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García-Machorro J, Gutiérrez-Sánchez M, Rojas-Ortega DA, Bello M, Andrade-Ochoa S, Díaz-Hernández S, Correa-Basurto J, Rojas-Hernández S. Identification of peptide epitopes of the gp120 protein of HIV-1 capable of inducing cellular and humoral immunity. RSC Adv 2023; 13:9078-9090. [PMID: 36950073 PMCID: PMC10025946 DOI: 10.1039/d2ra08160a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Accepted: 03/12/2023] [Indexed: 03/24/2023] Open
Abstract
The Human Immunodeficiency Virus (HIV-1) causes Acquired Immunodeficiency Syndrome (AIDS) and a high percentage of deaths. Therefore, it is necessary to design vaccines against HIV-1 for the prevention of AIDS. Bioinformatic tools and theoretical algorisms allow us to understand the structural proteins of viruses to develop vaccines based on immunogenic peptides (epitopes). In this work, we identified the epitopes: P1, P2, P10, P27 and P30 from the gp120 protein of HIV-1. These peptides were administered intranasally alone or with cholera toxin (CT) to BALB/c mice. The population of CD4+, CD8+ T lymphocytes and B cells (CD19/CD138+, IgA+ and IgG+) from nasal-associated lymphoid tissue, nasal passages, cervical and inguinal nodes was determined by flow cytometry. In addition, anti-peptides IgG and IgA from serum, nasal and vaginal washings were measured by ELISA. The results show that peptides administered by i.n. can modulate the immune response of T and B lymphocyte populations, as well as IgA and IgG antibodies secretion in the different sites analyzed. In conclusion, bioinformatics tools help us to select peptides with physicochemical properties that allow the induction of the humoral and cellular responses that depend on the peptide sequence.
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Affiliation(s)
- Jazmín García-Machorro
- Laboratorio de Medicina de Conservación, Escuela Superior de Medicina, Instituto Politécnico. Plan de San Luis y Díaz Mirón s/n Col. Casco de Santo Tomas Delegación Miguel Hidalgo C.P. 11340 Ciudad de México Mexico
| | - Mara Gutiérrez-Sánchez
- Laboratorio de Inmunobiología Molecular y Celular, Sección de Estudios de Posgrado e Investigación, Escuela Superior de Medicina, Instituto Politécnico Nacional México City Mexico
| | - Diego Alexander Rojas-Ortega
- Laboratorio de Inmunobiología Molecular y Celular, Sección de Estudios de Posgrado e Investigación, Escuela Superior de Medicina, Instituto Politécnico Nacional México City Mexico
| | - Martiniano Bello
- Laboratorio de Diseño y Desarrollo de Nuevos Fármacos e Innovación Biotécnológica (Laboratory for the Design and Development of New Drugs and Biotechnological Innovation), Escuela Superior de Medicina, Instituto Politécnico Nacional. Plan de San Luis y Díaz Mirón s/n Col. Casco de Santo Tomas Delegación Miguel Hidalgo C.P. 11340 Ciudad de México Mexico
| | - Sergio Andrade-Ochoa
- Facultad de Ciencias Químicas, Universidad Autónoma de Chihuahua, Circuito Universitario S/N 31125 Chihuahua México
- Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Prolongación de Carpio y Plan de Ayala S/N Colonia Santo Tomas 11340 Ciudad de México Mexico
| | - Sebastián Díaz-Hernández
- Laboratorio de Diseño y Desarrollo de Nuevos Fármacos e Innovación Biotécnológica (Laboratory for the Design and Development of New Drugs and Biotechnological Innovation), Escuela Superior de Medicina, Instituto Politécnico Nacional. Plan de San Luis y Díaz Mirón s/n Col. Casco de Santo Tomas Delegación Miguel Hidalgo C.P. 11340 Ciudad de México Mexico
| | - José Correa-Basurto
- Laboratorio de Diseño y Desarrollo de Nuevos Fármacos e Innovación Biotécnológica (Laboratory for the Design and Development of New Drugs and Biotechnological Innovation), Escuela Superior de Medicina, Instituto Politécnico Nacional. Plan de San Luis y Díaz Mirón s/n Col. Casco de Santo Tomas Delegación Miguel Hidalgo C.P. 11340 Ciudad de México Mexico
| | - Saúl Rojas-Hernández
- Laboratorio de Inmunobiología Molecular y Celular, Sección de Estudios de Posgrado e Investigación, Escuela Superior de Medicina, Instituto Politécnico Nacional México City Mexico
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García-Machorro J, Ramírez-Salinas GL, Martinez-Archundia M, Correa-Basurto J. The Advantage of Using Immunoinformatic Tools on Vaccine Design and Development for Coronavirus. Vaccines (Basel) 2022; 10:1844. [PMID: 36366353 PMCID: PMC9693616 DOI: 10.3390/vaccines10111844] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Revised: 10/21/2022] [Accepted: 10/27/2022] [Indexed: 10/28/2023] Open
Abstract
After the outbreak of SARS-CoV-2 by the end of 2019, the vaccine development strategies became a worldwide priority. Furthermore, the appearances of novel SARS-CoV-2 variants challenge researchers to develop new pharmacological or preventive strategies. However, vaccines still represent an efficient way to control the SARS-CoV-2 pandemic worldwide. This review describes the importance of bioinformatic and immunoinformatic tools (in silico) for guide vaccine design. In silico strategies permit the identification of epitopes (immunogenic peptides) which could be used as potential vaccines, as well as nonacarriers such as: vector viral based vaccines, RNA-based vaccines and dendrimers through immunoinformatics. Currently, nucleic acid and protein sequential as well structural analyses through bioinformatic tools allow us to get immunogenic epitopes which can induce immune response alone or in complex with nanocarriers. One of the advantages of in silico techniques is that they facilitate the identification of epitopes, while accelerating the process and helping to economize some stages of the development of safe vaccines.
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Affiliation(s)
- Jazmín García-Machorro
- Laboratorio de Medicina de Conservación, Escuela Superior de Medicina, Instituto Politécnico Nacional, Mexico City 11340, Mexico
| | - Gema Lizbeth Ramírez-Salinas
- Laboratorio de Diseño y Desarrollo de Nuevos Fármacos e Innovación Biotécnológica, Escuela Superior de Medicina, Instituto Politécnico Nacional, México City 11340, Mexico
| | - Marlet Martinez-Archundia
- Laboratorio de Diseño y Desarrollo de Nuevos Fármacos e Innovación Biotécnológica, Escuela Superior de Medicina, Instituto Politécnico Nacional, México City 11340, Mexico
| | - José Correa-Basurto
- Laboratorio de Diseño y Desarrollo de Nuevos Fármacos e Innovación Biotécnológica, Escuela Superior de Medicina, Instituto Politécnico Nacional, México City 11340, Mexico
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3
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Rodríguez-Mera IB, Carrasco-Yépez MM, Vásquez-Moctezuma I, Correa-Basurto J, Salinas GR, Castillo-Ramírez DA, Rosales-Cruz É, Rojas-Hernández S. Role of cathepsin B of Naegleria fowleri during primary amebic meningoencephalitis. Parasitol Res 2022; 121:3287-3303. [PMID: 36125528 PMCID: PMC9485797 DOI: 10.1007/s00436-022-07660-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Accepted: 09/06/2022] [Indexed: 11/25/2022]
Abstract
Naegleria fowleri causes primary amoebic meningoencephalitis in humans and experimental animals. It has been suggested that cysteine proteases of parasites play key roles in metabolism, nutrient uptake, host tissue invasion, and immune evasion. The aim of this work was to evaluate the presence, expression, and role of cathepsin B from N. fowleri in vitro and during PAM. Rabbit-specific polyclonal antibodies against cathepsin B were obtained from rabbit immunization with a synthetic peptide obtained by bioinformatic design. In addition, a probe was designed from mRNA for N. fowleri cathepsin B. Both protein and messenger were detected in fixed trophozoites, trophozoites interacted with polymorphonuclear and histological sections of infected mice. The main cathepsin B distribution was observed in cytoplasm or membrane mainly pseudopods and food-cups while messenger was in nucleus and cytoplasm. Surprisingly, both the messenger and enzyme were observed in extracellular medium. To determine cathepsin B release, we used trophozoites supernatant recovered from nasal passages or brain of infected mice. We observed the highest release in supernatant from recovered brain amoebae, and when we analyzed molecular weight of secreted proteins by immunoblot, we found 30 and 37 kDa bands which were highly immunogenic. Finally, role of cathepsin B during N. fowleri infection was determined; we preincubated trophozoites with E-64, pHMB or antibodies with which we obtained 60%, 100%, and 60% of survival, respectively, in infected mice. These results suggest that cathepsin B plays a role during pathogenesis caused by N. fowleri mainly in adhesion and contributes to nervous tissue damage.
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Affiliation(s)
- Itzel Berenice Rodríguez-Mera
- Laboratorio de Inmunología Molecular, Instituto Politécnico Nacional, Escuela Superior de Medicina, Salvador Díaz Mirón Esq. Plan de San Luis S/N, Miguel Hidalgo, Casco de Santo Tomas, Ciudad de México, CDMX, 11340, México
| | - María Maricela Carrasco-Yépez
- Laboratorio de Microbiología Ambiental, Estado de México, Universidad Nacional Autónoma de México, Grupo CyMA, UIICSE, FES Iztacala, Tlalnepantla de Baz, México
| | - Ismael Vásquez-Moctezuma
- Laboratorio de Bioquímica, Instituto Politécnico Nacional, Escuela Superior de Medicina, Ciudad de Mexico, México
| | - José Correa-Basurto
- Laboratorio de Modelado Molecular y Diseño de Fármacos, Instituto Politécnico Nacional, Escuela Superior de Medicina, Ciudad de Mexico, México
| | - Gema Ramírez- Salinas
- Laboratorio de Modelado Molecular y Diseño de Fármacos, Instituto Politécnico Nacional, Escuela Superior de Medicina, Ciudad de Mexico, México
| | - Diego Arturo Castillo-Ramírez
- Laboratorio de Inmunología Molecular, Instituto Politécnico Nacional, Escuela Superior de Medicina, Salvador Díaz Mirón Esq. Plan de San Luis S/N, Miguel Hidalgo, Casco de Santo Tomas, Ciudad de México, CDMX, 11340, México
| | - Érika Rosales-Cruz
- Instituto Politécnico Nacional, Escuela Nacional de Ciencias Biológicas, Ciudad de Mexico, México
| | - Saúl Rojas-Hernández
- Laboratorio de Inmunología Molecular, Instituto Politécnico Nacional, Escuela Superior de Medicina, Salvador Díaz Mirón Esq. Plan de San Luis S/N, Miguel Hidalgo, Casco de Santo Tomas, Ciudad de México, CDMX, 11340, México.
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4
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Roy U. Structural and molecular analyses of functional epitopes and escape mutants in Japanese encephalitis virus envelope protein domain III. Immunol Res 2021; 68:81-89. [PMID: 32445181 PMCID: PMC7243247 DOI: 10.1007/s12026-020-09130-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
The Japanese encephalitis virus (JEV) is one of the vector borne causes of encephalitis found in southeastern Asia. This positive single-stranded RNA virus is a member of the Flaviviridae family, which notably includes dengue, tick-borne, West Nile, Zika as well as yellow fever, and transmits to humans by infected mosquitos. The main site of interactions for antibodies against this virus is the envelope protein domain III (ED3). The present report investigates the time-dependent structural and conformational changes of JEV ED3 functional epitopes and escape mutants by computer simulations. The results indicate the presence of significant structural differences between the functional epitopes and the escape mutants. Mutation-induced structural/conformational instabilities of this type can decrease the antibody neutralization activity. Among the different escape mutants studied here, Ser40Lys/Asp41Arg appear to be most unstable, while Ser40Glu/Asp41Leu exhibit the lowest structural variations. The highest level of escape mutation observed in Ser40Lys is linked to the relatively higher values of root mean square deviation/fluctuation found in the molecular dynamics simulation of this protein. Secondary-structure deviations and depletion of H bonding are other contributing factors to the protein’s increased instability. Overall, the proteins with residue 41 mutations are found to be structurally more ordered than those with residue 40 mutations. The detailed time-based structural assessment of the mutant epitopes described here may contribute to the development of novel vaccines and antiviral drugs necessary to defend against future outbreaks of JEV escape mutants.
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Affiliation(s)
- Urmi Roy
- Department of Chemistry & Biomolecular Science, Clarkson University, 8 Clarkson Avenue, Potsdam, NY, 13699-5820, USA.
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Meshram RJ, Bagul KT, Aouti SU, Shirsath AM, Duggal H, Gacche RN. Modeling and simulation study to identify threonine synthase as possible drug target in Leishmania major. Mol Divers 2020; 25:1679-1700. [PMID: 32737682 DOI: 10.1007/s11030-020-10129-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Accepted: 07/22/2020] [Indexed: 01/16/2023]
Abstract
Leishmaniasis is one of the most neglected tropical diseases that demand immediate attention to the identification of new drug targets and effective drug candidates. The present study demonstrates the possibility of using threonine synthase (TS) as a putative drug target in leishmaniasis disease management. We report the construction of an effective homology model of the enzyme that appears to be structurally as well as functionally well conserved. The 200 nanosecond molecular dynamics data on TS with and without pyridoxal phosphate (PLP) shed light on mechanistic details of PLP-induced conformational changes. Moreover, we address some important structural and dynamic interactions in the PLP binding region of TS that are in good agreement with previously speculated crystallographic estimations. Additionally, after screening more than 44,000 compounds, we propose 10 putative inhibitor candidates for TS based on virtual screening data and refined Molecular Mechanics Generalized Born Surface Area calculations. We expect that structural and functional dynamics data disclosed in this study will help initiate experimental endeavors toward establishing TS as an effective antileishmanial drug target.
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Affiliation(s)
- Rohan J Meshram
- Bioinformatics Centre, Savitribai Phule Pune University, Pune, Maharashtra, 411007, India.
| | - Kamini T Bagul
- Bioinformatics Centre, Savitribai Phule Pune University, Pune, Maharashtra, 411007, India
| | - Snehal U Aouti
- Bioinformatics Centre, Savitribai Phule Pune University, Pune, Maharashtra, 411007, India
| | - Akshay M Shirsath
- Bioinformatics Centre, Savitribai Phule Pune University, Pune, Maharashtra, 411007, India
| | - Harleen Duggal
- Bioinformatics Centre, Savitribai Phule Pune University, Pune, Maharashtra, 411007, India
| | - Rajesh N Gacche
- Department of Biotechnology, Savitribai Phule Pune University, Pune, Maharashtra, 411007, India
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6
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Ramírez-Salinas GL, García-Machorro J, Rojas-Hernández S, Campos-Rodríguez R, de Oca ACM, Gomez MM, Luciano R, Zimic M, Correa-Basurto J. Bioinformatics design and experimental validation of influenza A virus multi-epitopes that induce neutralizing antibodies. Arch Virol 2020; 165:891-911. [PMID: 32060794 PMCID: PMC7222995 DOI: 10.1007/s00705-020-04537-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Accepted: 12/11/2019] [Indexed: 02/01/2023]
Abstract
Pandemics caused by influenza A virus (IAV) are responsible for the deaths of millions of humans around the world. One of these pandemics occurred in Mexico in 2009. Despite the impact of IAV on human health, there is no effective vaccine. Gene mutations and translocation of genome segments of different IAV subtypes infecting a single host cell make the development of a universal vaccine difficult. The design of immunogenic peptides using bioinformatics tools could be an interesting strategy to increase the success of vaccines. In this work, we used the predicted amino acid sequences of the neuraminidase (NA) and hemagglutinin (HA) proteins of different IAV subtypes to perform multiple alignments, epitope predictions, molecular dynamics simulations, and experimental validation. Peptide selection was based on the following criteria: promiscuity, protein surface exposure, and the degree of conservation among different medically relevant IAV strains. These peptides were tested using immunological assays to test their ability to induce production of antibodies against IAV. We immunized rabbits and mice and measured the levels of IgG and IgA antibodies in serum samples and nasal washes. Rabbit antibodies against the peptides P11 and P14 (both of which are hybrids of NA and HA) recognized HA from both group 1 (H1, H2, and H5) and group 2 (H3 and H7) IAV and also recognized the purified NA protein from the viral stock (influenza A Puerto Rico/916/34). IgG antibodies from rabbits immunized with P11 and P14 were capable of recognizing viral particles and inhibited virus hemagglutination. Additionally, intranasal immunization of mice with P11 and P14 induced specific IgG and IgA antibodies in serum and nasal mucosa, respectively. Interestingly, the IgG antibodies were found to have neutralizing capability. In conclusion, the peptides designed through in silico studies were validated in experimental assays.
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Affiliation(s)
- G Lizbeth Ramírez-Salinas
- Laboratorio de Diseño y Desarrollo de Nuevos Fármacos e Innovación Biotécnológica (Laboratory for the Design and Development of New Drugs and Biotechnological Innovation), Escuela Superior de Medicina, Instituto Politécnico Nacional, México City, 11340, México
| | - Jazmín García-Machorro
- Laboratorio de medicina de Conservación, Escuela Superior de Medicina, Instituto Politécnico Nacional, México City, 11340, México.
| | - Saúl Rojas-Hernández
- Laboratorio de Inmunología celular, Escuela Superior de Medicina, Instituto Politécnico Nacional, México City, 11340, México
| | - Rafael Campos-Rodríguez
- Laboratorio de Bioquímica. Escuela Superior de Medicina, Instituto Politécnico Nacional, México City, 11340, México
| | - Arturo Contis-Montes de Oca
- Laboratorio de Inmunología celular, Escuela Superior de Medicina, Instituto Politécnico Nacional, México City, 11340, México
| | - Miguel Medina Gomez
- Laboratorio de medicina de Conservación, Escuela Superior de Medicina, Instituto Politécnico Nacional, México City, 11340, México
| | - Rocío Luciano
- Laboratorio de medicina de Conservación, Escuela Superior de Medicina, Instituto Politécnico Nacional, México City, 11340, México
| | - Mirko Zimic
- Laboratorio de Bioinformática y Biología Molecular, Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, Perú
| | - José Correa-Basurto
- Laboratorio de Diseño y Desarrollo de Nuevos Fármacos e Innovación Biotécnológica (Laboratory for the Design and Development of New Drugs and Biotechnological Innovation), Escuela Superior de Medicina, Instituto Politécnico Nacional, México City, 11340, México.
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7
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Rojas-Osornio SA, Cruz-Hernández TR, Drago-Serrano ME, Campos-Rodríguez R. Immunity to influenza: Impact of obesity. Obes Res Clin Pract 2019; 13:419-429. [PMID: 31542241 DOI: 10.1016/j.orcp.2019.05.003] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/19/2018] [Revised: 05/14/2019] [Accepted: 05/19/2019] [Indexed: 12/27/2022]
Abstract
Obesity is a health concern that is recognized as a critical factor for vulnerability to influenza A/pdmH1N1 virus infection, with epidemiological and clinical impacts. In humans, obesity induces disturbances in inflammatory and immune responses to the influenza virus and in some cases, this leads to severe complications, with fatal outcomes. Obesity impairs immunity by altering the response of cytokines, resulting in a decrease in the cytotoxic cell response of immunocompetent cells which have a key anti-viral role. Additionally, obesity seems to disturb the balance of endocrine hormones, such as leptin, that affect the interplay between metabolic and immune systems. This contribution focuses on reviewing the current epidemiologic data for the immune response to immunity in obese humans and animal models. In doing so, we aim to provide potential mechanisms to enhance immunity to influenza A/pdmH1N1 virus infection and protective factors in obese people.
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Affiliation(s)
- Sandra Angélica Rojas-Osornio
- Sección de Estudios de Posgrado e Investigación, Escuela Superior de Medicina, Instituto Politécnico Nacional, Plan de San Luis y Díaz Mirón s/n, CP 11340, CDMX, Mexico
| | - Teresita Rocío Cruz-Hernández
- Sección de Estudios de Posgrado e Investigación, Escuela Superior de Medicina, Instituto Politécnico Nacional, Plan de San Luis y Díaz Mirón s/n, CP 11340, CDMX, Mexico
| | - Maria Elisa Drago-Serrano
- Departamento de Sistemas Biológicos, Universidad Autónoma Metropolitana, Unidad Xochimilco. Calzada del Hueso No. 1100, CP 04960, CDMX, Mexico
| | - Rafael Campos-Rodríguez
- Sección de Estudios de Posgrado e Investigación, Escuela Superior de Medicina, Instituto Politécnico Nacional, Plan de San Luis y Díaz Mirón s/n, CP 11340, CDMX, Mexico.
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8
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Meshram RJ, Bagul KT, Pawnikar SP, Barage SH, Kolte BS, Gacche RN. Known compounds and new lessons: structural and electronic basis of flavonoid-based bioactivities. J Biomol Struct Dyn 2019; 38:1168-1184. [DOI: 10.1080/07391102.2019.1597770] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Rohan J. Meshram
- Bioinformatics Centre, Savitribai Phule Pune University, Pune, Maharashtra, India
| | - Kamini T. Bagul
- Bioinformatics Centre, Savitribai Phule Pune University, Pune, Maharashtra, India
| | - Shristi P. Pawnikar
- Bioinformatics Centre, Savitribai Phule Pune University, Pune, Maharashtra, India
| | - Sagar H. Barage
- Amity Institute of Biotechnology, Amity University, Panvel, Maharashtra, India
| | - Baban S. Kolte
- Bioinformatics Centre, Savitribai Phule Pune University, Pune, Maharashtra, India
- Department of Biotechnology, Savitribai Phule Pune University, Pune, Maharashtra, India
| | - Rajesh N. Gacche
- Department of Biotechnology, Savitribai Phule Pune University, Pune, Maharashtra, India
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López-Contreras L, Hernández-Ramírez VI, Herrera-Martínez M, Montaño S, Constantino-Jonapa LA, Chávez-Munguía B, Talamás-Rohana P. Structural and functional characterization of the divergent Entamoeba Src using Src inhibitor-1. Parasit Vectors 2017; 10:500. [PMID: 29047404 PMCID: PMC5648430 DOI: 10.1186/s13071-017-2461-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2017] [Accepted: 10/09/2017] [Indexed: 12/14/2022] Open
Abstract
Background The abundant number of kinases that Entamoeba histolytica possesses allows us to assume that the regulation of cellular functions by phosphorylation-dephosphorylation processes is very important. However, the kinases responsible for the phosphorylation in Entamoeba spp. vary in the structure of their domains and, therefore, could be responsible for the unusual biological characteristics of this parasite. In higher eukaryotes, Src kinases share conserved structural domains and are very important in the regulation of the actin cytoskeleton. In both Entamoeba histolytica and Entamoeba invadens, the major Src kinase homologue of higher eukaryotes lacks SH3 and SH2 domains, but does have KELCH domains; the latter are part of actin cross-linking proteins in higher eukaryotic cells. Methods The function of the EhSrc protein kinase of Entamoeba spp. was evaluated using Src inhibitor-1, microscopy assays, Src kinase activity and western blot. In addition, to define the potential inhibitory mechanism of Src-inhibitor-1 for the amoebic EhSrc protein kinase, molecular dynamic simulations using NAnoscale Molecular Dynamics (NAMD2) program and docking studies were performed with MOE software. Results We demonstrate that Src inhibitor-1 is able to prevent the activity of EhSrc protein kinase, most likely by binding to the catalytic domain, which affects cell morphology via the disruption of actin cytoskeleton remodeling and the formation of phagocytic structures without an effect on cell adhesion. Furthermore, in E. invadens, Src inhibitor-1 inhibited the encystment process by blocking RhoA GTPase activity, a small GTPase protein of Rho family. Conclusions Even though the EhSrc molecule of Entamoeba is not a typical Src, because its divergent amino acid sequence, it is a critical factor in the biology of this parasite via the regulation of actin cytoskeleton remodeling via RhoA GTPase activation. Based on this, we conclude that EhSrc could become a target molecule for the future design of drugs that can prevent the transmission of the disease. Electronic supplementary material The online version of this article (10.1186/s13071-017-2461-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Luilli López-Contreras
- Área Académica de Medicina, Instituto de Ciencias de la Salud, Universidad Autónoma del Estado de Hidalgo, Camino a Tilcuatla s/n Municipio de San Agustín Tlaxiaca. C.P, 42160, Pachuca de Soto, Hidalgo, Mexico
| | - Verónica Ivonne Hernández-Ramírez
- Departamento de Infectómica y Patogénesis Molecular, Centro de Investigación y de Estudios Avanzados del I.P.N, Avenida Instituto Politécnico Nacional No. 2508, Col. San Pedro Zacatenco, Delegación Gustavo A. Madero, 07360, CDMX, CP, Mexico
| | - Mayra Herrera-Martínez
- Departamento de Infectómica y Patogénesis Molecular, Centro de Investigación y de Estudios Avanzados del I.P.N, Avenida Instituto Politécnico Nacional No. 2508, Col. San Pedro Zacatenco, Delegación Gustavo A. Madero, 07360, CDMX, CP, Mexico
| | - Sarita Montaño
- Facultad de Ciencias Químico Biológicas de la Universidad Autónoma de Sinaloa, Calz. de las Américas Norte 2771, Burócrata, 80030, Culiacán de Rosales, Sinaloa, Mexico
| | - Luis Alejandro Constantino-Jonapa
- Departamento de Infectómica y Patogénesis Molecular, Centro de Investigación y de Estudios Avanzados del I.P.N, Avenida Instituto Politécnico Nacional No. 2508, Col. San Pedro Zacatenco, Delegación Gustavo A. Madero, 07360, CDMX, CP, Mexico
| | - Bibiana Chávez-Munguía
- Departamento de Infectómica y Patogénesis Molecular, Centro de Investigación y de Estudios Avanzados del I.P.N, Avenida Instituto Politécnico Nacional No. 2508, Col. San Pedro Zacatenco, Delegación Gustavo A. Madero, 07360, CDMX, CP, Mexico
| | - Patricia Talamás-Rohana
- Departamento de Infectómica y Patogénesis Molecular, Centro de Investigación y de Estudios Avanzados del I.P.N, Avenida Instituto Politécnico Nacional No. 2508, Col. San Pedro Zacatenco, Delegación Gustavo A. Madero, 07360, CDMX, CP, Mexico.
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10
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Bello M, Correa-Basurto J. Energetic and flexibility properties captured by long molecular dynamics simulations of a membrane-embedded pMHCII-TCR complex. MOLECULAR BIOSYSTEMS 2016; 12:1350-66. [PMID: 26926952 DOI: 10.1039/c6mb00058d] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Although crystallographic data have provided important molecular insight into the interactions in the pMHC-TCR complex, the inherent features of this structural approach cause it to only provide a static picture of the interactions. While unbiased molecular dynamics simulations (UMDSs) have provided important information about the dynamic structural behavior of the pMHC-TCR complex, most of them have modeled the pMHC-TCR complex as soluble, when in physiological conditions, this complex is membrane bound; therefore, following this latter UMDS protocol might hamper important dynamic results. In this contribution, we performed three independent 300 ns-long UMDSs of the pMHCII-TCR complex anchored in two opposing membranes to explore the structural and energetic properties of the recognition of pMHCII by the TCR. The conformational ensemble generated through UMDSs was subjected to clustering and Cartesian principal component analyses (cPCA) to explore the dynamical behavior of the pMHCII-TCR association. Furthermore, based on the conformational population sampled through UMDSs, the effective binding free energy, per-residue free energy decomposition, and alanine scanning mutations were explored for the native pMHCII-TCR complex, as well as for 12 mutations (p1-p12MHCII-TCR) introduced in the native peptide. Clustering analyses and cPCA provide insight into the rocking motion of the TCR onto pMHCII, together with the presence of new electrostatic interactions not observed through crystallographic methods. Energetic results provide evidence of the main contributors to the pMHC-TCR complex formation as well as the key residues involved in this molecular recognition process.
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Affiliation(s)
- Martiniano Bello
- Laboratorio de Modelado Molecular, Bioinformática y Diseño de Fármacos de la Escuela Superior de Medicina, Instituto Politécnico Nacional, Plan de San Luis Y Diaz Mirón S/N, Col. Casco de Santo Tomas, Mexico City, CP: 11340, Mexico.
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11
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Bello M, Campos-Rodriguez R, Rojas-Hernandez S, Contis-Montes de Oca A, Correa-Basurto J. Predicting peptide vaccine candidates against H1N1 influenza virus through theoretical approaches. Immunol Res 2016; 62:3-15. [PMID: 25716614 DOI: 10.1007/s12026-015-8629-1] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Identification of potential epitopes that might activate the immune system has been facilitated by the employment of algorithms that use experimental data as templates. However, in order to prove the affinity and the map of interactions between the receptor (major histocompatibility complex, MHC, or T-cell receptor) and the potential epitope, further computational studies are required. Docking and molecular dynamics (MDs) simulations have been an effective source of generating structural information at molecular level in immunology. Herein, in order to provide a detailed understanding of the origins of epitope recognition and to select the best peptide candidate to develop an epitope-based vaccine, docking and MDs simulations in combination with MMGBSA free energy calculations and per-residue free energy decomposition were performed, taking as starting complexes those formed between four designed epitopes (P1-P4) from hemagglutinin (HA) of the H1N1 influenza virus and MHC-II anchored in POPC membrane. Our results revealed that the energetic contributions of individual amino acids within the pMHC-II complexes are mainly dictated by van der Waals interactions and the nonpolar part of solvation energy, whereas the electrostatic interactions corresponding to hydrogen bonds and salt bridges determine the binding specificity, being the most favorable interactions formed between p4 and MHC-II. Then, P1-P4 epitopes were synthesized and tested experimentally to compare theoretical and experimental results. Experimental results show that P4 elicited the highest strong humoral immune response to HA of the H1N1 and may induce antibodies that are cross-reactive to other influenza subtypes, suggesting that it could be a good candidate for the development of a peptide-based vaccine.
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Affiliation(s)
- Martiniano Bello
- Laboratorio de Modelado Molecular, Bioinformática y Diseño de Fármacos de la Escuela Superior de Medicina, Instituto Politécnico Nacional, Plan de San Luis y Diaz Mirón s/n, Col. Casco de Santo Tomas, CP 11340, Mexico City, Mexico,
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12
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Ramírez-Salinas GL, García-Machorro J, Quiliano M, Zimic M, Briz V, Rojas-Hernández S, Correa-Basurto J. Molecular modeling studies demonstrate key mutations that could affect the ligand recognition by influenza AH1N1 neuraminidase. J Mol Model 2015; 21:292. [PMID: 26499499 DOI: 10.1007/s00894-015-2835-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2014] [Accepted: 10/09/2015] [Indexed: 01/23/2023]
Abstract
The goal of this study was to identify neuraminidase (NA) residue mutants from human influenza AH1N1 using sequences from 1918 to 2012. Multiple alignment studies of complete NA sequences (5732) were performed. Subsequently, the crystallographic structure of the 1918 influenza (PDB ID: 3BEQ-A) was used as a wild-type structure and three-dimensional (3-D) template for homology modeling of the mutated selected NA sequences. The 3-D mutated NAs were refined using molecular dynamics (MD) simulations (50 ns). The refined 3-D models were used to perform docking studies using oseltamivir. Multiple sequence alignment studies showed seven representative mutations (A232V, K262R, V263I, T264V, S367L, S369N, and S369K). MD simulations applied to 3-D NAs showed that each NA had different active-site shapes according to structural surface visualization and docking results. Moreover, Cartesian principal component analyses (cPCA) show structural differences among these NA structures caused by mutations. These theoretical results suggest that the selected mutations that are located outside of the active site of NA could affect oseltamivir recognition and could be associated with resistance to oseltamivir.
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Affiliation(s)
- Gema L Ramírez-Salinas
- Laboratorio de Modelado Molecular y Bioinformática, Sección de Estudios de Posgrado e Investigación, Escuela Superior de Medicina, Instituto Politécnico Nacional, Plan de San Luis y Díaz Mirón, 11340, México City, Mexico
| | - J García-Machorro
- Laboratorio de Medicina de Conservación, Escuela Superior de Medicina, Instituto Politécnico Nacional, Plan de San Luis y Díaz Mirón, Mexico, DF, 11340, México
| | - Miguel Quiliano
- Unidad de Bioinformática y Biología Molecular, Laboratorios de Investigación y Desarrollo, Universidad Peruana Cayetano Heredia, Lima, Perú
| | - Mirko Zimic
- Unidad de Bioinformática y Biología Molecular, Laboratorios de Investigación y Desarrollo, Universidad Peruana Cayetano Heredia, Lima, Perú
| | - Verónica Briz
- Unidad de Infección Viral e Inmunidad, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, Madrid, España
| | - Saul Rojas-Hernández
- Laboratory of Immunology, School of Medicine, National Polytechnic Institute, Mexico, DF, Mexico
| | - J Correa-Basurto
- Laboratorio de Modelado Molecular y Bioinformática, Sección de Estudios de Posgrado e Investigación, Escuela Superior de Medicina, Instituto Politécnico Nacional, Plan de San Luis y Díaz Mirón, 11340, México City, Mexico.
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13
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Carrillo-Vazquez JP, Correa-Basurto J, García-Machorro J, Campos-Rodríguez R, Moreau V, Rosas-Trigueros JL, Reyes-López CA, Rojas-López M, Zamorano-Carrillo A. A continuous peptide epitope reacting with pandemic influenza AH1N1 predicted by bioinformatic approaches. J Mol Recognit 2015; 28:553-64. [DOI: 10.1002/jmr.2470] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2014] [Revised: 12/16/2014] [Accepted: 01/15/2015] [Indexed: 01/27/2023]
Affiliation(s)
| | - José Correa-Basurto
- Laboratorio de Modelado Molecular y Diseño de Fármacos; Escuela Superior de Medicina-IPN; Mexico, D.F. Mexico
| | - Jazmin García-Machorro
- Laboratorio de Medicina de Conservación; Escuela Superior de Medicina-IPN; Mexico, D.F. Mexico
| | | | | | - Jorge L. Rosas-Trigueros
- Laboratorio Transdisciplinario de Investigación en Sistemas Evolutivos SEPI-ESCOM-IPN; Mexico, D.F. Mexico
| | - Cesar A. Reyes-López
- Laboratorio de Bioquímica y Biofísica Computacional; Doctorado en Biotecnología ENMH-IPN; Mexico, D.F. Mexico
| | | | - Absalom Zamorano-Carrillo
- Laboratorio de Bioquímica y Biofísica Computacional; Doctorado en Biotecnología ENMH-IPN; Mexico, D.F. Mexico
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Gema LRS, Tolentino-Lopez LE, Martínez-Ramos F, Padilla-Martínez I, García-Machorro J, Correa-Basurto J. Targeting a cluster of arginine residues of neuraminidase to avoid oseltamivir resistance in influenza A (H1N1): a theoretical study. J Mol Model 2015; 21:8. [DOI: 10.1007/s00894-014-2525-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2014] [Accepted: 11/10/2014] [Indexed: 12/01/2022]
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15
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Bello M, Correa-Basurto J. Molecular dynamics simulations to provide insights into epitopes coupled to the soluble and membrane-bound MHC-II complexes. PLoS One 2013; 8:e72575. [PMID: 23977319 PMCID: PMC3747130 DOI: 10.1371/journal.pone.0072575] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2013] [Accepted: 07/10/2013] [Indexed: 11/24/2022] Open
Abstract
Epitope recognition by major histocompatibility complex II (MHC-II) is essential for the activation of immunological responses to infectious diseases. Several studies have demonstrated that this molecular event takes place in the MHC-II peptide-binding groove constituted by the α and β light chains of the heterodimer. This MHC-II peptide-binding groove has several pockets (P1-P11) involved in peptide recognition and complex stabilization that have been probed through crystallographic experiments and in silico calculations. However, most of these theoretical calculations have been performed without taking into consideration the heavy chains, which could generate misleading information about conformational mobility both in water and in the membrane environment. Therefore, in absence of structural information about the difference in the conformational changes between the peptide-free and peptide-bound states (pMHC-II) when the system is soluble in an aqueous environment or non-covalently bound to a cell membrane, as the physiological environment for MHC-II is. In this study, we explored the mechanistic basis of these MHC-II components using molecular dynamics (MD) simulations in which MHC-II was previously co-crystallized with a small epitope (P7) or coupled by docking procedures to a large (P22) epitope. These MD simulations were performed at 310 K over 100 ns for the water-soluble (MHC-IIw, MHC-II-P7w, and MHC-II-P22w) and 150 ns for the membrane-bound species (MHC-IIm, MHC-II-P7m, and MHC-II-P22m). Our results reveal that despite the different epitope sizes and MD simulation environments, both peptides are stabilized primarily by residues lining P1, P4, and P6-7, and similar noncovalent intermolecular energies were observed for the soluble and membrane-bound complexes. However, there were remarkably differences in the conformational mobility and intramolecular energies upon complex formation, causing some differences with respect to how the two peptides are stabilized in the peptide-binding groove.
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Affiliation(s)
- Martiniano Bello
- Laboratorio de Modelado Molecular y Bioinformática de la Escuela Superior de Medicina, Instituto Politécnico Nacional, México, Plan de San Luis Y Diaz Mirón S/N, Col. Casco de Santo Tomas, Mexico City, México.
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