1
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Eguchi M, Minami Y, Kuzume A, Chi S. Mechanisms Underlying Resistance to FLT3 Inhibitors in Acute Myeloid Leukemia. Biomedicines 2020; 8:biomedicines8080245. [PMID: 32722298 PMCID: PMC7459983 DOI: 10.3390/biomedicines8080245] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Revised: 07/10/2020] [Accepted: 07/16/2020] [Indexed: 01/03/2023] Open
Abstract
FLT3-ITD and FLT3-TKD mutations were observed in approximately 20 and 10% of acute myeloid leukemia (AML) cases, respectively. FLT3 inhibitors such as midostaurin, gilteritinib and quizartinib show excellent response rates in patients with FLT3-mutated AML, but its duration of response may not be sufficient yet. The majority of cases gain secondary resistance either by on-target and off-target abnormalities. On-target mutations (i.e., FLT3-TKD) such as D835Y keep the TK domain in its active form, abrogating pharmacodynamics of type II FLT3 inhibitors (e.g., midostaurin and quizartinib). Second generation type I inhibitors such as gilteritinib are consistently active against FLT3-TKD as well as FLT3-ITD. However, a “gatekeeper” mutation F691L shows universal resistance to all currently available FLT3 inhibitors. Off-target abnormalities are consisted with a variety of somatic mutations such as NRAS, AXL and PIM1 that bypass or reinforce FLT3 signaling. Off-target mutations can occur just in the primary FLT3-mutated clone or be gained by the evolution of other clones. A small number of cases show primary resistance by an FL-dependent, FGF2-dependent, and stromal CYP3A4-mediated manner. To overcome these mechanisms, the development of novel agents such as covalently-coupling FLT3 inhibitor FF-10101 and the investigation of combination therapy with different class agents are now ongoing. Along with novel agents, gene sequencing may improve clinical approaches by detecting additional targetable mutations and determining individual patterns of clonal evolution.
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Affiliation(s)
- Motoki Eguchi
- Department of Hematology, National Cancer Center Hospital East, Kashiwa 277-8577, Japan; (M.E.); (A.K.); (S.C.)
| | - Yosuke Minami
- Department of Hematology, National Cancer Center Hospital East, Kashiwa 277-8577, Japan; (M.E.); (A.K.); (S.C.)
- Correspondence: ; Tel.: +81-4-7133-1111; Fax: +81-7133-6502
| | - Ayumi Kuzume
- Department of Hematology, National Cancer Center Hospital East, Kashiwa 277-8577, Japan; (M.E.); (A.K.); (S.C.)
- Division of Hematology/Oncology, Department of Internal Medicine, Kameda Medical Center, Kamogawa 296-8602, Japan
| | - SungGi Chi
- Department of Hematology, National Cancer Center Hospital East, Kashiwa 277-8577, Japan; (M.E.); (A.K.); (S.C.)
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2
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Astolfi A, Kudolo M, Brea J, Manni G, Manfroni G, Palazzotti D, Sabatini S, Cecchetti F, Felicetti T, Cannalire R, Massari S, Tabarrini O, Loza MI, Fallarino F, Cecchetti V, Laufer SA, Barreca ML. Discovery of potent p38α MAPK inhibitors through a funnel like workflow combining in silico screening and in vitro validation. Eur J Med Chem 2019; 182:111624. [PMID: 31445234 DOI: 10.1016/j.ejmech.2019.111624] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2019] [Revised: 08/05/2019] [Accepted: 08/12/2019] [Indexed: 01/31/2023]
Abstract
This work describes the rational discovery of novel chemotypes of p38α MAPK inhibitors using a funnel approach consisting of several computer-aided drug discovery methods and biological experiments. Among the identified hits, four compounds belonging to different chemical families showed IC50 values lower than 10 μM. In particular, the 1,4-benzodioxane derivative 5 turned out to be a potent and efficient p38α MAPK inhibitor having IC50 = 0.07 μM, and LEexp and LipE values of 0.38 and 4.8, respectively; noteworthy, the compound had also a promising kinase selectivity profile and the capability to suppress p38α MAPK effects in human immune cells. Overall, the collected findings highlight that the applied strategy has been successful in generating chemical novelty in the inhibitor kinase field, providing suitable chemical candidates for further inhibitor optimization.
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Affiliation(s)
- Andrea Astolfi
- Department of Pharmaceutical Sciences, "Department of Excellence 2018-2022", University of Perugia, Via del Liceo 1, 06123, Perugia, Italy
| | - Mark Kudolo
- Department of Pharmaceutical & Medicinal Chemistry, Institute of Pharmacy, Eberhard-Karls University Tuebingen, Auf der Morgenstelle 8, 72076, Tuebingen, Germany
| | - Jose Brea
- CIMUS Research Center, University of Santiago de Compostela, Avda de Barcelona s/n, Planta 3, Despacho1, 15782, Santiago de Compostela, Spain
| | - Giorgia Manni
- Department of Experimental Medicine, University of Perugia, Piazzale Gambuli, 06100, Perugia, Italy
| | - Giuseppe Manfroni
- Department of Pharmaceutical Sciences, "Department of Excellence 2018-2022", University of Perugia, Via del Liceo 1, 06123, Perugia, Italy
| | - Deborah Palazzotti
- Department of Pharmaceutical Sciences, "Department of Excellence 2018-2022", University of Perugia, Via del Liceo 1, 06123, Perugia, Italy
| | - Stefano Sabatini
- Department of Pharmaceutical Sciences, "Department of Excellence 2018-2022", University of Perugia, Via del Liceo 1, 06123, Perugia, Italy
| | - Federica Cecchetti
- Department of Experimental Medicine, University of Perugia, Piazzale Gambuli, 06100, Perugia, Italy
| | - Tommaso Felicetti
- Department of Pharmaceutical Sciences, "Department of Excellence 2018-2022", University of Perugia, Via del Liceo 1, 06123, Perugia, Italy
| | - Rolando Cannalire
- Department of Pharmaceutical Sciences, "Department of Excellence 2018-2022", University of Perugia, Via del Liceo 1, 06123, Perugia, Italy
| | - Serena Massari
- Department of Pharmaceutical Sciences, "Department of Excellence 2018-2022", University of Perugia, Via del Liceo 1, 06123, Perugia, Italy
| | - Oriana Tabarrini
- Department of Pharmaceutical Sciences, "Department of Excellence 2018-2022", University of Perugia, Via del Liceo 1, 06123, Perugia, Italy
| | - Maria Isabel Loza
- CIMUS Research Center, University of Santiago de Compostela, Avda de Barcelona s/n, Planta 3, Despacho1, 15782, Santiago de Compostela, Spain
| | - Francesca Fallarino
- Department of Experimental Medicine, University of Perugia, Piazzale Gambuli, 06100, Perugia, Italy
| | - Violetta Cecchetti
- Department of Pharmaceutical Sciences, "Department of Excellence 2018-2022", University of Perugia, Via del Liceo 1, 06123, Perugia, Italy
| | - Stefan A Laufer
- Department of Pharmaceutical & Medicinal Chemistry, Institute of Pharmacy, Eberhard-Karls University Tuebingen, Auf der Morgenstelle 8, 72076, Tuebingen, Germany
| | - Maria Letizia Barreca
- Department of Pharmaceutical Sciences, "Department of Excellence 2018-2022", University of Perugia, Via del Liceo 1, 06123, Perugia, Italy.
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3
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Gilburt JAH, Girvan P, Blagg J, Ying L, Dodson CA. Ligand discrimination between active and inactive activation loop conformations of Aurora-A kinase is unmodified by phosphorylation. Chem Sci 2019; 10:4069-4076. [PMID: 31015948 PMCID: PMC6461105 DOI: 10.1039/c8sc03669a] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2018] [Accepted: 03/01/2019] [Indexed: 01/14/2023] Open
Abstract
Activation loop phosphorylation changes the position of equilibrium between DFG-in-like and DFG-out-like conformations but not the conformational preference of inhibitors.
Structure-based drug design is commonly used to guide the development of potent and specific enzyme inhibitors. Many enzymes – such as protein kinases – adopt multiple conformations, and conformational interconversion is expected to impact on the design of small molecule inhibitors. We measured the dynamic equilibrium between DFG-in-like active and DFG-out-like inactive conformations of the activation loop of unphosphorylated Aurora-A alone, in the presence of the activator TPX2, and in the presence of kinase inhibitors. The unphosphorylated kinase had a shorter residence time of the activation loop in the active conformation and a shift in the position of equilibrium towards the inactive conformation compared with phosphorylated kinase for all conditions measured. Ligand binding was associated with a change in the position of conformational equilibrium which was specific to each ligand and independent of the kinase phosphorylation state. As a consequence of this, the ability of a ligand to discriminate between active and inactive activation loop conformations was also independent of phosphorylation. Importantly, we discovered that the presence of multiple enzyme conformations can lead to a plateau in the overall ligand Kd, despite increasing affinity for the chosen target conformation, and modelled the conformational discrimination necessary for a conformation-promoting ligand.
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Affiliation(s)
- James A H Gilburt
- Molecular Medicine , National Heart & Lung Institute , Imperial College London , SAF Building , London SW7 2AZ , UK
| | - Paul Girvan
- Molecular Medicine , National Heart & Lung Institute , Imperial College London , SAF Building , London SW7 2AZ , UK
| | - Julian Blagg
- Cancer Research UK Cancer Therapeutics Unit , The Institute of Cancer Research , 15 Cotswold Road , Sutton , Surrey SM2 5NG , UK
| | - Liming Ying
- Molecular Medicine , National Heart & Lung Institute , Imperial College London , SAF Building , London SW7 2AZ , UK
| | - Charlotte A Dodson
- Molecular Medicine , National Heart & Lung Institute , Imperial College London , SAF Building , London SW7 2AZ , UK.,Department of Pharmacy and Pharmacology , University of Bath , Claverton Down , Bath BA2 7AY , UK .
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4
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Blaquiere N, Castanedo GM, Burch JD, Berezhkovskiy LM, Brightbill H, Brown S, Chan C, Chiang PC, Crawford JJ, Dong T, Fan P, Feng J, Ghilardi N, Godemann R, Gogol E, Grabbe A, Hole AJ, Hu B, Hymowitz SG, Alaoui Ismaili MH, Le H, Lee P, Lee W, Lin X, Liu N, McEwan PA, McKenzie B, Silvestre HL, Suto E, Sujatha-Bhaskar S, Wu G, Wu LC, Zhang Y, Zhong Z, Staben ST. Scaffold-Hopping Approach To Discover Potent, Selective, and Efficacious Inhibitors of NF-κB Inducing Kinase. J Med Chem 2018; 61:6801-6813. [PMID: 29940120 DOI: 10.1021/acs.jmedchem.8b00678] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
NF-κB-inducing kinase (NIK) is a protein kinase central to the noncanonical NF-κB pathway downstream from multiple TNF receptor family members, including BAFF, which has been associated with B cell survival and maturation, dendritic cell activation, secondary lymphoid organ development, and bone metabolism. We report herein the discovery of lead chemical series of NIK inhibitors that were identified through a scaffold-hopping strategy using structure-based design. Electronic and steric properties of lead compounds were modified to address glutathione conjugation and amide hydrolysis. These highly potent compounds exhibited selective inhibition of LTβR-dependent p52 translocation and transcription of NF-κB2 related genes. Compound 4f is shown to have a favorable pharmacokinetic profile across species and to inhibit BAFF-induced B cell survival in vitro and reduce splenic marginal zone B cells in vivo.
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Affiliation(s)
- Nicole Blaquiere
- Genentech, Inc. , 1 DNA Way , South San Francisco , California 94080 , United States
| | - Georgette M Castanedo
- Genentech, Inc. , 1 DNA Way , South San Francisco , California 94080 , United States
| | - Jason D Burch
- Genentech, Inc. , 1 DNA Way , South San Francisco , California 94080 , United States
| | | | - Hans Brightbill
- Genentech, Inc. , 1 DNA Way , South San Francisco , California 94080 , United States
| | - Suzanne Brown
- Genentech, Inc. , 1 DNA Way , South San Francisco , California 94080 , United States
| | - Connie Chan
- Genentech, Inc. , 1 DNA Way , South San Francisco , California 94080 , United States
| | - Po-Chang Chiang
- Genentech, Inc. , 1 DNA Way , South San Francisco , California 94080 , United States
| | - James J Crawford
- Genentech, Inc. , 1 DNA Way , South San Francisco , California 94080 , United States
| | - Teresa Dong
- Genentech, Inc. , 1 DNA Way , South San Francisco , California 94080 , United States
| | - Peter Fan
- Genentech, Inc. , 1 DNA Way , South San Francisco , California 94080 , United States
| | - Jianwen Feng
- Genentech, Inc. , 1 DNA Way , South San Francisco , California 94080 , United States
| | - Nico Ghilardi
- Genentech, Inc. , 1 DNA Way , South San Francisco , California 94080 , United States
| | - Robert Godemann
- Evotec AG , Manfred Eigen Campus, Essener Bogen , Hamburg 22419 , Germany
| | - Emily Gogol
- Genentech, Inc. , 1 DNA Way , South San Francisco , California 94080 , United States
| | - Alice Grabbe
- Evotec AG , Manfred Eigen Campus, Essener Bogen , Hamburg 22419 , Germany
| | - Alison J Hole
- Evotec AG , Manfred Eigen Campus, Essener Bogen , Hamburg 22419 , Germany
| | - Baihua Hu
- Pharmaron Beijing Co., Ltd. , 6 Taihe Road, BDA , Beijing 100176 , P. R. China
| | - Sarah G Hymowitz
- Genentech, Inc. , 1 DNA Way , South San Francisco , California 94080 , United States
| | | | - Hoa Le
- Genentech, Inc. , 1 DNA Way , South San Francisco , California 94080 , United States
| | - Patrick Lee
- Genentech, Inc. , 1 DNA Way , South San Francisco , California 94080 , United States
| | - Wyne Lee
- Genentech, Inc. , 1 DNA Way , South San Francisco , California 94080 , United States
| | - Xingyu Lin
- Pharmaron Beijing Co., Ltd. , 6 Taihe Road, BDA , Beijing 100176 , P. R. China
| | - Ning Liu
- Genentech, Inc. , 1 DNA Way , South San Francisco , California 94080 , United States
| | - Paul A McEwan
- Evotec AG , Manfred Eigen Campus, Essener Bogen , Hamburg 22419 , Germany
| | - Brent McKenzie
- Genentech, Inc. , 1 DNA Way , South San Francisco , California 94080 , United States
| | | | - Eric Suto
- Genentech, Inc. , 1 DNA Way , South San Francisco , California 94080 , United States
| | | | - Guosheng Wu
- Pharmaron Beijing Co., Ltd. , 6 Taihe Road, BDA , Beijing 100176 , P. R. China
| | - Lawren C Wu
- Genentech, Inc. , 1 DNA Way , South San Francisco , California 94080 , United States
| | - Yamin Zhang
- Pharmaron Beijing Co., Ltd. , 6 Taihe Road, BDA , Beijing 100176 , P. R. China
| | - Zoe Zhong
- Genentech, Inc. , 1 DNA Way , South San Francisco , California 94080 , United States
| | - Steven T Staben
- Genentech, Inc. , 1 DNA Way , South San Francisco , California 94080 , United States
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5
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Astolfi A, Manfroni G, Cecchetti V, Barreca ML. A Comprehensive Structural Overview of p38α Mitogen-Activated Protein Kinase in Complex with ATP-Site and Non-ATP-Site Binders. ChemMedChem 2017; 13:7-14. [PMID: 29210532 DOI: 10.1002/cmdc.201700636] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2017] [Revised: 12/01/2017] [Indexed: 12/18/2022]
Abstract
Herein we review all the currently available ATP-site and non-ATP-site ligands bound to p38α mitogen-activated protein kinase (MAPK) available in the RCSB Protein Data Bank (PDB). The co-crystallized inhibitors have been classified into different families according to their experimental binding mode and chemical structure, and the ligand-protein interactions are discussed using the most representative compounds. This systematic structural analysis could provide some take-home lessons for drug discovery programs aimed at the rational identification and optimization of new p38α MAPK inhibitors.
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Affiliation(s)
- Andrea Astolfi
- 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
| | - Violetta Cecchetti
- 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
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6
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Nishiguchi GA, Rico A, Tanner H, Aversa RJ, Taft BR, Subramanian S, Setti L, Burger MT, Wan L, Tamez V, Smith A, Lou Y, Barsanti PA, Appleton BA, Mamo M, Tandeske L, Dix I, Tellew JE, Huang S, Mathews Griner LA, Cooke VG, Van Abbema A, Merritt H, Ma S, Gampa K, Feng F, Yuan J, Wang Y, Haling JR, Vaziri S, Hekmat-Nejad M, Jansen JM, Polyakov V, Zang R, Sethuraman V, Amiri P, Singh M, Lees E, Shao W, Stuart DD, Dillon MP, Ramurthy S. Design and Discovery of N-(2-Methyl-5′-morpholino-6′-((tetrahydro-2H-pyran-4-yl)oxy)-[3,3′-bipyridin]-5-yl)-3-(trifluoromethyl)benzamide (RAF709): A Potent, Selective, and Efficacious RAF Inhibitor Targeting RAS Mutant Cancers. J Med Chem 2017; 60:4869-4881. [DOI: 10.1021/acs.jmedchem.6b01862] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Gisele A. Nishiguchi
- Global
Discovery Chemistry, Novartis Institutes for BioMedical Research, 250 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Alice Rico
- Global
Discovery Chemistry, Novartis Institutes for BioMedical Research, 5300 Chiron Way, Emeryville, California 94608, United States
| | - Huw Tanner
- Global
Discovery Chemistry, Novartis Institutes for BioMedical Research, 5300 Chiron Way, Emeryville, California 94608, United States
| | - Robert J. Aversa
- Global
Discovery Chemistry, Novartis Institutes for BioMedical Research, 250 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Benjamin R. Taft
- Global
Discovery Chemistry, Novartis Institutes for BioMedical Research, 5300 Chiron Way, Emeryville, California 94608, United States
| | - Sharadha Subramanian
- Global
Discovery Chemistry, Novartis Institutes for BioMedical Research, 5300 Chiron Way, Emeryville, California 94608, United States
| | - Lina Setti
- Global
Discovery Chemistry, Novartis Institutes for BioMedical Research, 5300 Chiron Way, Emeryville, California 94608, United States
| | - Matthew T. Burger
- Global
Discovery Chemistry, Novartis Institutes for BioMedical Research, 250 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Lifeng Wan
- Global
Discovery Chemistry, Novartis Institutes for BioMedical Research, 5300 Chiron Way, Emeryville, California 94608, United States
| | - Victoriano Tamez
- Global
Discovery Chemistry, Novartis Institutes for BioMedical Research, 250 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Aaron Smith
- Global
Discovery Chemistry, Novartis Institutes for BioMedical Research, 5300 Chiron Way, Emeryville, California 94608, United States
| | - Yan Lou
- Global
Discovery Chemistry, Novartis Institutes for BioMedical Research, 5300 Chiron Way, Emeryville, California 94608, United States
| | - Paul A. Barsanti
- Global
Discovery Chemistry, Novartis Institutes for BioMedical Research, 5300 Chiron Way, Emeryville, California 94608, United States
| | - Brent A. Appleton
- Global
Discovery Chemistry, Novartis Institutes for BioMedical Research, 5300 Chiron Way, Emeryville, California 94608, United States
| | - Mulugeta Mamo
- Global
Discovery Chemistry, Novartis Institutes for BioMedical Research, 5300 Chiron Way, Emeryville, California 94608, United States
| | - Laura Tandeske
- Oncology, Novartis Institutes for BioMedical Research, 5300 Chiron Way, Emeryville, California 94608, United States
| | - Ina Dix
- Global
Discovery Chemistry, Novartis Institutes for BioMedical Research, Novartis Pharma AG, Werk Klybeck, Postfach, CH-4002 Basel, Switzerland
| | - John E. Tellew
- Genomics
Institute of the Novartis Research Foundation, 10675 John Hopkins Drive, San Diego, California 92121, United States
| | - Shenlin Huang
- Genomics
Institute of the Novartis Research Foundation, 10675 John Hopkins Drive, San Diego, California 92121, United States
| | - Lesley A. Mathews Griner
- Oncology, Novartis Institutes for BioMedical Research, 250 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Vesselina G. Cooke
- Oncology, Novartis Institutes for BioMedical Research, 250 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Anne Van Abbema
- Oncology, Novartis Institutes for BioMedical Research, 5300 Chiron Way, Emeryville, California 94608, United States
| | - Hanne Merritt
- Oncology, Novartis Institutes for BioMedical Research, 5300 Chiron Way, Emeryville, California 94608, United States
| | - Sylvia Ma
- Oncology, Novartis Institutes for BioMedical Research, 5300 Chiron Way, Emeryville, California 94608, United States
| | - Kalyani Gampa
- Oncology, Novartis Institutes for BioMedical Research, 250 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Fei Feng
- Oncology, Novartis Institutes for BioMedical Research, 250 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Jing Yuan
- Oncology, Novartis Institutes for BioMedical Research, 250 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Yingyun Wang
- Oncology, Novartis Institutes for BioMedical Research, 5300 Chiron Way, Emeryville, California 94608, United States
| | - Jacob R. Haling
- Genomics
Institute of the Novartis Research Foundation, 10675 John Hopkins Drive, San Diego, California 92121, United States
| | - Sepideh Vaziri
- Genomics
Institute of the Novartis Research Foundation, 10675 John Hopkins Drive, San Diego, California 92121, United States
| | - Mohammad Hekmat-Nejad
- Oncology, Novartis Institutes for BioMedical Research, 5300 Chiron Way, Emeryville, California 94608, United States
| | - Johanna M. Jansen
- Global
Discovery Chemistry, Novartis Institutes for BioMedical Research, 5300 Chiron Way, Emeryville, California 94608, United States
| | - Valery Polyakov
- Global
Discovery Chemistry, Novartis Institutes for BioMedical Research, 5300 Chiron Way, Emeryville, California 94608, United States
| | - Richard Zang
- Global
Discovery Chemistry, Novartis Institutes for BioMedical Research, 5300 Chiron Way, Emeryville, California 94608, United States
| | - Vijay Sethuraman
- Oncology, Novartis Institutes for BioMedical Research, 5300 Chiron Way, Emeryville, California 94608, United States
| | - Payman Amiri
- Oncology, Novartis Institutes for BioMedical Research, 5300 Chiron Way, Emeryville, California 94608, United States
| | - Mallika Singh
- Oncology, Novartis Institutes for BioMedical Research, 5300 Chiron Way, Emeryville, California 94608, United States
| | - Emma Lees
- Oncology, Novartis Institutes for BioMedical Research, 250 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Wenlin Shao
- Oncology, Novartis Institutes for BioMedical Research, 250 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Darrin D. Stuart
- Oncology, Novartis Institutes for BioMedical Research, 250 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Michael P. Dillon
- Global
Discovery Chemistry, Novartis Institutes for BioMedical Research, 250 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Savithri Ramurthy
- Global
Discovery Chemistry, Novartis Institutes for BioMedical Research, 5300 Chiron Way, Emeryville, California 94608, United States
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7
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Lagunas-Rangel FA, Chávez-Valencia V. FLT3–ITD and its current role in acute myeloid leukaemia. Med Oncol 2017; 34:114. [DOI: 10.1007/s12032-017-0970-x] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2017] [Accepted: 04/25/2017] [Indexed: 01/20/2023]
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8
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Castanedo GM, Blaquiere N, Beresini M, Bravo B, Brightbill H, Chen J, Cui HF, Eigenbrot C, Everett C, Feng J, Godemann R, Gogol E, Hymowitz S, Johnson A, Kayagaki N, Kohli PB, Knüppel K, Kraemer J, Krüger S, Loke P, McEwan P, Montalbetti C, Roberts DA, Smith M, Steinbacher S, Sujatha-Bhaskar S, Takahashi R, Wang X, Wu LC, Zhang Y, Staben ST. Structure-Based Design of Tricyclic NF-κB Inducing Kinase (NIK) Inhibitors That Have High Selectivity over Phosphoinositide-3-kinase (PI3K). J Med Chem 2017; 60:627-640. [PMID: 28005357 DOI: 10.1021/acs.jmedchem.6b01363] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
We report here structure-guided optimization of a novel series of NF-κB inducing kinase (NIK) inhibitors. Starting from a modestly potent, low molecular weight lead, activity was improved by designing a type 11/2 binding mode that accessed a back pocket past the methionine-471 gatekeeper. Divergent binding modes in NIK and PI3K were exploited to dampen PI3K inhibition while maintaining NIK inhibition within these series. Potent compounds were discovered that selectively inhibit the nuclear translocation of NF-κB2 (p52/REL-B) but not canonical NF-κB1 (REL-A/p50).
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Affiliation(s)
| | - Nicole Blaquiere
- Genentech, Inc. 1 DNA Way, South San Francisco, California 94080, United States
| | - Maureen Beresini
- Genentech, Inc. 1 DNA Way, South San Francisco, California 94080, United States
| | - Brandon Bravo
- Genentech, Inc. 1 DNA Way, South San Francisco, California 94080, United States
| | - Hans Brightbill
- Genentech, Inc. 1 DNA Way, South San Francisco, California 94080, United States
| | - Jacob Chen
- Genentech, Inc. 1 DNA Way, South San Francisco, California 94080, United States
| | - Hai-Feng Cui
- Pharmaron Beijing Co., Ltd . 6 Taihe Road, BDA, Beijing 100176, P.R. China
| | - Charles Eigenbrot
- Genentech, Inc. 1 DNA Way, South San Francisco, California 94080, United States
| | - Christine Everett
- Genentech, Inc. 1 DNA Way, South San Francisco, California 94080, United States
| | - Jianwen Feng
- Genentech, Inc. 1 DNA Way, South San Francisco, California 94080, United States
| | - Robert Godemann
- Manfred Eigen Campus, Evotec AG , Essener Bogen, 22419 Hamburg, Germany
| | - Emily Gogol
- Genentech, Inc. 1 DNA Way, South San Francisco, California 94080, United States
| | - Sarah Hymowitz
- Genentech, Inc. 1 DNA Way, South San Francisco, California 94080, United States
| | - Adam Johnson
- Genentech, Inc. 1 DNA Way, South San Francisco, California 94080, United States
| | - Nobuhiko Kayagaki
- Genentech, Inc. 1 DNA Way, South San Francisco, California 94080, United States
| | - Pawan Bir Kohli
- Genentech, Inc. 1 DNA Way, South San Francisco, California 94080, United States
| | - Kathleen Knüppel
- Manfred Eigen Campus, Evotec AG , Essener Bogen, 22419 Hamburg, Germany
| | - Joachim Kraemer
- Manfred Eigen Campus, Evotec AG , Essener Bogen, 22419 Hamburg, Germany
| | - Susan Krüger
- Manfred Eigen Campus, Evotec AG , Essener Bogen, 22419 Hamburg, Germany
| | - Pui Loke
- Evotec (U.K.) Ltd , 114 Innovation Drive, Milton Park, Abingdon OX14 4Rz, U.K
| | - Paul McEwan
- Evotec (U.K.) Ltd , 114 Innovation Drive, Milton Park, Abingdon OX14 4Rz, U.K
| | | | - David A Roberts
- Genentech, Inc. 1 DNA Way, South San Francisco, California 94080, United States
| | - Myron Smith
- Evotec (U.K.) Ltd , 114 Innovation Drive, Milton Park, Abingdon OX14 4Rz, U.K
| | - Stefan Steinbacher
- Proteros Biostructures GmbH , Bunsenstrasse 7a, D-82152 Martinsried, Germany
| | | | - Ryan Takahashi
- Genentech, Inc. 1 DNA Way, South San Francisco, California 94080, United States
| | - Xiaolu Wang
- Manfred Eigen Campus, Evotec AG , Essener Bogen, 22419 Hamburg, Germany
| | - Lawren C Wu
- Genentech, Inc. 1 DNA Way, South San Francisco, California 94080, United States
| | - Yamin Zhang
- Pharmaron Beijing Co., Ltd . 6 Taihe Road, BDA, Beijing 100176, P.R. China
| | - Steven T Staben
- Genentech, Inc. 1 DNA Way, South San Francisco, California 94080, United States
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9
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Bethke E, Pinchuk B, Renn C, Witt L, Schlosser J, Peifer C. From Type I to Type II: Design, Synthesis, and Characterization of Potent Pyrazin-2-ones as DFG-Out Inhibitors of PDGFRβ. ChemMedChem 2016; 11:2664-2674. [PMID: 27885822 DOI: 10.1002/cmdc.201600494] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2016] [Revised: 10/30/2016] [Indexed: 11/09/2022]
Abstract
Reversible protein kinase inhibitors that bind in the ATP cleft can be classified as type I or type II binders. Of these, type I inhibitors address the active form, whereas type II inhibitors typically lock the kinase in an inactive form. At the molecular level, the conformation of the flexible activation loop holding the key DFG motif controls access to the ATP site, thereby determining an active or inactive kinase state. Accordingly, type I and type II kinase inhibitors bind to so-called DFG-in or DFG-out conformations, respectively. Based on our former study on highly selective platelet-derived growth factor receptor β (PDGFRβ) pyrazin-2-one type I inhibitors, we expanded this scaffold toward the deep pocket, yielding the highly potent and effective type II inhibitor 5 (4-[(4-methylpiperazin-1-yl)methyl]-N-[3-[[6-oxo-5-(3,4,5-trimethoxyphenyl)-1H-pyrazin-3-yl]methyl]phenyl]benzamide). In vitro characterization, including selectivity panel data from activity-based assays (300 kinases) and affinity-based assays (97 kinases) of these PDGFRβ type I (1; 5-(4-hydroxy-3-methoxy-phenyl)-3-(3,4,5-trimethoxyphenyl)-1H-pyrazin-2-one) and II (5) inhibitors showing the same pyrazin-2-one chemotype are compared. Implications are discussed regarding the data for selectivity and efficacy of type I and type II ligands.
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Affiliation(s)
- Eugen Bethke
- Christian Albrechts University of Kiel, Institute of Pharmacy, Gutenbergstr. 76, 24118, Kiel, Germany
| | - Boris Pinchuk
- Christian Albrechts University of Kiel, Institute of Pharmacy, Gutenbergstr. 76, 24118, Kiel, Germany
| | - Christian Renn
- Christian Albrechts University of Kiel, Institute of Pharmacy, Gutenbergstr. 76, 24118, Kiel, Germany
| | - Lydia Witt
- Christian Albrechts University of Kiel, Institute of Pharmacy, Gutenbergstr. 76, 24118, Kiel, Germany
| | - Joachim Schlosser
- Christian Albrechts University of Kiel, Institute of Pharmacy, Gutenbergstr. 76, 24118, Kiel, Germany
| | - Christian Peifer
- Christian Albrechts University of Kiel, Institute of Pharmacy, Gutenbergstr. 76, 24118, Kiel, Germany
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10
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Baby B, Antony P, Al Halabi W, Al Homedi Z, Vijayan R. Structural insights into the polypharmacological activity of quercetin on serine/threonine kinases. DRUG DESIGN DEVELOPMENT AND THERAPY 2016; 10:3109-3123. [PMID: 27729770 PMCID: PMC5045902 DOI: 10.2147/dddt.s118423] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Polypharmacology, the discovery or design of drug molecules that can simultaneously interact with multiple targets, is gaining interest in contemporary drug discovery. Serine/threonine kinases are attractive targets for therapeutic intervention in oncology due to their role in cellular phosphorylation and altered expression in cancer. Quercetin, a naturally occurring flavonoid, inhibits multiple cancer cell lines and is used as an anticancer drug in Phase I clinical trial. Quercetin glycosides have also received some attention due to their high bioavailability and activity against various diseases including cancer. However, these have been studied to a lesser extent. In this study, the structural basis of the multitarget inhibitory activity of quercetin and isoquercitrin, a glycoside derivative, on serine/threonine kinases using molecular modeling was explored. Structural analysis showed that both quercetin and isoquercitrin exhibited good binding energies and interacted with aspartate in the highly conserved Asp–Phe–Gly motif. The results indicate that isoquercitrin could be a more potent inhibitor of several members of the serine/threonine kinase family. In summary, the current structural evaluation highlights the multitarget inhibitory property of quercetin and its potential to be a chemical platform for oncological polypharmacology.
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Affiliation(s)
- Bincy Baby
- Department of Biology, College of Science, United Arab Emirates University, Al Ain, Abu Dhabi, United Arab Emirates
| | - Priya Antony
- Department of Biology, College of Science, United Arab Emirates University, Al Ain, Abu Dhabi, United Arab Emirates
| | - Walaa Al Halabi
- Department of Biology, College of Science, United Arab Emirates University, Al Ain, Abu Dhabi, United Arab Emirates
| | - Zahrah Al Homedi
- Department of Biology, College of Science, United Arab Emirates University, Al Ain, Abu Dhabi, United Arab Emirates
| | - Ranjit Vijayan
- Department of Biology, College of Science, United Arab Emirates University, Al Ain, Abu Dhabi, United Arab Emirates
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11
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Astolfi A, Iraci N, Sabatini S, Barreca ML, Cecchetti V. p38α MAPK and Type I Inhibitors: Binding Site Analysis and Use of Target Ensembles in Virtual Screening. Molecules 2015; 20:15842-61. [PMID: 26334265 PMCID: PMC6331920 DOI: 10.3390/molecules200915842] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2015] [Revised: 08/19/2015] [Accepted: 08/26/2015] [Indexed: 12/14/2022] Open
Abstract
Mitogen-activated protein kinase p38α plays an essential role in the regulation of pro-inflammatory signaling, and selective blockade of this kinase could be efficacious in many pathological processes. Despite considerable research efforts focused on the discovery and development of p38α MAPK inhibitors, no drug targeting this protein has been approved for clinical use so far. We herein analyze the available crystal structures of p38α MAPK in complex with ATP competitive type I inhibitors, getting insights into ATP binding site conformation and its influence on automated molecular docking results. The use of target ensembles, rather than single conformations, resulted in a performance improvement in both the ability to reproduce experimental bound conformations and the capability of mining active molecules from compound libraries. The information gathered from this study can be exploited in structure-based drug discovery programs having as the ultimate aim the identification of novel p38α MAPK type I inhibitors.
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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.
| | - Stefano Sabatini
- 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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12
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Ke YY, Singh VK, Coumar MS, Hsu YC, Wang WC, Song JS, Chen CH, Lin WH, Wu SH, Hsu JTA, Shih C, Hsieh HP. Homology modeling of DFG-in FMS-like tyrosine kinase 3 (FLT3) and structure-based virtual screening for inhibitor identification. Sci Rep 2015; 5:11702. [PMID: 26118648 PMCID: PMC4483777 DOI: 10.1038/srep11702] [Citation(s) in RCA: 57] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2014] [Accepted: 06/02/2015] [Indexed: 12/23/2022] Open
Abstract
The inhibition of FMS-like tyrosine kinase 3 (FLT3) activity using small-molecule inhibitors has emerged as a target-based alternative to traditional chemotherapy for the treatment of acute myeloid leukemia (AML). In this study, we report the use of structure-based virtual screening (SBVS), a computer-aided drug design technique for the identification of new chemotypes for FLT3 inhibition. For this purpose, homology modeling (HM) of the DFG-in FLT3 structure was carried using two template structures, including PDB ID: 1RJB (DFG-out FLT3 kinase domain) and PDB ID: 3LCD (DFG-in CSF-1 kinase domain). The modeled structure was able to correctly identify known DFG-in (SU11248, CEP-701, and PKC-412) and DFG-out (sorafenib, ABT-869 and AC220) FLT3 inhibitors, in docking studies. The modeled structure was then used to carry out SBVS of an HTS library of 125,000 compounds. The top scoring 97 compounds were tested for FLT3 kinase inhibition, and two hits (BPR056, IC50 = 2.3 and BPR080, IC50 = 10.7 μM) were identified. Molecular dynamics simulation and density functional theory calculation suggest that BPR056 (MW: 325.32; cLogP: 2.48) interacted with FLT3 in a stable manner and could be chemically optimized to realize a drug-like lead in the future.
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Affiliation(s)
- Yi-Yu Ke
- Institute of Biotechnology and Pharmaceutical Research, National Health Research Institutes, 35 Keyan Road, Zhunan, Miaoli County 350, Taiwan, ROC
| | - Vivek Kumar Singh
- Centre for Bioinformatics, School of Life Sciences, Pondicherry University, Kalapet, Puducherry 605014, India
| | - Mohane Selvaraj Coumar
- Centre for Bioinformatics, School of Life Sciences, Pondicherry University, Kalapet, Puducherry 605014, India
| | - Yung Chang Hsu
- Institute of Biotechnology and Pharmaceutical Research, National Health Research Institutes, 35 Keyan Road, Zhunan, Miaoli County 350, Taiwan, ROC
| | - Wen-Chieh Wang
- Institute of Biotechnology and Pharmaceutical Research, National Health Research Institutes, 35 Keyan Road, Zhunan, Miaoli County 350, Taiwan, ROC
| | - Jen-Shin Song
- Institute of Biotechnology and Pharmaceutical Research, National Health Research Institutes, 35 Keyan Road, Zhunan, Miaoli County 350, Taiwan, ROC
| | - Chun-Hwa Chen
- Institute of Biotechnology and Pharmaceutical Research, National Health Research Institutes, 35 Keyan Road, Zhunan, Miaoli County 350, Taiwan, ROC
| | - Wen-Hsing Lin
- Institute of Biotechnology and Pharmaceutical Research, National Health Research Institutes, 35 Keyan Road, Zhunan, Miaoli County 350, Taiwan, ROC
| | - Szu-Huei Wu
- Institute of Biotechnology and Pharmaceutical Research, National Health Research Institutes, 35 Keyan Road, Zhunan, Miaoli County 350, Taiwan, ROC
| | - John T A Hsu
- Institute of Biotechnology and Pharmaceutical Research, National Health Research Institutes, 35 Keyan Road, Zhunan, Miaoli County 350, Taiwan, ROC
| | - Chuan Shih
- Institute of Biotechnology and Pharmaceutical Research, National Health Research Institutes, 35 Keyan Road, Zhunan, Miaoli County 350, Taiwan, ROC
| | - Hsing-Pang Hsieh
- Institute of Biotechnology and Pharmaceutical Research, National Health Research Institutes, 35 Keyan Road, Zhunan, Miaoli County 350, Taiwan, ROC
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13
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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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14
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Rudolph J, Crawford JJ, Hoeflich KP, Wang W. Inhibitors of p21-activated kinases (PAKs). J Med Chem 2014; 58:111-29. [PMID: 25415869 DOI: 10.1021/jm501613q] [Citation(s) in RCA: 88] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The p21-activated kinase (PAK) family of serine/threonine protein kinases plays important roles in cytoskeletal organization, cellular morphogenesis, and survival, and members of this family have been implicated in many diseases including cancer, infectious diseases, and neurological disorders. Owing to their large and flexible ATP binding cleft, PAKs, particularly group I PAKs (PAK1, -2, and -3), are difficult to drug; hence, few PAK inhibitors with satisfactory kinase selectivity and druglike properties have been reported to date. Examples are a recently discovered group II PAK (PAK4, -5, -6) selective inhibitor series based on a benzimidazole core, a group I PAK selective series based on a pyrido[2,3-d]pyrimidine-7-one core, and an allosteric dibenzodiazepine PAK1 inhibitor series. Only one compound, an aminopyrazole based pan-PAK inhibitor, entered clinical trials but did not progress beyond phase I trials. Clinical proof of concept for pan-group I, pan-group II, or PAK isoform selective inhibition has yet to be demonstrated.
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Affiliation(s)
- Joachim Rudolph
- Discovery Chemistry, and ‡Structural Biology, Genentech , 1 DNA Way, South San Francisco, California 94080, United States
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15
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Staben ST, Feng JA, Lyle K, Belvin M, Boggs J, Burch JD, Chua CC, Cui H, DiPasquale AG, Friedman LS, Heise C, Koeppen H, Kotey A, Mintzer R, Oh A, Roberts DA, Rouge L, Rudolph J, Tam C, Wang W, Xiao Y, Young A, Zhang Y, Hoeflich KP. Back Pocket Flexibility Provides Group II p21-Activated Kinase (PAK) Selectivity for Type I 1/2 Kinase Inhibitors. J Med Chem 2014; 57:1033-45. [DOI: 10.1021/jm401768t] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
| | | | | | | | | | | | - Ching-ching Chua
- Medicinal
Chemistry, Evotec, Abingdon, Oxfordshire OX144SA, United Kingdom
| | - Haifeng Cui
- Pharmaron-Beijing, 6 Taihe Road, Beijing 100176, People’s Republic of China
| | - Antonio G. DiPasquale
- X-ray
Crystallography Facility, University of California, Berkeley, California 94720, United States
| | | | | | | | - Adrian Kotey
- Medicinal
Chemistry, Evotec, Abingdon, Oxfordshire OX144SA, United Kingdom
| | | | | | | | | | | | | | | | - Yisong Xiao
- Wuxi AppTec, 288 Fute Zhong
Road, Shanghai 200131, People’s Republic of China
| | | | - Yamin Zhang
- Pharmaron-Beijing, 6 Taihe Road, Beijing 100176, People’s Republic of China
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16
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Building structure-activity insights through patent mining. Pharm Pat Anal 2013; 1:545-54. [PMID: 24236924 DOI: 10.4155/ppa.12.60] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
One gap in current patent-mining practice is the lack of tools to build SAR knowledge. Here, we report a novel technique that enabled us to derive useful SAR information from the exemplified structures of a series of patents. In our approach, exemplified chemical structures were extracted from patent documents. They were grouped into structural series based on similarity and binding mode, after which the R-group table was generated. By analyzing R-group usages over time, we were able to build insights into SAR of a structural series, even though the biological activities were not available.
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17
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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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