1
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Zhang C, Yan W, Liu Y, Tang M, Teng Y, Wang F, Hu X, Zhao M, Yang J, Li Y. Structure-based design and synthesis of BML284 derivatives: A novel class of colchicine-site noncovalent tubulin degradation agents. Eur J Med Chem 2024; 268:116265. [PMID: 38430854 DOI: 10.1016/j.ejmech.2024.116265] [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: 12/19/2023] [Revised: 02/07/2024] [Accepted: 02/18/2024] [Indexed: 03/05/2024]
Abstract
Our previous studies have demonstrated that BML284 is a colchicine-site tubulin degradation agent. To improve its antiproliferative properties, 45 derivatives or analogs of BML284 were designed and synthesized based on the cocrystal structure of BML284 and tubulin. Among them, 5i was the most potent derivative, with IC50 values ranging from 0.02 to 0.05 μM against the five tested tumor cell lines. Structure-activity relationship studies verified that the N1 atom of the pyrimidine ring was the key functional group for its tubulin degradation ability. The 5i-tubulin cocrystal complex revealed that the binding pattern of 5i to tubulin is similar to that of BML284. However, replacing the benzodioxole ring with an indole ring strengthened the hydrogen bond formed by the 2-amino group with E198, which improved the antiproliferative activity of 5i. Compound 5i effectively suppressed tumor growth at an intravenous dose of 40 mg/kg (every 2 days) in paclitaxel sensitive A2780S and paclitaxel resistant A2780T ovarian xenograft models, with tumor growth inhibition values of 79.4% and 82.0%, respectively, without apparent side effects, showing its potential to overcome multidrug resistance. This study provided a successful example of crystal structure-guided discovery of 5i as a colchicine-targeted tubulin degradation agent, expanding the scope of targeted protein degradation.
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Affiliation(s)
- Chufeng Zhang
- Innovation Center of Nursing Research, Nursing Key Laboratory of Sichuan Province, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, and Collaborative Innovation Center of Biotherapy, Sichuan University, Chengdu, 610041, Sichuan, China
| | - Wei Yan
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, and Collaborative Innovation Center of Biotherapy, Sichuan University, Chengdu, 610041, Sichuan, China
| | - Yan Liu
- National Facility for Translational Medicine (Sichuan), West China Hospital, Sichuan University, 610041, Sichuan, China
| | - Minghai Tang
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, and Collaborative Innovation Center of Biotherapy, Sichuan University, Chengdu, 610041, Sichuan, China
| | - Yaxin Teng
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, and Collaborative Innovation Center of Biotherapy, Sichuan University, Chengdu, 610041, Sichuan, China
| | - Fang Wang
- Innovation Center of Nursing Research, Nursing Key Laboratory of Sichuan Province, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, and Collaborative Innovation Center of Biotherapy, Sichuan University, Chengdu, 610041, Sichuan, China
| | - Xiuying Hu
- Innovation Center of Nursing Research, Nursing Key Laboratory of Sichuan Province, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, and Collaborative Innovation Center of Biotherapy, Sichuan University, Chengdu, 610041, Sichuan, China
| | - Min Zhao
- Department of Urology, Institute of Urology (Laboratory of Reconstructive Urology), West China Hospital, Sichuan University, Chengdu, 610041, China.
| | - Jianhong Yang
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, and Collaborative Innovation Center of Biotherapy, Sichuan University, Chengdu, 610041, Sichuan, China.
| | - Yong Li
- Innovation Center of Nursing Research, Nursing Key Laboratory of Sichuan Province, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, and Collaborative Innovation Center of Biotherapy, Sichuan University, Chengdu, 610041, Sichuan, China.
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2
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Kohl PA, Song C, Fletcher BJ, Best RL, Tchounwou C, Garcia Arceo X, Chung PJ, Miller HP, Wilson L, Choi MC, Li Y, Feinstein SC, Safinya CR. Complexes of tubulin oligomers and tau form a viscoelastic intervening network cross-bridging microtubules into bundles. Nat Commun 2024; 15:2362. [PMID: 38491006 PMCID: PMC10943092 DOI: 10.1038/s41467-024-46438-x] [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: 02/09/2023] [Accepted: 02/28/2024] [Indexed: 03/18/2024] Open
Abstract
The axon-initial-segment (AIS) of mature neurons contains microtubule (MT) fascicles (linear bundles) implicated as retrograde diffusion barriers in the retention of MT-associated protein (MAP) tau inside axons. Tau dysfunction and leakage outside of the axon is associated with neurodegeneration. We report on the structure of steady-state MT bundles in varying concentrations of Mg2+ or Ca2+ divalent cations in mixtures containing αβ-tubulin, full-length tau, and GTP at 37 °C in a physiological buffer. A concentration-time kinetic phase diagram generated by synchrotron SAXS reveals a wide-spacing MT bundle phase (Bws), a transient intermediate MT bundle phase (Bint), and a tubulin ring phase. SAXS with TEM of plastic-embedded samples provides evidence of a viscoelastic intervening network (IN) of complexes of tubulin oligomers and tau stabilizing MT bundles. In this model, αβ-tubulin oligomers in the IN are crosslinked by tau's MT binding repeats, which also link αβ-tubulin oligomers to αβ-tubulin within the MT lattice. The model challenges whether the cross-bridging of MTs is attributed entirely to MAPs. Tubulin-tau complexes in the IN or bound to isolated MTs are potential sites for enzymatic modification of tau, promoting nucleation and growth of tau fibrils in tauopathies.
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Affiliation(s)
- Phillip A Kohl
- Materials Research Laboratory, University of California, Santa Barbara, Santa Barbara, CA, 93106, USA
| | - Chaeyeon Song
- Materials Department, University of California, Santa Barbara, Santa Barbara, CA, 93106, USA
- Biomolecular Science and Engineering, University of California, Santa Barbara, Santa Barbara, CA, 93106, USA
- Department of Molecular, Cellular, and Developmental Biology, University of California, Santa Barbara, Santa Barbara, CA, USA
- Department of Physics, University of California, Santa Barbara, Santa Barbara, CA, 93106, USA
- Amorepacific R&I Center, Yongin, 17074, Republic of Korea
| | - Bretton J Fletcher
- Materials Department, University of California, Santa Barbara, Santa Barbara, CA, 93106, USA
- Biomolecular Science and Engineering, University of California, Santa Barbara, Santa Barbara, CA, 93106, USA
- Department of Molecular, Cellular, and Developmental Biology, University of California, Santa Barbara, Santa Barbara, CA, USA
- Department of Physics, University of California, Santa Barbara, Santa Barbara, CA, 93106, USA
| | - Rebecca L Best
- Department of Molecular, Cellular, and Developmental Biology, University of California, Santa Barbara, Santa Barbara, CA, USA
- Neuroscience Research Institute, University of California, Santa Barbara, Santa Barbara, CA, 93106, USA
- Serimmune Inc., 150 Castilian Dr., Goleta, CA, 93117, USA
| | - Christine Tchounwou
- Materials Department, University of California, Santa Barbara, Santa Barbara, CA, 93106, USA
- Biomolecular Science and Engineering, University of California, Santa Barbara, Santa Barbara, CA, 93106, USA
- Department of Molecular, Cellular, and Developmental Biology, University of California, Santa Barbara, Santa Barbara, CA, USA
- Department of Physics, University of California, Santa Barbara, Santa Barbara, CA, 93106, USA
| | - Ximena Garcia Arceo
- Department of Physics, University of California, Santa Barbara, Santa Barbara, CA, 93106, USA
- Department of Chemistry and Biochemistry, University of California, San Diego, San Diego, CA, 93106, USA
| | - Peter J Chung
- Materials Department, University of California, Santa Barbara, Santa Barbara, CA, 93106, USA
- Biomolecular Science and Engineering, University of California, Santa Barbara, Santa Barbara, CA, 93106, USA
- Department of Molecular, Cellular, and Developmental Biology, University of California, Santa Barbara, Santa Barbara, CA, USA
- Department of Physics, University of California, Santa Barbara, Santa Barbara, CA, 93106, USA
- Department of Physics and Astronomy, University of Southern California, Los Angeles, CA, 90089, USA
| | - Herbert P Miller
- Department of Molecular, Cellular, and Developmental Biology, University of California, Santa Barbara, Santa Barbara, CA, USA
| | - Leslie Wilson
- Department of Molecular, Cellular, and Developmental Biology, University of California, Santa Barbara, Santa Barbara, CA, USA
- Neuroscience Research Institute, University of California, Santa Barbara, Santa Barbara, CA, 93106, USA
| | - Myung Chul Choi
- Department of Bio and Brain Engineering, Korea Advanced Institute of Science and Technology, 291 Daehak-ro, Daejeon, 34141, Korea
| | - Youli Li
- Materials Research Laboratory, University of California, Santa Barbara, Santa Barbara, CA, 93106, USA.
| | - Stuart C Feinstein
- Department of Molecular, Cellular, and Developmental Biology, University of California, Santa Barbara, Santa Barbara, CA, USA
- Neuroscience Research Institute, University of California, Santa Barbara, Santa Barbara, CA, 93106, USA
| | - Cyrus R Safinya
- Materials Department, University of California, Santa Barbara, Santa Barbara, CA, 93106, USA.
- Biomolecular Science and Engineering, University of California, Santa Barbara, Santa Barbara, CA, 93106, USA.
- Department of Molecular, Cellular, and Developmental Biology, University of California, Santa Barbara, Santa Barbara, CA, USA.
- Department of Physics, University of California, Santa Barbara, Santa Barbara, CA, 93106, USA.
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3
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Lucena-Agell D, Guillén MJ, Matesanz R, Álvarez-Bernad B, Hortigüela R, Avilés P, Martínez-Díez M, Santamaría-Núñez G, Contreras J, Plaza-Menacho I, Giménez-Abián JF, Oliva MA, Cuevas C, Díaz JF. PM534, an Optimized Target-Protein Interaction Strategy through the Colchicine Site of Tubulin. J Med Chem 2024; 67:2619-2630. [PMID: 38294341 PMCID: PMC10895673 DOI: 10.1021/acs.jmedchem.3c01775] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Revised: 01/02/2024] [Accepted: 01/10/2024] [Indexed: 02/01/2024]
Abstract
Targeting microtubules is the most effective wide-spectrum pharmacological strategy in antitumoral chemotherapy, and current research focuses on reducing main drawbacks: neurotoxicity and resistance. PM534 is a novel synthetic compound derived from the Structure-Activity-Relationship study on the natural molecule PM742, isolated from the sponge of the order Lithistida, family Theonellidae, genus Discodermia (du Bocage 1869). PM534 targets the entire colchicine binding domain of tubulin, covering four of the five centers of the pharmacophore model. Its nanomolar affinity and high retention time modulate a strikingly high antitumor activity that efficiently overrides two resistance mechanisms in cells (detoxification pumps and tubulin βIII isotype overexpression). Furthermore, PM534 induces significant inhibition of tumor growth in mouse xenograft models of human non-small cell lung cancer. Our results present PM534, a highly effective new compound in the preclinical evaluation that is currently in its first human Phase I clinical trial.
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Affiliation(s)
- Daniel Lucena-Agell
- Unidad
BICS. Centro de Investigaciones Biológicas Margarita Salas,
Consejo Superior de Investigaciones Científicas, Ramiro de Maeztu 9, 28040 Madrid, Spain
| | - María José Guillén
- PharmaMar
S.A., Avda de los Reyes
1, Colmenar Viejo, 28770 Madrid, Spain
| | - Ruth Matesanz
- Unidad
BICS. Centro de Investigaciones Biológicas Margarita Salas,
Consejo Superior de Investigaciones Científicas, Ramiro de Maeztu 9, 28040 Madrid, Spain
| | - Beatriz Álvarez-Bernad
- Unidad
BICS. Centro de Investigaciones Biológicas Margarita Salas,
Consejo Superior de Investigaciones Científicas, Ramiro de Maeztu 9, 28040 Madrid, Spain
| | - Rafael Hortigüela
- Unidad
BICS. Centro de Investigaciones Biológicas Margarita Salas,
Consejo Superior de Investigaciones Científicas, Ramiro de Maeztu 9, 28040 Madrid, Spain
| | - Pablo Avilés
- PharmaMar
S.A., Avda de los Reyes
1, Colmenar Viejo, 28770 Madrid, Spain
| | | | | | - Julia Contreras
- Centro
Nacional de Investigaciones Oncológicas (CNIO), Melchor Fernández Almagro
3, 28029 Madrid, Spain
| | - Iván Plaza-Menacho
- Centro
Nacional de Investigaciones Oncológicas (CNIO), Melchor Fernández Almagro
3, 28029 Madrid, Spain
| | - Juan F. Giménez-Abián
- Unidad
BICS. Centro de Investigaciones Biológicas Margarita Salas,
Consejo Superior de Investigaciones Científicas, Ramiro de Maeztu 9, 28040 Madrid, Spain
| | - María A. Oliva
- Unidad
BICS. Centro de Investigaciones Biológicas Margarita Salas,
Consejo Superior de Investigaciones Científicas, Ramiro de Maeztu 9, 28040 Madrid, Spain
| | - Carmen Cuevas
- PharmaMar
S.A., Avda de los Reyes
1, Colmenar Viejo, 28770 Madrid, Spain
| | - J. Fernando Díaz
- Unidad
BICS. Centro de Investigaciones Biológicas Margarita Salas,
Consejo Superior de Investigaciones Científicas, Ramiro de Maeztu 9, 28040 Madrid, Spain
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4
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Basu D, Dastidar SG. Molecular Dynamics and Machine Learning reveal distinguishing mechanisms of Competitive Ligands to perturb α,β-Tubulin. Comput Biol Chem 2024; 108:108004. [PMID: 38157659 DOI: 10.1016/j.compbiolchem.2023.108004] [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: 09/16/2023] [Revised: 11/25/2023] [Accepted: 12/08/2023] [Indexed: 01/03/2024]
Abstract
The mechanisms of action of ligands competing for the Colchicine Binding Site (CBS) of the α,β-Tubulin are non-standard compared to the commonly witnessed ligand-induced inhibition of proteins. This is because their potencies are not solely judged by the binding affinity itself, but also by their capacity to bias the conformational states of the dimer. Regarding the latter requirement, it is observed that ligands competing for the same pocket that binds colchicine exhibit divergence in potential clinical outcomes. Molecular dynamics-based ∼5.2 µs sampling of α,β-Tubulin complexed with four different ligands has revealed that each ligand has its customized way of influencing the complex. Primarily, it is the proportion of twisting and/or bending characteristic of modes of the intrinsic dynamics which is revealed to be 'fundamental' to tune this variation in the mechanism. The milder influence of 'bending' makes a ligand (TUB092), better classifiable under the group of vascular disrupting agents (VDAs), which are phenotypically effective on cytoskeletons; whereas a stronger impact of 'bending' makes the classical ligand Colchicine (COL) a better Anti-Mitotic agent (AMA). Two other ligands BAL27862 (2RR) and Nocodazole (NZO) fall in the intermediate zone as they fail to explicitly induce bending modes. Random Forest Classification method and K-means Clustering is applied to reveal the efficiency of Machine Learning methods in classifying the Tubulin conformations according to their ligand-specific perturbations and to highlight the significance of specific amino acid residues, mostly positioned in the α-β and β-β interfaces involved in the mechanism. These key residues responsible to yield discriminative actions of the ligands are likely to be highly useful in future endeavours to design more precise inhibitors.
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Affiliation(s)
- Debadrita Basu
- Biological Sciences, Bose Institute, EN 80, Sector V, Bidhan Nagar, Kolkata 700091, India
| | - Shubhra Ghosh Dastidar
- Biological Sciences, Bose Institute, EN 80, Sector V, Bidhan Nagar, Kolkata 700091, India.
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5
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Masci D, Puxeddu M, Di Magno L, D’Ambrosio M, Parisi A, Nalli M, Bai R, Coluccia A, Sciò P, Orlando V, D’Angelo S, Biagioni S, Urbani A, Hamel E, Nocentini A, Filiberti S, Turati M, Ronca R, Kopecka J, Riganti C, Fionda C, Bordone R, Della Rocca G, Canettieri G, Supuran CT, Silvestri R, La Regina G. 4-(3-Phenyl-4-(3,4,5-trimethoxybenzoyl)-1 H-pyrrol-1-yl)benzenesulfonamide, a Novel Carbonic Anhydrase and Wnt/β-Catenin Signaling Pathway Dual-Targeting Inhibitor with Potent Activity against Multidrug Resistant Cancer Cells. J Med Chem 2023; 66:14824-14842. [PMID: 37902628 PMCID: PMC10641813 DOI: 10.1021/acs.jmedchem.3c01424] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Revised: 10/11/2023] [Accepted: 10/12/2023] [Indexed: 10/31/2023]
Abstract
We synthesized new pyrrole and indole derivatives as human carbonic anhydrase (hCA) inhibitors with the potential to inhibit the Wnt/β-catenin signaling pathway. The presence of both N1-(4-sulfonamidophenyl) and 3-(3,4,5-trimethoxyphenyl) substituents was essential for strong hCA inhibitors. The most potent hCA XII inhibitor 15 (Ki = 6.8 nM) suppressed the Wnt/β-catenin signaling pathway and its target genes MYC, Fgf20, and Sall4 and exhibited the typical markers of apoptosis, cleaved poly(ADP-ribose)polymerase, and cleaved caspase-3. Compound 15 showed strong inhibition of viability in a panel of cancer cells, including colorectal cancer and triple-negative breast cancer cells, was effective against the NCI/ADR-RES DOX-resistant cell line, and restored the sensitivity to doxorubicin (DOX) in HT29/DX and MDCK/P-gp cells. Compound 15 is a novel dual-targeting compound with activity against hCA and Wnt/β-catenin. It thus has a broad targeting spectrum and is an anticancer agent with specific potential in P-glycoprotein overexpressing cell lines.
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Affiliation(s)
- Domiziana Masci
- Department
of Basic Biotechnological Sciences, Intensivological and Perioperative
Clinics, Catholic University of the Sacred
Heart, Largo Francesco
Vito 1, Rome 00168, Italy
| | - Michela Puxeddu
- Laboratory
Affiliated with the Institute Pasteur Italy—Cenci Bolognetti
Foundation, Department of Drug Chemistry and Technologies, Sapienza University of Rome, Piazzale Aldo Moro 5, Roma 00185, Italy
| | - Laura Di Magno
- Laboratory
Affiliated to Istituto Pasteur Italia—Fondazione Cenci Bolognetti,
Department of Molecular Medicine, Sapienza
University of Rome, Viale
Regina Elena 291, Rome 00161, Italy
| | - Michele D’Ambrosio
- Laboratory
Affiliated with the Institute Pasteur Italy—Cenci Bolognetti
Foundation, Department of Drug Chemistry and Technologies, Sapienza University of Rome, Piazzale Aldo Moro 5, Roma 00185, Italy
| | - Anastasia Parisi
- Laboratory
Affiliated with the Institute Pasteur Italy—Cenci Bolognetti
Foundation, Department of Drug Chemistry and Technologies, Sapienza University of Rome, Piazzale Aldo Moro 5, Roma 00185, Italy
| | - Marianna Nalli
- Laboratory
Affiliated with the Institute Pasteur Italy—Cenci Bolognetti
Foundation, Department of Drug Chemistry and Technologies, Sapienza University of Rome, Piazzale Aldo Moro 5, Roma 00185, Italy
| | - Ruoli Bai
- Molecular
Pharmacology Branch, Developmental Therapeutics Program, Division
of Cancer Treatment and Diagnosis, Frederick National Laboratory for
Cancer Research, National Cancer Institute,
National Institutes of Health, Frederick, Maryland 21702, United States
| | - Antonio Coluccia
- Laboratory
Affiliated with the Institute Pasteur Italy—Cenci Bolognetti
Foundation, Department of Drug Chemistry and Technologies, Sapienza University of Rome, Piazzale Aldo Moro 5, Roma 00185, Italy
| | - Pietro Sciò
- Laboratory
Affiliated with the Institute Pasteur Italy—Cenci Bolognetti
Foundation, Department of Drug Chemistry and Technologies, Sapienza University of Rome, Piazzale Aldo Moro 5, Roma 00185, Italy
| | - Viviana Orlando
- Department
of Biology and Biotechnologies “Charles Darwin”, Sapienza University of Rome, Piazzale Aldo Moro 5, Rome 00185, Italy
| | - Sara D’Angelo
- Department
of Biology and Biotechnologies “Charles Darwin”, Sapienza University of Rome, Piazzale Aldo Moro 5, Rome 00185, Italy
| | - Stefano Biagioni
- Department
of Biology and Biotechnologies “Charles Darwin”, Sapienza University of Rome, Piazzale Aldo Moro 5, Rome 00185, Italy
| | - Andrea Urbani
- Department
of Basic Biotechnological Sciences, Intensivological and Perioperative
Clinics, Catholic University of the Sacred
Heart, Largo Francesco
Vito 1, Rome 00168, Italy
| | - Ernest Hamel
- Molecular
Pharmacology Branch, Developmental Therapeutics Program, Division
of Cancer Treatment and Diagnosis, Frederick National Laboratory for
Cancer Research, National Cancer Institute,
National Institutes of Health, Frederick, Maryland 21702, United States
| | - Alessio Nocentini
- Dipartimento
Neurofarba, Sezione di Scienze Farmaceutiche e Nutraceutiche, Universitá degli Studi di Firenze, Via Ugo Schiff 6, Sesto Fiorentino I-50019, Firenze, Italy
| | - Serena Filiberti
- Experimental
Oncology and Immunology Unit, Department of Molecular and Translational
Medicine, University of Brescia, Via Branze 39, Brescia 25123, Italy
| | - Marta Turati
- Experimental
Oncology and Immunology Unit, Department of Molecular and Translational
Medicine, University of Brescia, Via Branze 39, Brescia 25123, Italy
| | - Roberto Ronca
- Experimental
Oncology and Immunology Unit, Department of Molecular and Translational
Medicine, University of Brescia, Via Branze 39, Brescia 25123, Italy
| | - Joanna Kopecka
- Department
of Oncology and Molecular Biotecnology Center “Guido Tarone″, Oncological Pharmacology Unit, Via Nizza 44, Torino 10126, Italy
| | - Chiara Riganti
- Department
of Oncology and Molecular Biotecnology Center “Guido Tarone″, Oncological Pharmacology Unit, Via Nizza 44, Torino 10126, Italy
| | - Cinzia Fionda
- Laboratory
Affiliated to Istituto Pasteur Italia—Fondazione Cenci Bolognetti,
Department of Molecular Medicine, Sapienza
University of Rome, Viale
Regina Elena 291, Rome 00161, Italy
| | - Rosa Bordone
- Laboratory
Affiliated to Istituto Pasteur Italia—Fondazione Cenci Bolognetti,
Department of Molecular Medicine, Sapienza
University of Rome, Viale
Regina Elena 291, Rome 00161, Italy
| | - Giorgia Della Rocca
- Laboratory
Affiliated to Istituto Pasteur Italia—Fondazione Cenci Bolognetti,
Department of Molecular Medicine, Sapienza
University of Rome, Viale
Regina Elena 291, Rome 00161, Italy
| | - Gianluca Canettieri
- Laboratory
Affiliated to Istituto Pasteur Italia—Fondazione Cenci Bolognetti,
Department of Molecular Medicine, Sapienza
University of Rome, Viale
Regina Elena 291, Rome 00161, Italy
| | - Claudiu T. Supuran
- Dipartimento
Neurofarba, Sezione di Scienze Farmaceutiche e Nutraceutiche, Universitá degli Studi di Firenze, Via Ugo Schiff 6, Sesto Fiorentino I-50019, Firenze, Italy
| | - Romano Silvestri
- Laboratory
Affiliated with the Institute Pasteur Italy—Cenci Bolognetti
Foundation, Department of Drug Chemistry and Technologies, Sapienza University of Rome, Piazzale Aldo Moro 5, Roma 00185, Italy
| | - Giuseppe La Regina
- Laboratory
Affiliated with the Institute Pasteur Italy—Cenci Bolognetti
Foundation, Department of Drug Chemistry and Technologies, Sapienza University of Rome, Piazzale Aldo Moro 5, Roma 00185, Italy
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6
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Velasco-Saavedra MA, Mar-Antonio E, Aguayo-Ortiz R. Molecular Insights into the Covalent Binding of Zoxamide to the β-Tubulin of Botrytis cinerea. J Chem Inf Model 2023; 63:6386-6395. [PMID: 37802126 DOI: 10.1021/acs.jcim.3c00911] [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: 10/08/2023]
Abstract
Botrytis cinerea is a fungal plant pathogen that causes significant economic losses in the agricultural industry worldwide. Fungicides that target microtubules, such as carbendazim (CBZ), diethofencarb (DEF), and zoxamide (ZOX), are widely used in crop protection against this pathogen. These groups of compounds exert their fungicidal activity by disrupting the microtubule assembly by binding to the β-tubulin subunit, provoking cell-cycle arrest and cell death. However, with the appearance of isolates resistant to these compounds, it is necessary to search for new alternatives to control this pathogenic fungus. In this work, we gained insight into the binding and stability of these fungicides in the benzimidazole binding site of B. cinerea β-tubulin through different computational approaches. Our molecular dynamics simulation replicas showed that R enantiomers of ZOX and its analog RH-4032 had better interaction profiles at the site compared to S enantiomers. The simulations also revealed that while the R-isomer fungicides formed H-bonds with the main chain carbonyl of V236 or the side chain residue of S314, only CBZ interacted with E198. Previous experimental data have identified key mutations in B. cinerea's β-tubulin gene that lead to the development of resistance or, on the contrary, increased sensitivity for treatment with these fungicide compounds. In agreement with experimental findings, alchemical free energy calculations showed that E198A and E198V mutations in B. cinerea β-tubulin have high sensitivity to (R)-ZOX, whereas the E198K mutation decreased its affinity. Similarly, the results obtained explain the resistance to CBZ of B. cinerea isolates with E198A/V/K mutations and the insensitivity of the wild-type organism to DEF. Our work provides a deeper insight into the molecular mechanism of action of these fungicides, highlighting the importance of understanding the interaction profiles to develop more effective antifungal agents.
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Affiliation(s)
- M Andrés Velasco-Saavedra
- Departamento de Farmacia, Facultad de Química, Universidad Nacional Autónoma de México, Mexico City 04510, Mexico
| | - Efrén Mar-Antonio
- 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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7
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Yamane T, Nakayama T, Ekimoto T, Inoue M, Ikezaki K, Sekiguchi H, Kuramochi M, Terao Y, Judai K, Saito M, Ikeguchi M, Sasaki YC. Comparison of the Molecular Motility of Tubulin Dimeric Isoforms: Molecular Dynamics Simulations and Diffracted X-ray Tracking Study. Int J Mol Sci 2023; 24:15423. [PMID: 37895101 PMCID: PMC10607685 DOI: 10.3390/ijms242015423] [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: 07/31/2023] [Revised: 10/11/2023] [Accepted: 10/19/2023] [Indexed: 10/29/2023] Open
Abstract
Tubulin has been recently reported to form a large family consisting of various gene isoforms; however, the differences in the molecular features of tubulin dimers composed of a combination of these isoforms remain unknown. Therefore, we attempted to elucidate the physical differences in the molecular motility of these tubulin dimers using the method of measurable pico-meter-scale molecular motility, diffracted X-ray tracking (DXT) analysis, regarding characteristic tubulin dimers, including neuronal TUBB3 and ubiquitous TUBB5. We first conducted a DXT analysis of neuronal (TUBB3-TUBA1A) and ubiquitous (TUBB5-TUBA1B) tubulin dimers and found that the molecular motility around the vertical axis of the neuronal tubulin dimer was lower than that of the ubiquitous tubulin dimer. The results of molecular dynamics (MD) simulation suggest that the difference in motility between the neuronal and ubiquitous tubulin dimers was probably caused by a change in the major contact of Gln245 in the T7 loop of TUBB from Glu11 in TUBA to Val353 in TUBB. The present study is the first report of a novel phenomenon in which the pico-meter-scale molecular motility between neuronal and ubiquitous tubulin dimers is different.
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Affiliation(s)
- Tsutomu Yamane
- Graduate School of Medical Life Science, Yokohama City University, 1-7-29 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan; (T.E.); (M.I.); (M.I.)
- HPC- and AI-Driven Drug Development Platform Division, Riken Center for Computational Science, RIKEN, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
| | - Takahiro Nakayama
- Department of Medical Physiology, Kyorin University School of Medicine, 6-20-2 Shinkawa, Mitaka 181-8611, Japan; (T.N.); (Y.T.)
| | - Toru Ekimoto
- Graduate School of Medical Life Science, Yokohama City University, 1-7-29 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan; (T.E.); (M.I.); (M.I.)
| | - Masao Inoue
- Graduate School of Medical Life Science, Yokohama City University, 1-7-29 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan; (T.E.); (M.I.); (M.I.)
| | - Keigo Ikezaki
- Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa 277-8568, Japan; (K.I.); (M.K.)
| | - Hiroshi Sekiguchi
- Japan Synchrotron Radiation Research Institute, SPring-8, 1-1-1 Kouto, Sayo 679-5198, Japan;
| | - Masahiro Kuramochi
- Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa 277-8568, Japan; (K.I.); (M.K.)
| | - Yasuo Terao
- Department of Medical Physiology, Kyorin University School of Medicine, 6-20-2 Shinkawa, Mitaka 181-8611, Japan; (T.N.); (Y.T.)
| | - Ken Judai
- Department of Physics, College of Humanities and Sciences, Nihon University, Sakurajosui 3-25-40, Tokyo 156-8550, Japan;
| | - Minoru Saito
- Department of Biosciences, College of Humanities and Sciences, Nihon University, Tokyo 156-8550, Japan;
| | - Mitsunori Ikeguchi
- Graduate School of Medical Life Science, Yokohama City University, 1-7-29 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan; (T.E.); (M.I.); (M.I.)
- HPC- and AI-Driven Drug Development Platform Division, Riken Center for Computational Science, RIKEN, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
| | - Yuji C. Sasaki
- Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa 277-8568, Japan; (K.I.); (M.K.)
- Japan Synchrotron Radiation Research Institute, SPring-8, 1-1-1 Kouto, Sayo 679-5198, Japan;
- AIST-UTokyo Advanced Operando-Measurement Technology Open Innovation Laboratory (OPERANDO-OIL), National Institute of Advanced Industrial Science and Technology (AIST), 6-2-3 Kashiwanoha, Chiba 277-0882, Japan
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8
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Zhang C, Zhao M, Wang G, Li Y. Recent Progress on Microtubule Degradation Agents. J Med Chem 2023; 66:13354-13368. [PMID: 37748178 DOI: 10.1021/acs.jmedchem.3c00517] [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: 09/27/2023]
Abstract
Targeted protein degradation (TPD) has emerged as the most promising approach for the specific knockdown of disease-associated proteins and is achieved by exploiting the cellular quality control machinery. TPD technologies are highly advantageous in overcoming drug resistance as they degrade the whole target protein. Microtubules play important roles in many cellular processes and are among the oldest and most well-established targets for tumor chemotherapy. However, the development of drug resistance, risk of hypersensitivity reactions, and intolerable toxicities severely restrict the clinical applications of microtubule-targeting agents (MTAs). Microtubule degradation agents (MDgAs) operate via completely different mechanisms compared with traditional MTAs and are capable of overcoming drug resistance. The emergence of MDgAs has expanded the scope of TPD and provided new avenues for the discovery of tubulin-targeted drugs. Herein, we summarized the development of MDgAs, and discussed their degradation mechanisms, mechanisms of action on the binding sites, potential opportunities, and challenges.
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Affiliation(s)
- Chufeng Zhang
- Innovation Center of Nursing Research, Nursing Key Laboratory of Sichuan Province, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, and Collaborative Innovation Center of Biotherapy, Sichuan University, Chengdu 610041, Sichuan, China
| | - Min Zhao
- Laboratory of Metabolomics and Drug-Induced Liver Injury, Department of Gastroenterology & Hepatology, Frontiers Science Center for Disease-Related Molecular Network, West China Hospital, Sichuan University, Chengdu 610041, Sichuan, China
| | - Guan Wang
- Innovation Center of Nursing Research, Nursing Key Laboratory of Sichuan Province, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, and Collaborative Innovation Center of Biotherapy, Sichuan University, Chengdu 610041, Sichuan, China
| | - Yong Li
- Innovation Center of Nursing Research, Nursing Key Laboratory of Sichuan Province, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, and Collaborative Innovation Center of Biotherapy, Sichuan University, Chengdu 610041, Sichuan, China
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9
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Martínez-Conde C, Colín-Lozano B, Gutiérrez-Hernández A, Hernández-Núñez E, Yépez-Mulia L, Colorado-Pablo LF, Aguayo-Ortiz R, Escalante J, Rivera-Leyva JC, Sánchez-Carranza JN, Barbosa-Cabrera E, Navarrete-Vazquez G. Enhancing Giardicidal Activity and Aqueous Solubility through the Development of "RetroABZ", a Regioisomer of Albendazole: In Vitro, In Vivo, and In Silico Studies. Int J Mol Sci 2023; 24:14949. [PMID: 37834396 PMCID: PMC10573946 DOI: 10.3390/ijms241914949] [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: 09/18/2023] [Revised: 10/03/2023] [Accepted: 10/04/2023] [Indexed: 10/15/2023] Open
Abstract
Parasitic diseases, including giardiasis caused by Giardia lamblia (G. lamblia), present a considerable global health burden. The limited effectiveness and adverse effects of current treatment options underscore the necessity for novel therapeutic compounds. In this study, we employed a rational design strategy to synthesize retroalbendazole (RetroABZ), aiming to address the limitations associated with albendazole, a commonly used drug for giardiasis treatment. RetroABZ exhibited enhanced in vitro activity against G. lamblia trophozoites, demonstrating nanomolar potency (IC50 = 83 nM), outperforming albendazole (189 nM). Moreover, our in vivo murine model of giardiasis displayed a strong correlation, supporting the efficacy of RetroABZ, which exhibited an eleven-fold increase in potency compared to albendazole, with median effective dose (ED50) values of 5 µg/kg and 55 µg/kg, respectively. A notable finding was RetroABZ's significantly improved water solubility (245.74 µg/mL), representing a 23-fold increase compared to albendazole, thereby offering potential opportunities for developing derivatives that effectively target invasive parasites. The molecular docking study revealed that RetroABZ displays an interaction profile with tubulin similar to albendazole, forming hydrogen bonds with Glu198 and Cys236 of the β-tubulin. Additionally, molecular dynamics studies demonstrated that RetroABZ has a greater number of hydrophobic interactions with the binding site in the β-tubulin, due to the orientation of the propylthio substituent. Consequently, RetroABZ exhibited a higher affinity compared to albendazole. Overall, our findings underscore RetroABZ's potential as a promising therapeutic candidate not only for giardiasis but also for other parasitic diseases.
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Affiliation(s)
- Carlos Martínez-Conde
- Facultad de Farmacia, Universidad Autónoma del Estado de Morelos, Cuernavaca 62209, Morelos, Mexico; (C.M.-C.); (B.C.-L.); (A.G.-H.); (J.C.R.-L.); (J.N.S.-C.)
| | - Blanca Colín-Lozano
- Facultad de Farmacia, Universidad Autónoma del Estado de Morelos, Cuernavaca 62209, Morelos, Mexico; (C.M.-C.); (B.C.-L.); (A.G.-H.); (J.C.R.-L.); (J.N.S.-C.)
| | - Abraham Gutiérrez-Hernández
- Facultad de Farmacia, Universidad Autónoma del Estado de Morelos, Cuernavaca 62209, Morelos, Mexico; (C.M.-C.); (B.C.-L.); (A.G.-H.); (J.C.R.-L.); (J.N.S.-C.)
| | - Emanuel Hernández-Núñez
- Departamento de Recursos del Mar, Centro de Investigación y de Estudios Avanzados, IPN, Unidad Mérida, Merida 97310, Yucatán, Mexico;
| | - Lilián Yépez-Mulia
- Unidad de Investigación Medica en Enfermedades Infecciosas y Parasitarias, Unidad Médica de Alta Especialidad-Hospital de Pediatría, Centro Médico Nacional Siglo XXI, Instituto Mexicano del Seguro Social, Mexico City 06720, Mexico;
| | - Luis Fernando Colorado-Pablo
- Departamento de Farmacia, Facultad de Química, Universidad Nacional Autónoma de Mexico, Mexico City 04510, Mexico; (L.F.C.-P.); (R.A.-O.)
| | - Rodrigo Aguayo-Ortiz
- Departamento de Farmacia, Facultad de Química, Universidad Nacional Autónoma de Mexico, Mexico City 04510, Mexico; (L.F.C.-P.); (R.A.-O.)
| | - Jaime Escalante
- Centro de Investigaciones Químicas-IICBA, Universidad Autónoma del Estado de Morelos, Av. Universidad 1001, Cuernavaca 62209, Morelos, Mexico;
| | - Julio C. Rivera-Leyva
- Facultad de Farmacia, Universidad Autónoma del Estado de Morelos, Cuernavaca 62209, Morelos, Mexico; (C.M.-C.); (B.C.-L.); (A.G.-H.); (J.C.R.-L.); (J.N.S.-C.)
| | - Jessica Nayelli Sánchez-Carranza
- Facultad de Farmacia, Universidad Autónoma del Estado de Morelos, Cuernavaca 62209, Morelos, Mexico; (C.M.-C.); (B.C.-L.); (A.G.-H.); (J.C.R.-L.); (J.N.S.-C.)
| | - Elizabeth Barbosa-Cabrera
- Sección de Estudios de Posgrado e Investigación, Escuela Superior de Medicina, IPN, Mexico City 11340, Mexico;
| | - Gabriel Navarrete-Vazquez
- Facultad de Farmacia, Universidad Autónoma del Estado de Morelos, Cuernavaca 62209, Morelos, Mexico; (C.M.-C.); (B.C.-L.); (A.G.-H.); (J.C.R.-L.); (J.N.S.-C.)
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10
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Uno N, Satofuka H, Miyamoto H, Honma K, Suzuki T, Yamazaki K, Ito R, Moriwaki T, Hamamichi S, Tomizuka K, Oshimura M, Kazuki Y. Treatment of CHO cells with Taxol and reversine improves micronucleation and microcell-mediated chromosome transfer efficiency. MOLECULAR THERAPY. NUCLEIC ACIDS 2023; 33:391-403. [PMID: 37547291 PMCID: PMC10403731 DOI: 10.1016/j.omtn.2023.07.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Accepted: 07/11/2023] [Indexed: 08/08/2023]
Abstract
Microcell-mediated chromosome transfer is an attractive technique for transferring chromosomes from donor cells to recipient cells and has enabled the generation of cell lines and humanized animal models that contain megabase-sized gene(s). However, improvements in chromosomal transfer efficiency are still needed to accelerate the production of these cells and animals. The chromosomal transfer protocol consists of micronucleation, microcell formation, and fusion of donor cells with recipient cells. We found that the combination of Taxol (paclitaxel) and reversine rather than the conventional reagent colcemid resulted in highly efficient micronucleation and substantially improved chromosomal transfer efficiency from Chinese hamster ovary donor cells to HT1080 and NIH3T3 recipient cells by up to 18.3- and 4.9-fold, respectively. Furthermore, chromosome transfer efficiency to human induced pluripotent stem cells, which rarely occurred with colcemid, was also clearly improved after Taxol and reversine treatment. These results might be related to Taxol increasing the number of spindle poles, leading to multinucleation and delaying mitosis, and reversine inducing mitotic slippage and decreasing the duration of mitosis. Here, we demonstrated that an alternative optimized protocol improved chromosome transfer efficiency into various cell lines. These data advance chromosomal engineering technology and the use of human artificial chromosomes in genetic and regenerative medical research.
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Affiliation(s)
- Narumi Uno
- Laboratory of Bioengineering, Faculty of Life Sciences, Tokyo University of Pharmacy and Life Sciences, 1432-1 Horinouchi, Hachioji, Tokyo 192-0392, Japan
- Chromosome Engineering Research Center, Tottori University, 86 Nishi-cho, Yonago, Tottori 683-8503, Japan
| | - Hiroyuki Satofuka
- Chromosome Engineering Research Center, Tottori University, 86 Nishi-cho, Yonago, Tottori 683-8503, Japan
| | - Hitomaru Miyamoto
- Department of Chromosome Biomedical Engineering, School of Life Science, Faculty of Medicine, Tottori University, 86 Nishi-cho, Yonago, Tottori 683-8503, Japan
| | - Kazuhisa Honma
- Department of Chromosome Biomedical Engineering, School of Life Science, Faculty of Medicine, Tottori University, 86 Nishi-cho, Yonago, Tottori 683-8503, Japan
| | - Teruhiko Suzuki
- Stem Cell Project, Tokyo Metropolitan Institute of Medical Science, Kamikitazawa, Setagaya-ku, Tokyo 156-8506, Japan
| | - Kyotaro Yamazaki
- Department of Chromosome Biomedical Engineering, School of Life Science, Faculty of Medicine, Tottori University, 86 Nishi-cho, Yonago, Tottori 683-8503, Japan
- Chromosome Engineering Research Group, The Exploratory Research Center on Life and Living Systems (ExCELLS), National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji, Okazaki, Aichi 444-8787, Japan
| | - Ryota Ito
- Laboratory of Bioengineering, Faculty of Life Sciences, Tokyo University of Pharmacy and Life Sciences, 1432-1 Horinouchi, Hachioji, Tokyo 192-0392, Japan
| | - Takashi Moriwaki
- Chromosome Engineering Research Center, Tottori University, 86 Nishi-cho, Yonago, Tottori 683-8503, Japan
- Department of Chromosome Biomedical Engineering, School of Life Science, Faculty of Medicine, Tottori University, 86 Nishi-cho, Yonago, Tottori 683-8503, Japan
| | - Shusei Hamamichi
- Chromosome Engineering Research Center, Tottori University, 86 Nishi-cho, Yonago, Tottori 683-8503, Japan
| | - Kazuma Tomizuka
- Laboratory of Bioengineering, Faculty of Life Sciences, Tokyo University of Pharmacy and Life Sciences, 1432-1 Horinouchi, Hachioji, Tokyo 192-0392, Japan
| | - Mitsuo Oshimura
- Chromosome Engineering Research Center, Tottori University, 86 Nishi-cho, Yonago, Tottori 683-8503, Japan
| | - Yasuhiro Kazuki
- Chromosome Engineering Research Center, Tottori University, 86 Nishi-cho, Yonago, Tottori 683-8503, Japan
- Department of Chromosome Biomedical Engineering, School of Life Science, Faculty of Medicine, Tottori University, 86 Nishi-cho, Yonago, Tottori 683-8503, Japan
- Chromosome Engineering Research Group, The Exploratory Research Center on Life and Living Systems (ExCELLS), National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji, Okazaki, Aichi 444-8787, Japan
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11
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Garman EF. Raimond B. G. Ravelli (25 March 1968-30 June 2023). Acta Crystallogr D Struct Biol 2023; 79:866-870. [PMID: 37561406 DOI: 10.1107/s2059798323006897] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/11/2023] Open
Abstract
Raimond B. G. Ravelli is remembered.
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Affiliation(s)
- Elspeth F Garman
- University of Oxford, Department of Biochemistry, Dorothy Crowfoot Hodgkin Building, Oxford OX1 3QU, United Kingdom
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12
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Chu Y, Tian Z, Yang M, Li W. Conformation and energy investigation of microtubule longitudinal dynamic instability induced by natural products. Chem Biol Drug Des 2023; 102:444-456. [PMID: 36509697 DOI: 10.1111/cbdd.14189] [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: 05/11/2022] [Revised: 08/29/2022] [Accepted: 11/28/2022] [Indexed: 12/15/2022]
Abstract
The natural products plinabulin, docetaxel, and vinblastine are microtubule targeting agents (MTAs). They have been used alone or in combination in cancer treatment. However, the exact nature of their effects on microtubule (MT) polymerization dynamics is poorly understood. To elucidate the longitudinal conformational and energetic changes during MT dynamics, a total of 140 ns molecular dynamic simulations combined with binding free energy calculations were performed on seven tubulin models. The results indicated that the drugs disrupted MT polymerization by altering both MT conformation and binding free energy of the neighboring tubulin subunits. The combination of plinabulin and docetaxel destabilized MT polymerization due to bending MT and weakening the polarity of tubulin polymerization. The new combination of docetaxel and vinblastine synergistically enhanced MT depolymerization and bending, while plinabulin and vinblastine had no synergistic inhibitory effects. The results were verified by the tubulin assembly assay. Our study obtained a comprehensive understanding of the action mechanisms of three natural drugs and their combinations on MT dynamic, provided theoretical guidance for new MTA combinations, and would promote the optimal use of MTA and contribute to developing new MTAs as anticancer agents.
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Affiliation(s)
- Yanyan Chu
- School of Medicine and Pharmacy, Ocean University of China, Qingdao, China
- Innovation Center for Marine Drug Screening and Evaluation, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Zhenhua Tian
- School of Medicine and Pharmacy, Ocean University of China, Qingdao, China
| | - Mengke Yang
- School of Medicine and Pharmacy, Ocean University of China, Qingdao, China
| | - Wenbao Li
- School of Medicine and Pharmacy, Ocean University of China, Qingdao, China
- Innovation Center for Marine Drug Screening and Evaluation, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
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13
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Ramakrishnan J, Chinnamadhu A, Suresh S, Poomani K. Probing the binding nature and stability of highly transmissible mutated variant alpha to omicron of SARS-CoV-2 RBD with ACE2 via molecular dynamics simulation. J Cell Biochem 2023; 124:1115-1134. [PMID: 37435893 DOI: 10.1002/jcb.30432] [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: 02/03/2023] [Revised: 05/20/2023] [Accepted: 05/23/2023] [Indexed: 07/13/2023]
Abstract
Currently, no approved drug is available as a causative agent of coronavirus disease 2019 (COVID-19) except for some repurposed drugs. The first structure of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was reported in late 2019, based on that some vaccines and repurposed drugs were approved to prevent people from COVID-19 during the pandemic situation. Since then, new types of variants emerged and notably, the receptor binding domain (RBD) adopted different binding modes with angiotensin-converting enzyme 2 (ACE2); this made significant changes in the progression of COVID-19. Some of the new variants are highly infectious spreading fast and dangerous. The present study is focused on understanding the binding mode of the RBD of different mutated SARS-CoV-2 variants of concern (alpha to omicron) with the human ACE2 using molecular dynamics simulation. Notably, some variants adopted a new binding mode of RBD with ACE2 and formed different interactions, which is unlike the wild type; this was confirmed from the comparison of interaction between RBD-ACE2 of all variants with its wild-type structure. Binding energy values confirm that some mutated variants exhibit high binding affinity. These findings demonstrate that the variations in the sequence of SARS-CoV-2 S-protein altered the binding mode of RBD; this may be the reason that the virus has high transmissibility and causes new infections. This in-silico study on mutated variants of SARS-CoV-2 RBD with ACE2 insights into their binding mode, binding affinity, and stability. This information may help to understand the RBD-ACE2 binding domains, which allows for designing newer drugs and vaccines.
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Affiliation(s)
- Jaganathan Ramakrishnan
- Laboratory of Biocrystallography and Computational Molecular Biology, Department of Physics, Periyar University, Salem, India
| | - Archana Chinnamadhu
- Laboratory of Biocrystallography and Computational Molecular Biology, Department of Physics, Periyar University, Salem, India
| | - Suganya Suresh
- Laboratory of Biocrystallography and Computational Molecular Biology, Department of Physics, Periyar University, Salem, India
| | - Kumaradhas Poomani
- Laboratory of Biocrystallography and Computational Molecular Biology, Department of Physics, Periyar University, Salem, India
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14
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Gallego-Yerga L, Ceña V, Peláez R. Potent and Selective Benzothiazole-Based Antimitotics with Improved Water Solubility: Design, Synthesis, and Evaluation as Novel Anticancer Agents. Pharmaceutics 2023; 15:1698. [PMID: 37376146 DOI: 10.3390/pharmaceutics15061698] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Revised: 06/06/2023] [Accepted: 06/06/2023] [Indexed: 06/29/2023] Open
Abstract
The design of colchicine site ligands on tubulin has proven to be a successful strategy to develop potent antiproliferative drugs against cancer cells. However, the structural requirements of the binding site endow the ligands with low aqueous solubility. In this work, the benzothiazole scaffold is used to design, synthesize, and evaluate a new family of colchicine site ligands exhibiting high water solubility. The compounds exerted antiproliferative activity against several human cancer cell lines, due to tubulin polymerization inhibition, showing high selectivity toward cancer cells in comparison with non-tumoral HEK-293 cells, as evidenced by MTT and LDH assays. The most potent derivatives, containing a pyridine moiety and ethylurea or formamide functionalities, displayed IC50 values in the nanomolar range even in the difficult-to-treat glioblastoma cells. Flow cytometry experiments on HeLa, MCF7, and U87MG cells showed that they arrest the cell cycle at the G2/M phases at an early time point (24 h), followed by apoptotic cell death 72 h after the treatment. Tubulin binding was confirmed by microtubule network disruption observed via confocal microscopy. Docking studies support favorable interaction of the synthesized ligands at the colchicine binding site. These results validate the proposed strategy to develop potent anticancer colchicine ligands with improved water solubility.
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Affiliation(s)
- Laura Gallego-Yerga
- Laboratorio de Química Orgánica y Farmacéutica, Departamento de Ciencias Farmacéuticas, Universidad de Salamanca, Campus Miguel de Unamuno, 37007 Salamanca, Spain
- Instituto de Investigación Biomédica de Salamanca (IBSAL), Facultad de Farmacia, Universidad de Salamanca, Campus Miguel de Unamuno, 37007 Salamanca, Spain
- Centro de Investigación de Enfermedades Tropicales de la Universidad de Salamanca (CIETUS), Facultad de Farmacia, Universidad de Salamanca, Campus Miguel de Unamuno, 37007 Salamanca, Spain
| | - Valentín Ceña
- Centro de Investigación Biomédica en Red Sobre Enfermedades Neurodegenerativas (CIBERNED), Instituto de Salud Carlos III, 28029 Madrid, Spain
- Unidad Asociada Neurodeath, Facultad de Medicina, Universidad de Castilla-La Mancha, 02006 Albacete, Spain
| | - Rafael Peláez
- Laboratorio de Química Orgánica y Farmacéutica, Departamento de Ciencias Farmacéuticas, Universidad de Salamanca, Campus Miguel de Unamuno, 37007 Salamanca, Spain
- Instituto de Investigación Biomédica de Salamanca (IBSAL), Facultad de Farmacia, Universidad de Salamanca, Campus Miguel de Unamuno, 37007 Salamanca, Spain
- Centro de Investigación de Enfermedades Tropicales de la Universidad de Salamanca (CIETUS), Facultad de Farmacia, Universidad de Salamanca, Campus Miguel de Unamuno, 37007 Salamanca, Spain
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15
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Borys F, Tobiasz P, Poterała M, Fabczak H, Krawczyk H, Joachimiak E. Systematic Studies on Anti-Cancer Evaluation of Stilbene and Dibenzo[ b,f]oxepine Derivatives. Molecules 2023; 28:molecules28083558. [PMID: 37110792 PMCID: PMC10146957 DOI: 10.3390/molecules28083558] [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: 03/06/2023] [Revised: 04/13/2023] [Accepted: 04/14/2023] [Indexed: 04/29/2023] Open
Abstract
Cancer is one of the most common causes of human death worldwide; thus, numerous therapies, including chemotherapy, have been and are being continuously developed. In cancer cells, an aberrant mitotic spindle-a microtubule-based structure necessary for the equal splitting of genetic material between daughter cells-leads to genetic instability, one of the hallmarks of cancer. Thus, the building block of microtubules, tubulin, which is a heterodimer formed from α- and β-tubulin proteins, is a useful target in anti-cancer research. The surface of tubulin forms several pockets, i.e., sites that can bind factors that affect microtubules' stability. Colchicine pockets accommodate agents that induce microtubule depolymerization and, in contrast to factors that bind to other tubulin pockets, overcome multi-drug resistance. Therefore, colchicine-pocket-binding agents are of interest as anti-cancer drugs. Among the various colchicine-site-binding compounds, stilbenoids and their derivatives have been extensively studied. Herein, we report systematic studies on the antiproliferative activity of selected stilbenes and oxepine derivatives against two cancer cell lines-HCT116 and MCF-7-and two normal cell lines-HEK293 and HDF-A. The results of molecular modeling, antiproliferative activity, and immunofluorescence analyses revealed that compounds 1a, 1c, 1d, 1i, 2i, 2j, and 3h were the most cytotoxic and acted by interacting with tubulin heterodimers, leading to the disruption of the microtubular cytoskeleton.
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Affiliation(s)
- Filip Borys
- Department of Organic Chemistry, Faculty of Chemistry, Warsaw University of Technology, 00-664 Warsaw, Poland
- Nencki Institute of Experimental Biology, Polish Academy of Sciences, 02-093 Warsaw, Poland
| | - Piotr Tobiasz
- Department of Organic Chemistry, Faculty of Chemistry, Warsaw University of Technology, 00-664 Warsaw, Poland
| | - Marcin Poterała
- Department of Organic Chemistry, Faculty of Chemistry, Warsaw University of Technology, 00-664 Warsaw, Poland
| | - Hanna Fabczak
- Nencki Institute of Experimental Biology, Polish Academy of Sciences, 02-093 Warsaw, Poland
| | - Hanna Krawczyk
- Department of Organic Chemistry, Faculty of Chemistry, Warsaw University of Technology, 00-664 Warsaw, Poland
| | - Ewa Joachimiak
- Nencki Institute of Experimental Biology, Polish Academy of Sciences, 02-093 Warsaw, Poland
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16
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Mahmoud EM, Shongwe M, Moghadam ES, Moghimi-Rad P, Stoll R, Abdel-Jalil R. Design, synthesis, and molecular docking study of novel cinnoline derivatives as potential inhibitors of tubulin polymerization. Z NATURFORSCH C 2023; 78:123-131. [PMID: 35993925 DOI: 10.1515/znc-2022-0087] [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: 04/26/2022] [Accepted: 07/18/2022] [Indexed: 11/15/2022]
Abstract
The preparation of a novel 4-methylbenzo[h] cinnolines entity via a three-step synthetic protocol is described. Cyclization of the naphthylamidrazones, in the presence of polyphosphoric acid (PPA), furnishes the respective target benzo[h]cinnolines directly. This one-pot synthesis involves intramolecular Friedel-Crafts acylation followed by instant elimination under heating conditions. It is noteworthy that the yield of the product from this step decreases dramatically if the heating is extended beyond 3 h. The target novel cinnolone derivatives were identified by mass spectrometry and their structures elucidated by spectroscopic techniques. Subsequently, molecular docking was performed to shed light on the putative binding mode of the newly synthesized cinnolines. The docking results indicate that these derivatives are potential inhibitors of tubulin polymerization and the best interaction was achieved with a computational ki = 0.5 nM and posed correctly over the lexibulin.
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Affiliation(s)
| | - Musa Shongwe
- Department of Chemistry, College of Science, Sultan Qaboos University, P.O. Box 36, P.C. 123, Muscat, Sultanate of Oman
| | - Ebrahim Saeedian Moghadam
- Department of Chemistry, College of Science, Sultan Qaboos University, P.O. Box 36, P.C. 123, Muscat, Sultanate of Oman.,Department of Medicinal Chemistry, Faculty of Pharmacy, Tehran University of Medical Sciences, Tehran, 1417614411, Iran
| | - Parsa Moghimi-Rad
- Department of Medicinal Chemistry, Faculty of Pharmacy, Tehran University of Medical Sciences, Tehran, 1417614411, Iran
| | - Raphael Stoll
- Biomolecular NMR, Ruhr University of Bochum, D-44780, Bochum, Germany
| | - Raid Abdel-Jalil
- Department of Chemistry, College of Science, Sultan Qaboos University, P.O. Box 36, P.C. 123, Muscat, Sultanate of Oman
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17
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Wranik M, Weinert T, Slavov C, Masini T, Furrer A, Gaillard N, Gioia D, Ferrarotti M, James D, Glover H, Carrillo M, Kekilli D, Stipp R, Skopintsev P, Brünle S, Mühlethaler T, Beale J, Gashi D, Nass K, Ozerov D, Johnson PJM, Cirelli C, Bacellar C, Braun M, Wang M, Dworkowski F, Milne C, Cavalli A, Wachtveitl J, Steinmetz MO, Standfuss J. Watching the release of a photopharmacological drug from tubulin using time-resolved serial crystallography. Nat Commun 2023; 14:903. [PMID: 36807348 PMCID: PMC9936131 DOI: 10.1038/s41467-023-36481-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Accepted: 02/02/2023] [Indexed: 02/19/2023] Open
Abstract
The binding and release of ligands from their protein targets is central to fundamental biological processes as well as to drug discovery. Photopharmacology introduces chemical triggers that allow the changing of ligand affinities and thus biological activity by light. Insight into the molecular mechanisms of photopharmacology is largely missing because the relevant transitions during the light-triggered reaction cannot be resolved by conventional structural biology. Using time-resolved serial crystallography at a synchrotron and X-ray free-electron laser, we capture the release of the anti-cancer compound azo-combretastatin A4 and the resulting conformational changes in tubulin. Nine structural snapshots from 1 ns to 100 ms complemented by simulations show how cis-to-trans isomerization of the azobenzene bond leads to a switch in ligand affinity, opening of an exit channel, and collapse of the binding pocket upon ligand release. The resulting global backbone rearrangements are related to the action mechanism of microtubule-destabilizing drugs.
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Affiliation(s)
- Maximilian Wranik
- Division of Biology and Chemistry, Paul Scherrer Institut, 5232, Villigen, Switzerland
| | - Tobias Weinert
- Division of Biology and Chemistry, Paul Scherrer Institut, 5232, Villigen, Switzerland
| | - Chavdar Slavov
- Institute of Physical and Theoretical Chemistry, Goethe University, Frankfurt am Main, Germany
| | - Tiziana Masini
- Computational & Chemical Biology, Istituto Italiano di Tecnologia, 16163, Genova, Italy
| | - Antonia Furrer
- Division of Biology and Chemistry, Paul Scherrer Institut, 5232, Villigen, Switzerland
| | - Natacha Gaillard
- Division of Biology and Chemistry, Paul Scherrer Institut, 5232, Villigen, Switzerland
| | - Dario Gioia
- Computational & Chemical Biology, Istituto Italiano di Tecnologia, 16163, Genova, Italy
| | - Marco Ferrarotti
- Computational & Chemical Biology, Istituto Italiano di Tecnologia, 16163, Genova, Italy
| | - Daniel James
- Division of Biology and Chemistry, Paul Scherrer Institut, 5232, Villigen, Switzerland
| | - Hannah Glover
- Division of Biology and Chemistry, Paul Scherrer Institut, 5232, Villigen, Switzerland
| | - Melissa Carrillo
- Division of Biology and Chemistry, Paul Scherrer Institut, 5232, Villigen, Switzerland
| | - Demet Kekilli
- Division of Biology and Chemistry, Paul Scherrer Institut, 5232, Villigen, Switzerland
| | - Robin Stipp
- Division of Biology and Chemistry, Paul Scherrer Institut, 5232, Villigen, Switzerland
| | - Petr Skopintsev
- Division of Biology and Chemistry, Paul Scherrer Institut, 5232, Villigen, Switzerland
| | - Steffen Brünle
- Division of Biology and Chemistry, Paul Scherrer Institut, 5232, Villigen, Switzerland
| | - Tobias Mühlethaler
- Division of Biology and Chemistry, Paul Scherrer Institut, 5232, Villigen, Switzerland
| | - John Beale
- Division of Biology and Chemistry, Paul Scherrer Institut, 5232, Villigen, Switzerland
| | - Dardan Gashi
- Photon Science Division, Paul Scherrer Institut, 5232, Villigen, Switzerland
| | - Karol Nass
- Photon Science Division, Paul Scherrer Institut, 5232, Villigen, Switzerland
| | - Dmitry Ozerov
- Scientific Computing, Theory and Data, Paul Scherrer Institut, 5232, Villigen, Switzerland
| | - Philip J M Johnson
- Photon Science Division, Paul Scherrer Institut, 5232, Villigen, Switzerland
| | - Claudio Cirelli
- Photon Science Division, Paul Scherrer Institut, 5232, Villigen, Switzerland
| | - Camila Bacellar
- Photon Science Division, Paul Scherrer Institut, 5232, Villigen, Switzerland
| | - Markus Braun
- Institute of Physical and Theoretical Chemistry, Goethe University, Frankfurt am Main, Germany
| | - Meitian Wang
- Photon Science Division, Paul Scherrer Institut, 5232, Villigen, Switzerland
| | - Florian Dworkowski
- Photon Science Division, Paul Scherrer Institut, 5232, Villigen, Switzerland
| | - Chris Milne
- Photon Science Division, Paul Scherrer Institut, 5232, Villigen, Switzerland
| | - Andrea Cavalli
- Computational & Chemical Biology, Istituto Italiano di Tecnologia, 16163, Genova, Italy
- Department of Pharmacy and Biotechnology, University of Bologna, 40126, Bologna, Italy
| | - Josef Wachtveitl
- Institute of Physical and Theoretical Chemistry, Goethe University, Frankfurt am Main, Germany
| | - Michel O Steinmetz
- Division of Biology and Chemistry, Paul Scherrer Institut, 5232, Villigen, Switzerland.
- Biozentrum, University of Basel, 4056, Basel, Switzerland.
| | - Jörg Standfuss
- Division of Biology and Chemistry, Paul Scherrer Institut, 5232, Villigen, Switzerland.
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18
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Computational Approaches to the Rational Design of Tubulin-Targeting Agents. Biomolecules 2023; 13:biom13020285. [PMID: 36830654 PMCID: PMC9952983 DOI: 10.3390/biom13020285] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Revised: 01/27/2023] [Accepted: 01/31/2023] [Indexed: 02/05/2023] Open
Abstract
Microtubules are highly dynamic polymers of α,β-tubulin dimers which play an essential role in numerous cellular processes such as cell proliferation and intracellular transport, making them an attractive target for cancer and neurodegeneration research. To date, a large number of known tubulin binders were derived from natural products, while only one was developed by rational structure-based drug design. Several of these tubulin binders show promising in vitro profiles while presenting unacceptable off-target effects when tested in patients. Therefore, there is a continuing demand for the discovery of safer and more efficient tubulin-targeting agents. Since tubulin structural data is readily available, the employment of computer-aided design techniques can be a key element to focus on the relevant chemical space and guide the design process. Due to the high diversity and quantity of structural data available, we compiled here a guide to the accessible tubulin-ligand structures. Furthermore, we review different ligand and structure-based methods recently used for the successful selection and design of new tubulin-targeting agents.
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19
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Shemesh A, Ghareeb H, Dharan R, Levi-Kalisman Y, Metanis N, Ringel I, Raviv U. Effect of tubulin self-association on GTP hydrolysis and nucleotide exchange reactions. BIOCHIMICA ET BIOPHYSICA ACTA. PROTEINS AND PROTEOMICS 2023; 1871:140869. [PMID: 36400388 DOI: 10.1016/j.bbapap.2022.140869] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2022] [Revised: 10/13/2022] [Accepted: 11/08/2022] [Indexed: 11/17/2022]
Abstract
We investigated how the self-association of isolated tubulin dimers affects the rate of GTP hydrolysis and the equilibrium of nucleotide exchange. Both reactions are relevant for microtubule (MT) dynamics. We used HPLC to determine the concentrations of GDP and GTP and thereby the GTPase activity of SEC-eluted tubulin dimers in assembly buffer solution, free of glycerol and tubulin aggregates. When GTP hydrolysis was negligible, the nucleotide exchange mechanism was studied by determining the concentrations of tubulin-free and tubulin-bound GTP and GDP. We observed no GTP hydrolysis below the critical conditions for MT assembly (either below the critical tubulin concentration and/or at low temperature), despite the assembly of tubulin 1D curved oligomers and single-rings, showing that their assembly did not involve GTP hydrolysis. Under conditions enabling spontaneous slow MT assembly, a slow pseudo-first-order GTP hydrolysis kinetics was detected, limited by the rate of MT assembly. Cryo-TEM images showed that GTP-tubulin 1D oligomers were curved also at 36 °C. Nucleotide exchange depended on the total tubulin concentration and the molar ratio between tubulin-free GDP and GTP. We used a thermodynamic model of isodesmic tubulin self-association, terminated by the formation of tubulin single-rings to determine the molar fractions of dimers with exposed and buried nucleotide exchangeable sites (E-sites). Our analysis shows that the GDP to GTP exchange reaction equilibrium constant was an order-of-magnitude larger for tubulin dimers with exposed E-sites than for assembled dimers with buried E-sites. This conclusion may have implications on the dynamics at the tip of the MT plus end.
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Affiliation(s)
- Asaf Shemesh
- Institute of Chemistry, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, Jerusalem 9190401, Israel; The Harvey M. Krueger Family Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, Jerusalem 9190401, Israel
| | - Hiba Ghareeb
- Institute of Chemistry, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, Jerusalem 9190401, Israel
| | - Raviv Dharan
- Institute of Chemistry, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, Jerusalem 9190401, Israel
| | - Yael Levi-Kalisman
- The Harvey M. Krueger Family Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, Jerusalem 9190401, Israel; Institute of Life Sciences, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, Jerusalem 9190401, Israel
| | - Norman Metanis
- Institute of Chemistry, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, Jerusalem 9190401, Israel
| | - Israel Ringel
- Institute for Drug Research, School of Pharmacy, The Hebrew University of Jerusalem, 9112102 Jerusalem, Israel
| | - Uri Raviv
- Institute of Chemistry, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, Jerusalem 9190401, Israel; The Harvey M. Krueger Family Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, Jerusalem 9190401, Israel.
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20
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Mukherjee S, Sawant AV, Prassanawar SS, Panda D. Copper-Plumbagin Complex Produces Potent Anticancer Effects by Depolymerizing Microtubules and Inducing Reactive Oxygen Species and DNA Damage. ACS OMEGA 2023; 8:3221-3235. [PMID: 36713695 PMCID: PMC9878539 DOI: 10.1021/acsomega.2c06691] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Accepted: 12/27/2022] [Indexed: 06/18/2023]
Abstract
Here, we have synthesized a copper complex of plumbagin (Cu-PLN) and investigated its antiproliferative activities in different cancer cells. The crystal structure of Cu-PLN showed that the complex was square planar with a binding stoichiometry of 1:2 (Cu/Plumbagin). Cu-PLN inhibited the proliferation of human cervical carcinoma (HeLa), human breast cancer (MCF-7), and murine melanoma (B16F10) cells with half-maximal inhibitory concentrations (IC50) of 0.85 ± 0.05, 2.3 ± 0.1, and 1.1 ± 0.1 μM, respectively. Plumbagin inhibited the proliferation of HeLa, MCF-7, and B16F10 cells with IC50 of 7 ± 0.1, 8.2 ± 0.2, and 6.2 ± 0.4 μM, respectively, showing that Cu-PLN is a stronger antiproliferative agent than plumbagin. Interestingly, Cu-PLN showed much stronger toxicity against breast carcinoma and skin melanoma cells than noncancerous breast epithelial and skin fibroblast cells, indicating its specific cytotoxicity toward cancer cells. A short exposure of Cu-PLN triggered microtubule disassembly in cultured cancer cells, and the complex also inhibited the polymerization of purified tubulin much more strongly than plumbagin. Furthermore, Cu-PLN inhibited the binding of colchicine to tubulin. In addition to microtubule depolymerization, the antiproliferative mechanism of Cu-PLN involved induction of reactive oxygen species, reduction of the mitochondrial membrane potential, and DNA damage. Moreover, the cytotoxic effects of Cu-PLN reduced significantly in cells pre-treated with N-acetyl cysteine, suggesting that reactive oxygen species generation is crucial in Cu-PLN's mode of action. Thus, the complexation of plumbagin with copper yields a promising antitumor agent having a stronger antiproliferative activity than cisplatin, a widely used anticancer drug.
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Affiliation(s)
- Sandipan Mukherjee
- Department
of Biosciences and Bioengineering, Indian
Institute of Technology Bombay, Mumbai 400076, India
| | - Avishkar V. Sawant
- Department
of Biosciences and Bioengineering, Indian
Institute of Technology Bombay, Mumbai 400076, India
| | - Shweta S. Prassanawar
- Department
of Biosciences and Bioengineering, Indian
Institute of Technology Bombay, Mumbai 400076, India
| | - Dulal Panda
- Department
of Biosciences and Bioengineering, Indian
Institute of Technology Bombay, Mumbai 400076, India
- National
Institute of Pharmaceutical Education and Research, SAS Nagar, Punjab 160062, India
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21
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Xanthatin and 8-epi-xanthatin as new potential colchicine binding site inhibitors: a computational study. J Mol Model 2023; 29:36. [PMID: 36627468 DOI: 10.1007/s00894-022-05428-w] [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: 08/17/2022] [Accepted: 12/19/2022] [Indexed: 01/12/2023]
Abstract
CONTEXT Phytocompounds xanthatin and 8-epi-xanthatin, obtained from Xanthium chinese Mill, showed antitumoral activity in vitro related to the microtubules destabilizing properties of these phytocompounds. Five binding sites for microtubule destabilizing agents have been characterized on tubulin by high-resolution X-ray crystallography: vinca domain, colchicine, pironetin, maytansine site, and more recently, the seventh site. This work aims to develop a comprehensive computational strategy to understand and eventually predict the interaction between xanthatin and 8-epi-xanthatin with the destabilizing-antimitotic binding domain of the tubulin heterodimer. In addition, we propose a putative binding site for these phytocompounds into the microtubule destabilizing binding sites on the tubulin heterodimer. Xanthanolides showed higher stability in the colchicine and pironetin binding sites, whit a greater affinity for the former. In addition, we found that xanthanolides and non-classical colchicine binding site inhibitors share a high structural similarity. METHODS The 3D structures for xanthatin and 8-epi-xanthatin were obtained using DFT with the hybrid functional B3LYP and the base 6-31G (d,p), implemented in Gaussian 09. The 3D coordinates for tubulin proteins were downloaded from PDB. The complexes tubulin-xanthanolides were predicted using a Monte-Carlo iterated search combined with the BFGS gradient-based optimizer implemented in the AutoDock Vina. The xanthanolides-tubulin complexes were energy minimized by molecular dynamics simulations at vacuum, and their stabilities were evaluated by solvated molecular dynamics simulations during 100 ns. All molecular dynamics simulations were performed using the conjugate gradient method implemented in NAMD2 and CHARMM36 forcefield.
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22
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Kumari A, Prassanawar SS, Panda D. β-III Tubulin Levels Determine the Neurotoxicity Induced by Colchicine-Site Binding Agent Indibulin. ACS Chem Neurosci 2023; 14:19-34. [PMID: 36541944 DOI: 10.1021/acschemneuro.2c00324] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Indibulin, a microtubule-depolymerizing agent, produces minimal neurotoxicity in animals. It is also less cytotoxic toward differentiated neuronal cells than undifferentiated cells. We found that the levels of β-III tubulin, acetylated tubulin, and polyglutamylated tubulin were significantly increased in differentiated neuroblastoma cells (SH-SY5Y). Since neuronal cells express β-tubulin isotypes differently from other cell types, we explored the binding of indibulin to different β-tubulin isotypes. Our molecular docking analysis suggested that indibulin binds to β-III tubulin with lower affinity than to other β-tubulin isotypes. We therefore studied the implications of different β-tubulin isotypes on the cytotoxic effects of indibulin, colchicine, and vinblastine in differentiated SH-SY5Y cells. Upon depletion of β-III tubulin in the differentiated cells, the toxicity of indibulin and colchicine significantly increased, while sensitivity to vinblastine was unaffected. Using biochemical, bioinformatics, and fluorescence spectroscopic techniques, we have identified the binding site of indibulin on tubulin, which had not previously been established. Indibulin inhibited the binding of colchicine and C12 (a colchicine-site binder) to tubulin and also increased the dissociation constant of the interaction between tubulin and colchicine. Indibulin did not inhibit the binding of vinblastine or taxol to tubulin. Interestingly, indibulin antagonized colchicine treatment but synergized with vinblastine treatment in a combination study performed in MDA-MB-231 cells. The results indicate that indibulin is a colchicine-site binder and that the efficacy of colchicine-site binders is affected by the β-III tubulin levels in the cells.
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Affiliation(s)
- Anuradha Kumari
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai 400076, India
| | - Shweta S Prassanawar
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai 400076, India
| | - Dulal Panda
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai 400076, India.,National Institute of Pharmaceutical Education and Research, SAS Nagar, Punjab 160062, India
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23
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Amini M, Barazandeh Tehrani M, Moghimirad P, Boumi S, Ostad S. Design, Synthesis, and Biological Evaluation of New Di-arylimidazole-quinazolinone Hybrid. HETEROCYCLES 2023. [DOI: 10.3987/com-22-14801] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
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24
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Leng J, Zhao Y, Sheng P, Xia Y, Chen T, Zhao S, Xie S, Yan X, Wang X, Yin Y, Kong L. Discovery of Novel N-Heterocyclic-Fused Deoxypodophyllotoxin Analogues as Tubulin Polymerization Inhibitors Targeting the Colchicine-Binding Site for Cancer Treatment. J Med Chem 2022; 65:16774-16800. [PMID: 36471625 DOI: 10.1021/acs.jmedchem.2c01595] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Natural products are a major source of anticancer agents and play critical roles in anticancer drug development. Inspired by the complexity-to-diversity strategy, novel deoxypodophyllotoxin (DPT) analogues were designed and synthesized. Among them, compound C3 exhibited the potent antiproliferative activity against four human cancer cell lines with IC50 values in the low nanomolar range. Additionally, it showed marked activity against paclitaxel-resistant MCF-7 cells and A549 cells. Moreover, compound C3 can inhibit tubulin polymerization by targeting the colchicine-binding site of tubulin. Further study revealed that compound C3 could arrest cancer cells in the G2/M phase and disrupt the angiogenesis in human umbilical vein endothelial cells. Meanwhile, C3 remarkably inhibited cancer cell motility and migration, as well as considerably inhibited tumor growth in MCF-7 and MCF-7/TxR xenograft model without obvious toxicity. Collectively, these results indicated that compound C3 may be a promising tubulin polymerization inhibitor development for cancer treatment.
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Affiliation(s)
- Jiafu Leng
- Jiangsu Key Laboratory of Bioactive Natural Product Research and State Key Laboratory of Natural Medicines, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing 210009, People's Republic of China
| | - Yongjun Zhao
- Jiangsu Key Laboratory of Bioactive Natural Product Research and State Key Laboratory of Natural Medicines, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing 210009, People's Republic of China
| | - Ping Sheng
- Jiangsu Key Laboratory of Bioactive Natural Product Research and State Key Laboratory of Natural Medicines, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing 210009, People's Republic of China
| | - Yuanzheng Xia
- Jiangsu Key Laboratory of Bioactive Natural Product Research and State Key Laboratory of Natural Medicines, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing 210009, People's Republic of China
| | - Tingting Chen
- Jiangsu Key Laboratory of Bioactive Natural Product Research and State Key Laboratory of Natural Medicines, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing 210009, People's Republic of China
| | - Shifang Zhao
- Jiangsu Key Laboratory of Bioactive Natural Product Research and State Key Laboratory of Natural Medicines, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing 210009, People's Republic of China
| | - Shanshan Xie
- Jiangsu Key Laboratory of Bioactive Natural Product Research and State Key Laboratory of Natural Medicines, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing 210009, People's Republic of China
| | - Xiangyu Yan
- Jiangsu Key Laboratory of Bioactive Natural Product Research and State Key Laboratory of Natural Medicines, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing 210009, People's Republic of China
| | - Xiaobing Wang
- Jiangsu Key Laboratory of Bioactive Natural Product Research and State Key Laboratory of Natural Medicines, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing 210009, People's Republic of China
| | - Yong Yin
- Jiangsu Key Laboratory of Bioactive Natural Product Research and State Key Laboratory of Natural Medicines, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing 210009, People's Republic of China
| | - Lingyi Kong
- Jiangsu Key Laboratory of Bioactive Natural Product Research and State Key Laboratory of Natural Medicines, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing 210009, People's Republic of China
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25
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Prudhomme V, Cucca M, Nauton L, Andrieu E, Fereyrolles M, Lamoine S, Michelin C, Bennis K, Collin A, De Ceuninck F, Botez I, Mallet C, Ducki S. Design, synthesis and biological evaluation of conformationnally-restricted analogues of E7010 as inhibitors of tubulin assembly (ITA) and vascular disrupting agents (VDA). Eur J Med Chem 2022; 244:114809. [DOI: 10.1016/j.ejmech.2022.114809] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Revised: 09/09/2022] [Accepted: 09/27/2022] [Indexed: 11/28/2022]
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26
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Riu F, Ibba R, Zoroddu S, Sestito S, Lai M, Piras S, Sanna L, Bordoni V, Bagella L, Carta A. Design, synthesis, and biological screening of a series of 4'-fluoro-benzotriazole-acrylonitrile derivatives as microtubule-destabilising agents (MDAs). J Enzyme Inhib Med Chem 2022; 37:2223-2240. [PMID: 35979600 PMCID: PMC9397482 DOI: 10.1080/14756366.2022.2111680] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022] Open
Abstract
Introduction: Colchicine-binding site inhibitors are some of the most interesting ligands belonging to the wider family of microtubule-destabilising agents.Results: A novel series of 4'-fluoro-substituted ligands (5-13) was synthesised. The antiproliferative activity assays resulted in nM values for the new benzotriazole-acrylonitrile derivatives. Compound 5, the hit compound, showed an evident blockade of HeLa cell cycle in the G2-M phase, but also a pro-apoptotic potential, and an increase of early and late apoptotic cells in HeLa and MCF-7 cell cycle analysis. Confocal microscopy analysis showed a segmented shape and a collapse of the cytoskeleton, as well as a consistent cell shrinkage after administration of 5 at 100 nM. Derivative 5 was also proved to compete with colchicine at colchicine-binding site, lowering its activity against tubulin polymerisation. In addition, co-administration of 5 and doxorubicin in drug-resistant A375 melanoma cell line highlighted a synergic potential in terms of inhibition of cell viability.Discussion: The 4'-fluoro substitution of benzotriazole-acrylonitrile scaffold brought us a step forward in the optimisation process to obtain compound 5 as promising MDA antiproliferative agent at nanomolar concentration.
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Affiliation(s)
- Federico Riu
- Department of Medicine, Surgery and Pharmacy, University of Sassari, Sassari, Italy
| | - Roberta Ibba
- Department of Medicine, Surgery and Pharmacy, University of Sassari, Sassari, Italy
| | - Stefano Zoroddu
- Department of Biomedical Sciences, University of Sassari, Sassari, Italy
| | - Simona Sestito
- Department of Chemical, Physical, Mathematical and Natural Sciences, University of Sassari, Sassari, Italy
| | - Michele Lai
- Department of Translational Medicine and New Technologies in Medicine and Surgery, Retrovirus Centre, University of Pisa, Pisa, Italy.,CISUP - Centre for Instrumentation Sharing - University of Pisa, Pisa, Italy
| | - Sandra Piras
- Department of Medicine, Surgery and Pharmacy, University of Sassari, Sassari, Italy
| | - Luca Sanna
- Department of Biomedical Sciences, University of Sassari, Sassari, Italy
| | - Valentina Bordoni
- Department of Biomedical Sciences, University of Sassari, Sassari, Italy
| | - Luigi Bagella
- Department of Biomedical Sciences, University of Sassari, Sassari, Italy.,Center for Biotechnology, College of Science and Technology, Sbarro Institute for Cancer Research and Molecular Medicine, Temple University, Philadelphia, PA, USA
| | - Antonio Carta
- Department of Medicine, Surgery and Pharmacy, University of Sassari, Sassari, Italy
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Chang J, Wang C, Yang S, Shi L, Zhang Y, Liu W, Meng J, Zeng J, Zhang R, Liu N, Xing D. Design, synthesis, and biological evaluation of diarylpyrazole derivatives as antitumor agents targeting microtubules. ARAB J CHEM 2022. [DOI: 10.1016/j.arabjc.2022.104253] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
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28
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Foroutan A, Corazzari M, Grolla AA, Colombo G, Travelli C, Genazzani AA, Theeramunkong S, Galli U, Tron GC. Identification of novel aza-analogs of TN-16 as disrupters of microtubule dynamics through a multicomponent reaction. Eur J Med Chem 2022; 245:114895. [DOI: 10.1016/j.ejmech.2022.114895] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Revised: 10/14/2022] [Accepted: 10/29/2022] [Indexed: 11/06/2022]
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29
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Doan NQH, Nguyen NTK, Duong VB, Nguyen HTT, Vong LB, Duong DN, Nguyen NTT, Nguyen TLT, Do TTH, Truong TN. Synthesis, Biological Evaluation, and Molecular Modeling Studies of 1-Aryl-1 H-pyrazole-Fused Curcumin Analogues as Anticancer Agents. ACS OMEGA 2022; 7:33963-33984. [PMID: 36188331 PMCID: PMC9520563 DOI: 10.1021/acsomega.2c02933] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Accepted: 09/08/2022] [Indexed: 05/28/2023]
Abstract
Addressing the growing burden of cancer and the shortcomings of chemotherapy in cancer treatment are the current research goals. Research to overcome the limitations of curcumin and to improve its anticancer activity via its heterocycle-fused monocarbonyl analogues (MACs) has immense potential. In this study, 32 asymmetric MACs fused with 1-aryl-1H-pyrazole (7a-10h) were synthesized and characterized to develop new curcumin analogues. Subsequently, via initial screening for cytotoxic activity, nine compounds exhibited potential growth inhibition against MDA-MB-231 (IC50 2.43-7.84 μM) and HepG2 (IC50 4.98-14.65 μM), in which seven compounds showing higher selectivities on two cancer cell lines than the noncancerous LLC-PK1 were selected for cell-free in vitro screening for effects on microtubule assembly activity. Among those, compounds 7d, 7h, and 10c showed effective inhibitions of microtubule assembly at 20.0 μM (40.76-52.03%), indicating that they could act as microtubule-destabilizing agents. From the screening results, three most potential compounds, 7d, 7h, and 10c, were selected for further evaluation of cellular effects on breast cancer MDA-MB-231 cells. The apoptosis-inducing study indicated that these three compounds could cause morphological changes at 1.0 μM and could enhance caspase-3 activity (1.33-1.57 times) at 10.0 μM in MDA-MB-231 cells, confirming their apoptosis-inducing activities. Additionally, in cell cycle analysis, compounds 7d and 7h at 2.5 μM and 10c at 5.0 μM also arrested MDA-MB-231 cells in the G2/M phase. Finally, the results from in silico studies revealed that the predicted absorption, distribution, metabolism, excretion, and the toxicity (ADMET) profile of the most potent MACs might have several advantages in addition to potential disadvantages, and compound 7h could bind into (ΔG -10.08 kcal·mol-1) and access wider space at the colchicine-binding site (CBS) than that of colchicine or nocodazole via molecular docking studies. In conclusion, our study serves as a basis for the design of promising synthetic compounds as anticancer agents in the future.
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Affiliation(s)
- Nam Q. H. Doan
- Faculty
of Pharmacy, Van Lang University, Ho Chi Minh City 700000, Vietnam
| | - Ngan T. K. Nguyen
- Department
of Organic Chemistry, Faculty of Pharmacy, University of Medicine and Pharmacy at Ho Chi Minh City, Ho Chi Minh City 700000, Vietnam
| | - Vu B. Duong
- Department
of Organic Chemistry, Faculty of Pharmacy, University of Medicine and Pharmacy at Ho Chi Minh City, Ho Chi Minh City 700000, Vietnam
| | - Ha T. T. Nguyen
- School
of Biomedical Engineering, International University, Vietnam National University Ho Chi Minh City, Ho Chi Minh City 700000, Vietnam
| | - Long B. Vong
- School
of Biomedical Engineering, International University, Vietnam National University Ho Chi Minh City, Ho Chi Minh City 700000, Vietnam
| | - Diem N. Duong
- Immunology
Lab, Vaccines and Biologicals Production Department, Pasteur Institute in Ho Chi Minh City, Ho Chi Minh City 700000, Vietnam
| | - Nguyet-Thu T. Nguyen
- Immunology
Lab, Vaccines and Biologicals Production Department, Pasteur Institute in Ho Chi Minh City, Ho Chi Minh City 700000, Vietnam
| | - Tuyen L. T. Nguyen
- Saigon
Pharmaceutical Sciences and Technologies Center, Ho Chi Minh City 700000, Vietnam
| | - Tuoi T. H. Do
- Department
of Pharmacology, Faculty of Pharmacy, University
of Medicine and Pharmacy at Ho Chi Minh City, Ho Chi Minh City 700000, Vietnam
| | - Tuyen N. Truong
- Department
of Organic Chemistry, Faculty of Pharmacy, University of Medicine and Pharmacy at Ho Chi Minh City, Ho Chi Minh City 700000, Vietnam
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30
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Lafanechère L. The microtubule cytoskeleton: An old validated target for novel therapeutic drugs. Front Pharmacol 2022; 13:969183. [PMID: 36188585 PMCID: PMC9521402 DOI: 10.3389/fphar.2022.969183] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Accepted: 08/30/2022] [Indexed: 12/02/2022] Open
Abstract
Compounds targeting microtubules are widely used in cancer therapy with a proven efficacy. However, because they also target non-cancerous cells, their administration leads to numerous adverse effects. With the advancement of knowledge on the structure of tubulin, the regulation of microtubule dynamics and their deregulation in pathological processes, new therapeutic strategies are emerging, both for the treatment of cancer and for other diseases, such as neuronal or even heart diseases and parasite infections. In addition, a better understanding of the mechanism of action of well-known drugs such as colchicine or certain kinase inhibitors contributes to the development of these new therapeutic approaches. Nowadays, chemists and biologists are working jointly to select drugs which target the microtubule cytoskeleton and have improved properties. On the basis of a few examples this review attempts to depict the panorama of these recent advances.
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31
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Dutta S, Bose D, Ghosh S, Chakrabarti A. Spectrin: an alternate target for cytoskeletal drugs. J Biomol Struct Dyn 2022:1-12. [PMID: 35994328 DOI: 10.1080/07391102.2022.2109063] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/15/2022]
Abstract
Cytoskeletal drugs having enormous therapeutic potential act on the cytoskeletal components like actin, tubulin either by promoting polymerization or destabilizing the same. Here we present the interaction of the popular cytoskeletal drugs such as taxol, latrunculin and cytochalasin with spectrin, a huge protein with multi domains that forms the cytoskeletal network. Particularly, the actin binding domain of spectrin regulates the dynamics of the actin cytoskeleton. We followed the binding of these drugs to its actin binding domain and intact spectrin as well. These drugs bind with moderate affinity (Kb ∼ 104 M-1) and the interaction with actin binding domain is entropy driven and hydrophobic in nature as determined by Van't Hoff plot. The docking studies and molecular dynamics simulations further corroborate the experimental findings. Particularly the higher binding constants in the case of latrunculin and cytochalasin to the actin binding domain of spectrin suggest the binding sites are presumably located in its actin binding domain.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Sansa Dutta
- Crystallography and Molecular Biology Division, Saha Institute of Nuclear Physics, Kolkata, West Bengal, India.,Department of Chemistry, Indian Institute of Technology, Kharagpur, West Bengal, India
| | - Dipayan Bose
- Crystallography and Molecular Biology Division, Saha Institute of Nuclear Physics, Kolkata, West Bengal, India.,Homi Bhabha National Institute, Mumbai, Maharashtra, India
| | - Semanti Ghosh
- Crystallography and Molecular Biology Division, Saha Institute of Nuclear Physics, Kolkata, West Bengal, India
| | - Abhijit Chakrabarti
- Crystallography and Molecular Biology Division, Saha Institute of Nuclear Physics, Kolkata, West Bengal, India.,Homi Bhabha National Institute, Mumbai, Maharashtra, India
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32
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Ranjan Dwivedi A, Singh Rawat S, Kumar V, Kumar N, Anand P, Prakash Yadav R, Barnwal S, Prasad A, Kumar V. Synthesis and Screening of Novel 4-N-Heterocyclic-2-aryl-6,7,8-trimethoxyquinazolines as Antiproliferative and Tubulin Polymerization Inhibitors. Bioorg Med Chem 2022; 72:116976. [DOI: 10.1016/j.bmc.2022.116976] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2022] [Revised: 08/04/2022] [Accepted: 08/19/2022] [Indexed: 11/02/2022]
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33
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Alpízar-Pedraza D, Veulens ADLN, Araujo EC, Piloto-Ferrer J, Sánchez-Lamar Á. Microtubules destabilizing agents binding sites in tubulin. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2022.132723] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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34
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An overview on the exploring the interaction of inorganic nanoparticles with microtubules for the advancement of cancer therapeutics. Int J Biol Macromol 2022; 212:358-369. [PMID: 35618086 DOI: 10.1016/j.ijbiomac.2022.05.150] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Revised: 05/17/2022] [Accepted: 05/21/2022] [Indexed: 01/01/2023]
Abstract
Targeting microtubules (MTs), dynamic and stable proteins in cells, by different ligands have been reported to be a potential strategy to combat cancer cells. Inorganic nanoparticles (NPs) have been widely used as anticancer, antibacterial, and free radical scavenging agents, where the come in contact with biological macromolecules. The interaction between the NPs and biological macromolecules like MTs frequently occurs through different mechanisms. A prerequisite for a detailed exploration of MT structures and functions for biomedical applications like cancer therapy is to investigate profoundly the mechanisms involved in MT-NP interactions, for which the full explanation and characterization of the parameters that are responsible for the formation of a NP-protein complex are crucial. Therefore, in view of the fact that the goal of the rational NP-based future drug design and new therapies is to rely on the information of the structural details and protein-NPs binding mechanisms to manipulate the process of developing new potential drugs, a comprehensive investigation of the essence of the molecular recognition/interaction is also of considerable importance. In the present review, first, the microtubule (MT) structure and its binding sites upon interaction with MT stabilizing agents (MSAs) and MT destabilizing agents (MDAs) are introduced and rationalized. Next, MT targeting in cancer therapy and interaction of NPs with MTs are discussed. Furthermore, interaction of NPs with proteins and the manipulation of protein corona (PC), experimental techniques, and direct interaction of NPs with MTs, are discussed, and finally the challenges and future perspective of the field are introduced. We envision this review can provide useful information on the manipulation of the MT lattice for the progress of cancer nanomedicine.
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35
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Boichuk S, Syuzov K, Bikinieva F, Galembikova A, Zykova S, Gankova K, Igidov S, Igidov N. Computational-Based Discovery of the Anti-Cancer Activities of Pyrrole-Based Compounds Targeting the Colchicine-Binding Site of Tubulin. Molecules 2022; 27:2873. [PMID: 35566235 PMCID: PMC9101527 DOI: 10.3390/molecules27092873] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2022] [Revised: 04/27/2022] [Accepted: 04/29/2022] [Indexed: 12/10/2022] Open
Abstract
Despite the tubulin-binding agents (TBAs) that are widely used in the clinic for cancer therapy, tumor resistance to TBAs (both inherited and acquired) significantly impairs their effectiveness, thereby decreasing overall survival (OS) and progression-free survival (PFS) rates, especially for the patients with metastatic, recurrent, and unresectable forms of the disease. Therefore, the development of novel effective drugs interfering with the microtubules' dynamic state remains a big challenge in current oncology. We report here about the novel ethyl 2-amino-1-(furan-2-carboxamido)-5-(2-aryl/tert-butyl-2-oxoethylidene)-4-oxo-4,5-dihydro-1H-pyrrole-3-carboxylates (EAPCs) exhibiting potent anti-cancer activities against the breast and lung cancer cell lines in vitro. This was due to their ability to inhibit tubulin polymerization and induce cell cycle arrest in M-phase. As an outcome, the EAPC-treated cancer cells exhibited a significant increase in apoptosis, which was evidenced by the expression of cleaved forms of PARP, caspase-3, and increased numbers of Annexin-V-positive cells. By using the in silico molecular modeling methods (e.g., induced-fit docking, binding metadynamics, and unbiased molecular dynamics), we found that EAPC-67 and -70 preferentially bind to the colchicine-binding site of tubulin. Lastly, we have shown that the EAPCs indicated above and colchicine utilizes a similar molecular mechanism to inhibit tubulin polymerization via targeting the T7 loop in the β-chain of tubulin, thereby preventing the conformational changes in the tubulin dimers required for their polymerization. Collectively, we identified the novel and potent TBAs that bind to the colchicine-binding site and disrupt the microtubule network. As a result of these events, the compounds induced a robust cell cycle arrest in M-phase and exhibited potent pro-apoptotic activities against the epithelial cancer cell lines in vitro.
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Affiliation(s)
- Sergei Boichuk
- Department of Pathology, Kazan State Medical University, 420012 Kazan, Russia; (K.S.); (F.B.); (A.G.)
- Department of Radiotherapy and Radiology, Russian Medical Academy of Continuous Professional Education, 125993 Moscow, Russia
- Biologically Active Terpenoids Laboratory, Kazan Federal University, 18 Kremlyovskaya St., 420008 Kazan, Russia
| | - Kirill Syuzov
- Department of Pathology, Kazan State Medical University, 420012 Kazan, Russia; (K.S.); (F.B.); (A.G.)
| | - Firuza Bikinieva
- Department of Pathology, Kazan State Medical University, 420012 Kazan, Russia; (K.S.); (F.B.); (A.G.)
| | - Aigul Galembikova
- Department of Pathology, Kazan State Medical University, 420012 Kazan, Russia; (K.S.); (F.B.); (A.G.)
| | - Svetlana Zykova
- Department of Pharmacology, Perm State Academy of Pharmacy, 614990 Perm, Russia; (S.Z.); (K.G.); (S.I.); (N.I.)
| | - Ksenia Gankova
- Department of Pharmacology, Perm State Academy of Pharmacy, 614990 Perm, Russia; (S.Z.); (K.G.); (S.I.); (N.I.)
| | - Sergei Igidov
- Department of Pharmacology, Perm State Academy of Pharmacy, 614990 Perm, Russia; (S.Z.); (K.G.); (S.I.); (N.I.)
| | - Nazim Igidov
- Department of Pharmacology, Perm State Academy of Pharmacy, 614990 Perm, Russia; (S.Z.); (K.G.); (S.I.); (N.I.)
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36
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Computational-Based Discovery of the Anti-Cancer Activities of Pyrrole-Based Compounds Targeting the Colchicine-Binding Site of Tubulin. Molecules 2022. [PMID: 35566235 DOI: 10.3390/molecules27092873.(] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/25/2023] Open
Abstract
Despite the tubulin-binding agents (TBAs) that are widely used in the clinic for cancer therapy, tumor resistance to TBAs (both inherited and acquired) significantly impairs their effectiveness, thereby decreasing overall survival (OS) and progression-free survival (PFS) rates, especially for the patients with metastatic, recurrent, and unresectable forms of the disease. Therefore, the development of novel effective drugs interfering with the microtubules' dynamic state remains a big challenge in current oncology. We report here about the novel ethyl 2-amino-1-(furan-2-carboxamido)-5-(2-aryl/tert-butyl-2-oxoethylidene)-4-oxo-4,5-dihydro-1H-pyrrole-3-carboxylates (EAPCs) exhibiting potent anti-cancer activities against the breast and lung cancer cell lines in vitro. This was due to their ability to inhibit tubulin polymerization and induce cell cycle arrest in M-phase. As an outcome, the EAPC-treated cancer cells exhibited a significant increase in apoptosis, which was evidenced by the expression of cleaved forms of PARP, caspase-3, and increased numbers of Annexin-V-positive cells. By using the in silico molecular modeling methods (e.g., induced-fit docking, binding metadynamics, and unbiased molecular dynamics), we found that EAPC-67 and -70 preferentially bind to the colchicine-binding site of tubulin. Lastly, we have shown that the EAPCs indicated above and colchicine utilizes a similar molecular mechanism to inhibit tubulin polymerization via targeting the T7 loop in the β-chain of tubulin, thereby preventing the conformational changes in the tubulin dimers required for their polymerization. Collectively, we identified the novel and potent TBAs that bind to the colchicine-binding site and disrupt the microtubule network. As a result of these events, the compounds induced a robust cell cycle arrest in M-phase and exhibited potent pro-apoptotic activities against the epithelial cancer cell lines in vitro.
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37
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Mol’kova EA, Shchegravina ES, Otvagin VF, Kuzmina NS, Malysheva YB, Svirshchevskaya EV, Zaburdaeva EA, Fedorov AY. Synthesis and biological evaluation of colchicine and thiocolchicine derivatives bearing a Michael acceptor moiety in ring A. Russ Chem Bull 2022. [DOI: 10.1007/s11172-022-3449-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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38
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Podophyllotoxin esters with alicyclic residues: an insight into the origin of microtubule-curling effect in cancer cells. MENDELEEV COMMUNICATIONS 2022. [DOI: 10.1016/j.mencom.2022.03.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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39
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Wang J, Miller DD, Li W. Molecular interactions at the colchicine binding site in tubulin: An X-ray crystallography perspective. Drug Discov Today 2022; 27:759-776. [PMID: 34890803 PMCID: PMC8901563 DOI: 10.1016/j.drudis.2021.12.001] [Citation(s) in RCA: 32] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Revised: 07/27/2021] [Accepted: 12/02/2021] [Indexed: 01/02/2023]
Abstract
Tubulin is an important cancer drug target. Compounds that bind at the colchicine site in tubulin have attracted significant interest as they are generally less affected by multidrug resistance than other potential drugs. Modeling is useful in understanding the interactions between tubulin and colchicine binding site inhibitors (CBSIs), but because the colchicine binding site contains two flexible loops whose conformations are highly ligand-dependent, modeling has its limitations. X-ray crystallography provides experimental pictures of tubulin-ligand interactions at this challenging colchicine site. Since 2004, when the first X-ray structure of tubulin in complex with N-deacetyl-N-(2-mercaptoacetyl)-colchicine (DAMA-colchicine) was published, many X-ray crystal structures have been reported for tubulin complexes involving the colchicine binding site. In this review, we summarize the crystal structures of tubulin in complexes with various CBSIs, aiming to facilitate the discovery of new generations of tubulin inhibitors.
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Affiliation(s)
- Jiaxing Wang
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Tennessee Health Science Center, Memphis, TN 38163, USA
| | - Duane D Miller
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Tennessee Health Science Center, Memphis, TN 38163, USA
| | - Wei Li
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Tennessee Health Science Center, Memphis, TN 38163, USA.
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40
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Mechanisms of influence of the microtubule over-stabilizing ligands on the structure and intrinsic dynamics of α,β-Tubulin. Comput Biol Chem 2021; 96:107617. [PMID: 34942453 DOI: 10.1016/j.compbiolchem.2021.107617] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Revised: 11/24/2021] [Accepted: 12/06/2021] [Indexed: 11/23/2022]
Abstract
The intervention into the cell cycle progression by administering microtubule over-stabilizing ligands that arrest the mitotic cell division by preventing spindle dissociation, is a promising strategy to fight against cancers. The building blocks of the microtubules and the spindles, i.e. the α,β-tubulin dimer, upon binding of such ligands, stay more comfortably in the microtubular multimeric form; the phenomenon of which is the key to the said over-stabilization. Using two such over-stabilizing ligands, Taxol and Taxotere, the present work reports the collective changes that these ligands induce on the structure and dynamics of the α,β-tubulin dimer which could be reconciled as the molecular basis of the over-stabilization of the microtubules; the trends have been found to be statistically significant across all independent calculations on them. The ligand binding increases the coherence between the residue communities of the two opposite faces of the β-subunit, which in a periodic arrangement in microtubule are knwon to form intermolecular contact with each other. This is likely to create an indirect cooperativity between those structural regions and this is a consequence of the reshuffling of the internal network of interactions upon ligand binding. Such reorganizations are also complemented by the increased contributions of the softer modes of the intrinsic dynamics more, which is likely to increase the plasticity of the system favourable for making structural adjustments in a multimer. Further, the ligands are able to compensate the drawback of lacking one phosphate group in protein-GDP interactions compared to the same for protein-GTP and this is in agreement with the hints form the earlier reports. The findings form a mechanistic basis of the enhanced capacity of the α,β-tubulin dimer to get more favourably accommodated into the microtubule superstructure upon binding either of Taxol and Taxotere.
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41
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Laisne MC, Michallet S, Lafanechère L. Characterization of Microtubule Destabilizing Drugs: A Quantitative Cell-Based Assay That Bridges the Gap between Tubulin Based- and Cytotoxicity Assays. Cancers (Basel) 2021; 13:cancers13205226. [PMID: 34680374 PMCID: PMC8533752 DOI: 10.3390/cancers13205226] [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: 08/25/2021] [Revised: 10/13/2021] [Accepted: 10/15/2021] [Indexed: 12/14/2022] Open
Abstract
Simple Summary The characterization of new microtubule depolymerizing agents relies mainly on purified tubulin assays in vitro and on cytotoxicity tests. However, the relationship between the in vitro effects of drugs and their effect on cell viability may not be direct. Here, we have systematically compared the effect of four reference drugs on tubulin polymerization in vitro and in cells, using a recently-developed quantitative assay of the cellular microtubule content. By comparing these results with cell viability assays, we found that this new cellular microtubule content test better predicts cellular drug toxicity than the in vitro tubulin polymerization assay. This test can thus be easily implemented in the process of discovery and characterization of novel microtubule poisons. Abstract (1) Background: Microtubule depolymerizing agents (MDAs) are commonly used for cancer treatment. However, the therapeutic use of such microtubule inhibitors is limited by their toxicity and the emergence of resistance. Thus, there is still a sustained effort to develop new MDAs. During the characterization of such agents, mainly through in vitro analyses using purified tubulin and cytotoxicity assays, quantitative comparisons are mandatory. The relationship between the effect of the drugs on purified tubulin and on cell viability are not always direct. (2) Methods: We have recently developed a cell-based assay that quantifies the cellular microtubule content. In this study, we have conducted a systematic comparative analysis of the effect of four well-characterized MDAs on the kinetics of in vitro tubulin assembly, on the cellular microtubule content (using our recently developed assay) and on cell viability. (3) Conclusions: These assays gave complementary results. Additionally, we found that the drugs’ effect on in vitro tubulin polymerization is not completely predictive of their relative cytotoxicity. Their effect on the cellular microtubule content, however, is closely related to their effect on cell viability. In conclusion, the assay we have recently developed can bridge the gap between in vitro tubulin assays and cell viability assays.
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42
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Banerjee S, Mahmud F, Deng S, Ma L, Yun MK, Fakayode SO, Arnst KE, Yang L, Chen H, Wu Z, Lukka PB, Parmar K, Meibohm B, White SW, Wang Y, Li W, Miller DD. X-ray Crystallography-Guided Design, Antitumor Efficacy, and QSAR Analysis of Metabolically Stable Cyclopenta-Pyrimidinyl Dihydroquinoxalinone as a Potent Tubulin Polymerization Inhibitor. J Med Chem 2021; 64:13072-13095. [PMID: 34406768 DOI: 10.1021/acs.jmedchem.1c01202] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Small molecules that interact with the colchicine binding site in tubulin have demonstrated therapeutic efficacy in treating cancers. We report the design, syntheses, and antitumor efficacies of new analogues of pyridopyrimidine and hydroquinoxalinone compounds with improved drug-like characteristics. Eight analogues, 5j, 5k, 5l, 5m, 5n, 5r, 5t, and 5u, showed significant improvement in metabolic stability and demonstrated strong antiproliferative potency in a panel of human cancer cell lines, including melanoma, lung cancer, and breast cancer. We report crystal structures of tubulin in complex with five representative compounds, 5j, 5k, 5l, 5m, and 5t, providing direct confirmation for their binding to the colchicine site in tubulin. A quantitative structure-activity relationship analysis of the synthesized analogues showed strong ability to predict potency. In vivo, 5m (4 mg/kg) and 5t (5 mg/kg) significantly inhibited tumor growth as well as melanoma spontaneous metastasis into the lung and liver against a highly paclitaxel-resistant A375/TxR xenograft model.
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Affiliation(s)
- Souvik Banerjee
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Tennessee Health Science Center, Memphis, Tennessee 38163, United States.,Department of Physical Sciences, College of STEM, University of Arkansas Fort Smith, Fort Smith, Arkansas 72913, United States
| | - Foyez Mahmud
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Tennessee Health Science Center, Memphis, Tennessee 38163, United States
| | - Shanshan Deng
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Tennessee Health Science Center, Memphis, Tennessee 38163, United States
| | - Lingling Ma
- Department of Respiratory and Critical Care Medicine, Targeted Tracer Research and Development Laboratory, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Mi-Kyung Yun
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, United States
| | - Sayo O Fakayode
- Department of Physical Sciences, College of STEM, University of Arkansas Fort Smith, Fort Smith, Arkansas 72913, United States
| | - Kinsie E Arnst
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Tennessee Health Science Center, Memphis, Tennessee 38163, United States
| | - Lei Yang
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, United States
| | - Hao Chen
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Tennessee Health Science Center, Memphis, Tennessee 38163, United States
| | - Zhongzhi Wu
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Tennessee Health Science Center, Memphis, Tennessee 38163, United States
| | - Pradeep B Lukka
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Tennessee Health Science Center, Memphis, Tennessee 38163, United States
| | - Keyur Parmar
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Tennessee Health Science Center, Memphis, Tennessee 38163, United States
| | - Bernd Meibohm
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Tennessee Health Science Center, Memphis, Tennessee 38163, United States
| | - Stephen W White
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, United States
| | - Yuxi Wang
- Department of Respiratory and Critical Care Medicine, Targeted Tracer Research and Development Laboratory, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Wei Li
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Tennessee Health Science Center, Memphis, Tennessee 38163, United States
| | - Duane D Miller
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Tennessee Health Science Center, Memphis, Tennessee 38163, United States
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43
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Potential colchicine binding site inhibitors unraveled by virtual screening, molecular dynamics and MM/PBSA. Comput Biol Med 2021; 137:104817. [PMID: 34488030 DOI: 10.1016/j.compbiomed.2021.104817] [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: 07/19/2021] [Revised: 08/26/2021] [Accepted: 08/26/2021] [Indexed: 11/22/2022]
Abstract
Microtubules have been widely studied in recent decades as an important pharmacological target for the treatment of cancer especially due to its key role in the mitosis process. Among the constituents of the microtubules, αβ-tubulin dimers stand out in view of their four distinct interaction sites, including the so-called colchicine binding site (CBS) - a promising target for the development of new tubulin modulators. When compared to other tubulin sites, targeting the CBS is advantageous because this site is able to host ligands with lower molecular volume and lipophilicity, thus reducing the chances of entailing the phenomenon of multiple drug resistance (MDR) - one of the main reasons of failure in chemotherapy. However, colchicine, the first ligand ever discovered with affinity towards the CBS, despite modulating the action of microtubules, has shown toxicity in clinical studies. Therefore, in order to expand the known chemical space of scaffolds capable of interacting with CBS and to design non-toxic colchicine binding site inhibitors, we conducted a robust virtual screening pipeline. This has been rigorously validated and consisted of ligand- and structure-based methodologies, which allowed us to select four promising CBS inhibitors called tubLCQF1-4. These four compounds were also evaluated with long trajectories molecular dynamics simulations and respective results were used for the theoretical determination of the free energy released in the formation of the complexes, using the Molecular Mechanics Poisson-Boltzmann Surface Area (MM/PBSA) methodology.
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Wang L, Zheng Y, Li D, Yang J, Lei L, Yan W, Zheng W, Tang M, Shi M, Zhang R, Cai X, Ni H, Ma X, Li N, Hong F, Ye H, Chen L. Design, Synthesis, and Bioactivity Evaluation of Dual-Target Inhibitors of Tubulin and Src Kinase Guided by Crystal Structure. J Med Chem 2021; 64:8127-8141. [PMID: 34081857 DOI: 10.1021/acs.jmedchem.0c01961] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Klisyri (KX01) is a dual tubulin/Src protein inhibitor that has shown potential therapeutic effects in several tumor models. However, a phase II clinical trial in patients with bone-metastatic castration-resistant prostate cancer was halted because of lack of efficacy. We previously reported that KX01 binds to the colchicine site of β-tubulin and its morpholine group lies close to α-tubulin's surface. Thus, we hypothesized that enhancing the interaction of KX01 with α-tubulin could increase tubulin inhibition and synthesized a series of KX01 derivatives directed by docking studies. Among these derivatives, 8a exhibited more than 10-fold antiproliferation activity in several tumor cells than KX01 and significantly improved in vivo antitumor effects. The X-ray crystal structure suggested that 8a both bound to the colchicine site and extended into the interior of α-tubulin to form potent interactions, presenting a novel binding mode. A potential clinical candidate for cancer therapy was identified in this study.
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Affiliation(s)
- Lun Wang
- State Key Laboratory of Biotherapy/Collaborative Innovation Center of Biotherapy and Cancer Center, West China Hospital of Sichuan University, Chengdu 610041, China
| | - Yunhua Zheng
- State Key Laboratory of Biotherapy/Collaborative Innovation Center of Biotherapy and Cancer Center, West China Hospital of Sichuan University, Chengdu 610041, China
| | - Dan Li
- State Key Laboratory of Biotherapy/Collaborative Innovation Center of Biotherapy and Cancer Center, West China Hospital of Sichuan University, Chengdu 610041, China
| | - Jianhong Yang
- State Key Laboratory of Biotherapy/Collaborative Innovation Center of Biotherapy and Cancer Center, West China Hospital of Sichuan University, Chengdu 610041, China
| | - Lei Lei
- State Key Laboratory of Biotherapy/Collaborative Innovation Center of Biotherapy and Cancer Center, West China Hospital of Sichuan University, Chengdu 610041, China
| | - Wei Yan
- State Key Laboratory of Biotherapy/Collaborative Innovation Center of Biotherapy and Cancer Center, West China Hospital of Sichuan University, Chengdu 610041, China
| | - Wei Zheng
- State Key Laboratory of Biotherapy/Collaborative Innovation Center of Biotherapy and Cancer Center, West China Hospital of Sichuan University, Chengdu 610041, China
| | - Minghai Tang
- State Key Laboratory of Biotherapy/Collaborative Innovation Center of Biotherapy and Cancer Center, West China Hospital of Sichuan University, Chengdu 610041, China
| | - Mingsong Shi
- State Key Laboratory of Biotherapy/Collaborative Innovation Center of Biotherapy and Cancer Center, West China Hospital of Sichuan University, Chengdu 610041, China
| | - Ruijia Zhang
- State Key Laboratory of Biotherapy/Collaborative Innovation Center of Biotherapy and Cancer Center, West China Hospital of Sichuan University, Chengdu 610041, China
| | - Xiaoying Cai
- State Key Laboratory of Biotherapy/Collaborative Innovation Center of Biotherapy and Cancer Center, West China Hospital of Sichuan University, Chengdu 610041, China
| | - Hengfan Ni
- The Ministry of Education Key Laboratory of Standardization of Chinese Herbal Medicine, State Key Laboratory, Breeding Base of Systematic Research Development and Utilization of Chinese Medicine Resources, School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, People's Republic of China
| | - Xu Ma
- State Key Laboratory of Biotherapy/Collaborative Innovation Center of Biotherapy and Cancer Center, West China Hospital of Sichuan University, Chengdu 610041, China
| | - Na Li
- State Key Laboratory of Biotherapy/Collaborative Innovation Center of Biotherapy and Cancer Center, West China Hospital of Sichuan University, Chengdu 610041, China
| | - Feng Hong
- State Key Laboratory of Biotherapy/Collaborative Innovation Center of Biotherapy and Cancer Center, West China Hospital of Sichuan University, Chengdu 610041, China
| | - Haoyu Ye
- State Key Laboratory of Biotherapy/Collaborative Innovation Center of Biotherapy and Cancer Center, West China Hospital of Sichuan University, Chengdu 610041, China
| | - Lijuan Chen
- State Key Laboratory of Biotherapy/Collaborative Innovation Center of Biotherapy and Cancer Center, West China Hospital of Sichuan University, Chengdu 610041, China
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Forero AM, Castellanos L, Sandoval-Hernández AG, Magalhães A, Tinoco LW, Lopez-Vallejo F, Ramos FA. Integration of NMR studies, computational predictions, and in vitro assays in the search of marine diterpenes with antitumor activity. Chem Biol Drug Des 2021; 98:507-521. [PMID: 34143939 DOI: 10.1111/cbdd.13907] [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: 01/16/2021] [Revised: 04/14/2021] [Accepted: 06/06/2021] [Indexed: 12/01/2022]
Abstract
Among the compounds of natural origin, diterpenes have proved useful as drugs for the treatment of cancer. Marine organisms, such as soft corals and algae, are a promising source of diterpenes, being a rich and unexplored source of cytotoxic agents. This study evaluated a library of 32 natural and semisynthetic marine diterpenes, including briarane, cembrane, and dolabellane nuclei, with the aim of determining their cytotoxicity against three human cancer cell lines (A549, MCF7, and PC3). The three most active compounds were submitted to a flow cytometry analysis in order to determine induction of apoptosis against the A549 cell line. An NMR analysis was conducted to determine and evaluate the interactions between active diterpenes and tubulin. These interactions were characterized by a computational study using molecular docking and MD simulations. With these results, two cembrane and one chlorinated briarane diterpenes were active against the three human cancer cell lines, induced apoptosis in the A549 cell line, and showed interactions with tubulin preferably at the taxane-binding site. This study is a starting point for the identification and optimization of the marine diterpenes selected for better antitumor activities. It also highlights the power of integrating NMR studies, computational predictions, and in vitro assays in the search for compounds with antitumor activity.
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Affiliation(s)
- Abel M Forero
- Departamento de Química, Facultad de Ciencias, Universidad Nacional de Colombia - Sede Bogotá, Bogotá, Colombia.,Departamento de Farmacia, Facultad de Ciencias, Universidad Nacional de Colombia - Sede Bogotá, Bogotá, Colombia
| | - Leonardo Castellanos
- Departamento de Química, Facultad de Ciencias, Universidad Nacional de Colombia - Sede Bogotá, Bogotá, Colombia
| | - Adrián G Sandoval-Hernández
- Departamento de Química, Facultad de Ciencias, Universidad Nacional de Colombia - Sede Bogotá, Bogotá, Colombia.,Instituto de Genética Humana, Universidad Nacional de Colombia - Sede Bogotá, Bogotá, Colombia
| | - Alvicler Magalhães
- Laboratório de Apoio ao Desenvolvimento Tecnológico (LADETEC), Instituto de Química, Avenida Horácio Macedo, Cidade Universitária, Rio de Janeiro, Brazil
| | - Luzineide W Tinoco
- Laboratório Multiusuário de Análises por RMN (LAMAR), Instituto de Pesquisas de Produtos Naturais (IPPN), Universidade Federal Do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Fabian Lopez-Vallejo
- Departamento de Química, Facultad de Ciencias, Universidad Nacional de Colombia - Sede Bogotá, Bogotá, Colombia
| | - Freddy A Ramos
- Departamento de Química, Facultad de Ciencias, Universidad Nacional de Colombia - Sede Bogotá, Bogotá, Colombia
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Albahde MAH, Abdrakhimov B, Li GQ, Zhou X, Zhou D, Xu H, Qian H, Wang W. The Role of Microtubules in Pancreatic Cancer: Therapeutic Progress. Front Oncol 2021; 11:640863. [PMID: 34094924 PMCID: PMC8176010 DOI: 10.3389/fonc.2021.640863] [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] [Accepted: 03/26/2021] [Indexed: 12/14/2022] Open
Abstract
Pancreatic cancer has an extremely low prognosis, which is attributable to its high aggressiveness, invasiveness, late diagnosis, and lack of effective therapies. Among all the drugs joining the fight against this type of cancer, microtubule-targeting agents are considered to be the most promising. They inhibit cancer cells although through different mechanisms such as blocking cell division, apoptosis induction, etc. Hereby, we review the functions of microtubule cytoskeletal proteins in tumor cells and comprehensively examine the effects of microtubule-targeting agents on pancreatic carcinoma.
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Affiliation(s)
- Mugahed Abdullah Hasan Albahde
- Department of Hepatobiliary and Pancreatic Surgery, The Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
- Key Laboratory of Precision Diagnosis and Treatment for Hepatobiliary and Pancreatic Tumor of Zhejiang Province, Hangzhou, China
- Research Center of Diagnosis and Treatment Technology for Hepatocellular Carcinoma of Zhejiang Province, Hangzhou, China
- Clinical Medicine Innovation Center of Precision Diagnosis and Treatment for Hepatobiliary and Pancreatic Disease of Zhejiang University, Hangzhou, China
| | - Bulat Abdrakhimov
- Department of Cardiovascular Surgery, Renmin Hospital of Wuhan University, Wuhan, China
| | - Guo-Qi Li
- Department of Hepatobiliary and Pancreatic Surgery, The Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
- Key Laboratory of Precision Diagnosis and Treatment for Hepatobiliary and Pancreatic Tumor of Zhejiang Province, Hangzhou, China
| | - Xiaohu Zhou
- Department of Hepatobiliary and Pancreatic Surgery, The Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
- Key Laboratory of Precision Diagnosis and Treatment for Hepatobiliary and Pancreatic Tumor of Zhejiang Province, Hangzhou, China
| | - Dongkai Zhou
- Department of Hepatobiliary and Pancreatic Surgery, The Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
- Key Laboratory of Precision Diagnosis and Treatment for Hepatobiliary and Pancreatic Tumor of Zhejiang Province, Hangzhou, China
| | - Hao Xu
- Department of Hepatobiliary and Pancreatic Surgery, The Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
- Key Laboratory of Precision Diagnosis and Treatment for Hepatobiliary and Pancreatic Tumor of Zhejiang Province, Hangzhou, China
| | - Huixiao Qian
- Department of Hepatobiliary and Pancreatic Surgery, The Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
- Key Laboratory of Precision Diagnosis and Treatment for Hepatobiliary and Pancreatic Tumor of Zhejiang Province, Hangzhou, China
| | - Weilin Wang
- Department of Hepatobiliary and Pancreatic Surgery, The Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
- Key Laboratory of Precision Diagnosis and Treatment for Hepatobiliary and Pancreatic Tumor of Zhejiang Province, Hangzhou, China
- Research Center of Diagnosis and Treatment Technology for Hepatocellular Carcinoma of Zhejiang Province, Hangzhou, China
- Clinical Medicine Innovation Center of Precision Diagnosis and Treatment for Hepatobiliary and Pancreatic Disease of Zhejiang University, Hangzhou, China
- Clinical Research Center of Hepatobiliary and Pancreatic Diseases of Zhejiang Province, Hangzhou, China
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New Estrone Oxime Derivatives: Synthesis, Cytotoxic Evaluation and Docking Studies. Molecules 2021; 26:molecules26092687. [PMID: 34064380 PMCID: PMC8125528 DOI: 10.3390/molecules26092687] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Revised: 04/28/2021] [Accepted: 05/01/2021] [Indexed: 01/09/2023] Open
Abstract
The interest in the introduction of the oxime group in molecules aiming to improve their biological effects is increasing. This work aimed to develop new steroidal oximes of the estrane series with potential antitumor interest. For this, several oximes were synthesized by reaction of hydroxylamine with the 17-ketone of estrone derivatives. Then, their cytotoxicity was evaluated in six cell lines. An estrogenicity assay, a cell cycle distribution analysis and a fluorescence microscopy study with Hoechst 3358 staining were performed with the most promising compound. In addition, molecular docking studies against estrogen receptor α, steroid sulfatase, 17β-hydroxysteroid dehydrogenase type 1 and β-tubulin were also accomplished. The 2-nitroestrone oxime showed higher cytotoxicity than the parent compound on MCF-7 cancer cells. Furthermore, the oximes bearing halogen groups in A-ring evidenced selectivity for HepaRG cells. Remarkably, the Δ9,11-estrone oxime was the most cytotoxic and arrested LNCaP cells in the G2/M phase. Fluorescence microscopy studies showed the presence of condensed DNA typical of prophase and condensed and fragmented nuclei characteristic of apoptosis. However, this oxime promoted the proliferation of T47-D cells. Interestingly, molecular docking studies estimated a strong interaction between Δ9,11-estrone oxime and estrogen receptor α and β-tubulin, which may account for the described effects.
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Recent advances in research of colchicine binding site inhibitors and their interaction modes with tubulin. Future Med Chem 2021; 13:839-858. [PMID: 33821673 DOI: 10.4155/fmc-2020-0376] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Microtubules have been a concerning target of cancer chemotherapeutics for decades, and several tubulin-targeted agents, such as paclitaxel, vincristine and vinorelbine, have been approved. The colchicine binding site is one of the primary targets on microtubules and possesses advantages compared with other tubulin-targeted agents, such as inhibitors of tumor vessels and overcoming P-glycoprotein overexpression-mediated multidrug resistance. This study reviews and summarizes colchicine binding site inhibitors reported in recent years with structural studies via the crystal structures of complexes or computer simulations to discover new lead compounds. We are attempting to resolve the challenge of colchicine site agent research.
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Zhu H, Li W, Shuai W, Liu Y, Yang L, Tan Y, Zheng T, Yao H, Xu J, Zhu Z, Yang DH, Chen ZS, Xu S. Discovery of novel N-benzylbenzamide derivatives as tubulin polymerization inhibitors with potent antitumor activities. Eur J Med Chem 2021; 216:113316. [PMID: 33676300 DOI: 10.1016/j.ejmech.2021.113316] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Revised: 02/16/2021] [Accepted: 02/17/2021] [Indexed: 01/17/2023]
Abstract
A series of novel N-benzylbenzamide derivatives were designed and synthesized as tubulin polymerization inhibitors. Among fifty-one target compounds, compound 20b exhibited significant antiproliferative activities with IC50 values ranging from 12 to 27 nM against several cancer cell lines, and possessed good plasma stability and satisfactory physicochemical properties. Mechanism studies demonstrated that 20b bound to the colchicine binding site and displayed potent anti-vascular activity. Notably, the corresponding disodium phosphate 20b-P exhibited an excellent safety profile with the LD50 value of 599.7 mg/kg (i.v. injection), meanwhile, it significantly inhibited tumor growth and decreased microvessel density in liver cancer cell H22 allograft mouse model without obvious toxicity. Collectively, 20b and 20b-P are novel promising anti-tubulin agents with more druggable properties and deserve to be further investigated for cancer therapy.
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Affiliation(s)
- Huajian Zhu
- State Key Laboratory of Natural Medicines and Department of Medicinal Chemistry, China Pharmaceutical University, 24 Tong Jia Xiang, Nanjing, 210009, PR China
| | - Wenlong Li
- State Key Laboratory of Natural Medicines and Department of Medicinal Chemistry, China Pharmaceutical University, 24 Tong Jia Xiang, Nanjing, 210009, PR China
| | - Wen Shuai
- State Key Laboratory of Natural Medicines and Department of Medicinal Chemistry, China Pharmaceutical University, 24 Tong Jia Xiang, Nanjing, 210009, PR China
| | - Yang Liu
- State Key Laboratory of Natural Medicines and Department of Medicinal Chemistry, China Pharmaceutical University, 24 Tong Jia Xiang, Nanjing, 210009, PR China
| | - Limei Yang
- State Key Laboratory of Natural Medicines and Department of Medicinal Chemistry, China Pharmaceutical University, 24 Tong Jia Xiang, Nanjing, 210009, PR China
| | - Yuchen Tan
- State Key Laboratory of Natural Medicines and Department of Medicinal Chemistry, China Pharmaceutical University, 24 Tong Jia Xiang, Nanjing, 210009, PR China
| | - Tiandong Zheng
- State Key Laboratory of Natural Medicines and Department of Medicinal Chemistry, China Pharmaceutical University, 24 Tong Jia Xiang, Nanjing, 210009, PR China
| | - Hong Yao
- State Key Laboratory of Natural Medicines and Department of Medicinal Chemistry, China Pharmaceutical University, 24 Tong Jia Xiang, Nanjing, 210009, PR China
| | - Jinyi Xu
- State Key Laboratory of Natural Medicines and Department of Medicinal Chemistry, China Pharmaceutical University, 24 Tong Jia Xiang, Nanjing, 210009, PR China
| | - Zheying Zhu
- Division of Molecular Therapeutics & Formulation, School of Pharmacy, The University of Nottingham, University Park Campus, Nottingham NG7 2RD, UK
| | - Dong-Hua Yang
- College of Pharmacy and Health Sciences, St. John's University, 8000 Utopia Parkway, Queens, New York, 11439, United States
| | - Zhe-Sheng Chen
- College of Pharmacy and Health Sciences, St. John's University, 8000 Utopia Parkway, Queens, New York, 11439, United States
| | - Shengtao Xu
- State Key Laboratory of Natural Medicines and Department of Medicinal Chemistry, China Pharmaceutical University, 24 Tong Jia Xiang, Nanjing, 210009, PR China.
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50
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Xian J, Bu F, Wang Y, Long F, Zhang Z, Wu C, Tao Y, Wang T, Wang G. A Rationale for Drug Design Provided by Co-Crystal Structure of IC261 in Complex with Tubulin. Molecules 2021; 26:946. [PMID: 33579052 PMCID: PMC7916759 DOI: 10.3390/molecules26040946] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2020] [Revised: 02/06/2021] [Accepted: 02/08/2021] [Indexed: 02/05/2023] Open
Abstract
Microtubules composed of α/β tubulin heterodimers are an essential part of the cytoskeleton of eukaryotic cells and are widely regarded as targets for cancer chemotherapy. IC261, which is discovered as an ATP-competitive inhibitor of serine/threonine-specific casein kinase 1 (CK1), has shown its inhibitory activity on microtubule polymerization in recent studies. However, the structural information of the interaction between tubulin and IC261 is still unclear. Here, we provided a high-resolution (2.85 Å) crystal structure of tubulin and IC261 complex, revealed the intermolecular interaction between tubulin and IC261, and analyzed the structure-activity relationship (SAR). Subsequently, the structure of tubulin-IC261 complex was compared with tubulin-colchicine complex to further elucidate the novelty of IC261. Furthermore, eight optimal candidate compounds of new IC261-based microtubule inhibitors were obtained through molecular docking studies. In conclusion, the co-crystal structure of tubulin-IC261 complex paves a way for the design and development of microtubule inhibitor drugs.
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Affiliation(s)
- Jinghong Xian
- Department of Clinical Research Management, Innovation Center of Nursing Research, Nursing Key Laboratory of Sichuan Province, West China Hospital, Collaborative Innovation Center of Biotherapy, Sichuan University, Chengdu 610041, China; (J.X.); (F.B.); (C.W.)
| | - Faqian Bu
- Department of Clinical Research Management, Innovation Center of Nursing Research, Nursing Key Laboratory of Sichuan Province, West China Hospital, Collaborative Innovation Center of Biotherapy, Sichuan University, Chengdu 610041, China; (J.X.); (F.B.); (C.W.)
- Precision Medicine Research Center, Department of Respiratory and Critical Care Medicine, West China Hospital, Sichuan University, Chengdu 610041, China; (Y.W.); (Z.Z.); (Y.T.)
| | - Yuxi Wang
- Precision Medicine Research Center, Department of Respiratory and Critical Care Medicine, West China Hospital, Sichuan University, Chengdu 610041, China; (Y.W.); (Z.Z.); (Y.T.)
| | - Fangyi Long
- Department of Pharmacy, Sichuan Cancer Hospital & Institution, Sichuan Cancer Center, School of Medicine, University of Electronic Science and Technology of China, Chengdu 610041, China;
| | - Zhixiong Zhang
- Precision Medicine Research Center, Department of Respiratory and Critical Care Medicine, West China Hospital, Sichuan University, Chengdu 610041, China; (Y.W.); (Z.Z.); (Y.T.)
| | - Chengyong Wu
- Department of Clinical Research Management, Innovation Center of Nursing Research, Nursing Key Laboratory of Sichuan Province, West China Hospital, Collaborative Innovation Center of Biotherapy, Sichuan University, Chengdu 610041, China; (J.X.); (F.B.); (C.W.)
- Precision Medicine Research Center, Department of Respiratory and Critical Care Medicine, West China Hospital, Sichuan University, Chengdu 610041, China; (Y.W.); (Z.Z.); (Y.T.)
| | - Yiran Tao
- Precision Medicine Research Center, Department of Respiratory and Critical Care Medicine, West China Hospital, Sichuan University, Chengdu 610041, China; (Y.W.); (Z.Z.); (Y.T.)
| | - Ting Wang
- Department of Pharmacy, Sichuan Cancer Hospital & Institution, Sichuan Cancer Center, School of Medicine, University of Electronic Science and Technology of China, Chengdu 610041, China;
| | - Guan Wang
- Department of Clinical Research Management, Innovation Center of Nursing Research, Nursing Key Laboratory of Sichuan Province, West China Hospital, Collaborative Innovation Center of Biotherapy, Sichuan University, Chengdu 610041, China; (J.X.); (F.B.); (C.W.)
- Precision Medicine Research Center, Department of Respiratory and Critical Care Medicine, West China Hospital, Sichuan University, Chengdu 610041, China; (Y.W.); (Z.Z.); (Y.T.)
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