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Nagare S, Lokhande KB, Swamy KV. Docking and simulation studies on cyclin D/CDK4 complex for targeting cell cycle arrest in cancer using flavanone and its congener. J Mol Model 2023; 29:90. [PMID: 36881272 DOI: 10.1007/s00894-023-05496-6] [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: 08/07/2022] [Accepted: 02/27/2023] [Indexed: 03/08/2023]
Abstract
Flavanone compounds are naturally occurring phytochemicals present in most of citrus fruits reported to be a potential anticancer moiety as it majorly participates in the inhibition of the cell cycle, apoptosis, and angiogenesis. Because of poor bioavailability, natural flavanones were not used as therapeutic targets so flavanone congeners were prepared by modifying at B-functional group using compound libraries such as PubChem Database. Cyclin-dependent kinase is primarily activating the cell cycle and potentiating the M phase, in order to control the cell cycle in cancer cyclin-dependent pathway was targeted and potential cyclin D/CDK4 receptor protein was retrieved from Protein Data Bank (PDBID:2W9Z). The binding site was determined using FlexX docking. Flavanone and its congeners were docked against the 2W9Z receptor protein with the docking software FlexX. For validation of docking results, molecular dynamics simulations of the best-fitting molecule were carried out using Desmond Package. Noncovalent interactions like hydrogen bonds, electrostatic interaction, and Van der walls potentials for stable conformations were calculated. Thus, upon docking and molecular dynamics studies, we discovered the potential flavanone derivatives such as Flavanone 20, Flavanone 25, and Flavanone 29, will become a potential drug target in controlling cell cycle arrest and may become a futuristic candidate in targeting cancer.
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Affiliation(s)
- Sagar Nagare
- School of Biotechnology and Bioinformatics, D.Y. Patil Deemed to Be University, CBD Belapur, Navi Mumbai, Maharashtra, India, 400614.,Bioinformatics Research Laboratory, Dr. D.Y. Patil Biotechnology and Bioinformatics Institute, Dr. D.Y. Patil Vidyapeeth, Tathawade Campus, Tathawade, Pune, Maharashtra, India, 411033
| | - Kiran Bharat Lokhande
- Bioinformatics Research Laboratory, Dr. D.Y. Patil Biotechnology and Bioinformatics Institute, Dr. D.Y. Patil Vidyapeeth, Tathawade Campus, Tathawade, Pune, Maharashtra, India, 411033.,Translational Bioinformatics and Computational Genomics Research Lab, Department of Life Sciences, Shiv Nadar Institution of Eminence, Gautam Buddha Nagar, UP, 201314, India
| | - K Venkateswara Swamy
- Bioinformatics and Drug Discovery Group, MIT School of Bioengineering Science and Research, MIT Art, Design and Technology University, Pune, Maharashtra, India, 412201.
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2
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Quandt E, Ribeiro MPC, Clotet J. Atypical cyclins in cancer: New kids on the block? Semin Cell Dev Biol 2020; 107:46-53. [PMID: 32417219 DOI: 10.1016/j.semcdb.2020.04.018] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2020] [Revised: 04/15/2020] [Accepted: 04/27/2020] [Indexed: 12/13/2022]
Abstract
Atypical cyclins have recently emerged as a new subfamily of cyclins characterized by common structural features and interactor pattern. Interestingly, atypical cyclins are phylogenetically close to canonical cyclins, which have well-established roles in cell cycle regulation and cancer. Therefore, although the function of atypical cyclins is still poorly characterized, it seems likely that they are involved in cancer pathogenesis as well. Here, we coupled gene expression and prognostic significance analysis to bibliographic search in order to provide new insights into the role of atypical cyclins in cancer. The information gathered suggests that atypical cyclins intervene in critical processes to sustain cancer growth and have potential to become novel prognostic markers and drug targets in cancer.
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Affiliation(s)
- Eva Quandt
- Faculty of Medicine and Health Sciences, Universitat Internacional De Catalunya, 08195, Sant Cugat Del Vallès, Barcelona, Spain
| | - Mariana P C Ribeiro
- Faculty of Medicine and Health Sciences, Universitat Internacional De Catalunya, 08195, Sant Cugat Del Vallès, Barcelona, Spain.
| | - Josep Clotet
- Faculty of Medicine and Health Sciences, Universitat Internacional De Catalunya, 08195, Sant Cugat Del Vallès, Barcelona, Spain.
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3
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Pellerano M, Naud-Martin D, Mahuteau-Betzer F, Morille M, Morris MC. Fluorescent Biosensor for Detection of the R248Q Aggregation-Prone Mutant of p53. Chembiochem 2019; 20:605-613. [PMID: 30548750 DOI: 10.1002/cbic.201800531] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2018] [Revised: 12/10/2018] [Indexed: 01/28/2023]
Abstract
The p53 tumour suppressor and guardian of the genome undergoes missense mutations that lead to functional inactivation in 50 % of human cancers. These mutations occur mostly in the DNA-binding domain of the protein, and several of these result in conformational changes that lead to amyloid-like protein aggregation. Herein, we describe a fluorescent biosensor that reports on the R248Q mutant of p53 in vitro and in living cells, engineered through conjugation of an environmentally sensitive probe onto a peptide derived from the primary aggregation segment of p53. This biosensor was characterised both in vitro and by means of fluorescence microscopy following facilitated delivery into cultured cells. It is shown that this biosensor preferentially reports on the p53 R248Q mutant in the PC9 lung cancer cell line compared with other lung cancer cell lines harbouring either wild-type or no p53.
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Affiliation(s)
- Morgan Pellerano
- Institut des Biomolécules Max Mousseron-IBMM-UMR 5247, Université de Montpellier, Faculté de Pharmacie, 15, Av. Charles Flahault, 34093, Montpellier, France
| | - Delphine Naud-Martin
- Institut Curie, PSL Research University, CNRS, INSERM, UMR9187-U1196, 91405, Orsay, France
| | | | - Marie Morille
- Institut Charles Gerhardt-UMR 5253 CNRS-UM-ENSCM, Université de Montpellier, Faculté de Pharmacie, 15, Av. Charles Flahault, 34093, Montpellier, France
| | - May C Morris
- Institut des Biomolécules Max Mousseron-IBMM-UMR 5247, Université de Montpellier, Faculté de Pharmacie, 15, Av. Charles Flahault, 34093, Montpellier, France
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4
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Li J, Ouyang Y, Zhang X, Zhou W, Wang F, Huang Z, Wang X, Chen Y, Zhang H, Fu L. Effect of HM910, a novel camptothecin derivative, on the inhibition of multiple myeloma cell growth in vitro and in vivo. Am J Cancer Res 2015; 5:1000-1016. [PMID: 26045982 PMCID: PMC4449431] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2014] [Accepted: 02/10/2015] [Indexed: 06/04/2023] Open
Abstract
Despite a variety of novel therapeutic agents, such as bortezomib, thalidomide and topotecan, multiple myeloma (MM) remains an incurable disease, thus the development of new chemotherapeutical agents is of high priority. We found HM910, a novel camptothecin (CPT) derivative, exhibited potent inhibition of MM cell growth in vitro and in xenografts of nude mice. Mechanistically, HM910 reduced the mitochondrial transmembrane potential (ΔΨm) via an increase in reactive oxygen species (ROS), which eventually resulting in the release of cytochrome c and the activation of mitochondrial-dependent apoptotic pathway. On the other hand, HM910 significantly triggered cell cycle arrest in G1 phase via downregulating the expressions of cyclin dependent kinase (CDK) 4 and 6, resulting in down-regulation of cyclin D1. Therefore, HM910 maybe a promising candidate for treating MM patients and is currently in phase I clinical trial in China.
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Affiliation(s)
- Juan Li
- First Affiliated Hospital, Sun Yat-sen UniversityGuangzhou 510080, China
| | - Yudan Ouyang
- First Affiliated Hospital, Sun Yat-sen UniversityGuangzhou 510080, China
- State Key Laboratory of Oncology in South China; Collaborative Innovation Center for Cancer Medicine; Cancer Center, Sun Yat-sen UniversityGuangzhou 510060, China
| | - Xu Zhang
- State Key Laboratory of Oncology in South China; Collaborative Innovation Center for Cancer Medicine; Cancer Center, Sun Yat-sen UniversityGuangzhou 510060, China
| | - Wenqiang Zhou
- Fangsheng Pharmaceuticals, IncChangsha 410000, China
| | - Fang Wang
- State Key Laboratory of Oncology in South China; Collaborative Innovation Center for Cancer Medicine; Cancer Center, Sun Yat-sen UniversityGuangzhou 510060, China
| | - Zhencong Huang
- State Key Laboratory of Oncology in South China; Collaborative Innovation Center for Cancer Medicine; Cancer Center, Sun Yat-sen UniversityGuangzhou 510060, China
| | - Xiaokun Wang
- State Key Laboratory of Oncology in South China; Collaborative Innovation Center for Cancer Medicine; Cancer Center, Sun Yat-sen UniversityGuangzhou 510060, China
| | - Yifan Chen
- State Key Laboratory of Oncology in South China; Collaborative Innovation Center for Cancer Medicine; Cancer Center, Sun Yat-sen UniversityGuangzhou 510060, China
| | - Hui Zhang
- State Key Laboratory of Oncology in South China; Collaborative Innovation Center for Cancer Medicine; Cancer Center, Sun Yat-sen UniversityGuangzhou 510060, China
| | - Liwu Fu
- State Key Laboratory of Oncology in South China; Collaborative Innovation Center for Cancer Medicine; Cancer Center, Sun Yat-sen UniversityGuangzhou 510060, China
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5
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Peyressatre M, Prével C, Pellerano M, Morris MC. Targeting cyclin-dependent kinases in human cancers: from small molecules to Peptide inhibitors. Cancers (Basel) 2015; 7:179-237. [PMID: 25625291 PMCID: PMC4381256 DOI: 10.3390/cancers7010179] [Citation(s) in RCA: 219] [Impact Index Per Article: 24.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2014] [Accepted: 01/12/2015] [Indexed: 12/12/2022] Open
Abstract
Cyclin-dependent kinases (CDK/Cyclins) form a family of heterodimeric kinases that play central roles in regulation of cell cycle progression, transcription and other major biological processes including neuronal differentiation and metabolism. Constitutive or deregulated hyperactivity of these kinases due to amplification, overexpression or mutation of cyclins or CDK, contributes to proliferation of cancer cells, and aberrant activity of these kinases has been reported in a wide variety of human cancers. These kinases therefore constitute biomarkers of proliferation and attractive pharmacological targets for development of anticancer therapeutics. The structural features of several of these kinases have been elucidated and their molecular mechanisms of regulation characterized in depth, providing clues for development of drugs and inhibitors to disrupt their function. However, like most other kinases, they constitute a challenging class of therapeutic targets due to their highly conserved structural features and ATP-binding pocket. Notwithstanding, several classes of inhibitors have been discovered from natural sources, and small molecule derivatives have been synthesized through rational, structure-guided approaches or identified in high throughput screens. The larger part of these inhibitors target ATP pockets, but a growing number of peptides targeting protein/protein interfaces are being proposed, and a small number of compounds targeting allosteric sites have been reported.
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Affiliation(s)
- Marion Peyressatre
- Institut des Biomolécules Max Mousseron, IBMM-CNRS-UMR5247, 15 Av. Charles Flahault, 34093 Montpellier, France.
| | - Camille Prével
- Institut des Biomolécules Max Mousseron, IBMM-CNRS-UMR5247, 15 Av. Charles Flahault, 34093 Montpellier, France.
| | - Morgan Pellerano
- Institut des Biomolécules Max Mousseron, IBMM-CNRS-UMR5247, 15 Av. Charles Flahault, 34093 Montpellier, France.
| | - May C Morris
- Institut des Biomolécules Max Mousseron, IBMM-CNRS-UMR5247, 15 Av. Charles Flahault, 34093 Montpellier, France.
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Premnath PN, Craig SN, Liu S, Anderson EL, Grigoroudis AI, Kontopidis G, Perkins TL, Wyatt MD, Pittman DL, McInnes C. Iterative conversion of cyclin binding groove peptides into druglike CDK inhibitors with antitumor activity. J Med Chem 2014; 58:433-42. [PMID: 25454794 PMCID: PMC4334226 DOI: 10.1021/jm5015023] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
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The cyclin groove is an important
recognition site for substrates
of the cell cycle cyclin dependent kinases and provides an opportunity
for highly selective inhibition of kinase activity through a non-ATP
competitive mechanism. The key peptide residues of the cyclin binding
motif have been studied in order to precisely define the structure–activity
relationship for CDK kinase inhibition. Through this information,
new insights into the interactions of peptide CDK inhibitors with
key subsites of the cyclin binding groove provide for the replacement
of binding determinants with more druglike functionality through REPLACE,
a strategy for the iterative conversion of peptidic blockers of protein–protein
interactions into pharmaceutically relevant compounds. As a result,
REPLACE is further exemplified in combining optimized peptidic sequences
with effective N-terminal capping groups to generate more stable compounds
possessing antitumor activity consistent with on-target inhibition
of cell cycle CDKs. The compounds described here represent prototypes
for a next generation of kinase therapeutics with high efficacy and
kinome selectivity, thus avoiding problems observed with first generation
CDK inhibitors.
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Affiliation(s)
- Padmavathy Nandha Premnath
- Department of Drug Discovery and Biomedical Sciences, South Carolina College of Pharmacy, University of South Carolina , Columbia, South Carolina 29208, United States
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Karthiga A, Tripathi SK, Shanmugam R, Suryanarayanan V, Singh SK. Targeting the cyclin-binding groove site to inhibit the catalytic activity of CDK2/cyclin A complex using p27(KIP1)-derived peptidomimetic inhibitors. J Chem Biol 2014; 8:11-24. [PMID: 25584078 DOI: 10.1007/s12154-014-0124-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2014] [Accepted: 09/02/2014] [Indexed: 01/24/2023] Open
Abstract
Functionally activated cyclin-dependent kinase 2 (CDK2)/cyclin A complex has been validated as an interesting therapeutic target to develop the efficient antineoplastic drug based on the cell cycle arrest. Cyclin A binds to CDK2 and activates the kinases as well as recruits the substrate and inhibitors using a hydrophobic cyclin-binding groove (CBG). Blocking the cyclin substrate recruitment on CBG is an alternative approach to override the specificity hurdle of the currently available ATP site targeting CDK2 inhibitors. Greater understanding of the interaction of CDK2/cyclin A complex with p27 (negative regulator) reveals that the Leu-Phe-Gly (LFG) motif region of p27 binds with the CBG site of cyclin A to arrest the malignant cell proliferation that induces apoptosis. In the present study, Replacement with Partial Ligand Alternatives through Computational Enrichment (REPLACE) drug design strategies have been applied to acquire LFG peptide-derived peptidomimetics library. The peptidomimetics function is equivalent with respect to substrate p27 protein fashion but does not act as an ATP antagonist. The combined approach of molecular docking, molecular dynamics (MD), and molecular electrostatic potential and ADME/T prediction were carried out to evaluate the peptidomimetics. Resultant interaction and electrostatic potential maps suggested that smaller substituent is desirable at the position of phenyl ring to interact with Trp217, Arg250, and Gln254 residues in the active site. The best docked poses were refined by the MD simulations which resulted in conformational changes. After equilibration, the structure of the peptidomimetic and receptor complex was stable. The results revealed that the various substrate protein-derived peptidomimetics could serve as perfect leads against CDK2 protein.
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Affiliation(s)
- Arumugasamy Karthiga
- Computer Aided Drug Designing and Molecular Modeling Lab, Department of Bioinformatics, Alagappa University, Karaikudi, 630 003 Tamil Nadu India
| | - Sunil Kumar Tripathi
- Computer Aided Drug Designing and Molecular Modeling Lab, Department of Bioinformatics, Alagappa University, Karaikudi, 630 003 Tamil Nadu India
| | - Ramasamy Shanmugam
- Department of Chemistry, Thiagarajar College, Madurai, 625009 Tamil Nadu India
| | - Venkatesan Suryanarayanan
- Computer Aided Drug Designing and Molecular Modeling Lab, Department of Bioinformatics, Alagappa University, Karaikudi, 630 003 Tamil Nadu India
| | - Sanjeev Kumar Singh
- Computer Aided Drug Designing and Molecular Modeling Lab, Department of Bioinformatics, Alagappa University, Karaikudi, 630 003 Tamil Nadu India
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Lou X, Zhang J, Liu S, Xu N, Liao DJ. The other side of the coin: the tumor-suppressive aspect of oncogenes and the oncogenic aspect of tumor-suppressive genes, such as those along the CCND-CDK4/6-RB axis. Cell Cycle 2014; 13:1677-93. [PMID: 24799665 DOI: 10.4161/cc.29082] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Although cancer-regulatory genes are dichotomized to oncogenes and tumor-suppressor gene s, in reality they can be oncogenic in one situation but tumor-suppressive in another. This dual-function nature, which sometimes hampers our understanding of tumor biology, has several manifestations: (1) Most canonically defined genes have multiple mRNAs, regulatory RNAs, protein isoforms, and posttranslational modifications; (2) Genes may interact at different levels, such as by forming chimeric RNAs or by forming different protein complexes; (3) Increased levels of tumor-suppressive genes in normal cells drive proliferation of cancer progenitor cells in the same organ or tissue by imposing compensatory proliferation pressure, which presents the dual-function nature as a cell-cell interaction. All these manifestations of dual functions can find examples in the genes along the CCND-CDK4/6-RB axis. The dual-function nature also underlies the heterogeneity of cancer cells. Gene-targeting chemotherapies, including that targets CDK4, are effective to some cancer cells but in the meantime may promote growth or progression of some others in the same patient. Redefining "gene" by considering each mRNA, regulatory RNA, protein isoform, and posttranslational modification from the same genomic locus as a "gene" may help in better understanding tumor biology and better selecting targets for different sub-populations of cancer cells in individual patients for personalized therapy.
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Affiliation(s)
- Xiaomin Lou
- CAS Key Laboratory of Genome Sciences and Information; Beijing Institute of Genomics; Chinese Academy of Sciences; Beijing, PR China
| | - Ju Zhang
- CAS Key Laboratory of Genome Sciences and Information; Beijing Institute of Genomics; Chinese Academy of Sciences; Beijing, PR China
| | - Siqi Liu
- CAS Key Laboratory of Genome Sciences and Information; Beijing Institute of Genomics; Chinese Academy of Sciences; Beijing, PR China
| | - Ningzhi Xu
- Laboratory of Cell and Molecular Biology; Cancer Institute; Chinese Academy of Medical Science; Beijing, PR China
| | - D Joshua Liao
- Hormel Institute; University of Minnesota; Austin, MN USA
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Kaushik A, Subramaniam S, Gupta D. In silico characterization and molecular dynamics simulation of Pfcyc-1, a cyclin homolog of Plasmodium falciparum. J Biomol Struct Dyn 2013; 32:1624-33. [PMID: 23998890 DOI: 10.1080/07391102.2013.831378] [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: 10/26/2022]
Abstract
Malaria is still one of the deadly diseases resulting in deaths of millions of people worldwide and situation has become worse due to alarming rise in anti-malarial drug resistance. Genome sequence availability of Plasmodium falciparum, the main causal organism of severe malaria in humans, has enabled identification of various parasite cell cycle regulators like several cyclins and cyclin dependent kinases or CDKs which are promising novel drug targets for Malaria. Here, we present in silico characterization of tertiary structure of Pfcyc-1, a P. falciparum cyclin homolog, which enables identification of key structural elements that contribute to its tertiary structure and function. We have investigated the structure and dynamics of Pfcyc-1 structural model by performing 10 ns molecular dynamics (MD) simulation. Our study indicates that despite poor sequence similarities with cyclin H and A, the characteristic structural cyclin domains are conserved in Pfcyc-1 too. The Pfcyc-1 model reveals a cyclin box, consisting of two tandemly repeating five-helix bundles separated by a linker hinge peptide. Furthermore, the amino acid residues in other known cyclins mediating cyclin-CDK interactions are conserved in Pfcyc-1. The model and its MD simulation offer a first ever structural annotation of any plasmodium cyclin, which along with sequence comparisons, helps in identification of important functional residues mediating the Pfcyc-1-CDK like interactions.
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Affiliation(s)
- Abhinav Kaushik
- a Bioinformatics Laboratory, Structural and Computational Biology Group , International Centre for Genetic Engineering and Biotechnology , Aruna Asaf Ali Marg, PB 10504, New Delhi , India
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Abate AA, Pentimalli F, Esposito L, Giordano A. ATP-noncompetitive CDK inhibitors for cancer therapy: an overview. Expert Opin Investig Drugs 2013; 22:895-906. [PMID: 23735075 DOI: 10.1517/13543784.2013.798641] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
INTRODUCTION Cyclin-dependent kinases (CDKs) are the key drivers of cell cycle progression and are often deregulated in cancer, therefore, targeting CDKs has long been pursued as a therapeutic strategy to tackle cancer. Unfortunately, however, none of the first-generation CDK inhibitors has yielded the expected efficacy to be successfully translated to the clinic mostly because, by targeting the very conserved kinase ATP-binding site resulted to be poorly specific and quite toxic. AREAS COVERED Here, the authors review recent approaches aimed at developing more specific CDK inhibitors mostly through the aid of computational drug design studies and report various small molecules and peptides, which resulted in promising CDK ATP-noncompetitive inhibitors. EXPERT OPINION Despite few successes, these new approaches still need additional considerations to generate effective antitumoral agents. The authors discuss some of the hurdles to overcome for a successful clinical translation.
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Affiliation(s)
- Agnese Anna Abate
- Sbarro Institute for Cancer Research and Molecular Medicine, Center for Biotechnology, College of Science and Technology, Temple University, Philadelphia, PA, USA
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Liu S, Premnath PN, Bolger JK, Perkins TL, Kirkland LO, Kontopidis G, McInnes C. Optimization of non-ATP competitive CDK/cyclin groove inhibitors through REPLACE-mediated fragment assembly. J Med Chem 2013; 56:1573-82. [PMID: 23323521 DOI: 10.1021/jm3013882] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
A major challenge in drug discovery is to develop and improve methods for targeting protein-protein interactions. Further exemplification of the REPLACE (REplacement with Partial Ligand Alternatives through Computational Enrichment) strategy for generating inhibitors of protein-protein interactions demonstrated that it can be used to optimize fragment alternatives of key determinants, to combine these in an effective way, and this was achieved for compounds targeting the cyclin-dependent kinase 2 (CDK2) substrate recruitment site on the cyclin regulatory subunit. Phenylheterocyclic isosteres replacing a critical charge-charge interaction provided new structural insights for binding to the cyclin groove. In particular, these results shed light onto the key contributions of a H-bond observed in crystal structures of N-terminally capped peptides. Furthermore, the structure-activity relationship of a bis(aryl) ether C-terminal capping group mimicking dipeptide interactions was probed through ring substitutions, allowing increased complementarity with the primary hydrophobic pocket. This study further validates REPLACE as an effective strategy for converting peptidic compounds to more pharmaceutically relevant compounds.
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Affiliation(s)
- Shu Liu
- Drug Discovery and Biomedical Sciences, South Carolina College of Pharmacy, University of South Carolina, Columbia, South Carolina 29208, United States
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Li H, Chadbourne FL, Lan R, Chan CF, Chan WL, Law GL, Lee CS, Cobb SL, Wong KL. Real time detection of cell cycle regulator cyclin A on living tumor cells with europium emission. Dalton Trans 2013; 42:13495-501. [DOI: 10.1039/c3dt51053k] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Affiliation(s)
- Hongguang Li
- Department of Chemistry, Hong Kong Baptist University, Kowloon Tong, Kowloon, Hong Kong
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Wang H, Chen X, Chen Y, Sun L, Li G, Zhai M, Zhai W, Kang Q, Gao Y, Qi Y. Antitumor activity of novel chimeric peptides derived from cyclinD/CDK4 and the protein transduction domain 4. Amino Acids 2012; 44:499-510. [DOI: 10.1007/s00726-012-1360-5] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2012] [Accepted: 06/29/2012] [Indexed: 12/30/2022]
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14
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Progress in the Development of Non-ATP-Competitive Protein Kinase Inhibitors for Oncology. ANNUAL REPORTS IN MEDICINAL CHEMISTRY 2012. [DOI: 10.1016/b978-0-12-396492-2.00029-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register]
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15
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Ou L, Ferreira AM, Otieno S, Xiao L, Bashford D, Kriwacki RW. Incomplete folding upon binding mediates Cdk4/cyclin D complex activation by tyrosine phosphorylation of inhibitor p27 protein. J Biol Chem 2011; 286:30142-51. [PMID: 21715330 DOI: 10.1074/jbc.m111.244095] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
p27(Kip1) (p27), an intrinsically disordered protein, regulates the various Cdk/cyclin complexes that control cell cycle progression. The kinase inhibitory domain of p27 contains a cyclin-binding subdomain (D1), a Cdk-binding subdomain (D2), and a linker helix subdomain that connects D1 and D2. Here, we report that, despite extensive sequence conservation between Cdk4/cyclin D1 (hereafter Cdk4/cyclin D) and Cdk2/cyclin A, the thermodynamic details describing how the individual p27 subdomains contribute to equally high affinity binding to these two Cdk/cyclin complexes are strikingly different. Differences in enthalpy/entropy compensation revealed that the D2 subdomain of p27 folds incompletely when binding Cdk4/cyclin D versus Cdk2/cyclin A. Incomplete binding-induced folding exposes tyrosine 88 of p27 for phosphorylation by the nonreceptor tyrosine kinase Abl. Importantly, tyrosine phosphorylation (of p27) relieves Cdk inhibition by p27, enabling cell cycle entry. Furthermore, the interaction between a conserved hydrophobic patch on cyclin D and subdomain D1 is much weaker than that with cyclin A; consequently, a construct containing subdomains D1 and LH (p27-D1LH) does not inhibit substrate binding to Cdk4/cyclin D as it does to Cdk2/cyclin A. Our results provide a mechanism by which Cdk4 (within the p27/Cdk4/cyclin D complex) is poised to be activated by extrinsic mitogenic signals that impinge upon p27 at the earliest stage of cell division. More broadly, our results further illustrate the regulatory versatility of intrinsically disordered proteins.
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Affiliation(s)
- Li Ou
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, USA
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