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Zeng Y, Ren X, Jin P, Fan Z, Liu M, Zhang Y, Li L, Zhuo M, Wang J, Li Z, Wu M. Inhibitors and PROTACs of CDK2: challenges and opportunities. Expert Opin Drug Discov 2024; 19:1125-1148. [PMID: 38994606 DOI: 10.1080/17460441.2024.2376655] [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: 04/28/2024] [Accepted: 07/02/2024] [Indexed: 07/13/2024]
Abstract
INTRODUCTION Abundant evidence suggests that the overexpression of CDK2-cyclin A/E complex disrupts normal cell cycle regulation, leading to uncontrolled proliferation of cancer cells. Thus, CDK2 has become a promising therapeutic target for cancer treatment. In recent years, insights into the structures of the CDK2 catalytic site and allosteric pockets have provided notable opportunities for developing more effective clinical candidates of CDK2 inhibitors. AREA COVERED This article reviews the latest CDK2 inhibitors that have entered clinical trials and discusses the design and discovery of the most promising new preclinical CDK2 inhibitors in recent years. Additionally, it summarizes the development of allosteric CDK2 inhibitors and CDK2-targeting PROTACs. The review encompasses strategies for inhibitor and PROTAC design, structure-activity relationships, as well as in vitro and in vivo biological assessments. EXPERT OPINION Despite considerable effort, no CDK2 inhibitor has yet received FDA approval for marketing due to poor selectivity and observed toxicity in clinical settings. Future research must prioritize the optimization of the selectivity, potency, and pharmacokinetics of CDK2 inhibitors and PROTACs. Moreover, exploring combination therapies incorporating CDK2 inhibitors with other targeted agents, or the design of multi-target inhibitors, presents significant promise for advancing cancer treatment strategies.
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Affiliation(s)
- Yangjie Zeng
- Medical College, Guizhou University, Guiyang, China
| | - Xiaodong Ren
- Medical College, Guizhou University, Guiyang, China
| | - Pengyao Jin
- Medical College, Guizhou University, Guiyang, China
| | - Zhida Fan
- Medical College, Guizhou University, Guiyang, China
| | | | - Yali Zhang
- Medical College, Guizhou University, Guiyang, China
| | - Linzhao Li
- Medical College, Guizhou University, Guiyang, China
| | - Ming Zhuo
- Medical College, Guizhou University, Guiyang, China
| | - Jubo Wang
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing, China
| | - Zhiyu Li
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing, China
| | - Min Wu
- Department of Neurosurgery, Guizhou Provincial People's Hospital, Guiyang, China
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2
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Foschi F, Tinivella A, Crippa V, Pinzi L, Mologni L, Passarella D, Rastelli G. Structure-activity exploration of a small-molecule allosteric inhibitor of T790M/L858R double mutant EGFR. J Enzyme Inhib Med Chem 2023; 38:239-245. [PMID: 36373202 PMCID: PMC9665079 DOI: 10.1080/14756366.2022.2145284] [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: 11/16/2022] Open
Abstract
EGFR is a protein kinase whose aberrant activity is frequently involved in the development of non-small lung cancer (NSCLC) drug resistant forms. The allosteric inhibition of this enzyme is currently one among the most attractive approaches to design and develop anticancer drugs. In a previous study, we reported the identification of a hit compound acting as type III allosteric inhibitor of the L858R/T790M double mutant EGFR. Herein, we report the design, synthesis and in vitro testing of a series of analogues of the previously identified hit with the aim of exploring the structure-activity relationships (SAR) around this scaffold. The performed analyses allowed us to identify two compounds 15 and 18 showing improved inhibition of double mutant EGFR with respect to the original hit, as well as interesting antiproliferative activity against H1975 NSCLC cancer cells expressing double mutant EGFR. The newly discovered compounds represent promising starting points for further hit-to-lead optimisation.
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Affiliation(s)
- Francesca Foschi
- Department of Life Sciences, University of Modena and Reggio Emilia, Modena, Italy.,Department of Chemistry, University of Milano, Milano, Italy
| | - Annachiara Tinivella
- Department of Life Sciences, University of Modena and Reggio Emilia, Modena, Italy
| | - Valentina Crippa
- School of Medicine and Surgery, University of Milano-Bicocca, Monza, Italy
| | - Luca Pinzi
- Department of Life Sciences, University of Modena and Reggio Emilia, Modena, Italy
| | - Luca Mologni
- School of Medicine and Surgery, University of Milano-Bicocca, Monza, Italy
| | | | - Giulio Rastelli
- Department of Life Sciences, University of Modena and Reggio Emilia, Modena, Italy
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Ahmad B, Saeed A, Castrosanto MA, Amir Zia M, Farooq U, Abbas Z, Khan S. Identification of natural marine compounds as potential inhibitors of CDK2 using molecular docking and molecular dynamics simulation approach. J Biomol Struct Dyn 2023; 41:8506-8516. [PMID: 36300512 DOI: 10.1080/07391102.2022.2135594] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Accepted: 10/08/2022] [Indexed: 10/31/2022]
Abstract
The multifunctional enzyme cyclin-dependent kinase 2 (CDK2) protein is essential for cell proliferation, transcription and modulation of the cell cycle. There is a dysfunction that is connected to various diseases, such as cancer, making it an important treatment target in oncology and beyond. The goal of this study is to identify novel CDK2 ATP binding site inhibitors using in silico drug designing. To find competitive inhibitors for the ATP site, molecular docking, molecular dynamics (MD) simulation and free-binding energy calculations were used. Natural compounds retrieved from marine sources (fungi and algae) were docked against protein, and the best-binding compounds were further evaluated using MD simulations. LIG1, LIG2 and LIG3 (ΔGPB = -19.98, -15.82 and -12.98 kcal/mol, respectively) were placed in the top positions based on their overall binding energy calculated using MMPBSA approach. Stability of the complexes was confirmed by carefully analyzing the rmsd and rmsf patterns retrieved from the MD trajectories. Several residues and areas (Leu124, Val123, Phe80, Leu83, Glu81, Arg 126, Asn132, Leu134, Gln131, Lys88 and Glu195) appear to be critical for inhibitor retention across the active pocket, according to RMSD and RMSF. The dynamics of the ligands inside the active pocket were mapped using principle component analysis. It has been observed that LIG1-3 appear to be the best possible inhibitors due to their high binding energies, interaction pattern and retention inside the active pocket.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Basharat Ahmad
- National Institute for Genomics and Advanced Biotechnology (NIGAB), National Agricultural Research Centre (NARC), Islamabad, Pakistan
- Department of Bioinformatics, Hazara University Mansehra, Mansehra, Pakistan
| | - Aamir Saeed
- Department of Bioinformatics, Hazara University Mansehra, Mansehra, Pakistan
| | - Melvin A Castrosanto
- College of Arts and Sciences, Institute of Chemistry, University of the Philippines Los Banos, Laguna, Philippines
| | - Muhammad Amir Zia
- National Institute for Genomics and Advanced Biotechnology (NIGAB), National Agricultural Research Centre (NARC), Islamabad, Pakistan
| | - Umar Farooq
- Department of Chemistry, COMSATS University Islamabad - Abbottabad Campus, Abbottabad, Pakistan
| | - Zaheer Abbas
- National Institute for Genomics and Advanced Biotechnology (NIGAB), National Agricultural Research Centre (NARC), Islamabad, Pakistan
| | - Sara Khan
- Department of Chemistry, COMSATS University Islamabad - Abbottabad Campus, Abbottabad, Pakistan
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Faber EB, Wang N, John K, Sun L, Wong HL, Burban D, Francis R, Tian D, Hong KH, Yang A, Wang L, Elsaid M, Khalid H, Levinson NM, Schönbrunn E, Hawkinson JE, Georg GI. Screening through Lead Optimization of High Affinity, Allosteric Cyclin-Dependent Kinase 2 (CDK2) Inhibitors as Male Contraceptives That Reduce Sperm Counts in Mice. J Med Chem 2023; 66:1928-1940. [PMID: 36701569 DOI: 10.1021/acs.jmedchem.2c01731] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Although cyclin-dependent kinase 2 (CDK2) is a validated target for both cancer and contraception, developing a CDK2 inhibitor with exquisite selectivity has been challenging due to the structural similarity of the ATP-binding site, where most kinase inhibitors bind. We previously discovered an allosteric pocket in CDK2 with the potential to bind a selective compound and then discovered and structurally confirmed an anthranilic acid scaffold that binds this pocket with high affinity. These allosteric inhibitors are selective for CDK2 over structurally similar CDK1 and show contraceptive potential. Herein, we describe the screening and optimization that led to compounds like EF-4-177 with nanomolar affinity for CDK2. EF-4-177 is metabolically stable, orally bioavailable, and significantly disrupts spermatogenesis, demonstrating this series' therapeutic potential. This work details the discovery of the highest affinity allosteric CDK inhibitors reported and shows promise for this series to yield an efficacious and selective allosteric CDK2 inhibitor.
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Affiliation(s)
- Erik B Faber
- Department of Medicinal Chemistry and Institute for Therapeutics Discovery and Development, University of Minnesota College of Pharmacy─Twin Cities, Minneapolis, Minnesota55414, United States
- Medical Scientist Training Program, University of Minnesota Medical School─Twin Cities, Minneapolis, Minnesota55455, United States
| | - Nan Wang
- Department of Medicinal Chemistry and Institute for Therapeutics Discovery and Development, University of Minnesota College of Pharmacy─Twin Cities, Minneapolis, Minnesota55414, United States
| | - Kristen John
- Department of Medicinal Chemistry and Institute for Therapeutics Discovery and Development, University of Minnesota College of Pharmacy─Twin Cities, Minneapolis, Minnesota55414, United States
| | - Luxin Sun
- Drug Discovery Department, Moffitt Cancer Center, Tampa, Florida33612, United States
| | - Henry L Wong
- Department of Medicinal Chemistry and Institute for Therapeutics Discovery and Development, University of Minnesota College of Pharmacy─Twin Cities, Minneapolis, Minnesota55414, United States
| | - David Burban
- Department of Pharmacology, University of Minnesota Medical School─Twin Cities, Minneapolis, Minnesota55455, United States
| | - Rawle Francis
- Department of Medicinal Chemistry and Institute for Therapeutics Discovery and Development, University of Minnesota College of Pharmacy─Twin Cities, Minneapolis, Minnesota55414, United States
| | - Defeng Tian
- Department of Medicinal Chemistry and Institute for Therapeutics Discovery and Development, University of Minnesota College of Pharmacy─Twin Cities, Minneapolis, Minnesota55414, United States
| | - Kwon H Hong
- Department of Medicinal Chemistry and Institute for Therapeutics Discovery and Development, University of Minnesota College of Pharmacy─Twin Cities, Minneapolis, Minnesota55414, United States
| | - An Yang
- Department of Medicinal Chemistry and Institute for Therapeutics Discovery and Development, University of Minnesota College of Pharmacy─Twin Cities, Minneapolis, Minnesota55414, United States
| | - Liming Wang
- Department of Medicinal Chemistry and Institute for Therapeutics Discovery and Development, University of Minnesota College of Pharmacy─Twin Cities, Minneapolis, Minnesota55414, United States
| | - Mazen Elsaid
- Department of Medicinal Chemistry and Institute for Therapeutics Discovery and Development, University of Minnesota College of Pharmacy─Twin Cities, Minneapolis, Minnesota55414, United States
| | - Hira Khalid
- Department of Medicinal Chemistry and Institute for Therapeutics Discovery and Development, University of Minnesota College of Pharmacy─Twin Cities, Minneapolis, Minnesota55414, United States
| | - Nicholas M Levinson
- Department of Pharmacology, University of Minnesota Medical School─Twin Cities, Minneapolis, Minnesota55455, United States
| | - Ernst Schönbrunn
- Drug Discovery Department, Moffitt Cancer Center, Tampa, Florida33612, United States
| | - Jon E Hawkinson
- Department of Medicinal Chemistry and Institute for Therapeutics Discovery and Development, University of Minnesota College of Pharmacy─Twin Cities, Minneapolis, Minnesota55414, United States
| | - Gunda I Georg
- Department of Medicinal Chemistry and Institute for Therapeutics Discovery and Development, University of Minnesota College of Pharmacy─Twin Cities, Minneapolis, Minnesota55414, United States
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Abstract
B-Raf is a protein kinase participating to the regulation of many biological processes in cells. Several studies have demonstrated that this protein is frequently upregulated in human cancers, especially when it bears activating mutations. In the last years, few ATP-competitive inhibitors of B-Raf have been marketed for the treatment of melanoma and are currently under clinical evaluation on a variety of other types of cancer. Although the introduction of drugs targeting B-Raf has provided significant advances in cancer treatment, responses to ATP-competitive inhibitors remain limited, mainly due to selectivity issues, side effects, narrow therapeutic windows, and the insurgence of drug resistance. Impressive research efforts have been made so far towards the identification of novel ATP-competitive modulators with improved efficacy against cancers driven by mutant Raf monomers and dimers, some of them showing good promises. However, several limitations could still be envisioned for these compounds, according to literature data. Besides, increased attentions have arisen around approaches based on the design of allosteric modulators, polypharmacology, proteolysis targeting chimeras (PROTACs) and drug repurposing for the targeting of B-Raf proteins. The design of compounds acting through such innovative mechanisms is rather challenging. However, valuable therapeutic opportunities can be envisioned on these drugs, as they act through innovative mechanisms in which limitations typically observed for approved ATP-competitive B-Raf inhibitors are less prone to emerge. In this article, current approaches adopted for the design of non-ATP competitive inhibitors targeting B-Raf are described, discussing also on the possibilities, ligands acting through such innovative mechanisms could provide for the obtainment of more effective therapies.
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Affiliation(s)
- Luca Pinzi
- Department of Life Sciences, University of Modena and Reggio Emilia, Via Giuseppe Campi 103, 41125, Modena, Italy
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Abstract
With several marketed drugs, allosteric inhibition of kinases has translated to pharmacological effects and clinical benefits comparable to those from orthosteric inhibition. However, despite much effort over more than 20 years, the number of kinase targets associated with FDA-approved allosteric drugs is limited, suggesting the challenges in identifying and validating allosteric inhibitors. Here we review the principles of allosteric inhibition, summarize the discovery of allosteric MEK1/2 and BCR-ABL1 inhibitors, and discuss the approaches to screening and demonstrating the functional activity of allosteric pocket ligands.
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Affiliation(s)
- Yue Pan
- Relay Therapeutics, 399 Binney Street, Cambridge, Massachusetts 02139, United States
| | - Mary M Mader
- Relay Therapeutics, 399 Binney Street, Cambridge, Massachusetts 02139, United States
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7
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Xie Z, Hou S, Yang X, Duan Y, Han J, Wang Q, Liao C. Lessons Learned from Past Cyclin-Dependent Kinase Drug Discovery Efforts. J Med Chem 2022; 65:6356-6389. [PMID: 35235745 DOI: 10.1021/acs.jmedchem.1c02190] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Inhibition of cyclin-dependent kinases (CDKs) has become an effective therapeutic strategy for treating various diseases, especially cancer. Over almost three decades, although great efforts have been made to discover CDK inhibitors, many of which have entered clinical trials, only four CDK inhibitors have been approved. In the process of CDK inhibitor development, many difficulties and misunderstandings have hampered their discovery and clinical applications, which mainly include inadequate understanding of the biological functions of CDKs, less attention paid to pan- and multi-CDK inhibitors, nonideal isoform selectivity of developed selective CDK inhibitors, overlooking the metabolic stability of early discovered CDK inhibitors, no effective resistance solutions, and a lack of available combination therapy and effective biomarkers for CDK therapies. After reviewing the mechanisms of CDKs and the research progress of CDK inhibitors, this perspective summarizes and discusses these difficulties or lessons, hoping to facilitate the successful discovery of more useful CDK inhibitors.
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Affiliation(s)
- Zhouling Xie
- Department of Pharmaceutical Sciences and Engineering, School of Food and Biological Engineering, Hefei University of Technology, Hefei 230009, P. R. China
| | - Shuzeng Hou
- Department of Pharmaceutical Sciences and Engineering, School of Food and Biological Engineering, Hefei University of Technology, Hefei 230009, P. R. China
| | - Xiaoxiao Yang
- Department of Pharmaceutical Sciences and Engineering, School of Food and Biological Engineering, Hefei University of Technology, Hefei 230009, P. R. China
| | - Yajun Duan
- Department of Pharmaceutical Sciences and Engineering, School of Food and Biological Engineering, Hefei University of Technology, Hefei 230009, P. R. China
| | - Jihong Han
- Department of Pharmaceutical Sciences and Engineering, School of Food and Biological Engineering, Hefei University of Technology, Hefei 230009, P. R. China
| | - Qin Wang
- Department of Otolaryngology─Head and Neck Surgery, The First Affiliated Hospital of Anhui Medical University, Hefei, 230022, P. R. China
| | - Chenzhong Liao
- Department of Pharmaceutical Sciences and Engineering, School of Food and Biological Engineering, Hefei University of Technology, Hefei 230009, P. R. China
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Faber EB, Wang N, Georg GI. Review of rationale and progress toward targeting cyclin-dependent kinase 2 (CDK2) for male contraception†. Biol Reprod 2021; 103:357-367. [PMID: 32543655 PMCID: PMC7523694 DOI: 10.1093/biolre/ioaa107] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2020] [Revised: 06/03/2020] [Accepted: 04/19/2020] [Indexed: 12/30/2022] Open
Abstract
Cyclin-dependent kinase 2 (CDK2) is a member of the larger cell cycle regulating CDK family of kinases, activated by binding partner cyclins as its name suggests. Despite its canonical role in mitosis, CDK2 knockout mice are viable but sterile, suggesting compensatory mechanisms for loss of CDK2 in mitosis but not meiosis. Here, we review the literature surrounding the role of CDK2 in meiosis, particularly a cyclin-independent role in complex with another activator, Speedy 1 (SPY1). From this evidence, we suggest that CDK2 could be a viable nonhormonal male contraceptive target. Finally, we review the literature of pertinent CDK2 inhibitors from the preclinical to clinical stages, mostly developed to treat various cancers. To date, there is no potent yet selective CDK2 inhibitor that could be repurposed as a contraceptive without appreciable off-target toxicity. To achieve selectivity for CDK2 over closely related kinases, developing compounds that bind outside the conserved adenosine triphosphate-binding site may be necessary.
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Affiliation(s)
- Erik B Faber
- Department of Medicinal Chemistry, College of Pharmacy, University of Minnesota-Twin Cities, Minneapolis, MN, USA.,Medical-Scientist Training Program, University of Minnesota Medical School, University of Minnesota-Twin Cities, Minneapolis, MN, USA
| | - Nan Wang
- Department of Medicinal Chemistry, College of Pharmacy, University of Minnesota-Twin Cities, Minneapolis, MN, USA
| | - Gunda I Georg
- Department of Medicinal Chemistry, College of Pharmacy, University of Minnesota-Twin Cities, Minneapolis, MN, USA
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MYBL2 amplification in breast cancer: Molecular mechanisms and therapeutic potential. Biochim Biophys Acta Rev Cancer 2020; 1874:188407. [DOI: 10.1016/j.bbcan.2020.188407] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Revised: 07/21/2020] [Accepted: 07/21/2020] [Indexed: 02/08/2023]
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Mou J, Chen D, Deng Y. Inhibitors of Cyclin-Dependent Kinase 1/2 for Anticancer Treatment. Med Chem 2020; 16:307-325. [PMID: 31241436 DOI: 10.2174/1573406415666190626113900] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2018] [Revised: 03/05/2019] [Accepted: 05/14/2019] [Indexed: 12/13/2022]
Abstract
BACKGROUND The cell cycle is regulated by cyclin-dependent kinases (CDKs) and their cognate cyclins, along with their endogenous inhibitors (CDKIs). CDKs act as central regulators in this process. Different CDKs play relevant roles in different phases. Among all CDKs, CDK1 is indispensible, which can drive all events that are required in the cell cycle in the absence of interphase CDKs (CDK2, CDK3, CDK4 and CDK6). So, CDK1 is an attractive target for anticancer drug development. METHODS CDK1 and CDK2 have 89.19% similar residues and 74.32% identical residues, their structures especially the ATP-binding sites are of great similarity. So, it is difficult to inhibit CDK1 and CDK2 individually. In this review, recent advances about CDK1/2 inhibitors were summarized. The chemical structures of different classes of CDK1/2 inhibitors and their structure activity are presented. RESULTS 19 kinds of CDK1/2 or CDK1 inhibitors with different scaffolds, including CDK2 allosteric inhibitors, were summarized. Some inhibitors are nature derived, for example, phenanthrene derivatives, nortopsentin derivatives, variolin B derivatives and meridians. CONCLUSION Nature products, especially marine ones are potential resources for CDK1 inhibitors development. The findings of CDK2 allosteric inhibitors open an avenue to the discovery of novel selective CDK1 or other CDKs allosteric inhibitors.
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Affiliation(s)
- Jiajia Mou
- Department of Medicinal Chemistry, School of Chinese Materia Medica, Tianjin University of Traditional Chinese Medicine, Health Industry Park, Jinghai District, Tianjin, 301617, China
| | - Danghui Chen
- Department of Medicinal Chemistry, School of Chinese Materia Medica, Tianjin University of Traditional Chinese Medicine, Health Industry Park, Jinghai District, Tianjin, 301617, China
| | - Yanru Deng
- Department of Medicinal Chemistry, School of Chinese Materia Medica, Tianjin University of Traditional Chinese Medicine, Health Industry Park, Jinghai District, Tianjin, 301617, China
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Wang B, Peng F, Huang W, Zhou J, Zhang N, Sheng J, Haruehanroengra P, He G, Han B. Rational drug design, synthesis, and biological evaluation of novel chiral tetrahydronaphthalene-fused spirooxindole as MDM2-CDK4 dual inhibitor against glioblastoma. Acta Pharm Sin B 2020; 10:1492-1510. [PMID: 32963945 PMCID: PMC7488488 DOI: 10.1016/j.apsb.2019.12.013] [Citation(s) in RCA: 50] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2019] [Revised: 11/17/2019] [Accepted: 12/12/2019] [Indexed: 02/08/2023] Open
Abstract
Simultaneous inhibition of MDM2 and CDK4 may be an effective treatment against glioblastoma. A collection of chiral spirocyclic tetrahydronaphthalene (THN)-oxindole hybrids for this purpose have been developed. Appropriate stereochemistry in THN-fused spirooxindole compounds is key to their inhibitory activity: selectivity differed by over 40-fold between the least and most potent stereoisomers in time-resolved FRET and KINOMEscan® in vitro assays. Studies in glioblastoma cell lines showed that the most active compound ent-4g induced apoptosis and cell cycle arrest by interfering with MDM2 -P53 interaction and CDK4 activation. Cells treated with ent-4g showed up-regulation of proteins involved in P53 and cell cycle pathways. The compound showed good anti-tumor efficacy against glioblastoma xenografts in mice. These results suggested that rational design, asymmetric synthesis and biological evaluation of novel tetrahydronaphthalene fused spirooxindoles could generate promising MDM2-CDK4 dual inhibitors in glioblastoma therapy.
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Faber EB, Tian D, Burban D, Levinson NM, Hawkinson JE, Georg GI. Cooperativity Between Orthosteric Inhibitors and Allosteric Inhibitor 8-Anilino-1-Naphthalene Sulfonic Acid (ANS) in Cyclin-Dependent Kinase 2. ACS Chem Biol 2020; 15:1759-1764. [PMID: 32433863 DOI: 10.1021/acschembio.0c00169] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
While kinases have been attractive targets to combat many diseases, including cancer, selective kinase inhibition has been challenging, because of the high degree of structural homology in the active site, where many kinase inhibitors bind. We have previously discovered that 8-anilino-1-naphthalene sulfonic acid (ANS) binds an allosteric pocket in cyclin-dependent kinase 2 (Cdk2). Here, we detail the positive cooperativity between ANS and orthosteric Cdk2 inhibitors dinaciclib and roscovitine, which increase the affinity of ANS toward Cdk2 5-fold to 10-fold, and the relatively noncooperative effects of ATP. We observe these effects using a fluorescent binding assay and heteronuclear single quantum correlation nuclear magnetic resonance (HSQC NMR), where we noticed a shift from fast exchange to slow exchange upon ANS titration in the presence of roscovitine but not with an ATP mimic. The discovery of cooperative relationships between orthosteric and allosteric kinase inhibitors could further the development of selective kinase inhibitors in general.
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Affiliation(s)
- Erik B. Faber
- Institute for Therapeutics Discovery and Development, Department of Medicinal Chemistry, College of Pharmacy, University of Minnesota, Minneapolis, Minnesota 55414, United States
| | - Defeng Tian
- Institute for Therapeutics Discovery and Development, Department of Medicinal Chemistry, College of Pharmacy, University of Minnesota, Minneapolis, Minnesota 55414, United States
| | - David Burban
- Department of Pharmacology, School of Medicine, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Nicholas M. Levinson
- Department of Pharmacology, School of Medicine, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Jon E. Hawkinson
- Institute for Therapeutics Discovery and Development, Department of Medicinal Chemistry, College of Pharmacy, University of Minnesota, Minneapolis, Minnesota 55414, United States
| | - Gunda I. Georg
- Institute for Therapeutics Discovery and Development, Department of Medicinal Chemistry, College of Pharmacy, University of Minnesota, Minneapolis, Minnesota 55414, United States
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Avoiding or Co-Opting ATP Inhibition: Overview of Type III, IV, V, and VI Kinase Inhibitors. NEXT GENERATION KINASE INHIBITORS 2020. [PMCID: PMC7359047 DOI: 10.1007/978-3-030-48283-1_3] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
As described in the previous chapter, most kinase inhibitors that have been developed for use in the clinic act by blocking ATP binding; however, there is growing interest in identifying compounds that target kinase activities and functions without interfering with the conserved features of the ATP-binding site. This chapter will highlight alternative approaches that exploit unique kinase structural features that are being targeted to identify more selective and potent inhibitors. The figure below, adapted from (Sammons et al., Molecular Carcinogenesis 58:1551–1570, 2019), provides a graphical description of the various approaches to manipulate kinase activity. In addition to the type I and II inhibitors, type III kinase inhibitors have been identified to target sites adjacent to the ATP-binding site in the catalytic domain. New information on kinase structure and substrate-binding sites has enabled the identification of type IV kinase inhibitor compounds that target regions outside the catalytic domain. The combination of targeting unique allosteric sites outside the catalytic domain with ATP-targeted compounds has yielded a number of novel bivalent type V kinase inhibitors. Finally, emerging interest in the development of irreversible compounds that form selective covalent interactions with key amino acids involved in kinase functions comprise the class of type VI kinase inhibitors.
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Gagic Z, Ruzic D, Djokovic N, Djikic T, Nikolic K. In silico Methods for Design of Kinase Inhibitors as Anticancer Drugs. Front Chem 2020; 7:873. [PMID: 31970149 PMCID: PMC6960140 DOI: 10.3389/fchem.2019.00873] [Citation(s) in RCA: 62] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2019] [Accepted: 12/04/2019] [Indexed: 12/11/2022] Open
Abstract
Rational drug design implies usage of molecular modeling techniques such as pharmacophore modeling, molecular dynamics, virtual screening, and molecular docking to explain the activity of biomolecules, define molecular determinants for interaction with the drug target, and design more efficient drug candidates. Kinases play an essential role in cell function and therefore are extensively studied targets in drug design and discovery. Kinase inhibitors are clinically very important and widely used antineoplastic drugs. In this review, computational methods used in rational drug design of kinase inhibitors are discussed and compared, considering some representative case studies.
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Affiliation(s)
- Zarko Gagic
- Department of Pharmaceutical Chemistry, Faculty of Medicine, University of Banja Luka, Banja Luka, Bosnia and Herzegovina
| | - Dusan Ruzic
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Belgrade, Belgrade, Serbia
| | - Nemanja Djokovic
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Belgrade, Belgrade, Serbia
| | - Teodora Djikic
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Belgrade, Belgrade, Serbia
| | - Katarina Nikolic
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Belgrade, Belgrade, Serbia
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15
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In Silico Repositioning of Cannabigerol as a Novel Inhibitor of the Enoyl Acyl Carrier Protein (ACP) Reductase (InhA). Molecules 2019; 24:molecules24142567. [PMID: 31311157 PMCID: PMC6680637 DOI: 10.3390/molecules24142567] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Revised: 07/08/2019] [Accepted: 07/13/2019] [Indexed: 12/22/2022] Open
Abstract
Cannabigerol (CBG) and cannabichromene (CBC) are non-psychoactive cannabinoids that have raised increasing interest in recent years. These compounds exhibit good tolerability and low toxicity, representing promising candidates for drug repositioning. To identify novel potential therapeutic targets for CBG and CBC, an integrated ligand-based and structure-based study was performed. The results of the analysis led to the identification of CBG as a low micromolar inhibitor of the Enoyl acyl carrier protein (ACP) reductase (InhA) enzyme.
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16
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Rastelli G, Pinzi L. Refinement and Rescoring of Virtual Screening Results. Front Chem 2019; 7:498. [PMID: 31355188 PMCID: PMC6637856 DOI: 10.3389/fchem.2019.00498] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Accepted: 06/28/2019] [Indexed: 12/13/2022] Open
Abstract
High-throughput docking is an established computational screening approach in drug design. This methodology enables a rapid identification of biologically active hit compounds, providing an efficient and cost-effective complement or alternative to experimental high-throughput screenings. However, limitations inherent to the methodology make docking results inevitably approximate. Two major Achille's heels include the use of approximated scoring functions and the limited sampling of the ligand-target complexes. Therefore, docking results require careful evaluation and further post-docking analyses. In this article, we will overview our approach to post-docking analysis in virtual screenings. BEAR (Binding Estimation After Refinement) was developed as a post-docking processing tool that refines docking poses by means of molecular dynamics (MD) and then rescores the ligands based on more accurate scoring functions (MM-PB(GB)SA). The tool has been validated and used prospectively in drug discovery applications. Future directions regarding refinement and rescoring in virtual screening are discussed.
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Affiliation(s)
- Giulio Rastelli
- Department of Life Sciences, University of Modena and Reggio Emilia, Modena, Italy
| | - Luca Pinzi
- Department of Life Sciences, University of Modena and Reggio Emilia, Modena, Italy
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17
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Dissecting a novel allosteric mechanism of cruzain: A computer-aided approach. PLoS One 2019; 14:e0211227. [PMID: 30682119 PMCID: PMC6347273 DOI: 10.1371/journal.pone.0211227] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2018] [Accepted: 01/09/2019] [Indexed: 02/08/2023] Open
Abstract
Trypanosoma cruzi is the causative agent of Chagas disease, a neglected infection affecting millions of people in tropical regions. There are several chemotherapeutic agents for the treatment of this disease, but most of them are highly toxic and generate resistance. Currently, the development of allosteric inhibitors constitutes a promising research field, since it can improve the accessibility to more selective and less toxic medicines. To date, the allosteric drugs prediction is a state-of-the-art topic in rational structure-based computational design. In this work, a simulation strategy was developed for computational discovery of allosteric inhibitors, and it was applied to cruzain, a promising target and the major cysteine protease of T. cruzi. Molecular dynamics simulations, binding free energy calculations and network-based modelling of residue interactions were combined to characterize and compare molecular distinctive features of the apo form and the cruzain-allosteric inhibitor complexes. By using geometry-based criteria on trajectory snapshots, we predicted two main allosteric sites suitable for drug targeting. The results suggest dissimilar mechanisms exerted by the same allosteric site when binding different potential allosteric inhibitors. Finally, we identified the residues involved in suboptimal paths linking the identified site and the orthosteric site. The present study constitutes the first approximation to the design of cruzain allosteric inhibitors and may serve for future pharmacological intervention. Here, no major effects on active site structure were observed due to compound binding (modification of distance and angles between catalytic residues), which indicates that allosteric regulation in cruzain might be mediated via alterations of its dynamical properties similarly to allosteric inhibition of human cathepsin K (HCatK). The current findings are particularly relevant for the design of allosteric modulators of papain-like cysteine proteases.
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18
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Panicker RC, Chattopadhaya S, Coyne AG, Srinivasan R. Allosteric Small-Molecule Serine/Threonine Kinase Inhibitors. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1163:253-278. [PMID: 31707707 DOI: 10.1007/978-981-13-8719-7_11] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Deregulation of protein kinase activity has been linked to many diseases ranging from cancer to AIDS and neurodegenerative diseases. Not surprisingly, drugging the human kinome - the complete set of kinases encoded by the human genome - has been one of the major drug discovery pipelines. Majority of the approved clinical kinase inhibitors target the ATP binding site of kinases. However, the remarkable sequence and structural similarity of ATP binding pockets of kinases make selective inhibition of kinases a daunting task. To circumvent these issues, allosteric inhibitors that target sites other than the orthosteric ATP binding pocket have been developed. The structural diversity of the allosteric sites allows these inhibitors to have higher selectivity, lower toxicity and improved physiochemical properties and overcome drug resistance associated with the use of conventional kinase inhibitors. In this chapter, we will focus on the allosteric inhibitors of selected serine/threonine kinases, outline the benefits of using these inhibitors and discuss the challenges and future opportunities.
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Affiliation(s)
- Resmi C Panicker
- School of Pharmaceutical Science and Technology, Tianjin University, Tianjin, People's Republic of China
| | | | - Anthony G Coyne
- University Chemical Laboratory, University of Cambridge, Cambridge, UK
| | - Rajavel Srinivasan
- School of Pharmaceutical Science and Technology, Tianjin University, Tianjin, People's Republic of China.
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Astl L, Tse A, Verkhivker GM. Interrogating Regulatory Mechanisms in Signaling Proteins by Allosteric Inhibitors and Activators: A Dynamic View Through the Lens of Residue Interaction Networks. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1163:187-223. [DOI: 10.1007/978-981-13-8719-7_9] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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20
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Tadesse S, Caldon EC, Tilley W, Wang S. Cyclin-Dependent Kinase 2 Inhibitors in Cancer Therapy: An Update. J Med Chem 2018; 62:4233-4251. [PMID: 30543440 DOI: 10.1021/acs.jmedchem.8b01469] [Citation(s) in RCA: 159] [Impact Index Per Article: 26.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Cyclin-dependent kinase 2 (CDK2) drives the progression of cells into the S- and M-phases of the cell cycle. CDK2 activity is largely dispensable for normal development, but it is critically associated with tumor growth in multiple cancer types. Although the role of CDK2 in tumorigenesis has been controversial, emerging evidence proposes that selective CDK2 inhibition may provide a therapeutic benefit against certain tumors, and it continues to appeal as a strategy to exploit in anticancer drug development. Several small-molecule CDK2 inhibitors have progressed to the clinical trials. However, a CDK2-selective inhibitor is yet to be discovered. Here, we discuss the latest understandings of the role of CDK2 in normal and cancer cells, review the core pharmacophores used to target CDK2, and outline strategies for the rational design of CDK2 inhibitors. We attempt to provide an outlook on how CDK2-selective inhibitors may open new avenues for cancer therapy.
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Affiliation(s)
- Solomon Tadesse
- Centre for Drug Discovery and Development , University of South Australia Cancer Research Institute , Adelaide , SA 5000 , Australia
| | - Elizabeth C Caldon
- The Kinghorn Cancer Centre , Garvan Institute of Medical Research , Darlinghurst , NSW 2010 , Australia.,St Vincent's Clinical School, UNSW Medicine , UNSW Sydney , Darlinghurst , NSW 2010 , Australia
| | - Wayne Tilley
- Adelaide Medical School , University of Adelaide , Adelaide , SA 5000 , Australia
| | - Shudong Wang
- Centre for Drug Discovery and Development , University of South Australia Cancer Research Institute , Adelaide , SA 5000 , Australia
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21
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Carlino L, Christodoulou MS, Restelli V, Caporuscio F, Foschi F, Semrau MS, Costanzi E, Tinivella A, Pinzi L, Lo Presti L, Battistutta R, Storici P, Broggini M, Passarella D, Rastelli G. Structure-Activity Relationships of Hexahydrocyclopenta[c
]quinoline Derivatives as Allosteric Inhibitors of CDK2 and EGFR. ChemMedChem 2018; 13:2627-2634. [DOI: 10.1002/cmdc.201800687] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2018] [Indexed: 01/11/2023]
Affiliation(s)
- Luca Carlino
- Dipartimento di Scienze della Vita; Università degli Studi di Modena e Reggio Emilia; Via Campi 103 41125 Modena Italy
| | - Michael S. Christodoulou
- Dipartimento di Scienze della Vita; Università degli Studi di Modena e Reggio Emilia; Via Campi 103 41125 Modena Italy
- Dipartimento di Chimica, Università degli Studi di Milano; Via Golgi 19 20133 Milano Italy
| | - Valentina Restelli
- IRCSS Istituto di Ricerche Farmacologiche Mario Negri; Via La Masa 19 20156 Milano Italy
| | - Fabiana Caporuscio
- Dipartimento di Scienze della Vita; Università degli Studi di Modena e Reggio Emilia; Via Campi 103 41125 Modena Italy
| | - Francesca Foschi
- Dipartimento di Scienze della Vita; Università degli Studi di Modena e Reggio Emilia; Via Campi 103 41125 Modena Italy
- Dipartimento di Chimica, Università degli Studi di Milano; Via Golgi 19 20133 Milano Italy
| | - Marta S. Semrau
- Structural Biology Lab; Elettra Sincrotrone Trieste S.C.p.A.; SS 14 km 163.5, AREA Science Park 34149 Trieste Italy
| | - Elisa Costanzi
- Dipartimento di Scienze Chimiche; Università degli Studi di Padova; Via Marzolo 1 35131 Padova Italy
| | - Annachiara Tinivella
- Dipartimento di Scienze della Vita; Università degli Studi di Modena e Reggio Emilia; Via Campi 103 41125 Modena Italy
| | - Luca Pinzi
- Dipartimento di Scienze della Vita; Università degli Studi di Modena e Reggio Emilia; Via Campi 103 41125 Modena Italy
| | - Leonardo Lo Presti
- Dipartimento di Chimica, Università degli Studi di Milano; Via Golgi 19 20133 Milano Italy
- Istituto di Scienze e Tecnologie Molecolari, Consiglio Nazionale delle Ricerche; Via Golgi 19 20133 Milano Italy
| | - Roberto Battistutta
- Dipartimento di Scienze Chimiche; Università degli Studi di Padova; Via Marzolo 1 35131 Padova Italy
| | - Paola Storici
- Structural Biology Lab; Elettra Sincrotrone Trieste S.C.p.A.; SS 14 km 163.5, AREA Science Park 34149 Trieste Italy
| | - Massimo Broggini
- IRCSS Istituto di Ricerche Farmacologiche Mario Negri; Via La Masa 19 20156 Milano Italy
| | - Daniele Passarella
- Dipartimento di Chimica, Università degli Studi di Milano; Via Golgi 19 20133 Milano Italy
| | - Giulio Rastelli
- Dipartimento di Scienze della Vita; Università degli Studi di Modena e Reggio Emilia; Via Campi 103 41125 Modena Italy
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22
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Identification of small-molecule EGFR allosteric inhibitors by high-throughput docking. Future Med Chem 2018; 10:1545-1553. [DOI: 10.4155/fmc-2018-0063] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Aim: The EGFR inhibitors represent the first-line treatment of non-small-cell lung cancer. However, the emergence of resistance urgently requires the development of new inhibitors targeting drug-resistant mutants. Methodology: A recently released structure of an EGFR kinase domain in complex with an allosteric inhibitor and a mutant protein model derived from it were used to set up a low-cost high-throughput docking protocol for the fast identification of EGFR allosteric inhibitors. Conclusion: The virtual screening of commercially available compounds led to the identification of interesting new hit compounds. The most promising hit was confirmed to be a new allosteric inhibitor of wild-type and T790M/L858R double mutant EGFR which was able to inhibit the growth of non-small-cell lung cancer cell lines.
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23
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Sturm N, Tinivella A, Rastelli G. Exploration and Comparison of the Geometrical and Physicochemical Properties of an αC Allosteric Pocket in the Structural Kinome. J Chem Inf Model 2018; 58:1094-1103. [DOI: 10.1021/acs.jcim.7b00735] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Affiliation(s)
- Noé Sturm
- Department of Life Sciences, University of Modena and Reggio Emilia, Via Campi 103, 41125 Modena, Italy
| | - Annachiara Tinivella
- Department of Life Sciences, University of Modena and Reggio Emilia, Via Campi 103, 41125 Modena, Italy
| | - Giulio Rastelli
- Department of Life Sciences, University of Modena and Reggio Emilia, Via Campi 103, 41125 Modena, Italy
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24
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Craven GB, Affron DP, Allen CE, Matthies S, Greener JG, Morgan RML, Tate EW, Armstrong A, Mann DJ. High-Throughput Kinetic Analysis for Target-Directed Covalent Ligand Discovery. Angew Chem Int Ed Engl 2018; 57:5257-5261. [PMID: 29480525 PMCID: PMC5947712 DOI: 10.1002/anie.201711825] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2017] [Revised: 01/16/2018] [Indexed: 01/10/2023]
Abstract
Cysteine‐reactive small molecules are used as chemical probes of biological systems and as medicines. Identifying high‐quality covalent ligands requires comprehensive kinetic analysis to distinguish selective binders from pan‐reactive compounds. Quantitative irreversible tethering (qIT), a general method for screening cysteine‐reactive small molecules based upon the maximization of kinetic selectivity, is described. This method was applied prospectively to discover covalent fragments that target the clinically important cell cycle regulator Cdk2. Crystal structures of the inhibitor complexes validate the approach and guide further optimization. The power of this technique is highlighted by the identification of a Cdk2‐selective allosteric (type IV) kinase inhibitor whose novel mode‐of‐action could be exploited therapeutically.
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Affiliation(s)
- Gregory B. Craven
- Department of ChemistryImperial College LondonSouth Kensington CampusLondonSW7 2AZUK
- Department of Life SciencesImperial College LondonSouth Kensington CampusLondonSW7 2AZUK
| | - Dominic P. Affron
- Department of ChemistryImperial College LondonSouth Kensington CampusLondonSW7 2AZUK
| | - Charlotte E. Allen
- Department of ChemistryImperial College LondonSouth Kensington CampusLondonSW7 2AZUK
| | - Stefan Matthies
- Department of ChemistryImperial College LondonSouth Kensington CampusLondonSW7 2AZUK
| | - Joe G. Greener
- Department of Life SciencesImperial College LondonSouth Kensington CampusLondonSW7 2AZUK
| | - Rhodri M. L. Morgan
- Department of Life SciencesImperial College LondonSouth Kensington CampusLondonSW7 2AZUK
| | - Edward W. Tate
- Department of ChemistryImperial College LondonSouth Kensington CampusLondonSW7 2AZUK
| | - Alan Armstrong
- Department of ChemistryImperial College LondonSouth Kensington CampusLondonSW7 2AZUK
| | - David J. Mann
- Department of Life SciencesImperial College LondonSouth Kensington CampusLondonSW7 2AZUK
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25
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Craven GB, Affron DP, Allen CE, Matthies S, Greener JG, Morgan RML, Tate EW, Armstrong A, Mann DJ. High-Throughput Kinetic Analysis for Target-Directed Covalent Ligand Discovery. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201711825] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Gregory B. Craven
- Department of Chemistry; Imperial College London; South Kensington Campus London SW7 2AZ UK
- Department of Life Sciences; Imperial College London; South Kensington Campus London SW7 2AZ UK
| | - Dominic P. Affron
- Department of Chemistry; Imperial College London; South Kensington Campus London SW7 2AZ UK
| | - Charlotte E. Allen
- Department of Chemistry; Imperial College London; South Kensington Campus London SW7 2AZ UK
| | - Stefan Matthies
- Department of Chemistry; Imperial College London; South Kensington Campus London SW7 2AZ UK
| | - Joe G. Greener
- Department of Life Sciences; Imperial College London; South Kensington Campus London SW7 2AZ UK
| | - Rhodri M. L. Morgan
- Department of Life Sciences; Imperial College London; South Kensington Campus London SW7 2AZ UK
| | - Edward W. Tate
- Department of Chemistry; Imperial College London; South Kensington Campus London SW7 2AZ UK
| | - Alan Armstrong
- Department of Chemistry; Imperial College London; South Kensington Campus London SW7 2AZ UK
| | - David J. Mann
- Department of Life Sciences; Imperial College London; South Kensington Campus London SW7 2AZ UK
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26
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Kalra S, Joshi G, Munshi A, Kumar R. Structural insights of cyclin dependent kinases: Implications in design of selective inhibitors. Eur J Med Chem 2017; 142:424-458. [PMID: 28911822 DOI: 10.1016/j.ejmech.2017.08.071] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2017] [Revised: 08/31/2017] [Accepted: 08/31/2017] [Indexed: 12/17/2022]
Abstract
There are around 20 Cyclin-dependent kinases (CDKs) known till date, and various research groups have reported their role in different types of cancer. The X-ray structures of some CDKs especially CDK2 was exploited in the past few years, and several inhibitors have been found, e.g., flavopiridol, indirubicin, roscovitine, etc., but due to the specificity issues of these inhibitors (binding to all CDKs), these were called as pan inhibitors. The revolutionary outcome of palbociclib in 2015 as CDK4/6 inhibitor added a new charm to the specific inhibitor design for CDKs. Computer-aided drug design (CADD) tools added a benefit to the design and development of new CDK inhibitors by studying the binding pattern of the inhibitors to the ATP binding domain of CDKs. Herein, we have attempted a comparative analysis of structural differences between several CDKs ATP binding sites and their inhibitor specificity by depicting the important ligand-receptor interactions for a particular CDK to be targeted. This perspective provides futuristic implications in the design of inhibitors considering the spatial features and structural insights of the specific CDK.
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Affiliation(s)
- Sourav Kalra
- Centre for Human Genetics and Molecular Medicine, School of Health Sciences, Central University of Punjab, Bathinda, India
| | - Gaurav Joshi
- Centre for Pharmaceutical Sciences and Natural Products, School of Basic and Applied Sciences, Central University of Punjab, Bathinda, India
| | - Anjana Munshi
- Centre for Human Genetics and Molecular Medicine, School of Health Sciences, Central University of Punjab, Bathinda, India.
| | - Raj Kumar
- Centre for Pharmaceutical Sciences and Natural Products, School of Basic and Applied Sciences, Central University of Punjab, Bathinda, India.
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27
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Tutone M, Almerico AM. Recent advances on CDK inhibitors: An insight by means of in silico methods. Eur J Med Chem 2017; 142:300-315. [PMID: 28802482 DOI: 10.1016/j.ejmech.2017.07.067] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2017] [Revised: 07/19/2017] [Accepted: 07/28/2017] [Indexed: 02/06/2023]
Abstract
The cyclin dependent kinases (CDKs) are a small family of serine/threonine protein kinases that can act as a potential therapeutic target in several proliferative diseases, including cancer. This short review is a survey on the more recent research progresses in the field achieved by using in silico methods. All the "armamentarium" available to the medicinal chemists (docking protocols and molecular dynamics, fragment-based, de novo design, virtual screening, and QSAR) has been employed to the discovery of new, potent, and selective inhibitors of cyclin dependent kinases. The results cited herein can be useful to understand the nature of the inhibitor-target interactions, and furnish an insight on the structural/molecular requirements necessary to achieve the required selectivity against cyclin dependent kinases over other types of kinases.
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Affiliation(s)
- Marco Tutone
- Dipartimento di Scienze e Tecnologie Biologiche Chimiche e Farmaceutiche (STEBICEF), Università di Palermo, Via Archirafi 32, 90123 Palermo, Italy
| | - Anna Maria Almerico
- Dipartimento di Scienze e Tecnologie Biologiche Chimiche e Farmaceutiche (STEBICEF), Università di Palermo, Via Archirafi 32, 90123 Palermo, Italy.
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28
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Pellerano M, Tcherniuk S, Perals C, Ngoc Van TN, Garcin E, Mahuteau-Betzer F, Teulade-Fichou MP, Morris MC. Targeting Conformational Activation of CDK2 Kinase. Biotechnol J 2017; 12. [PMID: 28430399 DOI: 10.1002/biot.201600531] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2016] [Revised: 04/20/2017] [Accepted: 04/21/2017] [Indexed: 01/12/2023]
Abstract
Cyclin-dependent kinases constitute attractive pharmacological targets for cancer therapeutics, yet inhibitors in clinical trials target the ATP-binding pocket of the CDK and therefore suffer from limited selectivity and emergence of resistance. The more recent development of allosteric inhibitors targeting conformational plasticity of protein kinases offers promising perspectives for therapeutics. In particular tampering with T-loop dynamics of CDK2 kinase would provide a selective means of inhibiting this kinase, by preventing its conformational activation. To this aim we engineered a fluorescent biosensor that specifically reports on conformational changes of CDK2 activation loop and is insensitive to ATP or ATP-competitive inhibitors, which constitutes a highly sensitive probe for identification of selective T-loop modulators. This biosensor was successfully applied to screen a library of small chemical compounds leading to discovery of a family of quinacridine analogs, which potently inhibit cancer cell proliferation, and promote accumulation of cells in S phase and G2. These compounds bind CDK2/ Cyclin A, inhibit its kinase activity, compete with substrate binding, but not with ATP, and dock onto the T-loop of CDK2. The best compound also binds CDK4 and CDK4/Cyclin D1, but not CDK1. The strategy we describe opens new doors for the discovery of a new class of allosteric CDK inhibitors for cancer therapeutics.
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Affiliation(s)
- Morgan Pellerano
- Institut des Biomolécules Max Mousseron, Université de Montpellier, Faculté de Pharmacie, Montpellier, France
| | - Sergey Tcherniuk
- Institut des Biomolécules Max Mousseron, Université de Montpellier, Faculté de Pharmacie, Montpellier, France
| | - Corine Perals
- Centre de Physiopathologie de Toulouse Purpan, Université de Toulouse Paul Sabatier, CHU Purpan, Toulouse Cedex 3, France
| | - Thi Nhu Ngoc Van
- Institut des Biomolécules Max Mousseron, Université de Montpellier, Faculté de Pharmacie, Montpellier, France
| | - Elsa Garcin
- Department of Chemistry and Biochemistry, University of Maryland Baltimore County (UMBC), Baltimore, USA
| | | | | | - May C Morris
- Institut des Biomolécules Max Mousseron, Université de Montpellier, Faculté de Pharmacie, Montpellier, France
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29
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Greener JG, Filippis I, Sternberg MJE. Predicting Protein Dynamics and Allostery Using Multi-Protein Atomic Distance Constraints. Structure 2017; 25:546-558. [PMID: 28190781 PMCID: PMC5343748 DOI: 10.1016/j.str.2017.01.008] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2016] [Revised: 11/24/2016] [Accepted: 01/19/2017] [Indexed: 11/16/2022]
Abstract
The related concepts of protein dynamics, conformational ensembles and allostery are often difficult to study with molecular dynamics (MD) due to the timescales involved. We present ExProSE (Exploration of Protein Structural Ensembles), a distance geometry-based method that generates an ensemble of protein structures from two input structures. ExProSE provides a unified framework for the exploration of protein structure and dynamics in a fast and accessible way. Using a dataset of apo/holo pairs it is shown that existing coarse-grained methods often cannot span large conformational changes. For T4-lysozyme, ExProSE is able to generate ensembles that are more native-like than tCONCOORD and NMSim, and comparable with targeted MD. By adding additional constraints representing potential modulators, ExProSE can predict allosteric sites. ExProSE ranks an allosteric pocket first or second for 27 out of 58 allosteric proteins, which is similar and complementary to existing methods. The ExProSE source code is freely available.
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Affiliation(s)
- Joe G Greener
- Centre for Integrative Systems Biology and Bioinformatics, Department of Life Sciences, Imperial College London, London SW7 2AZ, UK.
| | - Ioannis Filippis
- Centre for Integrative Systems Biology and Bioinformatics, Department of Life Sciences, Imperial College London, London SW7 2AZ, UK
| | - Michael J E Sternberg
- Centre for Integrative Systems Biology and Bioinformatics, Department of Life Sciences, Imperial College London, London SW7 2AZ, UK
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30
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Christodoulou MS, Caporuscio F, Restelli V, Carlino L, Cannazza G, Costanzi E, Citti C, Lo Presti L, Pisani P, Battistutta R, Broggini M, Passarella D, Rastelli G. Probing an Allosteric Pocket of CDK2 with Small Molecules. ChemMedChem 2016; 12:33-41. [DOI: 10.1002/cmdc.201600474] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2016] [Revised: 11/16/2016] [Indexed: 12/21/2022]
Affiliation(s)
- Michael S. Christodoulou
- Dipartimento di Scienze della Vita; Università degli Studi di Modena e Reggio Emilia; Via Campi 103 41125 Modena Italy
- Dipartimento di Chimica; Università degli Studi di Milano; Via Golgi 19 20133 Milano Italy
| | - Fabiana Caporuscio
- Dipartimento di Scienze della Vita; Università degli Studi di Modena e Reggio Emilia; Via Campi 103 41125 Modena Italy
| | - Valentina Restelli
- Istituto di Ricerche Farmacologiche Mario Negri; Via La Masa 19 20156 Milano Italy
| | - Luca Carlino
- Dipartimento di Scienze della Vita; Università degli Studi di Modena e Reggio Emilia; Via Campi 103 41125 Modena Italy
| | - Giuseppe Cannazza
- Dipartimento di Scienze della Vita; Università degli Studi di Modena e Reggio Emilia; Via Campi 103 41125 Modena Italy
| | - Elisa Costanzi
- Dipartimento di Scienze Chimiche; Università degli Studi di Padova; Via Marzolo 1 35131 Padova Italy
| | - Cinzia Citti
- Dipartimento di Scienze e Tecnologie Biologiche e Ambientali; Università del Salento; Via per Monteroni 73100 Lecce Italy
| | - Leonardo Lo Presti
- Dipartimento di Chimica; Università degli Studi di Milano; Via Golgi 19 20133 Milano Italy
| | - Pasquale Pisani
- Dipartimento di Scienze della Vita; Università degli Studi di Modena e Reggio Emilia; Via Campi 103 41125 Modena Italy
| | - Roberto Battistutta
- Dipartimento di Scienze Chimiche; Università degli Studi di Padova; Via Marzolo 1 35131 Padova Italy
| | - Massimo Broggini
- Istituto di Ricerche Farmacologiche Mario Negri; Via La Masa 19 20156 Milano Italy
| | - Daniele Passarella
- Dipartimento di Chimica; Università degli Studi di Milano; Via Golgi 19 20133 Milano Italy
| | - Giulio Rastelli
- Dipartimento di Scienze della Vita; Università degli Studi di Modena e Reggio Emilia; Via Campi 103 41125 Modena Italy
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31
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Recent progress of cyclin-dependent kinase inhibitors as potential anticancer agents. Future Med Chem 2016; 8:2047-2076. [DOI: 10.4155/fmc-2016-0129] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Deregulation of the cell cycle is a common feature in human cancer. The inhibition of cyclin-dependent kinases (CDKs), which play a crucial role in control of the cell cycle, has always been one of the most promising areas in cancer chemotherapy. This review first summarizes the biology of CDKs and then focuses on the recent advances in both broad-range and selective CDK inhibitors during the last 5 years. The design rationale, structural optimization and structure–activity relationships analysis of these small molecules have been discussed in detail and the key interactions with the amino-acid residues of the most important compounds are highlighted. Future perspectives for CDKs inhibitors will be defined in the development of highly selective CDK inhibitors, an accurate knowledge of gene control mechanism and further predictive biomarker research.
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Lu F, Luo G, Qiao L, Jiang L, Li G, Zhang Y. Virtual Screening for Potential Allosteric Inhibitors of Cyclin-Dependent Kinase 2 from Traditional Chinese Medicine. Molecules 2016; 21:molecules21091259. [PMID: 27657032 PMCID: PMC6274045 DOI: 10.3390/molecules21091259] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2016] [Revised: 09/01/2016] [Accepted: 09/17/2016] [Indexed: 01/16/2023] Open
Abstract
Cyclin-dependent kinase 2 (CDK2), a member of Cyclin-dependent kinases (CDKs), plays an important role in cell division and DNA replication. It is regarded as a desired target to treat cancer and tumor by interrupting aberrant cell proliferation. Compared to lower subtype selectivity of CDK2 ATP-competitive inhibitors, CDK2 allosteric inhibitor with higher subtype selectivity has been used to treat CDK2-related diseases. Recently, the first crystal structure of CDK2 with allosteric inhibitor has been reported, which provides new opportunities to design pure allosteric inhibitors of CDK2. The binding site of the ATP-competition inhibitors and the allosteric inhibitors are partially overlapped in space position, so the same compound might interact with the two binding sites. Thus a novel screening strategy was essential for the discovery of pure CDK2 allosteric inhibitors. In this study, pharmacophore and molecular docking were used to screen potential CDK2 allosteric inhibitors and ATP-competition inhibitors from Traditional Chinese Medicine (TCM). In the docking result of the allosteric site, the compounds which can act with the CDK2 ATP site were discarded, and the remaining compounds were regarded as the potential pure allosteric inhibitors. Among the results, prostaglandin E1 and nordihydroguaiaretic acid (NDGA) were available and their growth inhibitory effect on human HepG2 cell lines was determined by MTT assay. The two compounds could substantially inhibit the growth of HepG2 cell lines with an estimated IC50 of 41.223 μmol/L and 45.646 μmol/L. This study provides virtual screening strategy of allosteric compounds and a reliable method to discover potential pure CDK2 allosteric inhibitors from TCM. Prostaglandin E1 and NDGA could be regarded as promising candidates for CDK2 allosteric inhibitors.
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Affiliation(s)
- Fang Lu
- Beijing Key Laboratory of TCM Foundation and New Drug Research, School of Chinese Material Medica, Beijing University of Chinese Medicine, Beijing 100102, China.
| | - Ganggang Luo
- Beijing Key Laboratory of TCM Foundation and New Drug Research, School of Chinese Material Medica, Beijing University of Chinese Medicine, Beijing 100102, China.
| | - Liansheng Qiao
- Beijing Key Laboratory of TCM Foundation and New Drug Research, School of Chinese Material Medica, Beijing University of Chinese Medicine, Beijing 100102, China.
| | - Ludi Jiang
- Beijing Key Laboratory of TCM Foundation and New Drug Research, School of Chinese Material Medica, Beijing University of Chinese Medicine, Beijing 100102, China.
| | - Gongyu Li
- Beijing Key Laboratory of TCM Foundation and New Drug Research, School of Chinese Material Medica, Beijing University of Chinese Medicine, Beijing 100102, China.
| | - Yanling Zhang
- Beijing Key Laboratory of TCM Foundation and New Drug Research, School of Chinese Material Medica, Beijing University of Chinese Medicine, Beijing 100102, China.
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33
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Exploiting computationally derived out-of-the-box protein conformations for drug design. Future Med Chem 2016; 8:1887-1897. [PMID: 27629935 DOI: 10.4155/fmc-2016-0098] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Structural plasticity is an intrinsic property of proteins that allows each gene product to accomplish its tasks in a strictly regulated manner at a precise time and cellular location. Moreover, protein motions allow protein-ligand and protein-protein recognition. The knowledge of the conformational ensemble that a drug target populates may be crucial for the design of small molecules that can differently modulate its function. X-ray crystallography and NMR have endlessly provided snapshots of protein states. However, experimental structure determination is not always straightforward. Therefore, attempts have been made to depict protein conformational landscapes through molecular dynamics and enhanced sampling methods. Here, we review how accounting for protein dynamics through in silico generated out-of-the-box protein conformations has started to impact on drug discovery.
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Chilà R, Guffanti F, Damia G. Role and therapeutic potential of CDK12 in human cancers. Cancer Treat Rev 2016; 50:83-88. [PMID: 27662623 DOI: 10.1016/j.ctrv.2016.09.003] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2016] [Revised: 08/30/2016] [Accepted: 09/01/2016] [Indexed: 12/31/2022]
Abstract
Phosphorylation of the RNA polymerase II C-terminal domain by cyclin-dependent kinases (CDKs) is important for productive transcription. Deregulated transcription-CDKs have been reported in different human cancers. Until recently CDK9 was the only transcription-CDK with a causative role in cancer, but evidence is cumulating of the importance of CDK12. This review summarizes the role of CDK12 in transcription and RNA processing, in maintaining genomic stability/integrity and in tumorigenesis. CDK12 mutations have been reported in many cancers and have been suggested as a cause of defective DNA repair in ovarian carcinoma. CDK12 may have a role as a new therapeutic target in oncology.
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Affiliation(s)
- Rosaria Chilà
- Laboratory of Molecular Pharmacology, Oncology Department, IRCCS - Istituto di Ricerche Farmacologiche Mario Negri, Milan, Italy
| | - Federica Guffanti
- Laboratory of Molecular Pharmacology, Oncology Department, IRCCS - Istituto di Ricerche Farmacologiche Mario Negri, Milan, Italy
| | - Giovanna Damia
- Laboratory of Molecular Pharmacology, Oncology Department, IRCCS - Istituto di Ricerche Farmacologiche Mario Negri, Milan, Italy.
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35
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Carlino L, Rastelli G. Dual Kinase-Bromodomain Inhibitors in Anticancer Drug Discovery: A Structural and Pharmacological Perspective. J Med Chem 2016; 59:9305-9320. [DOI: 10.1021/acs.jmedchem.6b00438] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Luca Carlino
- Department
of Life Sciences, University of Modena and Reggio Emilia, Modena 41125, Italy
| | - Giulio Rastelli
- Department
of Life Sciences, University of Modena and Reggio Emilia, Modena 41125, Italy
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36
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Abstract
Small-molecule kinase inhibitors are invaluable targeted therapeutics for the treatment of various human diseases, especially cancers. While the majority of approved and developed preclinical small-molecule inhibitors are characterized as type I or type II inhibitors that target the ATP-binding pocket of kinases, the remarkable sequential and structural similarity among ATP pockets renders the selective inhibition of kinases a daunting challenge. Therefore, targeting allosteric pockets of kinases outside the highly conversed ATP pocket has been proposed as a promising alternative to overcome current barriers of kinase inhibitors, including poor selectivity and emergence of drug resistance. In spite of the small number of identified allosteric inhibitors in comparison with that of inhibitors targeting the ATP pocket, encouraging results, such as the FDA-approval of the first small-molecule allosteric inhibitor trametinib in 2013, the progress of more than 10 other allosteric inhibitors in clinical trials, and the emergence of a pipeline of highly selective and potent preclinical molecules, have been reported in the past decade. In this article, we present the current knowledge on allosteric inhibition in terms of conception, classification, potential advantages, and summarized debatable topics in the field. Recent progress and allosteric inhibitors that were identified in the past three years are highlighted in this paper.
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Affiliation(s)
- Peng Wu
- Department of Chemistry, Technical University of Denmark, Kgs. Lyngby DK-2800, Denmark.
| | - Mads H Clausen
- Department of Chemistry, Technical University of Denmark, Kgs. Lyngby DK-2800, Denmark; Center for Nanomedicine and Theranostics, Technical University of Denmark, Kgs. Lyngby DK-2800, Denmark
| | - Thomas E Nielsen
- Protein and Peptide Chemistry, Novo Nordisk A/S, Måløv DK-2760, Denmark
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37
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Cyclin dependent kinase (CDK) inhibitors as anticancer drugs. Bioorg Med Chem Lett 2015; 25:3420-35. [PMID: 26115571 DOI: 10.1016/j.bmcl.2015.05.100] [Citation(s) in RCA: 179] [Impact Index Per Article: 19.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2015] [Revised: 05/21/2015] [Accepted: 05/30/2015] [Indexed: 02/01/2023]
Abstract
Sustained proliferative capacity is a hallmark of cancer. In mammalian cells proliferation is controlled by the cell cycle, where cyclin-dependent kinases (CDKs) regulate critical checkpoints. CDK4 and CDK6 are considered highly validated anticancer drug targets due to their essential role regulating cell cycle progression at the G1 restriction point. This review provides an overview of recent advances on cyclin dependent kinase inhibitors in general with special emphasis on CDK4 and CDK6 inhibitors and compounds under clinical evaluation. Chemical structures, structure activity relationships, and relevant preclinical properties will be described.
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38
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Insights on Structural Characteristics and Ligand Binding Mechanisms of CDK2. Int J Mol Sci 2015; 16:9314-40. [PMID: 25918937 PMCID: PMC4463590 DOI: 10.3390/ijms16059314] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2015] [Revised: 04/01/2015] [Accepted: 04/15/2015] [Indexed: 12/20/2022] Open
Abstract
Cyclin-dependent kinase 2 (CDK2) is a crucial regulator of the eukaryotic cell cycle. However it is well established that monomeric CDK2 lacks regulatory activity, which needs to be aroused by its positive regulators, cyclins E and A, or be phosphorylated on the catalytic segment. Interestingly, these activation steps bring some dynamic changes on the 3D-structure of the kinase, especially the activation segment. Until now, in the monomeric CDK2 structure, three binding sites have been reported, including the adenosine triphosphate (ATP) binding site (Site I) and two non-competitive binding sites (Site II and III). In addition, when the kinase is subjected to the cyclin binding process, the resulting structural changes give rise to a variation of the ATP binding site, thus generating an allosteric binding site (Site IV). All the four sites are demonstrated as being targeted by corresponding inhibitors, as is illustrated by the allosteric binding one which is targeted by inhibitor ANS (fluorophore 8-anilino-1-naphthalene sulfonate). In the present work, the binding mechanisms and their fluctuations during the activation process attract our attention. Therefore, we carry out corresponding studies on the structural characterization of CDK2, which are expected to facilitate the understanding of the molecular mechanisms of kinase proteins. Besides, the binding mechanisms of CDK2 with its relevant inhibitors, as well as the changes of binding mechanisms following conformational variations of CDK2, are summarized and compared. The summary of the conformational characteristics and ligand binding mechanisms of CDK2 in the present work will improve our understanding of the molecular mechanisms regulating the bioactivities of CDK2.
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