Multi-Epitope-Based Vaccine Candidate for Monkeypox: An In Silico Approach

Delineating multi-epitopes vaccine designing from membrane protein CL5 against all monkeypox strains: a pangenome reverse vaccinology approach

The recently identified monkeypox virus (MPXV or mpox) is a zoonotic orthopox virus that infects humans and causes diseases with traits like smallpox. The world health organization (WHO) estimates that 3-6% of MPXV cases result in death. As it might impact everyone globally, like COVID, and become the next pandemic, the cure for this disease is important for global public health. The high incidence and disease ratio of MPXV necessitates immediate efforts to design a unique vaccine candidate capable of addressing MPXV diseases. Here, we used a computational pan-genome-based vaccine design strategy for all currently reported 19 MPXV strains acquired from different regions of the world. Thus, this study's objective was to develop a new and safe vaccine candidate against MPXV by targeting the membrane CL5 protein; identified after the pangenome analysis. Proteomics and reverse vaccinology have covered up all of the MPXV epitopes that would usually stimulate robust host immune responses. Following this, only two mapped (MHC-I, MHC-II, and B-cell) epitopes were observed to be extremely effective that can be used in the construction of CL5 protein vaccine candidates. The suggested vaccine (V5) candidate from eight vaccine models was shown to be antigenic, non-allergenic, and stable (with 213 amino acids). The vaccine's candidate efficacy was evaluated by using many in silico methods to predict, improve, and validate its 3D structure. Molecular docking and molecular dynamics simulations further reveal that the proposed vaccine candidate ensemble has a high interaction energy with the HLAs and TRL2/4 immunological receptors under study. Later, the vaccine sequence was used to generate an expression vector for the E. coli K12 strain. Further study uncovers that V5 was highly immunogenic because it produced robust primary, secondary, and tertiary immune responses. Eventually, the use of computer-aided vaccine designing may significantly reduce costs and speed up the process of developing vaccines. Although, the results of this research are promising, however, more research (experimental; in vivo, and in vitro studies) is needed to verify the biological efficacy of the proposed vaccine against MPXV.Communicated by Ramaswamy H. Sarma.

Using a dual immunoinformatics and bioinformatics approach to design a novel and effective multi-epitope vaccine against human torovirus disease

Human Torovirus (HToV), a member of the Coronaviridae family, causes severe enteric diseases with no specific medication available. To develop novel preventative measures, we employed immunoinformatics techniques to design a multi-epitope-based subunit vaccine (HToV-MEV) triggering diverse immune responses. We selected non-allergenic, non-toxic, and antigenic epitopes from structural polyproteins, joined them with suitable linkers, and added an adjuvant 50S ribosomal L7/L12 peptide. The vaccine's solubility score of 0.903678 and physiochemical properties were found effective. Molecular dynamics simulations and free energy calculations revealed strong binding affinity for Toll-like receptor 3 (TLR-3), with a lowest energy score of -303.88, indicating high affinity. In-silico cloning and codon optimization showed significant production potential in E. coli. Immune simulations predicted a human immunological response. Our results are promising, but subsequent in vivo research is recommended. The HToV-MEV vaccine design demonstrates potential for preventing HToV-related diseases, and further investigation is warranted to explore its therapeutic applications.

Human monkeypox virus: A systematic critical review during the pandemic peak

BACKGROUND

In July 2022, the world health organization (WHO) announced the monkeypox virus (MPXV) as a public health emergency of international concern, due to the unprecedented global transmission of the disease beyond previously endemic countries in Africa.

METHODS

For this systematic review, the author searched the "web of science" (WoS) database, which retrieves 138 articles on MPXV, published between 01-04-2022 and 22-09-2022. This period witnessed the maximum cases of infection as confirmed by the WHO. Seventy articles were used for in-depth analysis, after excluding papers not highly relevant to the topic.

RESULTS AND CONCLUSIONS

The current review demonstrates different types of MPXV identification analysis, transmission of MPXV, clinical features, immune responses against MPXV, the mutations, and phylogenetic analysis. It also identifies the patients with high-risk complications and determines the other diseases related to MPXV. This paper provides suggestions for the suitable usage of vaccines or antiviral drugs as a procedure to control the outbreak and preventive strategies related to the humans. This research discusses significant implications and recommendations to contribute in reducing the spread of MPXV and presents avenues for upcoming MPXV research.

The N and C-terminal deleted variant of the dengue virus NS1 protein is a potential candidate for dengue vaccine development

NS1 is an elusive dengue protein, involved in viral replication, assembly, pathogenesis, and immune evasion. Its levels in blood plasm are positively related to disease severity like thrombocytopenia, hemorrhage, and vascular leakage. Despite its pathogenic roles, NS1 is being used in various vaccine formulations due to its sequence conservancy, ability to produce protective antibodies and low risk for inducing antibody-dependent enhancement. In this study, we have used bioinformatics tools and reported literature to develop an NS1 variant (dNS1). Molecular docking studies were performed to evaluate the receptor-binding ability of the NS1 and dNS1 with TLR4. NS1 and dNS1 (153 to 312 amino acid region) genes were cloned, expressed and protein was purified followed by refolding. Docking studies showed the binding of NS1 and dNS1 with the TLR4 receptor which suggests that N and C-terminal sequences of NS1 are not critical for receptor binding. Antibodies against NS1 and dNS1 were raised in rabbits and binding affinity of anti-dNS1 anti-NS1 sera was evaluated against both NS1 and dNS1. Similar results were observed through western blotting which highlight that N and C-terminal deletion of NS1 does not compromise the immunogenic potential of dNS1 hence, supports its use in future vaccine formulations as a substitute for NS1.

A novel multi-epitope peptide vaccine targeting immunogenic antigens of Ebola and monkeypox viruses with potential of immune responses provocation in silico

The emergence or reemergence of monkeypox (Mpox) and Ebola virus (EBOV) agents causing zoonotic diseases remains a huge threat to human health. Our study aimed at designing a multi-epitope vaccine (MEV) candidate to target both the Mpox and EBOV agents using immunoinformatics tools. Viral protein sequences were retrieved, and potential nonallergenic, nontoxic, and antigenic epitopes were obtained. Next, cytotoxic and helper T-cell (CTL and HTL, respectively) and B-cell (BCL) epitopes were predicted, and those potential epitopes were fused utilizing proper linkers. The in silico cloning and expression processes were implemented using Escherichia coli K12. The immune responses were prognosticated using the C-ImmSim server. The MEV construct (29.53 kDa) included four BCL, two CTL, and four HTL epitopes and adjuvant. The MEV traits were pertinent in terms of antigenicity, non-allergenicity, nontoxicity, physicochemical characters, and stability. The MEV candidate was also highly expressed in E. coli K12. The strong affinity of MEV-TLR3 was confirmed using molecular docking and molecular dynamics simulation analyses. Immune simulation analyses unraveled durable activation and responses of cellular and humoral arms alongside innate immune responses. The designed MEV candidate demonstrated appropriate traits and was promising in the prediction of immune responses against both Mpox and EBOV agents. Further experimental assessments of the MEV are required to verify its efficacy.

Identification of novel potential inhibitors of monkeypox virus thymidine kinase using molecular docking, molecular dynamics simulation and MM/PBSA methods

The monkeypox spread has been announced a public health emergency of international concern (PHEIC) by the World Health Organization (WHO). Both monkeypox and smallpox viruses are placed in the genus Orthopoxvirus. Despite recommendations for the administration of smallpox drugs versus monkeypox, no specific drug for monkeypox has yet been introduced. A reliable and effective method against this outbreak can be the use of natural products. This study aimed for identification of natural flavonoid derivatives as potential thymidine kinase inhibitors, the main drug target of monkeypox virus. Thymidine kinase protein structure was predicted by homology modeling and the quality of generated model was evaluated. Then, the interaction between natural flavonoids and the modeled thymidine kinase was explored by molecular docking. Based on docking results, more than half of the flavonoids with higher docking scores compared to reference drug (ganciclovir) were exhibited better binding affinities toward the protein. In addition, stability of the top flavonoids including eupatorin, fisetin, rhamnetin and scutellarein, was confirmed by MD simulations and binding free energy calculations using MM/PBSA analysis. These selected compounds were also shown acceptable results for drug likeness and ADMET analysis. Therefore, the results of the study showed that these flavonoids could be considered as potential thymidine kinase inhibitors for use against monkeypox virus.

Design of multi-epitope vaccine against porcine rotavirus using computational biology and molecular dynamics simulation approaches

Porcine Rotavirus (PoRV) is a significant pathogen affecting swine-rearing regions globally, presenting a substantial threat to the economic development of the livestock sector. At present, no specific pharmaceuticals are available for this disease, and treatment options remain exceedingly limited. This study seeks to design a multi-epitope peptide vaccine for PoRV employing bioinformatics approaches to robustly activate T-cell and B-cell immune responses. Two antigenic proteins, VP7 and VP8*, were selected from PoRV, and potential immunogenic T-cell and B-cell epitopes were predicted using immunoinformatic tools. These epitopes were further screened according to non-toxicity, antigenicity, non-allergenicity, and immunogenicity criteria. The selected epitopes were linked with linkers to form a novel multi-epitope vaccine construct, with the PADRE sequence (AKFVAAWTLKAAA) and RS09 peptide attached at the N-terminus of the designed peptide chain to enhance the vaccine's antigenicity. Protein-protein docking of the vaccine constructs with toll-like receptors (TLR3 and TLR4) was conducted using computational methods, with the lowest energy docking results selected as the optimal predictive model. Subsequently, molecular dynamics (MD) simulation methods were employed to assess the stability of the protein vaccine constructs and TLR3 and TLR4 receptors. The results indicated that the vaccine-TLR3 and vaccine-TLR4 docking models remained stable throughout the simulation period. Additionally, the C-IMMSIM tool was utilized to determine the immunogenic triggering capability of the vaccine protein, demonstrating that the constructed vaccine protein could induce both cell-mediated and humoral immune responses, thereby playing a role in eliciting host immune responses. In conclusion, this study successfully constructed a multi-epitope vaccine against PoRV and validated the stability and efficacy of the vaccine through computational analysis. However, as the study is purely computational, experimental evaluation is required to validate the safety and immunogenicity of the newly constructed vaccine protein.

An immuno-informatics approach for annotation of hypothetical proteins and multi-epitope vaccine designed against the Mpox virus

A worrying new outbreak of Monkeypox (Mpox) in humans is caused by the Mpox virus (MpoxV). The pathogen has roughly 28 hypothetical proteins of unknown structure, function, and pathogenicity. Using reliable bioinformatics tools, we attempted to analyze the MpoxV genome, identify the role of hypothetical proteins (HPs), and design a potential candidate vaccine. Out of 28, we identified seven hypothetical proteins using multi-server validation with high confidence for the occurrence of conserved domains. Their physical, chemical, and functional characterizations, including molecular weight, theoretical isoelectric point, 3D structures, GRAVY value, subcellular localization, functional motifs, antigenicity, and virulence factors, were performed. We predicted possible cytotoxic T cell (CTL), helper T cell (HTL) and linear and conformational B cell epitopes, which were combined in a 219 amino acid multiepitope vaccine with human β defensin as a linker. This multi-epitopic vaccine was structurally modelled and docked with toll-like receptor-3 (TLR-3). The dynamical stability of the vaccine-TLR-3 docked complexes exhibited stable interactions based on RMSD and RMSF tests. Additionally, the modelled vaccine was cloned in-silico in an E. coli host to check the appropriate expression of the final vaccine built. Our results might conform to an immunogenic and safe vaccine, which would require further experimental validation.Communicated by Ramaswamy H. Sarma.

Formulation of next-generation polyvalent vaccine candidates against three important poxviruses by targeting DNA-dependent RNA polymerase using an integrated immunoinformatics and molecular modeling approach

BACKGROUND

Poxviruses comprise a group of large double-stranded DNA viruses and are known to cause diseases in humans, livestock animals, and other animal species. The Mpox virus (MPXV; formerly Monkeypox), variola virus (VARV), and volepox virus (VPXV) are among the prevalent poxviruses of the Orthopoxviridae genera. The ongoing Mpox infectious disease pandemic caused by the Mpox virus has had a major impact on public health across the globe. To date, only limited repurposed antivirals and vaccines are available for the effective treatment of Mpox and other poxviruses that cause contagious diseases.

METHODS

The present study was conducted with the primary goal of formulating multi-epitope vaccines against three evolutionary closed poxviruses i.e., MPXV, VARV, and VPXV using an integrated immunoinformatics and molecular modeling approach. DNA-dependent RNA polymerase (DdRp), a potential vaccine target of poxviruses, has been used to determine immunodominant B and T-cell epitopes followed by interactions analysis with Toll-like receptor 2 at the atomic level.

RESULTS

Three multi-epitope vaccine constructs, namely DdRp_MPXV (V1), DdRp_VARV (V2), and DdRp_VPXV (V3) were designed. These vaccine constructs were found to be antigenic, non-allergenic, non-toxic, and soluble with desired physicochemical properties. Protein-protein docking and interaction profiling analysis depicts a strong binding pattern between the targeted immune receptor TLR2 and the structural models of the designed vaccine constructs, and manifested a number of biochemical bonds (hydrogen bonds, salt bridges, and non-bonded contacts). State-of-the-art all-atoms molecular dynamics simulations revealed highly stable interactions of vaccine constructs with TLR2 at the atomic level throughout the simulations on 300 nanoseconds. Additionally, the outcome of the immune simulation analysis suggested that designed vaccines have the potential to induce protective immunity against targeted poxviruses.

CONCLUSIONS

Taken together, formulated next-generation polyvalent vaccines were found to have good efficacy against closely related poxviruses (MPXV, VARV, and VPXV) as demonstrated by our extensive immunoinformatics and molecular modeling evaluations; however, further experimental investigations are still needed.

In-silico formulation of a next-generation polyvalent vaccine against multiple strains of monkeypox virus and other related poxviruses

Mpox (formerly known as monkeypox) virus and some related poxviruses including smallpox virus pose a significant threat to public health, and effective prevention and treatment strategies are needed. This study utilized a reverse vaccinology approach to retrieve conserved epitopes for monkeypox virus and construct a vaccine that could provide cross-protection against related viruses with similar antigenic properties. The selected virulent proteins of monkeypox virus, MPXVgp165, and Virion core protein P4a, were subjected to epitope mapping for vaccine construction. Two vaccines were constructed using selected T cell epitopes and B cell epitopes with PADRE and human beta-defensins adjuvants conjugated in the vaccine sequence. Both constructs were found to be highly antigenic, non-allergenic, nontoxic, and soluble, suggesting their potential to generate an adequate immune response and be safe for humans. Vaccine construct 1 was selected for molecular dynamic simulation studies. The simulation studies revealed that the TLR8-vaccine complex was more stable than the TLR3-vaccine complex. The lower RMSD and RMSF values of the TLR8 bound vaccine compared to the TLR3 bound vaccine suggested better stability and consistency of hydrogen bonds. The Rg values of the vaccine chain bound to TLR8 indicated overall stability, whereas the vaccine chain bound to TLR3 showed deviations throughout the simulation. These results suggest that the constructed vaccine could be a potential preventive measure against monkeypox and related viruses however, further experimental validation is required to confirm these findings.

Design of multi-epitope chimeric vaccine against Monkeypox virus and SARS-CoV-2: A vaccinomics perspective

The current era we experience is full with pandemic infectious agents that no longer threatens the major local source but the whole globe. Almost the most emerging infectious agents are severe acute respiratory syndrome coronavirus-2 (SARS CoV-2), followed by monkeypox virus (MPXV). Since no approved antiviral drugs nor licensed active vaccines are yet available, we aimed to utilize immunoinformatics approach to design chimeric vaccine against the two mentioned viruses. This is the first study to deal with design divalent vaccine against SARS-CoV-2 and MPXV. ORF8, E and M proteins from Omicron SARS-CoV-2 and gp182 from MPXV were used as the protein precursor from which multi-epitopes (inducing B-cell, helper T cells, cytotoxic T cells and interferon-ɣ) chimeric vaccine was contrived. The structure of the vaccine construct was predicted, validated, and docked to toll-like receptor-2 (TLR-2). Moreover, its sequence was also used to examine the immune simulation profile and was then inserted into the pET-28a plasmid for in silico cloning. The vaccine construct was probable antigen (0.543) and safe (non-allergen) with strong binding energy to TLR-2 (-1169.8 kcal/mol) and found to have significant immune simulation profile. In conclusion, the designed chimeric vaccine was potent and safe against SARS-CoV-2 and MPXV, which deserves further consideration.

Development of membrane protein-based vaccine against lumpy skin disease virus (LSDV) using immunoinformatic tools

INTRODUCTION

Lumpy skin disease, an economically significant bovine illness, is now found in previously unheard-of geographic regions. Vaccination is one of the most important ways to stop its further spread.

AIM

Therefore, in this study, we applied advanced immunoinformatics approaches to design and develop an effective lumpy skin disease virus (LSDV) vaccine.

METHODS

The membrane glycoprotein was selected for prediction of the different B- and T-cell epitopes by using the immune epitope database. The selected B- and T-cell epitopes were combined with the appropriate linkers and adjuvant resulted in a vaccine chimera construct. Bioinformatics tools were used to predict, refine and validate the 2D, 3D structures and for molecular docking with toll-like receptor 4 using different servers. The constructed vaccine candidate was further processed on the basis of antigenicity, allergenicity, solubility, different physiochemical properties and molecular docking scores.

RESULTS

The in silico immune simulation induced significant response for immune cells. In silico cloning and codon optimization were performed to express the vaccine candidate in Escherichia coli. This study highlights a good signal for the design of a peptide-based LSDV vaccine.

CONCLUSION

Thus, the present findings may indicate that the engineered multi-epitope vaccine is structurally stable and can induce a strong immune response, which should help in developing an effective vaccine towards controlling LSDV infection.

In silico designing a novel TLR4-mediating multiepitope vaccine against monkeypox via advanced immunoinformatics and bioinformatics approaches

Monkeypox virus is a member of the Poxviridae family, which causes monkeypox zoonotic disease. Since July 2022, the prevention of monkeypox have become more considerable due to the new outbreak, making it a global concern. Therefore, we used an in silico-based method, including immunoinformatics, bioinformatics, molecular docking, and gene cloning approaches to design a novel multiepitope vaccine against monkeypox. Three immunogenic envelope proteins of monkeypox virus, including G10R, E8L, and A30L, were selected to predict appropriate immune system stimulator epitopes. The A30L is common between smallpox and monkeypox virus, so the proposed vaccine may be effective against smallpox too. There is no evidence of allergenicity and toxicity of the vaccine epitopes. To boost the immunogenicity of the designed vaccine, we used the helper epitope of PADRE and RS01as adjuvants. Furthermore, some linkers are used to link epitopes and adjuvants together. The physicochemical futures of the designed vaccine were assessed. The tertiary structure of the vaccine was modeled and then refined to improve its structure and physicochemical properties. To analyze the vaccine construct and TLR4 complex affinity, they were docked to gather. Besides, the vaccine was cloned into E.coli. pET-21b(+) plasmid to reveal that it can be expressed and stimulate the immune system. Immune stimulation evaluation showed that the candidate vaccine could induce the production of IgM, IgG1, and IgG2 antibodies. Overall, we suggested an effective vaccine candidate against monkeypox. However, Future studies and clinical trials should be done to ensure the efficacy and safety of this vaccine.Communicated by Ramaswamy H. Sarma.

Current Status of Vaccine Development for Monkeypox Virus

Monkeypox virus (MPXV) of poxviridae family causes a zoonotic disease called monkeypox (Mpox). MPXV cases have a fatality ratio ranging from 0 to 11% globally and have been more prevalent in children. There are three generations of smallpox vaccines that protect against MPXV. First and second generation of the vaccinia virus (VACV) vaccine protects MPXV. However, various adverse side effects were associated with the first and second generations of vaccines. In contrast, the Modified Vaccinia Ankara-Bavarian Nordic (MVA-BN) replication-incompetent vaccine shows fewer adverse effects and a significant amount of neutralizing antibodies in mammalian cells. A third-generation Modified Vaccinia Ankara-Bavarian Nordic (MVA-BN) was approved to prevent Mpox in 2019. Recently, MVA-BN-based Imvanex, Imvamune, and JYNNEOS vaccines have also been administered against MPXV. Globally, the World Health Organization (WHO) declared a global health emergency in May 2022 due to increased MPXV cases. Various computational studies have also designed a multi-epitope-based vaccine against the MPXV. In the multi-epitope-based vaccine, different epitopes like B-cell, Cytotoxic T Lymphocyte (CTL), CD8+, and CD4+ epitopes were derived from MPXV proteins. Further, these epitopes were linked with the help of various linkers to design a multi-epitope vaccine against MPXV. In summary, we have provided an overview of the current status of the vaccine against MPXV.

Computer-Aided Multi-Epitope Based Vaccine Design Against Monkeypox Virus Surface Protein A30L: An Immunoinformatics Approach

Monkeypox, a viral zoonotic disease resembling smallpox, has emerged as a significant national epidemic primarily in Africa. Nevertheless, the recent global dissemination of this pathogen has engendered apprehension regarding its capacity to metamorphose into a sweeping pandemic. To effectively combat this menace, a multi-epitope vaccine has been meticulously engineered with the specific aim of targeting the cell envelope protein of Monkeypox virus (MPXV), thereby stimulating a potent immunological response while mitigating untoward effects. This new vaccine uses T-cell and B-cell epitopes from a highly antigenic, non-allergenic, non-toxic, conserved, and non-homologous A30L protein to provide protection against the virus. In order to ascertain the vaccine design with the utmost efficacy, protein-protein docking methodologies were employed to anticipate the intricate interactions with Toll-like receptors (TLR) 2, 3, 4, 6, and 8. This meticulous approach led the researchers to discern an optimal vaccine architecture, bolstered by affirmative prognostications derived from both molecular dynamics (MD) simulations and immune simulations. The current research findings indicate that the peptides ATHAAFEYSK, FFIVVATAAV, and MNSLSIFFV exhibited antigenic properties and were determined to be non-allergenic and non-toxic. Through the utilization of codon optimization and in-silico cloning techniques, our investigation revealed that the prospective vaccine exhibited a remarkable expression level within Escherichia coli. Moreover, upon conducting immune simulations, we observed the induction of a robust immune response characterized by elevated levels of both B-cell and T-cell mediated immunity. Moreover, as the initial prediction with in-silico techniques has yielded promising results these epitope-based vaccines can be recommended to in vitro and in silico studies to validate their immunogenic properties.

Development of multi-epitope based subunit vaccine against Mycobacterium Tuberculosis using immunoinformatics approach

The etiological agent of tuberculosis (TB), Mycobacterium tuberculosis, is a deadly pathogen that adapts to thrive within the host. Since 2020, the COVID-19 pandemic has had colossal health, societal, and economic consequences, which have affected the reporting of new incidences and mortality cases of TB. As per the WHO 2022 report, 10.6 million people were diagnosed with TB, and 1.6 million died worldwide. The increase in resistant strains of tuberculosis is making it more burdensome to reach the End TB strategy. A reliable and efficient TB vaccine that may avert both primary infection and recurrence of latent TB in adults and adolescents is of the utmost importance. In this study, we used computational techniques to predict the ability of HLA molecules to display epitopes for six TB proteins (PPE68, PE_PGRS17, EspC, LDT4, RpfD, and RpfC) to design the multi-epitope subunit vaccine. From the aimed proteins, the potential B-cell, helper T lymphocyte (HTL), and cytotoxic T lymphocyte (CTL) epitopes were predicted and linked together with LPA adjuvant, and the vaccine was designed. The vaccine's physicochemical analysis demonstrates that it is non-allergic, non-toxic, and antigenic. Then, the vaccine structure was predicted, improved, and verified to yield the optimal structure. The developed vaccine's binding mechanism with distinct immunogenic receptors (Tlr2 and MHC-II) was assessed utilizing molecular docking. The molecular dynamic simulation and MMPBSA analysis were performed to comprehend the complexes' dynamics and stability. The immune simulation was utilized to anticipate the vaccine's immunogenic attributes. In silico cloning was employed to demonstrate the efficient expression of the designed vaccine in E. coli as a host. Moreover, in vitro and in vivo animal testing is required to determine the efficacy of the in silico developed vaccine.Communicated by Ramaswamy H. Sarma.

Computational design of a multi-epitope vaccine candidate against Langya henipavirus using surface proteins

In July 2022, Langya henipavirus (LayV) was identified in febrile patients in China. There is currently no approved vaccine against this virus. Therefore, this research aimed to design a multi-epitope vaccine against LayV using reverse vaccinology. The best epitopes were selected from LayV's fusion protein (F) and glycoprotein (G), and a multi-epitope vaccine was designed using these epitopes, adjuvant, and appropriate linkers. The physicochemical properties, antigenicity, allergenicity, toxicity, and solubility of the vaccine were evaluated. The vaccine's secondary and 3D structures were predicted, and molecular docking and molecular dynamics (MD) simulations were used to assess the vaccine's interaction and stability with toll-like receptor 4 (TLR4). Immune simulation, codon optimization, and in silico cloning of the vaccine were also performed. The vaccine candidate showed good physicochemical properties, as well as being antigenic, non-allergenic, and non-toxic, with acceptable solubility. Molecular docking and MD simulation revealed that the vaccine and TLR4 have stable interactions. Furthermore, immunological simulation of the vaccine indicated its ability to elicit immune responses against LayV. The vaccine's increased expression was also ensured using codon optimization. This study's findings were encouraging, but in vitro and in vivo tests are needed to confirm the vaccine's protective effect.Communicated by Ramaswamy H. Sarma.

Are Saudi Healthcare Workers Willing to Receive the Monkeypox Virus Vaccine? Evidence from a Descriptive-Baseline Survey

Since Saudi Arabia has already confirmed multiple monkeypox (Mpox) cases, it is essential to initiate timely preventive measures, including the implementation of vaccines. In this cross-sectional study, an online survey was conducted among healthcare workers (HCWs) in Saudi Arabia to understand their willingness to receive the Mpox vaccine. A structured questionnaire was used to gather the data. The study comprised 734 samples. Our study found that among study participants, 52.7% were willing to receive the Mpox vaccine and showed that sociodemographic factors were not significantly associated with vaccine willingness. Previous vaccination history (such as influenza and COVID-19) was significantly associated with Mpox vaccine willingness. The respondents reported that the main reasons for receiving the Mpox vaccine were their trust in the Saudi Health Ministry (57.7%) and their understanding that the vaccine was a social responsibility (44.6%). Furthermore, the majority of the respondents (74.7%) reported that they were motivated by the need to protect themselves, their family and their friends. Insufficient vaccine information and fear of unknown adverse reactions were the most reported reasons for an unwillingness to receive the Mpox vaccine. In conclusion, increasing Mpox vaccine-related awareness and focusing on greater information dissemination to reduce fear and increase vaccine uptake is highly recommended.

Construction, Expression, and Evaluation of the Naturally Acquired Humoral Immune Response against Plasmodium vivax RMC-1, a Multistage Chimeric Protein

The PvCelTOS, PvCyRPA, and Pvs25 proteins play important roles during the three stages of the P. vivax lifecycle. In this study, we designed and expressed a P. vivax recombinant modular chimeric protein (PvRMC-1) composed of the main antigenic regions of these vaccine candidates. After structure modelling by prediction, the chimeric protein was expressed, and the antigenicity was assessed by IgM and IgG (total and subclass) ELISA in 301 naturally exposed individuals from the Brazilian Amazon. The recombinant protein was recognized by IgG (54%) and IgM (40%) antibodies in the studied individuals, confirming the natural immunogenicity of the epitopes that composed PvRMC-1 as its maintenance in the chimeric structure. Among responders, a predominant cytophilic response mediated by IgG1 (70%) and IgG3 (69%) was observed. IgM levels were inversely correlated with age and time of residence in endemic areas (p < 0.01). By contrast, the IgG and IgM reactivity indexes were positively correlated with each other, and both were inversely correlated with the time of the last malaria episode. Conclusions: The study demonstrates that PvRMC-1 was successfully expressed and targeted by natural antibodies, providing important insights into the construction of a multistage chimeric recombinant protein and the use of naturally acquired antibodies to validate the construction.

Molecular recognition of SARS-CoV-2 spike protein with three essential partners: exploring possible immune escape mechanisms of viral mutants

OBJECTIVE

The COVID-19 epidemic is raging around the world, with the emergence of viral mutant strains such as Delta and Omicron, posing severe challenges to people's health and quality of life. A full understanding life cycle of the virus in host cells helps to reveal inactivation mechanism of antibody and provide inspiration for the development of a new-generation vaccines.

METHODS

In this work, molecular recognitions and conformational changes of SARS-CoV-2 spike protein mutants (i.e., Delta, Mu, and Omicron) and three essential partners (i.e., membrane receptor hACE2, protease TMPRSS2, and antibody C121) both were compared and analyzed using molecular simulations.

RESULTS

Water basin and binding free energy calculations both show that the three mutants possess higher affinity for hACE2 than WT, exhibiting stronger virus transmission. The descending order of cleavage ability by TMPRSS2 is Mu, Delta, Omicron, and WT, which is related to the new S1/S2 cutting site induced by transposition effect. The inefficient utilization of TMPRSS2 by Omicron is consistent with its primary entry into cells via the endosomal pathway. In addition, RBD-directed antibody C121 showed obvious resistance to Omicron, which may have originated from high fluctuation of approaching angles, high flexibility of I472-F490 loop, and reduced binding ability.

CONCLUSIONS

According to the overall characteristics of the three mutants, high infectivity, high immune escape, and low virulence may be the future evolutionary selection of SARS-CoV-2. In a word, this work not only proposes the possible resistance mechanism of SARS-CoV-2 mutants, but also provides theoretical guidance for the subsequent drug design against COVID-19 based on S protein structure.

Design of multi-epitope based vaccine against Mycobacterium tuberculosis: a subtractive proteomics and reverse vaccinology based immunoinformatics approach

Tuberculosis is an airborne transmissible disease caused by Mycobacterium tuberculosis that infects millions of lives worldwide. There is still no single comprehensive therapy or preventative available for the lethal illness. Currently, the available vaccine, BCG is ineffectual in preventing the prophylactic adult pulmonary TB and reactivation of latent tuberculosis. Therefore, this investigation was intended to design a new multi-epitope vaccine that can address the existing problems. The subtractive proteomics approach was implemented to prioritize essential, virulence, druggable, and antigenic proteins as suitable vaccine candidates. Furthermore, a reverse vaccinology-based immunoinformatics technique was employed to identify potential B-cell, helper T lymphocytes (HTL), and cytotoxic T lymphocytes (CTL) epitopes from the target proteins. Immune-stimulating adjuvant, linkers, and PADRE (Pan HLA-DR epitopes) amino acid sequences along with the selected epitopes were used to construct a chimeric multi-epitope vaccine. The molecular docking and normal mode analysis (NMA) were carried out to evaluate the binding mode of the designed vaccine with different immunogenic receptors (MHC-I, MHC-II, and Tlr4). In addition, the MD simulation, followed by essential dynamics study and MMPBSA analysis, was carried out to understand the dynamics and stability of the complexes. In-silico cloning was accomplished using E.coli as an expression system to express the designed vaccine successfully. Finally, the immune simulation study has foreseen that our designed vaccine could induce a significant immune response by elevation of different immunoglobulins in the host. However, there is an imperative need for the experimental validation of the designed vaccine in animal models to confer effectiveness and safety.HIGHLIGHTSMulti-epitope based vaccine was designed against Mycobacterium tuberculosis using subtractive proteomics and Immunoinformatics approach.The vaccine was found to be antigenic, non-allergenic, immunogenic, and stable based on in-silico prediction.Population coverage analysis of the proposed vaccine predicts an effective response in the world population.The molecular docking, MD simulation, and MM-PBSA study confirm the stable interaction of the vaccine with immunogenic receptors.In silico cloning and immune simulation of the vaccine demonstrated its successful expression in E.coli and induction of immune response in the host. Communicated by Ramaswamy H. Sarma.

An immunoinformatic approach towards development of a potent and effective multi-epitope vaccine against monkeypox virus (MPXV)

Monkeypox is a viral zoonotic disease, often transmitted to humans from animals. While the whole world is haggling with the COVID-19 pandemic, the emergence of the monkeypox virus (MPXV) arose as a new challenge to mankind. Till date, numerous cases related to the MPXV have been reported in several countries across the globe, but, its momentary distribution in the current time has left everyone in fright with increasing mortality and limited clinically approved treatments. Therefore, it is of immense importance to develop a potent and highly effective vaccine capable of inducing desired immunogenic responses against the highly contagious MPXV. Herein, using various immunoinformatic and computational biology tools, we made an attempt to develop a multi-epitope vaccine construct against the MPXV which is antigenic, non-allergen and non-toxic in nature and capable of exhibiting immunogenic behavior. The sequence of vaccine construct was designed using the proposed 4 MHC-I, 3 MHC-II and 4 B-cell epitopes linked with suitable adjuvant and linkers. The modeled structure of the vaccine construct was used to assess its interaction with the Toll-like Receptor 4 (TLR4) using ClusPro and HADDOCK. All-atoms molecular dynamics simulation of the MPXV vaccine construct-TLR4 complex followed by a high level of gene expression of the construct within the bacterial system affirmed its stability along with induction of immunogenic response within the host cell. Altogether, our immunoinformatic approach aid in the development of a stable chimeric vaccine construct against MPXV and needs further experimental validation for its immunological relevance and usefulness as a vaccine candidate.Communicated by Ramaswamy H. Sarma.

Identification of B and T Cell Epitopes to Design an Epitope-Based Peptide Vaccine against the Cell Surface Binding Protein of Monkeypox Virus: An Immunoinformatics Study

Background

Although the monkeypox virus-associated illness was previously confined to Africa, recently, it has started to spread across the globe and become a significant threat to human lives. Hence, this study was designed to identify the B and T cell epitopes and develop an epitope-based peptide vaccine against this virus's cell surface binding protein through an in silico approach to combat monkeypox-associated diseases.

Results

The analysis revealed that the cell surface binding protein of the monkeypox virus contains 30 B cell and 19 T cell epitopes within the given parameter. Among the T cell epitopes, epitope "ILFLMSQRY" was found to be one of the most potential peptide vaccine candidates. The docking analysis revealed an excellent binding affinity of this epitope with the human receptor HLA-B^∗15:01 with a very low binding energy (-7.5 kcal/mol).

Conclusion

The outcome of this research will aid the development of a T cell epitope-based peptide vaccine, and the discovered B and T cell epitopes will facilitate the creation of other epitope and multi-epitope-based vaccines in the future. This research will also serve as a basis for further in vitro and in vivo analysis to develop a vaccine that is effective against the monkeypox virus.

Computational Repurposing of Mitoxantrone-Related Structures against Monkeypox Virus: A Molecular Docking and 3D Pharmacophore Study

Monkeypox is caused by a DNA virus known as the monkeypox virus (MPXV) belonging to the Orthopoxvirus genus of the Poxviridae family. Monkeypox is a zoonotic disease where the primary significant hosts are rodents and non-human primates. There is an increasing global incidence with a 2022 outbreak that has spread to Europe in the middle of the COVID-19 pandemic. The new outbreak has novel, previously undiscovered mutations and variants. Currently, the US Food and Drug Administration (FDA) approved poxvirus treatment involving the use of tecovirimat. However, there has otherwise been limited research interest in monkeypox. Mitoxantrone (MXN), an anthracycline derivative, an FDA-approved therapeutic for treating cancer and multiple sclerosis, was previously reported to exhibit antiviral activity against the vaccinia virus and monkeypox virus. In this study, virtual screening, molecular docking analysis, and pharmacophore ligand-based modelling were employed on anthracene structures (1-13) closely related to MXN to explore the potential repurposing of multiple compounds from the PubChem library. Four chemical structures (2), (7), (10) and (12) show a predicted high binding potential to suppress viral replication.

Multi-Epitope Vaccine for Monkeypox Using Pan-Genome and Reverse Vaccinology Approaches

Outbreaks of monkeypox virus infections have imposed major health concerns worldwide, with high morbidity threats to children and immunocompromised adults. Although repurposed drugs and vaccines are being used to curb the disease, the evolving traits of the virus, exhibiting considerable genetic dynamicity, challenge the limits of a targeted treatment. A pan-genome-based reverse vaccinology approach can provide fast and efficient solutions to resolve persistent inconveniences in experimental vaccine design during an outbreak-exigency. The approach encompassed screening of available monkeypox whole genomes (n = 910) to identify viral targets. From 102 screened viral targets, viral proteins L5L, A28, and L5 were finalized based on their location, solubility, and antigenicity. The potential T-cell and B-cell epitopes were extracted from the proteins using immunoinformatics tools and algorithms. Multiple vaccine constructs were designed by combining the epitopes. Based on immunological properties, chemical stability, and structural quality, a novel multi-epitopic vaccine construct, V4, was finalized. Flexible-docking and coarse-dynamics simulation portrayed that the V4 had high binding affinity towards human HLA-proteins (binding energy < -15.0 kcal/mol) with low conformational fluctuations (<1 Å). Thus, the vaccine construct (V4) may act as an efficient vaccine to induce immunity against monkeypox, which encourages experimental validation and similar approaches against emerging viral infections.

Immunoinformatics-Aided Design of a Peptide Based Multiepitope Vaccine Targeting Glycoproteins and Membrane Proteins against Monkeypox Virus

Monkeypox is a self-limiting zoonotic viral disease and causes smallpox-like symptoms. The disease has a case fatality ratio of 3-6% and, recently, a multi-country outbreak of the disease has occurred. The currently available vaccines that have provided immunization against monkeypox are classified as live attenuated vaccinia virus-based vaccines, which pose challenges of safety and efficacy in chronic infections. In this study, we have used an immunoinformatics-aided design of a multi-epitope vaccine (MEV) candidate by targeting monkeypox virus (MPXV) glycoproteins and membrane proteins. From these proteins, seven epitopes (two T-helper cell epitopes, four T-cytotoxic cell epitopes and one linear B cell epitopes) were finally selected and predicted as antigenic, non-allergic, interferon-γ activating and non-toxic. These epitopes were linked to adjuvants to design a non-allergic and antigenic candidate MPXV-MEV. Further, molecular docking and molecular dynamics simulations predicted stable interactions between predicted MEV and human receptor TLR5. Finally, the immune-simulation analysis showed that the candidate MPXV-MEV could elicit a human immune response. The results obtained from these in silico experiments are promising but require further validation through additional in vivo experiments.