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Shawan MMAK, Sharma AR, Bhattacharya M, Mallik B, Akhter F, Shakil MS, Hossain MM, Banik S, Lee SS, Hasan MA, Chakraborty C. Designing an effective therapeutic siRNA to silence RdRp gene of SARS-CoV-2. INFECTION GENETICS AND EVOLUTION 2021; 93:104951. [PMID: 34089909 PMCID: PMC8170914 DOI: 10.1016/j.meegid.2021.104951] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Revised: 05/17/2021] [Accepted: 05/31/2021] [Indexed: 02/07/2023]
Abstract
The devastating outbreak of COVID-19 has spread all over the world and has become a global health concern. There is no specific therapeutics to encounter the COVID-19. Small interfering RNA (siRNA)-based therapy is an efficient strategy to control human viral infections employing post-transcriptional gene silencing (PTGS) through neutralizing target complementary mRNA. RNA-dependent RNA polymerase (RdRp) encoded by the viral RdRp gene as a part of the replication-transcription complex can be adopted as an acceptable target for controlling SARS-CoV-2 mediated infection. Therefore, in the current study, accessible siRNA designing tools, including significant algorithms and parameters, were rationally used to design the candidate siRNAs against SARS-COV-2 encoded RdRp. The designed siRNA molecules possessed adequate nucleotide-based and other features for potent gene silencing. The targets of the designed siRNAs revealed no significant matches within the whole human genome, ruling out any possibilities for off-target silencing by the siRNAs. Characterization with different potential parameters of efficacy allowed selecting the finest siRNA among all the designed siRNA molecules. Further, validation assessment and target site accessibility prediction also rationalized the suitability of this siRNA molecule. Molecular docking study between the selected siRNA molecule and component of RNA interference (RNAi) pathway gave an excellent outcome. Molecular dynamics of two complexes: siRNA and argonaute complex, guide RNA, and target protein complex, have shown structural stability of these proteins. Therefore, the designed siRNA molecule might act as an effective therapeutic agent against the SARS-CoV-2 at the genome level and can prevent further outbreaks of COVID-19 in humans.
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Chakraborty C, Sharma AR, Bhattacharya M, Agoramoorthy G, Lee SS. All Nations Must Prioritize the COVID-19 Vaccination Program for Elderly Adults Urgently. Aging Dis 2021; 12:688-690. [PMID: 34094633 PMCID: PMC8139210 DOI: 10.14336/ad.2021.0426] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Accepted: 04/26/2021] [Indexed: 12/04/2022] Open
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Chakraborty C, Sharma AR, Sharma G, Bhattacharya M, Patra BC, Sarkar BK, Banerjee S, Banerjee K, Lee SS. Understanding the molecular evolution of tiger diversity through DNA barcoding marker ND4 and NADH dehydrogenase complex using computational biology. Genes Genomics 2021; 43:759-773. [PMID: 33884571 DOI: 10.1007/s13258-021-01089-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2020] [Accepted: 03/19/2021] [Indexed: 10/21/2022]
Abstract
BACKGROUND Currently, Tigers (the top predator of an ecosystem) are on the list of endangered species. Thus the need is to understand the tiger's population genomics to design their conservation strategies. OBJECTIVE We analyzed the molecular evolution of tiger diversity using NADH dehydrogenase subunit 4 (ND4), a significant electron transport chain component. METHODS We have analyzed nucleotide composition and distribution pattern of ND genes, molecular evolution, evolutionary conservation pattern and conserved blocks of NADH, phylogenomics of ND4, and estimating species divergence, etc., using different bioinformatics tools and software, and MATLAB programming and computing environment. RESULTS The nucleotide composition and distribution pattern of ND genes in the tiger genome demonstrated an increase in the number of adenine (A) and a lower trend of A+T content in some place of the distribution analysis. However, the observed distributions were not significant (P > 0.05). Evolutionary conservation analysis showed three highly align blocks (186 to 198, 406 to 416, and 527 to 545). On mapping the molecular evolution of ND4 among model species (n = 30), we observed its presence in a broader range of species. ND4 based molecular evolution of tiger diversity and time divergence for a tiger (20 different other species) shows that genus Panthera originated more or less at a similar time. CONCLUSIONS The nucleotide composition and nucleotide distribution pattern of tiger ND genes showed the evolutionary pattern and origin of tiger and Panthera lineage concerning the molecular clock, which will help to understand their adaptive evolution.
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Abi B, Albahri T, Al-Kilani S, Allspach D, Alonzi LP, Anastasi A, Anisenkov A, Azfar F, Badgley K, Baeßler S, Bailey I, Baranov VA, Barlas-Yucel E, Barrett T, Barzi E, Basti A, Bedeschi F, Behnke A, Berz M, Bhattacharya M, Binney HP, Bjorkquist R, Bloom P, Bono J, Bottalico E, Bowcock T, Boyden D, Cantatore G, Carey RM, Carroll J, Casey BCK, Cauz D, Ceravolo S, Chakraborty R, Chang SP, Chapelain A, Chappa S, Charity S, Chislett R, Choi J, Chu Z, Chupp TE, Convery ME, Conway A, Corradi G, Corrodi S, Cotrozzi L, Crnkovic JD, Dabagov S, De Lurgio PM, Debevec PT, Di Falco S, Di Meo P, Di Sciascio G, Di Stefano R, Drendel B, Driutti A, Duginov VN, Eads M, Eggert N, Epps A, Esquivel J, Farooq M, Fatemi R, Ferrari C, Fertl M, Fiedler A, Fienberg AT, Fioretti A, Flay D, Foster SB, Friedsam H, Frlež E, Froemming NS, Fry J, Fu C, Gabbanini C, Galati MD, Ganguly S, Garcia A, Gastler DE, George J, Gibbons LK, Gioiosa A, Giovanetti KL, Girotti P, Gohn W, Gorringe T, Grange J, Grant S, Gray F, Haciomeroglu S, Hahn D, Halewood-Leagas T, Hampai D, Han F, Hazen E, Hempstead J, Henry S, Herrod AT, Hertzog DW, Hesketh G, Hibbert A, Hodge Z, Holzbauer JL, Hong KW, Hong R, Iacovacci M, Incagli M, Johnstone C, Johnstone JA, Kammel P, Kargiantoulakis M, Karuza M, Kaspar J, Kawall D, Kelton L, Keshavarzi A, Kessler D, Khaw KS, Khechadoorian Z, Khomutov NV, Kiburg B, Kiburg M, Kim O, Kim SC, Kim YI, King B, Kinnaird N, Korostelev M, Kourbanis I, Kraegeloh E, Krylov VA, Kuchibhotla A, Kuchinskiy NA, Labe KR, LaBounty J, Lancaster M, Lee MJ, Lee S, Leo S, Li B, Li D, Li L, Logashenko I, Lorente Campos A, Lucà A, Lukicov G, Luo G, Lusiani A, Lyon AL, MacCoy B, Madrak R, Makino K, Marignetti F, Mastroianni S, Maxfield S, McEvoy M, Merritt W, Mikhailichenko AA, Miller JP, Miozzi S, Morgan JP, Morse WM, Mott J, Motuk E, Nath A, Newton D, Nguyen H, Oberling M, Osofsky R, Ostiguy JF, Park S, Pauletta G, Piacentino GM, Pilato RN, Pitts KT, Plaster B, Počanić D, Pohlman N, Polly CC, Popovic M, Price J, Quinn B, Raha N, Ramachandran S, Ramberg E, Rider NT, Ritchie JL, Roberts BL, Rubin DL, Santi L, Sathyan D, Schellman H, Schlesier C, Schreckenberger A, Semertzidis YK, Shatunov YM, Shemyakin D, Shenk M, Sim D, Smith MW, Smith A, Soha AK, Sorbara M, Stöckinger D, Stapleton J, Still D, Stoughton C, Stratakis D, Strohman C, Stuttard T, Swanson HE, Sweetmore G, Sweigart DA, Syphers MJ, Tarazona DA, Teubner T, Tewsley-Booth AE, Thomson K, Tishchenko V, Tran NH, Turner W, Valetov E, Vasilkova D, Venanzoni G, Volnykh VP, Walton T, Warren M, Weisskopf A, Welty-Rieger L, Whitley M, Winter P, Wolski A, Wormald M, Wu W, Yoshikawa C. Measurement of the Positive Muon Anomalous Magnetic Moment to 0.46 ppm. PHYSICAL REVIEW LETTERS 2021; 126:141801. [PMID: 33891447 DOI: 10.1103/physrevlett.126.141801] [Citation(s) in RCA: 111] [Impact Index Per Article: 37.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2021] [Accepted: 03/25/2021] [Indexed: 06/12/2023]
Abstract
We present the first results of the Fermilab National Accelerator Laboratory (FNAL) Muon g-2 Experiment for the positive muon magnetic anomaly a_{μ}≡(g_{μ}-2)/2. The anomaly is determined from the precision measurements of two angular frequencies. Intensity variation of high-energy positrons from muon decays directly encodes the difference frequency ω_{a} between the spin-precession and cyclotron frequencies for polarized muons in a magnetic storage ring. The storage ring magnetic field is measured using nuclear magnetic resonance probes calibrated in terms of the equivalent proton spin precession frequency ω[over ˜]_{p}^{'} in a spherical water sample at 34.7 °C. The ratio ω_{a}/ω[over ˜]_{p}^{'}, together with known fundamental constants, determines a_{μ}(FNAL)=116 592 040(54)×10^{-11} (0.46 ppm). The result is 3.3 standard deviations greater than the standard model prediction and is in excellent agreement with the previous Brookhaven National Laboratory (BNL) E821 measurement. After combination with previous measurements of both μ^{+} and μ^{-}, the new experimental average of a_{μ}(Exp)=116 592 061(41)×10^{-11} (0.35 ppm) increases the tension between experiment and theory to 4.2 standard deviations.
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Choudhury A, Das NC, Patra R, Bhattacharya M, Ghosh P, Patra BC, Mukherjee S. Exploring the binding efficacy of ivermectin against the key proteins of SARS-CoV-2 pathogenesis: an in silico approach. Future Virol 2021. [PMCID: PMC7996102 DOI: 10.2217/fvl-2020-0342] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Aim: COVID-19 is currently the biggest threat to mankind. Recently, ivermectin (a US FDA-approved antiparasitic drug) has been explored as an anti-SARS-CoV-2 agent. Herein, we have studied the possible mechanism of action of ivermectin using in silico approaches. Materials & methods: Interaction of ivermectin against the key proteins involved in SARS-CoV-2 pathogenesis were investigated through molecular docking and molecular dynamic simulation. Results: Ivermectin was found as a blocker of viral replicase, protease and human TMPRSS2, which could be the biophysical basis behind its antiviral efficiency. The antiviral action and ADMET profile of ivermectin was on par with the currently used anticorona drugs such as hydroxychloroquine and remdesivir. Conclusion: Our study enlightens the candidature of ivermectin as an effective drug for treating COVID-19.
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Sharma AR, Sharma G, Bhattacharya M, Lee SS, Chakraborty C. Circulating miRNA in atherosclerosis: a clinical biomarker and early diagnostic tool. Curr Mol Med 2021; 22:250-262. [PMID: 33719955 DOI: 10.2174/1566524021666210315124438] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Revised: 02/01/2021] [Accepted: 02/02/2021] [Indexed: 11/22/2022]
Abstract
Atherosclerosis, which is a vascular disease, is characterized by narrowing the arteries and forming plaque inside arteries. There is a record 17.5 million associated deaths recorded annually, representing 31% of global death. It has been noted that there is an association between vascular fibrosis and atherosclerosis. The thickening of the arterial wall and reduction of the lumen diameter may cause unwarranted deposition of extracellular matrix (ECM), and these conditions help in the progression of many clinical diseases and pathological conditions such as atherosclerosis. Here, we reviewed the involvement of various circulating microRNAs (miRNAs) in the very early diagnosis of atherosclerosis. We have also tried to provide an insight into the advantages and validation of circulating miRNAs through different techniques. We have discussed different circulating miRNAs, such as miR-17, miR-17-5p, miR-29b, miR-30, miR-92a, miR-126, miR-143, miR-145, miR-146a, miR-212, miR-218, miR-221, miR-222, miR-361-5p, as a biomarker for clinical diagnosis of atherosclerosis. The insightful demonstration in this review will offer a better opportunity for the researchers and technology developers in understanding the current scenario of circulating miRNA, which could facilitate them in improving the current diagnostic technologies of atherosclerosis in clinics.
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Chakraborty C, Sharma AR, Mallick B, Bhattacharya M, Sharma G, Lee SS. Evaluation of molecular interaction, physicochemical parameters and conserved pattern of SARS-CoV-2 Spike RBD and hACE2: in silico and molecular dynamics approach. EUROPEAN REVIEW FOR MEDICAL AND PHARMACOLOGICAL SCIENCES 2021; 25:1708-1723. [PMID: 33629340 DOI: 10.26355/eurrev_202102_24881] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
OBJECTIVE Recent pandemic virus SARS-CoV-2 is a global warning for the healthcare system. The spike protein of virus SARS-CoV-2 is significant because of two reasons. Firstly, the spike protein of this virus binds with the human ACE2 (hACE2) receptor. Secondly, it has several antigenic regions that might be targeted for vaccine development. However, the structural analytical data for the spike protein of this virus is not available. MATERIALS AND METHODS Here, we performed an analysis to understand the structural two subunits of S glycoprotein (S gp) of SARS-CoV-2. Further, an analysis of secondary structure components and the tertiary structure analysis of RBD was carried out. We also performed molecular interaction analysis between S gp of this virus and hACE2 as well as between SARS-CoV S gp and hACE2 to compare the binding properties of these two viruses. RESULTS We noted that the molecular interaction of SARS-CoV-2 S gp and hACE2 form eleven hydrogen bonds, while the molecular interaction of SARS-CoV S gp and hACE2 receptor form seven hydrogen bonds, indicating that the molecular interaction of SARS-CoV-2 S gp and hACE2 receptor is more stable than SARS-CoV S gp and hACE2 receptor. The pairwise sequence alignment of S gp SARS-CoV and SARS-CoV-2 shows several conserved residues of these two proteins. Besides, conserved pattern analysis of SARS-CoV-2 S gp and hACE2 revealed the presence of several highly conserved regions for these two proteins. The molecular dynamics simulation shows a stable interplay between SARS-CoV-2 S gp with the hACE2 receptor. CONCLUSIONS The present study might help determine the SARS-CoV-2 virus entrance mechanism into the human cell. Moreover, the understanding of the conserved regions may help in the process of therapeutic development from the infection of the deadly virus.
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Chakraborty C, Ranjan Sharma A, Bhattacharya M, Lee SS, Agoramoorthy G. COVID-19 vaccine: Challenges in developing countries and India's initiatives. LE INFEZIONI IN MEDICINA 2021; 29:165-166. [PMID: 33664189] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Not available.
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Sharma G, Sharma AR, Bhattacharya M, Lee SS, Chakraborty C. CRISPR-Cas9: A Preclinical and Clinical Perspective for the Treatment of Human Diseases. Mol Ther 2021; 29:571-586. [PMID: 33238136 PMCID: PMC7854284 DOI: 10.1016/j.ymthe.2020.09.028] [Citation(s) in RCA: 92] [Impact Index Per Article: 30.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2020] [Revised: 07/12/2020] [Accepted: 09/16/2020] [Indexed: 12/21/2022] Open
Abstract
At present, the idea of genome modification has revolutionized the modern therapeutic research era. Genome modification studies have traveled a long way from gene modifications in primary cells to genetic modifications in animals. The targeted genetic modification may result in the modulation (i.e., either upregulation or downregulation) of the predefined gene expression. Clustered regularly interspaced short palindromic repeats (CRISPR)-CRISPR-associated nuclease 9 (Cas9) is a promising genome-editing tool that has therapeutic potential against incurable genetic disorders by modifying their DNA sequences. In comparison with other genome-editing techniques, CRISPR-Cas9 is simple, efficient, and very specific. This enabled CRISPR-Cas9 genome-editing technology to enter into clinical trials against cancer. Besides therapeutic potential, the CRISPR-Cas9 tool can also be applied to generate genetically inhibited animal models for drug discovery and development. This comprehensive review paper discusses the origin of CRISPR-Cas9 systems and their therapeutic potential against various genetic disorders, including cancer, allergy, immunological disorders, Duchenne muscular dystrophy, cardiovascular disorders, neurological disorders, liver-related disorders, cystic fibrosis, blood-related disorders, eye-related disorders, and viral infection. Finally, we discuss the different challenges, safety concerns, and strategies that can be applied to overcome the obstacles during CRISPR-Cas9-mediated therapeutic approaches.
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Chakraborty C, Sharma AR, Bhattacharya M, Sharma G, Lee SS. Immunoinformatics Approach for the Identification and Characterization of T Cell and B Cell Epitopes towards the Peptide-Based Vaccine against SARS-CoV-2. Arch Med Res 2021; 52:362-370. [PMID: 33546870 PMCID: PMC7846223 DOI: 10.1016/j.arcmed.2021.01.004] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Accepted: 01/14/2021] [Indexed: 02/07/2023]
Abstract
Presently, immunoinformatics is playing a significant role in epitope identification and vaccine designing for various critical diseases. Using immunoinformatics, several scientists are trying to identify and characterize T cell and B cell epitopes as well as design peptide-based vaccine against SARS-CoV-2. In this review article, we have tried to discuss the importance in adaptive immunity and its significance for designing the SARS-CoV-2 vaccine. Moreover, we have attempted to illustrate several significant key points for utilizing immunoinformatics for vaccine designing, such as the criteria for selection and identification of epitopes, T cell epitope, and B cell epitope prediction and different emerging tools/databases for immunoinformatics. In the current scenario, a few immunoinformatics studies have been performed for various infectious pathogens and related diseases. Thus, we have also summarized and included these current immunoinformatics studies in this review article. Finally, we have discussed about the probable T cell and B cell epitopes and their identification and characterization for vaccine designing against SARS-CoV-2.
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Chakraborty C, Bhattacharya M, Mallick B, Sharma AR, Lee SS, Agoramoorthy G. SARS-CoV-2 protein drug targets landscape: a potential pharmacological insight view for the new drug development. Expert Rev Clin Pharmacol 2021; 14:225-238. [PMID: 33423554 DOI: 10.1080/17512433.2021.1874348] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Introduction: Protein drug targets play a significant choice in different stages of the drug discovery process. There is an urgent need to understand the drug discovery approaches and protein drug targets (PDT) of SARS-CoV-2, with structural insights for the development of SARS-CoV-2 drugs through targeted therapeutic approach.Areas covered: We have described the protein as a drug target class and also discussed various drug discovery approaches for SARS-CoV-2 involving the protein drug targets such as drug repurposing study, designing of viral entry inhibitors, viral replication inhibitors, and different enzymes of the virus. We have performed comprehensive literature search from the popular databases such as PubMed Google scholar, Web of Science, and Scopus. Finally, we have illustrated the structural landscape of different significant viral proteins (3 CLpro or Mpro, PLpro, RdRp, helicase, S protein) and host proteins as drug targets (cathepsin L, furin, TMPRSS2, ACE2).Expert opinion: The structural landscape of PDT with their binding pockets, and significant residues involved in binding has been discussed further to better understand the PDT and the structure-based drug discovery for SARS-CoV-2. This attempt will increase more therapeutic options, and combination therapies with a multi-target strategy.
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Ghosh P, Bhakta S, Bhattacharya M, Sharma AR, Sharma G, Lee SS, Chakraborty C. A Novel Multi-Epitopic Peptide Vaccine Candidate Against Helicobacter pylori: In-Silico Identification, Design, Cloning and Validation Through Molecular Dynamics. Int J Pept Res Ther 2021; 27:1149-1166. [PMID: 33495694 PMCID: PMC7816556 DOI: 10.1007/s10989-020-10157-w] [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] [Accepted: 12/30/2020] [Indexed: 01/22/2023]
Abstract
Helicobacter pylori is a highly potential pathogen to colonize in the human stomach. This bacterial strain is now alarming serious health concern all over the world. Combating through available drugs is a difficult task due to lack of appropriate common targets against genetically diverse strains. Therefore, the developments of effective targets vaccines require alternative strategies to eliminate the H. pylori infection. In this study, we developed a novel vaccine construct using B-cell derived T-cell epitopes from four target antigenic proteins (HpaA, FlaA, FlaB and Omp18), and found the induction of possible immune response using advanced immunoinformatics approaches. In order to boost immune system, we tagged adjuvant (50S ribosomal protein L7/L12) with a suitable linker at the N-terminus side of vaccine sequence. Protein–protein docking between human Toll like receptor 5 (TLR5) and vaccine construct help to predict the way of inductive signaling that leads to immune-response. The calculated negative score (− 151.4, + / − 8.7) of molecular docking complex signify the best binding interface. Molecular dynamics simulation studies confirmed the proper docking between TLR5 and vaccine candidate. Moreover, Normal mode analysis (NMA) calculates the molecular motion of the docking complex. The low eigenvalue (2.935e−05) indicates the stable and flexible molecular motion in the binding interaction side. Finally, in-silico cloning of vaccine candidate was performed using expression vector pET28b (+) with the optimized restriction sites.
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Chakraborty C, Sharma AR, Bhattacharya M, Sharma G, Saha RP, Lee SS. Ongoing Clinical Trials of Vaccines to Fight against COVID-19 Pandemic. Immune Netw 2021; 21:e5. [PMID: 33728098 PMCID: PMC7937508 DOI: 10.4110/in.2021.21.e5] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Revised: 12/02/2020] [Indexed: 02/06/2023] Open
Abstract
Coronavirus disease 2019 (COVID-19) has developed as a pandemic, and it created an outrageous effect on the current healthcare and economic system throughout the globe. To date, there is no appropriate therapeutics or vaccines against the disease. The entire human race is eagerly waiting for the development of new therapeutics or vaccines against severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2). Efforts are being taken to develop vaccines at a rapid rate for fighting against the ongoing pandemic situation. Amongst the various vaccines under consideration, some are either in the preclinical stage or in the clinical stages of development (phase-I, -II, and -III). Even, phase-III trials are being conducted for some repurposed vaccines like Bacillus Calmette–Guérin, polio vaccine, and measles-mumps-rubella. We have highlighted the ongoing clinical trial landscape of the COVID-19 as well as repurposed vaccines. An insight into the current status of the available antigenic epitopes for SARS-CoV-2 and different types of vaccine platforms of COVID-19 vaccines has been discussed. These vaccines are highlighted throughout the world by different news agencies. Moreover, ongoing clinical trials for repurposed vaccines for COVID-19 and critical factors associated with the development of COVID-19 vaccines have also been described.
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Mallick B, Ranjan Sharma A, Bhattacharya M, Lee SS, Chakraborty C. PPARγ LBD and its ligand specificity reveal a selection of potential partial agonist: Molecular dynamics based T2D drug discovery initiative. BIOCELL 2021. [DOI: 10.32604/biocell.2021.015530] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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Patra P, Bhattacharya M, Sharma AR, Ghosh P, Sharma G, Patra BC, Mallick B, Lee SS, Chakraborty C. Identification and Design of a Next-Generation Multi Epitopes Bases Peptide Vaccine Candidate Against Prostate Cancer: An In Silico Approach. Cell Biochem Biophys 2020; 78:495-509. [PMID: 32347457 DOI: 10.1007/s12013-020-00912-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2020] [Accepted: 04/07/2020] [Indexed: 12/28/2022]
Abstract
Prostate cancer (PCa) is the second most diagnosed cancer in men and ranked fifth in overall cancer diagnosis. During the past decades, it has arisen as a significant life-threatening disease in men at an older age. At the early onset of illness when it is in localized form, radiation and surgical treatments are applied against this disease. In case of adverse situations androgen deprivation therapy, chemotherapy, hormonal therapy, etc. are widely used as a therapeutic element. However, studies found the occurrences of several side effects after applying these therapies. In current work, several immunoinformatic techniques were applied to formulate a multi-epitopic vaccine from the overexpressed antigenic proteins of PCa. A total of 13 epitopes were identified from the five prostatic antigenic proteins (PSA, PSMA, PSCA, STEAP, and PAP), after validation with several in silico tools. These epitopes were fused to form a vaccine element by (GGGGS)3 peptide linker. Afterward, 5, 6-dimethylxanthenone-4-acetic acid (DMXAA) was used as an adjuvant to initiate and induce STING-mediated cytotoxic cascade. In addition, molecular docking was performed between the vaccine element and HLA class I antigen with the low ACE value of -251 kcal/mol which showed a significant binding. Molecular simulation using normal mode analysis (NMA) illustrated the docking complex as a stable one. Therefore, this observation strongly indicated that our multi epitopes bases peptide vaccine molecule will be an effective candidate for the treatment of the PCa.
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Chakraborty C, Sharma AR, Bhattacharya M, Sharma G, Agoramoorthy G, Lee SS. Diabetes and COVID-19: a major challenge in pandemic period? EUROPEAN REVIEW FOR MEDICAL AND PHARMACOLOGICAL SCIENCES 2020; 24:11409-11420. [PMID: 33215463 DOI: 10.26355/eurrev_202011_23634] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
OBJECTIVE Diabetes is a lifestyle disease and it has become an epidemic worldwide in recent decades. In the ongoing COVID-19 pandemic situation, diabetes has become a serious health concern since large numbers of patients are vulnerable to die from the virus. Thus, diabetic patients affected by COVID-19 cause a major health crisis now. Reports show that large occurrence of diabetes makes it a serious comorbidity in COVID-19 patients. MATERIALS AND METHODS It is crucial to understand how COVID-19 affects diabetes patients. This paper has reviewed published literature extensively to understand the pattern, importance, care, and medication. RESULTS This review summarizes the association between COVID-19 and diabetes in terms of susceptibility for pneumonia and other diseases. It also discusses the harshness of COVID-19 with diabetes populations and immunological impacts. It further adds the ACE2 receptor role in diabetes with COVID-19 patients. CONCLUSIONS Finally, this paper illustrates different types of diabetes management techniques, such as blood glucose management, self-management, mental health management, and therapeutic management. It also summarizes the current knowledge about diabetic patients with COVID-19 to fight this pandemic.
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Das NC, Patra R, Gupta PSS, Ghosh P, Bhattacharya M, Rana MK, Mukherjee S. Designing of a novel multi-epitope peptide based vaccine against Brugia malayi: An in silico approach. INFECTION GENETICS AND EVOLUTION 2020; 87:104633. [PMID: 33181335 DOI: 10.1016/j.meegid.2020.104633] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2020] [Revised: 10/18/2020] [Accepted: 11/06/2020] [Indexed: 01/19/2023]
Abstract
In spite of the tremendous efforts of the World Health Organization, scientific and medical community to eradicate lymphatic filariasis (LF) within 2020, the disease is still taking a huge toll on mankind throughout the globe. The current therapeutic strategies and solution measures against this alarming condition are suffering from a number of limitations such as inadequate effectiveness of the drugs against the adult-stage parasites, low bioavailability, and emergence of resistance. Considering this situation, development of the new therapeutics are urgently needed to combat human LF, especially targeting the adult filarial nematodes. Brugia malayi, the causative parasite for the human brugian filariasis majorly found in the countries of the South-Asia. In this study, we have designed a vaccine candidate using B-cell and T-cell epitopes derived from the aspartic protease of B. malayi (BmASP-1) and found to display significant humoral and cell mediated immune responses using in-silico approaches. Protein-protein docking between the human Toll-like receptor 4 (TLR4) and the vaccine candidate helped us to predict the way of inductive signaling that leads to immune-response. Molecular dynamics (MD) simulation studies further confirmed the proper docking between the TLR4 and vaccine candidate. Moreover, in-silico cloning of the vaccine element within the expression vector was found useful to optimize the restriction sites as well as to determine the primer location. Taken together, the in-silico vaccine candidate depicted in this study promises could be a useful therapeutic option for treating LF and experimental validation of this study is expected to strengthen the candidature of the said vaccine in the future.
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Bhattacharya M, Sharma AR, Mallick B, Sharma G, Lee SS, Chakraborty C. Immunoinformatics approach to understand molecular interaction between multi-epitopic regions of SARS-CoV-2 spike-protein with TLR4/MD-2 complex. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2020; 85:104587. [PMID: 33039603 PMCID: PMC7543713 DOI: 10.1016/j.meegid.2020.104587] [Citation(s) in RCA: 60] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Revised: 10/02/2020] [Accepted: 10/05/2020] [Indexed: 12/17/2022]
Abstract
BACKGROUND The coronavirus (CoV) spike (S) protein is critical for receptor binding, membrane fusion and internalization of the virus into the human cells. We have tried to search the epitopic component of the S-protein that might be served as crucial targets for the vaccine development and also tried to understand the molecular mechanism of epitopes and TLR4/MD-2 complex for adaptive immunity. MATERIAL AND METHODS Here we identified the antigenicity and the epitopic divergence of S-protein via immunoinformatics approach. The study was performed to identify the epitopes, composition of amino acids and its distribution in epitopic regions, composition of amino acid between the identified epitopes, secondary structure architecture of epitopes, physicochemical and biochemical parameters and molecular interaction between the identified epitope and TLR4/MD-2 complex. The SARS-CoV-2 can be possibly recognised by TLR4 of host immune cells that are responsible for the adaptive immune response. RESULTS We identified four SARS-CoV-2 S-protein 9mer antigenic epitopes and observed that they bind with the TLR4/MD-2 complex by varied stable molecular bonding interactions. Molecular interaction between these characterized epitopes with TLR4/MD-2 complex might be indicated the binding affinity and downstream signalling of adaptive immune response. Different physicochemical and biochemical parameters such as O-glycosylation and N-glycosylation, Hydrophobicity, GRAVY were identified within epitopic regions of S-protein. These parameters help to understand the protein-protein interaction between epitopes and TLR4/MD-2 complex. The study also revealed different epitopic binding pockets of TLR4/MD-2 complex. CONCLUSIONS The identified epitopes impart suitable prospects for the development of novel peptide-based epitopic vaccine for the control of COVID-19 infection.
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Saha A, Sharma AR, Bhattacharya M, Sharma G, Lee SS, Chakraborty C. Response to: Status of Remdesivir: Not Yet Beyond Question! Arch Med Res 2020; 52:104-106. [PMID: 32948379 PMCID: PMC7492007 DOI: 10.1016/j.arcmed.2020.09.005] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Accepted: 09/04/2020] [Indexed: 01/29/2023]
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Saha RP, Sharma AR, Singh MK, Samanta S, Bhakta S, Mandal S, Bhattacharya M, Lee SS, Chakraborty C. Repurposing Drugs, Ongoing Vaccine, and New Therapeutic Development Initiatives Against COVID-19. Front Pharmacol 2020; 11:1258. [PMID: 32973505 PMCID: PMC7466451 DOI: 10.3389/fphar.2020.01258] [Citation(s) in RCA: 75] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2020] [Accepted: 07/30/2020] [Indexed: 12/15/2022] Open
Abstract
As the COVID-19 is still growing throughout the globe, a thorough investigation into the specific immunopathology of SARS-CoV-2, its interaction with the host immune system and pathogen evasion mechanism may provide a clear picture of how the pathogen can breach the host immune defenses in elderly patients and patients with comorbid conditions. Such studies will also reveal the underlying mechanism of how children and young patients can withstand the disease better. The study of the immune defense mechanisms and the prolonged immune memory from patients population with convalescent plasma may help in designing a suitable vaccine candidate not only for the current outbreak but also for similar outbreaks in the future. The vital drug candidates, which are being tested as potential vaccines or therapeutics against COVID-19, include live attenuated vaccine, inactivated or killed vaccine, subunit vaccine, antibodies, interferon treatment, repurposing existing drugs, and nucleic acid-based vaccines. Several organizations around the world have fast-tracked the development of a COVID-19 vaccine, and some drugs already went to phase III of clinical trials. Hence, here, we have tried to take a quick glimpse of the development stages of vaccines or therapeutic approaches to treat this deadly disease.
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Saha A, Sharma AR, Bhattacharya M, Sharma G, Lee SS, Chakraborty C. Tocilizumab: A Therapeutic Option for the Treatment of Cytokine Storm Syndrome in COVID-19. Arch Med Res 2020; 51:595-597. [PMID: 32482373 PMCID: PMC7241374 DOI: 10.1016/j.arcmed.2020.05.009] [Citation(s) in RCA: 69] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Accepted: 05/15/2020] [Indexed: 02/06/2023]
Abstract
Presently, we need more therapeutic molecules for this COVID-19 outbreak. The severity and mortality of the disease is associated with a high level of release of cytokine in the patients which is known as CRS (cytokine release syndrome) or cytokine storm syndrome. IL-6 is a type of pro-inflammatory cytokine which release in the severe COVID-19 patients. This cytokine initiates CRS the JAK-STAT or MAPK/NF-κB-IL-6 pathway. Tocilizumab, a humanized monoclonal antibody, is designed to bind both mIL-6R (membrane bound receptor for IL-6) and sIL-6R (soluble receptor for IL-6) and inhibit the JAK-STAT or MAPK/NF-κB-IL-6 signaling pathway. It finally stops the cytokine storm syndrome. However, we need to understand that how tocilizumab is bound with mIL-6R or sIL-6R. Similarly, we also need to understand more about the real molecular mechanism of activity of tocilizumab.
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Bhattacharya M, Sharma AR, Patra P, Ghosh P, Sharma G, Patra BC, Saha RP, Lee SS, Chakraborty C. A SARS-CoV-2 vaccine candidate: In-silico cloning and validation. INFORMATICS IN MEDICINE UNLOCKED 2020; 20:100394. [PMID: 32835079 PMCID: PMC7361115 DOI: 10.1016/j.imu.2020.100394] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Revised: 07/05/2020] [Accepted: 07/05/2020] [Indexed: 01/12/2023] Open
Abstract
SARS-CoV-2 is spreading globally at a rapid pace. To contain its spread and prevent further fatalities, the development of a vaccine against SARS-CoV-2 is an urgent prerequisite. Thus, in this article, by utilizing the in-silico approach, a vaccine candidate for SARS-CoV-2 has been proposed. Moreover, the effectiveness and safety measures of our proposed epitopic vaccine candidate have been evaluated by in-silico tools and servers (AllerTOP and AllergenFP servers). We observed that the vaccine candidate has no allergenicity and successfully combined with Toll-like receptor (TLR) protein to elicit an inflammatory immune response. Stable, functional mobility of the vaccine-TLR protein binding interface was confirmed by the Normal Mode Analysis. The in-silico cloning model demonstrated the efficacy of the construct vaccine along with the identified epitopes against SARS-CoV-2. Taken together, our proposed in-silico vaccine candidate has potent efficacy against COVID-19 infection, and successive research work might validate its effectiveness in in vitro and in vivo models.
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Chakraborty C, Sharma AR, Bhattacharya M, Sharma G, Lee SS, Agoramoorthy G. COVID-19: Consider IL-6 receptor antagonist for the therapy of cytokine storm syndrome in SARS-CoV-2 infected patients. J Med Virol 2020; 92:2260-2262. [PMID: 32462717 PMCID: PMC7283789 DOI: 10.1002/jmv.26078] [Citation(s) in RCA: 53] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2020] [Accepted: 05/26/2020] [Indexed: 12/12/2022]
Abstract
COVID‐19 leads to mortality of several patients and the cytokine storm is reportedly critical in the patients. To reduce the cytokine storm, we would like to propose the interleukin (IL) 6 receptor (IL‐6R) antagonist therapy for the COVID‐19 patients. Two humanized monoclonal antibodies are in clinical trial following IL‐6R antagonist therapies namely tocilizumab and sarilumab. However, researchers and physicians should look for more IL‐6R antagonists for the therapy of cytokine storm syndrome severe acute respiratory syndrome coronavirus 2 infected persons to enhance the therapeutic options for cytokine storm. Cytokine storm syndrome or cytokine release syndrome (CRS) is often observed in severe COVID‐19 patients. CRS may be the leading cause of the deaths of severe COVID‐19 patients. IL6 receptor antagonist molecules may be helpful for the therapy for containing CRS. Two humanized monoclonal antibodies (IL6 receptor antagonists), namely, tocilizumab and sarilumab, are in the clinical trials for the treatment of CRS of COVID‐19 patients.
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Chakraborty C, Sharma AR, Sharma G, Bhattacharya M, Saha RP, Lee SS. Extensive Partnership, Collaboration, and Teamwork is Required to Stop the COVID-19 Outbreak. Arch Med Res 2020; 51:728-730. [PMID: 32532523 PMCID: PMC7260497 DOI: 10.1016/j.arcmed.2020.05.021] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Accepted: 05/26/2020] [Indexed: 12/13/2022]
Abstract
The COVID-19 outbreak is a disaster now throughout the world. To stop this outbreak, we appeal through the paper for extensive partnership, collaboration and teamwork among the all levels of workers such as scientist, doctors, medical professionals, social workers, policy makers, governments, pharmaceutical firms, funding aid agencies to stop the pandemic immediately.
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Chakraborty C, Sharma AR, Bhattacharya M, Sharma G, Lee SS, Agoramoorthy G. Consider TLR5 for new therapeutic development against COVID-19. J Med Virol 2020; 92:2314-2315. [PMID: 32391920 PMCID: PMC7272826 DOI: 10.1002/jmv.25997] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Revised: 05/07/2020] [Accepted: 05/08/2020] [Indexed: 12/16/2022]
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