1
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Nwosu GO, Ross DM, Powell JA, Pitson SM. Venetoclax therapy and emerging resistance mechanisms in acute myeloid leukaemia. Cell Death Dis 2024; 15:413. [PMID: 38866760 DOI: 10.1038/s41419-024-06810-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2024] [Revised: 06/05/2024] [Accepted: 06/05/2024] [Indexed: 06/14/2024]
Abstract
Acute myeloid leukaemia (AML) is a highly aggressive and devastating malignancy of the bone marrow and blood. For decades, intensive chemotherapy has been the frontline treatment for AML but has yielded only poor patient outcomes as exemplified by a 5-year survival rate of < 30%, even in younger adults. As knowledge of the molecular underpinnings of AML has advanced, so too has the development new strategies with potential to improve the treatment of AML patients. To date the most promising of these targeted agents is the BH3-mimetic venetoclax which in combination with standard of care therapies, has manageable non-haematological toxicity and exhibits impressive efficacy. However, approximately 30% of AML patients fail to respond to venetoclax-based regimens and almost all treatment responders eventually relapse. Here, we review the emerging mechanisms of intrinsic and acquired venetoclax resistance in AML and highlight recent efforts to identify novel strategies to overcome resistance to venetoclax.
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Affiliation(s)
- Gus O Nwosu
- Centre for Cancer Biology, University of South Australia and SA Pathology, Adelaide, SA, Australia
- Clinical and Health Sciences, University of South Australia, Adelaide, SA, Australia
| | - David M Ross
- Centre for Cancer Biology, University of South Australia and SA Pathology, Adelaide, SA, Australia
- Adelaide Medical School, Faculty of Health Sciences, University of Adelaide, Adelaide, SA, Australia
- Department of Haematology, Royal Adelaide Hospital, Central Adelaide Local Health Network, Adelaide, SA, Australia
- Department of Haematology, Flinders University and Medical Centre, Adelaide, SA, Australia
| | - Jason A Powell
- Centre for Cancer Biology, University of South Australia and SA Pathology, Adelaide, SA, Australia.
- Adelaide Medical School, Faculty of Health Sciences, University of Adelaide, Adelaide, SA, Australia.
| | - Stuart M Pitson
- Centre for Cancer Biology, University of South Australia and SA Pathology, Adelaide, SA, Australia.
- Adelaide Medical School, Faculty of Health Sciences, University of Adelaide, Adelaide, SA, Australia.
- School of Biological Sciences, University of Adelaide, Adelaide, SA, Australia.
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2
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Huang Y, Liu W, Zhao C, Shi X, Zhao Q, Jia J, Wang A. Targeting cyclin-dependent kinases: From pocket specificity to drug selectivity. Eur J Med Chem 2024; 275:116547. [PMID: 38852339 DOI: 10.1016/j.ejmech.2024.116547] [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: 03/01/2024] [Revised: 05/28/2024] [Accepted: 05/28/2024] [Indexed: 06/11/2024]
Abstract
The development of selective modulators of cyclin-dependent kinases (CDKs), a kinase family with numerous members and functional variations, is a significant preclinical challenge. Recent advancements in crystallography have revealed subtle differences in the highly conserved CDK pockets. Exploiting these differences has proven to be an effective strategy for achieving excellent drug selectivity. While previous reports briefly discussed the structural features that lead to selectivity in individual CDK members, attaining inhibitor selectivity requires consideration of not only the specific structures of the target CDK but also the features of off-target members. In this review, we summarize the structure-activity relationships (SARs) that influence selectivity in CDK drug development and analyze the pocket features that lead to selectivity using molecular-protein binding models. In addition, in recent years, novel CDK modulators have been developed, providing more avenues for achieving selectivity. These cases were also included. We hope that these efforts will assist in the development of novel CDK drugs.
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Affiliation(s)
- Yaoguang Huang
- School of Traditional Chinese Materia Medica, Shenyang Pharmaceutical University, Shenyang, 110016, People's Republic of China
| | - Wenwu Liu
- School of Pharmaceutical Sciences, Tsinghua University, Haidian Dist., Beijing, 100084, People's Republic of China
| | - Changhao Zhao
- Department of Pharmacy, General Hospital of Northern Theater Command, Shenyang, 110840, People's Republic of China
| | - Xiaoyu Shi
- School of Traditional Chinese Materia Medica, Shenyang Pharmaceutical University, Shenyang, 110016, People's Republic of China
| | - Qingchun Zhao
- School of Traditional Chinese Materia Medica, Shenyang Pharmaceutical University, Shenyang, 110016, People's Republic of China; Department of Pharmacy, General Hospital of Northern Theater Command, Shenyang, 110840, People's Republic of China.
| | - Jingming Jia
- School of Traditional Chinese Materia Medica, Shenyang Pharmaceutical University, Shenyang, 110016, People's Republic of China.
| | - Anhua Wang
- School of Traditional Chinese Materia Medica, Shenyang Pharmaceutical University, Shenyang, 110016, People's Republic of China.
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3
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Taghizadeh MS, Taherishirazi M, Niazi A, Afsharifar A, Moghadam A. Structure-guided design and cloning of peptide inhibitors targeting CDK9/cyclin T1 protein-protein interaction. Front Pharmacol 2024; 15:1327820. [PMID: 38808256 PMCID: PMC11130503 DOI: 10.3389/fphar.2024.1327820] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Accepted: 01/18/2024] [Indexed: 05/30/2024] Open
Abstract
CDK9 (cyclin-dependent kinase 9) plays a significant role in numerous pathological conditions, such as HIV-1 infection and cancer. The interaction between CDK9 and cyclin T1 is crucial for maintaining the kinase's active state. Therefore, targeting this protein-protein interaction offers a promising strategy for inhibiting CDK9. In this study, we aimed to design and characterize a library of mutant peptides based on the binding region of cyclin T1 to CDK9. Using Osprey software, a total of 7,776 mutant peptides were generated. After conducting a comprehensive analysis, three peptides, namely, mp3 (RAADVEGQRKRRE), mp20 (RAATVEGQRKRRE), and mp29 (RAADVEGQDKRRE), were identified as promising inhibitors that possess the ability to bind to CDK9 with high affinity and exhibit low free binding energy. These peptides exhibited favorable safety profiles and displayed promising dynamic behaviors. Notably, our findings revealed that the mp3 and mp29 peptides interacted with a conserved sequence in CDK9 (residues 60-66). In addition, by designing the structure of potential peptides in the plasmid vector pET28a (+), we have been able to pave the way for facilitating the process of their recombinant production in an Escherichia coli expression system in future studies. Predictions indicated good solubility upon overexpression, further supporting their potential for downstream applications. While these results demonstrate the promise of the designed peptides as blockers of CDK9 with high affinity, additional experimental studies are required to validate their biological activity and assess their selectivity. Such investigations will provide valuable insights into their therapeutic potential and pave the way for the future development of peptide-based inhibitors targeting the CDK9-cyclin T1 complex.
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Affiliation(s)
| | | | - Ali Niazi
- Institute of Biotechnology, Shiraz University, Shiraz, Iran
| | - Alireza Afsharifar
- Plant Virology Research Center, School of Agriculture, Shiraz University, Shiraz, Iran
| | - Ali Moghadam
- Institute of Biotechnology, Shiraz University, Shiraz, Iran
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4
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Zhang Y, Shan L, Tang W, Ge Y, Li C, Zhang J. Recent Discovery and Development of Inhibitors that Target CDK9 and Their Therapeutic Indications. J Med Chem 2024; 67:5185-5215. [PMID: 38564299 DOI: 10.1021/acs.jmedchem.4c00312] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
CDK9 is a cyclin-dependent kinase that plays pivotal roles in multiple cellular functions including gene transcription, cell cycle regulation, DNA damage repair, and cellular differentiation. Targeting CDK9 is considered an attractive strategy for antitumor therapy, especially for leukemia and lymphoma. Several potent small molecule inhibitors, exemplified by TG02 (4), have progressed to clinical trials. However, many of them face challenges such as low clinical efficacy and multiple adverse reactions and may necessitate the exploration of novel strategies to lead to success in the clinic. In this perspective, we present a comprehensive overview of the structural characteristics, biological functions, and preclinical status of CDK9 inhibitors. Our focus extends to various types of inhibitors, including pan-inhibitors, selective inhibitors, dual-target inhibitors, degraders, PPI inhibitors, and natural products. The discussion encompasses chemical structures, structure-activity relationships (SARs), biological activities, selectivity, and therapeutic potential, providing detailed insight into the diverse landscape of CDK9 inhibitors.
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Affiliation(s)
- Yuming Zhang
- Department of Neurology, Neuro-system and Multimorbidity Laboratory and State Key Laboratory of Biotherapy and Cancer Center and National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, 610041 Sichuan, China
- West China College of Medicine, West China Hospital, Sichuan University, Chengdu, 610041 Sichuan, China
| | - Lianhai Shan
- School of Life Science and Engineering, Southwest Jiaotong University, Chengdu, 610031 Sichuan, China
| | - Wentao Tang
- Department of Neurology, Neuro-system and Multimorbidity Laboratory and State Key Laboratory of Biotherapy and Cancer Center and National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, 610041 Sichuan, China
| | - Yating Ge
- Department of Neurology, Neuro-system and Multimorbidity Laboratory and State Key Laboratory of Biotherapy and Cancer Center and National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, 610041 Sichuan, China
| | - ChengXian Li
- Department of Neurology, Neuro-system and Multimorbidity Laboratory and State Key Laboratory of Biotherapy and Cancer Center and National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, 610041 Sichuan, China
| | - Jifa Zhang
- Department of Neurology, Neuro-system and Multimorbidity Laboratory and State Key Laboratory of Biotherapy and Cancer Center and National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, 610041 Sichuan, China
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5
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Wang S, Liu F, Li P, Wang JN, Mo Y, Lin B, Mei Y. Potent inhibitors targeting cyclin-dependent kinase 9 discovered via virtual high-throughput screening and absolute binding free energy calculations. Phys Chem Chem Phys 2024; 26:5377-5386. [PMID: 38269624 DOI: 10.1039/d3cp05582e] [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: 01/26/2024]
Abstract
Due to the crucial regulatory mechanism of cyclin-dependent kinase 9 (CDK9) in mRNA transcription, the development of kinase inhibitors targeting CDK9 holds promise as a potential treatment strategy for cancer. A structure-based virtual screening approach has been employed for the discovery of potential novel CDK9 inhibitors. First, compounds with kinase inhibitor characteristics were identified from the ZINC15 database via virtual high-throughput screening. Next, the predicted binding modes were optimized by molecular dynamics simulations, followed by precise estimation of binding affinities using absolute binding free energy calculations based on the free energy perturbation scheme. The binding mode of molecule 006 underwent an inward-to-outward flipping, and the new binding mode exhibited binding affinity comparable to the small molecule T6Q in the crystal structure (PDB ID: 4BCF), highlighting the essential role of molecular dynamics simulation in capturing a plausible binding pose bridging docking and absolute binding free energy calculations. Finally, structural modifications based on these findings further enhanced the binding affinity with CDK9. The results revealed that enhancing the molecule's rigidity through ring formation, while maintaining the major interactions, reduced the entropy loss during the binding process and, thus, enhanced binding affinities.
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Affiliation(s)
- Shipeng Wang
- School of Chemistry and Chemical Engineering, Shanghai University of Engineering Science, Shanghai 201620, China.
| | - Fengjiao Liu
- School of Chemistry and Chemical Engineering, Shanghai University of Engineering Science, Shanghai 201620, China.
| | - Pengfei Li
- Single Particle, LLC, 10531 4S Commons Dr 166-629, San Diego, CA 92127, USA
| | - Jia-Ning Wang
- State Key Laboratory of Precision Spectroscopy, School of Physics and Electronic Science, East China Normal University, Shanghai 200241, China
| | - Yan Mo
- State Key Laboratory of Precision Spectroscopy, School of Physics and Electronic Science, East China Normal University, Shanghai 200241, China
- NYU-ECNU Center for Computational Chemistry at NYU Shanghai, Shanghai 200062, China
- Collaborative Innovation Center of Extreme Optics, Shanxi University, Taiyuan, Shanxi 030006, China
| | - Bin Lin
- Wuya College of Innovation, Shenyang Pharmaceutical University, Shenyang 110016, China.
| | - Ye Mei
- State Key Laboratory of Precision Spectroscopy, School of Physics and Electronic Science, East China Normal University, Shanghai 200241, China
- NYU-ECNU Center for Computational Chemistry at NYU Shanghai, Shanghai 200062, China
- Collaborative Innovation Center of Extreme Optics, Shanxi University, Taiyuan, Shanxi 030006, China
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6
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Yuan H, Yao W, Zhang X, Wei Z, Xi J, Hao Y, Liu X, Jiang R, Nie H. Highly Enantioselective Ir-Catalyzed Hydrogenation of Pyrazolo[1,5- a]pyrimidine for the Synthesis of Zanubrutinib. J Org Chem 2024; 89:1748-1752. [PMID: 38262733 DOI: 10.1021/acs.joc.3c02446] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2024]
Abstract
A highly enantioselective catalytic reduction of pyrazolo[1,5-a]pyrimidine to zanubrutinib has been realized by the Ir/(R)-t-Bu-FcPhox complex. This chiral product could be obtained in up to >99% ee in the asymmetric transformation without any other additives, providing a new route for the asymmetric synthesis of zanubrutinib.
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Affiliation(s)
- Haohuan Yuan
- Department of Medicinal Chemistry, School of Pharmacy, Fourth Military Medical University, Xi'an 710032, China
| | - Wei Yao
- Department of Medicinal Chemistry, School of Pharmacy, Fourth Military Medical University, Xi'an 710032, China
| | - Xiaomin Zhang
- Department of Medicinal Chemistry, School of Pharmacy, Fourth Military Medical University, Xi'an 710032, China
| | - Zhao Wei
- Department of Medicinal Chemistry, School of Pharmacy, Fourth Military Medical University, Xi'an 710032, China
| | - Jiayue Xi
- Department of Medicinal Chemistry, School of Pharmacy, Fourth Military Medical University, Xi'an 710032, China
| | | | - Xian Liu
- Department of Pharmaceutical Sciences, Beijing Institute of Radiation Medicine, Beijing 100850, China
| | - Ru Jiang
- Department of Medicinal Chemistry, School of Pharmacy, Fourth Military Medical University, Xi'an 710032, China
| | - Huifang Nie
- Department of Medicinal Chemistry, School of Pharmacy, Fourth Military Medical University, Xi'an 710032, China
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7
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Habib I, Chohan TA, Chohan TA, Batool F, Khurshid U, Khursheed A, Raza A, Ansari M, Hussain A, Anwar S, Awadh Ali NA, Saleem H. Integrated computational approaches for designing potent pyrimidine-based CDK9 inhibitors: 3D-QSAR, docking, and molecular dynamics simulations. Comput Biol Chem 2024; 108:108003. [PMID: 38159453 DOI: 10.1016/j.compbiolchem.2023.108003] [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: 08/28/2023] [Revised: 11/24/2023] [Accepted: 12/06/2023] [Indexed: 01/03/2024]
Abstract
CDK9 is an emerging target for the development of anticancer drugs. The development of CDK9 inhibitors with significant potency had consistently posed a formidable challenge. In the current research, a number of computational methodologies, such as, 3D-QSAR, molecular docking, fingerprint analysis, molecular dynamic (MD) simulations followed by MMGB/PBSA and ADMET studies were used systemically to uncover the binding mechanism of pyrimidine derivatives against CDK9. The CoMFA and CoMSIA models having high q2 (0.53, 0.54) and r2 values (0.96, 0.93) respectively indicating that model could accurately predict the bioactivities of CDK9 inhibitors. Using the R-group exploration technique implemented by the Spark™ by Cresset group, the structural requirements revealed by the contour maps of model were utilized strategically to create an in-house library of 100 new CDK9 inhibitors. Additionally, the compounds from the in-house library were mapped into 3D-QSAR model which predicted pIC50 values comparable to the experimental values. A comparison between 3D-QSAR generated contours and molecular docking conformation of ligands was performed to elucidate the essentials of CDK9 inhibitor design. MD simulations (100 ns) were performed on the selected docked complexes A21, A14 and D98 which contributed in validating the binding interactions. According to the findings of binding free energy analysis (MMGB/PBSA), It was observed that residues CYS106 and GLU107 had a considerable tendency to facilitate ligand-protein interactions via H-bond interactions. The aforementioned findings have the potential to enhance researchers comprehension of the mechanism underlying CDK9 inhibition and may be utilized in the development of innovative and efficacious CDK9 inhibitors.
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Affiliation(s)
- Iffat Habib
- Institute of Pharmaceutical Sciences (IPS), University of Veterinary and Animal Sciences (UVAS), Lahore 5400, Pakistan
| | - Tahir Ali Chohan
- Institute of Pharmaceutical Sciences (IPS), University of Veterinary and Animal Sciences (UVAS), Lahore 5400, Pakistan.
| | - Talha Ali Chohan
- Institute of Molecular Biology and Biotechnology, The University of Lahore, Lahore, Pakistan
| | - Fakhra Batool
- Department of Pharmacy, The Women university Multan, Multan, Pakistan
| | - Umair Khurshid
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, The Islamia University of Bahawalpur, Bahawalpur 63100 , Pakistan
| | - Anjum Khursheed
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, The Islamia University of Bahawalpur, Bahawalpur 63100 , Pakistan
| | - Ali Raza
- Institute of Pharmaceutical Sciences (IPS), University of Veterinary and Animal Sciences (UVAS), Lahore 5400, Pakistan
| | - Mukhtar Ansari
- Department of Clinical Pharmacy, College of Pharmacy, University of Ha'il, Ha'il, Saudi Arabia
| | - Arshad Hussain
- Department of Clinical Pharmacy, College of Pharmacy, University of Ha'il, Ha'il, Saudi Arabia
| | - Sirajudheen Anwar
- Department of Pharmacology, College of Pharmacy, University of Ha'il, Ha'il, Saudi Arabia.
| | - Nasser A Awadh Ali
- Department of Pharmacognosy and Medicinal Herbs, Faculty of Pharmacy, Al Baha University, Al Baha, Saudi Arabia
| | - Hammad Saleem
- Institute of Pharmaceutical Sciences (IPS), University of Veterinary and Animal Sciences (UVAS), Lahore 5400, Pakistan.
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8
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Bhutada I, Khambati F, Cheng SY, Tiek DM, Duckett D, Lawrence H, Vogelbaum MA, Mo Q, Chellappan SP, Padmanabhan J. CDK7 and CDK9 inhibition interferes with transcription, translation, and stemness, and induces cytotoxicity in GBM irrespective of temozolomide sensitivity. Neuro Oncol 2024; 26:70-84. [PMID: 37551745 PMCID: PMC10768977 DOI: 10.1093/neuonc/noad143] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2023] [Indexed: 08/09/2023] Open
Abstract
BACKGROUND Glioblastoma (GBM) is refractory to current treatment modalities while side effects of treatments result in neurotoxicity and cognitive impairment. Here we test the hypothesis that inhibiting CDK7 or CDK9 would effectively combat GBM with reduced neurotoxicity. METHODS We examined the effect of a CDK7 inhibitor, THZ1, and multiple CDK9 inhibitors (SNS032, AZD4573, NVP2, and JSH150) on GBM cell lines, patient-derived temozolomide (TMZ)-resistant and responsive primary tumor cells and glioma stem cells (GSCs). Biochemical changes were assessed by western blotting, immunofluorescence, multispectral imaging, and RT-PCR. In vivo, efficacy was assessed in orthotopic and subcutaneous xenograft models. RESULTS CDK7 and CDK9 inhibitors suppressed the viability of TMZ-responsive and resistant GBM cells and GSCs at low nanomolar concentrations, with limited cytotoxic effects in vivo. The inhibitors abrogated RNA Pol II and p70S6K phosphorylation and nascent protein synthesis. Furthermore, the self-renewal of GSCs was significantly reduced with a corresponding reduction in Sox2 and Sox9 levels. Analysis of TCGA data showed increased expression of CDK7, CDK9, SOX2, SOX9, and RPS6KB1 in GBM; supporting this, multispectral imaging of a TMA revealed increased levels of CDK9, Sox2, Sox9, phospho-S6, and phospho-p70S6K in GBM compared to normal brains. RNA-Seq results suggested that inhibitors suppressed tumor-promoting genes while inducing tumor-suppressive genes. Furthermore, the studies conducted on subcutaneous and orthotopic GBM tumor xenograft models showed that administration of CDK9 inhibitors markedly suppressed tumor growth in vivo. CONCLUSIONS Our results suggest that CDK7 and CDK9 targeted therapies may be effective against TMZ-sensitive and resistant GBM.
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Affiliation(s)
- Isha Bhutada
- Department of Tumor Biology, Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | - Fatema Khambati
- Department of Tumor Biology, Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | - Shi-Yuan Cheng
- The Ken and Ruth Devee Department of Neurology, Lou and Jean Malnati Brain Tumor Institute Northwestern Medicine, The Robert H. Lurie Comprehensive Cancer Center, Simpson Querrey Institute for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Deanna M Tiek
- The Ken and Ruth Devee Department of Neurology, Lou and Jean Malnati Brain Tumor Institute Northwestern Medicine, The Robert H. Lurie Comprehensive Cancer Center, Simpson Querrey Institute for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Derek Duckett
- Department of Drug Discovery, Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | - Harshani Lawrence
- Department of Drug Discovery, Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | - Michael A Vogelbaum
- Department of Neuro-Oncology and Neuro-Oncology Program, Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | - Qianxing Mo
- Department of Biostatistics and Bioinformatics, Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | - Srikumar P Chellappan
- Department of Tumor Biology, Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | - Jaya Padmanabhan
- Department of Tumor Biology, Moffitt Cancer Center and Research Institute, Tampa, FL, USA
- Department of Molecular Medicine, University of South Florida, Tampa, FL, USA
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9
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Mustafa EH, Laven-Law G, Kikhtyak Z, Nguyen V, Ali S, Pace AA, Iggo R, Kebede A, Noll B, Wang S, Winter JM, Dwyer AR, Tilley WD, Hickey TE. Selective inhibition of CDK9 in triple negative breast cancer. Oncogene 2024; 43:202-215. [PMID: 38001268 PMCID: PMC10786725 DOI: 10.1038/s41388-023-02892-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Revised: 11/02/2023] [Accepted: 11/10/2023] [Indexed: 11/26/2023]
Abstract
Targeted therapy for triple-negative breast cancers (TNBC) remains a clinical challenge due to tumour heterogeneity. Since TNBC have key features of transcriptionally addicted cancers, targeting transcription via regulators such as cyclin-dependent kinase 9 (CDK9) has potential as a therapeutic strategy. Herein, we preclinically tested a new selective CDK9 inhibitor (CDDD11-8) in TNBC using cell line, patient-derived organoid, and patient-derived explant models. In vitro, CDDD11-8 dose-dependently inhibited proliferation (IC50 range: 281-734 nM), induced cell cycle arrest, and increased apoptosis of cell lines, which encompassed the three major molecular subtypes of TNBC. On target inhibition of CDK9 activity was demonstrated by reduced RNAPII phosphorylation at a CDK9 target peptide and down-regulation of the MYC and MCL1 oncogenes at the mRNA and protein levels in all cell line models. Drug induced RNAPII pausing was evident at gene promoters, with strongest pausing at MYC target genes. Growth of five distinct patient-derived organoid models was dose-dependently inhibited by CDDD11-8 (IC50 range: 272-771 nM), including three derived from MYC amplified, chemo-resistant TNBC metastatic lesions. Orally administered CDDD11-8 also inhibited growth of mammary intraductal TNBC xenograft tumours with no overt toxicity in vivo (mice) or ex vivo (human breast tissues). In conclusion, our studies indicate that CDK9 is a viable therapeutic target in TNBC and that CDDD11-8, a novel selective CDK9 inhibitor, has efficacy in TNBC without apparent toxicity to normal tissues.
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Affiliation(s)
- Ebtihal H Mustafa
- Dame Roma Mitchell Cancer Research Laboratories, Adelaide Medical School, University of Adelaide, Adelaide, SA, Australia
| | - Geraldine Laven-Law
- Dame Roma Mitchell Cancer Research Laboratories, Adelaide Medical School, University of Adelaide, Adelaide, SA, Australia
| | - Zoya Kikhtyak
- Dame Roma Mitchell Cancer Research Laboratories, Adelaide Medical School, University of Adelaide, Adelaide, SA, Australia
| | - Van Nguyen
- Department of Surgery & Cancer, Imperial College London, London, UK
| | - Simak Ali
- Department of Surgery & Cancer, Imperial College London, London, UK
| | - Alex A Pace
- Dame Roma Mitchell Cancer Research Laboratories, Adelaide Medical School, University of Adelaide, Adelaide, SA, Australia
| | - Richard Iggo
- Dame Roma Mitchell Cancer Research Laboratories, Adelaide Medical School, University of Adelaide, Adelaide, SA, Australia
- Institut Bergonié, University of Bordeaux, Bordeaux, France
| | - Alemwork Kebede
- Drug Discovery and Development, Clinical and Health Sciences, University of South Australia, Adelaide, SA, Australia
| | - Ben Noll
- Drug Discovery and Development, Clinical and Health Sciences, University of South Australia, Adelaide, SA, Australia
| | - Shudong Wang
- Drug Discovery and Development, Clinical and Health Sciences, University of South Australia, Adelaide, SA, Australia
| | - Jean M Winter
- Dame Roma Mitchell Cancer Research Laboratories, Adelaide Medical School, University of Adelaide, Adelaide, SA, Australia
| | - Amy R Dwyer
- Dame Roma Mitchell Cancer Research Laboratories, Adelaide Medical School, University of Adelaide, Adelaide, SA, Australia
| | - Wayne D Tilley
- Dame Roma Mitchell Cancer Research Laboratories, Adelaide Medical School, University of Adelaide, Adelaide, SA, Australia
| | - Theresa E Hickey
- Dame Roma Mitchell Cancer Research Laboratories, Adelaide Medical School, University of Adelaide, Adelaide, SA, Australia.
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10
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Potapova TA, Unruh JR, Conkright-Fincham J, Banks CAS, Florens L, Schneider DA, Gerton JL. Distinct states of nucleolar stress induced by anticancer drugs. eLife 2023; 12:RP88799. [PMID: 38099650 PMCID: PMC10723795 DOI: 10.7554/elife.88799] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2023] Open
Abstract
Ribosome biogenesis is a vital and highly energy-consuming cellular function occurring primarily in the nucleolus. Cancer cells have an elevated demand for ribosomes to sustain continuous proliferation. This study evaluated the impact of existing anticancer drugs on the nucleolus by screening a library of anticancer compounds for drugs that induce nucleolar stress. For a readout, a novel parameter termed 'nucleolar normality score' was developed that measures the ratio of the fibrillar center and granular component proteins in the nucleolus and nucleoplasm. Multiple classes of drugs were found to induce nucleolar stress, including DNA intercalators, inhibitors of mTOR/PI3K, heat shock proteins, proteasome, and cyclin-dependent kinases (CDKs). Each class of drugs induced morphologically and molecularly distinct states of nucleolar stress accompanied by changes in nucleolar biophysical properties. In-depth characterization focused on the nucleolar stress induced by inhibition of transcriptional CDKs, particularly CDK9, the main CDK that regulates RNA Pol II. Multiple CDK substrates were identified in the nucleolus, including RNA Pol I- recruiting protein Treacle, which was phosphorylated by CDK9 in vitro. These results revealed a concerted regulation of RNA Pol I and Pol II by transcriptional CDKs. Our findings exposed many classes of chemotherapy compounds that are capable of inducing nucleolar stress, and we recommend considering this in anticancer drug development.
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Affiliation(s)
| | - Jay R Unruh
- Stowers Institute for Medical ResearchKansas CityUnited States
| | | | | | | | - David Alan Schneider
- Department of Biochemistry and Molecular Genetics, University of Alabama at BirminghamBirminghamUnited States
| | - Jennifer L Gerton
- Stowers Institute for Medical ResearchKansas CityUnited States
- Department of Biochemistry and Molecular Biology, University of Kansas Medical CenterKansas CityUnited States
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11
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Freeman DB, Hopkins TD, Mikochik PJ, Vacca JP, Gao H, Naylor-Olsen A, Rudra S, Li H, Pop MS, Villagomez RA, Lee C, Li H, Zhou M, Saffran DC, Rioux N, Hood TR, Day MAL, McKeown MR, Lin CY, Bischofberger N, Trotter BW. Discovery of KB-0742, a Potent, Selective, Orally Bioavailable Small Molecule Inhibitor of CDK9 for MYC-Dependent Cancers. J Med Chem 2023; 66:15629-15647. [PMID: 37967851 PMCID: PMC10726352 DOI: 10.1021/acs.jmedchem.3c01233] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Revised: 10/06/2023] [Accepted: 10/11/2023] [Indexed: 11/17/2023]
Abstract
Transcriptional deregulation is a hallmark of many cancers and is exemplified by genomic amplifications of the MYC family of oncogenes, which occur in at least 20% of all solid tumors in adults. Targeting of transcriptional cofactors and the transcriptional cyclin-dependent kinase (CDK9) has emerged as a therapeutic strategy to interdict deregulated transcriptional activity including oncogenic MYC. Here, we report the structural optimization of a small molecule microarray hit, prioritizing maintenance of CDK9 selectivity while improving on-target potency and overall physicochemical and pharmacokinetic (PK) properties. This led to the discovery of the potent, selective, orally bioavailable CDK9 inhibitor 28 (KB-0742). Compound 28 exhibits in vivo antitumor activity in mouse xenograft models and a projected human PK profile anticipated to enable efficacious oral dosing. Notably, 28 is currently being investigated in a phase 1/2 dose escalation and expansion clinical trial in patients with relapsed or refractory solid tumors.
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Affiliation(s)
- David B. Freeman
- Kronos
Bio, Inc., 301 Binney
Street, 2nd Floor East, Cambridge, Massachusetts 02142, United States
- Kronos
Bio, Inc., 1300 So. El
Camino Real Suite 400, San Mateo, California 94402, United States
| | - Tamara D. Hopkins
- Kronos
Bio, Inc., 301 Binney
Street, 2nd Floor East, Cambridge, Massachusetts 02142, United States
- Kronos
Bio, Inc., 1300 So. El
Camino Real Suite 400, San Mateo, California 94402, United States
| | - Peter J. Mikochik
- Kronos
Bio, Inc., 301 Binney
Street, 2nd Floor East, Cambridge, Massachusetts 02142, United States
- Kronos
Bio, Inc., 1300 So. El
Camino Real Suite 400, San Mateo, California 94402, United States
| | - Joseph P. Vacca
- Kronos
Bio, Inc., 301 Binney
Street, 2nd Floor East, Cambridge, Massachusetts 02142, United States
- Kronos
Bio, Inc., 1300 So. El
Camino Real Suite 400, San Mateo, California 94402, United States
| | - Hua Gao
- Kronos
Bio, Inc., 301 Binney
Street, 2nd Floor East, Cambridge, Massachusetts 02142, United States
- Kronos
Bio, Inc., 1300 So. El
Camino Real Suite 400, San Mateo, California 94402, United States
| | - Adel Naylor-Olsen
- Naylor
Olsen Consulting, LLC, 3369 Saddle Wood Court, Lansdale, Pennsylvania 19446, United States
| | - Sonali Rudra
- TCG
Lifesciences Private Limited, Block BN, Plot 7, Salt-lake Electronics Complex, Sector V, Kolkata 700091, West Bengal, India
| | - Huixu Li
- WuXi
AppTec (Tianjin) Co., Ltd., 168 NanHai Road, 10th Avenue, TEDA, Tianjin 300457, P. R. China
| | - Marius S. Pop
- Kronos
Bio, Inc., 301 Binney
Street, 2nd Floor East, Cambridge, Massachusetts 02142, United States
- Kronos
Bio, Inc., 1300 So. El
Camino Real Suite 400, San Mateo, California 94402, United States
| | - Rosa A. Villagomez
- Kronos
Bio, Inc., 301 Binney
Street, 2nd Floor East, Cambridge, Massachusetts 02142, United States
- Kronos
Bio, Inc., 1300 So. El
Camino Real Suite 400, San Mateo, California 94402, United States
| | - Christina Lee
- Kronos
Bio, Inc., 301 Binney
Street, 2nd Floor East, Cambridge, Massachusetts 02142, United States
- Kronos
Bio, Inc., 1300 So. El
Camino Real Suite 400, San Mateo, California 94402, United States
| | - Heng Li
- Kronos
Bio, Inc., 301 Binney
Street, 2nd Floor East, Cambridge, Massachusetts 02142, United States
- Kronos
Bio, Inc., 1300 So. El
Camino Real Suite 400, San Mateo, California 94402, United States
| | - Minyun Zhou
- Kronos
Bio, Inc., 301 Binney
Street, 2nd Floor East, Cambridge, Massachusetts 02142, United States
- Kronos
Bio, Inc., 1300 So. El
Camino Real Suite 400, San Mateo, California 94402, United States
| | - Douglas C. Saffran
- Kronos
Bio, Inc., 301 Binney
Street, 2nd Floor East, Cambridge, Massachusetts 02142, United States
- Kronos
Bio, Inc., 1300 So. El
Camino Real Suite 400, San Mateo, California 94402, United States
| | - Nathalie Rioux
- Certara
Strategic Consulting, 100 Overlook Center, Suite 101, Princeton, New Jersey 08540, United States
| | - Tressa R. Hood
- Kronos
Bio, Inc., 301 Binney
Street, 2nd Floor East, Cambridge, Massachusetts 02142, United States
- Kronos
Bio, Inc., 1300 So. El
Camino Real Suite 400, San Mateo, California 94402, United States
| | - Melinda A. L. Day
- Kronos
Bio, Inc., 301 Binney
Street, 2nd Floor East, Cambridge, Massachusetts 02142, United States
- Kronos
Bio, Inc., 1300 So. El
Camino Real Suite 400, San Mateo, California 94402, United States
| | - Michael R. McKeown
- Kronos
Bio, Inc., 301 Binney
Street, 2nd Floor East, Cambridge, Massachusetts 02142, United States
- Kronos
Bio, Inc., 1300 So. El
Camino Real Suite 400, San Mateo, California 94402, United States
| | - Charles Y. Lin
- Kronos
Bio, Inc., 301 Binney
Street, 2nd Floor East, Cambridge, Massachusetts 02142, United States
- Kronos
Bio, Inc., 1300 So. El
Camino Real Suite 400, San Mateo, California 94402, United States
| | - Norbert Bischofberger
- Kronos
Bio, Inc., 301 Binney
Street, 2nd Floor East, Cambridge, Massachusetts 02142, United States
- Kronos
Bio, Inc., 1300 So. El
Camino Real Suite 400, San Mateo, California 94402, United States
| | - B. Wesley Trotter
- Kronos
Bio, Inc., 301 Binney
Street, 2nd Floor East, Cambridge, Massachusetts 02142, United States
- Kronos
Bio, Inc., 1300 So. El
Camino Real Suite 400, San Mateo, California 94402, United States
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12
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Dominguez EC, Roleder C, Ball B, Danilov AV. Cyclin-dependent kinase-9 in B-cell malignancies: pathogenic role and therapeutic implications. Leuk Lymphoma 2023; 64:1893-1904. [PMID: 37552126 DOI: 10.1080/10428194.2023.2244102] [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: 06/02/2023] [Accepted: 07/29/2023] [Indexed: 08/09/2023]
Abstract
Cyclin-dependent kinases (CDK) regulate cell cycle and transcriptional activity. Pan-CDK inhibitors demonstrated early efficacy in lymphoid malignancies, but also have been associated with narrow therapeutic index. Among transcriptional CDKs, CDK7 and CDK9 emerged as promising targets. CDK9 serves as a component of P-TEFb elongation complex and thus is indispensable in mRNA transcription. Selective CDK9 inhibitors demonstrated pre-clinical efficacy in in vitro and in vivo models of B-cell non-Hodgkin lymphoma. CDK9 inhibition results in transcriptional pausing with rapid downmodulation of short-lived oncogenic proteins, e.g. Myc and Mcl-1, followed by cell apoptosis. Early phase clinical trials established safety of CDK9 inhibitors, with manageable neutropenia, infections and gastrointestinal toxicities. In this review, we summarize the rationale of targeting CDK9 in lymphoid malignancies, as well as pre-clinical and early clinical data with pan-CDK and selective CDK9 inhibitors.
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Affiliation(s)
| | - Carly Roleder
- City of Hope National Medical Center, Duarte, CA, USA
| | - Brian Ball
- City of Hope National Medical Center, Duarte, CA, USA
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13
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Wu T, Yu B, Xu Y, Du Z, Zhang Z, Wang Y, Chen H, Zhang LA, Chen R, Ma F, Gong W, Yu S, Qiu Z, Wu H, Xu X, Wang J, Li Z, Bian J. Discovery of Selective and Potent Macrocyclic CDK9 Inhibitors for the Treatment of Osimertinib-Resistant Non-Small-Cell Lung Cancer. J Med Chem 2023; 66:15340-15361. [PMID: 37870244 DOI: 10.1021/acs.jmedchem.3c01400] [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: 10/24/2023]
Abstract
Effectiveness of epidermal growth factor receptor (EGFR) inhibitors, including Osimertinib, for treating non-small-cell lung cancer (NSCLC) is limited due to the continuous emergence of drug resistance. Hence, it is urgent to develop new therapeutic approaches. CDK9, a key regulator of RNA transcription, has emerged as a promising target for the development of antitumor drugs due to its crucial role in modulating the levels of antiapoptotic protein Mcl-1. Herein, we present the synthesis, optimization, and evaluation of selective CDK9 inhibitors with a macrocyclic scaffold that effectively suppresses the growth of NSCLC cells. Notably, compound Z11, a potent CDK9 inhibitor (IC50 = 3.20 nM) with good kinase selectivity, significantly inhibits cell proliferation and colony formation and induces apoptosis in Osimertinib-resistant H1975 cells. Furthermore, Z11 demonstrates a significant suppression of tumor growth in six patient-derived organoids, including three organoids resistant to Osimertinib. Overall, Z11 served as a promising macrocycle-based CDK9 inhibitor for treating Osimertinib-resistant NSCLC.
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Affiliation(s)
- Tizhi Wu
- Jiangsu Key Laboratory of Drug Design and Optimization, Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, P. R. China
| | - Bin Yu
- Jiangsu Key Laboratory of Drug Design and Optimization, Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, P. R. China
| | - Yifan Xu
- Jiangsu Key Laboratory of Drug Design and Optimization, Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, P. R. China
| | - Zekun Du
- Jiangsu Key Laboratory of Drug Design and Optimization, Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, P. R. China
| | - Zhiming Zhang
- Jiangsu Key Laboratory of Drug Design and Optimization, Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, P. R. China
| | - Yuxiao Wang
- Jiangsu Key Laboratory of Drug Design and Optimization, Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, P. R. China
| | - Haoming Chen
- Jiangsu Key Laboratory of Drug Design and Optimization, Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, P. R. China
| | - Li Ao Zhang
- Jiangsu Key Laboratory of Drug Design and Optimization, Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, P. R. China
| | - Rui Chen
- Jiangsu Key Laboratory of Drug Design and Optimization, Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, P. R. China
| | - Feihai Ma
- Jiangsu Key Laboratory of Drug Design and Optimization, Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, P. R. China
| | - Weihong Gong
- Jiangsu Key Laboratory of Drug Design and Optimization, Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, P. R. China
| | - Sixian Yu
- Jiangsu Key Laboratory of Drug Design and Optimization, Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, P. R. China
| | - Zhixia Qiu
- Jiangsu Key Laboratory of Drug Design and Optimization, Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, P. R. China
| | - Hongxi Wu
- Jiangsu Key Laboratory of Drug Design and Optimization, Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, P. R. China
| | - Xi Xu
- Jiangsu Key Laboratory of Drug Design and Optimization, Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, P. R. China
| | - Jubo Wang
- Jiangsu Key Laboratory of Drug Design and Optimization, Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, P. R. China
| | - Zhiyu Li
- Jiangsu Key Laboratory of Drug Design and Optimization, Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, P. R. China
| | - Jinlei Bian
- Jiangsu Key Laboratory of Drug Design and Optimization, Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, P. R. China
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14
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Wu T, Zhang Z, Gong G, Du Z, Xu Y, Yu S, Ma F, Zhang X, Wang Y, Chen H, Wu S, Xu X, Qiu Z, Li Z, Wu H, Bian J, Wang J. Discovery of novel flavonoid-based CDK9 degraders for prostate cancer treatment via a PROTAC strategy. Eur J Med Chem 2023; 260:115774. [PMID: 37672930 DOI: 10.1016/j.ejmech.2023.115774] [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: 06/29/2023] [Revised: 08/08/2023] [Accepted: 08/28/2023] [Indexed: 09/08/2023]
Abstract
CDK9 plays a vital role in regulating RNA transcription and significantly impacts the expression of short-lived proteins such as Mcl-1 and c-Myc. Thus, targeting CDK9 holds great promise for the development of antitumor drugs. Natural flavonoid derivatives have recently gained considerable attention in the field of antitumor drug research due to their broad bioactivity and low toxicity. In this study, the PROTAC strategy was used to perform structural modifications of the flavonoid derivative LWT-111 to design a series of flavonoid-based CDK9 degraders. Notably, compound CP-07 emerged as a potent CDK9 degrader, effectively suppressing the proliferation and colony formation of 22RV1 cells by downregulating Mcl-1 and c-Myc. Moreover, CP-07 exhibited significant tumor growth inhibition with a TGI of 75.1% when administered at a dose of 20 mg/kg in the 22RV1 xenograft tumor model. These findings demonstrated the potential of CP-07 as a powerful flavonoid-based CDK9 degrader for prostate cancer therapy.
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Affiliation(s)
- Tizhi Wu
- Jiangsu Key Laboratory of Drug Design and Optimization, Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing, 210009, PR China
| | - Zhiming Zhang
- Jiangsu Key Laboratory of Drug Design and Optimization, Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing, 210009, PR China
| | - Guangyue Gong
- Jiangsu Key Laboratory of Drug Design and Optimization, Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing, 210009, PR China
| | - Zekun Du
- Jiangsu Key Laboratory of Drug Design and Optimization, Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing, 210009, PR China
| | - Yifan Xu
- Jiangsu Key Laboratory of Drug Design and Optimization, Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing, 210009, PR China
| | - Sixian Yu
- Jiangsu Key Laboratory of Drug Design and Optimization, Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing, 210009, PR China
| | - Feihai Ma
- Jiangsu Key Laboratory of Drug Design and Optimization, Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing, 210009, PR China
| | - Xuan Zhang
- Jiangsu Key Laboratory of Drug Design and Optimization, Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing, 210009, PR China
| | - Yuxiao Wang
- Jiangsu Key Laboratory of Drug Design and Optimization, Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing, 210009, PR China
| | - Haoming Chen
- Jiangsu Key Laboratory of Drug Design and Optimization, Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing, 210009, PR China
| | - Shiqi Wu
- Jiangsu Key Laboratory of Drug Design and Optimization, Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing, 210009, PR China
| | - Xi Xu
- Jiangsu Key Laboratory of Drug Design and Optimization, Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing, 210009, PR China
| | - Zhixia Qiu
- Jiangsu Key Laboratory of Drug Design and Optimization, Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing, 210009, PR China
| | - Zhiyu Li
- Jiangsu Key Laboratory of Drug Design and Optimization, Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing, 210009, PR China
| | - Hongxi Wu
- Jiangsu Key Laboratory of Drug Design and Optimization, Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing, 210009, PR China.
| | - Jinlei Bian
- Jiangsu Key Laboratory of Drug Design and Optimization, Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing, 210009, PR China.
| | - Jubo Wang
- Jiangsu Key Laboratory of Drug Design and Optimization, Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing, 210009, PR China.
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15
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Kattar SD, Gulati A, Margrey KA, Keylor MH, Ardolino M, Yan X, Johnson R, Palte RL, McMinn SE, Nogle L, Su J, Xiao D, Piesvaux J, Lee S, Hegde LG, Woodhouse JD, Faltus R, Moy LY, Xiong T, Ciaccio PJ, Pearson K, Patel M, Otte KM, Leyns CEG, Kennedy ME, Bennett DJ, DiMauro EF, Fell MJ, Fuller PH. Discovery of MK-1468: A Potent, Kinome-Selective, Brain-Penetrant Amidoisoquinoline LRRK2 Inhibitor for the Potential Treatment of Parkinson's Disease. J Med Chem 2023; 66:14912-14927. [PMID: 37861679 DOI: 10.1021/acs.jmedchem.3c01486] [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: 10/21/2023]
Abstract
Genetic mutation of the leucine-rich repeat kinase 2 (LRRK2) protein has been associated with Parkinson's disease (PD), a disabling and progressive neurodegenerative disorder that is devoid of efficacious disease-modifying therapies. Herein, we describe the invention of an amidoisoquinoline (IQ)-derived LRRK2 inhibitor lead chemical series. Knowledge-, structure-, and property-based drug design in concert with rigorous application of in silico calculations and presynthesis predictions enabled the prioritization of molecules with favorable CNS "drug-like" physicochemical properties. This resulted in the discovery of compound 8, which was profiled extensively before human ether-a-go-go (hERG) ion channel inhibition halted its progression. Strategic reduction of lipophilicity and basicity resulted in attenuation of hERG ion channel inhibition while maintaining a favorable CNS efflux transporter profile. Further structure- and property-based optimizations resulted in the discovery of preclinical candidate MK-1468. This exquisitely selective LRRK2 inhibitor has a projected human dose of 48 mg BID and a preclinical safety profile that supported advancement toward GLP toxicology studies.
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Affiliation(s)
- Solomon D Kattar
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts 02115, United States
| | - Anmol Gulati
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts 02115, United States
| | - Kaila A Margrey
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts 02115, United States
| | - Mitchell H Keylor
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts 02115, United States
| | - Michael Ardolino
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts 02115, United States
| | - Xin Yan
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts 02115, United States
| | - Rebecca Johnson
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts 02115, United States
| | - Rachel L Palte
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts 02115, United States
| | - Spencer E McMinn
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts 02115, United States
| | - Lisa Nogle
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts 02115, United States
| | - Jing Su
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts 02115, United States
| | - Dong Xiao
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts 02115, United States
| | - Jennifer Piesvaux
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts 02115, United States
| | - Susi Lee
- Merck & Co., Inc., 126 E. Lincoln Ave., Rahway, New Jersey 07065, United States
| | - Laxminarayan G Hegde
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts 02115, United States
| | - Janice D Woodhouse
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts 02115, United States
| | - Robert Faltus
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts 02115, United States
| | - Lily Y Moy
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts 02115, United States
| | - Tina Xiong
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts 02115, United States
| | - Paul J Ciaccio
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts 02115, United States
| | - Kara Pearson
- Merck & Co., Inc., 770 Sumneytown Pike., West Point, Pennsylvania 19486, United States
| | - Mayankbhai Patel
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts 02115, United States
| | - Karin M Otte
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts 02115, United States
| | - Cheryl E G Leyns
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts 02115, United States
| | - Matthew E Kennedy
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts 02115, United States
| | | | - Erin F DiMauro
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts 02115, United States
| | - Matthew J Fell
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts 02115, United States
| | - Peter H Fuller
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts 02115, United States
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16
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Wu T, Yu B, Gong W, Zhang J, Yu S, Tian Y, Zhao T, Li Z, Wang J, Bian J. Design and optimization of selective and potent CDK9 inhibitors with flavonoid scaffold for the treatment of acute myeloid leukemia. Eur J Med Chem 2023; 259:115711. [PMID: 37572539 DOI: 10.1016/j.ejmech.2023.115711] [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: 06/12/2023] [Revised: 08/03/2023] [Accepted: 08/03/2023] [Indexed: 08/14/2023]
Abstract
Acute myeloid leukemia (AML) is a prevalent hematological tumor associated with a high morbidity and mortality rate. CDK9, functioning as a pivotal transcriptional regulator, facilitates transcriptional elongation through phosphorylation of RNA polymerase II, which further governs the protein levels of Mcl-1 and c-Myc. Therefore, CDK9 has been considered as a promising therapeutic target for AML treatment. Here, we present the design, synthesis, and evaluation of CDK9 inhibitors bearing a flavonoid scaffold. Among them, compound 21a emerged as a highly selective CDK9 inhibitor (IC50 = 6.7 nM), exhibiting over 80-fold selectivity towards most other CDK family members and high kinase selectivity. In Mv4-11 cells, 21a effectively hindered cell proliferation (IC50 = 60 nM) and induced apoptosis by down-regulating Mcl-1 and c-Myc. Notably, 21a demonstrated significant inhibition of tumor growth in the Mv4-11 xenograft tumor model. These findings indicate that compound 21a holds promise as a potential candidate for treating AML.
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Affiliation(s)
- Tizhi Wu
- Jiangsu Key Laboratory of Drug Design and Optimization, Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing, 210009, PR China
| | - Bin Yu
- Jiangsu Key Laboratory of Drug Design and Optimization, Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing, 210009, PR China
| | - Weihong Gong
- Jiangsu Key Laboratory of Drug Design and Optimization, Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing, 210009, PR China
| | - Jing Zhang
- Jiangsu Key Laboratory of Drug Design and Optimization, Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing, 210009, PR China
| | - Sixian Yu
- Jiangsu Key Laboratory of Drug Design and Optimization, Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing, 210009, PR China
| | - Yucheng Tian
- Jiangsu Key Laboratory of Drug Design and Optimization, Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing, 210009, PR China
| | - Tengteng Zhao
- Jiangsu Key Laboratory of Drug Design and Optimization, Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing, 210009, PR China
| | - Zhiyu Li
- Jiangsu Key Laboratory of Drug Design and Optimization, Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing, 210009, PR China.
| | - Jubo Wang
- Jiangsu Key Laboratory of Drug Design and Optimization, Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing, 210009, PR China.
| | - Jinlei Bian
- Jiangsu Key Laboratory of Drug Design and Optimization, Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing, 210009, PR China.
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17
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Atiya A, Shahidi H, Mohammad T, Sharaf SE, Abdulmonem WA, Ashraf GM, Elasbali AM, Alharethi SH, Alhumaydhi FA, Baeesa SS, Rehan M, Shamsi A, Shahwan M. A virtual screening investigation to identify bioactive natural compounds as potential inhibitors of cyclin-dependent kinase 9. J Biomol Struct Dyn 2023; 41:10202-10213. [PMID: 36562191 DOI: 10.1080/07391102.2022.2153921] [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: 07/21/2022] [Accepted: 11/25/2022] [Indexed: 12/24/2022]
Abstract
Cyclin-dependent kinase 9 (CDK9) is a transcription-associated protein involved in controlling the cell cycle and is often deregulated in stress conditions. CDK9 is being studied as a well-known druggable target for developing effective therapeutics against a wide range of cancer, cardiac dysfunction and inflammatory diseases. Owing to the significance of CDK9 in the etiology of hematological and solid malignancies, its structure, biological activity, regulation and its pharmacological inhibition are being explored for therapeutic management of cancer. We employed a structure-based virtual high-throughput screening of bioactive compounds from the IMPPAT database to discover potential bioactive inhibitors of CDK9. The preliminary results were obtained from the Lipinski criteria, ADMET parameters and sorting compounds without any PAINS patterns. Subsequently, binding affinity and selectivity analyses were used to find effective CDK9 hits. This screening resulted in the identification of two natural compounds, Glabrene and Guggulsterone with high affinity and specificity for the CDK9 binding site. Both compounds exhibit drug-like characteristics, as projected by ADMET analysis, physicochemical data and PASS evaluation. Both compounds preferentially bind to the ATP-binding pocket of CDK9 and interact with functionally important residues. Further, the dynamics and consistency of CDK9 interaction with Glabrene and Guggulsteron were evaluated through all-atom molecular dynamic (MD) simulations which suggested the stability of both complexes. The results might be deployed to introduce novel CDK9 inhibitors that may treat life-threatening diseases, including cancer.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Akhtar Atiya
- Department of Pharmacognosy, College of Pharmacy, King Khalid University (KKU), Abha, Saudi Arabia
| | - Habiba Shahidi
- Department of Computer Science, Jamia Millia Islamia, New Delhi, India
| | - Taj Mohammad
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, India
| | - Sharaf E Sharaf
- Pharmaceutical Chemistry Department, College of Pharmacy Umm Al-Qura University Makkah, Saudi Arabia
- Clinical Research Adminstration Executive Adminstration of Research and Innovation King Abdullah Medical City in the Holy Capital Makkah, Makkah, Saudi Arabia
| | - Waleed Al Abdulmonem
- Department of Pathology, College of Medicine, Qassim University, Buraidah, Kingdom of Saudia Arabia
| | - Ghulam Md Ashraf
- Department of Medical Laboratory Sciences, College of Health Sciences, and Sharjah Institute for Medical Research, University of Sharjah, Sharjah, United Arab Emirates
| | | | - Salem Hussain Alharethi
- Department of Biological Science, College of Arts and Science, Najran University, Najran, Saudia Arabia
| | - Fahad A Alhumaydhi
- Department of Medical Laboratories, College of Applied Medical Sciences, Qassim University, Buraidah, Saudi Arabia
| | - Saleh Salem Baeesa
- Division of Neurosurgery, College of Medicine, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Mohd Rehan
- King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
- Department of Medical Laboratory Sciences, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Anas Shamsi
- Centre of Medical and Bio-Allied Health Sciences Research, Ajman University, Ajman, United Arab Emirates
| | - Moyad Shahwan
- Centre of Medical and Bio-Allied Health Sciences Research, Ajman University, Ajman, United Arab Emirates
- College of Pharmacy, Ajman University, Ajman, United Arab Emirates
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18
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Abrisqueta P, Nadeu F, Bosch-Schips J, Iacoboni G, Serna A, Cabirta A, Yáñez L, Quintanilla-Martínez L, Bosch F. From genetics to therapy: Unraveling the complexities of Richter transformation in chronic lymphocytic leukemia. Cancer Treat Rev 2023; 120:102619. [PMID: 37660626 DOI: 10.1016/j.ctrv.2023.102619] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Revised: 08/22/2023] [Accepted: 08/24/2023] [Indexed: 09/05/2023]
Abstract
Richter transformation (RT) refers to the progression of chronic lymphocytic leukemia, the most prevalent leukemia among adults, into a highly aggressive lymphoproliferative disorder, primarily a diffuse large B-cell lymphoma. This is a severe complication that continues to be a therapeutic challenge and remains an unmet medical need. Over the last five years, significant advances have occurred in uncovering the biological processes leading to the RT, refining criteria for properly diagnose RT from other entities, and exploring new therapeutic options beyond the ineffective chemotherapy. This review summarizes current knowledge in RT, including recent advances in the understanding of the pathogenesis of RT, in the classification of RT, and in the development of novel therapeutic strategies for this grave complication.
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Affiliation(s)
- Pau Abrisqueta
- Department of Hematology, Vall d'Hebron Hospital Universitari, Experimental Hematology, Vall d'Hebron Institute of Oncology (VHIO), Vall d'Hebron Barcelona Hospital Campus, Passeig Vall d'Hebron 119-129, 08035 Barcelona, Spain; Departament de Medicina, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain
| | - Ferran Nadeu
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), 08036 Barcelona, Spain; Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain
| | - Jan Bosch-Schips
- Department of Pathology, Hospital Universitari de Bellvitge-Bellvitge Biomedical Research Institute (IDIBELL), L'Hospitalet de Llobregat, 08907 Barcelona, Spain
| | - Gloria Iacoboni
- Department of Hematology, Vall d'Hebron Hospital Universitari, Experimental Hematology, Vall d'Hebron Institute of Oncology (VHIO), Vall d'Hebron Barcelona Hospital Campus, Passeig Vall d'Hebron 119-129, 08035 Barcelona, Spain; Departament de Medicina, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain
| | - Angel Serna
- Department of Hematology, Vall d'Hebron Hospital Universitari, Experimental Hematology, Vall d'Hebron Institute of Oncology (VHIO), Vall d'Hebron Barcelona Hospital Campus, Passeig Vall d'Hebron 119-129, 08035 Barcelona, Spain; Departament de Medicina, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain
| | - Alba Cabirta
- Department of Hematology, Vall d'Hebron Hospital Universitari, Experimental Hematology, Vall d'Hebron Institute of Oncology (VHIO), Vall d'Hebron Barcelona Hospital Campus, Passeig Vall d'Hebron 119-129, 08035 Barcelona, Spain; Departament de Medicina, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain
| | - Lucrecia Yáñez
- Department of Hematology, Hospital Universitario Marqués de Valdecilla, Santander, Spain
| | - Leticia Quintanilla-Martínez
- Institute of Pathology and Neuropathology, Tübingen University Hospital and Comprehensive Cancer Center Tübingen-Stuttgart, 72076 Tübingen, Germany
| | - Francesc Bosch
- Department of Hematology, Vall d'Hebron Hospital Universitari, Experimental Hematology, Vall d'Hebron Institute of Oncology (VHIO), Vall d'Hebron Barcelona Hospital Campus, Passeig Vall d'Hebron 119-129, 08035 Barcelona, Spain; Departament de Medicina, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain.
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19
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Xie C, Xiao G, Guo Q, Wu X, Zi G, Ding W, Hou G. Highly enantioselective Rh-catalyzed asymmetric reductive dearomatization of multi-nitrogen polycyclic pyrazolo[1,5- a]pyrimidines. Chem Sci 2023; 14:9048-9054. [PMID: 37655036 PMCID: PMC10466315 DOI: 10.1039/d3sc02086j] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2023] [Accepted: 07/20/2023] [Indexed: 09/02/2023] Open
Abstract
A highly enantioselective rhodium-catalyzed reductive dearomatization of 7-substituted pyrazolo[1,5-a]pyrimidines has been realized for the first time by two strategies to afford chiral 4,5,6,7-tetrahydropyrazolo[1,5-a]pyrimidines with excellent enantioselectivities of up to 98% ee. This method also provides an efficient approach for the synthesis of the powerful BTK inhibitor, zanubrutinib.
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Affiliation(s)
- Chaochao Xie
- Key Laboratory of Radiopharmaceuticals, College of Chemistry, Beijing Normal University No. 19 Xinjiekouwai St. Beijing 100875 China
| | - Guiying Xiao
- Key Laboratory of Radiopharmaceuticals, College of Chemistry, Beijing Normal University No. 19 Xinjiekouwai St. Beijing 100875 China
| | - Qianling Guo
- Key Laboratory of Radiopharmaceuticals, College of Chemistry, Beijing Normal University No. 19 Xinjiekouwai St. Beijing 100875 China
| | - Xiaoxue Wu
- Key Laboratory of Radiopharmaceuticals, College of Chemistry, Beijing Normal University No. 19 Xinjiekouwai St. Beijing 100875 China
| | - Guofu Zi
- Key Laboratory of Radiopharmaceuticals, College of Chemistry, Beijing Normal University No. 19 Xinjiekouwai St. Beijing 100875 China
| | - Wanjian Ding
- Key Laboratory of Radiopharmaceuticals, College of Chemistry, Beijing Normal University No. 19 Xinjiekouwai St. Beijing 100875 China
| | - Guohua Hou
- Key Laboratory of Radiopharmaceuticals, College of Chemistry, Beijing Normal University No. 19 Xinjiekouwai St. Beijing 100875 China
- Shanghai Key Laboratory for Molecular Engineering of Chiral Drugs, School of Chemistry and Chemical Engineering, Shanghai Jiao Tong University Shanghai 200240 China
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20
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Wang B, Zhou X, Kettenbach AN, Mitchell HD, Markillie LM, Loros JJ, Dunlap JC. A crucial role for dynamic expression of components encoding the negative arm of the circadian clock. Nat Commun 2023; 14:3371. [PMID: 37291101 PMCID: PMC10250352 DOI: 10.1038/s41467-023-38817-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Accepted: 05/17/2023] [Indexed: 06/10/2023] Open
Abstract
In the Neurospora circadian system, the White Collar Complex (WCC) drives expression of the principal circadian negative arm component frequency (frq). FRQ interacts with FRH (FRQ-interacting RNA helicase) and CKI, forming a stable complex that represses its own expression by inhibiting WCC. In this study, a genetic screen identified a gene, designated as brd-8, that encodes a conserved auxiliary subunit of the NuA4 histone acetylation complex. Loss of brd-8 reduces H4 acetylation and RNA polymerase (Pol) II occupancy at frq and other known circadian genes, and leads to a long circadian period, delayed phase, and defective overt circadian output at some temperatures. In addition to strongly associating with the NuA4 histone acetyltransferase complex, BRD-8 is also found complexed with the transcription elongation regulator BYE-1. Expression of brd-8, bye-1, histone h2a.z, and several NuA4 subunits is controlled by the circadian clock, indicating that the molecular clock both regulates the basic chromatin status and is regulated by changes in chromatin. Taken together, our data identify auxiliary elements of the fungal NuA4 complex having homology to mammalian components, which along with conventional NuA4 subunits, are required for timely and dynamic frq expression and thereby a normal and persistent circadian rhythm.
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Affiliation(s)
- Bin Wang
- Department of Molecular and Systems Biology, Geisel School of Medicine at Dartmouth, Hanover, NH, 03755, USA.
| | - Xiaoying Zhou
- Department of Molecular and Systems Biology, Geisel School of Medicine at Dartmouth, Hanover, NH, 03755, USA
| | - Arminja N Kettenbach
- Department of Biochemistry and Cell Biology, Geisel School of Medicine at Dartmouth, Hanover, NH, 03755, USA
| | - Hugh D Mitchell
- Biological Sciences Divisions, Pacific Northwest National Laboratory, Richland, WA, 99352, USA
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, 99352, USA
| | - Lye Meng Markillie
- Biological Sciences Divisions, Pacific Northwest National Laboratory, Richland, WA, 99352, USA
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, 99352, USA
| | - Jennifer J Loros
- Department of Molecular and Systems Biology, Geisel School of Medicine at Dartmouth, Hanover, NH, 03755, USA
- Department of Biochemistry and Cell Biology, Geisel School of Medicine at Dartmouth, Hanover, NH, 03755, USA
| | - Jay C Dunlap
- Department of Molecular and Systems Biology, Geisel School of Medicine at Dartmouth, Hanover, NH, 03755, USA.
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21
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Abstract
An analysis of 156 published clinical candidates from the Journal of Medicinal Chemistry between 2018 and 2021 was conducted to identify lead generation strategies most frequently employed leading to drug candidates. As in a previous publication, the most frequent lead generation strategies resulting in clinical candidates were from known compounds (59%) followed by random screening approaches (21%). The remainder of the approaches included directed screening, fragment screening, DNA-encoded library screening (DEL), and virtual screening. An analysis of similarity was also conducted based on Tanimoto-MCS and revealed most clinical candidates were distant from their original hits; however, most shared a key pharmacophore that translated from hit-to-clinical candidate. An examination of frequency of oxygen, nitrogen, fluorine, chlorine, and sulfur incorporation in clinical candidates was also conducted. The three most similar and least similar hit-to-clinical pairs from random screening were examined to provide perspective on changes that occur that lead to successful clinical candidates.
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Affiliation(s)
- Dean G Brown
- Jnana Therapeutics, One Design Center Pl Suite 19-400, Boston, Massachusetts 02210, United States
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22
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Wu T, Wu X, Xu Y, Chen R, Wang J, Li Z, Bian J. A patent review of selective CDK9 inhibitors in treating cancer. Expert Opin Ther Pat 2023; 33:309-322. [PMID: 37128897 DOI: 10.1080/13543776.2023.2208747] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
INTRODUCTION The dysregulation of CDK9 protein is greatly related to the proliferation and differentiation of various cancers due to its key role in the regulation of RNA transcription. Moreover, CDK9 inhibition can markedly downregulate the anti-apoptotic protein Mcl-1 which is essential for the survival of tumors. Thus, targeting CDK9 is considered to be a promising strategy for antitumor drug development, and the development of selective CDK9 inhibitors has gained increasing attention. AREAS COVERED This review focuses on the development of selective CDK9 inhibitors reported in patent publications during the period 2020-2022, which were searched from SciFinder and Cortellis Drug Discovery Intelligence. EXPERT OPINION Given that pan-CDK9 inhibitors may lead to serious side effects due to poor selectivity, the investigation of selective CDK9 inhibitors has attracted widespread attention. CDK9 inhibitors make some advance in treating solid tumors and possess the therapeutic potential in EGFR-mutant lung cancer. CDK9 inhibitors with short half-life and intravenous administration might result in transient target engagement and contribute to a better safety profile in vivo. However, more efforts are urgently needed to accelerate the development of CDK9 inhibitors, including the research on new binding modes between ligand and receptor or new protein binding sites.
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Affiliation(s)
- Tizhi Wu
- State Key Laboratory of Natural Medicines and Jiang Su Key Laboratory of Drug Design and Optimization, Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing, China
| | - Xiaowei Wu
- State Key Laboratory of Natural Medicines and Jiang Su Key Laboratory of Drug Design and Optimization, Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing, China
| | - Yifan Xu
- State Key Laboratory of Natural Medicines and Jiang Su Key Laboratory of Drug Design and Optimization, Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing, China
| | - Rui Chen
- State Key Laboratory of Natural Medicines and Jiang Su Key Laboratory of Drug Design and Optimization, Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing, China
| | - Jubo Wang
- State Key Laboratory of Natural Medicines and Jiang Su Key Laboratory of Drug Design and Optimization, Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing, China
| | - Zhiyu Li
- State Key Laboratory of Natural Medicines and Jiang Su Key Laboratory of Drug Design and Optimization, Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing, China
| | - Jinlei Bian
- State Key Laboratory of Natural Medicines and Jiang Su Key Laboratory of Drug Design and Optimization, Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing, China
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23
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Wang B, Zhou X, Kettenbach AN, Mitchell HD, Markillie LM, Loros JJ, Dunlap JC. A crucial role for dynamic expression of components encoding the negative arm of the circadian clock. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.24.538162. [PMID: 37162945 PMCID: PMC10168201 DOI: 10.1101/2023.04.24.538162] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
In the Neurospora circadian system, the White Collar Complex (WCC) drives expression of the principal circadian negative arm component frequency ( frq ). FRQ interacts with FRH (FRQ-interacting helicase) and CK-1 forming a stable complex that represses its own expression by inhibiting WCC. In this study, a genetic screen identified a gene, designated as brd-8 , that encodes a conserved auxiliary subunit of the NuA4 histone acetylation complex. Loss of brd-8 reduces H4 acetylation and RNA polymerase (Pol) II occupancy at frq and other known circadian genes, and leads to a long circadian period, delayed phase, and defective overt circadian output at some temperatures. In addition to strongly associating with the NuA4 histone acetyltransferase complex, BRD-8 is also found complexed with the transcription elongation regulator BYE-1. Expression of brd-8, bye-1, histone hH2Az , and several NuA4 subunits is controlled by the circadian clock, indicating that the molecular clock both regulates the basic chromatin status and is regulated by changes in chromatin. Taken together, our data identify new auxiliary elements of the fungal NuA4 complex having homology to mammalian components, which along with conventional NuA4 subunits, are required for timely and dynamic frq expression and thereby a normal and persistent circadian rhythm.
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24
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Thieme E, Bruss N, Sun D, Dominguez EC, Coleman D, Liu T, Roleder C, Martinez M, Garcia-Mansfield K, Ball B, Pirrotte P, Wang L, Xia Z, Danilov AV. CDK9 inhibition induces epigenetic reprogramming revealing strategies to circumvent resistance in lymphoma. Mol Cancer 2023; 22:64. [PMID: 36998071 PMCID: PMC10061728 DOI: 10.1186/s12943-023-01762-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Accepted: 03/14/2023] [Indexed: 03/31/2023] Open
Abstract
Diffuse large B-cell lymphoma (DLBCL) exhibits significant genetic heterogeneity which contributes to drug resistance, necessitating development of novel therapeutic approaches. Pharmacological inhibitors of cyclin-dependent kinases (CDK) demonstrated pre-clinical activity in DLBCL, however many stalled in clinical development. Here we show that AZD4573, a selective inhibitor of CDK9, restricted growth of DLBCL cells. CDK9 inhibition (CDK9i) resulted in rapid changes in the transcriptome and proteome, with downmodulation of multiple oncoproteins (eg, MYC, Mcl-1, JunB, PIM3) and deregulation of phosphoinotiside-3 kinase (PI3K) and senescence pathways. Following initial transcriptional repression due to RNAPII pausing, we observed transcriptional recovery of several oncogenes, including MYC and PIM3. ATAC-Seq and ChIP-Seq experiments revealed that CDK9i induced epigenetic remodeling with bi-directional changes in chromatin accessibility, suppressed promoter activation and led to sustained reprograming of the super-enhancer landscape. A CRISPR library screen suggested that SE-associated genes in the Mediator complex, as well as AKT1, confer resistance to CDK9i. Consistent with this, sgRNA-mediated knockout of MED12 sensitized cells to CDK9i. Informed by our mechanistic findings, we combined AZD4573 with either PIM kinase or PI3K inhibitors. Both combinations decreased proliferation and induced apoptosis in DLBCL and primary lymphoma cells in vitro as well as resulted in delayed tumor progression and extended survival of mice xenografted with DLBCL in vivo. Thus, CDK9i induces reprogramming of the epigenetic landscape, and super-enhancer driven recovery of select oncogenes may contribute to resistance to CDK9i. PIM and PI3K represent potential targets to circumvent resistance to CDK9i in the heterogeneous landscape of DLBCL.
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Affiliation(s)
- Elana Thieme
- grid.410425.60000 0004 0421 8357City of Hope National Medical Center, 1500 E Duarte Road, Duarte, CA 91010 USA
| | - Nur Bruss
- grid.410425.60000 0004 0421 8357City of Hope National Medical Center, 1500 E Duarte Road, Duarte, CA 91010 USA
| | - Duanchen Sun
- grid.516136.6Knight Cancer Institute, Oregon Health & Science University, Portland, OR USA
- grid.5288.70000 0000 9758 5690Division of Bioinformatics and Computational Biology, Department of Medical Informatics and Clinical Epidemiology, Oregon Health & Science University, Portland, OR USA
- grid.27255.370000 0004 1761 1174Present address: School of Mathematics, Shandong University, Jinan, 250100 Shandong China
| | - Edward C. Dominguez
- grid.410425.60000 0004 0421 8357City of Hope National Medical Center, 1500 E Duarte Road, Duarte, CA 91010 USA
| | - Daniel Coleman
- grid.516136.6Knight Cancer Institute, Oregon Health & Science University, Portland, OR USA
| | - Tingting Liu
- grid.410425.60000 0004 0421 8357City of Hope National Medical Center, 1500 E Duarte Road, Duarte, CA 91010 USA
| | - Carly Roleder
- grid.410425.60000 0004 0421 8357City of Hope National Medical Center, 1500 E Duarte Road, Duarte, CA 91010 USA
| | - Melissa Martinez
- grid.250942.80000 0004 0507 3225Translational Genomics Research Institute, Phoenix, AZ 85004 USA
- grid.410425.60000 0004 0421 8357Integrated Mass Spectrometry Shared Resource, City of Hope National Medical Center, Duarte, CA USA
| | - Krystine Garcia-Mansfield
- grid.250942.80000 0004 0507 3225Translational Genomics Research Institute, Phoenix, AZ 85004 USA
- grid.410425.60000 0004 0421 8357Integrated Mass Spectrometry Shared Resource, City of Hope National Medical Center, Duarte, CA USA
| | - Brian Ball
- grid.410425.60000 0004 0421 8357City of Hope National Medical Center, 1500 E Duarte Road, Duarte, CA 91010 USA
| | - Patrick Pirrotte
- grid.250942.80000 0004 0507 3225Translational Genomics Research Institute, Phoenix, AZ 85004 USA
- grid.410425.60000 0004 0421 8357Integrated Mass Spectrometry Shared Resource, City of Hope National Medical Center, Duarte, CA USA
| | - Lili Wang
- grid.410425.60000 0004 0421 8357City of Hope National Medical Center, 1500 E Duarte Road, Duarte, CA 91010 USA
| | - Zheng Xia
- grid.516136.6Knight Cancer Institute, Oregon Health & Science University, Portland, OR USA
- grid.5288.70000 0000 9758 5690Biomedical Engineering Department, Oregon Health & Science University, Portland, OR USA
| | - Alexey V. Danilov
- grid.410425.60000 0004 0421 8357City of Hope National Medical Center, 1500 E Duarte Road, Duarte, CA 91010 USA
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25
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Toure MA, Koehler AN. Addressing Transcriptional Dysregulation in Cancer through CDK9 Inhibition. Biochemistry 2023; 62:1114-1123. [PMID: 36854448 PMCID: PMC10035036 DOI: 10.1021/acs.biochem.2c00609] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/02/2023]
Abstract
Undermining transcriptional addiction, the dependence of cancers on selected transcriptional programs, is critically important for addressing cancers with high unmet clinical need. Cyclin-dependent kinase 9 (CDK9) has long been considered an actionable therapeutic target for modulating transcription in many diseases. This appeal is due to its role in coordinating the biochemical events that regulate RNA polymerase II (RNA Pol II) pause-release state, one that offers a way for attenuating transcriptional dysregulation driven by amplified or overexpressed transcription factors implicated in cancer. However, targeting CDK9 in the clinic has historically proven elusive, a challenge that stems from the often highly intolerable cytotoxicity attributed to its essentiality across many cell lineages and the polypharmacology of the first generation of pan-CDK inhibitors to reach the clinic. A new wave of highly selective molecules progressing through the early stages of clinical evaluation offers renewed hope.
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Affiliation(s)
- Mohammed A Toure
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
- The Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, United States
| | - Angela N Koehler
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
- The Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, United States
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26
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Zhuang HH, Qu Q, Teng XQ, Dai YH, Qu J. Superenhancers as master gene regulators and novel therapeutic targets in brain tumors. Exp Mol Med 2023; 55:290-303. [PMID: 36720920 PMCID: PMC9981748 DOI: 10.1038/s12276-023-00934-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2022] [Revised: 11/27/2022] [Accepted: 12/04/2022] [Indexed: 02/02/2023] Open
Abstract
Transcriptional deregulation, a cancer cell hallmark, is driven by epigenetic abnormalities in the majority of brain tumors, including adult glioblastoma and pediatric brain tumors. Epigenetic abnormalities can activate epigenetic regulatory elements to regulate the expression of oncogenes. Superenhancers (SEs), identified as novel epigenetic regulatory elements, are clusters of enhancers with cell-type specificity that can drive the aberrant transcription of oncogenes and promote tumor initiation and progression. As gene regulators, SEs are involved in tumorigenesis in a variety of tumors, including brain tumors. SEs are susceptible to inhibition by their key components, such as bromodomain protein 4 and cyclin-dependent kinase 7, providing new opportunities for antitumor therapy. In this review, we summarized the characteristics and identification, unique organizational structures, and activation mechanisms of SEs in tumors, as well as the clinical applications related to SEs in tumor therapy and prognostication. Based on a review of the literature, we discussed the relationship between SEs and different brain tumors and potential therapeutic targets, focusing on glioblastoma.
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Affiliation(s)
- Hai-Hui Zhuang
- Department of Pharmacy, the Second Xiangya Hospital, Central South University, Institute of Clinical Pharmacy, Central South University, Changsha, 410011, PR China
| | - Qiang Qu
- Department of Pharmacy, Xiangya Hospital, Central South University, Changsha, 410007, PR China.,Institute for Rational and Safe Medication Practices, National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, 410007, PR China
| | - Xin-Qi Teng
- Department of Pharmacy, the Second Xiangya Hospital, Central South University, Institute of Clinical Pharmacy, Central South University, Changsha, 410011, PR China
| | - Ying-Huan Dai
- Department of Pathology, the Second Xiangya Hospital, Central South University, Changsha, 410011, PR China
| | - Jian Qu
- Department of Pharmacy, the Second Xiangya Hospital, Central South University, Institute of Clinical Pharmacy, Central South University, Changsha, 410011, PR China.
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27
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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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28
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Wu L, Liu W, Huang Y, Zhu C, Ma Q, Wu Q, Tian L, Feng X, Liu M, Wang N, Xu X, Liu X, Xu C, Qiu J, Xu Z, Liu W, Zhao Q. Development and structure-activity relationship of tacrine derivatives as highly potent CDK2/9 inhibitors for the treatment of cancer. Eur J Med Chem 2022; 242:114701. [DOI: 10.1016/j.ejmech.2022.114701] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Revised: 08/15/2022] [Accepted: 08/17/2022] [Indexed: 11/27/2022]
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29
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Zhang H, Huang J, Chen R, Cai H, Chen Y, He S, Xu J, Zhang J, Wang L. Ligand- and structure-based identification of novel CDK9 inhibitors for the potential treatment of leukemia. Bioorg Med Chem 2022; 72:116994. [PMID: 36087428 DOI: 10.1016/j.bmc.2022.116994] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Revised: 08/21/2022] [Accepted: 08/29/2022] [Indexed: 11/02/2022]
Abstract
Cyclin-dependent kinase 9 (CDK9) plays a vital role in controlling cell transcription and has been an attractive target for cancer treatment. Herein, ten predictive models derived from 1330 unique molecules against CDK9 were constructed based on molecular fingerprints and graphs using two conventional machine learning and four deep learning methods. The evaluation results showed that FP-GNN deep learning architecture performed best for CDK9 inhibitors prediction with the highest BA and F1 values of 0.681 and 0.912 for testing set. We then performed virtual screening to identify new CDK9 inhibitors by incorporating the optimal established predictive model and molecular docking. Five compounds were identified to show broad anticancer activity against various cancer cell lines through bioassays. For example, C9 exhibited antiproliferative activities against HeLa, MOLM-13 and MDA-MB-231 with IC50 values of 2.53, 3.92 and 11.65 μM. Kinase inhibition assay results demonstrated that these compounds displayed submicromolar (214 ∼ 504 nM) inhibitory activities against CDK9. Further cellular mechanism evaluation revealed that C9 suppressed the activity of CDK9 and interfered with the expression of Mcl-1 and cleaved PARP in MOLM-13 cells, resulting in the induction of cellular apoptosis. In addition, C9 displayed a good stability in rat liver microsomes, artificial gastrointestinal fluid and plasm. An online platform (called DEEPCDK9Pred) was developed based on the FP-GNN models to predict or design new CDK9 inhibitors. Collectively, our findings demonstrated that FP-GNN algorithm can achieve accurate prediction of CDK9 inhibitors and the subsequent discovery of C9 as a new potential CDK9 inhibitor deserves further structural modification for the treatment of leukemia.
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Affiliation(s)
- Huimin Zhang
- Guangdong Provincial Key Laboratory of Fermentation and Enzyme Engineering, Joint International Research Laboratory of Synthetic Biology and Medicine, Guangdong Provincial Engineering and Technology Research Center of Biopharmaceuticals, School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, China
| | - Jindi Huang
- Guangdong Provincial Key Laboratory of Fermentation and Enzyme Engineering, Joint International Research Laboratory of Synthetic Biology and Medicine, Guangdong Provincial Engineering and Technology Research Center of Biopharmaceuticals, School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, China
| | - Rui Chen
- State Key Laboratory of Functions and Applications of Medicinal Plants & College of Pharmacy, Guizhou Provincial Engineering Technology Research Center for Chemical Drug R&D, Guizhou Medical University, Guiyang 550004, China
| | - Hanxuan Cai
- Guangdong Provincial Key Laboratory of Fermentation and Enzyme Engineering, Joint International Research Laboratory of Synthetic Biology and Medicine, Guangdong Provincial Engineering and Technology Research Center of Biopharmaceuticals, School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, China
| | - Yihao Chen
- Guangdong Provincial Key Laboratory of Fermentation and Enzyme Engineering, Joint International Research Laboratory of Synthetic Biology and Medicine, Guangdong Provincial Engineering and Technology Research Center of Biopharmaceuticals, School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, China
| | - Shuyun He
- Guangdong Provincial Key Laboratory of Fermentation and Enzyme Engineering, Joint International Research Laboratory of Synthetic Biology and Medicine, Guangdong Provincial Engineering and Technology Research Center of Biopharmaceuticals, School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, China
| | - Jianrong Xu
- Department of Pharmacology and Chemical Biology, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China; Academy of Integrative Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
| | - Jiquan Zhang
- State Key Laboratory of Functions and Applications of Medicinal Plants & College of Pharmacy, Guizhou Provincial Engineering Technology Research Center for Chemical Drug R&D, Guizhou Medical University, Guiyang 550004, China
| | - Ling Wang
- Guangdong Provincial Key Laboratory of Fermentation and Enzyme Engineering, Joint International Research Laboratory of Synthetic Biology and Medicine, Guangdong Provincial Engineering and Technology Research Center of Biopharmaceuticals, School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, China.
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Hang J, Ouyang H, Wei F, Zhong Q, Yuan W, Jiang L, Liu Z. Proteomics and phosphoproteomics of chordoma biopsies reveal alterations in multiple pathways and aberrant kinases activities. Front Oncol 2022; 12:941046. [PMID: 36248973 PMCID: PMC9563620 DOI: 10.3389/fonc.2022.941046] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Accepted: 09/14/2022] [Indexed: 11/26/2022] Open
Abstract
Background Chordoma is a slow-growing but malignant subtype of bone sarcoma with relatively high recurrence rates and high resistance to chemotherapy. It is urgent to understand the underlying regulatory networks to determine more effective potential targets. Phosphorylative regulation is currently regarded as playing a significant role in tumorigenesis, and the use of tyrosine kinase inhibitors in clinical practice has yielded new promise for the treatment of a variety of sarcoma types. Materials and methods We performed comprehensive proteomic and phosphoproteomic analyses of chordoma using four-dimensional label-free liquid chromatography–tandem mass spectrometry (LC-MS/MS) and bioinformatics analysis. The potential aberrantly expressed kinases and their functions were validated using western blotting and CCK-8 assays. Results Compared with paired normal muscle tissues, 1,139 differentially expressed proteins (DEPs) and 776 differentially phosphorylated proteins (DPPs) were identified in chordoma tumor tissues. The developmentally significant Wnt-signaling pathway and oxidative phosphorylation were aberrant in chordoma. Moreover, we predicted three kinases (AURA, CDK9, and MOK) with elevated activity by kinase-pathway network analysis (KiPNA) and verified their increased expression levels. The knockdown of these kinases markedly suppressed chordoma cell growth, and this was also the case for cells treated with the CDK9 inhibitor AZD4573. We additionally examined 208 proteins whose expression and phosphorylation levels were synergetically altered. Conclusions We herein depicted the collective protein profiles of chordomas, providing insight into chordomagenesis and the potential development of new therapeutic targets.
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Affiliation(s)
- Jing Hang
- Center for Reproductive Medicine, Department of Obstetrics and Gynecology, Peking University Third Hospital, Beijing, China
- Key Laboratory of Assisted Reproduction, Ministry of Education, Beijing, China
- Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproduction, Beijing, China
- National Clinical Research Center for Obstetrics and Gynecology, Beijing, China
| | - Hanqiang Ouyang
- Department of Orthopedics, Peking University Third Hospital, Beijing, China
- Beijing Key Laboratory of Spinal Disease, Beijing, China
- Engineering Research Center of Bone and Joint Precision Medicine, Beijing, China
| | - Feng Wei
- Department of Orthopedics, Peking University Third Hospital, Beijing, China
- Beijing Key Laboratory of Spinal Disease, Beijing, China
- Engineering Research Center of Bone and Joint Precision Medicine, Beijing, China
| | - Qihang Zhong
- Center for Reproductive Medicine, Department of Obstetrics and Gynecology, Peking University Third Hospital, Beijing, China
| | - Wanqiong Yuan
- Department of Orthopedics, Peking University Third Hospital, Beijing, China
- Beijing Key Laboratory of Spinal Disease, Beijing, China
- Engineering Research Center of Bone and Joint Precision Medicine, Beijing, China
- *Correspondence: Zhongjun Liu, ; Liang Jiang, ; Wanqiong Yuan,
| | - Liang Jiang
- Department of Orthopedics, Peking University Third Hospital, Beijing, China
- Beijing Key Laboratory of Spinal Disease, Beijing, China
- Engineering Research Center of Bone and Joint Precision Medicine, Beijing, China
- *Correspondence: Zhongjun Liu, ; Liang Jiang, ; Wanqiong Yuan,
| | - Zhongjun Liu
- Department of Orthopedics, Peking University Third Hospital, Beijing, China
- Beijing Key Laboratory of Spinal Disease, Beijing, China
- Engineering Research Center of Bone and Joint Precision Medicine, Beijing, China
- *Correspondence: Zhongjun Liu, ; Liang Jiang, ; Wanqiong Yuan,
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PRC1-independent binding and activity of RYBP on the KSHV genome during de novo infection. PLoS Pathog 2022; 18:e1010801. [PMID: 36026503 PMCID: PMC9455864 DOI: 10.1371/journal.ppat.1010801] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Revised: 09/08/2022] [Accepted: 08/08/2022] [Indexed: 11/19/2022] Open
Abstract
Kaposi’s sarcoma-associated herpesvirus (KSHV) is an oncogenic virus that causes lifelong infection in humans by establishing latency after primary infection. Latent infection is a prerequisite for both persistent infection and the development of KSHV-associated cancers. While viral lytic genes are transiently expressed after primary infection, their expression is significantly restricted and concomitant with the binding of host epigenetic repressors Polycomb Repressive Complex 1 and 2 (PRC1 and PRC2) to lytic genes. PRC1 and PRC2 mediate the repressive histone marks H2AK119ub and H3K27me3, respectively, and maintain heterochromatin structure on KSHV lytic genes to inhibit their expression. In contrast to PRC2, little is known about the recruitment and role of PRC1 factors on the KSHV genome following de novo infection. Thus, the goal of this study was to examine the function of PRC1 factors in the establishment of KSHV latency. To address this question, we performed an shRNA screen targeting 7 different components of the canonical and non-canonical PRC1 complexes during primary KSHV infection. We found that RYBP, a main subunit of the non-canonical PRC1 complexes, is a potent repressor of KSHV lytic genes that can bind to the viral genome and inhibit lytic genes as early as 4 hours post infection. Surprisingly, our ChIP analyses showed that RYBP binds to lytic viral gene promoters in a PRC1-independent manner, does not affect PRC1 activity on the KSHV genome, and can reduce the level of histone marks associated with transcription elongation. Our data also suggest that RYBP can repress the viral lytic cycle after primary infection by inhibiting the transcription elongation of the lytic cycle inducer KSHV gene RTA. Based on our results we propose that RYBP uses a PRC1-independent mechanism to block KSHV RTA expression thereby promoting the establishment of KSHV latency following de novo infection.
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Recyclization of Maleimides by Binucleophiles as a General Approach for Building Hydrogenated Heterocyclic Systems. Molecules 2022; 27:molecules27165268. [PMID: 36014507 PMCID: PMC9416709 DOI: 10.3390/molecules27165268] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Revised: 08/12/2022] [Accepted: 08/16/2022] [Indexed: 11/17/2022] Open
Abstract
The building of heterocyclic systems containing hydrogenated fragments is an important step towards the creation of biologically-active compounds with a wide spectrum of pharmacological activity. Among the numerous methods for creating such systems, a special place is occupied by processes using N-substituted maleimides as the initial substrate. This molecule easily reacts in Diels-Alder/retro-Diels-Alder reactions, Michael additions with various nucleophiles, and co-polymerization processes, as have been described in numerous detailed reviews. However, information on the use of maleimides in cascade heterocyclization reactions is currently limited. This study is devoted to a review and analysis of existing literature data on the processes of recyclization of N-substituted maleimides with various C,N-/N,N-/S,N-di- and polynucleophilic agents, such as amidines, guanidines, diamines, aliphatic ketazines, aminouracils, amino- and mercaptoazoles, aminothiourea, and thiocarbomoyl pyrazolines, among others. The significant structural diversity of the recyclization products described in this study illustrates the powerful potential of maleimides as a building block in the organic synthesis of biologically-active compounds with hydrogenated heterocyclic fragments.
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Synthesis of 4-(tert-Butyldimethylsilyl)-4,5,6,7-tetrahydro-[1,2,3]triazolo[1,5-a]pyridine. MOLBANK 2022. [DOI: 10.3390/m1427] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
SN2 rection between 4-(tert-butyldimethylsilyl)hex-5-yn-1-yl 4-methylbenzenesulfonate and NaN3 in DMF at 80 °C provided (6-azidohex-1-yn-3-yl)(tert-butyl)dimethylsilane intermediate, which underwent in situ intramolecular thermal Huisgen azide–alkyne cycloaddition reaction. This one-pot process gave 4-(tert-butyldimethylsilyl)-4,5,6,7-tetrahydro-[1,2,3]triazolo[1,5-a]pyridine in 78% yield.
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Wang X, Liu X, Huang J, Liu C, Li H, Wang C, Hong Q, Lei Y, Xia J, Yu Z, Dong R, Xu J, Tu Z, Duan C, Li S, Lu T, Tang W, Chen Y. Discovery of 2H-benzo[b][1,4]oxazin-3(4H)-one derivatives as potent and selective CDK9 inhibitors that enable transient target engagement for the treatment of hematologic malignancies. Eur J Med Chem 2022; 238:114461. [PMID: 35605362 DOI: 10.1016/j.ejmech.2022.114461] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Revised: 05/11/2022] [Accepted: 05/11/2022] [Indexed: 11/28/2022]
Abstract
Cyclin-dependent kinase 9 (CDK9) is a transcriptional regulator and a potential therapeutic target in hematologic malignancies. Selective and transient CDK9 inhibition reduces Mcl-1 expression and induces apoptosis in Mcl-1-dependent tumor cells for survival. Here, we describe our efforts to discover a novel series of 2H-benzo[b][1,4]oxazin-3(4H)-one as CDK9 inhibitors. Compound 32k was identified as a selective CDK9 inhibitor with short pharmacokinetic and physicochemical properties suitable for intravenous administration. Short-term treatment with 32k resulted in a rapid dose-dependent decrease in cellular p-Ser2-RNAPII, Mcl-1 and c-Myc, leading to apoptosis in the MV4-11 cell line. Correspondingly, significant in vivo antitumor efficacy was observed in xenograft models derived from multiple hematological tumors with intermittent 32k dosing. These results provide evidence that selective transient CDK9 inhibitors could be used for the treatment of hematologic malignancies.
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Affiliation(s)
- Xinren Wang
- School of Science, China Pharmaceutical University, 639 Longmian Avenue, Nanjing, 211198, PR China
| | - Xiaoyue Liu
- School of Science, China Pharmaceutical University, 639 Longmian Avenue, Nanjing, 211198, PR China
| | - Jianhang Huang
- School of Science, China Pharmaceutical University, 639 Longmian Avenue, Nanjing, 211198, PR China
| | - Chenhe Liu
- School of Science, China Pharmaceutical University, 639 Longmian Avenue, Nanjing, 211198, PR China
| | - Hongmei Li
- School of Science, China Pharmaceutical University, 639 Longmian Avenue, Nanjing, 211198, PR China
| | - Cong Wang
- School of Science, China Pharmaceutical University, 639 Longmian Avenue, Nanjing, 211198, PR China
| | - Qianqian Hong
- School of Science, China Pharmaceutical University, 639 Longmian Avenue, Nanjing, 211198, PR China
| | - Yan Lei
- School of Science, China Pharmaceutical University, 639 Longmian Avenue, Nanjing, 211198, PR China
| | - Jiawei Xia
- School of Science, China Pharmaceutical University, 639 Longmian Avenue, Nanjing, 211198, PR China
| | - Ziheng Yu
- School of Science, China Pharmaceutical University, 639 Longmian Avenue, Nanjing, 211198, PR China
| | - Ruinan Dong
- School of Science, China Pharmaceutical University, 639 Longmian Avenue, Nanjing, 211198, PR China
| | - Junyu Xu
- School of Science, China Pharmaceutical University, 639 Longmian Avenue, Nanjing, 211198, PR China
| | - Zhenlin Tu
- School of Science, China Pharmaceutical University, 639 Longmian Avenue, Nanjing, 211198, PR China
| | - ChunQi Duan
- School of Science, China Pharmaceutical University, 639 Longmian Avenue, Nanjing, 211198, PR China
| | - Shuwen Li
- School of Science, China Pharmaceutical University, 639 Longmian Avenue, Nanjing, 211198, PR China
| | - Tao Lu
- School of Science, China Pharmaceutical University, 639 Longmian Avenue, Nanjing, 211198, PR China; State Key Laboratory of Natural Medicines, China Pharmaceutical University, 24 Tongjiaxiang, Nanjing, 210009, PR China
| | - Weifang Tang
- School of Science, China Pharmaceutical University, 639 Longmian Avenue, Nanjing, 211198, PR China; State Key Laboratory of Natural Medicines, China Pharmaceutical University, 24 Tongjiaxiang, Nanjing, 210009, PR China
| | - Yadong Chen
- School of Science, China Pharmaceutical University, 639 Longmian Avenue, Nanjing, 211198, PR China; State Key Laboratory of Natural Medicines, China Pharmaceutical University, 24 Tongjiaxiang, Nanjing, 210009, PR China.
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Selective CDK9 Inhibition by Natural Compound Toyocamycin in Cancer Cells. Cancers (Basel) 2022; 14:cancers14143340. [PMID: 35884401 PMCID: PMC9324262 DOI: 10.3390/cancers14143340] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Revised: 06/24/2022] [Accepted: 07/04/2022] [Indexed: 11/30/2022] Open
Abstract
Simple Summary By combining drug screens, transcriptomic studies, and in vitro assays, our study identified the natural product toyocamycin as a potent and selective CDK9 inhibitor. Thus, toyocamycin can be used as a new small molecule to modulate CDK9 activity in preclinical research. Through docking simulations, we identified its specific binding sites, which could spark some interest to design novel small molecule CDK9 inhibitors. Abstract Aberrant transcription in cancer cells involves the silencing of tumor suppressor genes (TSGs) and activation of oncogenes. Transcriptomic changes are associated with epigenomic alterations such as DNA-hypermethylation, histone deacetylation, and chromatin condensation in promoter regions of silenced TSGs. To discover novel drugs that trigger TSG reactivation in cancer cells, we used a GFP-reporter system whose expression is silenced by promoter DNA hypermethylation and histone deacetylation. After screening a natural product drug library, we identified that toyocamycin, an adenosine-analog, induces potent GFP reactivation and loss of clonogenicity in human colon cancer cells. Connectivity-mapping analysis revealed that toyocamycin produces a pharmacological signature mimicking cyclin-dependent kinase (CDK) inhibitors. RNA-sequencing revealed that the toyocamycin transcriptomic signature resembles that of a specific CDK9 inhibitor (HH1). Specific inhibition of RNA Pol II phosphorylation level and kinase assays confirmed that toyocamycin specifically inhibits CDK9 (IC50 = 79 nM) with a greater efficacy than other CDKs (IC50 values between 0.67 and 15 µM). Molecular docking showed that toyocamycin efficiently binds the CDK9 catalytic site in a conformation that differs from other CDKs, explained by the binding contribution of specific amino acids within the catalytic pocket and protein backbone. Altogether, we demonstrated that toyocamycin exhibits specific CDK9 inhibition in cancer cells, highlighting its potential for cancer chemotherapy.
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Lemon LD, Kannan S, Mo KW, Adams M, Choi HG, Gulka AOD, Withers ES, Nurelegne HT, Gomez V, Ambrocio RE, Tumminkatti R, Lee RS, Wan M, Fasken MB, Spangle JM, Corbett AH. A Saccharomyces cerevisiae model and screen to define the functional consequences of oncogenic histone missense mutations. G3 GENES|GENOMES|GENETICS 2022; 12:6585874. [PMID: 35567477 PMCID: PMC9258546 DOI: 10.1093/g3journal/jkac120] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Accepted: 05/06/2022] [Indexed: 11/17/2022]
Abstract
Somatic missense mutations in histone genes turn these essential proteins into oncohistones, which can drive oncogenesis. Understanding how missense mutations alter histone function is challenging in mammals as mutations occur in a single histone gene. For example, described oncohistone mutations predominantly occur in the histone H3.3 gene, despite the human genome encoding 15 H3 genes. To understand how oncogenic histone missense mutations alter histone function, we leveraged the budding yeast model, which contains only 2 H3 genes, to explore the functional consequences of oncohistones H3K36M, H3G34W, H3G34L, H3G34R, and H3G34V. Analysis of cells that express each of these variants as the sole copy of H3 reveals that H3K36 mutants show different drug sensitivities compared to H3G34 mutants. This finding suggests that changes to proximal amino acids in the H3 N-terminal tail alter distinct biological pathways. We exploited the caffeine-sensitive growth of H3K36-mutant cells to perform a high copy suppressor screen. This screen identified genes linked to histone function and transcriptional regulation, including Esa1, a histone H4/H2A acetyltransferase; Tos4, a forkhead-associated domain-containing gene expression regulator; Pho92, an N6-methyladenosine RNA-binding protein; and Sgv1/Bur1, a cyclin-dependent kinase. We show that the Esa1 lysine acetyltransferase activity is critical for suppression of the caffeine-sensitive growth of H3K36R-mutant cells while the previously characterized binding interactions of Tos4 and Pho92 are not required for suppression. This screen identifies pathways that could be altered by oncohistone mutations and highlights the value of yeast genetics to identify pathways altered by such mutations.
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Affiliation(s)
- Laramie D Lemon
- Department of Biology, Emory University , Atlanta, GA 30322, USA
| | - Sneha Kannan
- Department of Biology, Emory University , Atlanta, GA 30322, USA
| | - Kim Wai Mo
- Department of Biology, Emory University , Atlanta, GA 30322, USA
| | - Miranda Adams
- Department of Biology, Emory University , Atlanta, GA 30322, USA
- Department of Radiation Oncology, Emory University , Atlanta, GA 30322, USA
- Graduate Program in Cancer Biology, Emory University , Atlanta, GA 30322, USA
| | - Haley G Choi
- Department of Biology, Emory University , Atlanta, GA 30322, USA
- Department of Radiation Oncology, Emory University , Atlanta, GA 30322, USA
| | - Alexander O D Gulka
- Department of Biology, Emory University , Atlanta, GA 30322, USA
- Graduate Program in Genetics and Molecular Biology, Emory University , Atlanta, GA 30322, USA
| | - Elise S Withers
- Department of Biology, Emory University , Atlanta, GA 30322, USA
| | | | - Valeria Gomez
- Department of Biology, Emory University , Atlanta, GA 30322, USA
| | - Reina E Ambrocio
- Department of Biology, Emory University , Atlanta, GA 30322, USA
| | - Rhea Tumminkatti
- Department of Biology, Emory University , Atlanta, GA 30322, USA
| | - Richard S Lee
- Department of Biology, Emory University , Atlanta, GA 30322, USA
- Department of Radiation Oncology, Emory University , Atlanta, GA 30322, USA
| | - Morris Wan
- Department of Biology, Emory University , Atlanta, GA 30322, USA
| | - Milo B Fasken
- Department of Biology, Emory University , Atlanta, GA 30322, USA
| | - Jennifer M Spangle
- Department of Radiation Oncology, Emory University , Atlanta, GA 30322, USA
| | - Anita H Corbett
- Department of Biology, Emory University , Atlanta, GA 30322, USA
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Targeting cyclin-dependent kinase 9 in cancer therapy. Acta Pharmacol Sin 2022; 43:1633-1645. [PMID: 34811514 PMCID: PMC9253122 DOI: 10.1038/s41401-021-00796-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Accepted: 10/12/2021] [Indexed: 12/12/2022] Open
Abstract
Cyclin-dependent kinase (CDK) 9 associates mainly with cyclin T1 and forms the positive transcription elongation factor b (p-TEFb) complex responsible for transcriptional regulation. It has been shown that CDK9 modulates the expression and activity of oncogenes, such as MYC and murine double minute 4 (MDM4), and it also plays an important role in development and/or maintenance of the malignant cell phenotype. Malfunction of CDK9 is frequently observed in numerous cancers. Recent studies have highlighted the function of CDK9 through a variety of mechanisms in cancers, including the formation of new complexes and epigenetic alterations. Due to the importance of CDK9 activation in cancer cells, CDK9 inhibitors have emerged as promising candidates for cancer therapy. Natural product-derived and chemically synthesized CDK9 inhibitors are being examined in preclinical and clinical research. In this review, we summarize the current knowledge on the role of CDK9 in transcriptional regulation, epigenetic regulation, and different cellular factor interactions, focusing on new advances. We show the importance of CDK9 in mediating tumorigenesis and tumor progression. Then, we provide an overview of some CDK9 inhibitors supported by multiple oncologic preclinical and clinical investigations. Finally, we discuss the perspective and challenge of CDK9 modulation in cancer.
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Transcription associated cyclin-dependent kinases as therapeutic targets for prostate cancer. Oncogene 2022; 41:3303-3315. [PMID: 35568739 PMCID: PMC9187515 DOI: 10.1038/s41388-022-02347-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Revised: 04/21/2022] [Accepted: 05/04/2022] [Indexed: 11/08/2022]
Abstract
Transcriptional deregulation has emerged as a hallmark of several cancer types. In metastatic castration-resistant prostate cancer, a stage in which systemic androgen deprivation therapies fail to show clinical benefit, transcriptional addiction to the androgen receptor is maintained in most patients. This has led to increased efforts to find novel therapies that prevent oncogenic transactivation of the androgen receptor. In this context, a group of druggable protein kinases, known as transcription associated cyclin-dependent kinases (tCDKs), show great potential as therapeutic targets. Despite initial reservations about targeting tCDKs due to their ubiquitous and prerequisite nature, preclinical studies showed that selectively inhibiting such kinases could provide sufficient therapeutic window to exert antitumour effects in the absence of systemic toxicity. As a result, several highly specific inhibitors are currently being trialled in solid tumours, including prostate cancer. This article summarises the roles of tCDKs in regulating gene transcription and highlights rationales for their targeting in prostate cancer. It provides an overview of the most recent developments in this therapeutic area, including the most recent clinical advances, and discusses the utility of tCDK inhibitors in combination with established cancer agents.
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Gao W, Hu H, Dai L, He M, Yuan H, Zhang H, Liao J, Wen B, Li Y, Palmisano M, Traore MDM, Zhou S, Sun D. Structure‒tissue exposure/selectivity relationship (STR) correlates with clinical efficacy/safety. Acta Pharm Sin B 2022; 12:2462-2478. [PMID: 35646532 PMCID: PMC9136610 DOI: 10.1016/j.apsb.2022.02.015] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2021] [Revised: 01/23/2022] [Accepted: 02/12/2022] [Indexed: 11/17/2022] Open
Abstract
Drug optimization, which improves drug potency/specificity by structure‒activity relationship (SAR) and drug-like properties, is rigorously performed to select drug candidates for clinical trials. However, the current drug optimization may overlook the structure‒tissue exposure/selectivity-relationship (STR) in disease-targeted tissues vs. normal tissues, which may mislead the drug candidate selection and impact the balance of clinical efficacy/toxicity. In this study, we investigated the STR in correlation with observed clinical efficacy/toxicity using seven selective estrogen receptor modulators (SERMs) that have similar structures, same molecular target, and similar/different pharmacokinetics. The results showed that drug's plasma exposure was not correlated with drug's exposures in the target tissues (tumor, fat pad, bone, uterus), while tissue exposure/selectivity of SERMs was correlated with clinical efficacy/safety. Slight structure modifications of four SERMs did not change drug's plasma exposure but altered drug's tissue exposure/selectivity. Seven SERMs with high protein binding showed higher accumulation in tumors compared to surrounding normal tissues, which is likely due to tumor EPR effect of protein-bound drugs. These suggest that STR alters drug's tissue exposure/selectivity in disease-targeted tissues vs. normal tissues impacting clinical efficacy/toxicity. Drug optimization needs to balance the SAR and STR in selecting drug candidate for clinical trial to improve success of clinical drug development.
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Affiliation(s)
- Wei Gao
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Michigan, Ann Arbor, MI 48109, USA
| | - Hongxiang Hu
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Michigan, Ann Arbor, MI 48109, USA
| | - Lipeng Dai
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Michigan, Ann Arbor, MI 48109, USA
| | - Miao He
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Michigan, Ann Arbor, MI 48109, USA
| | - Hebao Yuan
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Michigan, Ann Arbor, MI 48109, USA
| | - Huixia Zhang
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Michigan, Ann Arbor, MI 48109, USA
| | - Jinhui Liao
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Michigan, Ann Arbor, MI 48109, USA
| | - Bo Wen
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Michigan, Ann Arbor, MI 48109, USA
| | - Yan Li
- Translational Development and Clinical Pharmacology, Bristol Myers Squibb, Summit, NJ 07920, USA
| | - Maria Palmisano
- Translational Development and Clinical Pharmacology, Bristol Myers Squibb, Summit, NJ 07920, USA
| | - Mohamed Dit Mady Traore
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Michigan, Ann Arbor, MI 48109, USA
| | - Simon Zhou
- Translational Development and Clinical Pharmacology, Bristol Myers Squibb, Summit, NJ 07920, USA
| | - Duxin Sun
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Michigan, Ann Arbor, MI 48109, USA
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40
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Karlsson S, Benson H, Cook C, Currie G, Dubiez J, Emtenäs H, Hawkins J, Meadows R, Smith PD, Varnes J. From Milligram to Kilogram Manufacture of AZD4573: Making It Possible by Application of Enzyme-, Iridium-, and Palladium-Catalyzed Key Transformations. Org Process Res Dev 2022. [DOI: 10.1021/acs.oprd.1c00058] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Staffan Karlsson
- Early Chemical Development, Pharmaceutical Sciences, Biopharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Helen Benson
- Early Chemical Development, Pharmaceutical Sciences, Biopharmaceuticals R&D, AstraZeneca, Macclesfield, United Kingdom
| | - Calum Cook
- Early Chemical Development, Pharmaceutical Sciences, Biopharmaceuticals R&D, AstraZeneca, Macclesfield, United Kingdom
| | - Gordon Currie
- Early Chemical Development, Pharmaceutical Sciences, Biopharmaceuticals R&D, AstraZeneca, Macclesfield, United Kingdom
| | - Jerome Dubiez
- Early Chemical Development, Pharmaceutical Sciences, Biopharmaceuticals R&D, AstraZeneca, Macclesfield, United Kingdom
| | - Hans Emtenäs
- Early Chemical Development, Pharmaceutical Sciences, Biopharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Janet Hawkins
- Medicinal Chemistry, Oncology R&D, AstraZeneca, Cambridge, United Kingdom
| | - Rebecca Meadows
- Chemical Development, Pharmaceutical Technology & Development, Operations, AstraZeneca, Macclesfield, United Kingdom
| | - Peter D. Smith
- Early Chemical Development, Pharmaceutical Sciences, Biopharmaceuticals R&D, AstraZeneca, Macclesfield, United Kingdom
| | - Jeffrey Varnes
- Medicinal Chemistry, Oncology R&D, AstraZeneca, Boston, Massachusetts 02451, United States
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41
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Sun D, Gao W, Hu H, Zhou S. Why 90% of clinical drug development fails and how to improve it? Acta Pharm Sin B 2022; 12:3049-3062. [PMID: 35865092 PMCID: PMC9293739 DOI: 10.1016/j.apsb.2022.02.002] [Citation(s) in RCA: 296] [Impact Index Per Article: 148.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2021] [Revised: 02/03/2022] [Accepted: 02/06/2022] [Indexed: 12/14/2022] Open
Abstract
Ninety percent of clinical drug development fails despite implementation of many successful strategies, which raised the question whether certain aspects in target validation and drug optimization are overlooked? Current drug optimization overly emphasizes potency/specificity using structure‒activity-relationship (SAR) but overlooks tissue exposure/selectivity in disease/normal tissues using structure‒tissue exposure/selectivity–relationship (STR), which may mislead the drug candidate selection and impact the balance of clinical dose/efficacy/toxicity. We propose structure‒tissue exposure/selectivity–activity relationship (STAR) to improve drug optimization, which classifies drug candidates based on drug's potency/selectivity, tissue exposure/selectivity, and required dose for balancing clinical efficacy/toxicity. Class I drugs have high specificity/potency and high tissue exposure/selectivity, which needs low dose to achieve superior clinical efficacy/safety with high success rate. Class II drugs have high specificity/potency and low tissue exposure/selectivity, which requires high dose to achieve clinical efficacy with high toxicity and needs to be cautiously evaluated. Class III drugs have relatively low (adequate) specificity/potency but high tissue exposure/selectivity, which requires low dose to achieve clinical efficacy with manageable toxicity but are often overlooked. Class IV drugs have low specificity/potency and low tissue exposure/selectivity, which achieves inadequate efficacy/safety, and should be terminated early. STAR may improve drug optimization and clinical studies for the success of clinical drug development.
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42
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Borowczak J, Szczerbowski K, Ahmadi N, Szylberg Ł. CDK9 inhibitors in multiple myeloma: a review of progress and perspectives. Med Oncol 2022; 39:39. [PMID: 35092513 PMCID: PMC8800928 DOI: 10.1007/s12032-021-01636-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Accepted: 12/21/2021] [Indexed: 12/05/2022]
Abstract
Currently, multiple myeloma is not yet considered a curable disease. Despite the recent advances in therapy, the average patient lifespan is still unsatisfactory. Recently, CDK9 inhibitors emerged as a suitable agent to overcome resistance and prolong survival in patients with poor diagnoses. Downregulation of c-MYC, XIAP, Mcl-1 and restoration of p53 tumor-suppressive functions seems to play a key role in achieving clinical response. The applicability of the first generation of CDK9 inhibitors was limited due to relatively high toxicity, but the introduction of novel, highly selective drugs, seems to reduce the effects of off-target inhibition. CDK9 inhibitors were able to induce dose-dependent cytotoxicity in Doxorubicin-resistant, Lenalidomide-resistant and Bortezomib-resistant cell lines. They seem to be effective in cell lines with unfavorable prognostic factors, such as p53 deletion, t(4; 14) and t(14; 16). In preclinical trials, the application of CDK9 inhibitors led to tumor cells apoptosis, tumor growth inhibition and tumor mass reduction. Synergistic effects between CDK9 inhibitors and either Venetoclax, Bortezomib, Lenalidomide or Erlotinib have been proven and are awaiting verification in clinical trials. Although conclusions should be drawn with due care, obtained reports suggest that including CDK9 inhibitors into the current drug regimen may turn out to be beneficial, especially in poor prognosis patients.
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Affiliation(s)
- Jędrzej Borowczak
- Department of Clinical Pathomorphology, Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University in Torun, Bydgoszcz, Poland.
| | - Krzysztof Szczerbowski
- Department of Clinical Pathomorphology, Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University in Torun, Bydgoszcz, Poland
| | - Navid Ahmadi
- Department of Cardiothoracic Surgery, Royal Papworth Hospital, Cambridge, UK
| | - Łukasz Szylberg
- Department of Clinical Pathomorphology, Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University in Torun, Bydgoszcz, Poland
- Department of Tumor Pathology and Pathomorphology, Oncology Centre-Prof. Franciszek Łukaszczyk Memorial Hospital, Bydgoszcz, Poland
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43
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Hendricks JA, Beaton N, Chernobrovkin A, Miele E, Hamza GM, Ricchiuto P, Tomlinson RC, Friman T, Borenstain C, Barlaam B, Hande S, Lamb ML, De Savi C, Davies R, Main M, Hellner J, Beeler K, Feng Y, Bruderer R, Reiter L, Molina DM, Castaldi MP. Mechanistic Insights into a CDK9 Inhibitor Via Orthogonal Proteomics Methods. ACS Chem Biol 2022; 17:54-67. [PMID: 34955012 DOI: 10.1021/acschembio.1c00488] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Cyclin-dependent-kinases (CDKs) are members of the serine/threonine kinase family and are highly regulated by cyclins, a family of regulatory subunits that bind to CDKs. CDK9 represents one of the most studied examples of these transcriptional CDKs. CDK9 forms a heterodimeric complex with its regulatory subunit cyclins T1, T2 and K to form the positive transcription elongation factor b (P-TEFb). This complex regulates transcription via the phosphorylation of RNA polymerase II (RNAPolII) on Ser-2, facilitating promoter clearance and transcription elongation and thus remains an attractive therapeutic target. Herein, we have utilized classical affinity purification chemical proteomics, kinobeads assay, compressed CEllular Thermal Shift Assay (CETSA)-MS and Limited Proteolysis (LiP) to study the selectivity, target engagement and downstream mechanistic insights of a CDK9 tool compound. The above experiments highlight the value of quantitative mass spectrometry approaches to drug discovery, specifically proteome wide target identification and selectivity profiling. The approaches utilized in this study unanimously indicated that the CDK family of kinases are the main target of the compound of interest, with CDK9, showing the highest target affinity with remarkable consistency across approaches. We aim to provide guidance to the scientific community on the available chemical biology/proteomic tools to study advanced lead molecules and to highlight pros and cons of each technology while describing our findings in the context of the CDKs biology.
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Affiliation(s)
- J. Adam Hendricks
- Discovery Sciences, AstraZeneca, Boston, Massachusetts 02451, United States
| | - Nigel Beaton
- Biognosys AG, Wagistrasse 21, Schlieren 8952, Switzerland
| | | | - Eric Miele
- Discovery Sciences, AstraZeneca, Boston, Massachusetts 02451, United States
| | - Ghaith M. Hamza
- Discovery Sciences, AstraZeneca, Boston, Massachusetts 02451, United States
- Molecular, Cellular and Biomedical Sciences, University of New Hampshire, Durham, New Hampshire 03824, United States
| | | | | | - Tomas Friman
- Pelago Bioscience AB, Banvaktsvägen 20, Solna 17148, Sweden
| | | | | | - Sudhir Hande
- Oncology R&D, Boston, Massachusetts 02451, United States
| | | | - Chris De Savi
- Oncology R&D, Boston, Massachusetts 02451, United States
| | - Rick Davies
- Discovery Sciences, AstraZeneca, Cambridge CB4 0WG, U.K
| | - Martin Main
- Discovery Sciences, AstraZeneca, Cambridge CB4 0WG, U.K
| | - Joakim Hellner
- Pelago Bioscience AB, Banvaktsvägen 20, Solna 17148, Sweden
| | | | - Yuehan Feng
- Biognosys AG, Wagistrasse 21, Schlieren 8952, Switzerland
| | | | - Lukas Reiter
- Biognosys AG, Wagistrasse 21, Schlieren 8952, Switzerland
| | | | - M. Paola Castaldi
- Discovery Sciences, AstraZeneca, Boston, Massachusetts 02451, United States
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44
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Vervoort SJ, Devlin JR, Kwiatkowski N, Teng M, Gray NS, Johnstone RW. Targeting transcription cycles in cancer. Nat Rev Cancer 2022; 22:5-24. [PMID: 34675395 DOI: 10.1038/s41568-021-00411-8] [Citation(s) in RCA: 50] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 09/09/2021] [Indexed: 12/15/2022]
Abstract
Accurate control of gene expression is essential for normal development and dysregulation of transcription underpins cancer onset and progression. Similar to cell cycle regulation, RNA polymerase II-driven transcription can be considered as a unidirectional multistep cycle, with thousands of unique transcription cycles occurring in concert within each cell. Each transcription cycle comprises recruitment, initiation, pausing, elongation, termination and recycling stages that are tightly controlled by the coordinated action of transcriptional cyclin-dependent kinases and their cognate cyclins as well as the opposing activity of transcriptional phosphatases. Oncogenic dysregulation of transcription can entail defective control of gene expression, either at select loci or more globally, impacting a large proportion of the genome. The resultant dependency on the core-transcriptional machinery is believed to render 'transcriptionally addicted' cancers sensitive to perturbation of transcription. Based on these findings, small molecules targeting transcriptional cyclin-dependent kinases and associated proteins hold promise for the treatment of cancer. Here, we utilize the transcription cycles concept to explain how dysregulation of these finely tuned gene expression processes may drive tumorigenesis and how therapeutically beneficial responses may arise from global or selective transcriptional perturbation. This conceptual framework helps to explain tumour-selective transcriptional dependencies and facilitates the rational design of combination therapies.
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Affiliation(s)
- Stephin J Vervoort
- Gene Regulation Laboratory, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
- The Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, VIC, Australia
| | - Jennifer R Devlin
- Gene Regulation Laboratory, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
- The Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, VIC, Australia
| | - Nicholas Kwiatkowski
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Mingxing Teng
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Nathanael S Gray
- Department of Chemical and Systems Biology, CHEM-H and SCI, Stanford Medical School, Stanford University, Stanford, CA, USA.
| | - Ricky W Johnstone
- Gene Regulation Laboratory, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia.
- The Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, VIC, Australia.
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45
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Liu W, Huang Y, Wu L, Liu W, Jiang X, Xu Z, Zhao Q. Novel tacrine derivatives as potential CDK9 inhibitors with low cholinesterase inhibitory properties: design, synthesis, and biological evaluation. NEW J CHEM 2022. [DOI: 10.1039/d2nj03667c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Novel tacrine derivative ZLWT-48 possessed potent CDK9 inhibition activity (8.639 nM) and good selectivity over CDK2 (SI > 57).
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Affiliation(s)
- Wenwu Liu
- Teaching Hospital of Shenyang Pharmaceutical University, General Hospital of Northern Theater Command, Shenyang 110840, People's Republic of China
- School of Traditional Chinese Materia Medica, Shenyang Pharmaceutical University, Shenyang 110016, People's Republic of China
| | - Yaoguang Huang
- School of Traditional Chinese Materia Medica, Shenyang Pharmaceutical University, Shenyang 110016, People's Republic of China
| | - Limeng Wu
- School of Traditional Chinese Materia Medica, Shenyang Pharmaceutical University, Shenyang 110016, People's Republic of China
| | - Wenjie Liu
- School of Traditional Chinese Materia Medica, Shenyang Pharmaceutical University, Shenyang 110016, People's Republic of China
| | - Xiaowen Jiang
- School of Traditional Chinese Materia Medica, Shenyang Pharmaceutical University, Shenyang 110016, People's Republic of China
| | - Zihua Xu
- Teaching Hospital of Shenyang Pharmaceutical University, General Hospital of Northern Theater Command, Shenyang 110840, People's Republic of China
- School of Pharmacy, Shenyang Pharmaceutical University, Shenyang 110016, People's Republic of China
| | - Qingchun Zhao
- Teaching Hospital of Shenyang Pharmaceutical University, General Hospital of Northern Theater Command, Shenyang 110840, People's Republic of China
- School of Traditional Chinese Materia Medica, Shenyang Pharmaceutical University, Shenyang 110016, People's Republic of China
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46
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Huang Z, Wang T, Wang C, Fan Y. CDK9 Inhibitors in Cancer Research. RSC Med Chem 2022; 13:688-710. [PMID: 35814933 PMCID: PMC9215160 DOI: 10.1039/d2md00040g] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Accepted: 04/16/2022] [Indexed: 11/21/2022] Open
Abstract
Cyclin dependent kinase 9 (CDK9) played an essential role in regulating transcriptional elongation. Aberrations in CDK9 activity have been observed in various cancers, which made CDK9 was an attractive therapeutic...
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Affiliation(s)
- Zhi Huang
- Department of Medicinal Chemistry, School of Medicine, Nankai University 94 Weijin Road Tianjin 300071 China
- Anhui Province Key Laboratory of Medical Physics and Technology, Institute of Health and Medical Technology, Hefei Institutes of Physical Science, Chinese Academy of Sciences Hefei 230031 China
| | - Tianqi Wang
- Department of Medicinal Chemistry, School of Medicine, Nankai University 94 Weijin Road Tianjin 300071 China
| | - Cheng Wang
- Department of Medicinal Chemistry, School of Medicine, Nankai University 94 Weijin Road Tianjin 300071 China
| | - Yan Fan
- Department of Medicinal Chemistry, School of Medicine, Nankai University 94 Weijin Road Tianjin 300071 China
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47
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Andrews DM, Cartic S, Cosulich S, Divecha N, Faulder P, Flemington V, Kern O, Kettle JG, MacDonald E, McKelvie J, Pike KG, Roberts B, Rowlinson R, Smith JM, Stockley M, Swarbrick ME, Treinies I, Waring MJ. Identification and optimization of a novel series of selective PIP5K inhibitors. Bioorg Med Chem 2021; 54:116557. [PMID: 34922306 DOI: 10.1016/j.bmc.2021.116557] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Revised: 12/02/2021] [Accepted: 12/03/2021] [Indexed: 11/02/2022]
Abstract
Phosphatidyl inositol (4,5)-bisphosphate (PI(4,5)P2) plays several key roles in human biology and the lipid kinase that produces PI(4,5)P2, PIP5K, has been hypothesized to provide a potential therapeutic target of interest in the treatment of cancers. To better understand and explore the role of PIP5K in human cancers there remains an urgent need for potent and specific PIP5K inhibitor molecules. Following a high throughput screen of the AstraZeneca collection, a novel, moderately potent and selective inhibitor of PIP5K, 1, was discovered. Detailed exploration of the SAR for this novel scaffold resulted in the considerable optimization of both potency for PIP5K, and selectivity over the closely related kinase PI3Kα, as well as identifying several opportunities for the continued optimization of drug-like properties. As a result, several high quality in vitro tool compounds were identified (8, 20 and 25) that demonstrate the desired biochemical and cellular profiles required to aid better understanding of this complex area of biology.
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Affiliation(s)
- David M Andrews
- Medicinal Chemistry, Oncology R&D, Research and Early Development, AstraZeneca, Cambridge Science Park, Unit 310 Darwin Building, Cambridge CB4 0WG, UK
| | - Sharon Cartic
- Cancer Research UK Therapeutic Discovery Laboratories, Jonas Webb Building, Babraham Research Campus, Cambridge CB22 3AT, UK
| | - Sabina Cosulich
- Medicinal Chemistry, Oncology R&D, Research and Early Development, AstraZeneca, Cambridge Science Park, Unit 310 Darwin Building, Cambridge CB4 0WG, UK
| | - Nullin Divecha
- Inositide Laboratory, School of Biological Sciences, Faculty of Environmental and Life Sciences, Life Sciences Building 85, University of Southampton, Highfield Campus, Southampton, SO17 1BJ, UK
| | - Paul Faulder
- Medicinal Chemistry, Oncology R&D, Research and Early Development, AstraZeneca, Cambridge Science Park, Unit 310 Darwin Building, Cambridge CB4 0WG, UK
| | - Vikki Flemington
- Medicinal Chemistry, Oncology R&D, Research and Early Development, AstraZeneca, Cambridge Science Park, Unit 310 Darwin Building, Cambridge CB4 0WG, UK
| | - Oliver Kern
- Cancer Research UK Therapeutic Discovery Laboratories, Jonas Webb Building, Babraham Research Campus, Cambridge CB22 3AT, UK
| | - Jason G Kettle
- Medicinal Chemistry, Oncology R&D, Research and Early Development, AstraZeneca, Cambridge Science Park, Unit 310 Darwin Building, Cambridge CB4 0WG, UK
| | - Ellen MacDonald
- Cancer Research UK Therapeutic Discovery Laboratories, Jonas Webb Building, Babraham Research Campus, Cambridge CB22 3AT, UK
| | - Jennifer McKelvie
- Cancer Research UK Therapeutic Discovery Laboratories, Jonas Webb Building, Babraham Research Campus, Cambridge CB22 3AT, UK
| | - Kurt G Pike
- Medicinal Chemistry, Oncology R&D, Research and Early Development, AstraZeneca, Cambridge Science Park, Unit 310 Darwin Building, Cambridge CB4 0WG, UK
| | - Bryan Roberts
- Medicinal Chemistry, Oncology R&D, Research and Early Development, AstraZeneca, Cambridge Science Park, Unit 310 Darwin Building, Cambridge CB4 0WG, UK
| | - Rachel Rowlinson
- Medicinal Chemistry, Oncology R&D, Research and Early Development, AstraZeneca, Cambridge Science Park, Unit 310 Darwin Building, Cambridge CB4 0WG, UK
| | - James M Smith
- Medicinal Chemistry, Oncology R&D, Research and Early Development, AstraZeneca, Cambridge Science Park, Unit 310 Darwin Building, Cambridge CB4 0WG, UK.
| | - Martin Stockley
- Cancer Research UK Therapeutic Discovery Laboratories, Jonas Webb Building, Babraham Research Campus, Cambridge CB22 3AT, UK
| | - Martin E Swarbrick
- Cancer Research UK Therapeutic Discovery Laboratories, Jonas Webb Building, Babraham Research Campus, Cambridge CB22 3AT, UK
| | - Iris Treinies
- Cancer Research UK Therapeutic Discovery Laboratories, Jonas Webb Building, Babraham Research Campus, Cambridge CB22 3AT, UK
| | - Michael J Waring
- Medicinal Chemistry, Oncology R&D, Research and Early Development, AstraZeneca, Cambridge Science Park, Unit 310 Darwin Building, Cambridge CB4 0WG, UK
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48
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Fairlie WD, Lee EF. Targeting the BCL-2-regulated apoptotic pathway for the treatment of solid cancers. Biochem Soc Trans 2021; 49:2397-2410. [PMID: 34581776 PMCID: PMC8589438 DOI: 10.1042/bst20210750] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Revised: 08/31/2021] [Accepted: 09/02/2021] [Indexed: 12/14/2022]
Abstract
The deregulation of apoptosis is a key contributor to tumourigenesis as it can lead to the unwanted survival of rogue cells. Drugs known as the BH3-mimetics targeting the pro-survival members of the BCL-2 protein family to induce apoptosis in cancer cells have achieved clinical success for the treatment of haematological malignancies. However, despite our increasing knowledge of the pro-survival factors mediating the unwanted survival of solid tumour cells, and our growing BH3-mimetics armamentarium, the application of BH3-mimetic therapy in solid cancers has not reached its full potential. This is mainly attributed to the need to identify clinically safe, yet effective, combination strategies to target the multiple pro-survival proteins that typically mediate the survival of solid tumours. In this review, we discuss current and exciting new developments in the field that has the potential to unleash the full power of BH3-mimetic therapy to treat currently recalcitrant solid malignancies.
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Affiliation(s)
- W. Douglas Fairlie
- Cell Death and Survival Laboratory, Olivia Newton-John Cancer Research Institute, Heidelberg, Victoria 3084, Australia
- Cell Death and Survival Laboratory, School of Cancer Medicine, La Trobe University, Bundoora, Victoria 3086, Australia
- La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria 3086, Australia
| | - Erinna F. Lee
- Cell Death and Survival Laboratory, Olivia Newton-John Cancer Research Institute, Heidelberg, Victoria 3084, Australia
- Cell Death and Survival Laboratory, School of Cancer Medicine, La Trobe University, Bundoora, Victoria 3086, Australia
- La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria 3086, Australia
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49
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Barlaam B, De Savi C, Dishington A, Drew L, Ferguson AD, Ferguson D, Gu C, Hande S, Hassall L, Hawkins J, Hird AW, Holmes J, Lamb ML, Lister AS, McGuire TM, Moore JE, O'Connell N, Patel A, Pike KG, Sarkar U, Shao W, Stead D, Varnes JG, Vasbinder MM, Wang L, Wu L, Xue L, Yang B, Yao T. Discovery of a Series of 7-Azaindoles as Potent and Highly Selective CDK9 Inhibitors for Transient Target Engagement. J Med Chem 2021; 64:15189-15213. [PMID: 34647738 DOI: 10.1021/acs.jmedchem.1c01249] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Optimization of a series of azabenzimidazoles identified from screening hit 2 and the information gained from a co-crystal structure of the azabenzimidazole-based lead 6 bound to CDK9 led to the discovery of azaindoles as highly potent and selective CDK9 inhibitors. With the goal of discovering a highly selective and potent CDK9 inhibitor administrated intravenously that would enable transient target engagement of CDK9 for the treatment of hematological malignancies, further optimization focusing on physicochemical and pharmacokinetic properties led to azaindoles 38 and 39. These compounds are highly potent and selective CDK9 inhibitors having short half-lives in rodents, suitable physical properties for intravenous administration, and the potential to achieve profound but transient inhibition of CDK9 in vivo.
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Affiliation(s)
- Bernard Barlaam
- Oncology R&D, AstraZeneca, Cambridge CB4 0WG, United Kingdom
| | - Chris De Savi
- Oncology R&D, AstraZeneca, Boston, Massachusetts 02451, United States
| | | | - Lisa Drew
- Oncology R&D, AstraZeneca, Boston, Massachusetts 02451, United States
| | - Andrew D Ferguson
- Discovery Sciences, AstraZeneca, Boston, Massachusetts 02451, United States
| | - Douglas Ferguson
- Oncology R&D, AstraZeneca, Boston, Massachusetts 02451, United States
| | - Chungang Gu
- Oncology R&D, AstraZeneca, Boston, Massachusetts 02451, United States
| | - Sudhir Hande
- Oncology R&D, AstraZeneca, Boston, Massachusetts 02451, United States
| | | | - Janet Hawkins
- Oncology R&D, AstraZeneca, Cambridge CB4 0WG, United Kingdom
| | - Alexander W Hird
- Oncology R&D, AstraZeneca, Boston, Massachusetts 02451, United States
| | - Jane Holmes
- Oncology R&D, AstraZeneca, Cambridge CB4 0WG, United Kingdom
| | - Michelle L Lamb
- Oncology R&D, AstraZeneca, Boston, Massachusetts 02451, United States
| | - Andrew S Lister
- Oncology R&D, AstraZeneca, Cambridge CB4 0WG, United Kingdom
| | | | - Jane E Moore
- Oncology R&D, AstraZeneca, Cambridge CB4 0WG, United Kingdom
| | - Nichole O'Connell
- Discovery Sciences, AstraZeneca, Boston, Massachusetts 02451, United States
| | - Anil Patel
- Oncology R&D, AstraZeneca, Cambridge CB4 0WG, United Kingdom
| | - Kurt G Pike
- Oncology R&D, AstraZeneca, Cambridge CB4 0WG, United Kingdom
| | - Ujjal Sarkar
- Oncology R&D, AstraZeneca, Boston, Massachusetts 02451, United States
| | - Wenlin Shao
- Oncology R&D, AstraZeneca, Boston, Massachusetts 02451, United States
| | - Darren Stead
- Oncology R&D, AstraZeneca, Cambridge CB4 0WG, United Kingdom
| | - Jeffrey G Varnes
- Oncology R&D, AstraZeneca, Boston, Massachusetts 02451, United States
| | | | - Lei Wang
- Pharmaron Beijing Co., Ltd., 6 Taihe Road BDA, Beijing 100176, P. R. China
| | - Liangwei Wu
- Pharmaron Beijing Co., Ltd., 6 Taihe Road BDA, Beijing 100176, P. R. China
| | - Lin Xue
- Pharmaron Beijing Co., Ltd., 6 Taihe Road BDA, Beijing 100176, P. R. China
| | - Bin Yang
- Oncology R&D, AstraZeneca, Boston, Massachusetts 02451, United States
| | - Tieguang Yao
- Pharmaron Beijing Co., Ltd., 6 Taihe Road BDA, Beijing 100176, P. R. China
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50
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Subbaiah MAM, Meanwell NA. Bioisosteres of the Phenyl Ring: Recent Strategic Applications in Lead Optimization and Drug Design. J Med Chem 2021; 64:14046-14128. [PMID: 34591488 DOI: 10.1021/acs.jmedchem.1c01215] [Citation(s) in RCA: 134] [Impact Index Per Article: 44.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
The benzene moiety is the most prevalent ring system in marketed drugs, underscoring its historic popularity in drug design either as a pharmacophore or as a scaffold that projects pharmacophoric elements. However, introspective analyses of medicinal chemistry practices at the beginning of the 21st century highlighted the indiscriminate deployment of phenyl rings as an important contributor to the poor physicochemical properties of advanced molecules, which limited their prospects of being developed into effective drugs. This Perspective deliberates on the design and applications of bioisosteric replacements for a phenyl ring that have provided practical solutions to a range of developability problems frequently encountered in lead optimization campaigns. While the effect of phenyl ring replacements on compound properties is contextual in nature, bioisosteric substitution can lead to enhanced potency, solubility, and metabolic stability while reducing lipophilicity, plasma protein binding, phospholipidosis potential, and inhibition of cytochrome P450 enzymes and the hERG channel.
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Affiliation(s)
- Murugaiah A M Subbaiah
- Department of Medicinal Chemistry, Biocon-Bristol Myers Squibb Research and Development Centre, Biocon Park, Bommasandra IV Phase, Jigani Link Road, Bangalore, Karnataka 560099, India
| | - Nicholas A Meanwell
- Department of Small Molecule Drug Discovery, Bristol Myers Squibb Research and Early Development, P.O. Box 4000, Princeton, New Jersey 08543-4000, United States
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