1
|
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.
Collapse
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.
| |
Collapse
|
2
|
Zhang W, Liu Y, Jang H, Nussinov R. CDK2 and CDK4: Cell Cycle Functions Evolve Distinct, Catalysis-Competent Conformations, Offering Drug Targets. JACS AU 2024; 4:1911-1927. [PMID: 38818077 PMCID: PMC11134382 DOI: 10.1021/jacsau.4c00138] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/15/2024] [Revised: 04/08/2024] [Accepted: 05/06/2024] [Indexed: 06/01/2024]
Abstract
Cyclin-dependent kinases (CDKs), particularly CDK4 and CDK2, are crucial for cell cycle progression from the Gap 1 (G1) to the Synthesis (S) phase by phosphorylating targets such as the Retinoblastoma Protein (Rb). CDK4, paired with cyclin-D, operates in the long G1 phase, while CDK2 with cyclin-E, manages the brief G1-to-S transition, enabling DNA replication. Aberrant CDK signaling leads to uncontrolled cell proliferation, which is a hallmark of cancer. Exactly how they accomplish their catalytic phosphorylation actions with distinct efficiencies poses the fundamental, albeit overlooked question. Here we combined available experimental data and modeling of the active complexes to establish their conformational functional landscapes to explain how the two cyclin/CDK complexes differentially populate their catalytically competent states for cell cycle progression. Our premise is that CDK catalytic efficiencies could be more important for cell cycle progression than the cyclin-CDK biochemical binding specificity and that efficiency is likely the prime determinant of cell cycle progression. We observe that CDK4 is more dynamic than CDK2 in the ATP binding site, the regulatory spine, and the interaction with its cyclin partner. The N-terminus of cyclin-D acts as an allosteric regulator of the activation loop and the ATP-binding site in CDK4. Integrated with a suite of experimental data, we suggest that the CDK4 complex is less capable of remaining in the active catalytically competent conformation, and may have a lower catalytic efficiency than CDK2, befitting their cell cycle time scales, and point to critical residues and motifs that drive their differences. Our mechanistic landscape may apply broadly to kinases, and we propose two drug design strategies: (i) allosteric Inhibition by conformational stabilization for targeting allosteric CDK4 regulation by cyclin-D, and (ii) dynamic entropy-optimized targeting which leverages the dynamic, entropic aspects of CDK4 to optimize drug binding efficacy.
Collapse
Affiliation(s)
- Wengang Zhang
- Cancer
Innovation Laboratory, National Cancer Institute, Frederick, Maryland 21702, United States
| | - Yonglan Liu
- Cancer
Innovation Laboratory, National Cancer Institute, Frederick, Maryland 21702, United States
| | - Hyunbum Jang
- Computational
Structural Biology Section, Frederick National
Laboratory for Cancer Research, Frederick, Maryland 21702, United States
| | - Ruth Nussinov
- Computational
Structural Biology Section, Frederick National
Laboratory for Cancer Research, Frederick, Maryland 21702, United States
- Department
of Human Molecular Genetics and Biochemistry, Sackler School of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
| |
Collapse
|
3
|
Baker ZD, Rasmussen DM, Levinson NM. Exploring the conformational landscapes of protein kinases: perspectives from FRET and DEER. Biochem Soc Trans 2024:BST20230558. [PMID: 38778760 DOI: 10.1042/bst20230558] [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: 02/15/2024] [Revised: 05/08/2024] [Accepted: 05/10/2024] [Indexed: 05/25/2024]
Abstract
Conformational changes of catalytically-important structural elements are a key feature of the regulation mechanisms of protein kinases and are important for dictating inhibitor binding modes and affinities. The lack of widely applicable methods for tracking kinase conformational changes in solution has hindered our understanding of kinase regulation and our ability to design conformationally selective inhibitors. Here we provide an overview of two recently developed methods that detect conformational changes of the regulatory activation loop and αC-helix of kinases and that yield complementary information about allosteric mechanisms. An intramolecular Förster resonance energy transfer-based approach provides a scalable platform for detecting and classifying structural changes in high-throughput, as well as quantifying ligand binding cooperativity, shedding light on the energetics governing allostery. The pulsed electron paramagnetic resonance technique double electron-electron resonance provides lower throughput but higher resolution information on structural changes that allows for unambiguous assignment of conformational states and quantification of population shifts. Together, these methods are shedding new light on kinase regulation and drug interactions and providing new routes for the identification of novel kinase inhibitors and allosteric modulators.
Collapse
Affiliation(s)
- Zachary D Baker
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN 55455, U.S.A
| | - Damien M Rasmussen
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN 55455, U.S.A
| | - Nicholas M Levinson
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN 55455, U.S.A
- Department of Pharmacology, University of Minnesota, Minneapolis, MN 55455, U.S.A
| |
Collapse
|
4
|
Sobierajski T, Małolepsza J, Pichlak M, Gendaszewska-Darmach E, Błażewska KM. The impact of E3 ligase choice on PROTAC effectiveness in protein kinase degradation. Drug Discov Today 2024; 29:104032. [PMID: 38789027 DOI: 10.1016/j.drudis.2024.104032] [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: 02/02/2024] [Revised: 04/30/2024] [Accepted: 05/15/2024] [Indexed: 05/26/2024]
Abstract
Proteolysis targeting chimera (PROTACs) provide a novel therapeutic approach that is revolutionizing drug discovery. The success of PROTACs largely depends on the combination of their three fragments: E3 ligase ligand, linker and protein of interest (POI)-targeting ligand. We summarize the pivotal significance of the precise combination of the E3 ligase ligand with the POI-recruiting warhead, which is crucial for the successful execution of cellular processes and achieving the desired outcomes. Therefore, the key to our selection was the use of at least two ligands recruiting two different ligases. This approach enables a direct comparison of the impacts of the specific ligases on target degradation.
Collapse
Affiliation(s)
- Tomasz Sobierajski
- Institute of Organic Chemistry, Lodz University of Technology, Łódź, Poland
| | - Joanna Małolepsza
- Institute of Organic Chemistry, Lodz University of Technology, Łódź, Poland
| | - Marta Pichlak
- Institute of Molecular and Industrial Biotechnology, Lodz University of Technology, Łódź, Poland
| | | | | |
Collapse
|
5
|
Zeng WB, Ji TY, Zhang YT, Ma YF, Li R, You WW, Zhao PL. Design, synthesis, and biological evaluation of N-(pyridin-3-yl)pyrimidin-4-amine analogues as novel cyclin-dependent kinase 2 inhibitors for cancer therapy. Bioorg Chem 2024; 143:107019. [PMID: 38096683 DOI: 10.1016/j.bioorg.2023.107019] [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: 09/13/2023] [Revised: 11/25/2023] [Accepted: 12/03/2023] [Indexed: 01/24/2024]
Abstract
The discovery and development of CDK2 inhibitors has currently been validated as a hot topic in cancer therapy. Herein, a series of novel N-(pyridin-3-yl)pyrimidin-4-amine derivatives were designed and synthesized as potent CDK2 inhibitors. Among them, the most promising compound 7l presented a broad antiproliferative efficacy toward diverse cancer cells MV4-11, HT-29, MCF-7, and HeLa with IC50 values of 0.83, 2.12, 3.12, and 8.61 μM, respectively, which were comparable to that of Palbociclib and AZD5438. Interestingly, these compounds were less toxic on normal embryonic kidney cells HEK293 with high selectivity index. Further mechanistic studies indicated 7l caused cell cycle arrest and apoptosis on HeLa cells in a concentration-dependent manner. Moreover, 7l manifested potent and similar CDK2/cyclin A2 nhibitory activity to AZD5438 with an IC50 of 64.42 nM. These findings revealed that 7l could serve as ahighly promisingscaffoldfor CDK2 inhibitors as potential anticancer agents and functional probes.
Collapse
Affiliation(s)
- Wen-Bin Zeng
- Guangdong Provincial Key Laboratory of New Drug Screening, School of Pharmaceutical Science, Southern Medical University, Guangzhou 510515, PR China
| | - Tang-Yang Ji
- Guangdong Provincial Key Laboratory of New Drug Screening, School of Pharmaceutical Science, Southern Medical University, Guangzhou 510515, PR China
| | - Yan-Ting Zhang
- Guangdong Provincial Key Laboratory of New Drug Screening, School of Pharmaceutical Science, Southern Medical University, Guangzhou 510515, PR China
| | - Yu-Feng Ma
- Guangdong Provincial Key Laboratory of New Drug Screening, School of Pharmaceutical Science, Southern Medical University, Guangzhou 510515, PR China
| | - Rou Li
- Guangdong Provincial Key Laboratory of New Drug Screening, School of Pharmaceutical Science, Southern Medical University, Guangzhou 510515, PR China
| | - Wen-Wei You
- Guangdong Provincial Key Laboratory of New Drug Screening, School of Pharmaceutical Science, Southern Medical University, Guangzhou 510515, PR China
| | - Pei-Liang Zhao
- Guangdong Provincial Key Laboratory of New Drug Screening, School of Pharmaceutical Science, Southern Medical University, Guangzhou 510515, PR China.
| |
Collapse
|
6
|
Kuchukulla RR, Hwang I, Kim SH, Kye Y, Park N, Cha H, Moon S, Chung HW, Lee C, Kong G, Hur W. Identification of a novel potent CDK inhibitor degrading cyclinK with a superb activity to reverse trastuzumab-resistance in HER2-positive breast cancer in vivo. Eur J Med Chem 2024; 264:116014. [PMID: 38061230 DOI: 10.1016/j.ejmech.2023.116014] [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: 09/21/2023] [Revised: 11/19/2023] [Accepted: 11/26/2023] [Indexed: 12/30/2023]
Abstract
CDK12 is overexpressed in HER2-positive breast cancers and promotes tumorigenesis and trastuzumab resistance. Thus CDK12 is a good therapeutic target for the HER2-positive breast tumors resistant to trastuzumab. We previously reported a novel purine-based CDK inhibitor with an ability to degrade cyclinK. Herein, we further explored and synthesized new derivatives, and identified a new potent pan-CDK inhibitor degrading cyclinK (32e). Compound 32e potently inhibited CDK12/cyclinK with IC50 = 3 nM, and suppressed the growth of the both trastuzumab-sensitive and trastuzumab-resistant HER2-positive breast cancer cell lines (GI50's = 9-21 nM), which is superior to a potent, clinical pan-CDK inhibitor dinaciclib. Moreover, 32e (10, 20 mg/kg, ip, twice a week) showed a dose-dependent inhibition of tumor growth and a more dramatic anti-cancer effect than dinaciclib in mouse in vivo orthotopic breast cancer model of trastuzumab-resistant HCC1954 cells. Kinome-wide inhibition profiling revealed that 32e at 1 μM exhibits a decent selectivity toward CDK-family kinases including CDK12 over other wildtype protein kinases. Quantitative global proteomic analysis of 32e-treated HCC1954 cells demonstrated that 32e also showed a decent selectivity in degrading cyclinK over other cyclins. Compound 32e could be developed as a drug for intractable trastuzumab-resistant HER2-positive breast cancers. Our current study would provide a useful insight in designing potent cyclinK degraders.
Collapse
Affiliation(s)
- Ratnakar Reddy Kuchukulla
- HY-KIST Bioconvergence, Hanyang University, 222 Wangsimniro, Seongdong-gu, Seoul, 04763, Republic of Korea
| | - Injeoung Hwang
- HY-KIST Bioconvergence, Hanyang University, 222 Wangsimniro, Seongdong-gu, Seoul, 04763, Republic of Korea; Medicinal Materials Research Center, Korea Institute of Science and Technology (KIST), 5 Hwarangro 14 gil, Seongbuk-gu, Seoul, 02792, Republic of Korea
| | - Suhn Hyung Kim
- Medicinal Materials Research Center, Korea Institute of Science and Technology (KIST), 5 Hwarangro 14 gil, Seongbuk-gu, Seoul, 02792, Republic of Korea
| | - Younghyeon Kye
- HY-KIST Bioconvergence, Hanyang University, 222 Wangsimniro, Seongdong-gu, Seoul, 04763, Republic of Korea
| | - Narae Park
- Chemical & Biological Integrative Research Center, Korea Institute of Science and Technology (KIST), 5 Hwarangro 14 gil, Seongbuk-gu, Seoul, 02792, Republic of Korea; KHU-KIST Department of Converging Science and Technology, Kyung Hee University, 26 Kyungheedaero, Dongdaemun-gu, Seoul, 02447, Republic of Korea
| | - Heary Cha
- HY-KIST Bioconvergence, Hanyang University, 222 Wangsimniro, Seongdong-gu, Seoul, 04763, Republic of Korea
| | - Sojeong Moon
- HY-KIST Bioconvergence, Hanyang University, 222 Wangsimniro, Seongdong-gu, Seoul, 04763, Republic of Korea
| | - Hwan Won Chung
- Computational Science Research Center, Korea Institute of Science and Technology (KIST), 5 Hwarangro 14 gil, Seongbuk-gu, Seoul, 02792, Republic of Korea
| | - Cheolju Lee
- Chemical & Biological Integrative Research Center, Korea Institute of Science and Technology (KIST), 5 Hwarangro 14 gil, Seongbuk-gu, Seoul, 02792, Republic of Korea
| | - Gu Kong
- HY-KIST Bioconvergence, Hanyang University, 222 Wangsimniro, Seongdong-gu, Seoul, 04763, Republic of Korea; Medicinal Materials Research Center, Korea Institute of Science and Technology (KIST), 5 Hwarangro 14 gil, Seongbuk-gu, Seoul, 02792, Republic of Korea; Department of Pathology, Hanyang University College of Medicine, 222 Wangsimniro, Seongdong-gu, Seoul, 04763, Republic of Korea.
| | - Wooyoung Hur
- HY-KIST Bioconvergence, Hanyang University, 222 Wangsimniro, Seongdong-gu, Seoul, 04763, Republic of Korea; Medicinal Materials Research Center, Korea Institute of Science and Technology (KIST), 5 Hwarangro 14 gil, Seongbuk-gu, Seoul, 02792, Republic of Korea.
| |
Collapse
|