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Cano-González L, Espinosa-Mendoza JD, Matadamas-Martínez F, Romero-Velásquez A, Flores-Ramos M, Colorado-Pablo LF, Cerbón-Cervantes MA, Castillo R, González-Sánchez I, Yépez-Mulia L, Hernández-Campos A, Aguayo-Ortiz R. Structure-Based Optimization of Carbendazim-Derived Tubulin Polymerization Inhibitors through Alchemical Free Energy Calculations. J Chem Inf Model 2023; 63:7228-7238. [PMID: 37947759 DOI: 10.1021/acs.jcim.3c01379] [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: 11/12/2023]
Abstract
Carbendazim derivatives, commonly used as antiparasitic drugs, have shown potential as anticancer agents due to their ability to induce cell cycle arrest and apoptosis in human cancer cells by inhibiting tubulin polymerization. Crystallographic structures of α/β-tubulin multimers complexed with nocodazole and mebendazole, two carbendazim derivatives with potent anticancer activity, highlighted the possibility of designing compounds that occupy both benzimidazole- and colchicine-binding sites. In addition, previous studies have demonstrated that the incorporation of a phenoxy group at position 5/6 of carbendazim increases the antiproliferative activity in cancer cell lines. Despite the significant progress made in identifying new tubulin-targeting anticancer compounds, further modifications are needed to enhance their potency and safety. In this study, we explored the impact of modifying the phenoxy substitution pattern on antiproliferative activity. Alchemical free energy calculations were used to predict the binding free energy difference upon ligand modification and define the most viable path for structure optimization. Based on these calculations, seven compounds were synthesized and evaluated against lung and colon cancer cell lines. Our results showed that compound 5a, which incorporates an α-naphthyloxy substitution, exhibits the highest antiproliferative activity against both cancer lines (SK-LU-1 and SW620, IC50 < 100 nM) and induces morphological changes in the cells associated with mitotic arrest and mitotic catastrophe. Nevertheless, the tubulin polymerization assay showed that 5a has a lower inhibitory potency than nocodazole. Molecular dynamics simulations suggested that this low antitubulin activity could be associated with the loss of the key H-bond interaction with V236. This study provides insights into the design of novel carbendazim derivatives with anticancer activity.
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Affiliation(s)
- Lucia Cano-González
- Departamento de Farmacia, Facultad de Química, Universidad Nacional Autónoma de México, Mexico City 04510, Mexico
| | - Johan D Espinosa-Mendoza
- Departamento de Farmacia, Facultad de Química, Universidad Nacional Autónoma de México, Mexico City 04510, Mexico
| | - Félix Matadamas-Martínez
- Unidad de Investigación Médica en Enfermedades Infecciosas y Parasitarias, UMAE Hospital de Pediatría, Centro Médico Nacional Siglo XXI, Instituto Mexicano del Seguro Social, Mexico City 06720, Mexico
| | - Ariana Romero-Velásquez
- Departamento de Biología, Facultad de Química, Universidad Nacional Autónoma de México, Mexico City 04510, Mexico
| | - Miguel Flores-Ramos
- Escuela Nacional de Estudios Superiores, Unidad Mérida, Universidad Nacional Autónoma de México, Yucatán 97357, Mexico
| | - Luis Fernando Colorado-Pablo
- Departamento de Farmacia, Facultad de Química, Universidad Nacional Autónoma de México, Mexico City 04510, Mexico
| | | | - Rafael Castillo
- Departamento de Farmacia, Facultad de Química, Universidad Nacional Autónoma de México, Mexico City 04510, Mexico
| | - Ignacio González-Sánchez
- Departamento de Biología, Facultad de Química, Universidad Nacional Autónoma de México, Mexico City 04510, Mexico
| | - Lilián Yépez-Mulia
- Unidad de Investigación Médica en Enfermedades Infecciosas y Parasitarias, UMAE Hospital de Pediatría, Centro Médico Nacional Siglo XXI, Instituto Mexicano del Seguro Social, Mexico City 06720, Mexico
| | - Alicia Hernández-Campos
- Departamento de Farmacia, Facultad de Química, Universidad Nacional Autónoma de México, Mexico City 04510, Mexico
| | - Rodrigo Aguayo-Ortiz
- Departamento de Farmacia, Facultad de Química, Universidad Nacional Autónoma de México, Mexico City 04510, Mexico
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Montecinos F, Sackett DL. Structural Changes, Biological Consequences, and Repurposing of Colchicine Site Ligands. Biomolecules 2023; 13:biom13050834. [PMID: 37238704 DOI: 10.3390/biom13050834] [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: 04/17/2023] [Revised: 05/06/2023] [Accepted: 05/10/2023] [Indexed: 05/28/2023] Open
Abstract
Microtubule-targeting agents (MTAs) bind to one of several distinct sites in the tubulin dimer, the subunit of microtubules. The binding affinities of MTAs may vary by several orders of magnitude, even for MTAs that specifically bind to a particular site. The first drug binding site discovered in tubulin was the colchicine binding site (CBS), which has been known since the discovery of the tubulin protein. Although highly conserved throughout eukaryotic evolution, tubulins show diversity in their sequences between tubulin orthologs (inter-species sequence differences) and paralogs (intraspecies differences, such as tubulin isotypes). The CBS is promiscuous and binds to a broad range of structurally distinct molecules that can vary in size, shape, and affinity. This site remains a popular target for the development of new drugs to treat human diseases (including cancer) and parasitic infections in plants and animals. Despite the rich knowledge about the diversity of tubulin sequences and the structurally distinct molecules that bind to the CBS, a pattern has yet to be found to predict the affinity of new molecules that bind to the CBS. In this commentary, we briefly discuss the literature evidencing the coexistence of the varying binding affinities for drugs that bind to the CBS of tubulins from different species and within species. We also comment on the structural data that aim to explain the experimental differences observed in colchicine binding to the CBS of β-tubulin class VI (TUBB1) compared to other isotypes.
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Affiliation(s)
- Felipe Montecinos
- Protein Expression Laboratory, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Dan L Sackett
- Division of Basic and Translational Biophysics, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
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Kuczmera TJ, Dietz A, Boelke A, Nachtsheim BJ. Synthesis and reactivity of azole-based iodazinium salts. Beilstein J Org Chem 2023; 19:317-324. [PMID: 36960303 PMCID: PMC10028571 DOI: 10.3762/bjoc.19.27] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Accepted: 03/06/2023] [Indexed: 03/18/2023] Open
Abstract
A systematic investigation of imidazo- and pyrazoloiodazinium salts is presented. Besides a robust synthetic protocol that allowed us to synthesize these novel cyclic iodonium salts in their mono- and dicationic forms, we gained in-depth structural information through single-crystal analysis and demonstrated the ring opening of the heterocycle-bridged iodonium species. For an exclusive set of dicationic imidazoiodaziniums, we show highly delicate post-oxidation functionalizations retaining the hypervalent iodine center.
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Affiliation(s)
- Thomas J Kuczmera
- Institute for Organic and Analytical Chemistry, University of Bremen, 28359 Bremen, Germany
| | - Annalena Dietz
- Institute for Organic and Analytical Chemistry, University of Bremen, 28359 Bremen, Germany
| | - Andreas Boelke
- Institute for Organic and Analytical Chemistry, University of Bremen, 28359 Bremen, Germany
| | - Boris J Nachtsheim
- Institute for Organic and Analytical Chemistry, University of Bremen, 28359 Bremen, Germany
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Pallotto LM, Dilks CM, Park YJ, Smit RB, Lu B, Gopalakrishnan C, Gilleard JS, Andersen EC, Mains PE. Interactions of C. elegans β-tubulins with the microtubule inhibitor and anthelmintic drug albendazole. Genetics 2022; 221:6613138. [PMID: 35731216 DOI: 10.1093/genetics/iyac093] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Accepted: 06/08/2022] [Indexed: 11/14/2022] Open
Abstract
Parasitic nematodes are major human and agricultural pests, and benzimidazoles are amongst the most important broad spectrum anthelmintic drug class used for their control. Benzimidazole resistance is now widespread in many species of parasitic nematodes in livestock globally and an emerging concern for the sustainable control of human soil transmitted helminths. β-tubulin is the major benzimidazole target, although other genes may influence resistance. Among the six C. elegans β-tubulin genes, loss of ben-1 causes resistance without other apparent defects. Here, we explored the genetics of C. elegans β-tubulin genes in relation to the response to the benzimidazole derivative albendazole. The most highly expressed β-tubulin isotypes, encoded by tbb-1 and tbb-2, were known to be redundant with each other for viability, and their products are predicted not to bind benzimidazoles. We found that tbb-2 mutants, and to a lesser extent tbb-1 mutants, were hypersensitive to albendazole. The double mutant tbb-2 ben-1 is uncoordinated and short, resembling the wild type exposed to albendazole, but the tbb-1 ben-1 double mutant did not show the same phenotypes. These results suggest that tbb-2 is a modifier of ABZ sensitivity. To better understand how BEN-1 mutates to cause benzimidazole resistance, we isolated mutants resistant to albendazole and found that 15 of 16 mutations occurred in the ben-1 coding region. Mutations ranged from likely nulls to hypomorphs, and several corresponded to residues that cause resistance in other organisms. Null alleles of ben-1 are albendazole-resistant and BEN-1 shows high sequence identity with tubulins from other organisms, suggesting that many amino acid changes could cause resistance. However, our results suggest that missense mutations conferring resistance are not evenly distributed across all possible conserved sites. Independent of their roles in benzimidazole resistance, tbb-1 and tbb-2 may have specialized functions as null mutants of tbb-1 or tbb-2 were cold or heat sensitive, respectively.
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Affiliation(s)
- Linda M Pallotto
- Department of Biochemistry and Molecular Biology, University of Calgary, Calgary, Alberta T2N 4N1, Canada
| | - Clayton M Dilks
- Molecular Biosciences, Northwestern University, Evanston, IL, 60208, USA.,Interdisciplinary Biological Sciences Program, Northwestern University, Evanston, IL, 60208, USA
| | - Ye-Jean Park
- Department of Biochemistry and Molecular Biology, University of Calgary, Calgary, Alberta T2N 4N1, Canada
| | - Ryan B Smit
- Department of Biochemistry and Molecular Biology, University of Calgary, Calgary, Alberta T2N 4N1, Canada
| | - Brian Lu
- Department of Biochemistry and Molecular Biology, University of Calgary, Calgary, Alberta T2N 4N1, Canada
| | | | - John S Gilleard
- Department of Comparative Biology and Experimental Medicine, Host-Parasite Interactions (HPI) Program, Faculty of Veterinary Medicine, University of Calgary, Alberta, T2N 4N1 Canada
| | - Erik C Andersen
- Molecular Biosciences, Northwestern University, Evanston, IL, 60208, USA
| | - Paul E Mains
- Department of Biochemistry and Molecular Biology, University of Calgary, Calgary, Alberta T2N 4N1, Canada
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