1
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Cárdenas-Rodríguez N, Ignacio-Mejía I, Correa-Basurto J, Carrasco-Vargas H, Vargas-Hernández MA, Albores-Méndez EM, Mayen-Quinto RD, De La Paz-Valente R, Bandala C. Possible Role of Cannabis in the Management of Neuroinflammation in Patients with Post-COVID Condition. Int J Mol Sci 2024; 25:3805. [PMID: 38612615 PMCID: PMC11012123 DOI: 10.3390/ijms25073805] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2024] [Revised: 02/27/2024] [Accepted: 02/28/2024] [Indexed: 04/14/2024] Open
Abstract
The post-COVID condition (PCC) is a pathology stemming from COVID-19, and studying its pathophysiology, diagnosis, and treatment is crucial. Neuroinflammation causes the most common manifestations of this disease including headaches, fatigue, insomnia, depression, anxiety, among others. Currently, there are no specific management proposals; however, given that the inflammatory component involves cytokines and free radicals, these conditions must be treated to reduce the current symptoms and provide neuroprotection to reduce the risk of a long-term neurodegenerative disease. It has been shown that cannabis has compounds with immunomodulatory and antioxidant functions in other pathologies. Therefore, exploring this approach could provide a viable therapeutic option for PCC, which is the purpose of this review. This review involved an exhaustive search in specialized databases including PubMed, PubChem, ProQuest, EBSCO, Scopus, Science Direct, Web of Science, and Clinical Trials. Phytocannabinoids, including cannabidiol (CBD), cannabigerol (CBG), and Delta-9-tetrahydrocannabinol (THC), exhibit significant antioxidative and anti-inflammatory properties and have been shown to be an effective treatment for neuroinflammatory conditions. These compounds could be promising adjuvants for PCC alone or in combination with other antioxidants or therapies. PCC presents significant challenges to neurological health, and neuroinflammation and oxidative stress play central roles in its pathogenesis. Antioxidant therapy and cannabinoid-based approaches represent promising areas of research and treatment for mitigating adverse effects, but further studies are needed.
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Affiliation(s)
| | - Iván Ignacio-Mejía
- Laboratorio de Medicina Traslacional, Escuela Militar de Graduados de Sanidad, UDEFA, Mexico City 11200, Mexico;
| | - Jose Correa-Basurto
- Laboratorio de Diseño y Desarrollo de Nuevos Fármacos e Innovación Biotecnológica, Escuela Superior de Medicina, Instituto Politécnico Nacional, Mexico City 11340, Mexico;
| | | | - Marco Antonio Vargas-Hernández
- Subdirección de Investigación, Escuela Militar de Graduados en Sanidad, UDEFA, Mexico City 11200, Mexico; (M.A.V.-H.); (E.M.A.-M.)
| | - Exal Manuel Albores-Méndez
- Subdirección de Investigación, Escuela Militar de Graduados en Sanidad, UDEFA, Mexico City 11200, Mexico; (M.A.V.-H.); (E.M.A.-M.)
| | | | - Reynita De La Paz-Valente
- Laboratorio de Medicina Traslacional Aplicada a Neurociencias, Enfermedades Crónicas y Emergentes, Escuela superior de Medicina, Instituto Politécnico Nacional, Mexico City 11340, Mexico;
| | - Cindy Bandala
- Laboratorio de Medicina Traslacional Aplicada a Neurociencias, Enfermedades Crónicas y Emergentes, Escuela superior de Medicina, Instituto Politécnico Nacional, Mexico City 11340, Mexico;
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2
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Briseño-Díaz P, Schnoor M, Bello-Ramirez M, Correa-Basurto J, Rojo-Domínguez A, Arregui L, Vega L, Núñez-González E, Palau-Hernández LA, Parra-Torres CG, García Córdova OM, Zepeda-Castilla E, Torices-Escalante E, Domínguez-Camacho L, Xoconostle-Cazares B, Meraz-Ríos MA, Delfín-Azuara S, Carrión-Estrada DA, Villegas-Sepúlveda N, Hernández-Rivas R, Thompson-Bonilla MDR, Vargas M. Synergistic effect of antagonists to KRas4B/PDE6 molecular complex in pancreatic cancer. Life Sci Alliance 2023; 6:e202302019. [PMID: 37813486 PMCID: PMC10561825 DOI: 10.26508/lsa.202302019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 09/20/2023] [Accepted: 09/25/2023] [Indexed: 10/12/2023] Open
Abstract
Pancreatic ductal adenocarcinoma (PDAC) has the worst prognosis among all human cancers as it is highly resistant to chemotherapy. K-Ras mutations usually trigger the development and progression of PDAC. We hypothesized that compounds stabilizing the KRas4B/PDE6δ complex could serve as PDAC treatments. Using in silico approaches, we identified the small molecules C14 and P8 that reduced K-Ras activation in primary PDAC cells. Importantly, C14 and P8 significantly prevented tumor growth in patient-derived xenotransplants. Combined treatment with C14 and P8 strongly increased cytotoxicity in PDAC cell lines and primary cultures and showed strong synergistic antineoplastic effects in preclinical murine PDAC models that were superior to conventional therapeutics without causing side effects. Mechanistically, C14 and P8 reduced tumor growth by inhibiting AKT and ERK signaling downstream of K-RAS leading to apoptosis, specifically in PDAC cells. Thus, combined treatment with C14 and P8 may be a superior pharmaceutical strategy to improve the outcome of PDAC.
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Affiliation(s)
- Paola Briseño-Díaz
- https://ror.org/009eqmr18 Department of Molecular Biomedicine, Center for Research and Advanced Studies of the National Polytechnic Institute (CINVESTAV-IPN), México City, Mexico
| | - Michael Schnoor
- https://ror.org/009eqmr18 Department of Molecular Biomedicine, Center for Research and Advanced Studies of the National Polytechnic Institute (CINVESTAV-IPN), México City, Mexico
| | - Martiniano Bello-Ramirez
- Laboratory of Molecular Modeling and Drug Design of the Higher School of Medicine, National Polytechnic Institute, Mexico City, Mexico
| | - Jose Correa-Basurto
- Laboratory of Molecular Modeling and Drug Design of the Higher School of Medicine, National Polytechnic Institute, Mexico City, Mexico
| | - Arturo Rojo-Domínguez
- Department of Natural Sciences, Metropolitan Autonomous University, Mexico City, Mexico
| | - Leticia Arregui
- Department of Natural Sciences, Metropolitan Autonomous University, Mexico City, Mexico
| | - Libia Vega
- https://ror.org/009eqmr18 Toxicology Department, Center for Research and Advanced Studies of the National Polytechnic Institute (CINVESTAV-IPN), Mexico City, Mexico
| | - Enrique Núñez-González
- Department of Surgical Oncology and General Surgery, Hospital 1 de Octubre, ISSSTE, Mexico City, Mexico
| | | | | | | | - Ernesto Zepeda-Castilla
- Department of Surgical Oncology and General Surgery, Hospital 1 de Octubre, ISSSTE, Mexico City, Mexico
| | - Eduardo Torices-Escalante
- Department of Surgical Oncology and General Surgery, Hospital 1 de Octubre, ISSSTE, Mexico City, Mexico
| | - Leticia Domínguez-Camacho
- Department of Surgical Oncology and General Surgery, Hospital 1 de Octubre, ISSSTE, Mexico City, Mexico
| | - Beatriz Xoconostle-Cazares
- https://ror.org/009eqmr18 Department of Biotechnology, Center for Research and Advanced Studies of the National Polytechnic Institute (CINVESTAV-IPN), México City, Mexico
| | - Marco Antonio Meraz-Ríos
- https://ror.org/009eqmr18 Department of Molecular Biomedicine, Center for Research and Advanced Studies of the National Polytechnic Institute (CINVESTAV-IPN), México City, Mexico
| | - Sandra Delfín-Azuara
- https://ror.org/009eqmr18 Department of Molecular Biomedicine, Center for Research and Advanced Studies of the National Polytechnic Institute (CINVESTAV-IPN), México City, Mexico
| | - Dayan Andrea Carrión-Estrada
- https://ror.org/009eqmr18 Department of Molecular Biomedicine, Center for Research and Advanced Studies of the National Polytechnic Institute (CINVESTAV-IPN), México City, Mexico
| | - Nicolas Villegas-Sepúlveda
- https://ror.org/009eqmr18 Department of Molecular Biomedicine, Center for Research and Advanced Studies of the National Polytechnic Institute (CINVESTAV-IPN), México City, Mexico
| | - Rosaura Hernández-Rivas
- https://ror.org/009eqmr18 Department of Molecular Biomedicine, Center for Research and Advanced Studies of the National Polytechnic Institute (CINVESTAV-IPN), México City, Mexico
| | | | - Miguel Vargas
- https://ror.org/009eqmr18 Department of Molecular Biomedicine, Center for Research and Advanced Studies of the National Polytechnic Institute (CINVESTAV-IPN), México City, Mexico
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3
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Méndez-Morales S, Pérez-De Marco J, Rodríguez-Cortés O, Flores-Mejía R, Martínez-Venegas M, Sánchez-Vera Y, Tamay-Cach F, Lomeli-Gonzaléz J, Emilio Reyes A, Lehman-Mendoza R, Martínez-Arredondo H, Vazquez-Dávila R, Torres-Roldan J, Correa-Basurto J, Arellano-Mendoza M. Diabetic neuropathy: Molecular approach a treatment opportunity. Vascul Pharmacol 2022; 143:106954. [DOI: 10.1016/j.vph.2022.106954] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Revised: 01/11/2022] [Accepted: 01/13/2022] [Indexed: 12/15/2022]
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4
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Marcos X, Méndez-Luna D, Fragoso-Vázquez M, Rosales-Hernández M, Correa-Basurto J. Anti-breast cancer activity of novel compounds loaded in polymeric mixed micelles: Characterization and in vitro studies. J Drug Deliv Sci Technol 2021. [DOI: 10.1016/j.jddst.2021.102815] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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5
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Romo-Perez A, Dominguez-Gomez G, Chavez-Blanco A, Taja-Chayeb L, Gonzalez-Fierro A, Martinez EG, Correa-Basurto J, Duenas-Gonzalez A. BAPST. A Combo of Common use drugs as metabolic therapy of cancer-a theoretical proposal. Curr Mol Pharmacol 2021; 15:815-831. [PMID: 34620071 DOI: 10.2174/1874467214666211006123728] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Revised: 08/16/2021] [Accepted: 09/01/2021] [Indexed: 12/24/2022]
Abstract
Advances in cancer therapy have yet to impact worldwide cancer mortality. Poor cancer drug affordability is one of the factors limiting mortality burden strikes. Up to now, cancer drug repurposing had no meet expectations concerning drug affordability. The three FDA-approved cancer drugs developed under repurposing -all-trans-retinoic acid, arsenic trioxide, and thalidomide- do not differ in price from other drugs developed under the classical model. Though additional factors affect the whole process from inception to commercialization, the repurposing of widely used, commercially available, and cheap drugs may help. This work reviews the concept of the malignant metabolic phenotype and its exploitation by simultaneously blocking key metabolic processes altered in cancer. We elaborate on a combination called BAPST, which stands for the following drugs and pathways they inhibit: Benserazide (glycolysis), Apomorphine (glutaminolysis), Pantoprazole (Fatty-acid synthesis), Simvastatin (mevalonate pathway), and Trimetazidine (Fatty-acid oxidation). Their respective primary indications are: • Parkinson's disease (benserazide and apomorphine). • Peptic ulcer disease (pantoprazole). • Hypercholesterolemia (simvastatin). • Ischemic heart disease (trimetazidine). When used for their primary indication, the literature review on each of these drugs shows they have a good safety profile and lack predicted pharmacokinetic interaction among them. Most importantly, the inhibitory enzymatic concentrations required for inhibiting their cancer targets enzymes are below the plasma concentrations observed when these drugs are used for their primary indication. Based on that, we propose that the regimen BAPTS merits preclinical testing.
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Affiliation(s)
- Adriana Romo-Perez
- Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Mexico City. Mexico
| | | | - Alma Chavez-Blanco
- Subdirección de Investigación Básica, Instituto Nacional de Cancerología, Mexico City. Mexico
| | - Lucia Taja-Chayeb
- Subdirección de Investigación Básica, Instituto Nacional de Cancerología, Mexico City. Mexico
| | - Aurora Gonzalez-Fierro
- Subdirección de Investigación Básica, Instituto Nacional de Cancerología, Mexico City. Mexico
| | | | - Jose Correa-Basurto
- Laboratorio de Diseño y Desarrollo de Nuevos Fármacos e Innovación Biotecnológica, Escuela Superior de Medicina, Instituto Politécnico Nacional, Mexico City. Mexico
| | - Alfonso Duenas-Gonzalez
- Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Mexico City. Mexico
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6
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Flores-Mejía R, Fragoso-Vázquez MJ, Pérez-Blas LG, Parra-Barrera A, Hernández-Castro SS, Estrada-Pérez AR, Rodrígues J, Lara-Padilla E, Ortiz-Morales A, Correa-Basurto J. Chemical characterization (LC-MS-ESI), cytotoxic activity and intracellular localization of PAMAM G4 in leukemia cells. Sci Rep 2021; 11:8210. [PMID: 33859258 PMCID: PMC8050087 DOI: 10.1038/s41598-021-87560-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Accepted: 03/23/2021] [Indexed: 02/08/2023] Open
Abstract
Generation 4 of polyamidoamine dendrimer (G4-PAMAM) has several biological effects due to its tridimensional globular structure, repetitive branched amides, tertiary amines, and amino-terminal subunit groups liked to a common core. G4-PAMAM is cytotoxic due to its positive charges. However, its cytotoxicity could increase in cancer cells due to the excessive intracellular negative charges in these cells. Furthermore, this work reports G4-PAMAM chemical structural characterization using UHPLC-QTOF-MS/MS (LC-MS) by electrospray ionization to measure its population according to its positive charges. Additionally, the antiproliferative effects and intracellular localization were explored in the HMC-1 and K-562 cell lines by confocal microscopy. The LC-MS results show that G4-PAMAM generated multivalent mass spectrum values, and its protonated terminal amino groups produced numerous positive charges, which allowed us to determine its exact mass despite having a high molecular weight. Additionally, G4-PAMAM showed antiproliferative activity in the HMC-1 tumor cell line after 24 h (IC50 = 16.97 µM), 48 h (IC50 = 7.02 µM) and 72 h (IC50 = 5.98 µM) and in the K-562 cell line after 24 h (IC50 = 15.14 µM), 48 h (IC50 = 14.18 µM) and 72 h (IC50 = 9.91 µM). Finally, our results showed that the G4-PAMAM dendrimers were located in the cytoplasm and nucleus in both tumor cell lines studied.
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Affiliation(s)
- R Flores-Mejía
- Laboratorio 103, Sección de Estudios de Posgrado e Investigación, Escuela Superior de Medicina, Instituto Politécnico Nacional, CDMX, Mexico
| | - M J Fragoso-Vázquez
- Departamento de Química Orgánica, Escuela Nacional de Ciencias Biológicas del Instituto Politécnico Nacional, Ciudad de México, Mexico.
| | - L G Pérez-Blas
- Laboratorio 103, Sección de Estudios de Posgrado e Investigación, Escuela Superior de Medicina, Instituto Politécnico Nacional, CDMX, Mexico
| | - A Parra-Barrera
- Laboratorio de Medicina Regenerativa y Estudios del Cancer, Sección de Estudios de Posgrado e Investigación, Escuela Superior de Medicina, Instituto Politécnico Nacional, CDMX, Mexico
| | - S S Hernández-Castro
- 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, 11340, Ciudad de México, Mexico
| | - A R Estrada-Pérez
- 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, 11340, Ciudad de México, Mexico
| | - J Rodrígues
- CQM - Centro de Química da Madeira, Universidade da Madeira, Campus Universitário da Penteada, 9020-105, Funchal, Portugal
- School of Materials Science and Engineering/Center for Nano Energy Materials, Northwestern Polytechnical University, Xi'an, 710072, China
| | - E Lara-Padilla
- Laboratorio de Bioquímica de la Escuela Superior de Medicina, Instituto Politécnico Nacional, Ciudad de México, Mexico
| | - A Ortiz-Morales
- Laboratorio 103, Sección de Estudios de Posgrado e Investigación, Escuela Superior de Medicina, Instituto Politécnico Nacional, CDMX, Mexico
| | - J 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, 11340, Ciudad de México, Mexico.
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7
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Flores-Mejía R, Fragoso-Vázquez MJ, Pérez-Blas LG, Parra-Barrera A, Hernández-Castro SS, Estrada-Pérez AR, Rodrígues J, Lara-Padilla E, Ortiz-Morales A, Correa-Basurto J. Chemical characterization (LC–MS–ESI), cytotoxic activity and intracellular localization of PAMAM G4 in leukemia cells. Sci Rep 2021. [DOI: https://doi.org/10.1038/s41598-021-87560-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
AbstractGeneration 4 of polyamidoamine dendrimer (G4-PAMAM) has several biological effects due to its tridimensional globular structure, repetitive branched amides, tertiary amines, and amino-terminal subunit groups liked to a common core. G4-PAMAM is cytotoxic due to its positive charges. However, its cytotoxicity could increase in cancer cells due to the excessive intracellular negative charges in these cells. Furthermore, this work reports G4-PAMAM chemical structural characterization using UHPLC-QTOF-MS/MS (LC–MS) by electrospray ionization to measure its population according to its positive charges. Additionally, the antiproliferative effects and intracellular localization were explored in the HMC-1 and K-562 cell lines by confocal microscopy. The LC–MS results show that G4-PAMAM generated multivalent mass spectrum values, and its protonated terminal amino groups produced numerous positive charges, which allowed us to determine its exact mass despite having a high molecular weight. Additionally, G4-PAMAM showed antiproliferative activity in the HMC-1 tumor cell line after 24 h (IC50 = 16.97 µM), 48 h (IC50 = 7.02 µM) and 72 h (IC50 = 5.98 µM) and in the K-562 cell line after 24 h (IC50 = 15.14 µM), 48 h (IC50 = 14.18 µM) and 72 h (IC50 = 9.91 µM). Finally, our results showed that the G4-PAMAM dendrimers were located in the cytoplasm and nucleus in both tumor cell lines studied.
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8
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Martínez-Archundia M, Hernández Mojica TG, Correa-Basurto J, Montaño S, Camacho-Molina A. Molecular dynamics simulations reveal structural differences among wild-type NPC1 protein and its mutant forms. J Biomol Struct Dyn 2019; 38:3527-3532. [DOI: 10.1080/07391102.2019.1664324] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Affiliation(s)
- M. Martínez-Archundia
- Laboratorio de Modelado Molecular, Bioinformática y Diseño de fármacos, Sección de Estudios de Posgrado e Investigación, Escuela Superior de Medicina, Instituto Politécnico Nacional, México City, México
| | - T. G. Hernández Mojica
- Departamento de Genética, Instituto Nacional de Neurología y Neurocirugía Manuel Velasco Suárez, Secretaría de Salud, Mexico City, México, Facultad de Ciencias Químico Biológicas
| | - J. Correa-Basurto
- Laboratorio de Modelado Molecular, Bioinformática y Diseño de fármacos, Sección de Estudios de Posgrado e Investigación, Escuela Superior de Medicina, Instituto Politécnico Nacional, México City, México
| | - S. Montaño
- Universidad Autónoma de Sinaloa, Culiacán, Sinaloa, México
| | - A. Camacho-Molina
- Departamento de Genética, Instituto Nacional de Neurología y Neurocirugía Manuel Velasco Suárez, Secretaría de Salud, Mexico City, México, Facultad de Ciencias Químico Biológicas
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9
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Castro-Silva ES, Bello M, Hernández-Rodríguez M, Correa-Basurto J, Murillo-Álvarez JI, Rosales-Hernández MC, Muñoz-Ochoa M. In vitro and in silico evaluation of fucosterol from Sargassum horridum as potential human acetylcholinesterase inhibitor. J Biomol Struct Dyn 2019; 37:3259-3268. [PMID: 30088792 DOI: 10.1080/07391102.2018.1505551] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2018] [Accepted: 07/21/2018] [Indexed: 02/07/2023]
Abstract
The fucosterol has been reported numerous biological activities. In this study, the activity in vitro of the fucosterol from Sargassum horridum as potential human acetylcholinesterase inhibitor was evaluated. The structural identification was obtained by nuclear magnetic resonance (NMR) spectroscopy and based on experimental data, we combined docking and molecular dynamics simulations coupled to the molecular-mechanics-generalized-born-surface-area approach to evaluating the structural and energetic basis for the molecular recognition of fucosterol and neostigmine at the binding site of acetylcholinesterase (AChE). In addition, the Lineweaver-Burk plot showed the nature of a non-competitive inhibition. The maximum velocity (Vmax) and the constant of Michaelis-Menten (Km) estimated for fucosterol (0.006 µM) were 0.015 1/Vo (ΔA/h and 6.399 1/[ACh] mM-1, respectively. While, for neostigmine (0.14 µM), the Vmax was 0.022 1/Vo (ΔA/h) and Km of 6.726 1/[ACh] mM-1, these results showed a more effective inhibition by fucosterol respect to neostigmine. Structural analysis revealed that neostigmine reaches the AChE binding site reported elsewhere, whereas fucosterol can act as a no-competitive and competitive acetylcholinesterase inhibitor, in agree with kinetic enzymatic experiments. Binding free energy calculations revealed that fucosterol reaches the acetylcholinesterase binding site with higher affinity than neostigmine, which is according to experimental results. Whereas the per-residue decomposition free energy analysis let us identify crucial residues involved in the molecular recognition of ligands by AChE. Results corroborate the ability of theoretical methods to provide crucial information at the atomic level about energetic and structural differences in the binding interaction and affinity from fucosterol with AChE. Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- E S Castro-Silva
- a Laboratorio de Química de Macroalgas, Centro Interdisciplinario de Ciencias Marinas , Instituto Politécnico Nacional , La Paz , Mexico
| | - M Bello
- b Laboratorio de Modelado Molecular, Bioinformática y Diseño de Fármacos , Instituto Politécnico Nacional , Ciudad de México , Mexico
| | - M Hernández-Rodríguez
- c Laboratorio de Biofísica y Biocatálisis, Escuela Superior de Medicina , Instituto Politécnico Nacional , Ciudad de México , Mexico
| | - J Correa-Basurto
- b Laboratorio de Modelado Molecular, Bioinformática y Diseño de Fármacos , Instituto Politécnico Nacional , Ciudad de México , Mexico
| | - J I Murillo-Álvarez
- a Laboratorio de Química de Macroalgas, Centro Interdisciplinario de Ciencias Marinas , Instituto Politécnico Nacional , La Paz , Mexico
| | - M C Rosales-Hernández
- c Laboratorio de Biofísica y Biocatálisis, Escuela Superior de Medicina , Instituto Politécnico Nacional , Ciudad de México , Mexico
| | - M Muñoz-Ochoa
- a Laboratorio de Química de Macroalgas, Centro Interdisciplinario de Ciencias Marinas , Instituto Politécnico Nacional , La Paz , Mexico
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Martinez-Archundia M, Colin-Astudillo B, Gómez-Hernández L, Abarca-Rojano E, Correa-Basurto J. Docking analysis provide structural insights to design novel ligands that target PKM2 and HDC8 with potential use for cancer therapy. Molecular Simulation 2019. [DOI: 10.1080/08927022.2019.1579326] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Affiliation(s)
- M. Martinez-Archundia
- Laboratorio de Diseño y Desarrollo de Nuevos Fármacos e Innovación Biotécnológica, Escuela Superior de Medicina, Instituto Politécnico Nacional, México D.F., Mexico
| | - B. Colin-Astudillo
- Laboratorio de Diseño y Desarrollo de Nuevos Fármacos e Innovación Biotécnológica, Escuela Superior de Medicina, Instituto Politécnico Nacional, México D.F., Mexico
- Sección de Posgrado e Investigación, Escuela Superior de Medicina, Instituto Politécnico Nacional, Distrito Federal, México
| | - L. Gómez-Hernández
- Sección de Posgrado e Investigación, Escuela Superior de Medicina, Instituto Politécnico Nacional, Distrito Federal, México
| | - E. Abarca-Rojano
- Sección de Posgrado e Investigación, Escuela Superior de Medicina, Instituto Politécnico Nacional, Distrito Federal, México
| | - J. Correa-Basurto
- Laboratorio de Diseño y Desarrollo de Nuevos Fármacos e Innovación Biotécnológica, Escuela Superior de Medicina, Instituto Politécnico Nacional, México D.F., Mexico
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11
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Andrade-Ochoa S, Correa-Basurto J, Rodríguez-Valdez LM, Sánchez-Torres LE, Nogueda-Torres B, Nevárez-Moorillón GV. In vitro and in silico studies of terpenes, terpenoids and related compounds with larvicidal and pupaecidal activity against Culex quinquefasciatus Say (Diptera: Culicidae). Chem Cent J 2018; 12:53. [PMID: 29748726 PMCID: PMC5945571 DOI: 10.1186/s13065-018-0425-2] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2017] [Accepted: 04/30/2018] [Indexed: 11/10/2022] Open
Abstract
Background In order to develop new larvicidal agents derived from phytochemicals, the larvicidal activity of fifty molecules that are constituent of essential oils was evaluated against Culex quinquefasciatus Say. Terpenes, terpenoids and phenylpropanoids molecules were included in the in vitro evaluation, and QSAR models using genetic algorithms were built to identify molecular and structural properties of biological interest. Further, to obtain structural details on the possible mechanism of action, selected compounds were submitted to docking studies on sterol carrier protein-2 (SCP-2) as possible target. Results Results showed high larvicidal activity of carvacrol and thymol on the third and fourth larval stage with a median lethal concentration (LC50) of 5.5 and 11.1 µg/mL respectively. Myrcene and carvacrol were highly toxic for pupae, with LC50 values of 31.8 and 53.2 µg/mL. Structure–activity models showed that the structural property π-bonds is the largest contributor of larvicidal activity while ketone groups should be avoided. Similarly, property–activity models attributed to the molecular descriptor LogP the most contribution to larvicidal activity, followed by the absolute total charge (Qtot) and molar refractivity (AMR). The models were statistically significant; thus the information contributes to the design of new larvicidal agents. Docking studies show that all molecules tested have the ability to interact with the SCP-2 protein, wherein α-humulene and β-caryophyllene were the compounds with higher binding energy. Conclusions The description of the molecular properties and the structural characteristics responsible for larvicidal activity of the tested compounds were used for the development of mathematical models of structure–activity relationship. The identification of molecular and structural descriptors, as well as studies of molecular docking on the SCP-2 protein, provide insight on the mechanism of action of the active molecules, and the information can be used for the design of new structures for synthesis as potential new larvicidal agents. Electronic supplementary material The online version of this article (10.1186/s13065-018-0425-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- S Andrade-Ochoa
- Facultad de Ciencias Químicas, Universidad Autónoma de Chihuahua, Circuito Universitario S/N, Campus Universitario II., Chihuahua, Chihuahua, Mexico.,Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Prolongación de Carpio y Plan de Ayala S/N. Col. Santo Tomas, 11340, México, DF, Mexico
| | - J Correa-Basurto
- 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, México, DF, Mexico
| | - L M Rodríguez-Valdez
- Facultad de Ciencias Químicas, Universidad Autónoma de Chihuahua, Circuito Universitario S/N, Campus Universitario II., Chihuahua, Chihuahua, Mexico
| | - L E Sánchez-Torres
- Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Prolongación de Carpio y Plan de Ayala S/N. Col. Santo Tomas, 11340, México, DF, Mexico
| | - B Nogueda-Torres
- Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Prolongación de Carpio y Plan de Ayala S/N. Col. Santo Tomas, 11340, México, DF, Mexico
| | - G V Nevárez-Moorillón
- Facultad de Ciencias Químicas, Universidad Autónoma de Chihuahua, Circuito Universitario S/N, Campus Universitario II., Chihuahua, Chihuahua, Mexico.
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Sarmiento V, Ramirez-Sanchez I, Moreno-Ulloa A, Romero-Perez D, Chávez D, Ortiz M, Najera N, Correa-Basurto J, Villarreal F, Ceballos G. Synthesis of novel (-)-epicatechin derivatives as potential endothelial GPER agonists: Evaluation of biological effects. Bioorg Med Chem Lett 2018; 28:658-663. [PMID: 29395974 PMCID: PMC5817025 DOI: 10.1016/j.bmcl.2018.01.025] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2017] [Revised: 01/11/2018] [Accepted: 01/16/2018] [Indexed: 01/20/2023]
Abstract
To potentially identify proteins that interact (i.e. bind) and may contribute to mediate (-)-epicatechin (Epi) responses in endothelial cells we implemented the following strategy: 1) synthesis of novel Epi derivatives amenable to affinity column use, 2) in silico molecular docking studies of the novel derivatives on G protein-coupled estrogen receptor (GPER), 3) biological assessment of the derivatives on NO production, 4) implementation of an immobilized Epi derivative affinity column and, 5) affinity column based isolation of Epi interacting proteins from endothelial cell protein extracts. For these purposes, the Epi phenol and C3 hydroxyl groups were chemically modified with propargyl or mesyl groups. Docking studies of the novel Epi derivatives on GPER conformers at 14 ns and 70 ns demostrated favorable thermodynamic interactions reaching the binding site. Cultures of bovine coronary artery endothelial cells (BCAEC) treated with Epi derivatives stimulated NO production via Ser1179 phosphorylation of eNOS, effects that were attenuated by the use of the GPER blocker, G15. Epi derivative affinity columns yielded multiple proteins from BCAEC. Proteins were electrophoretically separated and inmmunoblotting analysis revealed GPER as an Epi derivative binding protein. Altogether, these results validate the proposed strategy to potentially isolate and identify novel Epi receptors that may account for its biological activity.
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Affiliation(s)
| | - Israel Ramirez-Sanchez
- Escuela Superior de Medicina del Instituto Politécnico Nacional, Sección de Posgrado, Mexico
| | - Aldo Moreno-Ulloa
- Departamento de Innovación Biomédica, Centro de Investigación Científica y de Educación Superior de Ensenada (CICESE), BC, Mexico
| | | | - Daniel Chávez
- Centro de Graduados e Investigación en Química del Instituto Tecnológico de Tijuana, Apartado Postal 1166, Tijuana, BC 22510, Mexico
| | - Miguel Ortiz
- Escuela Superior de Medicina del Instituto Politécnico Nacional, Sección de Posgrado, Mexico
| | - Nayelli Najera
- Escuela Superior de Medicina del Instituto Politécnico Nacional, Sección de Posgrado, Mexico
| | - Jose Correa-Basurto
- Escuela Superior de Medicina del Instituto Politécnico Nacional, Sección de Posgrado, Mexico
| | | | - Guillermo Ceballos
- Escuela Superior de Medicina del Instituto Politécnico Nacional, Sección de Posgrado, Mexico.
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Martínez-Archundia M, Bello M, Correa-Basurto J. Design of Drugs by Filtering Through ADMET, Physicochemical and Ligand-Target Flexibility Properties. Methods Mol Biol 2018; 1824:403-416. [PMID: 30039421 DOI: 10.1007/978-1-4939-8630-9_24] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
There is a synergistic interaction between medicinal chemistry, chemoinformatics, and bioinformatics. The last one includes analyses of sequences as well as structural analysis which employ computational techniques such as docking studies and molecular dynamics (MD) simulations. Over the last years these techniques have allowed the development of new accurate computational tools for drug design. As a result, there have been an increased number of publications where computational methods such as pharmacophore modeling, de novo drug design, evaluation of physicochemical properties, and analysis of ADMET (absorption, distribution, metabolism, excretion, and toxicity) properties have been quite useful for eliminating the compounds with poor physicochemical or toxicological properties. Furthermore, using MD simulations and docking analysis, it is possible to estimate the binding energy of the protein-ligand complexes by using scoring functions, as well as to structurally depict the binding pose of the compounds on proteins, in order to select the best evaluated compounds for subsequent synthetizing and evaluation through biological assays. In this work, we describe some computational tools that have been used for structure-based drug design of new compounds that target histone deacetylases (HDACs), which are known to be potential targets in cancer and parasitic diseases.
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Affiliation(s)
- Marlet Martínez-Archundia
- Laboratorio de Modelado Molecular, Bioinformática y Diseño de Fármacos, de la 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., Ciudad de México, Mexico
| | - 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 Díaz Mirón s/n, Col. Casco de Santo Tomas, Delegación Miguel Hidalgo, C.P., Ciudad de México, Mexico.
| | - Jose Correa-Basurto
- Laboratorio de Modelado Molecular, Bioinformática y Diseño de Fármacos, de la 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., Ciudad de México, Mexico.
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Rodríguez-Fonseca RA, Sixto-López Y, Fragoso-Vázquez MJ, Flores-Mejía R, Cabrera-Pérez LC, Vázquez-Moctezuma I, Rosales-Hernández MC, Bello M, Martínez-Archundia M, Trujillo-Ferrara JG, Becerra-Martínez E, Correa-Basurto J. Design, Synthesis and Biological Evaluation of a Phenyl Butyric Acid Derivative, N-(4-chlorophenyl)-4-phenylbutanamide: A HDAC6 Inhibitor with Anti-proliferative Activity on Cervix Cancer and Leukemia Cells. Anticancer Agents Med Chem 2017; 17:1441-1454. [PMID: 28044941 DOI: 10.2174/1871520617666170103092851] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2016] [Revised: 10/16/2016] [Accepted: 12/24/2016] [Indexed: 11/22/2022]
Abstract
BACKGROUND The epigenetic regulation of genes in cancer could be targeted by inhibiting Histone deacetylase 6 (HDAC6), an enzyme involved in several types of cancer such as lymphoma, leukemia, ovarian cancer, etc. OBJECTIVE Through in silico methods, a set of Phenyl butyric acid derivatives with possible HDAC6 inhibitory activity were designed, rendering monophenylamides and biphenylamides using tubacin (HDAC6 selective inhibitor) as reference. METHOD The target compounds were submitted to theoretical ADMET analyses and their binding properties on different HDAC6 conformers were evaluated through docking calculations. RESULTS These in silico studies allowed us to identify a compound named B-R2B. In order to have more information about the B-R2B binding recognition properties on HDAC6, the B-R2B-HDAC6 complex was submitted through 100 ns-long Molecular Dynamics (MD) simulation coupled to MMGBSA approach, revealing that B-R2B is located at the entrance of HDAC6 active pocket, blocking the passage of the substrate without reaching the HDAC6 binding site. Based on these results, B-R2B was synthesized, characterized and biologically tested. The HDAC6 fluorometric drug discovery kit Fluor-de-Lys (ENZO Life Sciences Inc.) was used to determine the HDAC6 human inhibitory activity (IC50 value) of B-R2B compound. In addition, B-R2B show IC50 values on cancer cell lines (HeLa; IC50 = 72.6 µM), acute myeloid leukemia (THP-1; IC50 = 16.5 µM), human mast leukemia (HMC; IC50 = 79.29 µM) and chronic myelogenous leukemia (Kasumi; IC50 = 101 µM). CONCLUSION These results show that B-R2B is a HDAC6 inhibitor, specifically a non-competitive type in a similar way that tubacin does, according to MD simulations.
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Affiliation(s)
- Rolando Alberto Rodríguez-Fonseca
- Laboratorio de Modelado Molecular, Diseno de farmacos y Bioinformatica, Escuela Superior de Medicina, Instituto Politecnico Nacional, Mexico, Plan de San Luis y Salvador Diaz Miron S/N, Col. Casco de Santo Tomas, Distrito Federal 11340. Mexico
| | - Yudibeth Sixto-López
- Laboratorio de Modelado Molecular, Diseno de farmacos y Bioinformatica, Escuela Superior de Medicina, Instituto Politecnico Nacional, Mexico, Plan de San Luis y Salvador Diaz Miron S/N, Col. Casco de Santo Tomas, Distrito Federal 11340. Mexico
| | - M Jonathan Fragoso-Vázquez
- Departamento de Quimica Organica, Escuela Nacional de Ciencias, Biologicas, Instituto Politecnico Nacional, Prolongacion de Carpio y Plan de Ayala, Col. Casco de Santo Thomas, Mexico City 11340. Mexico
| | - Raul Flores-Mejía
- Laboratorio de Inmunologia Medica, Escuela Superior de Medicina, Instituto Politecnico Nacional, Unidad Profesional Lazaro Cardenas, Avenida Salvador Diaz Miron s/n esquina Plan de San Luis, Col. Santo Tomas, Delegación Miguel Hidalgo 11340, Distrito Federal. Mexico
| | - Laura Cristina Cabrera-Pérez
- Laboratorio de Modelado Molecular, Diseno de farmacos y Bioinformatica, Escuela Superior de Medicina, Instituto Politecnico Nacional, Mexico, Plan de San Luis y Salvador Diaz Miron S/N, Col. Casco de Santo Tomas, Distrito Federal 11340. Mexico
| | - Ismael Vázquez-Moctezuma
- Laboratorio de Modelado Molecular, Diseno de farmacos y Bioinformatica, Escuela Superior de Medicina, Instituto Politecnico Nacional, Mexico, Plan de San Luis y Salvador Diaz Miron S/N, Col. Casco de Santo Tomas, Distrito Federal 11340. Mexico
| | - Martha Cecilia Rosales-Hernández
- Laboratorio de Modelado Molecular, Diseno de farmacos y Bioinformatica, Escuela Superior de Medicina, Instituto Politecnico Nacional, Mexico, Plan de San Luis y Salvador Diaz Miron S/N, Col. Casco de Santo Tomas, Distrito Federal 11340. Mexico
| | - Martiniano Bello
- Laboratorio de Modelado Molecular, Diseno de farmacos y Bioinformatica, Escuela Superior de Medicina, Instituto Politecnico Nacional, Mexico, Plan de San Luis y Salvador Diaz Miron S/N, Col. Casco de Santo Tomas, Distrito Federal 11340. Mexico
| | - M Martínez-Archundia
- Laboratorio de Modelado Molecular, Diseno de farmacos y Bioinformatica, Escuela Superior de Medicina, Instituto Politecnico Nacional, Mexico, Plan de San Luis y Salvador Diaz Miron S/N, Col. Casco de Santo Tomas, Distrito Federal 11340. Mexico
| | - Jose Guadalupe Trujillo-Ferrara
- Laboratorio de Modelado Molecular, Diseno de farmacos y Bioinformatica, Escuela Superior de Medicina, Instituto Politecnico Nacional, Mexico, Plan de San Luis y Salvador Diaz Miron S/N, Col. Casco de Santo Tomas, Distrito Federal 11340. Mexico
| | - Elvia Becerra-Martínez
- Centro de Nanociencias y Micro y Nanotecnologias (CNMN) del Instituto Politecnico Nacional, Av. Luis Enrique Erro S/N, Unidad Profesional Adolfo Lopez Mateos, Col. Zacatenco, Distrito Federal 07738. Mexico
| | - Jose Correa-Basurto
- Laboratorio de Modelado Molecular, Diseno de farmacos y Bioinformatica, Escuela Superior de Medicina, Instituto Politecnico Nacional, Mexico, Plan de San Luis y Salvador Diaz Miron S/N, Col. Casco de Santo Tomas, Distrito Federal 11340. Mexico
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Correa-Basurto J. Editorial: Pharmaceutical Applications of Dendrimers. Curr Pharm Des 2017; 23:3047. [PMID: 28990500 DOI: 10.2174/138161282321170830122757] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Affiliation(s)
- Jose Correa-Basurto
- Laboratorio de Modelado Molecular y Diseño de Fármacos (Laboratory of Molecular Modelling and Drug Design), Escuela Superior de Medicina del Instituto Politécnico Nacional, Plan de San Luis y Salvador Díaz Mirón s/n, Casco de Santo Tomás, Mexico city, 11340. Mexico
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Martínez-Pacheco H, Ramírez-Galicia G, Vergara-Arias M, Gertsch J, Fragoso-Vazquez JM, Mendez-Luna D, Abujamra AL, Cristina CPL, Cecilia RHM, Mendoza-Lujambio I, Correa-Basurto J. Docking and QSAR Studies of Aryl-valproic Acid Derivatives to Identify Antiproliferative Agents Targeting the HDAC8. Anticancer Agents Med Chem 2017; 17:927-940. [PMID: 27774878 DOI: 10.2174/1871520616666161019143219] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2016] [Revised: 09/30/2016] [Accepted: 10/04/2016] [Indexed: 11/22/2022]
Abstract
BACKGROUND Histone deacetylase 8 (HDAC8) is a plausible target for the development of novel anticancer drugs using a metal-chelating group and hydrophobic moieties as pharmacophores. It is known that valproic acid (administered as its salt, sodium valproate; VPANa+) is an HDAC8 inhibitor characterized by its hydrophobic chains. Nevertheless, VPA is hepatotoxic and VPA analogues might be explored for less hepatotoxic antiproliferative compounds. METHOD In this work, docking and QSAR studies of 500 aryl-VPA derivatives as possible HDAC8 inhibitors were performed in order to explore and select potential anti-proliferative compounds. Docking results identified π-π, hydrogen bonds as the most important noncovalent interactions between HDAC8 (PDB: 3F07) and the ligands tested, whereas Belm4 was the best QSAR descriptor and classified as a 2D-BCUT descriptor. RESULT Based on theoretical studies, compound DAVP042 was synthesized and evaluated in vitro for its antiproliferative activities on several cancer cell lines (A549-lung, MCF-7-breast, HCT116-colon and U937- lymphoid tissue) in comparison to VPA, as well as for its inhibitory activity on HDAC8 using in vitro models. DAVP042 demonstrated to have antiproliferative activity on all cancer cell lines employed, not only suggesting that this compound should be further studied, but also demonstrating that the methodology herein employed is appropriated to identify new therapeutic candidates.
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Affiliation(s)
- Heidy Martínez-Pacheco
- Universidad del Papaloapan, Circuito Central 200, Parque Industrial, 68301 Tuxtepec, Oaxaca. Mexico
| | - Guillermo Ramírez-Galicia
- Instituto de Química Aplicada, Universidad del Papaloapan, Circuito Central 200, Parque Industrial, 68301 Tuxtepec, Oaxaca. Mexico
| | - Midalia Vergara-Arias
- Laboratorio de Modelado Molecular y Diseño de Fármacos (Laboratory of Molecular Modelling and Drug Design), Escuela Superior de Medicina del Instituto Politécnico Nacional, Plan de San Luis y Salvador Díaz Mirón s/n, Casco de Santo Tomás, Mexico City, 11340. Mexico
| | - Jurg Gertsch
- Institute of Biochemistry and Molecular Medicine, NCCR TransCure, University of Bern, CH-3012 Bern. Switzerland
| | - Jonathan Manuel Fragoso-Vazquez
- Departamento de Química Orgánica, Escuela Nacional de Ciencias, Biológicas, Instituto Politécnico Nacional, Prolongación de Carpio y Plan de Ayala, Col. Casco de Santo Thomas. Mexico
| | - David Mendez-Luna
- Laboratorio de Modelado Molecular y Diseño de Fármacos (Laboratory of Molecular Modelling and Drug Design), Escuela Superior de Medicina del Instituto Politécnico Nacional, Plan de San Luis y Salvador Díaz Mirón s/n, Casco de Santo Tomás, Mexico City, 11340. Mexico
| | - A L Abujamra
- Graduate Program in Biotechnology, UNIVATES, Rio Grande do Sul. Brazil
| | - Cabrera-Perez Laura Cristina
- Laboratorio de Modelado Molecular y Diseño de Fármacos (Laboratory of Molecular Modelling and Drug Design), Escuela Superior de Medicina del Instituto Politécnico Nacional, Plan de San Luis y Salvador Díaz Mirón s/n, Casco de Santo Tomás, Mexico City, 11340. Mexico
| | - Rosales-Hernandez Martha Cecilia
- Laboratorio de Modelado Molecular y Diseño de Fármacos (Laboratory of Molecular Modelling and Drug Design), Escuela Superior de Medicina del Instituto Politécnico Nacional, Plan de San Luis y Salvador Díaz Mirón s/n, Casco de Santo Tomás, Mexico City, 11340. Mexico
| | - I Mendoza-Lujambio
- Laboratorio de Modelado Molecular y Diseño de Fármacos (Laboratory of Molecular Modelling and Drug Design), Escuela Superior de Medicina del Instituto Politécnico Nacional, Plan de San Luis y Salvador Díaz Mirón s/n, Casco de Santo Tomás, Mexico City, 11340. Mexico
| | - Jose Correa-Basurto
- Laboratorio de Modelado Molecular y Diseño de Fármacos (Laboratory of Molecular Modelling and Drug Design), Escuela Superior de Medicina del Instituto Politécnico Nacional, Plan de San Luis y Salvador Díaz Mirón s/n, Casco de Santo Tomás, Mexico City, 11340. Mexico
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Andrade-Ochoa S, García-Machorro J, Bello M, Rodríguez-Valdez L, Flores-Sandoval C, Correa-Basurto J. QSAR, DFT and molecular modeling studies of peptides from HIV-1 to describe their recognition properties by MHC-I. J Biomol Struct Dyn 2017; 36:2312-2330. [DOI: 10.1080/07391102.2017.1352538] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
- S. Andrade-Ochoa
- Laboratorio de Modelado Molecular, Bioinformática y Diseño de Fármacos, de la 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
- Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Prolongación de Carpio y Plan de Ayala S/N, Col. Santo Tomas 11340, Ciudad de México, Mexico
| | - J. García-Machorro
- Laboratorio de Medicina de Conservación, de la 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
| | - 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 Díaz Mirón s/n, Col. Casco de Santo Tomas, Delegación Miguel Hidalgo, C.P. 11340, Ciudad de México, Mexico
| | - L.M. Rodríguez-Valdez
- Facultad de Ciencias Químicas, Universidad Autónoma de Chihuahua, Circuito Universitario s/n, C.P. 31125, Chihuahua, Chih, Mexico
| | - C.A. Flores-Sandoval
- Instituto Mexicano del Petróleo, Eje Central Lázaro Cárdenas 152, Col. San Bartolo Atepehuacan 07730, Ciudad de México, Mexico
| | - J. Correa-Basurto
- Laboratorio de Modelado Molecular, Bioinformática y Diseño de Fármacos, de la 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
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Martínez-Ramos F, Luna-Palencia GR, Vásquez-Moctezuma I, Méndez-Luna D, Fragoso-Vázquez MJ, Trujillo-Ferrara J, Meraz-Ríos MA, Mendieta-Wejebe JE, Correa-Basurto J. Docking Studies of Glutamine Valproic Acid Derivative (S)-5- amino-2-(heptan-4-ylamino)-5-oxopentanoic Acid (Gln-VPA) on HDAC8 with Biological Evaluation in HeLa Cells. Anticancer Agents Med Chem 2017; 16:1485-1490. [PMID: 26845132 DOI: 10.2174/1871520616666160204111158] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2015] [Revised: 12/12/2015] [Accepted: 02/02/2016] [Indexed: 11/22/2022]
Abstract
In this contribution, we focused on evaluating a novel compound developed by our group. This molecule, derived from glutamine (Gln) and valproic acid (VPA), denominated (S)- 5-amino-2-(heptan-4-ylamino)-5-oxopentanoic acid (Gln-VPA), was submitted to docking studies on histone deacetylase 8 (HDAC8) to explore its non-bonded interactions. The theoretical results were validated in HeLa cells as a cancer cell model and in human dermal fibroblasts as a normal cell model. The effects of Gln-VPA on HeLa and normal fibroblasts in terms of cell survival and the ability to inhibit HDAC activity in nude nuclear proteins and in nuclear proteins of whole cells treated for 24 h were analyzed. The HeLa cell cycle was analyzed after 24 and 48 h of treatment with Gln-VPA. The docking studies show that Gln-VPA can reach the catalytic site of HDAC8. Gln-VPA was organically synthesized with a purity greater than 97%, and its structure was validated using mass spectrometry, nuclear magnetic resonance and infrared spectroscopy. Gln-VPA showed a similar effect to VPA as an HDAC inhibitor but with less toxicity to fibroblasts. Although Gln-VPA was less efficient than VPA in reducing the survival of HeLa cells, it could be studied for use as a cancer cell sensitizer.
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Affiliation(s)
| | | | | | | | | | | | | | | | - J Correa-Basurto
- Laboratorio de Bioquímica, Laboratorio de Modelado Molecular, Bioinformática y Diseño de Fármacos de la Escuela Superior de Medicina, Instituto Politécnico Nacional, Plan de San Luis y Díaz Mirón s/n, Casco de Santo Tomás, Distrito Federal, 11340, México
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Tamay-Cach F, L. Villa-Tanaca M, G. Trujillo-Ferrara J, Alemán-González-Duhart D, C. Quintana-Pérez J, A. González-Ramírez I, Correa-Basurto J. In Silico Studies Most Employed in the Discovery of New Antimicrobial Agents. Curr Med Chem 2016; 23:3360-3373. [DOI: 10.2174/0929867323666160210141912] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2015] [Revised: 02/10/2016] [Accepted: 05/19/2016] [Indexed: 11/22/2022]
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Correa-Basurto J. Meet Our Editorial Board Member. Anticancer Agents Med Chem 2016. [DOI: 10.2174/187152061608160712190331] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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Hernandez-Flores A, Almaraz-Barrera MDJ, Lozano-Amado D, Correa-Basurto J, Rojo-Dominguez A, Luna-Rivera E, Schnoor M, Guillen N, Hernandez-Rivas R, Vargas M. A new nucleocytoplasmic RhoGAP protein contributes to control the pathogenicity ofEntamoeba histolyticaby regulating EhRacC and EhRacD activity. Cell Microbiol 2016; 18:1653-1672. [DOI: 10.1111/cmi.12603] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2015] [Revised: 03/29/2016] [Accepted: 04/18/2016] [Indexed: 11/30/2022]
Affiliation(s)
- Araceli Hernandez-Flores
- Department of Molecular Biomedicine; Center of Research and Advanced Studies of the I.P.N; Mexico City, D.F. Mexico
| | - Ma de Jesus Almaraz-Barrera
- Department of Molecular Biomedicine; Center of Research and Advanced Studies of the I.P.N; Mexico City, D.F. Mexico
| | - Daniela Lozano-Amado
- Department of Molecular Biomedicine; Center of Research and Advanced Studies of the I.P.N; Mexico City, D.F. Mexico
| | - Jose Correa-Basurto
- High School of Medicine of the I.P.N; Molecular Modeling Laboratory and Drug Design; Mexico City, D.F. Mexico
| | - Arturo Rojo-Dominguez
- Cuajimalpa Unit., Department of Natural Sciences; Metropolitan Autonomous University; Mexico City, D.F. Mexico
| | - Eva Luna-Rivera
- Department of Molecular Biomedicine; Center of Research and Advanced Studies of the I.P.N; Mexico City, D.F. Mexico
| | - Michael Schnoor
- Department of Molecular Biomedicine; Center of Research and Advanced Studies of the I.P.N; Mexico City, D.F. Mexico
| | - Nancy Guillen
- Institut Pasteur; Department of Cell Biology and Infection; Paris France
| | - Rosaura Hernandez-Rivas
- Department of Molecular Biomedicine; Center of Research and Advanced Studies of the I.P.N; Mexico City, D.F. Mexico
| | - Miguel Vargas
- Department of Molecular Biomedicine; Center of Research and Advanced Studies of the I.P.N; Mexico City, D.F. Mexico
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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Sánchez-Guerrero E, Hernández-Campos ME, Correa-Basurto J, López-Sánchez P, Tolentino-López LE. Three-dimensional structure and molecular dynamics studies of prorrenin/renin receptor: description of the active site. Mol Biosyst 2015; 11:2520-8. [PMID: 26177886 DOI: 10.1039/c5mb00342c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The recent finding of a specific receptor for prorrenin/renin (PRR) has brought new insights into the physiology of the renin-angiotensin-aldosterone system. No undoubtable role has been described for this receptor so far. Its role seems to be important in chronic illnesses such as hypertension, possibly participating in the cardiovascular remodeling process, and diabetes where participation in inflammation development has been described. It is not possible, however, to explore the PRR function using classical pharmacological approaches due to the lack of specific agonists or antagonists. Two synthetic peptides have been described to accomplish these roles, but no conclusive data have been provided. There are no X-ray crystallography studies available to describe the structure and potential sites for drug development. So, the aim of this work was to model and theoretically describe the PRR. We describe and characterize the whole receptor protein, its spatial conformation and the potential interactions of PRR with the synthetic peptides available, describing the amino acid residues responsible for these interactions. This information provides the basis for directed development of drugs, seeking to agonize or antagonize PRR activity and study its function in health and ill stages.
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Affiliation(s)
- E Sánchez-Guerrero
- Sección de Estudios de Posgrado e Investigación, Escuela Superior de Medicina del IPN, Plan de San Luis y Díaz Mirón, Casco de Santo Tomás, México D.F. 11340, 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] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2014] [Accepted: 11/10/2014] [Indexed: 12/01/2022]
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25
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Méndez-Luna D, Martínez-Archundia M, Maroun RC, Ceballos-Reyes G, Fragoso-Vázquez MJ, González-Juárez DE, Correa-Basurto J. Deciphering the GPER/GPR30-agonist and antagonists interactions using molecular modeling studies, molecular dynamics, and docking simulations. J Biomol Struct Dyn 2015; 33:2161-72. [PMID: 25587872 DOI: 10.1080/07391102.2014.994102] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
The G-protein coupled estrogen receptor 1 GPER/GPR30 is a transmembrane seven-helix (7TM) receptor involved in the growth and proliferation of breast cancer. Due to the absence of a crystal structure of GPER/GPR30, in this work, molecular modeling studies have been carried out to build a three-dimensional structure, which was subsequently refined by molecular dynamics (MD) simulations (up to 120 ns). Furthermore, we explored GPER/GPR30's molecular recognition properties by using reported agonist ligands (G1, estradiol (E2), tamoxifen, and fulvestrant) and the antagonist ligands (G15 and G36) in subsequent docking studies. Our results identified the E2 binding site on GPER/GPR30, as well as other receptor cavities for accepting large volume ligands, through GPER/GPR30 π-π, hydrophobic, and hydrogen bond interactions. Snapshots of the MD trajectory at 14 and 70 ns showed almost identical binding motifs for G1 and G15. It was also observed that C107 interacts with the acetyl oxygen of G1 (at 14 ns) and that at 70 ns the residue E275 interacts with the acetyl group and with the oxygen from the other agonist whereas the isopropyl group of G36 is oriented toward Met141, suggesting that both C107 and E275 could be involved in the protein activation. This contribution suggest that GPER1 has great structural changes which explain its great capacity to accept diverse ligands, and also, the same ligand could be recognized in different binding pose according to GPER structural conformations.
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Affiliation(s)
- D Méndez-Luna
- a Laboratorio de modelado Molecular y Diseño de Fármacos (Laboratory of Molecular Modeling and Drug Design), Sección de Estudios de Posgrado e Investigación, Escuela Superior de Medicina , Instituto Politécnico Nacional , Plan de San Luis y Díaz Mirón, 11340 México, D.F. , Mexico
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Correa-Basurto J, Bello M, Rosales-Hernández M, Hernández-Rodríguez M, Nicolás-Vázquez I, Rojo-Domínguez A, Trujillo-Ferrara J, Miranda R, Flores-Sandoval C. QSAR, docking, dynamic simulation and quantum mechanics studies to explore the recognition properties of cholinesterase binding sites. Chem Biol Interact 2014; 209:1-13. [DOI: 10.1016/j.cbi.2013.12.001] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2013] [Revised: 11/25/2013] [Accepted: 12/02/2013] [Indexed: 11/30/2022]
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Luna-Palencia G, Martinez-Ramos F, Vasquez-Moctezuma I, Fragoso-Vazquez M, Mendieta-Wejebe J, Padilla-Martínez I, Sixto-Lopez Y, Mendez-Luna D, Trujillo-Ferrara J, Meraz-Rios M, Fonseca-Sabater Y, Correa-Basurto J. Three Amino Acid Derivatives of Valproic Acid: Design, Synthesis, Theoretical and Experimental Evaluation as Anticancer Agents. Anticancer Agents Med Chem 2014; 14:984-93. [DOI: 10.2174/1871520614666140127113218] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2013] [Revised: 01/15/2014] [Accepted: 01/20/2014] [Indexed: 11/22/2022]
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Segura-Cabrera A, García-Pérez C, Ciprés-Flores F, Cuevas-Hernández R, Trujillo-Ferrara J, Correa-Basurto J, Soriano-Ursúa M. Molecular dynamics simulations to explore the active/inactive conformers of guinea pig β2adrenoceptor for the selective design of agonists or antagonists. Molecular Simulation 2014. [DOI: 10.1080/08927022.2013.857771] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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30
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Bello M, Correa-Basurto J, Rudiño-Piñera E. Simulation of the cavity-binding site of three bacterial multicopper oxidases upon complex stabilization: interactional profile and electron transference pathways. J Biomol Struct Dyn 2013; 32:1303-17. [DOI: 10.1080/07391102.2013.817954] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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Correa-Basurto J. Editorial (Hot Topics: Molecular Modeling and QSAR Studies for Drug Design). Curr Pharm Des 2013; 19:2137. [DOI: 10.2174/1381612811319120001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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32
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Ramirez-Duran LA, Rosales-Hernandez MC, Hernandez-Rodriguez M, Elena Mendieta-Wejebe J, Trujillo-Ferrara J, Correa-Basurto J. Mapping Myeloperoxidase to Identify its Promiscuity Properties Using Docking and Molecular Dynamics Simulations. Curr Pharm Des 2013; 19:2204-15. [DOI: 10.2174/1381612811319120008] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2012] [Accepted: 09/23/2012] [Indexed: 11/22/2022]
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L. Rosas-Trigueros J, Ilizaliturri-Flores I, G. Benitez-Cardoza C, Correa-Basurto J, Zamorano-Carrillo A. Computational Modeling and Simulation of the Bcl-2 Family: Paving the Way for Rational Drug Design. Curr Med Chem 2012. [DOI: 10.2174/0929867311209066081] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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Rosas-Trigueros JL, Ilizaliturri-Flores I, Benítez-Cardoza CG, Correa-Basurto J, Zamorano-Carrillo A. Computational modeling and simulation of the Bcl-2 family: paving the way for rational drug design. Curr Med Chem 2012; 19:6081-94. [PMID: 23150945 DOI: 10.2174/092986712804485656] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2012] [Revised: 10/24/2012] [Accepted: 11/05/2012] [Indexed: 11/22/2022]
Abstract
Bcl-2 (B-cell lymphoma 2) family proteins have been studied intensively due to their association with cancer and other human diseases. These proteins were originally associated with the regulation of outer mitochondrial membrane integrity and apoptosis. However, there is experimental evidence that suggests that several members of this family play instrumental roles in other cellular pathways including autophagy, endoplasmic reticulum signaling, mitochondrial morphology and synaptic activity among others. Bcl-2 family proteins have been explored using diverse experimental and theoretical methods to obtain structural information that can provide valuable insight for drug development. This review is focused on computational studies related to Bcl-2 family proteins. Different strategies are described and evaluated, such as Molecular Dynamics simulations, docking, and rational drug design with the aim of demonstrating the importance of structural details of either ligands or proteins. The relevance of the knowledge obtained using these tools to drug design is discussed.
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Affiliation(s)
- J L Rosas-Trigueros
- SEPI de la ESCOM del Instituto Politécnico Nacional, México D.F. 07738, México
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Correa-Basurto J, Ramos-Morales FR, Matus MH, Rosales-Hernández MC, Mancilla-Percino T, Trujillo-Ferrara J, Ilizaliturri-Flores I. Docking and DFT Studies to explore the Topoisomerase II ATP Pocket employing 3-Substituted 2,6-Piperazindiones for drug design. Molecular Simulation 2012. [DOI: 10.1080/08927022.2012.690877] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
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Tolentino-Lopez L, Segura-Cabrera A, Reyes-Loyola P, Zimic M, Quiliano M, Briz V, Muñoz-Fernández A, Rodríguez-Pérez M, Ilizaliturri-Flores I, Correa-Basurto J. Outside-binding site mutations modify the active site's shapes in neuraminidase from influenza A H1N1. Biopolymers 2012; 99:10-21. [DOI: 10.1002/bip.22130] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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Jimenez-Botello L, Soriano-Ursua M, Avila-Costa, M, Picazo-Picazo O, Correa-Basurto J. 2.238 COFFEE OR CHOCOLATE, WHAT DO YOU LIKE TO DRINK WITH YOUR L-DOPA? Parkinsonism Relat Disord 2012. [DOI: 10.1016/s1353-8020(11)70562-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Soriano-Ursúa MA, Mancilla-Percino T, Correa-Basurto J, Querejeta E, Trujillo-Ferrara JG. Give boron a chance: boron containing compounds reach ionotropic and metabotropic transmembrane receptors. Mini Rev Med Chem 2011; 11:1031-8. [PMID: 21861808 DOI: 10.2174/138955711797247743] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2011] [Revised: 05/13/2011] [Accepted: 07/05/2011] [Indexed: 02/07/2023]
Abstract
The ligand-gated ion channels and seven transmembrane domain receptors are the greatest families of transmembrane receptors (TMR) expressed in mammalians and the major target of current available drugs. Recently, boron containing compounds (BCC) have shown capability of acting as ligands on these targets. This mini-review is focused on the description of BCC that target TMR which were evaluated under experimental models. The results in experimental models are related with the theoretical interaction studies of these ligands on the target proteins as 3D-models in order to explore the biological effects of BCC in molecular detail.
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Affiliation(s)
- M A Soriano-Ursúa
- Departamento de Bioquímica, Sección de Estudios de Posgrado e Investigación, Escuela Superior de Medicina, Instituto Politécnico Nacional, México city, México
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A. Bermudez-Lugo J, C. Rosales-Hernandez M, Deeb O, Trujillo-Ferrara J, Correa-Basurto J. In Silico Methods to Assist Drug Developers in Acetylcholinesterase Inhibitor Design. Curr Med Chem 2011; 18:1122-36. [DOI: 10.2174/092986711795029681] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2010] [Accepted: 02/26/2011] [Indexed: 11/22/2022]
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Soriano-Ursúa MA, Correa-Basurto J, Romero-Huerta J, Elizalde-Solis O, Galicia-Luna LA, Trujillo-Ferrara JG. Pharmacokinetic parameters and a theoretical study about metabolism of BR-AEA (a salbutamol derivative) in rabbit. J Enzyme Inhib Med Chem 2010; 25:340-6. [PMID: 19874116 DOI: 10.3109/14756360903179450] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
In this study, we report the pharmacokinetics of 1-(4-di-hydroxy-3,5-dioxa-4-borabicyclo[4.4.0]deca-7,9,11- trien-9-yl)-2-(tert-butylamino)ethanol (BR-AEA). This compound was identified as a more potent beta(2) adrenoceptor (beta(2)AR) agonist than salbutamol. A sensitive and reproducible high-performance liquid chromatography (HPLC) method was used for determining the time-dependent BR-AEA concentration in healthy rabbit plasma. The pharmacokinetic parameters obtained are explained in relation to the compound's metabolism by sulfotransferases. For this purpose, docking simulations were carried out on SULT1A3, SULT1C1, and SULT1A1 3-D models using the Autodock 3.0.5 program. According to the HPLC results, t(1/2) = 2.36 +/- 0.18 h and K(e) = 0.32 +/- 0.02 h(-1) for BR-AEA in rabbit plasma. Thus, BR-AEA has a greater half-life compared with salbutamol (t(1/2) = 0.66 +/- 0.08 h). This could be due to the protection that the boronic acid moiety of BR-AEA offers to the hydroxyl groups that would otherwise be susceptible to sulfation when exposed inside the active site of the sulfotransferase. This could be due to the fact that BR-AEA has a high affinity for the side-chain hydroxyl groups of Ser and Tyr residues of the enzymes, which are located outside the active site.
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Rosales-Hernandez MC, Bermudez-Lugo J, Garcia J, Trujillo-Ferrara J, Correa-Basurto J. Molecular Modeling Applied to Anti-Cancer Drug Development. Anticancer Agents Med Chem 2009; 9:230-8. [DOI: 10.2174/187152009787313819] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
In the past, anti-cancer drugs were identified and developed without focusing on a particular macromolecular target. Currently, the fields of molecular biochemistry, molecular biology, genetics and pharmacology, among other disciplines, have grown considerably in their ability to identify biological targets. These disciplines are now searching for specific targets to treat cancer. These targets exist in different cellular compartments (membrane, cytoplasm, nucleus) as proteins, glycoproteins, nucleic acids, etc. Computational tools have recently been used to explore such targets and to corroborate previously obtained experimental data. These methods have also been used to design new drugs with the aim of decreasing illness and the economic resources needed to discover drug candidates. Some of these computational methods include quantum mechanics (ab initio and density functional theories) and molecular mechanics (docking, molecular dynamics, and protein folding). Docking and molecular dynamics are the most commonly used computational tools for elucidating cancer targets. Using these tools, one can identify the recognition processes between ligands and targets at the atomic level. In addition, one can identify the affinity and conformational changes of these molecular complexes. In conclusion, we propose that the use of such tools is necessary in order to identify new anti-cancer drugs.
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Affiliation(s)
| | | | | | | | - J. Correa-Basurto
- Seccion de Estudios de Posgrado e Investigacion y Departamento de Bioquimica de la Escuela Superior de Medicina del IPN, Plan de San Luis y Diaz Miron s/n, Distrito Federal 11340, Mexico., Mexico
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Araujo-Alvarez JM, Trujillo-Ferrara JG, Ponce-Franco D, Correa-Basurto J, Delgado A, Querejeta E. (+)-(S)-trujillon, (+)-(S)-4-(2,2-diphenyl-1,3,2-oxazabolidin-5-oxo)propionic acid, a novel glutamatergic analog, modifies the activity of globus pallidus neurons by selective NMDA receptor activation. Chirality 2008; 23:429-37. [DOI: 10.1002/chir.20594] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2008] [Accepted: 04/15/2008] [Indexed: 11/06/2022]
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Correa-Basurto J, Rodríguez-Páez L, Aguiar-Moreno ES, López-Sánchez P, Espinoza-Fonseca LM, Wong C, Trujillo-Ferrara J. Computational and experimental evaluation of ornithine derivatives as ornithine decarboxylase inhibitors. Med Chem Res 2008. [DOI: 10.1007/s00044-008-9103-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Hulme R, Zamora O, Mota E, Pastén M, Contreras-Rojas R, Miranda R, Valencia-Hernández I, Correa-Basurto J, Trujillo-Ferrara J, Delgado F. Cyanamide: a convenient building block to synthesize 4-aryl-2-cyanoimino-3,4-dihydro-1H-pyrimidine systems via a multicomponent reaction. Tetrahedron 2008. [DOI: 10.1016/j.tet.2008.01.087] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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Rosales-Hernández MC, Mendieta-Wejebe JE, Correa-Basurto J, Vázquez-Alcántara JI, Terres-Rojas E, Trujillo-Ferrara J. Catalytic activity of acetylcholinesterase immobilized on mesoporous molecular sieves. Int J Biol Macromol 2007; 40:444-8. [PMID: 17208293 DOI: 10.1016/j.ijbiomac.2006.11.004] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2006] [Revised: 10/27/2006] [Accepted: 11/01/2006] [Indexed: 11/20/2022]
Abstract
MCM-41 and FSM-16 were used for enzyme immobilization on account of their good physical and chemical properties. In this work, the catalytic activity of acetylcholinesterase (AChE) immobilized on these materials was investigated, using neostigmina as AChE inhibitor. The results show that AChE was adsorbed on MCM-41 and on FSM-16-TIPB. AChE immobilized on the latter material maintained 70% of its activity and the material did not hydrolyze ACh (as MCM-41) by itself. Therefore, FSM-16-TIPB was the best material, considering also that when neostigmine was applied to AChE immobilized on FSM-16-TIPB, the activity of AChE decreased as occurs in its free from. Hence, this model could be useful in the evaluation of different kinds of AChE inhibitors, allowing the recycling of enzymes and making possible several assays and thereby, lowering cost.
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Affiliation(s)
- M C Rosales-Hernández
- Sección de Estudios de Posgrado e Investigación y Departamento de Bioquímica de la Escuela Superior de Medicina del Instituto Politécnico Nacional, Plan de San Luis y Díaz Mirón s/n, 11340 México, D.F., Mexico
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Espinosa Raya J, Correa-Basurto J, Vázquez Alcántara JI, Trujillo-Ferrara JG. (17) Effects of succinic acid derivatives on ex vivo acetylcholinesterase activity. Chem Biol Interact 2005; 157-158:379-80. [PMID: 16429502 DOI: 10.1016/j.cbi.2005.10.062] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
In the present study the acetylcholinesterase (AChE) inhibition and acute toxicity of two succinic acid derivatives were compared with tacrine. Administration of a single dose of each of two succinic acid derivatives produced a time and dose-dependent inhibition of brain AChE activity. Although the magnitude of the cholinergic effects observed with the two succinic acid derivatives was similar to that seen with tacrine and other AChE inhibitors, the toxicity study showed that the new inhibitors have less adverse side effects.
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Affiliation(s)
- J Espinosa Raya
- Sección de Graduados y Departamento de Bioquímica, Escuela Superior de Medicina, Instituto Politécnico Nacional. Plan de San Luis y Díaz Mirón, México, DF, 11340 México, Mexico
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Flores-Sandoval C, Zaragoza I, Marañón-Ruiz V, Correa-Basurto J, Trujillo-Ferrara J. Theoretical study of aryl succinic and maleic acid derivatives. ACTA ACUST UNITED AC 2005. [DOI: 10.1016/j.theochem.2004.11.004] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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