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Prado-Romero DL, Saldívar-González FI, López-Mata I, Laurel-García PA, Durán-Vargas A, García-Hernández E, Sánchez-Cruz N, Medina-Franco JL. De Novo Design of Inhibitors of DNA Methyltransferase 1: A Critical Comparison of Ligand- and Structure-Based Approaches. Biomolecules 2024; 14:775. [PMID: 39062489 PMCID: PMC11274800 DOI: 10.3390/biom14070775] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2024] [Revised: 06/14/2024] [Accepted: 06/26/2024] [Indexed: 07/28/2024] Open
Abstract
Designing and developing inhibitors against the epigenetic target DNA methyltransferase (DNMT) is an attractive strategy in epigenetic drug discovery. DNMT1 is one of the epigenetic enzymes with significant clinical relevance. Structure-based de novo design is a drug discovery strategy that was used in combination with similarity searching to identify a novel DNMT inhibitor with a novel chemical scaffold and warrants further exploration. This study aimed to continue exploring the potential of de novo design to build epigenetic-focused libraries targeted toward DNMT1. Herein, we report the results of an in-depth and critical comparison of ligand- and structure-based de novo design of screening libraries focused on DNMT1. The newly designed chemical libraries focused on DNMT1 are freely available on GitHub.
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Affiliation(s)
- Diana L. Prado-Romero
- DIFACQUIM Research Group, Department of Pharmacy, School of Chemistry, Universidad Nacional Autónoma de México, Avenida Universidad 3000, Mexico City 04510, Mexico; (D.L.P.-R.); (F.I.S.-G.); (P.A.L.-G.)
| | - Fernanda I. Saldívar-González
- DIFACQUIM Research Group, Department of Pharmacy, School of Chemistry, Universidad Nacional Autónoma de México, Avenida Universidad 3000, Mexico City 04510, Mexico; (D.L.P.-R.); (F.I.S.-G.); (P.A.L.-G.)
| | - Iván López-Mata
- División Académica de Ciencias Básicas, Universidad Juárez Autónoma de Tabasco, Carretera Cunduacán-Jalpa de Méndez, Km 1, Cunduacán 86690, Tabasco, Mexico;
- Instituto de Química, Unidad Mérida, Universidad Nacional Autónoma de México, Carretera Mérida-Tetiz Km. 4.5, Ucú 97357, Yucatán, Mexico;
| | - Pedro A. Laurel-García
- DIFACQUIM Research Group, Department of Pharmacy, School of Chemistry, Universidad Nacional Autónoma de México, Avenida Universidad 3000, Mexico City 04510, Mexico; (D.L.P.-R.); (F.I.S.-G.); (P.A.L.-G.)
| | - Adrián Durán-Vargas
- Instituto de Química, Universidad Nacional Autónoma de México, Ciudad Universitaria, Mexico City 04510, Mexico; (A.D.-V.); (E.G.-H.)
| | - Enrique García-Hernández
- Instituto de Química, Universidad Nacional Autónoma de México, Ciudad Universitaria, Mexico City 04510, Mexico; (A.D.-V.); (E.G.-H.)
| | - Norberto Sánchez-Cruz
- Instituto de Química, Unidad Mérida, Universidad Nacional Autónoma de México, Carretera Mérida-Tetiz Km. 4.5, Ucú 97357, Yucatán, Mexico;
- Instituto de Investigaciones en Matemáticas Aplicadas y en Sistemas, Unidad Mérida, Universidad Nacional Autónoma de México, Sierra Papacál 97302, Yucatán, Mexico
| | - José L. Medina-Franco
- DIFACQUIM Research Group, Department of Pharmacy, School of Chemistry, Universidad Nacional Autónoma de México, Avenida Universidad 3000, Mexico City 04510, Mexico; (D.L.P.-R.); (F.I.S.-G.); (P.A.L.-G.)
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Medrano‐Cerano JL, Cofas‐Vargas LF, Leyva E, Rauda‐Ceja JA, Calderón‐Vargas M, Cano‐Sánchez P, Titaux‐Delgado G, Melchor‐Meneses CM, Hernández‐Arana A, del Río‐Portilla F, García‐Hernández E. Decoding the mechanism governing the structural stability of wheat germ agglutinin and its isolated domains: A combined calorimetric, NMR, and MD simulation study. Protein Sci 2024; 33:e5020. [PMID: 38747397 PMCID: PMC11094770 DOI: 10.1002/pro.5020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Revised: 04/09/2024] [Accepted: 04/28/2024] [Indexed: 05/19/2024]
Abstract
Wheat germ agglutinin (WGA) demonstrates potential as an oral delivery agent owing to its selective binding to carbohydrates and its capacity to traverse biological membranes. In this study, we employed differential scanning calorimetry and molecular dynamics simulations to comprehensively characterize the thermal unfolding process of both the complete lectin and its four isolated domains. Furthermore, we present the nuclear magnetic resonance structures of three domains that were previously lacking experimental structures in their isolated forms. Our results provide a collective understanding of the energetic and structural factors governing the intricate unfolding mechanism of the complete agglutinin, shedding light on the specific role played by each domain in this process. The analysis revealed negligible interdomain cooperativity, highlighting instead significant coupling between dimer dissociation and the unfolding of the more labile domains. By comparing the dominant interactions, we rationalized the stability differences among the domains. Understanding the structural stability of WGA opens avenues for enhanced drug delivery strategies, underscoring its potential as a promising carrier throughout the gastrointestinal environment.
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Affiliation(s)
- Jorge Luis Medrano‐Cerano
- Universidad Nacional Autónoma de México, Instituto de Química, Ciudad UniversitariaCiudad de MéxicoMexico
| | | | - Eduardo Leyva
- Universidad Nacional Autónoma de México, Instituto de Química, Ciudad UniversitariaCiudad de MéxicoMexico
| | - Jesús Antonio Rauda‐Ceja
- Universidad Nacional Autónoma de México, Instituto de Química, Ciudad UniversitariaCiudad de MéxicoMexico
| | - Mateo Calderón‐Vargas
- Universidad Nacional Autónoma de México, Instituto de Química, Ciudad UniversitariaCiudad de MéxicoMexico
| | - Patricia Cano‐Sánchez
- Universidad Nacional Autónoma de México, Instituto de Química, Ciudad UniversitariaCiudad de MéxicoMexico
| | - Gustavo Titaux‐Delgado
- Universidad Nacional Autónoma de México, Instituto de Química, Ciudad UniversitariaCiudad de MéxicoMexico
| | | | - Andrés Hernández‐Arana
- Área de Biofisicoquímica, Departamento de QuímicaUniversidad Autónoma Metropolitana IztapalapaCiudad de MéxicoMexico
| | - Federico del Río‐Portilla
- Universidad Nacional Autónoma de México, Instituto de Química, Ciudad UniversitariaCiudad de MéxicoMexico
| | - Enrique García‐Hernández
- Universidad Nacional Autónoma de México, Instituto de Química, Ciudad UniversitariaCiudad de MéxicoMexico
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Agüero-Chapin G, Antunes A, Marrero-Ponce Y. A 2022 Update on Computational Approaches to the Discovery and Design of Antimicrobial Peptides. Antibiotics (Basel) 2023; 12:1011. [PMID: 37370330 DOI: 10.3390/antibiotics12061011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Accepted: 05/30/2023] [Indexed: 06/29/2023] Open
Abstract
The antimicrobial resistance process has been accelerated by the over-prescription and misuse of antibiotics [...].
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Affiliation(s)
- Guillermin Agüero-Chapin
- CIIMAR/CIMAR, Interdisciplinary Centre of Marine and Environmental Research, University of Porto, 4450-208 Porto, Portugal
- Department of Biology, Faculty of Sciences, University of Porto, 4169-007 Porto, Portugal
| | - Agostinho Antunes
- CIIMAR/CIMAR, Interdisciplinary Centre of Marine and Environmental Research, University of Porto, 4450-208 Porto, Portugal
- Department of Biology, Faculty of Sciences, University of Porto, 4169-007 Porto, Portugal
| | - Yovani Marrero-Ponce
- Universidad San Francisco de Quito (USFQ), Grupo de Medicina Molecular y Traslacional (MeM&T), Colegio de Ciencias de la Salud (COCSA), Escuela de Medicina, Edificio de Especialidades Médicas, Diego de Robles y vía Interoceánica, Quito 170157, Pichincha, Ecuador
- Departamento de Ciencias de la Computación, Centro de Investigación Científica y de Educación Superior de Ensenada (CICESE), Ensenada 22860, Baja California, Mexico
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Cofas-Vargas LF, Mendoza-Espinosa P, Avila-Barrientos LP, Prada-Gracia D, Riveros-Rosas H, García-Hernández E. Exploring the druggability of the binding site of aurovertin, an exogenous allosteric inhibitor of FOF1-ATP synthase. Front Pharmacol 2022; 13:1012008. [PMID: 36313289 PMCID: PMC9615146 DOI: 10.3389/fphar.2022.1012008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Accepted: 10/03/2022] [Indexed: 11/13/2022] Open
Abstract
In addition to playing a central role in the mitochondria as the main producer of ATP, FOF1-ATP synthase performs diverse key regulatory functions in the cell membrane. Its malfunction has been linked to a growing number of human diseases, including hypertension, atherosclerosis, cancer, and some neurodegenerative, autoimmune, and aging diseases. Furthermore, inhibition of this enzyme jeopardizes the survival of several bacterial pathogens of public health concern. Therefore, FOF1-ATP synthase has emerged as a novel drug target both to treat human diseases and to combat antibiotic resistance. In this work, we carried out a computational characterization of the binding sites of the fungal antibiotic aurovertin in the bovine F1 subcomplex, which shares a large identity with the human enzyme. Molecular dynamics simulations showed that although the binding sites can be described as preformed, the inhibitor hinders inter-subunit communications and exerts long-range effects on the dynamics of the catalytic site residues. End-point binding free energy calculations revealed hot spot residues for aurovertin recognition. These residues were also relevant to stabilize solvent sites determined from mixed-solvent molecular dynamics, which mimic the interaction between aurovertin and the enzyme, and could be used as pharmacophore constraints in virtual screening campaigns. To explore the possibility of finding species-specific inhibitors targeting the aurovertin binding site, we performed free energy calculations for two bacterial enzymes with experimentally solved 3D structures. Finally, an analysis of bacterial sequences was carried out to determine conservation of the aurovertin binding site. Taken together, our results constitute a first step in paving the way for structure-based development of new allosteric drugs targeting FOF1-ATP synthase sites of exogenous inhibitors.
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Affiliation(s)
- Luis Fernando Cofas-Vargas
- Universidad Nacional Autónoma de México, Instituto de Química, Ciudad Universitaria, Mexico City, Mexico
| | - Paola Mendoza-Espinosa
- Universidad Nacional Autónoma de México, Instituto de Química, Ciudad Universitaria, Mexico City, Mexico
- Tecnologico de Monterrey, The Institute for Obesity Research, Monterrey, Mexico
| | | | - Diego Prada-Gracia
- Unidad de Investigación en Biología Computacional y Diseño de Fármacos, Hospital Infantil de México Federico Gómez, Mexico City, Mexico
| | - Héctor Riveros-Rosas
- Departamento de Bioquímica, Facultad de Medicina, Universidad Nacional Autónoma de México, Avenida Universidad 3000, Cd. Universitaria, Mexico City, Mexico
| | - Enrique García-Hernández
- Universidad Nacional Autónoma de México, Instituto de Química, Ciudad Universitaria, Mexico City, Mexico
- *Correspondence: Enrique García-Hernández,
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Agüero-Chapin G, Galpert-Cañizares D, Domínguez-Pérez D, Marrero-Ponce Y, Pérez-Machado G, Teijeira M, Antunes A. Emerging Computational Approaches for Antimicrobial Peptide Discovery. Antibiotics (Basel) 2022; 11:antibiotics11070936. [PMID: 35884190 PMCID: PMC9311958 DOI: 10.3390/antibiotics11070936] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Revised: 07/01/2022] [Accepted: 07/08/2022] [Indexed: 02/05/2023] Open
Abstract
In the last two decades many reports have addressed the application of artificial intelligence (AI) in the search and design of antimicrobial peptides (AMPs). AI has been represented by machine learning (ML) algorithms that use sequence-based features for the discovery of new peptidic scaffolds with promising biological activity. From AI perspective, evolutionary algorithms have been also applied to the rational generation of peptide libraries aimed at the optimization/design of AMPs. However, the literature has scarcely dedicated to other emerging non-conventional in silico approaches for the search/design of such bioactive peptides. Thus, the first motivation here is to bring up some non-standard peptide features that have been used to build classical ML predictive models. Secondly, it is valuable to highlight emerging ML algorithms and alternative computational tools to predict/design AMPs as well as to explore their chemical space. Another point worthy of mention is the recent application of evolutionary algorithms that actually simulate sequence evolution to both the generation of diversity-oriented peptide libraries and the optimization of hit peptides. Last but not least, included here some new considerations in proteogenomic analyses currently incorporated into the computational workflow for unravelling AMPs in natural sources.
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Affiliation(s)
- Guillermin Agüero-Chapin
- CIIMAR—Centro Interdisciplinar de Investigação Marinha e Ambiental, Universidade do Porto, Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos, s/n, 4450-208 Porto, Portugal;
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre, 4169-007 Porto, Portugal
- Correspondence: (G.A.-C.); (A.A.); Tel.: +351-22-340-1813 (G.A.-C. & A.A.)
| | - Deborah Galpert-Cañizares
- Departamento de Ciencia de la Computación, Universidad Central Marta Abreu de Las Villas (UCLV), Santa Clara 54830, Cuba;
| | - Dany Domínguez-Pérez
- CIIMAR—Centro Interdisciplinar de Investigação Marinha e Ambiental, Universidade do Porto, Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos, s/n, 4450-208 Porto, Portugal;
- Proquinorte, Unipessoal, Lda, Avenida 5 de Outubro, 124, 7º Piso, Avenidas Novas, 1050-061 Lisboa, Portugal
| | - Yovani Marrero-Ponce
- Universidad San Francisco de Quito (USFQ), Grupo de Medicina Molecular y Translacional (MeM&T), Colegio de Ciencias de la Salud (COCSA), Escuela de Medicina, Edificio de Especialidades Médicas and Instituto de Simulación Computacional (ISC-USFQ), Diego de Robles y vía Interoceánica, Quito 170157, Ecuador;
| | - Gisselle Pérez-Machado
- EpiDisease S.L—Spin-Off of Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), 46980 Valencia, Spain;
| | - Marta Teijeira
- Departamento de Química Orgánica, Facultade de Química, Universidade de Vigo, 36310 Vigo, Spain;
- Instituto de Investigación Sanitaria Galicia Sur, Hospital Álvaro Cunqueiro, 36213 Vigo, Spain
| | - Agostinho Antunes
- CIIMAR—Centro Interdisciplinar de Investigação Marinha e Ambiental, Universidade do Porto, Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos, s/n, 4450-208 Porto, Portugal;
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre, 4169-007 Porto, Portugal
- Correspondence: (G.A.-C.); (A.A.); Tel.: +351-22-340-1813 (G.A.-C. & A.A.)
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