1
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Shahabipour S, Shamkhali AN, Razzaghi-Asl N. Cytotoxic monastrol derivatives as adjective inhibitors of drug-resistant Eg5: a molecular dynamics perspective. J Biomol Struct Dyn 2024:1-14. [PMID: 38450658 DOI: 10.1080/07391102.2024.2326195] [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: 11/06/2023] [Accepted: 02/27/2024] [Indexed: 03/08/2024]
Abstract
The mitotic kinesin Eg5 is a motor protein involved in the formation of bipolar spindle and cell division. Eg5 is overexpressed in various cancer cells and Eg5 targeting agents are promising candidates for cancer therapy. Subsequent to the discovery of monastrol as a small-molecule Eg5 modulator, numerous inhibitors/modulators have been reported from which a few entered clinical trials. Mutagenic investigations specified declined sensitivity of Eg5 allosteric site to monastrol due to the occurrence of drug-resistant mutations in some cell cultures. Accordingly, identification of tight binders to the mutant Eg5 allosteric site is an invaluable strategy to devise more efficient Eg5 modulators. We have previously synthesized a few dihydropyrimidinethione (DHPMT)-based 5-carboxamide monastrol derivatives (1-5) with higher cytotoxicities against AGS (IC50 9.90-98.48 µM) and MCF-7 (IC50 15.20-149.13 µM) cancer cell lines than monastrol. Within a current study, a structural insight was offered into the binding mechanism of intended derivatives inside the mutant Eg5 loop5/α2/α3 allosteric pocket. Molecular docking of the DHPMT R and S-enantiomers unraveled top-scored Eg5 complexes. Molecular dynamics (MD) simulations were carried out on 5 superior complexes as (R)-2/D130V-Eg5, (R)-4/D130V-Eg5, (R)-5/D130V-Eg5, (R)-5/L214I-Eg5, (R)-5/R119L-Eg5, and the control groups monastrol/D130V-Eg5, monastrol/L214I-Eg5, monastrol/R119L-Eg5. Free energy calculations were conducted through conformational sampling of MD-driven binding trajectories. Our results provided structural details on probable interaction mechanism of the cytotoxic DHPMTs that are difficult to address experimentally. The outputs of the current study propose new monastrol derivatives as probable resistance-overwhelming Eg5 modulators.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- S Shahabipour
- Department of Applied Chemistry, Faculty of Science, University of Mohaghegh Ardabili, Ardabil, Iran
| | - A N Shamkhali
- Department of Applied Chemistry, Faculty of Science, University of Mohaghegh Ardabili, Ardabil, Iran
- Neuroscience Research Center, Iran University of Medical Sciences, Tehran, Iran
| | - N Razzaghi-Asl
- Pharmaceutical Sciences Research Center, Ardabil University of Medical Sciences, Ardabil, Iran, Iran
- Department of Medicinal Chemistry, School of Pharmacy, Ardabil University of Medical Sciences, Ardabil, Iran
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2
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Indorato RL, DeBonis S, Garcia-Saez I, Skoufias DA. Drug resistance dependent on allostery: A P-loop rigor Eg5 mutant exhibits resistance to allosteric inhibition by STLC. Front Oncol 2022; 12:965455. [PMID: 36313676 PMCID: PMC9597087 DOI: 10.3389/fonc.2022.965455] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Accepted: 09/28/2022] [Indexed: 11/13/2022] Open
Abstract
The mitotic kinesin Eg5 has emerged as a potential anti-mitotic target for the purposes of cancer chemotherapy. Whether clinical resistance to these inhibitors can arise is unclear. We exploited HCT116 cancer cell line to select resistant clones to S-trityl-L-cysteine (STLC), an extensively studied Eg5 loop-L5 binding inhibitor. The STLC resistant clones differed in their resistance to other loop-L5 binding inhibitors but remained sensitive to the ATP class of competitive Eg5 specific inhibitors. Eg5 is still necessary for bipolar spindle formation in the resistant clones since the cells were sensitive to RNAi mediated depletion of Eg5. One clone expressing Eg5(T107N), a dominant point mutation in the P-loop of the ATP binding domain of the motor, appeared to be not only resistant but also dependent on the presence of STLC. Eg5(T107N) expression was associated also with resistance to the clinical relevant loop-L5 Eg5 inhibitors, Arry-520 and ispinesib. Ectopic expression of the Eg5(T107N) mutant in the absence of STLC was associated with strong non-exchangeable binding to microtubules causing them to bundle. Biochemical assays showed that in contrast to the wild type Eg5-STLC complex, the ATP binding site of the Eg5(T107N) is accessible for nucleotide exchange only when the inhibitor is present. We predict that resistance can be overcome by inhibitors that bind to other than the Eg5 loop-L5 binding site having different chemical scaffolds, and that allostery-dependent resistance to Eg5 inhibitors may also occur in cells and may have positive implications in chemotherapy since once diagnosed may be beneficial following cessation of the chemotherapeutic regimen.
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3
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Alexandar SP, Yennamalli RM, Ulaganathan V. Coarse grained modelling highlights the binding differences in the two different allosteric sites of the Human Kinesin EG5 and its implications in inhibitor design. Comput Biol Chem 2022; 99:107708. [PMID: 35717732 DOI: 10.1016/j.compbiolchem.2022.107708] [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: 03/26/2022] [Revised: 05/26/2022] [Accepted: 05/27/2022] [Indexed: 11/03/2022]
Abstract
Kinesins involved in mitotic cell division have gained prominence as promising chemotherapy targets. One such kinesin, EG5, a motor protein responsible for cell division, is a validated chemotherapy target with several compounds at various stages of clinical trials. EG5 has an active site and two different allosteric sites that are known to have ligand specificity. Upon ligand binding, EG5's motor domain will no longer undergo nucleotide-dependent conformational changes required to complete the catalytic cycle. However, there is a lack of in-depth knowledge on the mechanism of inhibitor binding to the two different allosteric sites. To understand the EG5's inhibition mechanism and interactions at allosteric sites and other functionally important regions, we generated two coarse-grained models, Gaussian Network Model (GNM) and Anisotropic Network Model (ANM), to identify the dynamics and its correlation to EG5's function. The first three slowest modes of GNM showed marked differences between the various models of EG5. In the first mode, when the inhibitor is bound at allosteric site 1, there is a presence of a hinge region around residue 166, which is not found when the inhibitor is bound at allosteric site 2 or allosteric sites 1 and 2. The third slowest mode showed a distinctive positively correlated region when the inhibitor is bound at allosteric site 2. These differences indicated that the mechanism of binding at allosteric site 1 and allosteric site 2 are unique. Further, it was observed that the simultaneous ligand binding at allosteric sites 1 and 2 shares structural dynamics and interactions that were found while ligand binds at allosteric sites 1 and 2 independently, leading to a new mechanism. Taken together, our observations suggest that there are different mechanisms at play in each inhibitor bound system considered.
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Affiliation(s)
- Soundarya Priya Alexandar
- Molecular Motors Lab, Department of Biotechnology, School of Chemical & Biotechnology, SASTRA Deemed to be University, Tirumalaisamudram, Thanjavur, Tamil Nadu 613401, India
| | - Ragothaman M Yennamalli
- Department of Bioinformatics, School of Chemical & Biotechnology, SASTRA Deemed to be University, Tirumalaisamudram, Thanjavur, Tamil Nadu 613401, India
| | - Venkatasubramanian Ulaganathan
- Molecular Motors Lab, Department of Biotechnology, School of Chemical & Biotechnology, SASTRA Deemed to be University, Tirumalaisamudram, Thanjavur, Tamil Nadu 613401, India.
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4
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She ZY, Zhong N, Wei YL. Kinesin-5 Eg5 mediates centrosome separation to control spindle assembly in spermatocytes. Chromosoma 2022; 131:87-105. [PMID: 35437661 DOI: 10.1007/s00412-022-00772-5] [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: 12/02/2021] [Revised: 03/12/2022] [Accepted: 04/08/2022] [Indexed: 11/25/2022]
Abstract
Timely and accurate centrosome separation is critical for bipolar spindle organization and faithful chromosome segregation during cell division. Kinesin-5 Eg5 is essential for centrosome separation and spindle organization in somatic cells; however, the detailed functions and mechanisms of Eg5 in spermatocytes remain unclear. In this study, we show that Eg5 proteins are located at spindle microtubules and centrosomes in spermatocytes both in vivo and in vitro. We reveal that the spermatocytes are arrested at metaphase I in seminiferous tubules after Eg5 inhibition. Eg5 ablation results in cell cycle arrest, the formation of monopolar spindle, and chromosome misalignment in cultured GC-2 spd cells. Importantly, we find that the long-term inhibition of Eg5 results in an increased number of centrosomes and chromosomal instability in spermatocytes. Our findings indicate that Eg5 mediates centrosome separation to control spindle assembly and chromosome alignment in spermatocytes, which finally contribute to chromosome stability and faithful cell division of the spermatocytes.
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Affiliation(s)
- Zhen-Yu She
- Department of Cell Biology and Genetics, The School of Basic Medical Sciences, Fujian Medical University, Fuzhou, 350122, Fujian, China.
- Key Laboratory of Stem Cell Engineering and Regenerative Medicine, Fujian Province University, Fuzhou, 350122, Fujian, China.
| | - Ning Zhong
- Department of Cell Biology and Genetics, The School of Basic Medical Sciences, Fujian Medical University, Fuzhou, 350122, Fujian, China
- Key Laboratory of Stem Cell Engineering and Regenerative Medicine, Fujian Province University, Fuzhou, 350122, Fujian, China
| | - Ya-Lan Wei
- Fujian Obstetrics and Gynecology Hospital, Fuzhou, 350011, Fujian, China
- Medical Research Center, Fujian Maternity and Child Health Hospital, Affiliated Hospital of Fujian Medical University, Fuzhou, 350001, Fujian, China
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5
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Alrazi IMD, Ogunwa TH, Kolawole AO, Elekofehinti OO, Omotuyi OI, Miyanishi T, Maruta S. Kolaflavanone, a biflavonoid derived from medicinal plant Garcinia, is an inhibitor of mitotic kinesin Eg5. J Biochem 2021; 170:611-622. [PMID: 34264310 DOI: 10.1093/jb/mvab083] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Accepted: 07/05/2021] [Indexed: 11/14/2022] Open
Abstract
Mitotic kinesin Eg5 remains a validated target in antimitotic therapy because of its essential role in the formation and maintenance of bipolar mitotic spindles. Although numerous Eg5 inhibitors of synthetic origin are known, only a few inhibitors derived from natural products have been reported. In our study, we focused on identifying novel Eg5 inhibitors from medicinal plants, particularly Garcinia species. Herein, we report the inhibitory effect of kolaflavanone (KLF), a Garcinia biflavonoid, on the ATPase and microtubule-gliding activities of mitotic kinesin Eg5. Additionally, we showed the interaction mechanism between Eg5 and KLF via in vitro and in silico analyses. The results revealed that KLF inhibited both the basal and microtubule-activated ATPase activities of Eg5. The inhibitory mechanism is allosteric, without a direct competition with adenosine-5'-diphosphate for the nucleotide-binding site. KLF also suppressed the microtubule gliding of Eg5 in vitro. The Eg5-KLF model obtained from molecular docking showed that the biflavonoid exists within the α2/α3/L5 (α2: Lys111-Glu116 and Ile135-Asp149, α3: Asn206-Thr226; L5: Gly117-Gly134) pocket, with a binding pose comparable to known Eg5 inhibitors. Overall, our data suggest that KLF is a novel allosteric inhibitor of mitotic kinesin Eg5.
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Affiliation(s)
- Islam M D Alrazi
- Department of Bioinformatics, Graduate School of Engineering, Soka University, 1-236 Tangi-cho, Hachioji, Tokyo 192-8577, Japan
| | - Tomisin H Ogunwa
- Department of Bioinformatics, Graduate School of Engineering, Soka University, 1-236 Tangi-cho, Hachioji, Tokyo 192-8577, Japan
| | - Ayodele O Kolawole
- Department of Biochemistry, The Federal University of Technology, Akure, Ondo State, PMB 704, Nigeria
| | - Olusola O Elekofehinti
- Department of Biochemistry, The Federal University of Technology, Akure, Ondo State, PMB 704, Nigeria
| | - Olaposi I Omotuyi
- Centre for Biocomputing and Drug Design, Biochemistry Department, Adekunle Ajasin University, Akungba-Akoko, Ondo State, PMB 001, Nigeria
| | - Takayuki Miyanishi
- Graduate School of Fisheries and Environmental Sciences, Nagasaki University, 1-14 Bunkyo-machi, Nagasaki, 852-8521, Japan
| | - Shinsaku Maruta
- Department of Bioinformatics, Graduate School of Engineering, Soka University, 1-236 Tangi-cho, Hachioji, Tokyo 192-8577, Japan
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6
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Cook AD, Roberts AJ, Atherton J, Tewari R, Topf M, Moores CA. Cryo-EM structure of a microtubule-bound parasite kinesin motor and implications for its mechanism and inhibition. J Biol Chem 2021; 297:101063. [PMID: 34375637 PMCID: PMC8526983 DOI: 10.1016/j.jbc.2021.101063] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Revised: 07/23/2021] [Accepted: 08/05/2021] [Indexed: 11/25/2022] Open
Abstract
Plasmodium parasites cause malaria and are responsible annually for hundreds of thousands of deaths. Kinesins are a superfamily of microtubule-dependent ATPases that play important roles in the parasite replicative machinery, which is a potential target for antiparasite drugs. Kinesin-5, a molecular motor that cross-links microtubules, is an established antimitotic target in other disease contexts, but its mechanism in Plasmodium falciparum is unclear. Here, we characterized P. falciparum kinesin-5 (PfK5) using cryo-EM to determine the motor's nucleotide-dependent microtubule-bound structure and introduced 3D classification of individual motors into our microtubule image processing pipeline to maximize our structural insights. Despite sequence divergence in PfK5, the motor exhibits classical kinesin mechanochemistry, including ATP-induced subdomain rearrangement and cover neck bundle formation, consistent with its plus-ended directed motility. We also observed that an insertion in loop5 of the PfK5 motor domain creates a different environment in the well-characterized human kinesin-5 drug-binding site. Our data reveal the possibility for selective inhibition of PfK5 and can be used to inform future exploration of Plasmodium kinesins as antiparasite targets.
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Affiliation(s)
- Alexander D Cook
- Institute of Structural and Molecular Biology, Department of Biological Sciences, Birkbeck, University of London, London, United Kingdom
| | - Anthony J Roberts
- Institute of Structural and Molecular Biology, Department of Biological Sciences, Birkbeck, University of London, London, United Kingdom
| | - Joseph Atherton
- Institute of Structural and Molecular Biology, Department of Biological Sciences, Birkbeck, University of London, London, United Kingdom
| | - Rita Tewari
- School of Life Sciences, University of Nottingham, Nottingham, United Kingdom
| | - Maya Topf
- Institute of Structural and Molecular Biology, Department of Biological Sciences, Birkbeck, University of London, London, United Kingdom
| | - Carolyn A Moores
- Institute of Structural and Molecular Biology, Department of Biological Sciences, Birkbeck, University of London, London, United Kingdom.
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7
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Fukai R, Ogo N, Ichida T, Yamane M, Sawada JI, Miyoshi N, Murakami H, Asai A. Design, synthesis, and evaluation of a novel prodrug, a S-trityl- l-cysteine derivative targeting kinesin spindle protein. Eur J Med Chem 2021; 215:113288. [PMID: 33640763 DOI: 10.1016/j.ejmech.2021.113288] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2020] [Revised: 01/30/2021] [Accepted: 02/03/2021] [Indexed: 11/29/2022]
Abstract
Kinesin spindle protein (KSP) is expressed only in cells undergoing cell division, and hence represents an attractive target for the treatment of cancer. Several KSP inhibitors have been developed and undergone clinical trial, but their clinical use is limited by their toxicity to rapidly proliferating non-cancerous cells. To create new KSP inhibitors that are highly selective for cancer cells, we optimized the amino acid moiety of S-trityl-l-cysteine (STLC) derivative 1 using in silico modeling. Molecular docking and molecular dynamics simulation were performed to investigate the binding mode of 1 with KSP. Consistent with the structure activity relationship studies, we found that a cysteine amino moiety plays an important role in stabilizing the interaction. Based on these findings and the structure of GSH, a substrate of γ-glutamyltransferase (GGT), we designed and synthesized the prodrug N-γ-glutamylated STLC derivative 9, which could be hydrolyzed by GGT to produce 1. The KSP ATPase inhibitory activity of 9 was lower than that of 1, and LC-MS analysis indicated that 9 was converted to 1 only in the presence of GGT in vitro. In addition, the cytotoxic activity of 9 was significantly attenuated in GGT-knockdown A549 cells. Since GGT is overexpressed on the cell membrane of various cancer cells, these results suggest that compound 9 could be a promising prodrug that selectively inhibits the proliferation of GGT-expressing cancer cells.
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Affiliation(s)
- Ryota Fukai
- Center for Drug Discovery, Graduate Division of Pharmaceutical Sciences, University of Shizuoka, Yada 52-1, Suruga-ku, Shizuoka, 422-8526, Japan
| | - Naohisa Ogo
- Center for Drug Discovery, Graduate Division of Pharmaceutical Sciences, University of Shizuoka, Yada 52-1, Suruga-ku, Shizuoka, 422-8526, Japan.
| | - Taiki Ichida
- Center for Drug Discovery, Graduate Division of Pharmaceutical Sciences, University of Shizuoka, Yada 52-1, Suruga-ku, Shizuoka, 422-8526, Japan
| | - Masayoshi Yamane
- Center for Drug Discovery, Graduate Division of Pharmaceutical Sciences, University of Shizuoka, Yada 52-1, Suruga-ku, Shizuoka, 422-8526, Japan
| | - Jun-Ichi Sawada
- Center for Drug Discovery, Graduate Division of Pharmaceutical Sciences, University of Shizuoka, Yada 52-1, Suruga-ku, Shizuoka, 422-8526, Japan
| | - Nao Miyoshi
- Center for Drug Discovery, Graduate Division of Pharmaceutical Sciences, University of Shizuoka, Yada 52-1, Suruga-ku, Shizuoka, 422-8526, Japan
| | - Hisashi Murakami
- Center for Drug Discovery, Graduate Division of Pharmaceutical Sciences, University of Shizuoka, Yada 52-1, Suruga-ku, Shizuoka, 422-8526, Japan
| | - Akira Asai
- Center for Drug Discovery, Graduate Division of Pharmaceutical Sciences, University of Shizuoka, Yada 52-1, Suruga-ku, Shizuoka, 422-8526, Japan.
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8
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Garcia-Saez I, Skoufias DA. Eg5 targeting agents: From new anti-mitotic based inhibitor discovery to cancer therapy and resistance. Biochem Pharmacol 2020; 184:114364. [PMID: 33310050 DOI: 10.1016/j.bcp.2020.114364] [Citation(s) in RCA: 52] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Revised: 12/04/2020] [Accepted: 12/08/2020] [Indexed: 12/13/2022]
Abstract
Eg5, the product of Kif11 gene, also known as kinesin spindle protein, is a motor protein involved in the proper establishment of a bipolar mitotic spindle. Eg5 is one of the 45 different kinesins coded in the human genome of the kinesin motor protein superfamily. Over the last three decades Eg5 has attracted great interest as a promising new mitotic target. The identification of monastrol as specific inhibitor of the ATPase activity of the motor domain of Eg5 inhibiting the Eg5 microtubule motility in vitro and in cellulo sparked an intense interest in academia and industry to pursue the identification of novel small molecules that target Eg5 in order to be used in cancer chemotherapy based on the anti-mitotic strategy. Several Eg5 inhibitors entered clinical trials. Currently the field is faced with the problem that most of the inhibitors tested exhibited only limited efficacy. However, one Eg5 inhibitor, Arry-520 (clinical name filanesib), has demonstrated clinical efficacy in patients with multiple myeloma and is scheduled to enter phase III clinical trials. At the same time, new trends in Eg5 inhibitor research are emerging, including an increased interest in novel inhibitor binding sites and a focus on drug synergy with established antitumor agents to improve chemotherapeutic efficacy. This review presents an updated view of the structure and function of Eg5-inhibitor complexes, traces the possible development of resistance to Eg5 inhibitors and their potential therapeutic applications, and surveys the current challenges and future directions of this active field in drug discovery.
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Affiliation(s)
- Isabel Garcia-Saez
- Université Grenoble Alpes, CNRS, CEA, Institut de Biologie Structurale (IBS), 38000 Grenoble, France
| | - Dimitrios A Skoufias
- Université Grenoble Alpes, CNRS, CEA, Institut de Biologie Structurale (IBS), 38000 Grenoble, France.
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9
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Makala H, Ulaganathan V, Sivasubramanian A, Rajendran N, Subramanian S. Evaluating Phenyl Propanoids Isolated from Citrus medica as Potential Inhibitors for Mitotic kinesin Eg5. LETT DRUG DES DISCOV 2020. [DOI: 10.2174/1570180817999200630125449] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Background:
Human mitotic kinesins play an essential role in mitotic cell division. Targeting
the spindle separation phase of mitosis has gained much attention in cancer chemotherapy.
Spindle segregation is carried out mainly by the kinesin, Eg5. Many Eg5 inhibitors are in different
phases of clinical trials as cancer drugs. This enzyme has two allosteric binding sites to which the
inhibitors can bind. The first site is formed by loop L5, helix α2 and helix α3 and all the current drug
candidates bind un-competitively to this site with ATP/ADP. The second site, formed by helix α4
and helix α6, which has gained attention recently, has not been explored well. Some inhibitors that
bind to this site are competitive, while others are uncompetitive to ATP/ADP. Phenylpropanoids are
pharmacologically active secondary metabolites.
Methods:
In this study, we have evaluated fourteen phenyl propanoids extracted from Citrus medica
for inhibitory activity against human mitotic kinesin Eg5 in vitro steady-state ATPase assay. Ther
interactions and stability using molecular docking and molecular dynamics simulations.
Results and Discussions:
Of the fourteen compounds tested, naringin and quercetin showed good
activity with IC50 values in the micromolar range. Molecular docking studies of these complexes
showed that both the molecules interact with the key residues of the active site predominantly thorough
hydrophobic & aromatic π–π interactions consistent with the known inhibitors. Besides, these
molecules also form hydrogen bonding interactions stabilizing the complexes. Molecular dynamics
simulations of these complexes confirm the stability of these interactions.
Conclusion:
These results can be used as a strong basis for further modification of these compounds
to design new inhibitors with higher potency using structure-based drug design.
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Affiliation(s)
- Himesh Makala
- Department of Biotechnology, School of Chemical and Biotechnology, SASTRA Deemed University, Thanjavur, Tamilnadu-613401, India
| | - Venkatasubramanian Ulaganathan
- Department of Biotechnology, School of Chemical and Biotechnology, SASTRA Deemed University, Thanjavur, Tamilnadu-613401, India
| | - Aravind Sivasubramanian
- Department of Biotechnology, School of Chemical and Biotechnology, SASTRA Deemed University, Thanjavur, Tamilnadu-613401, India
| | - Narendran Rajendran
- Department of Biotechnology, School of Chemical and Biotechnology, SASTRA Deemed University, Thanjavur, Tamilnadu-613401, India
| | - Shankar Subramanian
- Department of Biotechnology, School of Chemical and Biotechnology, SASTRA Deemed University, Thanjavur, Tamilnadu-613401, India
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Farias K, da Costa RF, Meira AS, Diniz-Filho J, Bezerra EM, Freire VN, Guest P, Nikahd M, Ma X, Gardiner MG, Banwell MG, de Oliveira MDCF, de Moraes MO, do Ó Pessoa C. Antitumor Potential of the Isoflavonoids (+)- and (-)-2,3,9-Trimethoxypterocarpan: Mechanism-of-Action Studies. ACS Med Chem Lett 2020; 11:1274-1280. [PMID: 32551011 DOI: 10.1021/acsmedchemlett.0c00097] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Accepted: 05/20/2020] [Indexed: 12/23/2022] Open
Abstract
Synthetically derived samples of (+)-(6aS,11aS)-2,3,9-trimethoxypterocarpan [(+)-1] and its enantiomer [(-)-1], both of which are examples of naturally occurring isoflavonoids, were evaluated, together with the corresponding racemate, as cytotoxic agents against the HL-60, HCT-116, OVCAR-8, and SF-295 tumor cell lines. As a result it was established that compound (+)-1 was particularly active with OVCAR-8 cells being the most sensitive and responding in a dose-dependent manner. A study of cell viability and drug-induced morphological changes revealed the compound causes cell death through a mechanism characteristic of apoptosis. Finally, a computational study of the interactions of compound (+)-1 and (S)-monastrol, an established, synthetically derived, potent, and cell-permeant inhibitor of mitosis, with the kinesin-type protein Eg5 revealed that both bind to this receptor in a similar manner. Significantly, compound (+)-1 binds with greater affinity, an effect attributed to the presence of the associated methoxy groups.
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Affiliation(s)
- Kaio Farias
- Department of Physiology and Pharmacology, Faculty of Medicine, Federal University of Ceará, Fortaleza, CE 60430-275, Brazil
| | - Roner F. da Costa
- Department of Natural Sciences, Mathematics and Statistics, Federal Rural University of the Semi-Arid Region - UFERSA, Mossoró - RN 59625-900, Brazil
| | - Assuero S. Meira
- Department of Physiology and Pharmacology, Faculty of Medicine, Federal University of Ceará, Fortaleza, CE 60430-275, Brazil
| | - Jairo Diniz-Filho
- Department of Physiology and Pharmacology, Faculty of Medicine, Federal University of Ceará, Fortaleza, CE 60430-275, Brazil
| | - Eveline M. Bezerra
- Department of Natural Sciences, Mathematics and Statistics, Federal Rural University of the Semi-Arid Region - UFERSA, Mossoró - RN 59625-900, Brazil
| | - Valder N. Freire
- Department of Physics, Science Center, Federal University of Ceará, Fortaleza, CE 60430-275, Brazil
| | - Prue Guest
- Research School of Chemistry, Institute of Advanced Studies, The Australian National University, Canberra, ACT 2601, Australia
| | - Maryam Nikahd
- Research School of Chemistry, Institute of Advanced Studies, The Australian National University, Canberra, ACT 2601, Australia
| | - Xinghua Ma
- Research School of Chemistry, Institute of Advanced Studies, The Australian National University, Canberra, ACT 2601, Australia
| | - Michael G. Gardiner
- Research School of Chemistry, Institute of Advanced Studies, The Australian National University, Canberra, ACT 2601, Australia
| | - Martin G. Banwell
- Research School of Chemistry, Institute of Advanced Studies, The Australian National University, Canberra, ACT 2601, Australia
- Institute for Advanced and Applied Chemical Synthesis, Jinan University, Guangzhou 510632, China
| | - Maria da C. F. de Oliveira
- Department of Organic and Inorganic Chemistry, Science Center, Federal University of Ceará, Fortaleza, CE 60430-275, Brazil
| | - Manoel O. de Moraes
- Department of Physiology and Pharmacology, Faculty of Medicine, Federal University of Ceará, Fortaleza, CE 60430-275, Brazil
| | - Claudia do Ó Pessoa
- Department of Physiology and Pharmacology, Faculty of Medicine, Federal University of Ceará, Fortaleza, CE 60430-275, Brazil
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11
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Ziemianowicz DS, MacCallum JL, Schriemer DC. Correlation between Labeling Yield and Surface Accessibility in Covalent Labeling Mass Spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2020; 31:207-216. [PMID: 32031402 DOI: 10.1021/jasms.9b00083] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
The functional properties of a protein are strongly influenced by its topography, or the solvent-facing contour map of its surface. Together with crosslinking, covalent labeling mass spectrometry (CL-MS) has the potential to contribute topographical data through the measurement of surface accessibility. However, recent efforts to correlate measures of surface accessibility with labeling yield have been met with mixed success. Most applications of CL-MS involve differential analysis of protein interactions (i.e., footprinting experiments) where such inconsistencies have limited effect. Extending CL-MS into structural analysis requires an improved evaluation of the relationship between labeling and surface exposure. In this study, we applied recently developed diazirine reagents to obtain deep coverage of the large motor domain of Eg5 (a mitotic kinesin), and together with computational methods we correlated labeling yields with accessibility data in a number of ways. We observe that correlations can indeed be seen at a local structural level, but these correlations do not extend across the structure. The lack of correlation arises from the influence of protein dynamics and chemical composition on reagent partitioning and, thus, also on labeling yield. We conclude that our use of CL-MS data should be considered in light of "chemical accessibility" rather than "solvent accessibility" and suggest that CL-MS data would be a useful tool in the fundamental study of protein-solute interactions.
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Affiliation(s)
- Daniel S Ziemianowicz
- Department of Biochemistry and Molecular Biology , University of Calgary , Calgary , Alberta , Canada T2N 4N1
- Robson DNA Science Centre, Arnie Charbonneau Cancer Institute , University of Calgary , Calgary , Alberta , Canada T2N 4N1
| | - Justin L MacCallum
- Department of Chemistry , University of Calgary , Calgary , Alberta , Canada T2N 4N1
| | - David C Schriemer
- Department of Biochemistry and Molecular Biology , University of Calgary , Calgary , Alberta , Canada T2N 4N1
- Robson DNA Science Centre, Arnie Charbonneau Cancer Institute , University of Calgary , Calgary , Alberta , Canada T2N 4N1
- Department of Chemistry , University of Calgary , Calgary , Alberta , Canada T2N 4N1
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12
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Kim CD, Kim ED, Liu L, Buckley RS, Parameswaran S, Kim S, Wojcik EJ. Small molecule allosteric uncoupling of microtubule depolymerase activity from motility in human Kinesin-5 during mitotic spindle assembly. Sci Rep 2019; 9:19900. [PMID: 31882607 PMCID: PMC6934681 DOI: 10.1038/s41598-019-56173-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2019] [Accepted: 12/06/2019] [Indexed: 01/22/2023] Open
Abstract
Human Kinesin-5 (Eg5) has a large number of known allosteric inhibitors that disrupt its mitotic function. Small-molecule inhibitors of Eg5 are candidate anti-cancer agents and important probes for understanding the cellular function. Here we show that Eg5 is capable of more than one type of microtubule interaction, and these activities can be controlled by allosteric agents. While both monastrol and S-trityl-L-cysteine inhibit Eg5 motility, our data reveal an unexpected ability of these loop5 targeting inhibitors to differentially control a novel Eg5 microtubule depolymerizing activity. Remarkably, small molecule loop5 effectors are able to independently modulate discrete functional interactions between the motor and microtubule track. We establish that motility can be uncoupled from the microtubule depolymerase activity and argue that loop5-targeting inhibitors of Kinesin-5 should not all be considered functionally synonymous. Also, the depolymerizing activity of the motor does not contribute to the genesis of monopolar spindles during allosteric inhibition of motility, but instead reveals a new function. We propose that, in addition to its canonical role in participating in the construction of the three-dimensional mitotic spindle structure, Eg5 also plays a distinct role in regulating the dynamics of individual microtubules, and thereby impacts the density of the mitotic spindle.
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Affiliation(s)
- Catherine D Kim
- Department of Biochemistry and Molecular Biology, LSU School of Medicine & Health Sciences Center, 1901 Perdido Street, New Orleans, LA, 70112, USA
| | - Elizabeth D Kim
- Department of Biochemistry and Molecular Biology, LSU School of Medicine & Health Sciences Center, 1901 Perdido Street, New Orleans, LA, 70112, USA
| | - Liqiong Liu
- Department of Biochemistry and Molecular Biology, LSU School of Medicine & Health Sciences Center, 1901 Perdido Street, New Orleans, LA, 70112, USA
| | - Rebecca S Buckley
- Department of Biochemistry and Molecular Biology, LSU School of Medicine & Health Sciences Center, 1901 Perdido Street, New Orleans, LA, 70112, USA
| | - Sreeja Parameswaran
- Department of Biochemistry and Molecular Biology, LSU School of Medicine & Health Sciences Center, 1901 Perdido Street, New Orleans, LA, 70112, USA
| | - Sunyoung Kim
- Department of Biochemistry and Molecular Biology, LSU School of Medicine & Health Sciences Center, 1901 Perdido Street, New Orleans, LA, 70112, USA
| | - Edward J Wojcik
- Department of Biochemistry and Molecular Biology, LSU School of Medicine & Health Sciences Center, 1901 Perdido Street, New Orleans, LA, 70112, USA.
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13
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Ogunwa TH, Taii K, Sadakane K, Kawata Y, Maruta S, Miyanishi T. Morelloflavone as a novel inhibitor of mitotic kinesin Eg5. J Biochem 2019; 166:129-137. [PMID: 30785183 DOI: 10.1093/jb/mvz015] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Accepted: 02/13/2019] [Indexed: 12/19/2022] Open
Abstract
Among 40 plant-derived biflavonoids with inhibitory potential against Eg5, morelloflavone from Garcinia dulcis leaves was selected for further testing based on in silico analysis of binding modes, molecular interactions, binding energies and functional groups that interact with Eg5. Computational models predicted that morelloflavone binds the putative allosteric pocket of Eg5, within the cavity surrounded by amino acid residues of Ile-136, Glu-116, Glu-118, Trp-127, Gly-117, Ala-133, Glu-215, Leu-214 and Tyr-211. Binding energy was -8.4 kcal/mol, with a single hydrogen bond formed between morelloflavone and Tyr-211. The binding configuration was comparable to that of a reference inhibitor, S-trityl-L-cysteine. Subsequent biochemical analysis in vitro confirmed that morelloflavone inhibited both the basal and microtubule-activated ATPase activity of Eg5 in a manner that does not compete with ATP binding. Morelloflavone also suppressed Eg5 gliding along microtubules. These results suggest that morelloflavone binds the allosteric binding site in Eg5 and thereby inhibits ATPase activity and motor function of Eg5.
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Affiliation(s)
- Tomisin Happy Ogunwa
- Department of Environmental Studies, Graduate School of Fisheries and Environmental Sciences, Nagasaki University, 1-14 Bunkyo-machi, Nagasaki, Japan
| | - Kenichi Taii
- Department of Bioinformatics, Graduate School of Engineering, Soka University, 1-236 Tangi-cho, Hachioji, Tokyo, Japan
| | - Kei Sadakane
- Department of Bioinformatics, Graduate School of Engineering, Soka University, 1-236 Tangi-cho, Hachioji, Tokyo, Japan
| | - Yuka Kawata
- Department of Environmental Studies, Graduate School of Fisheries and Environmental Sciences, Nagasaki University, 1-14 Bunkyo-machi, Nagasaki, Japan
| | - Shinsaku Maruta
- Department of Bioinformatics, Graduate School of Engineering, Soka University, 1-236 Tangi-cho, Hachioji, Tokyo, Japan
| | - Takayuki Miyanishi
- Department of Environmental Studies, Graduate School of Fisheries and Environmental Sciences, Nagasaki University, 1-14 Bunkyo-machi, Nagasaki, Japan
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14
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Indorato RL, Talapatra SK, Lin F, Haider S, Mackay SP, Kozielski F, Skoufias DA. Is the Fate of Clinical Candidate Arry-520 Already Sealed? Predicting Resistance in Eg5–Inhibitor Complexes. Mol Cancer Ther 2019; 18:2394-2406. [DOI: 10.1158/1535-7163.mct-19-0154] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2019] [Revised: 05/20/2019] [Accepted: 08/30/2019] [Indexed: 11/16/2022]
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15
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Mickolajczyk KJ, Cook ASI, Jevtha JP, Fricks J, Hancock WO. Insights into Kinesin-1 Stepping from Simulations and Tracking of Gold Nanoparticle-Labeled Motors. Biophys J 2019; 117:331-345. [PMID: 31301807 DOI: 10.1016/j.bpj.2019.06.010] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2018] [Revised: 06/04/2019] [Accepted: 06/10/2019] [Indexed: 02/02/2023] Open
Abstract
High-resolution tracking of gold nanoparticle-labeled proteins has emerged as a powerful technique for measuring the structural kinetics of processive enzymes and other biomacromolecules. These techniques use point spread function (PSF) fitting methods borrowed from single-molecule fluorescence imaging to determine molecular positions below the diffraction limit. However, compared to fluorescence, gold nanoparticle tracking experiments are performed at significantly higher frame rates and utilize much larger probes. In the current work, we use Brownian dynamics simulations of nanoparticle-labeled proteins to investigate the regimes in which the fundamental assumptions of PSF fitting hold and where they begin to break down. We find that because gold nanoparticles undergo tethered diffusion around their anchor point, PSF fitting cannot be extended to arbitrarily fast frame rates. Instead, camera exposure times that allow the nanoparticle to fully populate its stationary positional distribution achieve a spatial averaging that increases fitting precision. We furthermore find that changes in the rotational freedom of the tagged protein can lead to artifactual translations in the fitted particle position. Finally, we apply these lessons to dissect a standing controversy in the kinesin field over the structure of a dimer in the ATP waiting state. Combining new experiments with simulations, we determine that the rear kinesin head in the ATP waiting state is unbound but not displaced from its previous microtubule binding site and that apparent differences in separately published reports were simply due to differences in the gold nanoparticle attachment position. Our results highlight the importance of gold conjugation decisions and imaging parameters to high-resolution tracking results and will serve as a useful guide for the design of future gold nanoparticle tracking experiments.
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Affiliation(s)
- Keith J Mickolajczyk
- Department of Biomedical Engineering; Intercollege Graduate Degree Program in Bioengineering
| | - Annan S I Cook
- Department of Biomedical Engineering; Department of Physics, Pennsylvania State University, University Park, Pennsylvania
| | | | - John Fricks
- School of Mathematical and Statistical Sciences, Arizona State University, Tempe, Arizona
| | - William O Hancock
- Department of Biomedical Engineering; Intercollege Graduate Degree Program in Bioengineering.
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16
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Ogunwa TH, Laudadio E, Galeazzi R, Miyanishi T. Insights into the Molecular Mechanisms of Eg5 Inhibition by (+)-Morelloflavone. Pharmaceuticals (Basel) 2019; 12:ph12020058. [PMID: 30995725 PMCID: PMC6630617 DOI: 10.3390/ph12020058] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2019] [Revised: 04/10/2019] [Accepted: 04/12/2019] [Indexed: 12/17/2022] Open
Abstract
(+)-Morelloflavone (MF) is an antitumor biflavonoid that is found in the Garcinia species. Recently, we reported MF as a novel inhibitor of ATPase and microtubules-gliding activities of the kinesin spindle protein (Eg5) in vitro. Herein, we provide dynamical insights into the inhibitory mechanisms of MF against Eg5, which involves binding of the inhibitor to the loop5/α2/α3 allosteric pocket. Molecular dynamics simulations were carried out for 100 ns on eight complexes: Eg5-Adenosine diphosphate (Eg5-ADP), Eg5-ADP-S-trityl-l-cysteine (Eg5-ADP-STLC), Eg5-ADP-ispinesib, Eg5-ADP-MF, Eg5-Adenosine triphosphate (Eg5-ATP), Eg5-ATP-STLC, Eg5-ATP-ispinesib, and Eg5-ATP-MF complexes. Structural and energetic analyses were done using Umbrella sampling, Molecular Mechanics Poisson–Boltzmann Surface Area (MM/PBSA) method, GROMACS analysis toolkit, and virtual molecular dynamics (VMD) utilities. The results were compared with those of the known Eg5 inhibitors; ispinesib, and STLC. Our data strongly support a stable Eg5-MF complex, with significantly low binding energy and reduced flexibility of Eg5 in some regions, including loop5 and switch I. Furthermore, the loop5 Trp127 was trapped in a downward position to keep the allosteric pocket of Eg5 in the so-called “closed conformation”, comparable to observations for STLC. Altered structural conformations were also visible within various regions of Eg5, including switch I, switch II, α2/α3 helices, and the tubulin-binding region, indicating that MF might induce modifications in the Eg5 structure to compromise its ATP/ADP binding and conversion process as well as its interaction with microtubules. The described mechanisms are crucial for understanding Eg5 inhibition by MF.
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Affiliation(s)
- Tomisin Happy Ogunwa
- Department of Environmental Studies, Graduate School of Fisheries and Environmental Sciences, Nagasaki University, 1-14 Bunkyo-machi, Nagasaki 852-8521, Japan.
| | - Emiliano Laudadio
- Department of Life and Environmental Sciences, Università Politecnica delle Marche, 60131 Ancona, Italy.
| | - Roberta Galeazzi
- Department of Life and Environmental Sciences, Università Politecnica delle Marche, 60131 Ancona, Italy.
| | - Takayuki Miyanishi
- Department of Environmental Studies, Graduate School of Fisheries and Environmental Sciences, Nagasaki University, 1-14 Bunkyo-machi, Nagasaki 852-8521, Japan.
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17
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Sadakane K, Takaichi M, Maruta S. Photo-control of the mitotic kinesin Eg5 using a novel photochromic inhibitor composed of a spiropyran derivative. J Biochem 2018; 164:239-246. [PMID: 29718428 DOI: 10.1093/jb/mvy046] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2017] [Accepted: 04/21/2018] [Indexed: 11/13/2022] Open
Abstract
In this study, we synthesized a novel photochromic inhibitor of the mitotic kinesin Eg5, which is composed of the photochromic compound spiropyran to photo-control the function of Eg5. The compound (S)-2, 3-dispiropyran propionic acid (DSPPA) exhibits reversible spiropyran-merocyanine photo-isomerization upon irradiation with visible or ultra-violet light. DSPPA induced reversible changes in the inhibitory effect on Eg5 ATPase and motor activities, which correlates with the spiropyran-merocyanine photo-isomerization. Microtubule-dependent ATPase activity was significantly more inhibited by the spiropyran isomer of DSPPA than by the merocyanine isomer. Additionally, an in vitro motility assay revealed that the microtubule gliding velocity was reduced more by the spiropyran isomer than by the merocyanine isomer. This indicates that the spiropyran derivative may be useful in regulating the function of the mitotic kinesin.
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Affiliation(s)
- Kei Sadakane
- Department of Bioengineering, Graduate School of Engineering, Soka University, Hachioji, Tokyo, Japan
| | - Mao Takaichi
- Department of Bioengineering, Graduate School of Engineering, Soka University, Hachioji, Tokyo, Japan
| | - Shinsaku Maruta
- Department of Bioengineering, Graduate School of Engineering, Soka University, Hachioji, Tokyo, Japan
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18
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Yokoyama H, Sawada JI, Sato K, Ogo N, Kamei N, Ishikawa Y, Hara K, Asai A, Hashimoto H. Structural and Thermodynamic Basis of the Enhanced Interaction between Kinesin Spindle Protein Eg5 and STLC-type Inhibitors. ACS OMEGA 2018; 3:12284-12294. [PMID: 31459302 PMCID: PMC6644766 DOI: 10.1021/acsomega.8b00778] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/21/2018] [Accepted: 08/22/2018] [Indexed: 06/10/2023]
Abstract
For a better understanding of protein-inhibitor interactions, we report structural, thermodynamic, and biological analyses of the interactions between S-trityl-l-cysteine (STLC) derivatives and the motor domain of kinesin spindle protein Eg5. Binding of STLC-type inhibitors to Eg5 was enthalpically driven and entropically unfavorable. The introduction of a para-methoxy substituent in one phenyl ring of STLC enhances its inhibitory activity resulting from a larger enthalpy gain possibly due to the increased shape complementarity. The substituent fits to a recess in the binding pocket. To avoid steric hindrance, the substituted STLC is nudged toward the side opposite to the recess, which enhances the interaction of Eg5 with the remaining part of the inhibitor. Further introduction of an ethylene linkage between two phenyl rings enhances Eg5 inhibitory activity by reducing the loss of entropy in forming the complex. This study provides valuable examples of enhancing protein-inhibitor interactions without forming additional hydrogen bonds.
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Affiliation(s)
- Hideshi Yokoyama
- Faculty
of Pharmaceutical Sciences, Tokyo University
of Science, 2641 Yamazaki, Noda, Chiba 278-8510, Japan
- Department of Physical Biochemistry,
School of Pharmaceutical Sciences and Center for Drug
Discovery, Graduate School of Pharmaceutical Sciences, University of Shizuoka, 52-1 Yada, Suruga-ku, Shizuoka 422-8526, Japan
| | - Jun-ichi Sawada
- Department of Physical Biochemistry,
School of Pharmaceutical Sciences and Center for Drug
Discovery, Graduate School of Pharmaceutical Sciences, University of Shizuoka, 52-1 Yada, Suruga-ku, Shizuoka 422-8526, Japan
| | - Kohei Sato
- Department of Physical Biochemistry,
School of Pharmaceutical Sciences and Center for Drug
Discovery, Graduate School of Pharmaceutical Sciences, University of Shizuoka, 52-1 Yada, Suruga-ku, Shizuoka 422-8526, Japan
| | - Naohisa Ogo
- Department of Physical Biochemistry,
School of Pharmaceutical Sciences and Center for Drug
Discovery, Graduate School of Pharmaceutical Sciences, University of Shizuoka, 52-1 Yada, Suruga-ku, Shizuoka 422-8526, Japan
| | - Nanami Kamei
- Department of Physical Biochemistry,
School of Pharmaceutical Sciences and Center for Drug
Discovery, Graduate School of Pharmaceutical Sciences, University of Shizuoka, 52-1 Yada, Suruga-ku, Shizuoka 422-8526, Japan
| | - Yoshinobu Ishikawa
- Department of Physical Biochemistry,
School of Pharmaceutical Sciences and Center for Drug
Discovery, Graduate School of Pharmaceutical Sciences, University of Shizuoka, 52-1 Yada, Suruga-ku, Shizuoka 422-8526, Japan
| | - Kodai Hara
- Department of Physical Biochemistry,
School of Pharmaceutical Sciences and Center for Drug
Discovery, Graduate School of Pharmaceutical Sciences, University of Shizuoka, 52-1 Yada, Suruga-ku, Shizuoka 422-8526, Japan
| | - Akira Asai
- Department of Physical Biochemistry,
School of Pharmaceutical Sciences and Center for Drug
Discovery, Graduate School of Pharmaceutical Sciences, University of Shizuoka, 52-1 Yada, Suruga-ku, Shizuoka 422-8526, Japan
| | - Hiroshi Hashimoto
- Department of Physical Biochemistry,
School of Pharmaceutical Sciences and Center for Drug
Discovery, Graduate School of Pharmaceutical Sciences, University of Shizuoka, 52-1 Yada, Suruga-ku, Shizuoka 422-8526, Japan
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19
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Talapatra SK, Tham CL, Guglielmi P, Cirilli R, Chandrasekaran B, Karpoormath R, Carradori S, Kozielski F. Crystal structure of the Eg5 - K858 complex and implications for structure-based design of thiadiazole-containing inhibitors. Eur J Med Chem 2018; 156:641-651. [DOI: 10.1016/j.ejmech.2018.07.006] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2018] [Revised: 06/20/2018] [Accepted: 07/03/2018] [Indexed: 10/28/2022]
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20
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Sadakane K, Alrazi IMD, Maruta S. Highly efficient photocontrol of mitotic kinesin Eg5 ATPase activity using a novel photochromic compound composed of two azobenzene derivatives. J Biochem 2018; 164:295-301. [DOI: 10.1093/jb/mvy051] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2018] [Accepted: 05/20/2018] [Indexed: 11/14/2022] Open
Affiliation(s)
- Kei Sadakane
- Department of Bioinformatics, Graduate School of Engineering Soka University, 1-236 Tangi-cho, Hachioji, Tokyo, Japan
| | - Islam M D Alrazi
- Department of Bioinformatics, Graduate School of Engineering Soka University, 1-236 Tangi-cho, Hachioji, Tokyo, Japan
| | - Shinsaku Maruta
- Department of Bioinformatics, Graduate School of Engineering Soka University, 1-236 Tangi-cho, Hachioji, Tokyo, Japan
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21
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Muthuraja P, Himesh M, Prakash S, Venkatasubramanian U, Manisankar P. Synthesis of N-(1-(6-acetamido-5-phenylpyrimidin-4-yl) piperidin-3-yl) amide derivatives as potential inhibitors for mitotic kinesin spindle protein. Eur J Med Chem 2018; 148:106-115. [DOI: 10.1016/j.ejmech.2018.02.010] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2017] [Revised: 01/25/2018] [Accepted: 02/04/2018] [Indexed: 12/18/2022]
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22
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Balakumar C, Ramesh M, Tham CL, Khathi SP, Kozielski F, Srinivasulu C, Hampannavar GA, Sayyad N, Soliman ME, Karpoormath R. Ligand- and structure-based in silico studies to identify kinesin spindle protein (KSP) inhibitors as potential anticancer agents. J Biomol Struct Dyn 2017; 36:3687-3704. [DOI: 10.1080/07391102.2017.1396255] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- Chandrasekaran Balakumar
- Discipline of Pharmaceutical Sciences, College of Health Sciences, University of KwaZulu-Natal (UKZN), Westville, Durban 4001, South Africa
| | - Muthusamy Ramesh
- Discipline of Pharmaceutical Sciences, College of Health Sciences, University of KwaZulu-Natal (UKZN), Westville, Durban 4001, South Africa
| | - Chuin Lean Tham
- Department of Pharmaceutical and Biological Chemistry, The School of Pharmacy, University College London, 29-39, Brunswick Square, London WC1N 1AX, UK
| | - Samukelisiwe Pretty Khathi
- Discipline of Pharmaceutical Sciences, College of Health Sciences, University of KwaZulu-Natal (UKZN), Westville, Durban 4001, South Africa
| | - Frank Kozielski
- Department of Pharmaceutical and Biological Chemistry, The School of Pharmacy, University College London, 29-39, Brunswick Square, London WC1N 1AX, UK
| | - Cherukupalli Srinivasulu
- Discipline of Pharmaceutical Sciences, College of Health Sciences, University of KwaZulu-Natal (UKZN), Westville, Durban 4001, South Africa
| | - Girish A. Hampannavar
- Discipline of Pharmaceutical Sciences, College of Health Sciences, University of KwaZulu-Natal (UKZN), Westville, Durban 4001, South Africa
| | - Nisar Sayyad
- Discipline of Pharmaceutical Sciences, College of Health Sciences, University of KwaZulu-Natal (UKZN), Westville, Durban 4001, South Africa
| | - Mahmoud E. Soliman
- Discipline of Pharmaceutical Sciences, College of Health Sciences, University of KwaZulu-Natal (UKZN), Westville, Durban 4001, South Africa
| | - Rajshekhar Karpoormath
- Discipline of Pharmaceutical Sciences, College of Health Sciences, University of KwaZulu-Natal (UKZN), Westville, Durban 4001, South Africa
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23
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Makala H, Ulaganathan V. Identification of novel scaffolds to inhibit human mitotic kinesin Eg5 targeting the second allosteric binding site using in silico methods. J Recept Signal Transduct Res 2017; 38:12-19. [PMID: 29041840 DOI: 10.1080/10799893.2017.1387922] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Human mitotic kinesins are potential anticancer drug targets because of their essential role in mitotic cell division. The kinesin Eg5 (Kinesin-5, kif11) has gained much attention in this regard and has many inhibitors in different phases of clinical trials. All drug candidates considered for Eg5 so far binds to the binding site (Site 1) formed by the loop L5, helices α2 and α3 and are uncompetitive to ATP/ADP. Recently, it has been reported that Eg5 also has a second binding site (Site 2) formed by helices α4 and α6. In the current work, we have screened the compounds in the diversity set-III from National Cancer Institute (NCI) and Zinc database to identify potential inhibitors for Eg5 that specifically binds to the site 2. The compounds were ranked based on the glide extra precision docking scores and the top ranked compounds were found to have pyridazine scaffold. The top five compounds were further evaluated for other drug like properties. Stability of protein-ligand complexes were analyzed using molecular dynamic simulations. Our studies suggest that pyridazine analogs have good MDCK, permeability properties and high binding affinity to the human Eg5.
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Affiliation(s)
- Himesh Makala
- a Department of Biotechnology , School of Chemical and Biotechnology, SASTRA University , Thanjavur , India
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24
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Bickel KG, Mann BJ, Waitzman JS, Poor TA, Rice SE, Wadsworth P. Src family kinase phosphorylation of the motor domain of the human kinesin-5, Eg5. Cytoskeleton (Hoboken) 2017. [PMID: 28646493 DOI: 10.1002/cm.21380] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Spindle formation in mammalian cells requires precise spatial and temporal regulation of the kinesin-5, Eg5, which generates outward force to establish spindle bipolarity. Our results demonstrate that Eg5 is phosphorylated in cultured cells by Src family kinases (SFKs) at three sites in the motor head: Y125, Y211, and Y231. Mutation of these sites diminishes motor activity in vitro, and replacement of endogenous Eg5 with phosphomimetic Y211 in LLC-Pk1 cells results in monopolar spindles, consistent with loss of Eg5 activity. Cells treated with SFK inhibitors show defects in spindle formation, similar to those in cells expressing the nonphosphorylatable Y211 mutant, and distinct from inhibition of other mitotic kinases. We propose that this phosphoregulatory mechanism tunes Eg5 enzymatic activity for optimal spindle morphology.
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Affiliation(s)
- Kathleen G Bickel
- Department of Cell and Molecular Biology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, 60611
| | - Barbara J Mann
- Department of Biology, University of Massachusetts, Amherst, Massachusetts, 01003
| | - Joshua S Waitzman
- Department of Medicine, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, 60611
| | - Taylor A Poor
- Department of Medicine, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, 60611
| | - Sarah E Rice
- Department of Cell and Molecular Biology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, 60611
| | - Patricia Wadsworth
- Department of Biology, University of Massachusetts, Amherst, Massachusetts, 01003
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25
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Carbajales C, Sawada JI, Marzaro G, Sotelo E, Escalante L, Sánchez-Díaz Marta A, García-Mera X, Asai A, Coelho A. Multicomponent Assembly of the Kinesin Spindle Protein Inhibitor CPUYJ039 and Analogues as Antimitotic Agents. ACS COMBINATORIAL SCIENCE 2017; 19:153-160. [PMID: 28135059 DOI: 10.1021/acscombsci.6b00166] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
The potent kinesin spindle protein inhibitor CPUYJ039 and a set of analogues were prepared by a target-oriented approach based on a Ugi reaction that uses 2-nitrophenyl isocyanides as key building blocks. The herein documented strategy provides straightforward and atom economical access to potent benzimidazole-based antimitotic agents by exploring the versatility and exploratory power of the Ugi reaction. The results of docking studies and biological activity evaluations of the benzimidazole compounds are also reported.
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Affiliation(s)
- Carlos Carbajales
- Center
for Research in Biological Chemistry and Molecular Materials, University of Santiago de Compostela, Jenaro de la Fuente s/n, Campus
Vida, Santiago de Compostela 15782, Spain
| | - Jun-ichi Sawada
- Graduate
School of Pharmaceutical Sciences, University of Shizuoka, Suruga-ku, Shizuoka 422-8526, Japan
| | - Giovanni Marzaro
- Department
of Pharmaceutical and Pharmacological Sciences, University of Padova, Via Marzolo 5, 35131 Padova, Italy
| | - Eddy Sotelo
- Center
for Research in Biological Chemistry and Molecular Materials, University of Santiago de Compostela, Jenaro de la Fuente s/n, Campus
Vida, Santiago de Compostela 15782, Spain
- Department
of Organic Chemistry, Faculty of Pharmacy, University of Santiago de Compostela, Avenida das Ciencias, s/n, Campus sur, Santiago de Compostela 15782, Spain
| | - Luz Escalante
- Center
for Research in Biological Chemistry and Molecular Materials, University of Santiago de Compostela, Jenaro de la Fuente s/n, Campus
Vida, Santiago de Compostela 15782, Spain
| | - Antonio Sánchez-Díaz Marta
- Center
for Research in Biological Chemistry and Molecular Materials, University of Santiago de Compostela, Jenaro de la Fuente s/n, Campus
Vida, Santiago de Compostela 15782, Spain
| | - Xerardo García-Mera
- Department
of Organic Chemistry, Faculty of Pharmacy, University of Santiago de Compostela, Avenida das Ciencias, s/n, Campus sur, Santiago de Compostela 15782, Spain
| | - Akira Asai
- Graduate
School of Pharmaceutical Sciences, University of Shizuoka, Suruga-ku, Shizuoka 422-8526, Japan
| | - Alberto Coelho
- Center
for Research in Biological Chemistry and Molecular Materials, University of Santiago de Compostela, Jenaro de la Fuente s/n, Campus
Vida, Santiago de Compostela 15782, Spain
- Department
of Organic Chemistry, Faculty of Pharmacy, University of Santiago de Compostela, Avenida das Ciencias, s/n, Campus sur, Santiago de Compostela 15782, Spain
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26
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Möckel MM, Hund C, Mayer TU. Chemical Genetics Approach to Engineer Kinesins with Sensitivity towards a Small-Molecule Inhibitor of Eg5. Chembiochem 2016; 17:2042-2045. [PMID: 27550380 DOI: 10.1002/cbic.201600451] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2016] [Indexed: 12/14/2022]
Abstract
Due to their fast and often reversible mode of action, small molecules are ideally suited to dissect biological processes. Yet, the validity of small-molecule studies is intimately tied to the specificity of the applied compounds, thus imposing a great challenge to screens for novel inhibitors. Here, we applied a chemical-genetics approach to render kinesin motor proteins sensitive to inhibition by the well-characterized small molecule S-Trityl-l-cysteine (STLC). STLC specifically inhibits the kinesin Eg5 through binding to a known allosteric site within the motor domain. Transfer of this allosteric binding site into the motor domain of the human kinesins Kif3A and Kif4A sensitizes them towards STLC. Single-molecule microscopy analyses confirmed that STLC inhibits the movement of chimeric but not wild-type Kif4A along microtubules. Thus, our proof-of-concept study revealed that this chemical-genetic approach provides a powerful strategy to specifically inhibit kinesins in vitro for which small-molecule inhibitors are not yet available.
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Affiliation(s)
- Martin M Möckel
- Department of Biology, University of Konstanz, Universitätsstrasse 10, 78457, Konstanz, Germany
| | - Corinna Hund
- Department of Biology, University of Konstanz, Universitätsstrasse 10, 78457, Konstanz, Germany.,FGen GmbH, Hochbergerstrasse 60C, 4057, Basel, Switzerland
| | - Thomas U Mayer
- Department of Biology, University of Konstanz, Universitätsstrasse 10, 78457, Konstanz, Germany.
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27
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Talapatra SK, Rath O, Clayton E, Tomasi S, Kozielski F. Depsidones from Lichens as Natural Product Inhibitors of M-Phase Phosphoprotein 1, a Human Kinesin Required for Cytokinesis. JOURNAL OF NATURAL PRODUCTS 2016; 79:1576-1585. [PMID: 27300079 DOI: 10.1021/acs.jnatprod.5b00962] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
M-Phase Phosphoprotein 1 (MPP1), a microtubule plus end directed kinesin, is required for the completion of cytokinesis. Previous studies have shown that MPP1 is upregulated in various types of bladder cancer. This article describes inhibitor screening leading to the identification of a new class of natural product inhibitors of MPP1. Two compounds with structural similarity, norlobaridone (1) and physodic acid (2), were found to inhibit MPP1. Physodic acid is not competitive with ATP, indicating the presence of an allosteric inhibitor-binding pocket. Initial drug-like property screening indicates that physodic acid is more soluble than norlobaridone and has more favorable lipophilicity. However, both suffer from high clearance in human microsomal stability assays mediated by the lability of the lactone ring as well as hydroxylation of the alkyl chains as shown by metabolite identification studies. In cell-based assays physodic acid is a weak inhibitor with EC50 values of about 30 μM in a range of tumor cell lines. The two depsidones identified and characterized here could be used for future improvement of their activity against MPP1 and will be useful chemical probes for studying this unique molecular motor in more depth.
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Affiliation(s)
- Sandeep K Talapatra
- Department of Pharmaceutical and Biological Chemistry, The School of Pharmacy, University College London , 29-39 Brunswick Square, London WC1N 1AX, U.K
- The Beatson Institute for Cancer Research , Garscube Estate, Switchback Road, Glasgow G61 1BD, Scotland, U.K
| | - Oliver Rath
- The Beatson Institute for Cancer Research , Garscube Estate, Switchback Road, Glasgow G61 1BD, Scotland, U.K
| | - Eddie Clayton
- Cyprotex Discovery Ltd , 15 Beech Lane, Macclesfield, Cheshire SK10 2DR, U.K
| | - Sophie Tomasi
- Equipe PNSCM "Produits Naturels - Synthèses - Chimie Médicinale", Unités Mixtes de Recherche, Centre National de la Recherche Scientifique, 6226 Sciences Chimiques de Rennes, UFR Sciences Pharmaceutiques et Biologiques, Univ. Rennes 1, Université Bretagne Loire , 2 Avenue du Pr. Léon Bernard, F-35043 Rennes, France
| | - Frank Kozielski
- Department of Pharmaceutical and Biological Chemistry, The School of Pharmacy, University College London , 29-39 Brunswick Square, London WC1N 1AX, U.K
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28
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Dube D, Tiwari P, Kaur P. The hunt for antimitotic agents: an overview of structure-based design strategies. Expert Opin Drug Discov 2016; 11:579-97. [PMID: 27077683 DOI: 10.1080/17460441.2016.1174689] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
INTRODUCTION Structure-based drug discovery offers a rational approach for the design and development of novel anti-mitotic agents which target specific proteins involved in mitosis. This strategy has paved the way for development of a new generation of chemotypes which selectively interfere with the target proteins. The interference of these anti-mitotic targets implicated in diverse stages of mitotic cell cycle progression culminates in cancer cell apoptosis. AREAS COVERED This review covers the various mitotic inhibitors developed against validated mitotic checkpoint protein targets using structure-based design and optimization strategies. The protein-ligand interactions and the insights gained from these studies, culminating in the development of more potent and selective inhibitors, have been presented. EXPERT OPINION The advent of structure-based drug design coupled with advances in X-ray crystallography has revolutionized the discovery of candidate lead molecules. The structural insights gleaned from the co-complex protein-drug interactions have provided a new dimension in the design of anti-mitotic molecules to develop drugs with a higher selectivity and specificity profile. Targeting non-catalytic domains has provided an alternate approach to address cross-reactivity and broad selectivity among kinase inhibitors. The elucidation of structures of emerging mitotic drug targets has opened avenues for the design of inhibitors that target cancer.
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Affiliation(s)
- D Dube
- a Department of Biophysics , All India Institute of Medical Sciences , New Delhi , India
| | - P Tiwari
- a Department of Biophysics , All India Institute of Medical Sciences , New Delhi , India
| | - P Kaur
- a Department of Biophysics , All India Institute of Medical Sciences , New Delhi , India
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29
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Recent findings and future directions for interpolar mitotic kinesin inhibitors in cancer therapy. Future Med Chem 2016; 8:463-89. [PMID: 26976726 PMCID: PMC4896392 DOI: 10.4155/fmc.16.5] [Citation(s) in RCA: 70] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
The kinesin class of microtubule-associated motor proteins present attractive anti-cancer targets owing to their roles in key functions in dividing cells. Two interpolar mitotic kinesins Eg5 and HSET have opposing motor functions in mitotic spindle assembly with respect to microtubule movement, but both offer opportunities to develop cancer selective therapeutic agents. Here, we summarize the progress to date in developing inhibitors of Eg5 and HSET, with an emphasis on structural biology insights into the binding modes of allosteric inhibitors, compound selectivity and mechanisms of action of different chemical scaffolds. We discuss translation of preclinical studies to clinical experience with Eg5 inhibitors, recent findings on potential resistance mechanisms, and explore the implications for future anticancer drug development against these targets.
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30
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Ogo N, Ishikawa Y, Sawada JI, Matsuno K, Hashimoto A, Asai A. Structure-Guided Design of Novel l-Cysteine Derivatives as Potent KSP Inhibitors. ACS Med Chem Lett 2015; 6:1004-9. [PMID: 26396688 DOI: 10.1021/acsmedchemlett.5b00221] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2015] [Accepted: 07/22/2015] [Indexed: 12/31/2022] Open
Abstract
Kinesin spindle protein (KSP), known as Hs Eg5, a member of the kinesin-5 family, plays an important role in the formation and maintenance of the bipolar spindle. We previously reported S-trityl-l-cysteine derivatives as selective KSP inhibitors. Here, we report further optimizations using docking modeling in the L5 allosteric binding site, which led to the discovery of several high affinity derivatives with two fused phenyl rings in the trityl group giving low nanomolar range KSP ATPase inhibition. The representative derivatives potently inhibited cell growth of HCT116 cells in correlation with KSP inhibitory activities and significantly suppressed tumor growth in the xenograft model in vivo.
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Affiliation(s)
- Naohisa Ogo
- Center for Drug Discovery, Graduate School of Pharmaceutical
Sciences, University of Shizuoka, Shizuoka 422-8526, Japan
| | - Yoshinobu Ishikawa
- Department of Physical Biochemistry, School
of Pharmaceutical Sciences, University of Shizuoka, Shizuoka 422-8526, Japan
| | - Jun-ichi Sawada
- Center for Drug Discovery, Graduate School of Pharmaceutical
Sciences, University of Shizuoka, Shizuoka 422-8526, Japan
| | - Kenji Matsuno
- Center for Drug Discovery, Graduate School of Pharmaceutical
Sciences, University of Shizuoka, Shizuoka 422-8526, Japan
| | - Akihiro Hashimoto
- Tsukuba Research Center, Taiho Pharmaceutical Co., Ltd., 3 Okubo, Tsukuba, Ibaraki 300-2611, Japan
| | - Akira Asai
- Center for Drug Discovery, Graduate School of Pharmaceutical
Sciences, University of Shizuoka, Shizuoka 422-8526, Japan
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31
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Yokoyama H, Sawada JI, Katoh S, Matsuno K, Ogo N, Ishikawa Y, Hashimoto H, Fujii S, Asai A. Structural basis of new allosteric inhibition in Kinesin spindle protein Eg5. ACS Chem Biol 2015; 10:1128-36. [PMID: 25622007 DOI: 10.1021/cb500939x] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Kinesin spindle protein Eg5 is a target for anticancer therapies, and small molecule inhibitors of its ATPase activity have been developed. We herein report for the first time the crystal structure of and biochemical studies on the Eg5 motor domain in complex with a new type of allosteric inhibitor. The biphenyl-type inhibitor PVZB1194 binds to the α4/α6 allosteric pocket 15 Å from the ATP-binding pocket, which differs from conventional allosteric inhibitors that bind to the allosteric L5/α2/α3 pocket of Eg5. Binding of the inhibitor is involved in the neck-linker conformation and also causes conformational changes around the ATP-binding pocket through Tyr104 to affect the interaction of ATP with the pocket. This structure provides useful information for the development of novel types of allosteric drugs as well as a novel insight into the molecular mechanism responsible for regulating the motor activity of kinesins.
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Affiliation(s)
- Hideshi Yokoyama
- Department
of Physical Biochemistry, School of Pharmaceutical Sciences, University of Shizuoka, Shizuoka 422-8526, Japan
| | - Jun-ichi Sawada
- Center
for Drug Discovery, Graduate School of Pharmaceutical Sciences, University of Shizuoka, Shizuoka 422-8526, Japan
| | - Shiori Katoh
- Department
of Physical Biochemistry, School of Pharmaceutical Sciences, University of Shizuoka, Shizuoka 422-8526, Japan
| | - Kenji Matsuno
- Center
for Drug Discovery, Graduate School of Pharmaceutical Sciences, University of Shizuoka, Shizuoka 422-8526, Japan
| | - Naohisa Ogo
- Center
for Drug Discovery, Graduate School of Pharmaceutical Sciences, University of Shizuoka, Shizuoka 422-8526, Japan
| | - Yoshinobu Ishikawa
- Department
of Physical Biochemistry, School of Pharmaceutical Sciences, University of Shizuoka, Shizuoka 422-8526, Japan
| | - Hiroshi Hashimoto
- Department
of Physical Biochemistry, School of Pharmaceutical Sciences, University of Shizuoka, Shizuoka 422-8526, Japan
| | - Satoshi Fujii
- Department
of Physical Biochemistry, School of Pharmaceutical Sciences, University of Shizuoka, Shizuoka 422-8526, Japan
| | - Akira Asai
- Center
for Drug Discovery, Graduate School of Pharmaceutical Sciences, University of Shizuoka, Shizuoka 422-8526, Japan
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32
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Carbajales C, Prado MÁ, Gutiérrez-de-Terán H, Cores Á, Azuaje J, Novio S, Nuñez MJ, Fernández-García B, Sotelo E, García-Mera X, Sánchez-Lazo P, Freire-Garabal M, Coelho A. Structure-Based Design of New KSP-Eg5 Inhibitors Assisted by a Targeted Multicomponent Reaction. Chembiochem 2014; 15:1471-80. [DOI: 10.1002/cbic.201402089] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2014] [Indexed: 11/06/2022]
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33
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Takeuchi T, Oishi S, Kaneda M, Misu R, Ohno H, Sawada JI, Asai A, Nakamura S, Nakanishi I, Fujii N. Optimization of diaryl amine derivatives as kinesin spindle protein inhibitors. Bioorg Med Chem 2014; 22:3171-9. [DOI: 10.1016/j.bmc.2014.04.008] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2014] [Revised: 04/05/2014] [Accepted: 04/05/2014] [Indexed: 10/25/2022]
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34
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Talapatra SK, Anthony NG, Mackay SP, Kozielski F. Mitotic kinesin Eg5 overcomes inhibition to the phase I/II clinical candidate SB743921 by an allosteric resistance mechanism. J Med Chem 2013; 56:6317-29. [PMID: 23875972 DOI: 10.1021/jm4006274] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Development of drug resistance during cancer chemotherapy is one of the major causes of chemotherapeutic failure for the majority of clinical agents. The aim of this study was to investigate the underlying molecular mechanism of resistance developed by the mitotic kinesin Eg5 against the potent second-generation ispinesib analogue SB743921 (1), a phase I/II clinical candidate. Biochemical and biophysical data demonstrate that point mutations in the inhibitor-binding pocket decrease the efficacy of 1 by several 1000-fold. Surprisingly, the structures of wild-type and mutant Eg5 in complex with 1 display no apparent structural changes in the binding configuration of the drug candidate. Furthermore, ITC and modeling approaches reveal that resistance to 1 is not through conventional steric effects at the binding site but through reduced flexibility and changes in energy fluctuation pathways through the protein that influence its function. This is a phenomenon we have called "resistance by allostery".
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Affiliation(s)
- Sandeep K Talapatra
- The Beatson Institute for Cancer Research, Garscube Estate, Switchback Road, Bearsden, Glasgow G61 1BS, Scotland, U.K.
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35
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STLC-resistant cell lines as tools to classify chemically divergent Eg5 targeting agents according to their mode of action and target specificity. Biochem Pharmacol 2013; 86:1441-51. [PMID: 24041742 DOI: 10.1016/j.bcp.2013.09.003] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2013] [Revised: 09/04/2013] [Accepted: 09/05/2013] [Indexed: 11/23/2022]
Abstract
Determining the mechanism of action of drugs and their target specificity in cells remains a major challenge. Here we describe the use of cell lines expressing two point mutations in the allosteric inhibitor binding pocket of the mitotic kinesin Eg5 (D130A, in the loop L5 region and L214A in helix α3), which following transfection, were selected for their ability to proliferate normally in the presence of STLC, a well known Eg5 inhibitor. The cell lines were used to discriminate the mechanism of action of other chemically distinct small molecule inhibitors of Eg5 that differ in their mode of action. The STLC resistant cells were capable of continuous proliferation in the presence of ATP uncompetitive inhibitors, such as K858 and dimethylenastron, but were still sensitive to ATP competitive inhibitors that are thought to bind to a distinct site on Eg5 than the allosteric binding pocket. The STLC resistant cell lines can therefore be used as a filter to distinguish Eg5 loop L5 binding drugs from drugs binding to other pockets without prior structural information. Additionally, the cells can be used to analyze whether inhibitors of Eg5 are specific to this potential drug target or whether they have additional targets in dividing cells.
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36
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Jiang C, You Q. Kinesin spindle protein inhibitors in cancer: a patent review (2008 - present). Expert Opin Ther Pat 2013; 23:1547-60. [PMID: 23978071 DOI: 10.1517/13543776.2013.833606] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
INTRODUCTION Inhibition of kinesin spindle protein (KSP) has emerged as a novel and validated therapeutic strategy against cancers. A lot of new KSP inhibitors have been identified in recent years and some of them have entered clinical trials. This may provide more selections in future cancer therapy. AREAS COVERED In the present review, the authors will describe the most recent classes of KSP inhibitors by reviewing about 96 literatures in which 24 patent applications were included from 2008 to now. EXPERT OPINION Many new KSP inhibitors have been discovered that act either by binding in an allosteric site of KSP or by ATP competitive inhibition. There are several ATP non-competitive KSP inhibitors entering clinical investigation. Although they were both well tolerated and showed acceptable pharmacokinetic profiles, limited clinical response was always the problem. Mutation of the binding pocket was also a hindrance in the development of these allosteric inhibitors. The appearance of ATP competitive KSP inhibitors was considered to be able to overcome mutation-mediated resistance to the allosteric inhibitors, which could be a new approach for the development of novel KSP inhibitors.
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Affiliation(s)
- Cheng Jiang
- China Pharmaceutical University, Department of Medicinal Chemistry and Jiangsu Key Laboratory of Carcinogenesis and Intervention, Jiangsu Key Laboratory of Drug Design and Optimization , Nanjing 210009 , China
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37
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Kaan HYK, Major J, Tkocz K, Kozielski F, Rosenfeld SS. "Snapshots" of ispinesib-induced conformational changes in the mitotic kinesin Eg5. J Biol Chem 2013; 288:18588-98. [PMID: 23658017 DOI: 10.1074/jbc.m113.462648] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Kinesins comprise a superfamily of molecular motors that drive a wide variety of cellular physiologies, from cytoplasmic transport to formation of the bipolar spindle in mitosis. These differing roles are reflected in corresponding polymorphisms in key kinesin structural elements. One of these is a unique loop and stem motif found in all kinesins and referred to as loop 5 (L5). This loop is longest in the mitotic kinesin Eg5 and is the target for a number of small molecule inhibitors, including ispinesib, which is being used in clinical trials in patients with cancer. In this study, we have used x-ray crystallography to identify a new structure of an Eg5-ispinesib complex and have combined this with transient state kinetics to identify a plausible sequence of conformational changes that occur in response to ispinesib binding. Our results demonstrate that ispinesib-induced structural changes in L5 from Eg5 lead to subsequent changes in the conformation of the switch II loop and helix and in the neck linker. We conclude that L5 in Eg5 simultaneously regulates the structure of both the ATP binding site and the motor's mechanical elements that generate force.
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Affiliation(s)
- Hung Yi Kristal Kaan
- Beatson Institute for Cancer Research, Garscube Estate, Switchback Road, Bearsden, Glasgow G61 1BD, Scotland, United Kingdom
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38
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Good JAD, Wang F, Rath O, Kaan HYK, Talapatra SK, Podgórski D, MacKay SP, Kozielski F. Optimized S-trityl-L-cysteine-based inhibitors of kinesin spindle protein with potent in vivo antitumor activity in lung cancer xenograft models. J Med Chem 2013; 56:1878-93. [PMID: 23394180 PMCID: PMC3759169 DOI: 10.1021/jm3014597] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
![]()
The mitotic kinesin Eg5 is critical
for the assembly of the mitotic
spindle and is a promising chemotherapy target. Previously, we identified S-trityl-l-cysteine as a selective inhibitor of
Eg5 and developed triphenylbutanamine analogues with improved potency,
favorable drug-like properties, but moderate in vivo activity. We
report here their further optimization to produce extremely potent
inhibitors of Eg5 (Kiapp <
10 nM) with broad-spectrum activity against cancer cell lines comparable
to the Phase II drug candidates ispinesib and SB-743921. They have
good oral bioavailability and pharmacokinetics and induced complete
tumor regression in nude mice explanted with lung cancer patient xenografts.
Furthermore, they display fewer liabilities with CYP-metabolizing
enzymes and hERG compared with ispinesib and SB-743921, which is important
given the likely application of Eg5 inhibitors in combination therapies.
We present the case for this preclinical series to be investigated
in single and combination chemotherapies, especially targeting hematological
malignancies.
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Affiliation(s)
- James A D Good
- Molecular Motors Laboratory, The Beatson Institute for Cancer Research, Garscube Estate, Switchback Road, Glasgow G61 1BD, Scotland, UK.
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39
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El-Nassan HB. Advances in the discovery of kinesin spindle protein (Eg5) inhibitors as antitumor agents. Eur J Med Chem 2013; 62:614-31. [PMID: 23434636 DOI: 10.1016/j.ejmech.2013.01.031] [Citation(s) in RCA: 89] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2012] [Revised: 01/22/2013] [Accepted: 01/26/2013] [Indexed: 10/27/2022]
Abstract
Cancer is considered as one of the most serious health problems. Despite the presence of many effective chemotherapeutic agents, their severe side effects together with the appearance of mutant tumors limit the use of these drugs and increase the need for new anticancer agents. Eg5 represents an attractive target for medicinal chemists since Eg5 is overexpressed in many proliferative tissues while almost no Eg5 is detected in nonproliferative tissues. Many Eg5 inhibitors displayed potent anticancer activity against some of the mutant tumors with limited side effects. The present review provides an overview about the progress in the discovery of Eg5 inhibitors especially from 2009 to 2012 as well as the clinical trials conducted on some of these inhibitors.
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Affiliation(s)
- Hala Bakr El-Nassan
- Pharmaceutical Organic Chemistry Department, Faculty of Pharmacy, Cairo University, 33 Kasr El-Aini Street, Cairo 11562, Egypt.
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40
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Ulaganathan V, Talapatra SK, Rath O, Pannifer A, Hackney DD, Kozielski F. Structural insights into a unique inhibitor binding pocket in kinesin spindle protein. J Am Chem Soc 2013; 135:2263-72. [PMID: 23305346 DOI: 10.1021/ja310377d] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Human kinesin Eg5 is a target for drug development in cancer chemotherapy with compounds in phase II clinical trials. These agents bind to a well-characterized allosteric pocket involving the loop L5 region, a structural element in kinesin-5 family members thought to provide inhibitor specificity. Using X-ray crystallography, kinetic, and biophysical methods, we have identified and characterized a distinct allosteric pocket in Eg5 able to bind inhibitors with nanomolar K(d). This pocket is formed by key structural elements thought to be pivotal for force generation in kinesins and may represent a novel site for therapeutic intervention in this increasingly well-validated drug target.
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Affiliation(s)
- Venkatasubramanian Ulaganathan
- The Molecular Motors Laboratory, The Beatson Institute for Cancer Research, Garscube Estate, Switchback Road, Glasgow G61 1BD, Scotland, UK
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41
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Goulet A, Moores C. New insights into the mechanism of force generation by kinesin-5 molecular motors. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2013; 304:419-66. [PMID: 23809441 DOI: 10.1016/b978-0-12-407696-9.00008-7] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Kinesin-5 motors are members of a superfamily of microtubule-dependent ATPases and are widely conserved among eukaryotes. Kinesin-5s typically form homotetramers with pairs of motor domains located at either end of a dumbbell-shaped molecule. This quaternary structure enables cross-linking and ATP-driven sliding of pairs of microtubules, although the exact molecular mechanism of this activity is still unclear. Kinesin-5 function has been characterized in greatest detail in cell division, although a number of interphase roles have also been defined. The kinesin-5 ATPase is tuned for slow microtubule sliding rather than cellular transport and-in vertebrates-can be inhibited specifically by allosteric small molecules currently in cancer clinical trials. The biophysical and structural basis of kinesin-5 mechanochemistry is being elucidated and has provided further insight into kinesin-5 activities. However, it is likely that the precise mechanism of these important motors has evolved according to functional context and regulation in individual organisms.
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Affiliation(s)
- Adeline Goulet
- Institute of Structural and Molecular Biology, Birkbeck College, London, United Kingdom
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42
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Goulet A, Behnke-Parks WM, Sindelar CV, Major J, Rosenfeld SS, Moores CA. The structural basis of force generation by the mitotic motor kinesin-5. J Biol Chem 2012; 287:44654-66. [PMID: 23135273 DOI: 10.1074/jbc.m112.404228] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Kinesin-5 is required for forming the bipolar spindle during mitosis. Its motor domain, which contains nucleotide and microtubule binding sites and mechanical elements to generate force, has evolved distinct properties for its spindle-based functions. In this study, we report subnanometer resolution cryoelectron microscopy reconstructions of microtubule-bound human kinesin-5 before and after nucleotide binding and combine this information with studies of the kinetics of nucleotide-induced neck linker and cover strand movement. These studies reveal coupled, nucleotide-dependent conformational changes that explain many of this motor's properties. We find that ATP binding induces a ratchet-like docking of the neck linker and simultaneous, parallel docking of the N-terminal cover strand. Loop L5, the binding site for allosteric inhibitors of kinesin-5, also undergoes a dramatic reorientation when ATP binds, suggesting that it is directly involved in controlling nucleotide binding. Our structures indicate that allosteric inhibitors of human kinesin-5, which are being developed as anti-cancer therapeutics, bind to a motor conformation that occurs in the course of normal function. However, due to evolutionarily defined sequence variations in L5, this conformation is not adopted by invertebrate kinesin-5s, explaining their resistance to drug inhibition. Together, our data reveal the precision with which the molecular mechanism of kinesin-5 motors has evolved for force generation.
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Affiliation(s)
- Adeline Goulet
- Institute of Structural and Molecular Biology, Birkbeck College, Malet Street, London WC1E 7HX, United Kingdom
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Talapatra SK, Schüttelkopf AW, Kozielski F. The structure of the ternary Eg5-ADP-ispinesib complex. ACTA CRYSTALLOGRAPHICA. SECTION D, BIOLOGICAL CRYSTALLOGRAPHY 2012; 68:1311-9. [PMID: 22993085 PMCID: PMC3447400 DOI: 10.1107/s0907444912027965] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/31/2012] [Accepted: 06/20/2012] [Indexed: 11/17/2022]
Abstract
The human kinesin Eg5 is responsible for bipolar spindle formation during early mitosis. Inhibition of Eg5 triggers the formation of monoastral spindles, leading to mitotic arrest that eventually causes apoptosis. There is increasing evidence that Eg5 constitutes a potential drug target for the development of cancer chemotherapeutics. The most advanced Eg5-targeting agent is ispinesib, which exhibits potent antitumour activity and is currently in multiple phase II clinical trials. In this study, the crystal structure of the Eg5 motor domain in complex with ispinesib, supported by kinetic and thermodynamic binding data, is reported. Ispinesib occupies the same induced-fit pocket in Eg5 as other allosteric inhibitors, making extensive hydrophobic interactions with the protein. The data for the Eg5-ADP-ispinesib complex suffered from pseudo-merohedral twinning and revealed translational noncrystallographic symmetry, leading to challenges in data processing, space-group assignment and structure solution as well as in refinement. These complications may explain the lack of available structural information for this important agent and its analogues. The present structure represents the best interpretation of these data based on extensive data-reduction, structure-solution and refinement trials.
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Affiliation(s)
- S. K. Talapatra
- Molecular Motor Laboratory, The Beatson Institute for Cancer Research, Garscube Estate, Switchback Road, Bearsden, Glasgow G61 1BD, Scotland, UK
| | - A. W. Schüttelkopf
- Molecular Motor Laboratory, The Beatson Institute for Cancer Research, Garscube Estate, Switchback Road, Bearsden, Glasgow G61 1BD, Scotland, UK
| | - F. Kozielski
- Molecular Motor Laboratory, The Beatson Institute for Cancer Research, Garscube Estate, Switchback Road, Bearsden, Glasgow G61 1BD, Scotland, UK
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Doing the methylene shuffle – Further insights into the inhibition of mitotic kinesin Eg5 with S-trityl l-cysteine. Eur J Med Chem 2012; 54:483-98. [DOI: 10.1016/j.ejmech.2012.05.034] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2011] [Revised: 05/23/2012] [Accepted: 05/23/2012] [Indexed: 11/22/2022]
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Abstract
Kinesins are a family of molecular motors that travel unidirectionally along microtubule tracks to fulfil their many roles in intracellular transport or cell division. Over the past few years kinesins that are involved in mitosis have emerged as potential targets for cancer drug development. Several compounds that inhibit two mitotic kinesins (EG5 (also known as KIF11) and centromere-associated protein E (CENPE)) have entered Phase I and II clinical trials either as monotherapies or in combination with other drugs. Additional mitotic kinesins are currently being validated as drug targets, raising the possibility that the range of kinesin-based drug targets may expand in the future.
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Affiliation(s)
- Oliver Rath
- The Beatson Institute for Cancer Research, Garscube Estate, Switchback Road, Bearsden, Glasgow G61 1BD, Scotland, UK
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Nagarajan S, Skoufias DA, Kozielski F, Pae AN. Receptor–Ligand Interaction-Based Virtual Screening for Novel Eg5/Kinesin Spindle Protein Inhibitors. J Med Chem 2012; 55:2561-73. [DOI: 10.1021/jm201290v] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Shanthi Nagarajan
- Neuro-Medicine Center, Life
Sciences Division, Korea Institute of Science and Technology, PO Box 131, Cheongryang, Seoul 130-650, Republic of Korea
- School of Science, Korea University of Science and Technology, 52 Eoeun
dongYuseong-gu, Daejeon 305-333, Republic of Korea
| | - Dimitrios A. Skoufias
- Institute for Structural Biology (CEA-CNRS-UJF), 41 rue Jules Horowitz, 38027
Grenoble Cedex 1, France,
| | - Frank Kozielski
- The Beatson Institute for Cancer Research, Garscube Estate, Switchback Road,
Bearsden, Glasgow, G61 1BD, Scotland, U.K
| | - Ae Nim Pae
- Neuro-Medicine Center, Life
Sciences Division, Korea Institute of Science and Technology, PO Box 131, Cheongryang, Seoul 130-650, Republic of Korea
- School of Science, Korea University of Science and Technology, 52 Eoeun
dongYuseong-gu, Daejeon 305-333, Republic of Korea
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3D-QSAR studies of dihydropyrazole and dihydropyrrole derivatives as inhibitors of human mitotic kinesin Eg5 based on molecular docking. Molecules 2012; 17:2015-29. [PMID: 22343406 PMCID: PMC6268882 DOI: 10.3390/molecules17022015] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2012] [Revised: 02/07/2012] [Accepted: 02/13/2012] [Indexed: 11/16/2022] Open
Abstract
Human mitotic kinesin Eg5 plays an essential role in mitoses and is an interesting drug target against cancer. To find the correlation between Eg5 and its inhibitors, structure-based 3D-quantitative structure-activity relationship (QSAR) studies were performed on a series of dihydropyrazole and dihydropyrrole derivatives using comparative molecular field analysis (CoMFA) and comparative molecular similarity indices analysis (CoMSIA) methods. Based on the LigandFit docking results, predictive 3D-QSAR models were established, with cross-validated coefficient values (q²) up to 0.798 for CoMFA and 0.848 for CoMSIA, respectively. Furthermore, the CoMFA and CoMSIA models were mapped back to the binding sites of Eg5, which could provide a better understanding of vital interactions between the inhibitors and the kinase. Ligands binding in hydrophobic part of the inhibitor-binding pocket were found to be crucial for potent ligand binding and kinases selectivity. The analyses may be used to design more potent EG5 inhibitors and predict their activities prior to synthesis.
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Wang F, Good JAD, Rath O, Kaan HYK, Sutcliffe OB, Mackay SP, Kozielski F. Triphenylbutanamines: kinesin spindle protein inhibitors with in vivo antitumor activity. J Med Chem 2012; 55:1511-25. [PMID: 22248262 PMCID: PMC3428805 DOI: 10.1021/jm201195m] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
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The human mitotic kinesin Eg5 represents a novel mitotic
spindle target for cancer chemotherapy. We previously identified S-trityl-l-cysteine (STLC) and related analogues
as selective potent inhibitors of Eg5. We herein report on the development
of a series of 4,4,4-triphenylbutan-1-amine inhibitors derived from
the STLC scaffold. This new generation systematically improves on
potency: the most potent C-trityl analogues exhibit Kiapp ≤ 10 nM and GI50 ≈ 50 nM, comparable to results from the phase II clinical
benchmark ispinesib. Crystallographic studies reveal that they adopt
the same overall binding configuration as S-trityl
analogues at an allosteric site formed by loop L5 of Eg5. Evaluation
of their druglike properties reveals favorable profiles for future
development and, in the clinical candidate ispinesib, moderate hERG
and CYP inhibition. One triphenylbutanamine analogue and ispinesib
possess very good bioavailability (51% and 45%, respectively), with
the former showing in vivo antitumor growth activity in nude mice
xenograft studies.
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Affiliation(s)
- Fang Wang
- Molecular Motor Laboratory, The Beatson Institute for Cancer Research, Garscube Estate, Switchback Road, Glasgow G61 1BD, Scotland, UK.
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Harrington TD, Naber N, Larson AG, Cooke R, Rice SE, Pate E. Analysis of the interaction of the Eg5 Loop5 with the nucleotide site. J Theor Biol 2011; 289:107-15. [PMID: 21872609 DOI: 10.1016/j.jtbi.2011.08.017] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2011] [Revised: 08/12/2011] [Accepted: 08/16/2011] [Indexed: 11/24/2022]
Abstract
Loop 5 (L5) is a conserved loop that projects from the α2-helix adjacent to the nucleotide site of all kinesin-family motors. L5 is critical to the function of the mitotic kinesin-5 family motors and is the binding site for several kinesin-5 inhibitors that are currently in clinical trials. Its conformational dynamics and its role in motor function are not fully understood. Our previous work using EPR spectroscopy suggested that L5 alters the nucleotide pocket conformation of the kinesin-5 motor Eg5 (Larson et al., 2010). EPR spectra of a spin-labeled nucleotide analog bound at the nucleotide site of Eg5 display a highly immobilized component that is absent if L5 is shortened or if the inhibitor STLC is added (Larson et al., 2010), which X-ray structures suggest stabilizes an L5 conformation pointing away from the nucleotide site. These data, coupled with the proximity of L5 to the nucleotide site suggest L5 could interact with a bound nucleotide, modulating function. Here we use molecular dynamics (MD) simulations of Eg5 to explore the interaction of L5 with the nucleotide site in greater detail. We performed MD simulations in which the L5-domain of the Eg5·ADP X-ray structure was manually deformed via backbone bond rotations. The L5-domain of Eg5 was sufficiently lengthy that portions of L5 could be located in proximity to bound ADP. The MD simulations evolved to thermodynamically stable structures at 300 K showing that L5 can interact directly with bound nucleotide with significant impingement on the ribose hydroxyls, consistent with the EPR spectroscopy results. Taken together, these data provide support for the hypothesis that L5 modulates Eg5 function via interaction with the nucleotide-binding site.
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Affiliation(s)
- Timothy D Harrington
- Voiland School of Chemical Engineering and Bioengineering, Washington State University, Pullman, WA 99164, USA
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Kaan HYK, Hackney DD, Kozielski F. The structure of the kinesin-1 motor-tail complex reveals the mechanism of autoinhibition. Science 2011; 333:883-5. [PMID: 21836017 PMCID: PMC3339660 DOI: 10.1126/science.1204824] [Citation(s) in RCA: 127] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
When not transporting cargo, kinesin-1 is autoinhibited by binding of a tail region to the motor domains, but the mechanism of inhibition is unclear. We report the crystal structure of a motor domain dimer in complex with its tail domain at 2.2 angstroms and compare it with a structure of the motor domain alone at 2.7 angstroms. These structures indicate that neither an induced conformational change nor steric blocking is the cause of inhibition. Instead, the tail cross-links the motor domains at a second position, in addition to the coiled coil. This "double lockdown," by cross-linking at two positions, prevents the movement of the motor domains that is needed to undock the neck linker and release adenosine diphosphate. This autoinhibition mechanism could extend to some other kinesins.
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Affiliation(s)
- Hung Yi Kristal Kaan
- The Beatson Institute for Cancer Research, Switchback Road, Bearsden, Glasgow G61 1BD, Scotland, UK
| | - David D. Hackney
- Department of Biological Sciences, Carnegie Mellon University, 4400 Fifth Avenue, Pittsburgh, PA 15213, USA
| | - Frank Kozielski
- The Beatson Institute for Cancer Research, Switchback Road, Bearsden, Glasgow G61 1BD, Scotland, UK
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