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Abu-Hashem AA, Hakami O, El-Shazly M, El-Nashar HAS, Yousif MNM. Caffeine and Purine Derivatives: A Comprehensive Review on the Chemistry, Biosynthetic Pathways, Synthesis-Related Reactions, Biomedical Prospectives and Clinical Applications. Chem Biodivers 2024; 21:e202400050. [PMID: 38719741 DOI: 10.1002/cbdv.202400050] [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: 01/09/2024] [Accepted: 05/06/2024] [Indexed: 06/13/2024]
Abstract
Caffeine and purine derivatives represent interesting chemical moieties, which show various biological activities. Caffeine is an alkaloid that belongs to the family of methylxanthine alkaloids and it is present in food, beverages, and drugs. Coffee, tea, and some other beverages are a major source of caffeine in the human diet. Caffeine can be extracted from tea or coffee using hot water with dichloromethane or chloroform and the leftover is known as decaffeinated coffee or tea. Caffeine and its derivatives were synthesized via different procedures on small and large scales. It competitively antagonizes the adenosine receptors (ARs), which are G protein-coupled receptors largely distributed in the human body, including the heart, vessels, brain, and kidneys. Recently, many reports showed the effect of caffeine derivatives in the treatment of many diseases such as Alzheimer's, asthma, parkinsonism, and cancer. Also, it is used as an antioxidant, anti-inflammatory, analgesic, and hypocholesterolemic agent. The present review article discusses the synthesis, reactivity, and biological and pharmacological properties of caffeine and its derivatives. The biosynthesis and biotransformation of caffeine in coffee and tea leaves and the human body were summarized in the review.
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Affiliation(s)
- Ameen A Abu-Hashem
- Photochemistry Department, National Research Centre, 12622, Dokki, Giza, Egypt
- Chemistry Department, Faculty of Science, Jazan University, 45142 and 2097, Jazan, KSA, Saudi Arabia
| | - Othman Hakami
- Chemistry Department, Faculty of Science, Jazan University, 45142 and 2097, Jazan, KSA, Saudi Arabia
| | - Mohamed El-Shazly
- Department of Pharmacognosy, Faculty of Pharmacy, Ain Shams University, Cairo, 11566, Egypt
| | - Heba A S El-Nashar
- Department of Pharmacognosy, Faculty of Pharmacy, Ain Shams University, Cairo, 11566, Egypt
| | - Mahmoud N M Yousif
- Photochemistry Department, National Research Centre, 12622, Dokki, Giza, Egypt
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Rana N, Grover P, Singh H. Recent Developments and Future Perspectives of Purine Derivatives as a Promising Scaffold in Drug Discovery. Curr Top Med Chem 2024; 24:541-579. [PMID: 38288806 DOI: 10.2174/0115680266290152240110074034] [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: 10/30/2023] [Revised: 12/17/2023] [Accepted: 12/27/2023] [Indexed: 05/31/2024]
Abstract
Numerous purine-containing compounds have undergone extensive investigation for their medical efficacy across various diseases. The swift progress in purine-based medicinal chemistry has brought to light the therapeutic capabilities of purine-derived compounds in addressing challenging medical conditions. Defined by a heterocyclic ring comprising a pyrimidine ring linked with an imidazole ring, purine exhibits a diverse array of therapeutic attributes. This review systematically addresses the multifaceted potential of purine derivatives in combating various diseases, including their roles as anticancer agents, antiviral compounds (anti-herpes, anti-HIV, and anti-influenzae), autoimmune and anti-inflammatory agents, antihyperuricemic and anti-gout solutions, antimicrobial agents, antitubercular compounds, anti-leishmanial agents, and anticonvulsants. Emphasis is placed on the remarkable progress made in developing purine-based compounds, elucidating their significant target sites. The article provides a comprehensive exploration of developments in both natural and synthetic purines, offering insights into their role in managing a diverse range of illnesses. Additionally, the discussion delves into the structure-activity relationships and biological activities of the most promising purine molecules. The intriguing capabilities revealed by these purine-based scaffolds unequivocally position them at the forefront of drug candidate development. As such, this review holds potential significance for researchers actively involved in synthesizing purine-based drug candidates, providing a roadmap for the continued advancement of this promising field.
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Affiliation(s)
- Neha Rana
- School of Pharmacy (SOP), Noida International University, Yamuna Expressway, Gautam Budh Nagar, 203201, India
| | - Parul Grover
- KIET School of Pharmacy, KIET Group of Institutions, Delhi-NCR, Ghaziabad, 201206, India
| | - Hridayanand Singh
- Dr. K. N. Modi Institute of Pharmaceutical Education and Research, Modinagar, 201204, Uttar Pradesh, India
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Nano-Zirconium Dioxide Catalyzed Multicomponent Synthesis of Bioactive Pyranopyrazoles That Target Cyclin Dependent Kinase 1 in Human Breast Cancer Cells. Biomedicines 2023; 11:biomedicines11010172. [PMID: 36672680 PMCID: PMC9856062 DOI: 10.3390/biomedicines11010172] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Accepted: 01/05/2023] [Indexed: 01/12/2023] Open
Abstract
Small molecules are being used to inhibit cyclin dependent kinase (CDK) enzymes in cancer treatment. There is evidence that CDK is a drug-target for cancer therapy across many tumor types because it catalyzes the transfer of the terminal phosphate of ATP to a protein that acts as a substrate. Herein, the identification of pyranopyrazoles that were CDK inhibitors was attempted, whose synthesis was catalyzed by nano-zirconium dioxide via multicomponent reaction. Additionally, we performed an in-situ analysis of the intermediates of multicomponent reactions, for the first-time, which revealed that nano-zirconium dioxide stimulated the reaction, as estimated by Gibbs free energy calculations of spontaneity. Functionally, the novel pyranopyrazoles were tested for a loss of cell viability using human breast cancer cells (MCF-7). It was observed that compounds 5b and 5f effectively produced loss of viability of MCF-7 cells with IC50 values of 17.83 and 23.79 µM, respectively. In vitro and in silico mode-of-action studies showed that pyranopyrazoles target CDK1 in human breast cancer cells, with lead compounds 5b and 5f having potent IC50 values of 960 nM and 7.16 μM, respectively. Hence, the newly synthesized bioactive pyranopyrazoles could serve as better structures to develop CDK1 inhibitors against human breast cancer cells.
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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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Havlíček L, Moravcová D, Kryštof V, Strnad M. The Identification of a Novel Highly Condensed Pentacyclic Heteroaromatic Ring System 1,3,5,5b,6,8,10,10b-Octaazacyclopenta[h,i]Aceanthrylene and its Application in the Synthesis of 5,7-Substituted Pyrazolo[4,3-d]Pyrimidines. J Heterocycl Chem 2014. [DOI: 10.1002/jhet.2147] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Libor Havlíček
- Isotope Laboratory; Institute of Experimental Botany ASCR; Videnska 1083 142 20 Prague Czech Republic
| | - Daniela Moravcová
- Isotope Laboratory; Institute of Experimental Botany ASCR; Videnska 1083 142 20 Prague Czech Republic
| | - Vladimír Kryštof
- Laboratory of Growth Regulators, Faculty of Science; Palacký University & Institute of Experimental Botany ASCR; Šlechtitelů 11 78371 Olomouc Czech Republic
| | - Miroslav Strnad
- Laboratory of Growth Regulators, Faculty of Science; Palacký University & Institute of Experimental Botany ASCR; Šlechtitelů 11 78371 Olomouc Czech Republic
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Kapdi AR, Fairlamb IJS. Anti-cancer palladium complexes: a focus on PdX2L2, palladacycles and related complexes. Chem Soc Rev 2014; 43:4751-77. [PMID: 24723061 DOI: 10.1039/c4cs00063c] [Citation(s) in RCA: 250] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Much success has been achieved with platinum-based chemotherapeutic agents, i.e. through interactions with DNA. The long-term application of Pt complexes is thwarted by issues, leading scientists to examine other metals such as palladium which could exhibit complementary modes of action (given emphasis wherever known). Over the last 10 years several research groups have focused on the application of an eclectic array of palladium complexes (of the type PdX2L2, palladacycles and related structures) as potential anti-cancer agents. This review therefore provides readers with an up to date account of the advances that have taken place over the past several decades.
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Affiliation(s)
- Anant R Kapdi
- Department of Chemistry, Institute of Chemical Technology, 302, Advance Centre, Nathalal Parekh Road, Matunga, Mumbai-400019, India.
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Casimiro MC, Velasco-Velázquez M, Aguirre-Alvarado C, Pestell RG. Overview of cyclins D1 function in cancer and the CDK inhibitor landscape: past and present. Expert Opin Investig Drugs 2014; 23:295-304. [PMID: 24387133 DOI: 10.1517/13543784.2014.867017] [Citation(s) in RCA: 132] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
INTRODUCTION Intensive efforts, over the last decade, have been made to inhibit the kinase activity of cyclins that act as mediators during cell-cycle progression. Activation of the cyclin D1 oncogene, often by amplification or rearrangement, is a major driver of multiple types of human tumors including breast and squamous cell cancers, B-cell lymphoma, myeloma and parathyroid adenoma. AREAS COVERED In this review, the authors summarize the activity of cyclins and cyclin-dependent kinases in cell-cycle progression and transcription. They focus on cyclin D1/CDK4/CDK6, a central mediator in the transition from G1 to S phase. Furthermore, the authors discuss the first generation of pan-cyclin-dependent kinase inhibitors that failed to meet expectation and discuss, in detail, the second generation of highly specific cyclin D1/CDK4/CDK6 inhibitors that are proving to be more efficacious. EXPERT OPINION The mechanism by which cyclin D1 drives tumorigenesis may be dependent on kinase and kinase-independent functions. Further evidence is necessary to delineate the roles of cyclin D1 in early pre-neoplastic lesions where its overexpression may promote genomic instability in a kinase-independent manner.
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Affiliation(s)
- Mathew C Casimiro
- Thomas Jefferson University & Hospital, Department of Cancer Biology , 233 South 10th Street, Philadelphia, PA 19107 , USA
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9
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Synthesis and anti-bacterial activities of some novel pyrazolobenzothiazine-based chalcones and their pyrimidine derivatives. Med Chem Res 2011. [DOI: 10.1007/s00044-011-9820-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/15/2022]
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Sadanandam P, Jyothi V, Adharvana Chari M, Das P, Mukkanti K. Synthesis and characterization of 9-methyl-2-morpholin-4-yl-8-substituted phenyl-1H-purine derivatives using polyphosphoric acid (PPA) as an efficient catalyst. Tetrahedron Lett 2011. [DOI: 10.1016/j.tetlet.2011.08.076] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Jorda R, Havlíček L, McNae IW, Walkinshaw MD, Voller J, Šturc A, Navrátilová J, Kuzma M, Mistrík M, Bártek J, Strnad M, Kryštof V. Pyrazolo[4,3-d]pyrimidine Bioisostere of Roscovitine: Evaluation of a Novel Selective Inhibitor of Cyclin-Dependent Kinases with Antiproliferative Activity. J Med Chem 2011; 54:2980-93. [DOI: 10.1021/jm200064p] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Radek Jorda
- Laboratory of Growth Regulators, Faculty of Science, Palacký University and Institute of Experimental Botany ASCR, Šlechtitelů 11, 78371 Olomouc, Czech Republic
| | - Libor Havlíček
- Laboratory of Growth Regulators, Faculty of Science, Palacký University and Institute of Experimental Botany ASCR, Šlechtitelů 11, 78371 Olomouc, Czech Republic
- Isotope Laboratory, Institute of Experimental Botany ASCR, Videnska 1083, 142 20 Prague, Czech Republic
| | - Iain W. McNae
- Structural Biochemistry Group, University of Edinburgh, Michael Swann Building, King’s Buildings, Edinburgh, EH9 3JR, Scotland
| | - Malcolm D. Walkinshaw
- Structural Biochemistry Group, University of Edinburgh, Michael Swann Building, King’s Buildings, Edinburgh, EH9 3JR, Scotland
| | - Jiří Voller
- Centre of the Region Haná for Biotechnological and Agricultural Research, Faculty of Science, Department of Growth Regulators, Palacký University, Šlechtitelů 11, Olomouc, CZ-783 71, Czech Republic
| | - Antonín Šturc
- Laboratory of Growth Regulators, Faculty of Science, Palacký University and Institute of Experimental Botany ASCR, Šlechtitelů 11, 78371 Olomouc, Czech Republic
| | - Jana Navrátilová
- Laboratory of Growth Regulators, Faculty of Science, Palacký University and Institute of Experimental Botany ASCR, Šlechtitelů 11, 78371 Olomouc, Czech Republic
| | - Marek Kuzma
- Laboratory of Molecular Structure Characterization, Institute of Microbiology ASCR, Videnska 1083, 142 20 Prague, Czech Republic
| | - Martin Mistrík
- Laboratory of Genome Integrity and Institute of Molecular and Translational Medicine, Palacký University, Šlechtitelů 11, 78371 Olomouc, Czech Republic
| | - Jiří Bártek
- Laboratory of Genome Integrity and Institute of Molecular and Translational Medicine, Palacký University, Šlechtitelů 11, 78371 Olomouc, Czech Republic
| | - Miroslav Strnad
- Laboratory of Growth Regulators, Faculty of Science, Palacký University and Institute of Experimental Botany ASCR, Šlechtitelů 11, 78371 Olomouc, Czech Republic
| | - Vladimír Kryštof
- Laboratory of Growth Regulators, Faculty of Science, Palacký University and Institute of Experimental Botany ASCR, Šlechtitelů 11, 78371 Olomouc, Czech Republic
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Zhong QF, Sun LP. An efficient synthesis of 6,9-disubstituted purin-8-ones via copper-catalyzed coupling/cyclization. Tetrahedron 2010. [DOI: 10.1016/j.tet.2010.04.106] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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Synthesis of new series of pyrazolo[4,3-d]pyrimidin-7-ones and pyrido[2,3-d]pyrimidin-4-ones for their bacterial and cyclin-dependent kinases (CDKs) inhibitory activities. Med Chem Res 2010. [DOI: 10.1007/s00044-010-9328-z] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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Trávnícek Z, Szucová L, Popa I. Synthesis, characterization and assessment of the cytotoxic properties of cis and trans-[Pd(L)2Cl2] complexes involving 6-benzylamino-9-isopropylpurine derivatives. J Inorg Biochem 2007; 101:477-92. [PMID: 17208304 DOI: 10.1016/j.jinorgbio.2006.11.010] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2006] [Revised: 11/15/2006] [Accepted: 11/16/2006] [Indexed: 11/15/2022]
Abstract
A series of square-planar Pd(II) complexes of the composition cis-[Pd(L(n))(2)Cl(2)] {L(1)=2-chloro-6-benzylamino-9-isopropylpurine (1), L(2)=2-chloro-6-[(4-methoxybenzyl)amino]-9-isopropylpurine (2), L(3)=2-chloro-6-[(2-methoxybenzyl)amino]-9-isopropylpurine (3) and 2-[(chloropropyl)amino]-6-benzylamino-9-isopropylpurine (6)} has been synthesized by the reaction of PdCl(2) with L(n) in a 1:2 molar ratio. In contrast, the same reaction followed by recrystallization of the product from N,N'-dimethylformamide (DMF) leads to trans-[Pd(L(n))(2)Cl(2)] x nDMF {L(3), n=0 (4), n=1(4( *)DMF); L(4)=2-chloro-6-[(2,3-dimethoxybenzyl)-amino]-9-isopropylpurine, n=0 (5), n=1.5 (5( *)DMF). The compounds have been characterized by elemental analyses, conductivity measurements, electrospray mass spectra in the positive ion mode (ES+MS), FTIR, (1)H and (13)C NMR spectra, thermogravimetric analysis (TGA) and differential scanning calorimetry (DSC). Moreover, the complexes 2 and 6 have been also investigated by (15)N NMR spectroscopy. The molecular structures of L(5), {(H(2+)L(5))(Cl(-))(2)} x H(2)O, i.e. the protonated form of L(5), trans-[Pd(L(3))(2)Cl(2)] (4) and trans-[Pd(L(4))(2)Cl(2)] (5) have been determined by single crystal X-ray analysis. NMR data and X-ray structures revealed that the organic molecules are coordinated to Pd via N7 atom of a purine moiety. All the complexes and the corresponding ligands have been tested in vitro for their cytotoxicity against four human cancer cell lines: breast adenocarcinoma (MCF7), malignant melanoma (G361), chronic myelogenous leukaemia (K562) and osteogenic sarcoma (HOS). Promising in vitro cytotoxic effect has been found for cis-[Pd(L(2))(2)Cl(2)] (2), having the IC(50) values of 12, 10, 25, and 14 microM against MCF7, G361, K562, and HOS, respectively, and for trans-[Pd(L(3))(2)Cl(2)].DMF (4) with the IC(50) value of 15 microM against G361.
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Affiliation(s)
- Zdenek Trávnícek
- Department of Inorganic Chemistry, Palacký University, Krízkovského 10, CZ-771 47 Olomouc, Czech Republic.
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Krystof V, Cankar P, Frysová I, Slouka J, Kontopidis G, Dzubák P, Hajdúch M, Srovnal J, de Azevedo WF, Orság M, Paprskárová M, Rolcík J, Látr A, Fischer PM, Strnad M. 4-arylazo-3,5-diamino-1H-pyrazole CDK inhibitors: SAR study, crystal structure in complex with CDK2, selectivity, and cellular effects. J Med Chem 2006; 49:6500-9. [PMID: 17064068 DOI: 10.1021/jm0605740] [Citation(s) in RCA: 135] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
In a routine screening of our small-molecule compound collection we recently identified 4-arylazo-3,5-diamino-1H-pyrazoles as a novel group of ATP antagonists with moderate potency against CDK2-cyclin E. A preliminary SAR study based on 35 analogues suggests ways in which the pharmacophore could be further optimized, for example, via substitutions in the 4-aryl ring. Enzyme kinetics studies with the lead compound and X-ray crystallography of an inhibitor-CDK2 complex demonstrated that its mode of inhibition is competitive. Functional kinase assays confirmed the selectivity toward CDKs, with a preference for CDK9-cyclin T1. The most potent inhibitor, 4-[(3,5-diamino-1H-pyrazol-4-yl)diazenyl]phenol 31b (CAN508), reduced the frequency of S-phase cells of the cancer cell line HT-29 in antiproliferation assays. Further observed cellular effects included decreased phosphorylation of the retinoblastoma protein and the C-terminal domain of RNA polymerase II, inhibition of mRNA synthesis, and induction of the tumor suppressor protein p53, all of which are consistent with inhibition of CDK9.
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Affiliation(s)
- Vladimír Krystof
- Laboratory of Growth Regulators, Faculty of Science, Palacký University and Institute of Experimental Botany, Slechtitelů 11, 783 71 Olomouc, Czech Republic
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Dobes P, Otyepka M, Strnad M, Hobza P. Interaction Energies for the Purine Inhibitor Roscovitine with Cyclin-Dependent Kinase 2: Correlated Ab Initio Quantum-Chemical, DFT and Empirical Calculations. Chemistry 2006; 12:4297-304. [PMID: 16575928 DOI: 10.1002/chem.200501269] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The interaction between roscovitine and cyclin-dependent kinase 2 (cdk2) was investigated by performing correlated ab initio quantum-chemical calculations. The whole protein was fragmented into smaller systems consisting of one or a few amino acids, and the interaction energies of these fragments with roscovitine were determined by using the MP2 method with the extended aug-cc-pVDZ basis set. For selected complexes, the complete basis set limit MP2 interaction energies, as well as the coupled-cluster corrections with inclusion of single, double and noninteractive triples contributions [CCSD(T)], were also evaluated. The energies of interaction between roscovitine and small fragments and between roscovitine and substantial sections of protein (722 atoms) were also computed by using density-functional tight-binding methods covering dispersion energy (DFTB-D) and the Cornell empirical potential. Total stabilisation energy originates predominantly from dispersion energy and methods that do not account for the dispersion energy cannot, therefore, be recommended for the study of protein-inhibitor interactions. The Cornell empirical potential describes reasonably well the interaction between roscovitine and protein; therefore, this method can be applied in future thermodynamic calculations. A limited number of amino acid residues contribute significantly to the binding of roscovitine and cdk2, whereas a rather large number of amino acids make a negligible contribution.
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Affiliation(s)
- Petr Dobes
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic and Center for Biomolecules and Complex Molecular Systems, 166 10 Prague 6, Czech Republic
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Legraverend M, Grierson DS. The purines: potent and versatile small molecule inhibitors and modulators of key biological targets. Bioorg Med Chem 2006; 14:3987-4006. [PMID: 16503144 DOI: 10.1016/j.bmc.2005.12.060] [Citation(s) in RCA: 258] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2005] [Revised: 12/29/2005] [Accepted: 12/29/2005] [Indexed: 11/24/2022]
Abstract
The goal of this review is to highlight the wide range of biological activities displayed by purines, with particular emphasis on new purine-based agents which find potential application as chemical-biology tools and/or therapeutic agents. The expanding interest in the biological properties of polyfunctionalized purine derivatives issues, in large part, from the development of rapid high-throughput screening essays for new protein targets, and the corresponding development of efficient synthetic methodology adapted to the construction of highly diverse purine libraries. Purine-based compounds have found new applications as inducers of interferon and lineage-committed cell dedifferentiation, agonists and antagonists of adenosine receptors, ligands of corticotropin-releasing hormone receptors, and as inhibitors of HSP90, Src kinase, p38alpha MAP kinase, sulfotransferases, phosphodiesterases, and Cdks. The scope of application of purines in biology is most certainly far from being exhausted. Testing purine derivatives against the multitude of biological targets for which small molecule probes have not yet been found should thus be a natural reflex.
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Affiliation(s)
- Michel Legraverend
- UMR 176 CNRS-Institut Curie, Laboratoire de Pharmacochimie, Bât. 110, Centre Universitaire, 91405 Orsay, France.
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Szucová L, Trávnícek Z, Zatloukal M, Popa I. Novel platinum(II) and palladium(II) complexes with cyclin-dependent kinase inhibitors: Synthesis, characterization and antitumour activity. Bioorg Med Chem 2006; 14:479-91. [PMID: 16198575 DOI: 10.1016/j.bmc.2005.08.033] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2005] [Revised: 07/18/2005] [Accepted: 08/16/2005] [Indexed: 11/26/2022]
Abstract
The Pt(II) and Pd(II) complexes of the types cis-[Pt(L(1))(2)Cl(2)].H(2)O (1), cis-[Pt(L(2))(2)Cl(2)].3H(2)O (2), trans-[Pd(L(1))(2)Cl(2)].H(2)O (3), trans-[Pd(L(2))(2)Cl(2)].H(2)O (4), trans-[Pd(L(3))(2)Cl(2)].2DMF (5) and trans-[Pd(L(4))(2)Cl(2)].2DMF (6) (L(1)-L(4)=cyclin-dependent kinase inhibitors derived from 6-benzylamino-9-isopropylpurine) have been prepared and characterized. The complexes have been studied by elemental analyses, conductivity measurements, ES+ MS, FT-IR, (1)H, (13)C and (195)Pt NMR spectra, differential scanning calorimetry and thermogravimetric analysis. The molecular structures of L(1), trans-[Pd(L(3))(2)Cl(2)].2DMF (5) and trans-[Pd(L(4))(2)Cl(2)].2DMF (6) have been determined by single crystal X-ray analysis. The complexes have been tested in vitro due to their presumable anticancer activity against the following human cancer cell lines: K-562, MCF7, G-361 and HOS. Satisfying results were obtained for the complex 1 with IC(50) values of 6 microM acquired against G-361 as well as against HOS cell lines. The lowest values of IC(50) were achieved for the complexes 3 and 4 against MCF 7 cell line with IC(50) 3 microM(for 3) and also 3 microM (for 4).
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Affiliation(s)
- Lucie Szucová
- Department of Inorganic Chemistry, Palacký University, Krízkovského 10, CZ-771 47 Olomouc, Czech Republic
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García-Sosa AT, Mancera RL. The effect of a tightly bound water molecule on scaffold diversity in the computer-aided de novo ligand design of CDK2 inhibitors. J Mol Model 2005; 12:422-31. [PMID: 16374623 DOI: 10.1007/s00894-005-0063-1] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2005] [Accepted: 07/21/2005] [Indexed: 11/27/2022]
Abstract
We have determined the effects that tightly bound water molecules have on the de novo design of cyclin-dependent kinase-2 (CDK2) ligands. In particular, we have analyzed the impact of a specific structural water molecule on the chemical diversity and binding mode of ligands generated through a de novo structure-based ligand generation method in the binding site of CDK2. The tightly bound water molecule modifies the size and shape of the binding site and we have found that it also imposed constraints on the observed binding modes of the generated ligands. This in turn had the indirect effect of reducing the chemical diversity of the underlying molecular scaffolds that were able to bind to the enzyme satisfactorily. [Figure: see text].
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Affiliation(s)
- Alfonso T García-Sosa
- Department of Pharmacology, University of Cambridge, Tennis Court Road, Cambridge, CB2 1PD, UK.
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Chapter 6.3 Triazines, tetrazines and fused ring polyaza systems. ACTA ACUST UNITED AC 2005. [DOI: 10.1016/s0959-6380(05)80056-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
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