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Jash M, Ghosh S, Roy R, Mukherjee N, Sen S, Ghosh S. Next generation antimitotic β-carboline derivatives modulate microtubule dynamics and downregulate NF-κB, ERK 1/2 and phospho HSP 27. Life Sci 2024; 351:122836. [PMID: 38879159 DOI: 10.1016/j.lfs.2024.122836] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2024] [Revised: 06/01/2024] [Accepted: 06/11/2024] [Indexed: 06/21/2024]
Abstract
AIM Exploring the efficacy of β-carboline-based molecular inhibitors in targeting microtubules for the development of novel anticancer therapeutics. MATERIALS AND METHODS We synthesized a series of 1-Aryl-N-substituted-β-carboline-3-carboxamide compounds and evaluated their cytotoxicity against human lung carcinoma (A549) cells using the MTT assay. Normal lung fibroblast cells (WI-38) were used to assess compound selectivity. The mechanism of action of MJ-211 was elucidated through Western blot analysis of key pro-apoptotic and cell cycle regulatory proteins. Additionally, the inhibitory effect of MJ-211 on multicellular 3D spheroid growth of A549 cells was evaluated. KEY FINDINGS Lead compound MJ-211 exhibited remarkable cytotoxicity against A549 cells with an IC50 of 4.075 μM at 24 h treatment and IC50 of 1.7 nM after 72 h of treatment, while demonstrating selectivity towards normal WI-38 cells. MJ-211 activated pro-apoptotic factors Bim and p53, and suppressed Cyclin B1, Phospho HSP 27, BubR1, Mad 2, ERK1/2, and NF-κB, indicating its potent antimitotic and pro-apoptotic effects. MJ-211 significantly suppressed the migration of cells and inhibited the growth of A549 cell-derived multicellular 3D spheroids, highlighting its efficacy in a more physiologically relevant model. SIGNIFICANCE Cytotoxic effect of MJ-211 against cancer cells, selectivity towards normal cells, and ability to modulate key regulatory proteins involved in apoptosis and cell cycle progression underscore its potential as a promising template for further anticancer lead optimization. Moreover, the inhibitory effect of MJ-211 on multicellular spheroid growth suggests its efficacy in combating tumor heterogeneity and resistance mechanisms, thereby offering a promising avenue for future anticancer drug development.
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Affiliation(s)
- Moumita Jash
- Department of Bioscience and Bioengineering, Indian Institute of Technology, Jodhpur, Rajasthan, India
| | - Satyajit Ghosh
- Department of Bioscience and Bioengineering, Indian Institute of Technology, Jodhpur, Rajasthan, India
| | - Rajsekhar Roy
- Department of Bioscience and Bioengineering, Indian Institute of Technology, Jodhpur, Rajasthan, India
| | - Nabanita Mukherjee
- Smart Healthcare Department, Interdisciplinary Research Platform, Indian Institute of Technology, Jodhpur, Rajasthan, India
| | - Samya Sen
- iHUB Drishti Foundation, Indian Institute of Technology, Jodhpur, Rajasthan, India
| | - Surajit Ghosh
- Department of Bioscience and Bioengineering, Indian Institute of Technology, Jodhpur, Rajasthan, India; Smart Healthcare Department, Interdisciplinary Research Platform, Indian Institute of Technology, Jodhpur, Rajasthan, India; iHUB Drishti Foundation, Indian Institute of Technology, Jodhpur, Rajasthan, India.
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2
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Blume RY, Rabokon AM, Pydiura M, Yemets AI, Pirko YV, Blume YB. Genome-wide identification and evolution of the tubulin gene family in Camelina sativa. BMC Genomics 2024; 25:599. [PMID: 38877397 PMCID: PMC11177405 DOI: 10.1186/s12864-024-10503-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2024] [Accepted: 06/06/2024] [Indexed: 06/16/2024] Open
Abstract
BACKGROUND Tubulins play crucial roles in numerous fundamental processes of plant development. In flowering plants, tubulins are grouped into α-, β- and γ-subfamilies, while α- and β-tubulins possess a large isotype diversity and gene number variations among different species. This circumstance leads to insufficient recognition of orthologous isotypes and significantly complicates extrapolation of obtained experimental results, and brings difficulties for the identification of particular tubulin isotype function. The aim of this research is to identify and characterize tubulins of an emerging biofuel crop Camelina sativa. RESULTS We report comprehensive identification and characterization of tubulin gene family in C. sativa, including analyses of exon-intron organization, duplicated genes comparison, proper isotype designation, phylogenetic analysis, and expression patterns in different tissues. 17 α-, 34 β- and 6 γ-tubulin genes were identified and assigned to a particular isotype. Recognition of orthologous tubulin isotypes was cross-referred, involving data of phylogeny, synteny analyses and genes allocation on reconstructed genomic blocks of Ancestral Crucifer Karyotype. An investigation of expression patterns of tubulin homeologs revealed the predominant role of N6 (A) and N7 (B) subgenomes in tubulin expression at various developmental stages, contrarily to general the dominance of transcripts of H7 (C) subgenome. CONCLUSIONS For the first time a complete set of tubulin gene family members was identified and characterized for allohexaploid C. sativa species. The study demonstrates the comprehensive approach of precise inferring gene orthology. The applied technique allowed not only identifying C. sativa tubulin orthologs in model Arabidopsis species and tracking tubulin gene evolution, but also uncovered that A. thaliana is missing orthologs for several particular isotypes of α- and β-tubulins.
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Affiliation(s)
- Rostyslav Y Blume
- Institute of Food Biotechnology and Genomics of National Academy of Sciences of Ukraine, Kyiv, 02000, Ukraine.
| | - Anastasiia M Rabokon
- Institute of Food Biotechnology and Genomics of National Academy of Sciences of Ukraine, Kyiv, 02000, Ukraine
| | - Mykola Pydiura
- Institute of Food Biotechnology and Genomics of National Academy of Sciences of Ukraine, Kyiv, 02000, Ukraine
- JSC "Farmak", Kyiv, 04080, Ukraine
| | - Alla I Yemets
- Institute of Food Biotechnology and Genomics of National Academy of Sciences of Ukraine, Kyiv, 02000, Ukraine
| | - Yaroslav V Pirko
- Institute of Food Biotechnology and Genomics of National Academy of Sciences of Ukraine, Kyiv, 02000, Ukraine
| | - Yaroslav B Blume
- Institute of Food Biotechnology and Genomics of National Academy of Sciences of Ukraine, Kyiv, 02000, Ukraine
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3
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Stathatos GG, Merriner DJ, O'Connor AE, Zenker J, Dunleavy JE, O'Bryan MK. Epsilon tubulin is an essential determinant of microtubule-based structures in male germ cells. EMBO Rep 2024; 25:2722-2742. [PMID: 38773322 PMCID: PMC11169422 DOI: 10.1038/s44319-024-00159-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2023] [Revised: 04/08/2024] [Accepted: 04/30/2024] [Indexed: 05/23/2024] Open
Abstract
Alpha, beta, and gamma tubulins are essential building blocks for all eukaryotic cells. The functions of the non-canonical tubulins, delta, epsilon, and zeta, however, remain poorly understood and their requirement in mammalian development untested. Herein we have used a spermatogenesis model to define epsilon tubulin (TUBE1) function in mice. We show that TUBE1 is essential for the function of multiple complex microtubule arrays, including the meiotic spindle, axoneme and manchette and in its absence, there is a dramatic loss of germ cells and male sterility. Moreover, we provide evidence for the interplay between TUBE1 and katanin-mediated microtubule severing, and for the sub-specialization of individual katanin paralogs in the regulation of specific microtubule arrays.
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Affiliation(s)
- G Gemma Stathatos
- School of BioSciences and Bio21 Institute of Molecular Science and Biotechnology, Faculty of Science, The University of Melbourne, Parkville, VIC, 3010, Australia
- Australian Regenerative Medicine Institute, Monash University, Clayton, VIC, 3800, Australia
| | - D Jo Merriner
- School of BioSciences and Bio21 Institute of Molecular Science and Biotechnology, Faculty of Science, The University of Melbourne, Parkville, VIC, 3010, Australia
| | - Anne E O'Connor
- School of BioSciences and Bio21 Institute of Molecular Science and Biotechnology, Faculty of Science, The University of Melbourne, Parkville, VIC, 3010, Australia
| | - Jennifer Zenker
- Australian Regenerative Medicine Institute, Monash University, Clayton, VIC, 3800, Australia
| | - Jessica Em Dunleavy
- School of BioSciences and Bio21 Institute of Molecular Science and Biotechnology, Faculty of Science, The University of Melbourne, Parkville, VIC, 3010, Australia.
| | - Moira K O'Bryan
- School of BioSciences and Bio21 Institute of Molecular Science and Biotechnology, Faculty of Science, The University of Melbourne, Parkville, VIC, 3010, Australia.
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4
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Babcock NS, Montes-Cabrera G, Oberhofer KE, Chergui M, Celardo GL, Kurian P. Ultraviolet Superradiance from Mega-Networks of Tryptophan in Biological Architectures. J Phys Chem B 2024; 128:4035-4046. [PMID: 38641327 DOI: 10.1021/acs.jpcb.3c07936] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/21/2024]
Abstract
Networks of tryptophan (Trp)─an aromatic amino acid with strong fluorescence response─are ubiquitous in biological systems, forming diverse architectures in transmembrane proteins, cytoskeletal filaments, subneuronal elements, photoreceptor complexes, virion capsids, and other cellular structures. We analyze the cooperative effects induced by ultraviolet (UV) excitation of several biologically relevant Trp mega-networks, thus giving insights into novel mechanisms for cellular signaling and control. Our theoretical analysis in the single-excitation manifold predicts the formation of strongly superradiant states due to collective interactions among organized arrangements of up to >105 Trp UV-excited transition dipoles in microtubule architectures, which leads to an enhancement of the fluorescence quantum yield (QY) that is confirmed by our experiments. We demonstrate the observed consequences of this superradiant behavior in the fluorescence QY for hierarchically organized tubulin structures, which increases in different geometric regimes at thermal equilibrium before saturation, highlighting the effect's persistence in the presence of disorder. Our work thus showcases the many orders of magnitude across which the brightest (hundreds of femtoseconds) and darkest (tens of seconds) states can coexist in these Trp lattices.
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Affiliation(s)
- N S Babcock
- Quantum Biology Laboratory, Howard University, Washington, D.C. 20060, United States
| | - G Montes-Cabrera
- Quantum Biology Laboratory, Howard University, Washington, D.C. 20060, United States
- Institute of Physics, Benemérita Universidad Autónoma de Puebla, Puebla 72570, Mexico
| | - K E Oberhofer
- Lausanne Centre for Ultrafast Science, École Polytechnique Fédérale de Lausanne, Lausanne CH-1015, Switzerland
| | - M Chergui
- Lausanne Centre for Ultrafast Science, École Polytechnique Fédérale de Lausanne, Lausanne CH-1015, Switzerland
| | - G L Celardo
- Department of Physics and Astronomy, Università degli Studi di Firenze, Florence 50019, Italy
| | - P Kurian
- Quantum Biology Laboratory, Howard University, Washington, D.C. 20060, United States
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5
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Yang C, Wang Y, Su Z, Xiong L, Wang P, Lei W, Yan X, Ma D, Zhao G, Zhou Z. Biosynthesis of the highly oxygenated tetracyclic core skeleton of Taxol. Nat Commun 2024; 15:2339. [PMID: 38490987 PMCID: PMC10942993 DOI: 10.1038/s41467-024-46583-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Accepted: 03/03/2024] [Indexed: 03/18/2024] Open
Abstract
Taxol is a widely-applied anticancer drug that inhibits microtubule dynamics in actively replicating cells. Although a minimum 19-step biosynthetic pathway has been proposed and 16 enzymes likely involved have been characterized, stepwise biosynthetic reactions from the well-characterized di-oxygenated taxoids to Taxol tetracyclic core skeleton are yet to be elucidated. Here, we uncover the biosynthetic pathways for a few tri-oxygenated taxoids via confirming the critical reaction order of the second and third hydroxylation steps, unearth a taxoid 9α-hydroxylase catalyzing the fourth hydroxylation, and identify CYP725A55 catalyzing the oxetane ester formation via a cascade oxidation-concerted acyl rearrangement mechanism. After identifying a acetyltransferase catalyzing the formation of C7-OAc, the pathway producing the highly-oxygenated 1β-dehydroxybaccatin VI with the Taxol tetracyclic core skeleton is elucidated and its complete biosynthesis from taxa-4(20),11(12)-diene-5α-ol is achieved in an engineered yeast. These systematic studies lay the foundation for the complete elucidation of the biosynthetic pathway of Taxol.
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Affiliation(s)
- Chengshuai Yang
- Key Laboratories of Plant Design and Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
| | - Yan Wang
- Key Laboratories of Plant Design and Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
| | - Zhen Su
- Key Laboratories of Plant Design and Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Lunyi Xiong
- Key Laboratories of Plant Design and Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Pingping Wang
- Key Laboratories of Plant Design and Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
| | - Wen Lei
- Shanghai Research Institute of Chemical Industry, Shanghai, China
| | - Xing Yan
- Key Laboratories of Plant Design and Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China.
| | - Dawei Ma
- State Key Laboratory of Chemical Biology, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai, China.
| | - Guoping Zhao
- Key Laboratories of Plant Design and Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China.
- Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China.
| | - Zhihua Zhou
- Key Laboratories of Plant Design and Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China.
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6
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Chen X, Varghese S, Zhang Z, Du J, Ruan B, Baell JB, Liu X. Drug discovery and optimization based on the co-crystal structure of natural product with target. Eur J Med Chem 2024; 266:116126. [PMID: 38232464 DOI: 10.1016/j.ejmech.2024.116126] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Revised: 01/03/2024] [Accepted: 01/03/2024] [Indexed: 01/19/2024]
Abstract
Due to their structural diversities and prevalent biological activities, natural products (NPs) are momentous resources for drug discovery. Although NPs have a wide range of biological activities, many exhibit structural complexity that leads to synthetic difficulties, which combines with inefficient biological activity, toxicity, and unfavorable pharmacokinetic characteristics and ultimately imparts poor safety and efficacy outcomes. Progress in crystallization and computational techniques allow crystallography to have a seasonable influences on drug discovery. By co-crystallizing with proteins, therapeutic targets of NPs in specific diseases can be identified. By analyzing the co-crystal information, the structure-activity relationships (SARs) of NPs targeting specific proteins can be grasped. Under the guidance of co-crystal information, directional structural modification and simplification are powerful strategies for overcoming limitations of NPs, improving the success rate of NP-based drug discovery, and obtaining NP-based drugs with high selectivity, low toxicity and favorable pharmacokinetic characteristics. Here, we review the co-crystal information of a selection of NPs, focusing on the SARs of NPs reflected by co-crystal information and the modification and simplification strategies of NPs, and discuss how to apply co-crystal information in the optimization of NP-based lead compound.
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Affiliation(s)
- Xing Chen
- School of Pharmacy, Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Anhui Medical University, Hefei, 230032, PR China; School of Public Health, Key Laboratory of Population Health Across Life Cycle, Anhui Medical University, Hefei, 230032, PR China.
| | - Swapna Varghese
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Melbourne, Victoria, 3052, Australia.
| | - Zhaoyan Zhang
- School of Pharmacy, Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Anhui Medical University, Hefei, 230032, PR China.
| | - Juncheng Du
- School of Pharmacy, Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Anhui Medical University, Hefei, 230032, PR China.
| | - Banfeng Ruan
- Key Lab of Biofabrication of Anhui Higher Education, Hefei University, Hefei, 230601, PR China.
| | - Jonathan B Baell
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Melbourne, Victoria, 3052, Australia.
| | - Xinhua Liu
- School of Pharmacy, Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Anhui Medical University, Hefei, 230032, PR China.
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7
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Taheri A, Wang Z, Singal B, Guo F, Al-Bassam J. Cryo-EM structures of the tubulin cofactors reveal the molecular basis for the biogenesis of alpha/beta-tubulin. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.29.577855. [PMID: 38405852 PMCID: PMC10889022 DOI: 10.1101/2024.01.29.577855] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/27/2024]
Abstract
Microtubule polarity and dynamic polymerization originate from the self-association properties of the a-tubulin heterodimer. For decades, it has remained poorly understood how the tubulin cofactors, TBCD, TBCE, TBCC, and the Arl2 GTPase mediate a-tubulin biogenesis from α- and β-tubulins. Here, we use cryogenic electron microscopy to determine structures of tubulin cofactors bound to αβ-tubulin. These structures show that TBCD, TBCE, and Arl2 form a heterotrimeric cage-like TBC-DEG assembly around the a-tubulin heterodimer. TBCD wraps around Arl2 and almost entirely encircles -tubulin, while TBCE forms a lever arm that anchors along the other end of TBCD and rotates α-tubulin. Structures of the TBC-DEG-αβ-tubulin assemblies bound to TBCC reveal the clockwise rotation of the TBCE lever that twists a-tubulin by pulling its C-terminal tail while TBCD holds -tubulin in place. Altogether, these structures uncover transition states in αβ-tubulin biogenesis, suggesting a vise-like mechanism for the GTP-hydrolysis dependent a-tubulin biogenesis mediated by TBC-DEG and TBCC. These structures provide the first evidence of the critical functions of the tubulin cofactors as enzymes that regulate the invariant organization of αβ-tubulin, by catalyzing α- and β-tubulin assembly, disassembly, and subunit exchange which are crucial for regulating the polymerization capacities of αβ-tubulins into microtubules.
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8
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Abbaali I, Truong D, Day SD, Mushayeed F, Ganesh B, Haro-Ramirez N, Isles J, Nag H, Pham C, Shah P, Tomar I, Manel-Romero C, Morrissette NS. The tubulin database: Linking mutations, modifications, ligands and local interactions. PLoS One 2023; 18:e0295279. [PMID: 38064432 PMCID: PMC10707541 DOI: 10.1371/journal.pone.0295279] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Accepted: 11/20/2023] [Indexed: 12/18/2023] Open
Abstract
Microtubules are polymeric filaments, constructed of α-β tubulin heterodimers that underlie critical subcellular structures in eukaryotic organisms. Four homologous proteins (γ-, δ-, ε- and ζ-tubulin) additionally contribute to specialized microtubule functions. Although there is an immense volume of publicly available data pertaining to tubulins, it is difficult to assimilate all potentially relevant information across diverse organisms, isotypes, and categories of data. We previously assembled an extensive web-based catalogue of published missense mutations to tubulins with >1,500 entries that each document a specific substitution to a discrete tubulin, the species where the mutation was described and the associated phenotype with hyperlinks to the amino acid sequence and citation(s) for research. This report describes a significant update and expansion of our online resource (TubulinDB.bio.uci.edu) to nearly 18,000 entries. It now encompasses a cross-referenced catalog of post-translational modifications (PTMs) to tubulin drawn from public datasets, primary literature, and predictive algorithms. In addition, tubulin protein structures were used to define local interactions with bound ligands (GTP, GDP and diverse microtubule-targeting agents) and amino acids at the intradimer interface, within the microtubule lattice and with associated proteins. To effectively cross-reference these datasets, we established a universal tubulin numbering system to map entries into a common framework that accommodates specific insertions and deletions to tubulins. Indexing and cross-referencing permitted us to discern previously unappreciated patterns. We describe previously unlinked observations of loss of PTM sites in the context of cancer cells and tubulinopathies. Similarly, we expanded the set of clinical substitutions that may compromise MAP or microtubule-motor interactions by collecting tubulin missense mutations that alter amino acids at the interface with dynein and doublecortin. By expanding the database as a curated resource, we hope to relate model organism data to clinical findings of pathogenic tubulin variants. Ultimately, we aim to aid researchers in hypothesis generation and design of studies to dissect tubulin function.
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Affiliation(s)
- Izra Abbaali
- Department of Molecular Biology and Biochemistry, University of California, Irvine, CA, United States of America
| | - Danny Truong
- Department of Molecular Biology and Biochemistry, University of California, Irvine, CA, United States of America
| | - Shania Deon Day
- Department of Molecular Biology and Biochemistry, University of California, Irvine, CA, United States of America
| | - Faliha Mushayeed
- Department of Molecular Biology and Biochemistry, University of California, Irvine, CA, United States of America
| | - Bhargavi Ganesh
- Department of Molecular Biology and Biochemistry, University of California, Irvine, CA, United States of America
| | - Nancy Haro-Ramirez
- Department of Molecular Biology and Biochemistry, University of California, Irvine, CA, United States of America
| | - Juliet Isles
- Department of Molecular Biology and Biochemistry, University of California, Irvine, CA, United States of America
| | - Hindol Nag
- Department of Molecular Biology and Biochemistry, University of California, Irvine, CA, United States of America
| | - Catherine Pham
- Department of Molecular Biology and Biochemistry, University of California, Irvine, CA, United States of America
| | - Priya Shah
- Department of Molecular Biology and Biochemistry, University of California, Irvine, CA, United States of America
| | - Ishaan Tomar
- Department of Molecular Biology and Biochemistry, University of California, Irvine, CA, United States of America
| | - Carolina Manel-Romero
- Department of Molecular Biology and Biochemistry, University of California, Irvine, CA, United States of America
| | - Naomi S. Morrissette
- Department of Molecular Biology and Biochemistry, University of California, Irvine, CA, United States of America
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Li D, Jiang W. Classification of helical polymers with deep-learning language models. J Struct Biol 2023; 215:108041. [PMID: 37939748 PMCID: PMC10843845 DOI: 10.1016/j.jsb.2023.108041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2023] [Revised: 10/11/2023] [Accepted: 10/31/2023] [Indexed: 11/10/2023]
Abstract
Many macromolecules in biological systems exist in the form of helical polymers. However, the inherent polymorphism and heterogeneity of samples complicate the reconstruction of helical polymers from cryo-EM images. Currently, available 2D classification methods are effective at separating particles of interest from contaminants, but they do not effectively differentiate between polymorphs, resulting in heterogeneity in the 2D classes. As such, it is crucial to develop a method that can computationally divide a dataset of polymorphic helical structures into homogenous subsets. In this work, we utilized deep-learning language models to embed the filaments as vectors in hyperspace and group them into clusters. Tests with both simulated and experimental datasets have demonstrated that our method - HLM (Helical classification with Language Model) can effectively distinguish different types of filaments, in the presence of many contaminants and low signal-to-noise ratios. We also demonstrate that HLM can isolate homogeneous subsets of particles from a publicly available dataset, resulting in the discovery of a previously unreported filament variant with an extra density around the tau filaments.
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Affiliation(s)
- Daoyi Li
- Department of Biological Sciences, Purdue University
| | - Wen Jiang
- Department of Biological Sciences, Purdue University.
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10
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Kharb S, Yadav S, Singh A, Sarkar A, Tomar R. Molecular docking and physicochemical studies of 1,3-benzodioxole tagged Dacarbazine derivatives as an anticancer agent. ARTIFICIAL CELLS, NANOMEDICINE, AND BIOTECHNOLOGY 2023; 51:520-530. [PMID: 37698454 DOI: 10.1080/21691401.2023.2253470] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Revised: 05/22/2023] [Accepted: 08/11/2023] [Indexed: 09/13/2023]
Abstract
Cancer, the biggest cause of death globally, remains a tough illness despite enormous advances in therapy. In the present study, 1,3-benzodioxole-tagged dacarbazine derivates were investigated as microtubule inhibitors in order to control cancer as microtubules are involved in cell proliferation. The tubulin protein was analyzed and its structure was validated by various protein validation tools. The binding potential of 1,3-benzodioxole-based dacarbazine-tagged derivatives with tubulin was checked using molecular docking software HEX 8.0 CUDA and AutoDock Vina. Swiss ADME online Web server and pkCSM are used for studying pharmacokinetic and pharmacological studies of compounds. The docking analysis ADME studies displayed that Compounds 1 and 2 bind effectively with the tubulin protein and showed potential properties to use as a potent anticancer drug.
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Affiliation(s)
- Sonaxi Kharb
- Department of Chemistry, Baba Mastnath University, Rohtak, India
| | - Sangeeta Yadav
- Department of Chemistry, Netaji Subhas University of Technology, Dwarka, India
| | - Anshul Singh
- Department of Chemistry, Baba Mastnath University, Rohtak, India
| | - Anjana Sarkar
- Department of Chemistry, Netaji Subhas University of Technology, Dwarka, India
| | - Ravi Tomar
- Department of Chemistry, Institute of Basic Sciences, Maharaja Surajmal Brij University, Bharatpur, Rajasthan-321201, India
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11
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Sánchez-Carranza JN, Redondo-Horcajo M, Barasoain I, Escobar-Aguilar EA, Millán-Pacheco C, Alvarez L, Salas Vidal E, Diaz JF, Gonzalez-Maya L. Tannic Acid and Ethyl Gallate Potentialize Paclitaxel Effect on Microtubule Dynamics in Hep3B Cells. Pharmaceuticals (Basel) 2023; 16:1579. [PMID: 38004444 PMCID: PMC10675698 DOI: 10.3390/ph16111579] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Revised: 10/31/2023] [Accepted: 11/01/2023] [Indexed: 11/26/2023] Open
Abstract
Among broad-spectrum anticancer agents, paclitaxel (PTX) has proven to be one of the most effective against solid tumors for which more specific treatments are lacking. However, drawbacks such as neurotoxicity and the development of resistance reduce its therapeutic efficacy. Therefore, there is a need for compounds able to improve its activity by synergizing with it or potentiating its effect, thus reducing the doses required. We investigated the interaction between PTX and tannins, other compounds with anticancer activity known to act as repressors of several proteins involved in oncological pathways. We found that both tannic acid (TA) and ethyl gallate (EG) strongly potentiate the toxicity of PTX in Hep3B cells, suggesting their utility in combination therapy. We also found that AT and EG promote tubulin polymerization and enhance the effect of PTX on tubulin, suggesting a direct interaction with tubulin. Biochemical experiments confirmed that TA, but not EG, binds tubulin and potentiates the apparent binding affinity of PTX for the tubulin binding site. Furthermore, the molecular docking of TA to tubulin suggests that TA can bind to two different sites on tubulin, one at the PTX site and the second at the interface of α and β-tubulin (cluster 2). The binding of TA to cluster 2 could explain the overstabilization in the tubulin + PTX combinatorial assay. Finally, we found that EG can inhibit PTX-induced expression of pAkt and pERK defensive protein kinases, which are involved in resistance to PXT, by limiting cell death (apoptosis) and favoring cell proliferation and cell cycle progression. Our results support that tannic acid and ethyl gallate are potential chemotherapeutic agents due to their potentiating effect on paclitaxel.
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Affiliation(s)
- Jessica Nayelli Sánchez-Carranza
- Facultad de Farmacia, Universidad Autónoma del Estado de Morelos, Av. Universidad 1001, Cuernavaca 62209, Morelos, Mexico; (J.N.S.-C.); (E.A.E.-A.); (C.M.-P.)
| | - Mariano Redondo-Horcajo
- Centro de Investigaciones Biológicas Margarita Salas—Consejo Superior de Investigaciones Científicas, 28040 Madrid, Spain; (M.R.-H.); (I.B.)
| | - Isabel Barasoain
- Centro de Investigaciones Biológicas Margarita Salas—Consejo Superior de Investigaciones Científicas, 28040 Madrid, Spain; (M.R.-H.); (I.B.)
| | - Ever Angel Escobar-Aguilar
- Facultad de Farmacia, Universidad Autónoma del Estado de Morelos, Av. Universidad 1001, Cuernavaca 62209, Morelos, Mexico; (J.N.S.-C.); (E.A.E.-A.); (C.M.-P.)
| | - César Millán-Pacheco
- Facultad de Farmacia, Universidad Autónoma del Estado de Morelos, Av. Universidad 1001, Cuernavaca 62209, Morelos, Mexico; (J.N.S.-C.); (E.A.E.-A.); (C.M.-P.)
| | - Laura Alvarez
- Centro de Investigaciones Químicas-IICBA, Universidad Autónoma del Estado de Morelos, Av. Universidad 1001, Cuernavaca 62209, Morelos, Mexico;
| | - Enrique Salas Vidal
- Departamento de Genética del Desarrollo y Fisiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca 62209, Morelos, Mexico;
| | - J. Fernando Diaz
- Centro de Investigaciones Biológicas Margarita Salas—Consejo Superior de Investigaciones Científicas, 28040 Madrid, Spain; (M.R.-H.); (I.B.)
| | - Leticia Gonzalez-Maya
- Facultad de Farmacia, Universidad Autónoma del Estado de Morelos, Av. Universidad 1001, Cuernavaca 62209, Morelos, Mexico; (J.N.S.-C.); (E.A.E.-A.); (C.M.-P.)
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12
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Ma Y, Josa-Prado F, Essif JN, Liu S, Li S, Lucena-Agell D, Chan PY, Goossens K, Hortigüela R, Matesanz R, Wang Y, Gago F, Wang H, Risinger A, Diaz JF, Fang WS. Modulation of taxane binding to tubulin curved and straight conformations by systematic 3'N modification provides for improved microtubule binding, persistent cytotoxicity and in vivo potency. Eur J Med Chem 2023; 259:115668. [PMID: 37490800 DOI: 10.1016/j.ejmech.2023.115668] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Revised: 07/13/2023] [Accepted: 07/18/2023] [Indexed: 07/27/2023]
Abstract
The taxane class of microtubule stabilizers are some of the most effective and widely used chemotherapeutics. The anticancer activity of taxanes arises from their ability to induce tubulin assembly by selectively recognizing the curved (c-) conformation in unassembled tubulin as compared to the straight (s-) conformation in assembled tubulin. We first designed and synthesized a series of 3'N-modified taxanes bearing covalent groups. Instead of discovering covalent taxanes, we found a series of non-covalent taxanes 2, in which the 3'N side chain was found to be essential for cytotoxicity due to its role in locking tubulin in the s-conformation. A representative compound bearing an acrylamide moiety (2h) exhibited increased binding affinity to the unassembled tubulin c-conformation and less cytotoxicity than paclitaxel. Further exploration of chemical space around 2h afforded a new series 3, in which derivatives such as 3l bind more tightly to both the s- and c-conformations of tubulin compared to paclitaxel, leading to more efficient promotion of tubulin polymerization and a greater persistence of in vitro efficacy against breast cancer cells after drug washout. Although 3l also had improved in vivo potency as compared to paclitaxel, it was also associated with increased systemic toxicity that required localized, intratumoral injection to observe potent and prolonged antitumor efficacy.
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Affiliation(s)
- Yuntao Ma
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines & Ministry of Health Key Laboratory of Biosynthesis of Natural Products, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, 2A Nan Wei Road, Beijing, 100050, China
| | - Fernando Josa-Prado
- Centro de Investigaciones Biológicas Margarita Salas, Consejo Superior de Investigaciones Científicas, Ramiro de Maeztu 9, Madrid, 28040, Spain
| | - Jacob Nathaniel Essif
- Department of Pharmacology, University of Texas Health Science Center at San Antonio, San Antonio, TX, 78229, United States
| | - Shuqi Liu
- Key Laboratory of Molecular Pharmacology and Drug Evaluation (Yantai University), Ministry of Education, Collaborative Innovation Center of Advanced Drug Delivery System and Biotech Drugs in Universities of Shandong, Yantai University, Yantai, 264005, China
| | - Shuo Li
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines & Ministry of Health Key Laboratory of Biosynthesis of Natural Products, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, 2A Nan Wei Road, Beijing, 100050, China
| | - Daniel Lucena-Agell
- Centro de Investigaciones Biológicas Margarita Salas, Consejo Superior de Investigaciones Científicas, Ramiro de Maeztu 9, Madrid, 28040, Spain
| | - Peter Yw Chan
- Department of Pharmacology, University of Texas Health Science Center at San Antonio, San Antonio, TX, 78229, United States
| | - Kenneth Goossens
- Centro de Investigaciones Biológicas Margarita Salas, Consejo Superior de Investigaciones Científicas, Ramiro de Maeztu 9, Madrid, 28040, Spain
| | - Rafael Hortigüela
- Centro de Investigaciones Biológicas Margarita Salas, Consejo Superior de Investigaciones Científicas, Ramiro de Maeztu 9, Madrid, 28040, Spain
| | - Ruth Matesanz
- Centro de Investigaciones Biológicas Margarita Salas, Consejo Superior de Investigaciones Científicas, Ramiro de Maeztu 9, Madrid, 28040, Spain
| | - Yingjie Wang
- Key Laboratory of Molecular Pharmacology and Drug Evaluation (Yantai University), Ministry of Education, Collaborative Innovation Center of Advanced Drug Delivery System and Biotech Drugs in Universities of Shandong, Yantai University, Yantai, 264005, China
| | - Federico Gago
- Área de Farmacología, Departamento de Ciencias Biomédicas, Unidad Asociada al Instituto de Química Médica del CSIC, Universidad de Alcalá, E-28805, Alcalá de Henares, Madrid, Spain
| | - Hongbo Wang
- Key Laboratory of Molecular Pharmacology and Drug Evaluation (Yantai University), Ministry of Education, Collaborative Innovation Center of Advanced Drug Delivery System and Biotech Drugs in Universities of Shandong, Yantai University, Yantai, 264005, China
| | - April Risinger
- Department of Pharmacology, University of Texas Health Science Center at San Antonio, San Antonio, TX, 78229, United States
| | - J Fernando Diaz
- Centro de Investigaciones Biológicas Margarita Salas, Consejo Superior de Investigaciones Científicas, Ramiro de Maeztu 9, Madrid, 28040, Spain.
| | - Wei-Shuo Fang
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines & Ministry of Health Key Laboratory of Biosynthesis of Natural Products, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, 2A Nan Wei Road, Beijing, 100050, China.
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13
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Xu C, Chen B, Huang S, Deng Z, Wang T. A point mutation in the rice alpha-tubulin gene OsTUBA3 causes grain notching. THE NEW PHYTOLOGIST 2023; 240:1052-1065. [PMID: 37615062 DOI: 10.1111/nph.19226] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Accepted: 07/28/2023] [Indexed: 08/25/2023]
Abstract
Grain notching is a common deformation that decreases rice (Oryza sativa) quality; however, the underlying molecular basis causing grain notching remains unclear. We report mechanisms underlying grain notching in Small and notched grain (Sng) mutants, which contained an arginine to histidine substitution at amino acid position 422 (R422H) of the α-tubulin protein OsTUBA3. The R422H mutation decreased cell length and increased cell width/height of glumes and caryopses, but led to elongated caryopses compressed within shortened glumes, thus giving rise to notched and small grains. Glume and caryopsis cells had different dimensional orientations relative to the directions of organ elongation. Thus, the abnormal cell expansion induced in glumes and caryopses by the R422H mutation had different effects on elongation of these organs. The R422H mutation in OsTUBA3 compromised β-tubulin binding and led to formation of defective heterodimers. This in turn affected tubulin incorporation and microtubule (MT) nucleation and regrowth, consequently leading to MT instability and reducing the transverse orientation. The defective MT dynamics affected cell expansion and shape, causing different alterations in glume and caryopsis dimensions and resulting in grain notching. These data indicate that Arg422 in OsTUBA3 is crucial for MT dynamics and that substitution with His causes grain notching, reducing grain quality and yield. These findings offer valuable insights into the molecular regulation underlying grain development in rice.
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Affiliation(s)
- Chenshan Xu
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- Dezhou University, Dezhou, Shandong, 253023, China
| | - Bingtang Chen
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Shanjin Huang
- Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Zhuyun Deng
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Tai Wang
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- College of Life Science, University of Chinese Academy of Sciences, Beijing, 100093, China
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14
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Diao L, Zheng W, Zhao Q, Liu M, Fu Z, Zhang X, Bao L, Cong Y. Cryo-EM of α-tubulin isotype-containing microtubules revealed a contracted structure of α4A/β2A microtubules. Acta Biochim Biophys Sin (Shanghai) 2023; 55:1551-1560. [PMID: 37439022 PMCID: PMC10577476 DOI: 10.3724/abbs.2023130] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Accepted: 04/14/2023] [Indexed: 07/14/2023] Open
Abstract
Microtubules are hollow α/β-tubulin heterodimeric polymers that play critical roles in cells. In vertebrates, both α- and β-tubulins have multiple isotypes encoded by different genes, which are intrinsic factors in regulating microtubule functions. However, the structures of microtubules composed of different tubulin isotypes, especially α-tubulin isotypes, remain largely unknown. Here, we purify recombinant tubulin heterodimers composed of different mouse α-tubulin isotypes, including α1A, α1C and α4A, with the β-tubulin isotype β2A. We further assemble and determine the cryo-electron microscopy (cryo-EM) structures of α1A/β2A, α1C/β2A, and α4A/β2A microtubules. Our structural analysis demonstrates that α4A/β2A microtubules exhibit longitudinal contraction between tubulin interdimers compared with α1A/β2A and α1C/β2A microtubules. Collectively, our findings reveal that α-tubulin isotype composition can tune microtubule structures, and also provide evidence for the "tubulin code" hypothesis.
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Affiliation(s)
- Lei Diao
- State Key Laboratory of Cell BiologyShanghai Institute of Biochemistry and Cell BiologyCenter for Excellence in Molecular Cell ScienceUniversity of Chinese Academy of SciencesChinese Academy of SciencesShanghai200031China
| | - Wei Zheng
- State Key Laboratory of Molecular BiologyShanghai Institute of Biochemistry and Cell BiologyCenter for Excellence in Molecular Cell ScienceUniversity of Chinese Academy of SciencesChinese Academy of SciencesShanghai200031China
| | - Qiaoyu Zhao
- State Key Laboratory of Molecular BiologyShanghai Institute of Biochemistry and Cell BiologyCenter for Excellence in Molecular Cell ScienceUniversity of Chinese Academy of SciencesChinese Academy of SciencesShanghai200031China
| | - Mingyi Liu
- State Key Laboratory of Cell BiologyShanghai Institute of Biochemistry and Cell BiologyCenter for Excellence in Molecular Cell ScienceUniversity of Chinese Academy of SciencesChinese Academy of SciencesShanghai200031China
- School of Life Science and TechnologyShanghaiTech UniversityShanghai201210China
| | - Zhenglin Fu
- State Key Laboratory of Molecular BiologyShanghai Institute of Biochemistry and Cell BiologyCenter for Excellence in Molecular Cell ScienceUniversity of Chinese Academy of SciencesChinese Academy of SciencesShanghai200031China
| | - Xu Zhang
- School of Life Science and TechnologyShanghaiTech UniversityShanghai201210China
- Shanghai Advanced Research InstituteChinese Academy of SciencesShanghai201210China
| | - Lan Bao
- State Key Laboratory of Cell BiologyShanghai Institute of Biochemistry and Cell BiologyCenter for Excellence in Molecular Cell ScienceUniversity of Chinese Academy of SciencesChinese Academy of SciencesShanghai200031China
- School of Life Science and TechnologyShanghaiTech UniversityShanghai201210China
| | - Yao Cong
- State Key Laboratory of Molecular BiologyShanghai Institute of Biochemistry and Cell BiologyCenter for Excellence in Molecular Cell ScienceUniversity of Chinese Academy of SciencesChinese Academy of SciencesShanghai200031China
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15
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Horgan MJ, Zell L, Siewert B, Stuppner H, Schuster D, Temml V. Identification of Novel β-Tubulin Inhibitors Using a Combined In Silico/ In Vitro Approach. J Chem Inf Model 2023; 63:6396-6411. [PMID: 37774242 PMCID: PMC10598795 DOI: 10.1021/acs.jcim.3c00939] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Indexed: 10/01/2023]
Abstract
Due to their potential as leads for various therapeutic applications, including as antimitotic and antiparasitic agents, the development of tubulin inhibitors offers promise for drug discovery. In this study, an in silico pharmacophore-based virtual screening approach targeting the colchicine binding site of β-tubulin was employed. Several structure- and ligand-based models for known tubulin inhibitors were generated. Compound databases were virtually screened against the models, and prioritized hits from the SPECS compound library were tested in an in vitro tubulin polymerization inhibition assay for their experimental validation. Out of the 41 SPECS compounds tested, 11 were active tubulin polymerization inhibitors, leading to a prospective true positive hit rate of 26.8%. Two novel inhibitors displayed IC50 values in the range of colchicine. The most potent of which was a novel acetamide-bridged benzodiazepine/benzimidazole derivative with an IC50 = 2.9 μM. The screening workflow led to the identification of diverse inhibitors active at the tubulin colchicine binding site. Thus, the pharmacophore models show promise as valuable tools for the discovery of compounds and as potential leads for the development of cancer therapeutic agents.
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Affiliation(s)
- Mark James Horgan
- Institute
of Pharmacy/Pharmacognosy, Center for Chemistry and Biomedicine, University of Innsbruck, Innrain 80-82, 6020 Innsbruck, Austria
| | - Lukas Zell
- Institute
of Pharmacy, Department of Pharmaceutical and Medicinal Chemistry, Paracelsus Medical University Salzburg, Strubergasse 21, 5020 Salzburg, Austria
| | - Bianka Siewert
- Institute
of Pharmacy/Pharmacognosy, Center for Chemistry and Biomedicine, University of Innsbruck, Innrain 80-82, 6020 Innsbruck, Austria
| | - Hermann Stuppner
- Institute
of Pharmacy/Pharmacognosy, Center for Chemistry and Biomedicine, University of Innsbruck, Innrain 80-82, 6020 Innsbruck, Austria
| | - Daniela Schuster
- Institute
of Pharmacy, Department of Pharmaceutical and Medicinal Chemistry, Paracelsus Medical University Salzburg, Strubergasse 21, 5020 Salzburg, Austria
| | - Veronika Temml
- Institute
of Pharmacy, Department of Pharmaceutical and Medicinal Chemistry, Paracelsus Medical University Salzburg, Strubergasse 21, 5020 Salzburg, Austria
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16
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Yamane T, Nakayama T, Ekimoto T, Inoue M, Ikezaki K, Sekiguchi H, Kuramochi M, Terao Y, Judai K, Saito M, Ikeguchi M, Sasaki YC. Comparison of the Molecular Motility of Tubulin Dimeric Isoforms: Molecular Dynamics Simulations and Diffracted X-ray Tracking Study. Int J Mol Sci 2023; 24:15423. [PMID: 37895101 PMCID: PMC10607685 DOI: 10.3390/ijms242015423] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Revised: 10/11/2023] [Accepted: 10/19/2023] [Indexed: 10/29/2023] Open
Abstract
Tubulin has been recently reported to form a large family consisting of various gene isoforms; however, the differences in the molecular features of tubulin dimers composed of a combination of these isoforms remain unknown. Therefore, we attempted to elucidate the physical differences in the molecular motility of these tubulin dimers using the method of measurable pico-meter-scale molecular motility, diffracted X-ray tracking (DXT) analysis, regarding characteristic tubulin dimers, including neuronal TUBB3 and ubiquitous TUBB5. We first conducted a DXT analysis of neuronal (TUBB3-TUBA1A) and ubiquitous (TUBB5-TUBA1B) tubulin dimers and found that the molecular motility around the vertical axis of the neuronal tubulin dimer was lower than that of the ubiquitous tubulin dimer. The results of molecular dynamics (MD) simulation suggest that the difference in motility between the neuronal and ubiquitous tubulin dimers was probably caused by a change in the major contact of Gln245 in the T7 loop of TUBB from Glu11 in TUBA to Val353 in TUBB. The present study is the first report of a novel phenomenon in which the pico-meter-scale molecular motility between neuronal and ubiquitous tubulin dimers is different.
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Affiliation(s)
- Tsutomu Yamane
- Graduate School of Medical Life Science, Yokohama City University, 1-7-29 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan; (T.E.); (M.I.); (M.I.)
- HPC- and AI-Driven Drug Development Platform Division, Riken Center for Computational Science, RIKEN, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
| | - Takahiro Nakayama
- Department of Medical Physiology, Kyorin University School of Medicine, 6-20-2 Shinkawa, Mitaka 181-8611, Japan; (T.N.); (Y.T.)
| | - Toru Ekimoto
- Graduate School of Medical Life Science, Yokohama City University, 1-7-29 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan; (T.E.); (M.I.); (M.I.)
| | - Masao Inoue
- Graduate School of Medical Life Science, Yokohama City University, 1-7-29 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan; (T.E.); (M.I.); (M.I.)
| | - Keigo Ikezaki
- Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa 277-8568, Japan; (K.I.); (M.K.)
| | - Hiroshi Sekiguchi
- Japan Synchrotron Radiation Research Institute, SPring-8, 1-1-1 Kouto, Sayo 679-5198, Japan;
| | - Masahiro Kuramochi
- Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa 277-8568, Japan; (K.I.); (M.K.)
| | - Yasuo Terao
- Department of Medical Physiology, Kyorin University School of Medicine, 6-20-2 Shinkawa, Mitaka 181-8611, Japan; (T.N.); (Y.T.)
| | - Ken Judai
- Department of Physics, College of Humanities and Sciences, Nihon University, Sakurajosui 3-25-40, Tokyo 156-8550, Japan;
| | - Minoru Saito
- Department of Biosciences, College of Humanities and Sciences, Nihon University, Tokyo 156-8550, Japan;
| | - Mitsunori Ikeguchi
- Graduate School of Medical Life Science, Yokohama City University, 1-7-29 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan; (T.E.); (M.I.); (M.I.)
- HPC- and AI-Driven Drug Development Platform Division, Riken Center for Computational Science, RIKEN, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
| | - Yuji C. Sasaki
- Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa 277-8568, Japan; (K.I.); (M.K.)
- Japan Synchrotron Radiation Research Institute, SPring-8, 1-1-1 Kouto, Sayo 679-5198, Japan;
- AIST-UTokyo Advanced Operando-Measurement Technology Open Innovation Laboratory (OPERANDO-OIL), National Institute of Advanced Industrial Science and Technology (AIST), 6-2-3 Kashiwanoha, Chiba 277-0882, Japan
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17
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Eren E, Watts NR, Randazzo D, Palmer I, Sackett DL, Wingfield PT. Structural basis of microtubule depolymerization by the kinesin-like activity of HIV-1 Rev. Structure 2023; 31:1233-1246.e5. [PMID: 37572662 PMCID: PMC10592302 DOI: 10.1016/j.str.2023.07.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Revised: 04/07/2023] [Accepted: 07/18/2023] [Indexed: 08/14/2023]
Abstract
HIV-1 Rev is an essential regulatory protein that transports unspliced and partially spliced viral mRNAs from the nucleus to the cytoplasm for the expression of viral structural proteins. During its nucleocytoplasmic shuttling, Rev interacts with several host proteins to use the cellular machinery for the advantage of the virus. Here, we report the 3.5 Å cryo-EM structure of a 4.8 MDa Rev-tubulin ring complex. Our structure shows that Rev's arginine-rich motif (ARM) binds to both the acidic surfaces and the C-terminal tails of α/β-tubulin. The Rev-tubulin interaction is functionally homologous to that of kinesin-13, potently destabilizing microtubules at sub-stoichiometric levels. Expression of Rev in astrocytes and HeLa cells shows that it can modulate the microtubule cytoskeleton within the cellular environment. These results show a previously undefined regulatory role of Rev.
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Affiliation(s)
- Elif Eren
- Protein Expression Laboratory, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD 20892, USA.
| | - Norman R Watts
- Protein Expression Laboratory, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Davide Randazzo
- Light Imaging Section, Office of Science and Technology, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Ira Palmer
- Protein Expression Laboratory, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Dan L Sackett
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
| | - Paul T Wingfield
- Protein Expression Laboratory, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD 20892, USA.
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18
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Ben Jdila M, Kammoun F, Abdelmaksoud-Dammak R, Triki C, Fakhfakh F. Mutation in the β-tubulin gene TUBB4A results in epileptic encephalopathy associated with hypomyelinated leucodystrophy: Unexpected findings reveal genetic mosaicism. Int J Dev Neurosci 2023; 83:532-545. [PMID: 37529938 DOI: 10.1002/jdn.10284] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2023] [Revised: 05/10/2023] [Accepted: 06/15/2023] [Indexed: 08/03/2023] Open
Abstract
INTRODUCTION Epileptic encephalopathies (EEs) are a group of heterogeneous epileptic syndromes characterized by early-onset refractory seizures, specific EEG abnormalities, developmental delay or regression and intellectual disability. The genetic spectrum of EE is very wide with mutations in a number of genes having various functions, such as those encoding AMPA ionotropic and glutamate receptors as well as voltage-gated ion channels. However, the list of EE-responsible genes could certainly be enlarged by next-generation sequencing. PATIENTS AND METHODS The present study reports a clinical investigation and a molecular analysis by the whole exome sequencing (WES) and pyrosequencing of a patient's family affected by epileptic spasms and severe psychomotor delay. RESULTS Clinical and radiological investigations revealed that the patient presented clinical features of severe and drug-resistant EE-type infantile epileptic spasm syndrome that evolved to Lennox Gastaut syndrome with radiological findings of hypomyelinated leukodystrophy. The results of WES revealed the presence of a novel heterozygous c.466C>T mutation in exon 4 of the TUBB4A gene in the patient. This transition led to the replacement of arginine by cysteine at position 156 (p.R156C) of the conserved helix 4 among the N-terminal domain of the TUBB4A protein. Bioinformatic tools predicted its deleterious effects on the structural arrangement and stability of the protein. The presence of the mutation in the asymptomatic father suggested the hypothesis of somatic mosaicism that was tested by pyrosequencing of DNA from two tissues of the patient and her father. The obtained results showed a lower rate of mutated alleles in the asymptomatic father compared with the affected daughter in both lymphocytes and buccal mucosa cells, confirming the occurrence of paternal mosaicism. The phenotypic features of the patient were also compared with those of previously described patients presenting TUBB4A mutations. CONCLUSIONS Our study is the first to report a disease-causing variant in the TUBB4A gene in a patient with EE associated with hypomyelinated leucodystrophy. In addition, we expanded the phenotypic spectrum associated with the TUBB4A gene.
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Affiliation(s)
- Marwa Ben Jdila
- Research Laboratory 'NeuroPédiatrie' (LR19ES15), Sfax Medical School, Sfax University, Sfax, Tunisia
- Laboratory of Molecular and Functional Genetics, Faculty of Science of Sfax, Sfax University, Sfax, Tunisia
| | - Fatma Kammoun
- Research Laboratory 'NeuroPédiatrie' (LR19ES15), Sfax Medical School, Sfax University, Sfax, Tunisia
- Child Neurology Department, Hedi Chaker University Hospital of Sfax, Sfax, Tunisia
| | - Rania Abdelmaksoud-Dammak
- Center of Biotechnology of Sfax, Laboratory of Eucaryotes Molecular Biotechnology, University of Sfax, Sfax, Tunisia
| | - Chahnez Triki
- Research Laboratory 'NeuroPédiatrie' (LR19ES15), Sfax Medical School, Sfax University, Sfax, Tunisia
- Child Neurology Department, Hedi Chaker University Hospital of Sfax, Sfax, Tunisia
| | - Faiza Fakhfakh
- Laboratory of Molecular and Functional Genetics, Faculty of Science of Sfax, Sfax University, Sfax, Tunisia
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Mansoor Hussain UH, Basheer Ahamed SI. Structural impact of pathogenic SNPs on β-tubulin using molecular dynamics study. J Biomol Struct Dyn 2023; 41:8230-8240. [PMID: 36218086 DOI: 10.1080/07391102.2022.2130986] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Accepted: 09/26/2022] [Indexed: 10/17/2022]
Abstract
Single nucleotide polymorphisms (SNPs) in the TUBB1 (β-tubulin) gene have been implicated as the primary cause of macro thrombocytopenia. Therefore it is essential to identify the potential SNPs which are harmful to cause diseases such as macro thrombocytopenia. The impact caused by these variants on β-tubulin is twofold, both structural and functional. Multiple in-silico tools were used to scrutinise the most deleterious nsSNPs (non-synonymous SNPs) via sequence and structure-based approaches. Further, the β-tubulin protein model incorporating identified mutants was subjected to MD (molecular dynamic) simulations to analyse the impact on protein structure. A total of 2974 SNPs of TUBB1 were retrieved from various sources, and 32 nsSNPs were identified. By screening through sequence-based technique, 13 variants were detected as deleterious and further structure-based filtration was carried out to find thermally destabilising variants. Finally, three variants have been detected as highly destabilising by the mCSM server and chosen for the MD study. All three variants are present in the N-terminal, Intermediate, and C-terminal regions, breaking the spatial arrangement required for microtubule assembly. The spatial arrangement of these variants is in deviation with respect to WT (wild type) β-tubulin. The protein model was subjected to a simulation period of 100 ns. The FEL analysis revealed multiple clusters with minor populations indicating the unstable conformation adapted by the β-tubulin. The normal mode vector analysis exhibited high-intensity flexible motions at the C-terminal end, responsible for binding with MAPs (microtubule-associated proteins), an essential region in microtubule assembly. All these results reveal that the SNP's predicted eventually influence the spatial arrangement of β-tubulin, which would disturb the stacking arrangement of αβ tubulin dimer in microtubule assembly. The present study may set a path to cure the diseases like macro thrombocytopenia.Communicated by Ramaswamy H. Sarma.
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20
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Kowalczyk K, Błauż A, Moscoh Ayine-Tora D, Hartinger CG, Rychlik B, Plażuk D. Design, Synthesis, and Evaluation of Biological Activity of Ferrocene-Ispinesib Hybrids: Impact of a Ferrocenyl Group on the Antiproliferative and Kinesin Spindle Protein Inhibitory Activity. Chemistry 2023; 29:e202300813. [PMID: 37332065 DOI: 10.1002/chem.202300813] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Revised: 05/31/2023] [Accepted: 06/15/2023] [Indexed: 06/20/2023]
Abstract
With the aim to combine more than one biologically-active component in a single molecule, derivatives of ispinesib and its (S) analogue were prepared that featured ferrocenyl moieties or bulky organic substituents. Inspired by the strong kinesin spindle protein (KSP) inhibitory activity of ispinesib, the compounds were investigated for their antiproliferative activity. Among these compounds, several derivatives demonstrated significantly higher antiproliferative activity than ispinesib with nanomolar IC50 values against cell lines. Further evaluation indicated that the antiproliferative activity is not directly correlated with their KSP inhibitory activity while docking suggested that several of the derivatives may bind in a manner similar to ispinesib. In order to investigate the mode of action further, cell cycle analysis and reactive oxygen species formation were investigated. The improved antiproliferative activity of the most active compounds may be assigned to synergic effects of various factors such as KSP inhibitory activity due to the ispinesib core and ability to generate ROS and induce mitotic arrest.
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Affiliation(s)
- Karolina Kowalczyk
- Laboratory of Molecular Spectroscopy, Department of Organic Chemistry Faculty of Chemistry, University of Lodz ul. Tamka 12, 91-403, Łódź, Poland
| | - Andrzej Błauż
- Cytometry Lab, Department of Oncobiology and Epigenetics, Faculty of Biology and Environmental Protection, University of Lodz ul. Pomorska 141/143, 90-236, Łódź, Poland
| | | | - Christian G Hartinger
- School of Chemical Sciences, The University of Auckland, Private Bag 92019, Auckland, 1142, New Zealand
| | - Błażej Rychlik
- Cytometry Lab, Department of Oncobiology and Epigenetics, Faculty of Biology and Environmental Protection, University of Lodz ul. Pomorska 141/143, 90-236, Łódź, Poland
| | - Damian Plażuk
- Laboratory of Molecular Spectroscopy, Department of Organic Chemistry Faculty of Chemistry, University of Lodz ul. Tamka 12, 91-403, Łódź, Poland
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21
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Chu Y, Tian Z, Yang M, Li W. Conformation and energy investigation of microtubule longitudinal dynamic instability induced by natural products. Chem Biol Drug Des 2023; 102:444-456. [PMID: 36509697 DOI: 10.1111/cbdd.14189] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Revised: 08/29/2022] [Accepted: 11/28/2022] [Indexed: 12/15/2022]
Abstract
The natural products plinabulin, docetaxel, and vinblastine are microtubule targeting agents (MTAs). They have been used alone or in combination in cancer treatment. However, the exact nature of their effects on microtubule (MT) polymerization dynamics is poorly understood. To elucidate the longitudinal conformational and energetic changes during MT dynamics, a total of 140 ns molecular dynamic simulations combined with binding free energy calculations were performed on seven tubulin models. The results indicated that the drugs disrupted MT polymerization by altering both MT conformation and binding free energy of the neighboring tubulin subunits. The combination of plinabulin and docetaxel destabilized MT polymerization due to bending MT and weakening the polarity of tubulin polymerization. The new combination of docetaxel and vinblastine synergistically enhanced MT depolymerization and bending, while plinabulin and vinblastine had no synergistic inhibitory effects. The results were verified by the tubulin assembly assay. Our study obtained a comprehensive understanding of the action mechanisms of three natural drugs and their combinations on MT dynamic, provided theoretical guidance for new MTA combinations, and would promote the optimal use of MTA and contribute to developing new MTAs as anticancer agents.
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Affiliation(s)
- Yanyan Chu
- School of Medicine and Pharmacy, Ocean University of China, Qingdao, China
- Innovation Center for Marine Drug Screening and Evaluation, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Zhenhua Tian
- School of Medicine and Pharmacy, Ocean University of China, Qingdao, China
| | - Mengke Yang
- School of Medicine and Pharmacy, Ocean University of China, Qingdao, China
| | - Wenbao Li
- School of Medicine and Pharmacy, Ocean University of China, Qingdao, China
- Innovation Center for Marine Drug Screening and Evaluation, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
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22
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Olivares-Ferretti P, Beltrán JF, Salazar LA, Fonseca-Salamanca F. Protein Modelling and Molecular Docking Analysis of Fasciola hepatica β-Tubulin's Interaction Sites, with Triclabendazole, Triclabendazole Sulphoxide and Triclabendazole Sulphone. Acta Parasitol 2023; 68:535-547. [PMID: 37330945 DOI: 10.1007/s11686-023-00692-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Accepted: 05/29/2023] [Indexed: 06/20/2023]
Abstract
PURPOSE Fasciola hepatica is a globally distributed trematode that causes significant economic losses. Triclabendazole is the primary pharmacological treatment for this parasite. However, the increasing resistance to triclabendazole limits its efficacy. Previous pharmacodynamics studies suggested that triclabendazole acts by interacting mainly with the β monomer of tubulin. METHODS We used a high-quality method to model the six isotypes of F. hepatica β-tubulin in the absence of three-dimensional structures. Molecular dockings were conducted to evaluate the destabilization regions in the molecule against the ligands triclabendazole, triclabendazole sulphoxide and triclabendazole sulphone. RESULTS The nucleotide binding site demonstrates higher affinity than the binding sites of colchicine, albendazole, the T7 loop and pβVII (p < 0.05). We suggest that the binding of the ligands to the polymerization site of β-tubulin can lead a microtubule disruption. Furthermore, we found that triclabendazole sulphone exhibited significantly higher binding affinity than other ligands (p < 0.05) across all isotypes of β-tubulin. CONCLUSIONS Our investigation has yielded new insight on the mechanism of action of triclabendazole and its sulphometabolites on F. hepatica β-tubulin through computational tools. These findings have significant implications for ongoing scientific research ongoing towards the discovery of novel therapeutics to treat F. hepatica infections.
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Affiliation(s)
- Pamela Olivares-Ferretti
- Laboratory of Molecular Immunoparasitology, Center of Excellence in Translational Medicine-Scientific and Technological Bioresource Nucleus (CEMT-BIOREN), Temuco, Chile
| | - Jorge F Beltrán
- Chemical Engineering Department, Faculty of Engineering and Science, Universidad de La Frontera, Temuco, Chile
| | - Luis A Salazar
- Center of Molecular Biology and Pharmacogenetics, Scientific and Technological Bioresource Nucleus (BIOREN), Universidad de La Frontera, Avenida Francisco Salazar 01145, 4811230, Temuco, Chile
| | - Flery Fonseca-Salamanca
- Laboratory of Molecular Immunoparasitology, Center of Excellence in Translational Medicine-Scientific and Technological Bioresource Nucleus (CEMT-BIOREN), Temuco, Chile.
- Preclinical Sciences Department, Faculty of Medicine, Universidad de La Frontera, Temuco, Chile.
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23
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Zha J, Xia F. Developing Hybrid All-Atom and Ultra-Coarse-Grained Models to Investigate Taxol-Binding and Dynein Interactions on Microtubules. J Chem Theory Comput 2023; 19:5621-5632. [PMID: 37489636 DOI: 10.1021/acs.jctc.3c00275] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/26/2023]
Abstract
Simulating the conformations and functions of biological macromolecules by using all-atom (AA) models is a challenging task due to expensive computational costs. One possible strategy to solve this problem is to develop hybrid all-atom and ultra-coarse-grained (AA/UCG) models of the biological macromolecules. In the AA/UCG scheme, the interest regions are described by AA models, while the other regions are described in the UCG representation. In this study, we develop the hybrid AA/UCG models and apply them to investigate the conformational changes of microtubule-bound tubulins. The simulation results of the hybrid models elucidated the mechanism of why the taxol molecules selectively bound microtubules but not tubulin dimers. In addition, we also explore the interactions of the microtubules and dyneins. Our study shows that the hybrid AA/UCG model has great application potential in studying the function of complex biological systems.
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Affiliation(s)
- Jinyin Zha
- School of Chemistry and Molecular Engineering, NYU-ECNU Center for Computational Chemistry at NYU Shanghai, East China Normal University, Shanghai 200062, China
- Medicinal Chemistry and Bioinformatics Center, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Fei Xia
- School of Chemistry and Molecular Engineering, NYU-ECNU Center for Computational Chemistry at NYU Shanghai, East China Normal University, Shanghai 200062, China
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24
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Puri D, Barry BJ, Engle EC. TUBB3 and KIF21A in neurodevelopment and disease. Front Neurosci 2023; 17:1226181. [PMID: 37600020 PMCID: PMC10436312 DOI: 10.3389/fnins.2023.1226181] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Accepted: 07/17/2023] [Indexed: 08/22/2023] Open
Abstract
Neuronal migration and axon growth and guidance require precise control of microtubule dynamics and microtubule-based cargo transport. TUBB3 encodes the neuronal-specific β-tubulin isotype III, TUBB3, a component of neuronal microtubules expressed throughout the life of central and peripheral neurons. Human pathogenic TUBB3 missense variants result in altered TUBB3 function and cause errors either in the growth and guidance of cranial and, to a lesser extent, central axons, or in cortical neuronal migration and organization, and rarely in both. Moreover, human pathogenic missense variants in KIF21A, which encodes an anterograde kinesin motor protein that interacts directly with microtubules, alter KIF21A function and cause errors in cranial axon growth and guidance that can phenocopy TUBB3 variants. Here, we review reported TUBB3 and KIF21A variants, resulting phenotypes, and corresponding functional studies of both wildtype and mutant proteins. We summarize the evidence that, in vitro and in mouse models, loss-of-function and missense variants can alter microtubule dynamics and microtubule-kinesin interactions. Lastly, we highlight additional studies that might contribute to our understanding of the relationship between specific tubulin isotypes and specific kinesin motor proteins in health and disease.
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Affiliation(s)
- Dharmendra Puri
- Department of Neurology, Boston Children’s Hospital, Harvard Medical School, Boston, MA, United States
- F. M. Kirby Neurobiology Center, Boston Children’s Hospital, Boston, MA, United States
- Howard Hughes Medical Institute, Chevy Chase, MD, United States
| | - Brenda J. Barry
- Department of Neurology, Boston Children’s Hospital, Harvard Medical School, Boston, MA, United States
- F. M. Kirby Neurobiology Center, Boston Children’s Hospital, Boston, MA, United States
- Howard Hughes Medical Institute, Chevy Chase, MD, United States
| | - Elizabeth C. Engle
- Department of Neurology, Boston Children’s Hospital, Harvard Medical School, Boston, MA, United States
- F. M. Kirby Neurobiology Center, Boston Children’s Hospital, Boston, MA, United States
- Howard Hughes Medical Institute, Chevy Chase, MD, United States
- Department of Ophthalmology, Boston Children’s Hospital, Harvard Medical School, Boston, MA, United States
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25
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Maksudov F, Kliuchnikov E, Marx KA, Purohit PK, Barsegov V. Mechanical fatigue testing in silico: Dynamic evolution of material properties of nanoscale biological particles. Acta Biomater 2023; 166:326-345. [PMID: 37142109 DOI: 10.1016/j.actbio.2023.04.042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Revised: 04/01/2023] [Accepted: 04/26/2023] [Indexed: 05/06/2023]
Abstract
Biological particles have evolved to possess mechanical characteristics necessary to carry out their functions. We developed a computational approach to "fatigue testing in silico", in which constant-amplitude cyclic loading is applied to a particle to explore its mechanobiology. We used this approach to describe dynamic evolution of nanomaterial properties and low-cycle fatigue in the thin spherical encapsulin shell, thick spherical Cowpea Chlorotic Mottle Virus (CCMV) capsid, and thick cylindrical microtubule (MT) fragment over 20 cycles of deformation. Changing structures and force-deformation curves enabled us to describe their damage-dependent biomechanics (strength, deformability, stiffness), thermodynamics (released and dissipated energies, enthalpy, and entropy) and material properties (toughness). Thick CCMV and MT particles experience material fatigue due to slow recovery and damage accumulation over 3-5 loading cycles; thin encapsulin shells show little fatigue due to rapid remodeling and limited damage. The results obtained challenge the existing paradigm: damage in biological particles is partially reversible owing to particle's partial recovery; fatigue crack may or may not grow with each loading cycle and may heal; and particles adapt to deformation amplitude and frequency to minimize the energy dissipated. Using crack size to quantitate damage is problematic as several cracks might form simultaneously in a particle. Dynamic evolution of strength, deformability, and stiffness, can be predicted by analyzing the cycle number (N) dependent damage, [Formula: see text] , where α is a power law and Nf is fatigue life. Fatigue testing in silico can now be used to explore damage-induced changes in the material properties of other biological particles. STATEMENT OF SIGNIFICANCE: Biological particles possess mechanical characteristics necessary to perform their functions. We developed "fatigue testing in silico" approach, which employes Langevin Dynamics simulations of constant-amplitude cyclic loading of nanoscale biological particles, to explore dynamic evolution of the mechanical, energetic, and material properties of the thin and thick spherical particles of encapsulin and Cowpea Chlorotic Mottle Virus, and the microtubule filament fragment. Our study of damage growth and fatigue development challenge the existing paradigm. Damage in biological particles is partially reversible as fatigue crack might heal with each loading cycle. Particles adapt to deformation amplitude and frequency to minimize energy dissipation. The evolution of strength, deformability, and stiffness, can be accurately predicted by analyzing the damage growth in particle structure.
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Affiliation(s)
- Farkhad Maksudov
- Department of Chemistry, University of Massachusetts, Lowell, MA 01854, United States
| | - Evgenii Kliuchnikov
- Department of Chemistry, University of Massachusetts, Lowell, MA 01854, United States
| | - Kenneth A Marx
- Department of Chemistry, University of Massachusetts, Lowell, MA 01854, United States
| | - Prashant K Purohit
- Department of Mechanical Engineering and Applied Mechanics, University of Pennsylvania, PA, United States
| | - Valeri Barsegov
- Department of Chemistry, University of Massachusetts, Lowell, MA 01854, United States.
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26
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Zhang X, Li X, Chen W, Wang Y, Diao L, Gao Y, Wang H, Bao L, Liang X, Wu HY. The distinct initiation sites and processing activities of TTLL4 and TTLL7 in glutamylation of brain tubulin. J Biol Chem 2023; 299:104923. [PMID: 37321451 PMCID: PMC10404701 DOI: 10.1016/j.jbc.2023.104923] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Revised: 06/05/2023] [Accepted: 06/07/2023] [Indexed: 06/17/2023] Open
Abstract
Mammalian brain tubulins undergo a reversible posttranslational modification-polyglutamylation-which attaches a secondary polyglutamate chain to the primary sequence of proteins. Loss of its erasers can disrupt polyglutamylation homeostasis and cause neurodegeneration. Tubulin tyrosine ligase like 4 (TTLL4) and TTLL7 were known to modify tubulins, both with preference for the β-isoform, but differently contribute to neurodegeneration. However, differences in their biochemical properties and functions remain largely unknown. Here, using an antibody-based method, we characterized the properties of a purified recombinant TTLL4 and confirmed its sole role as an initiator, unlike TTLL7, which both initiates and elongates the side chains. Unexpectedly, TTLL4 produced stronger glutamylation immunosignals for α-isoform than β-isoform in brain tubulins. Contrarily, the recombinant TTLL7 raised comparable glutamylation immunoreactivity for two isoforms. Given the site selectivity of the glutamylation antibody, we analyzed modification sites of two enzymes. Tandem mass spectrometry analysis revealed their incompatible site selectivity on synthetic peptides mimicking carboxyl termini of α1- and β2-tubulins and a recombinant tubulin. Particularly, in the recombinant α1A-tubulin, a novel region was found glutamylated by TTLL4 and TTLL7, that again at distinct sites. These results pinpoint different site specificities between two enzymes. Moreover, TTLL7 exhibits less efficiency to elongate microtubules premodified by TTLL4, suggesting possible regulation of TTLL7 elongation activity by TTLL4-initiated sites. Finally, we showed that kinesin behaves differentially on microtubules modified by two enzymes. This study underpins the different reactivity, site selectivity, and function of TTLL4 and TTLL7 on brain tubulins and sheds light on their distinct role in vivo.
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Affiliation(s)
- Xinyue Zhang
- School of Pharmaceutical Science and Technology, Tianjin University, Tianjin, China
| | - Xiangxiao Li
- School of Pharmaceutical Science and Technology, Tianjin University, Tianjin, China
| | - Wei Chen
- IDG/McGovern Institute for Brain Research, School of Life Sciences, Tsinghua University, Beijing, China
| | - Yujuan Wang
- School of Pharmaceutical Science and Technology, Tianjin University, Tianjin, China
| | - Lei Diao
- State Key Laboratory of Cell Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai, China
| | - Yan Gao
- School of Pharmaceutical Science and Technology, Tianjin University, Tianjin, China
| | - Heyi Wang
- School of Pharmaceutical Science and Technology, Tianjin University, Tianjin, China
| | - Lan Bao
- State Key Laboratory of Cell Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai, China
| | - Xin Liang
- IDG/McGovern Institute for Brain Research, School of Life Sciences, Tsinghua University, Beijing, China
| | - Hui-Yuan Wu
- School of Pharmaceutical Science and Technology, Tianjin University, Tianjin, China.
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27
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Amărandi RM, Al-Matarneh MC, Popovici L, Ciobanu CI, Neamțu A, Mangalagiu II, Danac R. Exploring Pyrrolo-Fused Heterocycles as Promising Anticancer Agents: An Integrated Synthetic, Biological, and Computational Approach. Pharmaceuticals (Basel) 2023; 16:865. [PMID: 37375812 DOI: 10.3390/ph16060865] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Revised: 05/17/2023] [Accepted: 06/09/2023] [Indexed: 06/29/2023] Open
Abstract
Five new series of pyrrolo-fused heterocycles were designed through a scaffold hybridization strategy as analogs of the well-known microtubule inhibitor phenstatin. Compounds were synthesized using the 1,3-dipolar cycloaddition of cycloimmonium N-ylides to ethyl propiolate as a key step. Selected compounds were then evaluated for anticancer activity and ability to inhibit tubulin polymerization in vitro. Notably, pyrrolo[1,2-a]quinoline 10a was active on most tested cell lines, performing better than control phenstatin in several cases, most notably on renal cancer cell line A498 (GI50 27 nM), while inhibiting tubulin polymerization in vitro. In addition, this compound was predicted to have a promising ADMET profile. The molecular details of the interaction between compound 10a and tubulin were investigated through in silico docking experiments, followed by molecular dynamics simulations and configurational entropy calculations. Of note, we found that some of the initially predicted interactions from docking experiments were not stable during molecular dynamics simulations, but that configurational entropy loss was similar in all three cases. Our results suggest that for compound 10a, docking experiments alone are not sufficient for the adequate description of interaction details in terms of target binding, which makes subsequent scaffold optimization more difficult and ultimately hinders drug design. Taken together, these results could help shape novel potent antiproliferative compounds with pyrrolo-fused heterocyclic cores, especially from an in silico methodological perspective.
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Affiliation(s)
- Roxana-Maria Amărandi
- TRANSCEND Research Center, Regional Institute of Oncology Iasi, 2-4 General Henri Mathias Berthelot Street, 700483 Iasi, Romania
| | - Maria-Cristina Al-Matarneh
- "Petru Poni" Institute of Macromolecular Chemistry of Romanian Academy, 41A Grigore Ghica Voda Alley, 700487 Iasi, Romania
- Faculty of Chemistry, Alexandru Ioan Cuza University of Iasi, 11 Carol I, 700506 Iasi, Romania
| | - Lăcrămioara Popovici
- Faculty of Chemistry, Alexandru Ioan Cuza University of Iasi, 11 Carol I, 700506 Iasi, Romania
| | - Catalina Ionica Ciobanu
- Institute of Interdisciplinary Research-CERNESIM Centre, Alexandru Ioan Cuza University of Iasi, 11 Carol I, 700506 Iasi, Romania
| | - Andrei Neamțu
- TRANSCEND Research Center, Regional Institute of Oncology Iasi, 2-4 General Henri Mathias Berthelot Street, 700483 Iasi, Romania
| | - Ionel I Mangalagiu
- Faculty of Chemistry, Alexandru Ioan Cuza University of Iasi, 11 Carol I, 700506 Iasi, Romania
| | - Ramona Danac
- Faculty of Chemistry, Alexandru Ioan Cuza University of Iasi, 11 Carol I, 700506 Iasi, Romania
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28
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Beckett D, Voth GA. Unveiling the Catalytic Mechanism of GTP Hydrolysis in Microtubules. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.01.538927. [PMID: 37205601 PMCID: PMC10187240 DOI: 10.1101/2023.05.01.538927] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Microtubules (MTs) are large cytoskeletal polymers, composed of αβ-tubulin heterodimers, capable of stochastically converting from polymerizing to depolymerizing states and vice-versa. Depolymerization is coupled with hydrolysis of GTP within β-tubulin. Hydrolysis is favored in the MT lattice compared to free heterodimer with an experimentally observed rate increase of 500 to 700 fold, corresponding to an energetic barrier lowering of 3.8 to 4.0 kcal/mol. Mutagenesis studies have implicated α-tubulin residues, α:E254 and α:D251, as catalytic residues completing the β-tubulin active site of the lower heterodimer in the MT lattice. The mechanism for GTP hydrolysis in the free heterodimer, however, is not understood. Additionally, there has been debate concerning whether the GTP-state lattice is expanded or compacted relative to the GDP-state and whether a "compacted" GDP-state lattice is required for hydrolysis. In this work, extensive QM/MM simulations with transition-tempered metadynamics free energy sampling of compacted and expanded inter-dimer complexes, as well as free heterodimer, have been carried out to provide clear insight into the GTP hydrolysis mechanism. α:E254 was found to be the catalytic residue in a compacted lattice, while in the expanded lattice disruption of a key salt bridge interaction renders α:E254 less effective. The simulations reveal a barrier decrease of 3.8 ± 0.5 kcal/mol for the compacted lattice compared to free heterodimer, in good agreement with experimental kinetic measurements. Additionally, the expanded lattice barrier was found to be 6.3 ± 0.5 kcal/mol higher than compacted, demonstrating that GTP hydrolysis is variable with lattice state and slower at the MT tip. Significance Statement Microtubules (MTs) are large and dynamic components of the eukaryotic cytoskeleton with the ability to stochastically convert from a polymerizing to a depolymerizing state and vice-versa. Depolymerization is coupled to the hydrolysis of guanosine-5'-triphosphate (GTP), which is orders of magnitude faster in the MT lattice than in free tubulin heterodimers. Our results computationally ascertain the catalytic residue contacts in the MT lattice that accelerate GTP hydrolysis compared to the free heterodimer as well as confirm that a compacted MT lattice is necessary for hydrolysis while a more expanded lattice is unable to form the necessary contacts and thereby hydrolyze GTP.
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29
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Nogales E. The tubulin structure, a quarter of a century later. Mol Biol Cell 2023; 34:rt2. [PMID: 36913319 PMCID: PMC10092645 DOI: 10.1091/mbc.e23-01-0005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 02/13/2023] [Accepted: 02/23/2023] [Indexed: 03/14/2023] Open
Abstract
This retrospective on the 25th anniversary of the publication of the first structure of tubulin is shaped by my own personal experiences rather than being a strict and complete historical account of the event. It is a reflection on how working in science felt many years ago, on the struggles and the joys of reaching for the high-hanging fruit, and, ultimately, on how relevant or not our personal scientific contributions are to the broader scientific community. Writing it brought back memories of my unique and sadly lost postdoctoral advisor Ken Downing, who dreamt of this structure and brought it to fruition against all odds.
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Affiliation(s)
- Eva Nogales
- Molecular and Cell Biology Department, University of California, Berkeley
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory
- Howard Hughes Medical Institute, University of California Berkeley, Berkeley, CA 94720-3220
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30
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Kalra A, Benny A, Travis SM, Zizzi EA, Morales-Sanchez A, Oblinsky DG, Craddock TJA, Hameroff SR, MacIver MB, Tuszyński JA, Petry S, Penrose R, Scholes GD. Electronic Energy Migration in Microtubules. ACS CENTRAL SCIENCE 2023; 9:352-361. [PMID: 36968538 PMCID: PMC10037452 DOI: 10.1021/acscentsci.2c01114] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Indexed: 05/29/2023]
Abstract
The repeating arrangement of tubulin dimers confers great mechanical strength to microtubules, which are used as scaffolds for intracellular macromolecular transport in cells and exploited in biohybrid devices. The crystalline order in a microtubule, with lattice constants short enough to allow energy transfer between amino acid chromophores, is similar to synthetic structures designed for light harvesting. After photoexcitation, can these amino acid chromophores transfer excitation energy along the microtubule like a natural or artificial light-harvesting system? Here, we use tryptophan autofluorescence lifetimes to probe energy hopping between aromatic residues in tubulin and microtubules. By studying how the quencher concentration alters tryptophan autofluorescence lifetimes, we demonstrate that electronic energy can diffuse over 6.6 nm in microtubules. We discover that while diffusion lengths are influenced by tubulin polymerization state (free tubulin versus tubulin in the microtubule lattice), they are not significantly altered by the average number of protofilaments (13 versus 14). We also demonstrate that the presence of the anesthetics etomidate and isoflurane reduce exciton diffusion. Energy transport as explained by conventional Förster theory (accommodating for interactions between tryptophan and tyrosine residues) does not sufficiently explain our observations. Our studies indicate that microtubules are, unexpectedly, effective light harvesters.
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Affiliation(s)
- Aarat
P. Kalra
- Department
of Chemistry, New Frick Chemistry Building, Princeton University, Princeton, New Jersey08544, United States
| | - Alfy Benny
- Department
of Chemistry, New Frick Chemistry Building, Princeton University, Princeton, New Jersey08544, United States
| | - Sophie M. Travis
- Department
of Molecular Biology, Schultz Laboratory, Princeton University, Princeton, New Jersey08544, United States
| | - Eric A. Zizzi
- Department
of Mechanical and Aerospace Engineering (DIMEAS), Politecnico di Torino, Torino10129, Italy
| | - Austin Morales-Sanchez
- Department
of Chemistry, New Frick Chemistry Building, Princeton University, Princeton, New Jersey08544, United States
| | - Daniel G. Oblinsky
- Department
of Chemistry, New Frick Chemistry Building, Princeton University, Princeton, New Jersey08544, United States
| | - Travis J. A. Craddock
- Departments
of Psychology & Neuroscience, Computer Science, and Clinical Immunology, Nova Southeastern University, Ft. Lauderdale, Florida33314, United States
| | - Stuart R. Hameroff
- Department
of Anesthesiology, Center for Consciousness Studies, University of Arizona, Tucson, Arizona85721, United States
| | - M. Bruce MacIver
- Department
of Anesthesiology, Stanford University School
of Medicine, Stanford, California94305, United States
| | - Jack A. Tuszyński
- Department
of Mechanical and Aerospace Engineering (DIMEAS), Politecnico di Torino, Torino10129, Italy
- Department
of Physics, University of Alberta, Edmonton, AlbertaT6G 2E1, Canada
- Department
of Oncology, University of Alberta, Edmonton, AlbertaT6G 1Z2, Canada
| | - Sabine Petry
- Department
of Molecular Biology, Schultz Laboratory, Princeton University, Princeton, New Jersey08544, United States
| | - Roger Penrose
- Mathematical
Institute, Andrew Wiles Building, University
of Oxford, Radcliffe Observatory Quarter, Woodstock Road, Oxford, OX2 6GG, United
Kingdom
| | - Gregory D. Scholes
- Department
of Chemistry, New Frick Chemistry Building, Princeton University, Princeton, New Jersey08544, United States
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31
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Han W, Jin M, Liu C, Zhao Q, Wang S, Wang Y, Yin Y, Peng C, Wang Y, Cong Y. Structural basis of plp2-mediated cytoskeletal protein folding by TRiC/CCT. SCIENCE ADVANCES 2023; 9:eade1207. [PMID: 36921056 PMCID: PMC10017041 DOI: 10.1126/sciadv.ade1207] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Accepted: 02/14/2023] [Indexed: 06/18/2023]
Abstract
The cytoskeletal proteins tubulin and actin are the obligate substrates of TCP-1 ring complex/Chaperonin containing TCP-1 (TRiC/CCT), and their folding involves co-chaperone. Through cryo-electron microscopy analysis, we present a more complete picture of TRiC-assisted tubulin/actin folding along TRiC adenosine triphosphatase cycle, under the coordination of co-chaperone plp2. In the open S1/S2 states, plp2 and tubulin/actin engaged within opposite TRiC chambers. Notably, we captured an unprecedented TRiC-plp2-tubulin complex in the closed S3 state, engaged with a folded full-length β-tubulin and loaded with a guanosine triphosphate, and a plp2 occupying opposite rings. Another closed S4 state revealed an actin in the intermediate folding state and a plp2. Accompanying TRiC ring closure, plp2 translocation could coordinate substrate translocation on the CCT6 hemisphere, facilitating substrate stabilization and folding. Our findings reveal the folding mechanism of the major cytoskeletal proteins tubulin/actin under the coordination of the biogenesis machinery TRiC and plp2 and extend our understanding of the links between cytoskeletal proteostasis and related human diseases.
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Affiliation(s)
- Wenyu Han
- State Key Laboratory of Molecular Biology, National Center for Protein Science Shanghai, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai 200031, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Mingliang Jin
- State Key Laboratory of Molecular Biology, National Center for Protein Science Shanghai, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai 200031, China
| | - Caixuan Liu
- State Key Laboratory of Molecular Biology, National Center for Protein Science Shanghai, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai 200031, China
| | - Qiaoyu Zhao
- State Key Laboratory of Molecular Biology, National Center for Protein Science Shanghai, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai 200031, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Shutian Wang
- State Key Laboratory of Molecular Biology, National Center for Protein Science Shanghai, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai 200031, China
| | - Yifan Wang
- State Key Laboratory of Molecular Biology, National Center for Protein Science Shanghai, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai 200031, China
| | - Yue Yin
- National Facility for Protein Science in Shanghai, Zhangjiang Lab, Shanghai Advanced Research Institute, CAS, Shanghai 201210, China
| | - Chao Peng
- National Facility for Protein Science in Shanghai, Zhangjiang Lab, Shanghai Advanced Research Institute, CAS, Shanghai 201210, China
| | - Yanxing Wang
- State Key Laboratory of Molecular Biology, National Center for Protein Science Shanghai, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai 200031, China
| | - Yao Cong
- State Key Laboratory of Molecular Biology, National Center for Protein Science Shanghai, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai 200031, China
- University of Chinese Academy of Sciences, Beijing 100049, China
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Saibu OA, Hammed SO, Oladipo OO, Odunitan TT, Ajayi TM, Adejuyigbe AJ, Apanisile BT, Oyeneyin OE, Oluwafemi AT, Ayoola T, Olaoba OT, Alausa AO, Omoboyowa DA. Protein-protein interaction and interference of carcinogenesis by supramolecular modifications. Bioorg Med Chem 2023; 81:117211. [PMID: 36809721 DOI: 10.1016/j.bmc.2023.117211] [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: 10/25/2022] [Revised: 02/06/2023] [Accepted: 02/07/2023] [Indexed: 02/18/2023]
Abstract
Protein-protein interactions (PPIs) are essential in normal biological processes, but they can become disrupted or imbalanced in cancer. Various technological advancements have led to an increase in the number of PPI inhibitors, which target hubs in cancer cell's protein networks. However, it remains difficult to develop PPI inhibitors with desired potency and specificity. Supramolecular chemistry has only lately become recognized as a promising method to modify protein activities. In this review, we highlight recent advances in the use of supramolecular modification approaches in cancer therapy. We make special note of efforts to apply supramolecular modifications, such as molecular tweezers, to targeting the nuclear export signal (NES), which can be used to attenuate signaling processes in carcinogenesis. Finally, we discuss the strengths and weaknesses of using supramolecular approaches to targeting PPIs.
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Affiliation(s)
- Oluwatosin A Saibu
- Department of Environmental Toxicology, Universitat Duisburg-Essen, NorthRhine-Westphalia, Germany
| | - Sodiq O Hammed
- Genomics Unit, Helix Biogen Institute, Ogbomoso, Oyo State, Nigeria; Department of Physiology, Ladoke Akintola University of Technology, Ogbomoso, Oyo State, Nigeria
| | - Oladapo O Oladipo
- Department of Physiology, Ladoke Akintola University of Technology, Ogbomoso, Oyo State, Nigeria.
| | - Tope T Odunitan
- Genomics Unit, Helix Biogen Institute, Ogbomoso, Oyo State, Nigeria; Department of Biochemistry, Ladoke Akintola University of Technology, Ogbomoso, Oyo State, Nigeria
| | - Temitope M Ajayi
- Department of Biochemistry, Ladoke Akintola University of Technology, Ogbomoso, Oyo State, Nigeria
| | - Aderonke J Adejuyigbe
- Department of Physiology, Ladoke Akintola University of Technology, Ogbomoso, Oyo State, Nigeria
| | - Boluwatife T Apanisile
- Department of Nutrition and Dietetics, Ladoke Akintola University of Technology, Ogbomoso, Oyo State, Nigeria
| | - Oluwatoba E Oyeneyin
- Theoretical and Computational Chemistry Unit, Adekunle Ajasin University, Akungba-Akoko, Ondo State, Nigeria
| | - Adenrele T Oluwafemi
- Department of Biochemistry, Ladoke Akintola University of Technology, Ogbomoso, Oyo State, Nigeria
| | - Tolulope Ayoola
- Department of Biochemistry, Ladoke Akintola University of Technology, Ogbomoso, Oyo State, Nigeria
| | - Olamide T Olaoba
- Department of Molecular Pathogenesis and Therapeutics, University of Missouri-Columbia, Columbia, MO 65211, USA
| | - Abdullahi O Alausa
- Department of Molecular Biology and Biotechnology, ITMO University, St Petersburg, Russia
| | - Damilola A Omoboyowa
- Department of Biochemistry, Adekunle Ajasin University, Akungba-Akoko, Ondo State, Nigeria
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Computational Approaches to the Rational Design of Tubulin-Targeting Agents. Biomolecules 2023; 13:biom13020285. [PMID: 36830654 PMCID: PMC9952983 DOI: 10.3390/biom13020285] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Revised: 01/27/2023] [Accepted: 01/31/2023] [Indexed: 02/05/2023] Open
Abstract
Microtubules are highly dynamic polymers of α,β-tubulin dimers which play an essential role in numerous cellular processes such as cell proliferation and intracellular transport, making them an attractive target for cancer and neurodegeneration research. To date, a large number of known tubulin binders were derived from natural products, while only one was developed by rational structure-based drug design. Several of these tubulin binders show promising in vitro profiles while presenting unacceptable off-target effects when tested in patients. Therefore, there is a continuing demand for the discovery of safer and more efficient tubulin-targeting agents. Since tubulin structural data is readily available, the employment of computer-aided design techniques can be a key element to focus on the relevant chemical space and guide the design process. Due to the high diversity and quantity of structural data available, we compiled here a guide to the accessible tubulin-ligand structures. Furthermore, we review different ligand and structure-based methods recently used for the successful selection and design of new tubulin-targeting agents.
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Zocchi R, Compagnucci C, Bertini E, Sferra A. Deciphering the Tubulin Language: Molecular Determinants and Readout Mechanisms of the Tubulin Code in Neurons. Int J Mol Sci 2023; 24:ijms24032781. [PMID: 36769099 PMCID: PMC9917122 DOI: 10.3390/ijms24032781] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2022] [Revised: 01/17/2023] [Accepted: 01/27/2023] [Indexed: 02/04/2023] Open
Abstract
Microtubules (MTs) are dynamic components of the cell cytoskeleton involved in several cellular functions, such as structural support, migration and intracellular trafficking. Despite their high similarity, MTs have functional heterogeneity that is generated by the incorporation into the MT lattice of different tubulin gene products and by their post-translational modifications (PTMs). Such regulations, besides modulating the tubulin composition of MTs, create on their surface a "biochemical code" that is translated, through the action of protein effectors, into specific MT-based functions. This code, known as "tubulin code", plays an important role in neuronal cells, whose highly specialized morphologies and activities depend on the correct functioning of the MT cytoskeleton and on its interplay with a myriad of MT-interacting proteins. In recent years, a growing number of mutations in genes encoding for tubulins, MT-interacting proteins and enzymes that post-translationally modify MTs, which are the main players of the tubulin code, have been linked to neurodegenerative processes or abnormalities in neural migration, differentiation and connectivity. Nevertheless, the exact molecular mechanisms through which the cell writes and, downstream, MT-interacting proteins decipher the tubulin code are still largely uncharted. The purpose of this review is to describe the molecular determinants and the readout mechanisms of the tubulin code, and briefly elucidate how they coordinate MT behavior during critical neuronal events, such as neuron migration, maturation and axonal transport.
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Affiliation(s)
- Riccardo Zocchi
- Unit of Neuromuscular Disorders, Translational Pediatrics and Clinical Genetics, Bambino Gesù Children’s Hospital, IRCCS, 00146 Rome, Italy
| | - Claudia Compagnucci
- Molecular Genetics and Functional Genomics, Bambino Gesù Children’s Research Hospital, IRCCS, 00146 Rome, Italy
| | - Enrico Bertini
- Unit of Neuromuscular Disorders, Translational Pediatrics and Clinical Genetics, Bambino Gesù Children’s Hospital, IRCCS, 00146 Rome, Italy
- Correspondence: (E.B.); or (A.S.); Tel.: +39-06-6859-2104 (E.B. & A.S.)
| | - Antonella Sferra
- Unit of Neuromuscular Disorders, Translational Pediatrics and Clinical Genetics, Bambino Gesù Children’s Hospital, IRCCS, 00146 Rome, Italy
- Correspondence: (E.B.); or (A.S.); Tel.: +39-06-6859-2104 (E.B. & A.S.)
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35
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Shemesh A, Ghareeb H, Dharan R, Levi-Kalisman Y, Metanis N, Ringel I, Raviv U. Effect of tubulin self-association on GTP hydrolysis and nucleotide exchange reactions. BIOCHIMICA ET BIOPHYSICA ACTA. PROTEINS AND PROTEOMICS 2023; 1871:140869. [PMID: 36400388 DOI: 10.1016/j.bbapap.2022.140869] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2022] [Revised: 10/13/2022] [Accepted: 11/08/2022] [Indexed: 11/17/2022]
Abstract
We investigated how the self-association of isolated tubulin dimers affects the rate of GTP hydrolysis and the equilibrium of nucleotide exchange. Both reactions are relevant for microtubule (MT) dynamics. We used HPLC to determine the concentrations of GDP and GTP and thereby the GTPase activity of SEC-eluted tubulin dimers in assembly buffer solution, free of glycerol and tubulin aggregates. When GTP hydrolysis was negligible, the nucleotide exchange mechanism was studied by determining the concentrations of tubulin-free and tubulin-bound GTP and GDP. We observed no GTP hydrolysis below the critical conditions for MT assembly (either below the critical tubulin concentration and/or at low temperature), despite the assembly of tubulin 1D curved oligomers and single-rings, showing that their assembly did not involve GTP hydrolysis. Under conditions enabling spontaneous slow MT assembly, a slow pseudo-first-order GTP hydrolysis kinetics was detected, limited by the rate of MT assembly. Cryo-TEM images showed that GTP-tubulin 1D oligomers were curved also at 36 °C. Nucleotide exchange depended on the total tubulin concentration and the molar ratio between tubulin-free GDP and GTP. We used a thermodynamic model of isodesmic tubulin self-association, terminated by the formation of tubulin single-rings to determine the molar fractions of dimers with exposed and buried nucleotide exchangeable sites (E-sites). Our analysis shows that the GDP to GTP exchange reaction equilibrium constant was an order-of-magnitude larger for tubulin dimers with exposed E-sites than for assembled dimers with buried E-sites. This conclusion may have implications on the dynamics at the tip of the MT plus end.
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Affiliation(s)
- Asaf Shemesh
- Institute of Chemistry, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, Jerusalem 9190401, Israel; The Harvey M. Krueger Family Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, Jerusalem 9190401, Israel
| | - Hiba Ghareeb
- Institute of Chemistry, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, Jerusalem 9190401, Israel
| | - Raviv Dharan
- Institute of Chemistry, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, Jerusalem 9190401, Israel
| | - Yael Levi-Kalisman
- The Harvey M. Krueger Family Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, Jerusalem 9190401, Israel; Institute of Life Sciences, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, Jerusalem 9190401, Israel
| | - Norman Metanis
- Institute of Chemistry, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, Jerusalem 9190401, Israel
| | - Israel Ringel
- Institute for Drug Research, School of Pharmacy, The Hebrew University of Jerusalem, 9112102 Jerusalem, Israel
| | - Uri Raviv
- Institute of Chemistry, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, Jerusalem 9190401, Israel; The Harvey M. Krueger Family Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, Jerusalem 9190401, Israel.
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36
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Estévez-Gallego J, Álvarez-Bernad B, Pera B, Wullschleger C, Raes O, Menche D, Martínez JC, Lucena-Agell D, Prota AE, Bonato F, Bargsten K, Cornelus J, Giménez-Abián JF, Northcote P, Steinmetz MO, Kamimura S, Altmann KH, Paterson I, Gago F, Van der Eycken J, Díaz JF, Oliva MÁ. Chemical modulation of microtubule structure through the laulimalide/peloruside site. Structure 2023; 31:88-99.e5. [PMID: 36462501 DOI: 10.1016/j.str.2022.11.006] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Revised: 08/23/2022] [Accepted: 11/08/2022] [Indexed: 12/05/2022]
Abstract
Taxanes are microtubule-stabilizing agents used in the treatment of many solid tumors, but they often involve side effects affecting the peripheral nervous system. It has been proposed that this could be related to structural modifications on the filament upon drug binding. Alternatively, laulimalide and peloruside bind to a different site also inducing stabilization, but they have not been exploited in clinics. Here, we use a combination of the parental natural compounds and derived analogs to unravel the stabilization mechanism through this site. These drugs settle lateral interactions without engaging the M loop, which is part of the key and lock involved in the inter-protofilament contacts. Importantly, these drugs can modulate the angle between protofilaments, producing microtubules of different diameters. Among the compounds studied, we have found some showing low cytotoxicity and able to induce stabilization without compromising microtubule native structure. This opens the window of new applications for microtubule-stabilizing agents beyond cancer treatment.
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Affiliation(s)
- Juan Estévez-Gallego
- Centro de Investigaciones Biológicas Margarita Salas - Consejo Superior de Investigaciones Científicas, Madrid 28040, Spain
| | - Beatriz Álvarez-Bernad
- Centro de Investigaciones Biológicas Margarita Salas - Consejo Superior de Investigaciones Científicas, Madrid 28040, Spain
| | - Benet Pera
- Centro de Investigaciones Biológicas Margarita Salas - Consejo Superior de Investigaciones Científicas, Madrid 28040, Spain
| | - Christoph Wullschleger
- Department of Chemistry and Applied Biosciences, Institute of Pharmaceutical Sciences - ETH Zurich, Zürich 8093, Switzerland
| | - Olivier Raes
- Department of Organic and Macromolecular Chemistry, Ghent University, Gent 9000, Belgium
| | - Dirk Menche
- Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, UK
| | | | - Daniel Lucena-Agell
- Centro de Investigaciones Biológicas Margarita Salas - Consejo Superior de Investigaciones Científicas, Madrid 28040, Spain
| | - Andrea E Prota
- Laboratory of Biomolecular Research, Division of Biology and Chemistry, Paul Scherrer Institut, Villigen 5232, Switzerland
| | - Francesca Bonato
- Centro de Investigaciones Biológicas Margarita Salas - Consejo Superior de Investigaciones Científicas, Madrid 28040, Spain
| | - Katja Bargsten
- Laboratory of Biomolecular Research, Division of Biology and Chemistry, Paul Scherrer Institut, Villigen 5232, Switzerland
| | - Jelle Cornelus
- Department of Organic and Macromolecular Chemistry, Ghent University, Gent 9000, Belgium
| | - Juan Francisco Giménez-Abián
- Centro de Investigaciones Biológicas Margarita Salas - Consejo Superior de Investigaciones Científicas, Madrid 28040, Spain
| | - Peter Northcote
- Ferrier Research Institute, University of Wellington, Lower Hutt 5010, New Zealand
| | - Michel O Steinmetz
- Laboratory of Biomolecular Research, Division of Biology and Chemistry, Paul Scherrer Institut, Villigen 5232, Switzerland; University of Basel, Biozentrum, Basel 4056, Switzerland
| | - Shinji Kamimura
- Department of Biological Sciences, Faculty of Science and Engineering, Chuo University, Tokyo 192-0393, Japan
| | - Karl-Heinz Altmann
- Department of Chemistry and Applied Biosciences, Institute of Pharmaceutical Sciences - ETH Zurich, Zürich 8093, Switzerland
| | - Ian Paterson
- Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, UK
| | - Federico Gago
- Department of Biomedical Sciences and Associated Unit IQM-UAH, Universidad de Alcalá, Alcalá de Henares 28805, Spain
| | - Johan Van der Eycken
- Department of Organic and Macromolecular Chemistry, Ghent University, Gent 9000, Belgium
| | - J Fernando Díaz
- Centro de Investigaciones Biológicas Margarita Salas - Consejo Superior de Investigaciones Científicas, Madrid 28040, Spain
| | - María Ángela Oliva
- Centro de Investigaciones Biológicas Margarita Salas - Consejo Superior de Investigaciones Científicas, Madrid 28040, Spain.
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37
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Cushion TD, Leca I, Keays DA. MAPping tubulin mutations. Front Cell Dev Biol 2023; 11:1136699. [PMID: 36875768 PMCID: PMC9975266 DOI: 10.3389/fcell.2023.1136699] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Accepted: 02/02/2023] [Indexed: 02/17/2023] Open
Abstract
Microtubules are filamentous structures that play a critical role in a diverse array of cellular functions including, mitosis, nuclear translocation, trafficking of organelles and cell shape. They are composed of α/β-tubulin heterodimers which are encoded by a large multigene family that has been implicated in an umbrella of disease states collectively known as the tubulinopathies. De novo mutations in different tubulin genes are known to cause lissencephaly, microcephaly, polymicrogyria, motor neuron disease, and female infertility. The diverse clinical features associated with these maladies have been attributed to the expression pattern of individual tubulin genes, as well as their distinct Functional repertoire. Recent studies, however, have highlighted the impact of tubulin mutations on microtubule-associated proteins (MAPs). MAPs can be classified according to their effect on microtubules and include polymer stabilizers (e.g., tau, MAP2, doublecortin), destabilizers (e.g., spastin, katanin), plus-end binding proteins (e.g., EB1-3, XMAP215, CLASPs) and motor proteins (e.g., dyneins, kinesins). In this review we analyse mutation-specific disease mechanisms that influence MAP binding and their phenotypic consequences, and discuss methods by which we can exploit genetic variation to identify novel MAPs.
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Affiliation(s)
- Thomas D Cushion
- Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, United Kingdom.,Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), Vienna, Austria
| | - Ines Leca
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), Vienna, Austria
| | - David A Keays
- Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, United Kingdom.,Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), Vienna, Austria.,Division of Neurobiology, Department Biology II, Ludwig-Maximilians-University Munich, Munich, Germany
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38
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Marotta C, Giorgi E, Binacchi F, Cirri D, Gabbiani C, Pratesi A. An overview of recent advancements in anticancer Pt(IV) prodrugs: New smart drug combinations, activation and delivery strategies. Inorganica Chim Acta 2023. [DOI: 10.1016/j.ica.2023.121388] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
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39
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Chai P, Rao Q, Zhang K. Multi-curve fitting and tubulin-lattice signal removal for structure determination of large microtubule-based motors. J Struct Biol 2022; 214:107897. [PMID: 36089228 DOI: 10.1016/j.jsb.2022.107897] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2022] [Revised: 08/05/2022] [Accepted: 09/03/2022] [Indexed: 12/30/2022]
Abstract
Revealing high-resolution structures of microtubule-associated proteins (MAPs) is critical for understanding their fundamental roles in various cellular activities, such as cell motility and intracellular cargo transport. Nevertheless, large flexible molecular motors that dynamically bind and release microtubule networks are challenging for cryo-electron microscopy (cryo-EM). Traditional structure determination of MAPs bound to microtubules needs alignment information from the reconstruction of microtubules, which cannot be readily applied to large MAPs without a fixed binding pattern. Here, we developed a comprehensive approach to estimate the microtubule networks (multi-curve fitting), model the tubulin-lattice signals, and remove them (tubulin-lattice subtraction) from the raw cryo-EM micrographs. The approach does not require an ordered binding pattern of MAPs on microtubules, nor does it need a reconstruction of the microtubules. We demonstrated the capability of our approach using the reconstituted outer-arm dynein (OAD) bound to microtubule doublets. The tubulin-lattice subtraction improves the OAD alignment, thus leading to high-resolution reconstructions. In addition, the multi-curve fitting approach provides an accurate automatic alternative method to pick or segment filaments in 2D images and potentially in 3D tomograms. The accuracy of our approach has been demonstrated by using several other biological filaments. Our work provides a new tool to determine high-resolution structures of large MAPs bound to curved microtubule networks.
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Affiliation(s)
- Pengxin Chai
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06511, USA
| | - Qinhui Rao
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06511, USA
| | - Kai Zhang
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06511, USA.
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40
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Hoff KJ, Neumann AJ, Moore JK. The molecular biology of tubulinopathies: Understanding the impact of variants on tubulin structure and microtubule regulation. Front Cell Neurosci 2022; 16:1023267. [PMID: 36406756 PMCID: PMC9666403 DOI: 10.3389/fncel.2022.1023267] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Accepted: 09/30/2022] [Indexed: 11/24/2022] Open
Abstract
Heterozygous, missense mutations in both α- and β-tubulin genes have been linked to an array of neurodevelopment disorders, commonly referred to as "tubulinopathies." To date, tubulinopathy mutations have been identified in three β-tubulin isotypes and one α-tubulin isotype. These mutations occur throughout the different genetic domains and protein structures of these tubulin isotypes, and the field is working to address how this molecular-level diversity results in different cellular and tissue-level pathologies. Studies from many groups have focused on elucidating the consequences of individual mutations; however, the field lacks comprehensive models for the molecular etiology of different types of tubulinopathies, presenting a major gap in diagnosis and treatment. This review highlights recent advances in understanding tubulin structural dynamics, the roles microtubule-associated proteins (MAPs) play in microtubule regulation, and how these are inextricably linked. We emphasize the value of investigating interactions between tubulin structures, microtubules, and MAPs to understand and predict the impact of tubulinopathy mutations at the cell and tissue levels. Microtubule regulation is multifaceted and provides a complex set of controls for generating a functional cytoskeleton at the right place and right time during neurodevelopment. Understanding how tubulinopathy mutations disrupt distinct subsets of those controls, and how that ultimately disrupts neurodevelopment, will be important for establishing mechanistic themes among tubulinopathies that may lead to insights in other neurodevelopment disorders and normal neurodevelopment.
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Affiliation(s)
| | | | - Jeffrey K. Moore
- Department of Cell and Developmental Biology, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
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41
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Tan CH, Sim DSY, Lim SH, Mohd Mohidin TB, Mohan G, Low YY, Kam TS, Sim KS. Antiproliferative and Microtubule-stabilizing Activities of Two Iboga-vobasine Bisindoles Alkaloids from Tabernaemontana corymbosa in Colorectal Adenocarcinoma HT-29 Cells. PLANTA MEDICA 2022; 88:1325-1340. [PMID: 35100653 DOI: 10.1055/a-1755-5605] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Two iboga-vobasine bisindoles, 16'-decarbomethoxyvoacamine (1: ) and its 19,20-dihydro derivative, 16'-decarbomethoxydihydrovoacamine (2: ) from Tabernaemontana corymbosa exhibited potent cytotoxicity against the human colorectal adenocarcinoma HT-29 cells in our previous studies. Bisindoles 1: and 2: selectively inhibited the growth of HT-29 cells without significant cytotoxicity to normal human colon fibroblasts CCD-18Co. Treatment with bisindoles 1: and 2: suppressed the formation of HT-29 colonies via G0/G1 cell cycle arrest and induction of mitochondrial apoptosis. Owing to its higher antiproliferative activity, bisindole 2: was chosen for the subsequent studies. Bisindole 2: inhibited the formation of HT-29 spheroids (tumor-like cell aggregates) in 3D experiments in a dose-dependent manner, while an in vitro tubulin polymerization assay and molecular docking analysis showed that bisindole 2: is a microtubule-stabilizing agent which is predicted to bind at the β-tubulin subunit at the taxol-binding site. The binding resulted in the generation of ROS, which consequently activated the oxidative stress-related cell cycle arrest and apoptotic pathways, viz., JNK/p38, p21Cip1/Chk1, and p21Cip1/Rb/E2F, as shown by microarray profiling.
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Affiliation(s)
- Chun Hoe Tan
- Institute of Biological Sciences, Faculty of Science, Universiti Malaya, Jalan Profesor Diraja Ungku Aziz, Kuala Lumpur, Wilayah Persekutuan Kuala Lumpur, Malaysia
| | - Dawn Su Yin Sim
- Department of Chemistry, Faculty of Science, Universiti Malaya, Jalan Profesor Diraja Ungku Aziz, Kuala Lumpur, Wilayah Persekutuan Kuala Lumpur, Malaysia
| | - Siew Huah Lim
- Department of Chemistry, Faculty of Science, Universiti Malaya, Jalan Profesor Diraja Ungku Aziz, Kuala Lumpur, Wilayah Persekutuan Kuala Lumpur, Malaysia
| | - Taznim Begam Mohd Mohidin
- Institute of Biological Sciences, Faculty of Science, Universiti Malaya, Jalan Profesor Diraja Ungku Aziz, Kuala Lumpur, Wilayah Persekutuan Kuala Lumpur, Malaysia
| | - Gokula Mohan
- Institute of Biological Sciences, Faculty of Science, Universiti Malaya, Jalan Profesor Diraja Ungku Aziz, Kuala Lumpur, Wilayah Persekutuan Kuala Lumpur, Malaysia
| | - Yun Yee Low
- Department of Chemistry, Faculty of Science, Universiti Malaya, Jalan Profesor Diraja Ungku Aziz, Kuala Lumpur, Wilayah Persekutuan Kuala Lumpur, Malaysia
| | - Toh Seok Kam
- Department of Chemistry, Faculty of Science, Universiti Malaya, Jalan Profesor Diraja Ungku Aziz, Kuala Lumpur, Wilayah Persekutuan Kuala Lumpur, Malaysia
| | - Kae Shin Sim
- Institute of Biological Sciences, Faculty of Science, Universiti Malaya, Jalan Profesor Diraja Ungku Aziz, Kuala Lumpur, Wilayah Persekutuan Kuala Lumpur, Malaysia
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42
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Jaragh-Alhadad LA, Ali MS, Moustafa MS, Harisa GI, Alanazi FK, Karnik S. Sulfonamide derivatives mediate breast and lung cancer cell line killing through tubulin inhibition. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2022.133699] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
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43
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Ahmed Khalil A, Rauf A, Alhumaydhi FA, Aljohani ASM, Javed MS, Khan MA, Khan IA, El-Esawi MA, Bawazeer S, Bouyahya A, Rebezov M, Shariati MA, Thiruvengadam M. Recent Developments and Anticancer Therapeutics of Paclitaxel: An Update. Curr Pharm Des 2022; 28:3363-3373. [PMID: 36330627 DOI: 10.2174/1381612829666221102155212] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Revised: 09/19/2022] [Accepted: 09/26/2022] [Indexed: 11/06/2022]
Abstract
Plants are a source of diverse classes of secondary metabolites with anticancer properties. Paclitaxel (Taxol) is an anticancer drug isolated from various Taxus species and is used as a chemotherapeutic agent against various cancers. The biosynthesis of paclitaxel is a complex pathway, making its total chemical synthesis commercially non-viable; hence, alternative novel sources - like plant cell culture and heterologous expression systems, are being investigated to overcome this issue. Advancements in the field of genetic engineering, microbial fermentation engineering, and recombinant techniques have significantly increased the achievable yields of paclitaxel. Indeed, paclitaxel selectively targets microtubules and causes cell cycle arrest in the G2/M phase, inducing a cytotoxic effect in a concentration and time-dependent manner. Innovative drug delivery formulations, like the development of albumin-bound nanoparticles, nano-emulsions, nano-suspensions, liposomes, and polymeric micelles, have been applied to enhance the delivery of paclitaxel to tumor cells. This review focuses on the production, biosynthesis, mechanism of action, and anticancer effects of paclitaxel.
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Affiliation(s)
- Anees Ahmed Khalil
- University Institute of Diet and Nutritional Sciences, Faculty of Allied Health Sciences, The University of Lahore, Pakistan
| | - Abdur Rauf
- Department of Chemistry, University of Swabi, Anbar-23561, K.P.K, Pakistan
| | - Fahad A Alhumaydhi
- Department of Medical Laboratories, College of Applied Medical Sciences, Qassim University, Buraydah, Saudi Arabia
| | - Abdullah S M Aljohani
- Department of Veterinary Medicine, College of Agriculture and Veterinary Medicine, Qassim University, Buraydah, Saudi Arabia
| | - Muhammad Sameem Javed
- Institute of Food Science and Nutrition, Bahauddin Zakariya University, Multan, Pakistan
| | | | - Imtiaz Ali Khan
- Department of Entomology, University of Peshawar, KP, Pakistan
| | - Mohamed A El-Esawi
- Botany Department, Faculty of Science, Tanta University, Tanta, 31527, Egypt
| | - Sami Bawazeer
- Department of Pharmacognosy, Faculty of Pharmacy, Umm Al-Qura University, Makkah, P.O. Box 42, Saudi Arabia
| | - Abdelhakim Bouyahya
- Department of Biology, Laboratory of Human Pathologies Biology, Faculty of Sciences, and Genomic Center of Human Pathologies, Faculty of Medicine and Pharmacy, Mohammed V University in Rabat, 10106 Morocco
| | - Maksim Rebezov
- V.M. Gorbatov Federal Research Center for Food Systems of Russian Academy of Sciences, Moscow, Russian Federation.,Prokhorov General Physics Institute, Russian Academy of Sciences, Moscow, Russian Federation
| | - Mohammad Ali Shariati
- K.G. Razumovsky Moscow State University of Technologies and management (the First Cossack University), Moscow, Russian Federation
| | - Muthu Thiruvengadam
- Department of Applied Bioscience, College of Life and Environmental Sciences, Konkuk University, Seoul 05029, South Korea.,Department of Microbiology, Saveetha Dental College and Hospital, Saveetha Institute of Medical and Technical Sciences (SIMATS), Chennai 600077, India
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44
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Attard TJ, Welburn JPI, Marsh JA. Understanding molecular mechanisms and predicting phenotypic effects of pathogenic tubulin mutations. PLoS Comput Biol 2022; 18:e1010611. [PMID: 36206299 PMCID: PMC9581425 DOI: 10.1371/journal.pcbi.1010611] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Revised: 10/19/2022] [Accepted: 09/28/2022] [Indexed: 11/21/2022] Open
Abstract
Cells rely heavily on microtubules for several processes, including cell division and molecular trafficking. Mutations in the different tubulin-α and -β proteins that comprise microtubules have been associated with various diseases and are often dominant, sporadic and congenital. While the earliest reported tubulin mutations affect neurodevelopment, mutations are also associated with other disorders such as bleeding disorders and infertility. We performed a systematic survey of tubulin mutations across all isotypes in order to improve our understanding of how they cause disease, and increase our ability to predict their phenotypic effects. Both protein structural analyses and computational variant effect predictors were very limited in their utility for differentiating between pathogenic and benign mutations. This was even worse for those genes associated with non-neurodevelopmental disorders. We selected tubulin-α and -β disease mutations that were most poorly predicted for experimental characterisation. These mutants co-localise to the mitotic spindle in HeLa cells, suggesting they may exert dominant-negative effects by altering microtubule properties. Our results show that tubulin mutations represent a blind spot for current computational approaches, being much more poorly predicted than mutations in most human disease genes. We suggest that this is likely due to their strong association with dominant-negative and gain-of-function mechanisms.
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Affiliation(s)
- Thomas J. Attard
- Wellcome Trust Centre for Cell Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, Scotland, United Kingdom
| | - Julie P. I. Welburn
- Wellcome Trust Centre for Cell Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, Scotland, United Kingdom
| | - Joseph A. Marsh
- MRC Human Genetics Unit, Institute of Genetics & Cancer, University of Edinburgh, Edinburgh, United Kingdom
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45
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Vélëz H, Gauchan DP, García-Gil MDR. Taxol and β-tubulins from endophytic fungi isolated from the Himalayan Yew, Taxus wallichiana Zucc. Front Microbiol 2022; 13:956855. [PMID: 36246258 PMCID: PMC9557061 DOI: 10.3389/fmicb.2022.956855] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Accepted: 09/08/2022] [Indexed: 11/13/2022] Open
Abstract
Paclitaxel, better known as the anticancer drug Taxol®, has been isolated from several plant species and has been shown to be produced by fungi, actinomycetes, and even bacteria isolated from marine macroalgae. Given its cytostatic effect, studies conducted in the 1990's showed that paclitaxel was toxic to many pathogenic fungi and oomycetes. Further studies led to the idea that the differences in paclitaxel sensitivity exhibited by different fungi were due to differences in the β-tubulin protein sequence. With the recent isolation of endophytic fungi from the leaves and bark of the Himalayan Yew, Taxus wallichiana Zucc., and the availability of genomes from paclitaxel-producing fungi, we decided to further explore the idea that endophytic fungi isolated from Yews should be well-adapted to their environment by encoding β-tubulin proteins that are insensitive to paclitaxel. Our results found evidence of episodic positive/diversifying selection at 10 sites (default p-value threshold of 0.1) in the β-tubulin sequences, corresponding to codon positions 33, 55, 172, 218, 279, 335, 359, 362, 379, and 406. Four of these positions (i.e., 172, 279, 359, and 362) have been implicated in the binding of paclitaxel by β-tubulin or formed part of the binding pocket. As expected, all the fungal endophytes grew in different media regardless of the paclitaxel concentration tested. Furthermore, our results also showed that Taxomyces andreanae CBS 279.92, the first fungus shown to produce paclitaxel, is a Basidiomycete fungus as the two beta tubulins encoded by the fungus clustered together with other Basidiomycete fungi.
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Affiliation(s)
- Heriberto Vélëz
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala, Sweden
- *Correspondence: Heriberto Vélëz
| | - Dhurva Prasad Gauchan
- Department of Biotechnology, School of Science, Kathmandu University, Dhulikhel, Nepal
| | - María del Rosario García-Gil
- Department of Forest Genetics and Plant Physiology, Umeå Plant Science Centre, Swedish University of Agricultural Sciences, Umeå, Sweden
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Andres AE, Mariano A, Rane D, Peterson BR. Quantification of Engagement of Microtubules by Small Molecules in Living Cells by Flow Cytometry. ACS BIO & MED CHEM AU 2022; 2:529-537. [PMID: 36281300 PMCID: PMC9585582 DOI: 10.1021/acsbiomedchemau.2c00031] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Revised: 07/25/2022] [Accepted: 07/27/2022] [Indexed: 11/29/2022]
Abstract
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Drugs such as paclitaxel (Taxol) that bind microtubules
are widely
used for the treatment of cancer. Measurements of the affinity and
selectivity of these compounds for their targets are largely based
on studies of purified proteins, and only a few quantitative methods
for the analysis of interactions of small molecules with microtubules
in living cells have been reported. We describe here a novel method
for rapidly quantifying the affinities of compounds that bind polymerized
tubulin in living HeLa cells. This method uses the fluorescent molecular
probe Pacific Blue-GABA-Taxol in conjunction with verapamil to block
cellular efflux. Under physiologically relevant conditions of 37 °C,
this combination allowed quantification of equilibrium saturation
binding of this probe to cellular microtubules (Kd = 1.7 μM) using flow cytometry. Competitive binding
of the microtubule stabilizers paclitaxel (cellular Ki = 22 nM), docetaxel (cellular Ki = 16 nM), cabazitaxel (cellular Ki = 6 nM), and ixabepilone (cellular Ki = 10 nM) revealed intracellular affinities for microtubules that
closely matched previously reported biochemical affinities. By including
a cooperativity factor (α) for curve fitting of allosteric modulators,
this probe also allowed quantification of binding (Kb) of the microtubule destabilizers colchicine (Kb = 80 nM, α = 0.08), vinblastine (Kb = 7 nM, α = 0.18), and maytansine (Kb = 3 nM, α = 0.21). Screening of this
assay against 1008 NCI diversity compounds identified NSC 93427 as
a novel microtubule destabilizer (Kb =
485 nM, α = 0.02), illustrating the potential of this approach
for drug discovery.
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Affiliation(s)
- Angelo E. Andres
- Division of Medicinal Chemistry and Pharmacognosy, The Ohio State University, Columbus, Ohio 43210, United States
| | - Andres Mariano
- Division of Medicinal Chemistry and Pharmacognosy, The Ohio State University, Columbus, Ohio 43210, United States
| | - Digamber Rane
- Division of Medicinal Chemistry and Pharmacognosy, The Ohio State University, Columbus, Ohio 43210, United States
| | - Blake R. Peterson
- Division of Medicinal Chemistry and Pharmacognosy, The Ohio State University, Columbus, Ohio 43210, United States
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47
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Noman MAA, Huang DS, Coulup SK, Syeda SS, Henry, Wong L, Georg GI. Cytotoxicity of phenylpironetin analogs and the metabolic fate of pironetin and phenylpironetin. Bioorg Chem 2022; 125:105915. [DOI: 10.1016/j.bioorg.2022.105915] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2022] [Revised: 05/10/2022] [Accepted: 05/24/2022] [Indexed: 11/02/2022]
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48
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Mitchell CW, Czajewski I, van Aalten DM. Bioinformatic prediction of putative conveyers of O-GlcNAc transferase intellectual disability. J Biol Chem 2022; 298:102276. [PMID: 35863433 PMCID: PMC9428853 DOI: 10.1016/j.jbc.2022.102276] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Revised: 07/12/2022] [Accepted: 07/14/2022] [Indexed: 02/09/2023] Open
Abstract
Protein O-GlcNAcylation is a dynamic posttranslational modification that is catalyzed by the enzyme O-GlcNAc transferase (OGT) and is essential for neurodevelopment and postnatal neuronal function. Missense mutations in OGT segregate with a novel X-linked intellectual disability syndrome, the OGT congenital disorder of glycosylation (OGT-CDG). One hypothesis for the etiology of OGT-CDG is that loss of OGT activity leads to hypo-O-GlcNAcylation of as yet unidentified, specific neuronal proteins, affecting essential embryonic, and postnatal neurodevelopmental processes; however, the identity of these O-GlcNAcylated proteins is not known. Here, we used bioinformatic techniques to integrate sequence conservation, structural data, clinical data, and the available literature to identify 22 candidate proteins that convey OGT-CDG. We found using gene ontology and PANTHER database data that these candidate proteins are involved in diverse processes including Ras/MAPK signaling, translational repression, cytoskeletal dynamics, and chromatin remodeling. We also identify pathogenic missense variants at O-GlcNAcylation sites that segregate with intellectual disability. This work establishes a preliminary platform for the mechanistic dissection of the links between protein O-GlcNAcylation and neurodevelopment in OGT-CDG.
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Affiliation(s)
- Conor W. Mitchell
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark,Division of Cell and Developmental Biology, School of Life Sciences, University of Dundee, Dundee, United Kingdom
| | - Ignacy Czajewski
- Division of Cell and Developmental Biology, School of Life Sciences, University of Dundee, Dundee, United Kingdom
| | - Daan M.F. van Aalten
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark,Division of Cell and Developmental Biology, School of Life Sciences, University of Dundee, Dundee, United Kingdom,For correspondence: Daan M. F. van Aalten
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49
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Maddula V, Holtzman NS, Nagan MC, Rotenberg SA. Phosphomimetic Mutation at Ser165 of α-Tubulin Promotes the Persistence of GTP Caps in Microtubules. Biochemistry 2022; 61:1508-1516. [PMID: 35799350 DOI: 10.1021/acs.biochem.2c00154] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Protein kinase C (PKC)-mediated phosphorylation of α-tubulin at Ser165 or expression of phosphomimetic (S165D)-α-tubulin stimulates microtubule (MT) polymerization (Cytoskeleton 2014, 71, 257-272). Ser165 lies near the interface between adjacent αβ-tubulin heterodimers and helix H8, which contains Glu254, the catalytic residue in α-tubulin that hydrolyzes the exchangeable GTP in β-tubulin (β:GTP) and triggers MT depolymerization. It was hypothesized that S165D, a phosphomimetic variant of α-tubulin, perturbs the alignment of α:Glu254 with respect to β:GTP, thereby impairing its hydrolysis. Molecular simulations were performed with cryoEM structures of MTs (PDB ID: 3J6E) in which phosphomimetic S165D or control S165N had been substituted. Unlike native and S165N structures, the distance between S165D and α:Glu254 increased by 0.6 Å, while the distance between α:Glu254 and β:GTP decreased by 0.4 Å. Rotation of β:GTP by 4 Å occurred in the S165D variant, whereas β:GTP in the S165N control was unchanged from the native structure. Additionally, the S165D variant exhibited an altered pattern of H-bonding to β:GTP, including the loss of three H-bonds. The significance of these findings to β:GTP hydrolysis was analyzed in MCF-10A human breast cells treated with an antibody that detects GTP-bound tubulin. Compared with controls, GTP-tubulin signals were at higher levels in cells that ectopically expressed S165D-α-tubulin (TUBA1C) or had been treated with PKC activator DAG-lactone to induce phosphorylation of Ser165 in native α-tubulin. These findings support a model whereby conformational changes induced by Ser165 phosphorylation alter the spatial relationship between β:GTP and α:Glu254, thereby slowing GTP hydrolysis and promoting GTP caps.
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Affiliation(s)
- Vinay Maddula
- Department of Chemistry, Adelphi University, One South Ave, Garden City, New York 11530, United States
| | - Nathalia S Holtzman
- Department of Biology, Queens College - The City University of New York, Flushing, New York 11367-1597, United States.,PhD Program in Biochemistry, The Graduate Center of The City University of New York, 365 5th Ave, New York, New York 10016, United States
| | - Maria C Nagan
- Department of Chemistry, Stony Brook University, Stony Brook, New York 11794-3400, United States
| | - Susan A Rotenberg
- Department of Chemistry & Biochemistry, Queens College - The City University of New York, Flushing, New York 11367-1597, United States.,PhD Program in Biochemistry, The Graduate Center of The City University of New York, 365 5th Ave, New York, New York 10016, United States
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50
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Kumari G, Jain R, Kumar Sah R, Kalia I, Vashistha M, Singh P, Prasad Singh A, Samby K, Burrows J, Singh S. Multistage and transmission-blocking tubulin targeting potent antimalarial discovered from the open access MMV pathogen box. Biochem Pharmacol 2022; 203:115154. [PMID: 35798201 DOI: 10.1016/j.bcp.2022.115154] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2022] [Revised: 06/08/2022] [Accepted: 06/23/2022] [Indexed: 11/28/2022]
Abstract
The development of resistance to current antimalarial therapies remains a significant source of concern. To address this risk,newdrugswithnoveltargetsin distinct developmental stages ofPlasmodiumparasites are required. In the current study,we have targetedP. falciparumTubulin(PfTubulin)proteins which represent some of thepotentialdrug targetsfor malaria chemotherapy. PlasmodialMicrotubules (MTs) play a crucial role during parasite proliferation, growth, and transmission, which render them highlydesirabletargets for the development ofnext-generation chemotherapeutics. Towards this,we have evaluated the antimalarial activity ofTubulintargetingcompounds received from theMedicines for Malaria Venture (MMV)"Pathogen Box"against the human malaria parasite,P. falciparumincluding 3D7 (chloroquine and artemisinin sensitive strain), RKL-9 (chloroquine-resistant strain), and R539T (artemisinin-resistant strain). At nanomolar concentrations, the filtered-out compounds exhibitedpronouncedmultistage antimalarialeffects across the parasite life cycle, including intra-erythrocytic blood stages, liver stage parasites, gametocytes, and ookinetes. Concomitantly, these compoundswere found toimpedemale gamete ex-flagellation, thus showingtheir transmission-blocking potential. Target mining of these potent compounds, by combining in silico, biochemical and biophysical assays,implicatedPfTubulinas their moleculartarget, which may possibly act bydisruptingMT assembly dynamics by binding at the interface of α-βTubulin-dimer.Further, the promising ADME profile of the parent scaffold supported its consideration as a lead compound for further development.Thus, our work highlights the potential of targetingPfTubulin proteins in discovering and developing next-generation, multistage antimalarial agents against Multi-Drug Resistant (MDR) malaria parasites.
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Affiliation(s)
- Geeta Kumari
- Special Centre for Molecular Medicine, Jawaharlal Nehru University, New Delhi 110067, India
| | - Ravi Jain
- Special Centre for Molecular Medicine, Jawaharlal Nehru University, New Delhi 110067, India
| | - Raj Kumar Sah
- Special Centre for Molecular Medicine, Jawaharlal Nehru University, New Delhi 110067, India
| | | | - Manu Vashistha
- Advanced Instrumentation Research Facility, Jawaharlal Nehru University, New Delhi 110067, India
| | - Pooja Singh
- National Institute of Immunology, New Delhi 110067, India
| | | | | | | | - Shailja Singh
- Special Centre for Molecular Medicine, Jawaharlal Nehru University, New Delhi 110067, India.
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