151
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Numerical Parameter Space Compression and Its Application to Biophysical Models. Biophys J 2020; 118:1455-1465. [PMID: 32070477 DOI: 10.1016/j.bpj.2020.01.023] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2019] [Revised: 12/07/2019] [Accepted: 01/14/2020] [Indexed: 11/20/2022] Open
Abstract
Physical models of biological systems can become difficult to interpret when they have a large number of parameters. But the models themselves actually depend on (i.e., are sensitive to) only a subset of those parameters. This phenomenon is due to parameter space compression (PSC), in which a subset of parameters emerges as "stiff" as a function of time or space. PSC has only been used to explain analytically solvable physics models. We have generalized this result by developing a numerical approach to PSC that can be applied to any computational model. We validated our method against analytically solvable models of a random walk with drift and protein production and degradation. We then applied our method to a simple computational model of microtubule dynamic instability. We propose that numerical PSC has the potential to identify the low-dimensional structure of many computational models in biophysics. The low-dimensional structure of a model is easier to interpret and identifies the mechanisms and experiments that best characterize the system.
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152
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Tobias LM, Spokevicius AV, McFarlane HE, Bossinger G. The Cytoskeleton and Its Role in Determining Cellulose Microfibril Angle in Secondary Cell Walls of Woody Tree Species. PLANTS (BASEL, SWITZERLAND) 2020; 9:E90. [PMID: 31936868 PMCID: PMC7020502 DOI: 10.3390/plants9010090] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Revised: 01/06/2020] [Accepted: 01/10/2020] [Indexed: 12/28/2022]
Abstract
Recent advances in our understanding of the molecular control of secondary cell wall (SCW) formation have shed light on molecular mechanisms that underpin domestication traits related to wood formation. One such trait is the cellulose microfibril angle (MFA), an important wood quality determinant that varies along tree developmental phases and in response to gravitational stimulus. The cytoskeleton, mainly composed of microtubules and actin filaments, collectively contribute to plant growth and development by participating in several cellular processes, including cellulose deposition. Studies in Arabidopsis have significantly aided our understanding of the roles of microtubules in xylem cell development during which correct SCW deposition and patterning are essential to provide structural support and allow for water transport. In contrast, studies relating to SCW formation in xylary elements performed in woody trees remain elusive. In combination, the data reviewed here suggest that the cytoskeleton plays important roles in determining the exact sites of cellulose deposition, overall SCW patterning and more specifically, the alignment and orientation of cellulose microfibrils. By relating the reviewed evidence to the process of wood formation, we present a model of microtubule participation in determining MFA in woody trees forming reaction wood (RW).
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Affiliation(s)
- Larissa Machado Tobias
- School of Ecosystem and Forest Sciences, The University of Melbourne, Creswick, Victoria 3363, Australia; (A.V.S.); (G.B.)
| | - Antanas V. Spokevicius
- School of Ecosystem and Forest Sciences, The University of Melbourne, Creswick, Victoria 3363, Australia; (A.V.S.); (G.B.)
| | - Heather E. McFarlane
- Department of Cell and Systems Biology, University of Toronto, Toronto, ON M5S 3B2, Canada
| | - Gerd Bossinger
- School of Ecosystem and Forest Sciences, The University of Melbourne, Creswick, Victoria 3363, Australia; (A.V.S.); (G.B.)
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153
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Structures of β-glycosidase LXYL-P1-2 reveals the product binding state of GH3 family and a specific pocket for Taxol recognition. Commun Biol 2020; 3:22. [PMID: 31925310 PMCID: PMC6954215 DOI: 10.1038/s42003-019-0744-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2019] [Accepted: 12/16/2019] [Indexed: 11/08/2022] Open
Abstract
LXYL-P1-2 is one of the few xylosidases that efficiently catalyze the reaction from 7-β-xylosyl-10-deacetyltaxol (XDT) to 10-deacetyltaxol (DT), and is a potential enzyme used in Taxol industrial production. Here we report the crystal structure of LXYL-P1-2 and its XDT binding complex. These structures reveal an enzyme/product complex with the sugar conformation different from the enzyme/substrate complex reported previously in GH3 enzymes, even in the whole glycohydrolases family. In addition, the DT binding pocket is identified as the structural basis for the substrate specificity. Further structure analysis reveals common features in LXYL-P1-2 and Taxol binding protein tubulin, which might provide useful information for designing new Taxol carrier proteins for drug delivery.
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154
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Guo Q, Luo Y, Zhai S, Jiang Z, Zhao C, Xu J, Wang L. Discovery, biological evaluation, structure-activity relationships and mechanism of action of pyrazolo[3,4-b]pyridin-6-one derivatives as a new class of anticancer agents. Org Biomol Chem 2020; 17:6201-6214. [PMID: 31179474 DOI: 10.1039/c9ob00616h] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
We have recently reported computational models for prediction of cell-based anticancer activity using machine learning methods. Herein, we have developed an integrated strategy to discover new anticancer agents using a cascade of the established screening models. Application of this strategy identified 17 compounds with antitumor activity. Among these compounds, h2 (containing a pyrazolo[3,4-b]pyridin-6-one scaffold) exhibited anticancer activity against six tumor cell lines, including MDA-MB-231, HeLa, MCF-7, HepG2, CNE2 and HCT116, with IC50 values of 13.37, 13.04, 15.45, 7.05, 9.30 and 8.93 μM. Subsequently, a total of 61 h2 analogues were obtained by similarity searching and tested for their anticancer activities. I2 was identified as a novel anticancer agent having activity against MDA-MB-231, HeLa, MCF-7, HepG2, CNE2 and HCT116 tumor cell lines with IC50 values of 3.30, 5.04, 5.08, 3.71, 2.99 and 5.72 μM. I2 also showed potent cytotoxicity against adriamycin-resistant human breast and hepatocarcinoma cells. Further investigation revealed that I2 inhibited the microtubule polymerization by binding to the colchicine site, resulting in inhibition of cell migration, cell cycle arrest in the G2/M phase and apoptosis of cancer cells. Finally, molecular docking and molecular dynamics provided insights into the binding interactions of I2 with tubulin. This study identified I2 as a novel starting point for further development of anticancer agents that target tubulin.
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Affiliation(s)
- Qingqing Guo
- Joint International Research Laboratory of Synthetic Biology and Medicine, Guangdong Provincial Engineering and Technology Research Center of Biopharmaceuticals, School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, China.
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155
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Tryptophan Improves Memory Independent of Its Role as a Serotonin Precursor: Potential Involvement of Microtubule Proteins. J Mol Neurosci 2020; 70:559-567. [DOI: 10.1007/s12031-019-01457-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2019] [Accepted: 11/28/2019] [Indexed: 12/17/2022]
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156
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Buschmann H, Borchers A. Handedness in plant cell expansion: a mutant perspective on helical growth. THE NEW PHYTOLOGIST 2020; 225:53-69. [PMID: 31254400 DOI: 10.1111/nph.16034] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2019] [Accepted: 06/04/2019] [Indexed: 06/09/2023]
Abstract
Many plant mutants are known that exhibit some degree of helical growth. This 'twisted' phenotype has arisen frequently in mutant screens of model organisms, but it is also found in cultivars of ornamental plants, including trees. The phenomenon, in many cases, is based on defects in cell expansion symmetry. Any complete model which explains the anisotropy of plant cell growth must ultimately explain how helical cell expansion comes into existence - and how it is normally avoided. While the mutations observed in model plants mainly point to the microtubule system, additional affected components involve cell wall functions, auxin transport and more. Evaluation of published data suggests a two-way mechanism underlying the helical growth phenomenon: there is, apparently, a microtubular component that determines handedness, but there is also an influence arising in the cell wall that feeds back into the cytoplasm and affects cellular handedness. This idea is supported by recent reports demonstrating the involvement of the cell wall integrity pathway. In addition, there is mounting evidence that calcium is an important relayer of signals relating to the symmetry of cell expansion. These concepts suggest experimental approaches to untangle the phenomenon of helical cell expansion in plant mutants.
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Affiliation(s)
- Henrik Buschmann
- Botanical Institute, Biology and Chemistry Department, University of Osnabrück, 49076, Osnabrück, Germany
| | - Agnes Borchers
- Botanical Institute, Biology and Chemistry Department, University of Osnabrück, 49076, Osnabrück, Germany
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157
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Sarker SD, Nahar L, Miron A, Guo M. Anticancer natural products. ANNUAL REPORTS IN MEDICINAL CHEMISTRY 2020. [DOI: 10.1016/bs.armc.2020.02.001] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
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158
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Pietra F. Fighting cancer with microtubule-stabilizing agents: a computational investigation of the complex between β-tubulin and the microtubule-stabilizing, antitumor marine diterpenoid sarcodictyin A. Struct Chem 2019. [DOI: 10.1007/s11224-019-01440-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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159
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Wang C, Wang X, Sun Y, Taouil AK, Yan S, Botchkina GI, Ojima I. Design, synthesis and SAR study of 3rd-generation taxoids bearing 3-CH 3, 3-CF 3O and 3-CHF 2O groups at the C2-benzoate position. Bioorg Chem 2019; 95:103523. [PMID: 31911305 DOI: 10.1016/j.bioorg.2019.103523] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Revised: 12/18/2019] [Accepted: 12/18/2019] [Indexed: 12/11/2022]
Abstract
It has been shown that inclusion of CF3O and CHF2O groups to drug candidates often improve their pharmacological properties, especially metabolic stability, membrane permeability and PK profile. Moreover, the unique non-spherical structure of the OCHF2 group can provide interesting and beneficial characteristics. Accordingly, new 3rd-generation taxoids, bearing 3-OCF3 or 3-OCF2H (and 3-CH3 for comparison) at the C2 benzoate moiety, were synthesized and their potencies against drug-sensitive and drug-resistant cancer cell lines examined. In this study, our previous SAR studies on 3rd-generation taxoids were expanded to disclose that CH3, CF3O and CHF2O groups are well tolerated at this position and enhance potency, especially against MDR-cancer cell lines so that these taxoids can virtually overcome MDR. These new taxoids exhibit up to 7 times higher cytotoxicity (IC50) than paclitaxel against drug-sensitive cancer cell lines (MCF7 and LCC6-WT) and 2-3 orders of magnitude higher potency than paclitaxel against drug-resistant ovarian, breast and colon cancer cell lines with MDR-phenotype (NCI/ADR, LCC6-MDR and LDL-1), as well as pancreatic cancer cell line, CFPAC-1. Since it has been shown that a bulky group at this position reduces potency, it is noteworthy that rather bulky CF3O and CHF2O groups are well tolerated. Molecular modeling analysis indicated the favorable van der Waals interactions of CF3O and CHF2O groups in the binding site. It is also worthy of note that new taxoids, bearing a CHF2O group at the C2 benzoate position (1-06 series), exhibited the highest potencies against MDR-cancer cell lines and cancer stem cell (CSC)-enriched cancer cell lines. These new 3rd-generation taxoids are promising candidates for highly potent chemotherapeutic agents, as well as payloads for tumor-targeting drug conjugates such as antibody-drug conjugates (ADCs).
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Affiliation(s)
- Changwei Wang
- Department of Chemistry, Stony Brook University, Stony Brook, NY 11794-3400, USA; Institute of Chemical Biology and Drug Discovery, Stony Brook University, Stony Brook, NY 11794-3400, USA; Drug Discovery Pipeline, Guangzhou Institute of Biomedicine and Health, Chinese Academy of Science, Guangzhou 510530, China
| | - Xin Wang
- Department of Chemistry, Stony Brook University, Stony Brook, NY 11794-3400, USA; Institute of Chemical Biology and Drug Discovery, Stony Brook University, Stony Brook, NY 11794-3400, USA
| | - Yi Sun
- Department of Chemistry, Stony Brook University, Stony Brook, NY 11794-3400, USA; Institute of Chemical Biology and Drug Discovery, Stony Brook University, Stony Brook, NY 11794-3400, USA
| | - Adam K Taouil
- Department of Chemistry, Stony Brook University, Stony Brook, NY 11794-3400, USA
| | - Su Yan
- Department of Chemistry, Stony Brook University, Stony Brook, NY 11794-3400, USA; Institute of Chemical Biology and Drug Discovery, Stony Brook University, Stony Brook, NY 11794-3400, USA
| | - Galina I Botchkina
- Institute of Chemical Biology and Drug Discovery, Stony Brook University, Stony Brook, NY 11794-3400, USA; Department of Pathology, Renaissance School of Medicine, Stony Brook University, Stony Brook, NY 11794-3400, USA
| | - Iwao Ojima
- Department of Chemistry, Stony Brook University, Stony Brook, NY 11794-3400, USA; Institute of Chemical Biology and Drug Discovery, Stony Brook University, Stony Brook, NY 11794-3400, USA.
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160
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Safinya CR, Chung PJ, Song C, Li Y, Miller HP, Choi MC, Raviv U, Ewert KK, Wilson L, Feinstein SC. Minireview - Microtubules and Tubulin Oligomers: Shape Transitions and Assembly by Intrinsically Disordered Protein Tau and Cationic Biomolecules. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2019; 35:15970-15978. [PMID: 31539262 PMCID: PMC6988848 DOI: 10.1021/acs.langmuir.9b02208] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
In this minireview, which is part of a special issue in honor of Jacob N. Israelachvili's remarkable research career on intermolecular forces and interfacial science, we present studies of structures, phase behavior, and forces in reaction mixtures of microtubules (MTs) and tubulin oligomers with either intrinsically disordered protein (IDP) Tau, cationic vesicles, or the polyamine spermine (4+). Bare MTs consist of 13 protofilaments (PFs), on average, where each PF is made of a linear stack of αβ-tubulin dimers (i.e., tubulin oligomers). We begin with a series of experiments which demonstrate the flexibility of PFs toward shape changes in response to local environmental cues. First, studies show that MT-associated protein (MAP) Tau controls the diameter of microtubules upon binding to the outer surface, implying a shape change in the cross-sectional area of PFs forming the MT perimeter. The diameter of a MT may also be controlled by the charge density of a lipid bilayer membrane that coats the outer surface. We further describe an experimental study where it is unexpectedly found that the biologically relevant polyamine spermine (+4e) is able to depolymerize taxol-stabilized microtubules with efficiency that increases with decreasing temperature. This MT destabilization drives a dynamical structural transition where inside-out curving of PFs, during the depolymerization peeling process, is followed by reassembly of ring-like curved PF building blocks into an array of helical inverted tubulin tubules. We finally turn to a very recent study on pressure-distance measurements in bundles of MTs employing the small-angle X-ray scattering (SAXS)-osmotic pressure technique, which complements the surface-forces-apparatus technique developed by Jacob N. Israelachvili. These latter studies are among the very few which are beginning to shed light on the precise nature of the interactions between MTs mediated by MAP Tau in 37 °C reaction mixtures containing GTP and lacking taxol.
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Affiliation(s)
- Cyrus R. Safinya
- Materials Department, Physics Department, Molecular, Cellular, and Developmental Biology Department, University of California, Santa Barbara, California 93106, USA
| | - Peter J. Chung
- James Franck Institute and Department of Chemistry, University of Chicago, Illinois 60637, USA
| | - Chaeyeon Song
- Amorepacific Corporation R&D Center, Yongin 17074, Republic of Korea
| | - Youli Li
- Materials Research Laboratory, University of California, Santa Barbara, California 93106, USA
| | - Herbert P. Miller
- Neuroscience Research Institute and Molecular, Cellular, and Developmental Biology Department, University of California, Santa Barbara, California 93106, USA
| | - Myung Chul Choi
- Department of Bio and Brain Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 305-701, Republic of Korea
| | - Uri Raviv
- Institute of Chemistry and the Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, Jerusalem 9190401, Israel
| | - Kai K. Ewert
- Materials Department, Physics Department, Molecular, Cellular, and Developmental Biology Department, University of California, Santa Barbara, California 93106, USA
| | - Leslie Wilson
- Neuroscience Research Institute and Molecular, Cellular, and Developmental Biology Department, University of California, Santa Barbara, California 93106, USA
| | - Stuart C. Feinstein
- Neuroscience Research Institute and Molecular, Cellular, and Developmental Biology Department, University of California, Santa Barbara, California 93106, USA
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161
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Kumari N, Yadav S. Modulation of protein oligomerization: An overview. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2019; 149:99-113. [DOI: 10.1016/j.pbiomolbio.2019.03.003] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2018] [Revised: 03/05/2019] [Accepted: 03/06/2019] [Indexed: 12/21/2022]
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162
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Chattopadhyaya S, Chakravorty D, Basu G. A collective motion description of tubulin βT7 loop dynamics. Biophys Physicobiol 2019; 16:264-273. [PMID: 31984180 PMCID: PMC6976021 DOI: 10.2142/biophysico.16.0_264] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2019] [Accepted: 07/18/2019] [Indexed: 12/01/2022] Open
Abstract
Tubulin is a hetero-dimeric protein that polymerizes into microtubules and facilitates, among other things, eukaryotic cell division. Thus, any agent that interferes with tubulin polymerization is of therapeutic interest, vis-à-vis cancer. For example, colchicine is known to prevent tubulin polymerization by binding at the heterodimeric interface of αβ-tubulin. Crystal structures of tubulin bound to colchicine have shown that the dynamical conformation of a loop (βT7) plays an important role in colchicine binding. The βT7 loop dynamics also plays an important role in yielding curved versus straight αβ-tubulin dimers, only the latter being compatible with the microtubule assembly. Understanding the molecular mechanism of inhibition of microtubule assembly can lead to development of better therapeutic agents. In this work we were able to capture the βT7 loop flip by performing 200 ns molecular dynamics simulation of ligand-free αβ-tubulins. The loop flip could be described by only two independent collective vectors, obtained from principal component analysis. The first vector describes the flip while the second vector describes the trigger. The collective variables identified in this work is a natural reaction coordinate for functionally important tubulin dynamics, which allowed us to describe in detail the interaction network associated with the flip and the overall straight/curved conformational equilibrium.
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Affiliation(s)
| | | | - Gautam Basu
- Department of Biophysics, Bose Institute, VIIM, Kolkata 700054, India
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163
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Sachdeva T, Low ML, Mai C, Cheong SL, Liew YK, Milton MD. Design, Synthesis and Characterisation of Novel Phenothiazine‐Based Triazolopyridine Derivatives: Evaluation of Anti‐Breast Cancer Activity on Human Breast Carcinoma. ChemistrySelect 2019. [DOI: 10.1002/slct.201903203] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Affiliation(s)
| | - May Lee Low
- Department of Pharmaceutical ChemistrySchool of PharmacyInternational Medical University, No. 126 Jalan Jalil Perkasa 19, Bukit Jalil 57000 Kuala Lumpur Malaysia
| | - Chun‐Wai Mai
- Department of Pharmaceutical ChemistrySchool of PharmacyInternational Medical University, No. 126 Jalan Jalil Perkasa 19, Bukit Jalil 57000 Kuala Lumpur Malaysia
- Center for Cancer and Stem Cell ResearchInstitute for Research, Development and InnovationInternational Medical University, No. 126 Jalan Jalil Perkasa 19, Bukit Jalil 57000 Kuala Lumpur Malaysia
| | - Siew Lee Cheong
- Department of Pharmaceutical ChemistrySchool of PharmacyInternational Medical University, No. 126 Jalan Jalil Perkasa 19, Bukit Jalil 57000 Kuala Lumpur Malaysia
| | - Yun Khoon Liew
- Department of Life SciencesSchool of PharmacyInternational Medical University, No. 126, Jalan Jalil Perkasa 19, Bukit Jalil 57000 Kuala Lumpur Malaysia
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164
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Atherton J, Luo Y, Xiang S, Yang C, Rai A, Jiang K, Stangier M, Vemu A, Cook AD, Wang S, Roll-Mecak A, Steinmetz MO, Akhmanova A, Baldus M, Moores CA. Structural determinants of microtubule minus end preference in CAMSAP CKK domains. Nat Commun 2019; 10:5236. [PMID: 31748546 PMCID: PMC6868217 DOI: 10.1038/s41467-019-13247-6] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2019] [Accepted: 10/23/2019] [Indexed: 12/20/2022] Open
Abstract
CAMSAP/Patronins regulate microtubule minus-end dynamics. Their end specificity is mediated by their CKK domains, which we proposed recognise specific tubulin conformations found at minus ends. To critically test this idea, we compared the human CAMSAP1 CKK domain (HsCKK) with a CKK domain from Naegleria gruberi (NgCKK), which lacks minus-end specificity. Here we report near-atomic cryo-electron microscopy structures of HsCKK- and NgCKK-microtubule complexes, which show that these CKK domains share the same protein fold, bind at the intradimer interprotofilament tubulin junction, but exhibit different footprints on microtubules. NMR experiments show that both HsCKK and NgCKK are remarkably rigid. However, whereas NgCKK binding does not alter the microtubule architecture, HsCKK remodels its microtubule interaction site and changes the underlying polymer structure because the tubulin lattice conformation is not optimal for its binding. Thus, in contrast to many MAPs, the HsCKK domain can differentiate subtly specific tubulin conformations to enable microtubule minus-end recognition.
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Affiliation(s)
- Joseph Atherton
- Institute of Structural and Molecular Biology, Birkbeck, University of London, Malet Street, London, UK.
| | - Yanzhang Luo
- NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands
| | - Shengqi Xiang
- NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands
- MOE Key Lab for biomolecular Condensates & Cellular Dynamics, School of Life Sciences, University of Science and Technology of China, 96 Jinzhai Road, Hefei, 230026, Anhui, China
| | - Chao Yang
- Cell Biology, Department of Biology, Faculty of Science, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands
| | - Ankit Rai
- Cell Biology, Department of Biology, Faculty of Science, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands
| | - Kai Jiang
- Medical Research Institute, School of Medicine, Wuhan University, 430071, Wuhan, China
| | - Marcel Stangier
- Laboratory of Biomolecular Research, Division of Biology and Chemistry, Paul Scherrer Institut, Villigen, PSI, Switzerland
| | - Annapurna Vemu
- Cell Biology and Biophysics Unit, National Institute of Neurological Disorders and Stroke, Bethesda, MD, 20892, USA
| | - Alexander D Cook
- Institute of Structural and Molecular Biology, Birkbeck, University of London, Malet Street, London, UK
| | - Su Wang
- Institute of Structural and Molecular Biology, Birkbeck, University of London, Malet Street, London, UK
| | - Antonina Roll-Mecak
- Cell Biology and Biophysics Unit, National Institute of Neurological Disorders and Stroke, Bethesda, MD, 20892, USA
- Biophysics Center, National Heart, Lung and Blood Institute, Bethesda, MD, 20892, USA
| | - Michel O Steinmetz
- Laboratory of Biomolecular Research, Division of Biology and Chemistry, Paul Scherrer Institut, Villigen, PSI, Switzerland
- University of Basel, Biozentrum, CH-4056, Basel, Switzerland
| | - Anna Akhmanova
- Cell Biology, Department of Biology, Faculty of Science, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands
| | - Marc Baldus
- NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands.
| | - Carolyn A Moores
- Institute of Structural and Molecular Biology, Birkbeck, University of London, Malet Street, London, UK.
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165
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Aiken J, Buscaglia G, Aiken AS, Moore JK, Bates EA. Tubulin mutations in brain development disorders: Why haploinsufficiency does not explain TUBA1A tubulinopathies. Cytoskeleton (Hoboken) 2019; 77:40-54. [PMID: 31574570 DOI: 10.1002/cm.21567] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2019] [Revised: 09/09/2019] [Accepted: 09/17/2019] [Indexed: 12/12/2022]
Abstract
The neuronal cytoskeleton performs incredible feats during nervous system development. Extension of neuronal processes, migration, and synapse formation rely on the proper regulation of microtubules. Mutations that disrupt the primary α-tubulin expressed during brain development, TUBA1A, are associated with a spectrum of human brain malformations. One model posits that TUBA1A mutations lead to a reduction in tubulin subunits available for microtubule polymerization, which represents a haploinsufficiency mechanism. We propose an alternative model for the majority of tubulinopathy mutations, in which the mutant tubulin polymerizes into the microtubule lattice to dominantly "poison" microtubule function. Nine distinct α-tubulin and ten β-tubulin genes have been identified in the human genome. These genes encode similar tubulin proteins, called isotypes. Multiple tubulin isotypes may partially compensate for heterozygous deletion of a tubulin gene, but may not overcome the disruption caused by missense mutations that dominantly alter microtubule function. Here, we describe disorders attributed to haploinsufficiency versus dominant negative mechanisms to demonstrate the hallmark features of each disorder. We summarize literature on mouse models that represent both knockout and point mutants in tubulin genes, with an emphasis on how these mutations might provide insight into the nature of tubulinopathy patient mutations. Finally, we present data from a panel of TUBA1A tubulinopathy mutations generated in yeast α-tubulin that demonstrate that α-tubulin mutants can incorporate into the microtubule network and support viability of yeast growth. This perspective on tubulinopathy mutations draws on previous studies and additional data to provide a fresh perspective on how TUBA1A mutations disrupt neurodevelopment.
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Affiliation(s)
- Jayne Aiken
- Department of Cell and Developmental Biology, University of Colorado School of Medicine, Aurora, Colorado
| | - Georgia Buscaglia
- Department of Pediatrics, University of Colorado Anschutz Medical Campus, Aurora, Colorado
| | - A Sophie Aiken
- Department of Cell and Developmental Biology, University of Colorado School of Medicine, Aurora, Colorado
| | - Jeffrey K Moore
- Department of Cell and Developmental Biology, University of Colorado School of Medicine, Aurora, Colorado
| | - Emily A Bates
- Department of Pediatrics, University of Colorado Anschutz Medical Campus, Aurora, Colorado
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166
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Murphy BP, Tranel PJ. Target-Site Mutations Conferring Herbicide Resistance. PLANTS 2019; 8:plants8100382. [PMID: 31569336 PMCID: PMC6843678 DOI: 10.3390/plants8100382] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 09/04/2019] [Revised: 09/25/2019] [Accepted: 09/26/2019] [Indexed: 12/01/2022]
Abstract
Mutations conferring evolved herbicide resistance in weeds are known in nine different herbicide sites of action. This review summarizes recently reported resistance-conferring mutations for each of these nine target sites. One emerging trend is an increase in reports of multiple mutations, including multiple amino acid changes at the glyphosate target site, as well as mutations involving two nucleotide changes at a single amino acid codon. Standard reference sequences are suggested for target sites for which standards do not already exist. We also discuss experimental approaches for investigating cross-resistance patterns and for investigating fitness costs of specific target-site mutations.
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Affiliation(s)
- Brent P Murphy
- Department of Crop Sciences, University of Illinois, Urbana, IL 61801, USA.
| | - Patrick J Tranel
- Department of Crop Sciences, University of Illinois, Urbana, IL 61801, USA.
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167
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A high-performance haptic rendering system for virtual reality molecular modeling. ARTIFICIAL LIFE AND ROBOTICS 2019. [DOI: 10.1007/s10015-019-00555-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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168
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Reid TA, Coombes C, Mukherjee S, Goldblum RR, White K, Parmar S, McClellan M, Zanic M, Courtemanche N, Gardner MK. Structural state recognition facilitates tip tracking of EB1 at growing microtubule ends. eLife 2019; 8:48117. [PMID: 31478831 PMCID: PMC6742484 DOI: 10.7554/elife.48117] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2019] [Accepted: 08/23/2019] [Indexed: 11/13/2022] Open
Abstract
The microtubule binding protein EB1 specifically targets the growing ends of microtubules in cells, where EB1 facilitates the interactions of cellular proteins with microtubule plus-ends. Microtubule end targeting of EB1 has been attributed to high-affinity binding of EB1 to GTP-tubulin that is present at growing microtubule ends. However, our 3D single-molecule diffusion simulations predicted a ~ 6000% increase in EB1 arrivals to open, tapered microtubule tip structures relative to closed lattice conformations. Using quantitative fluorescence, single-molecule, and electron microscopy experiments, we found that the binding of EB1 onto opened, structurally disrupted microtubules was dramatically increased relative to closed, intact microtubules, regardless of hydrolysis state. Correspondingly, in cells, the blunting of growing microtubule plus-ends by Vinblastine was correlated with reduced EB1 targeting. Together, our results suggest that microtubule structural recognition, based on a fundamental diffusion-limited binding model, facilitates the tip tracking of EB1 at growing microtubule ends.
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Affiliation(s)
- Taylor A Reid
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, United States
| | - Courtney Coombes
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, United States
| | - Soumya Mukherjee
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, United States
| | - Rebecca R Goldblum
- Medical Scientist Training Program, University of Minnesota, Minneapolis, United States.,Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, United States
| | - Kyle White
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, United States
| | - Sneha Parmar
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, United States
| | - Mark McClellan
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, United States
| | - Marija Zanic
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, United States
| | - Naomi Courtemanche
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, United States
| | - Melissa K Gardner
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, United States
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169
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Sahakyan H, Abelyan N, Arakelov V, Arakelov G, Nazaryan K. In silico study of colchicine resistance molecular mechanisms caused by tubulin structural polymorphism. PLoS One 2019; 14:e0221532. [PMID: 31442266 PMCID: PMC6707608 DOI: 10.1371/journal.pone.0221532] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2019] [Accepted: 08/08/2019] [Indexed: 11/18/2022] Open
Abstract
Starting from 1972, colchicine is known as the most useful drug for prevention of familial Mediterranean fever attacks. However, some patients do not respond to colchicine treatment, even taken in high doses. Despite the fact, that different hypotheses have been proposed, the molecular mechanisms of colchicine resistance are not completely clear. It is generally known, that colchicine binds β-tubulin and inhibits microtubules polymerization. The β-tubulin gene has SNPs, which lead to amino acid substitutions, and some of them are located in colchicine binding site (CBS). We have assumed, that this SNPs can affect tubulin-colchicine interaction and might be the reason for colchicine resistance. With this in mind, we modeled 7 amino acid substitutions in CBS, performed molecular dynamics simulations of tubulin-colchicine complex and calculated binding energies for every amino acid substitution. Thus, our study shows, that two amino acid substitutions in the β-tubulin, namely A248T and M257V, reduce binding energy for approximately 2-fold. Based on this, we assume, that these amino acid substitutions could be the reason for colchicine resistance. Thus, our study gives a new insight into colchicine resistance mechanism and provides information for designing colchicine alternatives, that could be effective for colchicine resistant patients.
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Affiliation(s)
- Harutyun Sahakyan
- Department of Bioengineering, Bioinformatics and Molecular Biology, Russian-Armenian University, Yerevan, Armenia
| | - Narek Abelyan
- Department of Bioengineering, Bioinformatics and Molecular Biology, Russian-Armenian University, Yerevan, Armenia.,Laboratory of Computational Modeling of Biological Process, Institute of Molecular Biology, Yerevan, Armenia
| | - Vahram Arakelov
- Department of Bioengineering, Bioinformatics and Molecular Biology, Russian-Armenian University, Yerevan, Armenia.,Laboratory of Computational Modeling of Biological Process, Institute of Molecular Biology, Yerevan, Armenia
| | - Grigor Arakelov
- Department of Bioengineering, Bioinformatics and Molecular Biology, Russian-Armenian University, Yerevan, Armenia.,Laboratory of Computational Modeling of Biological Process, Institute of Molecular Biology, Yerevan, Armenia
| | - Karen Nazaryan
- Department of Bioengineering, Bioinformatics and Molecular Biology, Russian-Armenian University, Yerevan, Armenia.,Laboratory of Computational Modeling of Biological Process, Institute of Molecular Biology, Yerevan, Armenia
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170
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Hemmat M, Castle BT, Sachs JN, Odde DJ. Multiscale Computational Modeling of Tubulin-Tubulin Lateral Interaction. Biophys J 2019; 117:1234-1249. [PMID: 31493861 DOI: 10.1016/j.bpj.2019.08.011] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2019] [Revised: 07/26/2019] [Accepted: 08/13/2019] [Indexed: 10/26/2022] Open
Abstract
Microtubules are multistranded polymers in eukaryotic cells that support key cellular functions such as chromosome segregation, motor-based cargo transport, and maintenance of cell polarity. Microtubules self-assemble via "dynamic instability," in which the dynamic plus ends switch stochastically between alternating phases of polymerization and depolymerization. A key question in the field is what are the atomistic origins of this switching, i.e., what is different between the GTP- and GDP-tubulin states that enables microtubule growth and shortening, respectively? More generally, a major challenge in biology is how to connect theoretical frameworks across length- and timescales, from atoms to cellular behavior. In this study, we describe a multiscale model by linking atomistic molecular dynamics (MD), molecular Brownian dynamics (BD), and cellular-level thermokinetic modeling of microtubules. Here, we investigated the underlying interaction energy when tubulin dimers associate laterally by performing all-atom MD simulations. We found that the lateral potential energy is not significantly different among three nucleotide states of tubulin, GTP, GDP, and GMPCPP and is estimated to be ≅ -11 kBT. Furthermore, using MD potential energy in our BD simulations of tubulin dimers confirms that the lateral bond is weak on its own, with a mean lifetime of ∼0.1 μs, implying that the longitudinal bond is required for microtubule assembly. We conclude that nucleotide-dependent lateral-bond strength is not the key mediator microtubule dynamic instability, implying that GTP acts elsewhere to exert its stabilizing influence on microtubule polymer. Furthermore, the estimated lateral-bond strength (ΔGlat0≅ -5 kBT) is well-aligned with earlier estimates based on thermokinetic modeling and light microscopy measurements. Thus, we have computationally connected atomistic-level structural information, obtained by cryo-electron microscopy, to cellular-scale microtubule assembly dynamics using a combination of MD, BD, and thermokinetic models to bridge from Ångstroms to micrometers and from femtoseconds to minutes.
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Affiliation(s)
- Mahya Hemmat
- Department of Mechanical Engineering, University of Minnesota, Minneapolis, Minnesota
| | - Brian T Castle
- Department of Biomedical Engineering, University of Minnesota, Minneapolis, Minnesota
| | - Jonathan N Sachs
- Department of Biomedical Engineering, University of Minnesota, Minneapolis, Minnesota
| | - David J Odde
- Department of Biomedical Engineering, University of Minnesota, Minneapolis, Minnesota.
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171
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Molecular understanding of label-free second harmonic imaging of microtubules. Nat Commun 2019; 10:3530. [PMID: 31387998 PMCID: PMC6684603 DOI: 10.1038/s41467-019-11463-8] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2018] [Accepted: 07/03/2019] [Indexed: 11/30/2022] Open
Abstract
Microtubules are a vital component of the cell’s cytoskeleton and their organization is crucial for healthy cell functioning. The use of label-free SH imaging of microtubules remains limited, as sensitive detection is required and the true molecular origin and main determinants required to generate SH from microtubules are not fully understood. Using advanced correlative imaging techniques, we identified the determinants of the microtubule-dependent SH signal. Microtubule polarity, number and organization determine SH signal intensity in biological samples. At the molecular level, we show that the GTP-bound tubulin dimer conformation is fundamental for microtubules to generate detectable SH signals. We show that SH imaging can be used to study the effects of microtubule-targeting drugs and proteins and to detect changes in tubulin conformations during neuronal maturation. Our data provide a means to interpret and use SH imaging to monitor changes in the microtubule network in a label-free manner. Microtubules (MTs) are well-studied cytoskeleton components, but have primarily been investigated using fixation or invasive techniques. Here, the authors use label-free second harmonic (SH) fluorescence and correlative light electron microscopy to pinpoint determinants required for SH from MTs.
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172
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Synthesis of Pyrrolo[3,4- b]pyridin-5-ones via Multicomponent Reactions and In Vitro-In Silico Studies Against SiHa, HeLa, and CaSki Human Cervical Carcinoma Cell Lines. Molecules 2019; 24:molecules24142648. [PMID: 31336585 PMCID: PMC6680468 DOI: 10.3390/molecules24142648] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2019] [Revised: 07/08/2019] [Accepted: 07/18/2019] [Indexed: 12/29/2022] Open
Abstract
A series of 12 polysubstituted pyrrolo[3,4-b]pyridin-5-ones were synthesized via a one-pot cascade process (Ugi–3CR/aza Diels-Alder/N-acylation/decarboxylation/dehydration) and studied in vitro using human epithelial cervical carcinoma SiHa, HeLa, and CaSki cell line cultures. Three compounds of the series exhibited significative cytotoxicity against the three cell lines, with HeLa being the most sensitive one. Then, based on these results, in silico studies by docking techniques were performed using Paclitaxel as a reference and αβ-tubulin as the selected biological target. Worth highlighting is that strong hydrophobic interactions were observed between the three active molecules and the reference drug Paclitaxel, to the αβ-tubulin. In consequence, it was determined that hydrophobic–aromatic moieties of bioactive compounds and Paclitaxel play a key role in making stronger interactions to the ligand–target complex. A quantitative structure activity relationship (QSAR) study revealed that the six membered rings are the most significant molecular frameworks, being present in all proposed models for the in vitro-studied cell lines. Finally, also from the docking interpretation, a ligand-based pharmacophore model is proposed in order to find further potential polyheterocyclic candidates to bind stronger to the αβ-tubulin.
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173
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Tubulin response to intense nanosecond-scale electric field in molecular dynamics simulation. Sci Rep 2019; 9:10477. [PMID: 31324834 PMCID: PMC6642143 DOI: 10.1038/s41598-019-46636-4] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2019] [Accepted: 06/18/2019] [Indexed: 12/12/2022] Open
Abstract
Intense pulsed electric fields are known to act at the cell membrane level and are already being exploited in biomedical and biotechnological applications. However, it is not clear if electric pulses within biomedically-attainable parameters could directly influence intra-cellular components such as cytoskeletal proteins. If so, a molecular mechanism of action could be uncovered for therapeutic applications of such electric fields. To help clarify this question, we first identified that a tubulin heterodimer is a natural biological target for intense electric fields due to its exceptional electric properties and crucial roles played in cell division. Using molecular dynamics simulations, we then demonstrated that an intense - yet experimentally attainable - electric field of nanosecond duration can affect the bβ-tubulin’s C-terminus conformations and also influence local electrostatic properties at the GTPase as well as the binding sites of major tubulin drugs site. Our results suggest that intense nanosecond electric pulses could be used for physical modulation of microtubule dynamics. Since a nanosecond pulsed electric field can penetrate the tissues and cellular membranes due to its broadband spectrum, our results are also potentially significant for the development of new therapeutic protocols.
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174
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C SK, Gadewal N, Choudhary RK, Dasgupta D. Insights into the flexibility of the T3 loop and GTPase activating protein (GAP) domain of dimeric α and β tubulins from a molecular dynamics perspective. Comput Biol Chem 2019; 82:37-43. [PMID: 31255973 DOI: 10.1016/j.compbiolchem.2019.06.006] [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: 12/02/2017] [Revised: 03/09/2019] [Accepted: 06/12/2019] [Indexed: 10/26/2022]
Abstract
Tubulin protein is the fundamental unit of microtubules, and comprises of α and β subunits arranged in an alternate manner forming protofilaments. These longitudinal protofilaments are made up of intra- (α-β) and inter-dimer (β-α) interactions. Literature review confirms that GTP hydrolysis results in considerable structural rearrangement within GTP binding site of β-α dimer interface after the release of γ phosphate. In addition to this, the intra-dimer interface exhibits structural rigidity which needs further investigation. In this study, we explored the reasons for the flexibility and the rigidity of the β-α dimer and the α-β dimer respectively through molecular simulation and Anisotropic Normal Mode based analysis. As per the sequence alignment report, two glycine residues (Gly96 and Gly98) were observed in the T3 loop of the β subunit which get substituted by Asp98 and Ala100 in the T3 loop of the α subunit. The higher mobility of glycine residues contributes to the flexibility of the T3 loop of inter-dimer when they come in direct contact with the GTPase Activating Protein (GAP) domain of the subunit. This was confirmed through RMSD, RMSF and Radius of Gyration based studies. Conversely, the intra-dimer exhibited a lower mobility in the absence of glycine residues. As per ANM based analysis, positive domain correlations were observed between T3 loop and GAP domain of intra- and inter- dimeric contact regions. However, these correlation motions were higher in the intra-dimer as compared to the inter-dimer interface. Thus on the basis of our findings, we hypothesize that the higher flexibility of T3 loop and the GAP domain of the inter-dimer is required for structural rearrangement and protofilament stability during hydrolysis. Furthermore, the slightly rigid nature of the T3 loop and the GAP domain of the intra-dimer assists in enhancing the monomer-monomer interaction through the higher positive domain correlation.
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Affiliation(s)
- Selvaa Kumar C
- School of Biotechnology and Bioinformatics, D.Y. Patil Deemed to be University, CBD Belapur, Navi Mumbai, India.
| | - Nikhil Gadewal
- Advanced Centre for Treatment, Research and Education in Cancer (ACTREC), Kharghar, Navi Mumbai, India.
| | - Rajan Kumar Choudhary
- Advanced Centre for Treatment, Research and Education in Cancer (ACTREC), Kharghar, Navi Mumbai, India
| | - Debjani Dasgupta
- School of Biotechnology and Bioinformatics, D.Y. Patil Deemed to be University, CBD Belapur, Navi Mumbai, India
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175
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Acharya S, Maji M, Ruturaj, Purkait K, Gupta A, Mukherjee A. Synthesis, Structure, Stability, and Inhibition of Tubulin Polymerization by Ru II- p-Cymene Complexes of Trimethoxyaniline-Based Schiff Bases. Inorg Chem 2019; 58:9213-9224. [PMID: 31241921 DOI: 10.1021/acs.inorgchem.9b00853] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Four trimethoxy- and dimethoxyphenylamine-based Schiff base (L1-L4)-bearing RuII-p-cymene complexes (1-4) of the chemical formula [RuII(η6-p-cymene)(L)(Cl)] were synthesized, isolated in pure form, and structurally characterized using single-crystal X-ray diffraction and other analytical techniques. The complexes showed excellent in vitro antiproliferative activity against various forms of cancer that are difficult to cure, viz., triple negative human metastatic breast carcinoma MDA-MB-231, human pancreatic carcinoma MIA PaCa-2, and hepatocellular carcinoma Hep G2. The 1H nuclear magnetic resonance data in the presence of 10% dimethylformamide-d7 or dimethyl sulfoxide-d6 in phosphate buffer (pD 7.4, containing 4 mM NaCl) showed that the complexes immediately generate the aquated species that is stable for at least 24 h. Electrospray ionization mass spectrometry data showed that they do not bind with guanine nitrogen even in the presence of 5 molar equivalents of 9-EtG, during a period of 24 h. The best complex in the series, 1, exhibits an IC50 of approximately 10-15 μM in the panel of tested cancer cell lines. The complexes do not enhance the production of reactive oxygen species in the cells. Docking studies with a tubulin crystal structure (Protein Data Bank entry 1SAO ) revealed that 1 and 3 as well as L1 and L3 have a high affinity for the interface of the α and β tubulin dimer in the colchicine binding site. The immunofluorescence studies showed that 1 and 3 strongly inhibited microtubule network formation in MDA-MB-231 cells after treatment with an IC20 or IC50 dose for 12 h. The cell cycle analysis upon treatment with 1 showed that the complexes inhibit the mitotic phase because the arrest was observed in the G2/M phase. In summary, 1 and 3 are RuII half-sandwich complexes that are capable of disrupting a microtubule network in a dose-dependent manner. They depolarize the mitochondria, arrest the cell cycle in the G2/M phase, and kill the cells by an apoptotic pathway.
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Affiliation(s)
- Sourav Acharya
- Department of Chemical Sciences , Indian Institute of Science Education and Research Kolkata , Mohanpur , Nadia, West Bengal 741246 , India
| | - Moumita Maji
- Department of Chemical Sciences , Indian Institute of Science Education and Research Kolkata , Mohanpur , Nadia, West Bengal 741246 , India
| | - Ruturaj
- Department of Biological Sciences , Indian Institute of Science Education and Research Kolkata , Mohanpur , Nadia, West Bengal 741246 , India
| | - Kallol Purkait
- Department of Chemical Sciences , Indian Institute of Science Education and Research Kolkata , Mohanpur , Nadia, West Bengal 741246 , India
| | - Arnab Gupta
- Department of Biological Sciences , Indian Institute of Science Education and Research Kolkata , Mohanpur , Nadia, West Bengal 741246 , India
| | - Arindam Mukherjee
- Department of Chemical Sciences , Indian Institute of Science Education and Research Kolkata , Mohanpur , Nadia, West Bengal 741246 , India.,Center for Advanced Functional Materials (CAFM) , Indian Institute of Science Education and Research Kolkata , Mohanpur , Nadia, West Bengal 741246 , India
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176
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Mondal P, Khan J, Gupta V, Ghosh S. In Silico Approach for Designing Potent Neuroprotective Hexapeptide. ACS Chem Neurosci 2019; 10:3018-3030. [PMID: 31117343 DOI: 10.1021/acschemneuro.9b00251] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Alzheimer's disease (AD) is a constantly recurring neurodegenerative disease that deteriorates over a period of time. In this pathology, connections between neurons become extremely damaged due to the deposition of senile plaques in the membrane region, which results in abnormal signal transduction processes. Also, the intracellular microtubule networks are disrupted in the hyperphosphorylated tau cascade of AD. Therefore, design and development of potent neuroprotective molecules that can instantaneously target multiple facets of AD pathogenesis are greatly needed to tackle this unmet medical need. Here, we have implemented a pharmacophore based in silico analysis of various neuroprotective peptides known for neurotherapeutic application in AD. Fascinatingly, we have identified an active core of these peptides and designed a library of hexapeptides. We observed that peptide "LETVNQ" (LE6) has shown significant protection ability against degeneration of neurons. Experimental evidence suggests that this peptide immensely reduced the aggregation rate of amyloid-β (Aβ) and helped in microtubule polymerization. Intriguingly, this newly designed peptide does not have any cytotoxicity toward differentiated PC12 neurons; rather it helps in neurite outgrowth. Further, LE6 helps to maintain the complex microtubule network in cells by promoting the polymerization rate of intracellular microtubules and mediates excellent protection of neurons even after removal of nerve growth factor (NGF). Finally, we observed that this LE6 peptide has substantial stability under physiological conditions and helps to retain healthy morphology of primary rat cortical neurons. This excellent piece of work identifies a potent hexapeptide, which has exceptional ability to protect neurons as well as microtubule from degeneration and may become potent therapeutics against AD pathogenesis in the future.
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Affiliation(s)
- Prasenjit Mondal
- Organic and Medicinal Chemistry Division and Structural Biology and Bioinformatics Division, CSIR-Indian Institute of Chemical Biology, 4, Raja S. C. Mullick Road, Jadavpur, Kolkata, 700 032 WB, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Juhee Khan
- Organic and Medicinal Chemistry Division and Structural Biology and Bioinformatics Division, CSIR-Indian Institute of Chemical Biology, 4, Raja S. C. Mullick Road, Jadavpur, Kolkata, 700 032 WB, India
| | - Varsha Gupta
- Organic and Medicinal Chemistry Division and Structural Biology and Bioinformatics Division, CSIR-Indian Institute of Chemical Biology, 4, Raja S. C. Mullick Road, Jadavpur, Kolkata, 700 032 WB, India
| | - Surajit Ghosh
- Organic and Medicinal Chemistry Division and Structural Biology and Bioinformatics Division, CSIR-Indian Institute of Chemical Biology, 4, Raja S. C. Mullick Road, Jadavpur, Kolkata, 700 032 WB, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
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177
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Kazan F, Yagci ZB, Bai R, Ozkirimli E, Hamel E, Ozkirimli S. Synthesis and biological evaluation of indole-2-carbohydrazides and thiazolidinyl-indole-2-carboxamides as potent tubulin polymerization inhibitors. Comput Biol Chem 2019; 80:512-523. [DOI: 10.1016/j.compbiolchem.2019.05.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2018] [Revised: 02/12/2019] [Accepted: 05/06/2019] [Indexed: 12/31/2022]
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178
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Sánchez-Murcia PA, Mills A, Cortés-Cabrera Á, Gago F. Unravelling the covalent binding of zampanolide and taccalonolide AJ to a minimalist representation of a human microtubule. J Comput Aided Mol Des 2019; 33:627-644. [DOI: 10.1007/s10822-019-00208-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Accepted: 05/24/2019] [Indexed: 01/27/2023]
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179
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Guzman-Sepulveda JR, Wu R, Kalra AP, Aminpour M, Tuszynski JA, Dogariu A. Tubulin Polarizability in Aqueous Suspensions. ACS OMEGA 2019; 4:9144-9149. [PMID: 31460002 PMCID: PMC6648103 DOI: 10.1021/acsomega.9b00137] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Accepted: 05/13/2019] [Indexed: 05/10/2023]
Abstract
We report accurate optical measurements of tubulin polarizability in aqueous suspensions. We determined the dependence of polarizability on tubulin concentration and on the suspension's pH, providing benchmark numbers for quantifying the optical response of this protein in various artificial and cellular environments. We compare our measurement data with a few estimates found in the previous literature and also with our simplified model estimations.
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Affiliation(s)
| | - Ruitao Wu
- CREOL,
The College of Optics and Photonics, University
of Central Florida, Orlando 32816, United States
| | - Aarat P. Kalra
- Department of Physics and Department of Oncology, University
of Alberta, Edmonton T6G 2R3, Canada
| | - Maral Aminpour
- Department of Physics and Department of Oncology, University
of Alberta, Edmonton T6G 2R3, Canada
| | - Jack A. Tuszynski
- Department of Physics and Department of Oncology, University
of Alberta, Edmonton T6G 2R3, Canada
- Department
of Mechanical and Aerospace Engineering, Politecnico di Torino, Turin 10129, Italy
| | - Aristide Dogariu
- CREOL,
The College of Optics and Photonics, University
of Central Florida, Orlando 32816, United States
- E-mail:
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180
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Mondal P, Das G, Khan J, Pradhan K, Mallesh R, Saha A, Jana B, Ghosh S. Potential Neuroprotective Peptide Emerged from Dual Neurotherapeutic Targets: A Fusion Approach for the Development of Anti-Alzheimer's Lead. ACS Chem Neurosci 2019; 10:2609-2620. [PMID: 30840820 DOI: 10.1021/acschemneuro.9b00115] [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] [Indexed: 01/01/2023] Open
Abstract
Amyloid-beta (Aβ) peptide misfolds into fibrillary aggregates (β-sheet) and is deposited as amyloid plaques in the cellular environment, which severely damages intraneuronal connections leading to Alzheimer's disease (AD) pathogenesis. Furthermore, neurons are rich in tubulin/microtubules, and the intracellular network of microtubules also gets disrupted by the accumulation of Aβ fiber in the brain. Hence, development of new potent molecules, which can simultaneously inhibit Aβ fibrillations and stabilize microtubules, is particularly needed for the efficient therapeutic application in AD. To address these issues, here we introduced an innovative fusion strategy to design and develop next generation anti-AD therapeutic leads. This unexplored fusion strategy entails design and development of a potent nonapeptide by taking into account both the hydrophobic core (17-21) of Aβ peptide and the taxol binding region of β-tubulin. In vitro results suggest that this newly designed peptide interacts at the taxol binding region of β-tubulin with a moderate binding affinity and promotes microtubule polymerization. It has the ability to bind at the hydrophobic core (17-21) of Aβ, responsible for its aggregation, and prevent amyloid fibril as well as plaque formation. In addition, it interacts at the CAS site (catalytic anionic site) of acetylcholinesterase (AChE) and significantly inhibits AChE induced Aβ fibrillation, stimulates neurite branching, and provides stability to intracellular microtubules and extensive protection of neurons against nerve growth factor (NGF) deprived neuron toxicity. Moreover, this newly designed peptide shows good stability in serum obtained from humans and efficiently permeates the blood-brain barrier (BBB) without showing any toxicity toward differentiated PC12 neurons as well as primary rat cortical neurons. This excellent feature of protecting the neurons by stabilizing the microtubules without showing any toxicity toward neurons will make this peptide a potent therapeutic agent of AD in the near future.
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Affiliation(s)
- Prasenjit Mondal
- Organic & Medicinal Chemistry Division, CSIR-Indian Institute of Chemical Biology, 4, Raja S. C. Mullick Road, Jadavpur, Kol-32, West Bengal, India
- Academy of Scientific and Innovative Research (AcSIR), CSIR-Indian Institute of Chemical Biology Campus, 4, Raja S. C. Mullick Road, Jadavpur, Kol-32, West Bengal, India
| | - Gaurav Das
- Organic & Medicinal Chemistry Division, CSIR-Indian Institute of Chemical Biology, 4, Raja S. C. Mullick Road, Jadavpur, Kol-32, West Bengal, India
- Academy of Scientific and Innovative Research (AcSIR), CSIR-Indian Institute of Chemical Biology Campus, 4, Raja S. C. Mullick Road, Jadavpur, Kol-32, West Bengal, India
| | - Juhee Khan
- Organic & Medicinal Chemistry Division, CSIR-Indian Institute of Chemical Biology, 4, Raja S. C. Mullick Road, Jadavpur, Kol-32, West Bengal, India
| | - Krishnangsu Pradhan
- Organic & Medicinal Chemistry Division, CSIR-Indian Institute of Chemical Biology, 4, Raja S. C. Mullick Road, Jadavpur, Kol-32, West Bengal, India
| | - Rathnam Mallesh
- Organic & Medicinal Chemistry Division, CSIR-Indian Institute of Chemical Biology, 4, Raja S. C. Mullick Road, Jadavpur, Kol-32, West Bengal, India
- National Institute of Pharmaceutical Education and Research, Kolkata, CSIR-Indian Institute of Chemical Biology Campus, 4, Raja S. C. Mullick Road, Jadavpur, Kol-32, West Bengal, India
| | - Abhijit Saha
- Organic & Medicinal Chemistry Division, CSIR-Indian Institute of Chemical Biology, 4, Raja S. C. Mullick Road, Jadavpur, Kol-32, West Bengal, India
| | - Batakrishna Jana
- Organic & Medicinal Chemistry Division, CSIR-Indian Institute of Chemical Biology, 4, Raja S. C. Mullick Road, Jadavpur, Kol-32, West Bengal, India
| | - Surajit Ghosh
- Organic & Medicinal Chemistry Division, CSIR-Indian Institute of Chemical Biology, 4, Raja S. C. Mullick Road, Jadavpur, Kol-32, West Bengal, India
- Academy of Scientific and Innovative Research (AcSIR), CSIR-Indian Institute of Chemical Biology Campus, 4, Raja S. C. Mullick Road, Jadavpur, Kol-32, West Bengal, India
- National Institute of Pharmaceutical Education and Research, Kolkata, CSIR-Indian Institute of Chemical Biology Campus, 4, Raja S. C. Mullick Road, Jadavpur, Kol-32, West Bengal, India
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181
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Ma X, Özliseli E, Zhang Y, Pan G, Wang D, Zhang H. Fabrication of redox-responsive doxorubicin and paclitaxel prodrug nanoparticles with microfluidics for selective cancer therapy. Biomater Sci 2019; 7:634-644. [PMID: 30534690 DOI: 10.1039/c8bm01333k] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Cancer is an exceptionally confounding disease that demands the development of powerful drug/drugs, without inducing heavy adverse side effects. Thus, different approaches have been applied to improve the targeted delivery of cancer drugs: for example by using nanocarriers. However, nanocarriers are foreign materials, which need further validation for their biocompatibility and biodegradability. In this study, we have chemically conjugated the hydrophilic anticancer drug doxorubicin (DOX) with the hydrophobic drug paclitaxel (PTX) through a redox-sensitive disulfide bond, abbreviated to DOX-S-S-PTX. Subsequently, due to its amphiphilic characterization, the prodrug can self-assemble into nanoparticles under microfluidic nanoprecipitation. These novel prodrug nanoparticles have a super-high drug loading degree of 89%, which is impossible to achieve by any nanocarrier systems, and can be tailored to 180 nm to deliver themselves to the target, and release DOX and PTX under redox conditions, which are often found in cancer cells. By evaluating cell viability in MDA-MB-231, MDA-MB-231/ADR and MEF cell lines, we observed that the prodrug nanoparticles effectively killed the cancer cells, and selectively conquered the MDA-MB-231/ADR. Meanwhile, MEF cells were spared due to their lack of a redox condition. The cell interaction results show that the reduced intermediate of the prodrug can also bind to parent drug biological targets. The hemolysis results show that the nanoparticles are biocompatible in blood. Computer modelling suggested that the prodrug is unlikely to bind to biological targets that parent drugs still strongly interact with. Finally, we confirm that the prodrug nanoparticles have no therapeutic effect in blood or healthy cells, but can selectively eliminate the cancer cells that meet the redox conditions to cleave the disulfide bond and release the drugs DOX and PTX.
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Affiliation(s)
- Xiaodong Ma
- Department of Radiology affiliated Hospital of Jiangsu University Jiangsu University, 212001 Zhenjiang, P.R. China
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182
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Huang L, Hu C, Chao H, Wang R, Lu H, Li H, Chen H. miR-29c regulates resistance to paclitaxel in nasopharyngeal cancer by targeting ITGB1. Exp Cell Res 2019; 378:1-10. [DOI: 10.1016/j.yexcr.2019.02.012] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2018] [Revised: 02/14/2019] [Accepted: 02/15/2019] [Indexed: 01/20/2023]
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183
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A Survey on Tubulin and Arginine Methyltransferase Families Sheds Light on P. lividus Embryo as Model System for Antiproliferative Drug Development. Int J Mol Sci 2019; 20:ijms20092136. [PMID: 31052191 PMCID: PMC6539552 DOI: 10.3390/ijms20092136] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2019] [Accepted: 04/27/2019] [Indexed: 01/18/2023] Open
Abstract
Tubulins and microtubules (MTs) represent targets for taxane-based chemotherapy. To date, several lines of evidence suggest that effectiveness of compounds binding tubulin often relies on different post-translational modifications on tubulins. Among them, methylation was recently associated to drug resistance mechanisms impairing taxanes binding. The sea urchin is recognized as a research model in several fields including fertilization, embryo development and toxicology. To date, some α- and β-tubulin genes have been identified in P. lividus, while no data are available in echinoderms for arginine methyl transferases (PRMT). To evaluate the exploiting of the sea urchin embryo in the field of antiproliferative drug development, we carried out a survey of the expressed α- and β-tubulin gene sets, together with a comprehensive analysis of the PRMT gene family and of the methylable arginine residues in P. lividus tubulins. Because of their specificities, the sea urchin embryo may represent an interesting tool for dissecting mechanisms of tubulin targeting drug action. Therefore, results herein reported provide evidences supporting the P. lividus embryo as animal system for testing antiproliferative drugs.
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184
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Horenberg AL, Houghton AM, Pandey S, Seshadri V, Guilford WH. S-nitrosylation of cytoskeletal proteins. Cytoskeleton (Hoboken) 2019; 76:243-253. [PMID: 30969482 DOI: 10.1002/cm.21520] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2019] [Revised: 03/05/2019] [Accepted: 03/27/2019] [Indexed: 12/30/2022]
Abstract
Nitric oxide has pronounced effects on cellular functions normally associated with the cytoskeleton, including cell motility, shape, contraction, and mitosis. Protein S-nitrosylation, the covalent addition of a NO group to a cysteine sulfur, is a signaling pathway for nitric oxide that acts in parallel to cyclic guanosine monophosphate (cGMP), but is poorly studied compared to the latter. There is growing evidence that S-nitrosylation of cytoskeletal proteins selectively alters their function. We review that evidence, and find that S-nitrosylation of cytoskeletal targets has complementary but distinct effects to cyclic-GMP in motile and contractile cells-promoting cell migration, and biasing muscle contraction toward relaxation. However, the effects of S-nitrosylation on a host of cytoskeletal proteins and functions remains to be explored.
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Affiliation(s)
- Allison L Horenberg
- Department of Biomedical Engineering, University of Virginia, Charlottesville, Virginia
| | - Alisa M Houghton
- Department of Biomedical Engineering, University of Virginia, Charlottesville, Virginia
| | - Saurav Pandey
- Department of Biomedical Engineering, University of Virginia, Charlottesville, Virginia
| | - Vikram Seshadri
- Department of Biomedical Engineering, University of Virginia, Charlottesville, Virginia
| | - William H Guilford
- Department of Biomedical Engineering, University of Virginia, Charlottesville, Virginia
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185
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Silva-García EM, Cerda-García-Rojas CM, Del Río RE, Joseph-Nathan P. Parvifoline Derivatives as Tubulin Polymerization Inhibitors. JOURNAL OF NATURAL PRODUCTS 2019; 82:840-849. [PMID: 30883116 DOI: 10.1021/acs.jnatprod.8b00860] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
A series of functionalized sesquiterpenoids derived from benzocyclooctene, including natural parvifoline (1), isoparvifoline (3), epoxyparvifoline (5), epoxyisoparvifoline (7), 8,12-oxyparfivoline (9), 8,14-oxyparvifoline (11), and the respective benzoyl derivatives 2, 4, 6, 8, 10, and 12, were prepared and tested for their inhibitory effect on the in vitro α,β-tubulin polymerization process. The structural analysis and characterization of the new compounds 5-7 and 9-12 were achieved by 1D and 2D NMR spectroscopy, mass spectrometry, and X-ray diffraction analysis of 6, 7, and 9. Preparation of 9 and 12 involved molecular rearrangements of the epoxide group with transannular 1,5-hydride shifts. At 10 μM compounds 1, 5, and 8 inhibited the polymerization of the α,β-tubulin heterodimer by 24%, 49%, and 90% as compared to colchicine. These compounds were subjected to docking analysis that supported their interactions in a colchicine binding site located in the α-tubulin subunit, in the pocket formed by Phe296, Pro298, Pro307, His309, Tyr312, Lys338, Thr340, Ile341, and Gln342. Competitive inhibition assays with colchicine were also performed for the three compounds, which supported their binding at the colchicine secondary site in α-tubulin. Also, evaluations of their cytotoxicity on MCF7 breast carcinoma, HeLa cervix carcinoma, and HCT 116 colon carcinoma cell lines were carried out and showed that 8 is active against the HeLa and HCT 116 cell lines with IC50 3.3 ± 0.2 and 5.0 ± 0.5 μM, respectively.
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Affiliation(s)
- Edna M Silva-García
- Departamento de Química y Programa de Posgrado en Farmacología , Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional , Apartado 14-740 , Mexico City 07000 , Mexico
| | - Carlos M Cerda-García-Rojas
- Departamento de Química y Programa de Posgrado en Farmacología , Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional , Apartado 14-740 , Mexico City 07000 , Mexico
| | - Rosa E Del Río
- Instituto de Investigaciones Químico-Biológicas , Universidad Michoacana de San Nicolás de Hidalgo , Ciudad Universitaria , Morelia , Michoacán 58030 , Mexico
| | - Pedro Joseph-Nathan
- Departamento de Química y Programa de Posgrado en Farmacología , Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional , Apartado 14-740 , Mexico City 07000 , Mexico
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186
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Xie Y, Kril LM, Yu T, Zhang W, Frasinyuk MS, Bondarenko SP, Kondratyuk KM, Hausman E, Martin ZM, Wyrebek PP, Liu X, Deaciuc A, Dwoskin LP, Chen J, Zhu H, Zhan CG, Sviripa VM, Blackburn J, Watt DS, Liu C. Semisynthetic aurones inhibit tubulin polymerization at the colchicine-binding site and repress PC-3 tumor xenografts in nude mice and myc-induced T-ALL in zebrafish. Sci Rep 2019; 9:6439. [PMID: 31015569 PMCID: PMC6478746 DOI: 10.1038/s41598-019-42917-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2018] [Accepted: 12/17/2018] [Indexed: 02/07/2023] Open
Abstract
Structure-activity relationships (SAR) in the aurone pharmacophore identified heterocyclic variants of the (Z)-2-benzylidene-6-hydroxybenzofuran-3(2H)-one scaffold that possessed low nanomolar in vitro potency in cell proliferation assays using various cancer cell lines, in vivo potency in prostate cancer PC-3 xenograft and zebrafish models, selectivity for the colchicine-binding site on tubulin, and absence of appreciable toxicity. Among the leading, biologically active analogs were (Z)-2-((2-((1-ethyl-5-methoxy-1H-indol-3-yl)methylene)-3-oxo-2,3-dihydrobenzofuran-6-yl)oxy)acetonitrile (5a) and (Z)-6-((2,6-dichlorobenzyl)oxy)-2-(pyridin-4-ylmethylene)benzofuran-3(2H)-one (5b) that inhibited in vitro PC-3 prostate cancer cell proliferation with IC50 values below 100 nM. A xenograft study in nude mice using 10 mg/kg of 5a had no effect on mice weight, and aurone 5a did not inhibit, as desired, the human ether-à-go-go-related (hERG) potassium channel. Cell cycle arrest data, comparisons of the inhibition of cancer cell proliferation by aurones and known antineoplastic agents, and in vitro inhibition of tubulin polymerization indicated that aurone 5a disrupted tubulin dynamics. Based on molecular docking and confirmed by liquid chromatography-electrospray ionization-tandem mass spectrometry studies, aurone 5a targets the colchicine-binding site on tubulin. In addition to solid tumors, aurones 5a and 5b strongly inhibited in vitro a panel of human leukemia cancer cell lines and the in vivo myc-induced T cell acute lymphoblastic leukemia (T-ALL) in a zebrafish model.
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Affiliation(s)
- Yanqi Xie
- Department of Molecular and Cellular Biochemistry, College of Medicine, University of Kentucky, Lexington, KY, 40536-0509, USA
- Center for Pharmaceutical Research and Innovation, College of Pharmacy, University of Kentucky, Lexington, KY, 40536-0596, USA
| | - Liliia M Kril
- Department of Molecular and Cellular Biochemistry, College of Medicine, University of Kentucky, Lexington, KY, 40536-0509, USA
- Center for Pharmaceutical Research and Innovation, College of Pharmacy, University of Kentucky, Lexington, KY, 40536-0596, USA
| | - Tianxin Yu
- Department of Molecular and Cellular Biochemistry, College of Medicine, University of Kentucky, Lexington, KY, 40536-0509, USA
- Lucille Parker Markey Cancer Center, University of Kentucky, Lexington, KY, 40536-0093, USA
| | - Wen Zhang
- Department of Molecular and Cellular Biochemistry, College of Medicine, University of Kentucky, Lexington, KY, 40536-0509, USA
- Lucille Parker Markey Cancer Center, University of Kentucky, Lexington, KY, 40536-0093, USA
| | - Mykhaylo S Frasinyuk
- Department of Molecular and Cellular Biochemistry, College of Medicine, University of Kentucky, Lexington, KY, 40536-0509, USA
- Center for Pharmaceutical Research and Innovation, College of Pharmacy, University of Kentucky, Lexington, KY, 40536-0596, USA
- Institute of Bioorganic Chemistry and Petrochemistry, National Academy of Science of Ukraine, Kyiv, 02094, Ukraine
| | | | - Kostyantyn M Kondratyuk
- Institute of Bioorganic Chemistry and Petrochemistry, National Academy of Science of Ukraine, Kyiv, 02094, Ukraine
| | - Elizabeth Hausman
- Department of Molecular and Cellular Biochemistry, College of Medicine, University of Kentucky, Lexington, KY, 40536-0509, USA
| | - Zachary M Martin
- Department of Molecular and Cellular Biochemistry, College of Medicine, University of Kentucky, Lexington, KY, 40536-0509, USA
- Center for Pharmaceutical Research and Innovation, College of Pharmacy, University of Kentucky, Lexington, KY, 40536-0596, USA
| | - Przemyslaw P Wyrebek
- Department of Molecular and Cellular Biochemistry, College of Medicine, University of Kentucky, Lexington, KY, 40536-0509, USA
- Center for Pharmaceutical Research and Innovation, College of Pharmacy, University of Kentucky, Lexington, KY, 40536-0596, USA
| | - Xifu Liu
- Center for Drug Innovation and Discovery, Hebei Normal University, Shijiazhuang, Hebei, 050024, People's Republic of China
| | - Agripina Deaciuc
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, Lexington, KY, 40536-0596, USA
| | - Linda P Dwoskin
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, Lexington, KY, 40536-0596, USA
| | - Jing Chen
- Department of Molecular and Cellular Biochemistry, College of Medicine, University of Kentucky, Lexington, KY, 40536-0509, USA
| | - Haining Zhu
- Department of Molecular and Cellular Biochemistry, College of Medicine, University of Kentucky, Lexington, KY, 40536-0509, USA
| | - Chang-Guo Zhan
- Center for Pharmaceutical Research and Innovation, College of Pharmacy, University of Kentucky, Lexington, KY, 40536-0596, USA
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, Lexington, KY, 40536-0596, USA
- Molecular Modeling and Pharmaceutical Center, College of Pharmacy, University of Kentucky, Lexington, KY, 40536-0596, USA
| | - Vitaliy M Sviripa
- Center for Pharmaceutical Research and Innovation, College of Pharmacy, University of Kentucky, Lexington, KY, 40536-0596, USA
- Lucille Parker Markey Cancer Center, University of Kentucky, Lexington, KY, 40536-0093, USA
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, Lexington, KY, 40536-0596, USA
| | - Jessica Blackburn
- Department of Molecular and Cellular Biochemistry, College of Medicine, University of Kentucky, Lexington, KY, 40536-0509, USA
| | - David S Watt
- Department of Molecular and Cellular Biochemistry, College of Medicine, University of Kentucky, Lexington, KY, 40536-0509, USA.
- Center for Pharmaceutical Research and Innovation, College of Pharmacy, University of Kentucky, Lexington, KY, 40536-0596, USA.
- Lucille Parker Markey Cancer Center, University of Kentucky, Lexington, KY, 40536-0093, USA.
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, Lexington, KY, 40536-0596, USA.
| | - Chunming Liu
- Department of Molecular and Cellular Biochemistry, College of Medicine, University of Kentucky, Lexington, KY, 40536-0509, USA.
- Lucille Parker Markey Cancer Center, University of Kentucky, Lexington, KY, 40536-0093, USA.
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187
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A high-affinity peptide substrate for G protein-coupled receptor kinase 2 (GRK2). Amino Acids 2019; 51:973-976. [PMID: 31004228 DOI: 10.1007/s00726-019-02735-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2019] [Accepted: 04/09/2019] [Indexed: 01/07/2023]
Abstract
We synthesized a previously identified β-tubulin-derived G protein-coupled receptor kinase 2 (GKR2) peptide (GR-11-1; DEMEFTEAESNMN) and its amino-terminal extension (GR-11-1-N; GEGMDEMEFTEAESNMN) and carboxyl-terminal extension (GR-11-1-C; DEMEFTEAESNMNDLVSEYQ) peptides with the aim of finding a high-affinity peptide substrate for GRK2. GR-11-1-C showed high affinity for GRK2, but very low affinity for GKR5. Its specificity and sensitivity for GKR2 were greater than those of GR-11-1 and GR-11-1-N. These findings should be useful in designing tools for probing GKR2-mediated intracellular signaling pathways, as well as GRK2-specific drugs.
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188
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Schummel PH, Anders C, Jaworek MW, Winter R. Cosolvent and Crowding Effects on the Temperature- and Pressure-Dependent Dissociation Process of the α/β-Tubulin Heterodimer. Chemphyschem 2019; 20:1098-1109. [PMID: 30829441 DOI: 10.1002/cphc.201900115] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2019] [Revised: 03/01/2019] [Indexed: 11/09/2022]
Abstract
Tubulin is one of the main components of the cytoskeleton of eukaryotic cells. The formation of microtubules depends strongly on environmental and solution conditions, and has been found to be among the most pressure sensitive processes in vivo. We explored the effects of different types of cosolvents, such as trimethylamine-N-oxide (TMAO), sucrose and urea, and crowding agents to mimic cell-like conditions, on the temperature and pressure stability of the building block of microtubules, i. e. the α/β-tubulin heterodimer. To this end, fluorescence and FTIR spectroscopy, differential scanning and pressure perturbation calorimetry as well as fluorescence anisotropy and correlation spectroscopies were applied. The pressure and temperature of dissociation of α/β-tubulin as well as the underlying thermodynamic parameters upon dissociation, such as volume and enthalpy changes, have been determined for the different solution conditions. The temperature and pressure of dissociation of the α/β-tubulin heterodimer and hence its stability increases dramatically in the presence of TMAO and the nanocrowder sucrose. We show that by adjusting the levels of compatible cosolutes and crowders, cells are able to withstand deteriorating effects of pressure even up to the kbar-range.
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Affiliation(s)
- Paul Hendrik Schummel
- Faculty of Chemistry and Chemical Biology, Physical Chemistry-Biophysical Chemistry, TU Dortmund University, Otto-Hahn-Str. 4a, 44227, Dortmund, Germany
| | - Christian Anders
- Faculty of Chemistry and Chemical Biology, Physical Chemistry-Biophysical Chemistry, TU Dortmund University, Otto-Hahn-Str. 4a, 44227, Dortmund, Germany
| | - Michel W Jaworek
- Faculty of Chemistry and Chemical Biology, Physical Chemistry-Biophysical Chemistry, TU Dortmund University, Otto-Hahn-Str. 4a, 44227, Dortmund, Germany
| | - Roland Winter
- Faculty of Chemistry and Chemical Biology, Physical Chemistry-Biophysical Chemistry, TU Dortmund University, Otto-Hahn-Str. 4a, 44227, Dortmund, Germany
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189
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Matsumura T, Nakamura-Ishizu A, Takaoka K, Maki H, Muddineni SSNA, Wang CQ, Suzushima H, Kawakita M, Asou N, Matsuoka M, Kurokawa M, Osato M, Suda T. TUBB1 dysfunction in inherited thrombocytopenia causes genome instability. Br J Haematol 2019; 185:888-902. [PMID: 30854628 DOI: 10.1111/bjh.15835] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Accepted: 12/18/2018] [Indexed: 12/20/2022]
Abstract
Inherited thrombocytopenia is a genetically heterogeneous disease characterized by varying degrees of thrombocytopenia and risk of haematological malignancy, and the genetic cause of many cases remains unknown. We performed whole-exome sequencing of a family with thrombocytopenia and myeloid malignancy and identified a novel TUBB1 variant, T149P. Screening of other thrombocytopenia pedigrees identified another TUBB1 variant, R251H. TUBB1 encodes the tubulin β-1 chain, a major component of microtubules abundant in megakaryocytes. Variant TUBB1 disrupted the normal assembly of microtubules and impaired proplatelet formation in vitro. In addition, DNA damage response was severely attenuated by loss of TUBB1. We found that the nuclear accumulation of p53 (also termed TP53) and the expression of pro-apoptotic genes triggered by genotoxic stress were blocked in TUBB1-deficient cells and, accordingly, apoptosis after DNA damage was diminished by knockdown of TUBB1. Thus, we have demonstrated that microtubule dysfunction confers resistance to apoptosis, even in DNA damage-accumulated cells, which explains genome instability in the affected individuals. These studies will lead us to a better understanding of how microtubule dysfunction can contribute to the accumulation of DNA damage, genetic instability and leukaemogenesis.
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Affiliation(s)
- Takayoshi Matsumura
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Ayako Nakamura-Ishizu
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore.,International Research Centre for Medical Sciences, Kumamoto University, Kumamoto, Japan
| | - Kensuke Takaoka
- Department of Haematology and Oncology, Graduate School of Medicine, the University of Tokyo, Tokyo, Japan
| | - Hiroaki Maki
- Department of Haematology and Oncology, Graduate School of Medicine, the University of Tokyo, Tokyo, Japan
| | - Siva S N A Muddineni
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Chelsia Q Wang
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | | | | | - Norio Asou
- International Medical Centre, Saitama Medical University, Saitama, Japan
| | - Masao Matsuoka
- Department of Haematology, Rheumatology, and Infectious Diseases, Kumamoto University School of Medicine, Kumamoto, Japan
| | - Mineo Kurokawa
- Department of Haematology and Oncology, Graduate School of Medicine, the University of Tokyo, Tokyo, Japan
| | - Motomi Osato
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore.,International Research Centre for Medical Sciences, Kumamoto University, Kumamoto, Japan.,Centre for Metabolic Regulation of Healthy Aging, Kumamoto University, Kumamoto, Japan
| | - Toshio Suda
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore.,International Research Centre for Medical Sciences, Kumamoto University, Kumamoto, Japan
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190
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Tajielyato N, Alexov E. Processivity vs. Beating: Comparing Cytoplasmic and Axonemal Dynein Microtubule Binding Domain Association with Microtubule. Int J Mol Sci 2019; 20:ijms20051090. [PMID: 30832428 PMCID: PMC6429364 DOI: 10.3390/ijms20051090] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Revised: 02/24/2019] [Accepted: 02/26/2019] [Indexed: 12/25/2022] Open
Abstract
This study compares the role of electrostatics in the binding process between microtubules and two dynein microtubule-binding domains (MTBDs): cytoplasmic and axonemal. These two dyneins are distinctively different in terms of their functionalities: cytoplasmic dynein is processive, while axonemal dynein is involved in beating. In both cases, the binding requires frequent association/disassociation between the microtubule and MTBD, and involves highly negatively charged microtubules, including non-structured C-terminal domains (E-hooks), and an MTBD interface that is positively charged. This indicates that electrostatics play an important role in the association process. Here, we show that the cytoplasmic MTBD binds electrostatically tighter to microtubules than to the axonemal MTBD, but the axonemal MTBD experiences interactions with microtubule E-hooks at longer distances compared with the cytoplasmic MTBD. This allows the axonemal MTBD to be weakly bound to the microtubule, while at the same time acting onto the microtubule via the flexible E-hooks, even at MTBD⁻microtubule distances of 45 Å. In part, this is due to the charge distribution of MTBDs: in the cytoplasmic MTBD, the positive charges are concentrated at the binding interface with the microtubule, while in the axonemal MTBD, they are more distributed over the entire structure, allowing E-hooks to interact at longer distances. The dissimilarities of electrostatics in the cases of axonemal and cytoplasmic MTBDs were found not to result in a difference in conformational dynamics on MTBDs, while causing differences in the conformational states of E-hooks. The E-hooks' conformations in the presence of the axonemal MTBD were less restricted than in the presence of the cytoplasmic MTBD. In parallel with the differences, the common effect was found that the structural fluctuations of MTBDs decrease as either the number of contacts with E-hooks increases or the distance to the microtubule decreases.
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Affiliation(s)
- Nayere Tajielyato
- Department of Physics and Astronomy, Clemson University, Clemson, SC 29630, USA.
| | - Emil Alexov
- Department of Physics and Astronomy, Clemson University, Clemson, SC 29630, USA.
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191
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van Haren J, Wittmann T. Microtubule Plus End Dynamics - Do We Know How Microtubules Grow?: Cells boost microtubule growth by promoting distinct structural transitions at growing microtubule ends. Bioessays 2019; 41:e1800194. [PMID: 30730055 PMCID: PMC7021488 DOI: 10.1002/bies.201800194] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2018] [Revised: 12/22/2018] [Indexed: 12/31/2022]
Abstract
Microtubules form a highly dynamic filament network in all eukaryotic cells. Individual microtubules grow by tubulin dimer subunit addition and frequently switch between phases of growth and shortening. These unique dynamics are powered by GTP hydrolysis and drive microtubule network remodeling, which is central to eukaryotic cell biology and morphogenesis. Yet, our knowledge of the molecular events at growing microtubule ends remains incomplete. Here, recent ultrastructural, biochemical and cell biological data are integrated to develop a realistic model of growing microtubule ends comprised of structurally distinct but biochemically overlapping zones. Proteins that recognize microtubule lattice conformations associated with specific tubulin guanosine nucleotide states may independently control major structural transitions at growing microtubule ends. A model is proposed in which tubulin dimer addition and subsequent closure of the MT wall are optimized in cells to achieve rapid physiological microtubule growth.
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Affiliation(s)
- Jeffrey van Haren
- Department of Cell and Tissue Biology, University of California San Francisco, 513 Parnassus Avenue, San Francisco, CA, 94143, USA
| | - Torsten Wittmann
- Department of Cell and Tissue Biology, University of California San Francisco, 513 Parnassus Avenue, San Francisco, CA, 94143, USA
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192
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Li S, Wang C, Nithiarasu P. Electromechanical vibration of microtubules and its application in biosensors. J R Soc Interface 2019; 16:20180826. [PMID: 30958194 PMCID: PMC6408348 DOI: 10.1098/rsif.2018.0826] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2018] [Accepted: 01/16/2019] [Indexed: 01/03/2023] Open
Abstract
An electric field (EF) has the potential to excite the vibration of polarized microtubules (MTs) and thus enable their use as a biosensor for the biophysical properties of MTs or cells. To facilitate the development, this paper aims to capture the EF-induced vibration modes and the associated frequency for MTs. The analyses were carried out based on a molecular structural mechanics model accounting for the structural details of MTs. Transverse vibration, radial breathing vibration and axial vibration were achieved for MTs subject to a transverse or an axial EF. The frequency shift and stiffness alteration of MTs were also examined due to the possible changes of the tubulin interactions in physiological or pathological processes. The strong correlation achieved between the tubulin interaction and MT vibration excited by EF provides a new avenue to a non-contacting technique for the structural or property changes in MTs, where frequency shift is used as a biomarker. This technique can be used for individual MTs and is possible for those in cells when the cytosol damping on MT vibrations is largely reduced by the unique features of MT-cytosol interface.
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Affiliation(s)
| | - Chengyuan Wang
- Zienkiewicz Centre for Computational Engineering, College of Engineering, Swansea University, Bay Campus, Fabian Way, Swansea SA1 8EN, UK
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193
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Zeng QZ, Yang F, Li CG, Xu LH, He XH, Mai FY, Zeng CY, Zhang CC, Zha QB, Ouyang DY. Paclitaxel Enhances the Innate Immunity by Promoting NLRP3 Inflammasome Activation in Macrophages. Front Immunol 2019; 10:72. [PMID: 30761140 PMCID: PMC6361797 DOI: 10.3389/fimmu.2019.00072] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2018] [Accepted: 01/11/2019] [Indexed: 12/22/2022] Open
Abstract
Microtubules play critical roles in regulating the activation of NLRP3 inflammasome and microtubule-destabilizing agents such as colchicine have been shown to suppress the activation of this inflammasome. However, it remains largely unknown whether paclitaxel, a microtubule-stabilizing agent being used in cancer therapy, has any influences on NLRP3 inflammasome activation. Here we showed that paclitaxel pre-treatment greatly enhanced ATP- or nigericin-induced NLRP3 inflammasome activation as indicated by increased release of cleaved caspase-1 and mature IL-1β, enhanced formation of ASC speck, and increased gasdermin D cleavage and pyroptosis. Paclitaxel time- and dose-dependently induced α-tubulin acetylation in LPS-primed murine and human macrophages and further increased ATP- or nigericin-induced α-tubulin acetylation. Such increased α-tubulin acetylation was significantly suppressed either by resveratrol or NAD+ (coenzyme required for deacetylase activity of SIRT2), or by genetic knockdown of MEC-17 (gene encoding α-tubulin acetyltransferase 1). Concurrently, the paclitaxel-mediated enhancement of NLRP3 inflammasome activation was significantly suppressed by resveratrol, NAD+, or MEC-17 knockdown, indicating the involvement of paclitaxel-induced α-tubulin acetylation in the augmentation of NLRP3 inflammasome activation. Similar to paclitaxel, epothilone B that is another microtubule-stabilizing agent also induced α-tubulin acetylation and increased NLRP3 inflammasome activation in macrophages in response to ATP treatment. Consistent with the in vitro results, intraperitoneal administration of paclitaxel significantly increased serum IL-1β levels, reduced bacterial burden, dampened infiltration of inflammatory cells in the liver, and improved animal survival in a mouse model of bacterial infection. Collectively, our data indicate that paclitaxel potentiated NLRP3 inflammasome activation by inducing α-tubulin acetylation and thereby conferred enhanced antibacterial innate responses, suggesting its potential application against pathogenic infections beyond its use as a chemotherapeutic agent.
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Affiliation(s)
- Qiong-Zhen Zeng
- Department of Immunobiology, College of Life Science and Technology, Jinan University, Guangzhou, China
| | - Fan Yang
- Department of Immunobiology, College of Life Science and Technology, Jinan University, Guangzhou, China
| | - Chen-Guang Li
- Department of Immunobiology, College of Life Science and Technology, Jinan University, Guangzhou, China
| | - Li-Hui Xu
- Department of Cell Biology, College of Life Science and Technology, Jinan University, Guangzhou, China
| | - Xian-Hui He
- Department of Immunobiology, College of Life Science and Technology, Jinan University, Guangzhou, China
| | - Feng-Yi Mai
- Department of Immunobiology, College of Life Science and Technology, Jinan University, Guangzhou, China
| | - Chen-Ying Zeng
- Department of Immunobiology, College of Life Science and Technology, Jinan University, Guangzhou, China
| | - Cheng-Cheng Zhang
- Department of Immunobiology, College of Life Science and Technology, Jinan University, Guangzhou, China
| | - Qing-Bing Zha
- Department of Fetal Medicine, the First Affiliated Hospital of Jinan University, Guangzhou, China
| | - Dong-Yun Ouyang
- Department of Immunobiology, College of Life Science and Technology, Jinan University, Guangzhou, China
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194
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de Vink PJ, Andrei SA, Higuchi Y, Ottmann C, Milroy LG, Brunsveld L. Cooperativity basis for small-molecule stabilization of protein-protein interactions. Chem Sci 2019; 10:2869-2874. [PMID: 30996864 PMCID: PMC6429609 DOI: 10.1039/c8sc05242e] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2018] [Accepted: 01/25/2019] [Indexed: 12/14/2022] Open
Abstract
A cooperativity framework to describe and interpret small-molecule stabilization of protein–protein interactions (PPI) is presented, which allows elucidating structure–activity relationships regarding cooperativity and intrinsic affinity.
A cooperativity framework to describe and interpret small-molecule stabilization of protein–protein interactions (PPI) is presented. The stabilization of PPIs is a versatile and emerging therapeutic strategy to target specific combinations of protein partners within the protein interactome. Currently, the potency of PPI stabilizers is typically expressed by their apparent affinity or EC50. Here, we propose that the effect of a PPI stabilizer be best described involving the cooperativity factor, α, between the stabilizer and binding partners in addition to the intrinsic affinity, KDII, of the stabilizer for one of the apo-proteins. By way of illustration, we combine fluorescence polarization measurements with thermodynamic modeling to determine the α and KDII for the PPI stabilization of 14-3-3 and TASK3 by fusicoccin-A (FC-A) and validate our approach by studying other PPI-partners of 14-3-3 proteins. Finally, we characterize a library of different stabilizer compounds, and perform structure–activity relationship studies in which molecular changes could be attributed to either changes in cooperativity or intrinsic affinity. Such insights should aid in the development of more effective protein–protein stabilizer drugs.
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Affiliation(s)
- Pim J de Vink
- Laboratory of Chemical Biology , Department of Biomedical Engineering and Institute for Complex Molecular Systems , Eindhoven University of Technology , P. O. Box 513 , 5600MB , Eindhoven , The Netherlands .
| | - Sebastian A Andrei
- Laboratory of Chemical Biology , Department of Biomedical Engineering and Institute for Complex Molecular Systems , Eindhoven University of Technology , P. O. Box 513 , 5600MB , Eindhoven , The Netherlands .
| | - Yusuke Higuchi
- The Institute of Scientific and Industrial Research , Osaka University , Ibaraki , Japan
| | - Christian Ottmann
- Laboratory of Chemical Biology , Department of Biomedical Engineering and Institute for Complex Molecular Systems , Eindhoven University of Technology , P. O. Box 513 , 5600MB , Eindhoven , The Netherlands . .,Department of Organic Chemistry , University of Duisburg-Essen , Germany
| | - Lech-Gustav Milroy
- Laboratory of Chemical Biology , Department of Biomedical Engineering and Institute for Complex Molecular Systems , Eindhoven University of Technology , P. O. Box 513 , 5600MB , Eindhoven , The Netherlands .
| | - Luc Brunsveld
- Laboratory of Chemical Biology , Department of Biomedical Engineering and Institute for Complex Molecular Systems , Eindhoven University of Technology , P. O. Box 513 , 5600MB , Eindhoven , The Netherlands .
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195
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Campanacci V, Urvoas A, Consolati T, Cantos-Fernandes S, Aumont-Nicaise M, Valerio-Lepiniec M, Surrey T, Minard P, Gigant B. Selection and Characterization of Artificial Proteins Targeting the Tubulin α Subunit. Structure 2019; 27:497-506.e4. [PMID: 30661854 PMCID: PMC6408325 DOI: 10.1016/j.str.2018.12.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2018] [Revised: 10/24/2018] [Accepted: 12/03/2018] [Indexed: 11/08/2022]
Abstract
Microtubules are cytoskeletal filaments of eukaryotic cells made of αβ-tubulin heterodimers. Structural studies of non-microtubular tubulin rely mainly on molecules that prevent its self-assembly and are used as crystallization chaperones. Here we identified artificial proteins from an αRep library that are specific to α-tubulin. Turbidity experiments indicate that these αReps impede microtubule assembly in a dose-dependent manner and total internal reflection fluorescence microscopy further shows that they specifically block growth at the microtubule (−) end. Structural data indicate that they do so by targeting the α-tubulin longitudinal surface. Interestingly, in one of the complexes studied, the α subunit is in a conformation that is intermediate between the ones most commonly observed in X-ray structures of tubulin and those seen in the microtubule, emphasizing the plasticity of tubulin. These α-tubulin-specific αReps broaden the range of tools available for the mechanistic study of microtubule dynamics and its regulation. Selection of α-tubulin-specific artificial αRep proteins The αReps inhibit microtubule assembly and specifically block growth at the (−) end The αReps target the longitudinal surface of α-tubulin The αReps are useful tools for the mechanistic study of microtubule dynamics
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Affiliation(s)
- Valérie Campanacci
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette Cedex 91198, France
| | - Agathe Urvoas
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette Cedex 91198, France
| | - Tanja Consolati
- The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Soraya Cantos-Fernandes
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette Cedex 91198, France
| | - Magali Aumont-Nicaise
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette Cedex 91198, France
| | - Marie Valerio-Lepiniec
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette Cedex 91198, France
| | - Thomas Surrey
- The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Philippe Minard
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette Cedex 91198, France.
| | - Benoît Gigant
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette Cedex 91198, France.
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196
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Sosonyuk SE, Peshich A, Tutushkina AV, Khlevin DA, Lozinskaya NA, Gracheva YA, Glazunova VA, Osolodkin DI, Semenova MN, Semenov VV, Palyulin VA, Proskurnina MV, Shtil AA, Zefirov NS. Synthesis and cytotoxicity of novel simplified eleutherobin analogues as potential antitumour agents. Org Biomol Chem 2019; 17:2792-2797. [DOI: 10.1039/c8ob02915f] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Synthesis of title compounds based on adamantane and 8-oxabicyclo[3.2.1]octane scaffolds and evaluation of their biological activity.
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197
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Donhauser ZJ, Appadoo V, Kliman EJ, Jobs WB, Sheffield EC. Structural Changes in Tubulin Sheets Caused by Immobilization on Solid Supports. ACS OMEGA 2018; 3:18196-18202. [PMID: 30613819 PMCID: PMC6312633 DOI: 10.1021/acsomega.8b02475] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/21/2018] [Accepted: 12/11/2018] [Indexed: 06/09/2023]
Abstract
In the presence of zinc, the protein tubulin assembles into two-dimensional sheets that are a useful model system for the study of both tubulin and microtubule structure. Tubulin sheets present an ideal protein structure for study with atomic force microscopy because they contain a two-dimensional crystalline protein lattice and retain many of the structural features of tubulin and microtubules. However, high-resolution imaging requires nonperturbative immobilization onto an appropriate imaging substrate. In this report, several substrates commonly used for scanning probe microscopy are evaluated for their ability to effectively immobilize tubulin sheets: mica, gold, highly ordered pyrolytic graphite, and carbon-coated electron microscopy grids. We hypothesize that the different intermolecular interactions presented by these substrates will affect the morphology of adsorbed tubulin sheets as well as the amount of other contaminating adsorbates. Tubulin sheets were successfully imaged on all of these substrates and structural characterization is reported. The most consistent results were obtained on carbon-coated electron microscopy grids, which preserved fine structural features of the sheets and had the least amount of contamination from the adsorption of unpolymerized tubulin. Images of tubulin sheets obtained with atomic force microscopy also compare favorably with published electron micrographs of sheets produced using similar procedures. This work demonstrates the importance of assessing substrate effects when studying two-dimensional protein crystals and identifies suitable substrates for immobilizing tubulin sheets.
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Affiliation(s)
| | | | - Elysa J. Kliman
- Vassar College, 124 Raymond Avenue, Poughkeepsie, New York 12604, United States
| | - William B. Jobs
- Vassar College, 124 Raymond Avenue, Poughkeepsie, New York 12604, United States
| | - Evan C. Sheffield
- Vassar College, 124 Raymond Avenue, Poughkeepsie, New York 12604, United States
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198
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Majumdar S, Basu D, Ghosh Dastidar S. Conformational States of E7010 Is Complemented by Microclusters of Water Inside the α,β-Tubulin Core. J Chem Inf Model 2018; 59:2274-2286. [PMID: 30516382 DOI: 10.1021/acs.jcim.8b00538] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The α,β-tubulin is the building block of microtubules, which is associated with and dissociated from the microtubular architecture complying with the dynamic instability of the microtubules. This dynamic instability has a direct relation with the spindle formation by the microtubules and cell division kinetics. E7010 is one of the promising ligands of an α,β-tubulin protein that binds at the core of this protein and can diminish the protein's ability to fit to a growing microtubule, thus frustrating cell division. Although X-ray crystallography has reported a specific binding conformation of E7010 in PDB, molecular dynamics (MD) simulations have revealed two other conformational states of the ligand capable of binding to tubulin with stabilities close to that state reported in PDB. To rationalize this quasidegeneracy of ligand binding modes, MD simulations have further revealed that the understanding of the mechanism of E7010-tubulin binding remains incomplete unless the role of water molecules to bridge this interaction is taken into consideration, a very critical insight that was not visible from the PDB structure. Further, these water molecules differ from the standard examples of "bridging" waters which generally exist as isolated water molecules between the receptor and the ligand. In the present case, the water molecules sandwiched between ligand and protein, sequestered from the bulk solvent, integrate with each other by an H-bonds network forming a group, which appear as microclusters of water. The structural packing with the ligand binding pocket and the bridging interactions between protein and ligand take place through such clusters. The presence of this microcluster of water is not just cosmetic, instead they have a crucial impact on the ligand binding thermodynamics. Only with the explicit consideration of these water clusters in the binding energy calculations (MMGBSA) is the stability of the native mode of ligand binding reported in PDB rationalized. At the same time, two other binding modes are elucidated to be quasi-degenerate with the native state and that indicates the further possibility in gaining more entropic stabilization of the complex. The role of such "bridging" water clusters to enhance the protein-ligand interaction will be insightful for designing the next generation prospective compounds in the field of cancer therapeutics.
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Affiliation(s)
- Sarmistha Majumdar
- Division of Bioinformatics , Bose Institute , P-1/12 C.I.T. Scheme VII M , Kolkata 700054 , India
| | - Debadrita Basu
- Division of Bioinformatics , Bose Institute , P-1/12 C.I.T. Scheme VII M , Kolkata 700054 , India
| | - Shubhra Ghosh Dastidar
- Division of Bioinformatics , Bose Institute , P-1/12 C.I.T. Scheme VII M , Kolkata 700054 , India
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199
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Manka SW, Moores CA. Microtubule structure by cryo-EM: snapshots of dynamic instability. Essays Biochem 2018; 62:737-751. [PMID: 30315096 PMCID: PMC6281474 DOI: 10.1042/ebc20180031] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2018] [Revised: 09/14/2018] [Accepted: 09/19/2018] [Indexed: 01/24/2023]
Abstract
The development of cryo-electron microscopy (cryo-EM) allowed microtubules to be captured in their solution-like state, enabling decades of insight into their dynamic mechanisms and interactions with binding partners. Cryo-EM micrographs provide 2D visualization of microtubules, and these 2D images can also be used to reconstruct the 3D structure of the polymer and any associated binding partners. In this way, the binding sites for numerous components of the microtubule cytoskeleton-including motor domains from many kinesin motors, and the microtubule-binding domains of dynein motors and an expanding collection of microtubule associated proteins-have been determined. The effects of various microtubule-binding drugs have also been studied. High-resolution cryo-EM structures have also been used to probe the molecular basis of microtubule dynamic instability, driven by the GTPase activity of β-tubulin. These studies have shown the conformational changes in lattice-confined tubulin dimers in response to steps in the tubulin GTPase cycle, most notably lattice compaction at the longitudinal inter-dimer interface. Although work is ongoing to define a complete structural model of dynamic instability, attention has focused on the role of gradual destabilization of lateral contacts between tubulin protofilaments, particularly at the microtubule seam. Furthermore, lower resolution cryo-electron tomography 3D structures are shedding light on the heterogeneity of microtubule ends and how their 3D organization contributes to dynamic instability. The snapshots of these polymers captured using cryo-EM will continue to provide critical insights into their dynamics, interactions with cellular components, and the way microtubules contribute to cellular functions in diverse physiological contexts.
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Affiliation(s)
- Szymon W Manka
- Institute of Structural and Molecular Biology, Department of Biological Sciences, Birkbeck, University of London, London, U.K.
| | - Carolyn A Moores
- Institute of Structural and Molecular Biology, Department of Biological Sciences, Birkbeck, University of London, London, U.K
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200
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Nile Tilapia Derived Antimicrobial Peptide TP4 Exerts Antineoplastic Activity Through Microtubule Disruption. Mar Drugs 2018; 16:md16120462. [PMID: 30469546 PMCID: PMC6315541 DOI: 10.3390/md16120462] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2018] [Revised: 11/16/2018] [Accepted: 11/16/2018] [Indexed: 01/04/2023] Open
Abstract
Some antimicrobial peptides (AMPs) exhibit anti-cancer activity, acting on cancer cells either by causing membrane lysis or via intracellular effects. While intracellular penetration of AMPs has been shown to cause cancer cell death, the mechanisms of toxicity remain largely unknown. Here we show that a tilapia-derived AMP, Tilapia piscidin (TP) 4, penetrates intracellularly and targets the microtubule network. A pull-down assay identified α-Tubulin as a major interaction partner for TP4, and molecular docking analysis suggested that Phe1, Ile16, and Arg23 on TP4 are required for the interaction. TP4 treatment in A549 cells was found to disrupt the microtubule network in cells, and mutation of the essential TP4 residues prevented microtubule depolymerization in vitro. Importantly, the TP4 mutants also showed decreased cytotoxicity in A549 cells, suggesting that microtubule disruption is a major mechanistic component of TP4-mediated death in lung carcinoma cells.
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