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Tan C, xiao Y, Liu T, Chen S, Zhou J, Zhang S, Hu Y, Wu A, Li C. Development of multi-epitope mRNA vaccine against Clostridioides difficile using reverse vaccinology and immunoinformatics approaches. Synth Syst Biotechnol 2024; 9:667-683. [PMID: 38817826 PMCID: PMC11137598 DOI: 10.1016/j.synbio.2024.05.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2024] [Revised: 04/28/2024] [Accepted: 05/15/2024] [Indexed: 06/01/2024] Open
Abstract
Clostridioides difficile (C. difficile), as the major pathogen of diarrhea in healthcare settings, has become increasingly prevalent within community populations, resulting in significant morbidity and mortality. However, the therapeutic options for Clostridioides difficile infection (CDI) remain limited, and as of now, no authorized vaccine is available to combat this disease. Therefore, the development of a novel vaccine against C. difficile is of paramount importance. In our study, the complete proteome sequences of 118 strains of C. difficile were downloaded and analyzed. We found four antigenic proteins that were highly conserved and can be used for epitope identification. We designed two vaccines, WLcd1 and WLcd2, that contain the ideal T-cell and B-cell epitopes, adjuvants, and the pan HLA DR-binding epitope (PADRE) sequences. The biophysical and chemical assessments of these vaccine candidates indicated that they were suitable for immunogenic applications. Molecular docking analyses revealed that WLcd1 bonded with higher affinity to Toll-like receptors (TLRs) than WLcd2. Furthermore, molecular dynamics (MD) simulations, performed using Gmx_MMPBSA v1.56, confirmed the binding stability of WLcd1 with TLR2 and TLR4. The preliminary findings suggested that this multi-epitope vaccine could be a promising candidate for protection against CDI; however, experimental studies are necessary to confirm these predictions.
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Affiliation(s)
- Caixia Tan
- Infection Control Center, Xiangya Hospital, Central South University, Changsha, Hunan Province, 410008, China
- National Clinical Research Center for Geriatric Disorders (XiangYa Hospital), Changsha, Hunan Province, 410008, China
| | - Yuanyuan xiao
- Infection Control Center, Xiangya Hospital, Central South University, Changsha, Hunan Province, 410008, China
- National Clinical Research Center for Geriatric Disorders (XiangYa Hospital), Changsha, Hunan Province, 410008, China
| | - Ting Liu
- Infection Control Center, Xiangya Hospital, Central South University, Changsha, Hunan Province, 410008, China
- National Clinical Research Center for Geriatric Disorders (XiangYa Hospital), Changsha, Hunan Province, 410008, China
| | - Siyao Chen
- Infection Control Center, Xiangya Hospital, Central South University, Changsha, Hunan Province, 410008, China
- National Clinical Research Center for Geriatric Disorders (XiangYa Hospital), Changsha, Hunan Province, 410008, China
| | - Juan Zhou
- Infection Control Center, Xiangya Hospital, Central South University, Changsha, Hunan Province, 410008, China
- National Clinical Research Center for Geriatric Disorders (XiangYa Hospital), Changsha, Hunan Province, 410008, China
| | - Sisi Zhang
- Infection Control Center, Xiangya Hospital, Central South University, Changsha, Hunan Province, 410008, China
- National Clinical Research Center for Geriatric Disorders (XiangYa Hospital), Changsha, Hunan Province, 410008, China
| | - Yiran Hu
- Infection Control Center, Xiangya Hospital, Central South University, Changsha, Hunan Province, 410008, China
- National Clinical Research Center for Geriatric Disorders (XiangYa Hospital), Changsha, Hunan Province, 410008, China
| | - Anhua Wu
- Infection Control Center, Xiangya Hospital, Central South University, Changsha, Hunan Province, 410008, China
- National Clinical Research Center for Geriatric Disorders (XiangYa Hospital), Changsha, Hunan Province, 410008, China
| | - Chunhui Li
- Infection Control Center, Xiangya Hospital, Central South University, Changsha, Hunan Province, 410008, China
- National Clinical Research Center for Geriatric Disorders (XiangYa Hospital), Changsha, Hunan Province, 410008, China
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Rahman JF, Hoque H, Jubayer AA, Jewel NA, Hasan MN, Chowdhury AT, Prodhan SH. Alfin-like (AL) transcription factor family in Oryza sativa L.: Genome-wide analysis and expression profiling under different stresses. BIOTECHNOLOGY REPORTS (AMSTERDAM, NETHERLANDS) 2024; 43:e00845. [PMID: 38962072 PMCID: PMC11217604 DOI: 10.1016/j.btre.2024.e00845] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/25/2024] [Revised: 04/24/2024] [Accepted: 05/29/2024] [Indexed: 07/05/2024]
Abstract
Oryza sativa L. is the world's most essential and economically important food crop. Climate change and ecological imbalances make rice plants vulnerable to abiotic and biotic stresses, threatening global food security. The Alfin-like (AL) transcription factor family plays a crucial role in plant development and stress responses. This study comprehensively analyzed this gene family and their expression profiles in rice, revealing nine AL genes, classifying them into three distinct groups based on phylogenetic analysis and identifying four segmental duplication events. RNA-seq data analysis revealed high expression levels of OsALs in different tissues, growth stages, and their responsiveness to stresses. RT-qPCR data showed significant expression of OsALs in different abiotic stresses. Identification of potential cis-regulatory elements in promoter regions has also unveiled their involvement. Tertiary structures of the proteins were predicted. These findings would lay the groundwork for future research to reveal their molecular mechanism in stress tolerance and plant development.
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Affiliation(s)
- Jeba Faizah Rahman
- Department of Genetic Engineering and Biotechnology, Shahjalal University of Science and Technology, Sylhet, 3114, Bangladesh
| | - Hammadul Hoque
- Department of Genetic Engineering and Biotechnology, Shahjalal University of Science and Technology, Sylhet, 3114, Bangladesh
| | - Abdullah -Al- Jubayer
- Department of Biotechnology and Genetic Engineering, Bangabandhu Sheikh Mujibur Rahman Science and Technology University, Gopalganj, 8100, Bangladesh
| | - Nurnabi Azad Jewel
- Department of Genetic Engineering and Biotechnology, Shahjalal University of Science and Technology, Sylhet, 3114, Bangladesh
| | - Md. Nazmul Hasan
- Department of Genetic Engineering and Biotechnology, Shahjalal University of Science and Technology, Sylhet, 3114, Bangladesh
| | - Aniqua Tasnim Chowdhury
- Department of Genetic Engineering and Biotechnology, Shahjalal University of Science and Technology, Sylhet, 3114, Bangladesh
| | - Shamsul H. Prodhan
- Department of Genetic Engineering and Biotechnology, Shahjalal University of Science and Technology, Sylhet, 3114, Bangladesh
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3
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Nguyen TL, Kim H. Discovering peptides and computational investigations of a multiepitope vaccine target Mycobacterium tuberculosis. Synth Syst Biotechnol 2024; 9:391-405. [PMID: 38585591 PMCID: PMC10997871 DOI: 10.1016/j.synbio.2024.03.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Revised: 03/09/2024] [Accepted: 03/12/2024] [Indexed: 04/09/2024] Open
Abstract
Mycobacterium tuberculosis (MTB) is the causative agent of tuberculosis (TB), a prevalent airborne infectious disease. Despite the availability of the Bacille Calmette-Guerin vaccine, its global efficacy remains modest, and tuberculosis persists as a significant global public health threat. Addressing this challenge and advancing towards the End MTB Strategy, we developed a multiepitope vaccine (MEV) based on immunoinformatics and computational approaches. Immunoinformatics screening of MBT protein identified immune-dominant epitopes based on Major Histocompatibility Complex (MHC) allele binding, immunogenicity, antigenicity, allergenicity, toxicity, and cytokine inducibility. Selected epitopes were integrated into an MEV construct with adjuvant and linkers, forming a fully immunogenic vaccine candidate. Comprehensive analyses encompassed the evaluation of immunological and physicochemical properties, determination of tertiary structure, molecular docking with Toll-Like Receptors (TLR), molecular dynamics (MD) simulations for all atoms, and immune simulations. Our MEV comprises 534 amino acids, featuring 6 cytotoxic T lymphocyte, 8 helper T lymphocyte, and 7 linear B lymphocyte epitopes, demonstrating high antigenicity and stability. Notably, molecular docking studies and triplicate MD simulations revealed enhanced interactions and stability of MEV with the TLR4 complex compared to TLR2. In addition, the immune simulation indicated the capacity to effectively induce elevated levels of antibodies and cytokines, emphasizing the vaccine's robust immunogenic response. This study presents a promising MEV against TB, exhibiting favorable immunological and physicochemical attributes. The findings provide theoretical support for TB vaccine development. Our study aligns with the global initiative of the End MTB Strategy, emphasizing its potential impact on addressing persistent challenges in TB control.
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Affiliation(s)
- Truc Ly Nguyen
- Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, 08826, Republic of Korea
| | - Heebal Kim
- Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, 08826, Republic of Korea
- Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul, 08826, Republic of Korea
- eGnome, Inc., Seoul, 05836, Republic of Korea
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Nguyen TL, Kim H. Integrating immunoinformatics and computational epitope prediction for a vaccine candidate against respiratory syncytial virus. Infect Dis Model 2024; 9:763-774. [PMID: 38708060 PMCID: PMC11068479 DOI: 10.1016/j.idm.2024.04.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2024] [Revised: 04/04/2024] [Accepted: 04/10/2024] [Indexed: 05/07/2024] Open
Abstract
Respiratory syncytial virus (RSV) poses a significant global health threat, especially affecting infants and the elderly. Addressing this, the present study proposes an innovative approach to vaccine design, utilizing immunoinformatics and computational strategies. We analyzed RSV's structural proteins across both subtypes A and B, identifying potential helper T lymphocyte, cytotoxic T lymphocyte, and linear B lymphocyte epitopes. Criteria such as antigenicity, allergenicity, toxicity, and cytokine-inducing potential were rigorously examined. Additionally, we evaluated the conservancy of these epitopes and their population coverage across various RSV strains. The comprehensive analysis identified six major histocompatibility complex class I (MHC-I) binding, five MHC-II binding, and three B-cell epitopes. These were integrated with suitable linkers and adjuvants to form the vaccine. Further, molecular docking and molecular dynamics simulations demonstrated stable interactions between the vaccine candidate and human Toll-like receptors (TLR4 and TLR5), with a notable preference for TLR4. Immune simulation analysis underscored the vaccine's potential to elicit a strong immune response. This study presents a promising RSV vaccine candidate and offers theoretical support, marking a significant advancement in vaccine development efforts. However, the promising in silico findings need to be further validated through additional in vivo studies.
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Affiliation(s)
- Truc Ly Nguyen
- Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, 08826, Republic of Korea
| | - Heebal Kim
- Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, 08826, Republic of Korea
- Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul, 08826, Republic of Korea
- eGnome, Inc., Seoul, 05836, Republic of Korea
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Vouzina OD, Tafanidis A, Glykos NM. The Curious Case of A31P, a Topology-Switching Mutant of the Repressor of Primer Protein: A Molecular Dynamics Study of Its Folding and Misfolding. J Chem Inf Model 2024; 64:6081-6091. [PMID: 39052910 PMCID: PMC11323272 DOI: 10.1021/acs.jcim.4c00575] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2024] [Revised: 07/18/2024] [Accepted: 07/18/2024] [Indexed: 07/27/2024]
Abstract
The effect of mutations on protein structures is usually rather localized and minor. Finding a mutation that can single-handedly change the fold and/or topology of a protein structure is a rare exception. The A31P mutant of the homodimeric Repressor of primer (Rop) protein is one such exception: This single mutation ─and as demonstrated by two independent crystal structure determinations─ can convert the canonical (left-handed/all-antiparallel) 4-α-helical bundle of Rop to a new form (right-handed/mixed parallel and antiparallel bundle) displaying a previously unobserved "bisecting U" topology. The main problem with understanding the dramatic effect of this mutation on the folding of Rop is to understand its very existence: Most computational methods appear to agree that the mutation should have had no appreciable effect, with the majority of energy minimization methods and protein structure prediction protocols indicating that this mutation is fully consistent with the native Rop structure, requiring only a local and minor change at the mutation site. Here we use two long (10 μs each) molecular dynamics simulations to compare the stability and dynamics of the native Rop versus a hypothetical structure that is identical with the native Rop but is carrying this single Alanine31 to Proline mutation. Comparative analysis of the two trajectories convincingly shows that, in contrast to the indications from energy minimization ─but in agreement with the experimental data─, this hypothetical native-like A31P structure is unstable, with its turn regions almost completely unfolding, even under the relatively mild 320 K NpT simulations that we have used for this study. We discuss the implication of these findings for the folding of the A31P mutant, especially with respect to the proposed model of a double-funneled energy landscape.
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Affiliation(s)
- Olympia-Dialekti Vouzina
- Department of Molecular Biology and
Genetics, Democritus University of Thrace,
University campus, 68100 Alexandroupolis, Greece
| | - Alexandros Tafanidis
- Department of Molecular Biology and
Genetics, Democritus University of Thrace,
University campus, 68100 Alexandroupolis, Greece
| | - Nicholas M. Glykos
- Department of Molecular Biology and
Genetics, Democritus University of Thrace,
University campus, 68100 Alexandroupolis, Greece
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Ávila-Martínez EG, Cardoso TL, Pereira IL, Caballero PS, Wozeak DR, Neto ACPS, Pinto LDS, Hartwig DD. Immunoinformatic approaches for ErpY-LemA chimeric protein design for use in leptospirosis control. J Appl Microbiol 2024; 135:lxae179. [PMID: 39020252 DOI: 10.1093/jambio/lxae179] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2024] [Revised: 07/04/2024] [Accepted: 07/16/2024] [Indexed: 07/19/2024]
Abstract
AIMS Currently, immunoinformatic approaches have shown promise in rapidly and cost-effectively identifying new antigens from the Leptospira proteome. Chimeric multiepitope proteins offer a strategy with significant potential for implementation in diagnosis and vaccines development. METHODS AND RESULTS In this study, we detail the immunoinformatic analyses and design of a new recombinant chimeric protein constructed with epitopes identified from the sequences of ErpY-like and LemA proteins, previously identified as potential antigens for controlling leptospirosis. We expressed the chimeric protein using Escherichia coli heterologous systems, evaluated its antigenicity using serum from naturally infected patients, and its immunogenicity in mice as an animal model, with Freund as an adjuvant. The resulting recombinant chimeric protein, named rErpY-LemA, was successfully expressed and purified using a prokaryotic system, with an expected mass of 35 kDa. Serologic assays using serum samples from naturally infected patients demonstrated recognition of the chimera protein by antibodies present in sera. Animals immunized with the chimera exhibited a significant IgG antibody response from the 7th day (P < 0.001), persisting until day 49 of experimentation, with a titer of 1:12,800 (P < 0.05). Notably, significant production of IgA, IgM, and IgG subclasses was observed in animals immunized with the chimera. CONCLUSIONS These results highlight the promising role of immunoinformatics in rapidly identifying antigens and the potential of chimeric multiepitope proteins in developing effective strategies for leptospirosis control.
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Affiliation(s)
- Elsa Giovanna Ávila-Martínez
- Department of Microbiology and Parasitology, Institute of Biology, Federal University of Pelotas, CEP 96010-900, Pelotas, RS, Brazil
- Biotechnology Nucleus, Technological Development Center, Federal University of Pelotas, CEP 96010-900, Pelotas, RS, Brazil
| | - Thayná Laner Cardoso
- Department of Microbiology and Parasitology, Institute of Biology, Federal University of Pelotas, CEP 96010-900, Pelotas, RS, Brazil
- Biotechnology Nucleus, Technological Development Center, Federal University of Pelotas, CEP 96010-900, Pelotas, RS, Brazil
| | - Isabel Ladeira Pereira
- Department of Microbiology and Parasitology, Institute of Biology, Federal University of Pelotas, CEP 96010-900, Pelotas, RS, Brazil
- Biotechnology Nucleus, Technological Development Center, Federal University of Pelotas, CEP 96010-900, Pelotas, RS, Brazil
| | - Pâmela Scaraffuni Caballero
- Department of Microbiology and Parasitology, Institute of Biology, Federal University of Pelotas, CEP 96010-900, Pelotas, RS, Brazil
- Biotechnology Nucleus, Technological Development Center, Federal University of Pelotas, CEP 96010-900, Pelotas, RS, Brazil
| | - Daniela Rodriguero Wozeak
- Department of Microbiology and Parasitology, Institute of Biology, Federal University of Pelotas, CEP 96010-900, Pelotas, RS, Brazil
- Biotechnology Nucleus, Technological Development Center, Federal University of Pelotas, CEP 96010-900, Pelotas, RS, Brazil
| | - Amilton Clair Pinto Seixas Neto
- Department of Microbiology and Parasitology, Institute of Biology, Federal University of Pelotas, CEP 96010-900, Pelotas, RS, Brazil
| | - Luciano da Silva Pinto
- Biotechnology Nucleus, Technological Development Center, Federal University of Pelotas, CEP 96010-900, Pelotas, RS, Brazil
| | - Daiane Drawanz Hartwig
- Department of Microbiology and Parasitology, Institute of Biology, Federal University of Pelotas, CEP 96010-900, Pelotas, RS, Brazil
- Biotechnology Nucleus, Technological Development Center, Federal University of Pelotas, CEP 96010-900, Pelotas, RS, Brazil
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7
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Karkhane AA, Zargoosh S, Aliakbari M, Fatemi SSA, Aminzadeh S, Karkhaneh B. In Silico and Experimental Studies on the Effect of α3 and α5 Deletion on the Biochemical Properties of Bacillus thermocatenulatus Lipase. Mol Biotechnol 2024; 66:1894-1906. [PMID: 37479905 DOI: 10.1007/s12033-023-00804-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Accepted: 06/17/2023] [Indexed: 07/23/2023]
Abstract
To investigate the effect of α3 and α5 helices on the biochemical characterization of Bacillus thermocatenulatus lipase (BTL2), both helices were deleted from native BTL2 lipase. After structural modeling and characterization, the truncated btl2 gene (Δbtl2) was cloned into E. coli BL21 under the control of the T7 promoter. After cultivation and induction of the recombinant bacteria, the Δα3α5 lipase was purified by Ni-NTA column chromatography. Next, the biochemical properties of the Δα3α5 lipase were compared with the previously expressed and purified native lipase. In the presence of the substrate tributyrin (C4), the maximum activity of native and Δα3α5 lipase was 9360 and 5000 U/mg, respectively. The deletion changed the substrate specificity from tributyrin (C4) to tricaprylin (C8) substrate. Native and Δα3α5 lipase showed similar activity patterns at all temperatures and pH values, with the activity of Δα3α5 lipase being approximately 20% lower than native lipase. Triton X100 increased the activity of native and Δα3α5 lipases by 2.1- and 2.5-fold, respectively.
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Affiliation(s)
- Ali Asghar Karkhane
- Department of Systems Biotechnology, Institute of Industrial and Environmental Biotechnology, National Institute of Genetic Engineering and Biotechnology (NIGEB), Tehran, Iran.
- Department of Industrial and Environmental Biotechnology, National Institute of Genetic Engineering and Biotechnology (NIGEB), P.O. Box 14965/161, Tehran, Iran.
| | - Soha Zargoosh
- Department of Systems Biotechnology, Institute of Industrial and Environmental Biotechnology, National Institute of Genetic Engineering and Biotechnology (NIGEB), Tehran, Iran
| | - Moein Aliakbari
- Department of Systems Biotechnology, Institute of Industrial and Environmental Biotechnology, National Institute of Genetic Engineering and Biotechnology (NIGEB), Tehran, Iran
| | - Seyed Safa-Ali Fatemi
- Department of Systems Biotechnology, Institute of Industrial and Environmental Biotechnology, National Institute of Genetic Engineering and Biotechnology (NIGEB), Tehran, Iran
| | - Saeed Aminzadeh
- Department of Bioprocess Engineering, Institute of Industrial and Environmental Biotechnology, National Institute of Genetic Engineering and Biotechnology (NIGEB), Tehran, Iran
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Hossain FMA, Bappy MNI, Robin TB, Ahmad I, Patel H, Jahan N, Rabbi MGR, Roy A, Chowdhury W, Ahmed N, Prome AA, Rani NA, Khan P, Zinnah KMA. A review on computational studies and bioinformatics analysis of potential drugs against monkeypox virus. J Biomol Struct Dyn 2024; 42:6091-6107. [PMID: 37403283 DOI: 10.1080/07391102.2023.2231542] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Accepted: 06/23/2023] [Indexed: 07/06/2023]
Abstract
Monkeypox, a viral disease that is caused by monkeypox virus and occurs mainly in central and western Africa. However, recently it is spreading worldwide and took the focus of the scientific world towards it. Therefore, we made an attempt to cluster all the related information that may make it easy for the researchers to get the information easily and carry out their research smoothly to find prophylaxis against this emerging virus. There are very few researches found available on monkeypox. Almost all the studies were focused on smallpox virus and the recommended vaccines and therapeutics for monkeypox virus were originally developed for smallpox virus. Though these are recommended for emergency cases, they are not fully effective and specific against monkeypox. For this, here we also took the help of bioinformatics tools to screen potential drug candidates against this growing burden. Some potential antiviral plant metabolites, inhibitors and available drugs were scrutinized that can block the essential survival proteins of this virus. All the compounds Amentoflavone, Pseudohypericin, Adefovirdipiboxil, Fialuridin, Novobiocin and Ofloxacin showed elite binding efficiency with suitable ADME properties and Amentoflavone and Pseudohypericin showed stability in MD simulation study indicating their potency as probable drugs against this emerging virus.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Ferdaus Mohd Altaf Hossain
- Faculty of Veterinary, Animal and Biomedical Science, Sylhet Agricultural University, Sylhet, Bangladesh
- Department of Dairy Science, Sylhet Agricultural University, Sylhet, Bangladesh
| | - Md Nazmul Islam Bappy
- Faculty of Biotechnology and Genetic Engineering, Sylhet Agricultural University, Sylhet, Bangladesh
- Department of Animal and Fish Biotechnology, Sylhet Agricultural University, Sylhet, Bangladesh
| | - Tanjin Barketullah Robin
- Faculty of Biotechnology and Genetic Engineering, Sylhet Agricultural University, Sylhet, Bangladesh
| | - Iqrar Ahmad
- Department of Pharmaceutical Chemistry, Prof. Ravindra Nikam College of Pharmacy, Dhule, Maharashtra, India
| | - Harun Patel
- Department of Pharmaceutical Chemistry, Division of Computer Aided Drug Design, R. C. Patel Institute of Pharmaceutical Education and Research, Shirpur, Maharashtra, India
| | - Nusrat Jahan
- Faculty of Biotechnology and Genetic Engineering, Sylhet Agricultural University, Sylhet, Bangladesh
| | - Md Gulam Rabbany Rabbi
- Faculty of Biotechnology and Genetic Engineering, Sylhet Agricultural University, Sylhet, Bangladesh
| | - Anindita Roy
- Faculty of Biotechnology and Genetic Engineering, Sylhet Agricultural University, Sylhet, Bangladesh
| | - Wasima Chowdhury
- Faculty of Biotechnology and Genetic Engineering, Sylhet Agricultural University, Sylhet, Bangladesh
| | - Nadim Ahmed
- Faculty of Biotechnology and Genetic Engineering, Sylhet Agricultural University, Sylhet, Bangladesh
| | - Anindita Ash Prome
- Faculty of Biotechnology and Genetic Engineering, Sylhet Agricultural University, Sylhet, Bangladesh
| | - Nurul Amin Rani
- Faculty of Biotechnology and Genetic Engineering, Sylhet Agricultural University, Sylhet, Bangladesh
| | - Parvez Khan
- Department of Biochemistry & Molecular Biology, University of Nebraska Medical Center, Omaha, Nebraska, USA
| | - Kazi Md Ali Zinnah
- Faculty of Biotechnology and Genetic Engineering, Sylhet Agricultural University, Sylhet, Bangladesh
- Department of Animal and Fish Biotechnology, Sylhet Agricultural University, Sylhet, Bangladesh
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9
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Moqbel Hassan Alzubaydi N, Oun Ali Z, Al-Asadi S, Al-Kahachi R. Design and characterization of a multi-epitope vaccine targeting Chlamydia abortus using immunoinformatics approach. J Biomol Struct Dyn 2024; 42:6660-6677. [PMID: 37774751 DOI: 10.1080/07391102.2023.2240891] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Accepted: 07/06/2023] [Indexed: 10/01/2023]
Abstract
Chlamydiosis is a widespread ailment affecting humans, livestock, and wildlife, caused by C. abortus, a member of the Chlamydia genus. This disease leads to reproductive disorders in bovines and poses a zoonotic risk, resulting in adverse outcomes such as abortion, stillbirths, weak offspring, endometritis, repeat breeding, and perinatal mortality. However, current chlamydiosis vaccines have limitations in terms of safety, efficacy, and stability, necessitating the development of effective and safe alternatives. In this study, our objective was to design a multi-epitope vaccine (MEV) targeting all strains of C. abortus using bioinformatics and immunoinformatics approaches. We identified highly antigenic and non-allergic proteins (yidC, yajC, secY, CAB503, and CAB746) using VaxiJen and AlgPred tools. Physicochemical analyses and secondary structure predictions confirmed protein stability through ProtParam and SOPMA methods. Furthermore, we employed IEDB-AR, NETMHCpan, and ToxinPred2 tools to predict cytotoxic T lymphocyte (CTL), helper T lymphocyte (HTL), and B-cell epitopes, resulting in the identification of conserved epitopes for further analysis. The MEV construct, consisting of 545 amino acids, incorporated the adjuvant Beta defensin-3, along with 9 CTL epitopes and 21 HTL epitopes linked by EAAAK, KK, and AAY linkers. We assessed the safety and immunogenicity of the vaccine through comprehensive evaluations of antigenicity, toxicity, allergenicity, and physicochemical properties. Structural stability and quality were examined using 3D modeling via the ab initio approach with the Robetta platform. Molecular docking analysis explored the compatibility of the MEV with Toll-like receptor 9 (TLR9) using ClusPro, while molecular dynamics simulation with the DESMOND Maestro software predicted the stability and flexibility of the docked complex. Despite promising in silico findings, further wet lab investigations are crucial to validate the safety and efficacy of the MEV. Successful development and validation of this MEV hold significant potential in combatting chlamydiosis in both animal and human populations.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
| | - Zainab Oun Ali
- Department of Radiology Techniques, College of Health and Medical Techniques, Middle Technical University, Baghdad, Iraq
| | - Sura Al-Asadi
- Department of Laboratory Techniques, College of Health and Medical Techniques, Middle Technical University, Baghdad, Iraq
| | - Rusul Al-Kahachi
- Department of Scholarships and Cultural Relationship, Republic of Iraq Ministry of Higher Education and Scientific Research, Baghdad, Iraq
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10
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Safarzadeh Kozani P, Safarzadeh Kozani P, Rahbarizadeh F. Humanization of the antigen-recognition domain does not impinge on the antigen-binding, cytokine secretion, and antitumor reactivity of humanized nanobody-based CD19-redirected CAR-T cells. J Transl Med 2024; 22:679. [PMID: 39054481 PMCID: PMC11271212 DOI: 10.1186/s12967-024-05461-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2024] [Accepted: 07/01/2024] [Indexed: 07/27/2024] Open
Abstract
BACKGROUND The immunogenicity of the antigen-recognition domains of chimeric antigen receptor (CAR)-T cells leads to immune responses that may compromise the antitumor effects of the adoptively transferred T cells. Herein, we attempt to humanize a CD19-specific VHH (named H85) using in silico techniques and investigate the impact of antigen-recognition domain humanization on CAR expression and density, cytokine secretion, and cytolytic reactivity of CAR-T cells based on the humanized VHH. METHODS H85 was humanized (named HuH85), and then HuH85 was compared with H85 in terms of conformational structure, physicochemical properties, antigenicity and immunogenicity, solubility, flexibility, stability, and CD19-binding capacity using in silico techniques. Next, H85CAR-T cells and HuH85CAR-T cells were developed and CAR expression and surface density were assessed via flow cytometry. Ultimately, the antitumor reactivity and secreted levels of IFN-γ, IL-2, and TNF-α were assessed following the co-cultivation of the CAR-T cells with Ramos, Namalwa, and K562 cells. RESULTS In silico findings demonstrated no negative impacts on HuH85 as a result of humanization. Ultimately, H85CAR and HuH85CAR could be surface-expressed on transduced T cells at comparable levels as assessed via mean fluorescence intensity. Moreover, H85CAR-T cells and HuH85CAR-T cells mediated comparable antitumor effects against Ramos and Namalwa cells and secreted comparable levels of IFN-γ, IL-2, and TNF-α following co-cultivation. CONCLUSION HuH85 can be used to develop immunotherapeutics against CD19-associated hematologic malignancies. Moreover, HuH85CAR-T cells must be further investigated in vitro and in preclinical xenograft models of CD19+ leukemias and lymphomas before advancing into clinical trials.
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Affiliation(s)
- Pooria Safarzadeh Kozani
- Department of Medical Biotechnology, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, Iran
- Research and Development Center of Biotechnology, Tarbiat Modares University, Tehran, Iran
| | - Pouya Safarzadeh Kozani
- Department of Medical Biotechnology, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, Iran
- Research and Development Center of Biotechnology, Tarbiat Modares University, Tehran, Iran
| | - Fatemeh Rahbarizadeh
- Department of Medical Biotechnology, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, Iran.
- Research and Development Center of Biotechnology, Tarbiat Modares University, Tehran, Iran.
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11
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Oladipo EK, Akinleye TM, Adeyemo SF, Akinboade MW, Siyanbola KF, Adetunji VA, Arowosegbe OA, Olatunji VK, Adaramola EO, Afolabi HO, Ajani CD, Siyanbola TP, Folakanmi EO, Irewolede BA, Okesanya OJ, Ajani OF, Ariyo OE, Jimah EM, Iwalokun BA, Kolawole OM, Oloke JK, Onyeaka H. mRNA vaccine design for Epstein-Barr virus: an immunoinformatic approach. In Silico Pharmacol 2024; 12:68. [PMID: 39070665 PMCID: PMC11269547 DOI: 10.1007/s40203-024-00244-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Accepted: 07/14/2024] [Indexed: 07/30/2024] Open
Abstract
Epstein-Barr Virus (EBV), structurally similar to other herpes viruses, possess significant global health challenges as it causes infectious mononucleosis and is also associated with various cancers. Due to this widespread impact, an effective messenger RNA (mRNA) vaccine is paramount to help curb its spread, further underscoring the need for its development. This study, following an immunoinformatic approach, aimed to design a comprehensive mRNA vaccine against the EBV by selecting antigenic proteins, predicting Linear B-cell epitopes, cytotoxic T-cell lymphocyte (CTL) and helper T-cell lymphocyte (HTL) epitopes, and assessing vaccine characteristics. Seventy-nine EBV isolates from diverse geographical regions were examined. Additionally, the vaccine construct's physicochemical properties, transmembrane domains, solubility, and secondary structures were analysed. Molecular docking was conducted with Toll-Like Receptor 5 (TLR-5). Population coverage was assessed for selected major histocompatibility complex (MHC) alleles, and immune response was simulated. The result of this study highlighted a vaccine construct with high antigenicity, non-toxicity, and non-allergenicity and possessed favourable physicochemical properties. The vaccine's 3D structure is native-like and strongly binds with TLR-5, indicating a solid affinity with TLR-5. The selected MHC alleles provided broad universal population coverage of 89.1%, and the immune simulations suggested a robust and wide-ranging immunogenic response, activating critical immune cells, antibodies, and cytokines. These findings provide a solid foundation for further development and testing of the EBV candidate vaccine, offering potential solutions for combating EBV infections.
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Affiliation(s)
- Elijah Kolawole Oladipo
- Laboratory of Molecular Biology, Immunology and Bioinformatics, Department of Microbiology, Adeleke University, Ede, Osun State Nigeria
- Genomics Unit, Helix Biogen Institute, Ogbomosho, Oyo State Nigeria
| | - Temitope Michael Akinleye
- Genomics Unit, Helix Biogen Institute, Ogbomosho, Oyo State Nigeria
- Department of Anatomy and Advanced Research Center for Tumor Immunology, Inje University College of Medicine, 75 Bokji-ro, Busanjin-gu, Busan, 47392 Republic of Korea
| | | | | | | | | | | | | | | | | | | | | | | | | | - Olalekan John Okesanya
- Faculty of Medicine, Department of Public Health and Maritime Transport, Laboratory of Hygiene and Epidemiology, University of Thessaly, Papakyriazi 22, Larissa, 41222 Greece
| | - Olumide Faith Ajani
- African Centre for Disease Control and Prevention (African CDC), Addis Ababa, Ethiopia
| | - Olumuyiwa Elijah Ariyo
- Department of Medicine, Infectious Diseases and Tropical Medicine Unit, Federal Teaching Hospital, Ido-Ekiti, Ekiti State Nigeria
| | | | - Bamidele Abiodun Iwalokun
- Molecular Biology and Biotechnology Department, Nigerian Institute of Medical Research, Lagos, Nigeria
| | | | - Julius Kola Oloke
- Department of Natural Science, Precious Cornerstone, Ibadan, 200132 Nigeria
| | - Helen Onyeaka
- School of Chemical Engineering, University of Birmingham, Edgbaston, Birmingham, B15 2TT UK
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12
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Choi S, Lee Y, Park S, Jang SY, Park J, Oh DW, Kim SM, Kim TH, Lee GS, Cho C, Kim BS, Lee D, Kim EH, Cheong HK, Moon JH, Song JJ, Hwang J, Kim MH. Dissemination of pathogenic bacteria is reinforced by a MARTX toxin effector duet. Nat Commun 2024; 15:6218. [PMID: 39043696 PMCID: PMC11266601 DOI: 10.1038/s41467-024-50650-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2024] [Accepted: 07/15/2024] [Indexed: 07/25/2024] Open
Abstract
Multiple bacterial genera take advantage of the multifunctional autoprocessing repeats-in-toxin (MARTX) toxin to invade host cells. Secretion of the MARTX toxin by Vibrio vulnificus, a deadly opportunistic pathogen that causes primary septicemia, the precursor of sepsis, is a major driver of infection; however, the molecular mechanism via which the toxin contributes to septicemia remains unclear. Here, we report the crystal and cryo-electron microscopy (EM) structures of a toxin effector duet comprising the domain of unknown function in the first position (DUF1)/Rho inactivation domain (RID) complexed with human targets. These structures reveal how the duet is used by bacteria as a potent weapon. The data show that DUF1 acts as a RID-dependent transforming NADase domain (RDTND) that disrupts NAD+ homeostasis by hijacking calmodulin. The cryo-EM structure of the RDTND-RID duet complexed with calmodulin and Rac1, together with immunological analyses in vitro and in mice, provide mechanistic insight into how V. vulnificus uses the duet to suppress ROS generation by depleting NAD(P)+ and modifying Rac1 in a mutually-reinforcing manner that ultimately paralyzes first line immune responses, promotes dissemination of invaders, and induces sepsis. These data may allow development of tools or strategies to combat MARTX toxin-related human diseases.
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Affiliation(s)
- Sanghyeon Choi
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Korea
- Microbiome Convergence Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Korea
| | - Youngjin Lee
- Microbiome Convergence Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Korea
| | - Shinhye Park
- Microbiome Convergence Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Korea
- Department of Microbiology and Molecular Biology, Chungnam National University, Daejeon, 34134, Korea
| | - Song Yee Jang
- Microbiome Convergence Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Korea
- Core Research Facility & Analysis Center, KRIBB, Daejeon, 34141, Korea
| | - Jongbin Park
- Microbiome Convergence Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Korea
| | - Do Won Oh
- Microbiome Convergence Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Korea
- Graduate School of Medical Science and Engineering, KAIST, Daejeon, 34141, Korea
| | - Su-Man Kim
- Microbiome Convergence Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Korea
- Department of Biology Education, Chonnam National University, Gwangju, 61186, Korea
| | - Tae-Hwan Kim
- Microbiome Convergence Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Korea
- College of Veterinary Medicine, Chungnam National University, Daejeon, 34134, Korea
| | - Ga Seul Lee
- Core Research Facility & Analysis Center, KRIBB, Daejeon, 34141, Korea
- College of Pharmacy, Chungbuk National University, Cheongju, Chungbuk, 28644, Korea
| | - Changyi Cho
- Department of Food Science and Biotechnology, Ewha Womans University, Seoul, 03760, Korea
| | - Byoung Sik Kim
- Department of Food Science and Biotechnology, Ewha Womans University, Seoul, 03760, Korea
| | - Donghan Lee
- Korea Basic Science Institute, Cheongju, Chungbuk, 28119, Korea
| | - Eun-Hee Kim
- Korea Basic Science Institute, Cheongju, Chungbuk, 28119, Korea
| | - Hae-Kap Cheong
- Korea Basic Science Institute, Cheongju, Chungbuk, 28119, Korea
| | - Jeong Hee Moon
- Core Research Facility & Analysis Center, KRIBB, Daejeon, 34141, Korea
| | - Ji-Joon Song
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Korea
| | - Jungwon Hwang
- Microbiome Convergence Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Korea.
| | - Myung Hee Kim
- Microbiome Convergence Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Korea.
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13
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Zhu X, Wang X, Liu T, Zhang D, Jin T. Design of multi-epitope vaccine against porcine rotavirus using computational biology and molecular dynamics simulation approaches. Virol J 2024; 21:160. [PMID: 39039549 PMCID: PMC11264426 DOI: 10.1186/s12985-024-02440-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2024] [Accepted: 07/16/2024] [Indexed: 07/24/2024] Open
Abstract
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.
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MESH Headings
- Animals
- Swine
- Molecular Dynamics Simulation
- Rotavirus/immunology
- Rotavirus/genetics
- Epitopes, T-Lymphocyte/immunology
- Epitopes, T-Lymphocyte/genetics
- Epitopes, T-Lymphocyte/chemistry
- Computational Biology
- Epitopes, B-Lymphocyte/immunology
- Epitopes, B-Lymphocyte/genetics
- Rotavirus Vaccines/immunology
- Rotavirus Vaccines/chemistry
- Rotavirus Vaccines/genetics
- Rotavirus Infections/prevention & control
- Rotavirus Infections/immunology
- Rotavirus Infections/virology
- Vaccines, Subunit/immunology
- Vaccines, Subunit/genetics
- Vaccines, Subunit/chemistry
- Antigens, Viral/immunology
- Antigens, Viral/genetics
- Antigens, Viral/chemistry
- Molecular Docking Simulation
- Swine Diseases/prevention & control
- Swine Diseases/immunology
- Swine Diseases/virology
- Capsid Proteins/immunology
- Capsid Proteins/genetics
- Capsid Proteins/chemistry
- Vaccine Development
- Immunogenicity, Vaccine
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Affiliation(s)
- Xiaochen Zhu
- Tianjin Key Laboratory of Agricultural Animal Breeding and Healthy Husbandry, College of Animal Science and Veterinary Medicine, Tianjin Agricultural University, Tianjin, 300392, China
| | - Xinyuan Wang
- Tianjin Key Laboratory of Agricultural Animal Breeding and Healthy Husbandry, College of Animal Science and Veterinary Medicine, Tianjin Agricultural University, Tianjin, 300392, China
| | - Tingting Liu
- Tianjin Key Laboratory of Agricultural Animal Breeding and Healthy Husbandry, College of Animal Science and Veterinary Medicine, Tianjin Agricultural University, Tianjin, 300392, China
| | - Dongchao Zhang
- Tianjin Key Laboratory of Agricultural Animal Breeding and Healthy Husbandry, College of Animal Science and Veterinary Medicine, Tianjin Agricultural University, Tianjin, 300392, China.
- Tianjin Engineering Technology Center of Livestock Pathogen Detection and Genetic Engineering Vaccine, College of Animal Science and Veterinary Medicine, Tianjin Agricultural University, Tianjin, 300392, China.
| | - Tianming Jin
- Tianjin Key Laboratory of Animal Molecular Breeding and Biotechnology, Institute of Animal Science and Veterinary, Tianjin Academy of Agricultural Sciences, Tianjin, 300381, China.
- Tianjin Engineering Technology Center of Livestock Pathogen Detection and Genetic Engineering Vaccine, College of Animal Science and Veterinary Medicine, Tianjin Agricultural University, Tianjin, 300392, China.
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14
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Parvaei M, Habibi M, Shahbazi S, Babaluei M, Farokhi M, Asadi Karam MR. Immunostimulatory chimeric protein encapsulated in gelatin nanoparticles elicits protective immunity against Pseudomonas aeruginosa respiratory tract infection. Int J Biol Macromol 2024; 277:133964. [PMID: 39029853 DOI: 10.1016/j.ijbiomac.2024.133964] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2024] [Revised: 06/19/2024] [Accepted: 07/16/2024] [Indexed: 07/21/2024]
Abstract
This study presents the design and fabrication of an innovative vaccine candidate targeting Pseudomonas aeruginosa (P. aeruginosa). The vaccine consists of gelatin nanoparticles (GNPs) encapsulating a chimeric protein (CP) derived from the ExoS and OprI proteins from P. aeruginosa. The physicochemical properties of the GNPs were assessed using dynamic light scattering (DLS) and electron microscopy. The toxicity, encapsulation efficacy, release profile, and effectiveness of CP-encapsulated GNPs (CP-GNPs) in an animal model were investigated. The resulting nanovaccine demonstrated uniform spherical particles with an average size of 135 nm and an encapsulation efficiency of 85 %. The release assay revealed that 23 % of the antigen was released from the CP-GNPs after 20 days. The GNPs did not exhibit any toxic effects on L929 cells in vitro. The formulation induced both systemic and mucosal antibody responses. Additionally, CP-GNPs stimulated cytokine responses, including IFN-γ, IL-4, and IL-17, indicating the induction of both humoral (Th2) and cellular (Th1) responses. The CP-encapsulated GNPs formulation effectively protected the mice lungs against experimental respiratory tract infection, reducing colony count and inflammation. These findings suggest that CP-GNPs hold promise as a potential strategy for preventing respiratory tract infections caused by P. aeruginosa. Further research is needed to explore its clinical application.
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Affiliation(s)
- Maryam Parvaei
- Department of Molecular Biology, Pasteur Institute of Iran, Tehran, Iran
| | - Mehri Habibi
- Department of Molecular Biology, Pasteur Institute of Iran, Tehran, Iran
| | - Shahla Shahbazi
- Department of Molecular Biology, Pasteur Institute of Iran, Tehran, Iran
| | | | - Mehdi Farokhi
- National Cell Bank of Iran, Pasteur Institute of Iran, Tehran, Iran.
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15
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Naskar S, Harsukhbhai Chandpa H, Agarwal S, Meena J. Super epitope dengue vaccine instigated serotype independent immune protection in-silico. Vaccine 2024; 42:3857-3873. [PMID: 38616437 DOI: 10.1016/j.vaccine.2024.04.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2024] [Revised: 03/21/2024] [Accepted: 04/04/2024] [Indexed: 06/14/2024]
Abstract
Dengue becomes the most common life-threatening infectious arbovirus disease globally, with prevalence in the tropical and subtropical areas. The major clinical features include dengue haemorrhagic fever (DHF) and dengue shock syndrome (DSS), a condition of hypovolemic shock. Four different serotypes of the dengue virus, known as dengue virus serotype (DENV)- 1, 2, 3 and 4 can infect humans. Only one vaccine is available in the market, named Dengvaxia by Sanofi Pasteur, but there is no desired outcome of this treatment due the antibody dependent enhancement (ADE) of the multiple dengue serotypes. As of now, there is no cure against dengue disease. Our goal in this work was to create a subunit vaccine based on several epitopes that would be effective against every serotype of the dengue virus. Here, computational methods like- immunoinformatics and bioinformatics were implemented to find out possible dominant epitopes. A total of 21 epitopes were chosen using various in-silico techniques from the expected 133 major histocompatibility complex (MHC)- I and major histocompatibility complex (MHC)- II epitopes, along with 95 B-cell epitopes which were greatly conserved. Immune stimulant, non-allergenic and non-toxic immunodominant epitopes (super epitopes) with a suitable adjuvant (Heparin-Binding Hemagglutinin Adhesin, HBHA) were used to construct the vaccine. Following the physicochemical analysis, vaccine construct was docked with Toll-like receptors (TLRs) to predict the immune stimulation. Consequently, the optimal docked complex that demonstrated the least amount of ligand-receptor complex deformability was used to conduct the molecular dynamics analysis. By following the codon optimization, the final vaccine molecule was administered into an expressing vector to perform in-silico cloning. The robust immune responses were generated in the in-silico immune simulation analysis. Hence, this study provides a hope to control the dengue infections. For validation of the immune outcomes, in-vitro as well as in-vivo investigations are essential.
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Affiliation(s)
- Shovan Naskar
- ImmunoEngineering and Therapeutics Laboratory, Department of Pharmaceutical Engineering and Technology, Indian Institute of Technology (Banaras Hindu University), Varanasi 221005, India
| | - Hitesh Harsukhbhai Chandpa
- ImmunoEngineering and Therapeutics Laboratory, Department of Pharmaceutical Engineering and Technology, Indian Institute of Technology (Banaras Hindu University), Varanasi 221005, India
| | - Shalini Agarwal
- ImmunoEngineering and Therapeutics Laboratory, Department of Pharmaceutical Engineering and Technology, Indian Institute of Technology (Banaras Hindu University), Varanasi 221005, India
| | - Jairam Meena
- ImmunoEngineering and Therapeutics Laboratory, Department of Pharmaceutical Engineering and Technology, Indian Institute of Technology (Banaras Hindu University), Varanasi 221005, India.
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16
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de Carvalho GA, Tambwe PM, Nascimento LRC, Campos BKP, Chiareli RA, Junior GPN, Menegatti R, Gomez RS, Pinto MCX. In silico evidence of bitopertin's broad interactions within the SLC6 transporter family. J Pharm Pharmacol 2024:rgae051. [PMID: 38982944 DOI: 10.1093/jpp/rgae051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2024] [Accepted: 04/16/2024] [Indexed: 07/11/2024]
Abstract
The Glycine Transporter Type 1 (GlyT1) significantly impacts central nervous system functions, influencing glycinergic and glutamatergic neurotransmission. Bitopertin, the first GlyT1 inhibitor in clinical trials, was developed for schizophrenia treatment but showed limited efficacy. Despite this, bitopertin's repositioning could advance treating various pathologies. This study aims to understand bitopertin's mechanism of action using computational methods, exploring off-target effects, and providing a comprehensive pharmacological profile. Similarity Ensemble Approach (SEA) and SwissTargetPrediction initially predicted targets, followed by molecular modeling on SWISS-MODEL and GalaxyWeb servers. Binding sites were identified using PrankWeb, and molecular docking was performed with DockThor and GOLD software. Molecular dynamics analyses were conducted on the Visual Dynamics platform. Reverse screening on SEA and SwissTargetPrediction identified GlyT1 (SLC6A9), GlyT2 (SLC6A5), PROT (SLC6A7), and DAT (SLC6A3) as potential bitopertin targets. Homology modeling on SwissModel generated high-resolution models, optimized further on GalaxyWeb. PrankWeb identified similar binding sites in GlyT1, GlyT2, PROT, and DAT, indicating potential interaction. Docking studies suggested bitopertin's interaction with GlyT1 and proximity to GlyT2 and PROT. Molecular dynamics confirmed docking results, highlighting bitopertin's target stability beyond GlyT1. The study concludes that bitopertin potentially interacts with multiple SLC6 family targets, indicating a broader pharmacological property.
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Affiliation(s)
- Gustavo Almeida de Carvalho
- Departamento de Farmacologia, Instituto de Ciências Biológicas, Universidade Federal de Goiás, CEP 74690-900, Goiânia-GO, Brazil
| | - Paul Magogo Tambwe
- Departamento de Farmacologia, Instituto de Ciências Biológicas, Universidade Federal de Goiás, CEP 74690-900, Goiânia-GO, Brazil
| | - Lucas Rodrigues Couto Nascimento
- Departamento de Farmacologia, Instituto de Ciências Biológicas, Universidade Federal de Goiás, CEP 74690-900, Goiânia-GO, Brazil
| | - Bruna Kelly Pedrosa Campos
- Departamento de Farmacologia, Instituto de Ciências Biológicas, Universidade Federal de Goiás, CEP 74690-900, Goiânia-GO, Brazil
| | - Raphaela Almeida Chiareli
- Departamento de Farmacologia, Instituto de Ciências Biológicas, Universidade Federal de Goiás, CEP 74690-900, Goiânia-GO, Brazil
| | - Guilhermino Pereira Nunes Junior
- Departamento de Farmacologia, Instituto de Ciências Biológicas, Universidade Federal de Goiás, CEP 74690-900, Goiânia-GO, Brazil
| | - Ricardo Menegatti
- Faculdade de Farmácia, Universidade Federal de Goiás, Rua 240, Setor Leste Universitário, 74605170 - Goiânia, GO, Brazil
| | - Renato Santiago Gomez
- Departamento de Cirurgia, Faculdade de Medicina, Universidade Federal de Minas Gerais, Av. Alfredo Balena, 190, 30130-100, Belo Horizonte-MG, Brazil
| | - Mauro Cunha Xavier Pinto
- Departamento de Farmacologia, Instituto de Ciências Biológicas, Universidade Federal de Goiás, CEP 74690-900, Goiânia-GO, Brazil
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Masum MHU, Wajed S, Hossain MI, Moumi NR, Talukder A, Rahman MM. An mRNA vaccine for pancreatic cancer designed by applying in silico immunoinformatics and reverse vaccinology approaches. PLoS One 2024; 19:e0305413. [PMID: 38976715 PMCID: PMC11230540 DOI: 10.1371/journal.pone.0305413] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2024] [Accepted: 05/30/2024] [Indexed: 07/10/2024] Open
Abstract
Pancreatic ductal adenocarcinoma is the most prevalent pancreatic cancer, which is considered a significant global health concern. Chemotherapy and surgery are the mainstays of current pancreatic cancer treatments; however, a few cases are suitable for surgery, and most of the cases will experience recurrent episodes. Compared to DNA or peptide vaccines, mRNA vaccines for pancreatic cancer have more promise because of their delivery, enhanced immune responses, and lower proneness to mutation. We constructed an mRNA vaccine by analyzing S100 family proteins, which are all major activators of receptors for advanced glycation end products. We applied immunoinformatic approaches, including physicochemical properties analysis, structural prediction and validation, molecular docking study, in silico cloning, and immune simulations. The designed mRNA vaccine was estimated to have a molecular weight of 165023.50 Da and was highly soluble (grand average of hydropathicity of -0.440). In the structural assessment, the vaccine seemed to be a well-stable and functioning protein (Z score of -8.94). Also, the docking analysis suggested that the vaccine had a high affinity for TLR-2 and TLR-4 receptors. Additionally, the molecular mechanics with generalized Born and surface area solvation analysis of the "Vaccine-TLR-2" (-141.07 kcal/mol) and "Vaccine-TLR-4" (-271.72 kcal/mol) complexes also suggests a strong binding affinity for the receptors. Codon optimization also provided a high expression level with a GC content of 47.04% and a codon adaptation index score 1.0. The appearance of memory B-cells and T-cells was also observed over a while, with an increased level of helper T-cells and immunoglobulins (IgM and IgG). Moreover, the minimum free energy of the mRNA vaccine was predicted at -1760.00 kcal/mol, indicating the stability of the vaccine following its entry, transcription, and expression. This hypothetical vaccine offers a groundbreaking tool for future research and therapeutic development of pancreatic cancer.
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Affiliation(s)
- Md Habib Ullah Masum
- Department of Microbiology, Noakhali Science and Technology University, Noakhali, Bangladesh
- Microbiology, Cancer and Bioinformatics Research Group, Noakhali Science and Technology University, Noakhali, Bangladesh
| | - Shah Wajed
- Department of Microbiology, Noakhali Science and Technology University, Noakhali, Bangladesh
- Microbiology, Cancer and Bioinformatics Research Group, Noakhali Science and Technology University, Noakhali, Bangladesh
- Infectiology: Biology of Infectious Diseases, Universite Paris-Saclay, Gif-sur-Yvette, France
| | - Md Imam Hossain
- Department of Microbiology, Noakhali Science and Technology University, Noakhali, Bangladesh
| | - Nusrat Rahman Moumi
- Medical Sciences, University of Central Lancashire, Preston, Lancashire, United Kingdom
| | - Asma Talukder
- Microbiology, Cancer and Bioinformatics Research Group, Noakhali Science and Technology University, Noakhali, Bangladesh
- Department of Biotechnology and Genetic Engineering, Noakhali Science and Technology University, Noakhali, Bangladesh
- School of Pharmacy and Medical Sciences, and Menzies Health Institute Queensland, Griffith University, Brisbane, Queensland, Australia
| | - Md Mijanur Rahman
- Department of Microbiology, Noakhali Science and Technology University, Noakhali, Bangladesh
- Microbiology, Cancer and Bioinformatics Research Group, Noakhali Science and Technology University, Noakhali, Bangladesh
- School of Pharmacy and Medical Sciences, and Menzies Health Institute Queensland, Griffith University, Brisbane, Queensland, Australia
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18
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Al Adawiah R, Zaenal Mustopa A, Budiarti S, Nur Umami R, Hertati A, Irawan H, Ikramullah MC, Arwansyah A, Mamangkey J, Kartikasari I, Salahudin Darusman H. Molecular dynamics simulation and purification of chimeric L1/L2 protein from human papillomavirus type 52 expressed in Escherichia coli BL21 (DE3). J Immunoassay Immunochem 2024:1-20. [PMID: 38965835 DOI: 10.1080/15321819.2024.2376034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/06/2024]
Abstract
The available prophylactic vaccines for human papillomavirus (HPV) in the market are only effective against specific types of HPV, rendering them ineffective for other types of HPV infections. The objective of this research is to investigate the stability of the recombinant protein constructed, namely chimeric L1/L2 protein from HPV type 52, with improved cross-neutralization ability. The 3D model, predicted using Alphafold, Robetta, I-Tasser, and refined with Galaxy Refinement, is validated using Ramachandran plot analysis. The stability is verified through molecular dynamics simulations, considering parameters such as RMSD, RMSF, Rg, and SASA, where stable conditions are observed. The chimeric L1/L2 protein from HPV type 52 is purified using affinity chromatography, and the His-tag is cleaved using SUMO protease to obtain pure chimeric protein with the size of ~ 55 kDa. Western blot analysis confirms binding to anti-L1 HPV type 52 polyclonal antibody. The obtained vaccine candidate can be utilized as an effective prophylactic vaccine against HPV.
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Affiliation(s)
| | - Apon Zaenal Mustopa
- Research Center for Genetic Engineering, National Research and Innovation Agency (BRIN), KST Soekarno, Cibinong, Bogor, Indonesia
| | - Sri Budiarti
- Department of Biology, IPB University, Bogor, Indonesia
| | - Rifqiyah Nur Umami
- Research Center for Genetic Engineering, National Research and Innovation Agency (BRIN), KST Soekarno, Cibinong, Bogor, Indonesia
| | - Ai Hertati
- Research Center for Genetic Engineering, National Research and Innovation Agency (BRIN), KST Soekarno, Cibinong, Bogor, Indonesia
| | - Herman Irawan
- Research Center for Genetic Engineering, National Research and Innovation Agency (BRIN), KST Soekarno, Cibinong, Bogor, Indonesia
| | - Muh Chaeril Ikramullah
- Biotechnology Study Program, Postgraduate School of Universitas Gadjah Mada, Yogyakarta, Indonesia
| | | | - Jendri Mamangkey
- Research Center for Genetic Engineering, National Research and Innovation Agency (BRIN), KST Soekarno, Cibinong, Bogor, Indonesia
- Department of Biology Education, Faculty of Education and Teacher Training, Universitas Kristen Indonesia, Jakarta, Indonesia
| | | | - Huda Salahudin Darusman
- Department of Anatomy, Physiology and Pharmacology, School of Veterinary Medicine and Biomedical, IPB University Indonesia,Bogor
- Primate Animal Study Center, Research Institution and Community Service (LPPM), IPB University, Bogor, Indonesia
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Bhattacharjee A, Hosen MR, Lamisa AB, Ahammad I, Chowdhury ZM, Jamal TB, Sohag MMH, Hossain MU, Das KC, Keya CA, Salimullah M. An integrated comparative genomics, subtractive proteomics and immunoinformatics framework for the rational design of a Pan-Salmonella multi-epitope vaccine. PLoS One 2024; 19:e0292413. [PMID: 38959229 PMCID: PMC11221655 DOI: 10.1371/journal.pone.0292413] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Accepted: 04/23/2024] [Indexed: 07/05/2024] Open
Abstract
Salmonella infections pose a significant global public health concern due to the substantial expenses associated with monitoring, preventing, and treating the infection. In this study, we explored the core proteome of Salmonella to design a multi-epitope vaccine through Subtractive Proteomics and immunoinformatics approaches. A total of 2395 core proteins were curated from 30 different isolates of Salmonella (strain NZ CP014051 was taken as reference). Utilizing the subtractive proteomics approach on the Salmonella core proteome, Curlin major subunit A (CsgA) was selected as the vaccine candidate. csgA is a conserved gene that is related to biofilm formation. Immunodominant B and T cell epitopes from CsgA were predicted using numerous immunoinformatics tools. T lymphocyte epitopes had adequate population coverage and their corresponding MHC alleles showed significant binding scores after peptide-protein based molecular docking. Afterward, a multi-epitope vaccine was constructed with peptide linkers and Human Beta Defensin-2 (as an adjuvant). The vaccine could be highly antigenic, non-toxic, non-allergic, and have suitable physicochemical properties. Additionally, Molecular Dynamics Simulation and Immune Simulation demonstrated that the vaccine can bind with Toll Like Receptor 4 and elicit a robust immune response. Using in vitro, in vivo, and clinical trials, our findings could yield a Pan-Salmonella vaccine that might provide protection against various Salmonella species.
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Affiliation(s)
- Arittra Bhattacharjee
- Bioinformatics Division, National Institute of Biotechnology, Ganakbari, Ashulia, Savar, Dhaka, Bangladesh
| | - Md. Rakib Hosen
- Department of Genetic Engineering and Biotechnology, Jagannath University, Dhaka, Bangladesh
| | - Anika Bushra Lamisa
- Bioinformatics Division, National Institute of Biotechnology, Ganakbari, Ashulia, Savar, Dhaka, Bangladesh
| | - Ishtiaque Ahammad
- Bioinformatics Division, National Institute of Biotechnology, Ganakbari, Ashulia, Savar, Dhaka, Bangladesh
| | - Zeshan Mahmud Chowdhury
- Bioinformatics Division, National Institute of Biotechnology, Ganakbari, Ashulia, Savar, Dhaka, Bangladesh
| | - Tabassum Binte Jamal
- Bioinformatics Division, National Institute of Biotechnology, Ganakbari, Ashulia, Savar, Dhaka, Bangladesh
| | - Md. Mehadi Hasan Sohag
- Department of Genetic Engineering and Biotechnology, Jagannath University, Dhaka, Bangladesh
| | - Mohammad Uzzal Hossain
- Bioinformatics Division, National Institute of Biotechnology, Ganakbari, Ashulia, Savar, Dhaka, Bangladesh
| | - Keshob Chandra Das
- Molecular Biotechnology Division, National Institute of Biotechnology, Ganakbari, Ashulia, Savar, Dhaka, Bangladesh
| | - Chaman Ara Keya
- Department of Biochemistry and Microbiology, North South University, Bashundhara, Dhaka, Bangladesh
| | - Md Salimullah
- Molecular Biotechnology Division, National Institute of Biotechnology, Ganakbari, Ashulia, Savar, Dhaka, Bangladesh
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20
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Ahmed MH, Samia NSN, Singh G, Gupta V, Mishal MFM, Hossain A, Suman KH, Raza A, Dutta AK, Labony MA, Sultana J, Faysal EH, Alnasser SM, Alam P, Azam F. An immuno-informatics approach for annotation of hypothetical proteins and multi-epitope vaccine designed against the Mpox virus. J Biomol Struct Dyn 2024; 42:5288-5307. [PMID: 37519185 DOI: 10.1080/07391102.2023.2239921] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2023] [Accepted: 06/09/2023] [Indexed: 08/01/2023]
Abstract
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.
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Affiliation(s)
- Md Hridoy Ahmed
- Department of Genetic Engineering and Biotechnology, University of Chittagong, Chittagong, Bangladesh
| | - Nure Sharaf Nower Samia
- Department of Life Sciences (DLS), School of Environment and Life Sciences (SELS), Independent University, Dhaka, Bangladesh
| | - Gagandeep Singh
- Kusuma School of Biological Sciences, Indian Institute of Technology, New Delhi, India
- Section of Microbiology, Central Ayurveda Research Institute, Jhansi CCRAS, Ministry of Ayush, India
| | - Vandana Gupta
- Department of Microbiology, Ram Lal Anand College, University of Delhi, New Delhi, India
| | | | - Alomgir Hossain
- Department of Genetic Engineering and Biotechnology, University of Rajshahi, Rajshahi, Bangladesh
| | | | - Adnan Raza
- Bioscience department, COMSATS University of Islamabad, Islamabad, Pakistan
| | - Amit Kumar Dutta
- Department of Microbiology, University of Rajshahi, Rajshahi, Bangladesh
| | - Moriom Akhter Labony
- Department of Genetic Engineering and Biotechnology, University of Chittagong, Chittagong, Bangladesh
| | - Jakia Sultana
- Department of Botany, University of Rajshahi, Rajshahi, Bangladesh
| | | | - Sulaiman Mohammed Alnasser
- Department of Pharmacology and Toxicology, Unaizah College of Pharmacy, Qassim University, Buraydah, Saudi Arabia
| | - Prawez Alam
- Department of Pharmacognosy, College of Pharmacy, Prince Sattam Bin Abdulaziz University, Al Kharj, Saudi Arabia
| | - Faizul Azam
- Department of Pharmaceutical Chemistry and Pharmacognosy, Unaizah College of Pharmacy, Qassim University, Buraydah, Saudi Arabia
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21
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Ezzemani W, Ouladlahsen A, Altawalah H, Saile R, Sarih M, Kettani A, Ezzikouri S. Identification of novel T-cell epitopes on monkeypox virus and development of multi-epitopes vaccine using immunoinformatics approaches. J Biomol Struct Dyn 2024; 42:5349-5364. [PMID: 37354141 DOI: 10.1080/07391102.2023.2226733] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Accepted: 06/10/2023] [Indexed: 06/26/2023]
Abstract
Monkeypox virus (MPV) is closely related to the smallpox virus, and previous data from Africa suggest that the smallpox vaccine (VARV) is at least 85% effective in preventing MPV. No multi-epitope vaccine has yet been developed to prevent MPV infection. In this work, we used in silico structural biology and advanced immunoinformatic strategies to design a multi-epitope subunit vaccine against MPV infection. The designed vaccine sequence is adjuvanted with CpG-ODN and includes HTL/CTL epitopes for similar proteins between vaccinia virus (VACV) that induced T-cell production in vaccinated volunteers and the first draft sequence of the MPV genome associated with the suspected outbreak in several countries, May 2022. In addition, the specific binding of the modified vaccine and the immune Toll-like receptor 9 (TLR9) was estimated by molecular interaction studies. Strong interaction in the binding groove as well as good docking scores confirmed the stringency of the modified vaccine. The stability of the interaction was confirmed by a classical molecular dynamics simulation and normal mode analysis. Then, the immune simulation also indicated the ability of this vaccine to induce an effective immune response against MPV. Codon optimization and in silico cloning of the vaccine into the pET-28a (+) vector also showed its expression potential in the E. coli K12 system. The promising data obtained from the various in silico studies indicate that this vaccine is effective against MPV. However, additional in vitro and in vivo studies are still needed to confirm its efficacy.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Wahiba Ezzemani
- Virology Unit, Viral Hepatitis Laboratory, Institut Pasteur du Maroc, Casablanca, Morocco
- Laboratoire de Biologie et Santé (URAC34), Départment de Biologie, Faculté des Sciences Ben Msik, Hassan II University of Casablanca, Casablanca, Morocco
| | - Ahd Ouladlahsen
- Faculté de médecine et de pharmacie, Université Hassan II, Casablanca, Morocco
- Service des maladies infectieuses, CHU Ibn Rochd, Casablanca, Morocco
| | - Haya Altawalah
- Department of Microbiology, Faculty of Medicine, Kuwait University, Kuwait City, Kuwait
- Virology Unit, Yacoub Behbehani Center, Sabah Hospital, Ministry of Health, Kuwait City, Kuwait
| | - Rachid Saile
- Laboratoire de Biologie et Santé (URAC34), Départment de Biologie, Faculté des Sciences Ben Msik, Hassan II University of Casablanca, Casablanca, Morocco
| | - M'hammed Sarih
- Service de Parasitologie et des Maladies Vectorielles, Institut Pasteur du Maroc, Casablanca, Morocco
| | - Anass Kettani
- Laboratoire de Biologie et Santé (URAC34), Départment de Biologie, Faculté des Sciences Ben Msik, Hassan II University of Casablanca, Casablanca, Morocco
| | - Sayeh Ezzikouri
- Virology Unit, Viral Hepatitis Laboratory, Institut Pasteur du Maroc, Casablanca, Morocco
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22
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Kolla HB, Dutt M, Kumar A, Hebbandi Nanjunadappa R, Karakach T, Singh KP, Kelvin D, Clement Mertens PP, Umeshappa CS. Immuno-informatics study identifies conserved T cell epitopes in non-structural proteins of Bluetongue virus serotypes: formulation of a computationally optimized next-generation broad-spectrum multi-epitope vaccine. Front Immunol 2024; 15:1424307. [PMID: 39011043 PMCID: PMC11246920 DOI: 10.3389/fimmu.2024.1424307] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2024] [Accepted: 06/13/2024] [Indexed: 07/17/2024] Open
Abstract
Introduction Bluetongue (BT) poses a significant threat to the livestock industry, affecting various animal species and resulting in substantial economic losses. The existence of numerous BT virus (BTV) serotypes has hindered control efforts, highlighting the need for broad-spectrum vaccines. Methodology In this study, we evaluated the conserved amino acid sequences within key non-structural (NS) proteins of BTV and identified numerous highly conserved murine- and bovine-specific MHC class I-restricted (MHC-I) CD8+ and MHC-II-restricted CD4+ epitopes. We then screened these conserved epitopes for antigenicity, allergenicity, toxicity, and solubility. Using these epitopes, we developed in silico-based broad-spectrum multiepitope vaccines with Toll-like receptor (TLR-4) agonists. The predicted proinflammatory cytokine response was assessed in silico using the C-IMMSIM server. Structural modeling and refinement were achieved using Robetta and GalaxyWEB servers. Finally, we assessed the stability of the docking complexes through extensive 100-nanosecond molecular dynamics simulations before considering the vaccines for codon optimization and in silico cloning. Results We found many epitopes that meet these criteria within NS1 and NS2 proteins and developed in silico broad-spectrum vaccines. The immune simulation studies revealed that these vaccines induce high levels of IFN-γ and IL-2 in the vaccinated groups. Protein-protein docking analysis demonstrated promising epitopes with strong binding affinities to TLR-4. The docked complexes were stable, with minimal Root Mean Square Deviation and Root Mean Square Fluctuation values. Finally, the in silico-cloned plasmids have high % of GC content with > 0.8 codon adaptation index, suggesting they are suitable for expressing the protein vaccines in prokaryotic system. Discussion These next-generation vaccine designs are promising and warrant further investigation in wet lab experiments to assess their immunogenicity, safety, and efficacy for practical application in livestock. Our findings offer a robust framework for developing a comprehensive, broad-spectrum vaccine, potentially revolutionizing BT control and prevention strategies in the livestock industry.
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Affiliation(s)
- Harish Babu Kolla
- Department of Microbiology, Immunology and Pediatrics, Dalhousie University, Halifax, NS, Canada
- Immunology Division, IWK Health Centre, Halifax, NS, Canada
| | - Mansi Dutt
- Department of Microbiology, Immunology and Pediatrics, Dalhousie University, Halifax, NS, Canada
- Immunology Division, IWK Health Centre, Halifax, NS, Canada
| | - Anuj Kumar
- Department of Microbiology, Immunology and Pediatrics, Dalhousie University, Halifax, NS, Canada
- Immunology Division, IWK Health Centre, Halifax, NS, Canada
| | - Roopa Hebbandi Nanjunadappa
- Department of Microbiology, Immunology and Pediatrics, Dalhousie University, Halifax, NS, Canada
- Immunology Division, IWK Health Centre, Halifax, NS, Canada
| | - Tobias Karakach
- Department of Pharmacology, Dalhousie University, Halifax, NS, Canada
| | - Karam Pal Singh
- Center for Animal Disease Research and Diagnosis, Indian Veterinary Research Institute, Bareilly, India
| | - David Kelvin
- Department of Microbiology, Immunology and Pediatrics, Dalhousie University, Halifax, NS, Canada
- Immunology Division, IWK Health Centre, Halifax, NS, Canada
| | | | - Channakeshava Sokke Umeshappa
- Department of Microbiology, Immunology and Pediatrics, Dalhousie University, Halifax, NS, Canada
- Immunology Division, IWK Health Centre, Halifax, NS, Canada
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23
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Lim CP, Leow CH, Lim HT, Kok BH, Chuah C, Oliveira JIN, Jones M, Leow CY. Insights into structural vaccinology harnessed for universal coronavirus vaccine development. Clin Exp Vaccine Res 2024; 13:202-217. [PMID: 39144127 PMCID: PMC11319108 DOI: 10.7774/cevr.2024.13.3.202] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2024] [Revised: 05/10/2024] [Accepted: 05/15/2024] [Indexed: 08/16/2024] Open
Abstract
Structural vaccinology is pivotal in expediting vaccine design through high-throughput screening of immunogenic antigens. Leveraging the structural and functional characteristics of antigens and immune cell receptors, this approach employs protein structural comparison to identify conserved patterns in key pathogenic components. Molecular modeling techniques, including homology modeling and molecular docking, analyze specific three-dimensional (3D) structures and protein interactions and offer valuable insights into the 3D interactions and binding affinity between vaccine candidates and target proteins. In this review, we delve into the utilization of various immunoinformatics and molecular modeling tools to streamline the development of broad-protective vaccines against coronavirus disease 2019 variants. Structural vaccinology significantly enhances our understanding of molecular interactions between hosts and pathogens. By accelerating the pace of developing effective and targeted vaccines, particularly against the rapidly mutating severe acute respiratory syndrome coronavirus 2 and other prevalent infectious diseases, this approach stands at the forefront of advancing immunization strategies. The combination of computational techniques and structural insights not only facilitates the identification of potential vaccine candidates but also contributes to the rational design of vaccines, fostering a more efficient and targeted approach to combatting infectious diseases.
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Affiliation(s)
- Chin Peng Lim
- School of Pharmaceutical Sciences, Universiti Sains Malaysia, Gelugor, Malaysia
- Institute for Research in Molecular Medicine, Universiti Sains Malaysia, Gelugor, Malaysia
| | - Chiuan Herng Leow
- Institute for Research in Molecular Medicine, Universiti Sains Malaysia, Gelugor, Malaysia
| | - Hui Ting Lim
- Institute for Research in Molecular Medicine, Universiti Sains Malaysia, Gelugor, Malaysia
| | - Boon Hui Kok
- Institute for Research in Molecular Medicine, Universiti Sains Malaysia, Gelugor, Malaysia
| | - Candy Chuah
- Faculty of Medicine, Asian Institute of Medical Science and Technology University, Bedong, Malaysia
| | - Jonas Ivan Nobre Oliveira
- Department of Biophysics and Pharmacology, Bioscience Center, Federal University of Rio Grande do Norte, Natal, Brazil
| | - Malcolm Jones
- School of Veterinary Science, The University of Queensland, Gatton, Australia
| | - Chiuan Yee Leow
- School of Pharmaceutical Sciences, Universiti Sains Malaysia, Gelugor, Malaysia
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24
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Liu Z, Zhang Z, Yang L, Zhang Y, Li D, Zhang Q, Niu C, Zhang B, Zhai Y, Wang Z. Effect and mechanism of C-terminal cysteine on the properties of HEV p222 protein. Virology 2024; 595:110091. [PMID: 38718446 DOI: 10.1016/j.virol.2024.110091] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2024] [Revised: 04/07/2024] [Accepted: 04/18/2024] [Indexed: 05/18/2024]
Abstract
Preliminary investigations have demonstrated that the cysteines located at the C-terminus of HEV ORF2 protein exhibits disulfide bonding capability during virus-like particles (VLPs) assembly. However, the effect and mechanism underlying the pairing of disulfide bonds formed by C627, C630, and C638 remains unclear. The p222 protein encompasses C-terminus and serves as a representative of HEV ORF2 to investigate the specific impacts of C627, C630, and C638. The three cysteines were subjected to site-directed mutagenesis and expressed in prokaryotes; Both the mutated proteins and p222 underwent polymerization except for p222A; Surprisingly, only p222 was observed as abundant spherical particles under transmission electron microscope (TEM); Stability and immunogenicity of the p222 exhibited higher than other mutated proteins; LC/MS/MS analysis identified four disulfide bonds in the p222. The novel findings suggest that the three cysteines contribute to structural and functional properties of ORF2 protein, highlighting the indispensability of each cysteine.
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Affiliation(s)
- Zhenzhen Liu
- College of Medicine, Henan Polytechnic University, Jiaozuo, 454000, Henan, China
| | - Zhenzhen Zhang
- College of Medicine, Henan Polytechnic University, Jiaozuo, 454000, Henan, China
| | - Lanping Yang
- College of Medicine, Henan Polytechnic University, Jiaozuo, 454000, Henan, China
| | - Yongwen Zhang
- College of Medicine, Henan Polytechnic University, Jiaozuo, 454000, Henan, China
| | - Dong Li
- College of Medicine, Henan Polytechnic University, Jiaozuo, 454000, Henan, China
| | - Qingling Zhang
- College of Medicine, Henan Polytechnic University, Jiaozuo, 454000, Henan, China
| | - Chao Niu
- College of Medicine, Henan Polytechnic University, Jiaozuo, 454000, Henan, China
| | - Baobao Zhang
- College of Medicine, Henan Polytechnic University, Jiaozuo, 454000, Henan, China
| | - Yangyang Zhai
- College of Medicine, Henan Polytechnic University, Jiaozuo, 454000, Henan, China
| | - Zhenhui Wang
- College of Medicine, Henan Polytechnic University, Jiaozuo, 454000, Henan, China.
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25
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Murmu S, Archak S. In-silico study of protein-protein interactions in wheat blast using docking and molecular dynamics simulation approach. J Biomol Struct Dyn 2024; 42:5747-5757. [PMID: 37357445 DOI: 10.1080/07391102.2023.2228907] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Accepted: 06/17/2023] [Indexed: 06/27/2023]
Abstract
Despite advancements in agricultural research and the introduction of modern biotechnological and farming techniques, food security remains a significant issue. Although the efforts of farmers to meet the demands of a growing population, many plant diseases caused by pathogens, through their effects on cell division and tissue growth, lead to the annual loss of countless food crops. The recently emerged wheat blast fungus Magnaporthe oryzae pathotype Triticum (MoT) poses a significant danger to worldwide wheat cultivation. The fungus is a highly varied lineage of the M. oryzae, responsible for causing rice blast disease. In spite of being a significant challenge to successful wheat production in South America since 1985, the underlying biology of the wheat blast pathogen is still not fully understood. The initial outbreak of the wheat blast in South Asia had a severe impact on wheat production, resulting in a complete loss of yield in affected fields. For the purpose of enhancing disease management, it's vital to acquire a comprehensive comprehension of the infection biology of the fungus and its interaction with wheat plants on molecular levels. Host-pathogen protein interactions (HPIs) have the potential to reveal the pathogens' mechanism for overcoming the host organism. The current study delves into the interactions between the host plant wheat and MoT through protein-protein interactions, molecular docking, and 100 ns molecular dynamic simulations. This research uncovers the structural and functional basis of these proteins, leading to improved plant health and production.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Sneha Murmu
- Division of Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Sunil Archak
- Division of Genomic Resources, ICAR-National Bureau of Plant Genetic Resources, New Delhi, India
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26
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Kaur B, Karnwal A, Bansal A, Malik T. An Immunoinformatic-Based In Silico Identification on the Creation of a Multiepitope-Based Vaccination Against the Nipah Virus. BIOMED RESEARCH INTERNATIONAL 2024; 2024:4066641. [PMID: 38962403 PMCID: PMC11221950 DOI: 10.1155/2024/4066641] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/07/2024] [Revised: 05/30/2024] [Accepted: 06/01/2024] [Indexed: 07/05/2024]
Abstract
The zoonotic viruses pose significant threats to public health. Nipah virus (NiV) is an emerging virus transmitted from bats to humans. The NiV causes severe encephalitis and acute respiratory distress syndrome, leading to high mortality rates, with fatality rates ranging from 40% to 75%. The first emergence of the disease was found in Malaysia in 1998-1999 and later in Bangladesh, Cambodia, Timor-Leste, Indonesia, Singapore, Papua New Guinea, Vietnam, Thailand, India, and other South and Southeast Asian nations. Currently, no specific vaccines or antiviral drugs are available. The potential advantages of epitope-based vaccines include their ability to elicit specific immune responses while minimizing potential side effects. The epitopes have been identified from the conserved region of viral proteins obtained from the UniProt database. The selection of conserved epitopes involves analyzing the genetic sequences of various viral strains. The present study identified two B cell epitopes, seven cytotoxic T lymphocyte (CTL) epitopes, and seven helper T lymphocyte (HTL) epitope interactions from the NiV proteomic inventory. The antigenic and physiological properties of retrieved protein were analyzed using online servers ToxinPred, VaxiJen v2.0, and AllerTOP. The final vaccine candidate has a total combined coverage range of 80.53%. The tertiary structure of the constructed vaccine was optimized, and its stability was confirmed with the help of molecular simulation. Molecular docking was performed to check the binding affinity and binding energy of the constructed vaccine with TLR-3 and TLR-5. Codon optimization was performed in the constructed vaccine within the Escherichia coli K12 strain, to eliminate the danger of codon bias. However, these findings must require further validation to assess their effectiveness and safety. The development of vaccines and therapeutic approaches for virus infection is an ongoing area of research, and it may take time before effective interventions are available for clinical use.
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Affiliation(s)
- Beant Kaur
- School of Bioengineering and BiosciencesLovely Professional University, Phagwara, Punjab 144411, India
| | - Arun Karnwal
- School of Bioengineering and BiosciencesLovely Professional University, Phagwara, Punjab 144411, India
| | - Anu Bansal
- School of Bioengineering and BiosciencesLovely Professional University, Phagwara, Punjab 144411, India
| | - Tabarak Malik
- Department of Biomedical SciencesInstitute of HealthJimma University, Jimma, Ethiopia
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27
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Hasan A, Alonazi WB, Ibrahim M, Bin L. Immunoinformatics and Reverse Vaccinology Approach for the Identification of Potential Vaccine Candidates against Vandammella animalimors. Microorganisms 2024; 12:1270. [PMID: 39065039 PMCID: PMC11278545 DOI: 10.3390/microorganisms12071270] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2024] [Revised: 06/17/2024] [Accepted: 06/19/2024] [Indexed: 07/28/2024] Open
Abstract
Vandammella animalimorsus is a Gram-negative and non-motile bacterium typically transmitted to humans through direct contact with the saliva of infected animals, primarily through biting, scratches, or licks on fractured skin. The absence of a confirmed post-exposure treatment of V. animalimorsus bacterium highlights the imperative for developing an effective vaccine. We intended to determine potential vaccine candidates and paradigm a chimeric vaccine against V. animalimorsus by accessible public data analysis of the strain by utilizing reverse vaccinology. By subtractive genomics, five outer membranes were prioritized as potential vaccine candidates out of 2590 proteins. Based on the instability index and transmembrane helices, a multidrug transporter protein with locus ID A0A2A2AHJ4 was designated as a potential candidate for vaccine construct. Sixteen immunodominant epitopes were retrieved by utilizing the Immune Epitope Database. The epitope encodes the strong binding affinity, nonallergenic properties, non-toxicity, high antigenicity scores, and high solubility revealing the more appropriate vaccine construct. By utilizing appropriate linkers and adjuvants alongside a suitable adjuvant molecule, the epitopes were integrated into a chimeric vaccine to enhance immunogenicity, successfully eliciting both adaptive and innate immune responses. Moreover, the promising physicochemical features, the binding confirmation of the vaccine to the major innate immune receptor TLR-4, and molecular dynamics simulations of the designed vaccine have revealed the promising potential of the selected candidate. The integration of computational methods and omics data has demonstrated significant advantages in discovering novel vaccine targets and mitigating vaccine failure rates during clinical trials in recent years.
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Affiliation(s)
- Ahmad Hasan
- State Key Laboratory of Rice Biology and Breeding, Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Biotechnology, Zhejiang University, Hangzhou 310058, China; (A.H.); (M.I.)
| | - Wadi B. Alonazi
- Health Administration Department, College of Business Administration, King Saud University, Riyadh 11421, Saudi Arabia;
| | - Muhammad Ibrahim
- State Key Laboratory of Rice Biology and Breeding, Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Biotechnology, Zhejiang University, Hangzhou 310058, China; (A.H.); (M.I.)
| | - Li Bin
- State Key Laboratory of Rice Biology and Breeding, Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Biotechnology, Zhejiang University, Hangzhou 310058, China; (A.H.); (M.I.)
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Thach T, Dhanabalan K, Nandekar PP, Stauffer S, Heisler I, Alvarado S, Snyder J, Subramanian R. A Second Drug Binding Site in P2X3. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.10.598171. [PMID: 38915546 PMCID: PMC11195084 DOI: 10.1101/2024.06.10.598171] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/26/2024]
Abstract
Purinergic P2X3 receptors form trimeric cation-gated channels, which are activated by extracellular ATP. P2X3 plays a crucial role in chronic cough and affects over 10% of the population. Despite considerable efforts to develop drugs targeting P2X3, the highly conserved structure within the P2X receptor family presents obstacles for achieving selectivity. Camlipixant, a potent and selective P2X3 antagonist, is currently in phase III clinical trials. However, the mechanisms underlying receptor desensitization, ion permeation, principles governing antagonism, and the structure of P2X3 when bound to camlipixant remain elusive. In this study, we established a stable cell line expressing homotrimeric P2X3 and utilized a peptide scaffold to purify the complex and determine its structure using cryo-electron microscopy (cryo-EM). P2X3 binds to camlipixant at a previously unidentified drug-binding site and functions as an allosteric inhibitor. Structure-activity studies combined with modeling and simulations have shed light on the mechanisms underlying the selective targeting and inhibition of P2X3 by camlipixant, distinguishing it from other members of the P2X receptor family.
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Affiliation(s)
- Trung Thach
- Department of Biological Sciences, Purdue University, West Lafayette, IN-47907, USA
| | | | | | - Seth Stauffer
- Elanco Animal Health, 2500 Innovation Way, Greenfield, IN-46140, USA
| | - Iring Heisler
- Elanco Animal Health, 2500 Innovation Way, Greenfield, IN-46140, USA
| | - Sarah Alvarado
- Elanco Animal Health, 2500 Innovation Way, Greenfield, IN-46140, USA
| | - Jonathan Snyder
- Elanco Animal Health, 2500 Innovation Way, Greenfield, IN-46140, USA
| | - Ramaswamy Subramanian
- Department of Biological Sciences, Purdue University, West Lafayette, IN-47907, USA
- Weldon School of Biomedical Engineering, Purdue University, West Lafayette, IN-47907, USA
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Yu C, Wu Q, Xin J, Yu Q, Ma Z, Xue M, Xu Q, Zheng C. Designing a smallpox B-cell and T-cell multi-epitope subunit vaccine using a comprehensive immunoinformatics approach. Microbiol Spectr 2024; 12:e0046524. [PMID: 38700327 PMCID: PMC11237557 DOI: 10.1128/spectrum.00465-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2024] [Accepted: 04/01/2024] [Indexed: 05/05/2024] Open
Abstract
Smallpox is a highly contagious human disease caused by the variola virus. Although the disease was eliminated in 1979 due to its highly contagious nature and historical pathogenicity, with a mortality rate of up to 30%, this virus is an important candidate for biological weapons. Currently, vaccines are the critical measures to prevent this virus infection and spread. In this study, we designed a peptide vaccine using immunoinformatics tools, which have the potential to activate human immunity against variola virus infection efficiently. The design of peptides derives from vaccine-candidate proteins showing protective potential in vaccinia WR strains. Potential non-toxic and nonallergenic T-cell and B-cell binding and cytokine-inducing epitopes were then screened through a priority prediction using special linkers to connect B-cell epitopes and T-cell epitopes, and an appropriate adjuvant was added to the vaccine construction to enhance the immunogenicity of the peptide vaccine. The 3D structure display, docking, and free energy calculation analysis indicate that the binding affinity between the vaccine peptide and Toll-like receptor 3 is high, and the vaccine receptor complex is highly stable. Notably, the vaccine we designed is obtained from the protective protein of the vaccinia and combined with preventive measures to avoid side effects. This vaccine is highly likely to produce an effective and safe immune response against the variola virus infection in the body. IMPORTANCE In this work, we designed a vaccine with a cluster of multiple T-cell/B-cell epitopes, which should be effective in inducing systematic immune responses against variola virus infection. Besides, this work also provides a reference in vaccine design for preventing monkeypox virus infection, which is currently prevalent.
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Affiliation(s)
- Changqing Yu
- State Key Laboratory for Animal Disease Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
- Engineering Center of Agricultural Biosafety Assessment and Biotechnology, School of Advanced Agricultural Sciences, Yibin Vocational and Technical College, Yibin, China
| | - Qi Wu
- State Key Laboratory for Animal Disease Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
| | - Jiuqing Xin
- State Key Laboratory for Animal Disease Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
| | - Qiujuan Yu
- Department of Dermatology, The First People's Hospital of Mudanjiang, Mudanjiang, China
| | - Zhixin Ma
- State Key Laboratory for Animal Disease Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
| | - Mengzhou Xue
- Department of Cerebrovascular Diseases, The Second Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Qingyuan Xu
- State Key Laboratory for Animal Disease Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
| | - Chunfu Zheng
- Department of Microbiology, Immunology and Infection Diseases, University of Calgary, Calgary, Canada
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Yazdani Z, Rafiei A, Momenizadeh M, Abediankenari S, Yazdani M, Lagzian M. Designing novel peptides for detecting the Omicron variant, specifying SARS-CoV-2, and simultaneously screening coronavirus infections. J Biomol Struct Dyn 2024; 42:4759-4768. [PMID: 37306566 DOI: 10.1080/07391102.2023.2222821] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2022] [Accepted: 06/02/2023] [Indexed: 06/13/2023]
Abstract
In this study in silico a candidate diagnostic peptide-based tool was designed in four stages including diagnosis of coronavirus diseases, simultaneously identifying of COVID-19 and SARS from other members of this family, specific identification of SARS-CoV2, and diagnosis of COVID-19 Omicron. Designed candidate peptides consist of four immunodominant peptides from the proteins of the SARS-CoV-2 spike (S) and membrane (M). The tertiary structure of each peptide was predicted. The stimulation ability of the humoral immunity for each peptide was evaluated. Finally, in silico cloning was performed to develop an expression strategy for each peptide. These four peptides have suitable immunogenicity, appropriate construct, and the ability to be expressed in E.coli. These results must be experimentally validated in vitro and in vivo to ensure the immunogenicity of the kit.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Zahra Yazdani
- Department of Immunology, Molecular and Cell Biology Research Center, School of Medicine, Mazandaran University of Medical Sciences, Sari, Iran
- Students Research Committee, Mazandaran University of Medical Sciences, Sari, Iran
| | - Alireza Rafiei
- Department of Immunology, Molecular and Cell Biology Research Center, School of Medicine, Mazandaran University of Medical Sciences, Sari, Iran
| | - Mahdi Momenizadeh
- Students Research Committee, Mazandaran University of Medical Sciences, Sari, Iran
| | - Saeid Abediankenari
- Immunogenetics Research Center, Department of Immunology, Faculty of Medicine, Mazandaran University of Medical Sciences, Sari, Iran
| | | | - Milad Lagzian
- Department of Biology, Faculty of Sciences, University of Sistan and Baluchestan, Zahedan, Iran
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Das A, Rajkhowa S, Sinha S, Zaki MEA. Unveiling potential repurposed drug candidates for Plasmodium falciparum through in silico evaluation: A synergy of structure-based approaches, structure prediction, and molecular dynamics simulations. Comput Biol Chem 2024; 110:108048. [PMID: 38471353 DOI: 10.1016/j.compbiolchem.2024.108048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Revised: 02/28/2024] [Accepted: 02/29/2024] [Indexed: 03/14/2024]
Abstract
The rise of drug resistance in Plasmodium falciparum, rendering current treatments ineffective, has hindered efforts to eliminate malaria. To address this issue, the study employed a combination of Systems Biology approach and a structure-based pharmacophore method to identify a target against P. falciparum. Through text mining, 448 genes were extracted, and it was discovered that plasmepsins, found in the Plasmodium genus, play a crucial role in the parasite's survival. The metabolic pathways of these proteins were determined using the PlasmoDB genomic database and recreated using CellDesigner 4.4.2. To identify a potent target, Plasmepsin V (PF13_0133) was selected and examined for protein-protein interactions (PPIs) using the STRING Database. Topological analysis and global-based methods identified PF13_0133 as having the highest centrality. Moreover, the static protein knockout PPIs demonstrated the essentiality of PF13_0133 in the modeled network. Due to the unavailability of the protein's crystal structure, it was modeled and subjected to a molecular dynamics simulation study. The structure-based pharmacophore modeling utilized the modeled PF13_0133 (PfPMV), generating 10 pharmacophore hypotheses with a library of active and inactive compounds against PfPMV. Through virtual screening, two potential candidates, hesperidin and rutin, were identified as potential drugs which may be repurposed as potential anti-malarial agents.
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Affiliation(s)
- Abhichandan Das
- Centre for Biotechnology and Bioinformatics, Dibrugarh University, Dibrugarh, Assam 786004, India
| | - Sanchaita Rajkhowa
- Centre for Biotechnology and Bioinformatics, Dibrugarh University, Dibrugarh, Assam 786004, India.
| | - Subrata Sinha
- Department of Computational Sciences, Brainware University, Barasat, Kolkata, West Bengal 700125, India
| | - Magdi E A Zaki
- Department of Chemistry, Imam Mohammad Ibn Saud Islamic University (IMSIU), Riyadh, Saudi Arabia
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Braz JDM, Batista MVDA. Immunoinformatics-Based Design of Multi-epitope DNA and mRNA Vaccines Against Zika Virus. Bioinform Biol Insights 2024; 18:11779322241257037. [PMID: 38827811 PMCID: PMC11143849 DOI: 10.1177/11779322241257037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Accepted: 05/07/2024] [Indexed: 06/05/2024] Open
Abstract
In this study, we used an immunoinformatics approach to predict antigenic epitopes of Zika virus (ZIKV) proteins to assist in designing a vaccine antigen against ZIKV. We performed the prediction of CD8+ T-lymphocyte and antigenic B-cell epitopes of ZIKV proteins. The binding interactions of T-cell epitopes with major histocompatibility complex class I (MHC-I) proteins were assessed. We selected the antigenic, conserved, nontoxic, and immunogenic epitopes, which indicated significant interactions with the human leucocyte antigen (HLA-A and HLA-B) alleles and worldwide population coverage of 76.35%. The predicted epitopes were joined with the help of linkers and an adjuvant. The vaccine antigen was then analyzed through molecular docking with TLR3 and TLR8, and it was in silico cloned in the pVAX1 vector to be used as a DNA vaccine and designed as a mRNA vaccine.
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Affiliation(s)
- Juciene de Matos Braz
- Laboratory of Molecular Genetics and Biotechnology (GMBio), Department of Biology, Center for Biological and Health Sciences, Federal University of Sergipe, São Cristóvão, Brazil
| | - Marcus Vinicius de Aragão Batista
- Laboratory of Molecular Genetics and Biotechnology (GMBio), Department of Biology, Center for Biological and Health Sciences, Federal University of Sergipe, São Cristóvão, Brazil
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Mugunthan SP, Venkatesan D, Govindasamy C, Selvaraj D, Harish MC. Systems approach to design multi-epitopic peptide vaccine candidate against fowl adenovirus structural proteins for Gallus gallus domesticus. Front Cell Infect Microbiol 2024; 14:1351303. [PMID: 38881736 PMCID: PMC11177691 DOI: 10.3389/fcimb.2024.1351303] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Accepted: 05/06/2024] [Indexed: 06/18/2024] Open
Abstract
Introduction Fowl adenovirus (FAdV) is a significant pathogen in poultry, causing various diseases such as hepatitis-hydropericardium, inclusion body hepatitis, and gizzard erosion. Different serotypes of FAdV are associated with specific conditions, highlighting the need for targeted prevention strategies. Given the rising prevalence of FAdV-related diseases globally, effective vaccination and biosecurity measures are crucial. In this study, we explore the potential of structural proteins to design a multi-epitope vaccine targeting FAdV. Methods We employed an in silico approach to design the multi-epitope vaccine. Essential viral structural proteins, including hexon, penton, and fiber protein, were selected as vaccine targets. T-cell and B-cell epitopes binding to MHC-I and MHC-II molecules were predicted using computational methods. Molecular docking studies were conducted to validate the interaction of the multi-epitope vaccine candidate with chicken Toll-like receptors 2 and 5. Results Our in silico methodology successfully identified potential T-cell and B-cell epitopes within the selected viral structural proteins. Molecular docking studies revealed strong interactions between the multi-epitope vaccine candidate and chicken Toll-like receptors 2 and 5, indicating the structural integrity and immunogenic potential of the designed vaccine. Discussion The designed multi-epitope vaccine presents a promising approach for combating FAdV infections in chickens. By targeting essential viral structural proteins, the vaccine is expected to induce a robust immunological response. The in silico methodology utilized in this study provides a rapid and cost-effective means of vaccine design, offering insights into potential vaccine candidates before experimental validation. Future studies should focus on in vitro and in vivo evaluations to further assess the efficacy and safety of the proposed vaccine.
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Affiliation(s)
| | | | - Chandramohan Govindasamy
- Department of Community Health Sciences, College of Applied Medical Sciences, King Saud University, Riyadh, Saudi Arabia
| | - Dhivya Selvaraj
- Artificial Intelligence Laboratory, School of Computer Information and Communication Engineering, Kunsan National University, Gunsan, Republic of Korea
| | - Mani Chandra Harish
- Department of Biotechnology, Thiruvalluvar University, Vellore, Tamil Nadu, India
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Elrashedy A, Nayel M, Salama A, Salama MM, Hasan ME. Bioinformatics approach for structure modeling, vaccine design, and molecular docking of Brucella candidate proteins BvrR, OMP25, and OMP31. Sci Rep 2024; 14:11951. [PMID: 38789443 PMCID: PMC11126717 DOI: 10.1038/s41598-024-61991-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Accepted: 05/13/2024] [Indexed: 05/26/2024] Open
Abstract
Brucellosis is a zoonotic disease with significant economic and healthcare costs. Despite the eradication efforts, the disease persists. Vaccines prevent disease in animals while antibiotics cure humans with limitations. This study aims to design vaccines and drugs for brucellosis in animals and humans, using protein modeling, epitope prediction, and molecular docking of the target proteins (BvrR, OMP25, and OMP31). Tertiary structure models of three target proteins were constructed and assessed using RMSD, TM-score, C-score, Z-score, and ERRAT. The best models selected from AlphaFold and I-TASSER due to their superior performance according to CASP 12 - CASP 15 were chosen for further analysis. The motif analysis of best models using MotifFinder revealed two, five, and five protein binding motifs, however, the Motif Scan identified seven, six, and eight Post-Translational Modification sites (PTMs) in the BvrR, OMP25, and OMP31 proteins, respectively. Dominant B cell epitopes were predicted at (44-63, 85-93, 126-137, 193-205, and 208-237), (26-46, 52-71, 98-114, 142-155, and 183-200), and (29-45, 58-82, 119-142, 177-198, and 222-251) for the three target proteins. Additionally, cytotoxic T lymphocyte epitopes were detected at (173-181, 189-197, and 202-210), (61-69, 91-99, 159-167, and 181-189), and (3-11, 24-32, 167-175, and 216-224), while T helper lymphocyte epitopes were displayed at (39-53, 57-65, 150-158, 163-171), (79-87, 95-108, 115-123, 128-142, and 189-197), and (39-47, 109-123, 216-224, and 245-253), for the respective target protein. Furthermore, structure-based virtual screening of the ZINC and DrugBank databases using the docking MOE program was followed by ADMET analysis. The best five compounds of the ZINC database revealed docking scores ranged from (- 16.8744 to - 15.1922), (- 16.0424 to - 14.1645), and (- 14.7566 to - 13.3222) for the BvrR, OMP25, and OMP31, respectively. These compounds had good ADMET parameters and no cytotoxicity, while DrugBank compounds didn't meet Lipinski's rule criteria. Therefore, the five selected compounds from the ZINC20 databases may fulfill the pharmacokinetics and could be considered lead molecules for potentially inhibiting Brucella's proteins.
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Affiliation(s)
- Alyaa Elrashedy
- Department of Animal Medicine and Infectious Diseases (Infectious Diseases), Faculty of Veterinary Medicine, University of Sadat City, Sadat City, Egypt.
| | - Mohamed Nayel
- Department of Animal Medicine and Infectious Diseases (Infectious Diseases), Faculty of Veterinary Medicine, University of Sadat City, Sadat City, Egypt
| | - Akram Salama
- Department of Animal Medicine and Infectious Diseases (Infectious Diseases), Faculty of Veterinary Medicine, University of Sadat City, Sadat City, Egypt
| | - Mohammed M Salama
- Physics Department, Medical Biophysics Division, Faculty of Science, Helwan University, Cairo, Egypt
| | - Mohamed E Hasan
- Bioinformatics Department, Genetic Engineering and Biotechnology Research Institute, University of Sadat City, Sadat City, Egypt
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Carpio LE, Olivares M, Benítez-Paez A, Serrano-Candelas E, Barigye SJ, Sanz Y, Gozalbes R. Comparative Binding Study of Gliptins to Bacterial DPP4-like Enzymes for the Treatment of Type 2 Diabetes Mellitus (T2DM). Int J Mol Sci 2024; 25:5744. [PMID: 38891933 PMCID: PMC11171585 DOI: 10.3390/ijms25115744] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2024] [Revised: 05/21/2024] [Accepted: 05/23/2024] [Indexed: 06/21/2024] Open
Abstract
The role of the gut microbiota and its interplay with host metabolic health, particularly in the context of type 2 diabetes mellitus (T2DM) management, is garnering increasing attention. Dipeptidyl peptidase 4 (DPP4) inhibitors, commonly known as gliptins, constitute a class of drugs extensively used in T2DM treatment. However, their potential interactions with gut microbiota remain poorly understood. In this study, we employed computational methodologies to investigate the binding affinities of various gliptins to DPP4-like homologs produced by intestinal bacteria. The 3D structures of DPP4 homologs from gut microbiota species, including Segatella copri, Phocaeicola vulgatus, Bacteroides uniformis, Parabacteroides merdae, and Alistipes sp., were predicted using computational modeling techniques. Subsequently, molecular dynamics simulations were conducted for 200 ns to ensure the stability of the predicted structures. Stable structures were then utilized to predict the binding interactions with known gliptins through molecular docking algorithms. Our results revealed binding similarities of gliptins toward bacterial DPP4 homologs compared to human DPP4. Specifically, certain gliptins exhibited similar binding scores to bacterial DPP4 homologs as they did with human DPP4, suggesting a potential interaction of these drugs with gut microbiota. These findings could help in understanding the interplay between gliptins and gut microbiota DPP4 homologs, considering the intricate relationship between the host metabolism and microbial communities in the gut.
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Affiliation(s)
- Laureano E. Carpio
- ProtoQSAR SL, CEEI (Centro Europeo de Empresas Innovadoras), Parque Tecnológico de Valencia, 46980 Valencia, Spain; (L.E.C.); (E.S.-C.)
- MolDrug AI Systems SL, 46018 Valencia, Spain
| | - Marta Olivares
- Microbial Ecology, Nutrition and Health Research Unit, Institute of Agrochemistry and Food Technology, Spanish National Research Council (IATA-CSIC), 46980 Valencia, Spain; (M.O.); (A.B.-P.); (Y.S.)
| | - Alfonso Benítez-Paez
- Microbial Ecology, Nutrition and Health Research Unit, Institute of Agrochemistry and Food Technology, Spanish National Research Council (IATA-CSIC), 46980 Valencia, Spain; (M.O.); (A.B.-P.); (Y.S.)
| | - Eva Serrano-Candelas
- ProtoQSAR SL, CEEI (Centro Europeo de Empresas Innovadoras), Parque Tecnológico de Valencia, 46980 Valencia, Spain; (L.E.C.); (E.S.-C.)
| | | | - Yolanda Sanz
- Microbial Ecology, Nutrition and Health Research Unit, Institute of Agrochemistry and Food Technology, Spanish National Research Council (IATA-CSIC), 46980 Valencia, Spain; (M.O.); (A.B.-P.); (Y.S.)
| | - Rafael Gozalbes
- ProtoQSAR SL, CEEI (Centro Europeo de Empresas Innovadoras), Parque Tecnológico de Valencia, 46980 Valencia, Spain; (L.E.C.); (E.S.-C.)
- MolDrug AI Systems SL, 46018 Valencia, Spain
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Greenwood JR, Lacorte-Apostol V, Kroj T, Padilla J, Telebanco-Yanoria MJ, Glaus AN, Roulin A, Padilla A, Zhou B, Keller B, Krattinger SG. Genome-wide association analysis uncovers rice blast resistance alleles of Ptr and Pia. Commun Biol 2024; 7:607. [PMID: 38769168 PMCID: PMC11106262 DOI: 10.1038/s42003-024-06244-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Accepted: 04/24/2024] [Indexed: 05/22/2024] Open
Abstract
A critical step to maximize the usefulness of genome-wide association studies (GWAS) in plant breeding is the identification and validation of candidate genes underlying genetic associations. This is of particular importance in disease resistance breeding where allelic variants of resistance genes often confer resistance to distinct populations, or races, of a pathogen. Here, we perform a genome-wide association analysis of rice blast resistance in 500 genetically diverse rice accessions. To facilitate candidate gene identification, we produce de-novo genome assemblies of ten rice accessions with various rice blast resistance associations. These genome assemblies facilitate the identification and functional validation of novel alleles of the rice blast resistance genes Ptr and Pia. We uncover an allelic series for the unusual Ptr rice blast resistance gene, and additional alleles of the Pia resistance genes RGA4 and RGA5. By linking these associations to three thousand rice genomes we provide a useful tool to inform future rice blast breeding efforts. Our work shows that GWAS in combination with whole-genome sequencing is a powerful tool for gene cloning and to facilitate selection of specific resistance alleles for plant breeding.
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Affiliation(s)
- Julian R Greenwood
- Department of Plant and Microbial Biology, University of Zürich, Zürich, Switzerland.
- Research School of Biology, Australian National University, Canberra, ACT, Australia.
| | | | - Thomas Kroj
- PHIM Plant Health Institute, University of Montpellier, INRAE, CIRAD, Institut Agro, IRD, Montpellier, France
| | - Jonas Padilla
- International Rice Research Institute, Los Baños, Philippines
| | | | - Anna N Glaus
- Department of Plant and Microbial Biology, University of Zürich, Zürich, Switzerland
| | - Anne Roulin
- Agroscope, Müller-Thurgau-Strasse 29, 8820, Wädenswil, Switzerland
| | - André Padilla
- Centre de Biologie Structurale, CBS, University of Montpellier, CNRS UMR 5048, INSERM U, 1054, Montpellier, France
| | - Bo Zhou
- International Rice Research Institute, Los Baños, Philippines.
| | - Beat Keller
- Department of Plant and Microbial Biology, University of Zürich, Zürich, Switzerland.
| | - Simon G Krattinger
- Plant Science Program, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia.
- Center for Desert Agriculture, KAUST, Thuwal, 23955-6900, Saudi Arabia.
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Moin AT, Rani NA, Patil RB, Robin TB, Ullah MA, Rahim Z, Rahman MF, Zubair T, Hossain M, Mollah AKMM, Absar N, Hossain M, Manchur MA, Islam NN. In-silico formulation of a next-generation polyvalent vaccine against multiple strains of monkeypox virus and other related poxviruses. PLoS One 2024; 19:e0300778. [PMID: 38758816 PMCID: PMC11101047 DOI: 10.1371/journal.pone.0300778] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Accepted: 03/05/2024] [Indexed: 05/19/2024] Open
Abstract
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.
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Affiliation(s)
- Abu Tayab Moin
- Faculty of Biological Sciences, Department of Genetic Engineering and Biotechnology, Laboratory of Clinical Genetics, Genomics and Enzyme Research (LCGGER), University of Chittagong, Chattogram, Bangladesh
| | - Nurul Amin Rani
- Faculty of Biotechnology and Genetic Engineering, Sylhet Agricultural University, Sylhet, Bangladesh
| | - Rajesh B. Patil
- Department of Pharmaceutical Chemistry, Sinhgad Technical Education Society’s, Sinhgad College of Pharmacy, Maharashtra, India
| | - Tanjin Barketullah Robin
- Faculty of Biotechnology and Genetic Engineering, Sylhet Agricultural University, Sylhet, Bangladesh
| | - Md. Asad Ullah
- Faculty of Biological Sciences, Department of Biotechnology and Genetic Engineering, Jahangirnagar University, Savar, Dhaka, Bangladesh
| | - Zahidur Rahim
- Department of Zoology, Jahangirnagar University, Dhaka, Bangladesh
| | - Md. Foyzur Rahman
- Department of Pharmacy, Dhaka International University, Dhaka, Bangladesh
| | | | - Mohabbat Hossain
- Faculty of Biological Sciences, Department of Genetic Engineering and Biotechnology, Laboratory of Clinical Genetics, Genomics and Enzyme Research (LCGGER), University of Chittagong, Chattogram, Bangladesh
| | | | - Nurul Absar
- Faculty of Basic Medical and Pharmaceutical Sciences, Department of Biochemistry and Biotechnology, University of Science & Technology Chittagong, Khulshi, Chittagong, Bangladesh
| | - Mahboob Hossain
- Department of Mathematics and Natural Sciences, Microbiology Program, School of Data and Sciences, BRAC University, Dhaka, Bangladesh
| | - Mohammed Abul Manchur
- Faculty of Biological Sciences, Department of Microbiology, University of Chittagong, Chattogram, Bangladesh
| | - Nazneen Naher Islam
- Faculty of Biological Sciences, Department of Genetic Engineering and Biotechnology, Laboratory of Clinical Genetics, Genomics and Enzyme Research (LCGGER), University of Chittagong, Chattogram, Bangladesh
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Xiao X, Fu Y, You W, Huang C, Zeng F, Gu X, Sun X, Li J, Zhang Q, Du W, Cheng G, Liu Z, Liu L. Inhibition of the RLR signaling pathway by SARS-CoV-2 ORF7b is mediated by MAVS and abrogated by ORF7b-homologous interfering peptide. J Virol 2024; 98:e0157323. [PMID: 38572974 PMCID: PMC11092349 DOI: 10.1128/jvi.01573-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Accepted: 03/15/2024] [Indexed: 04/05/2024] Open
Abstract
Coronavirus disease 2019 (COVID-19) is caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection and characterized by dysregulated immune response. Studies have shown that the SARS-CoV-2 accessory protein ORF7b induces host cell apoptosis through the tumor necrosis factor alpha (TNF-α) pathway and blocks the production of interferon beta (IFN-β). The underlying mechanism remains to be investigated. In this study, we found that ORF7b facilitated viral infection and production, and inhibited the RIG-I-like receptor (RLR) signaling pathway through selectively interacting with mitochondrial antiviral-signaling protein (MAVS). MAVS439-466 region and MAVS Lys461 were essential for the physical association between MAVS and ORF7b, and the inhibition of the RLR signaling pathway by ORF7b. MAVSK461/K63 ubiquitination was essential for the RLR signaling regulated by the MAVS-ORF7b complex. ORF7b interfered with the recruitment of tumor necrosis factor receptor-related factor 6 (TRAF6) and the activation of the RLR signaling pathway by MAVS. Furthermore, interfering peptides targeting the ORF7b complex reversed the ORF7b-suppressed MAVS-RLR signaling pathway. The most potent interfering peptide V disrupts the formation of ORF7b tetramers, reverses the levels of the ORF7b-inhibited physical association between MAVS and TRAF6, leading to the suppression of viral growth and infection. Overall, this study provides a mechanism for the suppression of innate immunity by SARS-CoV-2 infection and the mechanism-based approach via interfering peptides to potentially prevent SARS-CoV-2 infection.IMPORTANCEThe pandemic coronavirus disease 2019 (COVID-19) is caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection and continues to be a threat to public health. It is imperative to understand the biology of SARS-CoV-2 infection and find approaches to prevent SARS-CoV-2 infection and ameliorate COVID-19. Multiple SARS-CoV-2 proteins are known to function on the innate immune response, but the underlying mechanism remains unknown. This study shows that ORF7b inhibits the RIG-I-like receptor (RLR) signaling pathway through the physical association between ORF7b and mitochondrial antiviral-signaling protein (MAVS), impairing the K63-linked MAVS polyubiquitination and its recruitment of tumor necrosis factor receptor-related factor 6 (TRAF6) to MAVS. The most potent interfering peptide V targeting the ORF7b-MAVS complex may reverse the suppression of the MAVS-mediated RLR signaling pathway by ORF7b and prevent viral infection and production. This study may provide new insights into the pathogenic mechanism of SARS-CoV-2 and a strategy to develop new drugs to prevent SARS-CoV-2 infection.
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Affiliation(s)
- Xiao Xiao
- Department of Infectious Diseases, Renmin Hospital, School of Basic Medical Sciences, Hubei University of Medicine, Shiyan, China
- Institute of Virology, Shiyan Key Laboratory of Virology, Hubei University of Medicine, Shiyan, China
- Hubei Key Laboratory of Embryonic Stem Cell Research, Hubei University of Medicine, Shiyan, China
| | - Yanan Fu
- Department of Infectious Diseases, Renmin Hospital, School of Basic Medical Sciences, Hubei University of Medicine, Shiyan, China
- Institute of Virology, Shiyan Key Laboratory of Virology, Hubei University of Medicine, Shiyan, China
| | - Wanling You
- Department of Infectious Diseases, Renmin Hospital, School of Basic Medical Sciences, Hubei University of Medicine, Shiyan, China
- Institute of Virology, Shiyan Key Laboratory of Virology, Hubei University of Medicine, Shiyan, China
| | - Congcong Huang
- Department of Infectious Diseases, Renmin Hospital, School of Basic Medical Sciences, Hubei University of Medicine, Shiyan, China
- Institute of Virology, Shiyan Key Laboratory of Virology, Hubei University of Medicine, Shiyan, China
- Hubei Key Laboratory of Embryonic Stem Cell Research, Hubei University of Medicine, Shiyan, China
| | - Feng Zeng
- Department of Infectious Diseases, Renmin Hospital, School of Basic Medical Sciences, Hubei University of Medicine, Shiyan, China
- Institute of Virology, Shiyan Key Laboratory of Virology, Hubei University of Medicine, Shiyan, China
| | - Xinsheng Gu
- Department of Infectious Diseases, Renmin Hospital, School of Basic Medical Sciences, Hubei University of Medicine, Shiyan, China
| | - Xiaoguang Sun
- Department of Infectious Diseases, Renmin Hospital, School of Basic Medical Sciences, Hubei University of Medicine, Shiyan, China
- Institute of Virology, Shiyan Key Laboratory of Virology, Hubei University of Medicine, Shiyan, China
| | - Jian Li
- Department of Infectious Diseases, Renmin Hospital, School of Basic Medical Sciences, Hubei University of Medicine, Shiyan, China
- Institute of Virology, Shiyan Key Laboratory of Virology, Hubei University of Medicine, Shiyan, China
| | - Qiwei Zhang
- Guangdong Provincial Key Laboratory of Virology, Institute of Medical Microbiology, Jinan University, Guangzhou, China
| | - Weixing Du
- Department of Infectious Diseases, Renmin Hospital, School of Basic Medical Sciences, Hubei University of Medicine, Shiyan, China
| | - Gong Cheng
- New Cornerstone Science Laboratory, Tsinghua-Peking Joint Center for Life Sciences, School of Basic Medical Sciences, Tsinghua University, Beijing, China
| | - Zhixin Liu
- Department of Infectious Diseases, Renmin Hospital, School of Basic Medical Sciences, Hubei University of Medicine, Shiyan, China
- Institute of Virology, Shiyan Key Laboratory of Virology, Hubei University of Medicine, Shiyan, China
- Hubei Key Laboratory of Embryonic Stem Cell Research, Hubei University of Medicine, Shiyan, China
| | - Long Liu
- Department of Infectious Diseases, Renmin Hospital, School of Basic Medical Sciences, Hubei University of Medicine, Shiyan, China
- Institute of Virology, Shiyan Key Laboratory of Virology, Hubei University of Medicine, Shiyan, China
- Hubei Key Laboratory of Embryonic Stem Cell Research, Hubei University of Medicine, Shiyan, China
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Karkashan A. Immunoinformatics assisted profiling of West Nile virus proteome to determine immunodominant epitopes for the development of next-generation multi-peptide vaccine. Front Immunol 2024; 15:1395870. [PMID: 38799422 PMCID: PMC11116617 DOI: 10.3389/fimmu.2024.1395870] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2024] [Accepted: 04/22/2024] [Indexed: 05/29/2024] Open
Abstract
Emerging infectious diseases represent a significant threat to global health, with West Nile virus (WNV) being a prominent example due to its potential to cause severe neurological disorders alongside mild feverish conditions. Particularly prevalent in the continental United States, WNV has emerged as a global concern, with outbreaks indicating the urgent need for effective prophylactic measures. The current problem is that the absence of a commercial vaccine against WNV highlights a critical gap in preventive strategies against WNV. This study aims to address this gap by proposing a novel, multivalent vaccine designed using immunoinformatics approaches to elicit comprehensive humoral and cellular immune responses against WNV. The objective of the study is to provide a theoretical framework for experimental scientists to formulate of vaccine against WNV and tackle the current problem by generating an immune response inside the host. The research employs reverse vaccinology and subtractive proteomics methodologies to identify NP_041724.2 polyprotein and YP_009164950.1 truncated flavivirus polyprotein NS1 as the prime antigens. The selection process for epitopes focused on B and T-cell reactivity, antigenicity, water solubility, and non-allergenic properties, prioritizing candidates with the potential for broad immunogenicity and safety. The designed vaccine construct integrates these epitopes, connected via GPGPG linkers, and supplemented with an adjuvant with the help of another linker EAAAK, to enhance immunogenicity. Preliminary computational analyses suggest that the proposed vaccine could achieve near-universal coverage, effectively targeting approximately 99.74% of the global population, with perfect coverage in specific regions such as Sweden and Finland. Molecular docking and immune simulation studies further validate the potential efficacy of the vaccine, indicating strong binding affinity with toll-like receptor 3 (TLR-3) and promising immune response profiles, including significant antibody-mediated and cellular responses. These findings present the vaccine construct as a viable candidate for further development and testing. While the theoretical and computational results are promising, advancing from in-silico predictions to a tangible vaccine requires comprehensive laboratory validation. This next step is essential to confirm the vaccine's efficacy and safety in eliciting an immune response against WNV. Through this study, we propose a novel approach to vaccine development against WNV and contribute to the broader field of immunoinformatics, showcasing the potential to accelerate the design of effective vaccines against emerging viral threats. The journey from hypothesis to practical solution embodies the interdisciplinary collaboration essential for modern infectious disease management and prevention strategies.
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Affiliation(s)
- Alaa Karkashan
- Department of Biological Sciences, College of Sciences, University of Jeddah, Jeddah, Saudi Arabia
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Guo J, Zhong Y, Wang Y, Liu P, Jin H, Wang Y, Shi L, Wang P, Li W. Phylogenetic Relationships and Evolution of the Genus Eganvirus (186-Type) Yersinia pestis Bacteriophages. Viruses 2024; 16:748. [PMID: 38793629 PMCID: PMC11126057 DOI: 10.3390/v16050748] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2024] [Revised: 05/02/2024] [Accepted: 05/06/2024] [Indexed: 05/26/2024] Open
Abstract
Plague is an endemic infectious disease caused by Yersinia pestis. In this study, we isolated fourteen phages with similar sequence arrangements to phage 186; these phages exhibited different lytic abilities in Enterobacteriaceae strains. To illustrate the phylogenetic relationships and evolutionary relationships between previously designated 186-type phages, we analysed the complete sequences and important genes of the phages, including whole-genome average nucleotide identity (ANI) and collinearity comparison, evolutionary analysis of four conserved structural genes (V, T, R, and Q genes), and analysis of the regulatory genes (cI, apl, and cII) and integrase gene (int). Phylogenetic analysis revealed that thirteen of the newly isolated phages belong to the genus Eganvirus and one belongs to the genus Felsduovirus in the family Peduoviridae, and these Eganvirus phages can be roughly clustered into three subgroups. The topological relationships exhibited by the whole-genome and structural genes seemed similar and stable, while the regulatory genes presented different topological relationships with the structural genes, and these results indicated that there was some homologous recombination in the regulatory genes. These newly isolated 186-type phages were mostly isolated from dogs, suggesting that the resistance of Canidae to Y. pestis infection may be related to the wide distribution of phages with lytic capability.
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Affiliation(s)
- Jin Guo
- National Institute for Communicable Disease Control and Prevention, China CDC, Changping, Beijing 102206, China; (J.G.); (Y.W.); (H.J.); (Y.W.)
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, Beijing 102206, China
| | - Youhong Zhong
- Yunnan Institute for Endemic Disease Control and Prevention, Dali 671000, China; (Y.Z.); (P.L.); (L.S.)
- Yunnan Provincial Key Laboratory for Zoonosis Control and Prevention, Dali 671000, China
| | - Yiting Wang
- National Institute for Communicable Disease Control and Prevention, China CDC, Changping, Beijing 102206, China; (J.G.); (Y.W.); (H.J.); (Y.W.)
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, Beijing 102206, China
| | - Pan Liu
- Yunnan Institute for Endemic Disease Control and Prevention, Dali 671000, China; (Y.Z.); (P.L.); (L.S.)
- Yunnan Provincial Key Laboratory for Zoonosis Control and Prevention, Dali 671000, China
| | - Haixiao Jin
- National Institute for Communicable Disease Control and Prevention, China CDC, Changping, Beijing 102206, China; (J.G.); (Y.W.); (H.J.); (Y.W.)
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, Beijing 102206, China
| | - Yumeng Wang
- National Institute for Communicable Disease Control and Prevention, China CDC, Changping, Beijing 102206, China; (J.G.); (Y.W.); (H.J.); (Y.W.)
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, Beijing 102206, China
| | - Liyuan Shi
- Yunnan Institute for Endemic Disease Control and Prevention, Dali 671000, China; (Y.Z.); (P.L.); (L.S.)
- Yunnan Provincial Key Laboratory for Zoonosis Control and Prevention, Dali 671000, China
| | - Peng Wang
- Yunnan Institute for Endemic Disease Control and Prevention, Dali 671000, China; (Y.Z.); (P.L.); (L.S.)
- Yunnan Provincial Key Laboratory for Zoonosis Control and Prevention, Dali 671000, China
| | - Wei Li
- National Institute for Communicable Disease Control and Prevention, China CDC, Changping, Beijing 102206, China; (J.G.); (Y.W.); (H.J.); (Y.W.)
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, Beijing 102206, China
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Sarvmeili J, Baghban Kohnehrouz B, Gholizadeh A, Shanehbandi D, Ofoghi H. Immunoinformatics design of a structural proteins driven multi-epitope candidate vaccine against different SARS-CoV-2 variants based on fynomer. Sci Rep 2024; 14:10297. [PMID: 38704475 PMCID: PMC11069592 DOI: 10.1038/s41598-024-61025-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Accepted: 04/30/2024] [Indexed: 05/06/2024] Open
Abstract
The ideal vaccines for combating diseases that may emerge in the future require more than simply inactivating a few pathogenic strains. This study aims to provide a peptide-based multi-epitope vaccine effective against various severe acute respiratory syndrome coronavirus 2 strains. To design the vaccine, a library of peptides from the spike, nucleocapsid, membrane, and envelope structural proteins of various strains was prepared. Then, the final vaccine structure was optimized using the fully protected epitopes and the fynomer scaffold. Using bioinformatics tools, the antigenicity, allergenicity, toxicity, physicochemical properties, population coverage, and secondary and three-dimensional structures of the vaccine candidate were evaluated. The bioinformatic analyses confirmed the high quality of the vaccine. According to further investigations, this structure is similar to native protein and there is a stable and strong interaction between vaccine and receptors. Based on molecular dynamics simulation, structural compactness and stability in binding were also observed. In addition, the immune simulation showed that the vaccine can stimulate immune responses similar to real conditions. Finally, codon optimization and in silico cloning confirmed efficient expression in Escherichia coli. In conclusion, the fynomer-based vaccine can be considered as a new style in designing and updating vaccines to protect against coronavirus disease.
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Affiliation(s)
- Javad Sarvmeili
- Department of Plant Breeding and Biotechnology, University of Tabriz, Tabriz, 51666, Iran
| | | | - Ashraf Gholizadeh
- Department of Animal Biology, University of Tabriz, Tabriz, 51666, Iran
| | - Dariush Shanehbandi
- Department of Immunology, Tabriz University of Medical Sciences, Tabriz, 51666, Iran
| | - Hamideh Ofoghi
- Department of Biotechnology, Iranian Research Organization for Science and Technology, Tehran, 33131, Iran
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Wang J, Jiang F, Cheng P, Ye Z, Li L, Yang L, Zhuang L, Gong W. Construction of novel multi-epitope-based diagnostic biomarker HP16118P and its application in the differential diagnosis of Mycobacterium tuberculosis latent infection. MOLECULAR BIOMEDICINE 2024; 5:15. [PMID: 38679629 PMCID: PMC11056354 DOI: 10.1186/s43556-024-00177-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Accepted: 02/29/2024] [Indexed: 05/01/2024] Open
Abstract
Tuberculosis (TB) is an infectious disease that significantly threatens human health. However, the differential diagnosis of latent tuberculosis infection (LTBI) and active tuberculosis (ATB) remains a challenge for clinicians in early detection and preventive intervention. In this study, we developed a novel biomarker named HP16118P, utilizing 16 helper T lymphocyte (HTL) epitopes, 11 cytotoxic T lymphocyte (CTL) epitopes, and 8 B cell epitopes identified from 15 antigens associated with LTBI-RD using the IEDB database. We analyzed the physicochemical properties, spatial structure, and immunological characteristics of HP16118P using various tools, which indicated that it is a hydrophilic and relatively stable alkaline protein. Furthermore, HP16118P exhibited good antigenicity and immunogenicity, while being non-toxic and non-allergenic, with the potential to induce immune responses. We observed that HP16118P can stimulate the production of high levels of IFN-γ+ T lymphocytes in individuals with ATB, LTBI, and health controls. IL-5 induced by HP16118P demonstrated potential in distinguishing LTBI individuals and ATB patients (p=0.0372, AUC=0.8214, 95% CI [0.5843 to 1.000]) with a sensitivity of 100% and specificity of 71.43%. Furthermore, we incorporated the GM-CSF, IL-23, IL-5, and MCP-3 induced by HP16118P into 15 machine learning algorithms to construct a model. It was found that the Quadratic discriminant analysis model exhibited the best diagnostic performance for discriminating between LTBI and ATB, with a sensitivity of 1.00, specificity of 0.86, and accuracy of 0.93. In summary, HP16118P has demonstrated strong antigenicity and immunogenicity, with the induction of GM-CSF, IL-23, IL-5, and MCP-3, suggesting their potential for the differential diagnosis of LTBI and ATB.
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Affiliation(s)
- Jie Wang
- Beijing Key Laboratory of New Techniques of Tuberculosis Diagnosis and Treatment, Institute of Tuberculosis Research, Senior Department of Tuberculosis, The Eighth Medical Center of PLA General Hospital, 17#Heishanhu Road, Haidian District, Beijing, 100091, China
- Department of Clinical Laboratory, The Eighth Medical Center of PLA General Hospital, Beijing, 100091, China
| | - Fan Jiang
- Beijing Key Laboratory of New Techniques of Tuberculosis Diagnosis and Treatment, Institute of Tuberculosis Research, Senior Department of Tuberculosis, The Eighth Medical Center of PLA General Hospital, 17#Heishanhu Road, Haidian District, Beijing, 100091, China
- Section of Health, No. 94804 Unit of the Chinese People's Liberation Army, Shanghai, 200434, China
- Resident standardization training cadet corps, Air Force Hospital of Eastern Theater, Nanjing, 210002, China
| | - Peng Cheng
- Beijing Key Laboratory of New Techniques of Tuberculosis Diagnosis and Treatment, Institute of Tuberculosis Research, Senior Department of Tuberculosis, The Eighth Medical Center of PLA General Hospital, 17#Heishanhu Road, Haidian District, Beijing, 100091, China
| | - Zhaoyang Ye
- Beijing Key Laboratory of New Techniques of Tuberculosis Diagnosis and Treatment, Institute of Tuberculosis Research, Senior Department of Tuberculosis, The Eighth Medical Center of PLA General Hospital, 17#Heishanhu Road, Haidian District, Beijing, 100091, China
- Hebei North University, ZhangjiakouHebei, 075000, China
| | - Linsheng Li
- Beijing Key Laboratory of New Techniques of Tuberculosis Diagnosis and Treatment, Institute of Tuberculosis Research, Senior Department of Tuberculosis, The Eighth Medical Center of PLA General Hospital, 17#Heishanhu Road, Haidian District, Beijing, 100091, China
- Hebei North University, ZhangjiakouHebei, 075000, China
| | - Ling Yang
- Beijing Key Laboratory of New Techniques of Tuberculosis Diagnosis and Treatment, Institute of Tuberculosis Research, Senior Department of Tuberculosis, The Eighth Medical Center of PLA General Hospital, 17#Heishanhu Road, Haidian District, Beijing, 100091, China
- Hebei North University, ZhangjiakouHebei, 075000, China
| | - Li Zhuang
- Beijing Key Laboratory of New Techniques of Tuberculosis Diagnosis and Treatment, Institute of Tuberculosis Research, Senior Department of Tuberculosis, The Eighth Medical Center of PLA General Hospital, 17#Heishanhu Road, Haidian District, Beijing, 100091, China
- Hebei North University, ZhangjiakouHebei, 075000, China
| | - Wenping Gong
- Beijing Key Laboratory of New Techniques of Tuberculosis Diagnosis and Treatment, Institute of Tuberculosis Research, Senior Department of Tuberculosis, The Eighth Medical Center of PLA General Hospital, 17#Heishanhu Road, Haidian District, Beijing, 100091, China.
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Bernardes GPMDA, Serra GM, Silva LDSE, Martins MP, Perez LN, de Molfetta FA, Santos AV, Schneider MPC. Potential Involvement of the South American Lungfish Intelectin-2 in Innate-Associated Immune Modulation. Int J Mol Sci 2024; 25:4798. [PMID: 38732017 PMCID: PMC11084424 DOI: 10.3390/ijms25094798] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2024] [Revised: 04/16/2024] [Accepted: 04/17/2024] [Indexed: 05/13/2024] Open
Abstract
Intelectins belong to a family of lectins with specific and transitory carbohydrate interaction capabilities. These interactions are related to the activity of agglutinating pathogens, as intelectins play a significant role in immunity. Despite the prominent immune defense function of intelectins, limited information about its structural characteristics and carbohydrate interaction properties is available. This study investigated an intelectin transcript identified in RNA-seq data obtained from the South American lungfish (Lepidosiren paradoxa), namely LpITLN2-B. The structural analyses predicted LpITLN2-B to be a homo-trimeric globular protein with the fibrinogen-like functional domain (FReD), exhibiting a molecular mass of 57 kDa. The quaternary structure is subdivided into three monomers, A, B, and C, and each domain comprises 11 β-sheets: an anti-parallel β-sheet, a β-hairpin, and a disordered β-sheet structure. Molecular docking demonstrates a significant interaction with disaccharides rather than monosaccharides. The preferential interaction with disaccharides highlights the potential interaction with pathogen molecules, such as LPS and Poly(I:C). The hemagglutination assay inhibited lectins activity, especially maltose and sucrose, highlighting lectin activity in L. paradoxa samples. Overall, our results show the potential relevance of LpITLN2-B in L. paradoxa immune defense against pathogens.
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Affiliation(s)
| | - Gustavo Marques Serra
- Laboratory of Biotechnology of Enzymes and Biotransformation, Biological Sciences Institute, Federal University of Pará (UFPA), Belém 66075-110, PA, Brazil;
| | - Lucas da Silva e Silva
- Laboratory of Genomics and Biotechnology, Biological Sciences Institute, Federal University of Pará (UFPA), Belém 66075-110, PA, Brazil; (G.P.M.d.A.B.); (L.d.S.e.S.); (M.P.C.S.)
| | - Maíra Pompeu Martins
- Laboratory of Genomics and Biotechnology, Biological Sciences Institute, Federal University of Pará (UFPA), Belém 66075-110, PA, Brazil; (G.P.M.d.A.B.); (L.d.S.e.S.); (M.P.C.S.)
| | - Louise Neiva Perez
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA;
| | - Fábio Alberto de Molfetta
- Laboratory of Molecular Modeling, Exact and Natural Sciences Institute, Federal University of Pará (UFPA), Belém 66075-110, PA, Brazil;
| | - Agenor Valadares Santos
- Laboratory of Biotechnology of Enzymes and Biotransformation, Biological Sciences Institute, Federal University of Pará (UFPA), Belém 66075-110, PA, Brazil;
| | - Maria Paula Cruz Schneider
- Laboratory of Genomics and Biotechnology, Biological Sciences Institute, Federal University of Pará (UFPA), Belém 66075-110, PA, Brazil; (G.P.M.d.A.B.); (L.d.S.e.S.); (M.P.C.S.)
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Bhat RAH, Khangembam VC, Pant V, Tandel RS, Pandey PK, Thakuria D. Antibacterial activity of a short de novo designed peptide against fish bacterial pathogens. Amino Acids 2024; 56:28. [PMID: 38578302 PMCID: PMC10997546 DOI: 10.1007/s00726-024-03388-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Accepted: 03/06/2024] [Indexed: 04/06/2024]
Abstract
In the face of increasing antimicrobial resistance in aquaculture, researchers are exploring novel substitutes to customary antibiotics. One potential solution is the use of antimicrobial peptides (AMPs). We aimed to design and evaluate a novel, short, and compositionally simple AMP with potent activity against various bacterial pathogens in aquaculture. The resulting peptide, KK12YW, has an amphipathic nature and net charge of + 7. Molecular docking experiments disclosed that KK12YW has a strong affinity for aerolysin, a virulence protein produced by the bacterial pathogen Aeromonas sobria. KK12YW was synthesized using Fmoc chemistry and tested against a range of bacterial pathogens, including A. sobria, A. salmonicida, A. hydrophila, Edwardsiella tarda, Vibrio parahaemolyticus, Pseudomonas aeruginosa, Escherichia coli, Staphylococcus epidermidis, and methicillin-resistant S. aureus. The AMP showed promising antibacterial activity, with MIC and MBC values ranging from 0.89 to 917.1 µgmL-1 and 3.67 to 1100.52 µgmL-1, respectively. In addition, KK12YW exhibited resistance to high temperatures and remained effective even in the presence of serum and salt, indicating its stability. The peptide also demonstrated minimal hemolysis toward fish RBCs, even at higher concentrations. Taken together, these findings indicate that KK12YW could be a highly promising and viable substitute for conventional antibiotics to combat microbial infections in aquaculture.
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Affiliation(s)
| | - Victoria C Khangembam
- ICAR-Directorate of Coldwater Fisheries Research, Bhimtal, 263136, Uttarakhand, India
| | - Vinita Pant
- ICAR-Directorate of Coldwater Fisheries Research, Bhimtal, 263136, Uttarakhand, India
| | - Ritesh Shantilal Tandel
- ICAR-Directorate of Coldwater Fisheries Research, Bhimtal, 263136, Uttarakhand, India
- Navsari Gujarat Research Centre, ICAR-Central Institute of Brackishwater Aquaculture, Navsari, 396 450, Gujarat, India
| | - Pramod Kumar Pandey
- ICAR-Directorate of Coldwater Fisheries Research, Bhimtal, 263136, Uttarakhand, India
| | - Dimpal Thakuria
- ICAR-Directorate of Coldwater Fisheries Research, Bhimtal, 263136, Uttarakhand, India.
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Mishra N, Dubey S, Kumari A, Khan MA, Kuligina ES, Preobrazhenskaya EV, Romanko AA, Yadav LR, Sarin R, Imyanitov EN, Varma AK. Structural implications of amyloidogenic rare variants Ser282Leu and Gln356Arg identified in h-BRCA1. Proteins 2024; 92:540-553. [PMID: 38037760 DOI: 10.1002/prot.26638] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Revised: 11/03/2023] [Accepted: 11/06/2023] [Indexed: 12/02/2023]
Abstract
Preliminary studies have shown BRCA1 (170-1600) residues to be intrinsically disordered with unknown structural details. However, thousands of clinically reported variants have been identified in this central region of BRCA1. Therefore, we aimed to characterize h-BRCA1(260-553) to assess the structural basis for pathogenicity of two rare missense variants Ser282Leu, Gln356Arg identified from the Indian and Russian populations respectively. Small-angle X-ray scattering analysis revealed WT scores Rg -32 Å, Dmax -93 Å, and Rflex-51% which are partially disordered, whereas Ser282Leu variant displayed a higher degree of disorderedness and Gln356Arg was observed to be aggregated. WT protein also possesses an inherent propensity to undergo a disorder-to-order transition in the presence of cruciform DNA and 2,2,2-Trifluoroethanol (TFE). An increased alpha-helical pattern was observed with increasing concentration of TFE for the Gln356Arg mutant whereas Ser282Leu mutant showed significant differences only at the highest TFE concentration. Furthermore, higher thermal shift was observed for WT-DNA complex compared to the Gln356Arg and Ser282Leu protein-DNA complex. Moreover, mature amyloid-like fibrils were observed with 30 μM thioflavin T (ThT) at 37°C for Ser282Leu and Gln356Arg proteins while the WT protein exists in a protofibril state as observed by TEM. Gln356Arg formed higher-order aggregates with amyloidogenesis over time as monitored by ThT fluorescence. In addition, computational analyses confirmed larger conformational fluctuations for Ser282Leu and Gln356Arg mutants than for the WT. The global structural alterations caused by these variants provide a mechanistic approach for further classification of the variants of uncertain clinical significance in BRCA1 into amyloidogenic variants which may have a significant role in disease pathogenesis.
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Affiliation(s)
- Neha Mishra
- Advanced Center for Treatment, Research and Education in Cancer, Navi Mumbai, India
- Homi Bhabha National Institute, Training School Complex, Mumbai, India
| | - Suchita Dubey
- Advanced Center for Treatment, Research and Education in Cancer, Navi Mumbai, India
- Homi Bhabha National Institute, Training School Complex, Mumbai, India
| | - Anchala Kumari
- Advanced Center for Treatment, Research and Education in Cancer, Navi Mumbai, India
| | - Mudassar Ali Khan
- Advanced Center for Treatment, Research and Education in Cancer, Navi Mumbai, India
- Homi Bhabha National Institute, Training School Complex, Mumbai, India
| | - Ekaterina S Kuligina
- Laboratory of Molecular Oncology, Department of Tumor Growth Biology, N.N. Petrov Institute of Oncology, St. Petersburg, Russia
- Department of Medical Genetics, St.-Petersburg Pediatric Medical University, St. Petersburg, Russia
| | - Elena V Preobrazhenskaya
- Laboratory of Molecular Oncology, Department of Tumor Growth Biology, N.N. Petrov Institute of Oncology, St. Petersburg, Russia
- Department of Medical Genetics, St.-Petersburg Pediatric Medical University, St. Petersburg, Russia
| | - Alexandr A Romanko
- Laboratory of Molecular Oncology, Department of Tumor Growth Biology, N.N. Petrov Institute of Oncology, St. Petersburg, Russia
- Department of Medical Genetics, St.-Petersburg Pediatric Medical University, St. Petersburg, Russia
| | - Lumbini R Yadav
- Advanced Center for Treatment, Research and Education in Cancer, Navi Mumbai, India
| | - Rajiv Sarin
- Advanced Center for Treatment, Research and Education in Cancer, Navi Mumbai, India
- Homi Bhabha National Institute, Training School Complex, Mumbai, India
| | - Evgeny N Imyanitov
- Laboratory of Molecular Oncology, Department of Tumor Growth Biology, N.N. Petrov Institute of Oncology, St. Petersburg, Russia
- Department of Medical Genetics, St.-Petersburg Pediatric Medical University, St. Petersburg, Russia
- Department of Oncology, I.I. Mechnikov North-Western Medical University, St.-Petersburg, Russia
| | - Ashok K Varma
- Advanced Center for Treatment, Research and Education in Cancer, Navi Mumbai, India
- Homi Bhabha National Institute, Training School Complex, Mumbai, India
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46
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Darvishi F, Beiranvand E, Kalhor H, Shahbazi B, Mafakher L. Homology modeling and molecular docking studies to decrease glutamine affinity of Yarrowia lipolytica L-asparaginase. Int J Biol Macromol 2024; 263:130312. [PMID: 38403216 DOI: 10.1016/j.ijbiomac.2024.130312] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Revised: 01/10/2024] [Accepted: 02/18/2024] [Indexed: 02/27/2024]
Abstract
L-Asparaginase is a key component in the treatment of leukemias and lymphomas. However, the glutamine affinity of this therapeutic enzyme is an off-target activity that causes several side effects. The modeling and molecular docking study of Yarrowia lipolytica L-asparaginase (YL-ASNase) to reduce its l-glutamine affinity and increase its stability was the aim of this study. Protein-ligand interactions of wild-type and different mutants of YL-ASNase against L-asparagine compared to l-glutamine were assessed using AutoDock Vina tools because the crystal structure of YL-ASNase does not exist in the protein data banks. The results showed that three mutants, T171S, T171S-N60A, and T171A-T223A, caused a considerable increase in L-asparagine affinity and a decrease in l-glutamine affinity as compared to the wild-type and other mutants. Then, molecular dynamics simulation and MM/GBSA free energy were applied to assess the stability of protein structure and its interaction with ligands. The three mutated proteins, especially T171S-N60A, had higher stability and interactions with L-asparagine than l-glutamine in comparison with the wild-type. The YL-ASNase mutants could be introduced as appropriate therapeutic candidates that might cause lower side effects. However, the functional properties of these mutated enzymes need to be confirmed by genetic manipulation and in vitro and in vivo studies.
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Affiliation(s)
- Farshad Darvishi
- Department of Microbiology, Faculty of Biological Sciences, Alzahra University, Tehran, Iran; Research Center for Applied Microbiology and Microbial Biotechnology (CAMB), Alzahra University, Tehran, Iran.
| | - Elham Beiranvand
- Department of Microbiology, Faculty of Biological Sciences, Alzahra University, Tehran, Iran.
| | - Hourieh Kalhor
- Cellular and Molecular Research Center, Qom University of Medical Sciences, Qom, Iran
| | - Behzad Shahbazi
- School of Pharmacy, Semnan University of Medical Sciences, Semnan, Iran
| | - Ladan Mafakher
- Thalassemia and Hemoglobinopathy Research Center, Health Research Institute, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
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Panda SP, Roy P, Soren D, Ranjan Sahoo D, Dehury B, Rout AK, Behera BK, Das BK. Structural insights of Labeo catla (catla) myxovirus resistance protein,GTP binding recognition and constitutive expression induced with Poly I:C. J Biomol Struct Dyn 2024; 42:3520-3534. [PMID: 37227778 DOI: 10.1080/07391102.2023.2213345] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Accepted: 05/08/2023] [Indexed: 05/27/2023]
Abstract
The Myxovirus resistance (Mx) proteins are critical effectors belonging to the super-family of guanidine triphosphatase, often stimulated by type I interferon (IFN) and mediates antiviral responses to restrict the replication of numerous viral genes in fishes. In teleosts, Mx proteins display diverse and complicated antiviral activity in different species. The present investigation seeks to characterize the Mx gene from Labeo catla upon induction by double-stranded (ds) RNA, polyinosinic-polycytidylic acid, (poly I: C). Molecular modeling and all-atoms molecular dynamics (MD) simulations were employed to understand the architecture of the GTPase domain and its plausible mode of GTP recognition in Mx protein. The full-length L. catla Mx (LcMx) gene sequence (1821 bp nucleotides) encodes an open reading frame of 606 amino acids. Domain search indicated conserved tripartite domain architecture of LcMx and forms a major cluster with the Mx from other teleosts. The positively charged Arginine and polar Glutamine residues from helix 3 and 4 of stalk region LcMx aid in homo-oligomerization. MD simulation portrayed the role of conserved critical residues aid in GTP recognition by the GTPase domain which perfectly corroborates with experimental findings and prior MD studies. After injection of poly I:C, the temporal mRNA profile showed that LcMx expression was significantly elevated in the spleen, brain, kidney, liver, muscle, heart, intestine, and gill tissues. Collectively, these results suggest that the elevated expression of the major innate immune defense gene Mx was able to inhibit the poly I: C mediated virulence in fish.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Soumya Prasad Panda
- Fish Health Management Division, ICAR-Central Institute of Freshwater Aquaculture, Bhubaneswar, Odisha, India
- Biotechnology Division, ICAR-Central Inland Fisheries Research Institute, Kolkata, West Bengal, India
- Department of Zoology, Ravenshaw University, Cuttack, Odisha, India
| | - Pragyan Roy
- Fish Health Management Division, ICAR-Central Institute of Freshwater Aquaculture, Bhubaneswar, Odisha, India
| | - Dhananjay Soren
- Department of Zoology, Ravenshaw University, Cuttack, Odisha, India
| | | | - Budheswar Dehury
- Biotechnology Division, ICAR-Central Inland Fisheries Research Institute, Kolkata, West Bengal, India
- Bioinformatics Division, ICMR-Regional Medical Research Centre, Nalco Square, Bhubaneswar, Odisha, India
| | - Ajaya Kumar Rout
- Biotechnology Division, ICAR-Central Inland Fisheries Research Institute, Kolkata, West Bengal, India
| | - Bijay Kumar Behera
- Biotechnology Division, ICAR-Central Inland Fisheries Research Institute, Kolkata, West Bengal, India
| | - Basanta Kumar Das
- Biotechnology Division, ICAR-Central Inland Fisheries Research Institute, Kolkata, West Bengal, India
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Suleman M, Khan TA, Ejaz H, Maroof S, Alshammari A, Albekairi NA, Khan H, Waheed Y, Khan A, Wei DQ, Crovella S. Structural vaccinology, molecular simulation and immune simulation approaches to design multi-epitopes vaccine against John Cunningham virus. Microb Pathog 2024; 189:106572. [PMID: 38354987 DOI: 10.1016/j.micpath.2024.106572] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Revised: 12/23/2023] [Accepted: 02/11/2024] [Indexed: 02/16/2024]
Abstract
The JCV (John Cunningham Virus) is known to cause progressive multifocal leukoencephalopathy, a condition that results in the formation of tumors. Symptoms of this condition such as sensory defects, cognitive dysfunction, muscle weakness, homonosapobia, difficulties with coordination, and aphasia. To date, there is no specific and effective treatment to completely cure or prevent John Cunningham polyomavirus infections. Since the best way to control the disease is vaccination. In this study, the immunoinformatic tools were used to predict the high immunogenic and non-allergenic B cells, helper T cells (HTL), and cytotoxic T cells (CTL) epitopes from capsid, major capsid, and T antigen proteins of JC virus to design the highly efficient subunit vaccines. The specific immunogenic linkers were used to link together the predicted epitopes and subjected to 3D modeling by using the Robetta server. MD simulation was used to confirm that the newly constructed vaccines are stable and properly fold. Additionally, the molecular docking approach revealed that the vaccines have a strong binding affinity with human TLR-7. The codon adaptation index (CAI) and GC content values verified that the constructed vaccines would be highly expressed in E. coli pET28a (+) plasmid. The immune simulation analysis indicated that the human immune system would have a strong response to the vaccines, with a high titer of IgM and IgG antibodies being produced. In conclusion, this study will provide a pre-clinical concept to construct an effective, highly antigenic, non-allergenic, and thermostable vaccine to combat the infection of the John Cunningham virus.
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Affiliation(s)
- Muhammad Suleman
- Laboratory of Animal Research Center (LARC), Qatar University, Doha, Qatar; Center for Biotechnology and Microbiology, University of Swat, Swat, Pakistan.
| | - Tariq Aziz Khan
- Center for Biotechnology and Microbiology, University of Swat, Swat, Pakistan.
| | - Hadiqa Ejaz
- King Edward Medical University, Lahore, Pakistan.
| | - Sabahat Maroof
- Sharif Medical and Dental Colllege, Lahore, Punjab, Pakistan
| | - Abdulrahman Alshammari
- Department of Pharmacology and Toxicology, College of Pharmacy, King Saud University, Post Box 2455, Riyadh, 11451, Saudi Arabia.
| | - Norah A Albekairi
- Department of Pharmacology and Toxicology, College of Pharmacy, King Saud University, Post Box 2455, Riyadh, 11451, Saudi Arabia.
| | - Haji Khan
- Center for Biotechnology and Microbiology, University of Swat, Swat, Pakistan.
| | - Yasir Waheed
- Office of Research, Innovation, and Commercialization (ORIC), Shaheed Zulfiqar Ali Bhutto Medical University (SZABMU), Islamabad, 44000, Pakistan; Gilbert and Rose-Marie Chagoury School of Medicine, Lebanese American University, Byblos, 1401, Lebanon
| | - Abbas Khan
- Department of Bioinformatics and Biostatistics, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China; Sunway Microbiome Centre, School of Medical and Life Sciences, Sunway University, 47500, Sunway City, Malaysia.
| | - Dong-Qing Wei
- Department of Bioinformatics and Biostatistics, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Sergio Crovella
- Laboratory of Animal Research Center (LARC), Qatar University, Doha, Qatar.
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Yazdani Z, Rafiei A, Ghoreyshi M, Abediankenari S. In Silico Analysis of a Candidate Multi-epitope Peptide Vaccine Against Human Brucellosis. Mol Biotechnol 2024; 66:769-783. [PMID: 36940016 PMCID: PMC10026239 DOI: 10.1007/s12033-023-00698-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Accepted: 02/13/2023] [Indexed: 03/21/2023]
Abstract
Brucellosis is one of the neglected endemic zoonoses in the world. Vaccination appears to be a promising health strategy to prevent it. This study used advanced computational techniques to develop a potent multi-epitope vaccine for human brucellosis. Seven epitopes from four main brucella species that infect humans were selected. They had significant potential to induce cellular and humoral responses. They showed high antigenic ability without the allergenic characteristic. In order to improve its immunogenicity, suitable adjuvants were also added to the structure of the vaccine. The physicochemical and immunological properties of the vaccine were evaluated. Then its two and three-dimensional structure was predicted. The vaccine was docked with toll-like receptor4 to assess its ability to stimulate innate immune responses. For successful expression of the vaccine protein in Escherichia coli, in silico cloning, codon optimization, and mRNA stability were evaluated. The immune simulation was performed to reveal the immune response profile of the vaccine after injection. The designed vaccine showed the high ability to induce immune response, especially cellular responses to human brucellosis. It showed the appropriate physicochemical properties, a high-quality structure, and a high potential for expression in a prokaryotic system.
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Affiliation(s)
- Zahra Yazdani
- Department of Immunology, Molecular and Cell Biology Research Center, School of Medicine, Mazandaran University of Medical Sciences, Sari, Iran
- Students Research Committee, Mazandaran University of Medical Sciences, Sari, Iran
| | - Alireza Rafiei
- Department of Immunology, Molecular and Cell Biology Research Center, School of Medicine, Mazandaran University of Medical Sciences, Sari, Iran.
| | - Mehrafarin Ghoreyshi
- Students Research Committee, Mazandaran University of Medical Sciences, Sari, Iran
| | - Saeid Abediankenari
- Immunogenetics Research Center, Department of Immunology, Faculty of Medicine, Mazandaran University of Medical Sciences, Sari, Iran
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50
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Sarkar S, Kumari A, Tiwari M, Tiwari V. Interaction and simulation studies suggest the possible molecular targets of intrinsically disordered amyloidogenic antimicrobial peptides in Acinetobacter baumannii. J Biomol Struct Dyn 2024; 42:2747-2764. [PMID: 37144752 DOI: 10.1080/07391102.2023.2208219] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Accepted: 04/20/2023] [Indexed: 05/06/2023]
Abstract
Acinetobacter baumannii is one of the causing agents of nosocomial infections. A wide range of antibiotics fails to work against these pathogens. Hence, there is an urgent requirement to develop other therapeutics to solve this problem. Antimicrobial peptides (AMPs) are a diverse group of naturally occurring peptides that have the ability to kill diverse groups of microorganisms. The major challenge of using AMPs as therapeutics is their unstable nature and the fact that most of their molecular targets are still unknown. In this study, we have selected intrinsically disordered and amyloidogenic AMPs, showing activity against A. baumannii, that is, Bactenecin, Cath BF, Citropin 1.1, DP7, NA-CATH, Tachyplesin, and WAM-1. To identify the probable target of these AMPs in A. baumannii, calculation of docking score, binding energy, dissociation constant, and molecular dynamics analysis was performed with selected seventeen possible molecular targets. The result showed that the most probable molecular targets of most of the intrinsically disordered amyloidogenic AMPs were UDP-N-acetylenol-pyruvoyl-glucosamine reductase (MurB), followed by 33-36 kDa outer membrane protein (Omp 33-36), UDP-N-acetylmuramoyl-l-alanyl-d-glutamate-2,6-diaminopimelate ligase (MurE), and porin Subfamily Protein (PorinSubF). Further, molecular dynamics analysis concluded that the target of antimicrobial peptide Bactenecin is MurB of A. baumannii, and identified other molecular targets of selected AMPs. Additionally, the oligomerization capacity of the selected AMPs was also investigated, and it was shown that the selected AMPs form oligomeric states, and interact with their molecular targets in that state. Experimental validation using purified AMPs and molecular targets needs to be done to confirm the interaction.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Sayani Sarkar
- Department of Biochemistry, Central University of Rajasthan, Ajmer, India
| | - Aruna Kumari
- Department of Biochemistry, Central University of Rajasthan, Ajmer, India
| | - Monalisa Tiwari
- Department of Biochemistry, Central University of Rajasthan, Ajmer, India
| | - Vishvanath Tiwari
- Department of Biochemistry, Central University of Rajasthan, Ajmer, India
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