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Ortiz-Mahecha CA, Bohórquez HJ, Agudelo WA, Patarroyo MA, Patarroyo ME, Suárez CF. Assessing Peptide Binding to MHC II: An Accurate Semiempirical Quantum Mechanics Based Proposal. J Chem Inf Model 2019; 59:5148-5160. [DOI: 10.1021/acs.jcim.9b00672] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Affiliation(s)
| | - Hugo J. Bohórquez
- Fundación Instituto de Inmunología de Colombia (FIDIC), Bogotá D.C., Colombia
- Universidad de Ciencias Aplicadas y Ambientales (UDCA), Bogotá D.C., Colombia
| | - William A. Agudelo
- Fundación Instituto de Inmunología de Colombia (FIDIC), Bogotá D.C., Colombia
| | - Manuel A. Patarroyo
- Fundación Instituto de Inmunología de Colombia (FIDIC), Bogotá D.C., Colombia
- School of Medicine and Health Sciences, Universidad del Rosario, Bogotá D.C., Colombia
| | - Manuel E. Patarroyo
- Fundación Instituto de Inmunología de Colombia (FIDIC), Bogotá D.C., Colombia
- Universidad Nacional de Colombia, Bogotá D.C., Colombia
| | - Carlos F. Suárez
- Fundación Instituto de Inmunología de Colombia (FIDIC), Bogotá D.C., Colombia
- School of Medicine and Health Sciences, Universidad del Rosario, Bogotá D.C., Colombia
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Patarroyo ME, Bermúdez A, Alba MP, Vanegas M, Moreno-Vranich A, Poloche LA, Patarroyo MA. IMPIPS: the immune protection-inducing protein structure concept in the search for steric-electron and topochemical principles for complete fully-protective chemically synthesised vaccine development. PLoS One 2015; 10:e0123249. [PMID: 25879751 PMCID: PMC4400017 DOI: 10.1371/journal.pone.0123249] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2014] [Accepted: 02/28/2015] [Indexed: 01/14/2023] Open
Abstract
Determining immune protection-inducing protein structures (IMPIPS) involves defining the stereo-electron and topochemical characteristics which are essential in MHC-p-TCR complex formation. Modified high activity binding peptides (mHABP) were thus synthesised to produce a large panel of IMPIPS measuring 26.5 ±3.5Å between the farthest atoms fitting into Pockets 1 to 9 of HLA-DRβ1* structures. They displayed a polyproline II-like (PPIIL) structure with their backbone O and N atoms orientated to establish H-bonds with specific residues from HLA-DRβ1*-peptide binding regions (PBR). Residues having specific charge and gauche+ orientation regarding p3χ1, p5χ2, and p7χ1 angles determined appropriate rotamer orientation for perfectly fitting into the TCR to induce an appropriate immune response. Immunological assays in Aotus monkeys involving IMPIPS mixtures led to promising results; taken together with the aforementioned physicochemical principles, non-interfering, long-lasting, protection-inducing, multi-epitope, multistage, minimal subunit-based chemically-synthesised peptides can be designed against diseases scourging humankind.
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Affiliation(s)
- Manuel Elkin Patarroyo
- Fundación Instituto de Inmunología de Colombia (FIDIC), Bogotá, Colombia
- Universidad Nacional de Colombia, Bogotá, Colombia
- * E-mail:
| | - Adriana Bermúdez
- Fundación Instituto de Inmunología de Colombia (FIDIC), Bogotá, Colombia
- Universidad del Rosario, Bogotá, Colombia
| | - Martha Patricia Alba
- Fundación Instituto de Inmunología de Colombia (FIDIC), Bogotá, Colombia
- Universidad del Rosario, Bogotá, Colombia
| | - Magnolia Vanegas
- Fundación Instituto de Inmunología de Colombia (FIDIC), Bogotá, Colombia
- Universidad del Rosario, Bogotá, Colombia
| | | | | | - Manuel Alfonso Patarroyo
- Fundación Instituto de Inmunología de Colombia (FIDIC), Bogotá, Colombia
- Universidad del Rosario, Bogotá, Colombia
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Koutsogiannouli EA, Moutou KA, Stamatis C, Walter L, Mamuris Z. Genetic variation in the major histocompatibility complex of the European brown hare (Lepus europaeus) across distinct phylogeographic areas. Immunogenetics 2014; 66:379-92. [DOI: 10.1007/s00251-014-0772-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2014] [Accepted: 03/31/2014] [Indexed: 10/25/2022]
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Cárdenas C, Bidon-Chanal A, Conejeros P, Arenas G, Marshall S, Luque FJ. Molecular modeling of class I and II alleles of the major histocompatibility complex in Salmo salar. J Comput Aided Mol Des 2010; 24:1035-51. [DOI: 10.1007/s10822-010-9387-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2009] [Accepted: 09/22/2010] [Indexed: 10/19/2022]
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Patarroyo ME, Cifuentes G, Bermúdez A, Patarroyo MA. Strategies for developing multi-epitope, subunit-based, chemically synthesized anti-malarial vaccines. J Cell Mol Med 2009; 12:1915-35. [PMID: 19012725 PMCID: PMC4506160 DOI: 10.1111/j.1582-4934.2008.00174.x] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
An anti-malarial vaccine against the extremely lethal Plasmodium falciparum is desperately needed. Peptides from this parasite's proteins involved in invasion and having high red blood cell-binding ability were identified; these conserved peptides were not immun genic or protection-inducing when used for immunizing Aotus monkeys. Modifying some critical binding residues in these high-activi binding peptides' (HABPs') attachment to red blood cells (RBC) allowed them to induce immunogenicity and protection against expermental challenge and acquire the ability to bind to specific HLA-DRp1* alleles. These modified HABPs adopted certain characterist structural configurations as determined by circular dichroism (CD) and 1H nuclear magnetic resonance (NMR) associated with certain HLA-DRβ1* haplotype binding activities and characteristics, such as a 2-Å-distance difference between amino acids fitting into HLA-DRp1 Pockets 1 to 9, residues participating in binding to HLA-DR pockets and residues making contact with the TCR, suggesting haplotyp and allele-conscious TCR. This has been demonstrated in HLA-DR-like genotyped monkeys and provides the basis for designing high effective, subunit-based, multi-antigen, multi-stage, synthetic vaccines, for immediate human use, malaria being one of them.
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Affiliation(s)
- M E Patarroyo
- Fundación Instituto de Inmunólogia de Colombia (FIDIC), Bogotá, Colombia.
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Agudelo WA, Galindo JF, Ortiz M, Villaveces JL, Daza EE, Patarroyo ME. Variations in the electrostatic landscape of class II human leukocyte antigen molecule induced by modifications in the myelin basic protein peptide: a theoretical approach. PLoS One 2009; 4:e4164. [PMID: 19132105 PMCID: PMC2613560 DOI: 10.1371/journal.pone.0004164] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2008] [Accepted: 12/03/2008] [Indexed: 12/31/2022] Open
Abstract
The receptor-ligand interactions involved in the formation of the complex between Class II Major Histocompatibility Complex molecules and antigenic peptides, which are essential for establishing an adaptive immunological response, were analyzed in the Class II Human Leukocyte Antigen (HLA) - Myelin Basic Protein (MBP) peptide complex (HLA-DRβ1*1501-MBP) using a multipolar molecular electrostatic potential approach. The Human Leukocyte Antigen - peptide complex system was divided into four pockets together with their respective peptide fragment and the corresponding occupying amino acid was replaced by each of the remaining 19 amino acids. Partial atomic charges were calculated by a quantum chemistry approach at the Hatree Fock/3-21*G level, to study the behavior of monopole, dipole and quadrupole electrostatic multipolar moments. Two types of electrostatic behavior were distinguished in the pockets' amino acids: “anchoring” located in Pocket 1 and 4, and “recognition” located in Pocket 4 and 7. According to variations in the electrostatic landscape, pockets were ordered as: Pocket 1>Pocket 9≫Pocket 4≈Pocket 7 which is in agreement with the binding ability reported for Class II Major Histocompatibility Complex pockets. In the same way, amino acids occupying the polymorphic positions β13R, β26F, β28D, β9W, β74A, β47F and β57D were shown to be key for this Receptor-Ligand interaction. The results show that the multipolar molecular electrostatic potential approach is appropriate for characterizing receptor-ligand interactions in the MHC–antigenic peptide complex, which could have potential implications for synthetic vaccine design.
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Affiliation(s)
- William A. Agudelo
- Grupo de Biomatemáticas, Fundación Instituto de Inmunología de Colombia, Bogotá, Colombia
- Grupo de Química Teórica, Universidad Nacional de Colombia, Centro de Investigaciones en Sistemas complejos CEIBA, Bogotá, Colombia
| | - Johan F. Galindo
- Grupo de Biomatemáticas, Fundación Instituto de Inmunología de Colombia, Bogotá, Colombia
- Grupo de Química Teórica, Universidad Nacional de Colombia, Centro de Investigaciones en Sistemas complejos CEIBA, Bogotá, Colombia
| | - Marysol Ortiz
- Grupo de Biomatemáticas, Fundación Instituto de Inmunología de Colombia, Bogotá, Colombia
- Grupo de Química Teórica, Universidad Nacional de Colombia, Centro de Investigaciones en Sistemas complejos CEIBA, Bogotá, Colombia
| | - José L. Villaveces
- Grupo de Química Teórica, Universidad Nacional de Colombia, Centro de Investigaciones en Sistemas complejos CEIBA, Bogotá, Colombia
- Grupo de Química Teórica, Universidad de los Andes, Centro de Investigaciones en Sistemas Complejos CEIBA, Bogotá, Colombia
| | - Edgar E. Daza
- Grupo de Química Teórica, Universidad Nacional de Colombia, Centro de Investigaciones en Sistemas complejos CEIBA, Bogotá, Colombia
| | - Manuel E. Patarroyo
- Grupo de Biomatemáticas, Fundación Instituto de Inmunología de Colombia, Bogotá, Colombia
- * E-mail:
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Patarroyo ME, Cifuentes G, Baquero J. Comparative molecular and three-dimensional analysis of the peptide–MHC II binding region in both human and Aotus MHC-DRB molecules confirms their usefulness in antimalarial vaccine development. Immunogenetics 2006; 58:598-606. [PMID: 16791622 DOI: 10.1007/s00251-006-0128-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2006] [Accepted: 05/03/2006] [Indexed: 11/28/2022]
Abstract
A vaccine against malaria is desperately needed, and Aotus monkeys are highly susceptible to experimental infection with malarial parasites. A thorough analysis of this monkey's immune system molecules was thus undertaken in our institute. Cloning and sequencing, followed by three-dimensional analysis, has revealed high homology with some HLA-DRB1 molecules in terms of their peptide binding region pockets. Molecules such as HLA-DRB1*03, 11, 08, and HLA-DRB1*04 are so similar to Aotus MHC-DRB molecules that peptides identified as binding to these molecules and inducing protective immunity in these monkeys could be used in humans without further refinement, while small modifications seem to be needed for those binding to HLA-DRB1*07, HLA-DRB1*15, 16, and HLA-DRB1*10-like molecules, making this New World monkey an excellent model for tailor-made vaccine development, especially against malaria.
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Affiliation(s)
- M E Patarroyo
- Fundación Instituto de Inmunología de Colombia, Carrera. 50 No. 26-00 Bogotá, Colombia.
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Balbín A, Cárdenas C, Villaveces JL, Patarroyo ME. A theoretical analysis of HLA-DRbeta1*0301-CLIP complex using the first three multipolar moments of the electrostatic field. Biochimie 2006; 88:1307-11. [PMID: 16872734 DOI: 10.1016/j.biochi.2006.05.009] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2005] [Accepted: 05/11/2006] [Indexed: 11/27/2022]
Abstract
Interactions between the HLA-DRbeta1*0301 molecule and several occupying peptides obtained from computational substitutions made to the CLIP peptide are studied. The exploration was carried out using a vector composed of the first three terms of the multipolar expansion of the electrostatic field, namely, charge (q), dipole (d) and quadrupole (C). Comparisons between pocket-peptide interactions established that the binding pockets for this HLA molecule are ordered in terms of their importance for binding peptides, as follows: P1 >>> P4 > P6 > P7 > P9. A set of electrostatically distinct amino acids that determine interaction stability and specificity were identified for each pocket. The beta74R residue was especially identified as being the key amino acid mediating the occupying peptide binding for pocket 4; this residue has been recently associated with Graves' disease.
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Cárdenas C, Obregón M, Balbín A, Villaveces JL, Patarroyo ME. Wave function analysis of MHC-peptide interactions. J Mol Graph Model 2006; 25:605-15. [PMID: 16793298 DOI: 10.1016/j.jmgm.2006.04.005] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2005] [Revised: 04/07/2006] [Accepted: 04/10/2006] [Indexed: 10/24/2022]
Abstract
We have carried out an analysis of the wave function data for three MHC-peptide complexes: HLA-DRbeta1*0101-HA, HLA-DRbeta1*0401-HA and HLA-DRbeta1*0401-Col. We used quantum chemistry computer programs to generate wave function coefficients for these complexes, from which we obtained both molecular and atomic orbital data for both pocket and peptide amino acids within each pocket region. From these discriminated data, interaction molecular orbitals (IMOs) were identified as those with large and similar atomic orbital coefficient contributions from both pocket and peptide amino acids. The present results correlate well with our previous research where only electrostatic moments were used to explore molecular component interactions. Furthermore, we show a quantum chemical methodology to produce more fine-grained results concerning amino acid behavior in the MHC-peptide interaction.
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Cárdenas C, Ortiz M, Balbín A, Villaveces JL, Patarroyo ME. Allele effects in MHC–peptide interactions: A theoretical analysis of HLA-DRβ1*0101-HA and HLA-DRβ1*0401-HA complexes. Biochem Biophys Res Commun 2005; 330:1162-7. [PMID: 15823565 DOI: 10.1016/j.bbrc.2005.03.102] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2005] [Indexed: 10/25/2022]
Abstract
HLA-DRbeta1*0101-HA and HLA-DRbeta1*0401-HA complexes are studied and compared by means of their computationally derived multipolar moments and electrostatic potentials. Changes in electrostatic potential are associated with definite pocket interaction profiles. Thus, Pocket 1 projects itself as an anchoring pocket for both complexes, in accordance with experimental results. While Pocket 4 has an anchoring profile in the HLA-DRbeta1*0101 allele, it presents itself as modulating pocket-peptide interactions in HLA-DRbeta1*0401. Pockets 6 and 7 both strongly contribute to allele specificity, with Pocket 7 being very important for HLA-DRbeta1*0401-HA. Pocket 9 acts as a "double purpose" interaction site for both alleles. It both projects itself as an anchoring pocket as well as modulating pocket-peptide interactions.
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