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Singha M, Pu L, Srivastava G, Ni X, Stanfield BA, Uche IK, Rider PJF, Kousoulas KG, Ramanujam J, Brylinski M. Unlocking the Potential of Kinase Targets in Cancer: Insights from CancerOmicsNet, an AI-Driven Approach to Drug Response Prediction in Cancer. Cancers (Basel) 2023; 15:4050. [PMID: 37627077 PMCID: PMC10452340 DOI: 10.3390/cancers15164050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Revised: 07/16/2023] [Accepted: 07/26/2023] [Indexed: 08/27/2023] Open
Abstract
Deregulated protein kinases are crucial in promoting cancer cell proliferation and driving malignant cell signaling. Although these kinases are essential targets for cancer therapy due to their involvement in cell development and proliferation, only a small part of the human kinome has been targeted by drugs. A comprehensive scoring system is needed to evaluate and prioritize clinically relevant kinases. We recently developed CancerOmicsNet, an artificial intelligence model employing graph-based algorithms to predict the cancer cell response to treatment with kinase inhibitors. The performance of this approach has been evaluated in large-scale benchmarking calculations, followed by the experimental validation of selected predictions against several cancer types. To shed light on the decision-making process of CancerOmicsNet and to better understand the role of each kinase in the model, we employed a customized saliency map with adjustable channel weights. The saliency map, functioning as an explainable AI tool, allows for the analysis of input contributions to the output of a trained deep-learning model and facilitates the identification of essential kinases involved in tumor progression. The comprehensive survey of biomedical literature for essential kinases selected by CancerOmicsNet demonstrated that it could help pinpoint potential druggable targets for further investigation in diverse cancer types.
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Affiliation(s)
- Manali Singha
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA; (M.S.); (G.S.); (X.N.)
| | - Limeng Pu
- Center for Computation and Technology, Louisiana State University, Baton Rouge, LA 70803, USA; (L.P.); (J.R.)
| | - Gopal Srivastava
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA; (M.S.); (G.S.); (X.N.)
| | - Xialong Ni
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA; (M.S.); (G.S.); (X.N.)
| | - Brent A. Stanfield
- Department of Pathobiological Sciences, School of Veterinary Medicine, Louisiana State University, Baton Rouge, LA 70803, USA; (B.A.S.); (I.K.U.); (P.J.F.R.); (K.G.K.)
| | - Ifeanyi K. Uche
- Department of Pathobiological Sciences, School of Veterinary Medicine, Louisiana State University, Baton Rouge, LA 70803, USA; (B.A.S.); (I.K.U.); (P.J.F.R.); (K.G.K.)
- Division of Biotechnology and Molecular Medicine, Department of Pathobiological Sciences, School of Veterinary Medicine, Louisiana State University, Baton Rouge, LA 70803, USA
- School of Medicine, Louisiana State University Health Sciences Center, New Orleans, LA 70112, USA
| | - Paul J. F. Rider
- Department of Pathobiological Sciences, School of Veterinary Medicine, Louisiana State University, Baton Rouge, LA 70803, USA; (B.A.S.); (I.K.U.); (P.J.F.R.); (K.G.K.)
- Division of Biotechnology and Molecular Medicine, Department of Pathobiological Sciences, School of Veterinary Medicine, Louisiana State University, Baton Rouge, LA 70803, USA
| | - Konstantin G. Kousoulas
- Department of Pathobiological Sciences, School of Veterinary Medicine, Louisiana State University, Baton Rouge, LA 70803, USA; (B.A.S.); (I.K.U.); (P.J.F.R.); (K.G.K.)
- Division of Biotechnology and Molecular Medicine, Department of Pathobiological Sciences, School of Veterinary Medicine, Louisiana State University, Baton Rouge, LA 70803, USA
| | - J. Ramanujam
- Center for Computation and Technology, Louisiana State University, Baton Rouge, LA 70803, USA; (L.P.); (J.R.)
- Division of Electrical and Computer Engineering, Louisiana State University, Baton Rouge, LA 70803, USA
| | - Michal Brylinski
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA; (M.S.); (G.S.); (X.N.)
- Center for Computation and Technology, Louisiana State University, Baton Rouge, LA 70803, USA; (L.P.); (J.R.)
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Targeting Tyrosine Kinases in Ovarian Cancer: Small Molecule Inhibitor and Monoclonal Antibody, Where Are We Now? Biomedicines 2022; 10:biomedicines10092113. [PMID: 36140214 PMCID: PMC9495728 DOI: 10.3390/biomedicines10092113] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Revised: 08/15/2022] [Accepted: 08/19/2022] [Indexed: 12/27/2022] Open
Abstract
Ovarian cancer is one of the most lethal gynaecological malignancies worldwide. Despite high success rates following first time treatment, this heterogenous disease is prone to recurrence. Oncogenic activity of receptor tyrosine kinases is believed to drive the progression of ovarian cancer. Here we provide an update on the progress of the therapeutic targeting of receptor tyrosine kinases in ovarian cancer. Broadly, drug classes that inhibit tyrosine kinase/pathways can be classified as small molecule inhibitors, monoclonal antibodies, or immunotherapeutic vaccines. Small molecule inhibitors tested in clinical trials thus far include sorafenib, sunitinib, pazopanib, tivantinib, and erlotinib. Monoclonal antibodies include bevacizumab, cetuximab, pertuzumab, trastuzumab, and seribantumab. While numerous trials have been carried out, the results of monotherapeutic agents have not been satisfactory. For combination with chemotherapy, the monoclonal antibodies appear more effective, though the efficacy is limited by low frequency of target alteration and a lack of useful predictive markers for treatment stratification. There remain critical gaps for the treatment of platinum-resistant ovarian cancers; however, platinum-sensitive tumours may benefit from the combination of tyrosine kinase targeting drugs and PARP inhibitors. Immunotherapeutics such as a peptide B-cell epitope vaccine and plasmid-based DNA vaccine have shown some efficacy both as monotherapeutic agents and in combination therapy, but require further development to validate current findings. In conclusion, the tyrosine kinases remain attractive targets for treating ovarian cancers. Future development will need to consider effective drug combination, frequency of target, and developing predictive biomarker.
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Microtubule-affinity regulating kinase 4: A potential drug target for cancer therapy. Cell Signal 2022; 99:110434. [PMID: 35961526 DOI: 10.1016/j.cellsig.2022.110434] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Revised: 07/14/2022] [Accepted: 08/05/2022] [Indexed: 12/29/2022]
Abstract
The human genome encodes more than 500 protein kinases that work by transferring the γ-phosphate group from ATP to serine, threonine, or tyrosine (Ser/Thr/Tyr) residues. Various kinases are associated with the onset of cancer and its further progression. The recent advancements in developing small-molecule kinase inhibitors to treat different cancer types have shown noticeable results in clinical therapies. Microtubule-affinity regulating kinase 4 (MARK-4) is a Ser/Thr protein kinase that relates structurally to AMPK/Snf1 subfamily of the CaMK kinases. The protein kinase modulates major signalling pathways such as NF-κB, mTOR and the Hippo-signalling pathway. MARK4 is associated with various cancer types due to its important role in regulating microtubule dynamics and subsequent cell division. Aberrant expression of MARK4 is linked with several pathologies such as cancer, Alzheimer's disease, obesity, etc. This review provides detailed information on structural aspects of MARK4 and its role in various signalling pathways related to cancer. Several therapeutic molecules were designed to inhibit the MARK4 activity from controlling associated diseases. The review further highlights kinase-targeted drug discovery and development in oncology and cancer therapies. Finally, we summarize the latest findings regarding the role of MARK4 in cancer, diabetes, and neurodegenerative disease path to provide a solid rationale for future investigation and therapeutic intervention.
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Hoarau M, Suwanakitti N, Varatthan T, Thiabma R, Rattanajak R, Charoensetakul N, Redman EK, Khotavivattana T, Vilaivan T, Yuthavong Y, Kamchonwongpaisan S. Assay Development and Identification of the First Plasmodium falciparum 7,8-dihydro-6-hydroxymethylpterin-pyrophosphokinase Inhibitors. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27113515. [PMID: 35684452 PMCID: PMC9182141 DOI: 10.3390/molecules27113515] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Revised: 05/23/2022] [Accepted: 05/27/2022] [Indexed: 11/24/2022]
Abstract
In the fight towards eradication of malaria, identifying compounds active against new drug targets constitutes a key approach. Plasmodium falciparum 7,8-dihydro-6-hydroxymethylpterin-pyrophosphokinase (PfHPPK) has been advanced as a promising target, as being part of the parasite essential folate biosynthesis pathway while having no orthologue in the human genome. However, no drug discovery efforts have been reported on this enzyme. In this study, we conducted a three-step screening of our in-house antifolate library against PfHPPK using a newly designed PfHPPK-GFP protein construct. Combining virtual screening, differential scanning fluorimetry and enzymatic assay, we identified 14 compounds active against PfHPPK. Compounds’ binding modes were investigated by molecular docking, suggesting competitive binding with the HMDP substrate. Cytotoxicity and in vitro ADME properties of hit compounds were also assessed, showing good metabolic stability and low toxicity. The most active compounds displayed low micromolar IC50 against drug-resistant parasites. The reported hit compounds constitute a good starting point for inhibitor development against PfHPPK, as an alternative approach to tackle the malaria parasite.
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Affiliation(s)
- Marie Hoarau
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency, Pathum Thani 12120, Thailand; (N.S.); (T.V.); (R.T.); (R.R.); (N.C.); (Y.Y.); (S.K.)
- Correspondence:
| | - Nattida Suwanakitti
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency, Pathum Thani 12120, Thailand; (N.S.); (T.V.); (R.T.); (R.R.); (N.C.); (Y.Y.); (S.K.)
| | - Thaveechai Varatthan
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency, Pathum Thani 12120, Thailand; (N.S.); (T.V.); (R.T.); (R.R.); (N.C.); (Y.Y.); (S.K.)
| | - Ratthiya Thiabma
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency, Pathum Thani 12120, Thailand; (N.S.); (T.V.); (R.T.); (R.R.); (N.C.); (Y.Y.); (S.K.)
| | - Roonglawan Rattanajak
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency, Pathum Thani 12120, Thailand; (N.S.); (T.V.); (R.T.); (R.R.); (N.C.); (Y.Y.); (S.K.)
| | - Netnapa Charoensetakul
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency, Pathum Thani 12120, Thailand; (N.S.); (T.V.); (R.T.); (R.R.); (N.C.); (Y.Y.); (S.K.)
| | - Emily K. Redman
- Department of Chemistry, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand; (E.K.R.); (T.V.)
| | - Tanatorn Khotavivattana
- Center of Excellence in Natural Products Chemistry, Department of Chemistry, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand;
| | - Tirayut Vilaivan
- Department of Chemistry, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand; (E.K.R.); (T.V.)
| | - Yongyuth Yuthavong
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency, Pathum Thani 12120, Thailand; (N.S.); (T.V.); (R.T.); (R.R.); (N.C.); (Y.Y.); (S.K.)
| | - Sumalee Kamchonwongpaisan
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency, Pathum Thani 12120, Thailand; (N.S.); (T.V.); (R.T.); (R.R.); (N.C.); (Y.Y.); (S.K.)
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Ferrao Blanco MN, Domenech Garcia H, Legeai-Mallet L, van Osch GJVM. Tyrosine kinases regulate chondrocyte hypertrophy: promising drug targets for Osteoarthritis. Osteoarthritis Cartilage 2021; 29:1389-1398. [PMID: 34284112 DOI: 10.1016/j.joca.2021.07.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/11/2021] [Revised: 06/24/2021] [Accepted: 07/08/2021] [Indexed: 02/02/2023]
Abstract
Osteoarthritis (OA) is a major health problem worldwide that affects the joints and causes severe disability. It is characterized by pain and low-grade inflammation. However, the exact pathogenesis remains unknown and the therapeutic options are limited. In OA articular chondrocytes undergo a phenotypic transition becoming hypertrophic, which leads to cartilage damage, aggravating the disease. Therefore, a therapeutic agent inhibiting hypertrophy would be a promising disease-modifying drug. The therapeutic use of tyrosine kinase inhibitors has been mainly focused on oncology, but the Food and Drug Administration (FDA) approval of the Janus kinase inhibitor Tofacitinib in Rheumatoid Arthritis has broadened the applicability of these compounds to other diseases. Interestingly, tyrosine kinases have been associated with chondrocyte hypertrophy. In this review, we discuss the experimental evidence that implicates specific tyrosine kinases in signaling pathways promoting chondrocyte hypertrophy, highlighting their potential as therapeutic targets for OA.
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Affiliation(s)
- M N Ferrao Blanco
- Department of Orthopaedics and Sports Medicine, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands.
| | - H Domenech Garcia
- Department of Orthopaedics and Sports Medicine, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands.
| | - L Legeai-Mallet
- Université de Paris, INSERM U1163, Institut Imagine, Paris, France.
| | - G J V M van Osch
- Department of Orthopaedics and Sports Medicine, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands; Department of Otorhinolaryngology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands; Department of Biomechanical Engineering, Delft University of Technology, Delft, the Netherlands.
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Peerzada MN, Hamel E, Bai R, Supuran CT, Azam A. Deciphering the key heterocyclic scaffolds in targeting microtubules, kinases and carbonic anhydrases for cancer drug development. Pharmacol Ther 2021; 225:107860. [PMID: 33895188 DOI: 10.1016/j.pharmthera.2021.107860] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Revised: 03/31/2021] [Accepted: 04/06/2021] [Indexed: 12/17/2022]
Abstract
Heterocyclic scaffolds are widely utilized for drug design by taking into account the molecular structure of therapeutic targets that are related to a broad spectrum of ailments, including tumors. Such compounds display various covalent and non-covalent interactions with the specific residues of the target proteins while causing their inhibition. There is a substantial number of heterocyclic compounds approved for cancer treatment, and these compounds function by interacting with different therapeutic targets involved in tumorogenesis. In this review, we trace and emphasize the privileged heterocyclic pharmacophores that have immense potency against several essential chemotherapeutic tumor targets: microtubules, kinases and carbonic anhydrases. Potent compounds currently undergoing pre-clinical and clinical studies have also been assessed for ascertaining the effective class of chemical scaffolds that have significant therapeutic potential against multiple malignancies. In addition, we also describe briefly the role of heterocyclic compounds in various chemotherapy regimens. The optimized molecular hybridization of delineated motifs may result in the discovery of more active anticancer therapeutics and circumvent the development of resistance by specific targets in the future.
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Affiliation(s)
- Mudasir Nabi Peerzada
- Medicinal Chemistry Research Laboratory, Department of Chemistry, Jamia Millia Islamia, Jamia Nagar, New Delhi 110025, India
| | - Ernest Hamel
- Molecular Pharmacology Branch, Developmental Therapeutics Program, Division of Cancer Treatment and Diagnosis, Frederick National Laboratory for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD 21702, USA
| | - Ruoli Bai
- Molecular Pharmacology Branch, Developmental Therapeutics Program, Division of Cancer Treatment and Diagnosis, Frederick National Laboratory for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD 21702, USA
| | - Claudiu T Supuran
- Department of NEUROFARBA, Section of Pharmaceutical and Nutraceutical Sciences, University of Florence, Polo Scientifico, Via U. Schiff 6, 50019 Sesto Fiorentino, Florence, Italy.
| | - Amir Azam
- Medicinal Chemistry Research Laboratory, Department of Chemistry, Jamia Millia Islamia, Jamia Nagar, New Delhi 110025, India.
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Ling Y, Liu J, Qian J, Meng C, Guo J, Gao W, Xiong B, Ling C, Zhang Y. Recent Advances in Multi-target Drugs Targeting Protein Kinases and Histone Deacetylases in Cancer Therapy. Curr Med Chem 2021; 27:7264-7288. [PMID: 31894740 DOI: 10.2174/0929867327666200102115720] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2019] [Revised: 08/12/2019] [Accepted: 10/12/2019] [Indexed: 02/06/2023]
Abstract
Protein Kinase Inhibitors (PKIs) and Histone Deacetylase Inhibitors (HDACIs) are two important classes of anticancer agents and have provided a variety of small molecule drugs for the treatment of various types of human cancers. However, malignant tumors are of a multifactorial nature that can hardly be "cured" by targeting a single target, and treatment of cancers hence requires modulation of multiple biological targets to restore the physiological balance and generate sufficient therapeutic efficacy. Multi-target drugs have attracted great interest because of their advantages in the treatment of complex cancers by simultaneously targeting multiple signaling pathways and possibly leading to synergistic effects. Synergistic effects have been observed in the combination of kinase inhibitors, such as imatinib, dasatinib, or sorafenib, with an array of HDACIs including vorinostat, romidepsin, or panobinostat. A considerable number of multi-target agents based on PKIs and HDACIs have been developed. In this review, we summarize the recent literature on the development of multi-target kinase-HDAC inhibitors and provide our view on the challenges and future directions on this topic.
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Affiliation(s)
- Yong Ling
- School of Pharmacy and Jiangsu Province Key Laboratory for Inflammation and Molecular Drug Target, Nantong University, Nantong 226001, China
| | - Ji Liu
- School of Pharmacy and Jiangsu Province Key Laboratory for Inflammation and Molecular Drug Target, Nantong University, Nantong 226001, China
| | - Jianqiang Qian
- School of Pharmacy and Jiangsu Province Key Laboratory for Inflammation and Molecular Drug Target, Nantong University, Nantong 226001, China
| | - Chi Meng
- School of Pharmacy and Jiangsu Province Key Laboratory for Inflammation and Molecular Drug Target, Nantong University, Nantong 226001, China
| | - Jing Guo
- School of Pharmacy and Jiangsu Province Key Laboratory for Inflammation and Molecular Drug Target, Nantong University, Nantong 226001, China
| | - Weijie Gao
- School of Pharmacy and Jiangsu Province Key Laboratory for Inflammation and Molecular Drug Target, Nantong University, Nantong 226001, China
| | - Biao Xiong
- School of Pharmacy and Jiangsu Province Key Laboratory for Inflammation and Molecular Drug Target, Nantong University, Nantong 226001, China
| | - Changchun Ling
- The Affiliated Hospital of Nantong University, Nantong University, Nantong 226001, China
| | - Yanan Zhang
- School of Pharmacy and Jiangsu Province Key Laboratory for Inflammation and Molecular Drug Target, Nantong University, Nantong 226001, China
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Modi SJ, Kulkarni VM. Exploration of structural requirements for the inhibition of VEGFR-2 tyrosine kinase: Binding site analysis of type II, 'DFG-out' inhibitors. J Biomol Struct Dyn 2021; 40:5712-5727. [PMID: 33459187 DOI: 10.1080/07391102.2021.1872417] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The conserved three-dimensional structure of receptor tyrosine kinases (RTKs) has been varyingly observed in prokaryotes to humans that actively participate in the phosphorylation process of tyrosine residues in the protein, which results in the alteration of protein's function. Mutation and transcriptional or post-translational modifications lead to a deregulation of kinases, which ultimately fallout into the development of pathological conditions like cancer. The human genome encodes two kinds of tyrosine kinases: non-receptor tyrosine kinases (NRTKs) and receptor tyrosine kinases (RTKs). Among these kinases, VEGF/VEGFR-2 signaling cascade is an important target to develop novel small-molecule inhibitors for the therapy of abnormal angiogenesis incorporated with cancer. Due to advances in the knowledge of the catalytic domain and 'DFG-motif' region, selective 'DFG-in' (type I) and 'DFG-out' (type II) VEGFR-2/KDR inhibitors were successfully developed, and some are in different phases of a clinical trial. 'DFG-out' (inactive) confirmation has significant advantages over 'DFG-in' (active) confirmation concerning the affinity of the ATP at the catalytic domain. Further, in the catalytic domain, between front and back cleft, smaller gatekeeper residue (Val916) present; therefore, selectivity against VEGFR-2 could be precisely achieved. In this review, small molecule type II/'DFG-out' inhibitors, their conformation, interaction at receptor binding pocket, and structural requirements to inhibit VEGFR-2 at the molecular level are discussed.HighlightsVEGFR-2 is a type of membrane-bound receptor tyrosine kinases (RTKs) that regulates the process of vasculogenesis and angiogenesis.Small molecule first-generation type I, 'DFG-in' and second-generation type II, 'DFG-out' VEGFR-2 inhibitors exhibit clinical benefits in the treatment of aberrant angiogenesis associated with cancer.Molecular docking of FDA approved and novel type II inhibitors were performed using X-ray crystal structures of VEGFR-2; binding site analysis was carried out.Structural requirements for the inhibition of VEGFR-2 were identified.
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Affiliation(s)
- Siddharth J Modi
- Department of Pharmaceutical Chemistry, Poona College of Pharmacy, Bharati Vidyapeeth (Deemed to be University), Pune, Maharashtra, India
| | - Vithal M Kulkarni
- Department of Pharmaceutical Chemistry, Poona College of Pharmacy, Bharati Vidyapeeth (Deemed to be University), Pune, Maharashtra, India
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Xu X, Chen Y, Fu Q, Ni D, Zhang J, Li X, Lu S. The chemical diversity and structure-based discovery of allosteric modulators for the PIF-pocket of protein kinase PDK1. J Enzyme Inhib Med Chem 2019; 34:361-374. [PMID: 30734603 PMCID: PMC6327997 DOI: 10.1080/14756366.2018.1553167] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2018] [Revised: 11/18/2018] [Accepted: 11/19/2018] [Indexed: 01/06/2023] Open
Abstract
Phosphoinositide-dependent protein kinase-1 (PDK1) is an important protein in mediating the PI3K-AKT pathway and is thus identified as a promising target. The catalytic activity of PDK1 is tightly regulated by allosteric modulators, which bind to the PDK1 Interacting Fragment (PIF) pocket of the kinase domain that is topographically distinct from the orthosteric, ATP binding site. Allosteric modulators by attaching to the less conserved PIF-pocket have remarkable advantages such as higher selectivity, less side effect, and lower toxicity. Targeting allosteric PIF-pocket of PDK1 has become the focus of recent attention. In this review, we summarise the current advances in the structure-based discovery of PDK1 allosteric modulators. We will first present the three-dimensional structure of PDK1 and illustrate the allosteric regulatory mechanism of PDK1 through the modulation of the PIF-pocket. Then, the recent advances of PDK1 allosteric modulators targeting the PIF-pocket will be recapitulated detailly according to the structural similarity of allosteric modulators.
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Affiliation(s)
- Xinyuan Xu
- Department of Pathophysiology, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Shanghai Jiao Tong University, School of Medicine, Shanghai, China
| | - Yingyi Chen
- Department of Pathophysiology, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Shanghai Jiao Tong University, School of Medicine, Shanghai, China
| | - Qiang Fu
- Department of Orthopedics, Shanghai General Hospital, Shanghai Jiao Tong University, School of Medicine, Shanghai, China
| | - Duan Ni
- Department of Pathophysiology, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Shanghai Jiao Tong University, School of Medicine, Shanghai, China
| | - Jian Zhang
- Department of Pathophysiology, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Shanghai Jiao Tong University, School of Medicine, Shanghai, China
| | - Xiaolong Li
- Department of Orthopedics, Changhai Hospital, Naval Military Medical University, Shanghai, China
| | - Shaoyong Lu
- Department of Pathophysiology, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Shanghai Jiao Tong University, School of Medicine, Shanghai, China
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Liu S, Jiang Y, Yan R, Li Z, Wan S, Zhang T, Wu X, Hou J, Zhu Z, Tian Y, Zhang J. Design, synthesis and biological evaluations of 2-amino-4-(1-piperidine) pyridine derivatives as novel anti crizotinib-resistant ALK/ROS1 dual inhibitors. Eur J Med Chem 2019; 179:358-375. [PMID: 31260890 DOI: 10.1016/j.ejmech.2019.06.043] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2019] [Revised: 05/29/2019] [Accepted: 06/15/2019] [Indexed: 12/11/2022]
Abstract
ALK and ROS1 kinases have become promising therapeutic targets since Crizotinib was used to treat non-small-cell lung cancer clinically. Aiming to explore new potent inhibitors, a series of 2-amino-4-(1-piperidine) pyridine derivatives that stabilized a novel DFG-shifted conformation in the kinase domain of ALK were designed and synthesized on the base of lead compound A. Biological evaluation highlighted that most of these new compounds could also potently inhibit ROS1 kinase, leading to the promising inhibitors against both ROS1 and ALK. Among them, the representative compound 2e stood out potent anti-proliferative activity against ALK-addicted H3122 and ROS1-addicted HCC78 cell lines (IC50 = 6.27 μM and 10.71 μM, respectively), which were comparable to that of Crizotinib. Moreover, 2e showed impressive enzyme activity against clinically Crizotinib-resistant ALKL1196M with an IC50 value of 41.3 nM, which was about 2-fold more potent than that of Crizotinib. 2e also showed potent inhibitory activity in about 6-fold superior to Crizotinib (IC50: 104.7 nM vs. 643.5 nM) in Ba/F3 cell line harboring ROS1G2032R. Furthermore, molecular modeling disclosed that all the representative inhibitors could dock into the active site of ALK and ROS1, which gave a probable explanation of anti Crizotinib-resistant mutants. These results indicated that our work has established a path forward for the generation of anti Crizotinib-resistant ALK/ROS1 dual inhibitors.
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Affiliation(s)
- Siming Liu
- Guangdong Provincial Key Laboratory of New Drug Screening, School of Pharmaceutical Science, Southern Medical University, Guangzhou, 510515, PR China
| | - Ying Jiang
- Guangdong Provincial Key Laboratory of New Drug Screening, School of Pharmaceutical Science, Southern Medical University, Guangzhou, 510515, PR China
| | - Ruohong Yan
- Guangdong Provincial Key Laboratory of New Drug Screening, School of Pharmaceutical Science, Southern Medical University, Guangzhou, 510515, PR China
| | - Zhonghuang Li
- Guangdong Provincial Key Laboratory of New Drug Screening, School of Pharmaceutical Science, Southern Medical University, Guangzhou, 510515, PR China
| | - Shanhe Wan
- Guangdong Provincial Key Laboratory of New Drug Screening, School of Pharmaceutical Science, Southern Medical University, Guangzhou, 510515, PR China
| | - Tingting Zhang
- Guangdong Provincial Key Laboratory of New Drug Screening, School of Pharmaceutical Science, Southern Medical University, Guangzhou, 510515, PR China
| | - Xiaoyun Wu
- Guangdong Provincial Key Laboratory of New Drug Screening, School of Pharmaceutical Science, Southern Medical University, Guangzhou, 510515, PR China
| | - Ju Hou
- Guangdong Provincial Key Laboratory of New Drug Screening, School of Pharmaceutical Science, Southern Medical University, Guangzhou, 510515, PR China
| | - Zhengguang Zhu
- Guangdong Provincial Key Laboratory of New Drug Screening, School of Pharmaceutical Science, Southern Medical University, Guangzhou, 510515, PR China
| | - Yuanxin Tian
- Guangdong Provincial Key Laboratory of New Drug Screening, School of Pharmaceutical Science, Southern Medical University, Guangzhou, 510515, PR China.
| | - Jiajie Zhang
- Guangdong Provincial Key Laboratory of New Drug Screening, School of Pharmaceutical Science, Southern Medical University, Guangzhou, 510515, PR China.
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Hameed R, Khan A, Khan S, Perveen S. Computational Approaches Towards Kinases as Attractive Targets for Anticancer Drug Discovery and Development. Anticancer Agents Med Chem 2018; 19:592-598. [PMID: 30306880 DOI: 10.2174/1871520618666181009163014] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2017] [Revised: 04/09/2018] [Accepted: 09/03/2018] [Indexed: 01/07/2023]
Abstract
BACKGROUND One of the major goals of computational chemists is to determine and develop the pathways for anticancer drug discovery and development. In recent past, high performance computing systems elicited the desired results with little or no side effects. The aim of the current review is to evaluate the role of computational chemistry in ascertaining kinases as attractive targets for anticancer drug discovery and development. METHODS Research related to computational studies in the field of anticancer drug development is reviewed. Extensive literature on achievements of theorists in this regard has been compiled and presented with special emphasis on kinases being the attractive anticancer drug targets. RESULTS Different approaches to facilitate anticancer drug discovery include determination of actual targets, multi-targeted drug discovery, ligand-protein inverse docking, virtual screening of drug like compounds, formation of di-nuclear analogs of drugs, drug specific nano-carrier design, kinetic and trapping studies in drug design, multi-target QSAR (Quantitative Structure Activity Relationship) model, targeted co-delivery of anticancer drug and siRNA, formation of stable inclusion complex, determination of mechanism of drug resistance, and designing drug like libraries for the prediction of drug-like compounds. Protein kinases have gained enough popularity as attractive targets for anticancer drugs. These kinases are responsible for uncontrolled and deregulated differentiation, proliferation, and cell signaling of the malignant cells which result in cancer. CONCLUSION Interest in developing drugs through computational methods is a growing trend, which saves equally the cost and time. Kinases are the most popular targets among the other for anticancer drugs which demand attention. 3D-QSAR modelling, molecular docking, and other computational approaches have not only identified the target-inhibitor binding interactions for better anticancer drug discovery but are also designing and predicting new inhibitors, which serve as lead for the synthetic preparation of drugs. In light of computational studies made so far in this field, the current review highlights the importance of kinases as attractive targets for anticancer drug discovery and development.
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Affiliation(s)
- Rabia Hameed
- Department of Chemistry, COMSATS University Islamabad, Abbottabad Campus, Abbottabad 22060, Pakistan
| | - Afsar Khan
- Department of Chemistry, COMSATS University Islamabad, Abbottabad Campus, Abbottabad 22060, Pakistan
| | - Sehroon Khan
- Key Laboratory of Economic Plants and Biotechnology, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 560201, Yunnan, China
| | - Shagufta Perveen
- Department of Pharmacognosy, College of Pharmacy, King Saud University, P.O. Box 2457, Riyadh 11451, Saudi Arabia
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Cozza G, Fortuna M, Meggio F, Sarno S, Kubbutat MHG, Totzke F, Schaechtele C, Pinna LA, Olsufyeva EN, Preobrazhenskaya MN. Hydrophobic Derivatives of Glycopeptide Antibiotics as Inhibitors of Protein Kinases. BIOCHEMISTRY. BIOKHIMIIA 2018; 83:1222-1230. [PMID: 30472959 PMCID: PMC7088347 DOI: 10.1134/s0006297918100073] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 12/26/2017] [Revised: 05/17/2018] [Indexed: 01/01/2023]
Abstract
As key regulators of cell signaling, protein kinases (PKs) are attractive targets for therapeutic intervention in a variety of diseases. Herein, we report for the first time the inhibitory activity of polycyclic peptides, particularly, derivatives of glycopeptide antibiotics teicoplanin and eremomycin, against a panel of 12 recombinant human protein kinases and two protein kinases (CK1 and CK2) isolated from rat liver. Several of the investigated compounds inhibited various PKs with IC50 values below 10 μM and caused >90% suppression of the enzyme activity at 10 µM concentration. Kinetic analysis of the protein kinase CK2α inhibition by the teicoplanin aglycon analogue (7) demonstrated the non-competitive mechanism of inhibition (with regard to ATP). Interestingly, the inhibitory activity of some investigated compounds correlated with the earlier described antiviral activity against HIV, HCV, and other corona- and flaviviruses.
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Affiliation(s)
- G Cozza
- Department of Molecular Medicine, University of Padova, Padova, 35131, Italy
| | - M Fortuna
- Department of Biological Chemistry, University of Padova, Padova, 35131, Italy
| | - F Meggio
- Department of Biological Chemistry, University of Padova, Padova, 35131, Italy
| | - S Sarno
- Department of Biomedical Sciences, University of Padova, Padova, 35131, Italy
| | | | - F Totzke
- ProQinase GmbH, Freiburg, 79106, Germany
| | | | - L A Pinna
- Center for Neuroscience Research Neuroscience Institute, Padova, 35131, Italy
| | - E N Olsufyeva
- Gause Institute of New Antibiotics, Moscow, 119021, Russia.
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Bhullar KS, Lagarón NO, McGowan EM, Parmar I, Jha A, Hubbard BP, Rupasinghe HPV. Kinase-targeted cancer therapies: progress, challenges and future directions. Mol Cancer 2018; 17:48. [PMID: 29455673 PMCID: PMC5817855 DOI: 10.1186/s12943-018-0804-2] [Citation(s) in RCA: 680] [Impact Index Per Article: 113.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2017] [Accepted: 02/01/2018] [Indexed: 02/06/2023] Open
Abstract
The human genome encodes 538 protein kinases that transfer a γ-phosphate group from ATP to serine, threonine, or tyrosine residues. Many of these kinases are associated with human cancer initiation and progression. The recent development of small-molecule kinase inhibitors for the treatment of diverse types of cancer has proven successful in clinical therapy. Significantly, protein kinases are the second most targeted group of drug targets, after the G-protein-coupled receptors. Since the development of the first protein kinase inhibitor, in the early 1980s, 37 kinase inhibitors have received FDA approval for treatment of malignancies such as breast and lung cancer. Furthermore, about 150 kinase-targeted drugs are in clinical phase trials, and many kinase-specific inhibitors are in the preclinical stage of drug development. Nevertheless, many factors confound the clinical efficacy of these molecules. Specific tumor genetics, tumor microenvironment, drug resistance, and pharmacogenomics determine how useful a compound will be in the treatment of a given cancer. This review provides an overview of kinase-targeted drug discovery and development in relation to oncology and highlights the challenges and future potential for kinase-targeted cancer therapies.
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Affiliation(s)
- Khushwant S Bhullar
- Department of Pharmacology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB, Canada
| | - Naiara Orrego Lagarón
- Department of Pharmacy and Pharmaceutical Technology, Faculty of Pharmacy, University of Barcelona, Barcelona, Spain
| | - Eileen M McGowan
- Chronic Disease Solutions Team, School of Life Science, University of Technology, New South Wales, Australia
| | - Indu Parmar
- Division of Product Development, Radient Technologies, Edmonton, AB, Canada
| | - Amitabh Jha
- Department of Chemistry, Acadia University, Wolfville, NS, Canada
| | - Basil P Hubbard
- Department of Pharmacology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB, Canada
| | - H P Vasantha Rupasinghe
- Department of Plant, Food, and Environmental Sciences, Faculty of Agriculture, Dalhousie University, Truro, NS, Canada.
- Department of Pathology, Faculty of Medicine, Dalhousie University, Halifax, NS, Canada.
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14
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Chilà R, Guffanti F, Damia G. Role and therapeutic potential of CDK12 in human cancers. Cancer Treat Rev 2016; 50:83-88. [PMID: 27662623 DOI: 10.1016/j.ctrv.2016.09.003] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2016] [Revised: 08/30/2016] [Accepted: 09/01/2016] [Indexed: 12/31/2022]
Abstract
Phosphorylation of the RNA polymerase II C-terminal domain by cyclin-dependent kinases (CDKs) is important for productive transcription. Deregulated transcription-CDKs have been reported in different human cancers. Until recently CDK9 was the only transcription-CDK with a causative role in cancer, but evidence is cumulating of the importance of CDK12. This review summarizes the role of CDK12 in transcription and RNA processing, in maintaining genomic stability/integrity and in tumorigenesis. CDK12 mutations have been reported in many cancers and have been suggested as a cause of defective DNA repair in ovarian carcinoma. CDK12 may have a role as a new therapeutic target in oncology.
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Affiliation(s)
- Rosaria Chilà
- Laboratory of Molecular Pharmacology, Oncology Department, IRCCS - Istituto di Ricerche Farmacologiche Mario Negri, Milan, Italy
| | - Federica Guffanti
- Laboratory of Molecular Pharmacology, Oncology Department, IRCCS - Istituto di Ricerche Farmacologiche Mario Negri, Milan, Italy
| | - Giovanna Damia
- Laboratory of Molecular Pharmacology, Oncology Department, IRCCS - Istituto di Ricerche Farmacologiche Mario Negri, Milan, Italy.
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15
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Tadesse S, Yu M, Kumarasiri M, Le BT, Wang S. Targeting CDK6 in cancer: State of the art and new insights. Cell Cycle 2016; 14:3220-30. [PMID: 26315616 DOI: 10.1080/15384101.2015.1084445] [Citation(s) in RCA: 85] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Cyclin-dependent kinase 6 (CDK6) plays a vital role in regulating the progression of the cell cycle. More recently, CDK6 has also been shown to have a transcriptional role in tumor angiogenesis. Up-regulated CDK6 activity is associated with the development of several types of cancers. While CDK6 is over-expressed in cancer cells, it has a low detectable level in non-cancerous cells and CDK6-null mice develop normally, suggesting a specific oncogenic role of CDK6, and that its inhibition may represent an ideal mechanism-based and low toxic therapeutic strategy in cancer treatment. Identification of selective small molecule inhibitors of CDK6 is thus needed for drug development. Herein, we review the latest understandings of the biological regulation and oncogenic roles of CDK6. The potential clinical relevance of CDK6 inhibition, the progress in the development of small-molecule CDK6 inhibitors and the rational design of potential selective CDK6 inhibitors are also discussed.
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Affiliation(s)
- Solomon Tadesse
- a Center for Drug Discovery and Development, Sansom Institute for Health Research, Center for Cancer Biology; and School of Pharmacy and Medical Sciences, University of South Australia ; Adelaide , Australia
| | - Mingfeng Yu
- a Center for Drug Discovery and Development, Sansom Institute for Health Research, Center for Cancer Biology; and School of Pharmacy and Medical Sciences, University of South Australia ; Adelaide , Australia
| | - Malika Kumarasiri
- a Center for Drug Discovery and Development, Sansom Institute for Health Research, Center for Cancer Biology; and School of Pharmacy and Medical Sciences, University of South Australia ; Adelaide , Australia
| | - Bich Thuy Le
- a Center for Drug Discovery and Development, Sansom Institute for Health Research, Center for Cancer Biology; and School of Pharmacy and Medical Sciences, University of South Australia ; Adelaide , Australia
| | - Shudong Wang
- a Center for Drug Discovery and Development, Sansom Institute for Health Research, Center for Cancer Biology; and School of Pharmacy and Medical Sciences, University of South Australia ; Adelaide , Australia
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16
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Wu J, Ji J, Weng B, Qiu P, Kanchana K, Wei T, Wang Y, Cai Y, Li X, Liang G. Discovery of novel non-ATP competitive FGFR1 inhibitors and evaluation of their anti-tumor activity in non-small cell lung cancer in vitro and in vivo. Oncotarget 2015; 5:4543-53. [PMID: 24980830 PMCID: PMC4147344 DOI: 10.18632/oncotarget.2122] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Accumulating evidence suggests that high expression of FGFR1 is closely related to the development of lung cancer especially in non-small cell lung cancers (NSCLC), to which non-ATP competitive inhibitors represent an effective therapeutical approach due to their good specificity. Herein, a series of NDGA analogues with the framework of bisaryl-1,4-dien-3-one as novel FGFR1 inhibitors have been designed and screened. Among them Aea4 and Aea25 showed strong FGFR1 ‵inhibition and high selectivity over other receptor kinases. The kinase inhibitory assay in different ATP concentrations and computer-assistant molecular docking showed that the FGFR1 inhibition mode of both Aea4 and Aea25 was non-ATP-competitive. The in vitro and in vivo study on anticancer efficacy of Aea4 and Aea25 against non-small cell lung cancer involves inhibition of cell proliferation, apoptosis induction and cell cycle arrest with no toxicity. Thus, these two novel non-ATP competitive inhibitors derived from NDGA may have a great therapeutic potential in the treatment of NSCLC. This work also provides a structural lead for the design of new non-ATP-competitive FGFR1 inhibitors.
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Affiliation(s)
- Jianzhang Wu
- Chemical Biology Research Center, School of Pharmaceutical Sciences, WenzhouMedical Universtiy, Wenzhou zhejiang China. These Authors contributed equally to this work
| | - Jiansong Ji
- Department of Interventional Radiology, The Fifth Affiliated Hospital of Wenzhou Medical University, Lishui, Zhejiang, China. These Authors contributed equally to this work
| | - Bixia Weng
- Chemical Biology Research Center, School of Pharmaceutical Sciences, WenzhouMedical Universtiy, Wenzhou zhejiang China
| | - Peihong Qiu
- Chemical Biology Research Center, School of Pharmaceutical Sciences, WenzhouMedical Universtiy, Wenzhou zhejiang China
| | - Karvannan Kanchana
- Chemical Biology Research Center, School of Pharmaceutical Sciences, WenzhouMedical Universtiy, Wenzhou zhejiang China
| | - Tao Wei
- Chemical Biology Research Center, School of Pharmaceutical Sciences, WenzhouMedical Universtiy, Wenzhou zhejiang China
| | - Yi Wang
- Chemical Biology Research Center, School of Pharmaceutical Sciences, WenzhouMedical Universtiy, Wenzhou zhejiang China
| | - Yuepiao Cai
- Chemical Biology Research Center, School of Pharmaceutical Sciences, WenzhouMedical Universtiy, Wenzhou zhejiang China
| | - Xiaokun Li
- Chemical Biology Research Center, School of Pharmaceutical Sciences, WenzhouMedical Universtiy, Wenzhou zhejiang China
| | - Guang Liang
- Chemical Biology Research Center, School of Pharmaceutical Sciences, WenzhouMedical Universtiy, Wenzhou zhejiang China
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Foda ZH, Shan Y, Kim ET, Shaw DE, Seeliger MA. A dynamically coupled allosteric network underlies binding cooperativity in Src kinase. Nat Commun 2015; 6:5939. [PMID: 25600932 PMCID: PMC4300553 DOI: 10.1038/ncomms6939] [Citation(s) in RCA: 88] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2014] [Accepted: 11/22/2014] [Indexed: 01/16/2023] Open
Abstract
Protein tyrosine kinases are attractive drug targets because many human diseases are associated with the deregulation of kinase activity. However, how the catalytic kinase domain integrates different signals and switches from an active to an inactive conformation remains incompletely understood. Here we identify an allosteric network of dynamically coupled amino acids in Src kinase that connects regulatory sites to the ATP- and substrate-binding sites. Surprisingly, reactants (ATP and peptide substrates) bind with negative cooperativity to Src kinase while products (ADP and phosphopeptide) bind with positive cooperativity. We confirm the molecular details of the signal relay through the allosteric network by biochemical studies. Experiments on two additional protein tyrosine kinases indicate that the allosteric network may be largely conserved among these enzymes. Our work provides new insights into the regulation of protein tyrosine kinases and establishes a potential conduit by which resistance mutations to ATP-competitive kinase inhibitors can affect their activity. Protein tyrosine kinases are subject to multiple regulatory mechanisms. Foda et al. show that reactants and products of the tyrosine kinase Src bind its catalytic domain with opposite cooperativity, and identify an allosteric network of dynamically coupled amino acids that underlie this behaviour.
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Affiliation(s)
- Zachariah H Foda
- Department of Pharmacological Sciences, Stony Brook University, Stony Brook, New York 11794, USA
| | - Yibing Shan
- D. E. Shaw Research, New York, New York 10036, USA
| | - Eric T Kim
- D. E. Shaw Research, New York, New York 10036, USA
| | - David E Shaw
- 1] D. E. Shaw Research, New York, New York 10036, USA [2] Department of Biochemistry and Molecular Biophysics, Center for Computational Biology and Bioinformatics, Columbia University, New York, New York 10032, USA
| | - Markus A Seeliger
- Department of Pharmacological Sciences, Stony Brook University, Stony Brook, New York 11794, USA
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18
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Molecular dynamics simulation and free energy calculation studies of kinase inhibitors binding to active and inactive conformations of VEGFR-2. J Mol Graph Model 2014; 56:103-12. [PMID: 25594497 DOI: 10.1016/j.jmgm.2014.12.006] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2014] [Revised: 12/04/2014] [Accepted: 12/16/2014] [Indexed: 11/21/2022]
Abstract
Vascular endothelial growth factors receptor-2 (VEGFR-2) inhibitors have been proved as very effective anticancer agents. Structurally similar ligands 1 and 2 show almost the same inhibitory activities against VEGFR-2, but they bind to the enzyme in distinct binding mode. Ligand 1 targets DFG-in active conformation of VEGFR-2, known as Type I inhibitor. On the other hand, ligand 2 targets DFG-out inactive conformation of VEGFR-2, known as Type II inhibitor or allosteric kinase inhibitor. Ligand 2 shows high inhibitory activity, while the compound 3, a close analog of 2 with the cyclopropylamide replaced by tert-butylamide, exhibits drastically diminished potency. In this work, molecular dynamics simulations and free energy calculations were performed on inhibitors 1-3 binding to active and inactive conformation of VEGFR-2. Molecular dynamics simulations find that the active conformation binding to Type I inhibitor 1 appears more flexible when compared to the unbound form. In contrast, binding of Type II inhibitor 2 to the inactive conformation helps to stabilize the inactive conformation of the protein. Binding free energy calculations verify that inhibitors 1 and 2 have almost the same activities against VEGFR-2, and that ligand 1 binds to and stabilizes the DFG-in conformation of VEGFR-2, which is in agree with the experimental observation. Molecular dynamics simulations and binding free energy calculations of 3 binding to VEGFR-2 can give a good explanation of the drastically diminished potency. Free energy analysis revealed that van der Waals interactions provided the substantial driving force for the binding process. The important hydrophobic property of the terminal 4-Cl phenyl was required to be Type II inhibitors. Furthermore, per-residue free energy decomposition analysis revealed that the most favorable contribution came from Leu840, Val848, Ala866, Lys868, Leu889, Val899, Thr916, Phe918, Cys919, Leu1035, Cys1045, Asp1046, and Phe1047. These results are expected to be useful for future rational design of novel potent VEGFR-2 inhibitors.
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19
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Lu T, Laughton CA, Wang S, Bradshaw TD. In vitro antitumor mechanism of (E)-N-(2-methoxy-5-(((2,4,6-trimethoxystyryl)sulfonyl)methyl)pyridin-3-yl)methanesulfonamide. Mol Pharmacol 2014; 87:18-30. [PMID: 25316768 DOI: 10.1124/mol.114.093245] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
ON01910.Na [sodium (E)-2-(2-methoxy-5-((2,4,6-trimethoxystyrylsulfonyl)methyl)phenylamino)acetate; Rigosertib, Estybon], a styryl benzylsulfone, is a phase III stage anticancer agent. This non-ATP competitive kinase inhibitor has multitargeted activity, promoting mitotic arrest and apoptosis. Extensive phase I/II studies with ON01910.Na, conducted in patients with solid tumors and hematologic cancers, demonstrate excellent efficacy. However, issues remain affecting its development. These include incomplete understanding of antitumor mechanisms, low oral bioavailability, and unpredictable pharmacokinetics. We have identified a novel (E)-styrylsulfonyl methylpyridine [(E)-N-(2-methoxy-5-((2,4,6-trimethoxystyrylsulfonyl)methyl)pyridin-3-yl)methanesulfonamide (TL-77)] which has shown improved oral bioavailability compared with ON01910.Na. Here, we present detailed cellular mechanisms of TL-77 in comparison with ON01910.Na. TL-77 displays potent growth inhibitory activity in vitro (GI50 < 1μM against HCT-116 cells), demonstrating 3- to 10-fold greater potency against tumor cell lines when compared with normal cells. Cell-cycle analyses reveal that TL-77 causes significant G2/M arrest in cancer cells, followed by the onset of apoptosis. In cell-free conditions, TL-77 potently inhibits tubulin polymerization. Mitotically arrested cells display multipolar spindles and misalignment of chromosomes, indicating that TL-77 interferes with mitotic spindle assembly in cancer cells. These effects are accompanied by induction of DNA damage, inhibition of Cdc25C phosphorylation [indicative of Plk1 inhibition], and downstream inhibition of cyclin B1. However, kinase assays failed to confirm inhibition of Plk1. Nonsignificant effects on phosphoinositide 3-kinase/Akt signal transduction were observed after TL-77 treatment. Analysis of apoptotic signaling pathways reveals that TL-77 downregulates expression of B-cell lymphoma 2 family proteins (Bid, Bcl-xl, and Mcl-1) and stimulates caspase activation. Taken together, TL-77 represents a promising anticancer agent worthy of further evaluation.
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Affiliation(s)
- Tiangong Lu
- School of Pharmacy and Centre for Biomolecular Sciences, University of Nottingham, University Park, Nottingham, United Kingdom (T.L., C.A.L., T.D.B.); and Centre for Drug Discovery and Development, Sansom Institute for Health Research, and School of Pharmacy and Medical Sciences, University of South Australia, Adelaide, Australia (S.W.)
| | - Charles A Laughton
- School of Pharmacy and Centre for Biomolecular Sciences, University of Nottingham, University Park, Nottingham, United Kingdom (T.L., C.A.L., T.D.B.); and Centre for Drug Discovery and Development, Sansom Institute for Health Research, and School of Pharmacy and Medical Sciences, University of South Australia, Adelaide, Australia (S.W.)
| | - Shudong Wang
- School of Pharmacy and Centre for Biomolecular Sciences, University of Nottingham, University Park, Nottingham, United Kingdom (T.L., C.A.L., T.D.B.); and Centre for Drug Discovery and Development, Sansom Institute for Health Research, and School of Pharmacy and Medical Sciences, University of South Australia, Adelaide, Australia (S.W.)
| | - Tracey D Bradshaw
- School of Pharmacy and Centre for Biomolecular Sciences, University of Nottingham, University Park, Nottingham, United Kingdom (T.L., C.A.L., T.D.B.); and Centre for Drug Discovery and Development, Sansom Institute for Health Research, and School of Pharmacy and Medical Sciences, University of South Australia, Adelaide, Australia (S.W.)
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Kim YB, Kang CW, Ranatunga S, Yang H, Sebti SM, Del Valle JR. Imidazo[1,2-a]pyridine-based peptidomimetics as inhibitors of Akt. Bioorg Med Chem Lett 2014; 24:4650-4653. [PMID: 25205195 DOI: 10.1016/j.bmcl.2014.08.040] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2014] [Revised: 08/16/2014] [Accepted: 08/19/2014] [Indexed: 12/26/2022]
Abstract
We report the design, synthesis, and biological evaluation of imidazopyridine-based peptidomimetics based on the substrate consensus sequence of Akt, an AGC family serine/threonine kinase hyperactivated in over 50% of human tumors. Our ligand-based approach led to the identification of novel substrate mimetic inhibitors of Akt1 featuring an unnatural extended dipeptide surrogate. Compound 11 inhibits Akt isoforms in the sub-micromolar range and exhibits improved proteolytic stability relative to a parent pentapeptide.
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Affiliation(s)
- Young B Kim
- Drug Discovery Department, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL 33612, USA
| | - Chang Won Kang
- Drug Discovery Department, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL 33612, USA
| | - Sujeewa Ranatunga
- Drug Discovery Department, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL 33612, USA
| | - Hua Yang
- Drug Discovery Department, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL 33612, USA
| | - Said M Sebti
- Drug Discovery Department, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL 33612, USA
| | - Juan R Del Valle
- Drug Discovery Department, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL 33612, USA
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Premnath PN, Liu S, Perkins T, Abbott J, Anderson E, McInnes C. Fragment based discovery of arginine isosteres through REPLACE: towards non-ATP competitive CDK inhibitors. Bioorg Med Chem 2013; 22:616-22. [PMID: 24286762 DOI: 10.1016/j.bmc.2013.10.039] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2013] [Revised: 10/16/2013] [Accepted: 10/24/2013] [Indexed: 11/26/2022]
Abstract
In order to develop non-ATP competitive CDK2/cyclin A inhibitors, the REPLACE strategy has been applied to generate fragment alternatives for the N-terminal tetrapeptide of the cyclin binding motif (HAKRRLIF) involved in substrate recruitment prior to phosphotransfer. The docking approach used for the prediction of small molecule mimics for peptide determinants was validated through reproduction of experimental binding modes of known inhibitors and provides useful information for evaluating binding to protein-protein interaction sites. Further to this, potential arginine isosteres predicted using the validated LigandFit docking method were ligated to the truncated C-terminal peptide, RLIF using solid phase synthesis and evaluated in a competitive binding assay. After testing, identified fragments were shown to represent not only appropriate mimics for a critical arginine residue but also to interact effectively with a minor hydrophobic pocket present in the binding groove. Further evaluation of binding modes was undertaken to optimize the potency of these compounds. Through further application of the REPLACE strategy in this study, peptide-small molecule hybrid CDK2 inhibitors were identified that are more drug-like and suitable for further optimization as anti-tumor therapeutics.
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Affiliation(s)
- Padmavathy Nandha Premnath
- Drug Discovery and Biomedical Sciences, South Carolina College of Pharmacy, University of South Carolina, Columbia, SC 29208, United States
| | - Shu Liu
- Drug Discovery and Biomedical Sciences, South Carolina College of Pharmacy, University of South Carolina, Columbia, SC 29208, United States
| | - Tracy Perkins
- Drug Discovery and Biomedical Sciences, South Carolina College of Pharmacy, University of South Carolina, Columbia, SC 29208, United States
| | - Jennifer Abbott
- Drug Discovery and Biomedical Sciences, South Carolina College of Pharmacy, University of South Carolina, Columbia, SC 29208, United States
| | - Erin Anderson
- Drug Discovery and Biomedical Sciences, South Carolina College of Pharmacy, University of South Carolina, Columbia, SC 29208, United States
| | - Campbell McInnes
- Drug Discovery and Biomedical Sciences, South Carolina College of Pharmacy, University of South Carolina, Columbia, SC 29208, United States.
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Dykstra DW, Dalby KN, Ren P. Elucidating binding modes of zuonin A enantiomers to JNK1 via in silico methods. J Mol Graph Model 2013; 45:38-44. [PMID: 24001752 DOI: 10.1016/j.jmgm.2013.08.008] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2013] [Revised: 07/24/2013] [Accepted: 08/06/2013] [Indexed: 10/26/2022]
Abstract
Aberrant c-Jun N-terminal kinase (JNK) signaling is associated with a number of diseases, including neurological conditions and cancer. Enantiomers of the lignan zuonin A, (-)-zuonin A and (+)-zuonin A bind isoforms of JNK with similar affinity and disrupt protein-protein interactions at JNK's D-recruitment site. Thus, they are of interest as lead non-ATP competitive inhibitors of the JNKs. While (-)-zuonin A inhibits the activity of JNK toward c-Jun by 80% when saturating, (+)-zuonin A only inhibits by 15%. Molecular docking and molecular dynamics simulations were performed to gain a better understanding of how these inhibitors interact with JNK. The results of this study provide new insight into potential binding modes for (-)-zuonin A and suggest that (-)-zuonin A interacts with JNK via an induced fit mechanism near the highly conserved φA-X-φB recognition site. Binding of (+)-zuonin A to JNK displays no such dynamic feature. The different binding modes may help explain differences in the inhibitory properties of the enantiomers although further experimental work would be necessary to fully confirm this interpretation.
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Affiliation(s)
- Daniel W Dykstra
- Department of Biomedical Engineering, University of Texas at Austin, TX 78712, USA; Department of Biochemistry, University of Texas at Austin, TX 78712, USA
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Wu X, Wan S, Li Z, Yang L, Zhang J, Wu S. 3D-QSAR study on 2,3-dihydroimidazo[4,5]-pyridin-2-one derivatives with a meta substitution pattern as V600EBRAF inhibitors. Med Chem Res 2013. [DOI: 10.1007/s00044-013-0633-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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Bharate SB, Sawant SD, Singh PP, Vishwakarma RA. Kinase inhibitors of marine origin. Chem Rev 2013; 113:6761-815. [PMID: 23679846 DOI: 10.1021/cr300410v] [Citation(s) in RCA: 89] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Sandip B Bharate
- Medicinal Chemistry Division, Indian Institute of Integrative Medicine (Council of Scientific and Industrial Research), Canal Road, Jammu-180001, India
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25
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Abstract
VEGF is an important signaling protein involved in both vasculogenesis and angiogenesis. As an essential receptor protein tyrosine kinase propagating cellular signal transduction processes, VEGFR-2 is a central target for drug discovery against tumor-associated angiogenesis. Since the autophosphorylation of VEGFR-2 represents a key step in this signal pathway that contributes to angiogenesis, the discovery of small molecule inhibitors that block this reaction has attracted great interest for novel drugs research and development. Advances in the understanding of catalytic cleft and the conformational changes of DFG motif have resulted in the development of small molecule inhibitors known as type I and type II. High-resolution crystal structures of various inhibitors in complex with the receptor offer an insight into the relationship among binding modes, inhibition mechanisms, activity, selectivity and resistance. To control selectivity, improve activity and introduce intellectual property novelty, the strategies for the further development are discussed through structural and conformational analysis in this review.
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Hindie V, Lopez-Garcia LA, Biondi RM. Use of a fluorescent ATP analog to probe the allosteric conformational change in the active site of the protein kinase PDK1. METHODS IN MOLECULAR BIOLOGY (CLIFTON, N.J.) 2013; 928:133-41. [PMID: 22956138 DOI: 10.1007/978-1-62703-008-3_10] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/15/2023]
Abstract
There is growing interest in exploring allosteric sites on proteins for drug discovery. At the center of the regulation of many protein kinases from the AGC family there is an allosteric site termed "PIF-pocket." The regulated binding of a C-terminal region of the kinase to the PIF-pocket, within the small lobe of the catalytic core, modulates the activity of AGC kinases. Small compounds that bind to the PIF-pocket can mimic its physiological mechanism of regulation and modulate the kinase activity in vitro, e.g., small compounds can activate the phosphoinositide-dependent protein kinase 1 (PDK1). Compounds binding to an allosteric site on a protein kinase may produce conformational changes at the ATP-binding site within the active site of the kinase domain. We here describe a fluorescent method using the ATP analog TNP-ATP that allows evaluating the allosteric conformational changes at the ATP-binding site of PDK1 triggered by small compounds binding to the PIF-pocket.
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Affiliation(s)
- Valerie Hindie
- Department of Internal Medicine I, Research Group PhosphoSites, Universitätsklinikum Frankfurt, Frankfurt, Germany
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27
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Jin F, Gao D, Zhang C, Liu F, Chu B, Chen Y, Chen YZ, Tan C, Jiang Y. Exploration of 1-(3-chloro-4-(4-oxo-4H-chromen-2-yl)phenyl)-3-phenylurea derivatives as selective dual inhibitors of Raf1 and JNK1 kinases for anti-tumor treatment. Bioorg Med Chem 2013; 21:824-31. [DOI: 10.1016/j.bmc.2012.04.006] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2012] [Revised: 03/31/2012] [Accepted: 04/04/2012] [Indexed: 12/19/2022]
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Wu XY, Chen WH, Wu SG, Tian YX, Zhang JJ. Pyrrolo[3,2-d]pyrimidine derivatives as type II kinase insert domain receptor (KDR) inhibitors: CoMFA and CoMSIA studies. Int J Mol Sci 2012; 13:2387-2404. [PMID: 22408460 PMCID: PMC3292029 DOI: 10.3390/ijms13022387] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2011] [Revised: 02/13/2012] [Accepted: 02/16/2012] [Indexed: 11/16/2022] Open
Abstract
Kinase insert domain receptor (KDR) inhibitors have been proved to be very effective anticancer agents. Molecular docking, 3D-QSAR methods, CoMFA and CoMSIA were performed on pyrrolo[3,2-d]pyrimidine derivatives as non-ATP competitive KDR inhibitors (type II). The bioactive conformation was explored by docking one potent compound 20 into the active site of KDR in its DFG-out inactive conformation. The constructed CoMFA and CoMSIA models produced statistically significant results with the cross-validated correlation coefficients q2 of 0.542 and 0.552, non-cross-validated correlation coefficients r2 of 0.912 and 0.955, and predicted correction coefficients r2pred of 0.913 and 0.897, respectively. These results ensure the CoMFA and CoMSIA models as a tool to guide the design of a series of new potent KDR inhibitors.
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Affiliation(s)
- Xiao-Yun Wu
- Author to whom correspondence should be addressed; E-Mails: (X.-Y.W.); (W.-H.C.); (J.-J.Z.); Tel.: +86-20-6278-9490 (X.-Y.W.); +86-20-6164-8589 (W.-H.C.); +86-20-6164-8548 (J.-J.Z.)
| | - Wen-Hua Chen
- Author to whom correspondence should be addressed; E-Mails: (X.-Y.W.); (W.-H.C.); (J.-J.Z.); Tel.: +86-20-6278-9490 (X.-Y.W.); +86-20-6164-8589 (W.-H.C.); +86-20-6164-8548 (J.-J.Z.)
| | | | | | - Jia-Jie Zhang
- Author to whom correspondence should be addressed; E-Mails: (X.-Y.W.); (W.-H.C.); (J.-J.Z.); Tel.: +86-20-6278-9490 (X.-Y.W.); +86-20-6164-8589 (W.-H.C.); +86-20-6164-8548 (J.-J.Z.)
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Progress in the Development of Non-ATP-Competitive Protein Kinase Inhibitors for Oncology. ANNUAL REPORTS IN MEDICINAL CHEMISTRY 2012. [DOI: 10.1016/b978-0-12-396492-2.00029-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register]
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Millward SW, Henning RK, Kwong GA, Pitram S, Agnew HD, Deyle KM, Nag A, Hein J, Lee SS, Lim J, Pfeilsticker JA, Sharpless KB, Heath JR. Iterative in situ click chemistry assembles a branched capture agent and allosteric inhibitor for Akt1. J Am Chem Soc 2011; 133:18280-8. [PMID: 21962254 DOI: 10.1021/ja2064389] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
We describe the use of iterative in situ click chemistry to design an Akt-specific branched peptide triligand that is a drop-in replacement for monoclonal antibodies in multiple biochemical assays. Each peptide module in the branched structure makes unique contributions to affinity and/or specificity resulting in a 200 nM affinity ligand that efficiently immunoprecipitates Akt from cancer cell lysates and labels Akt in fixed cells. Our use of a small molecule to preinhibit Akt prior to screening resulted in low micromolar inhibitory potency and an allosteric mode of inhibition, which is evidenced through a series of competitive enzyme kinetic assays. To demonstrate the efficiency and selectivity of the protein-templated in situ click reaction, we developed a novel QPCR-based methodology that enabled a quantitative assessment of its yield. These results point to the potential for iterative in situ click chemistry to generate potent, synthetically accessible antibody replacements with novel inhibitory properties.
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Affiliation(s)
- Steven W Millward
- Nanosystems Biology Cancer Center, Division of Chemistry and Chemical Engineering, MC-127-72, California Institute of Technology, Pasadena, California 91125, United States
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31
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Abstract
INTRODUCTION because of their important roles in disease and excellent 'druggability', kinases have become the second largest drug target family. The great success of the BCR-ABL inhibitor imatinib in treating chronic myelogenous leukemia illustrates the high potential of kinase inhibitor (KI) therapeutics, but also unveils a major limitation: the development of drug resistance. This is a significant concern as KIs reach large patient populations for an expanding array of indications. AREAS COVERED we provide an up-to-date understanding of the mechanisms through which KIs function and through which cells can become KI-resistant. We review current and future approaches to overcome KI resistance, focusing on currently approved KIs and KIs in clinical trials. We then discuss approaches to improve KI efficacy and overcome drug resistance and novel approaches to develop less drug resistance-prone KI therapeutics. EXPERT OPINION although drug resistance is a concern for current KI therapeutics, recent progress in our understanding of the underlying mechanisms and promising technological advances may overcome this limitation and provide powerful new therapeutics.
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Affiliation(s)
- Rina Barouch-Bentov
- Stanford University School of Medicine, Division of Infectious Disease and Geographic Medicine, Department of Medicine, Stanford, California 94305, USA
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32
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McInnes C, Wyatt MD. PLK1 as an oncology target: current status and future potential. Drug Discov Today 2011; 16:619-25. [PMID: 21601650 DOI: 10.1016/j.drudis.2011.05.002] [Citation(s) in RCA: 71] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2011] [Revised: 03/24/2011] [Accepted: 05/06/2011] [Indexed: 10/18/2022]
Abstract
The Polo-like kinases (PLKs) have been investigated as oncology targets for several years; however, only recently have potent inhibitors been described. Here, we report on progress in the clinical validation of the PLKs as antitumor drug targets as well as recent understanding gained regarding their synergistic roles in the context of other molecular defects occurring in tumors. Also relevant to the development of PLK inhibitors as therapeutics are the putative roles of other members of this family as tumor suppressors. The resulting potential drawbacks of non-isoform selective compounds are presented. As an alternative approach to achieving PLK1 specificity, we discuss prospects for developing small molecule inhibitors of the crucial regulatory and subcellular targeting domain containing the Polo-boxes.
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Affiliation(s)
- Campbell McInnes
- Pharmaceutical and Biomedical Sciences, South Carolina College of Pharmacy, University of South Carolina, Columbia, SC 29208, USA.
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33
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Corbel C, Wang Q, Bousserouel H, Hamdi A, Zhang B, Lozach O, Ferandin Y, Tan VBC, Guéritte F, Colas P, Couturier C, Bach S. First BRET-based screening assay performed in budding yeast leads to the discovery of CDK5/p25 interaction inhibitors. Biotechnol J 2011; 6:860-70. [PMID: 21681968 DOI: 10.1002/biot.201100138] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2011] [Revised: 04/07/2011] [Accepted: 04/29/2011] [Indexed: 11/06/2022]
Abstract
The protein kinase CDK5 (cyclin-dependent kinase 5) is activated through its association with a cyclin-like protein p35 or p39. In pathological conditions (such as Alzheimer's disease and various other neuropathies), truncation of p35 leads to the appearance of the p25 protein. The interaction of p25 with CDK5 up-regulates the kinase activity and modifies the substrate specificity. ATP-mimetic inhibitors of CDK5 have already been developed. However, the lack of selectivity of such inhibitors is often a matter of concern. An alternative approach can be used to identify highly specific inhibitors that disrupt protein interactions involving protein kinases. We have developed a bioluminescence resonance energy transfer (BRET)-based screening assay in yeast to discover protein-protein interaction inhibitors (P2I2). Here, we present the first use of BRET in yeast for the screening of small molecule libraries. This screening campaign led to the discovery of one molecule that prevents the interaction between CDK5 and p25, thus inhibiting the protein kinase activity. This molecule may give rise to high-specificity drug candidates.
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Affiliation(s)
- Caroline Corbel
- CNRS USR 3151, Protein Phosphorylation and Disease Laboratory, Protein-Protein Interaction Inhibition P2I2 Group, Station Biologique, Roscoff, Bretagne, France
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Loughlin WA, Tyndall JDA, Glenn MP, Hill TA, Fairlie DP. Update 1 of: Beta-Strand Mimetics. Chem Rev 2011; 110:PR32-69. [DOI: 10.1021/cr900395y] [Citation(s) in RCA: 83] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Wendy A. Loughlin
- School of Science, Nathan Campus, Griffith University, Brisbane, QLD 4111, Australia, and Division of Chemistry and Structural Biology, Institute for Molecular Bioscience, University of Queensland, Brisbane, QLD 4072, Australia This is a Chemical Reviews Perennial Review. The root paper of this title was published in Chem. Rev. 2004, 104 (12), 6085−6117, DOI: 10.1021/cr040648k; Published (Web) Nov. 4, 2004. Updates to the text appear in red type
| | - Joel D. A. Tyndall
- School of Science, Nathan Campus, Griffith University, Brisbane, QLD 4111, Australia, and Division of Chemistry and Structural Biology, Institute for Molecular Bioscience, University of Queensland, Brisbane, QLD 4072, Australia This is a Chemical Reviews Perennial Review. The root paper of this title was published in Chem. Rev. 2004, 104 (12), 6085−6117, DOI: 10.1021/cr040648k; Published (Web) Nov. 4, 2004. Updates to the text appear in red type
| | - Matthew P. Glenn
- School of Science, Nathan Campus, Griffith University, Brisbane, QLD 4111, Australia, and Division of Chemistry and Structural Biology, Institute for Molecular Bioscience, University of Queensland, Brisbane, QLD 4072, Australia This is a Chemical Reviews Perennial Review. The root paper of this title was published in Chem. Rev. 2004, 104 (12), 6085−6117, DOI: 10.1021/cr040648k; Published (Web) Nov. 4, 2004. Updates to the text appear in red type
| | - Timothy A. Hill
- School of Science, Nathan Campus, Griffith University, Brisbane, QLD 4111, Australia, and Division of Chemistry and Structural Biology, Institute for Molecular Bioscience, University of Queensland, Brisbane, QLD 4072, Australia This is a Chemical Reviews Perennial Review. The root paper of this title was published in Chem. Rev. 2004, 104 (12), 6085−6117, DOI: 10.1021/cr040648k; Published (Web) Nov. 4, 2004. Updates to the text appear in red type
| | - David P. Fairlie
- School of Science, Nathan Campus, Griffith University, Brisbane, QLD 4111, Australia, and Division of Chemistry and Structural Biology, Institute for Molecular Bioscience, University of Queensland, Brisbane, QLD 4072, Australia This is a Chemical Reviews Perennial Review. The root paper of this title was published in Chem. Rev. 2004, 104 (12), 6085−6117, DOI: 10.1021/cr040648k; Published (Web) Nov. 4, 2004. Updates to the text appear in red type
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35
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Radi M, Dreassi E, Brullo C, Crespan E, Tintori C, Bernardo V, Valoti M, Zamperini C, Daigl H, Musumeci F, Carraro F, Naldini A, Filippi I, Maga G, Schenone S, Botta M. Design, Synthesis, Biological Activity, and ADME Properties of Pyrazolo[3,4-d]pyrimidines Active in Hypoxic Human Leukemia Cells: A Lead Optimization Study. J Med Chem 2011; 54:2610-26. [DOI: 10.1021/jm1012819] [Citation(s) in RCA: 66] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- Marco Radi
- Dipartimento Farmaco Chimico Tecnologico, University of Siena,Via Alcide de Gasperi 2, I-53100 Siena, Italy
| | - Elena Dreassi
- Dipartimento Farmaco Chimico Tecnologico, University of Siena,Via Alcide de Gasperi 2, I-53100 Siena, Italy
| | - Chiara Brullo
- Dipartimento di Scienze Farmaceutiche, University of Genoa, Viale Benedetto XV 3, I-16132 Genova, Italy
| | - Emmanuele Crespan
- Istituto di Genetica Molecolare, IGM-CNR, Via Abbiategrasso 207, I-27100 Pavia, Italy
| | - Cristina Tintori
- Dipartimento Farmaco Chimico Tecnologico, University of Siena,Via Alcide de Gasperi 2, I-53100 Siena, Italy
| | - Vincenzo Bernardo
- Dipartimento Farmaco Chimico Tecnologico, University of Siena,Via Alcide de Gasperi 2, I-53100 Siena, Italy
| | - Massimo Valoti
- Dipartimento di Neuroscienze, University of Siena, Via Alcide de Gasperi 2, I-53100 Siena, Italy
| | - Claudio Zamperini
- Dipartimento Farmaco Chimico Tecnologico, University of Siena,Via Alcide de Gasperi 2, I-53100 Siena, Italy
| | - Henry Daigl
- Dipartimento Farmaco Chimico Tecnologico, University of Siena,Via Alcide de Gasperi 2, I-53100 Siena, Italy
| | - Francesca Musumeci
- Dipartimento di Scienze Farmaceutiche, University of Genoa, Viale Benedetto XV 3, I-16132 Genova, Italy
| | - Fabio Carraro
- Dipartimento di Fisiologia, Sezione di Neuroimmunofisiologia, University of Siena, Via Aldo Moro, I-53100 Siena, Italy
| | - Antonella Naldini
- Dipartimento di Fisiologia, Sezione di Neuroimmunofisiologia, University of Siena, Via Aldo Moro, I-53100 Siena, Italy
| | - Irene Filippi
- Dipartimento di Fisiologia, Sezione di Neuroimmunofisiologia, University of Siena, Via Aldo Moro, I-53100 Siena, Italy
| | - Giovanni Maga
- Istituto di Genetica Molecolare, IGM-CNR, Via Abbiategrasso 207, I-27100 Pavia, Italy
| | - Silvia Schenone
- Dipartimento di Scienze Farmaceutiche, University of Genoa, Viale Benedetto XV 3, I-16132 Genova, Italy
| | - Maurizio Botta
- Dipartimento Farmaco Chimico Tecnologico, University of Siena,Via Alcide de Gasperi 2, I-53100 Siena, Italy
- Sbarro Institute for Cancer Research and Molecular Medicine, Center for Biotechnology, College of Science and Technology, Temple University, BioLife Science Building, Suite 333, 1900 N 12th Street, Philadelphia, Pennsylvania 19122, United States
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36
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Shallal HM, Russu WA. Discovery, synthesis, and investigation of the antitumor activity of novel piperazinylpyrimidine derivatives. Eur J Med Chem 2011; 46:2043-57. [PMID: 21429632 DOI: 10.1016/j.ejmech.2011.02.057] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2010] [Revised: 02/19/2011] [Accepted: 02/22/2011] [Indexed: 12/20/2022]
Abstract
Protein kinases play several pertinent roles in cell proliferation, and targeting these proteins has been shown to be a successful strategy toward controlling different malignancies. Despite the great discovery stories during the last two decades, there is still a demand for anticancer small molecules with the potential of being selective on both the protein kinase and/or the cellular level. A series of novel piperazinylpyrimidine compounds were synthesized and tested for their potential to selectively inhibit the growth of certain tumor cell lines included within the NCI-60 cell line panel. MDA-MB-468, a triple-negative/basal-like breast carcinoma, cell line was among the most sensitive cell lines towards compounds 4 and 15. The three most interesting compounds identified in cellular screens (4, 15, and 16) were subjected to kinase profiling and found to have an interesting selective tendency to target certain kinase subfamily members; PDGFR, CK1, RAF and others. Compound 4 showed a selective tendency to bind to and/or inhibit the function of certain KIT and PDGFRA mutants compared to their wild-type isoforms. Piperazinylpyrimidine based derivatives represent a new class of selective kinase inhibitors. Significantly 4 is more potent at inhibiting oncogenic mutant forms of PDGFR family kinases, which is relevant in terms of its potential use in treating tumors that have become resistant to treatment or driven by such mutations. The clinical demand for agents useful in the control of triple-negative/basal-like breast cancer justifies our interest in compound 15 which is a potent growth inhibitor of MDA-MB-468 cell line.
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Affiliation(s)
- Hassan M Shallal
- Department of Pharmaceutics & Medicinal Chemistry, Thomas J. Long School of Pharmacy and Health Sciences, University of the Pacific, 3601 Pacific Ave., Stockton, CA 95211, USA
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Radi M, Crespan E, Falchi F, Bernardo V, Zanoli S, Manetti F, Schenone S, Maga G, Botta M. Design and synthesis of thiadiazoles and thiazoles targeting the Bcr-Abl T315I mutant: from docking false positives to ATP-noncompetitive inhibitors. ChemMedChem 2010; 5:1226-31. [PMID: 20509136 DOI: 10.1002/cmdc.201000066] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- Marco Radi
- Dipartimento Farmaco Chimico Tecnologico, University of Siena, Italy
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38
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Simard JR, Getlik M, Grütter C, Schneider R, Wulfert S, Rauh D. Fluorophore labeling of the glycine-rich loop as a method of identifying inhibitors that bind to active and inactive kinase conformations. J Am Chem Soc 2010; 132:4152-60. [PMID: 20201574 DOI: 10.1021/ja908083e] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Targeting protein kinases with small organic molecules is a promising strategy to regulate unwanted kinase activity in both chemical biology and medicinal chemistry research. Traditionally, kinase inhibitors are identified in activity-based screening assays using enzymatically active kinase preparations to measure the perturbation of substrate phosphorylation, often resulting in the enrichment of classical ATP competitive (Type I) inhibitors. However, addressing enzymatically incompetent kinase conformations offers new opportunities for targeted therapies and is moving to the forefront of kinase inhibitor research. Here we report the development of a new FLiK (Fluorescent Labels in Kinases) binding assay to detect small molecules that induce changes in the conformation of the glycine-rich loop. Due to cross-talk between the glycine-rich loop and the activation loop in kinases, this alternative labeling approach can also detect ligands that stabilize inactive kinase conformations, including slow-binding Type II and Type III kinase inhibitors. Protein X-ray crystallography validated the assay results and identified a novel DFG-out binding mode for a quinazoline-based inhibitor in p38alpha kinase. We also detected the high-affinity binding of a clinically relevant and specific VEGFR2 inhibitor, and we provide structural details of its binding mode in p38alpha, in which it stabilizes the DFG-out conformation. Last, we demonstrate the power of this new FLiK labeling strategy to detect the binding of Type I ligands that induce conformational changes in the glycine-rich loop as a means of gaining affinity for the target kinase. This approach may be a useful alternative to develop direct binding assays for kinases that do not adopt the DFG-out conformation while also avoiding the use of expensive kits, detection reagents, or radioactivity frequently employed with activity-based assays.
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Affiliation(s)
- Jeffrey R Simard
- Chemical Genomics Centre of the Max Planck Society, Otto-Hahn-Strasse 15, D-44227 Dortmund, Germany
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Simard JR, Grütter C, Pawar V, Aust B, Wolf A, Rabiller M, Wulfert S, Robubi A, Klüter S, Ottmann C, Rauh D. High-throughput screening to identify inhibitors which stabilize inactive kinase conformations in p38alpha. J Am Chem Soc 2010; 131:18478-88. [PMID: 19950957 DOI: 10.1021/ja907795q] [Citation(s) in RCA: 67] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Small molecule kinase inhibitors are an attractive means to modulate kinase activities in medicinal chemistry and chemical biology research. In the physiological setting of a cell, kinase function is orchestrated by a plethora of regulatory processes involving the structural transition of kinases between inactive and enzymatically competent conformations and vice versa. The development of novel kinase inhibitors is mainly fostered by high-throughput screening initiatives where the small molecule perturbation of the phosphorylation reaction is measured to identify inhibitors. Such setups require enzymatically active kinase preparations and present a risk of solely identifying classical ATP-competitive Type I inhibitors. Here we report the high-throughput screening of a library of approximately 35000 small organic molecules with an assay system that utilizes enzymatically inactive human p38alpha MAP kinase to detect stabilizers of the pharmacologically more desirable DFG-out conformation. We used protein X-ray crystallography to characterize the binding mode of hit compounds and reveal structural features which explain how these ligands stabilize and/or induce the DFG-out conformation. Lastly, we show that although some of the hit compounds were confirmed by protein X-ray crystallography, they were not detected in classic phosphorylation assays, thus validating the unique sensitivity of the assay system used in this study and highlighting the potential of screening with inactive kinase preparations.
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Affiliation(s)
- Jeffrey R Simard
- Chemical Genomics Centre of the Max Planck Society, Otto-Hahn-Strasse 15, D-44227 Dortmund, Germany
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40
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Simard JR, Getlik M, Grütter C, Pawar V, Wulfert S, Rabiller M, Rauh D. Development of a fluorescent-tagged kinase assay system for the detection and characterization of allosteric kinase inhibitors. J Am Chem Soc 2010; 131:13286-96. [PMID: 19572644 DOI: 10.1021/ja902010p] [Citation(s) in RCA: 113] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Kinase disregulation disrupts the intricate network of intracellular signaling pathways and contributes to the onset of diseases such as cancer. Although several kinase inhibitors are on the market, inhibitor selectivity and drug resistance mutations persist as fundamental challenges in the development of effective long-term treatments. Chemical entities binding to less conserved allosteric sites would be expected to offer new opportunities for scaffold development. Because no high-throughput method was previously available, we developed a fluorescence-based kinase binding assay for identifying and characterizing ligands which stabilize the inactive kinase conformation. Here, we present a description of the development and validation of this assay using the serine/threonine kinase p38alpha. By covalently attaching fluorophores to the activation loop of the kinase, we were able to detect conformational changes and measure the K(d), k(on), and k(off) associated with the binding and dissociation of ligands to the allosteric pocket. We report the SAR of a synthesized focused library of pyrazolourea derivatives, a scaffold known to bind with high affinity to the allosteric pocket of p38alpha. Additionally, we used protein X-ray crystallography together with our assay to examine the binding and dissociation kinetics to characterize potent quinazoline- and quinoline-based type II inhibitors, which also utilize this binding pocket in p38alpha. Last, we identified the b-Raf inhibitor sorafenib as a potent low nanomolar inhibitor of p38alpha and used protein X-ray crystallography to confirm a unique binding mode to the inactive kinase conformation.
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Affiliation(s)
- Jeffrey R Simard
- Chemical Genomics Centre of the Max Planck Society, Otto-Hahn-Strasse 15, D-44227 Dortmund, Germany
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