REFERENCES
  1. WHO/PAHO. Leishmaniases: Epidemiological Report of the Americas. Department of Neglected Infectious Diseases (2019) No 7. https://www.paho.org/en/topics/leishmaniasis. [Accessed September 30, 2022].
  2. SASIDHARAN, Santanu; SAUDAGAR, Prakash. Leishmaniasis: where are we and where are we heading?. Parasitology research, v. 120, p. 1541-1554, 2021.
  3. MOKNI, M. Cutaneous leishmaniasis. In: Annales de Dermatologie et de Venereologie. 2019. p. 232-246.
  4. HANDLER, Marc Z. et al. Cutaneous and mucocutaneous leishmaniasis: differential diagnosis, diagnosis, histopathology, and management. Journal of the American Academy of Dermatology, v. 73, n. 6, p. 911-926, 2015.
  5. Hurrell BP, Regli IB, Tacchini-Cottier F. Different Leishmania Species Drive Distinct Neutrophil Functions Trends Parasitol (2016) 32(5):392-401. doi: 10.1016/j.pt.2016.02.003
  6. SINGH S. New Developments in Diagnosis of Leishmaniasis. Indian Journal of Medical Research (2006) 123(3):311-30. PMID: 16778313
  7. Figueiredo MM, Dos Santos ARR, Godoi LC, de Castro NS, de Andrade BC, Sergio SAR, et al. Improved Performance of ELISA and Immunochromatographic Tests Using a New Chimeric A2-Based Protein for Human Visceral Leishmaniasis Diagnosis. J Immunol Res (2021) 28:5568077. doi: 10.1155/2021/5568077
  8. Zuben AP, Donalísio MR. Difficulties in Implementing the Guidelines of the Brazilian Visceral Leishmaniasis Control Program in large cities.Cad saude publica (2016) 20;32 (6):102-311. doi:10.1590/0102-311X00087415
  9. Aronso NE, Joya CA. Cutaneous leishmaniasis: Updates in diagnosis and management. Infectious Disease Clinics (2019) 33(1):101-117. doi.org/10.1016/j.idc.2018.10.004
  10. De Brito RCF, Aguiar-Soares RDO, Cardoso JMO, Coura-Vital W, Roatt BM, Reis AB. Recent advances and new strategies in Leishmaniasis diagnosis. Applied Microbiology and Biotechnology (2020) 104(19):8105-8116. doi: 10.1007/s00253-020-10846-y
  11. Pizza, M., Scarlato, V., Masignani, V., Giuliani, M. M., Arico, B., Comanducci, M., … & Rappuoli, R. (2000). Identification of vaccine candidates against serogroup B meningococcus by whole-genome sequencing. Science, 287(5459), 1816-1820.
  12. MENEZES-SOUZA, Daniel et al. Linear B-cell epitope mapping of MAPK3 and MAPK4 from Leishmania braziliensis: implications for the serodiagnosis of human and canine leishmaniasis. Applied microbiology and biotechnology, v. 99, p. 1323-1336, 2015.
  13. Souza AP, Soto M, Costa JML, Boaventura VS, de Oliveira CI, Cristal JR et al. Towards a More Precise Serological Diagnosis of Human Tegumentary Leishmaniasis Using Leishmania Recombinant Proteins.PLoS ONE (2013) 8(6): e66110. doi.org/10.1371/journal.pone.0066110
  14. Duarte MC, Pimenta DC, Menezes-Souza D, Magalhães RDM, Diniz JLCP, Costa LE, et al. Proteins Selected in Leishmania (Viannia) braziliensis by an Immunoproteomic Approach with Potential Serodiagnosis Applications for Tegumentary Leishmaniasis. Clin vaccine Immunol. (2015) 22(11):1187–1196 doi: 10.1128/CVI.00465-15
  15. Oualha R, Barhoumi M, Marzouki S, Harigua-Souiai E, Ben Ahmed , Guizani I. Infection of Human Neutrophils With Leishmania infantum or Leishmania major Strains Triggers Activation and Differential Cytokines Release. Front. Cell Infect. Microbiol(2019) 9:153. doi: 10.3389/fcimb.2019.00153
  16. Serrano-Coll H, Cardona-Castro N, Ramos AP, Llanos-Cuentas A. Innate immune response: ally or enemy in cutaneous leishmaniasis?Pathog Dis. (2021) 79(5):ftab028. doi: 10.1093/femspd/ftab028
  17. Abbas AK, Lichtman AH. Pillai S. Cellular and Molecular Immunology. 8th. Philadelphia: Elsevier Saunders (2015). 809-814.
  18. BACELLAR O, Lessa H, Schriefer A, Machado P, Jesus AR, Dutra WO, et al. Up-regulation of Th1-type responses in mucosal leishmaniasis patients. Infect Immun (2002) 70(12):6734-6740. doi: 10.1128/IAI.70.12.6734-6740.2002
  19. Toepp AJ, Petersen CA. The balancing act: Immunology of Leishmaniosis.Res. Vet. Sci (2020) 130:19-25. doi: 10.1016/j.rvsc.2020.02.004
  20. Novais FO, Carvalho LP, Graff JW, Beiting DP, Ruthel G, Roos DS, et al. Cytotoxic T cells mediate pathology and metastasis in cutaneous leishmaniasis. PLoS Pathog (2013) 9(7)):e1003504. doi: 10.1371/journal.ppat.1003504
  21. Rossi M, Fasel N. How to master the host immune system? Leishmania parasites have the solutions! Int Immunol (2018) 30(3):103-111. doi: 10.1093/intimm/dxx075.
  22. Miles SA, Conrado SM, Alves RG, Jeronimo SMB, Mosser DM. A role for IgG immune complexes during infection with the intracellular pathogen Leishmania. J. Exp. Med (2005) 201(5): 747-754. doi: 10.1084/jem.20041470
  23. Gonçalves R, Christensen SM, Mosser DM. Humoral immunity in leishmaniasis – Prevention or promotion of parasite growth?.Cytokine: X (2020) 2(4): 100046. doi: 10.1016/j.cytox.2020.100046
  24. Costa CH, Stewart JM, Gomes RB, Garcez LM, Ramos PK, Bozza M, et al. Asymptomatic human carriers of Leishmania chagasi. Am J Trop Med Hyg (2002) 66(4):334-7. doi: 10.4269/ajtmh.2002.66.334
  25. De Vries HJC, Schallig HD. Cutaneous Leishmaniasis: A 2022 Updated Narrative Review into Diagnosis and Management Developments.American Journal of Clinical Dermatology (2022) 23(6): 823-840. doi: 10.1007/s40257-022-00726-8
  26. KUMAR, Awanish; PANDEY, Satish Chandra; SAMANT, Mukesh. A spotlight on the diagnostic methods of a fatal disease Visceral Leishmaniasis.Parasite Immunol (2020) 42(10):e12727. doi: 10.1111/pim.12727
  27. Freire ML, De-Assis TM, Oliveira E, De Avelar DM, Siqueira IC, Barral A, et al Performance of serological tests available in Brazil for the diagnosis of human visceral leishmaniasis. PLoS Neglected Tropical Diseases (2019) 13(7):e0007484. doi.org/10.1371/journal.pntd.0007484
  28. Sato CM, Sanchez MCA, Celeste BJ, Duthie MS, Guderian J, Reed SG, et al. Use of Recombinant Antigens for Sensitive Serodiagnosis of American Tegumentary Leishmaniasis Caused by Different Leishmania Species. J Clin Microbiol (2017) 55(2): 495–503. doi: 10.1128/JCM.01904-16
  29. Souza AP, Soto M, Costa JML, Boaventura VS, de Oliveira CI, Cristal JR et al. Towards a More Precise Serological Diagnosis of Human Tegumentary Leishmaniasis Using Leishmania Recombinant Proteins.PLoS ONE (2013) 8(6): e66110. doi.org/10.1371/journal.pone.0066110
  30. Link JS, Alban SM, Soccol CR, Pereira GVM, Soccol VT. Synthetic peptides as potential antigens for cutaneous leishmaniosis diagnosis.Journal of immunology research (2017). doi: 10.1155/2017/5871043
  31. Yao B, Zhang L, Liang S, Zhang C. SVMTriP: A Method to Predict Antigenic Epitopes Using Support Vector Machine to Integrate Tri-Peptide Similarity and Propensity. PLoS One 2012; 7: e45152. doi:10.1371/journal.pone.0045152
  32. Hopp TP, Woods KR. Prediction of protein antigenic determinants from amino acid sequences. Proceedings of the National Academy of Sciences 1981; 78: 3824-3828. doi:10.1073/pnas.78.6.3824
  33. Hopp TP, Woods KR. A computer program for predicting protein antigenic determinants. Mol Immunol 1983; 20: 483-489. doi:10.1016/0161-5890(83)90029-9
  34. 34. El-Manzalawy Y, Honavar V. Recent advances in B-cell epitope prediction methods. Immunome Res. 2010; 6: 1-9. doi:10.1186/1745-7580-6-S2-S2
  35. Odorico M, Pellequer JL. BEPITOPE: Predicting the location of continuous epitopes and patterns in proteins. Journal of Molecular Recognition 2003; 16: 20-22. doi:10.1002/jmr.602
  36. Saha S, Raghava GPS. BcePred: Prediction of continuous B-cell epitopes in antigenic sequences using physico-chemical properties. Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). In Artificial Immune Systems: Third International Conference 2004; 3239: 197-204. doi:10.1007/978-3-540-30220-9_16
  37. Saha S, Raghava GPS. Prediction of continuous B-cell epitopes in an antigen using recurrent neural network. Proteins: Structure, Function and Genetics 2006; 65: 40-48. doi:10.1002/prot.21078
  38. Singh H, Ansari HR, Raghava GPS. Improved Method for Linear B-Cell Epitope Prediction Using Antigen’s Primary Sequence. PLoS One 2013; 8: e62216. doi:10.1371/journal.pone.0062216
  39. Jespersen MC, Peters B, Nielsen M, Marcatili P. BepiPred-2.0: Improving sequence-based B-cell epitope prediction using conformational epitopes. Nucleic Acids Res 2017; 45: W24-W29. doi:10.1093/nar/gkx346
  40. Sanchez-Trincado JL, Gomez-Perosanz M, Reche PA. Fundamentals and Methods for T- and B-Cell Epitope Prediction. J Immunol Res. 2017; 2017. doi:10.1155/2017/2680160
  41. Kulkarni-Kale U, Bhosle S, Kolaskar AS. CEP: A conformational epitope prediction server. Nucleic Acids Res 2005; 33 (suppl_2): W168-W171. doi:10.1093/nar/gki460
  42. Haste Andersen P, Nielsen M, Lund O. Prediction of residues in discontinuous B-cell epitopes using protein 3D structures. Protein Science 2006; 15: 2558-2567. doi:10.1110/ps.062405906
  43. Sun J, Wu D, Xu T, Wang X, Xu X, Tao L et al. SEPPA: A computational server for spatial epitope prediction of protein antigens. Nucleic Acids Res 2009; 37: W612-W616. doi:10.1093/nar/gkp417
  44. Rubinstein ND, Mayrose I, Martz E, Pupko T. Epitopia: A web-server for predicting B-cell epitopes. BMC Bioinformatics 2009; 10: 1-6. doi:10.1186/1471-2105-10-287
  45. Arab-Mazar Z, Mohebali M, Ranjbar MM, Tabaei SJS, Mamaghani AJ, Taghipour N. Design of a polytopic construct of LACK, TSA and GP63 proteins for the diagnosis of cutaneous leishmaniasis: An in silico strategy. J Asia Pac Entomol 2022; 25: 101982. doi:10.1016/j.aspen.2022.101982
  46. Assis LM, Sousa JR, Pinto NFS, Silva AA, Vaz AFM, Andrade PP et al. B-cell epitopes of antigenic proteins in Leishmania infantum: An in silico analysis. Parasite Immunol 2014; 36: 313-323. doi:10.1111/pim.12111
  47. Raybould MIJ, Marks C, Lewis AP, Shi J, Bujotzek A, Taddese B et al. Thera-SAbDab: The Therapeutic Structural Antibody Database. Nucleic Acids Res 2020; 48: D383-D388. doi:10.1093/nar/gkz827
  48. Poiron C, Wu Y, Ginestoux C, Ehrenmann F, Duroux P, Lefranc M-P. IMGT/mAb-DB: the IMGT® database for therapeutic monoclonal antibodies. Informatique et Mathématiques (JOBIM), Montpellier 2010; 11: 382
  49. Sela-Culang I, Benhnia MREI, Matho MH, Kaever T, Maybeno M, Schlossman A et al. Using a combined computational-experimental approach to predict antibody-specific B cell epitopes. Structure 2014; 22: 646-657. doi:10.1016/j.str.2014.02.003
  50. Kozakov D, Hall DR, Xia B, Porter KA, Padhorny D, Yueh C et al. The ClusPro web server for protein-protein docking. Nat Protoc 2017; 12: 255-278. doi:10.1038/nprot.2016.169
  51. Ramírez-Aportela E, López-Blanco JR, Chacón P. FRODOCK 2.0: Fast protein-protein docking server. Bioinformatics 2016; 32: 2386-2388. doi:10.1093/bioinformatics/btw141
  52. Schneidman-Duhovny D, Inbar Y, Nussinov R, Wolfson HJ. PatchDock and SymmDock: Servers for rigid and symmetric docking. Nucleic Acids Res 2005; 33: W363-W367. doi:10.1093/nar/gki481
  53. Chen R, Li L, Weng Z. ZDOCK: An initial-stage protein-docking algorithm. Proteins: Structure, Function and Genetics 2003; 52: 80-87. doi:10.1002/prot.10389
  54. Sircar A, Gray JJ. SnugDock: Paratope structural optimization during antibody-antigen docking compensates for errors in antibody homology models. PLoS Comput Biol 2010; 6: e1000644. doi:10.1371/journal.pcbi.1000644
  55. Van Zundert GCP, Rodrigues JPGLM, Trellet M, Schmitz C, Kastritis PL, Karaca E et al. The HADDOCK2.2 Web Server: User-Friendly Integrative Modeling of Biomolecular Complexes. J Mol Biol 2016; 428: 720–725. https://doi.org/10.1016/j.jmb.2015.09.014
  56. Jeliazkov JR, Frick R, Zhou J, Gray JJ. Robustification of rosetta antibody and rosetta snug dock. PLoS One 2021; 16: e0234282. doi:10.1371/journal.pone.0234282
  57. Méndez R, Leplae R, de Maria L, Wodak SJ. Assessment of blind predictions of protein-protein interactions: Current status of docking methods. Proteins: Structure, Function and Genetics 2003; 52: 51-67. doi:10.1002/prot.10393
  58. Guest JD, Vreven T, Zhou J, Moal I, Jeliazkov JR, Gray JJ et al. An expanded benchmark for antibody-antigen docking and affinity prediction reveals insights into antibody recognition determinants. Structure 2021; 29: 606-621. doi:10.1016/j.str.2021.01.005
  59. e Silva R de F, Ferreira LFGR, Hernandes MZ, de Brito MEF, de Oliveira BC, da Silva AA et al. Combination of in silico methods in the search for potential CD4+ and CD8+ T cell epitopes in the proteome of Leishmania braziliensis. Front Immunol 2016; 7: 327 doi:10.3389/fimmu.2016.00327
TABLE 1: List of proteins/peptides selected in silicoand used in the diagnosis of leishmaniasis