1
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Menchon G, Maveyraud L, Czaplicki G. Molecular Dynamics as a Tool for Virtual Ligand Screening. Methods Mol Biol 2024; 2714:33-83. [PMID: 37676592 DOI: 10.1007/978-1-0716-3441-7_3] [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] [Indexed: 09/08/2023]
Abstract
Rational drug design is essential for new drugs to emerge, especially when the structure of a target protein or nucleic acid is known. To that purpose, high-throughput virtual ligand screening campaigns aim at discovering computationally new binding molecules or fragments to modulate particular biomolecular interactions or biological activities, related to a disease process. The structure-based virtual ligand screening process primarily relies on docking methods which allow predicting the binding of a molecule to a biological target structure with a correct conformation and the best possible affinity. The docking method itself is not sufficient as it suffers from several and crucial limitations (lack of full protein flexibility information, no solvation and ion effects, poor scoring functions, and unreliable molecular affinity estimation).At the interface of computer techniques and drug discovery, molecular dynamics (MD) allows introducing protein flexibility before or after a docking protocol, refining the structure of protein-drug complexes in the presence of water, ions, and even in membrane-like environments, describing more precisely the temporal evolution of the biological complex and ranking these complexes with more accurate binding energy calculations. In this chapter, we describe the up-to-date MD, which plays the role of supporting tools in the virtual ligand screening (VS) process.Without a doubt, using docking in combination with MD is an attractive approach in structure-based drug discovery protocols nowadays. It has proved its efficiency through many examples in the literature and is a powerful method to significantly reduce the amount of required wet experimentations (Tarcsay et al, J Chem Inf Model 53:2990-2999, 2013; Barakat et al, PLoS One 7:e51329, 2012; De Vivo et al, J Med Chem 59:4035-4061, 2016; Durrant, McCammon, BMC Biol 9:71-79, 2011; Galeazzi, Curr Comput Aided Drug Des 5:225-240, 2009; Hospital et al, Adv Appl Bioinforma Chem 8:37-47, 2015; Jiang et al, Molecules 20:12769-12786, 2015; Kundu et al, J Mol Graph Model 61:160-174, 2015; Mirza et al, J Mol Graph Model 66:99-107, 2016; Moroy et al, Future Med Chem 7:2317-2331, 2015; Naresh et al, J Mol Graph Model 61:272-280, 2015; Nichols et al, J Chem Inf Model 51:1439-1446, 2011; Nichols et al, Methods Mol Biol 819:93-103, 2012; Okimoto et al, PLoS Comput Biol 5:e1000528, 2009; Rodriguez-Bussey et al, Biopolymers 105:35-42, 2016; Sliwoski et al, Pharmacol Rev 66:334-395, 2014).
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Affiliation(s)
- Grégory Menchon
- Inserm U1242, Oncogenesis, Stress and Signaling (OSS), Université de Rennes 1, Rennes, France
| | - Laurent Maveyraud
- Institut de Pharmacologie et de Biologie Structurale (IPBS), Université de Toulouse, CNRS, Université Toulouse III - Paul Sabatier (UT3), Toulouse, France
| | - Georges Czaplicki
- Institut de Pharmacologie et de Biologie Structurale (IPBS), Université de Toulouse, CNRS, Université Toulouse III - Paul Sabatier (UT3), Toulouse, France.
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2
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Microtubule nucleation by γ-tubulin complexes and beyond. Essays Biochem 2018; 62:765-780. [PMID: 30315097 PMCID: PMC6281477 DOI: 10.1042/ebc20180028] [Citation(s) in RCA: 75] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2018] [Revised: 09/05/2018] [Accepted: 09/13/2018] [Indexed: 12/21/2022]
Abstract
In this short review, we give an overview of microtubule nucleation within cells. It is nearly 30 years since the discovery of γ-tubulin, a member of the tubulin superfamily essential for proper microtubule nucleation in all eukaryotes. γ-tubulin associates with other proteins to form multiprotein γ-tubulin ring complexes (γ-TuRCs) that template and catalyse the otherwise kinetically unfavourable assembly of microtubule filaments. These filaments can be dynamic or stable and they perform diverse functions, such as chromosome separation during mitosis and intracellular transport in neurons. The field has come a long way in understanding γ-TuRC biology but several important and unanswered questions remain, and we are still far from understanding the regulation of microtubule nucleation in a multicellular context. Here, we review the current literature on γ-TuRC assembly, recruitment, and activation and discuss the potential importance of γ-TuRC heterogeneity, the role of non-γ-TuRC proteins in microtubule nucleation, and whether γ-TuRCs could serve as good drug targets for cancer therapy.
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3
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Cong H, Zhao X, Castle BT, Pomeroy EJ, Zhou B, Lee J, Wang Y, Bian T, Miao Z, Zhang W, Sham YY, Odde DJ, Eckfeldt CE, Xing C, Zhuang C. An Indole-Chalcone Inhibits Multidrug-Resistant Cancer Cell Growth by Targeting Microtubules. Mol Pharm 2018; 15:3892-3900. [PMID: 30048137 DOI: 10.1021/acs.molpharmaceut.8b00359] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Multidrug resistance and toxic side effects are the major challenges in cancer treatment with microtubule-targeting agents (MTAs), and thus, there is an urgent clinical need for new therapies. Chalcone, a common simple scaffold found in many natural products, is widely used as a privileged structure in medicinal chemistry. We have previously validated tubulin as the anticancer target for chalcone derivatives. In this study, an α-methyl-substituted indole-chalcone (FC77) was synthesized and found to exhibit an excellent cytotoxicity against the NCI-60 cell lines (average concentration causing 50% growth inhibition = 6 nM). More importantly, several multidrug-resistant cancer cell lines showed no resistance to FC77, and the compound demonstrated good selective toxicity against cancer cells versus normal CD34+ blood progenitor cells. A further mechanistic study demonstrated that FC77 could arrest cells that relate to the binding to tubulin and inhibit the microtubule dynamics. The National Cancer Institute COMPARE analysis and molecular modeling indicated that FC77 had a mechanism of action similar to that of colchicine. Overall, our data demonstrate that this indole-chalcone represents a novel MTA template for further development of potential drug candidates for the treatment of multidrug-resistant cancers.
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Affiliation(s)
- Hui Cong
- School of Pharmacy , Ningxia Medical University , Yinchuan , China
| | - Xinghua Zhao
- Department of Medicinal Chemistry , University of Minnesota , Minneapolis , Minnesota 55455 , United States.,College of Veterinary Medicine , Hebei Agricultural University , Baoding , China
| | - Brian T Castle
- Department of Biomedical Engineering , University of Minnesota , Minneapolis , Minnesota 55455 , United States
| | - Emily J Pomeroy
- Department of Medicine, Division of Hematology, Oncology, and Transplantation , University of Minnesota , Minneapolis , Minnesota 55455 , United States
| | - Bo Zhou
- Department of Medicinal Chemistry , University of Minnesota , Minneapolis , Minnesota 55455 , United States
| | - John Lee
- Department of Biochemistry, Molecular Biology and Biophysics , University of Minnesota , Minneapolis , Minnesota 55455 , United States
| | - Yi Wang
- Department of Medicinal Chemistry , University of Florida , Gainesville , Florida 32611 , United States
| | - Tengfei Bian
- Department of Medicinal Chemistry , University of Florida , Gainesville , Florida 32611 , United States
| | - Zhenyuan Miao
- School of Pharmacy , Second Military Medical University , Shanghai , China
| | - Wannian Zhang
- School of Pharmacy , Ningxia Medical University , Yinchuan , China.,School of Pharmacy , Second Military Medical University , Shanghai , China
| | - Yuk Yin Sham
- Department of Integrative Biology and Physiology , University of Minnesota , Minneapolis , Minnesota 55455 , United States
| | - David J Odde
- Department of Biomedical Engineering , University of Minnesota , Minneapolis , Minnesota 55455 , United States
| | - Craig E Eckfeldt
- Department of Medicine, Division of Hematology, Oncology, and Transplantation , University of Minnesota , Minneapolis , Minnesota 55455 , United States
| | - Chengguo Xing
- School of Pharmacy , Ningxia Medical University , Yinchuan , China.,Department of Medicinal Chemistry , University of Minnesota , Minneapolis , Minnesota 55455 , United States.,Department of Medicinal Chemistry , University of Florida , Gainesville , Florida 32611 , United States
| | - Chunlin Zhuang
- School of Pharmacy , Ningxia Medical University , Yinchuan , China.,School of Pharmacy , Second Military Medical University , Shanghai , China
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4
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Gervais V, Muller I, Mari PO, Mourcet A, Movellan KT, Ramos P, Marcoux J, Guillet V, Javaid S, Burlet-Schiltz O, Czaplicki G, Milon A, Giglia-Mari G. Small molecule-based targeting of TTD-A dimerization to control TFIIH transcriptional activity represents a potential strategy for anticancer therapy. J Biol Chem 2018; 293:14974-14988. [PMID: 30068551 DOI: 10.1074/jbc.ra118.003444] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2018] [Revised: 07/25/2018] [Indexed: 11/06/2022] Open
Abstract
The human transcription factor TFIIH is a large complex composed of 10 subunits that form an intricate network of protein-protein interactions critical for regulating its transcriptional and DNA repair activities. The trichothiodystrophy group A protein (TTD-A or p8) is the smallest TFIIH subunit, shuttling between a free and a TFIIH-bound state. Its dimerization properties allow it to shift from a homodimeric state, in the absence of a functional partner, to a heterodimeric structure, enabling dynamic binding to TFIIH. Recruitment of p8 at TFIIH stabilizes the overall architecture of the complex, whereas p8's absence reduces its cellular steady-state concentration and consequently decreases basal transcription, highlighting that p8 dimerization may be an attractive target for down-regulating transcription in cancer cells. Here, using a combination of molecular dynamics simulations to study p8 conformational stability and a >3000-member library of chemical fragments, we identified small-molecule compounds that bind to the dimerization interface of p8 and provoke its destabilization, as assessed by biophysical studies. Using quantitative imaging of TFIIH in living mouse cells, we found that these molecules reduce the intracellular concentration of TFIIH and its transcriptional activity to levels similar to that observed in individuals with trichothiodystrophy owing to mutated TTD-A Our results provide a proof of concept of fragment-based drug discovery, demonstrating the utility of small molecules for targeting p8 dimerization to modulate the transcriptional machinery, an approach that may help inform further development in anticancer therapies.
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Affiliation(s)
- Virginie Gervais
- From the Institut de Pharmacologie et de Biologie Structurale, IPBS, Université de Toulouse, CNRS, Université Paul Sabatier, BP-64182, F-31077 Toulouse, France,
| | - Isabelle Muller
- From the Institut de Pharmacologie et de Biologie Structurale, IPBS, Université de Toulouse, CNRS, Université Paul Sabatier, BP-64182, F-31077 Toulouse, France
| | - Pierre-Olivier Mari
- the Université Claude Bernard Lyon 1, INSERM U1217, Institut NeuroMyoGène, CNRS UMR 5310, F-69008 Lyon, France, and
| | - Amandine Mourcet
- From the Institut de Pharmacologie et de Biologie Structurale, IPBS, Université de Toulouse, CNRS, Université Paul Sabatier, BP-64182, F-31077 Toulouse, France
| | - Kumar Tekwani Movellan
- From the Institut de Pharmacologie et de Biologie Structurale, IPBS, Université de Toulouse, CNRS, Université Paul Sabatier, BP-64182, F-31077 Toulouse, France
| | - Pascal Ramos
- From the Institut de Pharmacologie et de Biologie Structurale, IPBS, Université de Toulouse, CNRS, Université Paul Sabatier, BP-64182, F-31077 Toulouse, France
| | - Julien Marcoux
- From the Institut de Pharmacologie et de Biologie Structurale, IPBS, Université de Toulouse, CNRS, Université Paul Sabatier, BP-64182, F-31077 Toulouse, France
| | - Valérie Guillet
- From the Institut de Pharmacologie et de Biologie Structurale, IPBS, Université de Toulouse, CNRS, Université Paul Sabatier, BP-64182, F-31077 Toulouse, France
| | - Sumaira Javaid
- From the Institut de Pharmacologie et de Biologie Structurale, IPBS, Université de Toulouse, CNRS, Université Paul Sabatier, BP-64182, F-31077 Toulouse, France.,the Dr. Panjwani Center for Molecular Medicine and Drug Research, International Center of Chemical and Biological Sciences, University of Karachi, Karachi-75270, Pakistan
| | - Odile Burlet-Schiltz
- From the Institut de Pharmacologie et de Biologie Structurale, IPBS, Université de Toulouse, CNRS, Université Paul Sabatier, BP-64182, F-31077 Toulouse, France
| | - Georges Czaplicki
- From the Institut de Pharmacologie et de Biologie Structurale, IPBS, Université de Toulouse, CNRS, Université Paul Sabatier, BP-64182, F-31077 Toulouse, France
| | - Alain Milon
- From the Institut de Pharmacologie et de Biologie Structurale, IPBS, Université de Toulouse, CNRS, Université Paul Sabatier, BP-64182, F-31077 Toulouse, France
| | - Giuseppina Giglia-Mari
- the Université Claude Bernard Lyon 1, INSERM U1217, Institut NeuroMyoGène, CNRS UMR 5310, F-69008 Lyon, France, and
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5
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Tovey CA, Tubman CE, Hamrud E, Zhu Z, Dyas AE, Butterfield AN, Fyfe A, Johnson E, Conduit PT. γ-TuRC Heterogeneity Revealed by Analysis of Mozart1. Curr Biol 2018; 28:2314-2323.e6. [PMID: 29983314 PMCID: PMC6065531 DOI: 10.1016/j.cub.2018.05.044] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2017] [Revised: 04/06/2018] [Accepted: 05/16/2018] [Indexed: 12/13/2022]
Abstract
Microtubules are essential for various cell processes [1] and are nucleated by multi-protein γ-tubulin ring complexes (γ-TuRCs) at various microtubule organizing centers (MTOCs), including centrosomes [2-6]. Recruitment of γ-TuRCs to different MTOCs at different times influences microtubule array formation, but how this is regulated remains an open question. It also remains unclear whether all γ-TuRCs within the same organism have the same composition and how any potential heterogeneity might influence γ-TuRC recruitment. MOZART1 (Mzt1) was recently identified as a γ-TuRC component [7, 8] and is conserved in nearly all eukaryotes [6, 9]. Mzt1 has so far been studied in cultured human cells, yeast, and plants; its absence leads to failures in γ-TuRC recruitment and cell division, resulting in cell death [7, 9-15]. Mzt1 is small (∼8.5 kDa), binds directly to core γ-TuRC components [9, 10, 14, 15], and appears to mediate the interaction between γ-TuRCs and proteins that tether γ-TuRCs to MTOCs [9, 15]. Here, we use Drosophila to investigate the function of Mzt1 in a multicellular animal for the first time. Surprisingly, we find that Drosophila Mzt1 is expressed only in the testes and is present in γ-TuRCs recruited to basal bodies, but not to mitochondria, in developing sperm cells. mzt1 mutants are viable but have defects in basal body positioning and γ-TuRC recruitment to centriole adjuncts; sperm formation is affected and mutants display a rapid age-dependent decline in sperm motility and male fertility. Our results reveal that tissue-specific and MTOC-specific γ-TuRC heterogeneity exist in Drosophila and highlight the complexity of γ-TuRC recruitment in a multicellular animal.
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Affiliation(s)
- Corinne A Tovey
- Department of Zoology, University of Cambridge, Downing Street, Cambridge CB2 3EJ, UK
| | - Chloe E Tubman
- Department of Zoology, University of Cambridge, Downing Street, Cambridge CB2 3EJ, UK
| | - Eva Hamrud
- Department of Zoology, University of Cambridge, Downing Street, Cambridge CB2 3EJ, UK
| | - Zihan Zhu
- Department of Zoology, University of Cambridge, Downing Street, Cambridge CB2 3EJ, UK
| | - Anna E Dyas
- Department of Zoology, University of Cambridge, Downing Street, Cambridge CB2 3EJ, UK
| | - Andrew N Butterfield
- Department of Zoology, University of Cambridge, Downing Street, Cambridge CB2 3EJ, UK
| | - Alex Fyfe
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, UK
| | - Errin Johnson
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, UK
| | - Paul T Conduit
- Department of Zoology, University of Cambridge, Downing Street, Cambridge CB2 3EJ, UK.
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6
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Menchon G, Maveyraud L, Czaplicki G. Molecular Dynamics as a Tool for Virtual Ligand Screening. Methods Mol Biol 2018; 1762:145-178. [PMID: 29594772 DOI: 10.1007/978-1-4939-7756-7_9] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Rational drug design is essential for new drugs to emerge, especially when the structure of a target protein or catalytic enzyme is known experimentally. To that purpose, high-throughput virtual ligand screening campaigns aim at discovering computationally new binding molecules or fragments to inhibit a particular protein interaction or biological activity. The virtual ligand screening process often relies on docking methods which allow predicting the binding of a molecule into a biological target structure with a correct conformation and the best possible affinity. The docking method itself is not sufficient as it suffers from several and crucial limitations (lack of protein flexibility information, no solvation effects, poor scoring functions, and unreliable molecular affinity estimation).At the interface of computer techniques and drug discovery, molecular dynamics (MD) allows introducing protein flexibility before or after a docking protocol, refining the structure of protein-drug complexes in the presence of water, ions and even in membrane-like environments, and ranking complexes with more accurate binding energy calculations. In this chapter we describe the up-to-date MD protocols that are mandatory supporting tools in the virtual ligand screening (VS) process. Using docking in combination with MD is one of the best computer-aided drug design protocols nowadays. It has proved its efficiency through many examples, described below.
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Affiliation(s)
- Grégory Menchon
- Laboratory of Biomolecular Research, Paul Scherrer Institute, Villigen PSI, Switzerland
| | - Laurent Maveyraud
- Institute of Pharmacology and Structural Biology, UMR 5089, University of Toulouse III, Toulouse, France
| | - Georges Czaplicki
- Institute of Pharmacology and Structural Biology, UMR 5089, University of Toulouse III, Toulouse, France.
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7
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Farache D, Jauneau A, Chemin C, Chartrain M, Rémy MH, Merdes A, Haren L. Functional Analysis of γ-Tubulin Complex Proteins Indicates Specific Lateral Association via Their N-terminal Domains. J Biol Chem 2016; 291:23112-23125. [PMID: 27660388 DOI: 10.1074/jbc.m116.744862] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2016] [Indexed: 11/06/2022] Open
Abstract
Microtubules are nucleated from multiprotein complexes containing γ-tubulin and associated γ-tubulin complex proteins (GCPs). Small complexes (γTuSCs) comprise two molecules of γ-tubulin bound to the C-terminal domains of GCP2 and GCP3. γTuSCs associate laterally into helical structures, providing a structural template for microtubule nucleation. In most eukaryotes γTuSCs associate with additional GCPs (4, 5, and 6) to form the core of the so-called γ-tubulin ring complex (γTuRC). GCPs 2-6 constitute a family of homologous proteins. Previous structural analysis and modeling of GCPs suggest that all family members can potentially integrate into the helical structure. Here we provide experimental evidence for this model. Using chimeric proteins in which the N- and C-terminal domains of different GCPs are swapped, we show that the N-terminal domains define the functional identity of GCPs, whereas the C-terminal domains are exchangeable. FLIM-FRET experiments indicate that GCP4 and GCP5 associate laterally within the complex, and their interaction is mediated by their N-terminal domains as previously shown for γTuSCs. Our results suggest that all GCPs are incorporated into the helix via lateral interactions between their N-terminal domains, whereas the C-terminal domains mediate longitudinal interactions with γ-tubulin. Moreover, we show that binding to γ-tubulin is not essential for integrating into the helical complex.
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Affiliation(s)
- Dorian Farache
- From the Centre de Biologie du Développement, CNRS-Université Toulouse III, 31062 Toulouse, France and
| | - Alain Jauneau
- Plateforme Imagerie-Microscopie, FR 3450 Pôle de Biotechnologie Végétale, 31326 Castanet-Tolosan, France
| | - Cécile Chemin
- From the Centre de Biologie du Développement, CNRS-Université Toulouse III, 31062 Toulouse, France and
| | - Marine Chartrain
- From the Centre de Biologie du Développement, CNRS-Université Toulouse III, 31062 Toulouse, France and
| | - Marie-Hélène Rémy
- From the Centre de Biologie du Développement, CNRS-Université Toulouse III, 31062 Toulouse, France and
| | - Andreas Merdes
- From the Centre de Biologie du Développement, CNRS-Université Toulouse III, 31062 Toulouse, France and
| | - Laurence Haren
- From the Centre de Biologie du Développement, CNRS-Université Toulouse III, 31062 Toulouse, France and
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8
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The C-terminal region of the transcriptional regulator THAP11 forms a parallel coiled-coil domain involved in protein dimerization. J Struct Biol 2016; 194:337-46. [DOI: 10.1016/j.jsb.2016.03.010] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2015] [Revised: 03/10/2016] [Accepted: 03/11/2016] [Indexed: 11/15/2022]
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9
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Overexpression and Nucleolar Localization of γ-Tubulin Small Complex Proteins GCP2 and GCP3 in Glioblastoma. J Neuropathol Exp Neurol 2015; 74:723-42. [PMID: 26079448 DOI: 10.1097/nen.0000000000000212] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
The expression, cellular distribution, and subcellular sorting of the microtubule (MT)-nucleating γ-tubulin small complex (γTuSC) proteins, GCP2 and GCP3, were studied in human glioblastoma cell lines and in clinical tissue samples representing all histologic grades of adult diffuse astrocytic gliomas (n = 54). Quantitative real-time polymerase chain reaction revealed a significant increase in the expression of GCP2 and GCP3 transcripts in glioblastoma cells versus normal human astrocytes; these were associated with higher amounts of both γTuSC proteins. GCP2 and GCP3 were concentrated in the centrosomes in interphase glioblastoma cells, but punctate and diffuse localizations were also detected in the cytosol and nuclei/nucleoli. Nucleolar localization was fixation dependent. GCP2 and GCP3 formed complexes with γ-tubulin in the nucleoli as confirmed by reciprocal immunoprecipitation experiments and immunoelectron microscopy. GCP2 and GCP3 depletion caused accumulation of cells in G2/M and mitotic delay but did not affect nucleolar integrity. Overexpression of GCP2 antagonized the inhibitory effect of the CDK5 regulatory subunit-associated tumor suppressor protein 3 (C53) on DNA damage G2/M checkpoint activity. Tumor cell GCP2 and GCP3 immunoreactivity was significantly increased over that in normal brains in glioblastoma samples; it was also associated with microvascular proliferation. These findings suggest that γTuSC protein dysregulation in glioblastomas may be linked to altered transcriptional checkpoint activity or interaction with signaling pathways associated with a malignant phenotype.
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Lindström L, Villoutreix BO, Lehn S, Hellsten R, Nilsson E, Crneta E, Olsson R, Alvarado-Kristensson M. Therapeutic Targeting of Nuclear γ-Tubulin in RB1-Negative Tumors. Mol Cancer Res 2015; 13:1073-82. [PMID: 25934692 DOI: 10.1158/1541-7786.mcr-15-0063-t] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2015] [Accepted: 03/28/2015] [Indexed: 11/16/2022]
Abstract
UNLABELLED In addition to its cytosolic function, γ-tubulin is a chromatin-associated protein. Reduced levels of nuclear γ-tubulin increase the activity of E2 promoter-binding factors (E2F) and raise the levels of retinoblastoma (RB1) tumor suppressor protein. In tumor cells lacking RB1 expression, decreased γ-tubulin levels induce cell death. Consequently, impairment of the nuclear activity of γ-tubulin has been suggested as a strategy for targeted chemotherapy of RB1-deficient tumors; thus, tubulin inhibitors were tested to identify compounds that interfere with γ-tubulin. Interestingly, citral increased E2F activity but impaired microtubule dynamics while citral analogues, such citral dimethyl acetal (CDA), increased E2F activity without affecting microtubules. The cytotoxic effect of CDA on tumor cells was attenuated by increased expression of either RB1 or γ-tubulin, and increased by reduced levels of either RB1 or γ-tubulin. Mechanistic study, in silico and in vitro, demonstrated that CDA prevents GTP binding to γ-tubulin and suggested that the FDA-approved drug dimethyl fumarate is also a γ-tubulin inhibitor. Finally, in vivo growth of xenograft tumors carrying defects in the RB1 signaling pathway were inhibited by CDA treatment. These results demonstrate that inhibition of γ-tubulin has the potential to specifically target tumor cells and may aid in the design of safer and more efficient chemotherapeutic regimes. IMPLICATIONS The in vivo antitumorigenic activity of γ-tubulin inhibitors paves the way for the development of a novel broad range targeted anticancer therapy that causes fewer side effects.
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Affiliation(s)
- Lisa Lindström
- Molecular Pathology, Department of Translational Medicine, Lund University, Skåne University Hospital, Malmö, Sweden
| | - Bruno O Villoutreix
- Université Paris Diderot, Sorbonne Paris Cité, UMRS 973 Inserm, Paris, France. Inserm, U973, Paris, France
| | - Sophie Lehn
- Molecular Pathology, Department of Translational Medicine, Lund University, Skåne University Hospital, Malmö, Sweden
| | - Rebecka Hellsten
- Division of Urological Cancers, Lund University, Skåne University Hospital, Malmö, Sweden
| | - Elise Nilsson
- Molecular Pathology, Department of Translational Medicine, Lund University, Skåne University Hospital, Malmö, Sweden
| | - Enisa Crneta
- Molecular Pathology, Department of Translational Medicine, Lund University, Skåne University Hospital, Malmö, Sweden
| | - Roger Olsson
- Chemical Biology and Therapeutics, Department of Experimental Medical Science, BMC, Lund University, Lund, Sweden
| | - Maria Alvarado-Kristensson
- Molecular Pathology, Department of Translational Medicine, Lund University, Skåne University Hospital, Malmö, Sweden.
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11
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Katsetos CD, Reginato MJ, Baas PW, D'Agostino L, Legido A, Tuszyn Ski JA, Dráberová E, Dráber P. Emerging microtubule targets in glioma therapy. Semin Pediatr Neurol 2015; 22:49-72. [PMID: 25976261 DOI: 10.1016/j.spen.2015.03.009] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Major advances in the genomics and epigenomics of diffuse gliomas and glioblastoma to date have not been translated into effective therapy, necessitating pursuit of alternative treatment approaches for these therapeutically challenging tumors. Current knowledge of microtubules in cancer and the development of new microtubule-based treatment strategies for high-grade gliomas are the topic in this review article. Discussed are cellular, molecular, and pharmacologic aspects of the microtubule cytoskeleton underlying mitosis and interactions with other cellular partners involved in cell cycle progression, directional cell migration, and tumor invasion. Special focus is placed on (1) the aberrant overexpression of βIII-tubulin, a survival factor associated with hypoxic tumor microenvironment and dynamic instability of microtubules; (2) the ectopic overexpression of γ-tubulin, which in addition to its conventional role as a microtubule-nucleating protein has recently emerged as a transcription factor interacting with oncogenes and kinases; (3) the microtubule-severing ATPase spastin and its emerging role in cell motility of glioblastoma cells; and (4) the modulating role of posttranslational modifications of tubulin in the context of interaction of microtubules with motor proteins. Specific antineoplastic strategies discussed include downregulation of targeted molecules aimed at achieving a sensitization effect on currently used mainstay therapies. The potential role of new classes of tubulin-binding agents and ATPase inhibitors is also examined. Understanding the cellular and molecular mechanisms underpinning the distinct behaviors of microtubules in glioma tumorigenesis and drug resistance is key to the discovery of novel molecular targets that will fundamentally change the prognostic outlook of patients with diffuse high-grade gliomas.
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Affiliation(s)
- Christos D Katsetos
- Department of Pediatrics, Drexel University College of Medicine, Section of Neurology and Pediatric Neuro-oncology Program, St Christopher's Hospital for Children, Philadelphia, PA; Department of Pathology and Laboratory Medicine, Drexel University College of Medicine, Philadelphia, PA.
| | - Mauricio J Reginato
- Department of Biochemistry and Molecular Biology, Drexel University College of Medicine, Philadelphia, PA
| | - Peter W Baas
- Department of Neurobiology and Anatomy, Drexel University College of Medicine, Philadelphia, PA
| | - Luca D'Agostino
- Department of Pediatrics, Drexel University College of Medicine, Section of Neurology and Pediatric Neuro-oncology Program, St Christopher's Hospital for Children, Philadelphia, PA
| | - Agustin Legido
- Department of Pediatrics, Drexel University College of Medicine, Section of Neurology and Pediatric Neuro-oncology Program, St Christopher's Hospital for Children, Philadelphia, PA
| | - Jack A Tuszyn Ski
- Department of Oncology, University of Alberta, Cross Cancer Institute, Edmonton, Alberta, Canada; Department of Physics, University of Alberta, Edmonton, Alberta, Canada
| | - Eduarda Dráberová
- Department of Biology of Cytoskeleton, Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, Prague, Czech Republic
| | - Pavel Dráber
- Department of Biology of Cytoskeleton, Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, Prague, Czech Republic
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Suri C, Joshi HC, Naik PK. Molecular modeling reveals binding interface of γ-tubulin with GCP4 and interactions with noscapinoids. Proteins 2015; 83:827-43. [DOI: 10.1002/prot.24773] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2014] [Revised: 01/15/2015] [Accepted: 01/28/2015] [Indexed: 11/06/2022]
Affiliation(s)
- Charu Suri
- Department of Biotechnology and Bioinformatics; Jaypee University of Information Technology; Waknaghat Solan 173234 Himachal Pradesh India
| | - Harish C. Joshi
- Department of Cell Biology; Emory University School of Medicine; Atlanta Georgia 30322
| | - Pradeep Kumar Naik
- Department of Biotechnology and Bioinformatics; Jaypee University of Information Technology; Waknaghat Solan 173234 Himachal Pradesh India
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Wang B, Buchman CD, Li L, Hurley TD, Meroueh SO. Enrichment of chemical libraries docked to protein conformational ensembles and application to aldehyde dehydrogenase 2. J Chem Inf Model 2014; 54:2105-16. [PMID: 24856086 PMCID: PMC4114474 DOI: 10.1021/ci5002026] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Molecular recognition is a complex process that involves a large ensemble of structures of the receptor and ligand. Yet, most structure-based virtual screening is carried out on a single structure typically from X-ray crystallography. Explicit-solvent molecular dynamics (MD) simulations offer an opportunity to sample multiple conformational states of a protein. Here we evaluate our recently developed scoring method SVMSP in its ability to enrich chemical libraries docked to MD structures of seven proteins from the Directory of Useful Decoys (DUD). SVMSP is a target-specific rescoring method that combines machine learning with statistical potentials. We find that enrichment power as measured by the area under the ROC curve (ROC-AUC) is not affected by increasing the number of MD structures. Among individual MD snapshots, many exhibited enrichment that was significantly better than the crystal structure, but no correlation between enrichment and structural deviation from crystal structure was found. We followed an innovative approach by training SVMSP scoring models using MD structures (SVMSPMD). The resulting models were applied to two difficult cases (p38 and CDK2) for which enrichment was not better than random. We found remarkable increase in enrichment power, particularly for p38, where the ROC-AUC increased by 0.30 to 0.85. Finally, we explored approaches for a priori identification of MD snapshots with high enrichment power from an MD simulation in the absence of active compounds. We found that the use of randomly selected compounds docked to the target of interest using SVMSP led to notable enrichment for EGFR and Src MD snapshots. SVMSP rescoring of protein-compound MD structures was applied for the search of small-molecule inhibitors of the mitochondrial enzyme aldehyde dehydrogenase 2 (ALDH2). Rank-ordering of a commercial library of 50 000 compounds docked to MD structures of ALDH2 led to five small-molecule inhibitors. Four compounds had IC50s below 5 μM. These compounds serve as leads for the design and synthesis of more potent and selective ALDH2 inhibitors.
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Affiliation(s)
- Bo Wang
- Department of Biochemistry and Molecular Biology, ‡Melvin and Bren Simon Cancer Center, §Center for Computational Biology and Bioinformatics, and ⊥Stark Neurosciences Institute, Indiana University School of Medicine , 535 Barnhill Drive, Indianapolis, Indiana 46202, United States
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