scholarly journals In silico trial to test COVID-19 candidate vaccines: a case study with UISS platform

2020 ◽  
Vol 21 (S17) ◽  
Author(s):  
Giulia Russo ◽  
Marzio Pennisi ◽  
Epifanio Fichera ◽  
Santo Motta ◽  
Giuseppina Raciti ◽  
...  
Keyword(s):  
Immune System ◽  
In Silico ◽  
Vaccination Strategy ◽  
Therapeutic Interventions ◽  
Effective Vaccine ◽  
Potential Candidate ◽  
Suggested Approach ◽  
Speed Up ◽  
Severe Respiratory Infection ◽  
Discovery Pipeline

Abstract Background SARS-CoV-2 is a severe respiratory infection that infects humans. Its outburst entitled it as a pandemic emergence. To get a grip on this outbreak, specific preventive and therapeutic interventions are urgently needed. It must be said that, until now, there are no existing vaccines for coronaviruses. To promptly and rapidly respond to pandemic events, the application of in silico trials can be used for designing and testing medicines against SARS-CoV-2 and speed-up the vaccine discovery pipeline, predicting any therapeutic failure and minimizing undesired effects. Results We present an in silico platform that showed to be in very good agreement with the latest literature in predicting SARS-CoV-2 dynamics and related immune system host response. Moreover, it has been used to predict the outcome of one of the latest suggested approach to design an effective vaccine, based on monoclonal antibody. Universal Immune System Simulator (UISS) in silico platform is potentially ready to be used as an in silico trial platform to predict the outcome of vaccination strategy against SARS-CoV-2. Conclusions In silico trials are showing to be powerful weapons in predicting immune responses of potential candidate vaccines. Here, UISS has been extended to be used as an in silico trial platform to speed-up and drive the discovery pipeline of vaccine against SARS-CoV-2.

scholarly journals In Silico Trial to test COVID-19 candidate vaccines: a case study with UISS platform

2020 ◽  
Author(s):  
Giulia Russo ◽  
Marzio Pennisi ◽  
Marco Viceconti ◽  
Francesco Pappalardo
Keyword(s):  
Immune System ◽  
In Silico ◽  
Vaccination Strategy ◽  
Therapeutic Interventions ◽  
Effective Vaccine ◽  
Suggested Approach ◽  
Speed Up ◽  
Severe Respiratory Infection ◽  
Good Agreement

AbstractSARS-CoV-2 is a severe respiratory infection that infects humans. Its outburst entitled it as a pandemic emergence. To get a grip on this outbreak, specific preventive and therapeutic interventions are urgently needed. It must be said that, until now, there are no existing vaccines for coronaviruses. To promptly and rapidly respond to pandemic events, the application of in silico trials can be used for designing and testing medicines against SARS-CoV-2 and speed-up the vaccine discovery pipeline, predicting any therapeutic failure and minimizing undesired effects. Here, we present an in silico platform that showed to be in very good agreement with the latest literature in predicting SARS-CoV-2 dynamics and related immune system host response. Moreover, it has been used to predict the outcome of one of the latest suggested approach to design an effective vaccine, based on monoclonal antibody. Universal Immune System Simulator (UISS) in silico platform is potentially ready to be used as an in silico trial platform to predict the outcome of vaccination strategy against SARS-CoV-2.

scholarly journals Designing of a next generation multiepitope based vaccine (MEV) against SARS-COV-2: Immunoinformatics and in silico approaches

PLoS ONE ◽  
2020 ◽  
Vol 15 (12) ◽  
pp. e0244176
Author(s):  
Muhammad Tahir ul Qamar ◽  
Abdur Rehman ◽  
Kishver Tusleem ◽  
Usman Ali Ashfaq ◽  
Muhammad Qasim ◽  
...  
Keyword(s):  
Mhc Class Ii ◽  
In Silico ◽  
Md Simulation ◽  
Effective Vaccine ◽  
Potential Candidate ◽  
Health Security ◽  
Antigenic Proteins ◽  
Hla Binding ◽  
K 12 ◽  
Respiratory Coronavirus

Coronavirus disease 2019 (COVID-19) pandemic caused by severe acute respiratory coronavirus 2 (SARS-COV-2) is a significant threat to global health security. Till date, no completely effective drug or vaccine is available to cure COVID-19. Therefore, an effective vaccine against SARS-COV-2 is crucially needed. This study was conducted to design an effective multiepitope based vaccine (MEV) against SARS-COV-2. Seven highly antigenic proteins of SARS-COV-2 were selected as targets and different epitopes (B-cell and T-cell) were predicted. Highly antigenic and overlapping epitopes were shortlisted. Selected epitopes indicated significant interactions with the HLA-binding alleles and 99.93% coverage of the world’s population. Hence, 505 amino acids long MEV was designed by connecting 16 MHC class I and eleven MHC class II epitopes with suitable linkers and adjuvant. MEV construct was non-allergenic, antigenic, stable and flexible. Furthermore, molecular docking followed by molecular dynamics (MD) simulation analyses, demonstrated a stable and strong binding affinity of MEV with human pathogenic toll-like receptors (TLR), TLR3 and TLR8. Finally, MEV codons were optimized for its in silico cloning into Escherichia coli K-12 system, to ensure its increased expression. Designed MEV in present study could be a potential candidate for further vaccine production process against COVID-19. However, to ensure its safety and immunogenic profile, the proposed MEV needs to be experimentally validated.

scholarly journals Designing of a next generation multiepitope based vaccine (MEV) against SARS-COV-2: Immunoinformatics and in silico approaches

2020 ◽  
Author(s):  
Muhammad Tahir ul Qamar ◽  
Abdur Rehman ◽  
Usman Ali Ashfaq ◽  
Muhammad Qasim Awan ◽  
Israr Fatima ◽  
...  
Keyword(s):  
Mhc Class Ii ◽  
In Silico ◽  
Simulation Analysis ◽  
Effective Vaccine ◽  
Potential Candidate ◽  
Antigenic Proteins ◽  
Structural Details ◽  
Hla Binding ◽  
K 12 ◽  
Respiratory Coronavirus

AbstractCoronavirus disease 2019 (COVID-19) associated pneumonia caused by severe acute respiratory coronavirus 2 (SARS-COV-2) was first reported in Wuhan, China in December 2019. Till date, no vaccine or completely effective drug is available to cure COVID-19. Therefore, an effective vaccine against SARS-COV-2 is crucially needed. This study was conducted to design an effective multiepitope based vaccine (MEV) against SARS-COV-2. Seven antigenic proteins were taken as targets and different epitopes (B-cell, T-cell and IFN-γ inducing) were predicted. Highly antigenic and overlapping epitopes were shortlisted. Selected epitopes indicated significant interactions with the HLA-binding alleles and 99.29% coverage of the world’s population. Finally, 505 amino acids long MEV was designed by connecting sixteen MHC class I and eleven MHC class II epitopes with suitable linkers and adjuvant. Linkers and adjuvant were added to enhance the immunogenicity response of the MEV. The antigenicity, allergenicity, physiochemical properties and structural details of MEV were analyzed in order to ensure safety and immunogenicity. MEV construct was non-allergenic, antigenic, stable and flexible. Molecular docking followed by molecular dynamics (MD) simulation analysis, demonstrated a stable and strong binding affinity of MEV with human pathogenic toll-like receptors (TLR), TLR3 and TLR8. Codon optimization and in silico cloning of MEV ensured increased expression in the Escherichia coli K-12 system. Designed MEV in present study could be a potential candidate for further vaccine production process against COVID-19. However, to ensure its safety and immunogenic profile, the proposed MEV needs to be experimentally validated.

scholarly journals Identification of Highly Conserved SARS-CoV-2 Antigenic Epitopes with Wide Coverage Using Reverse Vaccinology Approach

Viruses ◽  
2021 ◽  
Vol 13 (5) ◽  
pp. 787
Author(s):  
Yasmin Hisham ◽  
Yaqoub Ashhab ◽  
Sang-Hyun Hwang ◽  
Dong-Eun Kim
Keyword(s):  
Amino Acid ◽  
In Silico ◽  
Vaccine Development ◽  
Emerging Infectious Diseases ◽  
Vaccination Strategy ◽  
Viral Proteins ◽  
Reverse Vaccinology ◽  
Effective Vaccine ◽  
Amino Acid Substitutions ◽  
Time Required

One of the most effective strategies for eliminating new and emerging infectious diseases is effective immunization. The pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) warrants the need for a maximum coverage vaccine. Moreover, mutations that arise within the virus have a significant impact on the vaccination strategy. Here, we built a comprehensive in silico workflow pipeline to identify B-cell- and T-cell-stimulating antigens of SARS-CoV-2 viral proteins. Our in silico reverse vaccinology (RV) approach consisted of two parts: (1) analysis of the selected viral proteins based on annotated cellular location, antigenicity, allele coverage, epitope density, and mutation density and (2) analysis of the various aspects of the epitopes, including antigenicity, allele coverage, IFN-γ induction, toxicity, host homology, and site mutational density. After performing a mutation analysis based on the contemporary mutational amino acid substitutions observed in the viral variants, 13 potential epitopes were selected as subunit vaccine candidates. Despite mutational amino acid substitutions, most epitope sequences were predicted to retain immunogenicity without toxicity and host homology. Our RV approach using an in silico pipeline may potentially reduce the time required for effective vaccine development and can be applicable for vaccine development for other pathogenic diseases as well.

A COVID-19 vaccine—dare to dream

2020 ◽  
Vol 25 (12) ◽  
pp. 2-7
Author(s):  
Alison Phillis
Keyword(s):  
Infection Prevention ◽  
Vaccination Strategy ◽  
Therapeutic Interventions ◽  
Infection Prevention And Control ◽  
Effective Vaccine ◽  
Challenges And Opportunities ◽  
History Of ◽  
Serious Disease ◽  
The Uk ◽  
And Control

The global desire to produce and deploy a safe and effective vaccine to protect against SARS-CoV-2 infection and the morbidity and mortality subsequent to COVID-19 is unprecedented. The unparalleled speed of research development and access to funding is perhaps equally unique in the history of therapeutic achievement. This article, the third in a series of dedicated to exploring the origins and developments of SARS-CoV-2 within the context of the strategies of infection prevention and control, investigates the theatre behind the extraordinary efforts underpinning the research for therapeutic interventions to halt the COVID-19 pandemic. The Chair of the UK Vaccine Taskforce has stated that the exit strategy depends on a vaccine that is effective in reducing mortality, improving population health by reducing serious disease and protecting the NHS and social care system. This article introduces the major COVID-19 vaccine contenders and considers the challenges and opportunities of an effective global vaccination strategy.

scholarly journals Neonatal Immune System Ontogeny: The Role of Maternal Microbiota and Associated Factors. How Might the Non-Human Primate Model Enlighten the Path?

Vaccines ◽  
2021 ◽  
Vol 9 (6) ◽  
pp. 584
Author(s):  
Natalia Nunez ◽  
Louis Réot ◽  
Elisabeth Menu
Keyword(s):  
Immune System ◽  
Mode Of Delivery ◽  
Microbial Colonization ◽  
Therapeutic Interventions ◽  
Primate Model ◽  
Neonatal Immune System ◽  
Gastrointestinal Colonization ◽  
The Impact ◽  
Human Primate

Interactions between the immune system and the microbiome play a crucial role on the human health. These interactions start in the prenatal period and are critical for the maturation of the immune system in newborns and infants. Several factors influence the composition of the infant’s microbiota and subsequently the development of the immune system. They include maternal infection, antibiotic treatment, environmental exposure, mode of delivery, breastfeeding, and food introduction. In this review, we focus on the ontogeny of the immune system and its association to microbial colonization from conception to food diversification. In this context, we give an overview of the mother–fetus interactions during pregnancy, the impact of the time of birth and the mode of delivery, the neonate gastrointestinal colonization and the role of breastfeeding, weaning, and food diversification. We further review the impact of the vaccination on the infant’s microbiota and the reciprocal case. Finally, we discuss several potential therapeutic interventions that might help to improve the newborn and infant’s health and their responses to vaccination. Throughout the review, we underline the main scientific questions that are left to be answered and how the non-human primate model could help enlighten the path.

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.

Therapeutic cancer vaccines: reasons to believe

2021 ◽  
Author(s):  
Jonathan D. Moore
Keyword(s):  
Immune System ◽  
Cancer Vaccines ◽  
Disease Burden ◽  
Checkpoint Inhibitors ◽  
Effective Vaccine ◽  
Antigen Receptors ◽  
Engineered T Cells ◽  
The Right ◽  
Therapeutic Cancer Vaccines

Our hopes of using the power of the immune system to control tumours have been partially fulfilled with anti-PD1 antibodies and other checkpoint inhibitors and the use of engineered T cells targeting lineage-specific surface markers with chimeric antigen receptors. Can these successes be generalised? Therapeutic cancer vaccines aim to educate or re-educate the immune system to recognise tumour specific or tumour associated antigens. After many false dawns, some positive data for the effectiveness of such an approach is starting to emerge in advanced solid tumours, albeit as combination therapies with checkpoint inhibitors. But is the field targeting the right antigens? Interventions using the most effective vaccine platforms to target certain sets of antigens in patients with low disease burden might bring impressive long-term benefits to patients as single agents.

scholarly journals In Silico Prediction of T and B Cell Epitopes of SAG1-Related Sequence 3 (SRS3) Gene for Developing Toxoplasma gondii Vaccine

2020 ◽  
Vol In Press (In Press) ◽  
Author(s):  
Abolfazl Mirzadeh ◽  
Geita Saadatnia ◽  
Majid Golkar ◽  
Jalal Babaie ◽  
Samira Amiri ◽  
...  
Keyword(s):  
Toxoplasma Gondii ◽  
Dna Vaccine ◽  
In Silico ◽  
Effective Vaccine ◽  
T Cell Epitopes ◽  
In Silico Prediction ◽  
Vaccine Strategy ◽  
Related Sequence ◽  
Ideal Tool ◽  
Major Surface

: Toxoplasmosis is a worldwide infection that can lead to serious problems in immune-compromised individuals and fetuses. A DNA vaccine strategy would be an ideal tool against Toxoplasma gondii. One of the necessary measures to provide an effective vaccine is the selection of proteins with high antigenicity. The SAG1-related sequence 3 (SRS3) protein is a major surface antigen in T. gondii that can be used as a vaccine candidate. In the present study, bioinformatics and computational methods were utilized to predict protein characteristics, as well as secondary and tertiary structures. The in silico approach is highly suited to analyze, design, and evaluate DNA vaccine strategies. Hence, in silico prediction was used to identify B and T cell epitopes and compare the antigenicity of SRS3 and other candidate genes of Toxoplasma previously applied in the production of vaccines. The results of the analysis theoretically showed that SRS3 has multiple epitopes with high antigenicity, proposing that SRS3 is a promising immunogenic candidate for the development of DNA vaccines against toxoplasmosis.

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