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Steinmetz MO, Prota AE. Structure-based discovery and rational design of microtubule-targeting agents. Curr Opin Struct Biol 2024; 87:102845. [PMID: 38805950 DOI: 10.1016/j.sbi.2024.102845] [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: 02/29/2024] [Revised: 05/01/2024] [Accepted: 05/06/2024] [Indexed: 05/30/2024]
Abstract
Microtubule-targeting agents (MTAs) have demonstrated remarkable efficacy as antitumor, antifungal, antiparasitic, and herbicidal agents, finding applications in the clinical, veterinary, and agrochemical industry. Recent advances in tubulin and microtubule structural biology have provided powerful tools that pave the way for the rational design of innovative small-molecule MTAs for future basic and applied life science applications. In this mini-review, we present the current status of the tubulin and microtubule structural biology field, the recent impact it had on the discovery and rational design of MTAs, and exciting avenues for future MTA research.
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Affiliation(s)
- Michel O Steinmetz
- Laboratory of Biomolecular Research, Division of Biology and Chemistry, Paul Scherrer Institut, CH-5232 Villigen PSI, Switzerland; University of Basel, Biozentrum, 4056 Basel, Switzerland.
| | - Andrea E Prota
- Laboratory of Biomolecular Research, Division of Biology and Chemistry, Paul Scherrer Institut, CH-5232 Villigen PSI, Switzerland.
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2
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Bai QX, Zhang ZJ, Tang HP, Yang BY, Kuang HX, Wang M. Dryopteris crassirhizoma Nakai.: A review of its botany, traditional use, phytochemistry, pharmacological activity, toxicology and pharmacokinetics. JOURNAL OF ETHNOPHARMACOLOGY 2024; 328:118109. [PMID: 38570147 DOI: 10.1016/j.jep.2024.118109] [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: 11/16/2023] [Revised: 02/04/2024] [Accepted: 03/24/2024] [Indexed: 04/05/2024]
Abstract
ETHNOPHARMACOLOGICAL RELEVANCE The Dryopteris crassirhizoma Nakai., a commonly used herb, is known as "Guan Zhong" in China, "Oshida" in Japan and "Gwanjung" in Korea. It has long been used for parasitic infestation, hemorrhages and epidemic influenza. AIM OF THE REVIEW The present paper aims to provide an up-to-date review at the advancements of the investigations on the traditional use, phytochemistry, pharmacological activity, toxicology and pharmacokinetics of D. crassirhizoma. Besides, possible trends, therapeutic potentials, and perspectives for future research of this plant are also briefly discussed. MATERIALS AND METHODS Relevant information on traditional use, phytochemistry, pharmacological activity, toxicology and pharmacokinetics of D. crassirhizoma was collected through published materials and electronic databases, including the Chinese Pharmacopoeia, Flora of China, Web of Science, PubMed, Baidu Scholar, Google Scholar, and China National Knowledge Infrastructure. 109 papers included in the article and we determined that no major information was missing after many checks. All authors participated in the review process for this article and all research paper are from authoritative published materials and electronic databases. RESULTS 130 chemical components, among which phloroglucinols are the predominant groups, have been isolated and identified from D. crassirhizoma. D. crassirhizoma with its bioactive compounds is possessed of extensive biological activities, including anti-parasite, anti-microbial, anti-viral, anti-cancer, anti-inflammatory, anti-oxidant, anti-diabetic, bone protective, immunomodulatory, anti-platelet and anti-hyperuricemia activity. Besides, D. crassirhizoma has special toxicology and pharmacokinetics characterization. CONCLUSIONS D. crassirhizoma is a traditional Chinese medicine having a long history of application. This review mainly summarized the different chemical components extract from D. crassirhizoma and various reported pharmacological effects. Besides, the toxicology and pharmacokinetics of D. crassirhizoma also be analysed in this review. However, the chemical components of D. crassirhizoma are understudied and require further research to expand its medicinal potential, and it is urgent to design a new extraction scheme, so that the active ingredients can be obtained at a lower cost.
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Affiliation(s)
- Qian-Xiang Bai
- Key Laboratory of Basic and Application Research of Beiyao (Heilongjiang University of Chinese Medicine), Ministry of Education, Heilongjiang University of Chinese Medicine, Harbin, 150000, China
| | - Zhao-Jiong Zhang
- Key Laboratory of Basic and Application Research of Beiyao (Heilongjiang University of Chinese Medicine), Ministry of Education, Heilongjiang University of Chinese Medicine, Harbin, 150000, China
| | - Hai-Peng Tang
- Key Laboratory of Basic and Application Research of Beiyao (Heilongjiang University of Chinese Medicine), Ministry of Education, Heilongjiang University of Chinese Medicine, Harbin, 150000, China
| | - Bing-You Yang
- Key Laboratory of Basic and Application Research of Beiyao (Heilongjiang University of Chinese Medicine), Ministry of Education, Heilongjiang University of Chinese Medicine, Harbin, 150000, China
| | - Hai-Xue Kuang
- Key Laboratory of Basic and Application Research of Beiyao (Heilongjiang University of Chinese Medicine), Ministry of Education, Heilongjiang University of Chinese Medicine, Harbin, 150000, China
| | - Meng Wang
- Key Laboratory of Basic and Application Research of Beiyao (Heilongjiang University of Chinese Medicine), Ministry of Education, Heilongjiang University of Chinese Medicine, Harbin, 150000, China.
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3
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Salem FM, Martin WR, Zhao X, Adbus Sayeed SK, Ighneim S, Greene M, Mohamed E, Orahoske CM, Zhang W, Li B, Su B. Synthesis and biological evaluation of orally active anti-Trypanosoma agents. Bioorg Med Chem 2024; 107:117751. [PMID: 38762979 DOI: 10.1016/j.bmc.2024.117751] [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: 02/27/2024] [Revised: 05/01/2024] [Accepted: 05/06/2024] [Indexed: 05/21/2024]
Abstract
In previous studies, we developed anti-trypanosome tubulin inhibitors with promising in vitro selectivity and activity against Human African Trypanosomiasis (HAT). However, for such agents, oral activity is crucial. This study focused on further optimizing these compounds to enhance their ligand efficiency, aiming to reduce bulkiness and hydrophobicity, which should improve solubility and, consequently, oral bioavailability. Using Trypanosoma brucei brucei cells as the parasite model and human normal kidney cells and mouse macrophage cells as the host model, we evaluated 30 new analogs synthesized through combinatorial chemistry. These analogs have fewer aromatic moieties and lower molecular weights than their predecessors. Several new analogs demonstrated IC50s in the low micromolar range, effectively inhibiting trypanosome cell growth without harming mammalian cells at the same concentration. We conducted a detailed structure-activity relationship (SAR) analysis and a docking study to assess the compounds' binding affinity to trypanosome tubulin homolog. The results revealed a correlation between binding energy and anti-Trypanosoma activity. Importantly, compound 7 displayed significant oral activity, effectively inhibiting trypanosome cell proliferation in mice.
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Affiliation(s)
- Fatma M Salem
- Department of Chemistry, Center for Gene Regulation in Health and Disease, College of Arts and Sciences, Cleveland State University, 2121 Euclid Ave., Cleveland, OH 44115, USA
| | - William R Martin
- Department of Chemistry, Center for Gene Regulation in Health and Disease, College of Arts and Sciences, Cleveland State University, 2121 Euclid Ave., Cleveland, OH 44115, USA; Genomic Medicine Institute, Cleveland Clinic Genome Center, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Xiaotong Zhao
- Department of Chemistry, Center for Gene Regulation in Health and Disease, College of Arts and Sciences, Cleveland State University, 2121 Euclid Ave., Cleveland, OH 44115, USA
| | - S K Adbus Sayeed
- Department of Biology, Geo. & Env. Sciences, Center for Gene Regulation in Health and Disease, College of Arts and Sciences, Cleveland State University, 2121 Euclid Ave., Cleveland, OH 44115, USA
| | - Sabreena Ighneim
- Department of Chemistry, Center for Gene Regulation in Health and Disease, College of Arts and Sciences, Cleveland State University, 2121 Euclid Ave., Cleveland, OH 44115, USA
| | - McKenna Greene
- Department of Chemistry, Center for Gene Regulation in Health and Disease, College of Arts and Sciences, Cleveland State University, 2121 Euclid Ave., Cleveland, OH 44115, USA
| | - Eman Mohamed
- Department of Chemistry, Center for Gene Regulation in Health and Disease, College of Arts and Sciences, Cleveland State University, 2121 Euclid Ave., Cleveland, OH 44115, USA
| | - Cody M Orahoske
- Department of Chemistry, Center for Gene Regulation in Health and Disease, College of Arts and Sciences, Cleveland State University, 2121 Euclid Ave., Cleveland, OH 44115, USA
| | - Wenjing Zhang
- Department of Chemistry, Center for Gene Regulation in Health and Disease, College of Arts and Sciences, Cleveland State University, 2121 Euclid Ave., Cleveland, OH 44115, USA
| | - Bibo Li
- Department of Biology, Geo. & Env. Sciences, Center for Gene Regulation in Health and Disease, College of Arts and Sciences, Cleveland State University, 2121 Euclid Ave., Cleveland, OH 44115, USA.
| | - Bin Su
- Department of Chemistry, Center for Gene Regulation in Health and Disease, College of Arts and Sciences, Cleveland State University, 2121 Euclid Ave., Cleveland, OH 44115, USA.
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Abbaali I, Truong D, Wetzel DM, Morrissette NS. Toxoplasma replication is inhibited by MMV676477 without development of resistance. Cytoskeleton (Hoboken) 2024. [PMID: 38757481 DOI: 10.1002/cm.21876] [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: 01/05/2024] [Revised: 03/20/2024] [Accepted: 04/24/2024] [Indexed: 05/18/2024]
Abstract
Protozoan parasites cause life-threatening infections in both humans and animals, including agriculturally significant livestock. Available treatments are typically narrow spectrum and are complicated by drug toxicity and the development of resistant parasites. Protozoan tubulin is an attractive target for the development of broad-spectrum antimitotic agents. The Medicines for Malaria Pathogen Box compound MMV676477 was previously shown to inhibit replication of kinetoplastid parasites, such as Leishmania amazonensis and Trypanosoma brucei, and the apicomplexan parasite Plasmodium falciparum by selectively stabilizing protozoan microtubules. In this report, we show that MMV676477 inhibits intracellular growth of the human apicomplexan pathogen Toxoplasma gondii with an EC50 value of ~50 nM. MMV676477 does not stabilize vertebrate microtubules or cause other toxic effects in human fibroblasts. The availability of tools for genetic studies makes Toxoplasma a useful model for studies of the cytoskeleton. We conducted a forward genetics screen for MMV676477 resistance, anticipating that missense mutations would delineate the binding site on protozoan tubulin. Unfortunately, we were unable to use genetics to dissect target interactions because no resistant parasites emerged. This outcome suggests that future drugs based on the MMV676477 scaffold would be less likely to be undermined by the emergence of drug resistance.
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Affiliation(s)
- Izra Abbaali
- Department of Molecular Biology and Biochemistry, University of California, Irvine, California, USA
| | - Danny Truong
- Department of Molecular Biology and Biochemistry, University of California, Irvine, California, USA
| | - Dawn M Wetzel
- Department of Pediatrics and Biochemistry, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Naomi S Morrissette
- Department of Molecular Biology and Biochemistry, University of California, Irvine, California, USA
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5
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Tell I Puig A, Soldati-Favre D. Roles of the tubulin-based cytoskeleton in the Toxoplasma gondii apical complex. Trends Parasitol 2024; 40:401-415. [PMID: 38531711 DOI: 10.1016/j.pt.2024.02.010] [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: 01/08/2024] [Revised: 02/26/2024] [Accepted: 02/28/2024] [Indexed: 03/28/2024]
Abstract
Microtubules (MTs) play a vital role as key components of the eukaryotic cytoskeleton. The phylum Apicomplexa comprises eukaryotic unicellular parasitic organisms defined by the presence of an apical complex which consists of specialized secretory organelles and tubulin-based cytoskeletal elements. One apicomplexan parasite, Toxoplasma gondii, is an omnipresent opportunistic pathogen with significant medical and veterinary implications. To ensure successful infection and widespread dissemination, T. gondii heavily relies on the tubulin structures present in the apical complex. Recent advances in high-resolution imaging, coupled with reverse genetics, have offered deeper insights into the composition, functionality, and dynamics of these tubulin-based structures. The apicomplexan tubulins differ from those of their mammalian hosts, endowing them with unique attributes and susceptibility to specific classes of inhibitory compounds.
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Affiliation(s)
- Albert Tell I Puig
- Department of Microbiology and Molecular Medicine, CMU, University of Geneva, Geneva, Switzerland.
| | - Dominique Soldati-Favre
- Department of Microbiology and Molecular Medicine, CMU, University of Geneva, Geneva, Switzerland
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6
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Reber S, Singer M, Frischknecht F. Cytoskeletal dynamics in parasites. Curr Opin Cell Biol 2024; 86:102277. [PMID: 38048658 DOI: 10.1016/j.ceb.2023.102277] [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: 07/03/2023] [Revised: 10/12/2023] [Accepted: 10/17/2023] [Indexed: 12/06/2023]
Abstract
Cytoskeletal dynamics are essential for cellular homeostasis and development for both metazoans and protozoans. The function of cytoskeletal elements in protozoans can diverge from that of metazoan cells, with microtubules being more stable and actin filaments being more dynamic. This is particularly striking in protozoan parasites that evolved to enter metazoan cells. Here, we review recent progress towards understanding cytoskeletal dynamics in protozoan parasites, with a focus on divergent properties compared to classic model organisms.
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Affiliation(s)
- Simone Reber
- Max Planck Institute for Infection Biology, 10117 Berlin, Germany; University of Applied Sciences Berlin, 13353 Berlin, Germany
| | - Mirko Singer
- Integrative Parasitology, Center for Infectious Diseases, Heidelberg University Medical Faculty, Im Neuenheimer Feld 324, 69120 Heidelberg, Germany; German Center for Infection Research, DZIF Partner Site Heidelberg, Heidelberg, Germany.
| | - Friedrich Frischknecht
- Integrative Parasitology, Center for Infectious Diseases, Heidelberg University Medical Faculty, Im Neuenheimer Feld 324, 69120 Heidelberg, Germany; German Center for Infection Research, DZIF Partner Site Heidelberg, Heidelberg, Germany
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7
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Podolak M, Holota S, Deyak Y, Dziduch K, Dudchak R, Wujec M, Bielawski K, Lesyk R, Bielawska A. Tubulin inhibitors. Selected scaffolds and main trends in the design of novel anticancer and antiparasitic agents. Bioorg Chem 2024; 143:107076. [PMID: 38163424 DOI: 10.1016/j.bioorg.2023.107076] [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: 10/04/2023] [Revised: 12/02/2023] [Accepted: 12/27/2023] [Indexed: 01/03/2024]
Abstract
Design of tubulin inhibitors as anticancer drugs dynamically developed over the past 20 years. The modern arsenal of potential tubulin-targeting anticancer agents is represented by small molecules, monoclonal antibodies, and antibody-drug conjugates. Moreover, targeting tubulin has been a successful strategy in the development of antiparasitic drugs. In the present review, an overall picture of the research and development of potential tubulin-targeting agents using small molecules between 2018 and 2023 is provided. The data about some most often used and prospective chemotypes of small molecules (privileged heterocycles, moieties of natural molecules) and synthetic methodologies (analogue-based, fragment-based drug design, molecular hybridization) applied for the design of novel agents with an impact on the tubulin system are summarized. The design and prospects of multi-target agents with an impact on the tubulin system were also highlighted. Reported in the review data contribute to the "structure-activity" profile of tubulin-targeting small molecules as anticancer and antiparasitic agents and will be useful for the application by medicinal chemists in further exploration, design, improvement, and optimization of this class of molecules.
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Affiliation(s)
- Magdalena Podolak
- Department of Biotechnology, Medical University of Bialystok, Kilinskiego 1, 15-089 Bialystok, Poland
| | - Serhii Holota
- Department of Pharmaceutical, Organic and Bioorganic Chemistry, Danylo Halytsky Lviv National Medical University, Pekarska 69, 79010 Lviv, Ukraine
| | - Yaroslava Deyak
- Department of Pharmaceutical, Organic and Bioorganic Chemistry, Danylo Halytsky Lviv National Medical University, Pekarska 69, 79010 Lviv, Ukraine; Department of Pharmaceutical Disciplines, Uzhhorod National University, Narodna Square 3, 88000 Uzhhorod, Ukraine
| | - Katarzyna Dziduch
- Doctoral School, Medical University of Lublin, Chodzki 7, 20-093 Lublin, Poland
| | - Rostyslav Dudchak
- Department of Biotechnology, Medical University of Bialystok, Kilinskiego 1, 15-089 Bialystok, Poland
| | - Monika Wujec
- Department of Organic Chemistry, Medical University of Lublin, Chodzki 4a, 20-093 Lublin, Poland
| | - Krzysztof Bielawski
- Department of Synthesis and Technology of Drugs, Medical University of Bialystok, Kilinskiego 1, 15-089 Bialystok, Poland
| | - Roman Lesyk
- Department of Pharmaceutical, Organic and Bioorganic Chemistry, Danylo Halytsky Lviv National Medical University, Pekarska 69, 79010 Lviv, Ukraine.
| | - Anna Bielawska
- Department of Biotechnology, Medical University of Bialystok, Kilinskiego 1, 15-089 Bialystok, Poland
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8
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Montecinos F, Sackett DL. Structural Changes, Biological Consequences, and Repurposing of Colchicine Site Ligands. Biomolecules 2023; 13:biom13050834. [PMID: 37238704 DOI: 10.3390/biom13050834] [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: 04/17/2023] [Revised: 05/06/2023] [Accepted: 05/10/2023] [Indexed: 05/28/2023] Open
Abstract
Microtubule-targeting agents (MTAs) bind to one of several distinct sites in the tubulin dimer, the subunit of microtubules. The binding affinities of MTAs may vary by several orders of magnitude, even for MTAs that specifically bind to a particular site. The first drug binding site discovered in tubulin was the colchicine binding site (CBS), which has been known since the discovery of the tubulin protein. Although highly conserved throughout eukaryotic evolution, tubulins show diversity in their sequences between tubulin orthologs (inter-species sequence differences) and paralogs (intraspecies differences, such as tubulin isotypes). The CBS is promiscuous and binds to a broad range of structurally distinct molecules that can vary in size, shape, and affinity. This site remains a popular target for the development of new drugs to treat human diseases (including cancer) and parasitic infections in plants and animals. Despite the rich knowledge about the diversity of tubulin sequences and the structurally distinct molecules that bind to the CBS, a pattern has yet to be found to predict the affinity of new molecules that bind to the CBS. In this commentary, we briefly discuss the literature evidencing the coexistence of the varying binding affinities for drugs that bind to the CBS of tubulins from different species and within species. We also comment on the structural data that aim to explain the experimental differences observed in colchicine binding to the CBS of β-tubulin class VI (TUBB1) compared to other isotypes.
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Affiliation(s)
- Felipe Montecinos
- Protein Expression Laboratory, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Dan L Sackett
- Division of Basic and Translational Biophysics, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
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9
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Morrissette N, Abbaali I, Ramakrishnan C, Hehl AB. The Tubulin Superfamily in Apicomplexan Parasites. Microorganisms 2023; 11:microorganisms11030706. [PMID: 36985278 PMCID: PMC10056924 DOI: 10.3390/microorganisms11030706] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Revised: 03/03/2023] [Accepted: 03/06/2023] [Indexed: 03/11/2023] Open
Abstract
Microtubules and specialized microtubule-containing structures are assembled from tubulins, an ancient superfamily of essential eukaryotic proteins. Here, we use bioinformatic approaches to analyze features of tubulins in organisms from the phylum Apicomplexa. Apicomplexans are protozoan parasites that cause a variety of human and animal infectious diseases. Individual species harbor one to four genes each for α- and β-tubulin isotypes. These may specify highly similar proteins, suggesting functional redundancy, or exhibit key differences, consistent with specialized roles. Some, but not all apicomplexans harbor genes for δ- and ε-tubulins, which are found in organisms that construct appendage-containing basal bodies. Critical roles for apicomplexan δ- and ε-tubulin are likely to be limited to microgametes, consistent with a restricted requirement for flagella in a single developmental stage. Sequence divergence or the loss of δ- and ε-tubulin genes in other apicomplexans appears to be associated with diminished requirements for centrioles, basal bodies, and axonemes. Finally, because spindle microtubules and flagellar structures have been proposed as targets for anti-parasitic therapies and transmission-blocking strategies, we discuss these ideas in the context of tubulin-based structures and tubulin superfamily properties.
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Affiliation(s)
- Naomi Morrissette
- Molecular Biology and Biochemistry, University of California Irvine, Irvine, CA 92697, USA
- Correspondence: ; Tel.: +1-949-824-9243
| | - Izra Abbaali
- Molecular Biology and Biochemistry, University of California Irvine, Irvine, CA 92697, USA
| | - Chandra Ramakrishnan
- Institute for Parasitology, University of Zurich, Winterthurerstrasse 266a, 8057 Zürich, Switzerland
| | - Adrian B. Hehl
- Institute for Parasitology, University of Zurich, Winterthurerstrasse 266a, 8057 Zürich, Switzerland
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10
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Wranik M, Weinert T, Slavov C, Masini T, Furrer A, Gaillard N, Gioia D, Ferrarotti M, James D, Glover H, Carrillo M, Kekilli D, Stipp R, Skopintsev P, Brünle S, Mühlethaler T, Beale J, Gashi D, Nass K, Ozerov D, Johnson PJM, Cirelli C, Bacellar C, Braun M, Wang M, Dworkowski F, Milne C, Cavalli A, Wachtveitl J, Steinmetz MO, Standfuss J. Watching the release of a photopharmacological drug from tubulin using time-resolved serial crystallography. Nat Commun 2023; 14:903. [PMID: 36807348 PMCID: PMC9936131 DOI: 10.1038/s41467-023-36481-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Accepted: 02/02/2023] [Indexed: 02/19/2023] Open
Abstract
The binding and release of ligands from their protein targets is central to fundamental biological processes as well as to drug discovery. Photopharmacology introduces chemical triggers that allow the changing of ligand affinities and thus biological activity by light. Insight into the molecular mechanisms of photopharmacology is largely missing because the relevant transitions during the light-triggered reaction cannot be resolved by conventional structural biology. Using time-resolved serial crystallography at a synchrotron and X-ray free-electron laser, we capture the release of the anti-cancer compound azo-combretastatin A4 and the resulting conformational changes in tubulin. Nine structural snapshots from 1 ns to 100 ms complemented by simulations show how cis-to-trans isomerization of the azobenzene bond leads to a switch in ligand affinity, opening of an exit channel, and collapse of the binding pocket upon ligand release. The resulting global backbone rearrangements are related to the action mechanism of microtubule-destabilizing drugs.
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Affiliation(s)
- Maximilian Wranik
- Division of Biology and Chemistry, Paul Scherrer Institut, 5232, Villigen, Switzerland
| | - Tobias Weinert
- Division of Biology and Chemistry, Paul Scherrer Institut, 5232, Villigen, Switzerland
| | - Chavdar Slavov
- Institute of Physical and Theoretical Chemistry, Goethe University, Frankfurt am Main, Germany
| | - Tiziana Masini
- Computational & Chemical Biology, Istituto Italiano di Tecnologia, 16163, Genova, Italy
| | - Antonia Furrer
- Division of Biology and Chemistry, Paul Scherrer Institut, 5232, Villigen, Switzerland
| | - Natacha Gaillard
- Division of Biology and Chemistry, Paul Scherrer Institut, 5232, Villigen, Switzerland
| | - Dario Gioia
- Computational & Chemical Biology, Istituto Italiano di Tecnologia, 16163, Genova, Italy
| | - Marco Ferrarotti
- Computational & Chemical Biology, Istituto Italiano di Tecnologia, 16163, Genova, Italy
| | - Daniel James
- Division of Biology and Chemistry, Paul Scherrer Institut, 5232, Villigen, Switzerland
| | - Hannah Glover
- Division of Biology and Chemistry, Paul Scherrer Institut, 5232, Villigen, Switzerland
| | - Melissa Carrillo
- Division of Biology and Chemistry, Paul Scherrer Institut, 5232, Villigen, Switzerland
| | - Demet Kekilli
- Division of Biology and Chemistry, Paul Scherrer Institut, 5232, Villigen, Switzerland
| | - Robin Stipp
- Division of Biology and Chemistry, Paul Scherrer Institut, 5232, Villigen, Switzerland
| | - Petr Skopintsev
- Division of Biology and Chemistry, Paul Scherrer Institut, 5232, Villigen, Switzerland
| | - Steffen Brünle
- Division of Biology and Chemistry, Paul Scherrer Institut, 5232, Villigen, Switzerland
| | - Tobias Mühlethaler
- Division of Biology and Chemistry, Paul Scherrer Institut, 5232, Villigen, Switzerland
| | - John Beale
- Division of Biology and Chemistry, Paul Scherrer Institut, 5232, Villigen, Switzerland
| | - Dardan Gashi
- Photon Science Division, Paul Scherrer Institut, 5232, Villigen, Switzerland
| | - Karol Nass
- Photon Science Division, Paul Scherrer Institut, 5232, Villigen, Switzerland
| | - Dmitry Ozerov
- Scientific Computing, Theory and Data, Paul Scherrer Institut, 5232, Villigen, Switzerland
| | - Philip J M Johnson
- Photon Science Division, Paul Scherrer Institut, 5232, Villigen, Switzerland
| | - Claudio Cirelli
- Photon Science Division, Paul Scherrer Institut, 5232, Villigen, Switzerland
| | - Camila Bacellar
- Photon Science Division, Paul Scherrer Institut, 5232, Villigen, Switzerland
| | - Markus Braun
- Institute of Physical and Theoretical Chemistry, Goethe University, Frankfurt am Main, Germany
| | - Meitian Wang
- Photon Science Division, Paul Scherrer Institut, 5232, Villigen, Switzerland
| | - Florian Dworkowski
- Photon Science Division, Paul Scherrer Institut, 5232, Villigen, Switzerland
| | - Chris Milne
- Photon Science Division, Paul Scherrer Institut, 5232, Villigen, Switzerland
| | - Andrea Cavalli
- Computational & Chemical Biology, Istituto Italiano di Tecnologia, 16163, Genova, Italy
- Department of Pharmacy and Biotechnology, University of Bologna, 40126, Bologna, Italy
| | - Josef Wachtveitl
- Institute of Physical and Theoretical Chemistry, Goethe University, Frankfurt am Main, Germany
| | - Michel O Steinmetz
- Division of Biology and Chemistry, Paul Scherrer Institut, 5232, Villigen, Switzerland.
- Biozentrum, University of Basel, 4056, Basel, Switzerland.
| | - Jörg Standfuss
- Division of Biology and Chemistry, Paul Scherrer Institut, 5232, Villigen, Switzerland.
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11
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Lafanechère L. The microtubule cytoskeleton: An old validated target for novel therapeutic drugs. Front Pharmacol 2022; 13:969183. [PMID: 36188585 PMCID: PMC9521402 DOI: 10.3389/fphar.2022.969183] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Accepted: 08/30/2022] [Indexed: 12/02/2022] Open
Abstract
Compounds targeting microtubules are widely used in cancer therapy with a proven efficacy. However, because they also target non-cancerous cells, their administration leads to numerous adverse effects. With the advancement of knowledge on the structure of tubulin, the regulation of microtubule dynamics and their deregulation in pathological processes, new therapeutic strategies are emerging, both for the treatment of cancer and for other diseases, such as neuronal or even heart diseases and parasite infections. In addition, a better understanding of the mechanism of action of well-known drugs such as colchicine or certain kinase inhibitors contributes to the development of these new therapeutic approaches. Nowadays, chemists and biologists are working jointly to select drugs which target the microtubule cytoskeleton and have improved properties. On the basis of a few examples this review attempts to depict the panorama of these recent advances.
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Mühlethaler T, Milanos L, Ortega JA, Blum TB, Gioia D, Roy B, Prota AE, Cavalli A, Steinmetz MO. Rational Design of a Novel Tubulin Inhibitor with a Unique Mechanism of Action. Angew Chem Int Ed Engl 2022; 61:e202204052. [PMID: 35404502 PMCID: PMC9324959 DOI: 10.1002/anie.202204052] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Indexed: 11/16/2022]
Abstract
In this study, we capitalized on our previously performed crystallographic fragment screen and developed the antitubulin small molecule Todalam with only two rounds of straightforward chemical synthesis. Todalam binds to a novel tubulin site, disrupts microtubule networks in cells, arrests cells in G2/M, induces cell death, and synergizes with vinblastine. The compound destabilizes microtubules by acting as a molecular plug that sterically inhibits the curved-to-straight conformational switch in the α-tubulin subunit, and by sequestering tubulin dimers into assembly incompetent oligomers. Our results describe for the first time the generation of a fully rationally designed small molecule tubulin inhibitor from a fragment, which displays a unique molecular mechanism of action. They thus demonstrate the usefulness of tubulin-binding fragments as valuable starting points for innovative antitubulin drug and chemical probe discovery campaigns.
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Affiliation(s)
- Tobias Mühlethaler
- Laboratory of Biomolecular ResearchDepartment of Biology and ChemistryPaul Scherrer Institut5232Villigen PSISwitzerland
| | - Lampros Milanos
- Computational & Chemical BiologyIstituto Italiano di Tecnologiavia Morego 3016163GenovaItaly
| | - Jose Antonio Ortega
- Computational & Chemical BiologyIstituto Italiano di Tecnologiavia Morego 3016163GenovaItaly
| | - Thorsten B. Blum
- Laboratory of Biomolecular ResearchDepartment of Biology and ChemistryPaul Scherrer Institut5232Villigen PSISwitzerland
| | - Dario Gioia
- Computational & Chemical BiologyIstituto Italiano di Tecnologiavia Morego 3016163GenovaItaly
| | - Bibhas Roy
- Laboratory of Nanoscale BiologyDepartment of Biology and ChemistryPaul Scherrer Institut5232Villigen PSISwitzerland
| | - Andrea E. Prota
- Laboratory of Biomolecular ResearchDepartment of Biology and ChemistryPaul Scherrer Institut5232Villigen PSISwitzerland
| | - Andrea Cavalli
- Computational & Chemical BiologyIstituto Italiano di Tecnologiavia Morego 3016163GenovaItaly
- Department of Pharmacy and BiotechnologyAlma Mater StudiorumUniversity of Bolognavia Belmeloro 640126BolognaItaly
| | - Michel O. Steinmetz
- Laboratory of Biomolecular ResearchDepartment of Biology and ChemistryPaul Scherrer Institut5232Villigen PSISwitzerland
- University of Basel, Biozentrum4056BaselSwitzerland
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13
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Aguayo-Ortiz R, Dominguez L. Unveiling the Possible Oryzalin-Binding Site in the α-Tubulin of Toxoplasma gondii. ACS OMEGA 2022; 7:18434-18442. [PMID: 35694483 PMCID: PMC9178734 DOI: 10.1021/acsomega.2c00729] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Accepted: 05/11/2022] [Indexed: 06/09/2023]
Abstract
Dinitroaniline derivatives have been widely used as herbicidal agents to control weeds and grass. Previous studies demonstrated that these compounds also exhibit good antiparasitic activity against some protozoan parasites. Oryzalin (ORY), a representative dinitroaniline derivative, exerts its antiprotozoal activity against Toxoplasma gondii by inhibiting the microtubule polymerization process. Moreover, the identification of ORY-resistant T. gondii lines obtained by chemical mutagenesis confirmed that this compound binds selectively to α-tubulin. Based on experimental information reported so far and a multiple sequence analysis carried out in this work, we propose that the pironetin (PIR) site is the potential ORY-binding site. Therefore, we employed state-of-the-art computational approaches to characterize the interaction profile of ORY at the proposed site in the α-tubulin of T. gondii. An exhaustive search for other possible binding sites was performed using the Wrap "N" Shake method, which showed that ORY exhibits highest stability and affinity for the PIR site. Moreover, our molecular dynamics simulations revealed that the dipropylamine substituent of ORY interacts with a hydrophobic pocket, while the sulfonamide group formed hydrogen bonds with water molecules at the site entrance. Overall, our results suggest that ORY binds to the PIR site on the α-tubulin of the protozoan parasite T. gondii. This information will be very useful for designing less toxic and more potent antiprotozoal agents.
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Affiliation(s)
- Rodrigo Aguayo-Ortiz
- Departamento
de Farmacia, Facultad de Química, Universidad Nacional Autónoma de México, Mexico City 04510, Mexico
| | - Laura Dominguez
- Departamento
de Fisicoquímica, Facultad de Química, Universidad Nacional Autónoma de México, Mexico City 04510, Mexico
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14
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Mühlethaler T, Milanos L, Ortega JA, Blum TB, Gioia D, Roy B, Prota AE, Cavalli A, Steinmetz MO. Rational Design of a Novel Tubulin Inhibitor with a Unique Mechanism of Action. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202204052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Tobias Mühlethaler
- Laboratory of Biomolecular Research Department of Biology and Chemistry Paul Scherrer Institut 5232 Villigen PSI Switzerland
| | - Lampros Milanos
- Computational & Chemical Biology Istituto Italiano di Tecnologia via Morego 30 16163 Genova Italy
| | - Jose Antonio Ortega
- Computational & Chemical Biology Istituto Italiano di Tecnologia via Morego 30 16163 Genova Italy
| | - Thorsten B. Blum
- Laboratory of Biomolecular Research Department of Biology and Chemistry Paul Scherrer Institut 5232 Villigen PSI Switzerland
| | - Dario Gioia
- Computational & Chemical Biology Istituto Italiano di Tecnologia via Morego 30 16163 Genova Italy
| | - Bibhas Roy
- Laboratory of Nanoscale Biology Department of Biology and Chemistry Paul Scherrer Institut 5232 Villigen PSI Switzerland
| | - Andrea E. Prota
- Laboratory of Biomolecular Research Department of Biology and Chemistry Paul Scherrer Institut 5232 Villigen PSI Switzerland
| | - Andrea Cavalli
- Computational & Chemical Biology Istituto Italiano di Tecnologia via Morego 30 16163 Genova Italy
- Department of Pharmacy and Biotechnology Alma Mater Studiorum University of Bologna via Belmeloro 6 40126 Bologna Italy
| | - Michel O. Steinmetz
- Laboratory of Biomolecular Research Department of Biology and Chemistry Paul Scherrer Institut 5232 Villigen PSI Switzerland
- University of Basel, Biozentrum 4056 Basel Switzerland
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15
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Sinclair AN, de Graffenried CL. Cell division: Naegleria bundles up for mitosis. Curr Biol 2022; 32:R269-R271. [PMID: 35349811 DOI: 10.1016/j.cub.2022.01.079] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
How well do we understand the range of mechanisms used by eukaryotes for mitosis? A new study in a highly divergent eukaryote shows that unusual tubulin isoforms can create a mitotic spindle exclusively out of microtubule bundles.
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Affiliation(s)
- Amy N Sinclair
- Abveris, 480 Neponset Street Suite 10B, Canton, MA 02021, USA
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16
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Hirst WG, Fachet D, Kuropka B, Weise C, Saliba KJ, Reber S. Purification of functional Plasmodium falciparum tubulin allows for the identification of parasite-specific microtubule inhibitors. Curr Biol 2022; 32:919-926.e6. [PMID: 35051355 DOI: 10.1016/j.cub.2021.12.049] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Revised: 11/08/2021] [Accepted: 12/17/2021] [Indexed: 12/21/2022]
Abstract
Cytoskeletal proteins are essential for parasite proliferation, growth, and transmission, and therefore have the potential to serve as drug targets.1-5 While microtubules and their molecular building block αβ-tubulin are established drug targets in a variety of cancers,6,7 we still lack sufficient knowledge of the biochemistry of parasite tubulins to exploit the structural divergence between parasite and human tubulins. For example, it remains to be determined whether compounds of interest can specifically target parasite microtubules without affecting the host cell cytoskeleton. Such mechanistic insights have been limited by the lack of functional parasite tubulin. In this study, we report the purification and characterization of tubulin from Plasmodium falciparum, the causative agent of malaria. We show that the highly purified tubulin is fully functional, as it efficiently assembles into microtubules with specific parameters of dynamic instability. There is a high degree of amino-acid conservation between human and P. falciparum α- and β-tubulin, sharing approximately 83.7% and 88.5% identity, respectively. However, Plasmodium tubulin is more similar to plant than to mammalian tubulin, raising the possibility of identifying compounds that would selectively disrupt parasite microtubules without affecting the host cell cytoskeleton. As a proof of principle, we describe two compounds that exhibit selective toxicity toward parasite tubulin. Thus, the ability to specifically disrupt protozoan microtubule growth without affecting human microtubules provides an exciting opportunity for the development of novel antimalarials.
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Affiliation(s)
- William G Hirst
- IRI Life Sciences, Humboldt-Universität zu Berlin, 10115 Berlin, Germany; Research School of Biology, The Australian National University, Canberra, ACT 2601, Australia
| | - Dominik Fachet
- IRI Life Sciences, Humboldt-Universität zu Berlin, 10115 Berlin, Germany; Research School of Biology, The Australian National University, Canberra, ACT 2601, Australia
| | - Benno Kuropka
- Freie Universität Berlin, Institute of Chemistry and Biochemistry, Core Facility BioSupraMol, 14195 Berlin, Germany
| | - Christoph Weise
- Freie Universität Berlin, Institute of Chemistry and Biochemistry, Core Facility BioSupraMol, 14195 Berlin, Germany
| | - Kevin J Saliba
- Research School of Biology, The Australian National University, Canberra, ACT 2601, Australia
| | - Simone Reber
- IRI Life Sciences, Humboldt-Universität zu Berlin, 10115 Berlin, Germany; University of Applied Sciences Berlin, 13353 Berlin, Germany.
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Systematic Analysis of Clemastine, a Candidate Apicomplexan Parasite-Selective Tubulin-Targeting Agent. Int J Mol Sci 2021; 23:ijms23010068. [PMID: 35008492 PMCID: PMC8744746 DOI: 10.3390/ijms23010068] [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: 11/24/2021] [Revised: 12/15/2021] [Accepted: 12/20/2021] [Indexed: 11/24/2022] Open
Abstract
Apicomplexan parasites, such as Toxoplasma gondii, Plasmodium spp., Babesia spp., and Cryptosporidium spp., cause significant morbidity and mortality. Existing treatments are problematic due to toxicity and the emergence of drug-resistant parasites. Because protozoan tubulin can be selectively disrupted by small molecules to inhibit parasite growth, we assembled an in vitro testing cascade to fully delineate effects of candidate tubulin-targeting drugs on Toxoplasma gondii and vertebrate host cells. Using this analysis, we evaluated clemastine, an antihistamine that has been previously shown to inhibit Plasmodium growth by competitively binding to the CCT/TRiC tubulin chaperone as a proof-of-concept. We concurrently analyzed astemizole, a distinct antihistamine that blocks heme detoxification in Plasmodium. Both drugs have EC50 values of ~2 µM and do not demonstrate cytotoxicity or vertebrate microtubule disruption at this concentration. Parasite subpellicular microtubules are shortened by treatment with either clemastine or astemizole but not after treatment with pyrimethamine, indicating that this effect is not a general response to antiparasitic drugs. Immunoblot quantification indicates that the total α-tubulin concentration of 0.02 pg/tachyzoite does not change with clemastine treatment. In conclusion, the testing cascade allows profiling of small-molecule effects on both parasite and vertebrate cell viability and microtubule integrity.
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