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Combarel D, Dousset L, Bouchet S, Ferrer F, Tetu P, Lebbe C, Ciccolini J, Meyer N, Paci A. Tyrosine kinase inhibitors in cancers: Treatment optimization - Part I. Crit Rev Oncol Hematol 2024; 199:104384. [PMID: 38762217 DOI: 10.1016/j.critrevonc.2024.104384] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2024] [Revised: 05/02/2024] [Accepted: 05/03/2024] [Indexed: 05/20/2024] Open
Abstract
A multitude of TKI has been developed and approved targeting various oncogenetic alterations. While these have provided improvements in efficacy compared with conventional chemotherapies, resistance to targeted therapies occurs. Mutations in the kinase domain result in the inability of TKI to inactivate the protein kinase. Also, gene amplification, increased protein expression and downstream activation or bypassing of signalling pathways are commonly reported mechanisms of resistance. Improved understanding of mechanisms involved in TKI resistance has resulted in the development of new generations of targeted agents. In a race against time, the search for new, more potent and efficient drugs, and/or combinations of drugs, remains necessary as new resistance mechanisms to the latest generation of TKI emerge. This review examines the various generations of TKI approved to date and their common mechanisms of resistance, focusing on TKI targeting BCR-ABL, epidermal growth factor receptor, anaplastic lymphoma kinase and BRAF/MEK tyrosine kinases.
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Affiliation(s)
- David Combarel
- Service de Pharmacologie, Département de Biologie et Pathologie médicales, Gustave Roussy, Villejuif 94805, France; Service de Pharmacocinétique, Faculté de Pharmacie, Université Paris Saclay, Châtenay-Malabry 92 296, France
| | - Léa Dousset
- Dermatology Department, Bordeaux University Hospital, Bordeaux, France
| | - Stéphane Bouchet
- Département de Pharmacologie, Centre Hospitalier Universitaire de Bordeaux, Bordeaux, France
| | - Florent Ferrer
- Department of Pharmacology, Clermont-Ferrand University Hospital, Clermont-Ferrand, France; SMARTc Unit, CRCM Inserm U1068, Aix Marseille Univ and APHM, Marseille, France
| | - Pauline Tetu
- Department of Dermatology, APHP Dermatology, Paris 7 Diderot University, INSERM U976, Hôpital Saint-Louis, Paris, France
| | - Céleste Lebbe
- Department of Dermatology, APHP Dermatology, Paris 7 Diderot University, INSERM U976, Hôpital Saint-Louis, Paris, France
| | - Joseph Ciccolini
- SMARTc Unit, CRCM Inserm U1068, Aix Marseille Univ and APHM, Marseille, France
| | - Nicolas Meyer
- Université Paul Sabatier-Toulouse III, Institut National de la Santé et de la Recherche Médicale Unité Mixte de Recherche 1037-CRCT, Toulouse, France
| | - Angelo Paci
- Service de Pharmacologie, Département de Biologie et Pathologie médicales, Gustave Roussy, Villejuif 94805, France; Service de Pharmacocinétique, Faculté de Pharmacie, Université Paris Saclay, Châtenay-Malabry 92 296, France.
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Bahena Culhuac E, Bello M. Unveiling the Mechanisms of EGCG-p53 Interactions through Molecular Dynamics Simulations. ACS OMEGA 2024; 9:20066-20085. [PMID: 38737068 PMCID: PMC11080030 DOI: 10.1021/acsomega.3c10523] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/30/2023] [Revised: 03/24/2024] [Accepted: 03/27/2024] [Indexed: 05/14/2024]
Abstract
Green tea consumption is associated with protective and preventive effects against various types of cancer. These effects are attributed to polyphenols, particularly epigallocatechin-3-gallate (EGCG). EGCG acts by directly inhibiting tumor suppressor protein p53. The binding mechanism by which EGCG inhibits p53 activity is associated with residues Trp23-Lys24 and Pro47-Thr55 within the p53 N-terminal domain (NTD). However, the structural and thermodynamic aspects of the interaction between EGCG and p53 are poorly understood. Therefore, based on crystallographic data, we combine docking, molecular dynamics (MD) simulations, and molecular mechanics generalized Born surface area approaches to explore the intricacies of the EGCG-p53 binding mechanism. A triplicate microsecond MD simulation for each system is initially performed to capture diverse p53 NTD conformations. From the start, the most populated cluster of the second run (R2-1) stands out due to a unique opening between Trp23 and Trp53. During MD simulations, this conformation allows EGCG to sustain a high level of stability and affinity while interacting with both regions of interest and deepening the binding pocket. Structural analysis emphasizes the significance of pyrogallol motifs in EGCG binding. Therefore, the conformational shift in this gap is pivotal, enabling EGCG to impede p53 interactions and manifest its anticancer properties. These findings enhance the present comprehension of the anticancer properties of green tea polyphenols and pave the way for future therapeutic developments.
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Affiliation(s)
- Erick Bahena Culhuac
- Laboratorio
de Diseño y Desarrollo de Nuevos Fármacos e Innovación
Biotecnológica, Escuela Superior de Medicina, Instituto Politécnico Nacional, Ciudad de México 11340, Mexico
- Universidad
Autónoma del Estado de México Facultad de Ciencias, Toluca 50000, Mexico
| | - Martiniano Bello
- Laboratorio
de Diseño y Desarrollo de Nuevos Fármacos e Innovación
Biotecnológica, Escuela Superior de Medicina, Instituto Politécnico Nacional, Ciudad de México 11340, Mexico
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3
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Méndez-Luna D, Guzmán-Velázquez S, Padilla-Martínez II, García-Sánchez JR, Bello M, García-Vázquez JB, Mendoza-Figueroa HL, Correa-Basurto J. GPER binding site detection and description: A flavonoid-based docking and molecular dynamics simulations study. J Steroid Biochem Mol Biol 2024; 239:106474. [PMID: 38307214 DOI: 10.1016/j.jsbmb.2024.106474] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Revised: 01/12/2024] [Accepted: 01/29/2024] [Indexed: 02/04/2024]
Abstract
Flavonoids, a phenolic compounds class widely distributed in the plant kingdom, have attracted much interest for their implications on several health and disease processes. Usually, the consumption of this type of compounds is approximately 1 g/d, primarily obtained from cereals, chocolate, and dry legumes ensuring its beneficial role in maintaining the homeostasis of the human body. In this context, in cancer disease prominent data points to the role of flavonoids as adjuvant treatment aimed at the regression of the disease. GPER, an estrogen receptor on the cell surface, has been postulated as a probable orchestrator of the beneficial effects of several flavonoids through modulation/inhibition of various mechanisms that lead to cancer progression. Therefore, applying pocket and cavity protein detection and docking and molecular dynamics simulations (MD), we generate, from a cluster composed of 39 flavonoids, crucial insights into the potential role as GPER ligands, of Puerarin, Isoquercetin, Kaempferol 3-O-glucoside and Petunidin 3-O-glucoside, aglycones whose sugar moiety delimits a new described sugar-acceptor sub-cavity into the cavity binding site on the receptor, as well as of the probable activation mechanism of the receptor and the pivotal residues involved in it. Altogether, our results shed light on the potential use of the aforementioned flavonoids as GPER ligands and for further evaluations in in vitro and in vivo assays to elucidate their probable anti-cancer activity.
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Affiliation(s)
- David Méndez-Luna
- Laboratorio de Diseño y Desarrollo de Nuevos Fármacos e Innovación Biotecnológica, Escuela Superior de Medicina, Instituto Politécnico Nacional, Plan de San Luis y Díaz Mirón s/n, Col. Casco de Santo Tomas, Alcaldía Miguel Hidalgo, C.P. 11340 Ciudad de México, Mexico; Departamento de Fisiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Zacatenco, Av. Wilfrido Massieu 399, Col. Nueva Industrial Vallejo, Alcaldía Gustavo A. Madero, C.P. 07738 Ciudad de México, Mexico.
| | - Sonia Guzmán-Velázquez
- Departamento de Fisiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Zacatenco, Av. Wilfrido Massieu 399, Col. Nueva Industrial Vallejo, Alcaldía Gustavo A. Madero, C.P. 07738 Ciudad de México, Mexico.
| | - Itzia-Irene Padilla-Martínez
- Laboratorio de Química Supramolecular y Nanociencias, Unidad Profesional Interdisciplinaria de Biotecnología, Instituto Politécnico Nacional, Av. Acueducto s/n, Barrio la Laguna Ticomán, Alcaldía Gustavo A. Madero, C.P. 07340 Ciudad de México, Mexico.
| | - José-Rubén García-Sánchez
- Laboratorio de Oncología Molecular y Estrés Oxidativo, Escuela Superior de Medicina, Instituto Politécnico Nacional, Plan de San Luis y Díaz Mirón, s/n, Col. Casco de Santo Tomas, Alcaldía Miguel Hidalgo, C.P. 11340 Ciudad de México, Mexico.
| | - Martiniano Bello
- Laboratorio de Diseño y Desarrollo de Nuevos Fármacos e Innovación Biotecnológica, Escuela Superior de Medicina, Instituto Politécnico Nacional, Plan de San Luis y Díaz Mirón s/n, Col. Casco de Santo Tomas, Alcaldía Miguel Hidalgo, C.P. 11340 Ciudad de México, Mexico.
| | - Juan-Benjamín García-Vázquez
- Laboratorio de Diseño y Desarrollo de Nuevos Fármacos e Innovación Biotecnológica, Escuela Superior de Medicina, Instituto Politécnico Nacional, Plan de San Luis y Díaz Mirón s/n, Col. Casco de Santo Tomas, Alcaldía Miguel Hidalgo, C.P. 11340 Ciudad de México, Mexico.
| | - Humberto-Lubriel Mendoza-Figueroa
- Laboratorio de Diseño y Desarrollo de Nuevos Fármacos e Innovación Biotecnológica, Escuela Superior de Medicina, Instituto Politécnico Nacional, Plan de San Luis y Díaz Mirón s/n, Col. Casco de Santo Tomas, Alcaldía Miguel Hidalgo, C.P. 11340 Ciudad de México, Mexico.
| | - José Correa-Basurto
- Laboratorio de Diseño y Desarrollo de Nuevos Fármacos e Innovación Biotecnológica, Escuela Superior de Medicina, Instituto Politécnico Nacional, Plan de San Luis y Díaz Mirón s/n, Col. Casco de Santo Tomas, Alcaldía Miguel Hidalgo, C.P. 11340 Ciudad de México, Mexico.
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4
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Bello M. Evaluation of structural and thermodynamic insight of ERβ with DPN and derivatives through MMGBSA/MMPBSA methods. Steroids 2024; 201:109334. [PMID: 37949336 DOI: 10.1016/j.steroids.2023.109334] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Revised: 10/28/2023] [Accepted: 11/05/2023] [Indexed: 11/12/2023]
Abstract
Estrogen receptors (ERs) are nuclear factors that exist as two subtypes: ERα and ERβ. Among the different selective ERβ agonist ligands, the widely used ERβ-selective agonist DPN (diarylpropionitrile) is highlighted. Recent experimental and thermodynamic information between R-DPN and S-DPN enantiomers with ERβ is important for evaluating further the ability of MD simulations combined with end-point methods to reproduce experimental binding affinity and generate structural insight not provided through crystallographic data. In this research, starting from crystallographic data and experimental binding affinities, we explored the structural and thermodynamic basis of the molecular recognition of ERβ with DPN and derivatives through triplicate MD simulations combined with end-point methods. Conformational analysis showed some regions with the highest mobility linked to ligand association that, at the time, impacted the total protein fluctuation. Binding free energy (ΔG) analysis revealed that the Molecular Mechanics Generalized-Born Surface Area (MMGBSA) approach was able to reproduce the experimental tendency with a strong correlation (R = 0.778), whereas per-residue decomposition analysis revealed that all the systems interacted strongly with eight residues (L298, E305, L339, M340, L343, F356, H475, and L476). The comparison between theoretical studies using the MMGBSA approach with experimental results provides new insights for drug designing of new DPN derivatives.
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Affiliation(s)
- Martiniano Bello
- Laboratorio de Diseño y Desarrollo de Nuevos Fármacos e Innovación Biotecnológica, Escuela Superior de Medicina, Instituto Politécnico Nacional, Ciudad de México 11340, México.
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5
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Zhou H, Fu H, Shao X, Cai W. Binding Thermodynamics of Fourth-Generation EGFR Inhibitors Revealed by Absolute Binding Free Energy Calculations. J Chem Inf Model 2023; 63:7837-7846. [PMID: 38054791 DOI: 10.1021/acs.jcim.3c01636] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/07/2023]
Abstract
The overexpression or mutation of the kinase domain of the epidermal growth factor receptor (EGFR) is strongly associated with non-small-cell lung cancer (NSCLC). EGFR tyrosine kinase inhibitors (TKIs) have proven to be effective in treating NSCLC patients. However, EGFR mutations can result in drug resistance. To elucidate the mechanisms underlying this resistance and inform future drug development, we examined the binding affinities of BLU-945, a recently reported fourth-generation TKI, to wild-type EGFR (EGFRWT) and its double-mutant (L858R/T790M; EGFRDM) and triple-mutant (L858R/T790M/C797S; EGFRTM) forms. We compared the binding affinities of BLU-945, BLU-945 analogues, CH7233163 (another fourth-generation TKI), and erlotinib (a first-generation TKI) using absolute binding free energy calculations. Our findings reveal that BLU-945 and CH7233163 exhibit binding affinities to both EGFRDM and EGFRTM stronger than those of erlotinib, corroborating experimental data. We identified K745 and T854 as the key residues in the binding of fourth-generation EGFR TKIs. Electrostatic forces were the predominant driving force for the binding of fourth-generation TKIs to EGFR mutants. Furthermore, we discovered that the incorporation of piperidinol and sulfone groups in BLU-945 substantially enhanced its binding capacity to EGFR mutants. Our study offers valuable theoretical insights for optimizing fourth-generation EGFR TKIs.
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Affiliation(s)
- Huaxin Zhou
- Research Center for Analytical Sciences, Tianjin Key Laboratory of Biosensing and Molecular Recognition, State Key Laboratory of Medicinal Chemical Biology, College of Chemistry, Nankai University, Tianjin 300071, China
- Haihe Laboratory of Sustainable Chemical Transformations, Tianjin 300192, China
| | - Haohao Fu
- Research Center for Analytical Sciences, Tianjin Key Laboratory of Biosensing and Molecular Recognition, State Key Laboratory of Medicinal Chemical Biology, College of Chemistry, Nankai University, Tianjin 300071, China
- Haihe Laboratory of Sustainable Chemical Transformations, Tianjin 300192, China
- School of Materials Science and Engineering, Smart Sensing Interdisciplinary Science Center, Nankai University, Tianjin 300350, China
| | - Xueguang Shao
- Research Center for Analytical Sciences, Tianjin Key Laboratory of Biosensing and Molecular Recognition, State Key Laboratory of Medicinal Chemical Biology, College of Chemistry, Nankai University, Tianjin 300071, China
- Haihe Laboratory of Sustainable Chemical Transformations, Tianjin 300192, China
- School of Materials Science and Engineering, Smart Sensing Interdisciplinary Science Center, Nankai University, Tianjin 300350, China
| | - Wensheng Cai
- Research Center for Analytical Sciences, Tianjin Key Laboratory of Biosensing and Molecular Recognition, State Key Laboratory of Medicinal Chemical Biology, College of Chemistry, Nankai University, Tianjin 300071, China
- Haihe Laboratory of Sustainable Chemical Transformations, Tianjin 300192, China
- School of Materials Science and Engineering, Smart Sensing Interdisciplinary Science Center, Nankai University, Tianjin 300350, China
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6
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Morelos-Garnica LA, Guzmán-Velázquez S, Padilla-Martínez II, García-Sánchez JR, Bello M, Bakalara N, Méndez-Luna D, Correa-Basurto J. In silico design and cell-based evaluation of two dual anti breast cancer compounds targeting Bcl-2 and GPER. Sci Rep 2023; 13:17933. [PMID: 37863936 PMCID: PMC10589355 DOI: 10.1038/s41598-023-43860-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2023] [Accepted: 09/29/2023] [Indexed: 10/22/2023] Open
Abstract
According to WHO statistics, breast cancer (BC) disease represents about 2.3 million diagnosed and 685,000 deaths globally. Regarding histological classification of BC, the Estrogen (ER) and Progesterone (PR) receptors negative-expression cancer, named Triple-Negative BC (TNBC), represents the most aggressive type of this disease, making it a challenge for drug discovery. In this context, our research group, applying a well-established Virtual Screening (VS) protocol, in addition to docking and molecular dynamics simulations studies, yielded two ligands identified as 6 and 37 which were chemically synthesized and evaluated on MCF-7 and MDA-MB-231 cancer cell lines. Strikingly, 37 assayed on MDA-MB-231 (a TNBC cell model) depicted an outstanding value of 18.66 μM much lower than 65.67 μM yielded by Gossypol Bcl-2 inhibitor whose main disadvantage is to produce multiple toxic effects. Highlighted above, enforce the premise of the computational tools to find new therapeutic options against the most aggressive forms of breast cancer, as the results herein showed.
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Affiliation(s)
- Loreley-A Morelos-Garnica
- Laboratorio de Diseño y Desarrollo de Nuevos Fármacos e Innovación Biotecnológica, Escuela Superior de Medicina, Instituto Politécnico Nacional, Plan de San Luis y Díaz Mirón s/n, Col. Casco de Santo Tomas, Alcaldía Miguel Hidalgo, C.P. 11340, Mexico City, México
| | - Sonia Guzmán-Velázquez
- Departamento de Fisiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Zacatenco, Av. Wilfrido Massieu 399, Col. Nueva Industrial Vallejo, Alcaldía Gustavo A. Madero, C.P. 07738, Mexico City, México
| | - Itzia-I Padilla-Martínez
- Laboratorio de Química Supramolecular y Nanociencias, Unidad Profesional Interdisciplinaria de Biotecnología, Instituto Politécnico Nacional, Av. Acueducto s/n, Barrio la Laguna Ticomán, Alcaldía Gustavo A. Madero, C.P. 07340, Mexico City, México
| | - José-R García-Sánchez
- Laboratorio de Oncología Molecular y Estrés Oxidativo, Escuela Superior de Medicina, Instituto Politécnico Nacional, Plan de San Luis y Díaz Mirón, s/n, Col. Casco de Santo Tomas, Alcaldía Miguel Hidalgo, C.P. 11340, Mexico City, México
| | - Martiniano Bello
- Laboratorio de Diseño y Desarrollo de Nuevos Fármacos e Innovación Biotecnológica, Escuela Superior de Medicina, Instituto Politécnico Nacional, Plan de San Luis y Díaz Mirón s/n, Col. Casco de Santo Tomas, Alcaldía Miguel Hidalgo, C.P. 11340, Mexico City, México
| | - Norbert Bakalara
- Centre National de la Recherche Scientifique, École Nationale Supérieure de Technologie des Biomolécules de Bordeaux INP, Univeristé de Bordeaux, 146 Rue Léo Saignat, 33000, Bordeaux, France
| | - David Méndez-Luna
- Laboratorio de Diseño y Desarrollo de Nuevos Fármacos e Innovación Biotecnológica, Escuela Superior de Medicina, Instituto Politécnico Nacional, Plan de San Luis y Díaz Mirón s/n, Col. Casco de Santo Tomas, Alcaldía Miguel Hidalgo, C.P. 11340, Mexico City, México.
- Departamento de Fisiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Zacatenco, Av. Wilfrido Massieu 399, Col. Nueva Industrial Vallejo, Alcaldía Gustavo A. Madero, C.P. 07738, Mexico City, México.
| | - José Correa-Basurto
- Laboratorio de Diseño y Desarrollo de Nuevos Fármacos e Innovación Biotecnológica, Escuela Superior de Medicina, Instituto Politécnico Nacional, Plan de San Luis y Díaz Mirón s/n, Col. Casco de Santo Tomas, Alcaldía Miguel Hidalgo, C.P. 11340, Mexico City, México.
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Jazmin GM, Elaheh M, Manuel Jonathan FV, Martiniano B, David ML, Alám LC, José CB. In Silico Design of an Oseltamivir Derivative with Increased Affinity against Wild-Type and Mutant Variants of Neuraminidase and Hemagglutinin of Influenza A H1N1 Virus. Chem Biodivers 2023:e202201077. [PMID: 37377353 DOI: 10.1002/cbdv.202201077] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2022] [Accepted: 06/08/2023] [Indexed: 06/29/2023]
Abstract
Antiviral resistance has turned into a world concern nowadays. Influenza A H1N1 emerged as a problem at the world level due to the neuraminidase (NA) mutations. The NA mutants conferred resistance to oseltamivir and zanamivir. Several efforts were conducted to develop better anti-influenza A H1N1 drugs. Our research group combined in silico methods to create a compound derived from oseltamivir to be tested in vitro against influenza A H1N1. Here we show the results of a new compound derived from oseltamivir but with specific chemical modifications, with significant affinity either on NA (in silico and in vitro assays) or HA (in silico) from influenza A H1N1 strain. We include docking and molecular dynamics (MD) simulations of the oseltamivir derivative at the binding site onto NA and HA of influenza A H1N1. Additionally, the biological experimental results show that oseltamivir derivative decreases the lytic-plaque formation on viral susceptibility assays, and it does not show cytotoxicity. Finally, oseltamivir derivative assayed on viral NA showed a concentration-dependent inhibition behavior at nM, depicting a high affinity of the compound for the enzyme, corroborated with the MD simulations results, placing our designed oseltamivir derivative as a potential antiviral against influenza A H1N1.
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Affiliation(s)
- García-Machorro Jazmin
- Laboratorio de Medicina de Conservación, Escuela Superior de Medicina, Instituto Politécnico., Plan de San Luis y Díaz Mirón s/n, Col. Casco de Santo Tomas, Delegación Miguel Hidalgo, C.P. 11340, Ciudad de México, México
| | - Mirzaeicheshmeh Elaheh
- Laboratorio de Medicina de Conservación, Escuela Superior de Medicina, Instituto Politécnico., Plan de San Luis y Díaz Mirón s/n, Col. Casco de Santo Tomas, Delegación Miguel Hidalgo, C.P. 11340, Ciudad de México, México
- Laboratorio de Diseño y Desarrollo de Nuevos Fármacos e Innovación Biotecnológica (Laboratory for the Design and Development of New Drugs and Biotechnological Innovation), Escuela Superior de Medicina, Instituto Politécnico Nacional, Plan de San Luis y Salvador Díaz Mirón s/n, Casco de Santo Tomás, Ciudad de México, 11340, México
| | - Fragoso-Vázquez Manuel Jonathan
- Departamento de Química Orgánica, Escuela Nacional de Ciencias, Biológicas, Instituto Politécnico Nacional, Prolongación de Carpio y Plan de Ayala, Col. Casco de Santo Tomas, México City, CP 11340, México
| | - Bello Martiniano
- Laboratorio de Diseño y Desarrollo de Nuevos Fármacos e Innovación Biotecnológica (Laboratory for the Design and Development of New Drugs and Biotechnological Innovation), Escuela Superior de Medicina, Instituto Politécnico Nacional, Plan de San Luis y Salvador Díaz Mirón s/n, Casco de Santo Tomás, Ciudad de México, 11340, México
| | - Méndez-Luna David
- Laboratorio de Diseño y Desarrollo de Nuevos Fármacos e Innovación Biotecnológica (Laboratory for the Design and Development of New Drugs and Biotechnological Innovation), Escuela Superior de Medicina, Instituto Politécnico Nacional, Plan de San Luis y Salvador Díaz Mirón s/n, Casco de Santo Tomás, Ciudad de México, 11340, México
- Departamento de Fisiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Zacatenco, Av. Wilfrido Massieu 399, Col. Nueva Industrial Vallejo, Alcaldía Gustavo A. Madero, Ciudad de México, 07738, México
| | - León-Cardona Alám
- Laboratorio de Diseño y Desarrollo de Nuevos Fármacos e Innovación Biotecnológica (Laboratory for the Design and Development of New Drugs and Biotechnological Innovation), Escuela Superior de Medicina, Instituto Politécnico Nacional, Plan de San Luis y Salvador Díaz Mirón s/n, Casco de Santo Tomás, Ciudad de México, 11340, México
| | - Correa-Basurto José
- Laboratorio de Diseño y Desarrollo de Nuevos Fármacos e Innovación Biotecnológica (Laboratory for the Design and Development of New Drugs and Biotechnological Innovation), Escuela Superior de Medicina, Instituto Politécnico Nacional, Plan de San Luis y Salvador Díaz Mirón s/n, Casco de Santo Tomás, Ciudad de México, 11340, México
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8
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Kumar S, Sengupta S, Ali I, Gupta MK, Lalhlenmawia H, Azizov S, Kumar D. Identification and exploration of quinazoline-1,2,3-triazole inhibitors targeting EGFR in lung cancer. J Biomol Struct Dyn 2023; 41:11353-11372. [PMID: 37114510 DOI: 10.1080/07391102.2023.2204360] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Accepted: 12/17/2022] [Indexed: 04/29/2023]
Abstract
Epidermal growth factor receptor (EGFR) enhances lung cancer development, due to their inability to permeate the cell membrane, secreted growth factors work through specialized signal transduction pathways. The purpose of this study is to find out a novel anticancer agent that inhibits EGFR and reduces the chances of lung cancer. A series of triazole-substituted quinazoline hybrid compounds were designed by Chemdraw software and docked against five different crystallographic EGFR tyrosine kinase domain (TKD). For docking and visualization PyRx, Autodock vina, and Discovery studio visualizer were used. Molecule-14, Molecule-16, Molecule-19, Molecule-20, and Molecule-38 showed significant affinity but Molecule-19 showed excellent binding affinity (-12.4 kcal/mol) with crystallographic EGFR tyrosine kinase. The superimposition of the co-crystalized ligand with the hit compound shows similar conformation at the active site of EGFR (PDB ID: 4HJO) indicating excellent coupling and pharmaceutically active. The hit compound showed a good bioavailability score (0.55) with no sign of carcinogenesis, mutagenesis, or reproductive toxicity properties. MD simulation and MMGBSA represent good stability and binding free energy demonstrating that the hit (Molecule-19) may be used as a lead compound. Molecule-19 also showed good ADME properties, bioavailability scores, and synthetic accessibility with fewer signs of toxicity. It was observed that Molecule-19 may be a novel and potential inhibitor against EGFR with fewer side effects than the reference molecule. Additionally, the molecular dynamics simulation revealed the stable nature of protein-ligand interaction and provided information about the amino acid residues involved in binding. Overall, this study led to the identification of potential EGFR inhibitors with favorable pharmacokinetic properties. We believe that the outcome of this study can help to develop more potent drug-like molecules to tackle human lung cancer.
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Affiliation(s)
- Sunil Kumar
- Department of Pharmaceutical Chemistry, School of Pharmaceutical Sciences, Shoolini University, Solan, Himachal Pradesh, India
| | - Sounok Sengupta
- Department of Pharmacology, School of Pharmaceutical Sciences, Shoolini University, Solan, Himachal Pradesh, India
| | - Iqra Ali
- Department of Biosciences, COMSATS University Islamabad, Islamabad, Pakistan
| | - Manoj K Gupta
- Department of Chemistry, School of Basic Sciences, Central University of Haryana, Mahendergarh, Haryana, India
| | - H Lalhlenmawia
- Department of Pharmacy, Regional Institute of Paramedical and Nursing Sciences, Aizawl, Mizoram, India
| | - Shavkatjon Azizov
- Laboratory of Biological Active Macromolecular Systems, Institute of Bioorganic Chemistry, Academy of Sciences Uzbekistan, Tashkent, Uzbekistan
- Department of Pharmaceutical Chemistry, Tashkent Pharmaceutical Institute, Tashkent, Uzbekistan
| | - Deepak Kumar
- Department of Pharmaceutical Chemistry, School of Pharmaceutical Sciences, Shoolini University, Solan, Himachal Pradesh, India
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9
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Azam F, Bello M. Dynamic and thermodynamic impact of L94A, W100A, and W100L mutations on the D2 dopamine receptor bound to risperidone. RSC Adv 2022; 12:34359-34368. [PMID: 36545576 PMCID: PMC9709807 DOI: 10.1039/d2ra06694g] [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: 10/22/2022] [Accepted: 11/22/2022] [Indexed: 12/02/2022] Open
Abstract
DRD2 is an important receptor in the mediation of antipsychotic drugs but also in Parkinson medication, hyperprolactinemia, nausea and vomiting. Recently, crystallographic studies of the DRD2-risperidone complex have provided important information about risperidone recognition in wild-type and different stabilizing DRD2-risperidone residues. Using the crystallographic structure of the DRD2-risperidone complex as a starting point, we undertook molecular dynamics (MD) simulations to investigate the structural and thermodynamic basis of molecular recognition by risperidone at the ligand-binding sites of wild-type and mutant DRD2. A solvated phospholipid bilayer was used to construct DRD2-risperidone complexes, which were then subjected to several microsecond (μs) MD simulations in order to obtain realistic receptor-ligand conformations under the equilibrated simulation time. Risperidone had a higher affinity for wild-type and L94A mutant DRD2 than the W100L and W100A mutants, according to binding free energy calculations using the Molecular Mechanics Generalized-Born Surface Area (MMGBSA) method, explaining the experimental differences in ligand residence times. Principal component (PC) analysis revealed important conformational mobility upon molecular recognition of risperidone for the L94A mutant compared to the wild type, indicating an unfavorable entropic component that may contribute to improving risperidone affinity in the L94A DRD2 mutant.
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Affiliation(s)
- Faizul Azam
- Department of Pharmaceutical Chemistry and Pharmacognosy, Unaizah College of Pharmacy, Qassim UniversityUnaizah51911Saudi Arabia
| | - Martiniano Bello
- Laboratorio de Diseño y Desarrollo de Nuevos Fármacos e Innovación Biotecnológica, Escuela Superior de Medicina, Instituto Politécnico NacionalPlan de San Luis y Diaz Mirón, S/N, Col. Casco de Santo TomasCiudad de México 11340Mexico
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10
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Microsecond MD Simulations to Explore the Structural and Energetic Differences between the Human RXRα-PPARγ vs. RXRα-PPARγ-DNA. Molecules 2022; 27:molecules27185778. [PMID: 36144514 PMCID: PMC9503000 DOI: 10.3390/molecules27185778] [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: 08/08/2022] [Revised: 08/30/2022] [Accepted: 09/02/2022] [Indexed: 11/16/2022] Open
Abstract
The heterodimeric complex between retinoic X receptor alpha (RXRα) and peroxisome proliferator-activated receptor gamma (PPARγ) is one of the most important and predominant regulatory systems, controlling lipid metabolism by binding to specific DNA promoter regions. X-ray and molecular dynamics (MD) simulations have revealed the average conformation adopted by the RXRα-PPARγ heterodimer bound to DNA, providing information about how multiple domains communicate to regulate receptor properties. However, knowledge of the energetic basis of the protein-ligand and protein-protein interactions is still lacking. Here we explore the structural and energetic mechanism of RXRα-PPARγ heterodimer bound or unbound to DNA and forming complex with co-crystallized ligands (rosiglitazone and 9-cis-retinoic acid) through microsecond MD simulations, molecular mechanics generalized Born surface area binding free energy calculations, principal component analysis, the free energy landscape, and correlated motion analysis. Our results suggest that DNA binding alters correlated motions and conformational mobility within RXRα–PPARγ system that impact the dimerization and the binding affinity on both receptors. Intradomain correlated motions denotes a stronger correlation map for RXRα-PPARγ-DNA than RXRα-PPARγ, involving residues at the ligand binding site. In addition, our results also corroborated the greater role of PPARγ in regulation of the free and bound DNA state.
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11
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Bello M. Molecular Basis of Inhibitory Mechanism of Naltrexone and Its Metabolites through Structural and Energetic Analyses. Molecules 2022; 27:molecules27154919. [PMID: 35956868 PMCID: PMC9369988 DOI: 10.3390/molecules27154919] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Revised: 07/18/2022] [Accepted: 07/20/2022] [Indexed: 11/16/2022] Open
Abstract
Naltrexone is a potent opioid antagonist with good blood–brain barrier permeability, targeting different endogenous opioid receptors, particularly the mu-opioid receptor (MOR). Therefore, it represents a promising candidate for drug development against drug addiction. However, the details of the molecular interactions of naltrexone and its derivatives with MOR are not fully understood, hindering ligand-based drug discovery. In the present study, taking advantage of the high-resolution X-ray crystal structure of the murine MOR (mMOR), we constructed a homology model of the human MOR (hMOR). A solvated phospholipid bilayer was built around the hMOR and submitted to microsecond (µs) molecular dynamics (MD) simulations to obtain an optimized hMOR model. Naltrexone and its derivatives were docked into the optimized hMOR model and submitted to µs MD simulations in an aqueous membrane system. The MD simulation results were submitted to the molecular mechanics–generalized Born surface area (MMGBSA) binding free energy calculations and principal component analysis. Our results revealed that naltrexone and its derivatives showed differences in protein–ligand interactions; however, they shared contacts with residues at TM2, TM3, H6, and TM7. The binding free energy and principal component analysis revealed the structural and energetic effects responsible for the higher potency of naltrexone compared to its derivatives.
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Affiliation(s)
- Martiniano Bello
- Laboratorio de Diseño y Desarrollo de Nuevos Fármacos e Innovación Biotecnológica, Escuela Superior de Medicina, Instituto Politécnico Nacional, Plan de San Luis y Diaz Mirón, s/n, Col. Casco de Santo Tomas, Mexico City 11340, Mexico
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12
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Mahalapbutr P, Leechaisit R, Thongnum A, Todsaporn D, Prachayasittikul V, Rungrotmongkol T, Prachayasittikul S, Ruchirawat S, Prachayasittikul V, Pingaew R. Discovery of Anilino-1,4-naphthoquinones as Potent EGFR Tyrosine Kinase Inhibitors: Synthesis, Biological Evaluation, and Comprehensive Molecular Modeling. ACS OMEGA 2022; 7:17881-17893. [PMID: 35664590 PMCID: PMC9161259 DOI: 10.1021/acsomega.2c01188] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Accepted: 04/21/2022] [Indexed: 05/02/2023]
Abstract
Epidermal growth factor receptor (EGFR) has been recognized as one of the attractive targets for anticancer drug development. Herein, a set of anilino-1,4-naphthoquinone derivatives (3-18) was synthesized and investigated for their anticancer and EGFR inhibitory potentials. Among all tested compounds, three derivatives (3, 8, and 10) were selected for studying EGFR inhibitory activity (in vitro and in silico) due to their most potent cytotoxic activities against six tested cancer cell lines (i.e., HuCCA-1, HepG2, A549, MOLT-3, MDA-MB-231, and T47D; IC50 values = 1.75-27.91 μM), high selectivity index (>20), and good predicted drug-like properties. The experimental results showed that these three promising compounds are potent EGFR inhibitors with nanomolar IC50 values (3.96-18.64 nM). Interestingly, the most potent compound 3 bearing 4-methyl substituent on the phenyl ring displayed 4-fold higher potency than the known EGFR inhibitor, erlotinib. Molecular docking, molecular dynamics simulation, and MM/GBSA-based free energy calculation revealed that van der Waals force played a major role in the accommodations of compound 3 within the ATP-binding pocket of EGFR. Additionally, the 4-CH3 moiety of the compound was noted to be a key chemical feature contributing to the highly potent EGFR inhibitory activity via its formations of alkyl interactions with A743, K745, M766, and L788 residues as well as additional interactions with M766 and T790.
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Affiliation(s)
- Panupong Mahalapbutr
- Department
of Biochemistry, and Center for Translational Medicine, Faculty of
Medicine, Khon Kaen University, Khon Kaen 40002, Thailand
| | - Ronnakorn Leechaisit
- Department
of Chemistry, Faculty of Science, Srinakharinwirot
University, Bangkok 10110, Thailand
| | - Anusit Thongnum
- Department
of Physics, Faculty of Science, Srinakharinwirot
University, Bangkok 10110, Thailand
| | - Duangjai Todsaporn
- Structural
and Computational Biology Research Unit, Department of Biochemistry,
Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand
| | - Veda Prachayasittikul
- Center
of Data Mining and Biomedical Informatics, Faculty of Medical Technology, Mahidol University, Bangkok 10700, Thailand
| | - Thanyada Rungrotmongkol
- Structural
and Computational Biology Research Unit, Department of Biochemistry,
Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand
- Program
in Bioinformatics and Computational Biology, Graduate School, Chulalongkorn University, Bangkok 10330, Thailand
| | - Supaluk Prachayasittikul
- Center
of Data Mining and Biomedical Informatics, Faculty of Medical Technology, Mahidol University, Bangkok 10700, Thailand
| | - Somsak Ruchirawat
- Laboratory
of Medicinal Chemistry and Program in Chemical Sciences, Chulabhorn Research Institute, Chulabhorn Graduate
Institute, Bangkok 10210, Thailand
- Commission
on Higher Education, Ministry of Education, Center of Excellence on Environmental Health and Toxicology (EHT), Bangkok 10400, Thailand
| | - Virapong Prachayasittikul
- Department
of Clinical Microbiology and Applied Technology, Faculty of Medical
Technology, Mahidol University, Bangkok 10700, Thailand
| | - Ratchanok Pingaew
- Department
of Chemistry, Faculty of Science, Srinakharinwirot
University, Bangkok 10110, Thailand
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13
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Li Y, Fu R, Jiang T, Duan D, Wu Y, Li C, Li Z, Ni R, Li L, Liu Y. Mechanism of Lethal Skin Toxicities Induced by Epidermal Growth Factor Receptor Inhibitors and Related Treatment Strategies. Front Oncol 2022; 12:804212. [PMID: 35223483 PMCID: PMC8866822 DOI: 10.3389/fonc.2022.804212] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Accepted: 01/17/2022] [Indexed: 02/01/2023] Open
Abstract
Epidermal growth factor receptor (EGFR) inhibitors are widely used to treat various types of cancers such as non-small cell lung cancer, head and neck cancer, breast cancer, pancreatic cancer. Adverse reactions such as skin toxicity, interstitial lung disease, hepatotoxicity, ocular toxicity, hypomagnesemia, stomatitis, and diarrhea may occur during treatment. Because the EGFR signaling pathway is important for maintaining normal physiological skin function. Adverse skin reactions occurred in up to 90% of cancer patients treated with EGFR inhibitors, including common skin toxicities (such as papulopustular exanthemas, paronychia, hair changes) and rare fatal skin toxicities (e.g., Stevens–Johnson syndrome, toxic epidermal necrolysis, acute generalized exanthematous pustulosis). This has led to the dose reduction or discontinuation of EGFR inhibitors in the treatment of cancer. Recently, progress has been made about research on the skin toxicity of EGFR inhibitors. Here, we summarize the mechanism of skin toxicity caused by EGFR inhibitors, measures to prevent severe fatal skin toxicity, and provide reference for medical staff how to give care and treatment after adverse skin reactions.
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Affiliation(s)
- Yanping Li
- Department of Pharmacy, Daping Hospital, Army Medical University, Chongqing, China
| | - Ruoqiu Fu
- Department of Pharmacy, Daping Hospital, Army Medical University, Chongqing, China
| | - Tingting Jiang
- Department of Pharmacy, Daping Hospital, Army Medical University, Chongqing, China
| | - Dongyu Duan
- Department of Pharmacy, Daping Hospital, Army Medical University, Chongqing, China
| | - Yuanlin Wu
- Department of Pharmacy, Daping Hospital, Army Medical University, Chongqing, China
| | - Chen Li
- Department of Pharmacy, Daping Hospital, Army Medical University, Chongqing, China
| | - Ziwei Li
- Department of Pharmacy, Daping Hospital, Army Medical University, Chongqing, China
| | - Rui Ni
- Department of Pharmacy, Daping Hospital, Army Medical University, Chongqing, China
| | - Li Li
- Department of Pharmacy, Daping Hospital, Army Medical University, Chongqing, China
| | - Yao Liu
- Department of Pharmacy, Daping Hospital, Army Medical University, Chongqing, China
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14
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Kiriwan D, Seetaha S, Jiwacharoenchai N, Tabtimmai L, Sousa SF, Songtawee N, Choowongkomon K. Identification of tripeptides against tyrosine kinase domain of EGFR for lung cancer cell inhibition by in silico and in vitro studies. Chem Biol Drug Des 2021; 99:456-469. [PMID: 34923743 DOI: 10.1111/cbdd.14010] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Revised: 11/10/2021] [Accepted: 12/11/2021] [Indexed: 12/30/2022]
Abstract
Epidermal growth factor receptor tyrosine kinase domain (EGFR-TK) has been one of the prominent targets for therapeutics of several human cancers, in particular non-small cell lung cancer. Although several small chemical compounds targeting EGFR-TK have been approved by FDA for treatment of such a cancer, the discovery of a new class of EGFR-TK inhibitors, for example, small peptides, is still desired. In this study, using molecular docking-based virtual screening, we selected five small peptides with high docking scores from eight thousand peptides as candidate compounds against EGFR-TK. Among five, the tripeptide WFF had the most potency to suppress the survival of non-small cell lung cancer cells but had the least toxicity to human liver cancer cells. Our in vitro kinase assays showed that WFF exhibited much lower inhibitory activity against purified EGFR-TK than the drug erlotinib (i.e., IC50 values of ≈ 0.62 μM vs ≈ 7.57 nM, respectively). The relative free binding energies estimated from molecular dynamic simulations were consistent with the in vitro experiments in which the WFF bound had a lower affinity than erlotinib bound to EGFR-TK (i.e., ΔGbind values of -20.3 kJ/mol vs ≈ -126.8 kJ/mol, respectively). In addition, the simulation analyses demonstrated the difference in EGFR binding preference between the drug and tripeptide in which erlotinib was stably bound in the ATP-binding pocket for 4-anilinoquinazoline class of inhibitors, while WFF moved out of that pocket to interact with polar amino acid residues on the αC-helix, activation loop, and substrate-binding region. Our findings suggest preferable interactions of the potential tripeptide on enzyme inhibition that are useful for further development of a new class of inhibitors targeting EGFR-TK.
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Affiliation(s)
- Duangnapa Kiriwan
- Genetic Engineering and Bioinformatics Program, Kasetsart University, Bangkok, Thailand
| | - Supaphorn Seetaha
- Department of Biochemistry, Faculty of Science, Kasetsart University, Bangkok, Thailand
| | | | - Lueacha Tabtimmai
- Department of Biotechnology, Faculty of Applied Science, King Mongkut's University of Technology North Bangkok, Bangkok, Thailand
| | - Sérgio F Sousa
- Associate Laboratory i4HB-Institute for Health and Bioeconomy, Faculdade de Medicina, Universidade do Porto, Porto, Portugal.,UCIBIO-Applied Molecular Biosciences Unit, BioSIM-Departamento de Biomedicina, Faculdade de Medicina, Universidade do Porto, Porto, Portugal
| | - Napat Songtawee
- Department of Clinical Chemistry, Faculty of Medical Technology, Mahidol University, Nakhon Pathom, Thailand
| | - Kiattawee Choowongkomon
- Department of Biochemistry, Faculty of Science, Kasetsart University, Bangkok, Thailand.,Center for Advanced Studies in Nanotechnology for Chemical, Food and Agricultural Industries, KU Institute for Advanced Studies, Kasetsart University, Bangkok, Thailand
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15
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Balbuena-Rebolledo I, Padilla-Martínez II, Rosales-Hernández MC, Bello M. Repurposing FDA Drug Compounds against Breast Cancer by Targeting EGFR/HER2. Pharmaceuticals (Basel) 2021; 14:ph14080791. [PMID: 34451888 PMCID: PMC8401258 DOI: 10.3390/ph14080791] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2021] [Revised: 08/03/2021] [Accepted: 08/05/2021] [Indexed: 12/13/2022] Open
Abstract
Repurposing studies have identified several FDA-approved compounds as potential inhibitors of the intracellular domain of epidermal growth factor receptor 1 (EGFR) and human epidermal receptor 2 (HER2). EGFR and HER2 represent important targets for the design of new drugs against different types of cancer, and recently, differences in affinity depending on active or inactive states of EGFR or HER2 have been identified. In this study, we first identified FDA-approved compounds with similar structures in the DrugBank to lapatinib and gefitinib, two known inhibitors of EGFR and HER2. The selected compounds were submitted to docking and molecular dynamics MD simulations with the molecular mechanics generalized Born surface area approach to discover the conformational and thermodynamic basis for the recognition of these compounds on EGFR and HER2. These theoretical studies showed that compounds reached the ligand-binding site of EGFR and HER2, and some of the repurposed compounds did not interact with residues involved in drug resistance. An in vitro assay performed on two different breast cancer cell lines, MCF-7, and MDA-MB-23, showed growth inhibitory activity for these repurposed compounds on tumorigenic cells at micromolar concentrations. These repurposed compounds open up the possibility of generating new anticancer treatments by targeting HER2 and EGFR.
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Affiliation(s)
- Irving Balbuena-Rebolledo
- Laboratorio de Diseño y Desarrollo de Nuevos Fármacos e Innovación Biotecnológica, Escuela Superior de Medicina, Instituto Politécnico Nacional, Plan de San Luis y Diaz Mirón, s/n, Col. Casco de Santo Tomas, Ciudad de México 11340, Mexico;
- Laboratorio de Química Supramolecular y Nanociencias, Unidad Profesional Interdisciplinaria de Biotecnología, Instituto Politécnico Nacional, Av. Acueducto s/n, Barrio La Laguna Ticomán, Ciudad de México 07340, Mexico;
| | - Itzia Irene Padilla-Martínez
- Laboratorio de Química Supramolecular y Nanociencias, Unidad Profesional Interdisciplinaria de Biotecnología, Instituto Politécnico Nacional, Av. Acueducto s/n, Barrio La Laguna Ticomán, Ciudad de México 07340, Mexico;
| | - Martha Cecilia Rosales-Hernández
- Laboratorio de Biofísica y Biocatálisis, Sección de Estudios de Posgrado e Investigación, Escuela Superior de Medicina, Instituto Politécnico Nacional, Plan de San Luis y Diaz Mirón, s/n, Col. Casco de Santo Tomas, Ciudad de México 11340, Mexico;
| | - Martiniano Bello
- Laboratorio de Diseño y Desarrollo de Nuevos Fármacos e Innovación Biotecnológica, Escuela Superior de Medicina, Instituto Politécnico Nacional, Plan de San Luis y Diaz Mirón, s/n, Col. Casco de Santo Tomas, Ciudad de México 11340, Mexico;
- Correspondence: or
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16
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Topomer-CoMFA proposed as a tool to construct dual EGFR/HER-2 models. J Mol Model 2021; 27:239. [PMID: 34363097 DOI: 10.1007/s00894-021-04852-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Accepted: 07/06/2021] [Indexed: 10/20/2022]
Abstract
Protein kinases (in this case, HER-2 and EGFR) are involved in cancer-related diseases. Some reports have shown unique CoMFA models using the sum of activities expressed as pIC50 (-log IC50), as the classical CoMFA technique would not be the best strategy to construct models for multitarget therapy considering that the molecular alignment will not be the same for different targets. An alternative for this problem is the use of Topomer-CoMFA, a variation of CoMFA, which does not require the alignment step in the generation of 3D models. In this study, we propose the combined use of the sum of activities and Topomer-CoMFA for the construction of a unique dual 3D model considering the inhibitory activities against EGFR and HER-2. For this, 88 compounds from the literature were divided into two groups: training (71) and test (17) sets. The biological activity of each compound, expressed as IC50 for EGFR and HER-2, was transformed into pIC50, summed, and used as the dependent variable in the Topomer-CoMFA analyses. The obtained model was considered statistically robust in the prediction of the dual activity of new compounds. Finally, based on the obtained model, we proposed structural modifications to some of the compounds used to improve the biological data. From the 3D model, we suggested new derivative compounds with improved biological activity for both targets. Therefore, the combination of the techniques proposed in this study proves to be a good strategy to construct better statistical models that can predict biological activities in multitarget systems.
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17
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Hasan MK, Kamruzzaman M, Bin Manjur OH, Mahmud A, Hussain N, Alam Mondal MS, Hosen MI, Bello M, Rahman A. Structural analogues of existing anti-viral drugs inhibit SARS-CoV-2 RNA dependent RNA polymerase: A computational hierarchical investigation. Heliyon 2021; 7:e06435. [PMID: 33693066 PMCID: PMC7934700 DOI: 10.1016/j.heliyon.2021.e06435] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2020] [Revised: 02/16/2021] [Accepted: 03/03/2021] [Indexed: 01/18/2023] Open
Abstract
The Coronavirus Disease 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) became a pandemic, resulting in an exponentially increased mortality globally and scientists all over the world are struggling to find suitable solutions to combat it. Multiple repurposed drugs have already been in several clinical trials or recently completed. However, none of them shows any promising effect in combating COVID-19. Therefore, developing an effective drug is an unmet global need. RdRp (RNA dependent RNA polymerase) plays a pivotal role in viral replication. Therefore, it is considered as a prime target of drugs that may treat COVID-19. In this study, we have screened a library of compounds, containing approved RdRp inhibitor drugs that were or in use to treat other viruses (favipiravir, sofosbuvir, ribavirin, lopinavir, tenofovir, ritonavir, galidesivir and remdesivir) and their structural analogues, in order to identify potential inhibitors of SARS-CoV-2 RdRp. Extensive screening, molecular docking and molecular dynamics show that five structural analogues have notable inhibitory effects against RdRp of SARS-CoV-2. Importantly, comparative protein-antagonists interaction revealed that these compounds fit well in the pocket of RdRp. ADMET analysis of these compounds suggests their potency as drug candidates. Our identified compounds may serve as potential therapeutics for COVID-19.
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Affiliation(s)
- Md. Kamrul Hasan
- Department of Biochemistry and Molecular Biology, Tejgaon College, National University, Gazipur 1704, Bangladesh
| | - Mohammad Kamruzzaman
- Department of Biochemistry and Molecular Biology, University of Dhaka, Dhaka 1000, Bangladesh
| | - Omar Hamza Bin Manjur
- Department of Biochemistry and Molecular Biology, University of Dhaka, Dhaka 1000, Bangladesh
| | - Araf Mahmud
- Department of Genetic Engineering and Biotechnology, Shahjalal University of Science and Technology, Sylhet, 3114, Bangladesh
| | - Nazmul Hussain
- Department of Biochemistry and Molecular Biology, Tejgaon College, National University, Gazipur 1704, Bangladesh
| | | | - Md. Ismail Hosen
- Department of Biochemistry and Molecular Biology, University of Dhaka, Dhaka 1000, Bangladesh
| | - Martiniano Bello
- Laboratorio de Diseño y Desarrollo de Nuevos Fármacos e Innovación Biotécnológica (Laboratory for the Design and Development of New Drugs and Biotechnological Innovation), Escuela Superior de Medicina, Instituto Politécnico Nacional, Plan de San Luis y Díaz Mirón, Ciudad de México 11340, Mexico
| | - Atiqur Rahman
- Department of Biochemistry and Molecular Biology, University of Dhaka, Dhaka 1000, Bangladesh
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18
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Making NSCLC Crystal Clear: How Kinase Structures Revolutionized Lung Cancer Treatment. CRYSTALS 2020. [DOI: 10.3390/cryst10090725] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The parallel advances of different scientific fields provide a contemporary scenario where collaboration is not a differential, but actually a requirement. In this context, crystallography has had a major contribution on the medical sciences, providing a “face” for targets of diseases that previously were known solely by name or sequence. Worldwide, cancer still leads the number of annual deaths, with 9.6 million associated deaths, with a major contribution from lung cancer and its 1.7 million deaths. Since the relationship between cancer and kinases was unraveled, these proteins have been extensively explored and became associated with drugs that later attained blockbuster status. Crystallographic structures of kinases related to lung cancer and their developed and marketed drugs provided insight on their conformation in the absence or presence of small molecules. Notwithstanding, these structures were also of service once the initially highly successful drugs started to lose their effectiveness in the emergence of mutations. This review focuses on a subclassification of lung cancer, non-small cell lung cancer (NSCLC), and major oncogenic driver mutations in kinases, and how crystallographic structures can be used, not only to provide awareness of the function and inhibition of these mutations, but also how these structures can be used in further computational studies aiming at addressing these novel mutations in the field of personalized medicine.
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19
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Li DD, Wu TT, Yu P, Wang ZZ, Xiao W, Jiang Y, Zhao LG. Molecular Dynamics Analysis of Binding Sites of Epidermal Growth Factor Receptor Kinase Inhibitors. ACS OMEGA 2020; 5:16307-16314. [PMID: 32656454 PMCID: PMC7346266 DOI: 10.1021/acsomega.0c02183] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Accepted: 06/08/2020] [Indexed: 05/14/2023]
Abstract
The development of an epidermal growth factor receptor (EGFR) tyrosine kinase inhibitor (TKI) is an ongoing and challenging research field. However, the dynamic motion of the binding site of EGFR has not been accurately depicted, hindering the improvement of EGFR TKI. For this reason, about 33 protein complexes (32 EGFR proteins plus 1 ErbB4 protein) were carefully curated and subsequently studied for dynamic movements of their binding sites by molecular dynamics simulations in this study. The analysis of root mean square deviation (RMSD) revealed that T790M mutation can make an impact on dynamic motion of binding sites; the RMSD value of the EGFR binding site was unrelated to inhibitory activity. The analysis of the radius of gyration (R g) revealed that T790M can slightly shrink the value of R g, thereby influencing the shape of the EGFR binding site. More interestingly, the R g value can exhibit weak correlation with inhibitory activity of most inhibitors. The relationship between R g and biological activity deserve our serious interest since the best scoring function, Xscore, cannot distinguish highly active EGFR inhibitors. The root mean square fluctuation (RMSF) analysis of key residues derived from binding sites indicated that the most flexible residue was ASP800 with a large RMSF value against the steady residue ALA743 with a small RMSF value, and two other residues (MET793 and LEU844) were supposed to be involved with molecular recognition. In short, the obtained results would be more effective for guiding the development of a novel EGFR kinase inhibitor.
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Affiliation(s)
- Dong-Dong Li
- Jiangsu
Co-Innovation Center of Efficient Processing and Utilization of Forest
Resources, Nanjing Forestry University, Nanjing 210037, People’s Republic of China
- College
of Chemical Engineering, Nanjing Forestry
University, 159 Long Pan Road, Nanjing 210037, China
| | - Ting-Ting Wu
- Jiangsu
Co-Innovation Center of Efficient Processing and Utilization of Forest
Resources, Nanjing Forestry University, Nanjing 210037, People’s Republic of China
- College
of Chemical Engineering, Nanjing Forestry
University, 159 Long Pan Road, Nanjing 210037, China
| | - Pan Yu
- Jiangsu
Co-Innovation Center of Efficient Processing and Utilization of Forest
Resources, Nanjing Forestry University, Nanjing 210037, People’s Republic of China
- College
of Chemical Engineering, Nanjing Forestry
University, 159 Long Pan Road, Nanjing 210037, China
| | - Zhen-Zhong Wang
- Jiangsu
Kanion Pharmaceutical Co., Ltd., 58 Haichang South Road, Lianyungang 222001, Jiangsu Province, China
| | - Wei Xiao
- Jiangsu
Kanion Pharmaceutical Co., Ltd., 58 Haichang South Road, Lianyungang 222001, Jiangsu Province, China
- . Phone: +86-0518-81152227
| | - Yan Jiang
- College
of Chemical Engineering, Nanjing Forestry
University, 159 Long Pan Road, Nanjing 210037, China
- . Phone: +86-025-85427544
| | - Lin-Guo Zhao
- Jiangsu
Co-Innovation Center of Efficient Processing and Utilization of Forest
Resources, Nanjing Forestry University, Nanjing 210037, People’s Republic of China
- College
of Chemical Engineering, Nanjing Forestry
University, 159 Long Pan Road, Nanjing 210037, China
- . Phone: +86-025-85427962. Fax: +86-025-85418873
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Bello M, Guadarrama-García C, Rodriguez-Fonseca RA. Dissecting the molecular recognition of dual lapatinib derivatives for EGFR/HER2. J Comput Aided Mol Des 2019; 34:293-303. [DOI: 10.1007/s10822-019-00270-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2019] [Accepted: 12/06/2019] [Indexed: 01/22/2023]
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Zhang Z, Xu Y, Wu J, Shen Y, Cheng H, Xiang Y. Exploration of the selective binding mechanism of protein kinase Aurora A selectivity via a comprehensive molecular modeling study. PeerJ 2019; 7:e7832. [PMID: 31660263 PMCID: PMC6814069 DOI: 10.7717/peerj.7832] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2019] [Accepted: 09/04/2019] [Indexed: 12/12/2022] Open
Abstract
Background The kinase of Aurora A has been regarded as a promising therapeutic target due to its altered expression in various human cancers. However, given the high similarity of the active binding site of Aurora A to other kinases, designing highly selective inhibitors towards Aurora A remains a challenge. Recently, two potential small-molecule inhibitors named AT9283 and Danusertib were reported to exhibit significant selectivity to Aurora A, but not to Gleevec. It was argued that protein dynamics is crucial for drug selectivity to Aurora A. However, little computational research has been conducted to shed light on the underlying mechanisms. Methods In this study, MM/GBSA calculations based on conventional molecular dynamics (cMD) simulations and enhanced sampling simulations including Gaussian accelerated MD (GaMD) simulations and umbrella sampling were carried out to illustrate the selectivity of inhibitors to Aurora A. Results The calculation results from cMD simulation showed that the binding specificity is primarily controlled by conformational change of the kinase hinge. The protein dynamics and energetic differences were further supported by the GaMD simulations. Umbrella sampling further proved that AT9283 and Danusertib have similar potential of mean force (PMF) profiles toward Aurora A in terms of PMF depth. Compared with AT9283 and Danusertib, Gleevec has much lower PMF depth, indicating that Gleevec is more easily dissociated from Aurora A than AT9283 and Danusertib. These results not only show the selective determinants of Aurora A, but also provide valuable clues for the further development of novel potent Aurora A selective inhibitors.
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Affiliation(s)
- Zhe Zhang
- Department of Surgery, Clinical Medical College, Hubei University of Science and Technology, Xianning, Hubei, China
| | - Yafei Xu
- Department of Orthopedics, Nanhai Hospital, Southern Medical University, Foshan, Guangdong, China
| | - Jian Wu
- Department of Orthopedics, Xianning Central Hospital, Xianning, Hubei, China
| | - Ying Shen
- Department of Public Health, Xianning Central Hospital, Xianning, Hubei, China
| | - Hao Cheng
- Department of Surgery, Clinical Medical College, Hubei University of Science and Technology, Xianning, Hubei, China
| | - Yiming Xiang
- Department of Surgery, Second Affiliated Hospital of Hubei University of Science and Technology, Xianning, Hubei, China
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Ye L, Zhao T, Du W, Li A, Gao W, Li J, Wang L, Chen W. Discovery of aminopyridine-containing spiro derivatives as EGFR mutations inhibitors. J Enzyme Inhib Med Chem 2019; 34:1233-1246. [PMID: 31286784 PMCID: PMC6691816 DOI: 10.1080/14756366.2019.1634704] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Neratinib is an oral pan HER inhibitor, that irreversibly inhibits EGFR and HER2 and was proven to be effective against multiple EGFR mutations. In previous study, we reported spiro [indoline-3, 4′-piperidine]-2-ones as anticancer agents. In this study, we designed aminopyridine-containing spiro [indoline-3,4′-piperidine] derivatives A1-A4 using Neratinib and spiro [indoline-3, 4′-piperidine]-2-one compound patented as lead structure, then replaced piperidine with cyclopropane to obtain B1-B7 and replaced indoline with benzmorpholine to get C1-C4 and D1-D2. We synthesized these compounds and evaluated their residual activities under 0.5 M drug concentration on EGFR and ERBB2. Most of compounds showed stronger inhibition on EGFR-wt and ERBB2, in which A1-A4 showed excellent inhibitory activity with inhibition percentage on EGFR-wt kinase of 7%, 6%, 19%, 27%, respectively and 9%, 5%, 12%, 34% on ERBB2 kinase compared with 2% and 6% of Neratinib.
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Affiliation(s)
- Lianbao Ye
- a School of Pharmacy , Guangdong Pharmaceutical University , Guangzhou , China
| | - Tao Zhao
- a School of Pharmacy , Guangdong Pharmaceutical University , Guangzhou , China
| | - Wenjun Du
- a School of Pharmacy , Guangdong Pharmaceutical University , Guangzhou , China
| | - Anhu Li
- b Esa Biotech Co., LTD. , Guangzhou , China
| | - Wei Gao
- a School of Pharmacy , Guangdong Pharmaceutical University , Guangzhou , China
| | | | - Ling Wang
- d Joint International Research Laboratory of Synthetic Biology and Medicine, Guangdong Provincial Engineering and Technology Research Center of Biopharmaceuticals, School of Biology and Biological Engineering , South China University of Technology , Guangzhou , China
| | - Weiqiang Chen
- c School of Basic Courses , Guangdong Pharmaceutical University , Guangzhou , China
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Saldaña-Rivera L, Bello M, Méndez-Luna D. Structural insight into the binding mechanism of ATP to EGFR and L858R, and T790M and L858R/T790 mutants. J Biomol Struct Dyn 2019; 37:4671-4684. [PMID: 30558477 DOI: 10.1080/07391102.2018.1558112] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
The L858R mutation in EGFR is particularly responsive to small tyrosine kinase inhibitors (TKIs) such as gefitinib and erlotinib. This efficacy decreases due to drug resistance conferred by a second mutation, T790M, which subsequently produces a double mutant, L858R/T790M. Although this resistance was initially attributed to steric blocking by the T790M mutation, experimental studies have demonstrated that differences in the binding affinities of TKIs to T790M and L858R/T790M mutants are more a result of the increased sensitivity of these mutants to ATP than to a decrease in the affinity to TKIs. Regrettably, detailed information at the atomic level on the origins of the increased binding affinity of mutants for ATP is lacking. In this study, we have combined structural data and molecular dynamics simulations with the MMGBSA approach to determine how the L858R, T790M and L858R/T790 mutations impact the binding mechanism of ATP with respect to wild-type EGFR. Structural and energetic analyses provided novel information that helps to explain the increased affinity of ATP to T790M and L858R/T790 mutants with respect to L858R and wild-type systems. In addition, it was observed that dimerization of the wild-type and mutant systems exerts dissimilar effects on the ATP binding affinity characteristic of negative cooperativity. Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Lucia Saldaña-Rivera
- 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 , México City , México
| | - 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 , México City , México
| | - David Méndez-Luna
- 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 , México City , México
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Ma G, Zhu J, Liu F, Yang Y. Long Noncoding RNA LINC00460 Promotes the Gefitinib Resistance of Nonsmall Cell Lung Cancer Through Epidermal Growth Factor Receptor by Sponging miR-769-5p. DNA Cell Biol 2019; 38:176-183. [PMID: 30601026 PMCID: PMC6383575 DOI: 10.1089/dna.2018.4462] [Citation(s) in RCA: 53] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
The vital roles of long noncoding RNAs (lncRNAs) in the nonsmall cell lung cancer (NSCLC) tumorigenesis are increasingly important. This work aims to investigate the role of lncRNA LINC00460 in the gefitinib resistance of NSCLC cells and discover its relevant mechanism. Our finding reveals that the expression of lncRNA LINC00460 is upregulated in the gefitinib-resistant NSCLC tissue and cells, and closely correlated with advanced tumor stage and clinical poor prognosis outcome. Gain and loss functional assays are performed in gefitinib-resistant NSCLC cells (A549/GR), stating that LINC00460 facilitates the 50% inhibitive concentration of gefitinib for NSCLC cells, multidrug-resistant-related proteins (P-gp, MRP1, and BCRP), as well as the invasion. In vivo, LINC00460 silencing represses the tumor growth. Bioinformatics prediction tools and luciferase analysis confirm that the upregulated LINC00460 sponged miR-769-5p in NSCLC cells; moreover, epidermal growth factor receptor (EGFR) is identified as a direct target gene of miR-769-5p. Verification experiments confirm that the restoration of EGFR could weaken the sensibility of NSCLC cells toward the gefitinib. In conclusion, our result demonstrates that LINC00460 plays a pivotal role in gefitinib resistance of NSCLC cells by targeting EGFR through sponging miR-769-5p. This finding might serve as a therapeutic target for NSCLC.
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Affiliation(s)
- Guodong Ma
- 1 Department of Chest Surgery, Nanjing Chest Hospital, Nanjing, China
| | - Jiping Zhu
- 2 Department of Pneumology, Jiangsu Province Hospital of Traditional Chinese Medicine, Nanjing, China
| | - Feng Liu
- 1 Department of Chest Surgery, Nanjing Chest Hospital, Nanjing, China
| | - Yan Yang
- 3 Department of Radiation Oncology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
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