Abstract:SARS-CoV-2 infections have spread throughout the world and became a rapidly emerging public health issue. The immunoinformatics approach was applied to design a potent multi-epitope vaccine against this deadly virus.
“…The above-mentioned protocol and its variations have been used multiple times for vaccine design. Undoubtedly, vaccines against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) have received the most attention in recent years [80][81][82][83] . However, studies on other vaccine designs have also been carried out, both before and after the outbreak of COVID-19.…”
Section: Next-generation Vaccinesmentioning
confidence: 99%
“…Different groups focused on studies of multi-epitope vaccines against various TLRs. For instance, Oladipo et al 80 studied the TLR2, TLR3, TLR4 and TLR9, while Rafi et al 81 focused on TLR2 and TLR4, and Ysrafil et al 82 investigated TLR3, TLR4 and TLR8, as well as angiotensin-converting enzyme 2 (ACE2) as the entry receptors of SARS-CoV-2. Drawing upon the structure of the SARS-CoV-2 spike (S) glycoprotein (and nucleocapsid (N) protein and open reading frame 1a (ORF1a) protein in the case of Ysrafil et al 82 ), the authors tried to develop a potent multi-epitope subunit vaccine.…”
Section: Next-generation Vaccinesmentioning
confidence: 99%
“…In the second study, based on the detected correlations in the covariance matrix between pairs of residues, the authors confirmed the stability of the vaccine candidate model. Rafi et al 81 performed classical MD simulations to check the stability of the constructed vaccine with the extracellular subunit of TLR2 and TLR4/MD2. The results indicated that the TLR-vaccine complexes were both stable and compact during the simulations.…”
Toll-like receptors (TLRs) are transmembrane proteins which recognise various molecular patterns and activate signalling that triggers the immune response. In this review, our goal was to summarise how, in recent years, various computational solutions contributed to a better understanding of TLRs, regarding both their function and mechanism of action. We updated the recent information about small-molecule modulators and expanded the topic towards next- generation vaccine design, as well as studies of the dynamic nature of TLRs. Also, we underlined problems which remain unsolved.
“…The above-mentioned protocol and its variations have been used multiple times for vaccine design. Undoubtedly, vaccines against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) have received the most attention in recent years [80][81][82][83] . However, studies on other vaccine designs have also been carried out, both before and after the outbreak of COVID-19.…”
Section: Next-generation Vaccinesmentioning
confidence: 99%
“…Different groups focused on studies of multi-epitope vaccines against various TLRs. For instance, Oladipo et al 80 studied the TLR2, TLR3, TLR4 and TLR9, while Rafi et al 81 focused on TLR2 and TLR4, and Ysrafil et al 82 investigated TLR3, TLR4 and TLR8, as well as angiotensin-converting enzyme 2 (ACE2) as the entry receptors of SARS-CoV-2. Drawing upon the structure of the SARS-CoV-2 spike (S) glycoprotein (and nucleocapsid (N) protein and open reading frame 1a (ORF1a) protein in the case of Ysrafil et al 82 ), the authors tried to develop a potent multi-epitope subunit vaccine.…”
Section: Next-generation Vaccinesmentioning
confidence: 99%
“…In the second study, based on the detected correlations in the covariance matrix between pairs of residues, the authors confirmed the stability of the vaccine candidate model. Rafi et al 81 performed classical MD simulations to check the stability of the constructed vaccine with the extracellular subunit of TLR2 and TLR4/MD2. The results indicated that the TLR-vaccine complexes were both stable and compact during the simulations.…”
Toll-like receptors (TLRs) are transmembrane proteins which recognise various molecular patterns and activate signalling that triggers the immune response. In this review, our goal was to summarise how, in recent years, various computational solutions contributed to a better understanding of TLRs, regarding both their function and mechanism of action. We updated the recent information about small-molecule modulators and expanded the topic towards next- generation vaccine design, as well as studies of the dynamic nature of TLRs. Also, we underlined problems which remain unsolved.
“…B cell epitopes assist in the detection of viral infections in the immune system. At the 0.51 threshold, ABCpred ( http://crdd.osdd.net/raghava/abcpred/ ) was utilized to forecast 14-mer B cell epitopes for target proteins (Saha and Raghava, [ 50 ]; Ponomarenko et al, [ 51 ]; Rafi et al, [ 52 ]). T cell epitopes are important in the development of vaccines.…”
The global COVID-19 (coronavirus disease 2019) pandemic, which was caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has resulted in a significant loss of human life around the world. The SARS-CoV-2 has caused significant problems to medical systems and healthcare facilities due to its unexpected global expansion. Despite all of the efforts, developing effective treatments, diagnostic techniques, and vaccinations for this unique virus is a top priority and takes a long time. However, the foremost step in vaccine development is to identify possible antigens for a vaccine. The traditional method was time taking, but after the breakthrough technology of reverse vaccinology (RV) was introduced in 2000, it drastically lowers the time needed to detect antigens ranging from 5–15 years to 1–2 years. The different RV tools work based on machine learning (ML) and artificial intelligence (AI). Models based on AI and ML have shown promising solutions in accelerating the discovery and optimization of new antivirals or effective vaccine candidates. In the present scenario, AI has been extensively used for drug and vaccine research against SARS-COV-2 therapy discovery. This is more useful for the identification of potential existing drugs with inhibitory human coronavirus by using different datasets. The AI tools and computational approaches have led to speedy research and the development of a vaccine to fight against the coronavirus. Therefore, this paper suggests the role of artificial intelligence in the field of clinical trials of vaccines and clinical practices using different tools.
“…Immunoinformatic tools mostly rely on the availability of in vitro assay data of MHC−peptide binding and cytokine assays. These methods have advantages over traditional vaccinology as they reduce both time and cost [ 98 , 99 ]. Fig.…”
Section: In Silico Studies For Identification Of Probable Vaccine Can...mentioning
The emergence of COVID19 pandemic caused by SARS-CoV-2 virus has created a global public health and socio-economic crisis. Immunoinformatics-based approaches to investigate the potential antigens is the fastest way to move towards a multiepitope-based vaccine development. This review encompasses the underlying mechanisms of pathogenesis, innate and adaptive immune signaling along with evasion pathways of SARS-CoV-2. Furthermore, it compiles the promiscuous peptides from in silico studies which are subjected to prediction of cytokine milieu using web-based servers. Out of the 434 peptides retrieved from all studies, we have identified 33 most promising T cell vaccine candidates. This review presents a list of the most potential epitopes from several proteins of the virus based on their immunogenicity, homology, conservancy and population coverage studies. These epitopes can form a basis of second generation of vaccine development as the first generation vaccines in various stages of trials mostly focus only on Spike protein. We therefore, propose them as most potential candidates which can be taken up immediately for confirmation by experimental studies.
Supplementary Information
The online version contains supplementary material available at 10.1007/s00284-022-03003-3.
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