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Amărandi RM, Al-Matarneh MC, Popovici L, Ciobanu CI, Neamțu A, Mangalagiu II, Danac R. Exploring Pyrrolo-Fused Heterocycles as Promising Anticancer Agents: An Integrated Synthetic, Biological, and Computational Approach. Pharmaceuticals (Basel) 2023; 16:865. [PMID: 37375812 DOI: 10.3390/ph16060865] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Revised: 05/17/2023] [Accepted: 06/09/2023] [Indexed: 06/29/2023] Open
Abstract
Five new series of pyrrolo-fused heterocycles were designed through a scaffold hybridization strategy as analogs of the well-known microtubule inhibitor phenstatin. Compounds were synthesized using the 1,3-dipolar cycloaddition of cycloimmonium N-ylides to ethyl propiolate as a key step. Selected compounds were then evaluated for anticancer activity and ability to inhibit tubulin polymerization in vitro. Notably, pyrrolo[1,2-a]quinoline 10a was active on most tested cell lines, performing better than control phenstatin in several cases, most notably on renal cancer cell line A498 (GI50 27 nM), while inhibiting tubulin polymerization in vitro. In addition, this compound was predicted to have a promising ADMET profile. The molecular details of the interaction between compound 10a and tubulin were investigated through in silico docking experiments, followed by molecular dynamics simulations and configurational entropy calculations. Of note, we found that some of the initially predicted interactions from docking experiments were not stable during molecular dynamics simulations, but that configurational entropy loss was similar in all three cases. Our results suggest that for compound 10a, docking experiments alone are not sufficient for the adequate description of interaction details in terms of target binding, which makes subsequent scaffold optimization more difficult and ultimately hinders drug design. Taken together, these results could help shape novel potent antiproliferative compounds with pyrrolo-fused heterocyclic cores, especially from an in silico methodological perspective.
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Affiliation(s)
- Roxana-Maria Amărandi
- TRANSCEND Research Center, Regional Institute of Oncology Iasi, 2-4 General Henri Mathias Berthelot Street, 700483 Iasi, Romania
| | - Maria-Cristina Al-Matarneh
- "Petru Poni" Institute of Macromolecular Chemistry of Romanian Academy, 41A Grigore Ghica Voda Alley, 700487 Iasi, Romania
- Faculty of Chemistry, Alexandru Ioan Cuza University of Iasi, 11 Carol I, 700506 Iasi, Romania
| | - Lăcrămioara Popovici
- Faculty of Chemistry, Alexandru Ioan Cuza University of Iasi, 11 Carol I, 700506 Iasi, Romania
| | - Catalina Ionica Ciobanu
- Institute of Interdisciplinary Research-CERNESIM Centre, Alexandru Ioan Cuza University of Iasi, 11 Carol I, 700506 Iasi, Romania
| | - Andrei Neamțu
- TRANSCEND Research Center, Regional Institute of Oncology Iasi, 2-4 General Henri Mathias Berthelot Street, 700483 Iasi, Romania
| | - Ionel I Mangalagiu
- Faculty of Chemistry, Alexandru Ioan Cuza University of Iasi, 11 Carol I, 700506 Iasi, Romania
| | - Ramona Danac
- Faculty of Chemistry, Alexandru Ioan Cuza University of Iasi, 11 Carol I, 700506 Iasi, Romania
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Raj Shekhar B, Rupani K, Raghunath Parkar S, Sunil Nayak A, Vasant Kumbhar B, Khare SP, Menon S, Gawde H, Kumar Das D. Identifying Novel Risk Conferring Genes Involved in Glycosylation Processes with Familial Schizophrenia in an Indian Cohort: Prediction of ADAMTS9 gene Variant for Structural Stability. Gene 2023; 872:147443. [PMID: 37105505 DOI: 10.1016/j.gene.2023.147443] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Revised: 04/10/2023] [Accepted: 04/21/2023] [Indexed: 04/29/2023]
Abstract
Schizophrenia is a complex neuropsychiatric disorder and heritability is as high as 80% making it the most heritable mental disorder. Although GWAS has identified numerous variants, the pathophysiology is still elusive. Here, an attempt was made to identify genetic risk factors in familial cases of schizophrenia that are associated with a common causative pathway. To achieve this objective, exome sequencing was done in 4 familial cases and identified six unique coding variants in five genes. Among these genes, PIGQ gene has two pathogenic variants, one nonsense and in-frame deletion. One missense variant in GALNT16 and one in GALNT5 have variable damaging score, however, the other variants, in ADAMTS9 and in LTBP4 have the highest damaging score. Further analysis showed that the variant of LTBP4 was not present in the functional domain. The other missense variant in the ADAMTS9 gene was found to be significant and was present in the thrombospondin repeat motif, one of the important motifs. Detailed molecular dynamics simulation study on this variant showed a damaging effect on structural stability. Since, all these genes culminated into the glycosylation process, it was evident that an aberrant glycosylation process may be one of the risk factors. Although, extracellular matrix formation through glycosylation have been shown to be associated, the involvement of ADAMTS9 and PIGQ gene mediated glycosylation has not been reported. In this paper, a novel link between ADAMTS9 and PIGQ gene with schizophrenia have been reported. Therefore, this novel observation has contributed immensely to the existing knowledge on risk factor of Schizophrenia.
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Affiliation(s)
- Bipin Raj Shekhar
- Genetic Research Centre, ICMR-National Institute for Research in Reproductive and Child Health, Parel, Mumbai, Maharashtra-400012, India; Stem Cell Biology, ICMR-National Institute for Research in Reproductive and Child Health, Parel, Mumbai, Maharashtra-400012, India
| | - Karishma Rupani
- Department of Psychiatry, Seth GS Medical College and KEM Hospital, Parel, Mumbai, Maharashtra-400012, India
| | - Shubhangi Raghunath Parkar
- Department of Psychiatry, Seth GS Medical College and KEM Hospital, Parel, Mumbai, Maharashtra-400012, India
| | - Ajita Sunil Nayak
- Department of Psychiatry, Seth GS Medical College and KEM Hospital, Parel, Mumbai, Maharashtra-400012, India
| | - Bajarang Vasant Kumbhar
- Department of Biological Sciences, Sunandan Divatia School of Science, NMIMS University (Deemed), Mumbai, Maharashtra-400012, India
| | - Satyajeet P Khare
- Symbiosis School of Biological Sciences, Symbiosis International University, Pune, Maharashtra-412115, India
| | - Shyla Menon
- Stem Cell Biology, ICMR-National Institute for Research in Reproductive and Child Health, Parel, Mumbai, Maharashtra-400012, India
| | - Harshavardhan Gawde
- Genetic Research Centre, ICMR-National Institute for Research in Reproductive and Child Health, Parel, Mumbai, Maharashtra-400012, India
| | - Dhanjit Kumar Das
- Stem Cell Biology, ICMR-National Institute for Research in Reproductive and Child Health, Parel, Mumbai, Maharashtra-400012, India.
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In Silico Exploration of Microtubule Agent Griseofulvin and Its Derivatives Interactions with Different Human β-Tubulin Isotypes. Molecules 2023; 28:molecules28052384. [PMID: 36903629 PMCID: PMC10005519 DOI: 10.3390/molecules28052384] [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: 01/15/2023] [Revised: 03/01/2023] [Accepted: 03/03/2023] [Indexed: 03/08/2023] Open
Abstract
Tubulin isotypes are known to regulate microtubule stability and dynamics, as well as to play a role in the development of resistance to microtubule-targeted cancer drugs. Griseofulvin is known to disrupt cell microtubule dynamics and cause cell death in cancer cells through binding to tubulin protein at the taxol site. However, the detailed binding mode involved molecular interactions, and binding affinities with different human β-tubulin isotypes are not well understood. Here, the binding affinities of human β-tubulin isotypes with griseofulvin and its derivatives were investigated using molecular docking, molecular dynamics simulation, and binding energy calculations. Multiple sequence analysis shows that the amino acid sequences are different in the griseofulvin binding pocket of βI isotypes. However, no differences were observed at the griseofulvin binding pocket of other β-tubulin isotypes. Our molecular docking results show the favorable interaction and significant affinity of griseofulvin and its derivatives toward human β-tubulin isotypes. Further, molecular dynamics simulation results show the structural stability of most β-tubulin isotypes upon binding to the G1 derivative. Taxol is an effective drug in breast cancer, but resistance to it is known. Modern anticancer treatments use a combination of multiple drugs to alleviate the problem of cancer cells resistance to chemotherapy. Our study provides a significant understanding of the involved molecular interactions of griseofulvin and its derivatives with β-tubulin isotypes, which may help to design potent griseofulvin analogues for specific tubulin isotypes in multidrug-resistance cancer cells in future.
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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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Rai K, Kumbhar BV, Panda D, Kunwar A. Computational study of interactions of anti-cancer drug eribulin with human tubulin isotypes. Phys Chem Chem Phys 2022; 24:16694-16700. [PMID: 35766982 DOI: 10.1039/d1cp04454k] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Microtubules (MTs) are widely targeted for the treatment of various types of cancer due to their essential role in cell division. MTs are polymers made of αβ-tubulin heterodimers. These α- and β-tubulins have 8 and 10 different isotypes, respectively. It is known that a few tubulin isotypes have anti-cancer drug resistance properties, especially βIII, which shows poor sensitivity to many potent anti-cancer drugs such as eribulin. However, the molecular-level understanding of drug-resistance due to tubulin isotype variation is poorly understood. This paper presents the study of differential binding affinities of different tubulin isotypes with the potent anti-cancer drug eribulin. Eribulin (MT destabilizer) binds at the inter-dimer interface of MTs near the vinca site and induces a lattice deformation, which results in catastrophic events in MT dynamics. In this study, sequence analysis has been done throughway and the binding sites and based on that 2α-tubulin isotypes (αI and αVIII) and 7β tubulin isotypes (βI, βIIa, βIII, βIVa, βVI, βVII and βVIII) were selected. In total, 14 combinations were prepared after building homology models of these selected isotypes. Molecular docking and molecular dynamics simulations were performed to deeply understand the binding mode of eribulin at different MT compositions. RMSD, RMSF, radius of gyration, SASA, ligand-protein interactions, and calculations of binding free energy were performed to investigate the eribulin binding variations to tubulin isotypes and it was found that αIβII showed the maximum binding affinity among all 14 systems to eribulin. The βIII-tubulin isotype, which shows low sensitivity to eribulin in experimental results, had the least binding affinity in the system αVIIIβIII complex and the average binding affinity in the system αIβIII among all 14 systems. Additionally, we performed steered MD simulations and DynDom analysis of the systems with the lowest binding energy (αIβII) and the highest binding energy (αVIIIβIII) and extracted force, displacement, and H-bonding profiles during the pulling simulations to get a better insight.
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Affiliation(s)
- Khushnandan Rai
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, Maharashtra, India.
| | - Bajarang Vasant Kumbhar
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, Maharashtra, India.
| | - Dulal Panda
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, Maharashtra, India.
| | - Ambarish Kunwar
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, Maharashtra, India.
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6
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Evaluation of In Vitro Antiprotease Activity of Selected Traditional Medicinal Herbs in Dentistry and Its In Silico PASS Prediction. BIOMED RESEARCH INTERNATIONAL 2022; 2022:5870443. [PMID: 35707383 PMCID: PMC9192215 DOI: 10.1155/2022/5870443] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Revised: 05/06/2022] [Accepted: 05/24/2022] [Indexed: 11/17/2022]
Abstract
Background Dental/oral diseases are one of the significant public health problems globally. Herbal medicines for managing oral diseases are considered an effective alternative to synthetic compounds due to their lower side effect. Azadirachta indica, Terminalia chebula, Camellia sinensis, and Piper nigrum are used to control and prevent oral inflammations in dentistry. In this study, we have evaluated the protease inhibition activity of these plant extracts, and further, the binding mode of the active ingredient of these plants with trypsin was studied using molecular docking. Methods In this study, protease inhibition activity was carried out using aqueous extracts of the plant parts such as Azadirachta indica (neem) twig, Terminalia chebula (Haritaki) fruit, Camellia sinensis (green tea) powder, and Piper nigrum (kali miri) seed. Next, to explore the binding mode of active ingredients azadirachtin, chebuligenic acid, catechin, and piperine with trypsin, we employed a molecular docking study using AutoDock4.2. Results The results revealed that the Azadirachta indica plant extract showed an IC50 value of 96.19 μg mL−1, Camellia sinensis IC50 value of 188.50 μg mL−1, Piper nigrum IC50 value of 371.20 μg mL−1, and Terminalia chebula IC50 value of 639.48 μg mL−1, when compared with standard drug diclofenac sodium, had IC50 value 93.00 μg mL−1. Further, the docking result reveals that all the main active ingredients of these plants have significant binding affinity and prefer the same binding pocket of trypsin. Conclusion Hence, our results show the importance of traditional plants Azadirachta indica, Terminalia chebula, green tea, and Piper nigrum to control oral disease conditions. As they show significant protease inhibition activity, hence, the active ingredient could act as a potential anti-inflammatory agent and further help to prevent or control oral disease conditions such as gingivitis and periodontitis.
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7
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Patil AF, Patil VS, Jaiswal DP, Palakhe SS, Patil SP, Kumbhar BV. Investigating the novel acetonitrile derivatives as potential SARS-CoV-2 main protease inhibitor using molecular modeling approach. J Biomol Struct Dyn 2022; 41:3943-3955. [PMID: 35382699 DOI: 10.1080/07391102.2022.2059568] [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: 01/08/2023]
Abstract
The COVID-19 is declared a pandemic by World Health Organization (WHO). It causes respiratory illness which leads to oxygen deficiency; it has affected millions of lives all around the globe. It has also been observed that people with diabetes condition are more likely to have severe symptoms when infected with the SARS-CoV2. So, continued efforts are being taken to design and discover potential anti-covid drugs. Earlier, a study reveals that the acetonitrile (2-phenyl-4H-benzopyrimedo [2,1-b]-thiazol-4-yliden) derivatives have potential anti-diabetic activity. Hence, drugs repurpose approach was used to identify the potential acetonitrile derivative targeting the main protease of SARS-CoV2. Here, ADMET, molecular docking, and molecular dynamics simulation techniques were employed, to identify potential acetonitrile compounds against the main protease. The acetonitrile compounds (A to M) show the drug-likeness properties. Next, the molecular docking and dynamics simulation study reveals that acetonitrile compounds A, F, G, and L show a higher binding affinity and have an effect on the structure and dynamics of the main protease. Furthermore, binding energy calculations reveal that the acetonitrile derivative F has a higher binding affinity with the main protease and derivative L has a lower binding affinity with the main protease. The binding affinity of acetonitrile derivatives decreases in the order of F > A > G > L with the main protease. Thus, our computational modeling study provides valuable structural and energetic information of interaction of potential acetonitrile derivatives with the main protease which could be further used as potential lead molecules against the SARS-CoV2.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
| | - Vijay Shivaji Patil
- Department of Chemistry, Science College Akkalkuwa, K. B. C. N. M. U, Jalgaon, Maharashtra, India
| | - Dipak Premchand Jaiswal
- Department of Zoology, A. C. S. College Navapur, K. B. C. N. M. U, Jalgaon, Maharashtra, India
| | - Sandip Sumant Palakhe
- Department of Chemistry A. C. S. College Dharangaon, K. B. C. N. M. U, Jalgaon, Maharashtra, India
| | - Sandip Pandurang Patil
- Department of Chemistry G.T.P. College Nandurbar, K. B. C. N. M. U, Jalgaon, Maharashtra, India
| | - Bajarang Vasant Kumbhar
- Department of Biological Sciences, Sunandan Divatia School of Science, NMIMS University (Deemed to be), Mumbai, Maharashtra, India
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Formulation optimization and evaluation of glycyrrhetinic acid loaded PLARosome using factorial design: In-vitro anti-ulcer activity and in silico PASS prediction. J INDIAN CHEM SOC 2021. [DOI: 10.1016/j.jics.2021.100199] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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9
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Sardaru MC, Craciun AM, Al Matarneh CM, Sandu IA, Amarandi RM, Popovici L, Ciobanu CI, Peptanariu D, Pinteala M, Mangalagiu II, Danac R. Cytotoxic substituted indolizines as new colchicine site tubulin polymerisation inhibitors. J Enzyme Inhib Med Chem 2021; 35:1581-1595. [PMID: 32752898 PMCID: PMC7470029 DOI: 10.1080/14756366.2020.1801671] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
A potential microtubule destabilising series of new indolizine derivatives was synthesised and tested for their anticancer activity against a panel of 60 human cancer cell lines. Compounds 11a, 11b, 15a, and 15j showed a broad spectrum of growth inhibitory activity against cancer cell lines representing leukaemia, melanoma and cancer of lung, colon, central nervous system, ovary, kidney, breast, and prostate. Among them, compound 11a was distinguishable by its excellent cytostatic activity, showing GI50 values in the range of 10–100 nM on 43 cell lines. The less potent compounds 15a and 15j in terms of GI50 values showed a high cytotoxic effect against tested colon cancer, CNS cancer, renal cancer and melanoma cell lines and only on few cell lines from other types of cancer. In vitro assaying revealed tubulin polymerisation inhibition by all active compounds. Molecular docking showed good complementarity of active compounds with the colchicine binding site of tubulin.
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Affiliation(s)
- Monica-Cornelia Sardaru
- Department of Chemistry, Faculty of Chemistry, "Al. I. Cuza" University of Iasi, Iași, Romania.,"Petru Poni" Institute of Macromolecular Chemistry of Romanian Academy, Iași, Romania
| | - Anda Mihaela Craciun
- Department of Chemistry, Faculty of Chemistry, "Al. I. Cuza" University of Iasi, Iași, Romania.,"Petru Poni" Institute of Macromolecular Chemistry of Romanian Academy, Iași, Romania
| | - Cristina-Maria Al Matarneh
- Department of Chemistry, Faculty of Chemistry, "Al. I. Cuza" University of Iasi, Iași, Romania.,"Petru Poni" Institute of Macromolecular Chemistry of Romanian Academy, Iași, Romania
| | - Isabela Andreea Sandu
- "Petru Poni" Institute of Macromolecular Chemistry of Romanian Academy, Iași, Romania
| | - Roxana Maria Amarandi
- Department of Chemistry, Faculty of Chemistry, "Al. I. Cuza" University of Iasi, Iași, Romania.,TRANSCEND Research Center, Regional Institute of Oncology, Iași, Romania
| | - Lacramioara Popovici
- Department of Chemistry, Faculty of Chemistry, "Al. I. Cuza" University of Iasi, Iași, Romania
| | | | - Dragos Peptanariu
- "Petru Poni" Institute of Macromolecular Chemistry of Romanian Academy, Iași, Romania
| | - Mariana Pinteala
- "Petru Poni" Institute of Macromolecular Chemistry of Romanian Academy, Iași, Romania
| | - Ionel I Mangalagiu
- Department of Chemistry, Faculty of Chemistry, "Al. I. Cuza" University of Iasi, Iași, Romania
| | - Ramona Danac
- Department of Chemistry, Faculty of Chemistry, "Al. I. Cuza" University of Iasi, Iași, Romania
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Dwivedi A, Karulkar A, Ghosh S, Srinivasan S, Kumbhar BV, Jaiswal AK, Kizhakeyil A, Asija S, Rafiq A, Kumar S, Nisar A, Patil DP, Poojary MV, Jain H, Banavali SD, Highfill SL, Stroncek DF, Shah NN, Fry TJ, Narula G, Purwar R. Robust Antitumor Activity and Low Cytokine Production by Novel Humanized Anti-CD19 CAR T Cells. Mol Cancer Ther 2021; 20:846-858. [PMID: 33632869 DOI: 10.1158/1535-7163.mct-20-0476] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Revised: 01/06/2021] [Accepted: 02/17/2021] [Indexed: 11/16/2022]
Abstract
Recent studies have described the remarkable clinical outcome of anti-CD19 chimeric antigen receptor (CAR) T cells in treating B-cell malignancies. However, over 50% of patients develop life-threatening toxicities associated with cytokine release syndrome which may limit its utilization in low-resource settings. To mitigate the toxicity, we designed a novel humanized anti-CD19 CAR T cells by humanizing the framework region of single-chain variable fragment (scFv) derived from a murine FMC63 mAb and combining it with CD8α transmembrane domain, 4-1BB costimulatory domain, and CD3ζ signaling domain (h1CAR19-8BBζ). Docking studies followed by molecular dynamics simulation revealed that the humanized anti-CD19 scFv (h1CAR19) establishes higher binding affinity and has a flexible molecular structure with CD19 antigen compared with murine scFv (mCAR19). Ex vivo studies with CAR T cells generated from healthy donors and patients with relapsed/refractory B-cell acute lymphoblastic leukemia (B-ALL) expressing either h1CAR19 or mCAR19 showed comparable antitumor activity and proliferation. More importantly, h1CAR19-8BBζ T cells produced lower levels of cytokines (IFNγ, TNFα) upon antigen encounter and reduced the induction of IL6 cytokine from monocytes than mCAR19-8BBζ T cells. There was a comparable proliferation of h1CAR19-8BBζ T cells and mCAR19-8BBζ T cells upon repeated antigen encounter. Finally, h1CAR19-8BBζ T cells efficiently eliminated NALM6 tumor cells in a preclinical model. In conclusion, the distinct structural modification in CAR design confers the novel humanized anti-CD19 CAR with a favorable balance of efficacy to toxicity providing a rationale to test this construct in a phase I trial.
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Affiliation(s)
- Alka Dwivedi
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay (IIT Bombay), Mumbai, Maharashtra, India
| | - Atharva Karulkar
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay (IIT Bombay), Mumbai, Maharashtra, India
| | - Sarbari Ghosh
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay (IIT Bombay), Mumbai, Maharashtra, India
| | - Srisathya Srinivasan
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay (IIT Bombay), Mumbai, Maharashtra, India
| | | | - Ankesh Kumar Jaiswal
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay (IIT Bombay), Mumbai, Maharashtra, India
| | - Atish Kizhakeyil
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay (IIT Bombay), Mumbai, Maharashtra, India
| | - Sweety Asija
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay (IIT Bombay), Mumbai, Maharashtra, India
| | - Afrin Rafiq
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay (IIT Bombay), Mumbai, Maharashtra, India
| | - Sushant Kumar
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay (IIT Bombay), Mumbai, Maharashtra, India
| | - Albeena Nisar
- Department of Medical Oncology, Tata Memorial Center, Homi Bhabha National Institute, Mumbai, Maharashtra, India
| | - Deepali Pandit Patil
- Department of Medical Oncology, Tata Memorial Center, Homi Bhabha National Institute, Mumbai, Maharashtra, India
| | - Minal Vivek Poojary
- Department of Transfusion Medicine, ACTREC, Tata Memorial Center, Navi Mumbai, Homi Bhabha National Institute, Mumbai, Maharashtra, India
| | - Hasmukh Jain
- Department of Medical Oncology, Tata Memorial Center, Homi Bhabha National Institute, Mumbai, Maharashtra, India
| | - Shripad D Banavali
- Department of Medical Oncology, Tata Memorial Center, Homi Bhabha National Institute, Mumbai, Maharashtra, India
| | - Steven L Highfill
- Department of Transfusion Medicine, Clinical Center, National Institutes of Health, Center for Cellular Engineering, Bethesda, Maryland
| | - David F Stroncek
- Department of Transfusion Medicine, Clinical Center, National Institutes of Health, Center for Cellular Engineering, Bethesda, Maryland
| | - Nirali N Shah
- Pediatric Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Terry J Fry
- Department of Pediatrics, University of Colorado, Anschutz Medical Campus, Aurora, Colorado
| | - Gaurav Narula
- Department of Medical Oncology, Tata Memorial Center, Homi Bhabha National Institute, Mumbai, Maharashtra, India
| | - Rahul Purwar
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay (IIT Bombay), Mumbai, Maharashtra, India.
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11
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Zhu L, Zhang C, Lü X, Song C, Wang C, Zhang M, Xie Y, Schaefer HF. Binding modes of cabazitaxel with the different human β-tubulin isotypes: DFT and MD studies. J Mol Model 2020; 26:162. [DOI: 10.1007/s00894-020-04400-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2020] [Accepted: 04/28/2020] [Indexed: 12/27/2022]
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12
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Kumbhar BV, Bhandare VV. Exploring the interaction of Peloruside-A with drug resistant αβII and αβIII tubulin isotypes in human ovarian carcinoma using a molecular modeling approach. J Biomol Struct Dyn 2020; 39:1990-2002. [DOI: 10.1080/07391102.2020.1745689] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Affiliation(s)
- Bajarang Vasant Kumbhar
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, India
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13
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Muscat S, Pallante L, Stojceski F, Danani A, Grasso G, Deriu MA. The Impact of Natural Compounds on S-Shaped Aβ42 Fibril: From Molecular Docking to Biophysical Characterization. Int J Mol Sci 2020; 21:ijms21062017. [PMID: 32188076 PMCID: PMC7139307 DOI: 10.3390/ijms21062017] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Revised: 03/06/2020] [Accepted: 03/13/2020] [Indexed: 12/18/2022] Open
Abstract
The pursuit for effective strategies inhibiting the amyloidogenic process in neurodegenerative disorders, such as Alzheimer’s disease (AD), remains one of the main unsolved issues, and only a few drugs have demonstrated to delay the degeneration of the cognitive system. Moreover, most therapies induce severe side effects and are not effective at all stages of the illness. The need to find novel and reliable drugs appears therefore of primary importance. In this context, natural compounds have shown interesting beneficial effects on the onset and progression of neurodegenerative diseases, exhibiting a great inhibitory activity on the formation of amyloid aggregates and proving to be effective in many preclinical and clinical studies. However, their inhibitory mechanism is still unclear. In this work, ensemble docking and molecular dynamics simulations on S-shaped Aβ42 fibrils have been carried out to evaluate the influence of several natural compounds on amyloid conformational behaviour. A deep understanding of the interaction mechanisms between natural compounds and Aβ aggregates may play a key role to pave the way for design, discovery and optimization strategies toward an efficient destabilization of toxic amyloid assemblies.
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Affiliation(s)
- Stefano Muscat
- Dalle Molle Institute for Artificial Intelligence (IDSIA), University of Italian Switzerland (USI), University of Applied Science and Art of Southern Switzerland (SUPSI), CH-6928 Manno, Switzerland
| | - Lorenzo Pallante
- PolitoBIOMed Lab, Department of Mechanical and Aerospace Engineering, Politecnico di Torino, IT-10128 Torino, Italy
| | - Filip Stojceski
- Dalle Molle Institute for Artificial Intelligence (IDSIA), University of Italian Switzerland (USI), University of Applied Science and Art of Southern Switzerland (SUPSI), CH-6928 Manno, Switzerland
| | - Andrea Danani
- Dalle Molle Institute for Artificial Intelligence (IDSIA), University of Italian Switzerland (USI), University of Applied Science and Art of Southern Switzerland (SUPSI), CH-6928 Manno, Switzerland
| | - Gianvito Grasso
- Dalle Molle Institute for Artificial Intelligence (IDSIA), University of Italian Switzerland (USI), University of Applied Science and Art of Southern Switzerland (SUPSI), CH-6928 Manno, Switzerland
| | - Marco Agostino Deriu
- PolitoBIOMed Lab, Department of Mechanical and Aerospace Engineering, Politecnico di Torino, IT-10128 Torino, Italy
- Correspondence:
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14
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Pallante L, Rocca A, Klejborowska G, Huczynski A, Grasso G, Tuszynski JA, Deriu MA. In silico Investigations of the Mode of Action of Novel Colchicine Derivatives Targeting β-Tubulin Isotypes: A Search for a Selective and Specific β-III Tubulin Ligand. Front Chem 2020; 8:108. [PMID: 32154219 PMCID: PMC7047339 DOI: 10.3389/fchem.2020.00108] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2019] [Accepted: 02/04/2020] [Indexed: 01/04/2023] Open
Abstract
The cardinal role of microtubules in cell mitosis makes them interesting drug targets for many pharmacological treatments, including those against cancer. Moreover, different expression patterns between cell types for several tubulin isotypes represent a great opportunity to improve the selectivity and specificity of the employed drugs and to design novel compounds with higher activity only on cells of interest. In this context, tubulin isotype βIII represents an excellent target for anti-tumoral therapies since it is overexpressed in most cancer cells and correlated with drug resistance. Colchicine is a well-known antimitotic agent, which is able to bind the tubulin dimer and to halt the mitotic process. However, it shows high toxicity also on normal cells and it is not specific for isotype βIII. In this context, the search for colchicine derivatives is a matter of great importance in cancer research. In this study, homology modeling techniques, molecular docking, and molecular dynamics simulations have been employed to characterize the interaction between 55 new promising colchicine derivatives and tubulin isotype βIII. These compounds were screened and ranked based on their binding affinity and conformational stability in the colchicine binding site of tubulin βIII. Results from this study point the attention on an amide of 4-chlorine thiocolchicine. This colchicine-derivative is characterized by a unique mode of interaction with tubulin, compared to all other compounds considered, which is primarily characterized by the involvement of the α-T5 loop, a key player in the colchicine binding site. Information provided by the present study may be particularly important in the rational design of colchicine-derivatives targeting drug resistant cancer phenotypes.
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Affiliation(s)
- Lorenzo Pallante
- PolitoBIOMed Lab, Department of Mechanical and Aerospace Engineering, Politecnico di Torino, Turin, Italy
| | - Antonio Rocca
- PolitoBIOMed Lab, Department of Mechanical and Aerospace Engineering, Politecnico di Torino, Turin, Italy
| | | | - Adam Huczynski
- Department of Chemistry, Adam Mickiewicz University, Poznań, Poland
| | - Gianvito Grasso
- Dalle Molle Institute for Artificial Intelligence (IDSIA), University of Applied Sciences of Southern Switzerland (SUPSI), University of Italian Switzerland (USI), Manno, Switzerland
| | - Jack A Tuszynski
- PolitoBIOMed Lab, Department of Mechanical and Aerospace Engineering, Politecnico di Torino, Turin, Italy.,Department of Oncology, University of Alberta, Edmonton, AB, Canada
| | - Marco A Deriu
- PolitoBIOMed Lab, Department of Mechanical and Aerospace Engineering, Politecnico di Torino, Turin, Italy
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15
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Cury NM, Capitão RM, Almeida RDCBD, Artico LL, Corrêa JR, Simão dos Santos EF, Yunes JA, Correia CRD. Synthesis and evaluation of 2-carboxy indole derivatives as potent and selective anti-leukemic agents. Eur J Med Chem 2019; 181:111570. [DOI: 10.1016/j.ejmech.2019.111570] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2019] [Revised: 07/26/2019] [Accepted: 07/28/2019] [Indexed: 12/29/2022]
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16
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Chahal V, Nirwan S, Kakkar R. Combined approach of homology modeling, molecular dynamics, and docking: computer-aided drug discovery. PHYSICAL SCIENCES REVIEWS 2019. [DOI: 10.1515/psr-2019-0066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Abstract
With the continuous development in software, algorithms, and increase in computer speed, the field of computer-aided drug design has been witnessing reduction in the time and cost of the drug designing process. Structure based drug design (SBDD), which is based on the 3D structure of the enzyme, is helping in proposing novel inhibitors. Although a number of crystal structures are available in various repositories, there are various proteins whose experimental crystallization is difficult. In such cases, homology modeling, along with the combined application of MD and docking, helps in establishing a reliable 3D structure that can be used for SBDD. In this review, we have reported recent works, which have employed these three techniques for generating structures and further proposing novel inhibitors, for cytoplasmic proteins, membrane proteins, and metal containing proteins. Also, we have discussed these techniques in brief in terms of the theory involved and the various software employed. Hence, this review can give a brief idea about using these tools specifically for a particular problem.
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17
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Structural Basis of Colchicine-Site targeting Acylhydrazones active against Multidrug-Resistant Acute Lymphoblastic Leukemia. iScience 2019; 21:95-109. [PMID: 31655259 PMCID: PMC6820235 DOI: 10.1016/j.isci.2019.10.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2019] [Revised: 08/23/2019] [Accepted: 09/30/2019] [Indexed: 11/21/2022] Open
Abstract
Tubulin is one of the best validated anti-cancer targets, but most anti-tubulin agents have unfavorable therapeutic indexes. Here, we characterized the tubulin-binding activity, the mechanism of action, and the in vivo anti-leukemia efficacy of three 3,4,5-trimethoxy-N-acylhydrazones. We show that all compounds target the colchicine-binding site of tubulin and that none is a substrate of ABC transporters. The crystal structure of the tubulin-bound N-(1′-naphthyl)-3,4,5-trimethoxybenzohydrazide (12) revealed steric hindrance on the T7 loop movement of β-tubulin, thereby rendering tubulin assembly incompetent. Using dose escalation and short-term repeated dose studies, we further report that this compound class is well tolerated to >100 mg/kg in mice. We finally observed that intraperitoneally administered compound 12 significantly prolonged the overall survival of mice transplanted with both sensitive and multidrug-resistant acute lymphoblastic leukemia (ALL) cells. Taken together, this work describes promising colchicine-site-targeting tubulin inhibitors featuring favorable therapeutic effects against ALL and multidrug-resistant cells. 3,4,5-trimethoxy-N-acylhydrazones bind to the colchicine site of tubulin 12 forms a single H-bond with αThr179 and causes steric hindrance of tubulin βT7 loop 3,4,5-trimethoxy-N-acylhydrazones feature low toxicity 12 shows therapeutic effect against multidrug-resistant acute lymphoblastic leukemia
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18
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Kurek J, Kwaśniewska-Sip P, Myszkowski K, Cofta G, Barczyński P, Murias M, Kurczab R, Śliwa P, Przybylski P. Antifungal, anticancer, and docking studies of colchiceine complexes with monovalent metal cation salts. Chem Biol Drug Des 2019; 94:1930-1943. [PMID: 31260187 DOI: 10.1111/cbdd.13583] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2018] [Revised: 05/29/2019] [Accepted: 06/17/2019] [Indexed: 01/22/2023]
Abstract
Complexes of colchiceine with monovalent cation perchlorates and iodides have been obtained and characterized by spectroscopic methods. DFT and spectroscopic studies reveal that the dihedral angle ω1-1a-12-12a , crucial for colchicine biological mechanism of action, that is, binding to tubulins depends on the diameter of the complexed metal cation. Biological tests indicated no antifungal properties of colchicine (it was active only toward A.pullulans), in contrast to its derivative-(colchiceine). Complexation of colchiceine with metal cations improved significantly the antifungal potency, even below MIC <1 μg/ml. The colchiceine complexes were more potent than colchiceine, and some of them were even more potent than the fungicidal standard IPBC. The highest potency of colchiceine complexes was noted against A. pullulans (MIC = 0.5 μg/ml). In contrast to the findings concerning antifungal potency, the anticancer studies showed complexes of colchicine more active (~IC50 = 2 nM) than those of colchiceine (~IC50 = 6 μM). MDA-MB-231 breast cancer cell lines and human lung fibroblasts CCD39Lu were also tested.
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Affiliation(s)
- Joanna Kurek
- Faculty of Chemistry, Adam Mickiewicz University, Poznań, Poland
| | - Patrycja Kwaśniewska-Sip
- Wood Technology Institute, Environmental Protection and Wood Chemistry Department, Poznan, Poland
| | | | - Grzegorz Cofta
- Institute of Chemical Wood Technology, University of Life Science, Poznań, Poland
| | - Piotr Barczyński
- Faculty of Chemistry, Adam Mickiewicz University, Poznań, Poland
| | - Marek Murias
- Department of Toxicology, Poznan University of Medical Sciences, Poznań, Poland
| | - Rafał Kurczab
- Department of Medicinal Chemistry, Institute of Pharmacology, Polish Academy of Sciences, Kraków, Poland
| | - Paweł Śliwa
- Faculty of Chemical Engineering and Technology, Cracow University of Technology, Kraków, Poland
| | - Piotr Przybylski
- Faculty of Chemistry, Adam Mickiewicz University, Poznań, Poland
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19
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Bhandare VV, Kumbhar BV, Kunwar A. Differential binding affinity of tau repeat region R2 with neuronal-specific β-tubulin isotypes. Sci Rep 2019; 9:10795. [PMID: 31346240 PMCID: PMC6658543 DOI: 10.1038/s41598-019-47249-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2019] [Accepted: 07/05/2019] [Indexed: 12/14/2022] Open
Abstract
Tau is a microtubule-associated protein whose C-terminal domain consisting of four repeat regions R1, R2, R3 and R4 binds to microtubules to stabilize them. In several neurodegenerative diseases, tau detaches from microtubules to form insoluble aggregates leading to tauopathy. Microtubules are made up of αβ tubulin subunits. Seven α-tubulin and nine β-tubulin isotypes have been reported to be present in humans till date. These tubulin isotypes show residue composition variations mainly at C-terminal region and bind to motor proteins and anti-mitotic drugs differently. These tubulin isotypes show tissue specific expression as their relative proportion varies significantly in different type of cells. It is also known that tau binds differently to different cell lines and can either promote or demote microtubule polymerization. However, the relative binding affinity of tau to the different β-tubulin isotypes present in different cell lines is completely unknown. Here, we study relative binding affinity of Tau repeat region R2 to neuronal specific tubulin isotypes βI, βIIb, and βIII using molecular modelling approach. The order of binding energy of tau with tubulin is βIII > βIIb > βI. Our strategy can be potentially adapted to understand differential binding affinity of tau towards β-tubulin isotypes present in other cell lines.
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Affiliation(s)
- Vishwambhar Vishnu Bhandare
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, 400076, Maharashtra, India
| | - Bajarang Vasant Kumbhar
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, 400076, Maharashtra, India
| | - Ambarish Kunwar
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, 400076, Maharashtra, India.
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20
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Kumbhar BV, Bhandare VV, Panda D, Kunwar A. Delineating the interaction of combretastatin A-4 with αβ tubulin isotypes present in drug resistant human lung carcinoma using a molecular modeling approach. J Biomol Struct Dyn 2019; 38:426-438. [DOI: 10.1080/07391102.2019.1577174] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Bajarang Vasant Kumbhar
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, Maharashtra, India
| | - Vishwambhar Vishnu Bhandare
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, Maharashtra, India
| | - Dulal Panda
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, Maharashtra, India
| | - Ambarish Kunwar
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, Maharashtra, India
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21
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Richter M, Boldescu V, Graf D, Streicher F, Dimoglo A, Bartenschlager R, Klein CD. Synthesis, Biological Evaluation, and Molecular Docking of Combretastatin and Colchicine Derivatives and their hCE1-Activated Prodrugs as Antiviral Agents. ChemMedChem 2019; 14:469-483. [PMID: 30605241 DOI: 10.1002/cmdc.201800641] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2018] [Revised: 12/01/2018] [Indexed: 02/06/2023]
Abstract
Recent studies indicate that tubulin can be a host factor for vector-borne flaviviruses like dengue (DENV) and Zika (ZIKV), and inhibitors of tubulin polymerization such as colchicine have been demonstrated to decrease virus replication. However, toxicity limits the application of these compounds. Herein we report prodrugs based on combretastatin and colchicine derivatives that contain an ester cleavage site for human carboxylesterase, a highly abundant enzyme in monocytes and hepatocytes targeted by DENV. Relative to their parent compounds, the cytotoxicity of these prodrugs was reduced by several orders of magnitude. All synthesized prodrugs containing a leucine ester were hydrolyzed by the esterase in vitro. In contrast to previous reports, the phenylglycine esters were not cleaved by human carboxylesterase. The antiviral activity of combretastatin, colchicine, and selected prodrugs against DENV and ZIKV in cell culture was observed at low micromolar and sub-micromolar concentrations. In addition, docking studies were performed to understand the binding mode of the studied compounds to tubulin.
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Affiliation(s)
- Michael Richter
- Institute of Pharmacy and Molecular Biotechnology, Heidelberg University, INF 364, 69120, Heidelberg, Germany
| | - Veaceslav Boldescu
- Institute of Pharmacy and Molecular Biotechnology, Heidelberg University, INF 364, 69120, Heidelberg, Germany.,Institute of Chemistry, Laboratory of Organic Synthesis and Biopharmaceuticals, Moldova Academy of Sciences, Academiei str. 3, MD2028, Chisinau, Moldova
| | - Dominik Graf
- Institute of Pharmacy and Molecular Biotechnology, Heidelberg University, INF 364, 69120, Heidelberg, Germany
| | - Felix Streicher
- Institute of Pharmacy and Molecular Biotechnology, Heidelberg University, INF 364, 69120, Heidelberg, Germany
| | | | - Ralf Bartenschlager
- Department of Infectious Diseases, Molecular Virology, Heidelberg University, INF 344, 69120, Heidelberg, Germany), and German Center for Infection Research, Heidelberg Partner Site
| | - Christian D Klein
- Institute of Pharmacy and Molecular Biotechnology, Heidelberg University, INF 364, 69120, Heidelberg, Germany
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22
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Vicente-Blázquez A, González M, Álvarez R, Del Mazo S, Medarde M, Peláez R. Antitubulin sulfonamides: The successful combination of an established drug class and a multifaceted target. Med Res Rev 2018; 39:775-830. [PMID: 30362234 DOI: 10.1002/med.21541] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2018] [Revised: 09/02/2018] [Accepted: 09/06/2018] [Indexed: 12/13/2022]
Abstract
Tubulin, the microtubules and their dynamic behavior are amongst the most successful antitumor, antifungal, antiparasitic, and herbicidal drug targets. Sulfonamides are exemplary drugs with applications in the clinic, in veterinary and in the agrochemical industry. This review summarizes the actual state and recent progress of both fields looking from the double point of view of the target and its drugs, with special focus onto the structural aspects. The article starts with a brief description of tubulin structure and its dynamic assembly and disassembly into microtubules and other polymers. Posttranslational modifications and the many cellular means of regulating and modulating tubulin's biology are briefly presented in the tubulin code. Next, the structurally characterized drug binding sites, their occupying drugs and the effects they induce are described, emphasizing on the structural requirements for high potency, selectivity, and low toxicity. The second part starts with a summary of the favorable and highly tunable combination of physical-chemical and biological properties that render sulfonamides a prototypical example of privileged scaffolds with representatives in many therapeutic areas. A complete description of tubulin-binding sulfonamides is provided, covering the different species and drug sites. Some of the antimitotic sulfonamides have met with very successful applications and others less so, thus illustrating the advances, limitations, and future perspectives of the field. All of them combine in a mechanism of action and a clinical outcome that conform efficient drugs.
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Affiliation(s)
- Alba Vicente-Blázquez
- Laboratorio de Química Orgánica y Farmacéutica, Departamento de Ciencias Farmacéuticas, Universidad de Salamanca, Campus Miguel de Unamuno, Salamanca, Spain.,Facultad de Farmacia, Instituto de Investigación Biomédica de Salamanca (IBSAL), Universidad de Salamanca, Campus Miguel de Unamuno, Salamanca, Spain.,Facultad de Farmacia, Centro de Investigación de Enfermedades Tropicales de la Universidad de Salamanca (CIETUS), Universidad de Salamanca, Campus Miguel de Unamuno, Salamanca, Spain.,Laboratory of Cell Death and Cancer Therapy, Department of Molecular Biomedicine, Centro de Investigaciones Biológicas, Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain
| | - Myriam González
- Laboratorio de Química Orgánica y Farmacéutica, Departamento de Ciencias Farmacéuticas, Universidad de Salamanca, Campus Miguel de Unamuno, Salamanca, Spain.,Facultad de Farmacia, Instituto de Investigación Biomédica de Salamanca (IBSAL), Universidad de Salamanca, Campus Miguel de Unamuno, Salamanca, Spain.,Facultad de Farmacia, Centro de Investigación de Enfermedades Tropicales de la Universidad de Salamanca (CIETUS), Universidad de Salamanca, Campus Miguel de Unamuno, Salamanca, Spain
| | - Raquel Álvarez
- Laboratorio de Química Orgánica y Farmacéutica, Departamento de Ciencias Farmacéuticas, Universidad de Salamanca, Campus Miguel de Unamuno, Salamanca, Spain.,Facultad de Farmacia, Instituto de Investigación Biomédica de Salamanca (IBSAL), Universidad de Salamanca, Campus Miguel de Unamuno, Salamanca, Spain.,Facultad de Farmacia, Centro de Investigación de Enfermedades Tropicales de la Universidad de Salamanca (CIETUS), Universidad de Salamanca, Campus Miguel de Unamuno, Salamanca, Spain
| | - Sara Del Mazo
- Laboratorio de Química Orgánica y Farmacéutica, Departamento de Ciencias Farmacéuticas, Universidad de Salamanca, Campus Miguel de Unamuno, Salamanca, Spain.,Facultad de Farmacia, Instituto de Investigación Biomédica de Salamanca (IBSAL), Universidad de Salamanca, Campus Miguel de Unamuno, Salamanca, Spain.,Facultad de Farmacia, Centro de Investigación de Enfermedades Tropicales de la Universidad de Salamanca (CIETUS), Universidad de Salamanca, Campus Miguel de Unamuno, Salamanca, Spain
| | - Manuel Medarde
- Laboratorio de Química Orgánica y Farmacéutica, Departamento de Ciencias Farmacéuticas, Universidad de Salamanca, Campus Miguel de Unamuno, Salamanca, Spain.,Facultad de Farmacia, Instituto de Investigación Biomédica de Salamanca (IBSAL), Universidad de Salamanca, Campus Miguel de Unamuno, Salamanca, Spain.,Facultad de Farmacia, Centro de Investigación de Enfermedades Tropicales de la Universidad de Salamanca (CIETUS), Universidad de Salamanca, Campus Miguel de Unamuno, Salamanca, Spain
| | - Rafael Peláez
- Laboratorio de Química Orgánica y Farmacéutica, Departamento de Ciencias Farmacéuticas, Universidad de Salamanca, Campus Miguel de Unamuno, Salamanca, Spain.,Facultad de Farmacia, Instituto de Investigación Biomédica de Salamanca (IBSAL), Universidad de Salamanca, Campus Miguel de Unamuno, Salamanca, Spain.,Facultad de Farmacia, Centro de Investigación de Enfermedades Tropicales de la Universidad de Salamanca (CIETUS), Universidad de Salamanca, Campus Miguel de Unamuno, Salamanca, Spain
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23
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Kumbhar BV, Panda D, Kunwar A. Interaction of microtubule depolymerizing agent indanocine with different human αβ tubulin isotypes. PLoS One 2018; 13:e0194934. [PMID: 29584771 PMCID: PMC5870988 DOI: 10.1371/journal.pone.0194934] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2017] [Accepted: 03/13/2018] [Indexed: 12/02/2022] Open
Abstract
Tubulin isotypes are known to regulate the stability and dynamics of microtubules, and are also involved in the development of resistance against microtubule-targeted cancer drugs. Indanocine, a potent microtubule depolymerizing agent, is highly active against multidrug-resistant (MDR) cancer cells without affecting normal cells. It is known to disrupt microtubule dynamics in cells and induce apoptotic cell death. Indanocine is reported to bind to tubulin at the colchicine site i.e. at the interface of αβ tubulin heterodimer. However, it’s precise binding mode, involved molecular interactions and the binding affinities with different αβ-tubulin isotypes present in MDR cells are not well understood. Here, the binding affinities of human αβ-tubulin isotypes with indanocine were examined, employing the molecular modeling approach i.e. docking, molecular dynamics simulation and binding energy calculations. Multiple sequence analysis suggests that the amino acid sequences are different in the indanocine binding pockets of βI, βIIa, βIII and βVI isotypes. However, such differences are not observed in the amino acid sequences of βIVa, βIVb, and βV tubulin isotypes at indanocine binding pockets. Docking and molecular dynamics simulation results show that indanocine prefers the interface binding pocket of αβIIa, αβIII, αβIVb, αβV, and αβVI tubulin isotypes; whereas it is expelled from the interface binding pocket of αβIVa and αβI-tubulin isotypes. Further, binding free energy calculations show that αβVI has the highest binding affinity and αβI has the lowest binding affinity for indanocine among all β-tubulin isotypes. The binding free energy decreases in the order of αβVI > αβIVb > αβIIa > αβIII > αβV > αβIVa > αβI. Thus, our study provides a significant understanding of involved molecular interactions of indanocine with tubulin isotypes, which may help to design potent indanocine analogues for specific tubulin isotypes in MDR cells in future.
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Affiliation(s)
- Bajarang Vasant Kumbhar
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, Maharashtra, India
| | - Dulal Panda
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, Maharashtra, India
| | - Ambarish Kunwar
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, Maharashtra, India
- * E-mail:
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24
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Insight into microtubule destabilization mechanism of 3,4,5-trimethoxyphenyl indanone derivatives using molecular dynamics simulation and conformational modes analysis. J Comput Aided Mol Des 2018. [DOI: 10.1007/s10822-018-0109-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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25
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Hura N, Naaz A, Prassanawar SS, Guchhait SK, Panda D. Drug-Clinical Agent Molecular Hybrid: Synthesis of Diaryl(trifluoromethyl)pyrazoles as Tubulin Targeting Anticancer Agents. ACS OMEGA 2018; 3:1955-1969. [PMID: 30023819 PMCID: PMC6044759 DOI: 10.1021/acsomega.7b01784] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2017] [Accepted: 01/05/2018] [Indexed: 05/28/2023]
Abstract
Twenty-three combretastatin A-4 (CA-4) analogues were synthesized by judiciously incorporating a functional N-heterocyclic motif present in Celecoxib (a marketed drug) while retaining essential pharmacophoric features of CA-4. Combretastatin-(trifluoromethyl)pyrazole hybrid analogues, i.e., 5-trimethoxyphenyl-3-(trifluoromethyl)pyrazoles with a variety of relevantly substituted aryls and heteroaryls at 1-position were considered as potential tubulin polymerization inhibitors. The cytotoxicity of the compounds was evaluated using MCF-7 cells. Analog 23 (C-23) was found to be the most active among the tested compounds. It showed pronounced cytotoxicity against HeLa, B16F10, and multidrug-resistant mammary tumor cells EMT6/AR1. Interestingly, C-23 displayed significantly lower toxicity toward noncancerous cells, MCF10A and L929, than their cancerous counterparts, MCF-7 and B16F10, respectively. C-23 depolymerized interphase microtubules, disrupted mitotic spindle formation, and arrested MCF-7 cells at mitosis, leading to cell death. C-23 inhibited the assembly of tubulin in vitro. C-23 bound to tubulin at the colchicine binding site and altered the secondary structures of tubulin. The data revealed the importance of (trimethoxyphenyl)(trifluoromethyl)pyrazole as a cis-restricted double bond-alternative bridging motif, and carboxymethyl-substituted phenyl as ring B for activities and interaction with tubulin. The results indicated that the combretastatin-(trifluoromethyl)pyrazole hybrid class of analogues has the potential for further development as anticancer agents.
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Affiliation(s)
- Neha Hura
- Department
of Medicinal Chemistry, National Institute
of Pharmaceutical Education and Research (NIPER), S.A.S. Nagar, Punjab 160062, India
| | - Afsana Naaz
- Department
of Biosciences and Bioengineering, Indian
Institute of Technology Bombay, Powai, Mumbai 400076, India
| | - Shweta S. Prassanawar
- Department
of Biosciences and Bioengineering, Indian
Institute of Technology Bombay, Powai, Mumbai 400076, India
| | - Sankar K. Guchhait
- Department
of Medicinal Chemistry, National Institute
of Pharmaceutical Education and Research (NIPER), S.A.S. Nagar, Punjab 160062, India
| | - Dulal Panda
- Department
of Biosciences and Bioengineering, Indian
Institute of Technology Bombay, Powai, Mumbai 400076, India
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26
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Hemmat M, Castle BT, Odde DJ. Microtubule dynamics: moving toward a multi-scale approach. Curr Opin Cell Biol 2018; 50:8-13. [PMID: 29351860 PMCID: PMC5911414 DOI: 10.1016/j.ceb.2017.12.013] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2017] [Revised: 12/12/2017] [Accepted: 12/23/2017] [Indexed: 12/17/2022]
Abstract
Microtubule self-assembly dynamics serve to facilitate many vital cellular functions, such as chromosome segregation during mitosis and synaptic plasticity. However, the detailed atomistic basis of assembly dynamics has remained an unresolved puzzle. A key challenge is connecting together the vast range of relevant length-time scales, events happening at time scales ranging from nanoseconds, such as tubulin molecular interactions (Å-nm), to minutes-hours, such as the cellular response to microtubule dynamics during mitotic progression (μm). At the same time, microtubule interactions with associated proteins and binding agents, such as anti-cancer drugs, can strongly affect this dynamic process through atomic-level mechanisms that remain to be elucidated. New high-resolution technologies for investigating these interactions, including cryo-electron microscopy (EM) techniques and total internal reflection fluorescence (TIRF) microscopy, are yielding important new insights. Here, we focus on recent studies of microtubule dynamics, both theoretical and experimental, and how these findings shed new light on this complex phenomenon across length-time scales, from Å to μm and from nanoseconds to minutes.
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Affiliation(s)
- Mahya Hemmat
- Department of Mechanical Engineering, University of Minnesota, Minneapolis, MN 55455, USA
| | - Brian T Castle
- Department of Biomedical Engineering, University of Minnesota, Minneapolis, MN 55455, USA
| | - David J Odde
- Department of Biomedical Engineering, University of Minnesota, Minneapolis, MN 55455, USA.
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27
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Das S, Paul S. Exploring the binding sites and binding mechanism for hydrotrope encapsulated griseofulvin drug on γ-tubulin protein. PLoS One 2018; 13:e0190209. [PMID: 29324869 PMCID: PMC5764265 DOI: 10.1371/journal.pone.0190209] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2017] [Accepted: 12/11/2017] [Indexed: 01/10/2023] Open
Abstract
The protein γ-tubulin plays an important role in centrosomal clustering and this makes it an attractive therapeutic target for treating cancers. Griseofulvin, an antifungal drug, has recently been used to inhibit proliferation of various types of cancer cells. It can also affect the microtubule dynamics by targeting the γ-tubulin protein. So far, the binding pockets of γ-tubulin protein are not properly identified and the exact mechanism by which the drug binds to it is an area of intense speculation and research. The aim of the present study is to investigate the binding mechanism and binding affinity of griseofulvin on γ-tubulin protein using classical molecular dynamics simulations. Since the drug griseofulvin is sparingly soluble in water, here we also present a promising approach for formulating and achieving delivery of hydrophobic griseofulvin drug via hydrotrope sodium cumene sulfonate (SCS) cluster. We observe that the binding pockets of γ-tubulin protein are mainly formed by the H8, H9 helices and S7, S8, S14 strands and the hydrophobic interactions between the drug and γ-tubulin protein drive the binding process. The release of the drug griseofulvin from the SCS cluster is confirmed by the coordination number analysis. We also find hydrotrope-induced alteration of the binding sites of γ-tubulin protein and the weakening of the drug-protein interactions.
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Affiliation(s)
- Shubhadip Das
- Department of Chemistry, Indian Institute of Technology Guwahati, Guwahati, Assam, India
| | - Sandip Paul
- Department of Chemistry, Indian Institute of Technology Guwahati, Guwahati, Assam, India
- * E-mail:
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28
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Parker AL, Teo WS, McCarroll JA, Kavallaris M. An Emerging Role for Tubulin Isotypes in Modulating Cancer Biology and Chemotherapy Resistance. Int J Mol Sci 2017; 18:ijms18071434. [PMID: 28677634 PMCID: PMC5535925 DOI: 10.3390/ijms18071434] [Citation(s) in RCA: 91] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2017] [Revised: 06/24/2017] [Accepted: 06/27/2017] [Indexed: 12/19/2022] Open
Abstract
Tubulin proteins, as components of the microtubule cytoskeleton perform critical cellular functions throughout all phases of the cell cycle. Altered tubulin isotype composition of microtubules is emerging as a feature of aggressive and treatment refractory cancers. Emerging evidence highlighting a role for tubulin isotypes in differentially influencing microtubule behaviour and broader functional networks within cells is illuminating a complex role for tubulin isotypes regulating cancer biology and chemotherapy resistance. This review focuses on the role of different tubulin isotypes in microtubule dynamics as well as in oncogenic changes that provide a survival or proliferative advantage to cancer cells within the tumour microenvironment and during metastatic processes. Consideration of the role of tubulin isotypes beyond their structural function will be essential to improving the current clinical use of tubulin-targeted chemotherapy agents and informing the development of more effective cancer therapies.
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Affiliation(s)
- Amelia L Parker
- Tumour Biology and Targeting, Children's Cancer Institute, Lowy Cancer Research Centre, University of New South Wales, Sydney, NSW 2031, Australia.
- Australian Centre for NanoMedicine, ARC Centre of Excellence in Convergent Bio-Nano Science and Technology, University of New South Wales, Sydney, NSW 2052, Australia.
| | - Wee Siang Teo
- Tumour Biology and Targeting, Children's Cancer Institute, Lowy Cancer Research Centre, University of New South Wales, Sydney, NSW 2031, Australia.
- Australian Centre for NanoMedicine, ARC Centre of Excellence in Convergent Bio-Nano Science and Technology, University of New South Wales, Sydney, NSW 2052, Australia.
| | - Joshua A McCarroll
- Tumour Biology and Targeting, Children's Cancer Institute, Lowy Cancer Research Centre, University of New South Wales, Sydney, NSW 2031, Australia.
- Australian Centre for NanoMedicine, ARC Centre of Excellence in Convergent Bio-Nano Science and Technology, University of New South Wales, Sydney, NSW 2052, Australia.
| | - Maria Kavallaris
- Tumour Biology and Targeting, Children's Cancer Institute, Lowy Cancer Research Centre, University of New South Wales, Sydney, NSW 2031, Australia.
- Australian Centre for NanoMedicine, ARC Centre of Excellence in Convergent Bio-Nano Science and Technology, University of New South Wales, Sydney, NSW 2052, Australia.
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29
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Cirillo L, Gotta M, Meraldi P. The Elephant in the Room: The Role of Microtubules in Cancer. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2017; 1002:93-124. [DOI: 10.1007/978-3-319-57127-0_5] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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30
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Zúñiga MA, Alderete JB, Jaña GA, Jiménez VA. Structural insight into the role of Gln293Met mutation on the Peloruside A/Laulimalide association with αβ-tubulin from molecular dynamics simulations, binding free energy calculations and weak interactions analysis. J Comput Aided Mol Des 2017; 31:643-652. [DOI: 10.1007/s10822-017-0029-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2017] [Accepted: 05/28/2017] [Indexed: 01/27/2023]
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31
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Laurin Y, Eyer J, Robert CH, Prevost C, Sacquin-Mora S. Mobility and Core-Protein Binding Patterns of Disordered C-Terminal Tails in β-Tubulin Isotypes. Biochemistry 2017; 56:1746-1756. [PMID: 28290671 DOI: 10.1021/acs.biochem.6b00988] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Although they play a significant part in the regulation of microtubule structure, dynamics, and function, the disordered C-terminal tails of tubulin remain invisible to experimental structural methods and do not appear in the crystallographic structures that are currently available in the Protein Data Bank. Interestingly, these tails concentrate most of the sequence variability between tubulin isotypes and are the sites of the principal post-translational modifications undergone by this protein. Using homology modeling, we developed two complete models for the human αI/βI- and αI/βIII-tubulin isotypes that include their C-terminal tails. We then investigated the conformational variability of the two β-tails using long time-scale classical molecular dynamics simulations that revealed similar features, notably the unexpected presence of common anchoring regions on the surface of the tuulin dimer, but also distinctive mobility or interaction patterns, some of which could be related to the tail lengths and charge distributions. We also observed in our simulations that the C-terminal tail from the βI isotype, but not the βIII isotype, formed contacts in the putative binding site of a recently discovered peptide that disrupts microtubule formation in glioma cells. Hindering the binding site in the βI isotype would be consistent with this peptide's preferential disruption of microtubule formation in glioma, whose cells overexpress βIII, compared to normal glial cells. While these observations need to be confirmed with more intensive sampling, our study opens new perspectives for the development of isotype-specific chemotherapy drugs.
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Affiliation(s)
- Yoann Laurin
- Laboratoire de Biochimie Théorique, UPR 9080 CNRS, Institut de Biologie Physico-Chimique , 13 rue Pierre et Marie Curie, 75005 Paris, France
| | - Joel Eyer
- Laboratoire de Neurobiologie & Transgenèse, UPRES EA 3143, INSERM, Centre Hospitalier Universitaire , Angers, France
| | - Charles H Robert
- Laboratoire de Biochimie Théorique, UPR 9080 CNRS, Institut de Biologie Physico-Chimique , 13 rue Pierre et Marie Curie, 75005 Paris, France
| | - Chantal Prevost
- Laboratoire de Biochimie Théorique, UPR 9080 CNRS, Institut de Biologie Physico-Chimique , 13 rue Pierre et Marie Curie, 75005 Paris, France
| | - Sophie Sacquin-Mora
- Laboratoire de Biochimie Théorique, UPR 9080 CNRS, Institut de Biologie Physico-Chimique , 13 rue Pierre et Marie Curie, 75005 Paris, France
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32
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Rai A, Kapoor S, Naaz A, Kumar Santra M, Panda D. Enhanced stability of microtubules contributes in the development of colchicine resistance in MCF-7 cells. Biochem Pharmacol 2017; 132:38-47. [PMID: 28242250 DOI: 10.1016/j.bcp.2017.02.018] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2016] [Accepted: 02/22/2017] [Indexed: 10/20/2022]
Abstract
Understanding the mechanism of resistance to tubulin-targeted anticancer drugs is important for improved chemotherapy. In this work, a colchicine-resistant MCF-7 cell line (MCF-7Col30) was generated by the gradual increment of colchicine treatment and the MCF-7Col30 showed ∼8-fold resistance towards colchicine. MCF-7Col30 cells showed ∼2.5-fold resistance against microtubule depolymerizing agents, vinblastine, and nocodazole. In contrast, it displayed more sensitivity towards paclitaxel, a microtubule-polymerizing agent. MCF-7 and MCF-7Col30 cells showed similar sensitivity towards cisplatin. Further, the level of P-glycoprotein did not increase in MCF-7Col30 cells. MCF-7Col30 cells resisted the microtubule depolymerizing effects of colchicine. The time-lapse imaging of individual microtubules in live cells showed that the dynamics of microtubules in MCF-7Col30 cells was suppressed as compared to the parent MCF-7 cells. The levels of tubulin acetylation and glutamylation increased in MCF-7Col30 cells than the parent MCF-7 cells suggesting that microtubules are stabilized in MCF-7Col30 cells. Interestingly, the level of βIII tubulin was increased by 2.3 folds whereas that of βII and βIV tubulin was decreased by 55 and 150%, respectively in MCF-7Col30 cells. The results suggested that the changes in the level of β-tubulin isoforms and the post-translational modifications of microtubules altered the stability and dynamics of microtubules and contributed to the development of colchicine-resistance in MCF-7 cells.
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Affiliation(s)
- Ankit Rai
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, Maharashtra 400076, India
| | - Sonia Kapoor
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, Maharashtra 400076, India
| | - Afsana Naaz
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, Maharashtra 400076, India
| | - Manas Kumar Santra
- National Centre for Cell Science, University of Pune Campus, Ganeshkhind, Pune, Maharashtra 411007, India
| | - Dulal Panda
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, Maharashtra 400076, India.
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33
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Aguayo-Ortiz R, Cano-González L, Castillo R, Hernández-Campos A, Dominguez L. Structure-based approaches for the design of benzimidazole-2-carbamate derivatives as tubulin polymerization inhibitors. Chem Biol Drug Des 2017; 90:40-51. [PMID: 28004475 DOI: 10.1111/cbdd.12926] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2016] [Revised: 11/30/2016] [Accepted: 12/13/2016] [Indexed: 12/23/2022]
Abstract
Microtubules are highly dynamic assemblies of α/β-tubulin heterodimers whose polymerization inhibition is among one of the most successful approaches for anticancer drug development. Overexpression of the class I (βI) and class III (βIII) β-tubulin isotypes in breast and lung cancers and the highly expressed class VI (βVI) β-tubulin isotype in normal blood cells have increased the interest for designing specific tubulin-binding anticancer therapies. To this end, we employed our previously proposed model of the β-tubulin-nocodazole complex, supported by the recently determined X-ray structure, to identify the fundamental structural differences between β-tubulin isotypes. Moreover, we employed docking and molecular dynamics (MD) simulations to determine the binding mode of a series of benzimidazole-2-carbamete (BzC) derivatives in the βI-, βIII-, and βVI-tubulin isotypes. Our results demonstrate that Ala198 in the βVI isotype reduces the affinity of BzCs, explaining the low bone marrow toxicity for nocodazole. Additionally, no significant differences in the binding modes between βI- and βIII-BzC complexes were observed; however, Ser239 in the βIII isotype might be associated with the low affinity of BzCs to this isotype. Finally, our study provides insight into the β-tubulin-BzC interaction features essential for the development of more selective and less toxic anticancer therapeutics.
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Affiliation(s)
- Rodrigo Aguayo-Ortiz
- Facultad de Química, Departamento de Farmacia, Universidad Nacional Autónoma de México, CDMX, México, Mexico.,Facultad de Química, Departamento de Fisicoquímica, Universidad Nacional Autónoma de México, CDMX, México, Mexico
| | - Lucia Cano-González
- Facultad de Química, Departamento de Farmacia, Universidad Nacional Autónoma de México, CDMX, México, Mexico
| | - Rafael Castillo
- Facultad de Química, Departamento de Farmacia, Universidad Nacional Autónoma de México, CDMX, México, Mexico
| | - Alicia Hernández-Campos
- Facultad de Química, Departamento de Farmacia, Universidad Nacional Autónoma de México, CDMX, México, Mexico
| | - Laura Dominguez
- Facultad de Química, Departamento de Fisicoquímica, Universidad Nacional Autónoma de México, CDMX, México, Mexico
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34
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Pradhan M, Suri C, Choudhary S, Naik PK, Lopus M. Elucidation of the anticancer potential and tubulin isotype-specific interactions of β-sitosterol. J Biomol Struct Dyn 2016; 36:195-208. [DOI: 10.1080/07391102.2016.1271749] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Affiliation(s)
- Madhura Pradhan
- Experimental Cancer Therapeutics and Chemical Biology, UM-DAE Centre for Excellence in Basic Sciences, University of Mumbai Kalina Campus, Santacruz (E), Mumbai 400098, India
| | - Charu Suri
- Biotechnology and Bioinformatics, Jaypee University of Information Technology, Waknaghat, Solan 173234, Himachal Pradesh, India
| | - Sinjan Choudhary
- Experimental Cancer Therapeutics and Chemical Biology, UM-DAE Centre for Excellence in Basic Sciences, University of Mumbai Kalina Campus, Santacruz (E), Mumbai 400098, India
| | - Pradeep Kumar Naik
- School of Life Sciences, Sambalpur University, Jyoti Vihar, Sambalpur 768019, Odisha, India
| | - Manu Lopus
- Experimental Cancer Therapeutics and Chemical Biology, UM-DAE Centre for Excellence in Basic Sciences, University of Mumbai Kalina Campus, Santacruz (E), Mumbai 400098, India
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