In silico and immunoinformatics based multiepitope subunit vaccine design for protection against visceral leishmaniasis

References

• Aleem, M. T., Khan, A., Wen, Z., Yu, Z., Li, K., Shaukat, A., Chen, C., Rehman, T. U., Lu, M., Xu, L., Song, X., Li, X., & Yan, R. (2022). Molecular docking and in silico simulation of trichinella spiralis membrane-associated progesterone receptor component 2 (Ts-MAPRC2) and its interaction with human PGRMC1. BioMed Research International, 2022, 7414198–7414110. https://doi.org/10.1155/2022/7414198
   PubMed Web of Science ®Google Scholar
• Alford, R. F., Leaver-Fay, A., Jeliazkov, J. R., O'Meara, M. J., DiMaio, F. P., Park, H., Shapovalov, M. V., Renfrew, P. D., Mulligan, V. K., Kappel, K., Labonte, J. W., Pacella, M. S., Bonneau, R., Bradley, P., Dunbrack, R. L., Jr, Das, R., Baker, D., Kuhlman, B., Kortemme, T., & Gray, J. J. (2017). The Rosetta all-atom energy function for macromolecular modeling and design. Journal of Chemical Theory and Computation, 13(6), 3031–3048. https://doi.org/10.1021/acs.jctc.7b00125
   PubMed Web of Science ®Google Scholar
• Ali, M., Pandey, R. K., Khatoon, N., Narula, A., Mishra, A., & Prajapati, V. K. (2017). Exploring dengue genome to construct a multiepitope based subunit vaccine by utilizing immunoinformatics approach to battle against dengue infection. Scientific Reports, 7(1), 9232. https://doi.org/10.1038/s41598-017-09199-w
   PubMed Web of Science ®Google Scholar
• Al Zamane, S., Nobel, F. A., Jebin, R. A., Amin, M. B., Somadder, P. D., Antora, N. J., Hossain, M. I., Islam, M. J., Ahmed, K., & Moni, M. A. (2021). Development of an in silico multiepitope vaccine against SARS-COV-2 by précised immune-informatics approaches. Informatics in Medicine Unlocked, 27, 100781. https://doi.org/10.1016/j.imu.2021.100781
   PubMedGoogle Scholar
• Arezi, B., & Kuchta, R. D. (2000). Eukaryotic DNA primase. Trends in Biochemical Sciences, 25(11), 572–576. https://doi.org/10.1016/s0968-0004(00)01680-7
   PubMed Web of Science ®Google Scholar
• Awan, F. M., Obaid, A., Ikram, A., & Janjua, H. A. (2017). Mutation-structure-function relationship based integrated strategy reveals the potential impact of deleterious missense mutations in autophagy related proteins on hepatocellular carcinoma (HCC): A comprehensive informatics approach. International Journal of Molecular Sciences, 18(1), 139. https://doi.org/10.3390/ijms18010139
   PubMed Web of Science ®Google Scholar
• Bauer, J. A., Pavlović, J., & Bauerová-Hlinková, V. (2019). Normal mode analysis as a routine part of a structural investigation. Molecules, 24(18), 3293. https://doi.org/10.3390/molecules24183293
   PubMed Web of Science ®Google Scholar
• Beaumier, C. M., Gillespie, P. M., Hotez, P. J., & Bottazzi, M. E. (2013). New vaccines for neglected parasitic diseases and dengue. Translational Research: The Journal of Laboratory and Clinical Medicine, 162(3), 144–155. https://doi.org/10.1016/j.trsl.2013.03.006
   PubMed Web of Science ®Google Scholar
• Bhattacharya, M., Sharma, A. R., Patra, P., Ghosh, P., Sharma, G., Patra, B. C., Saha, R. P., Lee, S. S., & Chakraborty, C. (2020). A SARS-CoV-2 vaccine candidate: In-silico cloning and validation. Informatics in Medicine Unlocked, 20, 100394. https://doi.org/10.1016/j.imu.2020.100394
   PubMedGoogle Scholar
• Bhowmik, D., Jagadeesan, R., Rai, P., Nandi, R., Gugan, K., & Kumar, D. (2021). Evaluation of potential drugs against leishmaniasis targeting catalytic subunit of Leishmania donovani nuclear DNA primase using ligand based virtual screening, docking and molecular dynamics approaches. Journal of Biomolecular Structure & Dynamics, 39(5), 1838–1852. https://doi.org/10.1080/07391102.2020.1739557
   PubMed Web of Science ®Google Scholar
• Bonam, S. R., Partidos, C. D., Halmuthur, S., & Muller, S. (2017). An overview of novel adjuvants designed for improving vaccine efficacy. Trends in Pharmacological Sciences, 38(9), 771–793. https://doi.org/10.1016/j.tips.2017.06.002
   PubMed Web of Science ®Google Scholar
• Caro-Gomez, E., Gazi, M., Goez, Y., & Valbuena, G. (2014). Discovery of novel cross-protective Rickettsia prowazekii T-cell antigens using a combined reverse vaccinology and in vivo screening approach. Vaccine, 32(39), 4968–4976. https://doi.org/10.1016/j.vaccine.2014.06.089
   PubMed Web of Science ®Google Scholar
• Case, D. A., Cheatham, T. E., 3rd, Darden, T., Gohlke, H., Luo, R., Merz, K. M., Jr, Onufriev, A., Simmerling, C., Wang, B., & Woods, R. J. (2005). The Amber biomolecular simulation programs. Journal of Computational Chemistry, 26(16), 1668–1688. https://doi.org/10.1002/jcc.20290
   PubMed Web of Science ®Google Scholar
• Castiglione, F., Mantile, F., De Berardinis, P., & Prisco, A. (2012). How the interval between prime and boost injection affects the immune response in a computational model of the immune system. Computational and Mathematical Methods in Medicine, 2012, 842329–842329. https://doi.org/10.1155/2012/842329
   PubMed Web of Science ®Google Scholar
• Chakravarty, J., Kumar, S., Trivedi, S., Rai, V. K., Singh, A., Ashman, J. A., Laughlin, E. M., Coler, R. N., Kahn, S. J., Beckmann, A. M., Cowgill, K. D., Reed, S. G., Sundar, S., & Piazza, F. M. (2011). A clinical trial to evaluate the safety and immunogenicity of the LEISH-F1 + MPL-SE vaccine for use in the prevention of visceral leishmaniasis. Vaccine, 29(19), 3531–3537. https://doi.org/10.1016/j.vaccine.2011.02.096
   PubMed Web of Science ®Google Scholar
• Chaudhury, S., Berrondo, M., Weitzner, B. D., Muthu, P., Bergman, H., & Gray, J. J. (2011). Benchmarking and analysis of protein docking performance in Rosetta v3.2. PLoS One, 6(8), e22477. https://doi.org/10.1371/journal.pone.0022477
   PubMed Web of Science ®Google Scholar
• Chauhan, V., & Singh, M. P. (2020). Immuno-informatics approach to design a multiepitope vaccine to combat cytomegalovirus infection. European Journal of Pharmaceutical Sciences: Official Journal of the European Federation for Pharmaceutical Sciences, 147, 105279. https://doi.org/10.1016/j.ejps.2020.105279
   PubMed Web of Science ®Google Scholar
• Choudhury, A., Das, N. C., Patra, R., & Mukherjee, S. (2021). In silico analyses on the comparative sensing of SARS-CoV-2 mRNA by the intracellular TLRs of humans. Journal of Medical Virology, 93(4), 2476–2486. https://doi.org/10.1002/jmv.26776
   PubMed Web of Science ®Google Scholar
• Colovos, C., & Yeates, T. O. (1993). Verification of protein structures: Patterns of nonbonded atomic interactions. Protein Science: A Publication of the Protein Society, 2(9), 1511–1519. https://doi.org/10.1002/pro.5560020916
   PubMed Web of Science ®Google Scholar
• Croft, S. L., & Olliaro, P. (2011). Leishmaniasis chemotherapy–challenges and opportunities. Clinical Microbiology and Infection: The Official Publication of the European Society of Clinical Microbiology and Infectious Diseases, 17(10), 1478–1483. https://doi.org/10.1111/j.1469-0691.2011.03630.x
   PubMed Web of Science ®Google Scholar
• Das, N. C., Chakraborty, P., Bayry, J., & Mukherjee, S. (2021). In silico analyses on the comparative potential of therapeutic human monoclonal antibodies against newly emerged SARS-CoV-2 variants bearing mutant spike protein. Frontiers in Immunology, 12, 782506. https://doi.org/10.3389/fimmu.2021.782506
   PubMed Web of Science ®Google Scholar
• Das, N. C., Chakraborty, P., Bayry, J., & Mukherjee, S. (2023). Comparative binding ability of human monoclonal antibodies against omicron variants of SARS-CoV-2: An in silico investigation. Antibodies, 12(1), 17. https://doi.org/10.3390/antib12010017l
   Web of Science ®Google Scholar
• Das, N. C., Gupta, P. S. S., Panda, S. K., Rana, M. K., & Mukherjee, S. (2023). Reverse vaccinology assisted design of a novel multi-epitope vaccine to target Wuchereria bancrofti cystatin: An immunoinformatics approach. International Immunopharmacology, 115, 109639. https://doi.org/10.1016/j.intimp.2022.109639
   PubMed Web of Science ®Google Scholar
• Dawood, R. M., Moustafa, R. I., Abdelhafez, T. H., El-Shenawy, R., El-Abd, Y., Bader El Din, N. G., Dubuisson, J., & El Awady, M. K. (2019). A multiepitope peptide vaccine against HCV stimulates neutralizing humoral and persistent cellular responses in mice. BMC Infectious Diseases, 19(1), 932. https://doi.org/10.1186/s12879-019-4571-5
   PubMed Web of Science ®Google Scholar
• Deng, L., Thakur, A., Peng, J., Song, L., & Li, Z. (2023). Multi-omics analysis of DNA replication-associated primase polymerase (PRIMPOL) in pan-cancer: A potential target for prognosis and immune response. European Journal of Medical Research, 28(1), 207. https://doi.org/10.1186/s40001-023-01181-9
   PubMed Web of Science ®Google Scholar
• de Vries, S. J., van Dijk, M., & Bonvin, A. M. (2010). The HADDOCK web server for data-driven biomolecular docking. Nature Protocols, 5(5), 883–897. https://doi.org/10.1038/nprot.2010.32
   PubMed Web of Science ®Google Scholar
• Dimitrov, I., Bangov, I., Flower, D. R., & Doytchinova, I. (2014). AllerTOP v.2–A server for in silico prediction of allergens. Journal of Molecular Modeling, 20(6), 2278. https://doi.org/10.1007/s00894-014-2278-5
   PubMed Web of Science ®Google Scholar
• Dimitrov, I., Naneva, L., Doytchinova, I., & Bangov, I. (2014). AllergenFP: Allergenicity prediction by descriptor fingerprints. Bioinformatics, 30(6), 846–851. https://doi.org/10.1093/bioinformatics/btt619
   PubMed Web of Science ®Google Scholar
• Dong, R., Chu, Z., Yu, F., & Zha, Y. (2020). Contriving multi-epitope subunit of vaccine for COVID-19: Immunoinformatics approaches. Frontiers in Immunology, 11, 1784. https://doi.org/10.3389/fimmu.2020.01784
   PubMed Web of Science ®Google Scholar
• Doytchinova, I. A., & Flower, D. R. (2007). VaxiJen: A server for prediction of protective antigens, tumour antigens and subunit vaccines. BMC Bioinformatics, 8(1), 4. https://doi.org/10.1186/1471-2105-8-4
   PubMed Web of Science ®Google Scholar
• Duthie, M. S., Windish, H. P., Fox, C. B., & Reed, S. G. (2011). Use of defined TLR ligands as adjuvants within human vaccines. Immunological Reviews, 239(1), 178–196. https://doi.org/10.1111/j.1600-065X.2010.00978.x
   PubMed Web of Science ®Google Scholar
• El-Manzalawy, Y., Dobbs, D., & Honavar, V. (2008). Predicting linear B-cell epitopes using string kernels. Journal of Molecular Recognition: JMR, 21(4), 243–255. https://doi.org/10.1002/jmr.893
   PubMed Web of Science ®Google Scholar
• Enayatkhani, M., Hasaniazad, M., Faezi, S., Gouklani, H., Davoodian, P., Ahmadi, N., Einakian, M. A., Karmostaji, A., & Ahmadi, K. (2021). Reverse vaccinology approach to design a novel multiepitope vaccine candidate against COVID-19: An in silico study. Journal of Biomolecular Structure & Dynamics, 39(8), 2857–2872. https://doi.org/10.1080/07391102.2020.1756411
   PubMed Web of Science ®Google Scholar
• Engwerda, C. R., Murphy, M. L., Cotterell, S. E., Smelt, S. C., & Kaye, P. M. (1998). Neutralization of IL-12 demonstrates the existence of discrete organ-specific phases in the control of Leishmania donovani. European Journal of Immunology, 28(2), 669–680. https://doi.org/10.1002/(SICI)1521-4141(199802)28:02 ≤ 669::AID-IMMU669 ≥ 3.0.CO;2-N
   PubMed Web of Science ®Google Scholar
• Gaafar, B., Ali, S. A., Abd-Elrahman, K. A., & Almofti, Y. A. (2019). Immunoinformatics approach for multiepitope vaccine prediction from H, M, F, and N proteins of peste des petits ruminants virus. Journal of Immunology Research, 2019, 6124030–6124018. https://doi.org/10.1155/2019/6124030
   PubMed Web of Science ®Google Scholar
• García-Gómez, S., Reyes, A., Martínez-Jiménez, M. I., Chocrón, E. S., Mourón, S., Terrados, G., Powell, C., Salido, E., Méndez, J., Holt, I. J., & Blanco, L. (2013). PrimPol, an archaic primase/polymerase operating in human cells. Molecular Cell, 52(4), 541–553. https://doi.org/10.1016/j.molcel.2013.09.025
   PubMed Web of Science ®Google Scholar
• Ghorbani, M., & Farhoudi, R. (2018). Leishmaniasis in humans: Drug or vaccine therapy? Drug Design, Development and Therapy, 12, 25–40. volume https://doi.org/10.2147/dddt.s146521
   PubMed Web of Science ®Google Scholar
• Gillespie, P. M., Beaumier, C. M., Strych, U., Hayward, T., Hotez, P. J., & Bottazzi, M. E. (2016). Status of vaccine research and development of vaccines for leishmaniasis. Vaccine, 34(26), 2992–2995. https://doi.org/10.1016/j.vaccine.2015.12.071
   PubMed Web of Science ®Google Scholar
• Gorai, S., Das, N. C., Gupta, P. S. S., Panda, S. K., Rana, M. K., & Mukherjee, S. (2022). Designing efficient multi-epitope peptide-based vaccine by targeting the antioxidant thioredoxin of bancroftian filarial parasite. Infection, Genetics and Evolution: Journal of Molecular Epidemiology and Evolutionary Genetics in Infectious Diseases, 98, 105237. https://doi.org/10.1016/j.meegid.2022.105237
   PubMed Web of Science ®Google Scholar
• Gray, J. J., Moughon, S., Wang, C., Schueler-Furman, O., Kuhlman, B., Rohl, C. A., & Baker, D. (2003). Protein-protein docking with simultaneous optimization of rigid-body displacement and side-chain conformations. Journal of Molecular Biology, 331(1), 281–299. https://doi.org/10.1016/s0022-2836(03)00670-3
   PubMed Web of Science ®Google Scholar
• Grote, A., Hiller, K., Scheer, M., Münch, R., Nörtemann, B., Hempel, D. C., & Jahn, D. (2005). JCat: A novel tool to adapt codon usage of a target gene to its potential expression host. Nucleic Acids Research, 33(Web Server issue), W526–W531. https://doi.org/10.1093/nar/gki376
   PubMed Web of Science ®Google Scholar
• Gulsevin, A., & Meiler, J. (2020). An Investigation of three-finger toxin-nAChR interactions through Rosetta protein docking. Toxins, 12(9), 598. https://doi.org/10.3390/toxins12090598
   PubMed Web of Science ®Google Scholar
• Gupta, S., Kapoor, P., Chaudhary, K., Gautam, A., Kumar, R., & Raghava, G. P. (2013). In silico approach for predicting toxicity of peptides and proteins. PLoS One, 8(9), e73957. https://doi.org/10.1371/journal.pone.0073957
   PubMed Web of Science ®Google Scholar
• Gupta, S. K., Sisodia, B. S., Sinha, S., Hajela, K., Naik, S., Shasany, A. K., & Dube, A. (2007). Proteomic approach for identification and characterization of novel immunostimulatory proteins from soluble antigens of Leishmania donovani promastigotes. Proteomics, 7(5), 816–823. https://doi.org/10.1002/pmic.200600725
   PubMed Web of Science ®Google Scholar
• Hollup, S. M., Salensminde, G., & Reuter, N. (2005). WEBnm@: A web application for normal mode analyses of proteins. BMC Bioinformatics, 6(1), 52. https://doi.org/10.1186/1471-2105-6-52
   PubMedGoogle Scholar
• Humphrey, W., Dalke, A., & Schulten, K. (1996). VMD: Visual molecular dynamics. Journal of Molecular Graphics, 14(1), 33–38. https://doi.org/10.1016/0263-7855(96)00018-5
   PubMedGoogle Scholar
• Jain, K., & Jain, N. K. (2015). Vaccines for visceral leishmaniasis: A review. Journal of Immunological Methods, 422, 1–12. https://doi.org/10.1016/j.jim.2015.03.017
   PubMed Web of Science ®Google Scholar
• Joshi, T., Joshi, T., Sharma, P., Chandra, S., & Pande, V. (2021). Molecular docking and molecular dynamics simulation approach to screen natural compounds for inhibition of Xanthomonas oryzae pv. Oryzae by targeting peptide deformylase. Journal of Biomolecular Structure & Dynamics, 39(3), 823–840. https://doi.org/10.1080/07391102.2020.1719200
   PubMed Web of Science ®Google Scholar
• Kedzierska, K., & Koutsakos, M. (2020). The ABC of major histocompatibility complexes and T cell receptors in health and disease. Viral Immunology, 33(3), 160–178. https://doi.org/10.1089/vim.2019.0184
   PubMed Web of Science ®Google Scholar
• Khadem, F., & Uzonna, J. E. (2014). Immunity to visceral leishmaniasis: Implications for immunotherapy. Future Microbiology, 9(7), 901–915. https://doi.org/10.2217/fmb.14.43
   PubMed Web of Science ®Google Scholar
• Khan, M., Ami, J. Q., Faisal, K., Chowdhury, R., Ghosh, P., Hossain, F., Abd El Wahed, A., & Mondal, D. (2020). An immunoinformatic approach driven by experimental proteomics: In silico design of a subunit candidate vaccine targeting secretory proteins of Leishmania donovani amastigotes. Parasites & Vectors, 13(1), 196. https://doi.org/10.1186/s13071-020-04064-8
   PubMed Web of Science ®Google Scholar
• Khan, M., Khan, S., Ali, A., Akbar, H., Sayaf, A. M., Khan, A., & Wei, D. Q. (2019). Immunoinformatics approaches to explore Helicobacter pylori proteome (virulence factors) to design B and T cell multiepitope subunit vaccine. Scientific Reports, 9(1), 13321. https://doi.org/10.1038/s41598-019-49354-z
   PubMedGoogle Scholar
• Khatoon, N., Ojha, R., Mishra, A., & Prajapati, V. K. (2018). Examination of antigenic proteins of Trypanosoma cruzi to fabricate an epitope-based subunit vaccine by exploiting epitope mapping mechanism. Vaccine, 36(42), 6290–6300. https://doi.org/10.1016/j.vaccine.2018.09.004
   PubMed Web of Science ®Google Scholar
• Khatoon, N., Pandey, R. K., & Prajapati, V. K. (2017). Exploring Leishmania secretory proteins to design B and T cell multiepitope subunit vaccine using immunoinformatics approach. Scientific Reports, 7(1), 8285. https://doi.org/10.1038/s41598-017-08842-w
   PubMed Web of Science ®Google Scholar
• Krieger, E., Joo, K., Lee, J., Lee, J., Raman, S., Thompson, J., Tyka, M., Baker, D., & Karplus, K. (2009). Improving physical realism, stereochemistry, and side-chain accuracy in homology modeling: Four approaches that performed well in CASP8. Proteins, 77(Suppl 9), 114–122. https://doi.org/10.1002/prot.22570
   PubMed Web of Science ®Google Scholar
• Kroger, A. T. (2013). General recommendations on immunization. US Department of Health and Human Services, Public Health Service, Centers for Disease Control.
   Google Scholar
• Kumar, R., & Engwerda, C. (2014). Vaccines to prevent leishmaniasis. Clinical & Translational Immunology, 3(3), e13. https://doi.org/10.1038/cti.2014.4
   PubMedGoogle Scholar
• Kumari, R., Kumar, R., & Lynn, A. (2014). G-mmpbsa -A GROMACS tool for high-throughput MM-PBSA calculations. Journal of Chemical Information and Modeling, 54(7), 1951–1962. https://doi.org/10.1021/CI500020M
   PubMed Web of Science ®Google Scholar
• Kumbhar, B. V., & Bhandare, V. V. (2021). Exploring the interaction of Peloruside-A with drug resistant αβII and αβIII tubulin isotypes in human ovarian carcinoma using a molecular modeling approach. Journal of Biomolecular Structure & Dynamics, 39(6), 1990–2002. https://doi.org/10.1080/07391102.2020.1745689
   PubMed Web of Science ®Google Scholar
• Kuriata, A., Gierut, A. M., Oleniecki, T., Ciemny, M. P., Kolinski, A., Kurcinski, M., & Kmiecik, S. (2018). CABS-flex 2.0: A web server for fast simulations of flexibility of protein structures. Nucleic Acids Research, 46(W1), W338–W343. https://doi.org/10.1093/nar/gky356
   PubMed Web of Science ®Google Scholar
• Kushawaha, P. K., Gupta, R., Sundar, S., Sahasrabuddhe, A. A., & Dube, A. (2011). Elongation factor-2, a Th1 stimulatory protein of Leishmania donovani, generates strong IFN-γ and IL-12 response in cured Leishmania-infected patients/hamsters and protects hamsters against Leishmania challenge. Journal of Immunology, 187(12), 6417–6427. https://doi.org/10.4049/jimmunol.1102081
   PubMed Web of Science ®Google Scholar
• Lee, H., Heo, L., Lee, M. S., & Seok, C. (2015). GalaxyPepDock: A protein-peptide docking tool based on interaction similarity and energy optimization. Nucleic Acids Research, 43(W1), W431–W435. https://doi.org/10.1093/nar/gkv495
   PubMed Web of Science ®Google Scholar
• Lee, S., & Nguyen, M. T. (2015). Recent advances of vaccine adjuvants for infectious diseases. Immune Network, 15(2), 51–57. https://doi.org/10.4110/in.2015.15.2.51
   PubMed Web of Science ®Google Scholar
• Lengauer, T., & Rarey, M. (1996). Computational methods for biomolecular docking. Current Opinion in Structural Biology, 6(3), 402–406. https://doi.org/10.1016/s0959-440x(96)80061-3
   PubMed Web of Science ®Google Scholar
• Li, W., Joshi, M. D., Singhania, S., Ramsey, K. H., & Murthy, A. K. (2014). Peptide vaccine: Progress and challenges. Vaccines, 2(3), 515–536. https://doi.org/10.3390/vaccines2030515
   PubMedGoogle Scholar
• Liao, K. H., Chen, K.-B., Lee, W.-Y., Sun, M.-F., Lee, C.-C., & Chen, C. Y.-C. (2014). Ligand-based and structure-based investigation for Alzheimer’s disease from traditional Chinese medicine. Evidence-Based Complementary and Alternative Medicine: eCAM, 2014, 364819. https://doi.org/10.1155/2014/364819
   PubMed Web of Science ®Google Scholar
• Lill, M. A., & Danielson, M. L. (2011). Computer-aided drug design platform using PyMOL. Journal of Computer-Aided Molecular Design, 25(1), 13–19. https://doi.org/10.1007/s10822-010-9395-8
   PubMed Web of Science ®Google Scholar
• López-Blanco, J. R., Aliaga, J. I., Quintana-Ortí, E. S., & Chacón, P. (2014). iMODS: Internal coordinates normal mode analysis server. Nucleic Acids Research, 42(Web Server issue), W271–W276. https://doi.org/10.1093/nar/gku339
   PubMed Web of Science ®Google Scholar
• Lyskov, S., Chou, F. C., Conchúir, S. Ó., Der, B. S., Drew, K., Kuroda, D., Xu, J., Weitzner, B. D., Renfrew, P. D., Sripakdeevong, P., Borgo, B., Havranek, J. J., Kuhlman, B., Kortemme, T., Bonneau, R., Gray, J. J., & Das, R. (2013). Serverification of molecular modeling applications: The Rosetta Online Server that Includes Everyone (ROSIE). PLoS One, 8(5), e63906. https://doi.org/10.1371/journal.pone.0063906
   PubMed Web of Science ®Google Scholar
• Magnan, C. N., Randall, A., & Baldi, P. (2009). SOLpro: Accurate sequence-based prediction of protein solubility. Bioinformatics, 25(17), 2200–2207. https://doi.org/10.1093/bioinformatics/btp386
   PubMed Web of Science ®Google Scholar
• Maleki, A., Russo, G., Parasiliti Palumbo, G. A., & Pappalardo, F. (2022). In silico design of recombinant multiepitope vaccine against influenza A virus. BMC Bioinformatics, 22(S14), 617. https://doi.org/10.1186/s12859-022-04581-6
   PubMedGoogle Scholar
• Mann, S., Frasca, K., Scherrer, S., Henao-Martínez, A. F., Newman, S., Ramanan, P., & Suarez, J. A. (2021). A review of leishmaniasis: Current knowledge and future directions. Current Tropical Medicine Reports, 8(2), 121–132. https://doi.org/10.1007/s40475-021-00232-7
   PubMedGoogle Scholar
• Martinelli, D. D. (2022). In silico vaccine design: A tutorial in immunoinformatics. Health Care Analysis, 2, 100044. https://doi.org/10.1016/j.health.2022.100044
   Google Scholar
• Martins, V. T., Lage, D. P., Duarte, M. C., Costa, L. E., Garde, E., Rodrigues, M. R., Chávez-Fumagalli, M. A., Menezes-Souza, D., Roatt, B. M., Tavares, C. A., Soto, M., & Coelho, E. A. (2016). A new Leishmania-specific hypothetical protein, LiHyT, used as a vaccine antigen against visceral leishmaniasis. Acta Tropica, 154, 73–81. https://doi.org/10.1016/j.actatropica.2015.11.006
   PubMed Web of Science ®Google Scholar
• McGuffin, L. J., Bryson, K., & Jones, D. T. (2000). The PSIPRED protein structure prediction server. Bioinformatics, 16(4), 404–405. https://doi.org/10.1093/bioinformatics/16.4.404
   PubMed Web of Science ®Google Scholar
• Mehla, K., & Ramana, J. (2016). Identification of epitope-based peptide vaccine candidates against enterotoxigenic Escherichia coli: A comparative genomics and immunoinformatics approach. Molecular BioSystems, 12(3), 890–901. https://doi.org/10.1039/c5mb00745c
   PubMedGoogle Scholar
• Moafi, M., Rezvan, H., Sherkat, R., & Taleban, R. (2019). Leishmania vaccines entered in clinical trials: A review of literature. International Journal of Preventive Medicine, 10, 95. https://doi.org/10.4103/ijpvm.IJPVM_116_18
   PubMed Web of Science ®Google Scholar
• Mogensen, T. H. (2009). Pathogen recognition and inflammatory signaling in innate immune defenses. Clinical Microbiology Reviews, 22(2), 240–273, Table of Contents. https://doi.org/10.1128/CMR.00046-08
   PubMed Web of Science ®Google Scholar
• Murray, H. W. (1997). Endogenous interleukin-12 regulates acquired resistance in experimental visceral leishmaniasis. The Journal of Infectious Diseases, 175(6), 1477–1479. https://doi.org/10.1086/516482
   PubMed Web of Science ®Google Scholar
• Nain, Z., Abdulla, F., Rahman, M. M., Karim, M. M., Khan, M., Sayed, S. B., Mahmud, S., Rahman, S., Sheam, M. M., Haque, Z., & Adhikari, U. K. (2020). Proteome-wide screening for designing a multiepitope vaccine against emerging pathogen Elizabethkingia anophelis using immunoinformatic approaches. Journal of Biomolecular Structure & Dynamics, 38(16), 4850–4867. https://doi.org/10.1080/07391102.2019.1692072
   PubMed Web of Science ®Google Scholar
• Nivón, L. G., Moretti, R., & Baker, D. (2013). A pareto-optimal refinement method for protein design scaffolds. PLoS One, 8(4), e59004. https://doi.org/10.1371/journal.pone.0059004
   PubMed Web of Science ®Google Scholar
• Padma, S., Patra, R., Sen Gupta, P. S., Panda, S. K., Rana, M. K., & Mukherjee, S. (2023). Cell surface fibroblast activation protein-2 (Fap2) of Fusobacterium nucleatum as a vaccine candidate for therapeutic intervention of human colorectal cancer: An immunoinformatics approach. Vaccines, 11(3), 525. https://doi.org/10.3390/vaccines11030525
   Web of Science ®Google Scholar
• Pandey, R. K., Ojha, R., Aathmanathan, V. S., Krishnan, M., & Prajapati, V. K. (2018). Immunoinformatics approaches to design a novel multiepitope subunit vaccine against HIV infection. Vaccine, 36(17), 2262–2272. https://doi.org/10.1016/j.vaccine.2018.03.042
   PubMed Web of Science ®Google Scholar
• Patra, R., Das, N. C., & Mukherjee, S. (2021). Toll-like receptors (TLRs) as therapeutic targets for treating SARS-CoV-2: An immunobiological perspective. Advances in Experimental Medicine and Biology, 1352, 87–109. https://doi.org/10.1007/978-3-030-85109-5_6
   PubMedGoogle Scholar
• Peine, K. J., Gupta, G., Brackman, D. J., Papenfuss, T. L., Ainslie, K. M., Satoskar, A. R., & Bachelder, E. M. (2014). Liposomal resiquimod for the treatment of Leishmania donovani infection. The Journal of Antimicrobial Chemotherapy, 69(1), 168–175. https://doi.org/10.1093/jac/dkt320
   PubMed Web of Science ®Google Scholar
• Pinto-Martinez, A. K., Rodriguez-Durán, J., Serrano-Martin, X., Hernandez-Rodriguez, V., & Benaim, G. (2018). Mechanism of action of miltefosine on Leishmania donovani involves the impairment of acidocalcisome function and the activation of the sphingosine-dependent plasma membrane Ca 2+ channel. Antimicrobial Agents and Chemotherapy, 62(1). https://doi.org/10.1128/AAC.01614-17
   Google Scholar
• Pommier, Y. (2009). DNA topoisomerase I inhibitors: Chemistry, biology, and interfacial inhibition. Chemical Reviews, 109(7), 2894–2902. https://doi.org/10.1021/cr900097c
   PubMed Web of Science ®Google Scholar
• Pommier, Y., & Robert, D. (2001). Pharmacological agents that target DNA replication. In: M. L. DePamphilis (Ed.), DNA replication in eukaryotic cells (2nd ed. Chap. 26, pp. 1–28). Cold Spring Harbor Press.
   Google Scholar
• Ponomarenko, J., Bui, H. H., Li, W., Fusseder, N., Bourne, P. E., Sette, A., & Peters, B. (2008). ElliPro: A new structure-based tool for the prediction of antibody epitopes. BMC Bioinformatics, 9(1), 514. https://doi.org/10.1186/1471-2105-9-514
   PubMed Web of Science ®Google Scholar
• Ponte-Sucre, A., Gamarro, F., Dujardin, J. C., Barrett, M. P., López-Vélez, R., García-Hernández, R., Pountain, A. W., Mwenechanya, R., & Papadopoulou, B. (2017). Drug resistance and treatment failure in leishmaniasis: A 21st century challenge. PLoS Neglected Tropical Diseases, 11(12), e0006052. https://doi.org/10.1371/journal.pntd.0006052
   PubMed Web of Science ®Google Scholar
• Porollo, A., & Meller, J. (2007). Prediction-based fingerprints of protein-protein interactions. Proteins, 66(3), 630–645. https://doi.org/10.1002/prot.21248
   PubMed Web of Science ®Google Scholar
• Rahman, M. S., Hoque, M. N., Islam, M. R., Akter, S., Rubayet Ul Alam, A., Siddique, M. A., Saha, O., Rahaman, M. M., Sultana, M., Crandall, K. A., & Hossain, M. A. (2020). Epitope-based chimeric peptide vaccine design against S, M and E proteins of SARS-CoV-2, the etiologic agent of COVID-19 pandemic: An in silico approach. PeerJ. 8, e9572. https://doi.org/10.7717/peerj.9572
   PubMed Web of Science ®Google Scholar
• Rahman, N., Ali, F., Basharat, Z., Shehroz, M., Khan, M. K., Jeandet, P., Nepovimova, E., Kuca, K., & Khan, H. (2020). Vaccine design from the ensemble of surface glycoprotein epitopes of SARS-CoV-2: An immunoinformatics approach. Vaccines, 8(3), 423. https://doi.org/10.3390/vaccines8030423
   Web of Science ®Google Scholar
• Rashidi, S., Fernández-Rubio, C., Manzano-Román, R., Mansouri, R., Shafiei, R., Ali-Hassanzadeh, M., Barazesh, A., Karimazar, M., Hatam, G., & Nguewa, P. (2021). Potential therapeutic targets shared between leishmaniasis and cancer. Parasitology, 148(6), 655–671. https://doi.org/10.1017/S0031182021000160
   PubMed Web of Science ®Google Scholar
• Ribeiro, P., Dias, D. S., Lage, D. P., Costa, L. E., Martins, V. T., Tavares, G., Mendonça, D., Lima, M. P., Oliveira, J. S., Steiner, B. T., Machado-de-Ávila, R. A., Roatt, B. M., Chávez-Fumagalli, M. A., Menezes-Souza, D., Duarte, M. C., Teixeira, A. L., & Coelho, E. (2018). Evaluation of a Leishmania hypothetical protein administered as DNA vaccine or recombinant protein against Leishmania infantum infection and its immunogenicity in humans. Cellular Immunology, 331, 67–77. https://doi.org/10.1016/j.cellimm.2018.05.009
   PubMed Web of Science ®Google Scholar
• Rudd, S. G., Bianchi, J., & Doherty, A. J. (2014). PrimPol-A new polymerase on the block. Molecular & Cellular Oncology, 1(2), e960754. https://doi.org/10.4161/23723548.2014.960754
   PubMedGoogle Scholar
• Rudd, S. G., Glover, L., Jozwiakowski, S. K., Horn, D., & Doherty, A. J. (2013). PPL2 translesion polymerase is essential for the completion of chromosomal DNA replication in the African trypanosome. Molecular Cell, 52(4), 554–565. https://doi.org/10.1016/j.molcel.2013.10.034
   PubMed Web of Science ®Google Scholar
• Saha, S., & Raghava, G. P. (2006). Prediction of continuous B-cell epitopes in an antigen using recurrent neural network. Proteins, 65(1), 40–48. https://doi.org/10.1002/prot.21078
   PubMed Web of Science ®Google Scholar
• Sanchez-Trincado, J. L., Gomez-Perosanz, M., & Reche, P. A. (2017). Fundamentals and methods for T- and B-cell epitope prediction. Journal of Immunology Research, 2017, 2680160–2680114. https://doi.org/10.1155/2017/2680160
   PubMed Web of Science ®Google Scholar
• Sayed, S. B., Nain, Z., Khan, M., Abdulla, F., Tasmin, R., & Adhikari, U. K. (2020). Exploring lassa virus proteome to design a multi-epitope vaccine through immunoinformatics and immune simulation analyses. International Journal of Peptide Research and Therapeutics, 26(4), 2089–2107. https://doi.org/10.1007/s10989-019-10003-8
   PubMed Web of Science ®Google Scholar
• Sen, A., Sur, S., Tisa, L. S., Bothra, A. K., Thakur, S., & Mondal, U. K. (2010). Homology modelling of the Frankia nitrogenase iron protein. Symbiosis, 50(1-2), 37–44. https://doi.org/10.1007/s13199-009-0035-9
   Web of Science ®Google Scholar
• Sharma, S., Kumari, V., Kumbhar, B. V., Mukherjee, A., Pandey, R., & Kondabagil, K. (2021). Immunoinformatics approach for a novel multi-epitope subunit vaccine design against various subtypes of influenza A virus. Immunobiology, 226(2), 152053. https://doi.org/10.1016/j.imbio.2021.152053
   PubMed Web of Science ®Google Scholar
• Shey, R. A., Ghogomu, S. M., Esoh, K. K., Nebangwa, N. D., Shintouo, C. M., Nongley, N. F., Asa, B. F., Ngale, F. N., Vanhamme, L., & Souopgui, J. (2019). In-silico design of a multiepitope vaccine candidate against onchocerciasis and related filarial diseases. Scientific Reports, 9(1), 4409. https://doi.org/10.1038/s41598-019-40833-x
   PubMed Web of Science ®Google Scholar
• Shi, J., Zhang, J., Li, S., Sun, J., Teng, Y., Wu, M., Li, J., Li, Y., Hu, N., Wang, H., & Hu, Y. (2015). Epitope-based vaccine target screening against highly pathogenic MERS-CoV: An in silico approach applied to emerging infectious diseases. PLoS One, 10(12), e0144475. https://doi.org/10.1371/journal.pone.0144475
   PubMed Web of Science ®Google Scholar
• Singh, G., Pritam, M., Banerjee, M., Singh, A. K., & Singh, S. P. (2019). Genome based screening of epitope ensemble vaccine candidates against dreadful visceral leishmaniasis using immunoinformatics approach. Microbial Pathogenesis, 136, 103704. https://doi.org/10.1016/j.micpath.2019.103704
   PubMed Web of Science ®Google Scholar
• Singh, O. P., Singh, B., Chakravarty, J., & Sundar, S. (2016). Current challenges in treatment options for visceral leishmaniasis in India: A public health perspective. Infectious Diseases of Poverty, 5(1), 19. https://doi.org/10.1186/s40249-016-0112-2
   PubMed Web of Science ®Google Scholar
• Sinha, A. K., Singh, P., Prakash, A., Pal, D., Dube, A., & Kumar, A. (2017). Putative drug and vaccine target identification in Leishmania donovani membrane proteins using naïve bayes probabilistic classifier. IEEE/ACM Transactions on Computational Biology and Bioinformatics, 14(1), 204–211. https://doi.org/10.1109/TCBB.2016.2570217
   PubMed Web of Science ®Google Scholar
• Soltan, M. A., Elbassiouny, N., Gamal, H., Elkaeed, E. B., Eid, R. A., Eldeen, M. A., & Al-Karmalawy, A. A. (2021). In silico prediction of a multitope vaccine against Moraxella catarrhalis: Reverse vaccinology and immunoinformatics. Vaccines, 9(6), 669. https://doi.org/10.3390/vaccines9060669
   Web of Science ®Google Scholar
• Spriestersbach, A., Kubicek, J., Schäfer, F., Block, H., & Maertens, B. (2015). Purification of His-tagged proteins. Methods in Enzymology, 559, 1–15. https://doi.org/10.1016/bs.mie.2014.11.003
   Google Scholar
• Stäger, S., & Rafati, S. (2012). CD8(+) T cells in leishmania infections: Friends or foes? Frontiers in Immunology, 3, 5. https://doi.org/10.3389/fimmu.2012.00005
   PubMed Web of Science ®Google Scholar
• Stauch, A., Duerr, H. P., Dujardin, J. C., Vanaerschot, M., Sundar, S., & Eichner, M. (2012). Treatment of visceral leishmaniasis: Model-based analyses on the spread of antimony-resistant L. donovani in Bihar, India. PLoS Neglected Tropical Diseases, 6(12), e1973. https://doi.org/10.1371/journal.pntd.0001973
   PubMed Web of Science ®Google Scholar
• Stockdale, L., & Newton, R. (2013). A review of preventative methods against human leishmaniasis infection. PLoS Neglected Tropical Diseases, 7(6), e2278. https://doi.org/10.1371/journal.pntd.0002278
   PubMed Web of Science ®Google Scholar
• Sundar, S., & Chakravarty, J. (2010). Liposomal amphotericin B and leishmaniasis: Dose and response. Journal of Global Infectious Diseases, 2(2), 159–166. https://doi.org/10.4103/0974-777X.62886
   PubMedGoogle Scholar
• Tirosh, I., Barkai, N., & Verstrepen, K. J. (2009). Promoter architecture and the evolvability of gene expression. Journal of Biology, 8(11), 95. https://doi.org/10.1186/jbiol204
   PubMedGoogle Scholar
• Van Der Spoel, D., Lindahl, E., Hess, B., Groenhof, G., Mark, A. E., & Berendsen, H. J. (2005). GROMACS: Fast, flexible, and free. Journal of Computational Chemistry, 26(16), 1701–1718. https://doi.org/10.1002/jcc.20291
   PubMed Web of Science ®Google Scholar
• Vannier-Santos, M. A., Martiny, A., & de Souza, W. (2002). Cell biology of Leishmania spp.: invading and evading. Current Pharmaceutical Design, 8(4), 297–318. https://doi.org/10.2174/1381612023396230
   PubMed Web of Science ®Google Scholar
• van Zundert, G. C. P., Rodrigues, J. P. G. L. M., Trellet, M., Schmitz, C., Kastritis, P. L., Karaca, E., Melquiond, A. S. J., van Dijk, M., de Vries, S. J., & Bonvin, A. M. J. J. (2016). The HADDOCK2.2 web server: User-friendly integrative modeling of biomolecular complexes. Journal of Molecular Biology, 428(4), 720–725. https://doi.org/10.1016/j.jmb.2015.09.014
   PubMed Web of Science ®Google Scholar
• Velez, R., & Gállego, M. (2020). Commercially approved vaccines for canine leishmaniosis: A review of available data on their safety and efficacy. Tropical Medicine & International Health: TM & IH, 25(5), 540–557. https://doi.org/10.1111/tmi.13382
   PubMed Web of Science ®Google Scholar
• Wang, C., Schueler-Furman, O., & Baker, D. (2005). Improved side-chain modeling for protein-protein docking. Protein Science: A Publication of the Protein Society, 14(5), 1328–1339. https://doi.org/10.1110/ps.041222905
   PubMed Web of Science ®Google Scholar
• Wilkins, M. R., Gasteiger, E., Bairoch, A., Sanchez, J. C., Williams, K. L., Appel, R. D., & Hochstrasser, D. F. (1999). Protein identification and analysis tools in the ExPASy server. Methods in Molecular Biology, 112, 531–552. https://doi.org/10.1385/1-59259-584-7:531
   PubMedGoogle Scholar
• Williams, C. J., Headd, J. J., Moriarty, N. W., Prisant, M. G., Videau, L. L., Deis, L. N., Verma, V., Keedy, D. A., Hintze, B. J., Chen, V. B., Jain, S., Lewis, S. M., Arendall, W. B., Snoeyink, J., Adams, P. D., Lovell, S. C., Richardson, J. S., & Richardson, D. C. (2018). MolProbity: More and better reference data for improved all-atom structure validation. Protein Science: A Publication of the Protein Society, 27(1), 293–315. https://doi.org/10.1002/pro.3330
   PubMed Web of Science ®Google Scholar
• Xue, L. C., Rodrigues, J. P., Kastritis, P. L., Bonvin, A. M., & Vangone, A. (2016). PRODIGY: A web server for predicting the binding affinity of protein-protein complexes. Bioinformatics, 32(23), 3676–3678. https://doi.org/10.1093/bioinformatics/btw514
   PubMed Web of Science ®Google Scholar
• Yadagiri, G., Singh, A., Arora, K., & Mudavath, S. L. (2023). Immunotherapy and immunochemotherapy in combating visceral leishmaniasis. Frontiers in Medicine, 10, 1096458. https://doi.org/10.3389/fmed.2023.1096458
   Web of Science ®Google Scholar
• Yadav, S., Prakash, J., Shukla, H., Das, K. C., Tripathi, T., & Dubey, V. K. (2020). Design of a multiepitope subunit vaccine for immune-protection against Leishmania parasite. Pathogens and Global Health, 114(8), 471–481. https://doi.org/10.1080/20477724.2020.1842976
   PubMed Web of Science ®Google Scholar
• Yang, J., Zhang, Z., Yang, F., Zhang, H., Wu, H., Zhu, F., & Xue, W. (2021). Computational design and modeling of nanobodies toward SARS-CoV-2 receptor binding domain. Chemical Biology & Drug Design, 98(1), 1–18. https://doi.org/10.1111/cbdd.13847
   PubMed Web of Science ®Google Scholar
• Yang, J. X., Tseng, J. C., Yu, G. Y., Luo, Y., Huang, C. F., Hong, Y. R., & Chuang, T. H. (2022). Recent advances in the development of Toll-like receptor agonist-based vaccine adjuvants for infectious diseases. Pharmaceutics, 14(2), 423. https://doi.org/10.3390/pharmaceutics14020423
   PubMed Web of Science ®Google Scholar
• Yong, S., Anderson, D. E., Wei, W. E., Pang, J., Chia, W. N., Tan, C. W., Teoh, Y. L., Rajendram, P., Toh, M., Poh, C., Koh, V., Lum, J., Suhaimi, N. M., Chia, P. Y., Chen, M. I., Vasoo, S., Ong, B., Leo, Y. S., Wang, L., & Lee, V. (2020). Connecting clusters of COVID-19: An epidemiological and serological investigation. The Lancet. Infectious Diseases, 20(7), 809–815. https://doi.org/10.1016/S1473-3099(20)30273-5
   PubMed Web of Science ®Google Scholar
• Yu, C. S., Cheng, C. W., Su, W. C., Chang, K. C., Huang, S. W., Hwang, J. K., & Lu, C. H. (2014). CELLO2GO: A web server for protein subCELlular LOcalization prediction with functional gene ontology annotation. PLoS One, 9(6), e99368. https://doi.org/10.1371/journal.pone.0099368
   PubMed Web of Science ®Google Scholar