CI = 0.418, 0.657; p < 0.001), were significantly more physically inactive. Finally, the level of education and smoking habits significantly influenced the eating habits of university students during the extended strict lockdown in Bangladesh. Conclusion The current findings would be helpful tools and evidence for local and international public health experts and policymakers to reverse these worsening effects on students mediated by the prolonged lockdown. Several effective plans, programs, and combined attempts must be earnestly implemented to promote a smooth academic and daily life.
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Affiliation(s)
- Md. Jamal Hossain
- Department of Pharmacy, State University of Bangladesh, Dhaka, Bangladesh
- *Correspondence: Md. Jamal Hossain ; ; orcid.org/0000-0001-9706-207X
| | - Foyez Ahmmed
- Department of Statistics, Comilla University, Cumilla, Bangladesh
| | - Md. Robin Khan
- Bangladesh Reference Institute for Chemical Measurements, Dhaka, Bangladesh
| | | | - Sorif Hossain
- Institute of Statistical Research and Training, University of Dhaka, Dhaka, Bangladesh
- Department of Statistics, Noakhali Science and Technology University, Noakhali, Bangladesh
| | - Md. Oliullah Rafi
- Department of Genetic Engineering and Biotechnology, Jashore University of Science and Technology, Jashore, Bangladesh
| | - Md. Rabiul Islam
- Department of Pharmacy, University of Asia Pacific, Dhaka, Bangladesh
| | - Saikat Mitra
- Department of Pharmacy, Faculty of Pharmacy, University of Dhaka, Dhaka, Bangladesh
| | - Talha Bin Emran
- Department of Pharmacy, BGC Trust University Bangladesh, Chittagong, Bangladesh
| | - Fahadul Islam
- Department of Pharmacy, Faculty of Allied Health Sciences, Daffodil International University, Dhaka, Bangladesh
| | - Morshed Alam
- Institute of Education and Research, Jagannath University, Dhaka, Bangladesh
| | - Md. Moklesur Rahman Sarker
- Department of Pharmacy, State University of Bangladesh, Dhaka, Bangladesh
- Md. Moklesur Rahman Sarker ; ; orcid.org/0000-0001-9795-0608
| | - Isa Naina Mohamed
- Pharmacology Department, Medical Faculty, Universiti Kebangsaan Malaysia (The National University of Malaysia), Kuala Lumpur, Malaysia
- Isa Naina Mohamed ; orcid.org/0000-0001-8891-2423
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Hossain MJ, Ahmmed F, Sarker MMR, Sarwar S, Bari MS, Khan MR, Shahriar S, Rafi MO, Emran TB, Mitra S, Islam MR, Mohamed IN. Factors Associated With Underprivileged E-Learning, Session Jam Phobia, and the Subsequent Mental Distress Among Students Following the Extended University Closure in Bangladesh. Front Public Health 2022; 9:807474. [PMID: 35223762 PMCID: PMC8868938 DOI: 10.3389/fpubh.2021.807474] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Accepted: 12/16/2021] [Indexed: 12/23/2022] Open
Abstract
Severe session jam phobia (SJP), the extent of underprivileged online education, and subsequent mental health disorders among students have emerged as distinguished global problems due to the overwhelming effects of coronavirus disease 2019 (COVID-19). The purpose of this research was to evaluate the impact of extended COVID-19 lockdown and its mediating factors on current e-Learning activities, the prevalence of severe SJP and psychological distress among university students in Bangladesh. A web-based cross-sectional study was conducted to assemble responses through Google Form by applying a simple snowball sampling technique among university students aged 18 years or above in Bangladesh. All ethical considerations were maintained, and univariate, bivariate, and multivariate analyses were employed to analyze the acquired data set. Among the total analyzed data (n = 1,122), the male and female ratio was almost 1:1, and a remarkable segment (63.7%) was aged between 21-24 years. Alarmingly, around 50-60% of the students were suffering from severe SJP, prevailing underprivileged education in the e-Learning platform, and severe mental distress. Logistic regression analyses demonstrated that the students from public universities, lower- and mid-income families, lower-aged, and junior years education groups were significantly (p < 0.05) more underprivileged than their counter groups. Besides, the monthly family income and university type significantly influenced the extent of severe SJP. Finally, the students who were female, rustic, come from low-income families (below 25,000 BDT), who had academic uncertainty, job insecurity, online exam phobia, and dissatisfaction with e-Learning education, were significantly suffering from moderate to severe mental distress. The current evidence demonstrates that a substantial number of Bangladeshi university students are struggling with extreme session jam phobia, underprivileged e-Learning education, and subsequent psychological distress, which need to be immediately addressed through concerted efforts by the government, parents, and university authorities.
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Affiliation(s)
- Md. Jamal Hossain
- Department of Pharmacy, State University of Bangladesh, Dhaka, Bangladesh
| | - Foyez Ahmmed
- Department of Statistics, Comilla University, Cumilla, Bangladesh
| | | | - Sneha Sarwar
- Institute of Nutrition and Food Science, University of Dhaka, Dhaka, Bangladesh
| | - Md. Sazzadul Bari
- Department of Pharmacy, State University of Bangladesh, Dhaka, Bangladesh
| | - Md. Robin Khan
- Bangladesh Reference Institute for Chemical Measurements, Dhaka, Bangladesh
| | - Saimon Shahriar
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Dhaka, Dhaka, Bangladesh
| | - Md. Oliullah Rafi
- Department of Genetic Engineering and Biotechnology, Jashore University of Science and Technology, Jashore, Bangladesh
| | - Talha Bin Emran
- Department of Pharmacy, BGC Trust University Bangladesh, Chittagong, Bangladesh
| | - Saikat Mitra
- Department of Pharmacy, Faculty of Pharmacy, University of Dhaka, Dhaka, Bangladesh
| | - Md. Rabiul Islam
- Department of Pharmacy, University of Asia Pacific, Dhaka, Bangladesh
| | - Isa Naina Mohamed
- Pharmacology Department, Medical Faculty, Universiti Kebangsaan Malaysia (The National University of Malaysia), Kuala Lumpur, Malaysia
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Rafi MO, Al-Khafaji K, Sarker MT, Taskin-Tok T, Rana AS, Rahman MS. Design of a multi-epitope vaccine against SARS-CoV-2: immunoinformatic and computational methods. RSC Adv 2022; 12:4288-4310. [PMID: 35425433 PMCID: PMC8981096 DOI: 10.1039/d1ra06532g] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Accepted: 01/23/2022] [Indexed: 12/17/2022] Open
Abstract
A novel infectious agent, SARS-CoV-2, is responsible for causing the severe respiratory disease COVID-19 and death in humans. Spike glycoprotein plays a key role in viral particles entering host cells, mediating receptor recognition and membrane fusion, and are considered useful targets for antiviral vaccine candidates. Therefore, computational techniques can be used to design a safe, antigenic, immunogenic, and stable vaccine against this pathogen. Drawing upon the structure of the S glycoprotein, we are trying to develop a potent multi-epitope subunit vaccine against SARS-CoV-2. The vaccine was designed based on cytotoxic T-lymphocyte and helper T-lymphocyte epitopes with an N-terminal adjuvant via conducting immune filters and an extensive immunoinformatic investigation. The safety and immunogenicity of the designed vaccine were further evaluated via using various physicochemical, allergenic, and antigenic characteristics. Vaccine-target (toll-like receptors: TLR2 and TLR4) interactions, binding affinities, and dynamical stabilities were inspected through molecular docking and molecular dynamic (MD) simulation methods. Moreover, MD simulations for dimeric TLRs/vaccine in the membrane-aqueous environment were performed to understand the differential domain organization of TLRs/vaccine. Further, dynamical behaviors of vaccine/TLR systems were inspected via identifying the key residues (named HUB nodes) that control interaction stability and provide a clear molecular mechanism. The obtained results from molecular docking and MD simulation revealed a strong and stable interaction between vaccine and TLRs. The vaccine's ability to stimulate the immune response was assessed by using computational immune simulation. This predicted a significant level of cytotoxic T cell and helper T cell activation, as well as IgG, interleukin 2, and interferon-gamma production. This study shows that the designed vaccine is structurally and dynamically stable and can trigger an effective immune response against viral infections.
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Affiliation(s)
- Md Oliullah Rafi
- Department of Genetic Engineering and Biotechnology, Jashore University of Science and Technology Jashore 7408 Bangladesh
- Bioinformatics and Microbial Biotechnology Laboratory, Department of Genetic Engineering and Biotechnology, Jashore University of Science and Technology Jashore 7408 Bangladesh
| | - Khattab Al-Khafaji
- Department of Medical Laboratory Technology, AL-Nisour University College Baghdad Iraq
| | - Md Takim Sarker
- Department of Genetic Engineering and Biotechnology, Jashore University of Science and Technology Jashore 7408 Bangladesh
| | - Tugba Taskin-Tok
- Department of Bioinformatics and Computational Biology, Institute of Health Sciences, Gaziantep University Gaziantep 27310 Turkey
- Faculty of Arts and Sciences, Department of Chemistry, Gaziantep University Gaziantep Turkey
| | - Abdus Samad Rana
- School of Biotechnology, Jiangnan University Wuxi 214122 PR China
| | - Md Shahedur Rahman
- Department of Genetic Engineering and Biotechnology, Jashore University of Science and Technology Jashore 7408 Bangladesh
- Bioinformatics and Microbial Biotechnology Laboratory, Department of Genetic Engineering and Biotechnology, Jashore University of Science and Technology Jashore 7408 Bangladesh
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El-Mageed HRA, Abdelrheem DA, Rafi MO, Sarker MT, Al-Khafaji K, Hossain MJ, Capasso R, Emran TB. In Silico Evaluation of Different Flavonoids from Medicinal Plants for Their Potency against SARS-CoV-2. Biologics 2021; 1:416-434. [DOI: 10.3390/biologics1030024] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/01/2023]
Abstract
The ongoing pandemic situation of COVID-19 caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) poses a global threat to both the world economy and public health. Therefore, there is an urgent need to discover effective vaccines or drugs to fight against this virus. The flavonoids and their medicinal plant sources have already exhibited various biological effects, including antiviral, anti-inflammatory, antioxidant, etc. This study was designed to evaluate different flavonoids from medicinal plants as potential inhibitors against the spike protein (Sp) and main protease (Mpro) of SARS-CoV-2 using various computational approaches such as molecular docking, molecular dynamics. The binding affinity and inhibitory effects of all studied flavonoids were discussed and compared with some antiviral drugs that are currently being used in COVID-19 treatment namely favipiravir, lopinavir, and hydroxychloroquine, respectively. Among all studies flavonoids and proposed antiviral drugs, luteolin and mundulinol exhibited the highest binding affinity toward Mpro and Sp. Drug-likeness and ADMET studies revealed that the chosen flavonoids are safe and non-toxic. One hundred ns-MD simulations were implemented for luteolin-Mpro, mundulinol-Mpro, luteolin-Sp, and mundulinol-Sp complexes and the results revealed strong stability of these flavonoid-protein complexes. Furthermore, MM/PBSA confirms the stability of luteolin and mundulinol interactions within the active sites of this protein. In conclusion, our findings reveal that the promising activity of luteolin and mundulinol as inhibitors against COVID-19 via inhibiting the spike protein and major protease of SARS CoV-2, and we urge further research to achieve the clinical significance of our proposed molecular-based efficacy.
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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] [What about the content of this article? (0)] [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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Hossain MJ, Jannat T, Brishty SR, Roy U, Mitra S, Rafi MO, Islam MR, Nesa ML, Islam MA, Emran TB. Clinical Efficacy and Safety of Antiviral Drugs in the Extended Use against COVID-19: What We Know So Far. Biologics 2021; 1:252-284. [DOI: 10.3390/biologics1020016] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/01/2023]
Abstract
Human beings around the globe have been suffering from a devastating novel pandemic and public health emergency, coronavirus disease 2019 (COVID-19), for more than one and a half years due to the deadly and highly pathogenic severe acute respiratory coronavirus 2 (SARS-CoV-2) infection worldwide. Notably, no effective treatment strategy has been approved for the complete recovery of COVID-19 patients, though several vaccines have been rolled out around the world upon emergency use authorization. After the emergence of the COVID-19 outbreak globally, plenty of clinical investigations commenced to screen the safety and efficacy of several previously approved drugs to be repurposed against the SARS-CoV-2 pathogen. This concise review aims at exploring the current status of the clinical efficacy and safety profile of several antiviral medications for the treatment of patients with COVID-19 and other respiratory complications caused by SARS-CoV-2 infection. The paper covers all kinds of human studies (January 2020 to June 2021) except case reports/series to highlight the clear conclusion based on the current clinical evidence. Among the promising repositioned antivirals, remdesivir has been recommended in critical conditions to mitigate the fatality rate and improve clinical conditions. In addition, boosting the immune system is believed to be beneficial in treating COVID-19 patients, so interferon type I might exert immunomodulation through its antiviral effects by stimulating interferon-stimulated gene (ISG). However, more extensive clinical studies covering all ethnic groups globally are warranted based on current data to better understand the clinical efficacy of the currently proposed repurposed drugs against COVID-19.
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Mahmud S, Rafi MO, Paul GK, Promi MM, Shimu MSS, Biswas S, Emran TB, Dhama K, Alyami SA, Moni MA, Saleh MA. Designing a multi-epitope vaccine candidate to combat MERS-CoV by employing an immunoinformatics approach. Sci Rep 2021; 11:15431. [PMID: 34326355 PMCID: PMC8322212 DOI: 10.1038/s41598-021-92176-1] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Accepted: 05/21/2021] [Indexed: 01/26/2023] Open
Abstract
Currently, no approved vaccine is available against the Middle East respiratory syndrome coronavirus (MERS-CoV), which causes severe respiratory disease. The spike glycoprotein is typically considered a suitable target for MERS-CoV vaccine candidates. A computational strategy can be used to design an antigenic vaccine against a pathogen. Therefore, we used immunoinformatics and computational approaches to design a multi-epitope vaccine that targets the spike glycoprotein of MERS-CoV. After using numerous immunoinformatics tools and applying several immune filters, a poly-epitope vaccine was constructed comprising cytotoxic T-cell lymphocyte (CTL)-, helper T-cell lymphocyte (HTL)-, and interferon-gamma (IFN-γ)-inducing epitopes. In addition, various physicochemical, allergenic, and antigenic profiles were evaluated to confirm the immunogenicity and safety of the vaccine. Molecular interactions, binding affinities, and the thermodynamic stability of the vaccine were examined through molecular docking and dynamic simulation approaches, during which we identified a stable and strong interaction with Toll-like receptors (TLRs). In silico immune simulations were performed to assess the immune-response triggering capabilities of the vaccine. This computational analysis suggested that the proposed vaccine candidate would be structurally stable and capable of generating an effective immune response to combat viral infections; however, experimental evaluations remain necessary to verify the exact safety and immunogenicity profile of this vaccine.
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Affiliation(s)
- Shafi Mahmud
- Microbiology Laboratory, Department of Genetic Engineering and Biotechnology, University of Rajshahi, Rajshahi, 6505, Bangladesh
| | - Md Oliullah Rafi
- Department of Genetic Engineering and Biotechnology, Jashore University of Science and Technology, Jashore, 7408, Bangladesh
| | - Gobindo Kumar Paul
- Microbiology Laboratory, Department of Genetic Engineering and Biotechnology, University of Rajshahi, Rajshahi, 6505, Bangladesh
| | - Maria Meha Promi
- Department of Genetic Engineering and Biotechnology, University of Rajshahi, Rajshahi, 6505, Bangladesh
| | - Mst Sharmin Sultana Shimu
- Department of Genetic Engineering and Biotechnology, University of Rajshahi, Rajshahi, 6505, Bangladesh
| | - Suvro Biswas
- Department of Genetic Engineering and Biotechnology, University of Rajshahi, Rajshahi, 6505, Bangladesh
| | - Talha Bin Emran
- Department of Pharmacy, BGC Trust University Bangladesh, Chittagong, 4381, Bangladesh
| | - Kuldeep Dhama
- Division of Pathology, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, 243122, Uttar Pradesh, India
| | - Salem A Alyami
- Department of Mathematics and Statistics, Imam Mohammad Ibn Saud Islamic University, Riyadh, 11432, Saudi Arabia
| | - Mohammad Ali Moni
- Faculty of Medicine, WHO Collaborating Centre on eHealth, UNSW Digital Health, School of Public Health and Community Medicine, UNSW Sydney, Sydney, NSW, 2052, Australia.
| | - Md Abu Saleh
- Microbiology Laboratory, Department of Genetic Engineering and Biotechnology, University of Rajshahi, Rajshahi, 6505, Bangladesh.
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Rafi MO, Al-Khafaji K, Tok TT, Rahman MS. Computer-based identification of potential compounds from Salviae miltiorrhizae against Neirisaral adhesion A regulatory protein. J Biomol Struct Dyn 2020; 40:4301-4313. [PMID: 33289608 DOI: 10.1080/07391102.2020.1856189] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
In silico studies are attracting considerable interest due to their ability to understand protein-ligand interactions at the atomic level. The main principal tools of this in silico analyses are molecular docking and molecular dynamic (MD) simulation. This paper examines how can natural compounds that are derived from Salviae miltiorrhizae to block Neisseria adhesion A Regulatory protein (NadR). In molecular docking analysis, only four compounds were found in higher binding affinity with NadR among 10 candidates (tanshinol B, tanshinol A, lithospermic acid and tournefolal were -7.61, -7.56, -8.22 and -7.81 kcal/mol, respectively, compared to -7.23 kcal/mol of native ligand). Absorption, distribution, metabolism, excretion (ADME) and toxicity properties, medicinal chemistry profile, and physicochemical features were displayed that tournefolal contains good properties to work as a safe and good anti-adhesive drug. Therefore, the complexes of these four ligands with NadR protein were subjected to 100 ns of MD simulation. RMSD, RMSF, RG and hydrogen bonding exhibited that tournefolal showed stable binding affinity and molecular interaction with NadR protein. In light of these results, there is now a need to conduct much more in vitro and in vivo studies about the efficacy of tournefolal.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Md Oliullah Rafi
- Department of Genetic Engineering and Biotechnology, Jashore University of Science and Technology, Jashore, Bangladesh
| | - Khattab Al-Khafaji
- Faculty of Arts and Sciences, Department of Chemistry, Gaziantep University, Gaziantep, Turkey
| | - Tugba Taskin Tok
- Faculty of Arts and Sciences, Department of Chemistry, Gaziantep University, Gaziantep, Turkey.,Institute of Health Sciences, Department of Bioinformatics and Computational Biology, Gaziantep University, Gaziantep, Turkey
| | - Md Shahedur Rahman
- Department of Genetic Engineering and Biotechnology, Jashore University of Science and Technology, Jashore, Bangladesh
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12
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Rafi MO, Bhattacharje G, Al-Khafaji K, Taskin-Tok T, Alfasane MA, Das AK, Parvez MAK, Rahman MS. Combination of QSAR, molecular docking, molecular dynamic simulation and MM-PBSA: analogues of lopinavir and favipiravir as potential drug candidates against COVID-19. J Biomol Struct Dyn 2020; 40:3711-3730. [PMID: 33251975 PMCID: PMC7754938 DOI: 10.1080/07391102.2020.1850355] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Pandemic COVID-19 infections have spread throughout the world. There is no effective treatment against this disease. Viral RNA-dependent RNA polymerase (RdRp) catalyzes the replication of RNA from RNA and the main protease (Mpro) has a role in the processing of polyproteins that are translated from the RNA of SARS-CoV-2, and thus these two enzymes are strong candidates for targeting by anti-viral drugs. Small molecules such as lopinavir and favipiravir significantly inhibit the activity of Mpro and RdRp in vitro. Studies have shown that structurally modified lopinavir, favipiravir, and other similar compounds can inhibit COVID-19 main protease (Mpro) and RNA-dependent RNA polymerase (RdRp). In this study, lopinavir and its structurally similar compounds were chosen to bind the main protease, and favipiravir was chosen to target RNA-dependent RNA polymerase. Molecular docking and the quantitative structure-activity relationships (QSAR) study revealed that the selected candidates have favorable binding affinity but less druggable properties. To improve the druggability, four structural analogues of lopinavir and one structural analogue of favipiravir was designed by structural modification. Molecular interaction analyses have displayed that lopinavir and favipiravir analogues interact with the active site residues of Mpro and RdRp, respectively. Absorption, distribution, metabolism, excretion and toxicity (ADMET) properties, medicinal chemistry profile, and physicochemical features were shown that all structurally modified analogues are less toxic and contain high druggable properties than the selected candidates. Subsequently, 50 ns molecular dynamics simulation of the top four docked complexes demonstrated that CID44271905, a lopinavir analogue, forms the most stable complex with the Mpro. Further MMPBSA analyses using the MD trajectories also confirmed the higher binding affinity of CID44271905 towards Mpro. In summary, this study demonstrates a new way to identify leads for novel anti-viral drugs against COVID-19. Communicated by Ramaswamy H. Sarma
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Affiliation(s)
- Md Oliullah Rafi
- Department of Genetic Engineering and Biotechnology, Jashore University of Science and Technology, Jashore, Bangladesh
| | - Gourab Bhattacharje
- Department of Biotechnology, Indian Institute of Technology-Kharagpur, Kharagpur, India
| | - Khattab Al-Khafaji
- Department of Chemistry, Faculty of Arts and Sciences, Gaziantep University, Gaziantep, Turkey
| | - Tugba Taskin-Tok
- Department of Chemistry, Faculty of Arts and Sciences, Gaziantep University, Gaziantep, Turkey.,Department of Bioinformatics and Computational Biology, Institute of Health Sciences, Gaziantep University, Gaziantep, Turkey
| | | | - Amit Kumar Das
- Department of Biotechnology, Indian Institute of Technology-Kharagpur, Kharagpur, India
| | - Md Anowar Khasru Parvez
- Department of Microbiology, Jahangirnagar University, Dhaka, Bangladesh.,Treasurer Office, Pabna University of Science and Technology, Pabna, Bangladesh
| | - Md Shahedur Rahman
- Department of Genetic Engineering and Biotechnology, Jashore University of Science and Technology, Jashore, Bangladesh
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