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Lu T, Das S, Howlader DR, Picking WD, Picking WL. Shigella Vaccines: The Continuing Unmet Challenge. Int J Mol Sci 2024; 25:4329. [PMID: 38673913 PMCID: PMC11050647 DOI: 10.3390/ijms25084329] [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: 02/27/2024] [Revised: 04/09/2024] [Accepted: 04/11/2024] [Indexed: 04/28/2024] Open
Abstract
Shigellosis is a severe gastrointestinal disease that annually affects approximately 270 million individuals globally. It has particularly high morbidity and mortality in low-income regions; however, it is not confined to these regions and occurs in high-income nations when conditions allow. The ill effects of shigellosis are at their highest in children ages 2 to 5, with survivors often exhibiting impaired growth due to infection-induced malnutrition. The escalating threat of antibiotic resistance further amplifies shigellosis as a serious public health concern. This review explores Shigella pathology, with a primary focus on the status of Shigella vaccine candidates. These candidates include killed whole-cells, live attenuated organisms, LPS-based, and subunit vaccines. The strengths and weaknesses of each vaccination strategy are considered. The discussion includes potential Shigella immunogens, such as LPS, conserved T3SS proteins, outer membrane proteins, diverse animal models used in Shigella vaccine research, and innovative vaccine development approaches. Additionally, this review addresses ongoing challenges that necessitate action toward advancing effective Shigella prevention and control measures.
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Affiliation(s)
- Ti Lu
- Department of Veterinary Pathobiology and Bond Life Science Center, University of Missouri, Columbia, MO 65201, USA; (D.R.H.); (W.D.P.)
| | - Sayan Das
- Department of Microbial Pathogenesis, School of Dentistry, University of Maryland, Baltimore, MD 21201, USA;
| | - Debaki R. Howlader
- Department of Veterinary Pathobiology and Bond Life Science Center, University of Missouri, Columbia, MO 65201, USA; (D.R.H.); (W.D.P.)
| | - William D. Picking
- Department of Veterinary Pathobiology and Bond Life Science Center, University of Missouri, Columbia, MO 65201, USA; (D.R.H.); (W.D.P.)
| | - Wendy L. Picking
- Department of Veterinary Pathobiology and Bond Life Science Center, University of Missouri, Columbia, MO 65201, USA; (D.R.H.); (W.D.P.)
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Ullah H, Mahmud S, Hossain MJ, Islam MSB, Kibria KMK. Immunoinformatic identification of the epitope-based vaccine candidates from Maltoporin, FepA and OmpW of Shigella Spp, with molecular docking confirmation. INFECTION GENETICS AND EVOLUTION 2021; 96:105129. [PMID: 34737105 DOI: 10.1016/j.meegid.2021.105129] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Revised: 10/16/2021] [Accepted: 10/28/2021] [Indexed: 11/17/2022]
Abstract
Shigella is a bacterial pathogen that causes shigellosis, fatal bacillary dysentery, responsible for a higher level of mortality worldwide. We adopted a number of computational approaches to predict potential epitope-based vaccine candidates of immunogenic proteins of Shigella spp. We selected three cell surface proteins of the bacterium according to their antigenicity using the VaxiJen server, including, FepA, Maltoporin, and OmpW. The sequence analyses by the IEDB server resulted in three 15-mer peptides of the core epitope, FTAEHTQSV, FLVNQTLTL, and MRAGSATVR from FepA, Maltoporin, and OmpW, respectively, as the most potential epitopes that have an affinity with both cytotoxic and helper T-cells. Moreover, the epitopes showed 73.76%, 99.0%, and 93.07% world population coverage, along with 100% conservancy among the Shigella subspecies. The molecular docking simulation studies were performed to verify the interactions between the peptides and the respective HLAs. Docking analyses showed that the Epitope-MHC complexes had a higher level of global energy score dictating strong binding. We have also predicted B-cell epitopes from the sequences of these three proteins. In vivo study of the proposed epitope might contribute to the development of a functional and efficient vaccine, which might be an effective way to elude dysentery from the world.
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Affiliation(s)
- Hedayet Ullah
- Department of Biotechnology and Genetic Engineering, Faculty of Life Science, Mawlana Bhashani Science and Technology University, Tangail 1902, Bangladesh
| | - Shahin Mahmud
- Department of Biotechnology and Genetic Engineering, Faculty of Life Science, Mawlana Bhashani Science and Technology University, Tangail 1902, Bangladesh
| | - Md Jakir Hossain
- Department of Biotechnology and Genetic Engineering, Faculty of Life Science, Mawlana Bhashani Science and Technology University, Tangail 1902, Bangladesh
| | - Md Shaid Bin Islam
- Department of Biotechnology and Genetic Engineering, Faculty of Life Science, Mawlana Bhashani Science and Technology University, Tangail 1902, Bangladesh
| | - K M Kaderi Kibria
- Department of Biotechnology and Genetic Engineering, Faculty of Life Science, Mawlana Bhashani Science and Technology University, Tangail 1902, Bangladesh.
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Integrative Systems Biology Approaches to Identify Potential Biomarkers and Pathways of Cervical Cancer. J Pers Med 2021; 11:jpm11050363. [PMID: 33946372 PMCID: PMC8147030 DOI: 10.3390/jpm11050363] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Revised: 04/13/2021] [Accepted: 04/19/2021] [Indexed: 12/31/2022] Open
Abstract
Nowadays, cervical cancer (CC) is treated as the leading cancer among women throughout the world. Despite effective vaccination and improved surgery and treatment, CC retains its fatality rate of about half of the infected population globally. The major screening biomarkers and therapeutic target identification have now become a global concern. In the present study, we have employed systems biology approaches to retrieve the potential biomarkers and pathways from transcriptomic profiling. Initially, we have identified 76 of each up-regulated and down-regulated gene from a total of 4643 differentially expressed genes. The up-regulatory genes mainly concentrate on immune-inflammatory responses, and the down-regulatory genes are on receptor binding and gamma-glutamyltransferase. The involved pathways associated with these genes were also assessed through pathway enrichment, and we mainly focused on different cancer pathways, immunoresponse, and cell cycle pathways. After the subsequent enrichment of these genes, we have identified 12 hub genes, which play a crucial role in CC and are verified by expression profile analysis. From our study, we have found that genes LILRB2 and CYBB play crucial roles in CC, as reported here for the first time. Furthermore, the survivability of the hub genes was also assessed, and among them, finally, CXCR4 has been identified as one of the most potential differentially expressed genes that might play a vital role in the survival of CC patients. Thus, CXCR4 could be used as a prognostic and/or diagnostic biomarker and a drug target for CC.
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Pervin T, Oany AR. Vaccinomics approach for scheming potential epitope-based peptide vaccine by targeting l-protein of Marburg virus. In Silico Pharmacol 2021; 9:21. [PMID: 33717824 PMCID: PMC7936589 DOI: 10.1007/s40203-021-00080-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Accepted: 02/02/2021] [Indexed: 12/31/2022] Open
Abstract
Marburg virus is one of the world’s most threatening diseases, causing extreme hemorrhagic fever, with a death rate of up to 90%. The Food and Drug Administration (FDA) currently not authorized any treatments or vaccinations for the hindrance and post-exposure of the Marburg virus. In the present study, the vaccinomics methodology was adopted to design a potential novel peptide vaccine against the Marburg virus, targeting RNA-directed RNA polymerase (l). A total of 48 l-proteins from diverse variants of the Marburg virus were collected from the NCBI GenBank server and used to classify the best antigenic protein leading to predict equally T and B-cell epitopes. Initially, the top 26 epitopes were evaluated for the attraction with major histocompatibility complex (MHC) class I and II alleles. Finally, four prospective central epitopes NLSDLTFLI, FRYEFTRHF, YRLRNSTAL, and YRVRNVQTL were carefully chosen. Among these, FRYEFTRHF and YRVRNVQTL peptides showed 100% conservancy. Though YRLRNSTAL showed 95.74% conservancy, it demonstrated the highest combined score as T cell epitope (2.5461) and population coverage of 94.42% among the whole world population. The epitope was found non-allergenic, and docking interactions with human leukocyte antigens (HLAs) also verified. Finally, in vivo analysis of the recommended peptides might contribute to the advancement of an efficient and exclusively prevalent vaccine that would be an active route to impede the virus spreading.
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Affiliation(s)
- Tahmina Pervin
- Biotechnology and Genetic Engineering Discipline, Life Science School, Khulna University, Khulna, 9208 Bangladesh
| | - Arafat Rahman Oany
- Department of Biotechnology and Genetic Engineering, Faculty of Life Science, Mawlana Bhashani Science and Technology University, Tangail, 1902 Bangladesh.,Aristopharma Limited, Dhaka, Bangladesh
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Khan F, Kumar A. Vaccine Design and Immunoinformatics. Adv Bioinformatics 2021. [DOI: 10.1007/978-981-33-6191-1_8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
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Munia M, Mahmud S, Mohasin M, Kibria KK. In silico design of an epitope-based vaccine against choline binding protein A of Streptococcus pneumoniae. INFORMATICS IN MEDICINE UNLOCKED 2021. [DOI: 10.1016/j.imu.2021.100546] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
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Oany AR, Pervin T, Moni MA. Pharmacoinformatics based elucidation and designing of potential inhibitors against Plasmodium falciparum to target importin α/β mediated nuclear importation. INFECTION GENETICS AND EVOLUTION 2020; 88:104699. [PMID: 33385575 DOI: 10.1016/j.meegid.2020.104699] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2020] [Revised: 12/23/2020] [Accepted: 12/24/2020] [Indexed: 12/12/2022]
Abstract
Plasmodium falciparum, the prime causative agent of malaria, is responsible for 4, 05,000 deaths per year and fatality rates are higher among the children aged below 5 years. The emerging distribution of the multi-drug resistant P. falciparum becomes a worldwide concern, so the identification of unique targets and novel inhibitors is a prime need now. In the present study, we have employed pharmacoinformatics approaches to analyze 265 lead-like compounds from PubChem databases for virtual screening. Thereafter, 15 lead-like compounds were docked within the active side pocket of importin alpha. Comparative ligand properties and absorption, distribution, metabolism, excretion, and toxicity (ADMET) profile were also assessed. Finally, a novel inhibitor was designed and assessed computationally for its efficacy. From the comparative analysis we have found that our screened compounds possess better results than the existing lead ivermectin; having the highest binding energy of -15.6 kcal/mol, whereas ivermectin has -12.4 kcal/mol. The novel lead compound possessed more fascinating output without deviating any of the rules of Lipinski. It also possessed higher bioavailability and the drug-likeness score of 0.55 and 0.71, respectively compared to ivermectin. Furthermore, the binding study was confirmed by molecular dynamics simulation over 25 ns by evaluating the stability of the complex. Finally, all the screened compounds and the novel compound showed promising ADMET properties likewise. To end, we hope that our proposed screened compounds, as well as the novel compound, might give some advances to treat malaria efficiently in vitro and in vivo.
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Affiliation(s)
- Arafat Rahman Oany
- Department of Biotechnology and Genetic Engineering, Faculty of Life Science, Mawlana Bhashani Science and Technology University, Tangail, Bangladesh; Aristopharma Limited, Bangladesh.
| | - Tahmina Pervin
- Biotechnology and Genetic Engineering Discipline, Life Science School, Khulna University, Khulna, Bangladesh
| | - Mohammad Ali Moni
- Department of Computer Science & Engineering, Green University, Bangladesh; Department of Computer Science & Engineering, Pabna University of Science & Technology, Bangladesh; WHO Collaborating Centre on eHealth, UNSW Digital Health, School of Public Health and Community Medicine, Faculty of Medicine, UNSW, Sydney, Australia.
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Islam MSB, Miah M, Hossain ME, Kibria KMK. A conserved multi-epitope-based vaccine designed by targeting hemagglutinin protein of highly pathogenic avian H5 influenza viruses. 3 Biotech 2020; 10:546. [PMID: 33251084 PMCID: PMC7682764 DOI: 10.1007/s13205-020-02544-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2020] [Accepted: 11/03/2020] [Indexed: 11/29/2022] Open
Abstract
The highly pathogenic avian H5N1 influenza viruses have been recognized as a potential pandemic threat to humans, and to the poultry industry since 1997. H5 viruses consist of a high mutation rate, so universal vaccine designing is very challenging. Here, we describe a vaccinomics approach to design a novel multi-epitope influenza vaccine, based on the highly conserved regions of surface glycoprotein, Hemagglutinin (HA). Initially, the HA protein sequences from Bangladeshi origin were retrieved and aligned by ClustalW. The sequences of 100% conserved regions extracted and analyzed to select the highest potential T-cell and B-cell epitope. The HTL and CTL analyses using IEDB tools showed that DVWTYNAELLVLMEN possesses the highest affinity with MHC class I and II alleles, and it has the highest population coverage. The docking simulation study suggests that this epitope has the potential to interact with both MHC class I and MHC class II. The B-cell epitope prediction provides a potential peptide, GAIAGFIEGGWQGM. We further retrieved HA sequences of 3950 avian and 250 human H5 isolates from several populations of the world, where H5 was an epidemic. Surprisingly, these epitopes are more than 98% conserved in those regions which indicate their potentiality as a conserved vaccine. We have proposed a multi-epitope vaccine using these sequences and assess its stability and potentiality to induce B-cell immunity. In vivo study is necessary to corroborate this epitope as a vaccine, however, setting forth groundwork for wet-lab studies essential to mitigate pandemic threats and provide cross-protection of both avian and humans against H5 influenza viruses.
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Affiliation(s)
- Md. Shaid Bin Islam
- Department of Biotechnology and Genetic Engineering, Faculty of Life Science, Mawlana Bhashani Science and Technology University, Tangail, 1902 Bangladesh
| | - Mojnu Miah
- Infectious Diseases Division, International Centre for Diarrheal Diseases Research, Bangladesh (icddr,b), Dhaka, Bangladesh
| | - Mohammad Enayet Hossain
- Emerging Infections, Infectious Diseases Division, International Centre for Diarrheal Diseases Research, Bangladesh (icddr,b), Dhaka, Bangladesh
| | - K. M. Kaderi Kibria
- Department of Biotechnology and Genetic Engineering, Faculty of Life Science, Mawlana Bhashani Science and Technology University, Tangail, 1902 Bangladesh
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Smiline Girija AS. Delineating the Immuno-Dominant Antigenic Vaccine Peptides Against gacS -Sensor Kinase in Acinetobacter baumannii: An in silico Investigational Approach. Front Microbiol 2020; 11:2078. [PMID: 33013757 PMCID: PMC7506167 DOI: 10.3389/fmicb.2020.02078] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2019] [Accepted: 08/06/2020] [Indexed: 11/13/2022] Open
Abstract
Objectives To predict the novel vaccine peptide candidates against gacS protein involved with the citrate utilization in the two-component system of A. baumannii-associated virulence as an alternative strategy to combat the multi-drug resistant strains using an immuno-informatic approach. Methods The study is designed as an observational in silico study design with the application of BepiPred, AlgPred, VaxiJen, AntigenPro, SolPro, Expasy ProtParam server, IEDB database, and MHC cluster analytical tools and servers to predict the immuno-dominant B-cell and T-cell epitopes from gacS FASTA sequences retrieved from UNIPROT database. Further peptide interactions with TLR-4 was assessed based on the number of hydrogen bonds. Results Nine peptides (20aa) with the highest score of 1 were selected from the 137 epitopes, and five were predicted as antigenic epitopes (E1-E5). E3 was selected as the potent antigen (score: 0.939537) and E1 as the best vaccine candidate (score: 0.9803) under AntigenPro and Vaxijen server, respectively. SolPro predicted all epitopes as soluble peptides. ProtParam predictions showed E3 and E5 as stable proteins with a shelf life of 3.5 and 1.9 h and possessed negative GRAVY values. PsortB server predicted a final localization score of 7.88 for the gacS protein sequence as a cytoplasmic membrane protein. IEDB conservancy analysis showed 100% conserved sequences within the gacS sequence, and class I conservancy yielded positive values for all epitopes. Cluster analysis showed strong interactions, and the protein-peptide interactions with TLR-2 finally detected E5 as the best interacting peptide (H bonds = 14) followed by E3 (H bonds = 12). Conclusion The study suggests five antigenic peptides as promiscuous vaccine candidates to target the gacS of A. baumannii using immuno-informatic approach toward the peptide synthesis and in vitro analysis. However, the study recommends further experimental validation for immunological response and memory through in vivo studies.
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Affiliation(s)
- A S Smiline Girija
- Department of Microbiology, Saveetha Dental College and Hospitals, Saveetha Institute of Medical and Technical Sciences (SIMATS), Saveetha University, Chennai, India
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Intranasal Immunization of Mice with Multiepitope Chimeric Vaccine Candidate Based on Conserved Autotransporters SigA, Pic and Sap, Confers Protection against Shigella flexneri. Vaccines (Basel) 2020; 8:vaccines8040563. [PMID: 33019492 PMCID: PMC7712744 DOI: 10.3390/vaccines8040563] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Revised: 09/10/2020] [Accepted: 09/11/2020] [Indexed: 11/24/2022] Open
Abstract
Shigellosis is a diarrheal disease and the World Health Organization prompts the development of a vaccine against Shigella flexneri. The autotransporters SigA, Pic and Sap are conserved among Shigella spp. We previously designed an in silico vaccine with immunodominat epitopes from those autotransporters, and the GroEL protein of S. typhi as an adjuvant. Here, we evaluated the immunogenicity and protective efficacy of the chimeric multiepitope protein, named rMESF, in mice against lethal infection with S. flexneri. rMESF was administered to mice alone through the intranasal (i.n.) route or accompanied with Complete Freund’s adjuvant (CFA) intradermically (i.d.), subcutaneously (s.c.), and intramuscular (i.m.), as well as with Imject alum (i.m.). All immunized mice increased IgG, IgG1, IgG2a, IgA and fecal IgA titers compared to PBS+CFA and PBS+alum control groups. Furthermore, i.n. immunization of mice with rMESF alone presented the highest titers of serum and fecal IgA. Cytokine levels (IFN-γ, TNF-α, IL-4, and IL-17) and lymphocyte proliferation increased in all experimental groups, with the highest lymphoproliferative response in i.n. mice immunized with rMESF alone, which presented 100% protection against S. flexneri. In summary, this vaccine vests protective immunity and highlights the importance of mucosal immunity activation for the elimination of S. flexneri.
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Oany AR, Mia M, Pervin T, Junaid M, Hosen SMZ, Moni MA. Design of novel viral attachment inhibitors of the spike glycoprotein (S) of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) through virtual screening and dynamics. Int J Antimicrob Agents 2020; 56:106177. [PMID: 32987103 PMCID: PMC7518233 DOI: 10.1016/j.ijantimicag.2020.106177] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2020] [Revised: 09/14/2020] [Accepted: 09/20/2020] [Indexed: 12/12/2022]
Abstract
To date, the global COVID-19 pandemic has been associated with 11.8 million cases and over 545481 deaths. In this study, we have employed virtual screening approaches and selected 415 lead-like compounds from 103 million chemical substances, based on the existing drugs, from PubChem databases as potential candidates for the S protein-mediated viral attachment inhibition. Thereafter, based on drug-likeness and Lipinski's rules, 44 lead-like compounds were docked within the active side pocket of the viral-host attachment site of the S protein. Corresponding ligand properties and absorption, distribution, metabolism, excretion, and toxicity (ADMET) profile were measured. Furthermore, four novel inhibitors were designed and assessed computationally for efficacy. Comparative analysis showed the screened compounds in this study maintain better results than the proposed mother compounds, VE607 and SSAA09E2. The four designed novel lead compounds possessed more fascinating output without deviating from any of Lipinski's rules. They also showed higher bioavailability and the drug-likeness score was 0.56 and 1.81 compared with VE607 and SSAA09E2, respectively. All the screened compounds and novel compounds showed promising ADMET properties. Among them, the compound AMTM-02 was the best candidate, with a docking score of -7.5 kcal/mol. Furthermore, the binding study was verified by molecular dynamics simulation over 100 ns by assessing the stability of the complex. The proposed screened compounds and the novel compounds may give some breakthroughs for the development of a therapeutic drug to treat SARS-CoV-2 proficiently in vitro and in vivo.
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Affiliation(s)
- Arafat Rahman Oany
- Department of Biotechnology and Genetic Engineering, Faculty of Life Science, Mawlana Bhashani Science and Technology University, Tangail-1902, Bangladesh; Aristopharma Limited, Bangladesh.
| | - Mamun Mia
- Department of Biotechnology and Genetic Engineering, Faculty of Life Science, Mawlana Bhashani Science and Technology University, Tangail-1902, Bangladesh; Department of Medical Biotechnology, Bangladesh University of Health Sciences, Dhaka, Bangladesh
| | - Tahmina Pervin
- Biotechnology and Genetic Engineering Discipline, Life Science School, Khulna University, Khulna, Bangladesh
| | - Md Junaid
- Molecular Modeling Drug-design and Discovery Laboratory, Pharmacology Research Division, BCSIR Laboratories Chattogram, Bangladesh Council of Scientific and Industrial Research, Chattogram, Bangladesh
| | - S M Zahid Hosen
- Molecular Modeling Drug-design and Discovery Laboratory, Pharmacology Research Division, BCSIR Laboratories Chattogram, Bangladesh Council of Scientific and Industrial Research, Chattogram, Bangladesh; Pancreatic Research Group, South Western Sydney Clinical School, and Ingham Institute for Applied Medical Research, Faculty of Medicine, University of New South Wales, Sydney, Australia
| | - Mohammad Ali Moni
- WHO Collaborating Centre on eHealth, UNSW Digital Health, School of Public Health and Community Medicine, Faculty of Medicine, UNSW Sydney, Australia.
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SARS-CoV-2 transcriptome analysis and molecular cataloguing of immunodominant epitopes for multi-epitope based vaccine design. Genomics 2020; 112:5044-5054. [PMID: 32920121 PMCID: PMC7500163 DOI: 10.1016/j.ygeno.2020.09.019] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Revised: 08/18/2020] [Accepted: 09/08/2020] [Indexed: 01/12/2023]
Abstract
Genomics-led researches are engaged in tracing virus expression pattern, and induced immune responses in human to develop effective vaccine against COVID-19. In this study, targeted expression profiling and differential gene expression analysis of major histocompatibility complexes and innate immune system genes were performed through SARS-CoV-2 infected RNA-seq data of human cell line, and virus transcriptome was generated for T-and B-cell epitope prediction. Docking studies of epitopes with MHC and B-cell receptors were performed to identify potential T-and B-cell epitopes. Transcriptome analysis revealed the specific multiple allele expressions in cell line, genes for elicited induce immune response, and virus gene expression. Proposed T- and B-cell epitopes have high potential to elicit equivalent immune responses caused by SARS-CoV-2 infection which can be useful to provide links between elicited immune response and virus gene expression. This study will facilitate in vitro and in vivo vaccine related research studies in disease control. SARS-CoV-2 transcriptome construction from RNA-seq data of infected human cell-lines. T- and B-cell epitopes from SARS-CoV-2 transcriptome Gene expression profiling of MHC alleles and innate immune system genes
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León Y, Zapata L, Salas-Burgos A, Oñate A. In silico design of a vaccine candidate based on autotransporters and HSP against the causal agent of shigellosis, Shigella flexneri. Mol Immunol 2020; 121:47-58. [DOI: 10.1016/j.molimm.2020.02.008] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2019] [Revised: 02/10/2020] [Accepted: 02/12/2020] [Indexed: 12/19/2022]
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Peptide-Based Vaccination Therapy for Rheumatic Diseases. J Immunol Res 2020; 2020:8060375. [PMID: 32258176 PMCID: PMC7104265 DOI: 10.1155/2020/8060375] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Accepted: 02/28/2020] [Indexed: 02/06/2023] Open
Abstract
Rheumatic diseases are extremely heterogeneous diseases with substantial risks of morbidity and mortality, and there is a pressing need in developing more safe and cost-effective treatment strategies. Peptide-based vaccination is a highly desirable strategy in treating noninfection diseases, such as cancer and autoimmune diseases, and has gained increasing attentions. This review is aimed at providing a brief overview of the recent advances in peptide-based vaccination therapy for rheumatic diseases. Tremendous efforts have been made to develop effective peptide-based vaccinations against rheumatoid arthritis (RA) and systemic lupus erythematosus (SLE), while studies in other rheumatic diseases are still limited. Peptide-based active vaccination against pathogenic cytokines such as TNF-α and interferon-α (IFN-α) is shown to be promising in treating RA or SLE. Moreover, peptide-based tolerogenic vaccinations also have encouraging results in treating RA or SLE. However, most studies available now have been mainly based on animal models, while evidence from clinical studies is still lacking. The translation of these advances from experimental studies into clinical therapy remains impeded by some obstacles such as species difference in immunity, disease heterogeneity, and lack of safe delivery carriers or adjuvants. Nevertheless, advances in high-throughput technology, bioinformatics, and nanotechnology may help overcome these impediments and facilitate the successful development of peptide-based vaccination therapy for rheumatic diseases.
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Oli AN, Obialor WO, Ifeanyichukwu MO, Odimegwu DC, Okoyeh JN, Emechebe GO, Adejumo SA, Ibeanu GC. Immunoinformatics and Vaccine Development: An Overview. Immunotargets Ther 2020; 9:13-30. [PMID: 32161726 PMCID: PMC7049754 DOI: 10.2147/itt.s241064] [Citation(s) in RCA: 107] [Impact Index Per Article: 26.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2019] [Accepted: 01/25/2020] [Indexed: 12/11/2022] Open
Abstract
The use of vaccines have resulted in a remarkable improvement in global health. It has saved several lives, reduced treatment costs and raised the quality of animal and human lives. Current traditional vaccines came empirically with either vague or completely no knowledge of how they modulate our immune system. Even at the face of potential vaccine design advance, immune-related concerns (as seen with specific vulnerable populations, cases of emerging/re-emerging infectious disease, pathogens with complex lifecycle and antigenic variability, need for personalized vaccinations, and concerns for vaccines' immunological safety -specifically vaccine likelihood to trigger non-antigen-specific responses that may cause autoimmunity and vaccine allergy) are being raised. And these concerns have driven immunologists toward research for a better approach to vaccine design that will consider these challenges. Currently, immunoinformatics has paved the way for a better understanding of some infectious disease pathogenesis, diagnosis, immune system response and computational vaccinology. The importance of this immunoinformatics in the study of infectious diseases is diverse in terms of computational approaches used, but is united by common qualities related to host–pathogen relationship. Bioinformatics methods are also used to assign functions to uncharacterized genes which can be targeted as a candidate in vaccine design and can be a better approach toward the inclusion of women that are pregnant into vaccine trials and programs. The essence of this review is to give insight into the need to focus on novel computational, experimental and computation-driven experimental approaches for studying of host–pathogen interactions and thus making a case for its use in vaccine development.
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Affiliation(s)
- Angus Nnamdi Oli
- Department of Pharmaceutical Microbiology and Biotechnology, Faculty of Pharmaceutical Sciences, Nnamdi Azikiwe University, Awka, Nigeria
| | - Wilson Okechukwu Obialor
- Department of Pharmaceutical Microbiology and Biotechnology, Faculty of Pharmaceutical Sciences, Nnamdi Azikiwe University, Awka, Nigeria
| | - Martins Ositadimma Ifeanyichukwu
- Department of Immunology, College of Health Sciences, Faculty of Medicine, Nnamdi Azikiwe University, Anambra, Nigeria.,Department of Medical Laboratory Science,Faculty of Health Science and Technology, College of Health Sciences, Nnamdi Azikiwe University,Nnewi Campus, Nnewi, Nigeria
| | - Damian Chukwu Odimegwu
- Department of Pharmaceutical Microbiology and Biotechnology, Faculty of Pharmaceutical Sciences, University of Nigeria Nsukka, Enugu, Nigeria
| | - Jude Nnaemeka Okoyeh
- Department of Biology and Clinical Laboratory Science, Division of Arts and Sciences, Neumann University, Aston, PA 19014-1298, USA
| | - George Ogonna Emechebe
- Department of Pediatrics, Faculty of Clinical Medicine, Chukwuemeka Odumegwu Ojukwu University, Awka, Nigeria
| | - Samson Adedeji Adejumo
- Department of Pharmaceutical Microbiology and Biotechnology, Faculty of Pharmaceutical Sciences, Nnamdi Azikiwe University, Awka, Nigeria
| | - Gordon C Ibeanu
- Department of Pharmaceutical Science, North Carolina Central University, Durham, NC 27707, USA
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16
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Pokharel P, Habouria H, Bessaiah H, Dozois CM. Serine Protease Autotransporters of the Enterobacteriaceae (SPATEs): Out and About and Chopping It Up. Microorganisms 2019; 7:E594. [PMID: 31766493 PMCID: PMC6956023 DOI: 10.3390/microorganisms7120594] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2019] [Accepted: 11/13/2019] [Indexed: 02/06/2023] Open
Abstract
Autotransporters are secreted proteins with multiple functions produced by a variety of Gram-negative bacteria. In Enterobacteriaceae, a subgroup of these autotransporters are the SPATEs (serine protease autotransporters of Enterobacteriaceae). SPATEs play a crucial role in survival and virulence of pathogens such as Escherichia coli and Shigella spp. and contribute to intestinal and extra-intestinal infections. These high molecular weight proteases are transported to the external milieu by the type Va secretion system and function as proteases with diverse substrate specificities and biological functions including adherence and cytotoxicity. Herein, we provide an overview of SPATEs and discuss recent findings on the biological roles of these secreted proteins, including proteolysis of substrates, adherence to cells, modulation of the immune response, and virulence in host models. In closing, we highlight recent insights into the regulation of expression of SPATEs that could be exploited to understand fundamental SPATE biology.
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Affiliation(s)
- Pravil Pokharel
- Institut National de Recherche Scientifique (INRS)-Centre Armand-Frappier Santé Biotechnologie, Laval, QC H7V 1B7, Canada; (P.P.); (H.H.); (H.B.)
- Centre de Recherche en Infectiologie Porcine et Avicole (CRIPA), Saint-Hyacinthe, QC J2S 2M2, Canada
| | - Hajer Habouria
- Institut National de Recherche Scientifique (INRS)-Centre Armand-Frappier Santé Biotechnologie, Laval, QC H7V 1B7, Canada; (P.P.); (H.H.); (H.B.)
- Centre de Recherche en Infectiologie Porcine et Avicole (CRIPA), Saint-Hyacinthe, QC J2S 2M2, Canada
| | - Hicham Bessaiah
- Institut National de Recherche Scientifique (INRS)-Centre Armand-Frappier Santé Biotechnologie, Laval, QC H7V 1B7, Canada; (P.P.); (H.H.); (H.B.)
- Centre de Recherche en Infectiologie Porcine et Avicole (CRIPA), Saint-Hyacinthe, QC J2S 2M2, Canada
| | - Charles M. Dozois
- Institut National de Recherche Scientifique (INRS)-Centre Armand-Frappier Santé Biotechnologie, Laval, QC H7V 1B7, Canada; (P.P.); (H.H.); (H.B.)
- Centre de Recherche en Infectiologie Porcine et Avicole (CRIPA), Saint-Hyacinthe, QC J2S 2M2, Canada
- Institut Pasteur International Network, Laval, QC H7V 1B7, Canada
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17
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Muñoz González F, Sycz G, Alonso Paiva IM, Linke D, Zorreguieta A, Baldi PC, Ferrero MC. The BtaF Adhesin Is Necessary for Full Virulence During Respiratory Infection by Brucella suis and Is a Novel Immunogen for Nasal Vaccination Against Brucella Infection. Front Immunol 2019; 10:1775. [PMID: 31402921 PMCID: PMC6676368 DOI: 10.3389/fimmu.2019.01775] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2019] [Accepted: 07/15/2019] [Indexed: 01/18/2023] Open
Abstract
Brucella enters their hosts mostly through mucosae from where it spreads systemically. Adhesion to extracellular matrix (ECM) components or to host cells is important for the infectious process, and is mediated by several adhesins, including the BtaF trimeric autotransporter. Although Th1 responses and gamma interferon (IFN-γ) are important for protection, antibodies able to block adhesions might also contribute to prevent Brucella infection. We evaluated the importance of BtaF for respiratory Brucella infection, and characterized the immune response and protection from mucosal challenge induced by nasal vaccination with recombinant BtaF. While lung CFU numbers did not differ at day 1 p.i. between mice intratracheally inoculated with B. suis M1330 (wild type) and those receiving a ΔbtaF mutant, they were reduced in the latter group at 7 and 30 days p.i. For vaccination studies the BtaF passenger domain was engineered and expressed as a soluble trimeric protein. Mice were immunized by the nasal route with BtaF or saline (control group) plus the mucosal adjuvant c-di-AMP. Specific anti-BtaF antibodies (IgG and IgA) were increased in serum, including a mixed IgG2a/IgG1 response. In vitro, these antibodies reduced bacterial adhesion to A549 alveolar epithelial cells. Specific IgA antibodies were also increased in several mucosae. Spleen cells from BtaF immunized mice significantly increased their IL-2, IL-5, IL-17, and IFN-γ secretion upon antigen stimulation. In cervical draining lymph nodes, antigen-experienced CD4+ T cells were maintained mainly as central memory cells. A BtaF-specific delayed-type hypersensitivity response was detected in BtaF immunized mice. Lung cells from the latter produced high levels of IFN-γ upon antigen stimulation. Although nasal immunization with BtaF did not protect mice against B. suis respiratory challenge, it conferred significant protection from intragastric challenge; the splenic load of B. suis was reduced by 3.28 log CFU in immunized mice. This study shows that nasal vaccination with BtaF+c-di-AMP protects against intragastric challenge with B. suis by inducing local and systemic antibody responses, central memory CD4+ T cells and strong Th1 responses. Therefore, although BtaF vaccination did not protect from B. suis respiratory infection, this adhesin constitutes a promising immunogen against mucosal B. suis infection.
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Affiliation(s)
- Florencia Muñoz González
- Cátedra de Inmunología, Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, Buenos Aires, Argentina.,Instituto de Estudios de la Inmunidad Humoral (IDEHU), CONICET-Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Gabriela Sycz
- Fundación Instituto Leloir, IIBBA-CONICET, Buenos Aires, Argentina
| | - Iván M Alonso Paiva
- Cátedra de Inmunología, Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, Buenos Aires, Argentina.,Instituto de Estudios de la Inmunidad Humoral (IDEHU), CONICET-Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Dirk Linke
- Centre for Ecological and Evolutionary Synthesis, University of Oslo, Oslo, Norway
| | | | - Pablo C Baldi
- Cátedra de Inmunología, Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, Buenos Aires, Argentina.,Instituto de Estudios de la Inmunidad Humoral (IDEHU), CONICET-Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Mariana C Ferrero
- Cátedra de Inmunología, Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, Buenos Aires, Argentina.,Instituto de Estudios de la Inmunidad Humoral (IDEHU), CONICET-Universidad de Buenos Aires, Buenos Aires, Argentina
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18
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Wu Y, Zhai W, Zhou X, Wang Z, Lin Y, Ran L, Qi Y, Gao Y. HLA-A2-Restricted Epitopes Identified from MTA1 Could Elicit Antigen-Specific Cytotoxic T Lymphocyte Response. J Immunol Res 2018; 2018:2942679. [PMID: 30596107 PMCID: PMC6286779 DOI: 10.1155/2018/2942679] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2018] [Revised: 07/31/2018] [Accepted: 09/13/2018] [Indexed: 02/06/2023] Open
Abstract
Overexpression of metastasis-associated protein 1 (MTA1) has been observed in many human malignancies and is significantly related to tumor invasion and metastasis, therapeutic resistance to radiation and chemotherapy, making MTA1 an ideal candidate tumor antigen. We identified several human leukocyte antigen- (HLA-) A2-restricted epitopes in MTA1 and evaluated their binding ability to HLA-A∗0201 molecules. Subsequently, a recombinant fragment encompassing the dominant epitopes, MTA1(1-283), was expressed, and the abilities of the selected epitopes of MTA1 and the MTA1(1-283) fragment to induce cytotoxic T lymphocytes (CTLs) were examined. Our results indicated that the epitopes and MTA1(1-283) fragment elicited HLA-A2-restricted and antigen-specific CTL responses both in vitro and in vivo. The new epitopes identified here may help promote the development of new therapeutic vaccines for HLA-A2+ patients expressing MTA1.
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Affiliation(s)
- Yahong Wu
- School of Life Sciences, Zhengzhou University, Zhengzhou 450001, China
| | - Wenjie Zhai
- School of Life Sciences, Zhengzhou University, Zhengzhou 450001, China
| | - Xiuman Zhou
- School of Life Sciences, Zhengzhou University, Zhengzhou 450001, China
| | - Zhiwei Wang
- School of Life Sciences, Zhengzhou University, Zhengzhou 450001, China
| | - Yan Lin
- School of Life Sciences, Zhengzhou University, Zhengzhou 450001, China
| | - Ling Ran
- School of Life Sciences, Zhengzhou University, Zhengzhou 450001, China
| | - Yuanming Qi
- School of Life Sciences, Zhengzhou University, Zhengzhou 450001, China
| | - Yanfeng Gao
- School of Life Sciences, Zhengzhou University, Zhengzhou 450001, China
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19
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Immunoinformatics Approach for Epitope-Based Peptide Vaccine Design and Active Site Prediction against Polyprotein of Emerging Oropouche Virus. J Immunol Res 2018; 2018:6718083. [PMID: 30402510 PMCID: PMC6196980 DOI: 10.1155/2018/6718083] [Citation(s) in RCA: 87] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2018] [Accepted: 08/28/2018] [Indexed: 12/21/2022] Open
Abstract
Oropouche virus (OROV) is an emerging pathogen which causes Oropouche fever and meningitis in humans. Several outbreaks of OROV in South America, especially in Brazil, have changed its status as an emerging disease, but no vaccine or specific drug target is available yet. Our approach was to identify the epitope-based vaccine candidates as well as the ligand-binding pockets through the use of immunoinformatics. In this report, we identified both T-cell and B-cell epitopes of the most antigenic OROV polyprotein with the potential to induce both humoral and cell-mediated immunity. Eighteen highly antigenic and immunogenic CD8+ T-cell epitopes were identified, including three 100% conserved epitopes (TSSWGCEEY, CSMCGLIHY, and LAIDTGCLY) as the potential vaccine candidates. The selected epitopes showed 95.77% coverage for the mixed Brazilian population. The docking simulation ensured the binding interaction with high affinity. A total of five highly conserved and nontoxic linear B-cell epitopes "NQKIDLSQL," "HPLSTSQIGDRC," "SHCNLEFTAITADKIMSL," "PEKIPAKEGWLTFSKEHTSSW," and "HHYKPTKNLPHVVPRYH" were selected as potential vaccine candidates. The predicted eight conformational B-cell epitopes represent the accessibility for the entered virus. In the posttherapeutic strategy, ten ligand-binding pockets were identified for effective inhibitor design against emerging OROV infection. Collectively, this research provides novel candidates for epitope-based peptide vaccine design against OROV.
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20
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Allué-Guardia A, Koenig SSK, Quirós P, Muniesa M, Bono JL, Eppinger M. Closed Genome and Comparative Phylogenetic Analysis of the Clinical Multidrug Resistant Shigella sonnei Strain 866. Genome Biol Evol 2018; 10:2241-2247. [PMID: 30060169 PMCID: PMC6128377 DOI: 10.1093/gbe/evy168] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/28/2018] [Indexed: 01/10/2023] Open
Abstract
Shigella sonnei is responsible for the majority of shigellosis infections in the US with over 500,000 cases reported annually. Here, we present the complete genome of the clinical multidrug resistant (MDR) strain 866, which is highly susceptible to bacteriophage infections. The strain has a circular chromosome of 4.85 Mb and carries a 113 kb MDR plasmid. This IncB/O/K/Z-type plasmid, termed p866, confers resistance to five different classes of antibiotics including ß-lactamase, sulfonamide, tetracycline, aminoglycoside, and trimethoprim. Comparative analysis of the plasmid architecture and gene inventory revealed that p866 shares its plasmid backbone with previously described IncB/O/K/Z-type Shigella spp. and Escherichia coli plasmids, but is differentiated by the insertion of antibiotic resistance cassettes, which we found associated with mobile genetic elements such as Tn3, Tn7, and Tn10. A whole genome-derived phylogenetic reconstruction showed the evolutionary relationships of S. sonnei strain 866 and the four established Shigella species, highlighting the clonal nature of S. sonnei.
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Affiliation(s)
- Anna Allué-Guardia
- Department of Biology, University of Texas at San Antonio.,South Texas Center for Emerging Infectious Diseases (STCEID), San Antonio
| | - Sara S K Koenig
- Department of Biology, University of Texas at San Antonio.,South Texas Center for Emerging Infectious Diseases (STCEID), San Antonio
| | - Pablo Quirós
- Department of Genetics, Microbiology and Statistics, University of Barcelona, Spain
| | - Maite Muniesa
- Department of Genetics, Microbiology and Statistics, University of Barcelona, Spain
| | - James L Bono
- Agricultural Research Service, United States Department of Agriculture, U.S. Meat Animal Research Center, Clay Center, Nebraska
| | - Mark Eppinger
- Department of Biology, University of Texas at San Antonio.,South Texas Center for Emerging Infectious Diseases (STCEID), San Antonio
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21
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Solanki V, Tiwari V. Subtractive proteomics to identify novel drug targets and reverse vaccinology for the development of chimeric vaccine against Acinetobacter baumannii. Sci Rep 2018; 8:9044. [PMID: 29899345 PMCID: PMC5997985 DOI: 10.1038/s41598-018-26689-7] [Citation(s) in RCA: 127] [Impact Index Per Article: 21.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2018] [Accepted: 05/17/2018] [Indexed: 11/24/2022] Open
Abstract
The emergence of drug-resistant Acinetobacter baumannii is the global health problem associated with high mortality and morbidity. Therefore it is high time to find a suitable therapeutics for this pathogen. In the present study, subtractive proteomics along with reverse vaccinology approaches were used to predict suitable therapeutics against A. baumannii. Using subtractive proteomics, we have identified promiscuous antigenic membrane proteins that contain the virulence factors, resistance factors and essentiality factor for this pathogenic bacteria. Selected promiscuous targeted membrane proteins were used for the design of chimeric-subunit vaccine with the help of reverse vaccinology. Available best tools and servers were used for the identification of MHC class I, II and B cell epitopes. All selected epitopes were further shortlisted computationally to know their immunogenicity, antigenicity, allergenicity, conservancy and toxicity potentials. Immunogenic predicted promiscuous peptides used for the development of chimeric subunit vaccine with immune-modulating adjuvants, linkers, and PADRE (Pan HLA-DR epitopes) amino acid sequence. Designed vaccine construct V4 also interact with the MHC, and TLR4/MD2 complex as confirm by docking and molecular dynamics simulation studies. Therefore designed vaccine construct V4 can be developed to control the host-pathogen interaction or infection caused by A. baumannii.
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Affiliation(s)
- Vandana Solanki
- Department of Biochemistry, Central University of Rajasthan, Bandarsindri, Ajmer, 305817, India
| | - Vishvanath Tiwari
- Department of Biochemistry, Central University of Rajasthan, Bandarsindri, Ajmer, 305817, India.
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22
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Oany AR, Mia M, Pervin T, Hasan MN, Hirashima A. Identification of potential drug targets and inhibitor of the pathogenic bacteria Shigella flexneri 2a through the subtractive genomic approach. In Silico Pharmacol 2018; 6:11. [PMID: 30607324 DOI: 10.1007/s40203-018-0048-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2018] [Accepted: 05/28/2018] [Indexed: 01/09/2023] Open
Abstract
Shigella flexneri 2a is one of the most pathogenic bacteria among the Shigella spp., which is responsible for dysentery and causes masses of deaths throughout the world per year. A proper identification of the potential drug targets and inhibitors is crucial for the treatment of the shigellosis due to their emerging multidrug resistance (MDR) patterns. In this study, a systematic subtractive approach was implemented for the identification of novel therapeutic targets of S. flexneri 2a (301) through genome-wide metabolic pathway analysis of the essential genes and proteins. Ligand-based virtual screening and ADMET analyses were also made for the identification of potential inhibitors as well. Initially, we found 70 essential unique proteins as novel targets. After subsequent prioritization, finally we got six unique targets as the potential therapeutic targets and their three-dimensional models were built thereafter. Aspartate-β-semialdehyde dehydrogenase (ASD), was the most potent target among them and used for docking analysis through ligand-based virtual screening. The compound 3 (PubChem CID: 11319750) suited well as the best inhibitor of the ASD through ADMET and enzyme inhibition capacity analysis. To end, we hope that our proposed therapeutic targets and its inhibitors might give some breakthrough to treat shigellosis efficiently in in vitro.
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Affiliation(s)
- Arafat Rahman Oany
- 1Department of Biotechnology and Genetic Engineering, Life Science Faculty, Mawlana Bhashani Science and Technology University, Tangail, 1902 Bangladesh
| | - Mamun Mia
- 1Department of Biotechnology and Genetic Engineering, Life Science Faculty, Mawlana Bhashani Science and Technology University, Tangail, 1902 Bangladesh
| | - Tahmina Pervin
- 2Biotechnology and Genetic Engineering Discipline, Life Science School, Khulna University, Khulna, Bangladesh
| | - Md Nazmul Hasan
- 3Department of Genetic Engineering and Biotechnology, Jessore University of Science and Technology, Jessore, Bangladesh
| | - Akinori Hirashima
- 4Laboratory of Pesticide Chemistry, Division of Molecular Biosciences, Department of Bioscience and Biotechnology, Faculty of Agriculture, Kyushu University, Fukuoka, 812-8581 Japan
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