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Roy A, Swetha RG, Basu S, Biswas R, Ramaiah S, Anbarasu A. Integrating pan-genome and reverse vaccinology to design multi-epitope vaccine against Herpes simplex virus type-1. 3 Biotech 2024; 14:176. [PMID: 38855144 PMCID: PMC11153438 DOI: 10.1007/s13205-024-04022-6] [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: 03/08/2024] [Accepted: 05/27/2024] [Indexed: 06/11/2024] Open
Abstract
Herpes simplex virus type-1 (HSV-1), the etiological agent of sporadic encephalitis and recurring oral (sometimes genital) infections in humans, affects millions each year. The evolving viral genome reduces susceptibility to existing antivirals and, thus, necessitates new therapeutic strategies. Immunoinformatics strategies have shown promise in designing novel vaccine candidates in the absence of a clinically licensed vaccine to prevent HSV-1. However, to encourage clinical translation, the HSV-1 pan-genome was integrated with the reverse-vaccinology pipeline for rigorous screening of universal vaccine candidates. Viral targets were screened from 104 available complete genomes. Among 364 proteins, envelope glycoprotein D being an outer membrane protein with a high antigenicity score (> 0.4) and solubility (> 0.6) was selected for epitope screening. A total of 17 T-cell and 4 B-cell epitopes with highly antigenic, immunogenic, non-toxic properties and high global population coverage were identified. Furthermore, 8 vaccine constructs were designed using different combinations of epitopes and suitable linkers. VC-8 was identified as the most potential vaccine candidate regarding chemical and structural stability. Molecular docking revealed high interactive affinity (low binding energy: - 56.25 kcal/mol) of VC-8 with the target elicited by firm intermolecular H-bonds, salt-bridges, and hydrophobic interactions, which was validated with simulations. Compatibility of the vaccine candidate to be expressed in pET-29(a) + plasmid was established by in silico cloning studies. Immune simulations confirmed the potential of VC-8 to trigger robust B-cell, T-cell, cytokine, and antibody-mediated responses, thereby suggesting a promising candidate for the future of HSV-1 prevention. Supplementary Information The online version contains supplementary material available at 10.1007/s13205-024-04022-6.
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Affiliation(s)
- Aditi Roy
- Medical and Biological Computing Laboratory, School of Biosciences and Technology (SBST), Vellore Institute of Technology (VIT), Vellore, Tamil Nadu 632014 India
- Department of Biotechnology, SBST, VIT, Vellore, Tamil Nadu 632014 India
| | - Rayapadi G. Swetha
- Medical and Biological Computing Laboratory, School of Biosciences and Technology (SBST), Vellore Institute of Technology (VIT), Vellore, Tamil Nadu 632014 India
- Department of Biosciences, SBST, VIT, Vellore, Tamil Nadu 632014 India
| | - Soumya Basu
- Department of Biotechnology, NIST University, Berhampur, Odisha 761008 India
| | - Rhitam Biswas
- Medical and Biological Computing Laboratory, School of Biosciences and Technology (SBST), Vellore Institute of Technology (VIT), Vellore, Tamil Nadu 632014 India
- Department of Biotechnology, SBST, VIT, Vellore, Tamil Nadu 632014 India
| | - Sudha Ramaiah
- Medical and Biological Computing Laboratory, School of Biosciences and Technology (SBST), Vellore Institute of Technology (VIT), Vellore, Tamil Nadu 632014 India
- Department of Biosciences, SBST, VIT, Vellore, Tamil Nadu 632014 India
| | - Anand Anbarasu
- Medical and Biological Computing Laboratory, School of Biosciences and Technology (SBST), Vellore Institute of Technology (VIT), Vellore, Tamil Nadu 632014 India
- Department of Biotechnology, SBST, VIT, Vellore, Tamil Nadu 632014 India
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Kuri P, Goswami P. Current Update on Rotavirus in-Silico Multiepitope Vaccine Design. ACS OMEGA 2023; 8:190-207. [PMID: 36643547 PMCID: PMC9835168 DOI: 10.1021/acsomega.2c07213] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Accepted: 12/14/2022] [Indexed: 06/06/2023]
Abstract
Rotavirus gastroenteritis is one of the leading causes of pediatric morbidity and mortality worldwide in infants and under-five populations. The World Health Organization (WHO) recommended global incorporation of the rotavirus vaccine in national immunization programs to alleviate the burden of the disease. Implementation of the rotavirus vaccination in certain regions of the world brought about a significant and consistent reduction of rotavirus-associated hospitalizations. However, the efficacy of licensed vaccines remains suboptimal in low-income countries where the incidences of rotavirus gastroenteritis continue to happen unabated. The problem of low efficacy of currently licensed oral rotavirus vaccines in low-income countries necessitates continuous exploration, design, and development of new rotavirus vaccines. Traditional vaccine development is a complex, expensive, labor-intensive, and time-consuming process. Reverse vaccinology essentially utilizes the genome and proteome information on pathogens and has opened new avenues for in-silico multiepitope vaccine design for a plethora of pathogens, promising time reduction in the complete vaccine development pipeline by complementing the traditional vaccinology approach. A substantial number of reviews on licensed rotavirus vaccines and those under evaluation are already available in the literature. However, a collective account of rotavirus in-silico vaccines is lacking in the literature, and such an account may further fuel the interest of researchers to use reverse vaccinology to expedite the vaccine development process. Therefore, the main focus of this review is to summarize the research endeavors undertaken for the design and development of rotavirus vaccines by the reverse vaccinology approach utilizing the tools of immunoinformatics.
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Khan MS, Khan IM, Ahmad SU, Rahman I, Khan MZ, Khan MSZ, Abbas Z, Noreen S, Liu Y. Immunoinformatics design of B and T-cell epitope-based SARS-CoV-2 peptide vaccination. Front Immunol 2023; 13:1001430. [PMID: 36685569 PMCID: PMC9846236 DOI: 10.3389/fimmu.2022.1001430] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2022] [Accepted: 11/28/2022] [Indexed: 01/05/2023] Open
Abstract
SARS-COV-2 is a virulent respiratory virus, first identified in China (Wuhan) at the end of 2019. Scientists and researchers are trying to find any possible solution to this deadly viral disease. Different drug source agents have been identified, including western medicine, natural products, and traditional Chinese medicine. They have the potential to counteract COVID-19. This virus immediately affects the liver and causes a decrease in oxygen levels. In this study, multiple vacciome approaches were employed for designing a multi-epitope subunit vaccine for battling against SARS-COV-2. Vaccine designing, immunogenicity, allergenic, and physico-chemical assessment were performed by using the vacciome approach. The vaccine design is likely to be antigenic and produce potent interactions with ACE2 and NSP3 receptors. The developed vaccine has also been given to in-silico cloning models and immune response predictions. A total number of 12 CTL and 12 HTL antigenic epitopes were predicted from three selected covid-19 virulent proteins (spike protein, nucleocapsid protein, and membrane proteins, respectively) based on C-terminal cleavage and MHC binding scores. These predicted epitopes were amalgamated by AYY and GPGPG linkers, and a β-defensins adjuvant was inserted into the N-terminus of this vaccine. This analysis shows that the recommended vaccine can produce immune responses against SARS-COV-2. Designing and developing of the mentioned vaccine will require further experimental validation.
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Affiliation(s)
- Muhammad Shehzad Khan
- Anhui Province Key Laboratory of Embryo Development and Reproduction Regulation, Anhui Province Key Laboratory of Environmental Hormone and Reproduction, School of Biological and Food Engineering, Fuyang Normal University, Fuyang, China
- Department of Physics, College of Science, City University of Hong Kong, Kowloon, Hong Kong SAR, China
| | - Ibrar Muhammad Khan
- Anhui Province Key Laboratory of Embryo Development and Reproduction Regulation, Anhui Province Key Laboratory of Environmental Hormone and Reproduction, School of Biological and Food Engineering, Fuyang Normal University, Fuyang, China
| | - Syed Umair Ahmad
- Department of Bioinformatics Hazara University Mansehra, Mansehra, Pakistan
| | - Ishrat Rahman
- Department of Basic Dental Sciences, College of Dentistry, Princess Nourah Bint Abdulrahman University, Riyadh, Saudi Arabia
| | - Muhammad Zahoor Khan
- Department of Animal Breeding and Genetics, Faculty of Veterinary and Animal Sciences, University of Agriculture, Dera Ismail Khan, Pakistan
- State Key Laboratory of Animal Nutrition, Beijing Engineering Technology Research Center of Raw Milk Quality and Safety Control, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Muhammad Shah Zeb Khan
- Department of Biotechnology, University of Science and Technology of Bannu, Bannu, Pakistan
- School of Biomedical Science and Biomedical Engineering, Southeast University, Nanjing, China
| | - Zain Abbas
- Department of Life Sciences, University of Management and Technology, Lahore, Pakistan
| | - Shumaila Noreen
- Department of Zoology, Hazara University, Mansehra, Pakistan
| | - Yong Liu
- Anhui Province Key Laboratory of Embryo Development and Reproduction Regulation, Anhui Province Key Laboratory of Environmental Hormone and Reproduction, School of Biological and Food Engineering, Fuyang Normal University, Fuyang, China
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Awasthi A, Kumar N, Mishra A, Ravi R, Dalal A, Shankar S, Chandra R. Noscapine-Amino Acid Conjugates Suppress the Progression of Cancer Cells. ACS Pharmacol Transl Sci 2022; 5:1292-1304. [PMID: 36524011 PMCID: PMC9745893 DOI: 10.1021/acsptsci.2c00172] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Indexed: 11/16/2022]
Abstract
Lung cancer is the leading cause of cancer deaths globally; 1 in 16 people are diagnosed with lung cancer in their lifetime. Microtubules, a critical cytoskeletal assembly, have an essential role in cell division. Interference with the microtubule assembly leads to genetic instability during mitosis and cancer cell death. Currently, available antimitotic drugs such as vincas and taxanes are limited due to side effects such as alopecia, myelosuppression, and drug resistance. Noscapine, an opium alkaloid, is a tubulin-binding agent and can alter the microtubule assembly, causing cancer cell death. Amino acids are fundamental building blocks for protein synthesis, making them essential for the biosynthesis of cancer cells. However, the ability of amino acids in drug transportation has yet to be exploited in developing noscapine analogues as a potential drug candidate for cancer. Hence, in the present study, we have explored the ninth position of noscapine by introducing a hydroxymethylene group using the Blanc reaction and further coupled it with a series of amino acids to construct five target conjugates in good yields. The synthesized amino acid conjugate molecules were biologically evaluated against the A549 lung cancer cell line, among which the noscapine-tryptophan conjugate showed IC50 = 32 μM, as compared to noscapine alone (IC50 = 73 μM). Morphological changes in cancer cells, cell cycle arrest in the G1 phase, and ethidium bromide/acridine orange staining indicated promising anticancer properties. Molecular docking confirmed strong binding to tubulin, with a score of -41.47 kJ/mol with all 3D coordinates and significant involvement of molecular forces, including the hydrogen bonds and hydrophobic interactions. Molecular dynamics simulations demonstrated a stable binding of noscapine-tryptophan conjugate for a prolonged time (100 ns) with the involvement of free energy through the reaction coordinates analyses, solving the bioavailability of parent noscapine to the body.
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Affiliation(s)
- Amardeep Awasthi
- Department of Chemistry, University of Delhi, Delhi-110007, India
| | - Neeraj Kumar
- Department of Neurology, Northwestern University, Feinberg School of Medicine, Chicago, Illinois60611, United States
| | - Abhijeet Mishra
- Department of Biochemistry, Shivaji College, University of Delhi, Delhi-110027, India
| | - Rangnath Ravi
- Department of Chemistry, Shivaji College, University of Delhi, Delhi-110027, India
| | - Anu Dalal
- Department of Chemistry, Indian Institute of Technology, Delhi, Delhi-110016, India
| | - Saurav Shankar
- Department of Chemistry, University of Delhi, Delhi-110007, India
| | - Ramesh Chandra
- Department of Chemistry, University of Delhi, Delhi-110007, India
- Dr. B. R. Ambedkar Centre for Biomedical Research, University of Delhi, Delhi-110007, India
- Institute of Nano Medical Sciences, University of Delhi, Delhi-110007, India
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Salod Z, Mahomed O. Mapping Potential Vaccine Candidates Predicted by VaxiJen for Different Viral Pathogens between 2017-2021-A Scoping Review. Vaccines (Basel) 2022; 10:1785. [PMID: 36366294 PMCID: PMC9695814 DOI: 10.3390/vaccines10111785] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Revised: 10/16/2022] [Accepted: 10/18/2022] [Indexed: 09/29/2023] Open
Abstract
Reverse vaccinology (RV) is a promising alternative to traditional vaccinology. RV focuses on in silico methods to identify antigens or potential vaccine candidates (PVCs) from a pathogen's proteome. Researchers use VaxiJen, the most well-known RV tool, to predict PVCs for various pathogens. The purpose of this scoping review is to provide an overview of PVCs predicted by VaxiJen for different viruses between 2017 and 2021 using Arksey and O'Malley's framework and the Preferred Reporting Items for Systematic Reviews extension for Scoping Reviews (PRISMA-ScR) guidelines. We used the term 'vaxijen' to search PubMed, Scopus, Web of Science, EBSCOhost, and ProQuest One Academic. The protocol was registered at the Open Science Framework (OSF). We identified articles on this topic, charted them, and discussed the key findings. The database searches yielded 1033 articles, of which 275 were eligible. Most studies focused on severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), published between 2020 and 2021. Only a few articles (8/275; 2.9%) conducted experimental validations to confirm the predictions as vaccine candidates, with 2.2% (6/275) articles mentioning recombinant protein expression. Researchers commonly targeted parts of the SARS-CoV-2 spike (S) protein, with the frequently predicted epitopes as PVCs being major histocompatibility complex (MHC) class I T cell epitopes WTAGAAAYY, RQIAPGQTG, IAIVMVTIM, and B cell epitope IAPGQTGKIADY, among others. The findings of this review are promising for the development of novel vaccines. We recommend that vaccinologists use these findings as a guide to performing experimental validation for various viruses, with SARS-CoV-2 as a priority, because better vaccines are needed, especially to stay ahead of the emergence of new variants. If successful, these vaccines could provide broader protection than traditional vaccines.
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Affiliation(s)
- Zakia Salod
- Discipline of Public Health Medicine, University of KwaZulu-Natal, Durban 4051, South Africa
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Sehrawat H, Kumar N, Panchal S, Kumar L, Chandra R. Imperative persistent interaction analysis of anticancer noscapine-ionic liquid with calf thymus DNA. Int J Biol Macromol 2022; 220:415-425. [PMID: 35985396 DOI: 10.1016/j.ijbiomac.2022.08.106] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Revised: 08/10/2022] [Accepted: 08/15/2022] [Indexed: 11/25/2022]
Abstract
In this study, we have shown the interaction between opium poppy alkaloid noscapine-based ionic liquid [Pip-Nos]OTf and ct-DNA using UV-visible absorption spectroscopy, fluorescence spectroscopy, CD, and computational studies. The absorption spectra showed a hypochromic shift with no shift in the absorption maxima suggesting groove or electrostatic binding. Fluorescence spectra showed an enhancement in fluorescence emission suggesting that the probable mode of binding should be groove binding. Ethidium bromide (EB) competitive and Ionic strength study showed the absence of intercalative and electrostatic modes of interaction. Further, CD analysis of ct-DNA suggested a groove binding mode of interaction of [Pip-Nos]OTf with ct-DNA. [Pip-Nos]OTf displayed a strong binding with the target ct-DNA with a molecular docking score of -41.47 kJ/mol with all 3D coordinates and full conformation. Also, molecular binding contact analyses depicted the stable binding of drug and ct-DNA with potential hydrogen bonds and hydrophobic interactions. The structural superimposition dynamics analysis showed the stable binding of [Pip-Nos]OTf with the ct-DNA model through RMSD statistics. Moreover, the ligand interaction calculations revealed the involvement of large binding energy along with a high static number of molecular forces including the hydrogen bonds and hydrophobic interactions in their complexation. These significant results report the potency of [Pip-Nos]OTf and its important futuristic role in cancer therapeutics.
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Affiliation(s)
- Hitesh Sehrawat
- Drug Discovery & Development Laboratory, Department of Chemistry, University of Delhi, Delhi 110007, India.
| | - Neeraj Kumar
- Drug Discovery & Development Laboratory, Department of Chemistry, University of Delhi, Delhi 110007, India; Northwestern University, Feinberg School of Medicine, Department of Neurology, Chicago, IL 60611, USA
| | - Sagar Panchal
- Drug Discovery & Development Laboratory, Department of Chemistry, University of Delhi, Delhi 110007, India
| | - Loveneesh Kumar
- Drug Discovery & Development Laboratory, Department of Chemistry, University of Delhi, Delhi 110007, India
| | - Ramesh Chandra
- Drug Discovery & Development Laboratory, Department of Chemistry, University of Delhi, Delhi 110007, India; Dr. B. R. Ambedkar Center for Biomedical Research, University of Delhi, Delhi 110007, India; Institute of Nano Medical Sciences (INMS), University of Delhi, Delhi 110007, India.
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Ghahremanian S, Rashidi MM, Raeisi K, Toghraie D. Molecular dynamics simulation approach for discovering potential inhibitors against SARS-CoV-2: A structural review. J Mol Liq 2022; 354:118901. [PMID: 35309259 PMCID: PMC8916543 DOI: 10.1016/j.molliq.2022.118901] [Citation(s) in RCA: 32] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Revised: 03/04/2022] [Accepted: 03/06/2022] [Indexed: 01/11/2023]
Abstract
Since the commencement of the novel Coronavirus, the disease has quickly turned into a worldwide crisis so that there has been growing attention in discovering possible hit compounds for tackling this pandemic. Discovering standard treatment strategies is a serious challenge because little information is available about this emerged infectious virus. Regarding the high impact of time, applying computational procedures to choose promising drugs from a catalog of licensed medications provides a precious chance for combat against the life-threatening disorder of COVID-19. Molecular dynamics (MD) simulation is a promising approach for assessing the binding affinity of ligand-receptor as well as observing the conformational trajectory of docked complexes over time. Given that many computational studies are performed using MD along with the molecular docking on various candidates as antiviral inhibitors of COVID-19 protease, there is a demand to conduct a comprehensive review of the most important studies to reveal and compare the potential introduced agents that this study covers this defect. In this context, the present review intends to prepare an overview of these studies by considering RMSD, RMSF, radius of gyration, binding free energy, and Solvent-Accessible Surface Area (SASA) as effective parameters for evaluation. The outcomes will offer a road map for adjusting antiviral inhibitors, which can facilitate the selection and development of drug candidates for use in the medical therapy. Finally, the molecular modeling approaches rendered by this study may be valuable for future computational studies.
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Affiliation(s)
- Shabnam Ghahremanian
- Institute of Fundamental and Frontier Sciences, University of Electronic Science and Technology of China, Chengdu 610054, Sichuan, PR China
| | - Mohammad Mehdi Rashidi
- Institute of Fundamental and Frontier Sciences, University of Electronic Science and Technology of China, Chengdu 610054, Sichuan, PR China
- Faculty of Mechanical and Industrial Engineering, Quchan University of Technology, Quchan, Iran
| | - Kimai Raeisi
- Department of Basic Science, Shahrekord Branch, Islamic Azad University, Shahrekord, Iran
| | - Davood Toghraie
- Department of Mechanical Engineering, Khomeinishahr Branch, Islamic Azad University, Khomeinishahr, Iran
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Abdul-Hammed M, Adedotun IO, Falade VA, Adepoju AJ, Olasupo SB, Akinboade MW. Target-based drug discovery, ADMET profiling and bioactivity studies of antibiotics as potential inhibitors of SARS-CoV-2 main protease (M pro). Virusdisease 2021; 32:642-656. [PMID: 34226871 PMCID: PMC8246438 DOI: 10.1007/s13337-021-00717-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Accepted: 06/15/2021] [Indexed: 12/24/2022] Open
Abstract
A recent outbreak of a new strain of Coronavirus (SARS-CoV-2) has become a global health burden, which has resulted in deaths. No proven drug has been found to effectively cure this fast-spreading infection, hence the need to explore old drugs with the known profile in tackling this pandemic. A computer-aided drug design approach involving virtual screening was used to obtain the binding scores and inhibiting efficiencies of previously known antibiotics against SARS-CoV-2 main protease (Mpro). The drug-likeness analysis of the repurposed drugs were done using the Molinspiration chemoinformatics tool, while the Absorption, Distribution, Metabolism, Excretion, and Toxicity (ADMET) analysis was carried out using ADMET SAR-2 webserver. Other analyses performed include bioactivities of the repurposed drug as a probable anti-SARS-CoV-2 agent and oral bioavailability analyses among others. The results were compared with those of drugs currently involved in clinical trials in the ongoing pandemic. Although antibiotics have been speculated to be of no use in the treatment of viral infections, literature has emerged lately to reveal the antiviral potential and immune-boosting ability of antibiotics. This study identified Tarivid and Ciprofloxacin with binding affinities of - 8.3 kcal/mol and - 8.1 kcal/mol, respectively as significant inhibitors of SARS-CoV-2 (Mpro) with better pharmacokinetics, drug-likeness and oral bioavailability, bioactivity properties, ADMET properties and inhibitory strength compared to Remdesivir (- 7.6 kcal/mol) and Azithromycin (- 6.3 kcal/mol). These observations will provide insight for further research (clinical trial) in the cure and management of COVID-19.
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Affiliation(s)
- Misbaudeen Abdul-Hammed
- Department of Pure and Applied Chemistry, Ladoke Akintola University of Technology, P.M.B. 4000, Ogbomoso, Nigeria
| | - Ibrahim Olaide Adedotun
- Department of Pure and Applied Chemistry, Ladoke Akintola University of Technology, P.M.B. 4000, Ogbomoso, Nigeria
| | - Victoria Adeola Falade
- Department of Pure and Applied Chemistry, Ladoke Akintola University of Technology, P.M.B. 4000, Ogbomoso, Nigeria
| | - Adewusi John Adepoju
- Department of Pure and Applied Chemistry, Ladoke Akintola University of Technology, P.M.B. 4000, Ogbomoso, Nigeria
| | | | - Modinat Wuraola Akinboade
- Department of Biochemistry, Ladoke Akintola University of Technology, P.M.B. 4000, Ogbomoso, Nigeria
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Sehrawat H, Kumar N, Sood D, Kumar L, Tomar R, Chandra R. Unraveling the interaction of an opium poppy alkaloid noscapine ionic liquid with human hemoglobin: Biophysical and computational studies. J Mol Liq 2021. [DOI: 10.1016/j.molliq.2021.116710] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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Rahnama S, Azimzadeh Irani M, Amininasab M, Ejtehadi MR. S494 O-glycosylation site on the SARS-CoV-2 RBD affects the virus affinity to ACE2 and its infectivity; a molecular dynamics study. Sci Rep 2021; 11:15162. [PMID: 34312429 PMCID: PMC8313699 DOI: 10.1038/s41598-021-94602-w] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Accepted: 07/13/2021] [Indexed: 12/23/2022] Open
Abstract
SARS-CoV-2 is a strain of Coronavirus family that caused the ongoing pandemic of COVID-19. Several studies showed that the glycosylation of virus spike (S) protein and the Angiotensin-Converting Enzyme 2 (ACE2) receptor on the host cell is critical for the virus infectivity. Molecular Dynamics (MD) simulations were used to explore the role of a novel mutated O-glycosylation site (D494S) on the Receptor Binding Domain (RBD) of S protein. This site was suggested as a key mediator of virus-host interaction. By exploring the dynamics of three O-glycosylated models and the control systems of unglcosylated S4944 and S494D complexes, it was shown that the decoration of S494 with elongated O-glycans results in stabilized interactions on the direct RBD-ACE2. Calculation of the distances between RBD and two major H1, H2 helices of ACE2 and the interacting pairs of amino acids in the interface showed that the elongated O-glycan maintains these interactions by forming several polar contacts with the neighbouring residues while it would not interfere in the direct binding interface. Relative binding free energy of RBD-ACE2 is also more favorable in the O-glycosylated models with longer glycans. The increase of RBD binding affinity to ACE2 depends on the size of attached O-glycan. By increasing the size of O-glycan, the RBD-ACE2 binding affinity will increase. Hence, this crucial factor must be taken into account for any further inhibitory approaches towards RBD-ACE2 interaction.
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Affiliation(s)
- Shadi Rahnama
- Institute for Nanoscience and Nanotechnology, Sharif University of Technology, Tehran, 14588, Iran
| | | | - Mehriar Amininasab
- Department of Cell and Molecular Biology, School of Biology, College of Science, University of Tehran, Tehran, Iran
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Mugunthan SP, Harish MC. Multi-epitope-Based Vaccine Designed by Targeting Cytoadherence Proteins of Mycoplasma gallisepticum. ACS OMEGA 2021; 6:13742-13755. [PMID: 34095666 PMCID: PMC8173551 DOI: 10.1021/acsomega.1c01032] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Accepted: 05/04/2021] [Indexed: 05/18/2023]
Abstract
Mycoplasma gallisepticum causes chronic respiratory disease in chickens leading to large economic losses in the poultry industry, and the impacts remain to be a great challenge for a longer period. Among the other approaches, a vaccine targeting the adhesion proteins of M. gallisepticum would be a promising candidate in controlling the infection. Thus, the present study is aimed to design a multi-epitope vaccine candidate using cytoadhesion proteins of M. gallisepticum through an advanced immunoinformatics approach. As a result, the multi-epitope vaccine was constructed, which comprised potential T-cell and B-cell binding epitopes with appropriate adjuvants. The designed multi-epitope vaccine represented high antigenicity with viable physiochemical properties. The prospective three-dimensional structure of the epitope was predicted, refined, and validated. The molecular docking analysis of multi-epitope vaccine candidates with the chicken Toll-like receptor-5 predicted effective binding. Furthermore, codon optimization and in silico cloning ensured high expression. Thus, the present finding indicates that the engineered multi-epitope vaccine is structurally stable and can induce a strong immune response. Furthermore, the multi-epitope vaccine is suggested to be a suitable vaccine candidate for the M. gallisepticum infection due to its effective binding capacity and precise specificity.
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Affiliation(s)
- Susithra Priyadarshni Mugunthan
- Plant Genetic Engineering and Molecular Farming Lab, Department of Biotechnology, Thiruvalluvar University, Serkkadu, Vellore 632115, Tamil Nadu, India
| | - Mani Chandra Harish
- Plant Genetic Engineering and Molecular Farming Lab, Department of Biotechnology, Thiruvalluvar University, Serkkadu, Vellore 632115, Tamil Nadu, India
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Singh A, Kumar N, Singh S, Sewariya S, Sharma MK, Chandra R. High-valued pyrazinoindole analogues: Synthesis, antibacterial activity, structure activity relationship and molecular dynamics analyses. RESULTS IN CHEMISTRY 2021. [DOI: 10.1016/j.rechem.2021.100194] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022] Open
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13
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Rajapaksha H, Perera BT, Meepage J, Perera RT, Dissanayake C. Mitigate the cytokine storm due to the severe COVID-19: A computational investigation of possible allosteric inhibitory actions on IL-6R and IL-1R using selected phytochemicals. ACTA ACUST UNITED AC 2020. [DOI: 10.5155/eurjchem.11.4.351-363.2043] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The novel corona virus 2019 (COVID 19) is growing at an increasing rate with high mortality. Meanwhile, the cytokine storm is the most dangerous and potentially life-threatening event related to COVID 19. Phyto-compounds found in existing Ayurveda drugs have the ability to inhibit the Interleukin 6 (IL-6R) and Interleukin 1 (IL-1R) receptors. IL-6R and IL-1R receptors involve in cytokine storm and recognition of phytochemicals with proven safety profiles could open a pathway to the development of the most effective drugs against cytokine storm. In this study, we intend to perform an in silico investigation of effective phyto compounds, which can be isolated from selected medicinal herbs to avoid cytokine storm, inhibiting the IL-6 and IL-1 receptor binding process. An extensive literature survey followed by virtual screening was carried out to identify phytochemicals with potential anti-hyper-inflammatory action. Flexible docking was conducted for validated models of IL-1R and IL-6R-α with the most promising phytochemicals at possible allosteric sites using AutoDock Vina. Molecular dynamics (MD) studies were conducted for selected protein-ligand complexes using LARMD server and conformational changes were evaluated. According to the results, taepeenin J had Gibbs energy (ΔG) of -10.85 kcal/mol towards IL-1R but had limited oral bioavailability. MD analysis revealed that taepeenin J can cause significant conformational movements in IL-1R. Nortaepeenin B showed a ΔG of -8.5 kcal/mol towards IL-6R-α with an excellent oral bioavailability. MD analysis predicted that it can cause significant conformational movements in IL-6R-α. Hence, the evaluated phytochemicals are potential candidates for further in vitro studies for the development of medicine against cytokine storm on behalf of SARS-COV-2 infected patients.
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Affiliation(s)
- Harindu Rajapaksha
- Department of Chemistry, Faculty of Science, University of Kelaniya, Dalugama, 11 300, Sri Lanka
| | - Bingun Tharusha Perera
- Department of Chemistry, Faculty of Science, University of Kelaniya, Dalugama, 11 300, Sri Lanka
| | - Jeewani Meepage
- Department of Chemistry, Faculty of Science, University of Kelaniya, Dalugama, 11 300, Sri Lanka
| | - Ruwan Tharanga Perera
- Graduate Studies Division, Gampaha Wickramarachchi Ayurveda Institute, University of Kelaniya, Yakkala, 11870, Sri Lanka
| | - Chithramala Dissanayake
- Department of Cikitsa, Gampaha Wickramarachchi Ayurveda Institute, University of Kelaniya, Yakkala, 11870, Sri Lanka
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