scholarly journals In silico approach for designing of a multi-epitope based vaccine against novel Coronavirus (SARS-COV-2)

2020 ◽  
Author(s):  
Ratnadeep Saha ◽  
Burra V L S Prasad
Keyword(s):  
Immune Responses ◽  
In Silico ◽  
Tertiary Structure ◽  
Preventive Measure ◽  
Docking Studies ◽  
T Cell Epitopes ◽  
Mhc I ◽  
Host Immune Responses ◽  
Global Pandemic ◽  
Novel Coronavirus

AbstractA novel Coronavirus (SARS-COV-2) has now become a global pandemic. Considering the severity of infection and the associated mortalities, there is an urgent need to develop an effective preventive measure against this virus. In this study, we have designed a novel vaccine construct using computational strategies. Spike (S) glycoprotein is the major antigenic component that trigger the host immune responses. Detailed investigation of S protein with various immunoinformatics tools enabled us to identify 5 MHC I and 5 MHC II B-cell derived T-cell epitopes with VaxiJen score > 1 and IC50 value < 100nM. These epitopes were joined with a suitable adjuvant and appropriate linkers to form a multi-epitope based vaccine construct. Further, in silico testing of the vaccine construct for its antigenicity, allergenicity, solubility, and other physicochemical properties showed it to be safe and immunogenic. Suitable tertiary structure of the vaccine protein was generated using 3Dpro of SCRATCH suite, refined with GalaxyRefine, and validated with ProSA, PROCHECK, and ERRAT server. Finally, molecular docking studies were performed to ensure a favorable binding affinity between the vaccine construct and TLR3 receptor. The designed multi-epitope vaccine showed potential to elicit specific immune responses against the SARS-COV-2. However, further wet lab validation is necessary to confirm the actual effectiveness, safety and immunogenic potency of the vaccine construct against derived in this study.

In silico approach for designing a novel recombinant fusion protein as a Candidate Vaccine against HPV

2020 ◽  
Vol 17 ◽  
Author(s):  
Mohsen Sisakht ◽  
Amir Mahmoodzadeh ◽  
Mohammadsaeid Zahedi ◽  
Davood Rostamzadeh ◽  
Amin Moradi Hasan-Abad ◽  
...  
Keyword(s):  
Immune Responses ◽  
Fusion Protein ◽  
In Silico ◽  
Precancerous Lesions ◽  
Candidate Vaccine ◽  
T Cell Epitopes ◽  
Binding Interaction ◽  
Hpv16 E6 ◽  
E7 Proteins

Background: Human papillomavirus (HPV) is the main biological agent causing sexually transmitted diseases (STDs), including precancerous lesions and several types of prevalent cancers. To date, numerous types of vaccines are designed to prevent high-risk HPV. However, their prophylactic effect is not the same and does not clear previous infections. Therefore, there is an urgent need for developing therapeutic vaccines that trigger cell-mediated immune responses for the treatment of HPV. The HPV16 E6 and E7 proteins are ideal targets for vaccine therapy against HPV. Fusion protein vaccines, which include both immunogenic interest protein and an adjuvant for augmenting the immunogenicity effects, are theoretically capable of guarantee the power of the immune system against HPV. Method: A vaccine construct, including HPV16 E6/E7 proteins along with a heat shock protein GP96 (E6/E7-NTGP96 construct), was designed using in silico methods. By the aid of the SWISS-MODEL server, the optimal 3D model of the designed vaccine was selected, followed by physicochemical and molecular parameters were performed using bioinformatics tools. Docking studies were done to evaluate the binding interaction of the vaccine. Allergenicity, immunogenicity, B, and T cell epitopes of the designed construct were predicted. Results: Immunological and structural computational results illustrated that our designed construct is potentially proper for stimulation of cellular and humoral immune responses against HPV. Conclusion: Computational studies showed that the E6/E7-NTGP96 construct is a promising candidate vaccine that needs further in vitro and in vivo evaluations.

Screening of phytochemicals from Curcuma longa for their inhibitory activity on SARS-CoV-2: An in-silico study

2021 ◽  
Vol 19 ◽  
Author(s):  
Preeya Negi ◽  
Lalita Das ◽  
Surya Prakash ◽  
Vaishali M. Patil
Keyword(s):  
Drug Discovery ◽  
In Silico ◽  
Curcuma Longa ◽  
Docking Studies ◽  
Primary Objective ◽  
In Silico Screening ◽  
Rational Drug ◽  
In Silico Study ◽  
Speed Up ◽  
Novel Coronavirus

Introduction: Natural products or phytochemicals have always been useful as effective therapeutics and for providing the lead for rational drug discovery approaches specific to anti-viral therapeutics. Methods: The ongoing pandemic caused by novel coronavirus has created a demand for effective therapeutics. Thus, to achieve the primary objective to search for effective anti-viral therapeutics, in silico screening of phytochemicals present in Curcuma longa extract (ex. Curcumin) has been planned. Results: The present work involves the evaluation of ADME properties and molecular docking studies. Conclusion: The application of rationalized drug discovery approaches to screen the diverse natural resources will speed up the anti-COVID drug discovery efforts and benefit the global community.

scholarly journals Candidate targets for immune responses to 2019-Novel Coronavirus (nCoV): sequence homology- and bioinformatic-based predictions

2020 ◽  
Author(s):  
Alba Grifoni ◽  
John Sidney ◽  
Yun Zhang ◽  
Richard H Scheuermann ◽  
Bjoern Peters ◽  
...  
Keyword(s):  
Immune Responses ◽  
Sequence Similarity ◽  
Rapid Expansion ◽  
Immune Recognition ◽  
T Cell Epitopes ◽  
High Sequence Similarity ◽  
Essential Information ◽  
Viral Spread ◽  
Recent Emergence ◽  
Novel Coronavirus

ABSTRACTEffective countermeasures against the recent emergence and rapid expansion of the 2019-Novel Coronavirus (2019-nCoV) require the development of data and tools to understand and monitor viral spread and immune responses. However, little information about the targets of immune responses to 2019-nCoV is available. We used the Immune Epitope Database and Analysis Resource (IEDB) resource to catalog available data related to other coronaviruses, including SARS-CoV, which has high sequence similarity to 2019-nCoV, and is the best-characterized coronavirus in terms of epitope responses. We identified multiple specific regions in 2019-nCoV that have high homology to SARS virus. Parallel bionformatic predictions identified a priori potential B and T cell epitopes for 2019-nCoV. The independent identification of the same regions using two approaches reflects the high probability that these regions are targets for immune recognition of 2019-nCoV.ONE SENTENCE SUMMARYWe identified potential targets for immune responses to 2019-nCoV and provide essential information for understanding human immune responses to this virus and evaluation of diagnostic and vaccine candidates.

scholarly journals Myths versus Truths regarding the Novel Coronavirus Disease (COVID-2019) Outbreak

2020 ◽  
Vol 3 (1) ◽  
Author(s):  
Kapil Amgain ◽  
Sujana Neupane ◽  
Laxmi Panthi ◽  
Pooja Thapaliya
Keyword(s):  
Social Distance ◽  
Virus Disease ◽  
Rna Virus ◽  
Preventive Measure ◽  
Living Organism ◽  
Viral Disease ◽  
The Body ◽  
Global Public Health ◽  
Global Pandemic ◽  
Novel Coronavirus

Background: The Corona Virus Disease (COVID-19) is a novel infectious disease caused by the COVID-19 Virus. This virus belongs to the family of SARS (Severe Acute Respiratory Syndrome) and classified as SARS-CoV-2, a positive-sense single-stranded RNA virus that is causing an ongoing global pandemic. The outbreak of this novel Coronavirus (nCoV-19) is causing great fear in public due to its rapid spread over 200 countries worldwide and created a global Public Health Emergency. The virus is an intracellular obligatory parasite that can even infect bacteria called Bacteriophage. Unlike Bacteria, Virus is not a living microorganism and can’t multiply in the outer environment. If we draw a line in between the living and non-living, it lies in the border3. However, the peculiar characteristic of the virus is that it can be living after entering the body of the living organism, causing harmful effects. Since it behaves like dust or dirt outside of our body, it is better to wash them out and prevent it to enter our bodies. In this way, the best way of prevention of this novel COVID-19 viral disease is to wash it out from our hand, rather than killing it by using a disinfectant, hand sanitizer, alcohol-based rub, etc. Key Message: Don’t Get the Virus, Don’t Give the Virus. Since COVID-19 Virus can enter the body from the reservoir mainly through respiratory droplets during coughing, keeping social distance and proper hand-washing are the best way to preventive measure. To prevent the rapid spreading of COVID-19, please strictly follow the following five precautionary and preventive measures yourself and ask others too. HANDS – wash them often with soap and water ELBOW – cough into it FACE – don’t touch it SPACE – keep social distance (> 3feets) FEEL SICK? - Stay home (with proper nursing care)

scholarly journals Attenuated Subcomponent Vaccine Design Targeting the SARS-CoV-2 Nucleocapsid Phosphoprotein RNA Binding Domain: In silico analysis

2020 ◽  
Author(s):  
Onyeka S. Chukwudozie ◽  
Rebecca C. Chukwuanukwu ◽  
Iroanya O. Onyekachi ◽  
Eze M. Daniel ◽  
Duru C. Vincent ◽  
...  
Keyword(s):  
T Cell ◽  
In Silico ◽  
Rna Binding ◽  
Peptide Vaccine ◽  
In Silico Analysis ◽  
Dynamics Simulation ◽  
Effective Vaccine ◽  
Translation Efficiency ◽  
T Cell Epitopes ◽  
Mhc I

ABSTRACTThe novel coronavirus disease (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has previously never been identified with humans, thereby creating devastation in public health. The need for an effective vaccine to curb this pandemic cannot be overemphasized. In view of this, we, therefore, designed a subcomponent antigenic peptide vaccine targeting the N-terminal (NT) and C-terminal (CT) RNA binding domains of nucleocapsid protein that aid in viral replication. Promising antigenic B-cells and T cell epitopes were predicted using computational pipelines. The peptides “RIRGGDGKMKDL” and “AFGRRGPEQTQGNFG” were the B cell linear epitopes with good antigenic index and non-allergenic property. Two CD8+ and Three CD4+ T-cell epitopes were also selected considering their safe immunogenic profiling such as allergenicity, antigen level conservancy, antigenicity, peptide toxicity, and putative restrictions to a number of MHC-I and II alleles. With these selected epitopes, a non-allergenic chimeric peptide vaccine incapable of inducing a Type II hypersensitivity reaction was constructed. The molecular interaction between the toll-like receptor-5 (TLR5) which was triggered by the vaccine was analyzed by molecular docking and scrutinized using dynamics simulation. Finally, in silico cloning was performed to ensure the expression and translation efficiency of the vaccine, utilizing pET-28a vector. This research, therefore, provides a guide for experimental investigation and validation.

scholarly journals SeXX and COVID-19: Tussle between the Two

2020 ◽  
Author(s):  
Ashlesh Patil ◽  
Jaya Prasad Tripathy ◽  
Vishwajit Deshmukh ◽  
Bharat Sontakke ◽  
Satyendra C. Tripathi
Keyword(s):  
Immune Responses ◽  
Current Knowledge ◽  
Occupational Exposures ◽  
Point Of View ◽  
Host Immune Responses ◽  
Social Inequities ◽  
Biological Explanation ◽  
Novel Coronavirus ◽  
Biological Differences

Novel coronavirus disease (COVID-19) has affected nearly 7 million individuals and claimed more than 0.4 million lives to date. There are several reports of gender differences related to infection and death due to COVID-19. This raises important questions such as &ldquo;Whether there are differences based on gender in risk and severity of infection or mortality rate?&rdquo; and &ldquo;What are the biological explanation and mechanisms underlying these differences?&rdquo; Emerging evidence has proposed sex-based immunological, genetic, and hormonal differences to explain this ambiguity. Besides biological differences, women have also faced social inequities and economic hardships due to this pandemic. Several recent studies have shown that independent of age males are at higher risk for severity and mortality in COVID-19 patients. Although susceptibility to SARS-CoV-2 was found to be similar across both genders in several disease cohorts, a disproportionate death ratio in men can be partly explained by the higher burden of pre-existing diseases and occupational exposures among men. From an immunological point of view, females can engage a more active immune response, which may protect them and counter infectious diseases as compared to men. This attribute of better immune responses towards pathogens is thought to be due to high estrogen levels in females. Here we review the current knowledge about sex differences in susceptibility, the severity of infection and mortality, host immune responses, and the role of sex hormones in COVID-19 disease.

scholarly journals An Integrated In-Silico Approach to Develop Epitope-Based Peptide Vaccine against SARS-CoV-2

2020 ◽  
Author(s):  
Prekshi Garg ◽  
Neha Srivastava ◽  
Prachi Srivastava
Keyword(s):  
T Cell ◽  
B Cell ◽  
In Silico ◽  
3D Structure ◽  
Peptide Vaccine ◽  
Cell Epitope ◽  
Peptide Sequence ◽  
T Cell Epitopes ◽  
Mhc I ◽  
In Silico Study

SARS-CoV-2 has been the talk of the town ever since the beginning of 2020. The pandemic has brought the complete world on a halt. Every country is trying all possible steps to combat the disease ranging from shutting the complete economy of the country to repurposing of drugs and vaccine development. The rapid data analysis and widespread tools, software and databases have made bioinformatics capable of giving new insights to the researchers to deal with the current scenario more efficiently. Vaccinomics, the new emerging field of bioinformatics uses concepts of immunogenetics and immunogenomics with in silico tools to give promising results for wet lab experiments. This approach is highly validated for the designing and development of potent vaccines. The present in-silico study was attempted to identify peptide fragments from spike surface glycoprotein that can be efficiently used for the designing and development of epitope-based vaccine designing approach. Both B-cell and T-cell epitopes are predicted using integrated computational tools. VaxiJen server was used for prediction of protective antigenicity of the protein. NetCTL was studied for analyzing most potent T cell epitopes and its subsequent MHC-I interaction through tools provided by IEDB. 3D structure prediction of peptides and MHC-I alleles (HLA-C*03:03) was further done to carry out docking studies using AutoDock4.0. Various tools from IEDB were used to predict B-cell epitopes on the basis of different essential parameters like surface accessibility, beta turns and many more. Based on results interpretation, the peptide sequence from 1138-1145 amino acid and sequence WTAGAAAYY and YDPLQPEL were obtained as a potential B-cell epitope and T-cell epitope respectively. This in-silico study will help us to identify novel epitope-based peptide vaccine target in spike protein of SARS-CoV-2. Further, in-vitro and in-vivo study needed to validate the findings.

scholarly journals Targeting “Immunogenic Hotspots” in Dengue and Zika Virus:  A Novel Approach to a Common Vaccine

2021 ◽  
Author(s):  
Dhrubajyoti Mahata ◽  
Debangshu Mukherjee ◽  
Vanshika Malviya ◽  
Gayatri Mukherjee
Keyword(s):  
Immune Responses ◽  
B Cell ◽  
Sequence Similarity ◽  
Docking Studies ◽  
T Cell Epitopes ◽  
Biophysical Parameters ◽  
High Sequence Similarity ◽  
B Cell Epitopes ◽  
Denv Serotypes ◽  
Novel Approach

Diseases caused by Dengue (DENV) and Zika (ZIKV) viruses cause significant mortality and illness globally. Due to the high sequence similarity of the viral proteins and the purported cross-reactive immune responses against the viruses, we envisioned a common multi-epitope vaccine (MEV) against both viruses by adopting a novel approach of identifying “immunogenic hotspots”. These stretches of the structural and non-structural proteins are enriched with MHC class I and class II supertype-restricted T cell epitopes, and B cell epitopes, in addition to being highly conserved between different DENV serotypes and ZIKV. Such an approach ensures inclusion of multiple overlapping T and B cell epitopes common to both viruses, and also warrants high population coverage. Importantly, epitopes known to cause antibody-dependent-enhancement of infection have been excluded. These immunogenic hotspots have then been stitched together with linkers in-silico along with an adjuvant, CTxB to develop the MEV candidate. Four structural models of the MEV were selected on the basis of conformational preservation of CTxB, and their biophysical parameters, which also conserved the immunogenicity of the multiple epitopes. Importantly, each of the MEV candidates were found to interact with TLR4-MD2 complex by molecular docking studies, indicative of their ability to induce TLR-mediated immune responses.

scholarly journals Mini-Review: SARS-CoV-2 and COVID-19

2021 ◽  
pp. 7-13
Keyword(s):  
Immune Responses ◽  
International Committee ◽  
Unknown Etiology ◽  
Study Group ◽  
Wuhan City ◽  
Angiotensin Converting Enzyme 2 ◽  
Host Immune Responses ◽  
Worldwide Distribution ◽  
Close Relationship ◽  
Novel Coronavirus

On 31 December 2019, the cases of pneumonia caused by unknown etiology had emerged. These cases were reported in Wuhan city, Hubei Province of China. Chinese authorities identified the causative agent and announced to be a novel coronavirus. The tentative name of disease is COVID-19, abbreviating of coronavirus disease-19. The incubation period of the disease ranges from 2 to 14 days, however, 80% of the patients have mild or asymptomatic illness while 15 % and 5% of the patients had exhibited sever and critical cases respectively. The etiology of COVID-19 was known as SARS-CoV-2 and belongs to betacoranviruse as reported by the International Committee on Taxonomy of Viruses (ICTV) especially Coronaviridae Study Group (CSG). In addition, this virus is currently believed to be within bat-coronaviruses besides it possesses a close relationship with SARS-CoV more than MERS-CoV. Although, the majority of the diagnosed patients had symptoms, there were asymptomatic persons who can spread the SARS-CoV-2. Upon the emergence of worldwide distribution of this virus, the WHO had declared it as a global outbreak and pandemic. Unfortunately, at present time, there are neither vaccine and nor an approved COVID-19 specific drug against SARS-CoV-2. One of the remarkable pathogenesis mechanistic step of this virus is taking possession of the affinity to angiotensin-converting enzyme 2 (ACE2). This mini-review summarizes the origin and molecular identification of the virus as well as the host immune responses. SARS-CoV-2 , COVID-19, ACE2, origin

scholarly journals A Putative Prophylactic Solution for COVID-19: Development of Novel Multiepitope Vaccine Candidate against SARS-COV-2 by Comprehensive Immunoinformatic and Molecular Modelling Approach

Biology ◽  
2020 ◽  
Vol 9 (9) ◽  
pp. 296
Author(s):  
Hafiz Muzzammel Rehman ◽  
Muhammad Usman Mirza ◽  
Mian Azhar Ahmad ◽  
Mahjabeen Saleem ◽  
Matheus Froeyen ◽  
...  
Keyword(s):  
Molecular Modelling ◽  
In Silico ◽  
Vaccine Development ◽  
Adaptive Immune Response ◽  
World Health ◽  
Vector System ◽  
T Cell Epitopes ◽  
Novel Coronavirus ◽  
Health Organization ◽  
Dynamics Simulations

The outbreak of 2019-novel coronavirus (SARS-CoV-2) that causes severe respiratory infection (COVID-19) has spread in China, and the World Health Organization has declared it a pandemic. However, no approved drug or vaccines are available, and treatment is mainly supportive and through a few repurposed drugs. The urgency of the situation requires the development of SARS-CoV-2-based vaccines. Immunoinformatic and molecular modelling are time-efficient methods that are generally used to accelerate the discovery and design of the candidate peptides for vaccine development. In recent years, the use of multiepitope vaccines has proved to be a promising immunization strategy against viruses and pathogens, thus inducing more comprehensive protective immunity. The current study demonstrated a comprehensive in silico strategy to design stable multiepitope vaccine construct (MVC) from B-cell and T-cell epitopes of essential SARS-CoV-2 proteins with the help of adjuvants and linkers. The integrated molecular dynamics simulations analysis revealed the stability of MVC and its interaction with human Toll-like receptors (TLRs), which trigger an innate and adaptive immune response. Later, the in silico cloning in a known pET28a vector system also estimated the possibility of MVC expression in Escherichia coli. Despite that this study lacks validation of this vaccine construct in terms of its efficacy, the current integrated strategy encompasses the initial multiple epitope vaccine design concepts. After validation, this MVC can be present as a better prophylactic solution against COVID-19.

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