An integrative reverse vaccinology, immunoinformatic, docking and simulation approaches towards designing of multi-epitopes based vaccine against monkeypox virus

In silico analysis of identified molecules using LC-HR/MS of Cupressus sempervirens L. ethyl acetate fraction against three monkeypox virus targets

Monkeypox virus is a viral disease transmitted to humans through contact with infected animals, such as monkeys and rodents, or through direct contact with the bodily fluids or lesions of infected humans. The aim of this study is to evaluate in silico the inhibition effect of eight Cupressus sempervirens L. ethyl acetate fraction identified molecules using LC-MS on three monkeypox targets such as the vaccinia virus thymidylate kinase (VTK), the viral profilin-like protein (VPP), and the viral RNA polymerase (VRP). The study consist of using molecular docking with AutoDock vina based on the lowest energy value in kcal/mol, pharmacokinetics prediction with pre-ADMET v2.0 server, and prediction of biological activity with the PASS server tool. The best complexes were subjected to molecular dynamics simulation (MD) study to confirm their stability using Desmond software. The used molecules were vitamin C, vanillic acid (Pol), Flav1 (Catechin), Flav2 (Epicatechin), Flav3 (Hyperoside), Flav4 (Luteolin), Flav5 (Taxifolin), and Flav6 (Quercetin). The results show that flavonoids are potent to VTK, VPP and effectively block the VRP channel with energy values ranging from -7.0 to -9.3 kcal/mol. Further, MD simulation supports Flav1 and, Flav2 for notable stability in the VTK binding pocket through hydrogen and hydrophobic interactions. PASS results predicted various biological activities with promising VTK and VRP inhibition activities. The studied molecules could constitute a safer alternative to current drugs, which often cause adverse side effects.Communicated by Ramaswamy H. Sarma.

Immunoinformatic approach for multi-epitope vaccine design against Staphylococcus aureus based on hemolysin proteins

Staphylococcus aureus is a common bacterium that causes a variety of infections in humans. This microorganism produces several virulence factors, including hemolysins, which contribute to its disease-causing ability. The treatment of S. aureus infections typically involves the use of antibiotics. However, the emergence of antibiotic-resistant strains has become a major concern. Therefore, vaccination against S. aureus has gained attention as an alternative approach. Vaccination has the advantage of stimulating the immune system to produce specific antibodies that can neutralize bacteria and prevent infection. However, developing an effective vaccine against S. aureus has proven to be challenging. This study aimed to use in silico methods to design a multi-epitope vaccine against S. aureus infection based on hemolysin proteins. The designed vaccine contained four B-cell epitopes, four CTL epitopes, and four HTL epitopes, as well as the ribosomal protein L7/L12 and pan-HLA DR-binding epitope, included as adjuvants. Furthermore, the vaccine was non-allergenic and non-toxic with the potential to stimulate the TLR2-, TLR-4, and TLR-6 receptors. The predicted vaccine exhibited a high degree of antigenicity and stability, suggesting potential for further development as a viable vaccine candidate. The population coverage of the vaccine was 94.4 %, indicating potential widespread protection against S. aureus. Overall, these findings provide valuable insights into the design of an effective multi-epitope vaccine against S. aureus infection and pave the way for future experimental validations.

Advancements in monkeypox vaccines development: a critical review of emerging technologies

Monkeypox (mpox) is a zoonotic illness caused by the monkeypox virus (MPXV), with higher health concerns among people who are pregnant, children, and persons who are immunocompromised, including people with untreated and advanced HIV disease. Significant progress has been made in developing vaccines against mpox, yet critical challenges and limitations persist in ensuring their effectiveness, safety, and accessibility. The pertinence of this review is highlighted by the World Health Organization's declaration of a global health emergency on August 14, 2024, due to the recent mpox outbreak, underscoring the critical necessity for effective vaccine solutions in the face of a rapidly evolving virus. Here, we comprehensively analyze various vaccine platforms utilized in mpox prevention, including attenuated and non-replicating virus vaccines, viral vector-based vaccines, recombinant protein vaccines, and DNA and mRNA vaccines. We evaluate the advantages and limitations of each platform, highlighting the urgent need for ongoing research and innovation to enhance vaccine efficacy and safety. Recent advancements, such as incorporating immunostimulatory sequences, improved delivery systems, and developing polyvalent vaccines, are explored for their potential to offer broader protection against diverse orthopoxvirus strains. This work underscores the need to optimize currently available vaccines and investigate novel vaccination strategies to address future public health emergencies effectively. By focusing on these advanced methodologies, we aim to contribute to the development of robust and adaptable vaccine solutions for mpox and other related viral threats.

Design of an Epitope-Based Vaccine Against MERS-CoV

Background and Objectives: Middle East Respiratory Syndrome (MERS) is a viral respiratory illness caused by a coronavirus called Middle East respiratory syndrome. In the current study, immunoinformatics studies were applied to design an epitope-based vaccine construct against Middle East Respiratory Syndrome. Materials and Methods: In this study, epitopes base vaccine construct was designed against MERS using immunoinformatics approach. Results: In this approach, the targeted proteins were screened, and probable antigenic, non-allergenic, and good water-soluble epitopes were selected for vaccine construction. In vaccine construction, the selected epitopes were joined by GPGPG linkers, and a linear multi-epitope vaccine was constructed. The vaccine construct underwent a physiochemical property analysis. The 3D structure of the vaccine construct was predicted and subjected to refinement. After the refinement, the 3D model was subjected to a molecular docking analysis, TLRs (TLR-3 and TLR-9) were selected as receptors for vaccine construct, and the molecular docking analysis study determined that the vaccine construct has binding ability with the targeted receptor. Conclusions: The docking analysis also unveils that the vaccine construct can properly activate immune system against the target virus however experimental validation is needed to confirm the in silico findings further.

Exploring Monkeypox: prospects for therapeutics through computational-aided drug discovery

Monkeypox virus (MPXV) has emerged as a significant public health concern due to its potential for human transmission and its severe clinical manifestations. This review synthesizes findings from peer-reviewed articles spanning the last two decades, shedding light on diverse aspects of MPXV research. The exploration commences with an analysis of transmission dynamics, including zoonotic and human-to-human transmission, and potential reservoir hosts. Detailed insights into viral replication mechanisms illuminate its influence on disease progression and pathogenicity. Understanding the genomic and virion structure of MPXV is pivotal for targeted interventions. Genomic characteristics contributing to virulence are examined, alongside recent advancements in virion structure elucidation through cutting-edge imaging techniques. Emphasizing combat strategies, the review lists potential protein targets within the MPXV lifecycle for computer-aided drug design (CADD). The role of protein-ligand interactions and molecular docking simulations in identifying potential drug candidates is highlighted. Despite the absence of approved MPXV medications, the review outlines updates on ongoing small molecules and vaccine development efforts, spanning traditional and innovative platforms. The evolving landscape of computational drug research for MPXV is explored, encompassing advanced algorithms, machine learning, and high-performance computing. In conclusion, this review offers a holistic perspective on MPXV research by integrating insights spanning transmission dynamics to drug design. Equipping researchers with multifaceted understanding underscore the importance of innovative methodologies and interdisciplinary collaborations in addressing MPXV's challenges as research advances.

Exploring glutathione transferase and Cathepsin L-like proteinase for designing of epitopes-based vaccine against Fasciola hepatica by immunoinformatics and biophysics studies

Fasciolosis is a zoonotic infection and is considered a developing deserted tropical illness threatening ruminant productivity and causing financial losses. Herein, we applied immunoinformatics and biophysics studies to develop an epitopes vaccine against Fasciola hepatica using glutathione transferase and Cathepsin L-like proteinase as possible vaccine candidates. Using the selected proteins, B- and T-cell epitopes were predicted. After epitopes prediction, the epitopes were clarified over immunoinformatics screening, and only five epitopes, EFGRWQQEKCTIDLD, RRNIWEKNVKHIQEH, FKAKYLTEMSRASDI, TDMTFEEFKAKYLTE, and YTAVEGQCR were selected for vaccine construction; selected epitopes were linked with the help of a GPGPG linker and attached with an adjuvant through another linker, EAAAK linker. Cholera toxin B subunit was used as an adjuvant. The ExPASy ProtParam tool server predicted 234 amino acids, 25.86257 kDa molecular weight, 8.54 theoretical pI, 36.86 instability index, and -0.424 grand average of hydropathicity. Molecular docking analysis predicted that the vaccine could activate the immune system against F. hepatica. We calculated negative binding energy values. A biophysics study, likely molecular docking molecular dynamic simulation, further validated the docking results. In molecular dynamic simulation analysis, the top hit docked compounds with the lowest binding energy values were subjected to MD simulation; the simulation analysis showed that the vaccine and immune cell receptors are stable and can activate the immune system. MMGBSA of -146.27 net energy (kcal/mol) was calculated for the vaccine-TLR2 complex, while vaccine-TLR4 of -148.11 net energy (kcal/mol) was estimated. Furthermore, the C-ImmSim bioinformatics tool predicted that the vaccine construct can activate the immune system against F. hepatica, eradicate the infection caused by F. hepatica, and reduce financial losses that need to be spent while protecting against infections of F. hepatica. The computational immune simulation unveils that the vaccine model can activate the immune system against F. hepatica; hence, the experimental scientist can validate the finding accomplished through computational approaches.

Novel point-of-care rapid detection of monkeypox virus

Monkeypox, a viral zoonotic disease caused by MPXV, has emerged as a significant global health concern since the first outbreak outside Africa in 2003. As of the current data, there have been 30 189 confirmed cases of monkeypox in 88 countries, with 29 844 cases reported in 81 countries. Given the absence of prior documented instances of the disease, swift and accurate testing is imperative to contain the spread of monkeypox. In this study, we developed a LAMP detection reagent for monkeypox and evaluated its performance in terms of sensitivity, specificity, repeatability, stability, linear range, and linearity, utilizing a commercial magnetic bead-based nucleic acid extraction system. This has led to the establishment of an integrated on-site detection platform for the monkeypox virus, utilizing a closed cartridge. The sensitivity was found to be 100 copies per μL, with no cross-reactivity observed with three other viruses, indicating robust performance. The parameters of repeatability, stability, linear range, and linearity were also assessed. For 28 simulated samples, the detection results obtained from the integrated system were consistent with those from conventional laboratory methods, specifically qPCR and LAMP detection following nucleic acid extraction. The entire process can be completed in approximately one hour, making it highly suitable for immediate rapid testing.

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.

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.

A novel vaccine construct against Zika virus fever: insights from epitope-based vaccine discovery through molecular modeling and immunoinformatics approaches

The Zika virus (ZIKV) is an emerging virus associated with the Flaviviridae family that mainly causes infection in pregnant women and leads to several abnormalities during pregnancy. This virus has unique properties that may lead to pathological diseases. As the virus has the ability to evade immune response, a crucial effort is required to deal with ZIKV. Vaccines are a safe means to control different pathogenic infectious diseases. In the current research, a multi-epitope-based vaccination against ZIKV is being designed using in silico methods. For the epitope prediction and prioritization phase, ZIKV polyprotein (YP_002790881.1) and flavivirus polyprotein (>YP_009428568.1) were targeted. The predicted B-cell epitopes were used for MHC-I and MHC-II epitope prediction. Afterward, several immunoinformatics filters were applied and nine (REDLWCGSL, MQDLWLLRR, YKKSGITEV, TYTDRRWCF, RDAFPDSNS, KPSLGLINR, ELIGRARVS, AITQGKREE, and EARRSRRAV) epitopes were found to be probably antigenic in nature, non-allergenic, non-toxic, and water soluble without any toxins. Selected epitopes were joined using a particular GPGPG linker to create the base vaccination for epitopes, and an extra EAAAK linker was used to link the adjuvant. A total of 312 amino acids with a molecular weight (MW) of 31.62762 and an instability value of 34.06 were computed in the physicochemical characteristic analysis, indicating that the vaccine design is stable. The molecular docking analysis predicted a binding energy of -329.46 (kcal/mol) for TLR-3 and -358.54 (kcal/mol) for TLR-2. Moreover, the molecular dynamics simulation analysis predicted that the vaccine and receptor molecules have stable binding interactions in a dynamic environment. The C-immune simulation analysis predicted that the vaccine has the ability to generate both humoral and cellular immune responses. Based on the design, the vaccine construct has the best efficacy to evoke immune response in theory, but experimental analysis is required to validate the in silico base approach and ensure its safety.

Design and validation of a novel multi-epitopes vaccine against hantavirus

Hantavirus is a member of the order Bunyavirales and an emerging global pathogen. Hantavirus infections have affected millions of people globally based on available epidemiological data and research studies. Hemorrhagic fever with renal syndrome (HFRS) and hantavirus pulmonary syndrome (HPS) are the two main human diseases associated with hantavirus infections. Hence, efforts are required to develop a potent vaccine against the pathogen. The only vaccine that is in use for hantavirus is an inactivated virus vaccine, "Hantavax", but it failed to produce neutralizing antibodies. Vaccine development is of much importance in dealing with the surge of hantavirus globally. In this study, hantavirus five proteins (N protein, G1 and G2, L protein, and non-structural proteins) were used in NetCTL 1.2 program to predict T-cell epitopes. To predict major histocompatibility complex (MHC) binding alleles, an immune epitope database (IEDB) was used. All predicted epitopes were then investigated for different immunoinformatics analyses such as antigenicity and toxicity analyses. The good water-soluble, non-toxic, probable antigenic, and DRB*0101 binder was selected. A multi-epitopes-based vaccine designing was then done where linkers were used to connect the shortlisted epitopes. In addition, an adjuvant molecule was supplementary to the multi-epitopes peptide to improve the vaccine's immunogenic potential. The final vaccine construct's three-dimensional structure was modeled by ab initio method. The vaccine molecule was then evaluated for its binding potential with TLR-3 immune receptor, which is key for its recognition and processing by the host immune system. Docking studies were performed using HADDOCK software. The best-docked complex was selected and visualized for intermolecular binding and interactions using UCSF Chimera 1.16 software. The findings revealed that the designed vaccine might be a potential vaccine against hantavirus and can be used in experimental animal model testings.Communicated by Ramaswamy H. Sarma.

Design and computational evaluation of a novel multi-epitope hybrid vaccine against monkeypox virus: Potential targets and immunogenicity assessment for pandemic preparedness

Monkeypox is a type of DNA-enveloped virus that belongs to the orthopoxvirus family, closely related to the smallpox virus. It can cause an infectious disease in humans known as monkeypox disease. Although there are multiple drugs and vaccines designed to combat orthopoxvirus infections, with a primary focus on smallpox, the recent spread of the monkeypox virus to over 50 countries have ignited a mounting global concern. This unchecked viral proliferation has raised apprehensions about the potential for a pandemic corresponding to the catastrophic impact of COVID-19. This investigation explored the structural proteins of monkeypox virus as potential candidates for designing a novel hybrid multi-epitope vaccine. The epitopes obtained from the selected proteins were screened to ensure their non-allergenicity, non-toxicity, and antigenicity to trigger T and B-cell responses. The interaction of the vaccine with toll-like receptor-3 (TLR-3) and major histocompatibility complexes (MHCs) was assessed using Cluspro 2.0. To establish the reliability of the docked complexes, a comprehensive evaluation was conducted using Immune and MD Simulations and Normal Mode Analysis. However, to validate the computational results of this study, additional in-vitro and in-vivo research is essential.

Reverse engineering protection: A comprehensive survey of reverse vaccinology-based vaccines targeting viral pathogens

Vaccines have significantly reduced the impact of numerous deadly viral infections. However, there is an increasing need to expedite vaccine development in light of the recurrent pandemics and epidemics. Also, identifying vaccines against certain viruses is challenging due to various factors, notably the inability to culture certain viruses in cell cultures and the wide-ranging diversity of MHC profiles in humans. Fortunately, reverse vaccinology (RV) efficiently overcomes these limitations and has simplified the identification of epitopes from antigenic proteins across the entire proteome, streamlining the vaccine development process. Furthermore, it enables the creation of multiepitope vaccines that can effectively account for the variations in MHC profiles within the human population. The RV approach offers numerous advantages in developing precise and effective vaccines against viral pathogens, including extensive proteome coverage, accurate epitope identification, cross-protection capabilities, and MHC compatibility. With the introduction of RV, there is a growing emphasis among researchers on creating multiepitope-based vaccines aiming to stimulate the host's immune responses against multiple serotypes, as opposed to single-component monovalent alternatives. Regardless of how promising the RV-based vaccine candidates may appear, they must undergo experimental validation to probe their protection efficacy for real-world applications. The time, effort, and resources allocated to the laborious epitope identification process can now be redirected toward validating vaccine candidates identified through the RV approach. However, to overcome failures in the RV-based approach, efforts must be made to incorporate immunological principles and consider targeting the epitope regions involved in disease pathogenesis, immune responses, and neutralizing antibody maturation. Integrating multi-omics and incorporating artificial intelligence and machine learning-based tools and techniques in RV would increase the chances of developing an effective vaccine. This review thoroughly explains the RV approach, ideal RV-based vaccine construct components, RV-based vaccines designed to combat viral pathogens, its challenges, and future perspectives.

Immunoinformatic Approach for Rational Identification of Immunogenic Peptides Against Host Entry and/or Exit Mpox Proteins and Potential Multiepitope Vaccine Construction

COVID-19 has intensified humanity's concern about the emergence of new pandemics. Since 2018, epidemic outbreaks of the mpox virus have become worrisome. In June 2022, the World Health Organization declared the disease a global health emergency, with 14 500 cases reported by the Centers for Disease Control and Prevention in 60 countries. Therefore, the development of a vaccine based on the current virus genome is paramount in combating new cases. In view of this, we hypothesized the obtainment of rational immunogenic peptides predicted from proteins responsible for entry of the mpox virus into the host (A17L, A26L/A30L, A33R, H2R, L1R), exit (A27L, A35R, A36R, C19L), and both (B5R). To achieve this, we aligned the genome sequencing data of mpox virus isolated from an infected individual in the United States in June 2022 (ON674051.1) with the reference genome dated 2001 (NC_003310.1) for conservation analysis. The Immune Epitope Database server was used for the identification and characterization of the epitopes of each protein related to major histocompatibility complex I or II interaction and recognition by B-cell receptors, resulting in 138 epitopes for A17L, 233 for A28L, 48 for A33R, 77 for H2R, 77 for L1R, 270 for A27L, 72 for A35R, A36R, 148 for C19L, and 276 for B5R. These epitopes were tested in silico for antigenicity, physicochemical properties, and allergenicity, resulting in 51, 40, 10, 34, 38, 57, 25, 7, 47, and 53 epitopes, respectively. Additionally, to select an epitope with the highest promiscuity of binding to major histocompatibility complexes and B-cell receptor simultaneously, all epitopes of each protein were aligned, and the most repetitive and antigenic regions were identified. By classifying the results, we obtained 23 epitopes from the entry proteins, 16 from the exit proteins, and 7 from both. Subsequently, 1 epitope from each protein was selected, and all 3 were fused to construct a chimeric protein that has potential as a multiepitope vaccine. The constructed vaccine was then analyzed for its physicochemical, antigenic, and allergenic properties. Protein modeling, molecular dynamics, and molecular docking were performed on Toll-like receptors 2, 4, and 8, followed by in silico immune simulation of the vaccine. Finally, the results indicate an effective, stable, and safe vaccine that can be further tested, especially in vitro and in vivo, to validate the findings demonstrated in silico.

Multi-epitopes vaccine design for surface glycoprotein against SARS-CoV-2 using immunoinformatic approach

Background

The recent COVID vaccinations have successfully reduced death and severity but did not stop the transmission of viruses by the emerging SARS-CoV-2 strain. There is a need for better and long-lasting dynamic vaccines for numerous prevailing strains and the evolving SARS-CoV-2 virus, necessitating the development of broad-spectrum strains being used to stop infection by reducing the spread rate and re-infection. The spike (S) glycoprotein is one of the proteins expressed commonly in the early phases of SARS-CoV-2 infection. It has been identified as the most immunogenic protein of SARS-CoV-2.

Methods

In this study, advanced bioinformatics techniques have been exploited to design the novel multi-epitope vaccine using conserved S protein portions from widespread strains of SARS-CoV-2 to predict B cell and T cell epitopes. These epitopes were selected based on toxicity, antigenicity score and immunogenicity. Epitope combinations were used to construct the maximum potent multi-epitope construct with potential immunogenic features. EAAAK, AAY, and GPGPG were used as linkers to construct epitopes.

Results

The developed vaccine has shown positive results. After the chimeric vaccine construct was cloned into the PET28a (+) vector for expression screening in Escherichia coli, the potential expression of the construct was identified.

Conclusion

The construct vaccine performed well in computer-based immune response simulation and covered a variety of allelic populations. These computational results are more helpful for further analysis of our contract vaccine, which can finally help control and prevent SARS-CoV-2 infections worldwide.

Breaking Barriers: Current Advances and Future Directions in Mpox Therapy

BACKGROUND

Mpox, a newly discovered zoonotic infection, can be transmitted from animal to human and between humans. Serological and genomic studies are used to identify the virus.

OBJECTIVE

Currently, there are no proven effective treatments for Mpox. Also, the safety and efficacy of intravenous vaccinia immune globulin, oral Tecovirimat (an inhibitor of intracellular viral release), and oral Brincidofovir (a DNA polymerase inhibitor) against the Mpox virus are uncertain, highlighting the need for more effective and safe treatments. As a result, drug repurposing has emerged as a promising strategy to identify previously licensed drugs that can be repurposed to treat Mpox.

RESULTS

Various approaches have been employed to identify previously approved drugs that can target specific Mpox virus proteins, including thymidylate kinase, D9 decapping enzyme, E8 protein, Topoisomerase1, p37, envelope proteins (D13, A26, and H3), F13 protein, virus's main cysteine proteases, and DNA polymerase.

CONCLUSION

In this summary, we provide an overview of potential drugs that could be used to treat Mpox and discuss the underlying biological processes of their actions.

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.

Exploring the key genomic variation in monkeypox virus during the 2022 outbreak

BACKGROUND

In 2022, a global outbreak of monkeypox occurred with a significant shift in its epidemiological characteristics. The monkeypox virus (MPXV) belongs to the B.1 lineage, and its genomic variations that were linked to the outbreak were investigated in this study. Previous studies have suggested that viral genomic variation plays a crucial role in the pathogenicity and transmissibility of viruses. Therefore, understanding the genomic variation of MPXV is crucial for controlling future outbreaks.

METHODS

This study employed bioinformatics and phylogenetic approaches to evaluate the key genomic variation in the B.1 lineage of MPXV. A total of 979 MPXV strains were screened, and 212 representative strains were analyzed to identify specific substitutions in the viral genome. Reference sequences were constructed for each of the 10 lineages based on the most common nucleotide at each site. A total of 49 substitutions were identified, with 23 non-synonymous substitutions. Class I variants, which had significant effects on protein conformation likely to affect viral characteristics, were classified among the non-synonymous substitutions.

RESULTS

The phylogenetic analysis revealed 10 relatively monophyletic branches. The study identified 49 substitutions specific to the B.1 lineage, with 23 non-synonymous substitutions that were classified into Class I, II, and III variants. The Class I variants were likely responsible for the observed changes in the characteristics of circulating MPXV in 2022. These key mutations, particularly Class I variants, played a crucial role in the pathogenicity and transmissibility of MPXV.

CONCLUSION

This study provides an understanding of the genomic variation of MPXV in the B.1 lineage linked to the recent outbreak of monkeypox. The identification of key mutations, particularly Class I variants, sheds light on the molecular mechanisms underlying the observed changes in the characteristics of circulating MPXV. Further studies can focus on functional domains affected by these mutations, enabling the development of effective control strategies against future monkeypox outbreaks.

A novel therapeutic approach to prevent Helicobacter pylori induced gastric cancer using networking biology, molecular docking, and simulation approaches

Helicobacter pylori infects 50% of the world population and in 80% of cases, the infection progresses to the point where an ulcer develops leading to gastric cancer (GC). This study aimed to prevent GC by predicting Hub genes that are inducing GC. Furthermore, the study objective was to screen inhibitory molecules that block the function of predicted genes through several biophysical approaches. These proteins, such as Mucin 4 (MUC4) and Baculoviral IAP repeat containing 3 (BIRC3), had LogFC values of 2.28 and 3.39, respectively, and were found to be substantially expressed in those who had H. pylori infection. The MUC4 and BIRC3 inhibit apoptosis of infected cells and promote cancerous cell survival. The proteins were examined for their Physico-chemical characteristics, 3D structure and secondary structure analysis, solvent assessable surface area (SASA), active site identification, and network analysis. The MUC4 and BIRC3 expression was inhibited by docking eighty different compounds collected from the ZINC database. Fifty-seven compounds were successfully docked into the active site resulting in the lowest binding energy scores. The ZINC585267910 and ZINC585268691 compounds showed the lowest binding energy of -8.5 kcal/mol for MUC4 and -7.1 kcal/mol for BIRC3, respectively, and were considered best-docked solutions for molecular dynamics simulations. The mean root mean square deviation (RMSD) value for the ZINC585267910-MUC4 complex was 0.86 Å and the ZINC585268691-BIRC3 complex was 1.01 Å. The net MM/GBSA energy value of the ZINC585267910-MUC4 complex estimated was -46.84 kcal/mol and that of the ZINC585268691-BIRC3 complex was -44.84 kcal/mol. In a nutshell, the compounds might be investigated further as an inhibitor of the said proteins to stop the progress of GC induced by H. pylori.Communicated by Ramaswamy H. Sarma.

Immunoinformatics-based multi-epitope vaccine design for the re-emerging monkeypox virus

BACKGROUND

On May 7, 2022, WHO reported a new monkeypox case. By May 2023 over 80,000 cases had been reported worldwide outside previously endemic nations. (This primarily affected the men who have sex with men (MSM) community in rich nations). The present research aims to develop a multi-epitope vaccine for the monkeypox virus (MPXV) using structural and cell surface proteins.

METHODS

The first part of the research involved retrieving protein sequences. The Immune Epitope Database (IEDB) was then used to analyze the B and T lymphocyte epitopes. After analyzing the sensitizing properties, toxicity, antigenicity, and molecular binding, appropriate linkers were utilizedto connect selected epitopes to adjuvants, and the structure of the vaccine was formulated. Algorithms from the field of immunoinformatics predicted the secondary and tertiary structures of vaccines. The physical, chemical, and structural properties were refined and validated to achieve maximum stability. Molecular docking and molecular dynamic simulations were subsequently employed to assess the vaccine's efficacy. Afterward, the ability of the vaccine to interact with toll-like receptors 3 and 4 (TLR3 and TLR4) was evaluated. Finally, the optimized sequence was then introduced into the Escherichia coli (E. coli) PET30A + vector.

RESULTS

An immunoinformatics evaluation suggested that such a vaccine might be safe revealed that this vaccine is safe, hydrophilic, temperature- and condition-stable, and can stimulate innate immunity by binding to TLR3 and TLR4.

CONCLUSION

Our findings suggest that the first step in MPXV pathogenesis is structural and cell surface epitopes. In this study, the most effective and promising epitopes were selected and designed throughprecision servers. Furthermore,through the utilization of multi-epitope structures and a combination of two established adjuvants, this research has the potential to be a landmarkin developing an antiviralvaccine against MPXV. However, additional in vitro and in vivo tests are required to confirm these results.

In silico design and immunoinformatics analysis of a universal multi-epitope vaccine against monkeypox virus

Monkeypox virus (MPXV) outbreaks have been reported in various countries worldwide; however, there is no specific vaccine against MPXV. In this study, therefore, we employed computational approaches to design a multi-epitope vaccine against MPXV. Initially, cytotoxic T lymphocyte (CTL), helper T lymphocyte (HTL), linear B lymphocytes (LBL) epitopes were predicted from the cell surface-binding protein and envelope protein A28 homolog, both of which play essential roles in MPXV pathogenesis. All of the predicted epitopes were evaluated using key parameters. A total of 7 CTL, 4 HTL, and 5 LBL epitopes were chosen and combined with appropriate linkers and adjuvant to construct a multi-epitope vaccine. The CTL and HTL epitopes of the vaccine construct cover 95.57% of the worldwide population. The designed vaccine construct was found to be highly antigenic, non-allergenic, soluble, and to have acceptable physicochemical properties. The 3D structure of the vaccine and its potential interaction with Toll-Like receptor-4 (TLR4) were predicted. Molecular dynamics (MD) simulation confirmed the vaccine's high stability in complex with TLR4. Finally, codon adaptation and in silico cloning confirmed the high expression rate of the vaccine constructs in strain K12 of Escherichia coli (E. coli). These findings are very encouraging; however, in vitro and animal studies are needed to ensure the potency and safety of this vaccine candidate.

Application of Artificial Intelligence Techniques for Monkeypox: A Systematic Review

Monkeypox or Mpox is an infectious virus predominantly found in Africa. It has spread to many countries since its latest outbreak. Symptoms such as headaches, chills, and fever are observed in humans. Lumps and rashes also appear on the skin (similar to smallpox, measles, and chickenpox). Many artificial intelligence (AI) models have been developed for accurate and early diagnosis. In this work, we systematically reviewed recent studies that used AI for mpox-related research. After a literature search, 34 studies fulfilling prespecified criteria were selected with the following subject categories: diagnostic testing of mpox, epidemiological modeling of mpox infection spread, drug and vaccine discovery, and media risk management. In the beginning, mpox detection using AI and various modalities was described. Other applications of ML and DL in mitigating mpox were categorized later. The various machine and deep learning algorithms used in the studies and their performance were discussed. We believe that a state-of-the-art review will be a valuable resource for researchers and data scientists in developing measures to counter the mpox virus and its spread.

Targeted Protein-Specific Multi-Epitope-Based Vaccine Designing against Human Cytomegalovirus by Using Immunoinformatics Approaches

Cytomegaloviruses are emerging pathogenic agents known to cause congenital disorders in humans. In this study, immune epitopes (CTL, B cell and HTL) were screened for highly antigenic target proteins of the Human Cytomegalovirus. These shortlisted epitopes were then joined together through suitable linkers to construct multi epitope-based vaccine constructs (MEVCs). The functionality of each vaccine construct was evaluated through tertiary vaccine structure modelling and validations. Furthermore, physio-chemical properties including allergenicity, antigenicity molecular weight and many others were also predicted. The vaccine designs were also docked with the human TLR-4 receptor to demonstrate the receptor specific affinity and formed interactions. The vaccine peptides sequences were also subjected to codon optimization to confirm the potential vaccines expression in E. coli hosts. Additionally, all the MEVCs were also evaluated for immune response (IgG and IgM) induction. However, further in vivo tests are needed to ensure the efficacy of these vaccine designs.

An overview on Monkeypox, Current Paradigms and Advances in its Vaccination, Treatment and Clinical Management: Trends, Scope, Promise and Challenges

Monkeypox virus is an orthopoxvirus sharing the common genus with variola and vaccinia virus. Most of the monkeypox (MPX) cases had been reported from the central and west African region (the main endemic areas) prior to 2022 but there was a sudden outbreak in May, 2022 disseminating the infections to thousands of people even in non-endemic countries, posing a global public health emergency. MPX was considered a rae and neglected disease, however the 2022 MPX outbreaks in multiple countries attracted attention of worldwide researchers to pace up for carrying out researches on various aspects of MPXV including attempts to design and develop diagnostics, vaccines, drugs and therapeutics counteract MPX. Apart from being a zoonotic disease, the current outbreaks highlighted rapid human-to-human transmission of MPXV, besides the reverse zoonosis has also been documented with recent first report of human-to-dog transmission, urging a call for the importance of one health approach. Atypical and unusual disease manifestations as well asymptomatic MPXV infections have also been observed during 2022 MPX outbreak. The affected patients typically develop a rash resulting in a mild disease followed by recovery with some supportive care and use of antivirals such as tecovirimat, cidofovir and brincidofovir in severe disease cases. Modified vaccinia Ankara (MVA) vaccine with an excellent safety profile has been recommended to patients with higher risk exposure and immunocompromised individuals. Moreover, another vaccine the replication-competent vaccine (ACAM2000) could be a suitable alternative to MVA’s non-availability to some selective immunocompetent individuals. Current review highlights the salient aspects of management and treatment of monkeypox along with underlying promises in terms of therapeutics and a variety of challenges posed due to current global public health emergency situation to counteract MPX.

Saied A, Dhama K. Major Advances in Monkeypox Vaccine Research and Development – An Update

Monkeypox (MPX) is a zoonotic disease that is endemic to the western and central regions of Africa and it is caused by monkeypox virus (MPXV), which is classified as a member of the Poxviridae family, specifically the Chordopoxvirinae subfamily, and the Orthopoxvirus genus. The current multiregional outbreak of MPX, which started in May of 2022, has since swiftly spread across the globe and thus has been declared a global public health emergency by the World Health Organization (WHO). Protective immunity against MPXV can be achieved by administering a smallpox vaccination, as the two viruses share antigenic properties. Although smallpox was declared eradicated in 1980, the vaccine campaign was halted the following year, leaving the population with significantly less immunity than it had before. The potential for human-to-human transmission of MPXV has grown as a result. Due to the lack of a particular treatment for MPX infection, anti-viral medications initially designed for the smallpox virus are being employed. However, the prognosis for MPX may vary depending on factors like immunization history, pre-existing illnesses, and comorbidities, even though the majority of persons who develop MPX have a mild, self-limiting illness. Vaccines and antiviral drugs are being researched as potential responses to the latest 2022 MPX epidemic. The first-generation smallpox vaccinations maintained in national stockpiles of several countries are not recommended due to not meeting the current safety and manufacturing criteria, as stated by the WHO. Newer, safer (second- and third-generation) smallpox vaccines, such as JYNNEOSTM, which has been licensed for the prevention of MPX, are indicated as potentially useful in the interim guideline. Studies on vaccines and antiviral drugs are still being investigated as possible remedies to the recent MPX outbreak. This mini-review article serves as a retrospective look at the evolution of smallpox vaccines from their inception in the 1700s to the current trends up to the end of year 2022, specifically for developing monkeypox vaccines.

Design of a multi-epitope protein as a subunit vaccine against lumpy skin disease using an immunoinformatics approach

Lumpy skin disease (LSD) is a transboundary viral disease of cattle that causes substantial economic loss globally. There is no specific treatment and subunit vaccine for this disease to date. Reports of the global spread of this disease are worrisome. We designed a multi-epitope protein using an immunoinformatics approach in this study. We analyzed the proteome of LSDV and found 32 structural/surface proteins. Four of these 32 proteins were predicted as antigenic and non-homologous to bovine and highly conserved in 26 LSDV isolates. The predicted B-cell epitopes and CTL epitopes were stitched together with the help of an AAY linker leading to the formation of a multi-epitope protein. The in silico study revealed that the modeled subunit vaccine candidate and TLR4 receptor interact with high affinity. This interaction was also found to be stable using a molecular dynamics simulation study. Our study demonstrates a leap towards developing a subunit vaccine against LSD.

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.

Theoretical study of glycoluril by highly symmetrical magnesium oxide Mg12O12 nanostructure: adsorption, detection, SERS enhancement, and electrical conductivity study

Using metal substrates that are nanoscale in size, surface-enhanced Raman scattering (SERS) is a technique for enhancing the Raman signal of biomolecules. Numerous industries including sensing materials, adsorption and medical devices, use nanomaterials like nanocages and nanoclusters. To discover a possible novel sensor platform involving a small metal cluster and a curved rigid substrate, we used density functional theoretical (DFT) simulations to explore the adsorption of glycoluril (GLC), a prospective drug intermediate, on a pure magnesium oxide cage (Mg₁₂O₁₂). This well defined cage was used as (i) an exact probable structure that could be used as well as (ii) a general model for MgO nanostructures. We also investigated the mono Al-doped Mg₁₂O₁₂ nanocage version Mg₁₁AlO₁₂. All computations were performed at the M06-2X level of theory. The GLC binds to the Mg₁₂O₁₂ nanocage by way of strong donor-acceptor interactions. The adsorption is releasing - 45.80 kcal mol^-1 of energy. Due to Al doping, the energy gap of GLC-Mg₁₁AlO₁₂ (1.91 eV) is reduced from that of GLC-Mg₁₂O₁₂ (4.28 eV) and hence there is an increase in electrical conductivity of GLC-Mg₁₁AlO₁₂. The electronic change in the nanocage's conductivity can be transformed into an electrical signal which can be used to detect the presence of the drug analyte. In addition, when a GLC molecule is present, the work function of the nanocage is also reduced. The MgO nanocage, we conclude, is a work function type as well as a possible electronic sensor for GLC drug detection. GLC desorption from the Mg₁₁AlO₁₂ surface recovers more quickly in comparison with Mg₁₂O₁₂ recovery time. The AIM and NCIs assessed in this study were performed to help analyze the electronic structures of the complexes. Our findings pave the possibility for Mg₁₁AlO₁₂ nanostructures to be used in drug recognition.