Quantum Chemical Analysis of MHC-Peptide Interactions for Vaccine Design

The development of an adequate immune response against pathogens is mediated by molecular interactions between different cell types. Among them, binding of antigenic peptides to the Major Histocompatibility Complex (MHC) molecule expressed on the membrane of antigen presenting cells (APCs), and their subsequent recognition by the T cell receptor have been demonstrated to be crucial for developing an adequate immune response. The present review compiles computational quantum chemistry studies about the electrostatic potential variations induced on the MHC binding region by peptide’s amino acids, carried out with the aim of describing MHC–peptide binding interactions. The global idea is that the electrostatic potential can be represented in terms of a series expansion (charge, dipole, quadrupole, hexadecapole, etc.) whose three first terms provide a good local approximation to the molecular electrostatic ‘landscape’ and to the variations induced on such landscape by targeted modifications on the residues of the antigenic peptide. Studies carried out in four MHC class II human allele molecules, which are the most representative alleles of their corresponding haplotypes, showed that each of these molecules have conserved as well as specific electrostatic characteristics, which can be correlated at a good extent with the peptide binding profiles reported experimentally for these molecules. The information provided by such characteristics would help increase our knowledge about antigen binding and presentation, and could ultimately contribute to developing a logical and rational methodology for designing chemically synthesized, multi-antigenic, subunit-based vaccines, through the application of quantum chemistry methods

Quantum chemical analysis of MHC-peptide interactions for vaccine design

The development of an adequate immune response against pathogens is mediated by molecular interactions between different cell types. Among them, binding of antigenic peptides to the Major Histocompatibility Complex (MHC) molecule expressed on the membrane of antigen presenting cells (APCs), and their subsequent recognition by the T cell receptor have been demonstrated to be crucial for developing an adequate immune response. The present review compiles computational quantum chemistry studies about the electrostatic potential variations induced on the MHC binding region by peptide's amino acids, carried out with the aim of describing MHC-peptide binding interactions. The global idea is that the electrostatic potential can be represented in terms of a series expansion (charge, dipole, quadrupole, hexadecapole, etc.) whose three first terms provide a good local approximation to the molecular electrostatic 'landscape' and to the variations induced on such landscape by targeted modifications on the residues of the antigenic peptide. Studies carried out in four MHC class II human allele molecules, which are the most representative alleles of their corresponding haplotypes, showed that each of these molecules have conserved as well as specific electrostatic characteristics, which can be correlated at a good extent with the peptide binding profiles reported experimentally for these molecules. The information provided by such characteristics would help increase our knowledge about antigen binding and presentation, and could ultimately contribute to developing a logical and rational methodology for designing chemically synthesized, multiantigenic, subunit-based vaccines, through the application of quantum chemistry methods. © 2010 Bentham Science Publishers Ltd

Far from the madding crowd: The molecular basis for immunological escape of plasmodium falciparum

Like Thomas Hardy’s famous novel Far from the Madding Crowd, Plasmodium falciparum parasites display their most relevant survival structures (proteins) involved in host cell invasion far away from the immune system’s susceptible regions, displaying tremendous genetic variability, to attract the immune response and escape immune pressure. The 3D structure localisation of the conserved amino acid sequences of this deadly parasite’s most relevant proteins involved in host cell invasion, as well as the location of the highly polymorphic, highly immunogenic regions, clearly demonstrates that such structures are far apart, sometimes 90° to 180° opposite, thereby rendering the immune response useless. It is also shown here that these conserved, functionally-relevant structures are immunologically silent, since no immune response has been induced. © 2017, Caister Academic Press. All rights reserved

Well-defined regions of the Plasmodium falciparum reticulocyte binding protein homologue 4 mediate interaction with red blood cell membrane

Two widely studied parasite protein families are considered attractive targets for developing a fully effective antimalarial vaccine: the erythrocyte binding antigen (EBA) family defining a sialic acid-dependent invasion pathway, and reticulocyte-binding homologue (RH) proteins associated with sialic acid-independent red blood cell (RBC) invasion. In this study, the micronemal invasive PfRH4 protein was finely mapped using 20-mer-long synthetic peptides spanning the entire protein length to identify protein regions that establish high affinity interactions with human RBCs. Twenty conserved, mainly ?-helical high-activity binding peptides (HABPs) with nanomolar dissociation constants and recognizing 32, 25, 22, and 20 kDaRBCmembrane molecules in a chymotrypsin and/or trypsin-sensitive manner were identified in this protein. Anti-PfRH4 rabbit sera and PfRH4 HABPs inhibited merozoite invasion in vitro, therefore suggesting the implication of these HABPs in Plasmodium falciparum invasion and supporting their inclusion in further structural and immunological studies to design potential components of a minimal subunit-based, multiantigenic, chemically synthesized antimalarial vaccine. ©2009 American Chemical Society

Functional, immunological and three-dimensional analysis of chemically synthesisedsporozoite peptides as components of a fully-effective antimalarial vaccine

Our ongoing search for a fully-effective vaccine against the Plasmodium falciparum parasite (causing the most lethal form ofhuman malaria) has been focused on identifying and characterising proteins' amino acid sequences (high activity binding peptides orHABPs) involved in parasite invasion of red blood cells (RBC) by the merozoite and hepatocytes by the sporozoite. Many such merozoiteHABPs have been recognised and molecularly and structurally characterised; however, native HABPs are immunologically silentsince they do not induce any immune response or protection against P. falciparum malaria infection and they have to be structurallymodified to allow them to fit perfectly into immune system molecules.A deeply structural analysis of these conserved merozoite HABPs and their modified analogues has led to rules or principles becomingrecognised for constructing a logical and rational methodology for a minimal subunit-based, multi-epitope, multi-stage, chemicallysynthesisedvaccine. The same in-depth analysis of the most relevant sporozoite proteins involved in sporozoite cell-traversal and hepatocyteinvasion as well as the hepatic stage is shown here.Specifically modifying these HABPs has resulted in a new set of potential pre-erythrocyte targets which are able to induce high, longlastingantibody titres in Aotus monkeys, against their corresponding recombinant proteins and the complete parasite native molecules.This review shows how these rules may be applied against the first stage of parasite invasion (i.e. the sporozoite) to mount the first line ofdefence against the malarial parasite, which may indeed be the most effective one. Our results strongly support including some of thesemodified sporozoite HABPs in combination with the previously-described modified merozoite HABPs for obtaining the aforementionedfully-protective, multiepitope, multi-stage, minimal subunit-based, chemically-synthesized, antimalarial vaccine. © 2011 Bentham Science Publishers

Prevalence of infection with high-risk human papillomavirus in women in Colombia

AbstractThe prevalence of human papillomavirus (HPV) infections in 2109 females inhabiting five cities of Colombia was determined. Of the 49.2% with an HPV infection, 59.8% were infected with more than one viral type. Species 7 (of the the genus Alphapapillomavirus) was associated with multiple infections. Analysis of the socio-demographic data revealed a statistically significant protective effect associated with the status of civil union (civil recognition of cohabitation without marriage), and indigenous ethnicity proved to be a risk factor for HPV infection. This is the first study comparing HPV infection among women from geographical regions of Colombia with different socio-cultural structures

Emerging rules for subunit-based, multiantigenic, multistage chemically synthesized vaccines

(Figure Presented) Seventeen million people die of transmittable diseases and 2/3 of the world's population suffer them annually. Malaria, tuberculosis, AIDS, hepatitis, and reemerging and new diseases are a great threat to human-kind. A logical and rational approach for vaccine development is thus desperately needed. Protein chemistry provides the best tools for tackling these problems. The tremendous complexity of microbes, the different pathways they use for invading host cells, and the immune responses they induce can only be resolved by using the minimum subunit-based (chemically produced ?20-mer peptides), multiantigenic (most proteins involved in invasion), multistage (different invasion mechanisms) vaccine development approach. The most lethal form of malaria caused by Plasmodium falciparum (killing 3 million and affecting 500 million people worldwide annually) was used as target disease since many of its proteins, its invasion pathways, and its genome have been described recently. A New World primate (the Aotus monkey) is highly susceptibly to human malaria; its immune system molecules are 80-100% identical to those of its human counterpart, making it an excellent model for vaccine development. Chemically synthesized ?20-mer peptides, covering all the P. falciparum malaria proteins involved in red blood cell (RBC) invasion were synthesized by the classical t-Boc technology (based on synthetic SPf66 antimalarial vaccine information for identifying targets) and assayed in a highly sensitive, specific, and robust test for detecting receptor-ligand interactions between high-activity binding peptides (HABPs) and RBCs. HABPs were identified, some in which the molecule displays genetic variability (to be discarded due to their tremendous complexity) and elicits a strain-specific immune response and others that are conserved (no amino acid sequence variation). Conserved HABPs were synthesized in a polymeric form by adding cysteines at their N- and C-terminal ends to be used for monkey immunization. They became nonimmunogenic (no antibodies were induced) nonprotection inducers (monkeys were not protected against P. falciparum malaria challenge with a highly infective strain) suggesting a code of immunological silence or nonresponsiveness for these conserved HABPs. A large number of monkey trials involving a considerable number of Aotus monkeys were performed to break this code of immunological silence by replacing critical residues (determined by glycine peptide analogue scanning) to find that the following amino acid changes had to be made to render them antibody and protection inducing: F?R; W?Y; L?H; I?N; M?K; P?D; Q?E; C?T. The three-dimensional (3D) structure of and gt;100 of these native modified HABPs (determined by 1H NMR) revealed that the following structural changes had all to be achieved to allow a better fit into the major histocompatibility complex class II (MHC II)-peptide-TCR complex to properly activate the immune system: ?-helix shortening, modifying their ?-turn, adopting segmental ?-helix configuration, changing residue orientation, and increasing the distance of those residues fitting into the MHC II molecules from antigen-presenting cells. More than 100 such highly immunogenic, protection-inducing (against P. falciparum malaria) modified HABPs have been identified to date with this methodology, showing that it could lead to developing a highly effective subunit-based, multiantigenic, multistage synthetic vaccine against diseases scourging humankind, malaria being one of them. © 2008 American Chemical Society

Emerging rules for subunit-based, multiantigenic, multistage chemically synthesized vaccines

(Figure Presented) Seventeen million people die of transmittable diseases and 2/3 of the world's population suffer them annually. Malaria, tuberculosis, AIDS, hepatitis, and reemerging and new diseases are a great threat to human-kind. A logical and rational approach for vaccine development is thus desperately needed. Protein chemistry provides the best tools for tackling these problems. The tremendous complexity of microbes, the different pathways they use for invading host cells, and the immune responses they induce can only be resolved by using the minimum subunit-based (chemically produced ?20-mer peptides), multiantigenic (most proteins involved in invasion), multistage (different invasion mechanisms) vaccine development approach. The most lethal form of malaria caused by Plasmodium falciparum (killing 3 million and affecting 500 million people worldwide annually) was used as target disease since many of its proteins, its invasion pathways, and its genome have been described recently. A New World primate (the Aotus monkey) is highly susceptibly to human malaria; its immune system molecules are 80-100% identical to those of its human counterpart, making it an excellent model for vaccine development. Chemically synthesized ?20-mer peptides, covering all the P. falciparum malaria proteins involved in red blood cell (RBC) invasion were synthesized by the classical t-Boc technology (based on synthetic SPf66 antimalarial vaccine information for identifying targets) and assayed in a highly sensitive, specific, and robust test for detecting receptor-ligand interactions between high-activity binding peptides (HABPs) and RBCs. HABPs were identified, some in which the molecule displays genetic variability (to be discarded due to their tremendous complexity) and elicits a strain-specific immune response and others that are conserved (no amino acid sequence variation). Conserved HABPs were synthesized in a polymeric form by adding cysteines at their N- and C-terminal ends to be used for monkey immunization. They became nonimmunogenic (no antibodies were induced) nonprotection inducers (monkeys were not protected against P. falciparum malaria challenge with a highly infective strain) suggesting a code of immunological silence or nonresponsiveness for these conserved HABPs. A large number of monkey trials involving a considerable number of Aotus monkeys were performed to break this code of immunological silence by replacing critical residues (determined by glycine peptide analogue scanning) to find that the following amino acid changes had to be made to render them antibody and protection inducing: F?R; W?Y; L?H; I?N; M?K; P?D; Q?E; C?T. The three-dimensional (3D) structure of and gt;100 of these native modified HABPs (determined by 1H NMR) revealed that the following structural changes had all to be achieved to allow a better fit into the major histocompatibility complex class II (MHC II)-peptide-TCR complex to properly activate the immune system: ?-helix shortening, modifying their ?-turn, adopting segmental ?-helix configuration, changing residue orientation, and increasing the distance of those residues fitting into the MHC II molecules from antigen-presenting cells. More than 100 such highly immunogenic, protection-inducing (against P. falciparum malaria) modified HABPs have been identified to date with this methodology, showing that it could lead to developing a highly effective subunit-based, multiantigenic, multistage synthetic vaccine against diseases scourging humankind, malaria being one of them. © 2008 American Chemical Society

Structural and immunological principles leading to chemically synthesized, multiantigenic, multistage, minimal subunit-based vaccine development

Identifying the principles and rules for developing a logical, rational vaccine methodology against various diseases, is discussed. SPf66, the first multiantigenic, multistage, minimal subunit-based, chemically synthesized anti-P. falciparum malaria vaccine. A robust, sensitive, and specific methodology is developed for defining the intimate molecular interactions mediating merozoite invasion of RBC by synthesizing short merozoite-derived protein peptides binding specifically and with high affinity (HABP) to RBCs. Conserved HABP-mediated sporozoite binding to hepatic cells is identified in EBA-175 for developing a multiantigenic, multistage, fully protective antimalarial vaccine. for developing a logical and rational vaccine methodology at the molecular level, monkeys' immune system molecules is analyzed by cloning and sequencing the Aotus genes encoding immunoglobulins, cytokines, and Class I and II molecules

Structural and immunological principles leading to chemically synthesized, multiantigenic, multistage, minimal subunit-based vaccine development

Identifying the principles and rules for developing a logical, rational vaccine methodology against various diseases, is discussed. SPf66, the first multiantigenic, multistage, minimal subunit-based, chemically synthesized anti-P. falciparum malaria vaccine. A robust, sensitive, and specific methodology is developed for defining the intimate molecular interactions mediating merozoite invasion of RBC by synthesizing short merozoite-derived protein peptides binding specifically and with high affinity (HABP) to RBCs. Conserved HABP-mediated sporozoite binding to hepatic cells is identified in EBA-175 for developing a multiantigenic, multistage, fully protective antimalarial vaccine. for developing a logical and rational vaccine methodology at the molecular level, monkeys' immune system molecules is analyzed by cloning and sequencing the Aotus genes encoding immunoglobulins, cytokines, and Class I and II molecules