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Wu S, Wu Y, Deng S, Lei X, Yang X. Emerging roles of noncoding RNAs in human cancers. Discov Oncol 2023; 14:128. [PMID: 37439905 DOI: 10.1007/s12672-023-00728-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Accepted: 06/14/2023] [Indexed: 07/14/2023] Open
Abstract
Studies have found that RNA encoding proteins only account for a small part of the total number, most RNA is non-coding RNA, and non-coding RNA may affect the occurrence and development of human cancers by affecting gene expression, therefore play an important role in human pathology. At present, ncRNAs studied include miRNA, circRNA, lncRNA, piRNA, and snoRNA, etc. After decades of research, the basic role of these ncRNAs in many cancers has been clear. As far as we know, the role of miRNAs in cancer is one of the hottest research directions, however, it is also found that the imbalance of ncRNAs will affect the occurrence of gastric cancer, breast cancer, lung cancer, meanwhile, it may also affect the prognosis of these cancers. Therefore, the study of ncRNAs in cancers may help to find new cancer diagnostic and treatment methods. Here, we reviewed the biosynthesis and characteristics of miRNA, cricRNA, and lncRNA etc., their roles in human cancers, as well as the mechanism through which these ncRNAs affect human cancers.
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Affiliation(s)
- Shijie Wu
- School of Pharmaceutical Science, Hengyang Medical College, University of South China, 28 Western Changsheng Road, Hengyang, 421001, Hunan, People's Republic of China
| | - Yiwen Wu
- School of Pharmaceutical Science, Hengyang Medical College, University of South China, 28 Western Changsheng Road, Hengyang, 421001, Hunan, People's Republic of China
| | - Sijun Deng
- School of Pharmaceutical Science, Hengyang Medical College, University of South China, 28 Western Changsheng Road, Hengyang, 421001, Hunan, People's Republic of China
| | - Xiaoyong Lei
- School of Pharmaceutical Science, Hengyang Medical College, University of South China, 28 Western Changsheng Road, Hengyang, 421001, Hunan, People's Republic of China
- Hunan Provincial Key Laboratory of Tumor Microenvironment Responsive Drug Research, University of South China, 28 Western Changsheng Road, Hengyang, 421001, Hunan, People's Republic of China
| | - Xiaoyan Yang
- School of Pharmaceutical Science, Hengyang Medical College, University of South China, 28 Western Changsheng Road, Hengyang, 421001, Hunan, People's Republic of China.
- Hunan Provincial Key Laboratory of Tumor Microenvironment Responsive Drug Research, University of South China, 28 Western Changsheng Road, Hengyang, 421001, Hunan, People's Republic of China.
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2
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Hou W, Dai W, Huang H, Liu SL, Liu J, Huang LJ, Huang XH, Zeng JL, Gan ZW, Zhang ZY, Lan JX. Pharmacological activity and mechanism of pyrazines. Eur J Med Chem 2023; 258:115544. [PMID: 37300915 DOI: 10.1016/j.ejmech.2023.115544] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2023] [Revised: 05/25/2023] [Accepted: 06/03/2023] [Indexed: 06/12/2023]
Abstract
Heterocycles are common in the structure of drugs used clinically to deal with diseases. Such drugs usually contain nitrogen, oxygen and sulfur, which possess electron-accepting capacity and can form hydrogen bonds. These properties often bring enhanced target binding ability to these compounds when compared to alkanes. Pyrazine is a nitrogen-containing six-membered heterocyclic ring and many of its derivatives are identified as bioactive molecules. We review here the most active pyrazine compounds in terms of their structure, activity in vitro and in vivo (mainly antitumor activity) and the reported mechanisms of action. References have been downloaded through Web of Science, PubMed, Science Direct, Google Scholar and SciFinder Scholar. Publications reporting only the chemistry of pyrazine derivatives are beyond the scope of this review and have not been included. We found that compounds in which a pyrazine ring was fused into other heterocycles especially pyrrole or imidazole were the highly studied pyrazine derivatives, whose antineoplastic activity had been widely investigated. To the best of our knowledge, this is the first review of pyrazine derivatives and their bioactivity, especially their antitumor activity. This review should be useful for those engaged in development of medications based on heterocyclic compounds especially those based on pyrazine.
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Affiliation(s)
- Wen Hou
- College of Pharmacy, Gannan Medical University, Ganzhou, 341000, PR China
| | - Wei Dai
- College of Pharmacy, Gannan Medical University, Ganzhou, 341000, PR China
| | - Hao Huang
- College of Pharmacy, Gannan Medical University, Ganzhou, 341000, PR China
| | - Sheng-Lan Liu
- College of Pharmacy, Gannan Medical University, Ganzhou, 341000, PR China
| | - Jun Liu
- College of Pharmacy, Jinan University, Guangzhou, 510632, PR China
| | - Le-Jun Huang
- College of Rehabilitation, Gannan Medical University, Ganzhou, 341000, PR China
| | - Xian-Hua Huang
- College of Pharmacy, Gannan Medical University, Ganzhou, 341000, PR China
| | - Jun-Lin Zeng
- HuanKui Academy, Nanchang University, Nanchang, 330006, PR China
| | - Zhi-Wei Gan
- College of Pharmacy, Gannan Medical University, Ganzhou, 341000, PR China
| | - Zhen-Yu Zhang
- College of Pharmacy, Gannan Medical University, Ganzhou, 341000, PR China
| | - Jin-Xia Lan
- College of Public Health and Health Management, Gannan Medical University, Ganzhou, 341000, PR China.
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3
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Gangarapu NR, Ranganatham A, Reddy EK, Yellappa S, Chandrasekhar KB. 2-Aminoaryl-3,5-diaryl pyrazines: Synthesis, biological evaluation against Mycobacterium tuberculosis and docking studies. Arch Pharm (Weinheim) 2020; 353:e1900368. [PMID: 32399980 DOI: 10.1002/ardp.201900368] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2019] [Revised: 04/16/2020] [Accepted: 04/22/2020] [Indexed: 11/10/2022]
Abstract
Rationally designed Mycobacterium tuberculosis (Mtb) inhibitors were synthesized under Buchwald conditions using Pd2 (dba)3 /xantphos and the compounds were investigated for their biological activity against the Mtb standard strain H37Rv and two other clinically isolated multidrug-resistant strains with different drug resistance patterns. Compounds 5e, 6e, 7e, and 8e exhibited excellent antituberculosis activity against H37Rv with a minimum inhibitory concentration (MIC) value of 15 μg/ml. Compounds 5a, 6c, 7b, 8a, 8b, and 8d also displayed their potency with a MIC value in the range of 15-25 μg/ml. In addition to the Mtb studies, compounds 4e, 5e, 7e, and 8e were tested for cytotoxicity on HEK-293 cells and compounds 7e and 8e were identified to have low toxicities of up to 200 and 300 μM, respectively. The synthesized compounds docked with the 2FUM protein of Mtb and the docking studies revealed that compounds 5e, 6e, 7e, and 8e can bind strongly in the active site of the enzyme and showed binding energies of -9.62, -10.7, -11.48, and -12.06 kcal/mol, respectively. Compound 7e forms four hydrogen bonds, whereas compound 8e forms five hydrogen bonds with amino acids, respectively. Based on these results, compounds 7e and 8e might be considered potential lead compounds with good anti-Mtb potency.
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Affiliation(s)
- Nagaraja Reddy Gangarapu
- Department of Chemistry, Bangalore University, Bengaluru, Karnataka, India.,Department of Chemistry, Jawaharlal Nehru Technological University, Ananthapuramu, Andhra Pradesh, India
| | - Archakam Ranganatham
- Laboratory Division, National Tuberculosis Institute, Bangalore, Karnataka, India
| | - Eeda Koti Reddy
- Department of Science and Humanities, Division of Chemistry, Vignan's Foundation for Science, Technology and Research-VFSTR (Deemed to be University), Guntur, Andhra Pradesh, India
| | - Shivaraj Yellappa
- Department of Chemistry, Bangalore University, Bengaluru, Karnataka, India
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Mansi I, Al-Sha'er MA, Mhaidat N, Taha M. Ligand Based Pharmacophore Modeling Followed by Biological Screening Lead to Discovery of Novel PDK1 Inhibitors as Anticancer Agents. Anticancer Agents Med Chem 2020; 20:476-485. [PMID: 31889497 DOI: 10.2174/1871520620666191224110600] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2019] [Revised: 08/21/2019] [Accepted: 10/22/2019] [Indexed: 11/22/2022]
Abstract
BACKGROUND Phosphoinositide-Dependent Kinase-1 (PDK1) is a serine/threonine kinase, which belongs to AGC kinase family required by cancer cells. METHODS Pharmacophoric space of 86 PDK1 inhibitors using six diverse sets of inhibitors was explored to identify high-quality pharmacophores. The best combination of pharmacophoric models and physicochemical descriptors was selected by genetic algorithm-based QSAR analysis that can elucidate the variation of bioactivity within the training inhibitors. Two successful orthogonal pharmacophores emerged in the optimum QSAR equation (r2 69 = 0.90, r2 LOO= 0.86, F= 51.92, r2 PRESS against 17 test inhibitors = 0.79). Receiver Operating Characteristic (ROC) curve analyses were used to estimate the QSAR-selected pharmacophores. RESULTS 5 out of 11 compounds tested had shown potential intracellular PDK1 inhibition with the highest inhibition percent for compounds 92 and 93 as follows; 90 and 92% PDK1 inhibition, respectively. CONCLUSION PDK1 inhibitors are potential anticancer agents that can be discovered by combination method of ligand based design with QSAR and ROC analysis.
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Affiliation(s)
- Iman Mansi
- Faculty of Pharmaceutical Sciences, The Hashemite University, P.O. Box 330127 Zarqa, 13133, Jordan
| | | | - Nizar Mhaidat
- Clinical Pharmacy Department, Faculty of Pharmacy, Jordan University of Science & Technology, Irbid, Jordan
| | - Mutasem Taha
- Drug Design Center, Faculty of Pharmacy, University of Jordan, Amman, Jordan
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5
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Yu T, Wang Y, Fan Y, Fang N, Wang T, Xu T, Shu Y. CircRNAs in cancer metabolism: a review. J Hematol Oncol 2019; 12:90. [PMID: 31484561 PMCID: PMC6727394 DOI: 10.1186/s13045-019-0776-8] [Citation(s) in RCA: 269] [Impact Index Per Article: 53.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2019] [Accepted: 08/16/2019] [Indexed: 12/17/2022] Open
Abstract
Altered energy metabolism is a hallmark of tumors aiming at supplying necessary nutrients for tumorigenesis and development. These redirected metabolic pathways associated with carbohydrate, lipid and amino acid are orchestrated not only by carcinogenic proteins but by non-coding RNAs. Among them, circular RNA (circRNA), as a kind of novel identified non-coding RNAs, has become the focus of attention. Through binding with corresponding microRNAs or directly contacting proteins, circRNA plays a primarily important role in regulating cellular metabolism. Herein, we analyze the emerging findings and select circRNAs contributing to mutant glycolysis, lipogenesis and lipolysis, glutam inolysis, and oxidative respiration to deepen the understanding about the cancer metabolic regulatory network. In addition, we also discuss the possibility of circRNAs exerting their functions via exosomes and cancer stem cells. Owing to their unique structures and wide impacts, circRNAs may help reap huge fruits in developing clinical treatments targeting cancer metabolism.
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Affiliation(s)
- Tao Yu
- Department of Oncology, First Affiliated Hospital of Nanjing Medical University, #300 Guangzhou Road, Nanjing, 210029, China
| | - Yanfen Wang
- Department of Pathology, The Affiliated Hospital of Yangzhou University, Yangzhou, 225000, China
| | - Yu Fan
- Cancer Institute, The Affiliated People's Hospital of Jiangsu University, Zhenjiang, 212002, China
| | - Na Fang
- Cancer Institute, The Affiliated People's Hospital of Jiangsu University, Zhenjiang, 212002, China
| | - Tongshan Wang
- Department of Oncology, First Affiliated Hospital of Nanjing Medical University, #300 Guangzhou Road, Nanjing, 210029, China
| | - Tongpeng Xu
- Department of Oncology, First Affiliated Hospital of Nanjing Medical University, #300 Guangzhou Road, Nanjing, 210029, China.
| | - Yongqian Shu
- Department of Oncology, First Affiliated Hospital of Nanjing Medical University, #300 Guangzhou Road, Nanjing, 210029, China.
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6
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Mansi IA, Al-Sha'er MA, Mhaidat NM, Taha MO, Shahin R. Investigation of Binding Characteristics of Phosphoinositide-dependent Kinase-1 (PDK1) Co-crystallized Ligands Through Virtual Pharmacophore Modeling Leading to Novel Anti-PDK1 Hits. Med Chem 2019; 16:860-880. [PMID: 31339076 DOI: 10.2174/1573406415666190724131048] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2019] [Revised: 07/11/2019] [Accepted: 07/11/2019] [Indexed: 11/22/2022]
Abstract
BACKGROUND 3-Phosphoinositide Dependent Protein Kinase-1 (PDK1) is being lately considered as an attractive and forthcoming anticancer target. A Protein Data Bank (PDB) cocrystallized crystal provides not only rigid theoretical data but also a realistic molecular recognition data that can be explored and used to discover new hits. OBJECTIVE This incited us to investigate the co-crystallized ligands' contacts inside the PDK1 binding pocket via a structure-based receptor-ligand pharmacophore generation technique in Discovery Studio 4.5 (DS 4.5). METHODS Accordingly, 35 crystals for PDK1 were collected and studied. Every single receptorligand interaction was validated and the significant ones were converted into their corresponding pharmacophoric features. The generated pharmacophores were scored by the Receiver Operating Characteristic (ROC) curve analysis. RESULTS Consequently, 169 pharmacophores were generated and sorted, 11 pharmacophores acquired good ROC-AUC results of 0.8 and a selectivity value above 8. Pharmacophore 1UU3_2_01 was used in particular as a searching filter to screen NCI database because of its acceptable validity criteria and its distinctive positive ionizable feature. Several low micromolar PDK1 inhibitors were revealed. The most potent hit illustrated anti-PDK1 IC50 values of 200 nM with 70% inhibition against SW480 cell lines. CONCLUSION Eventually, the active hits were docked inside the PDK1 binding pocket and the recognition points between the active hits and the receptor were analyzed that led to the discovery of new scaffolds as potential PDK1 inhibitors.
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Affiliation(s)
- Iman A Mansi
- Faculty of Pharmaceutical Sciences, The Hashemite University, P.O. Box 330127 Zarqa, 13133 Jordan
| | | | - Nizar M Mhaidat
- Clinical Pharmacy Department, Faculty of Pharmacy, Jordan University of Science & Technology, Irbid, Jordan
| | - Mutasem O Taha
- Drug Design Center, Faculty of Pharmacy, University of Jordan, Amman, Jordan,Faculty of Pharmacy, Applied Science University, Amman, Jordan
| | - Rand Shahin
- Faculty of Pharmaceutical Sciences, The Hashemite University, P.O. Box 330127 Zarqa, 13133 Jordan
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7
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Preparation and biological evaluation of quinoline amines as anticancer agents and its molecular docking. Med Chem Res 2019. [DOI: 10.1007/s00044-019-02374-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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8
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Connelly RL, Knowles JP, Booker-Milburn KI. A Rapid Synthetic Approach to the ABCD Core of the Stemona Alkaloids. Org Lett 2019; 21:18-21. [PMID: 30560676 DOI: 10.1021/acs.orglett.8b03371] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A new Lewis acid-assisted Brønsted acid cascade approach for the stereoselective formation of the tetracyclic Stemona alkaloid skeleton is described in five steps from epoxide 15. Crucially, this tetracyclic product can be accessed as either C13 epimer, potentially serving as intermediates for the synthesis of a range of Stemona alkaloids.
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Affiliation(s)
- Rickki L Connelly
- School of Chemistry , University of Bristol , Cantock's Close, Bristol BS8 1TS , U.K
| | - Jonathan P Knowles
- School of Chemistry , University of Bristol , Cantock's Close, Bristol BS8 1TS , U.K
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9
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Fragment-based design, synthesis, biological evaluation, and SAR of 1 H -benzo[ d ]imidazol-2-yl)-1 H -indazol derivatives as potent PDK1 inhibitors. Bioorg Med Chem Lett 2017; 27:5473-5480. [DOI: 10.1016/j.bmcl.2017.10.041] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2017] [Revised: 10/03/2017] [Accepted: 10/19/2017] [Indexed: 11/19/2022]
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10
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Rhodium-Catalyzed Asymmetric Hydrogenation of Tetrasubstituted Cyclic Enamides: Efficient Access to Chiral Cycloalkylamine Derivatives. Adv Synth Catal 2017. [DOI: 10.1002/adsc.201601135] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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11
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Musumeci F, Fallacara AL, Brullo C, Grossi G, Botta L, Calandro P, Chiariello M, Kissova M, Crespan E, Maga G, Schenone S. Identification of new pyrrolo[2,3-d]pyrimidines as Src tyrosine kinase inhibitors in vitro active against Glioblastoma. Eur J Med Chem 2016; 127:369-378. [PMID: 28076826 DOI: 10.1016/j.ejmech.2016.12.036] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2016] [Revised: 12/14/2016] [Accepted: 12/17/2016] [Indexed: 01/01/2023]
Abstract
In the last few years, several pyrrolo-pyrimidine derivatives have been either approved by the US FDA and in other countries for the treatment of different diseases or are currently in phase I/II clinical trials. Herein we present the synthesis and the characterization of a novel series of pyrrolo[2,3-d]pyrimidines, compounds 8a-j, and their activity against Glioblastoma multiforme (GBM). Docking studies and MM-GBSA analysis revealed the ability of such compounds to efficiently interact with the ATP binding site of Src. Enzymatic assays against a mini-panel of kinases (Src, Fyn, EGFR, Kit, Flt3, Abl, AblT315I) have been performed, showing an unexpected selectivity of our pyrrolo[2,3-d]pyrimidines for Src. Finally, the derivatives were tested for their antiproliferative potency on U87 GBM cell line. Compound 8h showed a considerable cytotoxicity effect against U87 cell line with an IC50 value of 7.1 μM.
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Affiliation(s)
- Francesca Musumeci
- Dipartimento di Farmacia, Università degli Studi di Genova, Viale Benedetto XV, 3, 16132 Genova, Italy
| | - Anna Lucia Fallacara
- Dipartimento di Biotecnologie, Chimica e Farmacia, Università degli Studi di Siena, Via Aldo Moro 2, 53100 Siena, Italy
| | - Chiara Brullo
- Dipartimento di Farmacia, Università degli Studi di Genova, Viale Benedetto XV, 3, 16132 Genova, Italy
| | - Giancarlo Grossi
- Dipartimento di Farmacia, Università degli Studi di Genova, Viale Benedetto XV, 3, 16132 Genova, Italy
| | - Lorenzo Botta
- Dipartimento di Farmacia, Università"Federico II" di Napoli, Via D. Montesano 49, 80131 Napoli, Italy
| | - Pierpaolo Calandro
- Dipartimento di Biotecnologie, Chimica e Farmacia, Università degli Studi di Siena, Via Aldo Moro 2, 53100 Siena, Italy
| | - Mario Chiariello
- Consiglio Nazionale delle Ricerche, Istituto di Fisiologia Clinica and Istituto Toscano Tumori, Core Research Laboratory, Via Fiorentina 1, 53100 Siena, Italy
| | - Miroslava Kissova
- Consiglio Nazionale delle Ricerche, Istituto di Genetica Molecolare, IGM-CNR, Via Abbiategrasso 207, 27100 Pavia, Italy
| | - Emmanuele Crespan
- Consiglio Nazionale delle Ricerche, Istituto di Genetica Molecolare, IGM-CNR, Via Abbiategrasso 207, 27100 Pavia, Italy
| | - Giovanni Maga
- Consiglio Nazionale delle Ricerche, Istituto di Genetica Molecolare, IGM-CNR, Via Abbiategrasso 207, 27100 Pavia, Italy
| | - Silvia Schenone
- Dipartimento di Farmacia, Università degli Studi di Genova, Viale Benedetto XV, 3, 16132 Genova, Italy.
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Weng SS, Zhang JW. N-Oxyl-Radical-Catalyzed Intermolecular Aminooxygenation of Styrenes and Inter/intramolecular Aminoalkoxylation of Homoallylic Alcohols. ChemCatChem 2016. [DOI: 10.1002/cctc.201601183] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Affiliation(s)
- Shiue-Shien Weng
- Department of Chemistry; ROC Military Academy; Kaohsiung 830 Taiwan ROC
| | - Jia-Wei Zhang
- Department of Chemistry; ROC Military Academy; Kaohsiung 830 Taiwan ROC
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13
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Wucherer-Plietker M, Merkul E, Müller TJ, Esdar C, Knöchel T, Heinrich T, Buchstaller HP, Greiner H, Dorsch D, Finsinger D, Calderini M, Bruge D, Grädler U. Discovery of novel 7-azaindoles as PDK1 inhibitors. Bioorg Med Chem Lett 2016; 26:3073-3080. [DOI: 10.1016/j.bmcl.2016.05.005] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2016] [Revised: 05/02/2016] [Accepted: 05/03/2016] [Indexed: 11/30/2022]
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14
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Molecular Background of miRNA Role in Asthma and COPD: An Updated Insight. BIOMED RESEARCH INTERNATIONAL 2016; 2016:7802521. [PMID: 27376086 PMCID: PMC4916273 DOI: 10.1155/2016/7802521] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/16/2016] [Revised: 04/29/2016] [Accepted: 05/15/2016] [Indexed: 12/14/2022]
Abstract
Inflammatory airway diseases are a significant health problems requiring new approaches to the existing therapies and addressing fundamental issues. Difficulties in developing effective therapeutic strategies might be caused by lack of understanding of their exact molecular mechanism. MicroRNAs (miRNAs) are a class of regulators that already revolutionized the view of gene expression regulation. A cumulating number of investigations show a pivotal role of miRNAs in the pathogenesis of asthma, chronic obstructive pulmonary disease (COPD), or airway remodeling through the regulation of many pathways involved in their pathogenesis. Expression changes of several miRNAs have also been found to play a role in the development and/or improvement in asthma or COPD. Still, relatively little is known about the role of miRNAs in inflammatory disorders. The microRNA profiles may differ depending on the cell type or antigen-presenting cell. Based on the newest literature, this review discusses the current knowledge concerning miRNA contribution and influence on lung inflammation and chosen inflammatory airway diseases: asthma and COPD.
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15
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Sestito S, Daniele S, Nesi G, Zappelli E, Di Maio D, Marinelli L, Digiacomo M, Lapucci A, Martini C, Novellino E, Rapposelli S. Locking PDK1 in DFG-out conformation through 2-oxo-indole containing molecules: Another tools to fight glioblastoma. Eur J Med Chem 2016; 118:47-63. [PMID: 27123901 DOI: 10.1016/j.ejmech.2016.04.003] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2016] [Revised: 04/01/2016] [Accepted: 04/02/2016] [Indexed: 01/05/2023]
Abstract
The phosphoinositide-dependent kinase-1 (PDK1) is one of the main components of the PI3K/Akt pathway. Also named the "master kinase" of the AGC family, PDK1 plays a critical role in tumorigenesis, by enhancing cell proliferation and inhibiting apoptosis, as well as in cell invasion and metastasis formation. Although there have been done huge efforts in discovering specific compounds targeting PDK1, nowadays no PDK1 inhibitor has yet entered the clinic. With the aim to pick out novel and potent PDK1 inhibitors, herein we report the design and synthesis of a new class of molecules obtained by merging the 2-oxo-indole nucleus with the 2-oxo-pyridonyl fragment, two moieties with high affinity for the PDK1 hinge region and its DFG-out binding site, respectively. To this purpose, a small series of compounds were synthesised and a tandem application of docking and Molecular Dynamic (MD) was employed to get insight into their mode of binding. The OXID-pyridonyl hybrid 8, possessing the lower IC50 (IC50 = 112 nM), was also tested against recombinant kinases involved in the PI3K/PDK1/Akt pathway and was subjected to vitro studies to evaluate the cytotoxicity and the inhibition of tumour cell migration. All together the results let us to consider 8, as a lead compound of a new generation of PDK1 inhibitors and encourage us to further studies in this direction.
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Affiliation(s)
- Simona Sestito
- Department of Pharmacy, University of Pisa, Via Bonanno, 6, 56126 Pisa, Italy
| | - Simona Daniele
- Department of Pharmacy, University of Pisa, Via Bonanno, 6, 56126 Pisa, Italy
| | - Giulia Nesi
- Department of Pharmacy, University of Pisa, Via Bonanno, 6, 56126 Pisa, Italy
| | - Elisa Zappelli
- Department of Pharmacy, University of Pisa, Via Bonanno, 6, 56126 Pisa, Italy
| | - Danilo Di Maio
- Scuola Normale Superiore, Piazza dei Cavalieri 7, I-56126 Pisa, Italy; Istituto Nazionale di Fisica Nucleare (INFN), Largo Bruno Pontecorvo 3, 56127 Pisa, Italy
| | | | - Maria Digiacomo
- Department of Pharmacy, University of Pisa, Via Bonanno, 6, 56126 Pisa, Italy
| | - Annalina Lapucci
- Department of Pharmacy, University of Pisa, Via Bonanno, 6, 56126 Pisa, Italy
| | - Claudia Martini
- Department of Pharmacy, University of Pisa, Via Bonanno, 6, 56126 Pisa, Italy
| | | | - Simona Rapposelli
- Department of Pharmacy, University of Pisa, Via Bonanno, 6, 56126 Pisa, Italy.
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16
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Liu Y, Yang K, Sun X, Fang P, Shi H, Xu J, Xie M, Li M. MiR-138 suppresses airway smooth muscle cell proliferation through the PI3K/AKT signaling pathway by targeting PDK1. Exp Lung Res 2015; 41:363-9. [PMID: 26151666 DOI: 10.3109/01902148.2015.1041581] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
BACKGROUND Airway smooth muscle cells (ASMCs) play important physiological roles in the lung, and their abnormal proliferation directly contributes to airway remodeling during development of lung diseases such as asthma. MicroRNAs are small yet versatile gene tuners that regulate a variety of cellular processes, including cell growth and proliferation, but little is known about the precise role of microRNAs in the proliferation of ASMCs. METHODS In this study, human ASMCs from asthmatic and non-asthmatic donors were used. MicroRNA and mRNA expression were measured by quantitative real-time PCR. Dual-luciferase reporter assays were performed to determine whether microRNA-138 (miR-138) binds directly to 3-phosphoinositide-dependent protein kinase-1(PDK1) 3' untranslated region (3'-UTR) to alter gene expression. RESULTS The results showed that overexpression of miR-138 reduced proliferation of human ASMCs, whereas inhibition of miR-138 increased proliferation of ASMCs. MiR-138 directly suppressed PDK1 expression by targeting the 3'-UTR of the gene. MiR-138 controls ASMC proliferation through directly inhibiting the phosphoinositide 3-kinase (PI3K) pathway. CONCLUSIONS Our study indicated that miR-138 regulation of PI3K signaling in ASMCs by altering the expression of PDK1 can have a profound impact on cell proliferation.
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Affiliation(s)
- Yun Liu
- a 1 Department of Respiratory Medicine, The Second Affiliated Hospital , Xi'an Jiaotong University Medical College , Xi'an, Shaanxi, China
| | - Kunzheng Yang
- b 2 Department of Gastroenterology Medicine , Xi'an Beifang Hospital , Xi'an, Shaanxi, China
| | - Xiuzhen Sun
- a 1 Department of Respiratory Medicine, The Second Affiliated Hospital , Xi'an Jiaotong University Medical College , Xi'an, Shaanxi, China
| | - Ping Fang
- a 1 Department of Respiratory Medicine, The Second Affiliated Hospital , Xi'an Jiaotong University Medical College , Xi'an, Shaanxi, China
| | - Hongyang Shi
- a 1 Department of Respiratory Medicine, The Second Affiliated Hospital , Xi'an Jiaotong University Medical College , Xi'an, Shaanxi, China
| | - Jing Xu
- a 1 Department of Respiratory Medicine, The Second Affiliated Hospital , Xi'an Jiaotong University Medical College , Xi'an, Shaanxi, China
| | - Mei Xie
- a 1 Department of Respiratory Medicine, The Second Affiliated Hospital , Xi'an Jiaotong University Medical College , Xi'an, Shaanxi, China
| | - Manxiang Li
- a 1 Department of Respiratory Medicine, The Second Affiliated Hospital , Xi'an Jiaotong University Medical College , Xi'an, Shaanxi, China
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17
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Kotasthane A, Mulakala C, Viswanadhan VN. Applying conformational selection theory to improve crossdocking efficiency in 3-phosphoinositide dependent protein kinase-1. Proteins 2013; 82:436-51. [PMID: 23999908 DOI: 10.1002/prot.24410] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2013] [Revised: 08/22/2013] [Accepted: 08/23/2013] [Indexed: 11/11/2022]
Abstract
The emerging picture of biomolecular recognition is that of conformational selection followed by induced-fit. Conformational selection theory states that binding partners exist in various conformations in solution, with binding involving a "selection" between complementary conformers. In this study, we devise a docking protocol that mimics conformational selection in protein-ligand binding and demonstrate that it significantly enhances crossdocking accuracy over Glide's flexible docking protocol, which is widely used in the pharmaceutical industry. Our protocol uses a pregenerated conformational ensemble to simulate ligand flexibility. The ensemble was generated by thorough conformational sampling coupled with conformer minimization. The generated conformers were then rigidly docked in the active site of the protein along with a postdocking minimization step that allows limited induced fit effects to be modeled for the ligand. We illustrate the improved performance of our protocol through crossdocking of 31 ligands to cocomplexed proteins of the kinase 3-phosphoinositide dependent protein kinase-1 extracted from the crystal structures 1H1W (ATP bound), 1OKY (staurosporine bound) and 3QD0 (bound to a potent inhibitor). Consistent with conformational selection theory, the performance of our protocol was the best for crossdocking to the cognate protein bound to the natural ligand, ATP.
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Affiliation(s)
- Anuja Kotasthane
- Department of Computational Chemistry, Jubilant Biosys Limited, Yeshwanthpur, Bangalore, 560 022, Karnataka, India
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18
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van Linden OPJ, Kooistra AJ, Leurs R, de Esch IJP, de Graaf C. KLIFS: a knowledge-based structural database to navigate kinase-ligand interaction space. J Med Chem 2013; 57:249-77. [PMID: 23941661 DOI: 10.1021/jm400378w] [Citation(s) in RCA: 203] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Protein kinases regulate the majority of signal transduction pathways in cells and have become important targets for the development of designer drugs. We present a systematic analysis of kinase-ligand interactions in all regions of the catalytic cleft of all 1252 human kinase-ligand cocrystal structures present in the Protein Data Bank (PDB). The kinase-ligand interaction fingerprints and structure database (KLIFS) contains a consistent alignment of 85 kinase ligand binding site residues that enables the identification of family specific interaction features and classification of ligands according to their binding modes. We illustrate how systematic mining of kinase-ligand interaction space gives new insights into how conserved and selective kinase interaction hot spots can accommodate the large diversity of chemical scaffolds in kinase ligands. These analyses lead to an improved understanding of the structural requirements of kinase binding that will be useful in ligand discovery and design studies.
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Affiliation(s)
- Oscar P J van Linden
- Division of Medicinal Chemistry, Faculty of Sciences, Amsterdam Institute for Molecules, Medicines and Systems (AIMMS), VU University Amsterdam , De Boelelaan 1083, 1081 HV Amsterdam, The Netherlands
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19
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Multitargeted molecular docking study of plant-derived natural products on phosphoinositide-3 kinase pathway components. Med Chem Res 2013. [DOI: 10.1007/s00044-013-0774-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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20
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Welker ME, Kulik G. Recent syntheses of PI3K/Akt/mTOR signaling pathway inhibitors. Bioorg Med Chem 2013; 21:4063-91. [PMID: 23735831 PMCID: PMC3711139 DOI: 10.1016/j.bmc.2013.04.083] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2013] [Accepted: 04/30/2013] [Indexed: 12/20/2022]
Abstract
This review focuses on the syntheses of PI3K/Akt/mTOR inhibitors that have been reported outside of the patent literature in the last 5years but is largely centered on synthetic work reported in 2011 and 2012. While focused on syntheses of inhibitors, some information on in vitro and in vivo testing of compounds is also included. Many of these reported compounds are reversible, competitive adenosine triphosphate (ATP) binding inhibitors, so given the structural similarities of many of these compounds to the adenine core, this review presents recent work on inhibitors based on where the synthetic chemistry was started, that is, inhibitor syntheses which started with purines/pyrimidines are followed by inhibitor syntheses which began with pyridines, pyrazines, azoles, and triazines then moves to inhibitors which bear no structural resemblance to adenine: liphagal, wortmannin and quercetin analogs. The review then finishes with a short section on recent syntheses of phosphotidyl inositol (PI) analogs since competitive PI binding inhibitors represent an alternative to the competitive ATP binding inhibitors which have received the most attention.
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Affiliation(s)
- Mark E Welker
- Department of Chemistry, Wake Forest University, PO Box 7486, Winston-Salem, NC 27109, USA.
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21
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Medina JR. Selective 3-Phosphoinositide-Dependent Kinase 1 (PDK1) Inhibitors: Dissecting the Function and Pharmacology of PDK1. J Med Chem 2013; 56:2726-37. [DOI: 10.1021/jm4000227] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Jesús R. Medina
- Oncology Research, GlaxoSmithKline, Collegeville, Pennsylvania 19426, United States
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22
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Baxi SM, Tan W, Murphy ST, Smeal T, Yin MJ. Targeting 3-phosphoinoside-dependent kinase-1 to inhibit insulin-like growth factor-I induced AKT and p70 S6 kinase activation in breast cancer cells. PLoS One 2012; 7:e48402. [PMID: 23119004 PMCID: PMC3485233 DOI: 10.1371/journal.pone.0048402] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2012] [Accepted: 09/25/2012] [Indexed: 12/15/2022] Open
Abstract
Binding of IGF to IGF-IR activates PI3K to generate PIP3 which in turn recruits and activates proteins that contain a pleckstrin homology (PH) domain, including AKT and PDK1. PDK1 is highly expressed in breast tumor samples and breast cancer cell lines. Here we demonstrate that targeting PDK1 with the potent and selective PDK1 inhibitor PF-5177624 in the IGF-PI3K pathway blocks breast cancer cell proliferation and transformation. Breast cancer cell lines MCF7 and T47D, representing the luminal ER positive subtype and harboring PIK3CA mutations, were most responsive to IGF-I induction resulting in upregulated AKT and p70S6K phosphorylation via PDK1 activation. PF-5177624 downregulated AKT and p70S6K phosphorylation, blocked cell cycle progression, and decreased cell proliferation and transformation to block IGFR-I induced activation in breast cancer cells. These results may provide insight into clinical strategies for developing an IGFR-I inhibitor and/or a PDK1 inhibitor in luminal breast cancer patients.
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Affiliation(s)
- Sangita M. Baxi
- Oncology Research, Pfizer Worldwide Research and Development, San Diego, California, United States of America
| | - Wei Tan
- Oncology Research, Pfizer Worldwide Research and Development, San Diego, California, United States of America
| | - Sean T. Murphy
- Medicinal Chemistry, Pfizer Worldwide Research and Development, San Diego, California, United States of America
| | - Tod Smeal
- Oncology Research, Pfizer Worldwide Research and Development, San Diego, California, United States of America
| | - Min-Jean Yin
- Oncology Research, Pfizer Worldwide Research and Development, San Diego, California, United States of America
- * E-mail:
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23
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Brandvold KR, Steffey ME, Fox CC, Soellner MB. Development of a highly selective c-Src kinase inhibitor. ACS Chem Biol 2012; 7:1393-8. [PMID: 22594480 DOI: 10.1021/cb300172e] [Citation(s) in RCA: 93] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Generating highly selective probes to interrogate protein kinase function in biological studies remains a challenge, and new strategies are required. Herein, we describe the development of the first highly selective and cell-permeable inhibitor of c-Src, a key signaling kinase in cancer. Our strategy involves extension of traditional inhibitor design by appending functionality proposed to interact with the phosphate-binding loop of c-Src. Using our selective inhibitor, we demonstrate that selective inhibition is significantly more efficacious than pan-kinase inhibition in slowing the growth of cancer cells. We also show that inhibition of c-Abl kinase, an off-target of most c-Src inhibitors, promotes oncogenic cell growth.
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Affiliation(s)
- Kristoffer R. Brandvold
- Department
of Medicinal Chemistry and ‡Department of Chemistry, University of Michigan, 930 N. University Avenue, Ann
Arbor, Michigan 48109, United States
| | - Michael E. Steffey
- Department
of Medicinal Chemistry and ‡Department of Chemistry, University of Michigan, 930 N. University Avenue, Ann
Arbor, Michigan 48109, United States
| | - Christel C. Fox
- Department
of Medicinal Chemistry and ‡Department of Chemistry, University of Michigan, 930 N. University Avenue, Ann
Arbor, Michigan 48109, United States
| | - Matthew B. Soellner
- Department
of Medicinal Chemistry and ‡Department of Chemistry, University of Michigan, 930 N. University Avenue, Ann
Arbor, Michigan 48109, United States
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24
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Bhola NE, Freilino ML, Joyce SC, Sen M, Thomas SM, Sahu A, Cassell A, Chen CS, Grandis JR. Antitumor mechanisms of targeting the PDK1 pathway in head and neck cancer. Mol Cancer Ther 2012; 11:1236-46. [PMID: 22491800 DOI: 10.1158/1535-7163.mct-11-0936] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
G-protein-coupled receptors (GPCR) activate the epidermal growth factor receptor (EGFR) and mediate EGFR-independent signaling pathways to promote the growth of a variety of cancers, including head and neck squamous cell carcinoma (HNSCC). Identification of the common signaling mechanisms involved in GPCR-induced EGFR-dependent and EGFR-independent processes will facilitate the development of more therapeutic strategies. In this study, we hypothesized that phosphoinositide-dependent kinase 1 (PDK1) contributes to GPCR-EGFR cross-talk and signaling in the absence of EGFR and suggests that inhibition of the PDK1 pathway may be effective in the treatment of HNSCC. The contribution of PDK1 to the EGFR-dependent and EGFR-independent signaling in HNSCC was determined using RNA interference, a kinase-dead mutant, and pharmacologic inhibition. In vivo xenografts studies were also carried out to determine the efficacy of targeting PDK1 alone or in combination with the U.S. Food and Drug Administration-approved EGFR inhibitor cetuximab. PDK1 contributed to both GPCR-induced EGFR activation and cell growth. PDK1 also mediated activation of p70S6K in the absence of EGFR. Blockade of PDK1 with a small molecule inhibitor (AR-12) abrogated HNSCC growth, induced apoptosis, and enhanced the antiproliferative effects of EGFR tyrosine kinase inhibitors in vitro. HNSCC xenografts expressing kinase-dead PDK1 showed increased sensitivity to cetuximab compared with vector-transfected controls. Administration of AR-12 substantially decreased HNSCC tumor growth in vivo. These cumulative results show that PDK1 is a common signaling intermediate in GPCR-EGFR cross-talk and EGFR-independent signaling, and in which targeting the PDK1 pathway may represent a rational therapeutic strategy to enhance clinical responses to EGFR inhibitors in HNSCC.
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Affiliation(s)
- Neil E Bhola
- Department of Pharmacology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA
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