1
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Zhao S, Ali AS, Liu X, Yu Z, Kong X, Zhang Y, Paul Savage G, Xu Y, Lin B, Wu D, Francis CL. 1,3-Disubstituted-1,2,4-triazin-6-ones with potent activity against androgen receptor-dependent prostate cancer cells. Bioorg Med Chem 2024; 101:117634. [PMID: 38359754 DOI: 10.1016/j.bmc.2024.117634] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Revised: 01/31/2024] [Accepted: 02/05/2024] [Indexed: 02/17/2024]
Abstract
Synthesis and biological evaluation of a small, focused library of 1,3-disubstituted-1,2,4-triazin-6-ones for in vitro inhibitory activity against androgen-receptor-dependent (22Rv1) and androgen-receptor independent (PC3) castration-resistant prostate cancer (CRPC) cells led to highly active compounds with in vitro IC50 values against 22Rv1 cells of <200 nM, and with apparent selectivity for this cell type over PC3 cells. From metabolic/PK evaluations of these compounds, a 3-benzyl-1-(2,4-dichlorobenzyl) derivative had superior properties and showed considerably stronger activity, by nearly an order of magnitude, against AR-dependent LNCaP and C4-2B cells compared to AR-independent DU145 cells. This lead compound decreased AR expression in a dose and time dependent manner and displayed promising therapeutic effects in a 22Rv1 CRPC xenograft mouse model. Computational target prediction and subsequent docking studies suggested three potential known prostate cancer targets: p38a MAPK, TGF-β1, and HGFR/c-Met, with the latter case of c-Met appearing stronger, owing to close structural similarity of the lead compound to known pyridazin-3-one derivatives with potent c-Met inhibitory activity. RNA-seq analysis showed dramatic reduction of AR signalling pathway and/or target genes by the lead compound, subsequently confirmed by quantitative PCR analysis. The lead compound was highly inhibitory against HGF, the c-Met ligand, which fitted well with the computational target prediction and docking studies. These results suggest that this compound could be a promising starting point for the development of an effective therapy for the treatment of CRPC.
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Affiliation(s)
- Shiting Zhao
- Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China; Guangzhou Medical University, Guangzhou 511436, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Abdelsalam S Ali
- Drug Discovery Chemistry Team, CSIRO, Clayton, Victoria 3168, Australia
| | - Xiaomin Liu
- Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China; Guangzhou Medical University, Guangzhou 511436, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhiwei Yu
- Key Laboratory of Structure-Based Drug Design and Discovery of Ministry of Education, Wuya College of Innovation, Shenyang Pharmaceutical University, Shenyang 110016, China
| | - Xinyu Kong
- Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China; Guangzhou Medical University, Guangzhou 511436, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yan Zhang
- Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China; Guangzhou Medical University, Guangzhou 511436, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - G Paul Savage
- Drug Discovery Chemistry Team, CSIRO, Clayton, Victoria 3168, Australia
| | - Yong Xu
- Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China; Guangzhou Medical University, Guangzhou 511436, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Bin Lin
- Key Laboratory of Structure-Based Drug Design and Discovery of Ministry of Education, Wuya College of Innovation, Shenyang Pharmaceutical University, Shenyang 110016, China
| | - Donghai Wu
- Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China; Guangzhou Medical University, Guangzhou 511436, China; University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Craig L Francis
- Drug Discovery Chemistry Team, CSIRO, Clayton, Victoria 3168, Australia.
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2
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Zhou W, Ryan A, Janosko CP, Shoger KE, Haugh JM, Gottschalk RA, Deiters A. Isoform-specific optical activation of kinase function reveals p38-ERK signaling crosstalk. RSC Chem Biol 2023; 4:765-773. [PMID: 37799579 PMCID: PMC10549237 DOI: 10.1039/d2cb00157h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Accepted: 08/08/2023] [Indexed: 10/07/2023] Open
Abstract
Evolution has diversified the mammalian proteome by the generation of protein isoforms that originate from identical genes, e.g., through alternative gene splicing or post-translational modifications, or very similar genes found in gene families. Protein isoforms can have either overlapping or unique functions and traditional chemical, biochemical, and genetic techniques are often limited in their ability to differentiate between isoforms due to their high similarity. This is particularly true in the context of highly dynamic cell signaling cascades, which often require acute spatiotemporal perturbation to assess mechanistic details. To that end, we describe a method for the selective perturbation of the individual protein isoforms of the mitogen-activated protein kinase (MAPK) p38. The genetic installation of a photocaging group at a conserved active site lysine enables the precise light-controlled initiation of kinase signaling, followed by investigation of downstream events. Through optical control, we have identified a novel point of crosstalk between two major signaling cascades: the p38/MAPK pathway and the extracellular signal-regulated kinase (ERK)/MAPK pathway. Specifically, using the photoactivated p38 isoforms, we have found the p38γ and p38δ variants to be positive regulators of the ERK signaling cascade, while confirming the p38α and p38β variants as negative regulators.
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Affiliation(s)
- Wenyuan Zhou
- Department of Chemistry, University of Pittsburgh Pittsburgh PA 15260 USA
| | - Amy Ryan
- Department of Chemistry, University of Pittsburgh Pittsburgh PA 15260 USA
| | - Chasity P Janosko
- Department of Chemistry, University of Pittsburgh Pittsburgh PA 15260 USA
| | - Karsen E Shoger
- Department of Immunology, University of Pittsburgh School of Medicine Pittsburgh PA 15260 USA
- Center for Systems Immunology, University of Pittsburgh Pittsburgh PA 15261 USA
| | - Jason M Haugh
- Department of Chemical and Biomolecular Engineering, North Carolina State University Raleigh NC 27606 USA
| | - Rachel A Gottschalk
- Department of Immunology, University of Pittsburgh School of Medicine Pittsburgh PA 15260 USA
- Center for Systems Immunology, University of Pittsburgh Pittsburgh PA 15261 USA
| | - Alexander Deiters
- Department of Chemistry, University of Pittsburgh Pittsburgh PA 15260 USA
- Center for Systems Immunology, University of Pittsburgh Pittsburgh PA 15261 USA
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3
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Armani E, Capaldi C, Bagnacani V, Saccani F, Aquino G, Puccini P, Facchinetti F, Martucci C, Moretto N, Villetti G, Patacchini R, Civelli M, Hurley C, Jennings A, Alcaraz L, Bloomfield D, Briggs M, Daly S, Panchal T, Russell V, Wicks S, Finch H, Fitzgerald M, Fox C, Delcanale M. Design, Synthesis, and Biological Characterization of Inhaled p38α/β MAPK Inhibitors for the Treatment of Lung Inflammatory Diseases. J Med Chem 2022; 65:7170-7192. [PMID: 35546685 DOI: 10.1021/acs.jmedchem.2c00115] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The identification of novel inhaled p38α/β mitogen-activated protein kinases (MAPK) (MAPK14/11) inhibitors suitable for the treatment of pulmonary inflammatory conditions has been described. A rational drug design approach started from the identification of a novel tetrahydronaphthalene series, characterized by nanomolar inhibition of p38α with selectivity over p38γ and p38δ isoforms. SAR optimization of 1c is outlined, where improvements in potency against p38α and ligand-enzyme dissociation kinetics led to several compounds showing pronounced anti-inflammatory effects in vitro (inhibition of TNFα release). Targeting of the defined physicochemical properties allowed the identification of compounds 3h, 4e, and 4f, which showed, upon intratracheal instillation, low plasma levels, prolonged lung retention, and anti-inflammatory effects in a rat acute model of a bacterial endotoxin-induced pulmonary inflammation. Compound 4e, in particular, displayed remarkable efficacy and duration of action and was selected for progression in disease models of asthma and chronic obstructive pulmonary disease (COPD).
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Affiliation(s)
- Elisabetta Armani
- Chiesi Farmaceutici S.p.A, Centro Ricerche, Largo Belloli 11/a, 43122 Parma, Italy
| | - Carmelida Capaldi
- Chiesi Farmaceutici S.p.A, Centro Ricerche, Largo Belloli 11/a, 43122 Parma, Italy
| | - Valentina Bagnacani
- Chiesi Farmaceutici S.p.A, Centro Ricerche, Largo Belloli 11/a, 43122 Parma, Italy
| | - Francesca Saccani
- Chiesi Farmaceutici S.p.A, Centro Ricerche, Largo Belloli 11/a, 43122 Parma, Italy
| | - Giancarlo Aquino
- Chiesi Farmaceutici S.p.A, Centro Ricerche, Largo Belloli 11/a, 43122 Parma, Italy
| | - Paola Puccini
- Chiesi Farmaceutici S.p.A, Centro Ricerche, Largo Belloli 11/a, 43122 Parma, Italy
| | - Fabrizio Facchinetti
- Chiesi Farmaceutici S.p.A, Centro Ricerche, Largo Belloli 11/a, 43122 Parma, Italy
| | - Cataldo Martucci
- Chiesi Farmaceutici S.p.A, Centro Ricerche, Largo Belloli 11/a, 43122 Parma, Italy
| | - Nadia Moretto
- Chiesi Farmaceutici S.p.A, Centro Ricerche, Largo Belloli 11/a, 43122 Parma, Italy
| | - Gino Villetti
- Chiesi Farmaceutici S.p.A, Centro Ricerche, Largo Belloli 11/a, 43122 Parma, Italy
| | - Riccardo Patacchini
- Chiesi Farmaceutici S.p.A, Centro Ricerche, Largo Belloli 11/a, 43122 Parma, Italy
| | - Maurizio Civelli
- Chiesi Farmaceutici S.p.A, Centro Ricerche, Largo Belloli 11/a, 43122 Parma, Italy
| | - Chris Hurley
- Charles River Laboratories, 8/9 Spire Green Centre, Flex Meadow, Harlow CM19 5TR, United Kingdom
| | - Andrew Jennings
- Charles River Laboratories, 8/9 Spire Green Centre, Flex Meadow, Harlow CM19 5TR, United Kingdom
| | - Lilian Alcaraz
- Charles River Laboratories, 8/9 Spire Green Centre, Flex Meadow, Harlow CM19 5TR, United Kingdom
| | - Dawn Bloomfield
- Charles River Laboratories, 8/9 Spire Green Centre, Flex Meadow, Harlow CM19 5TR, United Kingdom
| | - Michael Briggs
- Charles River Laboratories, 8/9 Spire Green Centre, Flex Meadow, Harlow CM19 5TR, United Kingdom
| | - Stephen Daly
- Charles River Laboratories, 8/9 Spire Green Centre, Flex Meadow, Harlow CM19 5TR, United Kingdom
| | - Terry Panchal
- Charles River Laboratories, 8/9 Spire Green Centre, Flex Meadow, Harlow CM19 5TR, United Kingdom
| | - Vince Russell
- Charles River Laboratories, 8/9 Spire Green Centre, Flex Meadow, Harlow CM19 5TR, United Kingdom
| | - Sharon Wicks
- Charles River Laboratories, 8/9 Spire Green Centre, Flex Meadow, Harlow CM19 5TR, United Kingdom
| | - Harry Finch
- Pulmagen Therapeutics, The Coach House, Grenville Court Britwell Road, Burnham, Slough SL1 8DF, United Kingdom
| | - Mary Fitzgerald
- Pulmagen Therapeutics, The Coach House, Grenville Court Britwell Road, Burnham, Slough SL1 8DF, United Kingdom
| | - Craig Fox
- Pulmagen Therapeutics, The Coach House, Grenville Court Britwell Road, Burnham, Slough SL1 8DF, United Kingdom
| | - Maurizio Delcanale
- Chiesi Farmaceutici S.p.A, Centro Ricerche, Largo Belloli 11/a, 43122 Parma, Italy
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4
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Halim PA, Hassan RA, Mohamed KO, Hassanin SO, Khalil MG, Abdou AM, Osman EO. Synthesis and biological evaluation of halogenated phenoxychalcones and their corresponding pyrazolines as cytotoxic agents in human breast cancer. J Enzyme Inhib Med Chem 2021; 37:189-201. [PMID: 34894967 PMCID: PMC8667918 DOI: 10.1080/14756366.2021.1998023] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Novel halogenated phenoxychalcones 2a–f and their corresponding N-acetylpyrazolines 3a–f were synthesised and evaluated for their anticancer activities against breast cancer cell line (MCF-7) and normal breast cell line (MCF-10a), compared with staurosporine. All compounds showed moderate to good cytotoxic activity when compared to control. Compound 2c was the most active, with IC50 = 1.52 µM and selectivity index = 15.24. Also, chalcone 2f showed significant cytotoxic activity with IC50 = 1.87 µM and selectivity index = 11.03. Compound 2c decreased both total mitogen activated protein kinase (p38α MAPK) and phosphorylated enzyme in MCF-7 cells, suggesting its ability to decrease cell proliferation and survival. It also showed the ability to induce ROS in MCF-7 treated cells. Compound 2c exhibited apoptotic behaviour in MCF-7 cells due to cell accumulation in G2/M phase and elevation in late apoptosis 57.78-fold more than control. Docking studies showed that compounds 2c and 2f interact with p38alpha MAPK active sites.
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Affiliation(s)
- Peter A Halim
- Pharmaceutical Organic Chemistry Department, Faculty of Pharmacy, Cairo University, Cairo, Egypt
| | - Rasha A Hassan
- Pharmaceutical Organic Chemistry Department, Faculty of Pharmacy, Cairo University, Cairo, Egypt
| | - Khaled O Mohamed
- Pharmaceutical Organic Chemistry Department, Faculty of Pharmacy, Cairo University, Cairo, Egypt
| | - Soha O Hassanin
- Biochemistry Department, Faculty of Pharmacy, Modern University for Technology and Information, Cairo, Egypt
| | - Mona G Khalil
- Pharmacology and Toxicology Department, Faculty of Pharmacy, Modern University for Technology and Information, Cairo, Egypt
| | - Amr M Abdou
- Department of Microbiology and Immunology, National Research Centre, Dokki, Egypt
| | - Eman O Osman
- Pharmaceutical Organic Chemistry Department, Faculty of Pharmacy, Cairo University, Cairo, Egypt
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5
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Zhao L, Wang Y, Xu Y, Sun Q, Liu H, Chen Q, Liu B. BIRB796, an Inhibitor of p38 Mitogen-Activated Protein Kinase, Inhibits Proliferation and Invasion in Glioblastoma Cells. ACS OMEGA 2021; 6:11466-11473. [PMID: 34056302 PMCID: PMC8154025 DOI: 10.1021/acsomega.1c00521] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Accepted: 03/25/2021] [Indexed: 06/12/2023]
Abstract
Glioblastoma (GBM) is the most common malignant tumor, and it is characterized by high cellular proliferation and invasion in the central nervous system of adults. Due to its high degree of heterogeneity and mortality, there is no effective therapy for GBM. In our study, we investigated the effect of the p38-MAPK signaling pathway inhibitor BIRB796 on GBM cells. Cell Counting Kit-8 (CCK-8) assay, 5-ethynyl-2'-deoxyuridine (EDU) staining, and cell cycle distribution analysis were performed, and the results showed that BIRB796 decreased proliferation in U87 and U251 cells. Moreover, wound healing and invasion assays were performed, which showed that BIRB796 inhibited the migration and invasion of human GBM cells. We found that BIRB796 treatment significantly decreased the formation of the cytoskeleton and thus downregulated the movement ability of the cells, as shown by phalloidin staining and vimentin immunofluorescence staining. Real-time polymerase chain reaction showed that the mRNA levels of MMP-2, Vimentin, CyclinD1, and Snail-1 were downregulated. Consistently, the expressions of MMP-2, Vimentin, CyclinD1, and p-p38 were also decreased after BIRB796 treatment. Taken together, all our results demonstrated that BIRB796 could play an antitumor role by inhibiting the proliferation and invasion in GBM cells. Thus, BIRB796 may be used as an adjuvant therapy to improve the therapeutic efficacy of GBM treatment.
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Affiliation(s)
- Linyao Zhao
- Department
of Neurosurgery, Renmin Hospital of Wuhan
University, Hubei 430060, China
- Central
Laboratory, Renmin Hospital of Wuhan University, Wuhan, Hubei, 430060, PR China
| | - Yixuan Wang
- Department
of Neurosurgery, Renmin Hospital of Wuhan
University, Hubei 430060, China
- Central
Laboratory, Renmin Hospital of Wuhan University, Wuhan, Hubei, 430060, PR China
| | - Yang Xu
- Department
of Neurosurgery, Renmin Hospital of Wuhan
University, Hubei 430060, China
- Central
Laboratory, Renmin Hospital of Wuhan University, Wuhan, Hubei, 430060, PR China
| | - Qian Sun
- Department
of Neurosurgery, Renmin Hospital of Wuhan
University, Hubei 430060, China
- Central
Laboratory, Renmin Hospital of Wuhan University, Wuhan, Hubei, 430060, PR China
| | - Hao Liu
- Department
of Neurosurgery, Renmin Hospital of Wuhan
University, Hubei 430060, China
- Central
Laboratory, Renmin Hospital of Wuhan University, Wuhan, Hubei, 430060, PR China
| | - Qianxue Chen
- Department
of Neurosurgery, Renmin Hospital of Wuhan
University, Hubei 430060, China
- Central
Laboratory, Renmin Hospital of Wuhan University, Wuhan, Hubei, 430060, PR China
| | - Baohui Liu
- Department
of Neurosurgery, Renmin Hospital of Wuhan
University, Hubei 430060, China
- Central
Laboratory, Renmin Hospital of Wuhan University, Wuhan, Hubei, 430060, PR China
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6
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Selective targeting of the αC and DFG-out pocket in p38 MAPK. Eur J Med Chem 2020; 208:112721. [DOI: 10.1016/j.ejmech.2020.112721] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Revised: 07/31/2020] [Accepted: 08/01/2020] [Indexed: 12/25/2022]
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7
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Uwada J, Nakazawa H, Mikami D, Islam MS, Muramatsu I, Taniguchi T, Yazawa T. PNU-120596, a positive allosteric modulator of α7 nicotinic acetylcholine receptor, directly inhibits p38 MAPK. Biochem Pharmacol 2020; 182:114297. [DOI: 10.1016/j.bcp.2020.114297] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Revised: 10/19/2020] [Accepted: 10/20/2020] [Indexed: 10/23/2022]
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8
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Aoto PC, Stanfield RL, Wilson IA, Dyson HJ, Wright PE. A Dynamic Switch in Inactive p38γ Leads to an Excited State on the Pathway to an Active Kinase. Biochemistry 2019; 58:5160-5172. [PMID: 31794659 DOI: 10.1021/acs.biochem.9b00932] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
The inactive state of mitogen-activated protein kinases (MAPKs) adopts an open conformation while the active state exists in a compact form stabilized by phosphorylation. In the active state, eukaryotic kinases undergo breathing motions related to substrate binding and product release that have not previously been detected in the inactive state. However, docking interactions of partner proteins with inactive MAPK kinases exhibit allostery in binding of activating kinases. Interactions at a site distant from the activation loop are coupled to the configuration of the activation loop, suggesting that the inactive state may also undergo concerted dynamics. X-ray crystallographic studies of nonphosphorylated, inactive p38γ reveal differences in domain orientations and active site structure in the two molecules in the asymmetric unit. One molecule resembles an inactive kinase with an open active site. The second molecule has a rotation of the N-lobe that leads to partial compaction of the active site, resulting in a conformation that is intermediate between the inactive open state and the fully closed state of the activated kinase. Although the compact state of apo p38γ displays several of the features of the activated enzyme, it remains catalytically inert. In solution, the kinase fluctuates on a millisecond time scale between the open ground state and a weakly populated excited state that is similar in structure to the compact state observed in the crystal. The nuclear magnetic resonance and crystal structure data imply that interconversion between the open and compact states involves a molecular switch associated with the DFG loop.
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9
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Suplatov D, Kopylov K, Sharapova Y, Švedas V. Human p38α mitogen-activated protein kinase in the Asp168-Phe169-Gly170-in (DFG-in) state can bind allosteric inhibitor Doramapimod. J Biomol Struct Dyn 2018; 37:2049-2060. [PMID: 29749295 DOI: 10.1080/07391102.2018.1475260] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
Doramapimod (BIRB-796) is widely recognized as one of the most potent and selective type II inhibitors of human p38α mitogen-activated protein kinase (MAPK); however, the understanding of its binding mechanism remains incomplete. Previous studies indicated high affinity of the ligand to a so-called allosteric pocket revealed only in the 'out' state of the DFG motif (i.e. Asp168-Phe169-Gly170) when Phe169 becomes fully exposed to the solvent. The possibility of alternative binding in the DFG-in state was hypothesized, but the molecular mechanism was not known. Methods of bioinformatics, docking and long-time scale classical and accelerated molecular dynamics have been applied to study the interaction of Doramapimod with the human p38α MAPK. It was shown that Doramapimod can bind to the protein even when the Phe169 is fully buried inside the allosteric pocket and the kinase activation loop is in the DFG-in state. Orientation of the inhibitor in such a complex is significantly different from that in the known crystallographic complex formed by the kinase in the DFG-out state; however, the Doramapimod's binding is followed by the ligand-induced conformational changes, which finally improve accommodation of the inhibitor. Molecular modelling has confirmed that Doramapimod combines the features of type I and II inhibitors of p38α MAPK, i.e. can directly and indirectly compete with the ATP binding. It can be concluded that optimization of the initial binding in the DFG-in state and the final accommodation in the DFG-out state should be both considered at designing novel efficient type II inhibitors of MAPK and homologous proteins. Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Dmitry Suplatov
- a Faculty of Bioengineering and Bioinformatics, Belozersky Institute of Physicochemical Biology , Lomonosov Moscow State University , Vorobjev hills , Moscow , Russia
| | - Kirill Kopylov
- a Faculty of Bioengineering and Bioinformatics, Belozersky Institute of Physicochemical Biology , Lomonosov Moscow State University , Vorobjev hills , Moscow , Russia
| | - Yana Sharapova
- a Faculty of Bioengineering and Bioinformatics, Belozersky Institute of Physicochemical Biology , Lomonosov Moscow State University , Vorobjev hills , Moscow , Russia
| | - Vytas Švedas
- a Faculty of Bioengineering and Bioinformatics, Belozersky Institute of Physicochemical Biology , Lomonosov Moscow State University , Vorobjev hills , Moscow , Russia
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10
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Sturm N, Tinivella A, Rastelli G. Exploration and Comparison of the Geometrical and Physicochemical Properties of an αC Allosteric Pocket in the Structural Kinome. J Chem Inf Model 2018; 58:1094-1103. [DOI: 10.1021/acs.jcim.7b00735] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Affiliation(s)
- Noé Sturm
- Department of Life Sciences, University of Modena and Reggio Emilia, Via Campi 103, 41125 Modena, Italy
| | - Annachiara Tinivella
- Department of Life Sciences, University of Modena and Reggio Emilia, Via Campi 103, 41125 Modena, Italy
| | - Giulio Rastelli
- Department of Life Sciences, University of Modena and Reggio Emilia, Via Campi 103, 41125 Modena, Italy
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11
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Ebiike H, Taka N, Matsushita M, Ohmori M, Takami K, Hyohdoh I, Kohchi M, Hayase T, Nishii H, Morikami K, Nakanishi Y, Akiyama N, Shindoh H, Ishii N, Isobe T, Matsuoka H. Discovery of [5-Amino-1-(2-methyl-3H-benzimidazol-5-yl)pyrazol-4-yl]-(1H-indol-2-yl)methanone (CH5183284/Debio 1347), An Orally Available and Selective Fibroblast Growth Factor Receptor (FGFR) Inhibitor. J Med Chem 2016; 59:10586-10600. [DOI: 10.1021/acs.jmedchem.6b01156] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Hirosato Ebiike
- Research
Division, Chugai Pharmaceutical Co., Ltd., 200 Kajiwara, Kamakura, Kanagawa 247-8530, Japan
| | - Naoki Taka
- Research
Division, Chugai Pharmaceutical Co., Ltd., 1-135 Komakado, Gotemba, Shizuoka 412-8513, Japan
| | - Masayuki Matsushita
- Research
Division, Chugai Pharmaceutical Co., Ltd., 200 Kajiwara, Kamakura, Kanagawa 247-8530, Japan
| | - Masayuki Ohmori
- Research
Division, Chugai Pharmaceutical Co., Ltd., 200 Kajiwara, Kamakura, Kanagawa 247-8530, Japan
| | - Kyoko Takami
- Research
Division, Chugai Pharmaceutical Co., Ltd., 1-135 Komakado, Gotemba, Shizuoka 412-8513, Japan
| | - Ikumi Hyohdoh
- Research
Division, Chugai Pharmaceutical Co., Ltd., 200 Kajiwara, Kamakura, Kanagawa 247-8530, Japan
| | - Masami Kohchi
- Research
Division, Chugai Pharmaceutical Co., Ltd., 200 Kajiwara, Kamakura, Kanagawa 247-8530, Japan
| | - Tadakatsu Hayase
- Research
Division, Chugai Pharmaceutical Co., Ltd., 200 Kajiwara, Kamakura, Kanagawa 247-8530, Japan
| | - Hiroki Nishii
- Research
Division, Chugai Pharmaceutical Co., Ltd., 200 Kajiwara, Kamakura, Kanagawa 247-8530, Japan
| | - Kenji Morikami
- Research
Division, Chugai Pharmaceutical Co., Ltd., 1-135 Komakado, Gotemba, Shizuoka 412-8513, Japan
| | - Yoshito Nakanishi
- Research
Division, Chugai Pharmaceutical Co., Ltd., 200 Kajiwara, Kamakura, Kanagawa 247-8530, Japan
| | - Nukinori Akiyama
- Research
Division, Chugai Pharmaceutical Co., Ltd., 200 Kajiwara, Kamakura, Kanagawa 247-8530, Japan
| | - Hidetoshi Shindoh
- Research
Division, Chugai Pharmaceutical Co., Ltd., 200 Kajiwara, Kamakura, Kanagawa 247-8530, Japan
| | - Nobuya Ishii
- Research
Division, Chugai Pharmaceutical Co., Ltd., 200 Kajiwara, Kamakura, Kanagawa 247-8530, Japan
| | - Takehito Isobe
- Research
Division, Chugai Pharmaceutical Co., Ltd., 1-135 Komakado, Gotemba, Shizuoka 412-8513, Japan
| | - Hiroharu Matsuoka
- Research
Division, Chugai Pharmaceutical Co., Ltd., 1-135 Komakado, Gotemba, Shizuoka 412-8513, Japan
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12
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Kwarcinski FE, Brandvold KR, Phadke S, Beleh OM, Johnson TK, Meagher JL, Seeliger MA, Stuckey JA, Soellner MB. Conformation-Selective Analogues of Dasatinib Reveal Insight into Kinase Inhibitor Binding and Selectivity. ACS Chem Biol 2016; 11:1296-304. [PMID: 26895387 PMCID: PMC7306399 DOI: 10.1021/acschembio.5b01018] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
In the kinase field, there are many widely held tenets about conformation-selective inhibitors that have yet to be validated using controlled experiments. We have designed, synthesized, and characterized a series of kinase inhibitor analogues of dasatinib, an FDA-approved kinase inhibitor that binds the active conformation. This inhibitor series includes two Type II inhibitors that bind the DFG-out inactive conformation and two inhibitors that bind the αC-helix-out inactive conformation. Using this series of compounds, we analyze the impact that conformation-selective inhibitors have on target binding and kinome-wide selectivity.
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Affiliation(s)
- Frank E. Kwarcinski
- Department of Medicinal Chemistry, University of Michigan, Ann Arbor, MI 48109
| | | | - Sameer Phadke
- Department of Chemistry, University of Michigan, Ann Arbor, MI 48109
| | - Omar M. Beleh
- Department of Medicinal Chemistry, University of Michigan, Ann Arbor, MI 48109
| | - Taylor K. Johnson
- Department of Medicinal Chemistry, University of Michigan, Ann Arbor, MI 48109
| | | | - Markus A. Seeliger
- Department of Pharmacological Sciences, Stony Brook University, Stony Brook, NY 11794
| | - Jeanne A. Stuckey
- Center for Structural Biology, University of Michigan, Ann Arbor, MI 48109
| | - Matthew B. Soellner
- Department of Medicinal Chemistry, University of Michigan, Ann Arbor, MI 48109
- Department of Chemistry, University of Michigan, Ann Arbor, MI 48109
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13
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Foloppe N, Chen IJ. Towards understanding the unbound state of drug compounds: Implications for the intramolecular reorganization energy upon binding. Bioorg Med Chem 2016; 24:2159-89. [PMID: 27061672 DOI: 10.1016/j.bmc.2016.03.022] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2016] [Revised: 03/09/2016] [Accepted: 03/12/2016] [Indexed: 01/24/2023]
Abstract
There has been an explosion of structural information for pharmaceutical compounds bound to biological targets, but the conformations and dynamics of compounds free in solution are poorly characterized, if at all. Yet, knowledge of the unbound state is essential to understand the fundamentals of molecular recognition, including the much debated conformational intramolecular reorganization energy of a compound upon binding (ΔEReorg). Also, dependable observation of the unbound compounds is important for ligand-based drug discovery, e.g. with pharmacophore modelling. Here, these questions are addressed with long (⩾0.5μs) state-of-the-art molecular dynamics (MD) simulations of 26 compounds (including 7 approved drugs) unbound in explicit solvent. These compounds were selected to be chemically diverse, with a range of flexibility, and good quality bioactive X-ray structures. The MD-simulated free compounds are compared to their bioactive structure and conformers generated with ad hoc sampling in vacuo or with implicit generalized Born (GB) aqueous solvation models. The GB conformational models clearly depart from those obtained in explicit solvent, and suffer from conformational collapse almost as severe as in vacuo. Thus, the global energy minima in vacuo or with GB are not suitable representations of the unbound state, which can instead be extensively sampled by MD simulations. Many, but not all, MD-simulated compounds displayed some structural similarity to their bioactive structure, supporting the notion of conformational pre-organization for binding. The ligand-protein complexes were also simulated in explicit solvent, to estimate ΔEReorg as an enthalpic difference ΔHReorg between the intramolecular energies in the bound and unbound states. This fresh approach yielded ΔHReorg values⩽6kcal/mol for 18 out of 26 compounds. For three particularly polar compounds 15⩽ΔHReorg⩽20kcal/mol, supporting the notion that ΔHReorg can be substantial. Those large ΔHReorg values correspond to a redistribution of electrostatic interactions upon binding. Overall, the study illustrates how MD simulations offer a promising avenue to characterize the unbound state of medicinal compounds.
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Affiliation(s)
- Nicolas Foloppe
- Vernalis (R&D) Ltd, Granta Park, Abington, Cambridge CB21 6GB, UK.
| | - I-Jen Chen
- Vernalis (R&D) Ltd, Granta Park, Abington, Cambridge CB21 6GB, UK.
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14
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Ansideri F, Lange A, El-Gokha A, Boeckler FM, Koch P. Fluorescence polarization-based assays for detecting compounds binding to inactive c-Jun N-terminal kinase 3 and p38α mitogen-activated protein kinase. Anal Biochem 2016; 503:28-40. [PMID: 26954235 DOI: 10.1016/j.ab.2016.02.018] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2015] [Revised: 02/25/2016] [Accepted: 02/26/2016] [Indexed: 12/14/2022]
Abstract
Two fluorescein-labeled pyridinylimidazoles were synthesized and evaluated as probes for the binding affinity determination of potential kinase inhibitors to the c-Jun N-terminal kinase 3 (JNK3) and p38α mitogen-activated protein kinase (MAPK). Fluorescence polarization (FP)-based competition binding assays were developed for both enzymes using 1-(3',6'-dihydroxy-3-oxo-3H-spiro[isobenzofuran-1,9'-xanthen]-5-yl)-3-(4-((4-(4-(4-fluorophenyl)-2-(methylthio)-1H-imidazol-5-yl)pyridin-2-yl)amino)phenyl)thiourea (5) as an FP probe (JNK3: Kd = 3.0 nM; p38α MAPK: Kd = 5.7 nM). The validation of the assays with known inhibitors of JNK3 and p38α MAPK revealed that both FP assays correlate very well with inhibition data received by the activity assays. This, in addition to the viability of both FP-based binding assays for the high-throughput screening procedure, makes the assays suitable as inexpensive prescreening protocols for JNK3 and p38α MAPK inhibitors.
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Affiliation(s)
- Francesco Ansideri
- Institute of Pharmaceutical Sciences, Department of Medicinal and Pharmaceutical Chemistry, Eberhard Karls Universität Tübingen, 72076 Tübingen, Germany
| | - Andreas Lange
- Institute of Pharmaceutical Sciences, Molecular Design and Pharmaceutical Biophysics, Eberhard Karls Universität Tübingen, 72076 Tübingen, Germany
| | - Ahmed El-Gokha
- Institute of Pharmaceutical Sciences, Department of Medicinal and Pharmaceutical Chemistry, Eberhard Karls Universität Tübingen, 72076 Tübingen, Germany; Department of Chemistry, Faculty of Science, Menofia University, Menofia, Egypt
| | - Frank M Boeckler
- Institute of Pharmaceutical Sciences, Molecular Design and Pharmaceutical Biophysics, Eberhard Karls Universität Tübingen, 72076 Tübingen, Germany
| | - Pierre Koch
- Institute of Pharmaceutical Sciences, Department of Medicinal and Pharmaceutical Chemistry, Eberhard Karls Universität Tübingen, 72076 Tübingen, Germany.
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15
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Abstract
Protein tyrosine kinases differ widely in their propensity to undergo rearrangements
of the N-terminal Asp–Phe–Gly (DFG) motif of the activation
loop, with some, including FGFR1 kinase, appearing refractory to this so-called
‘DFG flip'. Recent inhibitor-bound structures have unexpectedly
revealed FGFR1 for the first time in a ‘DFG-out' state. Here we
use conformationally selective inhibitors as chemical probes for interrogation of
the structural and dynamic features that appear to govern the DFG flip in FGFR1. Our
detailed structural and biophysical insights identify contributions from altered
dynamics in distal elements, including the αH helix, towards the
outstanding stability of the DFG-out complex with the inhibitor ponatinib. We
conclude that the αC-β4 loop and ‘molecular
brake' regions together impose a high energy barrier for this
conformational rearrangement, and that this may have significance for maintaining
autoinhibition in the non-phosphorylated basal state of FGFR1. Receptor tyrosine kinases are key mediators of cell proliferation
that have been implicated in several disease states for which they represent promising
drug targets. Here the authors determine the thermodynamic basis for the low propensity
of FGFR1 to access the DFG-Phe-out conformation required to bind type-II
inhibitors.
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16
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Effects of p38α/β inhibition on acute lymphoblastic leukemia proliferation and survival in vivo. Leukemia 2015; 29:2307-16. [PMID: 26104660 DOI: 10.1038/leu.2015.153] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2014] [Revised: 06/03/2015] [Accepted: 06/11/2015] [Indexed: 12/24/2022]
Abstract
P38α/β has been described as a tumor-suppressor controlling cell cycle checkpoints and senescence in epithelial malignancies. However, p38α/β also regulates other cellular processes. Here, we describe a role of p38α/β as a regulator of acute lymphoblastic leukemia (ALL) proliferation and survival in experimental ALL models. We also report first evidence that p38α/β phosphorylation is associated with the occurrence of relapses in TEL-AML1-positive leukemia. First, in vitro experiments show that p38α/β signaling is induced in a cyclical manner upon initiation of proliferation and remains activated during log-phase of cell growth. Next, we provide evidence that growth-permissive signals in the bone marrow activate p38α/β in a novel avian ALL model, in which therapeutic targeting can be tested. We further demonstrate that p38α/β inhibition by small molecules can suppress leukemic expansion and prolong survival of mice bearing ALL cell lines and primary cells. Knockdown of p38α strongly delays leukemogenesis in mice xenografted with cell lines. Finally, we show that in xenografted TEL-AML1 patients, ex vivo p38α/β phosphorylation is associated with an inferior long-term relapse-free survival. We propose p38α/β as a mediator of proliferation and survival in ALL and show first preclinical evidence for p38α/β inhibition as an adjunct approach to conventional therapies.
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17
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Geschwindner S, Ulander J, Johansson P. Ligand Binding Thermodynamics in Drug Discovery: Still a Hot Tip? J Med Chem 2015; 58:6321-35. [DOI: 10.1021/jm501511f] [Citation(s) in RCA: 83] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
| | - Johan Ulander
- CVMD Innovative Medicines, AstraZeneca R&D Mölndal, S-43183 Mölndal, Sweden
| | - Patrik Johansson
- Discovery Sciences, AstraZeneca R&D Mölndal, S-43183 Mölndal, Sweden
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18
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Astolfi A, Iraci N, Manfroni G, Barreca ML, Cecchetti V. A Comprehensive Structural Overview of p38α MAPK in Complex with Type I Inhibitors. ChemMedChem 2015; 10:957-69. [PMID: 26012502 DOI: 10.1002/cmdc.201500030] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2015] [Revised: 03/05/2015] [Indexed: 12/12/2022]
Abstract
p38α mitogen-activated protein kinase (MAPK) is a well-recognized therapeutic target for the treatment of autoimmune and inflammatory diseases. Over the past two decades, tremendous efforts have been focused on the discovery and development of small-molecule p38α MAPK inhibitors, although currently no drugs targeting this protein are clinically available. Therefore, the identification of novel chemotypes that are able to inhibit p38α MAPK function is still of great therapeutic significance. With the objective to support drug discovery programs aimed at identifying new immunomodulators acting on p38α MAPK, herein we present a complete overview of the available crystal structures of this protein in complex with ATP-site type I inhibitors. The 85 available complexes are classified by chemotype and experimental binding mode, and the ligand-protein interactions are discussed using the most representative inhibitors. The type and frequency of key inhibitor features are analyzed to give a final summary of the chemical requirements of promising p38α MAPK inhibitors. The proposed pharmacophore can be exploited to enhance the opportunities to identify novel type I inhibitors of p38α MAPK.
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Affiliation(s)
- Andrea Astolfi
- Department of Pharmaceutical Sciences, University of Perugia, Via A. Fabretti 48, 06123 Perugia (Italy)
| | - Nunzio Iraci
- Department of Pharmaceutical Sciences, University of Perugia, Via A. Fabretti 48, 06123 Perugia (Italy)
| | - Giuseppe Manfroni
- Department of Pharmaceutical Sciences, University of Perugia, Via A. Fabretti 48, 06123 Perugia (Italy)
| | - Maria Letizia Barreca
- Department of Pharmaceutical Sciences, University of Perugia, Via A. Fabretti 48, 06123 Perugia (Italy).
| | - Violetta Cecchetti
- Department of Pharmaceutical Sciences, University of Perugia, Via A. Fabretti 48, 06123 Perugia (Italy)
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19
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Abstract
In this issue of Chemistry & Biology, Hari and colleagues show that conformation-selective ATP-competitive kinase inhibitors have distinct noncatalytic effects on Erk2, including the ability to modulate protein-protein interactions outside the ATP-binding site. These findings enhance our knowledge about the diverse array of activities in which kinase inhibitors can target signaling pathways.
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20
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Méndez-Lucio O, Kooistra AJ, Graaf CD, Bender A, Medina-Franco JL. Analyzing Multitarget Activity Landscapes Using Protein–Ligand Interaction Fingerprints: Interaction Cliffs. J Chem Inf Model 2015; 55:251-62. [DOI: 10.1021/ci500721x] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Oscar Méndez-Lucio
- Centre
for Molecular Informatics, Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - Albert J. Kooistra
- Division
of Medicinal Chemistry, Faculty of Sciences, Amsterdam Institute for
Molecules, Medicines and Systems (AIMMS), VU University Amsterdam, De Boelelaan 1083, 1081 HV Amsterdam, The Netherlands
| | - Chris de Graaf
- Division
of Medicinal Chemistry, Faculty of Sciences, Amsterdam Institute for
Molecules, Medicines and Systems (AIMMS), VU University Amsterdam, De Boelelaan 1083, 1081 HV Amsterdam, The Netherlands
| | - Andreas Bender
- Centre
for Molecular Informatics, Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - José L. Medina-Franco
- Facultad
de Química, Departamento de Farmacia, Universidad Nacional Autónoma de México, Avenida Universidad 3000, Mexico City 04510, Mexico
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21
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Cumming JG, Debreczeni JÉ, Edfeldt F, Evertsson E, Harrison M, Holdgate GA, James MJ, Lamont SG, Oldham K, Sullivan JE, Wells SL. Discovery and characterization of MAPK-activated protein kinase-2 prevention of activation inhibitors. J Med Chem 2014; 58:278-93. [PMID: 25255283 DOI: 10.1021/jm501038s] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Two structurally distinct series of novel, MAPK-activated kinase-2 prevention of activation inhibitors have been discovered by high throughput screening. Preliminary structure-activity relationship (SAR) studies revealed substructural features that influence the selective inhibition of the activation by p38α of the downstream kinase MK2 in preference to an alternative substrate, MSK1. Enzyme kinetics, surface plasmon resonance (SPR), 2D protein NMR, and X-ray crystallography were used to determine the binding mode and the molecular mechanism of action. The compounds bind competitively to the ATP binding site of p38α but unexpectedly with higher affinity in the p38α-MK2 complex compared with p38α alone. This observation is hypothesized to be the origin of the substrate selectivity. The two lead series identified are suitable for further investigation for their potential to treat chronic inflammatory diseases with improved tolerability over previously studied p38α inhibitors.
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Affiliation(s)
- John G Cumming
- AstraZeneca , Alderley Park, Macclesfield, Cheshire SK10 4TG, United Kingdom
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22
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Leonard SE, Register AC, Krishnamurty R, Brighty GJ, Maly DJ. Divergent modulation of Src-family kinase regulatory interactions with ATP-competitive inhibitors. ACS Chem Biol 2014; 9:1894-905. [PMID: 24946274 PMCID: PMC4136698 DOI: 10.1021/cb500371g] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
![]()
Multidomain protein kinases, central
controllers of signal transduction,
use regulatory domains to modulate catalytic activity in a complex
cellular environment. Additionally, these domains regulate noncatalytic
functions, including cellular localization and protein–protein
interactions. Src-family kinases (SFKs) are promising therapeutic
targets for a number of diseases and are an excellent model for studying
the regulation of multidomain kinases. Here, we demonstrate that the
regulatory domains of the SFKs Src and Hck are divergently affected
by ligands that stabilize two distinct inactive ATP-binding site conformations.
Conformation-selective, ATP-competitive inhibitors differentially
modulate the ability of the SH3 and SH2 domains of Src and Hck to
engage in intermolecular interactions and the ability of the kinase–inhibitor
complex to undergo post-translational modification by effector enzymes.
This surprising divergence in regulatory domain behavior by two classes
of inhibitors that each stabilize inactive ATP-binding site conformations
is found to occur through perturbation or stabilization of the αC
helix. These studies provide insight into how conformation-selective,
ATP-competitive inhibitors can be designed to modulate domain interactions
and post-translational modifications distal to the ATP-binding site
of kinases.
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Affiliation(s)
- Stephen E. Leonard
- Department
of Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - A. C. Register
- Department
of Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - Ratika Krishnamurty
- Department
of Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - Gabriel J. Brighty
- Department
of Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - Dustin J. Maly
- Department
of Chemistry, University of Washington, Seattle, Washington 98195, United States
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23
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Hari SB, Merritt EA, Maly DJ. Conformation-selective ATP-competitive inhibitors control regulatory interactions and noncatalytic functions of mitogen-activated protein kinases. ACTA ACUST UNITED AC 2014; 21:628-35. [PMID: 24704509 DOI: 10.1016/j.chembiol.2014.02.016] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2014] [Revised: 02/17/2014] [Accepted: 02/20/2014] [Indexed: 01/07/2023]
Abstract
Most potent protein kinase inhibitors act by competing with ATP to block the phosphotransferase activity of their targets. However, emerging evidence demonstrates that ATP-competitive inhibitors can affect kinase interactions and functions in ways beyond blocking catalytic activity. Here, we show that stabilizing alternative ATP-binding site conformations of the mitogen-activated protein kinases (MAPKs) p38α and Erk2 with ATP-competitive inhibitors differentially, and in some cases divergently, modulates the abilities of these kinases to interact with upstream activators and deactivating phosphatases. Conformation-selective ligands are also able to modulate Erk2's ability to allosterically activate the MAPK phosphatase DUSP6, highlighting how ATP-competitive ligands can control noncatalytic kinase functions. Overall, these studies underscore the relationship between the ATP-binding and regulatory sites of MAPKs and provide insight into how ATP-competitive ligands can be designed to confer graded control over protein kinase function.
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Affiliation(s)
- Sanjay B Hari
- Department of Chemistry, University of Washington, Seattle, WA 98195, USA
| | - Ethan A Merritt
- Department of Biological Structure, University of Washington, Seattle, WA 98195, USA
| | - Dustin J Maly
- Department of Chemistry, University of Washington, Seattle, WA 98195, USA.
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24
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Hari SB, Merritt EA, Maly DJ. Sequence determinants of a specific inactive protein kinase conformation. ACTA ACUST UNITED AC 2014; 20:806-15. [PMID: 23790491 DOI: 10.1016/j.chembiol.2013.05.005] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2013] [Revised: 04/18/2013] [Accepted: 05/09/2013] [Indexed: 02/07/2023]
Abstract
Only a small percentage of protein kinases have been shown to adopt a distinct inactive ATP-binding site conformation, called the Asp-Phe-Gly-out (DFG-out) conformation. Given the high degree of homology within this enzyme family, we sought to understand the basis of this disparity on a sequence level. We identified two residue positions that sensitize mitogen-activated protein kinases (MAPKs) to inhibitors that stabilize the DFG-out inactive conformation. After characterizing the structure and dynamics of an inhibitor-sensitive MAPK mutant, we demonstrated the generality of this strategy by sensitizing a kinase (apoptosis signal-regulating kinase 1) not in the MAPK family to several DFG-out stabilizing ligands, using the same residue positions. The use of specific inactive conformations may aid the study of noncatalytic roles of protein kinases, such as binding partner interactions and scaffolding effects.
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Affiliation(s)
- Sanjay B Hari
- Department of Chemistry, University of Washington, Seattle, WA 98195, USA
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25
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Hari SB, Perera BGK, Ranjitkar P, Seeliger MA, Maly DJ. Conformation-selective inhibitors reveal differences in the activation and phosphate-binding loops of the tyrosine kinases Abl and Src. ACS Chem Biol 2013; 8:2734-43. [PMID: 24106839 DOI: 10.1021/cb400663k] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Over the past decade, an increasingly diverse array of potent and selective inhibitors that target the ATP-binding sites of protein kinases have been developed. Many of these inhibitors, like the clinically approved drug imatinib (Gleevec), stabilize a specific catalytically inactive ATP-binding site conformation of their kinases targets. Imatinib is notable in that it is highly selective for its kinase target, Abl, over other closely related tyrosine kinases, such as Src. In addition, imatinib is highly sensitive to the phosphorylation state of Abl's activation loop, which is believed to be a general characteristic of all inhibitors that stabilize a similar inactive ATP-binding site conformation. In this report, we perform a systematic analysis of a diverse series of ATP-competitive inhibitors that stabilize a similar inactive ATP-binding site conformation as imatinib with the tyrosine kinases Src and Abl. In contrast to imatinib, many of these inhibitors have very similar potencies against Src and Abl. Furthermore, only a subset of this class of inhibitors is sensitive to the phosphorylation state of the activation loop of these kinases. In attempting to explain this observation, we have uncovered an unexpected correlation between Abl's activation loop and another flexible active site feature, called the phosphate-binding loop (p-loop). These studies shed light on how imatinib is able to obtain its high target selectivity and reveal how the conformational preference of flexible active site regions can vary between closely related kinases.
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Affiliation(s)
- Sanjay B. Hari
- Department
of Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - B. Gayani K. Perera
- Department
of Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - Pratistha Ranjitkar
- Department
of Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - Markus A. Seeliger
- Department
of Pharmacological Sciences, Stony Brook University Medical School, Stony
Brook, New York 11794, United States
| | - Dustin J. Maly
- Department
of Chemistry, University of Washington, Seattle, Washington 98195, United States
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26
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Okada O, Yamashita H, Takedomi K, Ono S, Sunada S, Kubodera H. Prediction of the binding affinity of compounds with diverse scaffolds by MP-CAFEE. Biophys Chem 2013; 180-181:119-26. [PMID: 23938954 DOI: 10.1016/j.bpc.2013.07.005] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2013] [Revised: 07/02/2013] [Accepted: 07/15/2013] [Indexed: 11/16/2022]
Abstract
Accurate methods to predict the binding affinities of compounds for target molecules are powerful tools in structure-based drug design (SBDD). A recently developed method called massively parallel computation of absolute binding free energy with a well-equilibrated system (MP-CAFEE) successfully predicted the binding affinities of compounds with relatively similar scaffolds. We investigate the applicability of MP-CAFEE for predicting the affinity of compounds having more diverse scaffolds for the target p38α, a mitogen-activated protein kinase. The calculated and experimental binding affinities correlate well, showing that MP-CAFEE can accurately rank the compounds with diverse scaffolds. We propose a method to determine the optimal number of sampling runs with respect to a predefined level of accuracy, which is established according to the stage in the SBDD process being considered. The optimal number of sampling runs for two key stages-lead identification and lead optimization-is estimated to be five and eight or more, respectively, in our model system using Cochrans sample size formula.
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Affiliation(s)
- Okimasa Okada
- Medicinal Chemistry Research Laboratories II, Mitsubishi Tanabe Pharma Corporation, Toda, Saitama 335-8505, Japan.
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27
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Backes A, Zech B, Felber B, Klebl B, Müller G. Small-molecule inhibitors binding to protein kinase. Part II: the novel pharmacophore approach of type II and type III inhibition. Expert Opin Drug Discov 2013; 3:1427-49. [PMID: 23506107 DOI: 10.1517/17460440802580106] [Citation(s) in RCA: 87] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
BACKGROUND Protein kinases are essential enzymes propagating cellular signal transduction processes and consequently emerged as central targets for drug discovery against a wide range of diseases with a strong historical focus on oncological disorders. Several high-resolution crystal structures of various ATP-competitive inhibitors in complex with their target protein kinases have been determined and represent a wealth of detailed information about binding modes, inhibition mechanisms, and associated structure- activity relationships of target-bound small molecules. OBJECTIVE In this second part of a two-part review, we discuss the binding mode of inhibitors that target protein kinases in their inactive state. METHODS The scope of this review covers inhibitors for which crystal structures in complex with their respective kinases in the inactive state are available. RESULTS Structural parameters of both inhibitors and kinases contribute to the complexity of designing kinase inhibitors. Kinase inhibitors that target the inactive state of a kinase have become a novel rule in the design of highly active and selective compounds. The combination of high-resolution structures of ligand-enzyme complexes with especially detailed kinetic studies will in the long-term help to develop new low-molecular weight type II inhibitors.
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Affiliation(s)
- Ac Backes
- Sandoz GmbH, Biochemiestrasse 10, 6336 Langkampfen, Austria +43 5338 200 5235 ; +43 5338 200 460 ;
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28
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Alton GR, Lunney EA. Targeting the unactivated conformations of protein kinases for small molecule drug discovery. Expert Opin Drug Discov 2013; 3:595-605. [PMID: 23506143 DOI: 10.1517/17460441.3.6.595] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
BACKGROUND The number of drugs in active clinical development or on the market that target the unactivated conformational states of protein kinases is growing and represents a significant portion of kinase research at biopharmaceutical companies. These non-classical kinase inhibitors have a mode of action which may overcome some of the liabilities of classical ATP-site inhibitors that substantially overlap the space that ATP occupies in the activated kinase. OBJECTIVE This review will discuss state-of-the-art methods of inhibiting protein kinases by targeting the unactivated conformations of the enzyme with small molecules directed to the ATP binding region. METHODS Biochemical and structural biology publications and public domain crystal structures were evaluated to identify key concepts in drug discovery for unactivated protein kinase inhibitors that target the ATP binding region. CONCLUSION The potential for enhanced selectivity, potency and duration of pharmacological action may allow non-classical kinase therapeutics to be used for chronic dosing in non-life-threatening indications. Moreover, by targeting additional conformational space on the kinase protein it is possible that new chemical matter will be discovered such that current intellectual property limitations on traditional ATP-site chemical scaffolds may be circumvented.
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Affiliation(s)
- Gordon R Alton
- Senior Principal Scientist Pfizer Global Research and Development, Department of Biochemical Pharmacology, 10628 Science Center Drive, San Diego, CA 92121, USA +1 858 526 4926 ; 858 526 4236 ;
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29
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Andrews SS, Hill ZB, Perera BGK, Maly DJ. Label transfer reagents to probe p38 MAPK binding partners. Chembiochem 2013; 14:209-16. [PMID: 23319368 DOI: 10.1002/cbic.201200673] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2012] [Indexed: 11/06/2022]
Abstract
Protein kinases are essential enzymes for cellular signaling, and are often regulated by participation in protein complexes. The mitogen-activated protein kinase (MAPK) p38 is involved in multiple pathways, and its regulation depends on its interactions with other signaling proteins. However, the identification of p38-interacting proteins is challenging. For this reason, we have developed label transfer reagents (LTRs) that allow labeling of p38 signaling complexes. These LTRs leverage the potency and selectivity of known p38 inhibitors to place a photo-crosslinker and tag in the vicinity of p38 and its binding partners. Upon UV irradiation, proteins that are in close proximity to p38 are covalently crosslinked, and labeled proteins are detected and/or purified with an orthogonal chemical handle. Here we demonstrate that p38-selective LTRs selectively label a diversity of p38 binding partners, including substrates, activators, and inactivators. Furthermore, these LTRs can be used in immunoprecipitations to provide low-resolution structural information on p38-containing complexes.
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Affiliation(s)
- Simeon S Andrews
- Department of Chemistry, University of Washington, Box 351700, Seattle, WA 98195-1700, USA
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30
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Ranjitkar P, Perera BGK, Swaney DL, Swaney DL, Hari SB, Larson ET, Krishnamurty R, Merritt EA, Villén J, Maly DJ. Affinity-based probes based on type II kinase inhibitors. J Am Chem Soc 2012; 134:19017-25. [PMID: 23088519 DOI: 10.1021/ja306035v] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Protein kinases are key components of most mammalian signal transduction networks and are therapeutically relevant drug targets. Efforts to study protein kinase function would benefit from new technologies that are able to profile kinases in complex proteomes. Here, we describe active site-directed probes for profiling kinases in whole cell extracts and live cells. These probes contain general ligands that stabilize a specific inactive conformation of the ATP-binding sites of protein kinases, as well as trifluoromethylphenyl diazirine and alkyne moieties that allow covalent modification and enrichment of kinases, respectively. A diverse group of serine/threonine and tyrosine kinases were identified as specific targets of these probes in whole cell extracts. In addition, a number of kinase targets were selectively labeled in live cells. Our chemical proteomics approach should be valuable for interrogating protein kinase active sites in physiologically relevant environments.
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Affiliation(s)
- Pratistha Ranjitkar
- Department of Chemistry, University of Washington, Seattle, Washington 98195, USA
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31
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Brown DS, Cumming JG, Bethel P, Finlayson J, Gerhardt S, Nash I, Pauptit RA, Pike KG, Reid A, Snelson W, Swallow S, Thompson C. The discovery of N-cyclopropyl-4-methyl-3-[6-(4-methylpiperazin-1-yl)-4-oxoquinazolin-3(4H)-yl]benzamide (AZD6703), a clinical p38α MAP kinase inhibitor for the treatment of inflammatory diseases. Bioorg Med Chem Lett 2012; 22:3879-83. [DOI: 10.1016/j.bmcl.2012.04.116] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2012] [Revised: 04/25/2012] [Accepted: 04/27/2012] [Indexed: 11/27/2022]
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Vinh NB, Simpson JS, Scammells PJ, Chalmers DK. Virtual screening using a conformationally flexible target protein: models for ligand binding to p38α MAPK. J Comput Aided Mol Des 2012; 26:409-23. [PMID: 22527960 DOI: 10.1007/s10822-012-9569-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2011] [Accepted: 03/26/2012] [Indexed: 12/25/2022]
Abstract
We have used virtual screening to develop models for the binding of aryl substituted heterocycles to p38α MAPK. Virtual screening was conducted on a number of p38α MAPK crystal structures using a library of 46 known p38α MAPK inhibitors containing a heterocyclic core substituted by pyridine and fluorophenyl rings (structurally related to SB203580) and a set of decoy compounds. Multiple protonation states and tautomers of active and decoy compounds were considered. Each docking model was evaluated using receiver operating characteristic (ROC) curves and enrichment factors. The two best performing single crystal structures were found to be 1BL7 and 2EWA, with enrichment factors of 14.1 and 13.0 at 2% of the virtual screen respectively. Ensembles of up to four receptors of similar conformations were generated, generally giving good or very good performances with high ROC AUCs and good enrichment. The 1BL7-2EWA ensemble was able to outperform each of its constituent receptors and gave high enrichment factors of 17.3, 12.0, 8.0 at 2, 5 and 10% respectively, of the virtual screen. A ROC AUC of 0.94 was obtained for this ensemble. This method may be applied to other proteins where there are a large number of inhibitor classes with different binding site conformations.
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Affiliation(s)
- Natalie B Vinh
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University (Parkville Campus), 381 Royal Parade, Parkville, VIC, 3052, Australia
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Hill ZB, Perera BGK, Andrews SS, Maly DJ. Targeting diverse signaling interaction sites allows the rapid generation of bivalent kinase inhibitors. ACS Chem Biol 2012; 7:487-95. [PMID: 22148755 DOI: 10.1021/cb200387g] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
The identification of potent and selective modulators of protein kinase function remains a challenge, and new strategies are needed for generating these useful ligands. Here, we describe the generation of bivalent inhibitors of three unrelated protein kinases: the CAMK family kinase Pim1, the mitogen-activated protein kinase (MAPK) p38α, and the receptor tyrosine kinase (RTK) epidermal growth factor receptor (EGFR). These bivalent inhibitors consist of an ATP-competitive inhibitor that is covalently tethered to an engineered form of the self-labeling protein O(6)-alkylguanine-DNA alkyltransferase (SNAP-tag). In each example, SNAP-tag is fused to a peptide ligand that binds to a signaling interaction site of the kinase being targeted. These interactions increase the overall selectivity and potency of the bivalent inhibitors that were generated. The ability to exploit disparate binding sites in diverse kinases points to the generality of the method described. Finally, we demonstrate that ATP-competitive inhibitors that are conjugated to the bio-orthogonal tag O(4)-benzyl-2-chloro-6-aminopyrimidine (CLP) are cell-permeable. The selective labeling of SNAP-tag with CLP conjugates allows the rapid assembly of bivalent inhibitors in living cells.
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Affiliation(s)
- Zachary B. Hill
- Department
of Chemistry, University of Washington, Box 351700, Seattle, Washington 98195-1700,
United States
| | - B. Gayani K. Perera
- Department
of Chemistry, University of Washington, Box 351700, Seattle, Washington 98195-1700,
United States
| | - Simeon S. Andrews
- Department
of Chemistry, University of Washington, Box 351700, Seattle, Washington 98195-1700,
United States
| | - Dustin J. Maly
- Department
of Chemistry, University of Washington, Box 351700, Seattle, Washington 98195-1700,
United States
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34
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Structure-based design, synthesis and biological evaluation of N-pyrazole, N′-thiazole urea inhibitors of MAP kinase p38α. Eur J Med Chem 2012; 48:1-15. [DOI: 10.1016/j.ejmech.2011.11.019] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2011] [Revised: 11/05/2011] [Accepted: 11/09/2011] [Indexed: 11/22/2022]
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Iwata H, Imamura S, Hori A, Hixon MS, Kimura H, Miki H. Biochemical characterization of a novel type-II VEGFR2 kinase inhibitor: comparison of binding to non-phosphorylated and phosphorylated VEGFR2. Bioorg Med Chem 2011; 19:5342-51. [PMID: 21885287 DOI: 10.1016/j.bmc.2011.08.002] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2011] [Accepted: 08/02/2011] [Indexed: 11/17/2022]
Abstract
A pyrrolo[3,2-d]pyrimidine-based type-II vascular endothelial growth factor receptor 2 (VEGFR2) kinase inhibitor, compound 20d, displayed time-dependent inhibition of the non-phosphorylated catalytic domain of VEGFR2. In contrast, 20d did not show time-dependent inhibition of the phosphorylated enzyme. Dissociation of 20d from non-phosphorylated VEGFR2 was slow and the half-life of the complex was longer than 4h. In contrast, dissociation of 20d from the phosphorylated enzyme was very fast (half-life <5min). A fluorescent tracer based displacement assay and surface plasmon resonance (SPR) analysis confirmed the slow dissociation of 20d from only non-phosphorylated VEGFR2. Thus, activity based and binding kinetic analyses both supported slow dissociation of 20d from only non-phosphorylated VEGFR2. Additionally SPR analysis revealed that association rates were rapid and nearly identical for these two phosphorylation forms of VEGFR2. From these results, the preferential effect of 20d on non-phosphorylated VEGFR2 is dominated by its slow dissociation from the enzyme and this characteristically long residence time may increase its potency in vivo. The present findings may assist in the design of novel type-II kinase inhibitors.
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Affiliation(s)
- Hidehisa Iwata
- Discovery Research Laboratories, Pharmaceutical Research Division, Takeda Pharmaceutical Company Ltd, 26-1, Muraoka-Higashi, 2-chome, Fujisawa, Kanagawa 251-8555, Japan
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36
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Backes AC, Müller G, Sennhenn PC. Design Principles of Deep Pocket-Targeting Protein Kinase Inhibitors. PROTEIN KINASES AS DRUG TARGETS 2011. [DOI: 10.1002/9783527633470.ch6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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Wodicka LM, Ciceri P, Davis MI, Hunt JP, Floyd M, Salerno S, Hua XH, Ford JM, Armstrong RC, Zarrinkar PP, Treiber DK. Activation state-dependent binding of small molecule kinase inhibitors: structural insights from biochemistry. ACTA ACUST UNITED AC 2011; 17:1241-9. [PMID: 21095574 DOI: 10.1016/j.chembiol.2010.09.010] [Citation(s) in RCA: 85] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2010] [Revised: 08/25/2010] [Accepted: 09/14/2010] [Indexed: 01/29/2023]
Abstract
Interactions between kinases and small molecule inhibitors can be activation state dependent. A detailed understanding of inhibitor binding therefore requires characterizing interactions across multiple activation states. We have systematically explored the effects of ABL1 activation loop phosphorylation and PDGFR family autoinhibitory juxtamembrane domain docking on inhibitor binding affinity. For a diverse compound set, the affinity patterns correctly classify inhibitors as having type I or type II binding modes, and we show that juxtamembrane domain docking can have dramatic negative effects on inhibitor affinity. The results have allowed us to associate ligand-induced conformational changes observed in cocrystal structures with specific energetic costs. The approach we describe enables investigation of the complex relationship between kinase activation state and compound binding affinity and should facilitate strategic inhibitor design.
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Affiliation(s)
- Lisa M Wodicka
- Ambit Biosciences, 4215 Sorrento Valley Boulevard, San Diego, CA 92121, USA
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38
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Targeting Protein–Protein Interactions and Fragment-Based Drug Discovery. Top Curr Chem (Cham) 2011; 317:145-79. [DOI: 10.1007/128_2011_265] [Citation(s) in RCA: 79] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
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39
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BAKAN AHMET, BAHAR IVET. Computational generation inhibitor-bound conformers of p38 MAP kinase and comparison with experiments. PACIFIC SYMPOSIUM ON BIOCOMPUTING. PACIFIC SYMPOSIUM ON BIOCOMPUTING 2011:181-92. [PMID: 21121046 PMCID: PMC4782186 DOI: 10.1142/9789814335058_0020] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/11/2023]
Abstract
The p38 MAP kinases play a critical role in regulating stress-activated pathways, and serve as molecular targets for controlling inflammatory diseases. Computer-aided efforts for developing p38 inhibitors have been hampered by the necessity to include the enzyme conformational flexibility in ligand docking simulations. A useful strategy in such complicated cases is to perform ensemble-docking provided that a representative set of conformers is available for the target protein either from computations or experiments. We explore here the abilities of two computational approaches, molecular dynamics (MD) simulations and anisotropic network model (ANM) normal mode analysis, for generating potential ligand-bound conformers starting from the apo state of p38, and benchmark them against the space of conformers (or the reference modes of structural changes) inferred from principal component analysis of 134 experimentally resolved p38 kinase structures. ANM-generated conformations are found to provide a significantly better coverage of the inhibitor-bound conformational space observed experimentally, compared to MD simulations performed in explicit water, suggesting that ANM-based sampling of conformations can be advantageously employed as input structural models in docking simulations.
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Affiliation(s)
- AHMET BAKAN
- Department of Computational and Systems Biology, School of Medicine, University of Pittsburgh, 3501 Fifth Ave, Suite 3064 BST3, Pittsburgh, PA, USA
| | - IVET BAHAR
- Department of Computational and Systems Biology, School of Medicine, University of Pittsburgh, 3501 Fifth Ave, Suite 3064 BST3, Pittsburgh, PA, USA
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40
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Optimization of α-ketoamide based p38 inhibitors through modifications to the region that binds to the allosteric site. Bioorg Med Chem Lett 2010; 20:4819-24. [DOI: 10.1016/j.bmcl.2010.06.102] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2010] [Revised: 06/14/2010] [Accepted: 06/21/2010] [Indexed: 11/20/2022]
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41
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Filomia F, De Rienzo F, Menziani MC. Insights into MAPK p38alpha DFG flip mechanism by accelerated molecular dynamics. Bioorg Med Chem 2010; 18:6805-12. [PMID: 20724167 DOI: 10.1016/j.bmc.2010.07.047] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2010] [Revised: 07/16/2010] [Accepted: 07/20/2010] [Indexed: 01/07/2023]
Abstract
The DFG motif at the beginning of the activation loop of the MAPK p38alpha undergoes a local structural reorganization upon binding of allosteric type-II and type-III inhibitors, which causes the residue F169 to move from a buried conformation (defined as DFG-in) to a solvent exposed conformation (defined as DFG-out). Although both experimental and computer simulation studies had been performed with the aim of unveiling the details of the DFG-in to DFG-out transition, the molecular mechanism is still far from being unequivocally depicted. Here, the accelerated molecular dynamics (AMD) technique has been applied to model the active loop flexibility of p38alpha and sample special protein conformations which can be accessible only in some conditions or time periods. Starting from the assumption of an experimentally known initial and final state of the protein, the study allowed the description of the interaction network and the structural intermediates which lead the protein to change its loop conformation and active site accessibility. Besides a few important hydrogen bond interactions, a primary role seems to be played by cation-pi interactions, involving the DFG-loop residue F(169), which participate in the stabilization of an intermediate conformation and in its consequent transition to the DFG-out conformation. From this study, insights which may prove useful for inhibitor design and/or site directed mutagenesis studies are derived.
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Affiliation(s)
- Federico Filomia
- Department of Chemistry, University of Modena & Reggio Emilia, Italy-Via Giuseppe Campi 183, 41100 Modena, Italy
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42
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Kuglstatter A, Ghate M, Tsing S, Villaseñor AG, Shaw D, Barnett JW, Browner MF. X-ray crystal structure of JNK2 complexed with the p38alpha inhibitor BIRB796: insights into the rational design of DFG-out binding MAP kinase inhibitors. Bioorg Med Chem Lett 2010; 20:5217-20. [PMID: 20655210 DOI: 10.1016/j.bmcl.2010.06.157] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2010] [Revised: 06/28/2010] [Accepted: 06/30/2010] [Indexed: 11/27/2022]
Abstract
JNK2 and p38alpha are closely related mitogen-activated protein kinases that regulate various cellular activities and are considered drug targets for inflammatory diseases. We have determined the X-ray crystal structure of the clinical phase II p38alpha inhibitor BIRB796 bound to its off-target JNK2. This shows for the first time a JNK subfamily member in the DFG-out conformation. The fully resolved activation loop reveals that BIRB796 inhibits JNK2 activation by stabilizing the loop in a position that does not allow its phosphorylation by upstream kinases. The structure suggests that substituents at the BIRB796 morpholino group and modifications of the t-butyl moiety should further increase the p38alpha to JNK2 potency ratio. For the design of selective DFG-out binding JNK2 inhibitors, the binding pocket of the BIRB796 tolyl group may have the best potential.
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43
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Holdgate GA, Anderson M, Edfeldt F, Geschwindner S. Affinity-based, biophysical methods to detect and analyze ligand binding to recombinant proteins: matching high information content with high throughput. J Struct Biol 2010; 172:142-57. [PMID: 20609391 DOI: 10.1016/j.jsb.2010.06.024] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2010] [Revised: 06/28/2010] [Accepted: 06/29/2010] [Indexed: 01/21/2023]
Abstract
Affinity-based technologies have become impactful tools to detect, monitor and characterize molecular interactions using recombinant target proteins. This can aid the understanding of biological function by revealing mechanistic details, and even more importantly, enables the identification of new improved ligands that can modulate the biological activity of those targets in a desired fashion. The selection of the appropriate technology is a key step in that process, as each one of the currently available technologies offers a characteristic type of biophysical information about the ligand-binding event. Alongside the indisputable advantages of each of those technologies they naturally display diverse restrictions that are quite frequently related to the target system to be studied but also to the affinity, solubility and molecular size of the ligands. This paper discusses some of the theoretical and experimental aspects of the most common affinity-based methods, what type of information can be gained from each one of those approaches, and what requirements as well as limitations are expected from working with recombinant proteins on those platforms and how those can be optimally addressed.
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Affiliation(s)
- Geoff A Holdgate
- Lead Generation Sciences, AstraZeneca R&D Alderley Park, Mereside, Alderley Park, United Kingdom
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44
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Ranjitkar P, Brock AM, Maly DJ. Affinity reagents that target a specific inactive form of protein kinases. ACTA ACUST UNITED AC 2010; 17:195-206. [PMID: 20189109 DOI: 10.1016/j.chembiol.2010.01.008] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2009] [Revised: 01/18/2010] [Accepted: 01/20/2010] [Indexed: 02/01/2023]
Abstract
A number of small-molecule inhibitors have been developed that target the catalytic domains of protein kinases that are not in an active conformation. An inactive form that has been observed in several kinases is the DFG-out conformation. This conformation is characterized by an almost 180 degrees rotation of the conserved Asp-Phe-Gly (DFG) motif in the ATP-binding cleft relative to the active form. However, the sequence and structural determinants that allow a kinase to stably adopt the DFG-out conformation are not known. Here, we characterize a series of inhibitors based on a general pharmacophore for this inactive form. We demonstrate that modified versions of these inhibitors can be used to study the thermodynamics and kinetics of ligand binding to DFG-out-adopting kinases and for enriching these kinases from complex protein mixtures.
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45
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Use of p38 MAPK Inhibitors for the Treatment of Werner Syndrome. Pharmaceuticals (Basel) 2010; 3:1842-1872. [PMID: 27713332 PMCID: PMC4033955 DOI: 10.3390/ph3061842] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2010] [Revised: 05/13/2010] [Accepted: 05/26/2010] [Indexed: 11/17/2022] Open
Abstract
Werner syndrome provides a convincing model for aspects of the normal ageing phenotype and may provide a suitable model for therapeutic interventions designed to combat the ageing process. Cultured primary fibroblast cells from Werner syndrome patients provide a powerful model system to study the link between replicative senescence in vitro and in vivo pathophysiology. Genome instability, together with an increased pro-oxidant state, and frequent replication fork stalling, all provide plausible triggers for intracellular stress in Werner syndrome cells, and implicates p38 MAPK signaling in their shortened replicative lifespan. A number of different p38 MAPK inhibitor chemotypes have been prepared rapidly and efficiently using microwave heating techniques for biological study in Werner syndrome cells, including SB203580, VX-745, RO3201195, UR-13756 and BIRB 796, and their selectivity and potency evaluated in this cellular context. Werner syndrome fibroblasts treated with a p38 MAPK inhibitor reveal an unexpected reversal of the accelerated ageing phenotype. Thus the study of p38 inhibition and its effect upon Werner pathophysiology is likely to provide new revelations into the biological mechanisms operating in cellular senescence and human ageing in the future.
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46
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The design, synthesis, and evaluation of 8 hybrid DFG-out allosteric kinase inhibitors: a structural analysis of the binding interactions of Gleevec, Nexavar, and BIRB-796. Bioorg Med Chem 2010; 18:5738-48. [PMID: 20621496 DOI: 10.1016/j.bmc.2010.05.063] [Citation(s) in RCA: 133] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2010] [Revised: 05/20/2010] [Accepted: 05/23/2010] [Indexed: 11/20/2022]
Abstract
The majority of kinase inhibitors developed to date are competitive inhibitors that target the ATP binding site; however, recent crystal structures of Gleevec (imatinib mesylate, STI571, PDB: 1IEP), Nexavar (Sorafenib tosylate, BAY 43-9006, PDB: 1UWJ), and BIRB-796 (PDB: 1KV2) have revealed a secondary binding site adjacent to the ATP binding site known as the DFG-out allosteric binding site. The recent successes of Gleevec and Nexavar for the treatment of chronic myeloid leukemia and renal cell carcinoma has generated great interest in the development of other kinase inhibitors that target this secondary binding site. Here, we present a structural comparison of the important and similar interactions necessary for Gleevec(R), Nexavar, and BIRB-796 to bind to their respective DFG-out allosteric binding pockets and the selectivity of each with respect to c-Abl, B-Raf, and p38alpha. A structural analysis of their selectivity profiles has been generated from the synthesis and evaluation of 8 additional DFG-out allosteric inhibitors that were developed directly from fragments of these successful scaffolds.
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47
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Fluorescence polarization binding assay to develop inhibitors of inactive p38α mitogen-activated protein kinase. Anal Biochem 2010; 401:125-33. [DOI: 10.1016/j.ab.2010.02.016] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2010] [Revised: 02/01/2010] [Accepted: 02/12/2010] [Indexed: 12/30/2022]
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48
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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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49
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Du Y, Tang J, Li G, Li G, Berti-Mattera L, Lee CA, Bartkowski D, Gale D, Monahan J, Niesman MR, Alton G, Kern TS. Effects of p38 MAPK inhibition on early stages of diabetic retinopathy and sensory nerve function. Invest Ophthalmol Vis Sci 2010; 51:2158-64. [PMID: 20071676 DOI: 10.1167/iovs.09-3674] [Citation(s) in RCA: 92] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Purpose. p38 mitogen-activated protein kinase (MAPK) is known to play a regulatory role in inflammatory processes in disease. Inflammation has been linked also to the development of diabetic retinopathy in rodents. This study was conducted to evaluate the effect of a p38 MAPK inhibitor on the development of early stages of diabetic retinopathy in rats. Methods. Streptozotocin-diabetic rats were assigned to two groups-treated with the p38 MAPK inhibitor PHA666859 (Pfizer, New York, NY) and untreated-and compared with age-matched nondiabetic control animals. Results. At 2 months of diabetes, insulin-deficient diabetic control rats exhibited significant increases in retinal superoxide, nitric oxide (NO), cyclooxygenase (COX)-2, and leukostasis within retinal microvessels. All these abnormalities were significantly inhibited by the p38 MAPK inhibitor (25 mg/kgBW/d). At 10 months of diabetes, significant increases in the number of degenerate (acellular) capillaries and pericyte ghosts were measured in control diabetic rats versus those in nondiabetic control animals, and pharmacologic inhibition of p38 MAPK significantly inhibited all these abnormalities (all P < 0.05). This therapy also had beneficial effects outside the eye in diabetes, as evidenced by the inhibition of a diabetes-induced hypersensitivity of peripheral nerves to light touch (tactile allodynia). Conclusions. p38 MAPK plays an important role in diabetes-induced inflammation in the retina, and inhibition of p38 MAPK offers a novel therapeutic approach to inhibiting the development of early stages of diabetic retinopathy and other complications of diabetes.
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Affiliation(s)
- Yunpeng Du
- Case Western Reserve University, Cleveland, Ohio, USA
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50
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Klüter S, Grütter C, Naqvi T, Rabiller M, Simard JR, Pawar V, Getlik M, Rauh D. Displacement Assay for the Detection of Stabilizers of Inactive Kinase Conformations. J Med Chem 2009; 53:357-67. [DOI: 10.1021/jm901297e] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Affiliation(s)
- Sabine Klüter
- Chemical Genomics Centre of the Max Planck Society, Otto-Hahn-Strasse 15, D-44227 Dortmund, Germany
| | - Christian Grütter
- Chemical Genomics Centre of the Max Planck Society, Otto-Hahn-Strasse 15, D-44227 Dortmund, Germany
| | - Tabassum Naqvi
- DiscoveRx Corporation, 42501 Albrae Street, Fremont, California 94538
| | - Matthias Rabiller
- Chemical Genomics Centre of the Max Planck Society, Otto-Hahn-Strasse 15, D-44227 Dortmund, Germany
| | - Jeffrey R. Simard
- Chemical Genomics Centre of the Max Planck Society, Otto-Hahn-Strasse 15, D-44227 Dortmund, Germany
| | - Vijaykumar Pawar
- Chemical Genomics Centre of the Max Planck Society, Otto-Hahn-Strasse 15, D-44227 Dortmund, Germany
| | - Matthäus Getlik
- Chemical Genomics Centre of the Max Planck Society, Otto-Hahn-Strasse 15, D-44227 Dortmund, Germany
| | - Daniel Rauh
- Chemical Genomics Centre of the Max Planck Society, Otto-Hahn-Strasse 15, D-44227 Dortmund, Germany
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