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Rusina P, Gandalipov E, Abdusheva Y, Panova M, Burdenkova A, Chaliy V, Brachs M, Stroganov O, Guzeeva K, Svitanko I, Shtil A, Novikov F. Imidazole-4-N-acetamide Derivatives as a Novel Scaffold for Selective Targeting of Cyclin Dependent Kinases. Cancers (Basel) 2023; 15:3766. [PMID: 37568583 PMCID: PMC10417023 DOI: 10.3390/cancers15153766] [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: 05/31/2023] [Revised: 07/16/2023] [Accepted: 07/21/2023] [Indexed: 08/13/2023] Open
Abstract
The rational design of cyclin-dependent protein kinase (CDK) inhibitors presumes the development of approaches for accurate prediction of selectivity and the activity of small molecular weight anticancer drug candidates. Aiming at attenuation of general toxicity of low selectivity compounds, we herein explored the new chemotype of imidazole-4-N-acetamide substituted derivatives of the pan-CDK inhibitor PHA-793887. Newly synthesized compounds 1-4 containing an aliphatic methyl group or aromatic radicals at the periphery of the scaffold were analyzed for the prediction of relative free energies of binding to CDK1, -2, -5, and -9 using a protocol based on non-equilibrium (NEQ) thermodynamics. This methodology allows for the demonstration of a good correlation between the calculated parameters of interaction of 1-4 with individual targets and the values of inhibitory potencies in in vitro kinase assays. We provide evidence in support of NEQ thermodynamics as a time sparing, precise, and productive approach for generating chemical inhibitors of clinically relevant anticancer targets.
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Affiliation(s)
- Polina Rusina
- Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, 47 Leninsky Avenue, 119991 Moscow, Russia
| | - Erik Gandalipov
- Laboratory of Solution Chemistry and Advanced Materials Technologies, ITMO University, 9 Lomonosov Street, 191002 Saint Petersburg, Russia
- PHARMENTERPRISES LLC, Skolkovo Innovation Center, 42 (1) Bolshoi Blvd., 143026 Moscow, Russia
| | - Yana Abdusheva
- Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, 47 Leninsky Avenue, 119991 Moscow, Russia
- PHARMENTERPRISES LLC, Skolkovo Innovation Center, 42 (1) Bolshoi Blvd., 143026 Moscow, Russia
- Higher School of Economics, National Research University, 20 Myasnitskaya Street, 101000 Moscow, Russia
| | - Maria Panova
- Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, 47 Leninsky Avenue, 119991 Moscow, Russia
- PHARMENTERPRISES LLC, Skolkovo Innovation Center, 42 (1) Bolshoi Blvd., 143026 Moscow, Russia
| | - Alexandra Burdenkova
- Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, 47 Leninsky Avenue, 119991 Moscow, Russia
- Higher School of Economics, National Research University, 20 Myasnitskaya Street, 101000 Moscow, Russia
| | - Vasiliy Chaliy
- Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, 47 Leninsky Avenue, 119991 Moscow, Russia
| | - Maria Brachs
- Treamid Therapeutics GmbH, c/o CoLaborator (Bayer), Building S141, Muellerstraβe 178, 13353 Berlin, Germany
| | | | - Ksenia Guzeeva
- Higher School of Economics, National Research University, 20 Myasnitskaya Street, 101000 Moscow, Russia
| | - Igor Svitanko
- Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, 47 Leninsky Avenue, 119991 Moscow, Russia
- Higher School of Economics, National Research University, 20 Myasnitskaya Street, 101000 Moscow, Russia
| | - Alexander Shtil
- Blokhin National Medical Research Center of Oncology, 24 Kashirskoye Shosse, 115522 Moscow, Russia
- Institute of Cyber Intelligence Systems, National Research Nuclear University MEPhI, 31 Kashirskoye Shosse, 115409 Moscow, Russia
| | - Fedor Novikov
- Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, 47 Leninsky Avenue, 119991 Moscow, Russia
- PHARMENTERPRISES LLC, Skolkovo Innovation Center, 42 (1) Bolshoi Blvd., 143026 Moscow, Russia
- Higher School of Economics, National Research University, 20 Myasnitskaya Street, 101000 Moscow, Russia
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2
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Wu X, Xie Y, Zhao K, Lu J. Targeting the super elongation complex for oncogenic transcription driven tumor malignancies: Progress in structure, mechanisms and small molecular inhibitor discovery. Adv Cancer Res 2023; 158:387-421. [PMID: 36990537 DOI: 10.1016/bs.acr.2022.12.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Oncogenic transcription activation is associated with tumor development and resistance derived from chemotherapy or target therapy. The super elongation complex (SEC) is an important complex regulating gene transcription and expression in metazoans closely related to physiological activities. In normal transcriptional regulation, SEC can trigger promoter escape, limit proteolytic degradation of transcription elongation factors and increase the synthesis of RNA polymerase II (POL II), and regulate many normal human genes to stimulate RNA elongation. Dysregulation of SEC accompanied by multiple transcription factors in cancer promotes rapid transcription of oncogenes and induce cancer development. In this review, we summarized recent progress in understanding the mechanisms of SEC in regulating normal transcription, and importantly its roles in cancer development. We also highlighted the discovery of SEC complex target related inhibitors and their potential applications in cancer treatment.
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Affiliation(s)
- Xinyu Wu
- School of Pharmacy, Key Laboratory of Molecular Pharmacology and Drug Evaluation (Yantai University), Ministry of Education, Collaborative Innovation Center of Advanced Drug Delivery System and Biotech Drugs in Universities of Shandong, Yantai University, Yantai, China; Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
| | - Yanqiu Xie
- School of Pharmacy, Key Laboratory of Molecular Pharmacology and Drug Evaluation (Yantai University), Ministry of Education, Collaborative Innovation Center of Advanced Drug Delivery System and Biotech Drugs in Universities of Shandong, Yantai University, Yantai, China; Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
| | - Kehao Zhao
- School of Pharmacy, Key Laboratory of Molecular Pharmacology and Drug Evaluation (Yantai University), Ministry of Education, Collaborative Innovation Center of Advanced Drug Delivery System and Biotech Drugs in Universities of Shandong, Yantai University, Yantai, China.
| | - Jing Lu
- School of Pharmacy, Key Laboratory of Molecular Pharmacology and Drug Evaluation (Yantai University), Ministry of Education, Collaborative Innovation Center of Advanced Drug Delivery System and Biotech Drugs in Universities of Shandong, Yantai University, Yantai, China.
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3
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Aoi Y, Takahashi YH, Shah AP, Iwanaszko M, Rendleman EJ, Khan NH, Cho BK, Goo YA, Ganesan S, Kelleher NL, Shilatifard A. SPT5 stabilization of promoter-proximal RNA polymerase II. Mol Cell 2021; 81:4413-4424.e5. [PMID: 34480849 PMCID: PMC8687145 DOI: 10.1016/j.molcel.2021.08.006] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Revised: 06/28/2021] [Accepted: 08/03/2021] [Indexed: 01/02/2023]
Abstract
Based on in vitro studies, it has been demonstrated that the DSIF complex, composed of SPT4 and SPT5, regulates the elongation stage of transcription catalyzed by RNA polymerase II (RNA Pol II). The precise cellular function of SPT5 is not clear, because conventional gene depletion strategies for SPT5 result in loss of cellular viability. Using an acute inducible protein depletion strategy to circumvent this issue, we report that SPT5 loss triggers the ubiquitination and proteasomal degradation of the core RNA Pol II subunit RPB1, a process that we show to be evolutionarily conserved from yeast to human cells. RPB1 degradation requires the E3 ligase Cullin 3, the unfoldase VCP/p97, and a novel form of CDK9 kinase complex. Our study demonstrates that SPT5 stabilizes RNA Pol II specifically at promoter-proximal regions, permitting RNA Pol II release from promoters into gene bodies and providing mechanistic insight into the cellular function of SPT5 in safeguarding accurate gene expression.
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Affiliation(s)
- Yuki Aoi
- Simpson Querrey Institute for Epigenetics, Department of Biochemistry and Molecular Genetics Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Yoh-Hei Takahashi
- Simpson Querrey Institute for Epigenetics, Department of Biochemistry and Molecular Genetics Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Avani P Shah
- Simpson Querrey Institute for Epigenetics, Department of Biochemistry and Molecular Genetics Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Marta Iwanaszko
- Simpson Querrey Institute for Epigenetics, Department of Biochemistry and Molecular Genetics Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Emily J Rendleman
- Simpson Querrey Institute for Epigenetics, Department of Biochemistry and Molecular Genetics Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Nabiha H Khan
- Simpson Querrey Institute for Epigenetics, Department of Biochemistry and Molecular Genetics Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Byoung-Kyu Cho
- Simpson Querrey Institute for Epigenetics, Department of Biochemistry and Molecular Genetics Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA; Proteomics Center of Excellence, Northwestern University, Evanston, IL 60611, USA
| | - Young Ah Goo
- Simpson Querrey Institute for Epigenetics, Department of Biochemistry and Molecular Genetics Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA; Proteomics Center of Excellence, Northwestern University, Evanston, IL 60611, USA
| | - Sheetal Ganesan
- Simpson Querrey Institute for Epigenetics, Department of Biochemistry and Molecular Genetics Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Neil L Kelleher
- Simpson Querrey Institute for Epigenetics, Department of Biochemistry and Molecular Genetics Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA; Proteomics Center of Excellence, Northwestern University, Evanston, IL 60611, USA
| | - Ali Shilatifard
- Simpson Querrey Institute for Epigenetics, Department of Biochemistry and Molecular Genetics Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA.
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4
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Freeman-Cook K, Hoffman RL, Miller N, Almaden J, Chionis J, Zhang Q, Eisele K, Liu C, Zhang C, Huser N, Nguyen L, Costa-Jones C, Niessen S, Carelli J, Lapek J, Weinrich SL, Wei P, McMillan E, Wilson E, Wang TS, McTigue M, Ferre RA, He YA, Ninkovic S, Behenna D, Tran KT, Sutton S, Nagata A, Ornelas MA, Kephart SE, Zehnder LR, Murray B, Xu M, Solowiej JE, Visswanathan R, Boras B, Looper D, Lee N, Bienkowska JR, Zhu Z, Kan Z, Ding Y, Mu XJ, Oderup C, Salek-Ardakani S, White MA, VanArsdale T, Dann SG. Expanding control of the tumor cell cycle with a CDK2/4/6 inhibitor. Cancer Cell 2021; 39:1404-1421.e11. [PMID: 34520734 DOI: 10.1016/j.ccell.2021.08.009] [Citation(s) in RCA: 73] [Impact Index Per Article: 24.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Revised: 06/03/2021] [Accepted: 08/17/2021] [Indexed: 12/12/2022]
Abstract
The CDK4/6 inhibitor, palbociclib (PAL), significantly improves progression-free survival in HR+/HER2- breast cancer when combined with anti-hormonals. We sought to discover PAL resistance mechanisms in preclinical models and through analysis of clinical transcriptome specimens, which coalesced on induction of MYC oncogene and Cyclin E/CDK2 activity. We propose that targeting the G1 kinases CDK2, CDK4, and CDK6 with a small-molecule overcomes resistance to CDK4/6 inhibition. We describe the pharmacodynamics and efficacy of PF-06873600 (PF3600), a pyridopyrimidine with potent inhibition of CDK2/4/6 activity and efficacy in multiple in vivo tumor models. Together with the clinical analysis, MYC activity predicts (PF3600) efficacy across multiple cell lineages. Finally, we find that CDK2/4/6 inhibition does not compromise tumor-specific immune checkpoint blockade responses in syngeneic models. We anticipate that (PF3600), currently in phase 1 clinical trials, offers a therapeutic option to cancer patients in whom CDK4/6 inhibition is insufficient to alter disease progression.
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Affiliation(s)
- Kevin Freeman-Cook
- Pfizer Global Research and Development La Jolla, 10770 Science Center Drive, San Diego, CA 92121, USA
| | - Robert L Hoffman
- Pfizer Global Research and Development La Jolla, 10770 Science Center Drive, San Diego, CA 92121, USA
| | - Nichol Miller
- Pfizer Global Research and Development La Jolla, 10770 Science Center Drive, San Diego, CA 92121, USA
| | - Jonathan Almaden
- Pfizer Global Research and Development La Jolla, 10770 Science Center Drive, San Diego, CA 92121, USA
| | - John Chionis
- Pfizer Global Research and Development La Jolla, 10770 Science Center Drive, San Diego, CA 92121, USA
| | - Qin Zhang
- Pfizer Global Research and Development La Jolla, 10770 Science Center Drive, San Diego, CA 92121, USA
| | - Koleen Eisele
- Pfizer Global Research and Development La Jolla, 10770 Science Center Drive, San Diego, CA 92121, USA
| | - Chaoting Liu
- Pfizer Global Research and Development La Jolla, 10770 Science Center Drive, San Diego, CA 92121, USA
| | - Cathy Zhang
- Pfizer Global Research and Development La Jolla, 10770 Science Center Drive, San Diego, CA 92121, USA
| | - Nanni Huser
- Pfizer Global Research and Development La Jolla, 10770 Science Center Drive, San Diego, CA 92121, USA
| | - Lisa Nguyen
- Pfizer Global Research and Development La Jolla, 10770 Science Center Drive, San Diego, CA 92121, USA
| | - Cinthia Costa-Jones
- Pfizer Global Research and Development La Jolla, 10770 Science Center Drive, San Diego, CA 92121, USA
| | - Sherry Niessen
- Pfizer Global Research and Development La Jolla, 10770 Science Center Drive, San Diego, CA 92121, USA
| | - Jordan Carelli
- Pfizer Global Research and Development La Jolla, 10770 Science Center Drive, San Diego, CA 92121, USA
| | - John Lapek
- Pfizer Global Research and Development La Jolla, 10770 Science Center Drive, San Diego, CA 92121, USA
| | - Scott L Weinrich
- Pfizer Global Research and Development La Jolla, 10770 Science Center Drive, San Diego, CA 92121, USA
| | - Ping Wei
- Pfizer Global Research and Development La Jolla, 10770 Science Center Drive, San Diego, CA 92121, USA
| | - Elizabeth McMillan
- Pfizer Global Research and Development La Jolla, 10770 Science Center Drive, San Diego, CA 92121, USA
| | - Elizabeth Wilson
- Pfizer Global Research and Development La Jolla, 10770 Science Center Drive, San Diego, CA 92121, USA
| | - Tim S Wang
- Pfizer Global Research and Development La Jolla, 10770 Science Center Drive, San Diego, CA 92121, USA
| | - Michele McTigue
- Pfizer Global Research and Development La Jolla, 10770 Science Center Drive, San Diego, CA 92121, USA
| | - Rose Ann Ferre
- Pfizer Global Research and Development La Jolla, 10770 Science Center Drive, San Diego, CA 92121, USA
| | - You-Ai He
- Pfizer Global Research and Development La Jolla, 10770 Science Center Drive, San Diego, CA 92121, USA
| | - Sacha Ninkovic
- Pfizer Global Research and Development La Jolla, 10770 Science Center Drive, San Diego, CA 92121, USA
| | - Douglas Behenna
- Pfizer Global Research and Development La Jolla, 10770 Science Center Drive, San Diego, CA 92121, USA
| | - Khanh T Tran
- Pfizer Global Research and Development La Jolla, 10770 Science Center Drive, San Diego, CA 92121, USA
| | - Scott Sutton
- Pfizer Global Research and Development La Jolla, 10770 Science Center Drive, San Diego, CA 92121, USA
| | - Asako Nagata
- Pfizer Global Research and Development La Jolla, 10770 Science Center Drive, San Diego, CA 92121, USA
| | - Martha A Ornelas
- Pfizer Global Research and Development La Jolla, 10770 Science Center Drive, San Diego, CA 92121, USA
| | - Susan E Kephart
- Pfizer Global Research and Development La Jolla, 10770 Science Center Drive, San Diego, CA 92121, USA
| | - Luke R Zehnder
- Pfizer Global Research and Development La Jolla, 10770 Science Center Drive, San Diego, CA 92121, USA
| | - Brion Murray
- Pfizer Global Research and Development La Jolla, 10770 Science Center Drive, San Diego, CA 92121, USA
| | - Meirong Xu
- Pfizer Global Research and Development La Jolla, 10770 Science Center Drive, San Diego, CA 92121, USA
| | - James E Solowiej
- Pfizer Global Research and Development La Jolla, 10770 Science Center Drive, San Diego, CA 92121, USA
| | - Ravi Visswanathan
- Pfizer Global Research and Development La Jolla, 10770 Science Center Drive, San Diego, CA 92121, USA
| | - Britton Boras
- Pfizer Global Research and Development La Jolla, 10770 Science Center Drive, San Diego, CA 92121, USA
| | - David Looper
- Pfizer Global Research and Development La Jolla, 10770 Science Center Drive, San Diego, CA 92121, USA
| | - Nathan Lee
- Pfizer Global Research and Development La Jolla, 10770 Science Center Drive, San Diego, CA 92121, USA
| | - Jadwiga R Bienkowska
- Pfizer Global Research and Development La Jolla, 10770 Science Center Drive, San Diego, CA 92121, USA
| | - Zhou Zhu
- Pfizer Global Research and Development La Jolla, 10770 Science Center Drive, San Diego, CA 92121, USA
| | - Zhengyan Kan
- Pfizer Global Research and Development La Jolla, 10770 Science Center Drive, San Diego, CA 92121, USA
| | - Ying Ding
- Pfizer Global Research and Development La Jolla, 10770 Science Center Drive, San Diego, CA 92121, USA
| | - Xinmeng Jasmine Mu
- Pfizer Global Research and Development La Jolla, 10770 Science Center Drive, San Diego, CA 92121, USA
| | - Cecilia Oderup
- Pfizer Global Research and Development La Jolla, 10770 Science Center Drive, San Diego, CA 92121, USA
| | - Shahram Salek-Ardakani
- Pfizer Global Research and Development La Jolla, 10770 Science Center Drive, San Diego, CA 92121, USA
| | - Michael A White
- Pfizer Global Research and Development La Jolla, 10770 Science Center Drive, San Diego, CA 92121, USA
| | - Todd VanArsdale
- Pfizer Global Research and Development La Jolla, 10770 Science Center Drive, San Diego, CA 92121, USA.
| | - Stephen G Dann
- Pfizer Global Research and Development La Jolla, 10770 Science Center Drive, San Diego, CA 92121, USA.
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Edwards DS, Maganti R, Tanksley JP, Luo J, Park JJH, Balkanska-Sinclair E, Ling J, Floyd SR. BRD4 Prevents R-Loop Formation and Transcription-Replication Conflicts by Ensuring Efficient Transcription Elongation. Cell Rep 2021; 32:108166. [PMID: 32966794 PMCID: PMC7507985 DOI: 10.1016/j.celrep.2020.108166] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Revised: 04/13/2020] [Accepted: 08/27/2020] [Indexed: 12/29/2022] Open
Abstract
Effective spatio-temporal control of transcription and replication during S-phase is paramount to maintaining genomic integrity and cell survival. Dysregulation of these systems can lead to conflicts between the transcription and replication machinery, causing DNA damage and cell death. BRD4 allows efficient transcriptional elongation by stimulating phosphorylation of RNA polymerase II (RNAPII). We report that bromodomain and extra-terminal domain (BET) protein loss of function (LOF) causes RNAPII pausing on the chromatin and DNA damage affecting cells in S-phase. This persistent RNAPII-dependent pausing leads to an accumulation of RNA:DNA hybrids (R-loops) at sites of BRD4 occupancy, leading to transcription-replication conflicts (TRCs), DNA damage, and cell death. Finally, our data show that the BRD4 C-terminal domain, which interacts with P-TEFb, is required to prevent R-loop formation and DNA damage caused by BET protein LOF.
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Affiliation(s)
- Drake S Edwards
- Medical Scientist Training Program, Duke University School of Medicine, Durham, NC 27710, USA; Department of Pharmacology and Cancer Biology, Duke University School of Medicine, Durham, NC 27710, USA; Department of Radiation Oncology, Duke University School of Medicine, Durham, NC 27710, USA
| | | | - Jarred P Tanksley
- Department of Radiation Oncology, Duke University School of Medicine, Durham, NC 27710, USA
| | - Jie Luo
- Department of Radiation Oncology, Duke University School of Medicine, Durham, NC 27710, USA
| | - James J H Park
- Department of Radiation Oncology, Duke University School of Medicine, Durham, NC 27710, USA
| | | | | | - Scott R Floyd
- Department of Pharmacology and Cancer Biology, Duke University School of Medicine, Durham, NC 27710, USA; Department of Radiation Oncology, Duke University School of Medicine, Durham, NC 27710, USA.
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6
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Broni E, Kwofie SK, Asiedu SO, Miller WA, Wilson MD. A Molecular Modeling Approach to Identify Potential Antileishmanial Compounds Against the Cell Division Cycle (cdc)-2-Related Kinase 12 (CRK12) Receptor of Leishmania donovani. Biomolecules 2021; 11:458. [PMID: 33803906 PMCID: PMC8003136 DOI: 10.3390/biom11030458] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2021] [Revised: 03/12/2021] [Accepted: 03/14/2021] [Indexed: 12/11/2022] Open
Abstract
The huge burden of leishmaniasis caused by the trypanosomatid protozoan parasite Leishmania is well known. This illness was included in the list of neglected tropical diseases targeted for elimination by the World Health Organization. However, the increasing evidence of resistance to existing antimonial drugs has made the eradication of the disease difficult to achieve, thus warranting the search for new drug targets. We report here studies that used computational methods to identify inhibitors of receptors from natural products. The cell division cycle-2-related kinase 12 (CRK12) receptor is a plausible drug target against Leishmania donovani. This study modelled the 3D molecular structure of the L. donovani CRK12 (LdCRK12) and screened for small molecules with potential inhibitory activity from African flora. An integrated library of 7722 African natural product-derived compounds and known inhibitors were screened against the LdCRK12 using AutoDock Vina after performing energy minimization with GROMACS 2018. Four natural products, namely sesamin (NANPDB1649), methyl ellagic acid (NANPDB1406), stylopine (NANPDB2581), and sennecicannabine (NANPDB6446) were found to be potential LdCRK12 inhibitory molecules. The molecular docking studies revealed two compounds NANPDB1406 and NANPDB2581 with binding affinities of -9.5 and -9.2 kcal/mol, respectively, against LdCRK12 which were higher than those of the known inhibitors and drugs, including GSK3186899, amphotericin B, miltefosine, and paromomycin. All the four compounds were predicted to have inhibitory constant (Ki) values ranging from 0.108 to 0.587 μM. NANPDB2581, NANPDB1649 and NANPDB1406 were also predicted as antileishmanial with Pa and Pi values of 0.415 and 0.043, 0.391 and 0.052, and 0.351 and 0.071, respectively. Molecular dynamics simulations coupled with molecular mechanics Poisson-Boltzmann surface area (MM/PBSA) computations reinforced their good binding mechanisms. Most compounds were observed to bind in the ATP binding pocket of the kinase domain. Lys488 was predicted as a key residue critical for ligand binding in the ATP binding pocket of the LdCRK12. The molecules were pharmacologically profiled as druglike with inconsequential toxicity. The identified molecules have scaffolds that could form the backbone for fragment-based drug design of novel leishmanicides but warrant further studies to evaluate their therapeutic potential.
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Affiliation(s)
- Emmanuel Broni
- Department of Biomedical Engineering, School of Engineering Sciences, College of Basic & Applied Sciences, University of Ghana, Legon, Accra LG 77, Ghana;
| | - Samuel K. Kwofie
- Department of Biomedical Engineering, School of Engineering Sciences, College of Basic & Applied Sciences, University of Ghana, Legon, Accra LG 77, Ghana;
- West African Center for Cell Biology of Infectious Pathogens, Department of Biochemistry, Cell and Molecular Biology, College of Basic and Applied Sciences, University of Ghana, Legon, Accra LG 54, Ghana
| | - Seth O. Asiedu
- Department of Parasitology, Noguchi Memorial Institute for Medical Research (NMIMR), College of Health Sciences (CHS), University of Ghana, Legon, Accra LG 581, Ghana; (S.O.A.); (M.D.W.)
| | - Whelton A. Miller
- Department of Medicine, Loyola University Medical Center, Maywood, IL 60153, USA;
- Department of Molecular Pharmacology and Neuroscience, Loyola University Medical Center, Maywood, IL 60153, USA
- Department of Chemical and Biomolecular Engineering, School of Engineering and Applied Science, University of Pennsylvania, Philadelphia, IL 19104, USA
| | - Michael D. Wilson
- Department of Parasitology, Noguchi Memorial Institute for Medical Research (NMIMR), College of Health Sciences (CHS), University of Ghana, Legon, Accra LG 581, Ghana; (S.O.A.); (M.D.W.)
- Department of Medicine, Loyola University Medical Center, Maywood, IL 60153, USA;
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7
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Abstract
The fundamental processes of cell-cycle regulation and transcription are linked by the heterotrimeric CDK-activating kinase (CAK) complex. We solved the crystal structure of the active CAK complex and provide a molecular rationale for CAK activation, regulation, and substrate recognition. Our data thus highly advance our understanding of this essential factor which is also a proven target for cancer therapy. Cyclin-dependent kinase 7 (CDK7), Cyclin H, and the RING-finger protein MAT1 form the heterotrimeric CDK-activating kinase (CAK) complex which is vital for transcription and cell-cycle control. When associated with the general transcription factor II H (TFIIH) it activates RNA polymerase II by hyperphosphorylation of its C-terminal domain (CTD). In the absence of TFIIH the trimeric complex phosphorylates the T-loop of CDKs that control cell-cycle progression. CAK holds a special position among the CDK branch due to this dual activity and the dependence on two proteins for activation. We solved the structure of the CAK complex from the model organism Chaetomium thermophilum at 2.6-Å resolution. Our structure reveals an intricate network of interactions between CDK7 and its two binding partners MAT1 and Cyclin H, providing a structural basis for the mechanism of CDK7 activation and CAK activity regulation. In vitro activity measurements and functional mutagenesis show that CDK7 activation can occur independent of T-loop phosphorylation and is thus exclusively MAT1-dependent by positioning the CDK7 T-loop in its active conformation.
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8
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Wood DJ, Endicott JA. Structural insights into the functional diversity of the CDK-cyclin family. Open Biol 2019; 8:rsob.180112. [PMID: 30185601 PMCID: PMC6170502 DOI: 10.1098/rsob.180112] [Citation(s) in RCA: 141] [Impact Index Per Article: 28.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2018] [Accepted: 08/10/2018] [Indexed: 12/17/2022] Open
Abstract
Since their characterization as conserved modules that regulate progression through the eukaryotic cell cycle, cyclin-dependent protein kinases (CDKs) in higher eukaryotic cells are now also emerging as significant regulators of transcription, metabolism and cell differentiation. The cyclins, though originally characterized as CDK partners, also have CDK-independent roles that include the regulation of DNA damage repair and transcriptional programmes that direct cell differentiation, apoptosis and metabolic flux. This review compares the structures of the members of the CDK and cyclin families determined by X-ray crystallography, and considers what mechanistic insights they provide to guide functional studies and distinguish CDK- and cyclin-specific activities. Aberrant CDK activity is a hallmark of a number of diseases, and structural studies can provide important insights to identify novel routes to therapy.
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Affiliation(s)
- Daniel J Wood
- Newcastle Cancer Centre, Northern Institute for Cancer Research, Medical School, Newcastle University, Paul O'Gorman Building, Framlington Place, Newcastle upon Tyne NE2 4HH, UK
| | - Jane A Endicott
- Newcastle Cancer Centre, Northern Institute for Cancer Research, Medical School, Newcastle University, Paul O'Gorman Building, Framlington Place, Newcastle upon Tyne NE2 4HH, UK
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9
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Ma X, Yang T, Luo Y, Wu L, Jiang Y, Song Z, Pan T, Liu B, Liu G, Liu J, Yu F, He Z, Zhang W, Yang J, Liang L, Guan Y, Zhang X, Li L, Cai W, Tang X, Gao S, Deng K, Zhang H. TRIM28 promotes HIV-1 latency by SUMOylating CDK9 and inhibiting P-TEFb. eLife 2019; 8:42426. [PMID: 30652970 PMCID: PMC6361614 DOI: 10.7554/elife.42426] [Citation(s) in RCA: 65] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2018] [Accepted: 01/16/2019] [Indexed: 12/19/2022] Open
Abstract
Comprehensively elucidating the molecular mechanisms of human immunodeficiency virus type 1 (HIV-1) latency is a priority to achieve a functional cure. As current 'shock' agents failed to efficiently reactivate the latent reservoir, it is important to discover new targets for developing more efficient latency-reversing agents (LRAs). Here, we found that TRIM28 potently suppresses HIV-1 expression by utilizing both SUMO E3 ligase activity and epigenetic adaptor function. Through global site-specific SUMO-MS study and serial SUMOylation assays, we identified that P-TEFb catalytic subunit CDK9 is significantly SUMOylated by TRIM28 with SUMO4. The Lys44, Lys56 and Lys68 residues on CDK9 are SUMOylated by TRIM28, which inhibits CDK9 kinase activity or prevents P-TEFb assembly by directly blocking the interaction between CDK9 and Cyclin T1, subsequently inhibits viral transcription and contributes to HIV-1 latency. The manipulation of TRIM28 and its consequent SUMOylation pathway could be the target for developing LRAs. The human immunodeficiency virus-1, or HIV-1, infects certain human cells, including white blood cells. One reason the infection is incurable is because the virus can integrate its genetic information into its host, and essentially ‘sleep’ within the host cell, a process called latency. This helps to hide HIV-1 from the immune system and stops it getting destroyed. Latency represents a critical challenge in treating and curing HIV-1. One proposed cure for HIV-1 involves ‘shocking’ the viruses out of latency so that they can be eliminated. Applying this so-called shock and kill approach means scientists need to understand more about how latency is maintained. Previous evidence shows that latency requires proteins known as histone deacetylases and histone methyltransferases. Certain gene-silencing proteins called transcription suppressors are also involved. Ma et al. have now examined latent HIV-1 in several kinds of human cells grown in the laboratory. The cells were modified to make certain proteins at much lower levels than normal. The experiments showed that the loss of a protein called TRIM28 ‘wakes up’ latent HIV-1. TRIM28 attaches chemical marks called SUMOylations to gene regulators in the cell. These SUMOylations restrict the activity of HIV-1’s genes, which is important to maintain latency. Specifically, TRIM28 adds SUMOylations to a protein named CDK9 at three key positions. Reducing the levels of TRIM28 made it easier to shock many HIV-1 in infected cells out of latency. With further investigation, targeting TRIM28 may one day be used to treat HIV-1 infection through a shock and kill method.
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Affiliation(s)
- Xiancai Ma
- Institute of Human Virology, Sun Yat-sen University, Guangzhou, China.,Key Laboratory of Tropical Disease Control of Ministry of Education, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Tao Yang
- Institute of Human Virology, Sun Yat-sen University, Guangzhou, China.,Key Laboratory of Tropical Disease Control of Ministry of Education, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Yuewen Luo
- Institute of Human Virology, Sun Yat-sen University, Guangzhou, China.,Key Laboratory of Tropical Disease Control of Ministry of Education, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Liyang Wu
- Institute of Human Virology, Sun Yat-sen University, Guangzhou, China.,Key Laboratory of Tropical Disease Control of Ministry of Education, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Yawen Jiang
- Institute of Human Virology, Sun Yat-sen University, Guangzhou, China.,Key Laboratory of Tropical Disease Control of Ministry of Education, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Zheng Song
- Institute of Human Virology, Sun Yat-sen University, Guangzhou, China.,Key Laboratory of Tropical Disease Control of Ministry of Education, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Ting Pan
- Institute of Human Virology, Sun Yat-sen University, Guangzhou, China.,Key Laboratory of Tropical Disease Control of Ministry of Education, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Bingfeng Liu
- Institute of Human Virology, Sun Yat-sen University, Guangzhou, China.,Key Laboratory of Tropical Disease Control of Ministry of Education, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Guangyan Liu
- College of Basic Medical Sciences, Shenyang Medical College, Shenyang, China
| | - Jun Liu
- Institute of Human Virology, Sun Yat-sen University, Guangzhou, China.,Key Laboratory of Tropical Disease Control of Ministry of Education, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Fei Yu
- Key Laboratory of Tropical Disease Control of Ministry of Education, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Zhangping He
- Key Laboratory of Tropical Disease Control of Ministry of Education, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Wanying Zhang
- Key Laboratory of Tropical Disease Control of Ministry of Education, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Jinyu Yang
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Liting Liang
- Key Laboratory of Tropical Disease Control of Ministry of Education, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Yuanjun Guan
- Core Laboratory Platform for Medical Science, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Xu Zhang
- Key Laboratory of Tropical Disease Control of Ministry of Education, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Linghua Li
- Department of Infectious Diseases, Guangzhou Eighth People's Hospital, Guangzhou, China
| | - Weiping Cai
- Department of Infectious Diseases, Guangzhou Eighth People's Hospital, Guangzhou, China
| | - Xiaoping Tang
- Department of Infectious Diseases, Guangzhou Eighth People's Hospital, Guangzhou, China
| | - Song Gao
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Kai Deng
- Key Laboratory of Tropical Disease Control of Ministry of Education, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Hui Zhang
- Key Laboratory of Tropical Disease Control of Ministry of Education, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
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10
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Cheng W, Yang Z, Wang S, Li Y, Wei H, Tian X, Kan Q. Recent development of CDK inhibitors: An overview of CDK/inhibitor co-crystal structures. Eur J Med Chem 2019; 164:615-639. [PMID: 30639897 DOI: 10.1016/j.ejmech.2019.01.003] [Citation(s) in RCA: 57] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2018] [Revised: 12/31/2018] [Accepted: 01/02/2019] [Indexed: 02/06/2023]
Abstract
The cyclin-dependent protein kinases (CDKs) are protein-serine/threonine kinases that display crucial effects in regulation of cell cycle and transcription. While the excessive expression of CDKs is intimate related to the development of diseases including cancers, which provides opportunities for disease treatment. A large number of small molecules are explored targeting CDKs. CDK/inhibitor co-crystal structures play an important role during the exploration of inhibitors. So far nine kinds of CDK/inhibitor co-crystals have been determined, they account for the highest proportion among the Protein Data Bank (PDB) deposited crystal structures. Herein, we review main co-crystals of CDKs in complex with corresponding inhibitors reported in recent years, focusing our attention on the binding models and the pharmacological activities of inhibitors.
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Affiliation(s)
- Weiyan Cheng
- Department of Pharmacy, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, China; Henan Key Laboratory of Precision Clinical Pharmacy, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, China
| | - Zhiheng Yang
- Department of Pharmacy, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, China; Henan Key Laboratory of Precision Clinical Pharmacy, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, China
| | - Suhua Wang
- Department of Pharmacy, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, China; Henan Key Laboratory of Precision Clinical Pharmacy, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, China
| | - Ying Li
- Department of Pharmacy, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, China; Henan Key Laboratory of Precision Clinical Pharmacy, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, China
| | - Han Wei
- Department of Pharmacy, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, China; Henan Key Laboratory of Precision Clinical Pharmacy, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, China
| | - Xin Tian
- Department of Pharmacy, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, China; Henan Key Laboratory of Precision Clinical Pharmacy, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, China.
| | - Quancheng Kan
- Department of Pharmacy, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, China; Henan Key Laboratory of Precision Clinical Pharmacy, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, China.
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11
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Ito M, Tanaka T, Toita A, Uchiyama N, Kokubo H, Morishita N, Klein MG, Zou H, Murakami M, Kondo M, Sameshima T, Araki S, Endo S, Kawamoto T, Morin GB, Aparicio SA, Nakanishi A, Maezaki H, Imaeda Y. Discovery of 3-Benzyl-1-( trans-4-((5-cyanopyridin-2-yl)amino)cyclohexyl)-1-arylurea Derivatives as Novel and Selective Cyclin-Dependent Kinase 12 (CDK12) Inhibitors. J Med Chem 2018; 61:7710-7728. [PMID: 30067358 DOI: 10.1021/acs.jmedchem.8b00683] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Cyclin-dependent kinase 12 (CDK12) plays a key role in the coordination of transcription with elongation and mRNA processing. CDK12 mutations found in tumors and CDK12 inhibition sensitize cancer cells to DNA-damaging reagents and DNA-repair inhibitors. This suggests that CDK12 inhibitors are potential therapeutics for cancer that may cause synthetic lethality. Here, we report the discovery of 3-benzyl-1-( trans-4-((5-cyanopyridin-2-yl)amino)cyclohexyl)-1-arylurea derivatives as novel and selective CDK12 inhibitors. Structure-activity relationship studies of a HTS hit, structure-based drug design, and conformation-oriented design using the Cambridge Structural Database afforded the optimized compound 2, which exhibited not only potent CDK12 (and CDK13) inhibitory activity and excellent selectivity but also good physicochemical properties. Furthermore, 2 inhibited the phosphorylation of Ser2 in the C-terminal domain of RNA polymerase II and induced growth inhibition in SK-BR-3 cells. Therefore, 2 represents an excellent chemical probe for functional studies of CDK12 and could be a promising lead compound for drug discovery.
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Affiliation(s)
- Masahiro Ito
- Pharmaceutical Research Division , Takeda Pharmaceutical Company Limited , 26-1, Muraoka-Higashi 2-chome , Fujisawa , Kanagawa 251-8555 , Japan
| | - Toshio Tanaka
- Pharmaceutical Research Division , Takeda Pharmaceutical Company Limited , 26-1, Muraoka-Higashi 2-chome , Fujisawa , Kanagawa 251-8555 , Japan
| | - Akinori Toita
- Pharmaceutical Research Division , Takeda Pharmaceutical Company Limited , 26-1, Muraoka-Higashi 2-chome , Fujisawa , Kanagawa 251-8555 , Japan
| | - Noriko Uchiyama
- Pharmaceutical Research Division , Takeda Pharmaceutical Company Limited , 26-1, Muraoka-Higashi 2-chome , Fujisawa , Kanagawa 251-8555 , Japan
| | - Hironori Kokubo
- Pharmaceutical Research Division , Takeda Pharmaceutical Company Limited , 26-1, Muraoka-Higashi 2-chome , Fujisawa , Kanagawa 251-8555 , Japan
| | - Nao Morishita
- Pharmaceutical Research Division , Takeda Pharmaceutical Company Limited , 26-1, Muraoka-Higashi 2-chome , Fujisawa , Kanagawa 251-8555 , Japan
| | - Michael G Klein
- Department of Structural Biology , Takeda California Inc. , 10410 Science Center Drive , San Diego , California 92121 , United States
| | - Hua Zou
- Department of Structural Biology , Takeda California Inc. , 10410 Science Center Drive , San Diego , California 92121 , United States
| | - Morio Murakami
- Pharmaceutical Research Division , Takeda Pharmaceutical Company Limited , 26-1, Muraoka-Higashi 2-chome , Fujisawa , Kanagawa 251-8555 , Japan
| | - Mitsuyo Kondo
- Pharmaceutical Research Division , Takeda Pharmaceutical Company Limited , 26-1, Muraoka-Higashi 2-chome , Fujisawa , Kanagawa 251-8555 , Japan
| | - Tomoya Sameshima
- Pharmaceutical Research Division , Takeda Pharmaceutical Company Limited , 26-1, Muraoka-Higashi 2-chome , Fujisawa , Kanagawa 251-8555 , Japan
| | - Shinsuke Araki
- Pharmaceutical Research Division , Takeda Pharmaceutical Company Limited , 26-1, Muraoka-Higashi 2-chome , Fujisawa , Kanagawa 251-8555 , Japan
| | - Satoshi Endo
- Pharmaceutical Research Division , Takeda Pharmaceutical Company Limited , 26-1, Muraoka-Higashi 2-chome , Fujisawa , Kanagawa 251-8555 , Japan
| | - Tomohiro Kawamoto
- Pharmaceutical Research Division , Takeda Pharmaceutical Company Limited , 26-1, Muraoka-Higashi 2-chome , Fujisawa , Kanagawa 251-8555 , Japan
| | - Gregg B Morin
- Genome Sciences Centre , British Columbia Cancer Agency , 675 West 10th Avenue , Vancouver , British Columbia V5Z 1L3 , Canada.,Department of Medical Genetics , University of British Columbia , Vancouver , British Columbia V6H 3N1 , Canada
| | - Samuel A Aparicio
- Department of Molecular Oncology , British Columbia Cancer Agency , 675 West 10th Avenue , Vancouver , British Columbia V5Z 1L3 , Canada
| | - Atsushi Nakanishi
- Pharmaceutical Research Division , Takeda Pharmaceutical Company Limited , 26-1, Muraoka-Higashi 2-chome , Fujisawa , Kanagawa 251-8555 , Japan
| | - Hironobu Maezaki
- Pharmaceutical Research Division , Takeda Pharmaceutical Company Limited , 26-1, Muraoka-Higashi 2-chome , Fujisawa , Kanagawa 251-8555 , Japan
| | - Yasuhiro Imaeda
- Pharmaceutical Research Division , Takeda Pharmaceutical Company Limited , 26-1, Muraoka-Higashi 2-chome , Fujisawa , Kanagawa 251-8555 , Japan
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12
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Martin MP, Endicott JA, Noble MEM. Structure-based discovery of cyclin-dependent protein kinase inhibitors. Essays Biochem 2017; 61:439-452. [PMID: 29118092 PMCID: PMC6248306 DOI: 10.1042/ebc20170040] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2017] [Revised: 09/24/2017] [Accepted: 09/25/2017] [Indexed: 01/02/2023]
Abstract
The cell fate-determining roles played by members of the cyclin-dependent protein kinase (CDK) family explain why their dysregulation can promote proliferative diseases, and identify them as potential targets for drug discovery in oncology and beyond. After many years of research, the first efficacious CDK inhibitors have now been registered for clinical use in a defined segment of breast cancer. Research is underway to identify inhibitors with appropriate CDK-inhibitory profiles to recapitulate this success in other disease settings. Here, we review the structural data that illustrate the interactions and properties that confer upon inhibitors affinity and/or selectivity toward different CDK family members. We conclude that where CDK inhibitors display selectivity, that selectivity derives from exploiting active site sequence peculiarities and/or from the capacity of the target CDK(s) to access conformations compatible with optimizing inhibitor-target interactions.
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Affiliation(s)
- Mathew P Martin
- Newcastle Cancer Centre, Northern Institute for Cancer Research, Paul O'Gorman Building, Medical School, Newcastle University, Framlington Place, Newcastle upon Tyne NE2 4HH, U.K
| | - Jane A Endicott
- Newcastle Cancer Centre, Northern Institute for Cancer Research, Paul O'Gorman Building, Medical School, Newcastle University, Framlington Place, Newcastle upon Tyne NE2 4HH, U.K
| | - Martin E M Noble
- Newcastle Cancer Centre, Northern Institute for Cancer Research, Paul O'Gorman Building, Medical School, Newcastle University, Framlington Place, Newcastle upon Tyne NE2 4HH, U.K.
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13
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Stetz G, Tse A, Verkhivker GM. Ensemble-based modeling and rigidity decomposition of allosteric interaction networks and communication pathways in cyclin-dependent kinases: Differentiating kinase clients of the Hsp90-Cdc37 chaperone. PLoS One 2017; 12:e0186089. [PMID: 29095844 PMCID: PMC5667858 DOI: 10.1371/journal.pone.0186089] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2017] [Accepted: 09/25/2017] [Indexed: 12/24/2022] Open
Abstract
The overarching goal of delineating molecular principles underlying differentiation of protein kinase clients and chaperone-based modulation of kinase activity is fundamental to understanding activity of many oncogenic kinases that require chaperoning of Hsp70 and Hsp90 systems to attain a functionally competent active form. Despite structural similarities and common activation mechanisms shared by cyclin-dependent kinase (CDK) proteins, members of this family can exhibit vastly different chaperone preferences. The molecular determinants underlying chaperone dependencies of protein kinases are not fully understood as structurally similar kinases may often elicit distinct regulatory responses to the chaperone. The regulatory divergences observed for members of CDK family are of particular interest as functional diversification among these kinases may be related to variations in chaperone dependencies and can be exploited in drug discovery of personalized therapeutic agents. In this work, we report the results of a computational investigation of several members of CDK family (CDK5, CDK6, CDK9) that represented a broad repertoire of chaperone dependencies—from nonclient CDK5, to weak client CDK6, and strong client CDK9. By using molecular simulations of multiple crystal structures we characterized conformational ensembles and collective dynamics of CDK proteins. We found that the elevated dynamics of CDK9 can trigger imbalances in cooperative collective motions and reduce stability of the active fold, thus creating a cascade of favorable conditions for chaperone intervention. The ensemble-based modeling of residue interaction networks and community analysis determined how differences in modularity of allosteric networks and topography of communication pathways can be linked with the client status of CDK proteins. This analysis unveiled depleted modularity of the allosteric network in CDK9 that alters distribution of communication pathways and leads to impaired signaling in the client kinase. According to our results, these network features may uniquely define chaperone dependencies of CDK clients. The perturbation response scanning and rigidity decomposition approaches identified regulatory hotspots that mediate differences in stability and cooperativity of allosteric interaction networks in the CDK structures. By combining these synergistic approaches, our study revealed dynamic and network signatures that can differentiate kinase clients and rationalize subtle divergences in the activation mechanisms of CDK family members. The therapeutic implications of these results are illustrated by identifying structural hotspots of pathogenic mutations that preferentially target regions of the increased flexibility to enable modulation of activation changes. Our study offers a network-based perspective on dynamic kinase mechanisms and drug design by unravelling relationships between protein kinase dynamics, allosteric communications and chaperone dependencies.
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Affiliation(s)
- Gabrielle Stetz
- Department of Computational and Data Sciences, Schmid College of Science and Technology, Chapman University, Orange, California, United States of America
| | - Amanda Tse
- Department of Computational and Data Sciences, Schmid College of Science and Technology, Chapman University, Orange, California, United States of America
| | - Gennady M. Verkhivker
- Department of Computational and Data Sciences, Schmid College of Science and Technology, Chapman University, Orange, California, United States of America
- Department of Biomedical and Pharmaceutical Sciences, Chapman University School of Pharmacy, Irvine, California, United States of America
- * E-mail:
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14
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Paparidis NFDS, Durvale MC, Canduri F. The emerging picture of CDK9/P-TEFb: more than 20 years of advances since PITALRE. MOLECULAR BIOSYSTEMS 2017; 13:246-276. [PMID: 27833949 DOI: 10.1039/c6mb00387g] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
CDK9 is a prominent member of the transcriptional CDKs subfamily, a group of kinases whose function is to control the primary steps of mRNA synthesis and processing by eukaryotic RNA polymerase II. As a cyclin-dependent kinase, CDK9 activation in vivo depends upon its association with T-type cyclins to assemble the positive transcription elongation factor (P-TEFb). Although CDK9/P-TEFb phosphorylates the C-terminal domain of RNAP II in the same positions targeted by CDK7 (TFIIH) and CDK8 (Mediator), the former does not participate in the transcription initiation, but rather plays a unique role by driving the polymerase to productive elongation. In addition to RNAP II CTD, the negative transcription elongation factors DSIF and NELF also represent major CDK9 substrates, whose phosphorylation is required to overcome the proximal pause of the polymerase. CDK9 is recruited to specific genes through proteins that interact with both P-TEFb and distinct elements in DNA, RNA or chromatin, where it modulates the activity of individual RNAP II transcription complexes. The regulation of CDK9 function is an intricate network that includes post-translational modifications (phosphorylation/dephosphorylation and acetylation/deacetylation of key residues) as well as the association of P-TEFb with various proteins that can stimulate or inhibit its kinase activity. Several cases of CDK9 deregulation have been linked to important human diseases, including various types of cancer and also AIDS (due to its essential role in HIV replication). Not only HIV, but also many other human viruses have been shown to depend strongly on CDK9 activity to be transcribed within host cells. This review summarizes the main advances made on CDK9/P-TEFb field in more than 20 years, introducing the structural, functional and genetic aspects that have been elucidated ever since.
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Affiliation(s)
- Nikolas Ferreira Dos Santos Paparidis
- Department of Chemistry and Molecular Physics, Institute of Chemistry of Sao Carlos, Sao Paulo University, Av. Trabalhador Sãocarlense, 400, Zip Code 780, 13560-970, São Carlos-SP, Brazil.
| | - Maxwell Castro Durvale
- Department of Biochemistry, Institute of Chemistry, Sao Paulo University, Av. Prof. Lineu Prestes, 748, 05508-000, Butantã - São Paulo - SP, Brazil
| | - Fernanda Canduri
- Department of Chemistry and Molecular Physics, Institute of Chemistry of Sao Carlos, Sao Paulo University, Av. Trabalhador Sãocarlense, 400, Zip Code 780, 13560-970, São Carlos-SP, Brazil.
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15
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Verkhivker GM. Network-based modelling and percolation analysis of conformational dynamics and activation in the CDK2 and CDK4 proteins: dynamic and energetic polarization of the kinase lobes may determine divergence of the regulatory mechanisms. MOLECULAR BIOSYSTEMS 2017; 13:2235-2253. [DOI: 10.1039/c7mb00355b] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Network modeling and percolation analysis of conformational dynamics and energetics of regulatory mechanisms in cyclin-dependent kinases.
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Affiliation(s)
- G. M. Verkhivker
- Graduate Program in Computational and Data Sciences
- Department of Computational Biosciences
- Schmid College of Science and Technology
- Chapman University
- Orange
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16
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Vos SM, Pöllmann D, Caizzi L, Hofmann KB, Rombaut P, Zimniak T, Herzog F, Cramer P. Architecture and RNA binding of the human negative elongation factor. eLife 2016; 5. [PMID: 27282391 PMCID: PMC4940160 DOI: 10.7554/elife.14981] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2016] [Accepted: 06/09/2016] [Indexed: 11/30/2022] Open
Abstract
Transcription regulation in metazoans often involves promoter-proximal pausing of RNA polymerase (Pol) II, which requires the 4-subunit negative elongation factor (NELF). Here we discern the functional architecture of human NELF through X-ray crystallography, protein crosslinking, biochemical assays, and RNA crosslinking in cells. We identify a NELF core subcomplex formed by conserved regions in subunits NELF-A and NELF-C, and resolve its crystal structure. The NELF-AC subcomplex binds single-stranded nucleic acids in vitro, and NELF-C associates with RNA in vivo. A positively charged face of NELF-AC is involved in RNA binding, whereas the opposite face of the NELF-AC subcomplex binds NELF-B. NELF-B is predicted to form a HEAT repeat fold, also binds RNA in vivo, and anchors the subunit NELF-E, which is confirmed to bind RNA in vivo. These results reveal the three-dimensional architecture and three RNA-binding faces of NELF. DOI:http://dx.doi.org/10.7554/eLife.14981.001
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Affiliation(s)
- Seychelle M Vos
- Department of Molecular Biology, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - David Pöllmann
- Department of Molecular Biology, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany.,Gene Center Munich, Ludwig-Maximilians-Universität München, Munich, Germany.,Department of Biochemistry, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Livia Caizzi
- Department of Molecular Biology, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Katharina B Hofmann
- Department of Molecular Biology, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Pascaline Rombaut
- Gene Center Munich, Ludwig-Maximilians-Universität München, Munich, Germany.,Department of Biochemistry, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Tomasz Zimniak
- Gene Center Munich, Ludwig-Maximilians-Universität München, Munich, Germany.,Department of Biochemistry, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Franz Herzog
- Gene Center Munich, Ludwig-Maximilians-Universität München, Munich, Germany.,Department of Biochemistry, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Patrick Cramer
- Department of Molecular Biology, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
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17
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Structural and Functional Analysis of the Cdk13/Cyclin K Complex. Cell Rep 2015; 14:320-31. [PMID: 26748711 DOI: 10.1016/j.celrep.2015.12.025] [Citation(s) in RCA: 88] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2015] [Revised: 10/29/2015] [Accepted: 11/30/2015] [Indexed: 12/20/2022] Open
Abstract
Cyclin-dependent kinases regulate the cell cycle and transcription in higher eukaryotes. We have determined the crystal structure of the transcription kinase Cdk13 and its Cyclin K subunit at 2.0 Å resolution. Cdk13 contains a C-terminal extension helix composed of a polybasic cluster and a DCHEL motif that interacts with the bound ATP. Cdk13/CycK phosphorylates both Ser5 and Ser2 of the RNA polymerase II C-terminal domain (CTD) with a preference for Ser7 pre-phosphorylations at a C-terminal position. The peptidyl-prolyl isomerase Pin1 does not change the phosphorylation specificities of Cdk9, Cdk12, and Cdk13 but interacts with the phosphorylated CTD through its WW domain. Using recombinant proteins, we find that flavopiridol inhibits Cdk7 more potently than it does Cdk13. Gene expression changes after knockdown of Cdk13 or Cdk12 are markedly different, with enrichment of growth signaling pathways for Cdk13-dependent genes. Together, our results provide insights into the structure, function, and activity of human Cdk13/CycK.
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18
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Structures of the CDK12/CycK complex with AMP-PNP reveal a flexible C-terminal kinase extension important for ATP binding. Sci Rep 2015; 5:17122. [PMID: 26597175 PMCID: PMC4656997 DOI: 10.1038/srep17122] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2015] [Accepted: 10/26/2015] [Indexed: 12/15/2022] Open
Abstract
Cyclin-dependent kinase 12 (CDK12) promotes transcriptional elongation by phosphorylation of the RNA polymerase II C-terminal domain (CTD). Structure-function studies show that this activity is dependent on a C-terminal kinase extension, as well as the binding of cyclin K (CycK). To better define these interactions we determined the crystal structure of the human CDK12/CycK complex with and without the kinase extension in the presence of AMP-PNP. The structures revealed novel features for a CDK, including a large β4-β5 loop insertion that contributes to the N-lobe interaction with the cyclin. We also observed two different conformations of the C-terminal kinase extension that effectively open and close the ATP pocket. Most notably, bound AMP-PNP was only observed when trapped in the closed state. Truncation of this C-terminal structure also diminished AMP-PNP binding, as well as the catalytic activity of the CDK12/CycK complex. Further kinetic measurements showed that the full length CDK12/CycK complex was significantly more active than the two crystallised constructs suggesting a critical role for additional domains. Overall, these results demonstrate the intrinsic flexibility of the C-terminal extension in CDK12 and highlight its importance for both ATP binding and kinase activity.
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19
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Jin HX, Go ML, Yin P, Qiu XT, Zhu P, Yan XJ. Determining the Functions of HIV-1 Tat and a Second Magnesium Ion in the CDK9/Cyclin T1 Complex: A Molecular Dynamics Simulation Study. PLoS One 2015; 10:e0124673. [PMID: 25909811 PMCID: PMC4409394 DOI: 10.1371/journal.pone.0124673] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2014] [Accepted: 03/16/2015] [Indexed: 11/18/2022] Open
Abstract
The current paradigm of cyclin-dependent kinase (CDK) regulation based on the well-established CDK2 has been recently expanded. The determination of CDK9 crystal structures suggests the requirement of an additional regulatory protein, such as human immunodeficiency virus type 1 (HIV-1) Tat, to exert its physiological functions. In most kinases, the exact number and roles of the cofactor metal ions remain unappreciated, and the repertoire has thus gained increasing attention recently. Here, molecular dynamics (MD) simulations were implemented on CDK9 to explore the functional roles of HIV-1 Tat and the second Mg2+ ion at site 1 (Mg12+). The simulations unveiled that binding of HIV-1 Tat to CDK9 not only stabilized hydrogen bonds (H-bonds) between ATP and hinge residues Asp104 and Cys106, as well as between ATP and invariant Lys48, but also facilitated the salt bridge network pertaining to the phosphorylated Thr186 at the activation loop. By contrast, these H-bonds cannot be formed in CDK9 owing to the absence of HIV-1 Tat. MD simulations further revealed that the Mg12+ ion, coupled with the Mg22+ ion, anchored to the triphosphate moiety of ATP in its catalytic competent conformation. This observation indicates the requirement of the Mg12+ ion for CDK9 to realize its function. Overall, the introduction of HIV-1 Tat and Mg12+ ion resulted in the active site architectural characteristics of phosphorylated CDK9. These data highlighted the functional roles of HIV-1 Tat and Mg12+ ion in the regulation of CDK9 activity, which contributes an important complementary understanding of CDK molecular underpinnings.
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Affiliation(s)
- Hai-Xiao Jin
- Key Laboratory of Applied Marine Biotechnology Ministry of Education, School of Marine Sciences, Ningbo University, Ningbo, China
| | - Mei-Lin Go
- Department of Pharmacy, National University of Singapore, Singapore, Singapore
| | - Peng Yin
- Key Laboratory of Chemical Biology and Traditional Chinese Medicine Research (Ministry of Education), College of Chemistry and Chemical Engineering, Hunan Normal University, Changsha, China
| | - Xiao-Ting Qiu
- Key Laboratory of Applied Marine Biotechnology Ministry of Education, School of Marine Sciences, Ningbo University, Ningbo, China
| | - Peng Zhu
- Key Laboratory of Applied Marine Biotechnology Ministry of Education, School of Marine Sciences, Ningbo University, Ningbo, China
| | - Xiao-Jun Yan
- Key Laboratory of Applied Marine Biotechnology Ministry of Education, School of Marine Sciences, Ningbo University, Ningbo, China
- * E-mail:
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20
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21
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Han Y, Zhan Y, Hou G, Li L. Cyclin-dependent kinase 9 may as a novel target in downregulating the atherosclerosis inflammation (Review). Biomed Rep 2014; 2:775-779. [PMID: 25279144 DOI: 10.3892/br.2014.322] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2014] [Accepted: 07/17/2014] [Indexed: 01/05/2023] Open
Abstract
Inflammation is a key component of atherosclerosis. Genes coding for inflammatory or anti-inflammatory molecules are considered good candidates for estimating the risk of developing atherosclerosis. Cyclin-dependent kinase 9 (CDK9), the kinase of positive transcription elongation factor b (P-TEFb), is crucial in the cell cycle and apoptosis. Previous studies have focused on its inhibition of immune cells for the resolution of inflammation. Considering the effects of inflammation in the pathogenicity of atherosclerosis, decreasing inflammation through the inhibition of CDK9 may be useful for the prognosis of atherosclerosis. The aim of this review was to examine whether inhibition of the CDK9 monocyte may affect the process of inflammation by acting on the cytokine secretion and interacting with endothelial cells (ECs). Thus, CDK9 may be a novel target for the diagnosis and therapy of atherosclerosis.
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Affiliation(s)
- Yeming Han
- Key Laboratory of Cardiovascular Remodeling and Function Research, Chinese Ministry of Education and Chinese Ministry of Public Health, Qilu Hospital, Shandong University, Jinan, Shandong 250012, P.R. China
| | - Yang Zhan
- Institute of Experimental Nuclear Medicine, School of Medicine, Shandong University, Jinan, Shandong 250012, P.R. China
| | - Guihua Hou
- Institute of Experimental Nuclear Medicine, School of Medicine, Shandong University, Jinan, Shandong 250012, P.R. China
| | - Li Li
- Key Laboratory of Cardiovascular Remodeling and Function Research, Chinese Ministry of Education and Chinese Ministry of Public Health, Qilu Hospital, Shandong University, Jinan, Shandong 250012, P.R. China
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22
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Bösken CA, Farnung L, Hintermair C, Merzel Schachter M, Vogel-Bachmayr K, Blazek D, Anand K, Fisher RP, Eick D, Geyer M. The structure and substrate specificity of human Cdk12/Cyclin K. Nat Commun 2014; 5:3505. [PMID: 24662513 PMCID: PMC3973122 DOI: 10.1038/ncomms4505] [Citation(s) in RCA: 136] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2013] [Accepted: 02/25/2014] [Indexed: 02/06/2023] Open
Abstract
Phosphorylation of the RNA polymerase II C-terminal domain (CTD) by cyclin-dependent kinases is important for productive transcription. Here we determine the crystal structure of Cdk12/CycK and analyse its requirements for substrate recognition. Active Cdk12/CycK is arranged in an open conformation similar to that of Cdk9/CycT but different from those of cell cycle kinases. Cdk12 contains a C-terminal extension that folds onto the N- and C-terminal lobes thereby contacting the ATP ribose. The interaction is mediated by an HE motif followed by a polybasic cluster that is conserved in transcriptional CDKs. Cdk12/CycK showed the highest activity on a CTD substrate prephosphorylated at position Ser7, whereas the common Lys7 substitution was not recognized. Flavopiridol is most potent towards Cdk12 but was still 10-fold more potent towards Cdk9. T-loop phosphorylation of Cdk12 required coexpression with a Cdk-activating kinase. These results suggest the regulation of Pol II elongation by a relay of transcriptionally active CTD kinases. Cyclin-dependent kinase 12 (Cdk12) phosphorylates the C-terminal domain (CTD) of RNA polymerase II to regulate transcription. Here, the authors solve the crystal structure of the Cdk12 kinase domain and show that Cdk12 has its highest activity on a CTD substrate that carries a serine 7 phosphorylation.
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Affiliation(s)
- Christian A Bösken
- 1] Group Physical Biochemistry, Center of Advanced European Studies and Research, Ludwig-Erhard-Allee 2, Bonn 53175, Germany [2] Department of Physical Biochemistry, Max Planck Institute of Molecular Physiology, Otto-Hahn-Strasse 11, Dortmund 44227, Germany
| | - Lucas Farnung
- Department of Physical Biochemistry, Max Planck Institute of Molecular Physiology, Otto-Hahn-Strasse 11, Dortmund 44227, Germany
| | - Corinna Hintermair
- Department of Molecular Epigenetics, Helmholtz Center Munich, Center for Integrated Protein Science (CIPSM), Marchioninistrasse 25, München 81377, Germany
| | - Miriam Merzel Schachter
- Department of Structural and Chemical Biology, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA
| | - Karin Vogel-Bachmayr
- Department of Physical Biochemistry, Max Planck Institute of Molecular Physiology, Otto-Hahn-Strasse 11, Dortmund 44227, Germany
| | - Dalibor Blazek
- Central European Institute of Technology (CEITEC), Masaryk University, Brno 62500, Czech Republic
| | - Kanchan Anand
- Group Physical Biochemistry, Center of Advanced European Studies and Research, Ludwig-Erhard-Allee 2, Bonn 53175, Germany
| | - Robert P Fisher
- Department of Structural and Chemical Biology, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA
| | - Dirk Eick
- Department of Molecular Epigenetics, Helmholtz Center Munich, Center for Integrated Protein Science (CIPSM), Marchioninistrasse 25, München 81377, Germany
| | - Matthias Geyer
- 1] Group Physical Biochemistry, Center of Advanced European Studies and Research, Ludwig-Erhard-Allee 2, Bonn 53175, Germany [2] Department of Physical Biochemistry, Max Planck Institute of Molecular Physiology, Otto-Hahn-Strasse 11, Dortmund 44227, Germany
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Walsby E, Pratt G, Shao H, Abbas AY, Fischer PM, Bradshaw TD, Brennan P, Fegan C, Wang S, Pepper C. A novel Cdk9 inhibitor preferentially targets tumor cells and synergizes with fludarabine. Oncotarget 2014; 5:375-85. [PMID: 24495868 PMCID: PMC3964214 DOI: 10.18632/oncotarget.1568] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2013] [Accepted: 12/18/2013] [Indexed: 01/22/2023] Open
Abstract
Cdk9 is a key elongation factor for RNA transcription and functions by phosphorylating the C-terminal domain of RNA polymerase II. Here we present direct evidence that cdk9 is important for cancer cell survival and describe the characterization of the potent cdk9 inhibitor CDKI-73 in primary human leukemia cells. CDKI-73 induced caspase-dependent apoptosis that was preceded by dephosphorylation of cdk9 and serine 2 of RNA polymerase II. CDKI-73 was more potent than the pan-cdk inhibitor flavopiridol and showed >200-fold selectivity against primary leukemia cells when compared with normal CD34+ cells. Furthermore, CDKI-73 was equipotent in poor prognostic sub-groups of leukemia patients and showed cytotoxic synergy with the nucleoside analog fludarabine. The Mechanism of synergy was associated with CDKI-73-mediated transcriptional inhibition of MCL1 and XIAP that was maintained when used in combination with fludarabine. Our data present a strong rationale for the development of cdk9 inhibitors such as CDKI-73 as anticancer therapeutics.
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MESH Headings
- Animals
- Antineoplastic Combined Chemotherapy Protocols/pharmacology
- Apoptosis
- Case-Control Studies
- Cyclin-Dependent Kinase 9/antagonists & inhibitors
- Cyclin-Dependent Kinase 9/genetics
- Drug Synergism
- HEK293 Cells
- Humans
- Leukemia, Lymphocytic, Chronic, B-Cell/drug therapy
- Leukemia, Lymphocytic, Chronic, B-Cell/enzymology
- Leukemia, Lymphocytic, Chronic, B-Cell/pathology
- Mice
- Phosphorylation
- Prognosis
- Protein Kinase Inhibitors/administration & dosage
- Protein Kinase Inhibitors/pharmacology
- Pyrimidines/administration & dosage
- Pyrimidines/pharmacology
- Sulfonamides/administration & dosage
- Sulfonamides/pharmacology
- Transcription, Genetic/drug effects
- Vidarabine/administration & dosage
- Vidarabine/analogs & derivatives
- Vidarabine/pharmacology
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Affiliation(s)
- Elisabeth Walsby
- Cardiff CLL Research Group, Institute of Cancer & Genetics, School of Medicine, Cardiff University, Heath Park, Cardiff, UK
| | - Guy Pratt
- CRUK Institute for Cancer Studies, University of Birmingham, Birmingham, UK
| | - Hao Shao
- School of Pharmacy and Centre for Biomolecular Sciences, University of Nottingham, Nottingham, UK
| | - Abdullah Y. Abbas
- School of Pharmacy and Centre for Biomolecular Sciences, University of Nottingham, Nottingham, UK
| | - Peter M. Fischer
- School of Pharmacy and Centre for Biomolecular Sciences, University of Nottingham, Nottingham, UK
| | - Tracey D. Bradshaw
- School of Pharmacy and Centre for Biomolecular Sciences, University of Nottingham, Nottingham, UK
| | - Paul Brennan
- Cardiff CLL Research Group, Institute of Cancer & Genetics, School of Medicine, Cardiff University, Heath Park, Cardiff, UK
| | - Chris Fegan
- Cardiff CLL Research Group, Institute of Cancer & Genetics, School of Medicine, Cardiff University, Heath Park, Cardiff, UK
| | - Shudong Wang
- School of Pharmacy and Centre for Biomolecular Sciences, University of Nottingham, Nottingham, UK
- School of Pharmacy and Medical Sciences, University of South Australia, Adelaide, Australia
| | - Chris Pepper
- Cardiff CLL Research Group, Institute of Cancer & Genetics, School of Medicine, Cardiff University, Heath Park, Cardiff, UK
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24
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Cross-talk of phosphorylation and prolyl isomerization of the C-terminal domain of RNA Polymerase II. Molecules 2014; 19:1481-511. [PMID: 24473209 PMCID: PMC4350670 DOI: 10.3390/molecules19021481] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2013] [Revised: 01/06/2014] [Accepted: 01/21/2014] [Indexed: 12/04/2022] Open
Abstract
Post-translational modifications of the heptad repeat sequences in the C-terminal domain (CTD) of RNA polymerase II (Pol II) are well recognized for their roles in coordinating transcription with other nuclear processes that impinge upon transcription by the Pol II machinery; and this is primarily achieved through CTD interactions with the various nuclear factors. The identification of novel modifications on new regulatory sites of the CTD suggests that, instead of an independent action for all modifications on CTD, a combinatorial effect is in operation. In this review we focus on two well-characterized modifications of the CTD, namely serine phosphorylation and prolyl isomerization, and discuss the complex interplay between the enzymes modifying their respective regulatory sites. We summarize the current understanding of how the prolyl isomerization state of the CTD dictates the specificity of writers (CTD kinases), erasers (CTD phosphatases) and readers (CTD binding proteins) and how that correlates to transcription status. Subtle changes in prolyl isomerization states cannot be detected at the primary sequence level, we describe the methods that have been utilized to investigate this mode of regulation. Finally, a general model of how prolyl isomerization regulates the phosphorylation state of CTD, and therefore transcription-coupled processes, is proposed.
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CDK/CK1 inhibitors roscovitine and CR8 downregulate amplified MYCN in neuroblastoma cells. Oncogene 2013; 33:5675-87. [PMID: 24317512 DOI: 10.1038/onc.2013.513] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2013] [Revised: 10/09/2013] [Accepted: 10/21/2013] [Indexed: 12/15/2022]
Abstract
To understand the mechanisms of action of (R)-roscovitine and (S)-CR8, two related pharmacological inhibitors of cyclin-dependent kinases (CDKs), we applied a variety of '-omics' techniques to the human neuroblastoma SH-SY5Y and IMR32 cell lines: (1) kinase interaction assays, (2) affinity competition on immobilized broad-spectrum kinase inhibitors, (3) affinity chromatography on immobilized (R)-roscovitine and (S)-CR8, (4) whole genome transcriptomics analysis and specific quantitative PCR studies, (5) global quantitative proteomics approach and western blot analysis of selected proteins. Altogether, the results show that the major direct targets of these two molecules belong to the CDKs (1,2,5,7,9,12), DYRKs, CLKs and CK1s families. By inhibiting CDK7, CDK9 and CDK12, these inhibitors transiently reduce RNA polymerase 2 activity, which results in downregulation of a large set of genes. Global transcriptomics and proteomics analysis converge to a central role of MYC transcription factors downregulation. Indeed, CDK inhibitors trigger rapid and massive downregulation of MYCN expression in MYCN-amplified neuroblastoma cells as well as in nude mice xenografted IMR32 cells. Inhibition of casein kinase 1 may also contribute to the antitumoral activity of (R)-roscovitine and (S)-CR8. This dual mechanism of action may be crucial in the use of these kinase inhibitors for the treatment of MYC-dependent cancers, in particular neuroblastoma where MYCN amplification is a strong predictor factor for high-risk disease.
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Abstract
Structural studies of members of the CDK (cyclin-dependent protein kinase) family have made a significant contribution to our understanding of the regulation of protein kinases. The structure of monomeric unphosphorylated CDK2 was the first of an inactive protein kinase to be determined and, since then, structures of other members of the CDK family, alone, in complex with regulatory proteins and in differing phosphorylation states, have enhanced our understanding of the molecular mechanisms regulating protein kinase activity. Recently, our knowledge of the structural biology of the CDK family has been extended by determination of structures for members of the transcriptional CDK and CDK-like kinase branches of the extended family. We include these recent structures in the present review and consider them in the light of current models for CDK activation and regulation.
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27
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Transcription factors mediate the enzymatic disassembly of promoter-bound 7SK snRNP to locally recruit P-TEFb for transcription elongation. Cell Rep 2013; 5:1256-68. [PMID: 24316072 DOI: 10.1016/j.celrep.2013.11.003] [Citation(s) in RCA: 73] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2013] [Revised: 10/02/2013] [Accepted: 11/02/2013] [Indexed: 12/19/2022] Open
Abstract
The transition from transcription initiation into elongation is controlled by transcription factors, which recruit positive transcription elongation factor b (P-TEFb) to promoters to phosphorylate RNA polymerase II. A fraction of P-TEFb is recruited as part of the inhibitory 7SK small nuclear ribonucleoprotein particle (snRNP), which inactivates the kinase and prevents elongation. However, it is unclear how P-TEFb is captured from the promoter-bound 7SK snRNP to activate elongation. Here, we describe a mechanism by which transcription factors mediate the enzymatic release of P-TEFb from the 7SK snRNP at promoters to trigger activation in a gene-specific manner. We demonstrate that Tat recruits PPM1G/PP2Cγ to locally disassemble P-TEFb from the 7SK snRNP at the HIV promoter via dephosphorylation of the kinase T loop. Similar to Tat, nuclear factor (NF)-κB recruits PPM1G in a stimulus-dependent manner to activate elongation at inflammatory-responsive genes. Recruitment of PPM1G to promoter-assembled 7SK snRNP provides a paradigm for rapid gene activation through transcriptional pause release.
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28
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Hole A, Baumli S, Shao H, Shi S, Huang S, Pepper C, Fischer P, Wang S, Endicott JA, Noble ME. Comparative structural and functional studies of 4-(thiazol-5-yl)-2-(phenylamino)pyrimidine-5-carbonitrile CDK9 inhibitors suggest the basis for isotype selectivity. J Med Chem 2013; 56:660-70. [PMID: 23252711 PMCID: PMC3579457 DOI: 10.1021/jm301495v] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2012] [Indexed: 01/08/2023]
Abstract
Cyclin-dependent kinase 9/cyclin T, the protein kinase heterodimer that constitutes positive transcription elongation factor b, is a well-validated target for treatment of several diseases, including cancer and cardiac hypertrophy. In order to aid inhibitor design and rationalize the basis for CDK9 selectivity, we have studied the CDK-binding properties of six different members of a 4-(thiazol-5-yl)-2-(phenylamino)pyrimidine-5-carbonitrile series that bind to both CDK9/cyclin T and CDK2/cyclin A. We find that for a given CDK, the melting temperature of a CDK/cyclin/inhibitor complex correlates well with inhibitor potency, suggesting that differential scanning fluorimetry (DSF) is a useful orthogonal measure of inhibitory activity for this series. We have used DSF to demonstrate that the binding of these compounds is independent of the presence or absence of the C-terminal tail region of CDK9, unlike the binding of the CDK9-selective inhibitor 5,6-dichlorobenzimidazone-1-β-d-ribofuranoside (DRB). Finally, on the basis of 11 cocrystal structures bound to CDK9/cyclin T or CDK2/cyclin A, we conclude that selective inhibition of CDK9/cyclin T by members of the 4-(thiazol-5-yl)-2-(phenylamino)pyrimidine-5-carbonitrile series results from the relative malleability of the CDK9 active site rather than from the formation of specific polar contacts.
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Affiliation(s)
- Alison
J. Hole
- Department
of Biochemistry, University of Oxford,
South Parks Road, Oxford OX1
3QU, U.K
| | - Sonja Baumli
- Department
of Biochemistry, University of Oxford,
South Parks Road, Oxford OX1
3QU, U.K
| | - Hao Shao
- School of Pharmacy
and Centre
for Biomolecular Sciences, University of Nottingham, University Park, Nottingham NG7 2RD, U.K
| | - Shenhua Shi
- School of Pharmacy
and Centre
for Biomolecular Sciences, University of Nottingham, University Park, Nottingham NG7 2RD, U.K
| | - Shiliang Huang
- School of Pharmacy
and Centre
for Biomolecular Sciences, University of Nottingham, University Park, Nottingham NG7 2RD, U.K
| | - Chris Pepper
- Institute of Cancer and Genetics,
School of Medicine, Cardiff University,
Heath Park, Cardiff CF14 4XN, U.K
| | - Peter
M. Fischer
- School of Pharmacy
and Centre
for Biomolecular Sciences, University of Nottingham, University Park, Nottingham NG7 2RD, U.K
| | - Shudong Wang
- School of Pharmacy
and Centre
for Biomolecular Sciences, University of Nottingham, University Park, Nottingham NG7 2RD, U.K
- School of Pharmacy and Medical
Sciences, University of South Australia, Adelaide SA 5001, Australia
| | - Jane A. Endicott
- Department
of Biochemistry, University of Oxford,
South Parks Road, Oxford OX1
3QU, U.K
| | - Martin E. Noble
- Department
of Biochemistry, University of Oxford,
South Parks Road, Oxford OX1
3QU, U.K
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