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Chen YT, Yang H, Chu JW. Trajectory Statistical Learning of the Potential Mean of Force and Diffusion Coefficient from Molecular Dynamics Simulations. J Phys Chem B 2024; 128:56-66. [PMID: 38165090 DOI: 10.1021/acs.jpcb.3c05245] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2024]
Abstract
Central to studying the conformational changes of a complex protein is understanding the dynamics and energetics involved. Phenomenologically, structural dynamics can be formulated using an overdamped Langevin model along an observable, e.g., the distance between two residues in the protein. The Langevin model is specified by the deterministic force (the potential of mean force, PMF) and stochastic force (characterized by the diffusion coefficient, D). It is therefore of great interest to be able to extract both PMF and D from an observable time series but under the same computational framework. Here, we approach this challenge in molecular dynamics (MD) simulations by treating it as a missing-data Bayesian estimation problem. An important distinction in our methodology is that the entire MD trajectory, as opposed to the individual data elements, is used as the statistical variable in Bayesian imputation. This idea is implemented through an eigen-decomposition procedure for a time-symmetrized Fokker-Planck equation, followed by maximizing the likelihood for parameter estimation. The mathematical expressions for the functional derivatives used in learning PMF and D also provide new physical insights for the manner by which the information on both the deterministic and stochastic forces is encoded in the dynamics data. An all-atom MD simulation of a nontrivial biomolecule case is used to illustrate the application of this approach. We show that, interestingly, the results of trajectory statistical learning can motivate new order parameters for an improved description of the kinetic bottlenecks in conformational changes. Complementing purely data-driven or black-box methods, this work underscores the advantages of physics-based machine learning in gaining chemical insights from quantitative parameter estimation.
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Affiliation(s)
- Yi-Tsao Chen
- Institute of Bioinformatics and Systems Biology, National Yang Ming Chiao Tung University, Hsinchu 30010, Taiwan, Republic of China
| | - Haw Yang
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, United States
| | - Jhih-Wei Chu
- Institute of Bioinformatics and Systems Biology, Department of Biological Science and Technology, Institute of Molecular Medicine and Bioengineering, and Center for Intelligent Drug Systems and Smart Bio-Devices (IDS2B), National Yang Ming Chiao Tung University, Hsinchu 30010, Taiwan, Republic of China
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2
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Aceves-Hernández JM, Inés Nicolás Vázquez M, Luis Garza Rivera J, Espinoza Godínez A, Mateo Flores J, de Jesús Cruz Guzmán J, Castaño VM. Palbociclib (PD 0332991) Interaction with Kinases. Theoretical and Comparative Molecular Docking Study. Chem Biodivers 2023; 20:e202200554. [PMID: 36799136 DOI: 10.1002/cbdv.202200554] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Accepted: 01/24/2023] [Indexed: 02/18/2023]
Abstract
The optimized geometry of palbociclib, (PD 0332991) (8-cyclopentyl-6-ethanoyl-5-methyl-2-(5-(piperazin-1-yl)pyridin-2-ylamino)pyrido[2,3-d]pyrimidin-7(8H)-one), electrostatic potential map, molecular orbitals were calculated using the density functional theory. The geometry was used in a molecular docking study of palbociclib-kinase complexes, results could be explained by the charge of the nitrogen and oxygen atoms within the palbociclib. Energy gap of HOMO-LUMO surfaces, could help to explain the reactivity of the ligand and the hydrogen bonding with three different kinases, two of CDK6 and one of CDK4 type. Docking results are similar and complementary with literature reports using molecular dynamics, were hydrogen bonding was obtained and analyzed. The promiscuity of three kinases with palbociclib was detected by the docking results, thus, palbociclib could be used in other types of cancer besides myeloid leukemia. Some similarities are found with CDK4/CDK6 kinases which allow us to determine that palbociclib could be used to control other resistant inhibitor types of cancer.
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Affiliation(s)
- Juan M Aceves-Hernández
- Departamento de Ciencias Químicas, Facultad de Estudios Superiores Cuautitlán Campo 1, Universidad Nacional Autónoma de México, Avenida 1o de Mayo s/n, Colonia Santa María las Torres, Cuautitlán Izcalli, Estado de México, 54740, México
| | - María Inés Nicolás Vázquez
- Departamento de Ciencias Químicas, Facultad de Estudios Superiores Cuautitlán Campo 1, Universidad Nacional Autónoma de México, Avenida 1o de Mayo s/n, Colonia Santa María las Torres, Cuautitlán Izcalli, Estado de México, 54740, México
| | - José Luis Garza Rivera
- Departamento de Ciencias Químicas, Facultad de Estudios Superiores Cuautitlán Campo 1, Universidad Nacional Autónoma de México, Avenida 1o de Mayo s/n, Colonia Santa María las Torres, Cuautitlán Izcalli, Estado de México, 54740, México
| | - Angélica Espinoza Godínez
- Departamento de Ciencias Químicas, Facultad de Estudios Superiores Cuautitlán Campo 1, Universidad Nacional Autónoma de México, Avenida 1o de Mayo s/n, Colonia Santa María las Torres, Cuautitlán Izcalli, Estado de México, 54740, México
| | - Juan Mateo Flores
- Departamento de Ciencias Químicas, Facultad de Estudios Superiores Cuautitlán Campo 1, Universidad Nacional Autónoma de México, Avenida 1o de Mayo s/n, Colonia Santa María las Torres, Cuautitlán Izcalli, Estado de México, 54740, México
| | - José de Jesús Cruz Guzmán
- Departamento de Ciencias Químicas, Facultad de Estudios Superiores Cuautitlán Campo 1, Universidad Nacional Autónoma de México, Avenida 1o de Mayo s/n, Colonia Santa María las Torres, Cuautitlán Izcalli, Estado de México, 54740, México
| | - Víctor M Castaño
- Centro de Física Aplicada y Tecnología Avanzada, Universidad Nacional Autónoma de México, Boulevard Juriquilla, Querétaro, 76230, México
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D’Incal C, Broos J, Torfs T, Kooy RF, Vanden Berghe W. Towards Kinase Inhibitor Therapies for Fragile X Syndrome: Tweaking Twists in the Autism Spectrum Kinase Signaling Network. Cells 2022; 11:cells11081325. [PMID: 35456004 PMCID: PMC9029738 DOI: 10.3390/cells11081325] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Revised: 04/01/2022] [Accepted: 04/03/2022] [Indexed: 12/12/2022] Open
Abstract
Absence of the Fragile X Mental Retardation Protein (FMRP) causes autism spectrum disorders and intellectual disability, commonly referred to as the Fragile X syndrome. FMRP is a negative regulator of protein translation and is essential for neuronal development and synapse formation. FMRP is a target for several post-translational modifications (PTMs) such as phosphorylation and methylation, which tightly regulate its cellular functions. Studies have indicated the involvement of FMRP in a multitude of cellular pathways, and an absence of FMRP was shown to affect several neurotransmitter receptors, for example, the GABA receptor and intracellular signaling molecules such as Akt, ERK, mTOR, and GSK3. Interestingly, many of these molecules function as protein kinases or phosphatases and thus are potentially amendable by pharmacological treatment. Several treatments acting on these kinase-phosphatase systems have been shown to be successful in preclinical models; however, they have failed to convincingly show any improvements in clinical trials. In this review, we highlight the different protein kinase and phosphatase studies that have been performed in the Fragile X syndrome. In our opinion, some of the paradoxical study conclusions are potentially due to the lack of insight into integrative kinase signaling networks in the disease. Quantitative proteome analyses have been performed in several models for the FXS to determine global molecular processes in FXS. However, only one phosphoproteomics study has been carried out in Fmr1 knock-out mouse embryonic fibroblasts, and it showed dysfunctional protein kinase and phosphatase signaling hubs in the brain. This suggests that the further use of phosphoproteomics approaches in Fragile X syndrome holds promise for identifying novel targets for kinase inhibitor therapies.
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Affiliation(s)
- Claudio D’Incal
- Protein Chemistry, Proteomics and Epigenetic Signaling (PPES), Department of Biomedical Sciences, University of Antwerp, 2000 Antwerp, Belgium; (C.D.); (J.B.); (T.T.)
- Department of Medical Genetics, University of Antwerp, 2000 Antwerp, Belgium;
| | - Jitse Broos
- Protein Chemistry, Proteomics and Epigenetic Signaling (PPES), Department of Biomedical Sciences, University of Antwerp, 2000 Antwerp, Belgium; (C.D.); (J.B.); (T.T.)
| | - Thierry Torfs
- Protein Chemistry, Proteomics and Epigenetic Signaling (PPES), Department of Biomedical Sciences, University of Antwerp, 2000 Antwerp, Belgium; (C.D.); (J.B.); (T.T.)
| | - R. Frank Kooy
- Department of Medical Genetics, University of Antwerp, 2000 Antwerp, Belgium;
| | - Wim Vanden Berghe
- Protein Chemistry, Proteomics and Epigenetic Signaling (PPES), Department of Biomedical Sciences, University of Antwerp, 2000 Antwerp, Belgium; (C.D.); (J.B.); (T.T.)
- Correspondence: ; Tel.: +0032-(0)-32-652-657
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Wei X, Wang Y, Zhang S, Gu T, Steinmetz G, Yu H, Guo G, Liu X, Fan S, Wang F, Gu Y, Xin F. Structural analysis of receptor-like kinase SOBIR1 reveals mechanisms that regulate its phosphorylation-dependent activation. PLANT COMMUNICATIONS 2022; 3:100301. [PMID: 35529948 PMCID: PMC9073325 DOI: 10.1016/j.xplc.2022.100301] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Revised: 11/04/2021] [Accepted: 01/15/2022] [Indexed: 05/20/2023]
Abstract
Plant leucine-rich repeat (LRR) receptor-like kinases (RLKs) and LRR receptor-like proteins (RLPs) comprise a large family of cell surface receptors that play critical roles in signal perception and transduction. Both LRR-RLKs and LRR-RLPs rely on regulatory LRR-RLKs to initiate downstream signaling pathways. BRASSINOSTEROID INSENSITIVE 1-ASSOCIATED KINASE 1/SOMATIC EMBRYOGENESIS RECEPTOR KINASE 3 (BAK1/SERK3) and SUPPRESSOR OF BIR1-1 (SOBIR1) are important and extensively studied regulatory LRR-RLKs with distinct functions. Although the regulatory mechanism of BAK1 activation has been studied in detail, the activation mechanism of SOBIR1 remains poorly understood. Here, the crystal structures of the catalytically inactive kinase domain of SOBIR1 (SOBIR1-KD) from Arabidopsis thaliana were determined in complexes with AMP-PNP and Mg2+. The results show that SOBIR1-KD contains a uniquely long β3-αC loop and adopts an Src-like inactive conformation with an unusual architecture at the activation segment, which comprises three helices. Biochemical studies revealed that SOBIR1 is transphosphorylated by BAK1 following its autophosphorylation via an intermolecular mechanism, and the phosphorylation of Thr529 in the activation segment and the β3-αC loop are critical for SOBIR1 phosphorylation. Further functional analysis confirmed the importance of Thr529 and the β3-αC loop for the SOBIR1-induced cell death response in Nicotiana benthamiana. Taken together, these findings provide a structural basis for the regulatory mechanism of SOBIR1 and reveal the important elements and phosphorylation events in the special stepwise activation of SOBIR1-KD, the first such processes found in regulatory LRR-RLKs.
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Affiliation(s)
- Xue Wei
- Laboratory of Biomanufacturing and Food Engineering, Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Yulu Wang
- Laboratory of Biomanufacturing and Food Engineering, Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Su Zhang
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing 100083, China
| | - Tianyi Gu
- Laboratory of Biomanufacturing and Food Engineering, Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Gabryel Steinmetz
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA
- Innovative Genomics Institute, University of California, Berkeley, CA 94720, USA
| | - Haiyan Yu
- Laboratory of Biomanufacturing and Food Engineering, Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Guoguang Guo
- Key Laboratory of Ministry of Education for Protein Science, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Xin Liu
- Hefei National Laboratory for Physical Sciences at the Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Shilong Fan
- The Center of Protein Science, Tsinghua University, Beijing 100084, China
| | - Fengzhong Wang
- Laboratory of Biomanufacturing and Food Engineering, Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Yangnan Gu
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA
- Innovative Genomics Institute, University of California, Berkeley, CA 94720, USA
| | - Fengjiao Xin
- Laboratory of Biomanufacturing and Food Engineering, Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, Beijing 100193, China
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Rajczewski AT, Jagtap PD, Griffin TJ. An overview of technologies for MS-based proteomics-centric multi-omics. Expert Rev Proteomics 2022; 19:165-181. [PMID: 35466851 PMCID: PMC9613604 DOI: 10.1080/14789450.2022.2070476] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
INTRODUCTION Mass spectrometry-based proteomics reveals dynamic molecular signatures underlying phenotypes reflecting normal and perturbed conditions in living systems. Although valuable on its own, the proteome has only one level of moleclar information, with the genome, epigenome, transcriptome, and metabolome, all providing complementary information. Multi-omic analysis integrating information from one or more of these other domains with proteomic information provides a more complete picture of molecular contributors to dynamic biological systems. AREAS COVERED Here, we discuss the improvements to mass spectrometry-based technologies, focused on peptide-based, bottom-up approaches that have enabled deep, quantitative characterization of complex proteomes. These advances are facilitating the integration of proteomics data with other 'omic information, providing a more complete picture of living systems. We also describe the current state of bioinformatics software and approaches for integrating proteomics and other 'omics data, critical for enabling new discoveries driven by multi-omics. EXPERT COMMENTARY Multi-omics, centered on the integration of proteomics information with other 'omic information, has tremendous promise for biological and biomedical studies. Continued advances in approaches for generating deep, reliable proteomic data and bioinformatics tools aimed at integrating data across 'omic domains will ensure the discoveries offered by these multi-omic studies continue to increase.
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Affiliation(s)
- Andrew T. Rajczewski
- Department of Biochemistry, Molecular and Cell Biology Building, University of Minnesota, 420 Washington Ave SE 7-129, Minneapolis, MN, 55455, USA
| | - Pratik D. Jagtap
- Department of Biochemistry, Molecular and Cell Biology Building, University of Minnesota, 420 Washington Ave SE 7-129, Minneapolis, MN, 55455, USA,Coauthor, Research Department of Biochemistry, Molecular and Cell Biology Building, University of Minnesota, 420 Washington Ave SE 7-129, Minneapolis, MN, 55455, USA
| | - Timothy J. Griffin
- Department of Biochemistry, Molecular and Cell Biology Building, University of Minnesota, 420 Washington Ave SE 7-129, Minneapolis, MN, 55455, USA,Department of Biochemistry, Molecular and Cell Biology Building, University of Minnesota, 420 Washington Ave SE 7-129, Minneapolis, MN, 55455, USA
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6
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Zhang Q, Liu X, Liu H, Zhang B, Yang H, Mi K, Guddat LW, Rao Z. Conformational Changes in a Macrolide Antibiotic Binding Protein From Mycobacterium smegmatis Upon ADP Binding. Front Microbiol 2021; 12:780954. [PMID: 34956144 PMCID: PMC8696161 DOI: 10.3389/fmicb.2021.780954] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Accepted: 11/15/2021] [Indexed: 11/13/2022] Open
Abstract
Rv3197 (MABP-1), a non-canonical ABC protein in Mycobacterium tuberculosis, has ATPase activity and confers inducible resistance to the macrolide family of antibiotics. Here we have shown that MSMEG_1954, the homolog of Rv3197 in M. smegmatis, has a similar function of conferring macrolide resistance. Crystal structures of apo-MSMEG_1954 (form1 and form 2) and MSMEG_1954 in complex with ADP have been determined. These three structures show that MSMEG_1954 has at least two different conformations we identify as closed state (MSMEG_1954-form 1) and open state (MSMEG_1954-form 2 and MSMEG_1954-ADP). Structural superimposition shows that the MSMEG_1954-form 2 and MSMEG_1954-ADP complex have similar conformation to that observed for MABP-1 and MABP-1-erythromicin complex structure. However, the antibiotic binding pocket in MSMEG_1954-form 1 is completely blocked by the N-terminal accessory domain. When bound by ADP, the N-terminal accessory domain undergoes conformational change, which results in the open of the antibiotic binding pocket. Because of the degradation of N terminal accessory domain in MSMSG_1954-form 2, it is likely to represent a transitional state between MSMEG_1954-form 1 and MSMEG_1954-ADP complex structure.
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Affiliation(s)
- Qingqing Zhang
- State Key Laboratory of Medicinal Chemical Biology, Frontiers Science Center for Cell Responses, College of Life Sciences, Nankai University, Tianjin, China.,Innovative Center for Pathogen Research, Guangzhou Laboratory, Guangzhou, China
| | - Xiang Liu
- State Key Laboratory of Medicinal Chemical Biology, Frontiers Science Center for Cell Responses, College of Life Sciences, Nankai University, Tianjin, China
| | - Huijuan Liu
- State Key Laboratory of Medicinal Chemical Biology, Frontiers Science Center for Cell Responses, College of Life Sciences, Nankai University, Tianjin, China
| | - Bingjie Zhang
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Haitao Yang
- Shanghai Institute for Advanced Immunochemical Studies and School of Life Sciences and Technology, ShanghaiTech University, Shanghai, China
| | - Kaixia Mi
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Luke W Guddat
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia
| | - Zihe Rao
- State Key Laboratory of Medicinal Chemical Biology, Frontiers Science Center for Cell Responses, College of Life Sciences, Nankai University, Tianjin, China.,Shanghai Institute for Advanced Immunochemical Studies and School of Life Sciences and Technology, ShanghaiTech University, Shanghai, China.,Laboratory of Structural Biology, School of Life Sciences and School of Medicine, Tsinghua University, Beijing, China
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7
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Carrasco E, Gomez-Gutierrez P, Campos PM, Vega M, Messeguer A, Perez JJ. Discovery of novel 2,3,5-trisubstituted pyridine analogs as potent inhibitors of IL-1β via modulation of the p38 MAPK signaling pathway. Eur J Med Chem 2021; 223:113620. [PMID: 34186234 DOI: 10.1016/j.ejmech.2021.113620] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Revised: 04/08/2021] [Accepted: 06/01/2021] [Indexed: 12/20/2022]
Abstract
Interleukin-1β is a central mediator of innate immune responses and inflammation. It plays a key role in a wide variety of pathologies, ranging from autoinflammatory diseases to metabolic syndrome and malignant tumors. It is well established that its inhibition results in a rapid and sustained reduction in disease severity, underlining the importance of having a repertoire of drugs of this class. At present, there are only three interleukin-1β blockers approved in the clinic. All of them are biologics, requiring parenteral administration and resulting in expensive treatments. In an exercise to identify small molecule allosteric inhibitors of MAP kinases, we discovered a series of compounds that block IL-1β release produced as a consequence of a stimulus involved in triggering an inflammatory response. The present study reports the hit-to-lead optimization process that permitted the identification of the compound 13b (AIK3-305) an orally available, potent and selective inhibitor of IL-1β. Furthermore, the study also reports the results of an in vivo efficacy study of 13b in a LPS endotoxic shock model in male BALB/c mice, where IL-1β inhibition is monitored in different tissues.
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Affiliation(s)
- Esther Carrasco
- Allinky Biopharma, Campus de Cantoblanco, Faraday 7, 28049, Madrid, Spain
| | - Patricia Gomez-Gutierrez
- Allinky Biopharma, Campus de Cantoblanco, Faraday 7, 28049, Madrid, Spain; Dept. of Chemical Engineering, Universitat Politecnica de Catalunya, 08028, Barcelona, Spain
| | - Pedro M Campos
- Allinky Biopharma, Campus de Cantoblanco, Faraday 7, 28049, Madrid, Spain
| | - Miguel Vega
- Allinky Biopharma, Campus de Cantoblanco, Faraday 7, 28049, Madrid, Spain
| | - Angel Messeguer
- IQAC CSIC, Institute of Advanced Chemistry of Catalonia, Dept. Biological Chemistry, Jordi Girona 18-26, 08034, Barcelona, Spain
| | - Juan J Perez
- Dept. of Chemical Engineering, Universitat Politecnica de Catalunya, 08028, Barcelona, Spain.
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Cellular model system to dissect the isoform-selectivity of Akt inhibitors. Nat Commun 2021; 12:5297. [PMID: 34489430 PMCID: PMC8421423 DOI: 10.1038/s41467-021-25512-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Accepted: 08/11/2021] [Indexed: 02/07/2023] Open
Abstract
The protein kinase Akt plays a pivotal role in cellular processes. However, its isoforms' distinct functions have not been resolved to date, mainly due to the lack of suitable biochemical and cellular tools. Against this background, we present the development of an isoform-dependent Ba/F3 model system to translate biochemical results on isoform specificity to the cellular level. Our cellular model system complemented by protein X-ray crystallography and structure-based ligand design results in covalent-allosteric Akt inhibitors with unique selectivity profiles. In a first proof-of-concept, the developed molecules allow studies on isoform-selective effects of Akt inhibition in cancer cells. Thus, this study will pave the way to resolve isoform-selective roles in health and disease and foster the development of next-generation therapeutics with superior on-target properties.
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Carrasco E, Gomez-Gutierrez P, Campos PM, Messeguer A, Perez JJ, Vega M. Structure-Activity Studies of Novel di-substituted [1,2,5]oxadiazolo[3,4-b]pyrazine Analogs Targeting the A-loop Regulatory Site of p38 MAP Kinase. Curr Med Chem 2021; 29:1640-1653. [PMID: 34931978 DOI: 10.2174/0929867328666210712165659] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2021] [Revised: 05/24/2021] [Accepted: 05/27/2021] [Indexed: 11/22/2022]
Abstract
INTRODUCTION In the quest for novel allosteric inhibitors of the p38 MAP kinase, we recently described the A-loop regulatory site, identified through molecular modeling studies together with the disclosure of a small molecule hit with a moderate inhibitory profile. Starting from this structure, we subsequently identified two additional hits with simpler molecular structures from an in silico screening study, using a substructure search in the SciFinder database. After corroboration of their inhibitory profile, analysis of their structures permitted to conclude about the suitability of the [1,2,5]oxadiazolo[3,4-b]pyrazine (furazano[3,4-b]pyrazine) scaffold for the development of potent A-loop regulatory site p38 MAP kinase inhibitors. Accordingly, we report the synthesis and pharmacological evaluation of a series of di-substituted analogs with a potent inhibitory profile of p38 MAP kinase, as shown by in vitro assays of their capability to inhibit IL-1β secretion in human monocyte-derived macrophages. BACKGROUND In the quest for novel allosteric inhibitors of the p38 MAP kinase, we recently described the A-loop regulatory site, identified through molecular modeling studies together with the disclosure of a small molecule hit with a moderate inhibitory profile. OBJECTIVE To find small molecule potent inhibitors of the p38 MAP kinase A-loop regulatory site. METHODS Starting from this structure, we subsequently identified two additional hits with simpler molecular structures from an in silico screening study, using a substructure search in the SciFinder database. After corroboration of their inhibitory profile, we carried out a hit-to-lead optimization process guided by molecular modeling using a [1,2,5]oxadiazolo[3,4-b]pyrazine (furazano[3,4-b]pyrazine) scaffold. RESULTS We report the synthesis and pharmacological evaluation of a series of di-substituted analogs with a potent inhibitory profile of p38 MAP kinase, as shown by in vitro assays of their capability to inhibit IL-1β secretion in human monocyte-derived macrophages. CONCLUSIONS We describe in the present work a series of [1,2,5]oxadiazolo[3,4-b]pyrazine (furazano[3,4-b]pyrazine), potent inhibitors of IL-1β secretion in human monocyte-derived macrophages allosteric modulators of the p38 MAP kinase A-loop regulatory site.
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Affiliation(s)
- Esther Carrasco
- Allinky Biopharma, Campus de Cantoblanco, Faraday 7, 28049 Madrid, Spain
| | | | - Pedro M Campos
- Allinky Biopharma, Campus de Cantoblanco, Faraday 7, 28049 Madrid, Spain
| | - Angel Messeguer
- IQAC CSIC, Institute of Advanced Chemistry of Catalonia, Dept. Biol. Chem., Jordi Girona 18-26, 08034 Barcelona, Spain
| | - Juan Jesus Perez
- Dept. of Chemical Engineering, Universitat Politecnica de Catalunya, 08028 Barcelona, Spain
| | - Miguel Vega
- Allinky Biopharma, Campus de Cantoblanco, Faraday 7, 28049 Madrid, Spain
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10
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Vásquez AF, González Barrios AF. Classical MD and metadynamics simulations on back-pocket binders of CDK2 and VEGFR2: a guidepost to design novel small-molecule dual inhibitors. J Biomol Struct Dyn 2021; 40:9030-9041. [PMID: 33949282 DOI: 10.1080/07391102.2021.1922311] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Cyclin-Dependent Kinase 2 (CDK2) and Vascular-Endothelial Growth Factor Receptor 2 (VEGFR2) are promising targets for the design of novel inhibitors in anticancer therapeutics. In a recent work, our group designed a set of potential dual inhibitors predicted to occupy an allosteric back pocket near the active site of both enzymes, but their dynamic and unbinding behavior was unclear. Here, we used molecular dynamics (MD) and metadynamics (meta-D) simulations to study two of these virtual candidates (herein called IQ2 and IQ3). Their binding mode was predicted to be similar to that observed in LQ5 and BAX, well-known back-pocket binders of CDK2 and VEGFR2, respectively, including H-bonding with critical residues such as Leu83/Cys113 and Asp145/Asp190 (but excepting H-bonding with Glu51/Glu111) in CDK2/VEGFR2, correspondingly. Likewise, while LQ5 and BAX unbound through the allosteric channel as expected for type-IIA inhibitors, IQ2 and IQ3 unbound via the ATP channel (except for CDK2-IQ2) as expected for type-I½A inhibitors. Interestingly, a C-C single/double bond difference between IQ2/IQ3, respectively, resulted associated with differences in the AS/T loop flexibility observed for CDK2. These insights will help developing scaffold modifications during an optimization stage, serving as a starting point to develop dual kinase inhibitors in challenging biological targets with a promising anticancer potential.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Andrés Felipe Vásquez
- Grupo de Diseño de Productos y Procesos (GDPP), Department of Chemical Engineering, Universidad de los Andes, Bogotá, Colombia
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11
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Łukasik P, Baranowska-Bosiacka I, Kulczycka K, Gutowska I. Inhibitors of Cyclin-Dependent Kinases: Types and Their Mechanism of Action. Int J Mol Sci 2021; 22:ijms22062806. [PMID: 33802080 PMCID: PMC8001317 DOI: 10.3390/ijms22062806] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Revised: 03/03/2021] [Accepted: 03/05/2021] [Indexed: 12/04/2022] Open
Abstract
Recent studies on cyclin-dependent kinase (CDK) inhibitors have revealed that small molecule drugs have become very attractive for the treatment of cancer and neurodegenerative disorders. Most CDK inhibitors have been developed to target the ATP binding pocket. However, CDK kinases possess a very similar catalytic domain and three-dimensional structure. These features make it difficult to achieve required selectivity. Therefore, inhibitors which bind outside the ATP binding site present a great interest in the biomedical field, both from the fundamental point of view and for the wide range of their potential applications. This review tries to explain whether the ATP competitive inhibitors are still an option for future research, and highlights alternative approaches to discover more selective and potent small molecule inhibitors.
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Affiliation(s)
- Paweł Łukasik
- Department of Medical Chemistry, Pomeranian Medical University in Szczecin, Powstancow Wlkp. 72 Av., 70-111 Szczecin, Poland;
| | - Irena Baranowska-Bosiacka
- Department of Biochemistry, Pomeranian Medical University in Szczecin, Powstancow Wlkp. 72 Av., 70-111 Szczecin, Poland;
| | - Katarzyna Kulczycka
- Department of Pharmaceutical Chemistry, Pomeranian Medical University in Szczecin, Powstancow Wlkp. 72 Av., 70-111 Szczecin, Poland;
| | - Izabela Gutowska
- Department of Medical Chemistry, Pomeranian Medical University in Szczecin, Powstancow Wlkp. 72 Av., 70-111 Szczecin, Poland;
- Correspondence:
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12
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Vásquez AF, Reyes Muñoz A, Duitama J, González Barrios A. Discovery of new potential CDK2/VEGFR2 type II inhibitors by fragmentation and virtual screening of natural products. J Biomol Struct Dyn 2020; 39:3285-3299. [DOI: 10.1080/07391102.2020.1763839] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Affiliation(s)
- Andrés Felipe Vásquez
- Grupo de Diseño de Productos y Procesos (GDPP), Department of Chemical Engineering, Universidad de los Andes, Bogotá, Colombia
| | - Alejandro Reyes Muñoz
- Grupo de Biología Computacional Ecología Microbiana (BCEM), Department of Biological Sciences, Universidad de los Andes, Bogotá, Colombia
- Max Planck Tandem Group in Computational Biology, Universidad de los Andes, Bogotá, Colombia
| | - Jorge Duitama
- Systems and Computing Engineering Department, Universidad de los Andes, Bogotá, Colombia
| | - Andrés González Barrios
- Grupo de Diseño de Productos y Procesos (GDPP), Department of Chemical Engineering, Universidad de los Andes, Bogotá, Colombia
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13
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Rao RN, Chanda K. An assessment study of known pyrazolopyrimidines: Chemical methodology and cellular activity. Bioorg Chem 2020; 99:103801. [PMID: 32278206 DOI: 10.1016/j.bioorg.2020.103801] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2019] [Revised: 03/22/2020] [Accepted: 03/24/2020] [Indexed: 10/24/2022]
Abstract
Heterocyclic compounds with nitrogen atom play a key role in the normal life cycle of a cell. Pyrazolopyrimidine is a privileged class of nitrogen containing fused heterocyclic compound contributing to a major portion of all lead molecules in medicinal chemistry. The thumbprint of pyrazolopyrimidine as a pharmacophore is always noticeable due to its analogy with the adenine base in DNA. Pyrazolopyrimidines are divided into five types [I, II, III, IV, V] based on the mechanism of action on the specific target conferring a wide scope of research which has accelerated the interest of researchers to investigate its biological profile. In 1956, the anti-cancer activity of pyrazolopyrimidine was evaluated for the first time with appreciable results. Since then, medicinal chemists centered their work on various methods of synthesis and evaluating the biological profile of pyrazolopyrimidine isomers. This report consists of novel methodologies followed to synthesize pyrazolopyrimidine isomers along with a note on their biological significance. To the best of our knowledge, this review article will be first of its kind to encompass different synthetic procedures along with anti-cancer, kinase inhibition, phosphodiesterase inhibition and receptor blocking activity of pyrazolopyrimidine moieties. IC50 values of potent compounds are added wherever necessary to understand the suitability of pyrazolopyrimidine skeletons for a specific biological activity.
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Affiliation(s)
- R Nishanth Rao
- Department of Chemistry, School of Advanced Sciences, Vellore Institute of Technology, Vellore 632014, India
| | - Kaushik Chanda
- Department of Chemistry, School of Advanced Sciences, Vellore Institute of Technology, Vellore 632014, India
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14
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Quambusch L, Landel I, Depta L, Weisner J, Uhlenbrock N, Müller MP, Glanemann F, Althoff K, Siveke JT, Rauh D. Covalent‐Allosteric Inhibitors to Achieve Akt Isoform‐Selectivity. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201909857] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Affiliation(s)
- Lena Quambusch
- Faculty of Chemistry and Chemical BiologyTU Dortmund University and Drug Discovery Hub Dortmund (DDHD)Zentrum für Integrierte Wirkstoffforschung (ZIW) Otto-Hahn-Strasse 4a 44227 Dortmund Germany
| | - Ina Landel
- Faculty of Chemistry and Chemical BiologyTU Dortmund University and Drug Discovery Hub Dortmund (DDHD)Zentrum für Integrierte Wirkstoffforschung (ZIW) Otto-Hahn-Strasse 4a 44227 Dortmund Germany
| | - Laura Depta
- Faculty of Chemistry and Chemical BiologyTU Dortmund University and Drug Discovery Hub Dortmund (DDHD)Zentrum für Integrierte Wirkstoffforschung (ZIW) Otto-Hahn-Strasse 4a 44227 Dortmund Germany
| | - Jörn Weisner
- Faculty of Chemistry and Chemical BiologyTU Dortmund University and Drug Discovery Hub Dortmund (DDHD)Zentrum für Integrierte Wirkstoffforschung (ZIW) Otto-Hahn-Strasse 4a 44227 Dortmund Germany
| | - Niklas Uhlenbrock
- Faculty of Chemistry and Chemical BiologyTU Dortmund University and Drug Discovery Hub Dortmund (DDHD)Zentrum für Integrierte Wirkstoffforschung (ZIW) Otto-Hahn-Strasse 4a 44227 Dortmund Germany
| | - Matthias P. Müller
- Faculty of Chemistry and Chemical BiologyTU Dortmund University and Drug Discovery Hub Dortmund (DDHD)Zentrum für Integrierte Wirkstoffforschung (ZIW) Otto-Hahn-Strasse 4a 44227 Dortmund Germany
| | - Franziska Glanemann
- Institute of Developmental Cancer TherapeuticsWest German Cancer Center, University Hospital Essen Essen Germany
- Division of Solid Tumor Translational OncologyGerman Cancer Consortium (DKTK, partner site Essen) and German Research Center (DKFZ) Heidelberg Germany
| | - Kristina Althoff
- Institute of Developmental Cancer TherapeuticsWest German Cancer Center, University Hospital Essen Essen Germany
- Division of Solid Tumor Translational OncologyGerman Cancer Consortium (DKTK, partner site Essen) and German Research Center (DKFZ) Heidelberg Germany
| | - Jens T. Siveke
- Institute of Developmental Cancer TherapeuticsWest German Cancer Center, University Hospital Essen Essen Germany
- Division of Solid Tumor Translational OncologyGerman Cancer Consortium (DKTK, partner site Essen) and German Research Center (DKFZ) Heidelberg Germany
| | - Daniel Rauh
- Faculty of Chemistry and Chemical BiologyTU Dortmund University and Drug Discovery Hub Dortmund (DDHD)Zentrum für Integrierte Wirkstoffforschung (ZIW) Otto-Hahn-Strasse 4a 44227 Dortmund Germany
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15
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Quambusch L, Landel I, Depta L, Weisner J, Uhlenbrock N, Müller MP, Glanemann F, Althoff K, Siveke JT, Rauh D. Covalent-Allosteric Inhibitors to Achieve Akt Isoform-Selectivity. Angew Chem Int Ed Engl 2019; 58:18823-18829. [PMID: 31584233 PMCID: PMC6972997 DOI: 10.1002/anie.201909857] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2019] [Revised: 09/24/2019] [Indexed: 02/03/2023]
Abstract
Isoforms of protein kinase Akt are involved in essential processes including cell proliferation, survival, and metabolism. However, their individual roles in health and disease have not been thoroughly evaluated. Thus, there is an urgent need for perturbation studies, preferably mediated by highly selective bioactive small molecules. Herein, we present a structure‐guided approach for the design of structurally diverse and pharmacologically beneficial covalent‐allosteric modifiers, which enabled an investigation of the isoform‐specific preferences and the important residues within the allosteric site of the different isoforms. The biochemical, cellular, and structural evaluations revealed interactions responsible for the selective binding profiles. The isoform‐selective covalent‐allosteric Akt inhibitors that emerged from this approach showed a conclusive structure–activity relationship and broke ground in the development of selective probes to delineate the isoform‐specific functions of Akt kinases.
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Affiliation(s)
- Lena Quambusch
- Faculty of Chemistry and Chemical Biology, TU Dortmund University and Drug Discovery Hub Dortmund (DDHD), Zentrum für Integrierte Wirkstoffforschung (ZIW), Otto-Hahn-Strasse 4a, 44227, Dortmund, Germany
| | - Ina Landel
- Faculty of Chemistry and Chemical Biology, TU Dortmund University and Drug Discovery Hub Dortmund (DDHD), Zentrum für Integrierte Wirkstoffforschung (ZIW), Otto-Hahn-Strasse 4a, 44227, Dortmund, Germany
| | - Laura Depta
- Faculty of Chemistry and Chemical Biology, TU Dortmund University and Drug Discovery Hub Dortmund (DDHD), Zentrum für Integrierte Wirkstoffforschung (ZIW), Otto-Hahn-Strasse 4a, 44227, Dortmund, Germany
| | - Jörn Weisner
- Faculty of Chemistry and Chemical Biology, TU Dortmund University and Drug Discovery Hub Dortmund (DDHD), Zentrum für Integrierte Wirkstoffforschung (ZIW), Otto-Hahn-Strasse 4a, 44227, Dortmund, Germany
| | - Niklas Uhlenbrock
- Faculty of Chemistry and Chemical Biology, TU Dortmund University and Drug Discovery Hub Dortmund (DDHD), Zentrum für Integrierte Wirkstoffforschung (ZIW), Otto-Hahn-Strasse 4a, 44227, Dortmund, Germany
| | - Matthias P Müller
- Faculty of Chemistry and Chemical Biology, TU Dortmund University and Drug Discovery Hub Dortmund (DDHD), Zentrum für Integrierte Wirkstoffforschung (ZIW), Otto-Hahn-Strasse 4a, 44227, Dortmund, Germany
| | - Franziska Glanemann
- Institute of Developmental Cancer Therapeutics, West German Cancer Center, University Hospital Essen, Essen, Germany.,Division of Solid Tumor Translational Oncology, German Cancer Consortium (DKTK, partner site Essen) and German Research Center (DKFZ), Heidelberg, Germany
| | - Kristina Althoff
- Institute of Developmental Cancer Therapeutics, West German Cancer Center, University Hospital Essen, Essen, Germany.,Division of Solid Tumor Translational Oncology, German Cancer Consortium (DKTK, partner site Essen) and German Research Center (DKFZ), Heidelberg, Germany
| | - Jens T Siveke
- Institute of Developmental Cancer Therapeutics, West German Cancer Center, University Hospital Essen, Essen, Germany.,Division of Solid Tumor Translational Oncology, German Cancer Consortium (DKTK, partner site Essen) and German Research Center (DKFZ), Heidelberg, Germany
| | - Daniel Rauh
- Faculty of Chemistry and Chemical Biology, TU Dortmund University and Drug Discovery Hub Dortmund (DDHD), Zentrum für Integrierte Wirkstoffforschung (ZIW), Otto-Hahn-Strasse 4a, 44227, Dortmund, Germany
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16
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Niggenaber J, Hardick J, Lategahn J, Rauh D. Structure Defines Function: Clinically Relevant Mutations in ErbB Kinases. J Med Chem 2019; 63:40-51. [DOI: 10.1021/acs.jmedchem.9b00964] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Janina Niggenaber
- Faculty of Chemistry and Chemical Biology, TU Dortmund University, Otto-Hahn-Strasse 4a, 44227 Dortmund, (Germany)
- Drug Discovery Hub Dortmund (DDHD) am Zentrum für Integrierte Wirkstoffforschung (ZIW), TU Dortmund University, 44227 Dortmund (Germany)
| | - Julia Hardick
- Faculty of Chemistry and Chemical Biology, TU Dortmund University, Otto-Hahn-Strasse 4a, 44227 Dortmund, (Germany)
- Drug Discovery Hub Dortmund (DDHD) am Zentrum für Integrierte Wirkstoffforschung (ZIW), TU Dortmund University, 44227 Dortmund (Germany)
| | - Jonas Lategahn
- Faculty of Chemistry and Chemical Biology, TU Dortmund University, Otto-Hahn-Strasse 4a, 44227 Dortmund, (Germany)
- Drug Discovery Hub Dortmund (DDHD) am Zentrum für Integrierte Wirkstoffforschung (ZIW), TU Dortmund University, 44227 Dortmund (Germany)
| | - Daniel Rauh
- Faculty of Chemistry and Chemical Biology, TU Dortmund University, Otto-Hahn-Strasse 4a, 44227 Dortmund, (Germany)
- Drug Discovery Hub Dortmund (DDHD) am Zentrum für Integrierte Wirkstoffforschung (ZIW), TU Dortmund University, 44227 Dortmund (Germany)
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17
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Suzuki M, Yoshida I, Suto K, Desaki Y, Shibuya N, Kaku H. AtCERK1 Phosphorylation Site S493 Contributes to the Transphosphorylation of Downstream Components for Chitin-Induced Immune Signaling. PLANT & CELL PHYSIOLOGY 2019; 60:1804-1810. [PMID: 31119298 DOI: 10.1093/pcp/pcz096] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2019] [Accepted: 05/11/2019] [Indexed: 06/09/2023]
Abstract
While ligand-induced autophosphorylation of receptor-like kinases (RLKs) is known to be critical for triggering the downstream responses, biochemical mechanism by which each phosphorylation site contributes to the initiation of corresponding signaling cascades is only poorly understood, except the involvement of some phosphorylation sites in the regulation of catalytic activity of these RLKs. In this article, we first confirmed that the phosphorylation of S493 of AtCERK1 is involved in the regulation of chitin-induced defense responses by the complementation of an atcerk1 mutant with AtCERK1(S493A) cDNA. In vitro kinase assay with the heterologously expressed kinase domain of AtCERK1, GST-AtCERK1cyt, showed that the S493A mutation did not affect the autophosphorylation of AtCERK1 itself but diminished the transphosphorylation of downstream signaling components, PBL27 and PUB4. On the other hand, a phosphomimetic mutant, GST-AtCERK1(S493D)cyt, transphosphorylated these substrates as similar to the wild type AtCERK1. These results suggested that the phosphorylation of S493 does not contribute to the regulation of catalytic activity but plays an important role for the transphosphorylation of the downstream signaling components, thus contributing to the initiation of chitin signaling. To our knowledge, it is a novel finding that a specific phosphorylation site contributes to the regulation of transphosphorylation activity of RLKs. Further studies on the structural basis by which S493 phosphorylation contributes to the regulation of transphosphorylation would contribute to the understanding how the ligand-induced autophosphorylation of RLKs properly regulates the downstream signaling.
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Affiliation(s)
- Maruya Suzuki
- Department of Life Sciences, School of Agriculture, Meiji University, 1-1-1 Higashi-Mita, Tama-ku, Kawasaki, Japan
| | - Issei Yoshida
- Department of Life Sciences, School of Agriculture, Meiji University, 1-1-1 Higashi-Mita, Tama-ku, Kawasaki, Japan
| | - Kenkichi Suto
- Department of Life Sciences, School of Agriculture, Meiji University, 1-1-1 Higashi-Mita, Tama-ku, Kawasaki, Japan
| | - Yoshitake Desaki
- Department of Life Sciences, School of Agriculture, Meiji University, 1-1-1 Higashi-Mita, Tama-ku, Kawasaki, Japan
| | - Naoto Shibuya
- Department of Life Sciences, School of Agriculture, Meiji University, 1-1-1 Higashi-Mita, Tama-ku, Kawasaki, Japan
| | - Hanae Kaku
- Department of Life Sciences, School of Agriculture, Meiji University, 1-1-1 Higashi-Mita, Tama-ku, Kawasaki, Japan
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18
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He X, Ni D, Lu S, Zhang J. Characteristics of Allosteric Proteins, Sites, and Modulators. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1163:107-139. [DOI: 10.1007/978-981-13-8719-7_6] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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19
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Kaitsiotou H, Keul M, Hardick J, Mühlenberg T, Ketzer J, Ehrt C, Krüll J, Medda F, Koch O, Giordanetto F, Bauer S, Rauh D. Inhibitors to Overcome Secondary Mutations in the Stem Cell Factor Receptor KIT. J Med Chem 2017; 60:8801-8815. [DOI: 10.1021/acs.jmedchem.7b00841] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- Helena Kaitsiotou
- Faculty
of Chemistry and Chemical Biology, TU Dortmund University, Otto-Hahn-Straße 4a, D-44227 Dortmund, Germany
| | - Marina Keul
- Faculty
of Chemistry and Chemical Biology, TU Dortmund University, Otto-Hahn-Straße 4a, D-44227 Dortmund, Germany
| | - Julia Hardick
- Faculty
of Chemistry and Chemical Biology, TU Dortmund University, Otto-Hahn-Straße 4a, D-44227 Dortmund, Germany
| | - Thomas Mühlenberg
- Department
of Medical Oncology, Sarcoma Centre West German Cancer Centre University Duisburg−Essen, Medical School, Hufelandstraße 55, D-45122 Essen, Germany
- Germany
and German Cancer Consortium (DKTK), Partner Site University Hospital Essen, D-45147 Essen, Germany
| | - Julia Ketzer
- Department
of Medical Oncology, Sarcoma Centre West German Cancer Centre University Duisburg−Essen, Medical School, Hufelandstraße 55, D-45122 Essen, Germany
- Germany
and German Cancer Consortium (DKTK), Partner Site University Hospital Essen, D-45147 Essen, Germany
| | - Christiane Ehrt
- Faculty
of Chemistry and Chemical Biology, TU Dortmund University, Otto-Hahn-Straße 4a, D-44227 Dortmund, Germany
| | - Jasmin Krüll
- Faculty
of Chemistry and Chemical Biology, TU Dortmund University, Otto-Hahn-Straße 4a, D-44227 Dortmund, Germany
| | - Federico Medda
- Taros Chemicals GmbH & Co. KG, Emil-Figge-Straße 76a, D-44227 Dortmund, Germany
| | - Oliver Koch
- Faculty
of Chemistry and Chemical Biology, TU Dortmund University, Otto-Hahn-Straße 4a, D-44227 Dortmund, Germany
| | | | - Sebastian Bauer
- Department
of Medical Oncology, Sarcoma Centre West German Cancer Centre University Duisburg−Essen, Medical School, Hufelandstraße 55, D-45122 Essen, Germany
- Germany
and German Cancer Consortium (DKTK), Partner Site University Hospital Essen, D-45147 Essen, Germany
| | - Daniel Rauh
- Faculty
of Chemistry and Chemical Biology, TU Dortmund University, Otto-Hahn-Straße 4a, D-44227 Dortmund, Germany
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20
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Ahrari S, Mogharrab N, Navapour L. Interconversion of inactive to active conformation of MARK2: Insights from molecular modeling and molecular dynamics simulation. Arch Biochem Biophys 2017; 630:66-80. [PMID: 28711359 DOI: 10.1016/j.abb.2017.07.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2016] [Revised: 07/09/2017] [Accepted: 07/10/2017] [Indexed: 12/18/2022]
Abstract
The Ser/Thr protein kinase MARK2, also known as Par1b, belongs to the highly-conserved family of PAR proteins which regulate cell polarity and partitioning through the animal kingdom. In the current study, inactive and active structures of human MARK2 were constructed by modeling and molecular dynamics simulation, based on available incomplete crystal structures in Protein Data Bank, to investigate local structural changes through which MARK2 switches from inactive to active state. None of the MARK2 wild type inactive crystal structures represent the position of activation segment. So, the contribution of this loop to the formation of inactive state is not clear. In the modeled structure of inactive MARK2, activation segment occludes the enzyme active site and assumes a relatively stable position. We also presented a detailed description of the major structural changes occur through the activation process and proposed a framework on how these deviations might be affected by the phosphorylation of Thr208 or existence of the UBA domain. Inspection of protein active state in the presence of Mg-ATP, demonstrated the precise arrangement of the various parts of enzyme around Mg-ATP and the importance of their stability in localization of the resulting complex. The results also confirmed the alleged mild auto-inhibitory role of the UBA domain and suggested a reason for the necessity of this role, based on structural similarities to other related kinases.
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Affiliation(s)
- Sajjad Ahrari
- Biophysics and Computational Biology Laboratory (BCBL), Department of Biology, College of Sciences, Shiraz University, Shiraz, Iran
| | - Navid Mogharrab
- Biophysics and Computational Biology Laboratory (BCBL), Department of Biology, College of Sciences, Shiraz University, Shiraz, Iran.
| | - Leila Navapour
- Biophysics and Computational Biology Laboratory (BCBL), Department of Biology, College of Sciences, Shiraz University, Shiraz, Iran
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21
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Gomez-Gutierrez P, Campos PM, Vega M, Perez JJ. Identification of a Novel Inhibitory Allosteric Site in p38α. PLoS One 2016; 11:e0167379. [PMID: 27898710 PMCID: PMC5127581 DOI: 10.1371/journal.pone.0167379] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2016] [Accepted: 11/14/2016] [Indexed: 11/29/2022] Open
Abstract
In the present study, we report the discovery of a novel allosteric inhibitory site for p38α, a subclass of the mitogen-activated protein kinases (MAPK) family. The putative site was discovered after inspection of the crystallographic structure of the p38α-MK2 complex. MK2 (MAPK-activated protein kinase 2) is an interesting protein playing a dual role as modulator and substrate of p38α. This intriguing behavior is due to the ability of the two proteins to form distinctive heterodimers when p38α is phosphorylated or not. We hypothesized that the regulatory action of MK2 is due to its capability to keep p38α in an inactive conformation and consequently, we investigated the atomic structure of the p38α-MK2 complex to understand such regulatory behavior at the molecular level. After inspection of the complex structure, two peptides designed from the MK2 regulatory loop in contact with p38α with sequences Tyr1-Ser2-Asn3-His4-Gly5-Leu6 (peptide-1) and [Phe0]-peptide-1 (peptide-2) in their zwitterionic form were investigated for their phosphorylation inhibitory capability in vitro. Since both peptides exhibited inhibitory capability of the p38α kinase mediated phosphorylation of MEF2A, in a subsequent step we pursued the discovery of small molecule peptidomimetics. For this purpose we characterized in detail the peptide-p38α interaction using molecular dynamics simulations, leading to the definition of a pharmacophore for the peptide-protein interaction. This hypothesis was used as query for a in silico screening, leading to the discovery of a fused ring compound with micromolar inhibitory activity. Site-directed mutagenesis studies support that the compound binds to the putative novel allosteric site in p38α.
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Affiliation(s)
- Patricia Gomez-Gutierrez
- Allinky Biopharma. Madrid Scientific Park. Faraday, 7. Campus de Cantoblanco, Spain
- Dept. of Chemical Engineering. Universitat Politecnica de Catalunya. ETSEIB. Av. Diagonal, Spain
| | - Pedro M. Campos
- Allinky Biopharma. Madrid Scientific Park. Faraday, 7. Campus de Cantoblanco, Spain
| | - Miguel Vega
- Allinky Biopharma. Madrid Scientific Park. Faraday, 7. Campus de Cantoblanco, Spain
| | - Juan J. Perez
- Dept. of Chemical Engineering. Universitat Politecnica de Catalunya. ETSEIB. Av. Diagonal, Spain
- * E-mail:
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22
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Suzuki M, Shibuya M, Shimada H, Motoyama N, Nakashima M, Takahashi S, Suto K, Yoshida I, Matsui S, Tsujimoto N, Ohnishi M, Ishibashi Y, Fujimoto Z, Desaki Y, Kaku H, Kito K, Shibuya N. Autophosphorylation of Specific Threonine and Tyrosine Residues in Arabidopsis CERK1 is Essential for the Activation of Chitin-Induced Immune Signaling. PLANT & CELL PHYSIOLOGY 2016; 57:2312-2322. [PMID: 27565204 DOI: 10.1093/pcp/pcw150] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2016] [Accepted: 08/17/2016] [Indexed: 05/06/2023]
Abstract
Pattern recognition receptors on the plant cell surface mediate the recognition of microbe/damage-associated molecular patterns (MAMPs/DAMPs) and activate downstream immune signaling. Autophosphorylation of signaling receptor-like kinases is a critical event for the activation of downstream responses but the function of each phosphorylation site in the regulation of immune signaling is not well understood. In this study, 41 Ser/Thr/Tyr and 15 Ser/Thr residues were identified as in vitro and in vivo autophosphorylation sites of Arabidopsis CERK1, which is essential for chitin signaling. Comprehensive analysis of transgenic plants expressing mutated CERK1 genes for each phosphorylation site in the cerk1-2 background indicated that the phosphorylation of T479 in the activation segment and Y428 located upstream of the catalytic loop is important for the activation of chitin-triggered defense responses. Contribution of the phosphorylation of T573 to the chitin responses was also suggested. In vitro evaluation of kinase activities of mutated kinase domains indicated that the phosphorylation of T479 and T573 is directly involved in the regulation of kinase activity of CERK1 but the phosphorylation of Y428 regulates chitin signaling independently of the regulation of kinase activity. These results indicated that the phosphorylation of specific residues in the kinase domain contributes to the regulation of downstream signaling either through the regulation of kinase activity or the different mechanisms, e.g. regulation of protein-protein interactions.
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Affiliation(s)
- Maruya Suzuki
- Department of Life Sciences, School of Agriculture, Meiji University, 1-1-1 Higashi-Mita, Tama-ku, Kawasaki, 214-8571, Japan
- These authors contributed equally to this work
| | - Masatoshi Shibuya
- Department of Life Sciences, School of Agriculture, Meiji University, 1-1-1 Higashi-Mita, Tama-ku, Kawasaki, 214-8571, Japan
- These authors contributed equally to this work
| | - Hikaru Shimada
- Department of Life Sciences, School of Agriculture, Meiji University, 1-1-1 Higashi-Mita, Tama-ku, Kawasaki, 214-8571, Japan
- These authors contributed equally to this work
| | - Noriko Motoyama
- Department of Life Sciences, School of Agriculture, Meiji University, 1-1-1 Higashi-Mita, Tama-ku, Kawasaki, 214-8571, Japan
- These authors contributed equally to this work
| | - Masato Nakashima
- Department of Life Sciences, School of Agriculture, Meiji University, 1-1-1 Higashi-Mita, Tama-ku, Kawasaki, 214-8571, Japan
| | - Shohei Takahashi
- Department of Life Sciences, School of Agriculture, Meiji University, 1-1-1 Higashi-Mita, Tama-ku, Kawasaki, 214-8571, Japan
| | - Kenkichi Suto
- Department of Life Sciences, School of Agriculture, Meiji University, 1-1-1 Higashi-Mita, Tama-ku, Kawasaki, 214-8571, Japan
| | - Issei Yoshida
- Department of Life Sciences, School of Agriculture, Meiji University, 1-1-1 Higashi-Mita, Tama-ku, Kawasaki, 214-8571, Japan
| | - Saki Matsui
- Department of Life Sciences, School of Agriculture, Meiji University, 1-1-1 Higashi-Mita, Tama-ku, Kawasaki, 214-8571, Japan
| | - Natsumi Tsujimoto
- Department of Life Sciences, School of Agriculture, Meiji University, 1-1-1 Higashi-Mita, Tama-ku, Kawasaki, 214-8571, Japan
| | - Mihoko Ohnishi
- Department of Life Sciences, School of Agriculture, Meiji University, 1-1-1 Higashi-Mita, Tama-ku, Kawasaki, 214-8571, Japan
| | - Yuko Ishibashi
- Department of Life Sciences, School of Agriculture, Meiji University, 1-1-1 Higashi-Mita, Tama-ku, Kawasaki, 214-8571, Japan
| | - Zui Fujimoto
- National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba, Ibaraki, 305-8602, Japan
| | - Yoshitake Desaki
- Department of Life Sciences, School of Agriculture, Meiji University, 1-1-1 Higashi-Mita, Tama-ku, Kawasaki, 214-8571, Japan
| | - Hanae Kaku
- Department of Life Sciences, School of Agriculture, Meiji University, 1-1-1 Higashi-Mita, Tama-ku, Kawasaki, 214-8571, Japan
| | - Keiji Kito
- Department of Life Sciences, School of Agriculture, Meiji University, 1-1-1 Higashi-Mita, Tama-ku, Kawasaki, 214-8571, Japan
| | - Naoto Shibuya
- Department of Life Sciences, School of Agriculture, Meiji University, 1-1-1 Higashi-Mita, Tama-ku, Kawasaki, 214-8571, Japan
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23
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Carlino L, Rastelli G. Dual Kinase-Bromodomain Inhibitors in Anticancer Drug Discovery: A Structural and Pharmacological Perspective. J Med Chem 2016; 59:9305-9320. [DOI: 10.1021/acs.jmedchem.6b00438] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Luca Carlino
- Department
of Life Sciences, University of Modena and Reggio Emilia, Modena 41125, Italy
| | - Giulio Rastelli
- Department
of Life Sciences, University of Modena and Reggio Emilia, Modena 41125, Italy
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24
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Shang J, Lu S, Jiang Y, Zhang J. Allosteric modulators of MEK1: drug design and discovery. Chem Biol Drug Des 2016; 88:485-97. [PMID: 27115708 DOI: 10.1111/cbdd.12780] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2015] [Revised: 04/01/2016] [Accepted: 04/18/2016] [Indexed: 12/20/2022]
Abstract
Mitogen-activated protein kinase kinase (MAPKK, MEK) mediates signal transduction, controlling cell proliferation and survival. MEK occupies a key downstream position in the Ras-Raf-MEK-ERK signaling pathway, implying that inhibition of MEK will potently suppress tumor cell growth, with potential applications in cancer therapy. Based on the promising therapeutic effects of MEK modulators, continued efforts have been made in this class. Here, we review the discovery and development of MEK1 allosteric modulators, classifying them into four structural groups. The allosteric mechanisms and recent clinical progress involving these modulators are also reviewed.
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Affiliation(s)
- Jialin Shang
- Department of Pathophysiology, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Shanghai Jiao Tong University, School of Medicine, Shanghai, China
| | - Shaoyong Lu
- Department of Pathophysiology, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Shanghai Jiao Tong University, School of Medicine, Shanghai, China
| | - Yongjun Jiang
- School of Biotechnology and Chemical Engineering, Ningbo Institute of Technology, Zhejiang University, Ningbo, China
| | - Jian Zhang
- Department of Pathophysiology, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Shanghai Jiao Tong University, School of Medicine, Shanghai, China. .,Medicinal Bioinformatics Center, Shanghai Jiao Tong University, School of Medicine, Shanghai, China.
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25
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Molecular Dynamics Simulations and Classical Multidimensional Scaling Unveil New Metastable States in the Conformational Landscape of CDK2. PLoS One 2016; 11:e0154066. [PMID: 27100206 PMCID: PMC4839568 DOI: 10.1371/journal.pone.0154066] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2016] [Accepted: 04/07/2016] [Indexed: 01/04/2023] Open
Abstract
Protein kinases are key regulatory nodes in cellular networks and their function has been shown to be intimately coupled with their structural flexibility. However, understanding the key structural mechanisms of large conformational transitions remains a difficult task. CDK2 is a crucial regulator of cell cycle. Its activity is finely tuned by Cyclin E/A and the catalytic segment phosphorylation, whereas its deregulation occurs in many types of cancer. ATP competitive inhibitors have failed to be approved for clinical use due to toxicity issues raised by a lack of selectivity. However, in the last few years type III allosteric inhibitors have emerged as an alternative strategy to selectively modulate CDK2 activity. In this study we have investigated the conformational variability of CDK2. A low dimensional conformational landscape of CDK2 was modeled using classical multidimensional scaling on a set of 255 crystal structures. Microsecond-scale plain and accelerated MD simulations were used to populate this landscape by using an out-of-sample extension of multidimensional scaling. CDK2 was simulated in the apo-form and in complex with the allosteric inhibitor 8-anilino-1-napthalenesulfonic acid (ANS). The apo-CDK2 landscape analysis showed a conformational equilibrium between an Src-like inactive conformation and an active-like form. These two states are separated by different metastable states that share hybrid structural features with both forms of the kinase. In contrast, the CDK2/ANS complex landscape is compatible with a conformational selection picture where the binding of ANS in proximity of the αC helix causes a population shift toward the inactive conformation. Interestingly, the new metastable states could enlarge the pool of candidate structures for the development of selective allosteric CDK2 inhibitors. The method here presented should not be limited to the CDK2 case but could be used to systematically unmask similar mechanisms throughout the human kinome.
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26
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Structural simulation of adenosine phosphate via plumbagin and zoledronic acid competitively targets JNK/Erk to synergistically attenuate osteoclastogenesis in a breast cancer model. Cell Death Dis 2016; 7:e2094. [PMID: 26866274 PMCID: PMC4849151 DOI: 10.1038/cddis.2016.11] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2015] [Revised: 01/04/2016] [Accepted: 01/05/2016] [Indexed: 12/18/2022]
Abstract
The treatment of breast cancer-induced osteolysis remains a challenge in clinical settings. Here, we explored the effect and mechanism of combined treatment with zoledronic acid (ZA) and plumbagin (PL), a widely investigated component derived from Plumbago zeylanica, against breast cancer-induced osteoclastogenesis. We found that the combined treatment with PL and ZA suppressed cell viability of precursor osteoclasts and synergistically inhibited MDA-MB-231-induced osteoclast formation (combination index=0.28) with the abrogation of recombinant mouse receptor activator of nuclear factor-κB ligand (RANKL)-induced activation of NF-κB/MAPK (nuclear factor-κB/mitogen-activated protein kinase) pathways. Molecular docking suggested a putative binding area within c-Jun N-terminal kinase/extracellular signal-regulated kinase (JNK/Erk) protease active sites through the structural mimicking of adenosine phosphate (ANP) by the spatial combination of PL with ZA. A homogeneous time-resolved fluorescence assay further illustrated the direct competitiveness of the dual drugs against ANP docking to phosphorylated JNK/Erk, contributing to the inhibited downstream expression of c-Jun/c-Fos/NFATc-1 (nuclear factor of activated T cells, cytoplasmic, calcineurin-dependent 1). Then, in vivo testing demonstrated that the combined administration of PL and ZA attenuated breast cancer growth in the bone microenvironment. Additionally, these molecules prevented the destruction of proximal tibia, with significant reduction of tartrate-resistant acid phosphatase (TRAcP)-positive osteoclast cells and potentiation of apoptotic cancer cells, to a greater extent when combined than when the drugs were applied independently. Altogether, the combination treatment with PL and ZA could significantly and synergistically suppress osteoclastogenesis and inhibit tumorigenesis both in vitro and in vivo by simulating the spatial structure of ANP to inhibit competitively phosphorylation of c-Jun N-terminal kinase/extracellular signal-regulated kinase (JNK/Erk).
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27
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Horbert R, Pinchuk B, Davies P, Alessi D, Peifer C. Photoactivatable Prodrugs of Antimelanoma Agent Vemurafenib. ACS Chem Biol 2015; 10:2099-107. [PMID: 26061392 DOI: 10.1021/acschembio.5b00174] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
In this study, we report on novel photoactivatable caged prodrugs of vemurafenib. This kinase inhibitor was the first approved drug for the personalized treatment of BRAF-mutated melanoma and showed impressive results in clinical studies. However, the occurrence of severe side effects and drug resistance illustrates the urgent need for innovative therapeutic approaches. To conquer these limitations, we implemented photoremovable protecting groups into vemurafenib. In general, this caging concept provides spatial and temporal control over the activation of molecules triggered by ultraviolet light. Thus, higher inhibitor concentrations in tumor tissues might be reached with less systemic effects. Our study describes the first development of caged vemurafenib prodrugs useful as pharmacological tools. We investigated their photochemical characteristics and photoactivation. In vitro evaluation proved the intended loss-of-function and the light-dependent recovery of efficacy in kinase and cellular assays. The reported vemurafenib photo prodrugs represent a powerful biological tool for novel pharmacological approaches in cancer research.
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Affiliation(s)
- Rebecca Horbert
- Pharmaceutical
Chemistry, Christian Albrechts University, Gutenbergstraße 76, 24118 Kiel, Germany
| | - Boris Pinchuk
- Pharmaceutical
Chemistry, Christian Albrechts University, Gutenbergstraße 76, 24118 Kiel, Germany
| | - Paul Davies
- MRC
Protein Phosphorylation and Ubiquitylation Unit, College of Life Sciences, University of Dundee, Dow Street, Dundee DD1
5EH, U.K
| | - Dario Alessi
- MRC
Protein Phosphorylation and Ubiquitylation Unit, College of Life Sciences, University of Dundee, Dow Street, Dundee DD1
5EH, U.K
| | - Christian Peifer
- Pharmaceutical
Chemistry, Christian Albrechts University, Gutenbergstraße 76, 24118 Kiel, Germany
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28
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Rzymski T, Mikula M, Wiklik K, Brzózka K. CDK8 kinase--An emerging target in targeted cancer therapy. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2015; 1854:1617-29. [PMID: 26006748 DOI: 10.1016/j.bbapap.2015.05.011] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2015] [Revised: 05/15/2015] [Accepted: 05/16/2015] [Indexed: 12/31/2022]
Abstract
Cyclin-dependent kinase (CDK) inhibitors have been developed as potential anticancer therapeutics and several nonselective compounds are currently in advanced clinical trials. This review is focused on the key biological roles of CDK8 kinase, which provide a proof-of-principle for continued efforts toward effective cancer treatment, targeting activity of this CDK family member. Among currently identified kinase inhibitors, several displayed significant selectivity for CDK8 and notably the effectiveness in targeting cancer specific gene expression programs. Structural features of CDK8 and available ligands were discussed from a perspective of the rational drug design process. Current state of the art confirms that further development of CDK8 inhibitors will translate into targeted therapies in oncology. This article is part of a Special Issue entitled:Inhibitors of Protein Kinases.
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Affiliation(s)
| | - Michał Mikula
- Maria Sklodowska-Curie Memorial Cancer Center and Institute of Oncology, Warsaw, Poland
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29
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Basu D, Richters A, Rauh D. Structure-based design and synthesis of covalent-reversible inhibitors to overcome drug resistance in EGFR. Bioorg Med Chem 2015; 23:2767-80. [PMID: 25975640 DOI: 10.1016/j.bmc.2015.04.038] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2015] [Revised: 04/12/2015] [Accepted: 04/14/2015] [Indexed: 01/04/2023]
Abstract
The clinical success of covalent kinase inhibitors in the treatment of EGFR-dependent non-small cell lung cancer (NSCLC) has rejuvenated the appreciation of reactive small molecules. Acquired drug resistance against first-line EGFR inhibitors remains the major bottleneck in NSCLC and is currently addressed by the application of fine-tuned covalent drugs. Here we report the design, synthesis and biochemical evaluation of a novel class of EGFR inhibitors with a covalent yet reversible warhead. A series of WZ4002 analogs, derived from anilinopyrimidine and 3-substituted-2-cyanoacrylamide scaffolds, exhibit strong and selective inhibitory activity against clinically relevant EGFR(L858R) and EGFR(L858R/T790M).
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Affiliation(s)
- Debjit Basu
- Department of Chemistry and Chemical Biology, Technische Universität Dortmund, Otto-Hahn-Straße 6, 44227 Dortmund, Germany
| | - André Richters
- Department of Chemistry and Chemical Biology, Technische Universität Dortmund, Otto-Hahn-Straße 6, 44227 Dortmund, Germany
| | - Daniel Rauh
- Department of Chemistry and Chemical Biology, Technische Universität Dortmund, Otto-Hahn-Straße 6, 44227 Dortmund, Germany.
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30
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Desogus A, Schenone S, Brullo C, Tintori C, Musumeci F. Bcr-Abl tyrosine kinase inhibitors: a patent review. Expert Opin Ther Pat 2015; 25:397-412. [PMID: 25656651 DOI: 10.1517/13543776.2015.1012155] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
INTRODUCTION Breakpoint cluster region Abelson (Bcr-Abl) tyrosine kinase (TK) is a constitutively activated cytoplasmic TK and is the underlying cause of chronic myeloid leukemia (CML). To date, imatinib represents the frontline treatment for CML therapy. The development of resistance has prompted the search for novel Bcr-Abl inhibitors. AREAS COVERED This review presents a short overview of drugs already approved for CML therapy and of the compounds that are in clinical trials. The body of the article deals with Bcr-Abl inhibitors patented since 2008, focusing on their chemical features. EXPERT OPINION The search for Bcr-Abl inhibitors is very active. We believe that a number of patented compounds could enter clinical trials and some could be approved for CML therapy in the next few years. Overall, Bcr-Abl inhibitors constitute a very appealing research field that can be expected to expand further.
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Affiliation(s)
- Andrea Desogus
- Università degli Studi di Genova, Dipartimento di Farmacia , Viale Benedetto XV 3, I-16132, Genova , Italy +0039 010 3538362 ;
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31
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Kothiwale S, Borza CM, Lowe EW, Pozzi A, Meiler J. Discoidin domain receptor 1 (DDR1) kinase as target for structure-based drug discovery. Drug Discov Today 2015; 20:255-61. [PMID: 25284748 PMCID: PMC4336622 DOI: 10.1016/j.drudis.2014.09.025] [Citation(s) in RCA: 59] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2014] [Revised: 08/08/2014] [Accepted: 09/26/2014] [Indexed: 11/18/2022]
Abstract
Discoidin domain receptor (DDR) 1 and 2 are transmembrane receptors that belong to the family of receptor tyrosine kinases (RTK). Upon collagen binding, DDRs transduce cellular signaling involved in various cell functions, including cell adhesion, proliferation, differentiation, migration, and matrix homeostasis. Altered DDR function resulting from either mutations or overexpression has been implicated in several types of disease, including atherosclerosis, inflammation, cancer, and tissue fibrosis. Several established inhibitors, such as imatinib, dasatinib, and nilotinib, originally developed as Abelson murine leukemia (Abl) kinase inhibitors, have been found to inhibit DDR kinase activity. As we review here, recent discoveries of novel inhibitors and their co-crystal structure with the DDR1 kinase domain have made structure-based drug discovery for DDR1 amenable.
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Affiliation(s)
| | - Corina M Borza
- Department of Medicine, Division of Nephrology, Vanderbilt University, Nashville, TN 37232, USA
| | - Edward W Lowe
- Department of Chemistry, Vanderbilt University, Nashville, TN 37232, USA
| | - Ambra Pozzi
- Department of Medicine, Division of Nephrology, Vanderbilt University, Nashville, TN 37232, USA; Department of Medicine, Veterans Affairs Hospital, Nashville, TN 37232, USA
| | - Jens Meiler
- Department of Chemistry, Vanderbilt University, Nashville, TN 37232, USA.
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32
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Fang Z, Simard JR, Plenker D, Nguyen HD, Phan T, Wolle P, Baumeister S, Rauh D. Discovery of inter-domain stabilizers-a novel assay system for allosteric akt inhibitors. ACS Chem Biol 2015; 10:279-88. [PMID: 24959717 DOI: 10.1021/cb500355c] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
In addition to the catalytically active kinase domain, most kinases feature regulatory domains that govern their activity. Modulating and interfering with these interdomain interactions presents a major opportunity for understanding biological systems and developing novel therapeutics. Therefore, small molecule inhibitors that target these interactions through an allosteric mode of action have high intrinsic selectivity, as these interactions are often unique to a single kinase or kinase family. Here we report the development of iFLiK (interface-Fluorescent Labels in Kinases), a fluorescence-based assay that can monitor such interdomain interactions. Using iFLiK, we have demonstrated selective detection of allosteric Akt inhibitors that induce an inactive closed conformation unique to Akt. This methodology easily distinguished small molecule allosteric inhibitors from classic ATP-competitive inhibitors. Screening an in-house compound library with iFLiK, we were able to identify novel compounds with a scaffold that has not been previously described for allosteric Akt inhibitors.
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Affiliation(s)
- Zhizhou Fang
- Technische Universität Dortmund, Fakultät
für Chemie und Chemische Biologie, Otto-Hahn-Strasse 6, 44227 Dortmund, Germany
- Chemical
Genomics
Centre of the Max Planck Society, Otto-Hahn-Strasse
15, 44227 Dortmund, Germany
| | - Jeffrey R. Simard
- Chemical
Genomics
Centre of the Max Planck Society, Otto-Hahn-Strasse
15, 44227 Dortmund, Germany
| | - Dennis Plenker
- University of Cologne, Medical Faculty, Department
of Translational Genomics, Weyertal 115b, 50931 Cologne, Germany
| | - Hoang D. Nguyen
- Chemical
Genomics
Centre of the Max Planck Society, Otto-Hahn-Strasse
15, 44227 Dortmund, Germany
| | - Trang Phan
- Chemical
Genomics
Centre of the Max Planck Society, Otto-Hahn-Strasse
15, 44227 Dortmund, Germany
| | - Patrik Wolle
- Technische Universität Dortmund, Fakultät
für Chemie und Chemische Biologie, Otto-Hahn-Strasse 6, 44227 Dortmund, Germany
| | - Stefan Baumeister
- Technische Universität Dortmund, Fakultät
für Chemie und Chemische Biologie, Otto-Hahn-Strasse 6, 44227 Dortmund, Germany
| | - Daniel Rauh
- Technische Universität Dortmund, Fakultät
für Chemie und Chemische Biologie, Otto-Hahn-Strasse 6, 44227 Dortmund, Germany
- Chemical
Genomics
Centre of the Max Planck Society, Otto-Hahn-Strasse
15, 44227 Dortmund, Germany
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33
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Badrinarayan P, Sastry GN. Specificity rendering 'hot-spots' for aurora kinase inhibitor design: the role of non-covalent interactions and conformational transitions. PLoS One 2014; 9:e113773. [PMID: 25485544 PMCID: PMC4259475 DOI: 10.1371/journal.pone.0113773] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2014] [Accepted: 10/29/2014] [Indexed: 11/19/2022] Open
Abstract
The present study examines the conformational transitions occurring among the major structural motifs of Aurora kinase (AK) concomitant with the DFG-flip and deciphers the role of non-covalent interactions in rendering specificity. Multiple sequence alignment, docking and structural analysis of a repertoire of 56 crystal structures of AK from Protein Data Bank (PDB) has been carried out. The crystal structures were systematically categorized based on the conformational disposition of the DFG-loop [in (DI) 42, out (DO) 5 and out-up (DOU) 9], G-loop [extended (GE) 53 and folded (GF) 3] and αC-helix [in (CI) 42 and out (CO) 14]. The overlapping subsets on categorization show the inter-dependency among structural motifs. Therefore, the four distinct possibilities a) 2W1C (DI, CI, GE) b) 3E5A (DI, CI, GF) c) 3DJ6 (DI, CO, GF) d) 3UNZ (DOU, CO, GF) along with their co-crystals and apo-forms were subjected to molecular dynamics simulations of 40 ns each to evaluate the variations of individual residues and their impact on forming interactions. The non-covalent interactions formed by the 157 AK co-crystals with different regions of the binding site were initially studied with the docked complexes and structure interaction fingerprints. The frequency of the most prominent interactions was gauged in the AK inhibitors from PDB and the four representative conformations during 40 ns. Based on this study, seven major non-covalent interactions and their complementary sites in AK capable of rendering specificity have been prioritized for the design of different classes of inhibitors.
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Affiliation(s)
- Preethi Badrinarayan
- Molecular Modeling Group, Organic Chemical Sciences, CSIR-Indian Institute of Chemical Technology, Tarnaka, Hyderabad- 500 607, India
| | - G. Narahari Sastry
- Molecular Modeling Group, Organic Chemical Sciences, CSIR-Indian Institute of Chemical Technology, Tarnaka, Hyderabad- 500 607, India
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34
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Feng Y, De Franceschi G, Kahraman A, Soste M, Melnik A, Boersema PJ, de Laureto PP, Nikolaev Y, Oliveira AP, Picotti P. Global analysis of protein structural changes in complex proteomes. Nat Biotechnol 2014; 32:1036-44. [PMID: 25218519 DOI: 10.1038/nbt.2999] [Citation(s) in RCA: 243] [Impact Index Per Article: 24.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2013] [Accepted: 07/25/2014] [Indexed: 01/28/2023]
Abstract
Changes in protein conformation can affect protein function, but methods to probe these structural changes on a global scale in cells have been lacking. To enable large-scale analyses of protein conformational changes directly in their biological matrices, we present a method that couples limited proteolysis with a targeted proteomics workflow. Using our method, we assessed the structural features of more than 1,000 yeast proteins simultaneously and detected altered conformations for ~300 proteins upon a change of nutrients. We find that some branches of carbon metabolism are transcriptionally regulated whereas others are regulated by enzyme conformational changes. We detect structural changes in aggregation-prone proteins and show the functional relevance of one of these proteins to the metabolic switch. This approach enables probing of both subtle and pronounced structural changes of proteins on a large scale.
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Affiliation(s)
- Yuehan Feng
- 1] Institute of Biochemistry, Department of Biology, ETH Zurich, Zurich, Switzerland. [2]
| | - Giorgia De Franceschi
- 1] Institute of Biochemistry, Department of Biology, ETH Zurich, Zurich, Switzerland. [2] CRIBI Biotechnology Centre, University of Padua, Padua, Italy. [3]
| | - Abdullah Kahraman
- 1] Institute of Biochemistry, Department of Biology, ETH Zurich, Zurich, Switzerland. [2]
| | - Martin Soste
- Institute of Biochemistry, Department of Biology, ETH Zurich, Zurich, Switzerland
| | - Andre Melnik
- Institute of Biochemistry, Department of Biology, ETH Zurich, Zurich, Switzerland
| | - Paul J Boersema
- Institute of Biochemistry, Department of Biology, ETH Zurich, Zurich, Switzerland
| | | | - Yaroslav Nikolaev
- Institute of Molecular Biology and Biophysics, Department of Biology, ETH Zurich, Zurich, Switzerland
| | - Ana Paula Oliveira
- Institute of Molecular Systems Biology, Department of Biology, ETH Zurich, Zurich, Switzerland
| | - Paola Picotti
- Institute of Biochemistry, Department of Biology, ETH Zurich, Zurich, Switzerland
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35
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Rastelli G, Anighoro A, Chripkova M, Carrassa L, Broggini M. Structure-based discovery of the first allosteric inhibitors of cyclin-dependent kinase 2. Cell Cycle 2014; 13:2296-305. [PMID: 24911186 DOI: 10.4161/cc.29295] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Allosteric targeting of protein kinases via displacement of the structural αC helix with type III allosteric inhibitors is currently gaining a foothold in drug discovery. Recently, the first crystal structure of CDK2 with an open allosteric pocket adjacent to the αC helix has been described, prospecting new opportunities to design more selective inhibitors, but the structure has not yet been exploited for the structure-based design of type III allosteric inhibitors. In this work we report the results of a virtual screening campaign that resulted in the discovery of the first-in-class type III allosteric ligands of CDK2. Using a combination of docking and post-docking analyses made with our tool BEAR, 7 allosteric ligands (hit rate of 20%) with micromolar affinity for CDK2 were identified, some of them inhibiting the growth of breast cancer cell lines in the micromolar range. Competition experiments performed in the presence of the ATP-competitive inhibitor staurosporine confirmed that the 7 ligands are truly allosteric, in agreement with their design. Of these, compound 2 bound CDK2 with an EC50 value of 3 μM and inhibited the proliferation of MDA-MB231 and ZR-75-1 breast cancer cells with IC50 values of approximately 20 μM, while compound 4 had an EC50 value of 71 μM and IC50 values around 4 μM. Remarkably, the most potent compound 4 was able to selectively inhibit CDK2-mediated Retinoblastoma phosphorylation, confirming that its mechanism of action is fully compatible with a selective inhibition of CDK2 phosphorylation in cells. Finally, hit expansion through analog search of the most potent inhibitor 4 revealed an additional ligand 4g with similar in vitro potency on breast cancer cells.
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Affiliation(s)
- Giulio Rastelli
- Life Sciences Department; University of Modena and Reggio Emilia; Modena, Italy
| | - Andrew Anighoro
- Life Sciences Department; University of Modena and Reggio Emilia; Modena, Italy
| | - Martina Chripkova
- IRCCS - Istituto di Ricerche Farmacologiche "Mario Negri"; Milan, Italy
| | - Laura Carrassa
- IRCCS - Istituto di Ricerche Farmacologiche "Mario Negri"; Milan, Italy
| | - Massimo Broggini
- IRCCS - Istituto di Ricerche Farmacologiche "Mario Negri"; Milan, Italy
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36
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Schenone S, Radi M, Musumeci F, Brullo C, Botta M. Biologically Driven Synthesis of Pyrazolo[3,4-d]pyrimidines As Protein Kinase Inhibitors: An Old Scaffold As a New Tool for Medicinal Chemistry and Chemical Biology Studies. Chem Rev 2014; 114:7189-238. [DOI: 10.1021/cr400270z] [Citation(s) in RCA: 92] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Silvia Schenone
- Dipartimento
di Farmacia, Università degli Studi di Genova Viale Benedetto
XV, 3, 16132 Genova, Italy
| | - Marco Radi
- Dipartimento
di Farmacia, Università degli Studi di Parma Viale delle
Scienze, 27/A, 43124 Parma, Italy
| | - Francesca Musumeci
- Dipartimento
di Farmacia, Università degli Studi di Genova Viale Benedetto
XV, 3, 16132 Genova, Italy
| | - Chiara Brullo
- Dipartimento
di Farmacia, Università degli Studi di Genova Viale Benedetto
XV, 3, 16132 Genova, Italy
| | - Maurizio Botta
- Dipartimento
di Biotecnologie, Chimica e Farmacia, Università degli Studi di Siena Via Aldo Moro, 2, 53100 Siena, Italy
- Sbarro
Institute for Cancer Research and Molecular Medicine, Center for Biotechnology,
College of Science and Technology, Temple University, BioLife Science
Building, Suite 333, 1900 N 12th Street, Philadelphia, Pennsylvania 19122, United States
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37
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Richters A, Nguyen HD, Phan T, Simard JR, Grütter C, Engel J, Rauh D. Identification of Type II and III DDR2 Inhibitors. J Med Chem 2014; 57:4252-62. [DOI: 10.1021/jm500167q] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Affiliation(s)
- André Richters
- Department
of Chemistry and Chemical Biology, Technical University of Dortmund, Otto-Hahn-Straße 6, 44227 Dortmund, Germany
| | - Hoang D. Nguyen
- Chemical
Genomics Centre of the Max Planck Society, Otto-Hahn-Straße 15, 44227 Dortmund, Germany
| | - Trang Phan
- Chemical
Genomics Centre of the Max Planck Society, Otto-Hahn-Straße 15, 44227 Dortmund, Germany
| | - Jeffrey R. Simard
- Chemical
Genomics Centre of the Max Planck Society, Otto-Hahn-Straße 15, 44227 Dortmund, Germany
| | - Christian Grütter
- Department
of Chemistry and Chemical Biology, Technical University of Dortmund, Otto-Hahn-Straße 6, 44227 Dortmund, Germany
| | - Julian Engel
- Department
of Chemistry and Chemical Biology, Technical University of Dortmund, Otto-Hahn-Straße 6, 44227 Dortmund, Germany
| | - Daniel Rauh
- Department
of Chemistry and Chemical Biology, Technical University of Dortmund, Otto-Hahn-Straße 6, 44227 Dortmund, Germany
- Chemical
Genomics Centre of the Max Planck Society, Otto-Hahn-Straße 15, 44227 Dortmund, Germany
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38
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Activation pathway of Src kinase reveals intermediate states as targets for drug design. Nat Commun 2014; 5:3397. [PMID: 24584478 PMCID: PMC4465921 DOI: 10.1038/ncomms4397] [Citation(s) in RCA: 266] [Impact Index Per Article: 26.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2013] [Accepted: 02/06/2014] [Indexed: 12/18/2022] Open
Abstract
Unregulated activation of Src kinases leads to aberrant signaling, uncontrolled growth, and differentiation of cancerous cells. Reaching a complete mechanistic understanding of large scale conformational transformations underlying the activation of kinases could greatly help in the development of therapeutic drugs for the treatment of these pathologies. In principle, the nature of conformational transition could be modeled in silico via atomistic molecular dynamics simulations, although this is very challenging due to the long activation timescales. Here, we employ a computational paradigm that couples transition pathway techniques and Markov state model-based massively distributed simulations for mapping the conformational landscape of c-src tyrosine kinase. The computations provide the thermodynamics and kinetics of kinase activation for the first time, and help identify key structural intermediates. Furthermore, the presence of a novel allosteric site in an intermediate state of c-src that could be potentially utilized for drug design is predicted.
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39
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Patel JS, Berteotti A, Ronsisvalle S, Rocchia W, Cavalli A. Steered molecular dynamics simulations for studying protein-ligand interaction in cyclin-dependent kinase 5. J Chem Inf Model 2014; 54:470-80. [PMID: 24437446 DOI: 10.1021/ci4003574] [Citation(s) in RCA: 115] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
In this study, we applied steered molecular dynamics (SMD) simulations to investigate the unbinding mechanism of nine inhibitors of the enzyme cyclin-dependent kinase 5 (CDK5). The study had two major objectives: (i) to create a correlation between the unbinding force profiles and the inhibition activities of these compounds expressed as IC50 values; (ii) to investigate the unbinding mechanism and to reveal atomistic insights, which could help identify accessory binding sites and transient interactions. Overall, we carried out 1.35 μs of cumulative SMD simulations. We showed that SMD could qualitatively discriminate binders from nonbinders, while it failed to properly rank series of inhibitors, particularly when IC50 values were too similar. From a mechanistic standpoint, SMD provided useful insights related to transient and dynamical interactions, which could complement static description obtained by X-ray crystallography experiments. In conclusion, the present study represents a further step toward a systematic exploitation of SMD and other dynamical approaches in structure-based drug design and computational medicinal chemistry.
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Affiliation(s)
- Jagdish Suresh Patel
- Department of Drug Discovery and Development, Istituto Italiano di Tecnologia , Via Morego 30, I-16163 Genova, Italy
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40
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Simard JR, Rauh D. FLiK: a direct-binding assay for the identification and kinetic characterization of stabilizers of inactive kinase conformations. Methods Enzymol 2014; 548:147-71. [PMID: 25399645 DOI: 10.1016/b978-0-12-397918-6.00006-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Despite the hundreds of kinase inhibitors currently in discovery and preclinical phases, the number of FDA-approved kinase inhibitors remains very low by comparison, a discrepancy which reflects the challenges which accompanies kinase inhibitor development. Targeting protein kinases with ATP-competitive inhibitors has been the classical approach to inhibit kinase activity, but the highly conserved nature of the ATP-binding site often contributes to the poor inhibitor selectivity. To address this problem, we developed a high-throughput screening technology that can discriminate for inhibitors, which stabilize inactive kinase conformations by binding within allosteric pockets in the kinase domain. Here, we describe how to use the Fluorescence Labels in Kinases approach to measure the K(d) of ligands as well as how to kinetically characterize the binding and dissociation of ligands to the kinase. We also describe how this technology can be used to rapidly screen small molecule libraries in high throughput.
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Affiliation(s)
- Jeffrey R Simard
- Chemical Genomics Centre of the Max Planck Society, Dortmund, Germany.
| | - Daniel Rauh
- Chemical Genomics Centre of the Max Planck Society, Dortmund, Germany; Fakultät Chemie, Chemische Biologie, Technische Universität Dortmund, Dortmund, Germany.
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41
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Abstract
Computer-aided drug discovery/design methods have played a major role in the development of therapeutically important small molecules for over three decades. These methods are broadly classified as either structure-based or ligand-based methods. Structure-based methods are in principle analogous to high-throughput screening in that both target and ligand structure information is imperative. Structure-based approaches include ligand docking, pharmacophore, and ligand design methods. The article discusses theory behind the most important methods and recent successful applications. Ligand-based methods use only ligand information for predicting activity depending on its similarity/dissimilarity to previously known active ligands. We review widely used ligand-based methods such as ligand-based pharmacophores, molecular descriptors, and quantitative structure-activity relationships. In addition, important tools such as target/ligand data bases, homology modeling, ligand fingerprint methods, etc., necessary for successful implementation of various computer-aided drug discovery/design methods in a drug discovery campaign are discussed. Finally, computational methods for toxicity prediction and optimization for favorable physiologic properties are discussed with successful examples from literature.
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Affiliation(s)
- Gregory Sliwoski
- Jr., Center for Structural Biology, 465 21st Ave South, BIOSCI/MRBIII, Room 5144A, Nashville, TN 37232-8725.
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42
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Grütter C, Sreeramulu S, Sessa G, Rauh D. Structural characterization of the RLCK family member BSK8: a pseudokinase with an unprecedented architecture. J Mol Biol 2013; 425:4455-67. [PMID: 23911552 DOI: 10.1016/j.jmb.2013.07.034] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2013] [Revised: 07/21/2013] [Accepted: 07/25/2013] [Indexed: 10/26/2022]
Abstract
Brassinosteroid signaling kinases (BSKs) are plant-specific receptor-like cytoplasmic protein kinases involved in the brassinosteroid signaling pathway. Unlike common protein kinases, they possess a naturally occurring alanine residue at the "gatekeeper" position, as well as other sequence variations. How BSKs activate downstream proteins such as BSU1, as well as the structural consequences of their unusual sequential features, was unclear. We crystallized the catalytic domain of BSK8 and solved its structure by multiple-wavelength anomalous dispersion phasing methods to a resolution of 1.5Å. In addition, a co-crystal structure of BSK8 with 5-adenylyl imidodiphosphate (AMP-PNP) revealed unusual conformational arrangements of the nucleotide phosphate groups and catalytic key motifs, typically not observed for active protein kinases. Sequential analysis and comparisons with known pseudokinase structures suggest that BSKs represent constitutively inactive protein kinases that regulate brassinosteroid signal transfer through an allosteric mechanism.
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Affiliation(s)
- Christian Grütter
- Technische Universität Dortmund Fakultät Chemie und Chemische Biologie, Otto-Hahn-Strasse 6, D-44227 Dortmund, Germany
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43
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Richters A, Ketzer J, Getlik M, Grütter C, Schneider R, Heuckmann JM, Heynck S, Sos ML, Gupta A, Unger A, Schultz-Fademrecht C, Thomas RK, Bauer S, Rauh D. Targeting Gain of Function and Resistance Mutations in Abl and KIT by Hybrid Compound Design. J Med Chem 2013; 56:5757-72. [DOI: 10.1021/jm4004076] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- André Richters
- Department of Chemistry and Chemical Biology, Technical University of Dortmund, Otto-Hahn-Strasse 6, D-44227 Dortmund, Germany
| | - Julia Ketzer
- Department of Medical Oncology,
Sarcoma Center, West German Cancer Center, University Duisburg-Essen Medical School, Hufelandstrasse 55, D-45122
Essen, Germany
| | - Matthäus Getlik
- Department of Chemistry and Chemical Biology, Technical University of Dortmund, Otto-Hahn-Strasse 6, D-44227 Dortmund, Germany
| | - Christian Grütter
- Department of Chemistry and Chemical Biology, Technical University of Dortmund, Otto-Hahn-Strasse 6, D-44227 Dortmund, Germany
| | - Ralf Schneider
- Chemical Genomics Centre of the Max-Planck-Society,
Otto-Hahn-Strasse 15, D-44227 Dortmund, Germany
| | - Johannes M. Heuckmann
- Department of Translational Genomics, University of Cologne, Weyertal 115b, D-50931 Cologne,
Germany
| | - Stefanie Heynck
- Department of Translational Genomics, University of Cologne, Weyertal 115b, D-50931 Cologne,
Germany
| | - Martin L. Sos
- Department of Translational Genomics, University of Cologne, Weyertal 115b, D-50931 Cologne,
Germany
| | - Anu Gupta
- Department of Molecular Genetics, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio 44195, United States
| | - Anke Unger
- Lead Discovery Center GmbH, Otto-Hahn-Strasse 15, D-44227 Dortmund, Germany
| | | | - Roman K. Thomas
- Department of Translational Genomics, University of Cologne, Weyertal 115b, D-50931 Cologne,
Germany
- Department of Pathology, University of Cologne, Joseph-Stelzmann Strasse 9,
D-50931 Cologne, Germany
| | - Sebastian Bauer
- Department of Medical Oncology,
Sarcoma Center, West German Cancer Center, University Duisburg-Essen Medical School, Hufelandstrasse 55, D-45122
Essen, Germany
| | - Daniel Rauh
- Department of Chemistry and Chemical Biology, Technical University of Dortmund, Otto-Hahn-Strasse 6, D-44227 Dortmund, Germany
- Chemical Genomics Centre of the Max-Planck-Society,
Otto-Hahn-Strasse 15, D-44227 Dortmund, Germany
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44
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Schneider R, Gohla A, Simard JR, Yadav DB, Fang Z, van Otterlo WAL, Rauh D. Overcoming compound fluorescence in the FLiK screening assay with red-shifted fluorophores. J Am Chem Soc 2013; 135:8400-8. [PMID: 23672540 DOI: 10.1021/ja403074j] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
In the attempt to discover novel chemical scaffolds that can modulate the activity of disease-associated enzymes, such as kinases, biochemical assays are usually deployed in high-throughput screenings. First-line assays, such as activity-based assays, often rely on fluorescent molecules by measuring a change in the total emission intensity, polarization state, or energy transfer to another fluorescent molecule. However, under certain conditions, intrinsic compound fluorescence can lead to difficult data analysis and to false-positive, as well as false-negative, hits. We have reported previously on a powerful direct binding assay called fluorescent labels in kinases ('FLiK'), which enables a sensitive measurement of conformational changes in kinases upon ligand binding. In this assay system, changes in the emission spectrum of the fluorophore acrylodan, induced by the binding of a ligand, are translated into a robust assay readout. However, under the excitation conditions of acrylodan, intrinsic compound fluorescence derived from highly conjugated compounds complicates data analysis. We therefore optimized this method by identifying novel fluorophores that excite in the far red, thereby avoiding compound fluorescence. With this advancement, even rigid compounds with multiple π-conjugated ring systems can now be measured reliably. This study was performed on three different kinase constructs with three different labeling sites, each undergoing distinct conformational changes upon ligand binding. It may therefore serve as a guideline for the establishment of novel fluorescence-based detection assays.
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Affiliation(s)
- Ralf Schneider
- Chemical Genomics Centre of the Max-Planck-Society , Otto-Hahn-Strasse 15, 44137 Dortmund, Germany
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45
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Urich R, Wishart G, Kiczun M, Richters A, Tidten-Luksch N, Rauh D, Sherborne B, Wyatt PG, Brenk R. De novo design of protein kinase inhibitors by in silico identification of hinge region-binding fragments. ACS Chem Biol 2013; 8:1044-52. [PMID: 23534475 PMCID: PMC3833278 DOI: 10.1021/cb300729y] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
![]()
Protein kinases constitute an attractive
family of enzyme targets
with high relevance to cell and disease biology. Small molecule inhibitors
are powerful tools to dissect and elucidate the function of kinases
in chemical biology research and to serve as potential starting points
for drug discovery. However, the discovery and development of novel
inhibitors remains challenging. Here, we describe a structure-based de novo design approach that generates novel, hinge-binding
fragments that are synthetically feasible and can be elaborated to
small molecule libraries. Starting from commercially available compounds,
core fragments were extracted, filtered for pharmacophoric properties
compatible with hinge-region binding, and docked into a panel of protein
kinases. Fragments with a high consensus score were subsequently short-listed
for synthesis. Application of this strategy led to a number of core
fragments with no previously reported activity against kinases. Small
libraries around the core fragments were synthesized, and representative
compounds were tested against a large panel of protein kinases and
subjected to co-crystallization experiments. Each of the tested compounds
was active against at least one kinase, but not all kinases in the
panel were inhibited. A number of compounds showed high ligand efficiencies
for therapeutically relevant kinases; among them were MAPKAP-K3, SRPK1,
SGK1, TAK1, and GCK for which only few inhibitors are reported in
the literature.
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Affiliation(s)
- Robert Urich
- Drug Discovery Unit (DDU), Division
of Biological Chemistry and Drug Discovery, College of Life Sciences, University of Dundee, Sir James Black Centre, DD1 5EH,
U.K
| | - Grant Wishart
- Department of Chemistry, MSD, Newhouse, Lanarkshire, ML1 5SH, U.K
| | - Michael Kiczun
- Department of Chemistry, MSD, Newhouse, Lanarkshire, ML1 5SH, U.K
| | - André Richters
- Fakultät Chemie - Chemische
Biologie, Technische Universität Dortmund, Otto-Hahn-Straße 6, 44227 Dortmund, Germany
| | - Naomi Tidten-Luksch
- Drug Discovery Unit (DDU), Division
of Biological Chemistry and Drug Discovery, College of Life Sciences, University of Dundee, Sir James Black Centre, DD1 5EH,
U.K
| | - Daniel Rauh
- Fakultät Chemie - Chemische
Biologie, Technische Universität Dortmund, Otto-Hahn-Straße 6, 44227 Dortmund, Germany
| | - Brad Sherborne
- Department of Chemistry, MSD, Newhouse, Lanarkshire, ML1 5SH, U.K
| | - Paul G. Wyatt
- Drug Discovery Unit (DDU), Division
of Biological Chemistry and Drug Discovery, College of Life Sciences, University of Dundee, Sir James Black Centre, DD1 5EH,
U.K
| | - Ruth Brenk
- Institut für Pharmazie
und Biochemie, Johannes Gutenberg-Universität Mainz, Staudinger Weg 5, 55128 Mainz, Germany
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46
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Palmieri L, Rastelli G. αC helix displacement as a general approach for allosteric modulation of protein kinases. Drug Discov Today 2013. [DOI: 10.1016/j.drudis.2012.11.009] [Citation(s) in RCA: 81] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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47
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De Munter S, Köhn M, Bollen M. Challenges and opportunities in the development of protein phosphatase-directed therapeutics. ACS Chem Biol 2013; 8:36-45. [PMID: 23214403 DOI: 10.1021/cb300597g] [Citation(s) in RCA: 84] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Protein phosphatases have both protective and promoting roles in the etiology of diseases. A prominent example is the existence of oncogenic as well as tumor-suppressing protein phosphatases. A few protein phosphatase activity modulators are already applied in therapies. These were however not developed in target-directed approaches, and the recent discovery of phosphatase involvement followed their application in therapy. Nevertheless, these examples demonstrate that small molecules can be generated that modulate the activity of protein phosphatases and are beneficial for the treatment of protein phosphorylation diseases. We describe here strategies for the development of activators and inhibitors of protein phosphatases and clarify some long-standing misconceptions concerning the druggability of these enzymes. Recent developments suggest that it is feasible to design potent and selective protein phosphatase modulators with a therapeutic potential.
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Affiliation(s)
- Sofie De Munter
- Laboratory of Biosignaling & Therapeutics, Department of Cellular and Molecular Medicine, University of Leuven, Leuven, Belgium
| | - Maja Köhn
- Genome Biology Unit, European Molecular Biology Laboratory, Heidelberg,
Germany
| | - Mathieu Bollen
- Laboratory of Biosignaling & Therapeutics, Department of Cellular and Molecular Medicine, University of Leuven, Leuven, Belgium
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48
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Fang Z, Grütter C, Rauh D. Strategies for the selective regulation of kinases with allosteric modulators: exploiting exclusive structural features. ACS Chem Biol 2013; 8:58-70. [PMID: 23249378 DOI: 10.1021/cb300663j] [Citation(s) in RCA: 149] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The modulation of kinase function has become an important goal in modern drug discovery and chemical biology research. In cancer-targeted therapies, kinase inhibitors have been experiencing an upsurge, which can be measured by the increasing number of kinase inhibitors approved by the FDA in recent years. However, lack of efficacy, limited selectivity, and the emergence of acquired drug resistance still represent major bottlenecks in the clinic and challenge inhibitor development. Most known kinase inhibitors target the active kinase and are ATP competitive. A second class of small organic molecules, which address remote sites of the kinase and stabilize enzymatically inactive conformations, is rapidly moving to the forefront of kinase inhibitor research. Such allosteric modulators bind to sites that are less conserved across the kinome and only accessible upon conformational changes. These molecules are therefore thought to provide various advantages such as higher selectivity and extended drug target residence times. This review highlights various strategies that have been developed to utilizing exclusive structural features of kinases and thereby modulating their activity allosterically.
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Affiliation(s)
- Zhizhou Fang
- Technische Universität Dortmund, Fakultät
Chemie − Chemische Biologie, Otto-Hahn-Strasse
6, D-44227 Dortmund, Germany
| | - Christian Grütter
- Technische Universität Dortmund, Fakultät
Chemie − Chemische Biologie, Otto-Hahn-Strasse
6, D-44227 Dortmund, Germany
| | - Daniel Rauh
- Technische Universität Dortmund, Fakultät
Chemie − Chemische Biologie, Otto-Hahn-Strasse
6, D-44227 Dortmund, Germany
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49
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West GM, Pascal BD, Ng LM, Soon FF, Melcher K, Xu HE, Chalmers MJ, Griffin PR. Protein conformation ensembles monitored by HDX reveal a structural rationale for abscisic acid signaling protein affinities and activities. Structure 2013; 21:229-35. [PMID: 23290725 DOI: 10.1016/j.str.2012.12.001] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2012] [Revised: 11/16/2012] [Accepted: 12/08/2012] [Indexed: 01/04/2023]
Abstract
Plants regulate growth and respond to environmental stress through abscisic acid (ABA) regulated pathways, and as such these pathways are of primary interest for biological and agricultural research. The ABA response is first perceived by the PYR/PYL/RCAR class of START protein receptors. These ABA activated receptors disrupt phosphatase inhibition of Snf1-related kinases (SnRKs), enabling kinase signaling. Here, insights into the structural mechanism of proteins in the ABA signaling pathway (the ABA receptor PYL2, HAB1 phosphatase, and two kinases, SnRK2.3 and 2.6) are discerned through hydrogen/deuterium exchange (HDX) mass spectrometry. HDX on the phosphatase in the presence of binding partners provides evidence for receptor-specific conformations involving the Trp385 "lock" that is necessary for signaling. Furthermore, kinase activity is linked to a more stable "closed" conformation. These solution-based studies complement the static crystal structures and provide a more detailed understanding of the ABA signaling pathway.
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Affiliation(s)
- Graham M West
- Department of Molecular Therapeutics, The Scripps Research Institute, Scripps Florida, Jupiter, FL 33458, USA
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50
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Fischer S, Wentsch HK, Mayer-Wrangowski SC, Zimmermann M, Bauer SM, Storch K, Niess R, Koeberle SC, Grütter C, Boeckler FM, Rauh D, Laufer SA. Dibenzosuberones as p38 mitogen-activated protein kinase inhibitors with low ATP competitiveness and outstanding whole blood activity. J Med Chem 2012; 56:241-53. [PMID: 23270382 DOI: 10.1021/jm301539x] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
p38α mitogen-activated protein (MAP) kinase is a main target in drug research concerning inflammatory diseases. Nevertheless, no inhibitor of p38α MAP kinase has been introduced to the market. This might be attributed to the fact that there is no inhibitor which combines outstanding activity in biological systems and selectivity. Herein an approach to the development of such inhibitors on the basis of the highly selective molecular probe Skepinone-L is described. Introduction of a "deep pocket" moiety addressing the DFG motif led to an increased activity of the compounds. Hydrophilic moieties, addressing the solvent-exposed area adjacent to hydrophilic region II, conserved a high activity of the compounds in a whole blood assay. Combined with their outstanding selectivity and low ATP competitiveness, these inhibitors are very interesting candidates for use in biological systems and in therapy.
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Affiliation(s)
- Stefan Fischer
- Institute of Pharmacy, University of Tübingen , Auf der Morgenstelle 8, D-72076 Tübingen, Germany
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