1
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Liu R, Li W, Yao Y, Wu Y, Luo HB, Li Z. Accelerating and Automating the Free Energy Perturbation Absolute Binding Free Energy Calculation with the RED-E Function. J Chem Inf Model 2023; 63:7755-7767. [PMID: 38048439 DOI: 10.1021/acs.jcim.3c01670] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/06/2023]
Abstract
The accurate prediction of the binding affinities between small molecules and biological macromolecules plays a fundamental role in structure-based drug design, which is still challenging. The free energy perturbation-based absolute binding free energy (FEP-ABFE) approach has shown potential in its reliability. To correctly calculate the energy related to the ligand being restrained by the receptor, additional restraints between the ligand and the receptor are needed. However, determining the restraint parameters for individual ligands empirically is too trivial to be automated, and usually gives rise to numerical instabilities, which set back the applications of FEP-ABFE. To address these issues, we derived the analytical expression for the probability distribution of energy differences, P(ΔU), during the process of restraint addition, which is called the RED-E (restraint energy distribution at equilibrium position) function. Simulations indicated that the RED-E function can accurately describe P(ΔU) when restraints are added at the equilibrium position. Based on the RED-E function, an automatic restraint selection method was proposed to select the best restraint. With this method, there is a high phase-space overlap between the free and restrained states, such that using a 2-λ perturbation can accurately calculate the free energy of the restraint addition, which is a nearly 6 times acceleration compared with current widely used 12-λ perturbation method. The RED-E function gives insight into the non-Gaussian behavior of the sampled P(ΔU) in certain FEP processes in an analytical way. The highly automated and accelerated restraint selection also makes it possible for the large-scale application of FEP-ABFE in real drug discovery practices.
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Affiliation(s)
- Runduo Liu
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China
| | - Wenchao Li
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China
| | - Yufen Yao
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China
| | - Yinuo Wu
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China
| | - Hai-Bin Luo
- Key Laboratory of Tropical Biological Resources of Ministry of Education, School of Pharmaceutical Sciences, Hainan University, Haikou, Hainan 570228, China
- Song Li' Academician Workstation of Hainan University (School of Pharmaceutical Sciences), Yazhou Bay, Sanya 572000, China
| | - Zhe Li
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China
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2
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Zhang T, Jiang S, Li T, Liu Y, Zhang Y. Identified Isosteric Replacements of Ligands' Glycosyl Domain by Data Mining. ACS OMEGA 2023; 8:25165-25184. [PMID: 37483233 PMCID: PMC10357434 DOI: 10.1021/acsomega.3c02243] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Accepted: 06/09/2023] [Indexed: 07/25/2023]
Abstract
Biologically equivalent replacements of key moieties in molecules rationalize scaffold hopping, patent busting, or R-group enumeration. Yet, this information may depend upon the expert-defined space, and might be subjective and biased toward the chemistries they get used to. Most importantly, these practices are often informatively incomplete since they are often compromised by a try-and-error cycle, and although they depict what kind of substructures are suitable for the replacement occurrence, they fail to explain the driving forces to support such interchanges. The protein data bank (PDB) encodes a receptor-ligand interaction pattern and could be an optional source to mine structural surrogates. However, manual decoding of PDB has become almost impossible and redundant to excavate the bioisosteric know-how. Therefore, a text parsing workflow has been developed to automatically extract the local structural replacement of a specific structure from PDB by finding spatial and steric interaction overlaps between the fragments in endogenous ligands and particular ligand fragments. Taking the glycosyl domain for instance, a total of 49 520 replacements that overlap on nucleotide ribose were identified and categorized based on their SMILE codes. A predominately ring system, such as aliphatic and aromatic rings, was observed; yet, amide and sulfonamide replacements also occur. We believe these findings may enlighten medicinal chemists on the structure design and optimization of ligands using the bioisosteric replacement strategy.
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Affiliation(s)
- Tinghao Zhang
- Xi’an
Institute of Flexible Electronics (IFE) and Xi’an Institute
of Biomedical Materials & Engineering (IBME), Northwestern Polytechnical
University, 127 West Youyi Road, Xi’an 710072, China
| | - Shenghao Jiang
- School of
Computer Science, Northwestern Polytechnical
University, 127 West
Youyi Road, Xi’an 710072, China
| | - Ting Li
- Xi’an
Institute of Flexible Electronics (IFE) and Xi’an Institute
of Biomedical Materials & Engineering (IBME), Northwestern Polytechnical
University, 127 West Youyi Road, Xi’an 710072, China
| | - Yan Liu
- Xi’an
Institute of Flexible Electronics (IFE) and Xi’an Institute
of Biomedical Materials & Engineering (IBME), Northwestern Polytechnical
University, 127 West Youyi Road, Xi’an 710072, China
| | - Yuezhou Zhang
- Xi’an
Institute of Flexible Electronics (IFE) and Xi’an Institute
of Biomedical Materials & Engineering (IBME), Northwestern Polytechnical
University, 127 West Youyi Road, Xi’an 710072, China
- Ningbo
Institute of Northwestern Polytechnical University, Frontiers Science
Center for Flexible Electronics (FSCFE), Key laboratory of Flexible
Electronics of Zhejiang Province, Ningbo Institute of Northwestern
Polytechnical University, 218 Qingyi Road, Ningbo 315103, China
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3
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Wang Q, Bode AM, Zhang T. Targeting CDK1 in cancer: mechanisms and implications. NPJ Precis Oncol 2023; 7:58. [PMID: 37311884 DOI: 10.1038/s41698-023-00407-7] [Citation(s) in RCA: 18] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Accepted: 05/25/2023] [Indexed: 06/15/2023] Open
Abstract
Cyclin dependent kinases (CDKs) are serine/threonine kinases that are proposed as promising candidate targets for cancer treatment. These proteins complexed with cyclins play a critical role in cell cycle progression. Most CDKs demonstrate substantially higher expression in cancer tissues compared with normal tissues and, according to the TCGA database, correlate with survival rate in multiple cancer types. Deregulation of CDK1 has been shown to be closely associated with tumorigenesis. CDK1 activation plays a critical role in a wide range of cancer types; and CDK1 phosphorylation of its many substrates greatly influences their function in tumorigenesis. Enrichment of CDK1 interacting proteins with Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis was conducted to demonstrate that the associated proteins participate in multiple oncogenic pathways. This abundance of evidence clearly supports CDK1 as a promising target for cancer therapy. A number of small molecules targeting CDK1 or multiple CDKs have been developed and evaluated in preclinical studies. Notably, some of these small molecules have also been subjected to human clinical trials. This review evaluates the mechanisms and implications of targeting CDK1 in tumorigenesis and cancer therapy.
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Affiliation(s)
- Qiushi Wang
- The Hormel Institute, University of Minnesota, 801 16th Ave NE, Austin, MN, 55912, USA
| | - Ann M Bode
- The Hormel Institute, University of Minnesota, 801 16th Ave NE, Austin, MN, 55912, USA.
| | - Tianshun Zhang
- The Hormel Institute, University of Minnesota, 801 16th Ave NE, Austin, MN, 55912, USA.
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4
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Mounika P, Gurupadayya B, Kumar HY, Namitha B. An Overview of CDK Enzyme Inhibitors in Cancer Therapy. Curr Cancer Drug Targets 2023; 23:603-619. [PMID: 36959160 DOI: 10.2174/1568009623666230320144713] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2022] [Revised: 01/12/2023] [Accepted: 01/25/2023] [Indexed: 03/25/2023]
Abstract
The ability to address the cell cycle in cancer therapy brings up new medication development possibilities. Cyclin-dependent kinases are a group of proteins that control the progression of the cell cycle. The CDK/cyclin complexes are activated when specific CDK sites are phosphorylated. Because of their non-selectivity and severe toxicity, most first-generation CDK inhibitors (also known as pan-CDK inhibitors) have not been authorized for clinical usage. Despite this, significant progress has been made in allowing pan-CDK inhibitors to be employed in clinical settings. Pan-CDK inhibitors' toxicity and side effects have been lowered in recent years because of the introduction of combination therapy techniques. As a result of this, pan-CDK inhibitors have regained a lot of clinical potential as a combination therapy approach. The CDK family members have been introduced in this overview, and their important roles in cell cycle control have been discussed. Then, we have described the current state of CDK inhibitor research, with a focus on inhibitors other than CDK4/6. We have mentioned first-generation pan-CDKIs, flavopiridol and roscovitine, as well as second-generation CDKIs, dinaciclib, P276-00, AT7519, TG02, roniciclib, and RGB-286638, based on their research phases, clinical trials, and cancer targeting. CDKIs are CDK4/6, CDK7, CDK9, and CDK12 inhibitors. Finally, we have looked into the efficacy of CDK inhibitors and PD1/PDL1 antibodies when used together, which could lead to the development of a viable cancer treatment strategy.
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Affiliation(s)
- Peddaguravagari Mounika
- Department of Pharmaceutical Chemistry, JSS College of Pharmacy, JSS Academy of Higher Education & Research, Mysuru, 570015, India
| | - Bannimath Gurupadayya
- Department of Pharmaceutical Chemistry, JSS College of Pharmacy, JSS Academy of Higher Education & Research, Mysuru, 570015, India
| | - Honnavalli Yogish Kumar
- Department of Pharmaceutical Chemistry, JSS College of Pharmacy, JSS Academy of Higher Education & Research, Mysuru, 570015, India
| | - Bannimath Namitha
- Department of Pharmacology, JSS College of Pharmacy, JSS Academy of Higher Education & Research, Mysuru, 570015, India
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5
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Bamou FZ, Le TM, Tayeb BA, Tahaei SAS, Minorics R, Zupkó I, Szakonyi Z. Antiproliferative Activity of (-)-Isopulegol-based 1,3-Oxazine, 1,3-Thiazine and 2,4-Diaminopyrimidine Derivatives. Chemistry 2022; 11:e202200169. [PMID: 36200514 PMCID: PMC9535514 DOI: 10.1002/open.202200169] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2022] [Revised: 08/25/2022] [Indexed: 11/08/2022]
Abstract
A series of novel heterocyclic structures, namely 1,3‐oxazines, 1,3‐thiazines and 2,4‐diaminopyrimidines, were designed and synthesised. The bioassay tests demonstrated that, among these analogues, 2,4‐diaminopyridine derivatives showed significant antiproliferative activity against different human cancer cell lines (A2780, SiHa, HeLa, MCF‐7 and MDA‐MB‐231). Pyrimidines substituted with N2‐(p‐trifluoromethyl)aniline, in particular, displayed a potent inhibitory effect on the growth of cancer cells. Structure–activity relationships were also studied from the aspects of stereochemistry on the aminodiol moiety as well as exploring the effects of substituents on the pyrimidine scaffold.
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Affiliation(s)
- Fatima Z. Bamou
- Institute of Pharmaceutical Chemistry andMTA-SZTE Stereochemistry Research GroupHungarian Academy of SciencesUniversity of SzegedEötvös u. 66720SzegedHungary
| | - Tam M. Le
- Institute of Pharmaceutical Chemistry andMTA-SZTE Stereochemistry Research GroupHungarian Academy of SciencesUniversity of SzegedEötvös u. 66720SzegedHungary
| | - Bizhar A. Tayeb
- Department of Pharmacodynamics and BiopharmacyUniversity of SzegedEötvös u. 66720SzegedHungary
| | - Seyyed A. S. Tahaei
- Department of Pharmacodynamics and BiopharmacyUniversity of SzegedEötvös u. 66720SzegedHungary
| | - Renáta Minorics
- Department of Pharmacodynamics and BiopharmacyUniversity of SzegedEötvös u. 66720SzegedHungary
| | - István Zupkó
- Department of Pharmacodynamics and BiopharmacyUniversity of SzegedEötvös u. 66720SzegedHungary
| | - Zsolt Szakonyi
- Institute of Pharmaceutical Chemistry andMTA-SZTE Stereochemistry Research GroupHungarian Academy of SciencesUniversity of SzegedEötvös u. 66720SzegedHungary
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6
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Mader L, Hayward JJ, Porter LA, Trant JF. A revised synthesis of 6-alkoxy-2-aminopurines with late-stage convergence allowing for increased molecular complexity. NEW J CHEM 2022. [DOI: 10.1039/d2nj02204d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
This streamlined synthesis allows the alcohol at the 6-position of 6-alkoxy-2-arylaminopurines to be used only in moderate excess, rather than as solvent, opening up the possibility of accessing more complicated molecules.
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Affiliation(s)
- Lavleen Mader
- Department of Chemistry and Biochemistry, University of Windsor, 401 Sunset Avenue, Windsor, ON, N9B 3P4, Canada
| | - John J. Hayward
- Department of Chemistry and Biochemistry, University of Windsor, 401 Sunset Avenue, Windsor, ON, N9B 3P4, Canada
| | - Lisa A. Porter
- Department of Biomedical Sciences, University of Windsor, 401 Sunset Avenue, Windsor, ON, N9B 3P4, Canada
| | - John F. Trant
- Department of Chemistry and Biochemistry, University of Windsor, 401 Sunset Avenue, Windsor, ON, N9B 3P4, Canada
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7
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Sherbiny FF, Bayoumi AH, El-Morsy AM, Sobhy M, Hagras M. Design, Synthesis, biological Evaluation, and molecular docking studies of novel Pyrazolo[3,4-d]Pyrimidine derivative scaffolds as potent EGFR inhibitors and cell apoptosis inducers. Bioorg Chem 2021; 116:105325. [PMID: 34507234 DOI: 10.1016/j.bioorg.2021.105325] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Revised: 12/27/2020] [Accepted: 08/30/2021] [Indexed: 12/14/2022]
Abstract
A series of novel hybrid pyrazolo[3,4-d]pyramidine derivatives was designed and chemically synthesized in useful yields. The synthesized compounds were structurally characterized by the usual techniques. All the new synthesized compounds were biologically screened in vitro for their antiproliferative activities against a panel of four cancer cell lines, namely HepG-2, MCF-7, HCT-116, and Hela. The results of cytotoxic evaluation indicated that compound 14d was appeared to be the most prominent broad-spectrum cytotoxic activity and significantly more potent than sorafenib with IC50 values of 4.28, 5.18, 3.97, and 9.85 µM against four cell lines (HePG2, Hela, HCT-116 and MCF-7). In addition, compound 15 was displayed promising antiproliferative effect against all tested cell lines with IC50 value less than 11 µM compared with sorafenib as a control drug. Besides, structurally pharmacophoric features indicated that pyrazolo[3,4-d]pyrimidine scaffold having an amide linker and substituted with phenyl moiety at the 5-position was more potent than those possessing azomethine methyl, azomethine proton and carbomethene linkers, which lead to significant decrease in antiproliferative activity. The most potent compounds were further selected and evaluated for their activities against epidermal growth factor receptor (EGFR) kinase inhibitors according to homogenous time resolved fluorescence (HTRF) assay. The most potent compound 14d exhibited the most promising inhibitory activity against EGFRWT with IC50 value of 56.02 ± 1.38 µM compared with gefitinib as control drug with IC50 value of 41.79 ± 1.07 µM. Moreover, the inhibition of cell cycle progression and induction of apoptosis in the A549 cell line at G2/M and pre-G1 phases of cell cycle might contribute to cancer treatment that evaluated by Annexin V-FITC/PI double staining detection method. Finally, molecular docking studies were conducted to investigate that probable binding conformations of these anticancer agents and ADME properties were calculated to predict pharmacokinetics and toxic properties of the target compounds.
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Affiliation(s)
- Farag F Sherbiny
- Pharmaceutical Organic Chemistry Department, Faculty of Pharmacy (Boys), Al-Azhar University, Cairo 11884, Egypt; Department of Chemistry, Basic Science Center and Pharmaceutical Organic Chemistry College of Pharmaceutical Science & Drug Manufacturing, Misr University for Science and Technology (MUST), Al-Motamayez District, 6(th) of October City 77, Egypt.
| | - Ashraf H Bayoumi
- Pharmaceutical Organic Chemistry Department, Faculty of Pharmacy (Boys), Al-Azhar University, Cairo 11884, Egypt
| | - Ahmed M El-Morsy
- Pharmaceutical Organic Chemistry Department, Faculty of Pharmacy (Boys), Al-Azhar University, Cairo 11884, Egypt; Pharmaceutical Chemistry Department, College of Pharmacy, The Islamic University, Najaf 54001, Iraq
| | - Mohamed Sobhy
- Pharmaceutical Organic Chemistry Department, Faculty of Pharmacy (Boys), Al-Azhar University, Cairo 11884, Egypt
| | - Mohamed Hagras
- Pharmaceutical Organic Chemistry Department, Faculty of Pharmacy (Boys), Al-Azhar University, Cairo 11884, Egypt
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8
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Etman AM, Abdel Mageed SS, Ali MA, El Hassab MAEM. Cyclin-Dependent Kinase as a Novel Therapeutic Target: An Endless Story. CURRENT CHEMICAL BIOLOGY 2021; 15:139-162. [DOI: 10.2174/2212796814999201123194016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Revised: 09/03/2020] [Accepted: 09/16/2020] [Indexed: 09/02/2023]
Abstract
Cyclin-Dependent Kinases (CDKs) are a family of enzymes that, along with their Cyclin
partners, play a crucial role in cell cycle regulation at many biological functions such as proliferation,
differentiation, DNA repair, and apoptosis. Thus, they are tightly regulated by a number of inhibitory
and activating enzymes. Deregulation of these kinases’ activity either by amplification,
overexpression or mutation of CDKs or Cyclins leads to uncontrolled proliferation of cancer cells.
Hyperactivity of these kinases has been reported in a wide variety of human cancers. Hence, CDKs
have been established as one of the most attractive pharmacological targets in the development of
promising anticancer drugs. The elucidated structural features and the well-characterized molecular
mechanisms of CDKs have been the guide in designing inhibitors to these kinases. Yet, they remain
a challenging therapeutic class as they share conserved structure similarity in their active site.
Several inhibitors have been discovered from natural sources or identified through high throughput
screening and rational drug design approaches. Most of these inhibitors target the ATP binding
pocket, therefore, they suffer from a number of limitations. Here, a growing number of ATP noncompetitive
peptides and small molecules has been reported.
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Affiliation(s)
- Ahmed Mohamed Etman
- Department of Pharmacology, Faculty of Pharmacy, Tanta University, Tanta, 31111,Egypt
| | - Sherif Sabry Abdel Mageed
- Department of Pharmacology, Faculty of Pharmacy, Badr University in Cairo (BUC), Badr city, Cairo, 11829,Egypt
| | - Mohamed Ahmed Ali
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Badr University in Cairo (BUC), Badr city, Cairo, 11829,Egypt
| | - Mahmoud Abd El Monem El Hassab
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Badr University in Cairo (BUC), Badr city, Cairo, 11829,Egypt
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9
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Rankine-Wilson LI, Shapira T, Sao Emani C, Av-Gay Y. From infection niche to therapeutic target: the intracellular lifestyle of Mycobacterium tuberculosis. MICROBIOLOGY (READING, ENGLAND) 2021; 167:001041. [PMID: 33826491 PMCID: PMC8289223 DOI: 10.1099/mic.0.001041] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Accepted: 02/15/2021] [Indexed: 12/16/2022]
Abstract
Mycobacterium tuberculosis (Mtb) is an obligate human pathogen killing millions of people annually. Treatment for tuberculosis is lengthy and complicated, involving multiple drugs and often resulting in serious side effects and non-compliance. Mtb has developed numerous complex mechanisms enabling it to not only survive but replicate inside professional phagocytes. These mechanisms include, among others, overcoming the phagosome maturation process, inhibiting the acidification of the phagosome and inhibiting apoptosis. Within the past decade, technologies have been developed that enable a more accurate understanding of Mtb physiology within its intracellular niche, paving the way for more clinically relevant drug-development programmes. Here we review the molecular biology of Mtb pathogenesis offering a unique perspective on the use and development of therapies that target Mtb during its intracellular life stage.
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Affiliation(s)
| | - Tirosh Shapira
- Division of Infectious Disease, Department of Medicine, The University of British Columbia, Vancouver, Canada
| | - Carine Sao Emani
- Division of Infectious Disease, Department of Medicine, The University of British Columbia, Vancouver, Canada
| | - Yossef Av-Gay
- Department of Microbiology & Immunology, The University of British Columbia, Vancouver, Canada
- Division of Infectious Disease, Department of Medicine, The University of British Columbia, Vancouver, Canada
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10
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Barnieh FM, Loadman PM, Falconer RA. Progress towards a clinically-successful ATR inhibitor for cancer therapy. CURRENT RESEARCH IN PHARMACOLOGY AND DRUG DISCOVERY 2021; 2:100017. [PMID: 34909652 PMCID: PMC8663972 DOI: 10.1016/j.crphar.2021.100017] [Citation(s) in RCA: 58] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 01/24/2021] [Accepted: 01/24/2021] [Indexed: 02/06/2023] Open
Abstract
The DNA damage response (DDR) is now known to play an important role in both cancer development and its treatment. Targeting proteins such as ATR (Ataxia telangiectasia mutated and Rad3-related) kinase, a major regulator of DDR, has demonstrated significant therapeutic potential in cancer treatment, with ATR inhibitors having shown anti-tumour activity not just as monotherapies, but also in potentiating the effects of conventional chemotherapy, radiotherapy, and immunotherapy. This review focuses on the biology of ATR, its functional role in cancer development and treatment, and the rationale behind inhibition of this target as a therapeutic approach, including evaluation of the progress and current status of development of potent and specific ATR inhibitors that have emerged in recent decades. The current applications of these inhibitors both in preclinical and clinical studies either as single agents or in combinations with chemotherapy, radiotherapy and immunotherapy are also extensively discussed. This review concludes with some insights into the various concerns raised or observed with ATR inhibition in both the preclinical and clinical settings, with some suggested solutions.
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Affiliation(s)
- Francis M. Barnieh
- Institute of Cancer Therapeutics, Faculty of Life Sciences, University of Bradford, Bradford, BD7 1DP, UK
| | - Paul M. Loadman
- Institute of Cancer Therapeutics, Faculty of Life Sciences, University of Bradford, Bradford, BD7 1DP, UK
| | - Robert A. Falconer
- Institute of Cancer Therapeutics, Faculty of Life Sciences, University of Bradford, Bradford, BD7 1DP, UK
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11
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Eco-friendly sequential one-pot synthesis, molecular docking, and anticancer evaluation of arylidene-hydrazinyl-thiazole derivatives as CDK2 inhibitors. Bioorg Chem 2021; 108:104615. [PMID: 33484942 DOI: 10.1016/j.bioorg.2020.104615] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2020] [Revised: 11/19/2020] [Accepted: 12/28/2020] [Indexed: 11/20/2022]
Abstract
One current approach in the treatment of cancer is the inhibition of cyclin dependent kinase (CDK) enzymes with small molecules. CDK are a class of enzymes, which catalyze the transfer of the terminal phosphate of a molecule of ATP to a protein that acts as a substrate. Among CDK enzymes, CDK2 has been implicated in a variety of cancers, supporting its potential as a novel target for cancer therapy across many tumor types. Here the discovery and development of arylidene-hydrazinyl-thiazole as a potentially CDK2 inhibitors is described, including details of the design and successful synthesis of the series analogs (27a-r) using one-pot approach under eco-friendly ultrasound and microwave conditions. Most of the newly synthesized compounds showed good growth inhibition when assayed for their in-vitro anti-proliferative activity against three cancer cell lines (HepG2, MCF-7 and HCT-116) compared to the reference drug roscovitine, with little toxicity on the normal fibroblast cell lines (WI-38). Furthermore, the compounds exhibiting the highest anti-proliferative activities were tested against a panel of kinase enzymes. These derivatives displayed an outstanding CDK2 inhibitory potential with varying degree of inhibition in the range of IC50 0.35-1.49 μM when compared with the standard inhibitor roscovitine having an IC50 value 0.71 μM. The most promising CDK2 inhibitor (27f) was selected for further studies to determine its effect on the cell cycle progression and apoptosis in HepG2 cell line. The results indicated that this compound implied inhibition in the G2/M phase of the cell cycle, and it is a good apoptotic agent. Finally, Molecular docking study was performed to identify the structural elements which involved in the inhibitory activity with the prospective target, CDK2, and to rationalize the structure-activity relationship (SAR).
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12
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Effects of Transient Receptor Potential Cation 5 (TRPC5) Inhibitor, NU6027, on Hippocampal Neuronal Death after Traumatic Brain Injury. Int J Mol Sci 2020; 21:ijms21218256. [PMID: 33158109 PMCID: PMC7662546 DOI: 10.3390/ijms21218256] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Revised: 10/30/2020] [Accepted: 11/03/2020] [Indexed: 12/20/2022] Open
Abstract
Traumatic brain injury (TBI) can cause physical, cognitive, social, and behavioral changes that can lead to permanent disability or death. After primary brain injury, translocated free zinc can accumulate in neurons and lead to secondary events such as oxidative stress, inflammation, edema, swelling, and cognitive impairment. Under pathological conditions, such as ischemia and TBI, excessive zinc release, and accumulation occurs in neurons. Based on previous research, it hypothesized that calcium as well as zinc would be influx into the TRPC5 channel. Therefore, we hypothesized that the suppression of TRPC5 would prevent neuronal cell death by reducing the influx of zinc and calcium. To test our hypothesis, we used a TBI animal model. After the TBI, we immediately injected NU6027 (1 mg/kg, intraperitoneal), TRPC5 inhibitor, and then sacrificed animals 24 h later. We conducted Fluoro-Jade B (FJB) staining to confirm the presence of degenerating neurons in the hippocampal cornus ammonis 3 (CA3). After the TBI, the degenerating neuronal cell count was decreased in the NU6027-treated group compared with the vehicle-treated group. Our findings suggest that the suppression of TRPC5 can open a new therapeutic window for a reduction of the neuronal death that may occur after TBI.
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13
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Guglielmo S, Cortese D, Cano C, Fruttero R. Molecular dynamics simulations reveal the determinants of cyclin-dependent kinase 2 inhibition by 5-nitrosopyrimidine derivatives. J Biomol Struct Dyn 2020; 38:4016-4024. [PMID: 31498033 DOI: 10.1080/07391102.2019.1666032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Revised: 09/02/2019] [Accepted: 09/03/2019] [Indexed: 10/26/2022]
Abstract
Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Stefano Guglielmo
- Dipartimento di Scienza e Tecnologia del Farmaco, Universita' degli Studi di Torino, Turin, Italy
- Scientific Computing Competence Centre (C3S), University of Turin, Turin, Italy
| | - Daniela Cortese
- Dipartimento di Scienza e Tecnologia del Farmaco, Universita' degli Studi di Torino, Turin, Italy
- Northern Institute for Cancer Research, School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - Celine Cano
- Northern Institute for Cancer Research, School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - Roberta Fruttero
- Dipartimento di Scienza e Tecnologia del Farmaco, Universita' degli Studi di Torino, Turin, Italy
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14
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NU-6027 Inhibits Growth of Mycobacterium tuberculosis by Targeting Protein Kinase D and Protein Kinase G. Antimicrob Agents Chemother 2019; 63:AAC.00996-19. [PMID: 31285226 DOI: 10.1128/aac.00996-19] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2019] [Accepted: 06/30/2019] [Indexed: 12/31/2022] Open
Abstract
Tuberculosis (TB) is a global health concern, and this situation has further worsened due to the emergence of drug-resistant strains and the failure of BCG vaccine to impart protection. There is an imperative need to develop highly sensitive, specific diagnostic tools, novel therapeutics, and vaccines for the eradication of TB. In the present study, a chemical screen of a pharmacologically active compound library was performed to identify antimycobacterial compounds. The phenotypic screen identified a few novel small-molecule inhibitors, including NU-6027, a known CDK-2 inhibitor. We demonstrate that NU-6027 inhibits Mycobacterium bovis BCG growth in vitro and also displayed cross-reactivity with Mycobacterium tuberculosis protein kinase D (PknD) and protein kinase G (PknG). Comparative structural and sequence analysis along with docking simulation suggest that the unique binding site stereochemistry of PknG and PknD accommodates NU-6027 more favorably than other M. tuberculosis Ser/Thr protein kinases. Further, we also show that NU-6027 treatment induces the expression of proapoptotic genes in macrophages. Finally, we demonstrate that NU-6027 inhibits M. tuberculosis growth in both macrophage and mouse tissues. Taken together, these results indicate that NU-6027 can be optimized further for the development of antimycobacterial agents.
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Wood DJ, Lopez-Fernandez JD, Knight LE, Al-Khawaldeh I, Gai C, Lin S, Martin MP, Miller DC, Cano C, Endicott JA, Hardcastle IR, Noble MEM, Waring MJ. FragLites-Minimal, Halogenated Fragments Displaying Pharmacophore Doublets. An Efficient Approach to Druggability Assessment and Hit Generation. J Med Chem 2019; 62:3741-3752. [PMID: 30860382 DOI: 10.1021/acs.jmedchem.9b00304] [Citation(s) in RCA: 54] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Identifying ligand binding sites on proteins is a critical step in target-based drug discovery. Current approaches to this require resource-intensive screening of large libraries of lead-like or fragment molecules. Here, we describe an efficient and effective experimental approach to mapping interaction sites using a set of halogenated compounds expressing paired hydrogen-bonding motifs, termed FragLites. The FragLites identify productive drug-like interactions, which are identified sensitively and unambiguously by X-ray crystallography, exploiting the anomalous scattering of the halogen substituent. This mapping of protein interaction surfaces provides an assessment of druggability and can identify efficient start points for the de novo design of hit molecules incorporating the interacting motifs. The approach is illustrated by mapping cyclin-dependent kinase 2, which successfully identifies orthosteric and allosteric sites. The hits were rapidly elaborated to develop efficient lead-like molecules. Hence, the approach provides a new method of identifying ligand sites, assessing tractability and discovering new leads.
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Affiliation(s)
- Daniel J Wood
- Northern Institute for Cancer Research, Medical School , Newcastle University , Paul O'Gorman Building, Framlington Place , Newcastle upon Tyne NE2 4HH , U.K
| | - J Daniel Lopez-Fernandez
- Northern Institute for Cancer Research, Chemistry, School of Natural and Environmental Sciences , Newcastle University , Bedson Building , Newcastle upon Tyne NE1 7RU , U.K
| | - Leanne E Knight
- Northern Institute for Cancer Research, Chemistry, School of Natural and Environmental Sciences , Newcastle University , Bedson Building , Newcastle upon Tyne NE1 7RU , U.K
| | - Islam Al-Khawaldeh
- Northern Institute for Cancer Research, Chemistry, School of Natural and Environmental Sciences , Newcastle University , Bedson Building , Newcastle upon Tyne NE1 7RU , U.K
| | - Conghao Gai
- Northern Institute for Cancer Research, Chemistry, School of Natural and Environmental Sciences , Newcastle University , Bedson Building , Newcastle upon Tyne NE1 7RU , U.K
| | - Shengying Lin
- Northern Institute for Cancer Research, Chemistry, School of Natural and Environmental Sciences , Newcastle University , Bedson Building , Newcastle upon Tyne NE1 7RU , U.K
| | - Mathew P Martin
- Northern Institute for Cancer Research, Medical School , Newcastle University , Paul O'Gorman Building, Framlington Place , Newcastle upon Tyne NE2 4HH , U.K
| | - Duncan C Miller
- Northern Institute for Cancer Research, Chemistry, School of Natural and Environmental Sciences , Newcastle University , Bedson Building , Newcastle upon Tyne NE1 7RU , U.K
| | - Céline Cano
- Northern Institute for Cancer Research, Chemistry, School of Natural and Environmental Sciences , Newcastle University , Bedson Building , Newcastle upon Tyne NE1 7RU , U.K
| | - Jane A Endicott
- Northern Institute for Cancer Research, Medical School , Newcastle University , Paul O'Gorman Building, Framlington Place , Newcastle upon Tyne NE2 4HH , U.K
| | - Ian R Hardcastle
- Northern Institute for Cancer Research, Chemistry, School of Natural and Environmental Sciences , Newcastle University , Bedson Building , Newcastle upon Tyne NE1 7RU , U.K
| | - Martin E M Noble
- Northern Institute for Cancer Research, Medical School , Newcastle University , Paul O'Gorman Building, Framlington Place , Newcastle upon Tyne NE2 4HH , U.K
| | - Michael J Waring
- Northern Institute for Cancer Research, Chemistry, School of Natural and Environmental Sciences , Newcastle University , Bedson Building , Newcastle upon Tyne NE1 7RU , U.K
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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: 139] [Impact Index Per Article: 23.2] [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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Jorda R, Hendrychová D, Voller J, Řezníčková E, Gucký T, Kryštof V. How Selective Are Pharmacological Inhibitors of Cell-Cycle-Regulating Cyclin-Dependent Kinases? J Med Chem 2018; 61:9105-9120. [PMID: 30234987 DOI: 10.1021/acs.jmedchem.8b00049] [Citation(s) in RCA: 58] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Cyclin-dependent kinases (CDKs) are an important and emerging class of drug targets for which many small-molecule inhibitors have been developed. However, there is often insufficient data available on the selectivity of CDK inhibitors (CDKi) to attribute the effects on the presumed target CDK to these inhibitors. Here, we highlight discrepancies between the kinase selectivity of CDKi and the phenotype exhibited; we evaluated 31 CDKi (claimed to target CDK1-4) for activity toward CDKs 1, 2, 4, 5, 7, 9 and for effects on the cell cycle. Our results suggest that most CDKi should be reclassified as pan-selective and should not be used as a tool. In addition, some compounds did not even inhibit CDKs as their primary cellular targets; for example, NU6140 showed potent inhibition of Aurora kinases. We also established an online database of commercially available CDKi for critical evaluation of their utility as molecular probes. Our results should help researchers select the most relevant chemical tools for their specific applications.
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Affiliation(s)
- Radek Jorda
- Laboratory of Growth Regulators, Centre of the Region Haná for Biotechnological and Agricultural Research , Palacký University and Institute of Experimental Botany ASCR , Šlechtitelů 27 , 78371 Olomouc , Czech Republic
| | - Denisa Hendrychová
- Laboratory of Growth Regulators, Centre of the Region Haná for Biotechnological and Agricultural Research , Palacký University and Institute of Experimental Botany ASCR , Šlechtitelů 27 , 78371 Olomouc , Czech Republic
| | - Jiří Voller
- Laboratory of Growth Regulators, Centre of the Region Haná for Biotechnological and Agricultural Research , Palacký University and Institute of Experimental Botany ASCR , Šlechtitelů 27 , 78371 Olomouc , Czech Republic
| | - Eva Řezníčková
- Laboratory of Growth Regulators, Centre of the Region Haná for Biotechnological and Agricultural Research , Palacký University and Institute of Experimental Botany ASCR , Šlechtitelů 27 , 78371 Olomouc , Czech Republic
| | - Tomáš Gucký
- Laboratory of Growth Regulators, Centre of the Region Haná for Biotechnological and Agricultural Research , Palacký University and Institute of Experimental Botany ASCR , Šlechtitelů 27 , 78371 Olomouc , Czech Republic
| | - Vladimír Kryštof
- Laboratory of Growth Regulators, Centre of the Region Haná for Biotechnological and Agricultural Research , Palacký University and Institute of Experimental Botany ASCR , Šlechtitelů 27 , 78371 Olomouc , Czech Republic
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p16 Ink4a and p21 Cip1/Waf1 promote tumour growth by enhancing myeloid-derived suppressor cells chemotaxis. Nat Commun 2017; 8:2050. [PMID: 29234059 PMCID: PMC5727112 DOI: 10.1038/s41467-017-02281-x] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2017] [Accepted: 11/17/2017] [Indexed: 01/06/2023] Open
Abstract
p16Ink4a and p21Cip1/Waf1 act as tumour suppressors through induction of cellular senescence. However, senescence-independent roles of these CDK inhibitors are not well understood. Here, we report an unexpected function of p16Ink4 and p21Cip1/Waf1, namely, tumour promotion through chemotaxis. In monocytic myeloid-derived suppressor cells (Mo-MDSCs), p16Ink4 and p21Cip1/Waf1 are highly expressed and stimulate CX3CR1 chemokine receptor expression by preventing CDK-mediated phosphorylation and inactivation of SMAD3. Thus, deletion of p16Ink4 and p21Cip1/Waf1 reduces CX3CR1 expression, thereby inhibiting Mo-MDSC accumulation in tumours expressing CX3CL1 and suppressing the tumour progression in mice. Notably, blockade of the CX3CL1/CX3CR1 axis suppresses tumour growth, whereas inactivation of CDKs elicits the opposite effect. These findings reveal an unexpected function of p16Ink4a and p21Waf1/Cip1 and indicate that regulation of Mo-MDSCs chemotaxis is a valuable potential strategy for control of tumour development. Both p16Ink4a and p21Cip1/Waf1 are known oncosuppressors and have a role in senescence. Here, the authors show a pro-tumorigenic role for these two proteins: high expression in myeloid-derived suppressor cells stimulates their chemotactic function, favouring tumour progression.
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Keretsu S, Balasubramanian PK, Bhujbal SP, Cho SJ. Receptor-guided 3D-Quantitative Structure-Activity Relationship and Docking Studies of 6-Substituted 2-Arylaminopurines as CDK2 Kinase Inhibitors. B KOREAN CHEM SOC 2017. [DOI: 10.1002/bkcs.11280] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Affiliation(s)
- Seketoulie Keretsu
- Department of Biomedical Sciences, College of Medicine; Chosun University; Gwangju 501-759 Republic of Korea
| | | | - Swapnil Pandurang Bhujbal
- Department of Biomedical Sciences, College of Medicine; Chosun University; Gwangju 501-759 Republic of Korea
| | - Seung Joo Cho
- Department of Biomedical Sciences, College of Medicine; Chosun University; Gwangju 501-759 Republic of Korea
- Department of Cellular and Molecular Medicine, College of Medicine; Chosun University; Gwangju 501-759 Republic of Korea
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Effect of cell cycle arrest on intermediate metabolism in the marine diatom Phaeodactylum tricornutum. Proc Natl Acad Sci U S A 2017; 114:E8007-E8016. [PMID: 28874574 DOI: 10.1073/pnas.1711642114] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The inhibitor NU 2058 [6-(cyclohexylmethoxy)-9H-purin-2-amine] leads to G1-phase cell cycle arrest in the marine diatom, Phaeodactylum tricornutum, by binding to two cyclin-dependent kinases, CDKA1 and CDKA2. NU 2058 has no effect on photosynthetic attributes, such as Fv/Fm, chlorophyll a/cell, levels of D2 PSII subunits, or RbcL; however, cell cycle arrest leads to unbalanced growth whereby photosynthetic products that can no longer be used for cell division are redirected toward carbohydrates and triacylglycerols (TAGs). Arrested cells up-regulate most genes involved in fatty acid synthesis, including acetyl-CoA carboxylase, and three out of five putative type II diglyceride acyltransferases (DGATs), the enzymes that catalyze TAG production. Correlation of transcriptomes in arrested cells with a flux balance model for P. tricornutum predicts that reactions in the mitochondrion that supply glycerate may support TAG synthesis. Our results reveal that sources of intermediate metabolites and macromolecular sinks are tightly coupled to the cell cycle in a marine diatom, and that arresting cells in the G1 phase leads to remodeling of intermediate metabolism and unbalanced growth.
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21
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Parveen I, Ahmed N, Idrees D, Khan P, Hassan MI. Synthesis, estrogen receptor binding affinity and molecular docking of pyrimidine-piperazine-chromene and -quinoline conjugates. Bioorg Med Chem Lett 2017; 27:4493-4499. [DOI: 10.1016/j.bmcl.2017.07.077] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2017] [Revised: 07/22/2017] [Accepted: 07/28/2017] [Indexed: 10/19/2022]
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22
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Coxon CR, Wong C, Bayliss R, Boxall K, Carr KH, Fry AM, Hardcastle IR, Matheson CJ, Newell DR, Sivaprakasam M, Thomas H, Turner D, Yeoh S, Wang LZ, Griffin RJ, Golding BT, Cano C. Structure-guided design of purine-based probes for selective Nek2 inhibition. Oncotarget 2017; 8:19089-19124. [PMID: 27833088 PMCID: PMC5386672 DOI: 10.18632/oncotarget.13249] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2016] [Accepted: 10/17/2016] [Indexed: 01/23/2023] Open
Abstract
Nek2 (NIMA-related kinase 2) is a cell cycle-dependent serine/threonine protein kinase that regulates centrosome separation at the onset of mitosis. Overexpression of Nek2 is common in human cancers and suppression can restrict tumor cell growth and promote apoptosis. Nek2 inhibition with small molecules, therefore, offers the prospect of a new therapy for cancer. To achieve this goal, a better understanding of the requirements for selective-inhibition of Nek2 is required. 6-Alkoxypurines were identified as ATP-competitive inhibitors of Nek2 and CDK2. Comparison with CDK2-inhibitor structures indicated that judicious modification of the 6-alkoxy and 2-arylamino substituents could achieve discrimination between Nek2 and CDK2. In this study, a library of 6-cyclohexylmethoxy-2-arylaminopurines bearing carboxamide, sulfonamide and urea substituents on the 2-arylamino ring was synthesized. Few of these compounds were selective for Nek2 over CDK2, with the best result being obtained for 3-((6-(cyclohexylmethoxy)-9H-purin-2-yl)amino)-N,N-dimethylbenzamide (CDK2 IC50 = 7.0 μM; Nek2 IC50 = 0.62 μM) with >10-fold selectivity. Deletion of the 6-substituent abrogated activity against both Nek2 and CDK2. Nine compounds containing an (E)-dialkylaminovinyl substituent at C-6, all showed selectivity for Nek2, e.g. (E)-6-(2-(azepan-1-yl)vinyl)-N-phenyl-9H-purin-2-amine (CDK2 IC50 = 2.70 μM; Nek2 IC50 = 0.27 μM). Structural biology of selected compounds enabled a partial rationalization of the observed structure activity relationships and mechanism of Nek2 activation. This showed that carboxamide 11 is the first reported inhibitor of Nek2 in the DFG-in conformation.
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Affiliation(s)
- Christopher R. Coxon
- Northern Institute for Cancer Research, School of Chemistry, Newcastle University, Newcastle upon Tyne, UK
| | - Christopher Wong
- Northern Institute for Cancer Research, School of Chemistry, Newcastle University, Newcastle upon Tyne, UK
| | - Richard Bayliss
- Department of Molecular and Cell Biology, University of Leicester, Leicester, UK
| | - Kathy Boxall
- Cancer Research UK Cancer Therapeutics Unit, The Institute of Cancer Research, London, UK
| | - Katherine H. Carr
- Department of Molecular and Cell Biology, University of Leicester, Leicester, UK
| | - Andrew M. Fry
- Department of Molecular and Cell Biology, University of Leicester, Leicester, UK
| | - Ian R. Hardcastle
- Northern Institute for Cancer Research, School of Chemistry, Newcastle University, Newcastle upon Tyne, UK
| | - Christopher J. Matheson
- Northern Institute for Cancer Research, School of Chemistry, Newcastle University, Newcastle upon Tyne, UK
| | - David R. Newell
- Northern Institute for Cancer Research, Newcastle University, Newcastle upon Tyne, UK
| | - Mangaleswaran Sivaprakasam
- Northern Institute for Cancer Research, School of Chemistry, Newcastle University, Newcastle upon Tyne, UK
| | - Huw Thomas
- Northern Institute for Cancer Research, Newcastle University, Newcastle upon Tyne, UK
| | - David Turner
- Northern Institute for Cancer Research, School of Chemistry, Newcastle University, Newcastle upon Tyne, UK
| | - Sharon Yeoh
- Department of Molecular and Cell Biology, University of Leicester, Leicester, UK
| | - Lan Z. Wang
- Northern Institute for Cancer Research, Newcastle University, Newcastle upon Tyne, UK
| | - Roger J. Griffin
- Northern Institute for Cancer Research, School of Chemistry, Newcastle University, Newcastle upon Tyne, UK
| | - Bernard T. Golding
- Northern Institute for Cancer Research, School of Chemistry, Newcastle University, Newcastle upon Tyne, UK
| | - Céline Cano
- Northern Institute for Cancer Research, School of Chemistry, Newcastle University, Newcastle upon Tyne, UK
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23
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Coxon C, Anscombe E, Harnor SJ, Martin MP, Carbain B, Golding BT, Hardcastle IR, Harlow LK, Korolchuk S, Matheson CJ, Newell DR, Noble MEM, Sivaprakasam M, Tudhope SJ, Turner DM, Wang LZ, Wedge SR, Wong C, Griffin RJ, Endicott JA, Cano C. Cyclin-Dependent Kinase (CDK) Inhibitors: Structure-Activity Relationships and Insights into the CDK-2 Selectivity of 6-Substituted 2-Arylaminopurines. J Med Chem 2017; 60:1746-1767. [PMID: 28005359 PMCID: PMC6111440 DOI: 10.1021/acs.jmedchem.6b01254] [Citation(s) in RCA: 64] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2016] [Indexed: 02/08/2023]
Abstract
Purines and related heterocycles substituted at C-2 with 4'-sulfamoylanilino and at C-6 with a variety of groups have been synthesized with the aim of achieving selectivity of binding to CDK2 over CDK1. 6-Substituents that favor competitive inhibition at the ATP binding site of CDK2 were identified and typically exhibited 10-80-fold greater inhibition of CDK2 compared to CDK1. Most impressive was 4-((6-([1,1'-biphenyl]-3-yl)-9H-purin-2-yl)amino) benzenesulfonamide (73) that exhibited high potency toward CDK2 (IC50 0.044 μM) but was ∼2000-fold less active toward CDK1 (IC50 86 μM). This compound is therefore a useful tool for studies of cell cycle regulation. Crystal structures of inhibitor-kinase complexes showed that the inhibitor stabilizes a glycine-rich loop conformation that shapes the ATP ribose binding pocket and that is preferred in CDK2 but has not been observed in CDK1. This aspect of the active site may be exploited for the design of inhibitors that distinguish between CDK1 and CDK2.
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Affiliation(s)
- Christopher
R. Coxon
- Newcastle
Cancer Centre, Northern Institute for Cancer Research, School of Chemistry, Newcastle University, Bedson Building, Newcastle
upon Tyne NE1 7RU, U.K.
| | - Elizabeth Anscombe
- Department
of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, U.K.
| | - Suzannah J. Harnor
- Newcastle
Cancer Centre, Northern Institute for Cancer Research, School of Chemistry, Newcastle University, Bedson Building, Newcastle
upon Tyne NE1 7RU, U.K.
| | - Mathew P. Martin
- Newcastle
Cancer Centre, Northern Institute for Cancer Research, Newcastle University Medical School, Paul O’Gorman Building, Framlington Place, Newcastle upon Tyne, NE2 4HH, U.K.
| | - Benoit Carbain
- Newcastle
Cancer Centre, Northern Institute for Cancer Research, School of Chemistry, Newcastle University, Bedson Building, Newcastle
upon Tyne NE1 7RU, U.K.
| | - Bernard T. Golding
- Newcastle
Cancer Centre, Northern Institute for Cancer Research, School of Chemistry, Newcastle University, Bedson Building, Newcastle
upon Tyne NE1 7RU, U.K.
| | - Ian R. Hardcastle
- Newcastle
Cancer Centre, Northern Institute for Cancer Research, School of Chemistry, Newcastle University, Bedson Building, Newcastle
upon Tyne NE1 7RU, U.K.
| | - Lisa K. Harlow
- Newcastle
Cancer Centre, Northern Institute for Cancer Research, School of Chemistry, Newcastle University, Bedson Building, Newcastle
upon Tyne NE1 7RU, U.K.
| | - Svitlana Korolchuk
- Newcastle
Cancer Centre, Northern Institute for Cancer Research, Newcastle University Medical School, Paul O’Gorman Building, Framlington Place, Newcastle upon Tyne, NE2 4HH, U.K.
| | - Christopher J. Matheson
- Newcastle
Cancer Centre, Northern Institute for Cancer Research, School of Chemistry, Newcastle University, Bedson Building, Newcastle
upon Tyne NE1 7RU, U.K.
| | - David R. Newell
- Newcastle
Cancer Centre, Northern Institute for Cancer Research, Newcastle University Medical School, Paul O’Gorman Building, Framlington Place, Newcastle upon Tyne, NE2 4HH, U.K.
| | - Martin E. M. Noble
- Department
of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, U.K.
| | - Mangaleswaran Sivaprakasam
- Newcastle
Cancer Centre, Northern Institute for Cancer Research, School of Chemistry, Newcastle University, Bedson Building, Newcastle
upon Tyne NE1 7RU, U.K.
| | - Susan J. Tudhope
- Newcastle
Cancer Centre, Northern Institute for Cancer Research, Newcastle University Medical School, Paul O’Gorman Building, Framlington Place, Newcastle upon Tyne, NE2 4HH, U.K.
| | - David M. Turner
- Newcastle
Cancer Centre, Northern Institute for Cancer Research, School of Chemistry, Newcastle University, Bedson Building, Newcastle
upon Tyne NE1 7RU, U.K.
| | - Lan Z. Wang
- Newcastle
Cancer Centre, Northern Institute for Cancer Research, Newcastle University Medical School, Paul O’Gorman Building, Framlington Place, Newcastle upon Tyne, NE2 4HH, U.K.
| | - Stephen R. Wedge
- Newcastle
Cancer Centre, Northern Institute for Cancer Research, Newcastle University Medical School, Paul O’Gorman Building, Framlington Place, Newcastle upon Tyne, NE2 4HH, U.K.
| | - Christopher Wong
- Newcastle
Cancer Centre, Northern Institute for Cancer Research, School of Chemistry, Newcastle University, Bedson Building, Newcastle
upon Tyne NE1 7RU, U.K.
| | - Roger J. Griffin
- Newcastle
Cancer Centre, Northern Institute for Cancer Research, School of Chemistry, Newcastle University, Bedson Building, Newcastle
upon Tyne NE1 7RU, U.K.
| | - Jane A. Endicott
- Department
of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, U.K.
| | - Céline Cano
- Newcastle
Cancer Centre, Northern Institute for Cancer Research, School of Chemistry, Newcastle University, Bedson Building, Newcastle
upon Tyne NE1 7RU, U.K.
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Synthesis, anti-17β-HSD and antiproliferative activity of new substituted 5-nitrosopyrimidine analogs. Med Chem Res 2017. [DOI: 10.1007/s00044-017-1795-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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DNA Damage Signaling Is Required for Replication of Human Bocavirus 1 DNA in Dividing HEK293 Cells. J Virol 2016; 91:JVI.01831-16. [PMID: 27733644 DOI: 10.1128/jvi.01831-16] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2016] [Accepted: 10/05/2016] [Indexed: 02/07/2023] Open
Abstract
Human bocavirus 1 (HBoV1), an emerging human-pathogenic respiratory virus, is a member of the genus Bocaparvovirus of the Parvoviridae family. In human airway epithelium air-liquid interface (HAE-ALI) cultures, HBoV1 infection initiates a DNA damage response (DDR), activating all three phosphatidylinositol 3-kinase-related kinases (PI3KKs): ATM, ATR, and DNA-PKcs. In this context, activation of PI3KKs is a requirement for amplification of the HBoV1 genome (X. Deng, Z. Yan, F. Cheng, J. F. Engelhardt, and J. Qiu, PLoS Pathog, 12:e1005399, 2016, https://doi.org/10.1371/journal.ppat.1005399), and HBoV1 replicates only in terminally differentiated, nondividing cells. This report builds on the previous discovery that the replication of HBoV1 DNA can also occur in dividing HEK293 cells, demonstrating that such replication is likewise dependent on a DDR. Transfection of HEK293 cells with the duplex DNA genome of HBoV1 induces hallmarks of DDR, including phosphorylation of H2AX and RPA32, as well as activation of all three PI3KKs. The large viral nonstructural protein NS1 is sufficient to induce the DDR and the activation of the three PI3KKs. Pharmacological inhibition or knockdown of any one of the PI3KKs significantly decreases both the replication of HBoV1 DNA and the downstream production of progeny virions. The DDR induced by the HBoV1 NS1 protein does not cause obvious damage to cellular DNA or arrest of the cell cycle. Notably, key DNA replication factors and major DNA repair DNA polymerases (polymerase η [Pol η] and polymerase κ [Pol κ]) are recruited to the viral DNA replication centers and facilitate HBoV1 DNA replication. Our study provides the first evidence of the DDR-dependent parvovirus DNA replication that occurs in dividing cells and is independent of cell cycle arrest. IMPORTANCE The parvovirus human bocavirus 1 (HBoV1) is an emerging respiratory virus that causes lower respiratory tract infections in young children worldwide. HEK293 cells are the only dividing cells tested that fully support the replication of the duplex genome of this virus and allow the production of progeny virions. In this study, we demonstrate that HBoV1 induces a DDR that plays significant roles in the replication of the viral DNA and the production of progeny virions in HEK293 cells. We also show that both cellular DNA replication factors and DNA repair DNA polymerases colocalize within centers of viral DNA replication and that Pol η and Pol κ play an important role in HBoV1 DNA replication. Whereas the DDR that leads to the replication of the DNA of other parvoviruses is facilitated by the cell cycle, the DDR triggered by HBoV1 DNA replication or NS1 is not. HBoV1 is the first parvovirus whose NS1 has been shown to be able to activate all three PI3KKs (ATM, ATR, and DNA-PKcs).
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Gerogiokas G, Southey MWY, Mazanetz MP, Heifetz A, Bodkin M, Law RJ, Henchman RH, Michel J. Assessment of Hydration Thermodynamics at Protein Interfaces with Grid Cell Theory. J Phys Chem B 2016; 120:10442-10452. [PMID: 27645529 DOI: 10.1021/acs.jpcb.6b07993] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Molecular dynamics simulations have been analyzed with the Grid Cell Theory (GCT) method to spatially resolve the binding enthalpies and entropies of water molecules at the interface of 17 structurally diverse proteins. Correlations between computed energetics and structural descriptors have been sought to facilitate the development of simple models of protein hydration. Little correlation was found between GCT-computed binding enthalpies and continuum electrostatics calculations. A simple count of contacts with functional groups in charged amino acids correlates well with enhanced water stabilization, but the stability of water near hydrophobic and polar residues depends markedly on its coordination environment. The positions of X-ray-resolved water molecules correlate with computed high-density hydration sites, but many unresolved waters are significantly stabilized at the protein surfaces. A defining characteristic of ligand-binding pockets compared to nonbinding pockets was a greater solvent-accessible volume, but average water thermodynamic properties were not distinctive from other interfacial regions. Interfacial water molecules are frequently stabilized by enthalpy and destabilized entropy with respect to bulk, but counter-examples occasionally occur. Overall detailed inspection of the local coordinating environment appears necessary to gauge the thermodynamic stability of water in protein structures.
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Affiliation(s)
- Georgios Gerogiokas
- EaStCHEM School of Chemistry , Joseph Black Building, The King's Buildings, Edinburgh EH9 3JJ, United Kingdom
| | - Michelle W Y Southey
- Evotec (U.K.) Limited , 114 Innovation Drive, Milton Park, Abingdon, Oxfordshire OX14 4SA, United Kingdom
| | - Michael P Mazanetz
- Evotec (U.K.) Limited , 114 Innovation Drive, Milton Park, Abingdon, Oxfordshire OX14 4SA, United Kingdom
| | - Alexander Heifetz
- Evotec (U.K.) Limited , 114 Innovation Drive, Milton Park, Abingdon, Oxfordshire OX14 4SA, United Kingdom
| | - Michael Bodkin
- Evotec (U.K.) Limited , 114 Innovation Drive, Milton Park, Abingdon, Oxfordshire OX14 4SA, United Kingdom
| | - Richard J Law
- Evotec (U.K.) Limited , 114 Innovation Drive, Milton Park, Abingdon, Oxfordshire OX14 4SA, United Kingdom
| | - Richard H Henchman
- Manchester Institute of Biotechnology, The University of Manchester , 131 Princess Street, Manchester M1 7DN, United Kingdom.,School of Chemistry, The University of Manchester , Oxford Road, Manchester M13 9PL, United Kingdom
| | - J Michel
- EaStCHEM School of Chemistry , Joseph Black Building, The King's Buildings, Edinburgh EH9 3JJ, United Kingdom
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Bazgier V, Berka K, Otyepka M, Banáš P. Exponential repulsion improves structural predictability of molecular docking. J Comput Chem 2016; 37:2485-94. [PMID: 27620738 DOI: 10.1002/jcc.24473] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2016] [Revised: 06/21/2016] [Accepted: 07/16/2016] [Indexed: 01/13/2023]
Abstract
Molecular docking is a powerful tool for theoretical prediction of the preferred conformation and orientation of small molecules within protein active sites. The obtained poses can be used for estimation of binding energies, which indicate the inhibition effect of designed inhibitors, and therefore might be used for in silico drug design. However, the evaluation of ligand binding affinity critically depends on successful prediction of the native binding mode. Contemporary docking methods are often based on scoring functions derived from molecular mechanical potentials. In such potentials, nonbonded interactions are typically represented by electrostatic interactions between atom-centered partial charges and standard 6-12 Lennard-Jones potential. Here, we present implementation and testing of a scoring function based on more physically justified exponential repulsion instead of the standard Lennard-Jones potential. We found that this scoring function significantly improved prediction of the native binding modes in proteins bearing narrow active sites such as serine proteases and kinases. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Václav Bazgier
- Laboratory of Growth Regulators, Centre of the Region Haná for Biotechnological and Agricultural Research, Institute of Experimental Botany ASCR & Palacky University, Šlechtitelů 11, Olomouc, 783 71, Czech Republic.,Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science, Palacký University Olomouc, 17. listopadu 12, Olomouc, 77146, Czech Republic
| | - Karel Berka
- Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science, Palacký University Olomouc, 17. listopadu 12, Olomouc, 77146, Czech Republic
| | - Michal Otyepka
- Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science, Palacký University Olomouc, 17. listopadu 12, Olomouc, 77146, Czech Republic
| | - Pavel Banáš
- Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science, Palacký University Olomouc, 17. listopadu 12, Olomouc, 77146, Czech Republic.
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Beale G, Haagensen EJ, Thomas HD, Wang LZ, Revill CH, Payne SL, Golding BT, Hardcastle IR, Newell DR, Griffin RJ, Cano C. Combined PI3K and CDK2 inhibition induces cell death and enhances in vivo antitumour activity in colorectal cancer. Br J Cancer 2016; 115:682-90. [PMID: 27529512 PMCID: PMC5023777 DOI: 10.1038/bjc.2016.238] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Revised: 05/31/2016] [Accepted: 07/14/2016] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND The phosphatidylinositol-3-kinase/mammalian target of rapamycin (PI3K/mTOR) pathway is commonly deregulated in human cancer, hence many PI3K and mTOR inhibitors have been developed and have now reached clinical trials. Similarly, CDKs have been investigated as cancer drug targets. METHODS We have synthesised and characterised a series of 6-aminopyrimidines identified from a kinase screen that inhibit PI3K and/or mTOR and/or CDK2. Kinase inhibition, tumour cell growth, cell cycle distribution, cytotoxicity and signalling experiments were undertaken in HCT116 and HT29 colorectal cancer cell lines, and in vivo HT29 efficacy studies. RESULTS 2,6-Diaminopyrimidines with an O(4)-cyclohexylmethyl substituent and a C-5-nitroso or cyano group (1,2,5) induced cell cycle phase alterations and were growth inhibitory (GI50<20 μM). Compound 1, but not 2 or 5, potently inhibits CDK2 (IC50=0.1 nM) as well as PI3K, and was cytotoxic at growth inhibitory concentrations. Consistent with kinase inhibition data, compound 1 reduced phospho-Rb and phospho-rS6 at GI50 concentrations. Combination of NU6102 (CDK2 inhibitor) and pictilisib (GDC-0941; pan-PI3K inhibitor) resulted in synergistic growth inhibition, and enhanced cytotoxicity in HT29 cells in vitro and HT29 tumour growth inhibition in vivo. CONCLUSIONS These studies identified a novel series of mixed CDK2/PI3K inhibitors and demonstrate that dual targeting of CDK2 and PI3K can result in enhanced antitumour activity.
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Affiliation(s)
- Gary Beale
- Newcastle Cancer Centre, Northern Institute for Cancer Research, Paul O'Gorman Building, Medical School, Newcastle University, Framlington Place, Newcastle-upon-Tyne NE2 4HH, UK
| | - Emma J Haagensen
- Newcastle Cancer Centre, Northern Institute for Cancer Research, Paul O'Gorman Building, Medical School, Newcastle University, Framlington Place, Newcastle-upon-Tyne NE2 4HH, UK
| | - Huw D Thomas
- Newcastle Cancer Centre, Northern Institute for Cancer Research, Paul O'Gorman Building, Medical School, Newcastle University, Framlington Place, Newcastle-upon-Tyne NE2 4HH, UK
| | - Lan-Zhen Wang
- Newcastle Cancer Centre, Northern Institute for Cancer Research, Paul O'Gorman Building, Medical School, Newcastle University, Framlington Place, Newcastle-upon-Tyne NE2 4HH, UK
| | - Charlotte H Revill
- Newcastle Cancer Centre, Northern Institute for Cancer Research, School of Chemistry, Newcastle University, Bedson Building, Newcastle NE1 7RU, UK
| | - Sara L Payne
- Newcastle Cancer Centre, Northern Institute for Cancer Research, School of Chemistry, Newcastle University, Bedson Building, Newcastle NE1 7RU, UK
| | - Bernard T Golding
- Newcastle Cancer Centre, Northern Institute for Cancer Research, School of Chemistry, Newcastle University, Bedson Building, Newcastle NE1 7RU, UK
| | - Ian R Hardcastle
- Newcastle Cancer Centre, Northern Institute for Cancer Research, School of Chemistry, Newcastle University, Bedson Building, Newcastle NE1 7RU, UK
| | - David R Newell
- Newcastle Cancer Centre, Northern Institute for Cancer Research, Paul O'Gorman Building, Medical School, Newcastle University, Framlington Place, Newcastle-upon-Tyne NE2 4HH, UK
| | - Roger J Griffin
- Newcastle Cancer Centre, Northern Institute for Cancer Research, School of Chemistry, Newcastle University, Bedson Building, Newcastle NE1 7RU, UK
| | - Celine Cano
- Newcastle Cancer Centre, Northern Institute for Cancer Research, School of Chemistry, Newcastle University, Bedson Building, Newcastle NE1 7RU, UK
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Cortese D, Chegaev K, Guglielmo S, Wang LZ, Golding BT, Cano C, Fruttero R. Synthesis and Biological Evaluation of N(2) -Substituted 2,4-Diamino-6-cyclohexylmethoxy-5-nitrosopyrimidines and Related 5-Cyano-NNO-azoxy Derivatives as Cyclin-Dependent Kinase 2 (CDK2) Inhibitors. ChemMedChem 2016; 11:1705-8. [PMID: 27355194 DOI: 10.1002/cmdc.201600108] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2016] [Revised: 06/07/2016] [Indexed: 11/09/2022]
Abstract
The potent and selective cyclin-dependent kinase 2 (CDK2) inhibitor NU6027 (6-cyclohexylmethoxy-5-nitroso-2,4-diaminopyrimidine) was used as the lead for the synthesis of a series of analogues in order to provide further insight into the structure-activity relationships for 2,4-diaminopyrimidine CDK2 inhibitors. Aliphatic amino substituents were introduced at position 2. The use of linear or less sterically hindered amines gave rise to compounds endowed with slightly better activity than the lead; on the other hand, the compounds were less active if a bulkier amino substituent was used. Substitution of the 5-nitroso group with a 5-cyano-NNO-azoxy moiety afforded a new class of inhibitors, the activity of which against CDK2 was found to be similar to that of the nitroso series. The most active nitroso compound was 8 b ((2S)-2-[(4-amino-6-cyclohexylmethoxy-5-nitrosopyrimidin-2-yl)amino]propan-1-ol; IC50 =0.16 μm), while in the 5-cyano-NNO-azoxy series the most active compound was 9 b (4-amino-5-[(Z)-cyano-NNO-azoxy]-2-{[(2S)-1-hydroxypropan-2-yl]amino}-6-cyclohexylmethoxypyrimidine; IC50 =0.30 μm). Taken together, these new analogues of NU6027 enhance our understanding of the structure-activity relationships for 2,4-diaminopyrimidine CDK2 inhibitors.
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Affiliation(s)
- Daniela Cortese
- Department of Drug Science and Technology, Università degli Studi di Torino, Via P. Giuria 9, 10125, Turin, Italy
| | - Konstantin Chegaev
- Department of Drug Science and Technology, Università degli Studi di Torino, Via P. Giuria 9, 10125, Turin, Italy
| | - Stefano Guglielmo
- Department of Drug Science and Technology, Università degli Studi di Torino, Via P. Giuria 9, 10125, Turin, Italy
| | - Lan Z Wang
- Northern Institute for Cancer Research, Paul O'Gorman Building, Medical School, Newcastle University, Framlington Place, Newcastle Upon Tyne, NE2 4HH, UK
| | - Bernard T Golding
- Northern Institute for Cancer Research, Bedson Building, School of Chemistry, Newcastle University, Newcastle Upon Tyne, NE1 7RU, UK
| | - Céline Cano
- Northern Institute for Cancer Research, Bedson Building, School of Chemistry, Newcastle University, Newcastle Upon Tyne, NE1 7RU, UK
| | - Roberta Fruttero
- Department of Drug Science and Technology, Università degli Studi di Torino, Via P. Giuria 9, 10125, Turin, Italy.
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30
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Drugging ATR: progress in the development of specific inhibitors for the treatment of cancer. Future Med Chem 2016; 7:873-91. [PMID: 26061106 DOI: 10.4155/fmc.15.33] [Citation(s) in RCA: 62] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
In this article, we review the ATR inhibitor field from initial pharmacological tools to first-generation clinical candidates with the potential to bring benefit to cancer patients. ATR is a critical part of the cell DNA-damage response. Over the past decade or more, compounds with weak ATR potency and low specificity have been used as tools in early studies to elucidate ATR pharmacology. More recently highly potent, selective and in vivo active ATR inhibitors have been developed enabling detailed preclinical in vitro and in vivo target assessment to be made. The published studies reveal the potential of ATR inhibitors for use as monotherapy or in combination with DNA-damaging agents. To date, VX-970 and AZD6738, have entered clinical assessment.
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31
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Xu X, Yao Q. Scaffold Hopping Approach to a New Series of Pyridine Derivatives as Potent Inhibitors of CDK2. Arch Pharm (Weinheim) 2016; 349:224-31. [DOI: 10.1002/ardp.201500335] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2015] [Revised: 01/14/2016] [Accepted: 01/20/2016] [Indexed: 11/07/2022]
Affiliation(s)
- Xiaojuan Xu
- School of Chemistry and Chemical Engineering; Yancheng Teachers University; Yancheng China
| | - Qizheng Yao
- Department of Medicinal Chemistry, School of Pharmacy; China Pharmaceutical University; Nanjing China
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32
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Replication of an Autonomous Human Parvovirus in Non-dividing Human Airway Epithelium Is Facilitated through the DNA Damage and Repair Pathways. PLoS Pathog 2016; 12:e1005399. [PMID: 26765330 PMCID: PMC4713420 DOI: 10.1371/journal.ppat.1005399] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2015] [Accepted: 12/22/2015] [Indexed: 01/11/2023] Open
Abstract
Human bocavirus 1 (HBoV1) belongs to the genus Bocaparvovirus of the Parvoviridae family, and is an emerging human pathogenic respiratory virus. In vitro, HBoV1 infects well-differentiated/polarized primary human airway epithelium (HAE) cultured at an air-liquid interface (HAE-ALI). Although it is well known that autonomous parvovirus replication depends on the S phase of the host cells, we demonstrate here that the HBoV1 genome amplifies efficiently in mitotically quiescent airway epithelial cells of HAE-ALI cultures. Analysis of HBoV1 DNA in infected HAE-ALI revealed that HBoV1 amplifies its ssDNA genome following a typical parvovirus rolling-hairpin DNA replication mechanism. Notably, HBoV1 infection of HAE-ALI initiates a DNA damage response (DDR) with activation of all three phosphatidylinositol 3-kinase–related kinases (PI3KKs). We found that the activation of the three PI3KKs is required for HBoV1 genome amplification; and, more importantly, we identified that two Y-family DNA polymerases, Pol η and Pol κ, are involved in HBoV1 genome amplification. Overall, we have provided an example of de novo DNA synthesis (genome amplification) of an autonomous parvovirus in non-dividing cells, which is dependent on the cellular DNA damage and repair pathways. Parvovirus is unique among DNA viruses. It has a single stranded DNA genome of ~5.5 kb in length. Autonomous parvoviruses, which replicate autonomously in cells, rely on the S phase cell cycle for genome amplification. In the current study, we demonstrated that human bocavirus 1 (HBoV1), an autonomous human Bocaparvovirus, replicates its genome in well-differentiated (non-dividing) primary human airway epithelial cells. HBoV1 infection of non-dividing human airway epithelial cells induces a DNA damage response. We provide evidence that HBoV1 genome amplification in non-dividing airway epithelial cells is facilitated by the DNA damage response-mediated signaling pathways. Importantly, we discovered that two Y-family DNA repair polymerases, but not cellular DNA replication polymerases, are directly involved in HBoV1 genome amplification. Therefore, our study is innovative because it is the first to show that an autonomous parvovirus amplifies its genome in non-dividing cells, and that the DNA repair polymerases are involved in viral genome amplification.
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33
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Affiliation(s)
- Daniel Beaudoin
- Département de Chimie, Université de Montréal, Montréal, Québec H3C 3J7, Canada
| | - James D. Wuest
- Département de Chimie, Université de Montréal, Montréal, Québec H3C 3J7, Canada
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34
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Banik R, Roy S, Kirillov AM, Bauza A, Frontera A, Rodríguez-Diéguez A, Salas JM, Maniukiewicz W, Das SK, Das S. Two mixed-ligand cadmium(ii) compounds bearing 5-nitrosopyrimidine and N-donor aromatic blocks: self-assembly generation, structural and topological features, DFT studies, and Hirshfeld surface analysis. CrystEngComm 2016. [DOI: 10.1039/c6ce00989a] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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35
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Wieringa HW, van der Zee AGJ, de Vries EGE, van Vugt MATM. Breaking the DNA damage response to improve cervical cancer treatment. Cancer Treat Rev 2015; 42:30-40. [PMID: 26643553 DOI: 10.1016/j.ctrv.2015.11.008] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2015] [Revised: 11/16/2015] [Accepted: 11/17/2015] [Indexed: 12/25/2022]
Abstract
Every year, cervical cancer affects ∼500,000 women worldwide, and ∼275,000 patients die of this disease. The addition of platin-based chemotherapy to primary radiotherapy has increased 5-year survival of advanced-stage cervical cancer patients, which is, however, still only 66%. One of the factors thought to contribute to treatment failure is the ability of tumor cells to repair chemoradiotherapy-induced DNA damage. Therefore, sensitization of tumor cells for chemoradiotherapy via inhibition of the DNA damage response (DDR) as a novel strategy to improve therapy effect, is currently studied pre-clinically as well as in the clinic. Almost invariably, cervical carcinogenesis involves infection with the human papillomavirus (HPV), which inactivates part of the DNA damage response. This HPV-mediated partial inactivation of the DDR presents therapeutic targeting of the residual DDR as an interesting approach to achieve chemoradio-sensitization for cervical cancer. How the DDR can be most efficiently targeted, however, remains unclear. The fact that cisplatin and radiotherapy activate multiple signaling axes within the DDR further complicates a rational choice of therapeutic targets within the DDR. In this review, we provide an overview of the current preclinical and clinical knowledge about targeting the DDR in cervical cancer.
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Affiliation(s)
- Hylke W Wieringa
- Department of Medical Oncology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands; Department of Gynecologic Oncology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Ate G J van der Zee
- Department of Gynecologic Oncology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Elisabeth G E de Vries
- Department of Medical Oncology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Marcel A T M van Vugt
- Department of Medical Oncology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands.
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36
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Yu FC, Hao XP, Huang R, Yan SJ, Lin J. Synthesis of 2-nitroso heterocyclic ketene aminals with (E)-1-nitro-4-(2-nitrovinyl)-benzene as the nitrosating agent. Tetrahedron 2015. [DOI: 10.1016/j.tet.2015.01.063] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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Xu W, Lucke AJ, Fairlie DP. Comparing sixteen scoring functions for predicting biological activities of ligands for protein targets. J Mol Graph Model 2015; 57:76-88. [PMID: 25682361 DOI: 10.1016/j.jmgm.2015.01.009] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2014] [Revised: 01/22/2015] [Accepted: 01/23/2015] [Indexed: 12/17/2022]
Abstract
Accurately predicting relative binding affinities and biological potencies for ligands that interact with proteins remains a significant challenge for computational chemists. Most evaluations of docking and scoring algorithms have focused on enhancing ligand affinity for a protein by optimizing docking poses and enrichment factors during virtual screening. However, there is still relatively limited information on the accuracy of commercially available docking and scoring software programs for correctly predicting binding affinities and biological activities of structurally related inhibitors of different enzyme classes. Presented here is a comparative evaluation of eight molecular docking programs (Autodock Vina, Fitted, FlexX, Fred, Glide, GOLD, LibDock, MolDock) using sixteen docking and scoring functions to predict the rank-order activity of different ligand series for six pharmacologically important protein and enzyme targets (Factor Xa, Cdk2 kinase, Aurora A kinase, COX-2, pla2g2a, β Estrogen receptor). Use of Fitted gave an excellent correlation (Pearson 0.86, Spearman 0.91) between predicted and experimental binding only for Cdk2 kinase inhibitors. FlexX and GOLDScore produced good correlations (Pearson>0.6) for hydrophilic targets such as Factor Xa, Cdk2 kinase and Aurora A kinase. By contrast, pla2g2a and COX-2 emerged as difficult targets for scoring functions to predict ligand activities. Although possessing a high hydrophobicity in its binding site, β Estrogen receptor produced reasonable correlations using LibDock (Pearson 0.75, Spearman 0.68). These findings can assist medicinal chemists to better match scoring functions with ligand-target systems for hit-to-lead optimization using computer-aided drug design approaches.
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Affiliation(s)
- Weijun Xu
- Division of Chemistry and Structural Biology, Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Andrew J Lucke
- Division of Chemistry and Structural Biology, Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
| | - David P Fairlie
- Division of Chemistry and Structural Biology, Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia.
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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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Chen L, Li J, Wu L, Yang M, Gao F, Yuan L. Synergistic actions of olomoucine and bone morphogenetic protein-4 in axonal repair after acute spinal cord contusion. Neural Regen Res 2014; 9:1830-8. [PMID: 25422646 PMCID: PMC4239774 DOI: 10.4103/1673-5374.143431] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/22/2014] [Indexed: 01/10/2023] Open
Abstract
To determine whether olomoucine acts synergistically with bone morphogenetic protein-4 in the treatment of spinal cord injury, we established a rat model of acute spinal cord contusion by impacting the spinal cord at the T8 vertebra. We injected a suspension of astrocytes derived from glial-restricted precursor cells exposed to bone morphogenetic protein-4 (GDAsBMP) into the spinal cord around the site of the injury, and/or olomoucine intraperitoneally. Olomoucine effectively inhibited astrocyte proliferation and the formation of scar tissue at the injury site, but did not prevent proliferation of GDAsBMP or inhibit their effects in reducing the spinal cord lesion cavity. Furthermore, while GDAsBMP and olomoucine independently resulted in small improvements in locomotor function in injured rats, combined administration of both treatments had a significantly greater effect on the restoration of motor function. These data indicate that the combined use of olomoucine and GDAsBMP creates a better environment for nerve regeneration than the use of either treatment alone, and contributes to spinal cord repair after injury.
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Affiliation(s)
- Liang Chen
- Capital Medical University School of Rehabilitation Medicine, Beijing, China ; Department of Spinal and Neural Function Reconstruction, China Rehabilitation Research Center, Beijing, China
| | - Jianjun Li
- Capital Medical University School of Rehabilitation Medicine, Beijing, China ; Department of Spinal and Neural Function Reconstruction, China Rehabilitation Research Center, Beijing, China ; Center of Neural Injury and Repair, Beijing Institute for Brain Disorders, Beijing, China
| | - Liang Wu
- Rehabilitation Center, Beijing Xiaotangshan Rehabilitation Hospital, Beijing, China
| | - Mingliang Yang
- Capital Medical University School of Rehabilitation Medicine, Beijing, China ; Department of Spinal and Neural Function Reconstruction, China Rehabilitation Research Center, Beijing, China ; Center of Neural Injury and Repair, Beijing Institute for Brain Disorders, Beijing, China
| | - Feng Gao
- Capital Medical University School of Rehabilitation Medicine, Beijing, China ; Department of Spinal and Neural Function Reconstruction, China Rehabilitation Research Center, Beijing, China
| | - Li Yuan
- Department of General Surgery, China Rehabilitation Research Center, Beijing, China
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40
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Chen H, Zhao Y, Li H, Zhang D, Huang Y, Shen Q, Van Duyne R, Kashanchi F, Zeng C, Liu S. Break CDK2/Cyclin E1 interface allosterically with small peptides. PLoS One 2014; 9:e109154. [PMID: 25290691 PMCID: PMC4188581 DOI: 10.1371/journal.pone.0109154] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2014] [Accepted: 09/03/2014] [Indexed: 02/07/2023] Open
Abstract
Most inhibitors of Cyclin-dependent kinase 2 (CDK2) target its ATP-binding pocket. It is difficult, however, to use this pocket to design very specific inhibitors because this catalytic pocket is highly conserved in the protein family of CDKs. Here we report some short peptides targeting a noncatalytic pocket near the interface of the CDK2/Cyclin complex. Docking and molecular dynamics simulations were used to select the peptides, and detailed dynamical network analysis revealed that these peptides weaken the complex formation via allosteric interactions. Our experiments showed that upon binding to the noncatalytic pocket, these peptides break the CDK2/Cyclin complex partially and diminish its kinase activity in vitro. The binding affinity of these peptides measured by Surface Plasmon Resonance can reach as low as 0.5 µM.
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Affiliation(s)
- Hao Chen
- Department of Physics, The George Washington University, Washington, D. C., United States of America
| | - Yunjie Zhao
- Department of Physics, The George Washington University, Washington, D. C., United States of America
| | - Haotian Li
- Department of Physics, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Dongyan Zhang
- Department of Physics, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Yanzhao Huang
- Department of Physics, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Qi Shen
- BNLMS, Center for Quantitative Biology, Peking University, Beijing, China
| | - Rachel Van Duyne
- George Mason University, National Center for Biodefense & Infectious Diseases, Manassas, Virginia, United States of America
- The George Washington University Medical Center, Department of Microbiology, Immunology, and Tropical Medicine, Washington, D. C., United States of America
| | - Fatah Kashanchi
- George Mason University, National Center for Biodefense & Infectious Diseases, Manassas, Virginia, United States of America
| | - Chen Zeng
- Department of Physics, Huazhong University of Science and Technology, Wuhan, Hubei, China
- Department of Physics, The George Washington University, Washington, D. C., United States of America
| | - Shiyong Liu
- Department of Physics, Huazhong University of Science and Technology, Wuhan, Hubei, China
- * E-mail:
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41
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Fluorescent biosensors for drug discovery new tools for old targets--screening for inhibitors of cyclin-dependent kinases. Eur J Med Chem 2014; 88:74-88. [PMID: 25314935 DOI: 10.1016/j.ejmech.2014.10.003] [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: 08/05/2014] [Revised: 09/29/2014] [Accepted: 10/01/2014] [Indexed: 12/12/2022]
Abstract
Cyclin-dependent kinases play central roles in regulation of cell cycle progression, transcriptional regulation and other major biological processes such as neuronal differentiation and metabolism. These kinases are hyperactivated in most human cancers and constitute attractive pharmacological targets. A large number of ATP-competitive inhibitors of CDKs have been identified from natural substances, in high throughput screening assays, or through structure-guided approaches. Alternative strategies have been explored to target essential protein/protein interfaces and screen for allosteric inhibitors that trap inactive intermediates or prevent conformational activation. However this remains a major challenge given the highly conserved structural features of these kinases, and calls for new and alternative screening technologies. Fluorescent biosensors constitute powerful tools for the detection of biomolecules in complex biological samples, and are well suited to study dynamic processes and highlight molecular alterations associated with pathological disorders. They further constitute sensitive and selective tools which can be readily implemented to high throughput and high content screens in drug discovery programmes. Our group has developed fluorescent biosensors to probe cyclin-dependent kinases and gain insight into their molecular behaviour in vitro and in living cells. These tools provide a means of monitoring subtle alterations in the abundance and activity of CDK/Cyclins and can respond to compounds that interfere with the conformational dynamics of these kinases. In this review we discuss the different strategies which have been devised to target CDK/Cyclins, and describe the implementation of our CDK/Cyclin biosensors to develop HTS/HCS assays in view of identifying new classes of inhibitors for cancer therapeutics.
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Gold(I)-triphenylphosphine complexes with hypoxanthine-derived ligands: in vitro evaluations of anticancer and anti-inflammatory activities. PLoS One 2014; 9:e107373. [PMID: 25226034 PMCID: PMC4167326 DOI: 10.1371/journal.pone.0107373] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2014] [Accepted: 08/11/2014] [Indexed: 01/19/2023] Open
Abstract
A series of gold(I) complexes involving triphenylphosphine (PPh3) and one N-donor ligand derived from deprotonated mono- or disubstituted hypoxanthine (HLn) of the general composition [Au(Ln)(PPh3)] (1–9) is reported. The complexes were thoroughly characterized, including multinuclear high resolution NMR spectroscopy as well as single crystal X-ray analysis (for complexes 1 and 3). The complexes were screened for their invitro cytotoxicity against human cancer cell lines MCF7 (breast carcinoma), HOS (osteosarcoma) and THP-1 (monocytic leukaemia), which identified the complexes 4–6 as the most promising representatives, who antiproliferative activity was further tested against A549 (lung adenocarcinoma), G-361 (melanoma), HeLa (cervical cancer), A2780 (ovarian carcinoma), A2780R (ovarian carcinoma resistant to cisplatin), 22Rv1 (prostate cancer) cell lines. Complexes 4–6 showed a significantly higher invitro anticancer effect against the employed cancer cells, except for G-361, as compared with the commercially used anticancer drug cisplatin, with IC50 ≈ 1–30 µM. Anti-inflammatory activity was evaluated invitro by the assessment of the ability of the complexes to modulate secretion of the pro-inflammatory cytokines, i.e. tumour necrosis factor-α (TNF-α) and interleukin-1β (IL-1β), in the lipopolysaccharide-activated macrophage-like THP-1 cell model. The results of this study identified the complexes as auspicious anti-inflammatory agents with similar or better activity as compared with the clinically applied gold-based antiarthritic drug Auranofin. In an effort to explore the possible mechanisms responsible for the biological effect, the products of interactions of selected complexes with sulfur-containing biomolecules (L-cysteine and reduced glutathione) were studied by means of the mass-spectrometry study.
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One-pot synthesis and antiproliferative activity of novel 2,4-diaminopyrimidine derivatives bearing piperidine and piperazine moieties. Eur J Med Chem 2014; 84:127-34. [DOI: 10.1016/j.ejmech.2014.07.017] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2014] [Revised: 06/10/2014] [Accepted: 07/06/2014] [Indexed: 02/06/2023]
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44
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Cytotoxicity, antioxidant and glutathione S-transferase inhibitory activity of palladium(II) chloride complexes bearing nucleobase ligands. TRANSIT METAL CHEM 2014. [DOI: 10.1007/s11243-014-9848-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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45
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Holcakova J, Muller P, Tomasec P, Hrstka R, Nekulova M, Krystof V, Strnad M, Wilkinson GWG, Vojtesek B. Inhibition of post-transcriptional RNA processing by CDK inhibitors and its implication in anti-viral therapy. PLoS One 2014; 9:e89228. [PMID: 24586613 PMCID: PMC3931720 DOI: 10.1371/journal.pone.0089228] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2013] [Accepted: 01/17/2014] [Indexed: 01/31/2023] Open
Abstract
Cyclin-dependent kinases (CDKs) are key regulators of the cell cycle and RNA polymerase II mediated transcription. Several pharmacological CDK inhibitors are currently in clinical trials as potential cancer therapeutics and some of them also exhibit antiviral effects. Olomoucine II and roscovitine, purine-based inhibitors of CDKs, were described as effective antiviral agents that inhibit replication of a broad range of wild type human viruses. Olomoucine II and roscovitine show high selectivity for CDK7 and CDK9, with important functions in the regulation of RNA polymerase II transcription. RNA polymerase II is necessary for viral transcription and following replication in cells. We analyzed the effect of inhibition of CDKs by olomoucine II on gene expression from viral promoters and compared its effect to widely-used roscovitine. We found that both roscovitine and olomoucine II blocked the phosphorylation of RNA polymerase II C-terminal domain. However the repression of genes regulated by viral promoters was strongly dependent on gene localization. Both roscovitine and olomoucine II inhibited expression only when the viral promoter was not integrated into chromosomal DNA. In contrast, treatment of cells with genome-integrated viral promoters increased their expression even though there was decreased phosphorylation of the C-terminal domain of RNA polymerase II. To define the mechanism responsible for decreased gene expression after pharmacological CDK inhibitor treatment, the level of mRNA transcription from extrachromosomal DNA was determined. Interestingly, our results showed that inhibition of RNA polymerase II C-terminal domain phosphorylation increased the number of transcribed mRNAs. However, some of these mRNAs were truncated and lacked polyadenylation, which resulted in decreased translation. These results suggest that phosphorylation of RNA polymerase II C-terminal domain is critical for linking transcription and posttrancriptional processing of mRNA expressed from extrachromosomal DNA.
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Affiliation(s)
- Jitka Holcakova
- Regional Centre for Applied Molecular Oncology, Masaryk Memorial Cancer Institute, Brno, Czech Republic
| | - Petr Muller
- Regional Centre for Applied Molecular Oncology, Masaryk Memorial Cancer Institute, Brno, Czech Republic
| | - Peter Tomasec
- School of Medicine, Cardiff University, Cardiff, United Kingdom
| | - Roman Hrstka
- Regional Centre for Applied Molecular Oncology, Masaryk Memorial Cancer Institute, Brno, Czech Republic
| | - Marta Nekulova
- Regional Centre for Applied Molecular Oncology, Masaryk Memorial Cancer Institute, Brno, Czech Republic
| | - Vladimir Krystof
- Laboratory of Growth Regulators, Faculty of Science, Palacky University, Olomouc, Czech Republic
- Institute of Experimental Botany AS CR, Olomouc, Czech Republic
| | - Miroslav Strnad
- Laboratory of Growth Regulators, Faculty of Science, Palacky University, Olomouc, Czech Republic
- Institute of Experimental Botany AS CR, Olomouc, Czech Republic
| | | | - Borivoj Vojtesek
- Regional Centre for Applied Molecular Oncology, Masaryk Memorial Cancer Institute, Brno, Czech Republic
- * E-mail:
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Carbain B, Paterson DJ, Anscombe E, Campbell AJ, Cano C, Echalier A, Endicott JA, Golding BT, Haggerty K, Hardcastle IR, Jewsbury PJ, Newell DR, Noble MEM, Roche C, Wang LZ, Griffin RJ. 8-Substituted O(6)-cyclohexylmethylguanine CDK2 inhibitors: using structure-based inhibitor design to optimize an alternative binding mode. J Med Chem 2014; 57:56-70. [PMID: 24304238 DOI: 10.1021/jm401555v] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Evaluation of the effects of purine C-8 substitution within a series of CDK1/2-selective O(6)-cyclohexylmethylguanine derivatives revealed that potency decreases initially with increasing size of the alkyl substituent. Structural analysis showed that C-8 substitution is poorly tolerated, and to avoid unacceptable steric interactions, these compounds adopt novel binding modes. Thus, 2-amino-6-cyclohexylmethoxy-8-isopropyl-9H-purine adopts a "reverse" binding mode where the purine backbone has flipped 180°. This provided a novel lead chemotype from which we have designed more potent CDK2 inhibitors using, in the first instance, quantum mechanical energy calculations. Introduction of an ortho-tolyl or ortho-chlorophenyl group at the purine C-8 position restored the potency of these "reverse" binding mode inhibitors to that of the parent 2-amino-6-cyclohexylmethoxy-9H-purine. By contrast, the corresponding 8-(2-methyl-3-sulfamoylphenyl)-purine derivative exhibited submicromolar CDK2-inhibitory activity by virtue of engineered additional interactions with Asp86 and Lys89 in the reversed binding mode, as confirmed by X-ray crystallography.
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Affiliation(s)
- Benoit Carbain
- Department of Biochemistry, University of Oxford , South Parks Road, Oxford OX1 3QU, U.K
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Adasme-Carreño F, Muñoz-Gutierrez C, Caballero J, Alzate-Morales JH. Performance of the MM/GBSA scoring using a binding site hydrogen bond network-based frame selection: the protein kinase case. Phys Chem Chem Phys 2014; 16:14047-58. [DOI: 10.1039/c4cp01378f] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Conformational clustering using hydrogen bond network analysis improved the MM/GBSA scoring for some protein-kinase–ligand systems used as case studies.
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Affiliation(s)
- Francisco Adasme-Carreño
- Centro de Bioinformática y Simulación Molecular (CBSM)
- Escuela de Ingeniería en Bioinformática
- Facultad de Ingeniería
- Universidad de Talca
- Talca, Chile
| | - Camila Muñoz-Gutierrez
- Centro de Bioinformática y Simulación Molecular (CBSM)
- Escuela de Ingeniería en Bioinformática
- Facultad de Ingeniería
- Universidad de Talca
- Talca, Chile
| | - Julio Caballero
- Centro de Bioinformática y Simulación Molecular (CBSM)
- Escuela de Ingeniería en Bioinformática
- Facultad de Ingeniería
- Universidad de Talca
- Talca, Chile
| | - Jans H. Alzate-Morales
- Centro de Bioinformática y Simulación Molecular (CBSM)
- Escuela de Ingeniería en Bioinformática
- Facultad de Ingeniería
- Universidad de Talca
- Talca, Chile
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48
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Yuan H, Liu H, Tai W, Wang F, Zhang Y, Yao S, Ran T, Lu S, Ke Z, Xiong X, Xu J, Chen Y, Lu T. Molecular modelling on small molecular CDK2 inhibitors: an integrated approach using a combination of molecular docking, 3D-QSAR and pharmacophore modelling. SAR AND QSAR IN ENVIRONMENTAL RESEARCH 2013; 24:795-817. [PMID: 23941641 DOI: 10.1080/1062936x.2013.815655] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Cyclin-dependent kinase 2 (CDK2) has been identified as an important target for developing novel anticancer agents. Molecular docking, three-dimensional quantitative structure-activity relationship (3D-QSAR) and pharmacophore modelling were combined with the ultimate goal of studying the structure-activity relationship of CDK2 inhibitors. The comparative molecular similarity indices analysis (CoMSIA) model constructed based on a set of 3-aminopyrazole derivatives as CDK2 inhibitors gave statistically significant results (q (2) = 0.700; r (2) = 0.982). A HypoGen pharmacophore model, constructed using diverse CDK2 inhibitors, also showed significant statistics ([Formula: see text]Cost = 61.483; RMSD = 0.53; Correlation coefficient = 0.98). The small residues and error values between the estimated and experimental activities of the training and test set compounds proved their strong capability of activity prediction. The structural insights obtained from these two models were consistent with each other. The pharmacophore model summarized the important pharmacophoric features required for protein-ligand binding. The 3D contour maps in combination with the comprehensive pharmacophoric features helped to better interpret the structure-activity relationship. The results will be beneficial for the discovery and design of novel CDK2 inhibitors. The simplicity of this approach provides expansion to its applicability in optimizing other classes of small molecular CDK2 inhibitors.
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Affiliation(s)
- H Yuan
- a Laboratory of Molecular Design and Drug Discovery, School of Science, China Pharmaceutical University , Nanjing , China
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49
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Boschi D, Tosco P, Chandra N, Chaurasia S, Fruttero R, Griffin R, Wang LZ, Gasco A. 6-Cyclohexylmethoxy-5-(cyano-NNO-azoxy)pyrimidine-4-amine: A new scaffold endowed with potent CDK2 inhibitory activity. Eur J Med Chem 2013; 68:333-8. [DOI: 10.1016/j.ejmech.2013.07.031] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2013] [Revised: 06/06/2013] [Accepted: 07/17/2013] [Indexed: 11/29/2022]
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50
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Procházková E, Čechová L, Janeba Z, Dračínský M. A Switchable Intramolecular Hydrogen Bond in Polysubstituted 5-Nitrosopyrimidines. J Org Chem 2013; 78:10121-33. [DOI: 10.1021/jo401441z] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Affiliation(s)
- Eliška Procházková
- Institute of Organic Chemistry
and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo
nam. 2, 166 10 Prague, Czech Republic
| | - Lucie Čechová
- Institute of Organic Chemistry
and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo
nam. 2, 166 10 Prague, Czech Republic
| | - Zlatko Janeba
- Institute of Organic Chemistry
and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo
nam. 2, 166 10 Prague, Czech Republic
| | - Martin Dračínský
- Institute of Organic Chemistry
and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo
nam. 2, 166 10 Prague, Czech Republic
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