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Rullah K, Shamsudin NF, Koeberle A, Tham CL, Fasihi Mohd Aluwi MF, Leong SW, Jantan I, Lam KW. Flavonoid diversity and roles in the lipopolysaccharide-mediated inflammatory response of monocytes and macrophages. Future Med Chem 2024; 16:75-99. [PMID: 38205612 DOI: 10.4155/fmc-2023-0174] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Accepted: 11/27/2023] [Indexed: 01/12/2024] Open
Abstract
Targeting lipopolysaccharide (LPS)/toll-like receptor 4 signaling in mononuclear phagocytes has been explored for the treatment of inflammation and inflammation-related disorders. However, only a few key targets have been translated into clinical applications. Flavonoids, a class of ubiquitous plant secondary metabolites, possess a privileged scaffold which serves as a valuable template for designing pharmacologically active compounds directed against diseases with inflammatory components. This perspective provides a general overview of the diversity of flavonoids and their multifaceted mechanisms that interfere with LPS-induced signaling in monocytes and macrophages. Focus is placed on flavonoids targeting MD-2, IκB kinases, c-Jun N-terminal kinases, extracellular signal-regulated kinase, p38 MAPK and PI3K/Akt or modulating LPS-related gene expression.
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Affiliation(s)
- Kamal Rullah
- Department of Pharmaceutical Chemistry, Kulliyyah of Pharmacy, International Islamic University Malaysia, 25200 Kuantan, Pahang, Malaysia
| | - Nur Farisya Shamsudin
- Department of Pharmaceutical Chemistry, Kulliyyah of Pharmacy, International Islamic University Malaysia, 25200 Kuantan, Pahang, Malaysia
| | - Andreas Koeberle
- Michael Popp Institute and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, 6020 Innsbruck, Austria
| | - Chau Ling Tham
- Department of Biomedical Science, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, 43400 Serdang, Selangor, Malaysia
| | - Mohd Fadhlizil Fasihi Mohd Aluwi
- Faculty of Industrial Sciences and Technology, Universiti Malaysia Pahang Al-Sultan Abdullah, Lebuhraya Tun Razak, 26300 Gambang, Kuantan, Pahang, Malaysia
| | - Sze-Wei Leong
- Department of Chemistry, Faculty of Science, University of Malaya, 50603 Kuala Lumpur, Malaysia
| | - Ibrahim Jantan
- Institute of Systems Biology (INBIOSIS), Universiti Kebangsaan Malaysia, 43600 Bangi, Malaysia
| | - Kok Wai Lam
- Centre for Drug & Herbal Development, Faculty of Pharmacy, Universiti Kebangsaan Malaysia, Jalan Raja Muda Abdul Aziz, 50300 Kuala Lumpur, Malaysia
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2
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González L, Díaz L, Pous J, Baginski B, Duran-Corbera A, Scarpa M, Brun-Heath I, Igea A, Martin-Malpartida P, Ruiz L, Pallara C, Esguerra M, Colizzi F, Mayor-Ruiz C, Biondi RM, Soliva R, Macias MJ, Orozco M, Nebreda AR. Characterization of p38α autophosphorylation inhibitors that target the non-canonical activation pathway. Nat Commun 2023; 14:3318. [PMID: 37308482 DOI: 10.1038/s41467-023-39051-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Accepted: 05/26/2023] [Indexed: 06/14/2023] Open
Abstract
p38α is a versatile protein kinase that can control numerous processes and plays important roles in the cellular responses to stress. Dysregulation of p38α signaling has been linked to several diseases including inflammation, immune disorders and cancer, suggesting that targeting p38α could be therapeutically beneficial. Over the last two decades, numerous p38α inhibitors have been developed, which showed promising effects in pre-clinical studies but results from clinical trials have been disappointing, fueling the interest in the generation of alternative mechanisms of p38α modulation. Here, we report the in silico identification of compounds that we refer to as non-canonical p38α inhibitors (NC-p38i). By combining biochemical and structural analyses, we show that NC-p38i efficiently inhibit p38α autophosphorylation but weakly affect the activity of the canonical pathway. Our results demonstrate how the structural plasticity of p38α can be leveraged to develop therapeutic opportunities targeting a subset of the functions regulated by this pathway.
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Affiliation(s)
- Lorena González
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, 08028, Barcelona, Spain
| | - Lucía Díaz
- Nostrum Biodiscovery, 08034, Barcelona, Spain
| | - Joan Pous
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, 08028, Barcelona, Spain
| | - Blazej Baginski
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, 08028, Barcelona, Spain
| | - Anna Duran-Corbera
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, 08028, Barcelona, Spain
| | - Margherita Scarpa
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, 08028, Barcelona, Spain
| | - Isabelle Brun-Heath
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, 08028, Barcelona, Spain
| | - Ana Igea
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, 08028, Barcelona, Spain
| | - Pau Martin-Malpartida
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, 08028, Barcelona, Spain
| | - Lidia Ruiz
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, 08028, Barcelona, Spain
| | | | | | - Francesco Colizzi
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, 08028, Barcelona, Spain
- Department of Marine Biology and Oceanography, Institute of Marine Sciences ICM-CSIC, 08003, Barcelona, Spain
| | - Cristina Mayor-Ruiz
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, 08028, Barcelona, Spain
| | - Ricardo M Biondi
- Instituto de Investigación en Biomedicina de Buenos Aires (IBioBA)-CONICET-Partner Institute of the Max Planck Society, Buenos Aires, Argentina
| | | | - Maria J Macias
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, 08028, Barcelona, Spain.
- ICREA, Pg. Lluís Companys 23, 08010, Barcelona, Spain.
| | - Modesto Orozco
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, 08028, Barcelona, Spain.
- Departament de Bioquímica i Biomedicina, Facultat de Biologia, Universitat de Barcelona, 08028, Barcelona, Spain.
| | - Angel R Nebreda
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, 08028, Barcelona, Spain.
- ICREA, Pg. Lluís Companys 23, 08010, Barcelona, Spain.
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3
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Tolomeu HV, Fraga CAM. Imidazole: Synthesis, Functionalization and Physicochemical Properties of a Privileged Structure in Medicinal Chemistry. MOLECULES (BASEL, SWITZERLAND) 2023; 28:molecules28020838. [PMID: 36677894 PMCID: PMC9865940 DOI: 10.3390/molecules28020838] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/10/2022] [Revised: 12/30/2022] [Accepted: 01/01/2023] [Indexed: 01/19/2023]
Abstract
Imidazole was first synthesized by Heinrich Debus in 1858 and was obtained by the reaction of glyoxal and formaldehyde in ammonia, initially called glyoxaline. The current literature provides much information about the synthesis, functionalization, physicochemical characteristics and biological role of imidazole. Imidazole is a structure that, despite being small, has a unique chemical complexity. It is a nucleus that is very practical and versatile in its construction/functionalization and can be considered a rich source of chemical diversity. Imidazole acts in extremely important processes for the maintenance of living organisms, such as catalysis in enzymatic processes. Imidazole-based compounds with antibacterial, anti-inflammatory, antidiabetic, antiparasitic, antituberculosis, antifungal, antioxidant, antitumor, antimalarial, anticancer, antidepressant and many others make up the therapeutic arsenal and new bioactive compounds proposed in the most diverse works. The interest and importance of imidazole-containing analogs in the field of medicinal chemistry is remarkable, and the understanding from the development of the first blockbuster drug cimetidine explores all the chemical and biological concepts of imidazole in the context of research and development of new drugs.
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Affiliation(s)
- Heber Victor Tolomeu
- Laboratório de Avaliação e Síntese de Substâncias Bioativas (LASSBio), Instituto de Ciências Biomédicas, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-909, Brazil
- Programa de Pós-Graduação em Farmacologia e Química Medicinal, Instituto de Ciências Biomédicas, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-909, Brazil
| | - Carlos Alberto Manssour Fraga
- Laboratório de Avaliação e Síntese de Substâncias Bioativas (LASSBio), Instituto de Ciências Biomédicas, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-909, Brazil
- Programa de Pós-Graduação em Farmacologia e Química Medicinal, Instituto de Ciências Biomédicas, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-909, Brazil
- Correspondence: ; Tel.: +55-21-39386447
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Design and synthesis of new triarylimidazole derivatives as dual inhibitors of BRAFV600E/p38α with potential antiproliferative activity. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2021.132218] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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5
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Song M, Fang S, Li Z, Wang N, Li X, Liu W, Zhang Y, Lin C, Miao W. CsAtf1, a bZIP transcription factor, is involved in fludioxonil sensitivity and virulence in the rubber tree anthracnose fungus Colletotrichum siamense. Fungal Genet Biol 2021; 158:103649. [PMID: 34921997 DOI: 10.1016/j.fgb.2021.103649] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Revised: 11/16/2021] [Accepted: 11/27/2021] [Indexed: 11/29/2022]
Abstract
In phytopathogenic fungi, the HOG MAPK pathway has roles in osmoregulation, fungicide sensitivity, and other processes. The ATF1/CREB-activating transcription factor Atf1 is a regulator that functions downstream of the HOG MAPK pathway. Here, we identified a gene, designated CsAtf1, that encodes a bZIP transcription factor in Colletotrichum siamense, which is the main pathogen that causes Colletotrichum leaf fall disease in rubber trees in China. CsAtf1 localizes to the nucleus. Its mRNA expression correlates positively with that of CsPbs2 and CsHog1 in the HOG MAPK pathway in response to activator (anisomycin), inhibitor (SB203580) and fludioxonil treatments. The CsAtf1 deletion mutant showed slightly retarded mycelial growth, small conidia, slow spore germination, and abnormal appressorium formation. This mutant showed the increased spore germination rate after fludioxonil treatment and more resistance to the fungicide fludioxonil than did the wild-type fungus. However, unlike deletion of Pbs2 or Hog1, which resulted in greater sensitivity to osmotic stress, the CsAtf1 deletion induced slightly increased resistance to osmotic stress and the cell wall stress response. The ΔCsAtf1 strain also exhibited significantly reduced virulence on rubber tree leaves. These data revealed that CsAtf1 plays a key role in the regulation of fludioxonil sensitivity and in pathogenicity regulation in C. siamense.
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Affiliation(s)
- Miao Song
- College of Plant Protection/Key Laboratory of Green Prevention and Control of Tropical Plant Diseases and Pests, Ministry of Education, Hainan University, Haikou 570228, China
| | - Siqi Fang
- College of Plant Protection/Key Laboratory of Green Prevention and Control of Tropical Plant Diseases and Pests, Ministry of Education, Hainan University, Haikou 570228, China
| | - Zhigang Li
- College of Plant Protection/Key Laboratory of Green Prevention and Control of Tropical Plant Diseases and Pests, Ministry of Education, Hainan University, Haikou 570228, China
| | - Na Wang
- College of Plant Protection/Key Laboratory of Green Prevention and Control of Tropical Plant Diseases and Pests, Ministry of Education, Hainan University, Haikou 570228, China
| | - Xiao Li
- College of Plant Protection/Key Laboratory of Green Prevention and Control of Tropical Plant Diseases and Pests, Ministry of Education, Hainan University, Haikou 570228, China
| | - Wenbo Liu
- College of Plant Protection/Key Laboratory of Green Prevention and Control of Tropical Plant Diseases and Pests, Ministry of Education, Hainan University, Haikou 570228, China
| | - Yu Zhang
- College of Plant Protection/Key Laboratory of Green Prevention and Control of Tropical Plant Diseases and Pests, Ministry of Education, Hainan University, Haikou 570228, China
| | - Chunhua Lin
- College of Plant Protection/Key Laboratory of Green Prevention and Control of Tropical Plant Diseases and Pests, Ministry of Education, Hainan University, Haikou 570228, China
| | - Weiguo Miao
- College of Plant Protection/Key Laboratory of Green Prevention and Control of Tropical Plant Diseases and Pests, Ministry of Education, Hainan University, Haikou 570228, China.
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6
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Zhang XH, Chen CH, Li H, Hsiang J, Wu X, Hu W, Horne D, Nam S, Shively J, Rosen ST. Targeting the non-ATP-binding pocket of the MAP kinase p38γ mediates a novel mechanism of cytotoxicity in cutaneous T-cell lymphoma (CTCL). FEBS Lett 2021; 595:2570-2592. [PMID: 34455585 PMCID: PMC8577799 DOI: 10.1002/1873-3468.14186] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Revised: 07/31/2021] [Accepted: 08/19/2021] [Indexed: 02/01/2023]
Abstract
We describe here for the first time a lipid‐binding‐domain (LBD) in p38γ mitogen‐activated protein kinase (MAPK) involved in the response of T cells to a newly identified inhibitor, CSH71. We describe how CSH71, which binds to both the LBD and the ATP‐binding pocket of p38γ, is selectively cytotoxic to CTCL Hut78 cells but spares normal healthy peripheral blood mononuclear (PBMC) cells, and propose possible molecular mechanisms for its action. p38γ is a key player in CTCL development, and we expect that the ability to regulate its expression by specifically targeting the lipid‐binding domain will have important clinical relevance. Our findings characterize novel mechanisms of gene regulation in T lymphoma cells and validate the use of computational screening techniques to identify inhibitors for therapeutic development.
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Affiliation(s)
| | - Chih-Hong Chen
- Beckman Research Institute of City of Hope, Duarte, CA, USA
| | - Hongzhi Li
- Beckman Research Institute of City of Hope, Duarte, CA, USA
| | - Jack Hsiang
- Beckman Research Institute of City of Hope, Duarte, CA, USA
| | - Xiwei Wu
- Beckman Research Institute of City of Hope, Duarte, CA, USA
| | - Weidong Hu
- Beckman Research Institute of City of Hope, Duarte, CA, USA
| | - David Horne
- Beckman Research Institute of City of Hope, Duarte, CA, USA
| | - Sangkil Nam
- Beckman Research Institute of City of Hope, Duarte, CA, USA
| | - Jack Shively
- Beckman Research Institute of City of Hope, Duarte, CA, USA
| | - Steven T Rosen
- Beckman Research Institute of City of Hope, Duarte, CA, USA
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7
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Huth HW, Castro-Gomes T, de Goes AM, Ropert C. Translocation of intracellular CD24 constitutes a triggering event for drug resistance in breast cancer. Sci Rep 2021; 11:17077. [PMID: 34426608 PMCID: PMC8382710 DOI: 10.1038/s41598-021-96449-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Accepted: 08/03/2021] [Indexed: 01/06/2023] Open
Abstract
The capacity of tumor cells to shift dynamically between different states could be responsible for chemoresistance and has been commonly linked to the acquisition of stem cell properties. Here, we have evaluated the phenotype switching associated with drug resistance in breast cancer cell lines and cell lineage obtained from Brazilian patients. We have highlighted the role of the cancer stem cell marker CD24 in the dynamics of cell plasticity and the acquirement of drug resistance. We showed that the translocation of CD24 from cytosol to cell membrane is a triggering event for the phenotype change of breast tumor cells exposed to drug stress. Here, we provide evidence that the phenotype switching is due to the presence of a cytosolic pool of CD24. Importantly, the cellular localization of CD24 was correlated with the changes in the dynamics of p38 MAPK activation. A strong and continuous phosphorylation of the p38 MAPK led to the overexpression of Bcl-2 after treatment in persistent cells presenting high density of CD24 on cell membrane. This phenotype enabled the cells to enter in slow-down of cell cycle, after which several weeks later, the dormant cells proliferated again. Importantly, the use of a p38 activity inhibitor sensitized cells to drug treatment and avoided chemoresistance.
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Affiliation(s)
- Hugo Werner Huth
- Departamento de Biologia Celular, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, 31270-910, Brazil
| | - Thiago Castro-Gomes
- Departamento de Parasitologia, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, 31270-910, Brazil
| | - Alfredo Miranda de Goes
- Departamento de Bioquímica e Imunologia, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, 31270-910, Brazil
| | - Catherine Ropert
- Departamento de Bioquímica e Imunologia, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, 31270-910, Brazil.
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8
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Brennan CM, Emerson CP, Owens J, Christoforou N. p38 MAPKs - roles in skeletal muscle physiology, disease mechanisms, and as potential therapeutic targets. JCI Insight 2021; 6:e149915. [PMID: 34156029 PMCID: PMC8262482 DOI: 10.1172/jci.insight.149915] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
p38 MAPKs play a central role in orchestrating the cellular response to stress and inflammation and in the regulation of myogenesis. Potent inhibitors of p38 MAPKs have been pursued as potential therapies for several disease indications due to their antiinflammatory properties, although none have been approved to date. Here, we provide a brief overview of p38 MAPKs, including their role in regulating myogenesis and their association with disease progression. Finally, we discuss targeting p38 MAPKs as a therapeutic approach for treating facioscapulohumeral muscular dystrophy and other muscular dystrophies by addressing multiple pathological mechanisms in skeletal muscle.
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Affiliation(s)
| | - Charles P Emerson
- Wellstone Muscular Dystrophy Program, Department of Neurology, University of Massachusetts Medical School, Worcester, Massachusetts, USA
| | - Jane Owens
- Rare Disease Research Unit, Pfizer Inc., Cambridge, Massachusetts, USA
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9
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Chen Z, Zhang J, Wei D, Chen J, Yang J. GCN2 Regulates ATF3-p38 MAPK Signaling Transduction in Pulmonary Veno-Occlusive Disease. J Cardiovasc Pharmacol Ther 2021; 26:677-689. [PMID: 33988041 DOI: 10.1177/10742484211015535] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Pulmonary veno-occlusive disease (PVOD) is a fatal disease of pulmonary vascular lesions leading to right heart failure. Heritable PVOD (hPVOD) is related to biallelic mutation of EIF2AK4 (encoding GCN2), but its molecular mechanism remains unclear. In this study, we aimed to investigate the pathogenesis of PVOD and to find potential drug targets for PVOD. GCN2 dysfunction led to an enhanced transcription of collagen I gene (col1a1 and col1a2) through decreasing ATF3-dependent p38 phosphorylation inhibition in PVOD, which promotes the collagen I synthesis in pulmonary arterial smooth muscle cells (PASMCs) and eventually leads to increased collagen deposition in pulmonary artery. Four GCN2 knockout (KO) cell lines (exon 15 or 33 mutation) were successfully constructed by epiCRISPR system. Two induced pluripotent stem cells (iPSCs) were generated by reprogramming peripheral blood mononuclear cells (PBMCs) of PVOD patient. It was also comfirmed that GCN2 dysfunction could lead to increased expression of collagen I in lateral plate mesoderm lineage-smooth muscle cells (LM-SMCs) differentiated from both GCN2 KO cell lines and iPSCs. SB203580 (a specific inhibitor of p38) improved hemodynamics and pulmonary vascular remodeling in mitomycin C (MMC)-induced PVOD rats by right ventricle echocardiography. On the whole, we proposed that GCN2 deficiency decreased ATF3-dependent p38 phosphorylation inhibition in PVOD development and suggested a potential therapeutic reagent of SB203580 for the treatment of the disease.
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Affiliation(s)
- Zhongqiu Chen
- Department of Cell Biology, State Key Laboratory of Medical Molecular Biology, 12501Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.,Department of Physiology, 26441Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Jingyuan Zhang
- Department of Physiology, 26441Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Dong Wei
- Wuxi Lung Transplant Center, 261546Wuxi People's Hospital affiliated to Nanjing Medical University, Wuxi, China
| | - Jingyu Chen
- Wuxi Lung Transplant Center, 261546Wuxi People's Hospital affiliated to Nanjing Medical University, Wuxi, China
| | - Jun Yang
- Department of Physiology, 26441Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
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10
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Chen J, Wang W, Sun H, Pang L, Bao H. Binding mechanism of inhibitors to p38α MAP kinase deciphered by using multiple replica Gaussian accelerated molecular dynamics and calculations of binding free energies. Comput Biol Med 2021; 134:104485. [PMID: 33993013 DOI: 10.1016/j.compbiomed.2021.104485] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Revised: 05/07/2021] [Accepted: 05/07/2021] [Indexed: 12/12/2022]
Abstract
The p38α MAP Kinase has been an important target of drug design for treatment of inflammatory diseases and cancers. This work applies multiple replica Gaussian accelerated molecular dynamics (MR-GaMD) simulations and the molecular mechanics generalized Born surface area (MM-GBSA) method to probe the binding mechanism of inhibitors L51, R24 and 1AU to p38α. Dynamics analyses show that inhibitor bindings exert significant effect on conformational changes of the active helix α2 and the conserved DFG loop. The rank of binding free energies calculated with MM-GBSA not only agrees well with that determined by the experimental IC50 values but also suggests that mutual compensation between the enthalpy and entropy changes can improve binding of inhibitors to p38α. The analyses of free energy landscapes indicate that the L51, R24 and 1AU bound p38α display a DFG-out conformation. The residue-based free energy decomposition method is used to evaluate contributions of separate residues to the inhibitor-p38α binding and the results imply that residues V30, V38, L74, L75, I84, T106, H107, L108, M109, L167, F169 and D168 can be utilized as efficient targets of potent inhibitors toward p38α.
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Affiliation(s)
- Jianzhong Chen
- School of Science, Shandong Jiaotong University, Jinan, 250357, China.
| | - Wei Wang
- School of Science, Shandong Jiaotong University, Jinan, 250357, China
| | - Haibo Sun
- School of Science, Shandong Jiaotong University, Jinan, 250357, China
| | - Laixue Pang
- School of Science, Shandong Jiaotong University, Jinan, 250357, China
| | - Huayin Bao
- School of Pharmacy, Shandong University of Traditional Chinese Medicine, Jinan, 250355, China.
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11
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Asiedu SO, Kwofie SK, Broni E, Wilson MD. Computational Identification of Potential Anti-Inflammatory Natural Compounds Targeting the p38 Mitogen-Activated Protein Kinase (MAPK): Implications for COVID-19-Induced Cytokine Storm. Biomolecules 2021; 11:653. [PMID: 33946644 PMCID: PMC8146027 DOI: 10.3390/biom11050653] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2021] [Revised: 04/24/2021] [Accepted: 04/26/2021] [Indexed: 02/06/2023] Open
Abstract
Severely ill coronavirus disease 2019 (COVID-19) patients show elevated concentrations of pro-inflammatory cytokines, a situation commonly known as a cytokine storm. The p38 MAPK receptor is considered a plausible therapeutic target because of its involvement in the platelet activation processes leading to inflammation. This study aimed to identify potential natural product-derived inhibitory molecules against the p38α MAPK receptor to mitigate the eliciting of pro-inflammatory cytokines using computational techniques. The 3D X-ray structure of the receptor with PDB ID 3ZS5 was energy minimized using GROMACS and used for molecular docking via AutoDock Vina. The molecular docking was validated with an acceptable area under the curve (AUC) of 0.704, which was computed from the receiver operating characteristic (ROC) curve. A compendium of 38,271 natural products originating from Africa and China together with eleven known p38 MAPK inhibitors were screened against the receptor. Four potential lead compounds ZINC1691180, ZINC5519433, ZINC4520996 and ZINC5733756 were identified. The compounds formed strong intermolecular bonds with critical residues Val38, Ala51, Lys53, Thr106, Leu108, Met109 and Phe169. Additionally, they exhibited appreciably low binding energies which were corroborated via molecular mechanics Poisson-Boltzmann surface area (MM-PBSA) calculations. The compounds were also predicted to have plausible pharmacological profiles with insignificant toxicity. The molecules were also predicted to be anti-inflammatory, kinase inhibitors, antiviral, platelet aggregation inhibitors, and immunosuppressive, with probable activity (Pa) greater than probable inactivity (Pi). ZINC5733756 is structurally similar to estradiol with a Tanimoto coefficient value of 0.73, which exhibits anti-inflammatory activity by targeting the activation of Nrf2. Similarly, ZINC1691180 has been reported to elicit anti-inflammatory activity in vitro. The compounds may serve as scaffolds for the design of potential biotherapeutic molecules against the cytokine storm associated with COVID-19.
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Affiliation(s)
- Seth O. Asiedu
- Department of Parasitology, Noguchi Memorial Institute for Medical Research, College of Health Sciences, University of Ghana, Legon, Accra P.O. Box LG 581, Ghana; (S.O.A); (M.D.W)
| | - Samuel K. Kwofie
- Department of Biomedical Engineering, School of Engineering Sciences, College of Basic and Applied Sciences, University of Ghana, Legon, Accra P.O. Box LG 77, Ghana;
- West African Centre for Cell Biology of Infectious Pathogens, Department of Biochemistry, Cell and Molecular Biology, College of Basic and Applied Sciences, University of Ghana, Accra P.O. Box LG 54, Ghana
| | - Emmanuel Broni
- Department of Biomedical Engineering, School of Engineering Sciences, College of Basic and Applied Sciences, University of Ghana, Legon, Accra P.O. Box LG 77, Ghana;
| | - Michael D. Wilson
- Department of Parasitology, Noguchi Memorial Institute for Medical Research, College of Health Sciences, University of Ghana, Legon, Accra P.O. Box LG 581, Ghana; (S.O.A); (M.D.W)
- Department of Medicine, Loyola University Medical Center, Maywood, IL 60153, USA
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12
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Roser P, Weisner J, Stehle J, Rauh D, Drescher M. Conformational selection vs. induced fit: insights into the binding mechanisms of p38α MAP Kinase inhibitors. Chem Commun (Camb) 2021; 56:8818-8821. [PMID: 32749403 DOI: 10.1039/d0cc02539a] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The conformational dynamics of a kinase's activation loop have been challenging to assess due to the activation loop's intrinsic flexibility. To directly probe the conformational equilibrium of the activation loop of mitogen-activated protein kinase p38α, we present an approach based on site-directed spin labeling, electron paramagnetic resonance (EPR) distance restraints, and multilateration. We demonstrate that the activation loop of apo p38α resides in a highly flexible equilibrium state and we reveal that binding of small molecules significantly alters this equilibrium and the populated sub-states.
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Affiliation(s)
- Patrick Roser
- Department of Chemistry and Konstanz Research School Chemical Biology (KoRS-CB), University of Konstanz, Universitätsstraße 10, 78457 Konstanz, Germany.
| | - Jörn Weisner
- Faculty of Chemistry and Chemical Biology, TU Dortmund University, Drug Discovery Hub Dortmund (DDHD) am Zentrum für Integrierte Wirkstoffforschung (ZIW), Otto-Hahn-Strasse 4a, 44227 Dortmund, Germany.
| | - Juliane Stehle
- Department of Chemistry and Konstanz Research School Chemical Biology (KoRS-CB), University of Konstanz, Universitätsstraße 10, 78457 Konstanz, Germany.
| | - Daniel Rauh
- Faculty of Chemistry and Chemical Biology, TU Dortmund University, Drug Discovery Hub Dortmund (DDHD) am Zentrum für Integrierte Wirkstoffforschung (ZIW), Otto-Hahn-Strasse 4a, 44227 Dortmund, Germany.
| | - Malte Drescher
- Department of Chemistry and Konstanz Research School Chemical Biology (KoRS-CB), University of Konstanz, Universitätsstraße 10, 78457 Konstanz, Germany.
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13
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Ali EMH, Abdel-Maksoud MS, Hassan RM, Mersal KI, Ammar UM, Se-In C, He-Soo H, Kim HK, Lee A, Lee KT, Oh CH. Design, synthesis and anti-inflammatory activity of imidazol-5-yl pyridine derivatives as p38α/MAPK14 inhibitor. Bioorg Med Chem 2021; 31:115969. [PMID: 33422910 DOI: 10.1016/j.bmc.2020.115969] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2020] [Revised: 12/20/2020] [Accepted: 12/21/2020] [Indexed: 01/12/2023]
Abstract
P38α/MAPK14 is intracellular signalling regulator involved in biosynthesis of inflammatory mediator cytokines (TNF-α, IL-1, IL-6, and IL-1b), which induce the production of inflammatory proteins (iNOS, NF-kB, and COX-2). In this study, drug repurposing strategies were followed to repositioning of a series of B-RAF V600E imidazol-5-yl pyridine inhibitors to inhibit P38α kinase. A group 25 reported P38α kinase inhibitors were used to build a pharmacophore model for mapping the target compounds and proving their affinity for binding in P38α active site. Target compounds were evaluated for their potency against P38α kinase, compounds 11a and 11d were the most potent inhibitors (IC50 = 47 nM and 45 nM, respectively). In addition, compound 11d effectively inhibited the production of proinflammatory cytokinesTNF-α, 1L-6, and 1L-1β in LPS-induced RAW 264.7 macrophages with IC50 values of 78.03 nM, 17.6 µM and 82.15 nM, respectively. The target compounds were tested for their anti-inflammatory activity by detecting the reduction of Nitric oxide (NO) and prostaglandin (PGE2) production in LPS-stimulated RAW 264.7 macrophages. Compound 11d exhibited satisfied inhibitory activity of the production of PGE2 and NO with IC50 values of 0.29 µM and 0.61 µM, respectively. Molecular dynamics simulations of the most potent inhibitor 11d were carried out to illustrate its conformational stability in the binding site of P38α kinase.
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Affiliation(s)
- Eslam M H Ali
- Center for Biomaterials, Korea Institute of Science & Technology (KIST School), Seoul, Seongbuk-gu, 02792, Republic of Korea; University of Science & Technology (UST), Daejeon, Yuseong-gu, 34113, Republic of Korea; Pharmaceutical Chemistry Department, Faculty of Pharmacy, Modern University for Technology and Information (MTI), Cairo 12055, Egypt
| | - Mohammed S Abdel-Maksoud
- Medicinal & Pharmaceutical Chemistry Department, Pharmaceutical and Drug Industries Research Division, National Research Centre (NRC), (ID: 60014618), P.O. 12622, Dokki, Giza, Egypt
| | - Rasha Mohamed Hassan
- Medicinal & Pharmaceutical Chemistry Department, Pharmaceutical and Drug Industries Research Division, National Research Centre (NRC), (ID: 60014618), P.O. 12622, Dokki, Giza, Egypt
| | - Karim I Mersal
- Center for Biomaterials, Korea Institute of Science & Technology (KIST School), Seoul, Seongbuk-gu, 02792, Republic of Korea; University of Science & Technology (UST), Daejeon, Yuseong-gu, 34113, Republic of Korea
| | - Usama M Ammar
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, 161 Cathedral Street, Glasgow G4 0NR, Scotland, United Kingdom
| | - Choi Se-In
- Department of Pharmaceutical Biochemistry, College of Pharmacy, Kyung Hee University, 1 Hoegi-dong, Dongdaemun-gu, Seoul 130-701, Republic of Korea
| | - Han He-Soo
- Department of Pharmaceutical Biochemistry, College of Pharmacy, Kyung Hee University, 1 Hoegi-dong, Dongdaemun-gu, Seoul 130-701, Republic of Korea
| | - Hee-Kwon Kim
- Department of Nuclear Medicine, Molecular Imaging & Therapeutic Medicine Research Center, Jeonbuk National University Medical School and Hospital, 20 Geonji-ro, Deokjin-gu, Jeonju 54907, Republic of Korea; Research Institute of Clinical Medicine of Jeonbuk National University-Biomedical Research Institute of Jeonbuk National University Hospital, 20 Geonji-ro, Deokjin-gu, Jeonju 54907, Republic of Korea
| | - Anna Lee
- Department of Chemistry, Hanseo University, Seosan 31962, Republic of Korea
| | - Kyung-Tae Lee
- Department of Pharmaceutical Biochemistry, College of Pharmacy, Kyung Hee University, 1 Hoegi-dong, Dongdaemun-gu, Seoul 130-701, Republic of Korea.
| | - Chang-Hyun Oh
- Center for Biomaterials, Korea Institute of Science & Technology (KIST School), Seoul, Seongbuk-gu, 02792, Republic of Korea; University of Science & Technology (UST), Daejeon, Yuseong-gu, 34113, Republic of Korea.
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14
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Selective targeting of the αC and DFG-out pocket in p38 MAPK. Eur J Med Chem 2020; 208:112721. [DOI: 10.1016/j.ejmech.2020.112721] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Revised: 07/31/2020] [Accepted: 08/01/2020] [Indexed: 12/25/2022]
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15
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Abstract
Malaria is one of the most impacting public health problems in tropical and subtropical areas of the globe, with approximately 200 million cases worldwide annually. In the absence of an effective vaccine, rapid treatment is vital for effective malaria control. However, parasite resistance to currently available drugs underscores the urgent need for identifying new antimalarial therapies with new mechanisms of action. Among potential drug targets for developing new antimalarial candidates, protein kinases are attractive. These enzymes catalyze the phosphorylation of several proteins, thereby regulating a variety of cellular processes and playing crucial roles in the development of all stages of the malaria parasite life cycle. Moreover, the large phylogenetic distance between Plasmodium species and its human host is reflected in marked differences in structure and function of malaria protein kinases between the homologs of both species, indicating that selectivity can be attained. In this review, we describe the functions of the different types of Plasmodium kinases and highlight the main recent advances in the discovery of kinase inhibitors as potential new antimalarial drug candidates.
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16
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Abdeldayem A, Raouf YS, Constantinescu SN, Moriggl R, Gunning PT. Advances in covalent kinase inhibitors. Chem Soc Rev 2020; 49:2617-2687. [DOI: 10.1039/c9cs00720b] [Citation(s) in RCA: 89] [Impact Index Per Article: 22.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
This comprehensive review details recent advances, challenges and innovations in covalent kinase inhibition within a 10 year period (2007–2018).
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Affiliation(s)
- Ayah Abdeldayem
- Department of Chemical & Physical Sciences
- University of Toronto
- Mississauga
- Canada
- Department of Chemistry
| | - Yasir S. Raouf
- Department of Chemical & Physical Sciences
- University of Toronto
- Mississauga
- Canada
- Department of Chemistry
| | | | - Richard Moriggl
- Institute of Animal Breeding and Genetics
- University of Veterinary Medicine
- 1210 Vienna
- Austria
| | - Patrick T. Gunning
- Department of Chemical & Physical Sciences
- University of Toronto
- Mississauga
- Canada
- Department of Chemistry
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17
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Röhm S, Berger BT, Schröder M, Chaikuad A, Winkel R, Hekking KFW, Benningshof JJC, Müller G, Tesch R, Kudolo M, Forster M, Laufer S, Knapp S. Fast Iterative Synthetic Approach toward Identification of Novel Highly Selective p38 MAP Kinase Inhibitors. J Med Chem 2019; 62:10757-10782. [DOI: 10.1021/acs.jmedchem.9b01227] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- Sandra Röhm
- Institute for Pharmaceutical Chemistry, Johann Wolfgang Goethe-University, Max-von-Laue-Str. 9, D-60438 Frankfurt am Main, Germany
- Structural Genomics Consortium (SGC), Buchmann Institute for Life Sciences, Johann Wolfgang Goethe-University, Max-von-Laue-Str. 15, D-60438 Frankfurt am Main, Germany
| | - Benedict-Tilman Berger
- Institute for Pharmaceutical Chemistry, Johann Wolfgang Goethe-University, Max-von-Laue-Str. 9, D-60438 Frankfurt am Main, Germany
- Structural Genomics Consortium (SGC), Buchmann Institute for Life Sciences, Johann Wolfgang Goethe-University, Max-von-Laue-Str. 15, D-60438 Frankfurt am Main, Germany
| | - Martin Schröder
- Institute for Pharmaceutical Chemistry, Johann Wolfgang Goethe-University, Max-von-Laue-Str. 9, D-60438 Frankfurt am Main, Germany
- Structural Genomics Consortium (SGC), Buchmann Institute for Life Sciences, Johann Wolfgang Goethe-University, Max-von-Laue-Str. 15, D-60438 Frankfurt am Main, Germany
| | - Apirat Chaikuad
- Institute for Pharmaceutical Chemistry, Johann Wolfgang Goethe-University, Max-von-Laue-Str. 9, D-60438 Frankfurt am Main, Germany
- Structural Genomics Consortium (SGC), Buchmann Institute for Life Sciences, Johann Wolfgang Goethe-University, Max-von-Laue-Str. 15, D-60438 Frankfurt am Main, Germany
| | - Rob Winkel
- Mercachem BV, Kerkenbos 1013, 6546 BB Nijmegen, The Netherlands
| | | | | | - Gerhard Müller
- Gotham Therapeutics, 430 East 29th Street, Alexandria Center, New York, New York 10016, United States
| | - Roberta Tesch
- Institute for Pharmaceutical Chemistry, Johann Wolfgang Goethe-University, Max-von-Laue-Str. 9, D-60438 Frankfurt am Main, Germany
- Structural Genomics Consortium (SGC), Buchmann Institute for Life Sciences, Johann Wolfgang Goethe-University, Max-von-Laue-Str. 15, D-60438 Frankfurt am Main, Germany
| | - Mark Kudolo
- Department of Pharmaceutical/Medicinal Chemistry, Eberhard Karls University Tübingen, Auf der Morgenstelle 8, 72076 Tübingen, Germany
| | - Michael Forster
- Department of Pharmaceutical/Medicinal Chemistry, Eberhard Karls University Tübingen, Auf der Morgenstelle 8, 72076 Tübingen, Germany
| | - Stefan Laufer
- Department of Pharmaceutical/Medicinal Chemistry, Eberhard Karls University Tübingen, Auf der Morgenstelle 8, 72076 Tübingen, Germany
| | - Stefan Knapp
- Institute for Pharmaceutical Chemistry, Johann Wolfgang Goethe-University, Max-von-Laue-Str. 9, D-60438 Frankfurt am Main, Germany
- Structural Genomics Consortium (SGC), Buchmann Institute for Life Sciences, Johann Wolfgang Goethe-University, Max-von-Laue-Str. 15, D-60438 Frankfurt am Main, Germany
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18
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Abdolmaleki A, Ghasemi JB. Inhibition activity prediction for a dataset of candidates' drug by combining fuzzy logic with MLR/ANN QSAR models. Chem Biol Drug Des 2019; 93:1139-1157. [PMID: 31343121 DOI: 10.1111/cbdd.13511] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2018] [Revised: 02/03/2019] [Accepted: 02/16/2019] [Indexed: 11/28/2022]
Abstract
A hybrid of artificial intelligence simple and low computational cost QSAR was used. Approximately 90 pyridinylimidazole-based drug candidates with a range of potencies against p38R MAP kinase were investigated. To obtain more flexibility and effective capability of handling and processing information about the real world, in this case, the fuzzy set theory was introduced into the QSAR. An integration of multiple linear regression and artificial neural network with adaptive neuro-fuzzy inference systems (ANFIS) was developed to predict the inhibition activity. The algorithm of ANFIS was applied to identify the suitable variables and then to find the optimal descriptors. The gradient descent with momentum backpropagation ANN was used to establish the nonlinear multivariate relationships between the chemical structural parameters and biological response. A comparison between the result of the proposed linear and nonlinear regression showed the superiority of QSAR modeling by ANFIS-ANN method over the MLR. The results demonstrated that the ANFIS could be applied successfully as a feature selection. The appearance of Diam, Homo, and LogP descriptors in the model showed the importance of the steric, electronic, and thermodynamic interactions between a drug and its target site in the distribution of a compound within a biosystem and its interaction with competing for binding sites.
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Affiliation(s)
- Azizeh Abdolmaleki
- Department of Chemistry, Tuyserkan Branch, Islamic Azad University, Tuyserkan, Iran
| | - Jahan B Ghasemi
- Drug Design in Silico Lab., Chemistry Faculty, University of Tehran, Tehran, Iran
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19
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Kumra H, Dinesh NEH, Reinhardt DP. Lessons from tracheal tube development for understanding congenital tracheal malformations. Eur Respir J 2019; 53:53/3/1900127. [PMID: 30846450 DOI: 10.1183/13993003.00127-2019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2019] [Accepted: 02/09/2019] [Indexed: 11/05/2022]
Affiliation(s)
- Heena Kumra
- Faculty of Medicine, Dept of Anatomy and Cell Biology, McGill University, Montreal, QC, Canada.,Both authors contributed equally
| | - Neha E H Dinesh
- Faculty of Medicine, Dept of Anatomy and Cell Biology, McGill University, Montreal, QC, Canada.,Both authors contributed equally
| | - Dieter P Reinhardt
- Faculty of Medicine, Dept of Anatomy and Cell Biology, McGill University, Montreal, QC, Canada.,Faculty of Dentistry, McGill University, Montreal, QC, Canada
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20
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Roser P, Weisner J, Simard JR, Rauh D, Drescher M. Direct monitoring of the conformational equilibria of the activation loop in the mitogen-activated protein kinase p38α. Chem Commun (Camb) 2018; 54:12057-12060. [PMID: 30295691 DOI: 10.1039/c8cc06128a] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Conformational transitions in protein kinases are crucial for the biological function of these enzymes. Here, we characterize and assess conformational equilibria of the activation loop and the effect of small molecule inhibitors in the MAP kinase p38α. Our work experimentally revealed the existence of a two-state equilibrium for p38α while the addition of inhibitors shifts the equilibrium between these two states.
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Affiliation(s)
- Patrick Roser
- Department of Chemistry and Konstanz Research School Chemical Biology, (KoRS-CB), University of Konstanz, Universitätsstraße 10, 78457 Konstanz, Germany.
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21
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Maruyama K, Sheng Y, Watanabe H, Fukuzawa K, Tanaka S. Application of singular value decomposition to the inter-fragment interaction energy analysis for ligand screening. COMPUT THEOR CHEM 2018. [DOI: 10.1016/j.comptc.2018.04.001] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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22
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Abrahams A, Mouchet N, Gouault N, Lohézic Le Dévéhat F, Le Roch M, Rouaud I, Gilot D, Galibert MD. Integrating targeted gene expression and a skin model system to identify functional inhibitors of the UV activated p38 MAP kinase. Photochem Photobiol Sci 2018; 15:1468-1475. [PMID: 27748490 DOI: 10.1039/c6pp00283h] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
The stress-activated p38α MAP Kinase is an integral and critical component of the UV-induced inflammatory response. Despite the advances in recent years in the development of p38 kinase inhibitors, validation of these compounds in the diseased models remains limited. Based on the pharmacological profile of p38α inhibitor lead compound, SB203580, we synthesized a series of pyrrole-derivatives. Using UV-irradiated human skin punch-biopsies and cell cultures, we identified and validated the inhibitory activity of the derivatives by quantitatively measuring their effect on the expression of p38α target genes using real-time PCR. This approach not only identified pyrrole-2 as a unique derivative of this series that specifically inhibited the UV-activated p38α kinase, but also documented the skin permeation, bioavailability and reversible properties of this derivative in a 3D structure. The successful skin permeation of pyrrole-2 and its impact on AREG, COX-2 and MMP-9 gene expression demonstrates its potential use in modulating inflammatory processes in the skin. This study underscored the importance of using adapted biological models to identify accurate bioactive compounds.
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Affiliation(s)
- Amaal Abrahams
- CNRS UMR6290, Institut de Génétique et Développement de Rennes, France. and University of Rennes1, France and University of Cape Town, Department of Human Biology, Cape Town, South Africa
| | - Nicolas Mouchet
- CNRS UMR6290, Institut de Génétique et Développement de Rennes, France. and University of Rennes1, France
| | - Nicolas Gouault
- University of Rennes1, France and CNRS UMR6226, Sciences Chimiques de Rennes, France
| | | | - Myriam Le Roch
- University of Rennes1, France and CNRS UMR6226, Sciences Chimiques de Rennes, France
| | - Isabelle Rouaud
- University of Rennes1, France and CNRS UMR6226, Sciences Chimiques de Rennes, France
| | - David Gilot
- CNRS UMR6290, Institut de Génétique et Développement de Rennes, France. and University of Rennes1, France
| | - Marie-Dominique Galibert
- CNRS UMR6290, Institut de Génétique et Développement de Rennes, France. and University of Rennes1, France and CHU-Pontchaillou, Rennes, France
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23
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Molina MD, Quirin M, Haillot E, Jimenez F, Chessel A, Lepage T. p38 MAPK as an essential regulator of dorsal-ventral axis specification and skeletogenesis during sea urchin development: a re-evaluation. Development 2017; 144:2270-2281. [PMID: 28507001 DOI: 10.1242/dev.152330] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2017] [Accepted: 05/08/2017] [Indexed: 12/15/2022]
Abstract
Dorsal-ventral axis formation in the sea urchin embryo relies on the asymmetrical expression of the TGFβ Nodal. The p38-MAPK pathway has been proposed to be essential for dorsal-ventral axis formation by acting upstream of nodal expression. Here, we report that, in contrast to previous studies that used pharmacological inhibitors of p38, manipulating the activity of p38 by genetic means has no obvious impact on morphogenesis. Instead, we discovered that p38 inhibitors strongly disrupt specification of all germ layers by blocking signalling from the Nodal receptor and by interfering with the ERK pathway. Strikingly, while expression of a mutant p38 that is resistant to SB203580 did not rescue dorsal-ventral axis formation or skeletogenesis in embryos treated with this inhibitor, expression of mutant Nodal receptors that are resistant to SB203580 fully restored nodal expression in SB203580-treated embryos. Taken together, these results establish that p38 activity is not required for dorsal-ventral axis formation through nodal expression nor for skeletogenesis. Our results prompt a re-evaluation of the conclusions of several recent studies that linked p38 activity to dorsal-ventral axis formation and to patterning of the skeleton.
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Affiliation(s)
| | - Magali Quirin
- Université Côte d'Azur, CNRS, INSERM iBV, 06108 Nice cedex 2, France
| | - Emmanuel Haillot
- Université Côte d'Azur, CNRS, INSERM iBV, 06108 Nice cedex 2, France
| | - Felipe Jimenez
- Université Côte d'Azur, CNRS, INSERM iBV, 06108 Nice cedex 2, France
| | - Aline Chessel
- Université Côte d'Azur, CNRS, INSERM iBV, 06108 Nice cedex 2, France
| | - Thierry Lepage
- Université Côte d'Azur, CNRS, INSERM iBV, 06108 Nice cedex 2, France
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24
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Norrie JL, Li Q, Co S, Huang BL, Ding D, Uy JC, Ji Z, Mackem S, Bedford MT, Galli A, Ji H, Vokes SA. PRMT5 is essential for the maintenance of chondrogenic progenitor cells in the limb bud. Development 2016; 143:4608-4619. [PMID: 27827819 DOI: 10.1242/dev.140715] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2016] [Accepted: 10/24/2016] [Indexed: 12/13/2022]
Abstract
During embryonic development, undifferentiated progenitor cells balance the generation of additional progenitor cells with differentiation. Within the developing limb, cartilage cells differentiate from mesodermal progenitors in an ordered process that results in the specification of the correct number of appropriately sized skeletal elements. The internal pathways by which these cells maintain an undifferentiated state while preserving their capacity to differentiate is unknown. Here, we report that the arginine methyltransferase PRMT5 has a crucial role in maintaining progenitor cells. Mouse embryonic buds lacking PRMT5 have severely truncated bones with wispy digits lacking joints. This novel phenotype is caused by widespread cell death that includes mesodermal progenitor cells that have begun to precociously differentiate into cartilage cells. We propose that PRMT5 maintains progenitor cells through its regulation of Bmp4 Intriguingly, adult and embryonic stem cells also require PRMT5 for maintaining pluripotency, suggesting that similar mechanisms might regulate lineage-restricted progenitor cells during organogenesis.
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Affiliation(s)
- Jacqueline L Norrie
- Department of Molecular Biosciences, University of Texas at Austin, 2500 Speedway Stop A4800, Austin, TX 78712, USA
| | - Qiang Li
- Department of Molecular Biosciences, University of Texas at Austin, 2500 Speedway Stop A4800, Austin, TX 78712, USA
| | - Swanie Co
- Department of Molecular Biosciences, University of Texas at Austin, 2500 Speedway Stop A4800, Austin, TX 78712, USA
| | - Bau-Lin Huang
- Cancer and Developmental Biology Laboratory, CCR, NCI, Frederick, MD 21702, USA
| | - Ding Ding
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, 615 North Wolfe Street, Room E3638, Baltimore, MD 21205, USA
| | - Jann C Uy
- Department of Molecular Biosciences, University of Texas at Austin, 2500 Speedway Stop A4800, Austin, TX 78712, USA
| | - Zhicheng Ji
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, 615 North Wolfe Street, Room E3638, Baltimore, MD 21205, USA
| | - Susan Mackem
- Cancer and Developmental Biology Laboratory, CCR, NCI, Frederick, MD 21702, USA
| | - Mark T Bedford
- Department of Epigenetics & Molecular Carcinogenesis, M.D. Anderson Cancer Center, 1808 Park Road 1C (P.O. Box 389), Smithville, TX 78957, USA
| | - Antonella Galli
- Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
| | - Hongkai Ji
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, 615 North Wolfe Street, Room E3638, Baltimore, MD 21205, USA
| | - Steven A Vokes
- Department of Molecular Biosciences, University of Texas at Austin, 2500 Speedway Stop A4800, Austin, TX 78712, USA
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25
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Comparative chemical array screening for p38γ/δ MAPK inhibitors using a single gatekeeper residue difference between p38α/β and p38γ/δ. Sci Rep 2016; 6:29881. [PMID: 27431267 PMCID: PMC4949465 DOI: 10.1038/srep29881] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2016] [Accepted: 06/23/2016] [Indexed: 11/08/2022] Open
Abstract
Mammalian p38 mitogen activated protein kinases (MAPKs) are responsive to a variety of cellular stresses. The development of specific pyridinyl imidazole inhibitors has permitted the characterization of the p38 MAPK isoform p38α, which is expressed in most cell types, whereas the physiological roles of p38γ and p38δ are poorly understood. In this study, we report an approach for identifying selective inhibitors against p38γ and p38δ by focusing on the difference in gatekeeper residues between p38α/β and p38γ/δ. Using GST-fused p38α wild type and T106M mutant constructs, wherein the p38α gatekeeper residue (Thr-106) was substituted by the p38γ/δ-type (Met), we performed comparative chemical array screening to identify specific binders of the mutant and identified SU-002 bound to p38αT106M specifically. SU-002 was found to inhibit p38αT106M but not p38α kinase activity in in vitro kinase assays. SU-005, the analog of SU-002, had inhibitory effects against the kinase activity of p38γ and p38δ in vitro but not p38α. In addition, SU-005 inhibited both p38γ and p38δ auto-phosphorylation in HeLa and HEK293T cells. These results demonstrate that the comparative chemical array screening approach is a powerful technique to explore specific inhibitors for mutant proteins with even single amino-acid substitutions in a high-throughput manner.
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26
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Kesarwani M, Huber E, Kincaid Z, Evelyn CR, Biesiada J, Rance M, Thapa MB, Shah NP, Meller J, Zheng Y, Azam M. Targeting substrate-site in Jak2 kinase prevents emergence of genetic resistance. Sci Rep 2015; 5:14538. [PMID: 26419724 PMCID: PMC4588578 DOI: 10.1038/srep14538] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2015] [Accepted: 08/18/2015] [Indexed: 12/13/2022] Open
Abstract
Emergence of genetic resistance against kinase inhibitors poses a great challenge for durable therapeutic response. Here, we report a novel mechanism of JAK2 kinase inhibition by fedratinib (TG101348) that prevents emergence of genetic resistance. Using in vitro drug screening, we identified 211 amino-acid substitutions conferring resistance to ruxolitinib (INCB018424) and cross-resistance to the JAK2 inhibitors AZD1480, CYT-387 and lestaurtinib. In contrast, these resistant variants were fully sensitive to fedratinib. Structural modeling, coupled with mutagenesis and biochemical studies, revealed dual binding sites for fedratinib. In vitro binding assays using purified proteins showed strong affinity for the substrate-binding site (Kd = 20 nM) while affinity for the ATP site was poor (Kd = ~8 μM). Our studies demonstrate that mutations affecting the substrate-binding pocket encode a catalytically incompetent kinase, thereby preventing emergence of resistant variants. Most importantly, our data suggest that in order to develop resistance-free kinase inhibitors, the next-generation drug design should target the substrate-binding site.
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Affiliation(s)
- Meenu Kesarwani
- Cincinnati Children's Hospital Medical Center, Cancer Blood Disease Institute, Divisions of Experimental Hematology and Cancer Pathology, Cincinnati, Ohio, 45229 USA
| | - Erika Huber
- Cincinnati Children's Hospital Medical Center, Cancer Blood Disease Institute, Divisions of Experimental Hematology and Cancer Pathology, Cincinnati, Ohio, 45229 USA
| | - Zachary Kincaid
- Cincinnati Children's Hospital Medical Center, Cancer Blood Disease Institute, Divisions of Experimental Hematology and Cancer Pathology, Cincinnati, Ohio, 45229 USA
| | - Chris R Evelyn
- Cincinnati Children's Hospital Medical Center, Cancer Blood Disease Institute, Divisions of Experimental Hematology and Cancer Pathology, Cincinnati, Ohio, 45229 USA
| | - Jacek Biesiada
- Cincinnati Children's Hospital Medical Center, Cancer Blood Disease Institute, Divisions of Experimental Hematology and Cancer Pathology, Cincinnati, Ohio, 45229 USA
| | - Mark Rance
- Department of Molecular Genetics, Biochemistry and Microbiology University of Cincinnati College of Medicine, University of Cincinnati, Ohio 45229 USA
| | - Mahendra B Thapa
- Department of Molecular Genetics, Biochemistry and Microbiology University of Cincinnati College of Medicine, University of Cincinnati, Ohio 45229 USA
| | - Neil P Shah
- Division of Hematology-Oncology UCSF School of Medicine, San Francisco, California, 94143 USA
| | - Jarek Meller
- Cincinnati Children's Hospital Medical Center, Cancer Blood Disease Institute, Divisions of Experimental Hematology and Cancer Pathology, Cincinnati, Ohio, 45229 USA
| | - Yi Zheng
- Cincinnati Children's Hospital Medical Center, Cancer Blood Disease Institute, Divisions of Experimental Hematology and Cancer Pathology, Cincinnati, Ohio, 45229 USA
| | - Mohammad Azam
- Cincinnati Children's Hospital Medical Center, Cancer Blood Disease Institute, Divisions of Experimental Hematology and Cancer Pathology, Cincinnati, Ohio, 45229 USA.,Department of Molecular Genetics, Biochemistry and Microbiology University of Cincinnati College of Medicine, University of Cincinnati, Ohio 45229 USA
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Design, Synthesis and Biological Evaluation of Novel Substituted N,N'-Diaryl ureas as Potent p38 Inhibitors. Molecules 2015; 20:16604-19. [PMID: 26378516 PMCID: PMC6332430 DOI: 10.3390/molecules200916604] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2015] [Revised: 09/07/2015] [Accepted: 09/09/2015] [Indexed: 11/16/2022] Open
Abstract
A novel series of substituted N,N'-diaryl ureas that act as p38α inhibitors have been designed and synthesized based on two key residues (Gly110 and Thr106) that are different in p38α MAPK than in other kinases. Preliminary biological evaluation indicated that most compounds possessed good p38α inhibitory potencies. Among these compounds, 9g appeared to be the most powerful and is the main compound that we will study in the future.
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Astolfi A, Iraci N, Manfroni G, Barreca ML, Cecchetti V. A Comprehensive Structural Overview of p38α MAPK in Complex with Type I Inhibitors. ChemMedChem 2015; 10:957-69. [PMID: 26012502 DOI: 10.1002/cmdc.201500030] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2015] [Revised: 03/05/2015] [Indexed: 12/12/2022]
Abstract
p38α mitogen-activated protein kinase (MAPK) is a well-recognized therapeutic target for the treatment of autoimmune and inflammatory diseases. Over the past two decades, tremendous efforts have been focused on the discovery and development of small-molecule p38α MAPK inhibitors, although currently no drugs targeting this protein are clinically available. Therefore, the identification of novel chemotypes that are able to inhibit p38α MAPK function is still of great therapeutic significance. With the objective to support drug discovery programs aimed at identifying new immunomodulators acting on p38α MAPK, herein we present a complete overview of the available crystal structures of this protein in complex with ATP-site type I inhibitors. The 85 available complexes are classified by chemotype and experimental binding mode, and the ligand-protein interactions are discussed using the most representative inhibitors. The type and frequency of key inhibitor features are analyzed to give a final summary of the chemical requirements of promising p38α MAPK inhibitors. The proposed pharmacophore can be exploited to enhance the opportunities to identify novel type I inhibitors of p38α MAPK.
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Affiliation(s)
- Andrea Astolfi
- Department of Pharmaceutical Sciences, University of Perugia, Via A. Fabretti 48, 06123 Perugia (Italy)
| | - Nunzio Iraci
- Department of Pharmaceutical Sciences, University of Perugia, Via A. Fabretti 48, 06123 Perugia (Italy)
| | - Giuseppe Manfroni
- Department of Pharmaceutical Sciences, University of Perugia, Via A. Fabretti 48, 06123 Perugia (Italy)
| | - Maria Letizia Barreca
- Department of Pharmaceutical Sciences, University of Perugia, Via A. Fabretti 48, 06123 Perugia (Italy).
| | - Violetta Cecchetti
- Department of Pharmaceutical Sciences, University of Perugia, Via A. Fabretti 48, 06123 Perugia (Italy)
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Sabatini S, Manfroni G, Barreca ML, Bauer SM, Gargaro M, Cannalire R, Astolfi A, Brea J, Vacca C, Pirro M, Massari S, Tabarrini O, Loza MI, Fallarino F, Laufer SA, Cecchetti V. The Pyrazolobenzothiazine Core as a New Chemotype of p38 Alpha Mitogen-Activated Protein Kinase Inhibitors. Chem Biol Drug Des 2015; 86:531-45. [DOI: 10.1111/cbdd.12516] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2014] [Revised: 12/19/2014] [Accepted: 01/05/2015] [Indexed: 12/23/2022]
Affiliation(s)
- Stefano Sabatini
- Department of Pharmaceutical Sciences; University of Perugia; Via A. Fabretti, 48 06123 Perugia Italy
| | - Giuseppe Manfroni
- Department of Pharmaceutical Sciences; University of Perugia; Via A. Fabretti, 48 06123 Perugia Italy
| | - Maria Letizia Barreca
- Department of Pharmaceutical Sciences; University of Perugia; Via A. Fabretti, 48 06123 Perugia Italy
| | - Silke M. Bauer
- Department of Pharmaceutical & Medicinal Chemistry; Institute of Pharmacy; Eberhard-Karls University Tuebingen; Auf der Morgenstelle 8 72076 Tuebingen Germany
| | - Marco Gargaro
- Department of Experimental Medicine; University of Perugia; Piazzale Gambuli 06100 Perugia Italy
| | - Rolando Cannalire
- Department of Pharmaceutical Sciences; University of Perugia; Via A. Fabretti, 48 06123 Perugia Italy
| | - Andrea Astolfi
- Department of Pharmaceutical Sciences; University of Perugia; Via A. Fabretti, 48 06123 Perugia Italy
| | - Jose Brea
- CIMUS Research Center; University of Santiago de Compostela; Avda de Barcelona s/n, Planta 3. Despacho 1 15782 Santiago de Compostela Spain
| | - Carmine Vacca
- Department of Experimental Medicine; University of Perugia; Piazzale Gambuli 06100 Perugia Italy
| | - Matteo Pirro
- Department of Medicine; University of Perugia; Piazzale Gambuli 06100 Perugia Italy
| | - Serena Massari
- Department of Pharmaceutical Sciences; University of Perugia; Via A. Fabretti, 48 06123 Perugia Italy
| | - Oriana Tabarrini
- Department of Pharmaceutical Sciences; University of Perugia; Via A. Fabretti, 48 06123 Perugia Italy
| | - Maria Isabel Loza
- CIMUS Research Center; University of Santiago de Compostela; Avda de Barcelona s/n, Planta 3. Despacho 1 15782 Santiago de Compostela Spain
| | - Francesca Fallarino
- Department of Experimental Medicine; University of Perugia; Piazzale Gambuli 06100 Perugia Italy
| | - Stefan A. Laufer
- Department of Pharmaceutical & Medicinal Chemistry; Institute of Pharmacy; Eberhard-Karls University Tuebingen; Auf der Morgenstelle 8 72076 Tuebingen Germany
| | - Violetta Cecchetti
- Department of Pharmaceutical Sciences; University of Perugia; Via A. Fabretti, 48 06123 Perugia Italy
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30
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p38δ MAPK: Emerging Roles of a Neglected Isoform. Int J Cell Biol 2014; 2014:272689. [PMID: 25313309 PMCID: PMC4182853 DOI: 10.1155/2014/272689] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2014] [Revised: 08/29/2014] [Accepted: 08/31/2014] [Indexed: 12/19/2022] Open
Abstract
p38δ mitogen activated protein kinase (MAPK) is a unique stress responsive protein kinase. While the p38 MAPK family as a whole has been implicated in a wide variety of biological processes, a specific role for p38δ MAPK in cellular signalling and its contribution to both physiological and pathological conditions are presently lacking. Recent emerging evidence, however, provides some insights into specific p38δ MAPK signalling. Importantly, these studies have helped to highlight functional similarities as well as differences between p38δ MAPK and the other members of the p38 MAPK family of kinases. In this review we discuss the current understanding of the molecular mechanisms underlying p38δ MAPK activity. We outline a role for p38δ MAPK in important cellular processes such as differentiation and apoptosis as well as pathological conditions such as neurodegenerative disorders, diabetes, and inflammatory disease. Interestingly, disparate roles for p38δ MAPK in tumour development have also recently been reported. Thus, we consider evidence which characterises p38δ MAPK as both a tumour promoter and a tumour suppressor. In summary, while our knowledge of p38δ MAPK has progressed somewhat since its identification in 1997, our understanding of this particular isoform in many cellular processes still strikingly lags behind that of its counterparts.
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Cao H, Zang KK, Han M, Zhao ZQ, Wu GC, Zhang YQ. Inhibition of p38 mitogen-activated protein kinase activation in the rostral anterior cingulate cortex attenuates pain-related negative emotion in rats. Brain Res Bull 2014; 107:79-88. [PMID: 25038392 DOI: 10.1016/j.brainresbull.2014.06.005] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2014] [Revised: 06/19/2014] [Accepted: 06/25/2014] [Indexed: 01/12/2023]
Abstract
The emotional components of pain are far less studied than the sensory components. Previous studies have indicated that the rostral anterior cingulate cortex (rACC) is implicated in the affective response to noxious stimuli. Activation of p38 mitogen-activated protein kinase (MAPK) in the spinal cord has been documented to play an important role in diverse kinds of pathological pain states. We used formalin-induced conditioned place aversion (F-CPA) in rats, an animal model believed to reflect the emotional response to pain, to investigate the involvement of p38 MAPK in the rACC after the induction of affective pain. Intraplantar formalin injection produced a significant activation of p38 MAPK, as well as mitogen-activated kinase kinase (MKK) 3 and MKK6, its upstream activators, in the bilateral rACC. p38 MAPK was elevated in both NeuN-positive neurons and Iba1-positive microglia in the rACC, but not GFAP-positive cells. Blocking p38 MAPK activation in the bilateral rACC using its specific inhibitor SB203580 or SB239063 dose-dependently suppressed the formation of F-CPA. Inhibiting p38 MAPK activation did not affect formalin-induced two-phase spontaneous nociceptive response and low intensity electric foot-shock induced CPA. The present study demonstrated that p38 MAPK signaling pathway in the rACC contributes to pain-related negative emotion. Thus, a new pharmacological strategy targeted at the p38 MAPK cascade may be useful in treating pain-related emotional disorders.
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Affiliation(s)
- Hong Cao
- Institute of Neurobiology, Institute of Brain Science and State Key Laboratory of Medical Neurobiology, Shanghai Medical College, Fudan University, Shanghai 200032, China.
| | - Kai-Kai Zang
- Institute of Neurobiology, Institute of Brain Science and State Key Laboratory of Medical Neurobiology, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Mei Han
- Institute of Neurobiology, Institute of Brain Science and State Key Laboratory of Medical Neurobiology, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Zhi-Qi Zhao
- Institute of Neurobiology, Institute of Brain Science and State Key Laboratory of Medical Neurobiology, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Gen-Cheng Wu
- Department of Integrative Medicine and Neurobiology, Institutes of Brain Research, State Key Laboratory of Medical Neurobiology, Fudan University, Shanghai 200032, China
| | - Yu-Qiu Zhang
- Institute of Neurobiology, Institute of Brain Science and State Key Laboratory of Medical Neurobiology, Shanghai Medical College, Fudan University, Shanghai 200032, China
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32
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Brown KM, Suvorova E, Farrell A, McLain A, Dittmar A, Wiley GB, Marth G, Gaffney PM, Gubbels MJ, White M, Blader IJ. Forward genetic screening identifies a small molecule that blocks Toxoplasma gondii growth by inhibiting both host- and parasite-encoded kinases. PLoS Pathog 2014; 10:e1004180. [PMID: 24945800 PMCID: PMC4055737 DOI: 10.1371/journal.ppat.1004180] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2013] [Accepted: 04/28/2014] [Indexed: 02/02/2023] Open
Abstract
The simultaneous targeting of host and pathogen processes represents an untapped approach for the treatment of intracellular infections. Hypoxia-inducible factor-1 (HIF-1) is a host cell transcription factor that is activated by and required for the growth of the intracellular protozoan parasite Toxoplasma gondii at physiological oxygen levels. Parasite activation of HIF-1 is blocked by inhibiting the family of closely related Activin-Like Kinase (ALK) host cell receptors ALK4, ALK5, and ALK7, which was determined in part by use of an ALK4,5,7 inhibitor named SB505124. Besides inhibiting HIF-1 activation, SB505124 also potently blocks parasite replication under normoxic conditions. To determine whether SB505124 inhibition of parasite growth was exclusively due to inhibition of ALK4,5,7 or because the drug inhibited a second kinase, SB505124-resistant parasites were isolated by chemical mutagenesis. Whole-genome sequencing of these mutants revealed mutations in the Toxoplasma MAP kinase, TgMAPK1. Allelic replacement of mutant TgMAPK1 alleles into wild-type parasites was sufficient to confer SB505124 resistance. SB505124 independently impacts TgMAPK1 and ALK4,5,7 signaling since drug resistant parasites could not activate HIF-1 in the presence of SB505124 or grow in HIF-1 deficient cells. In addition, TgMAPK1 kinase activity is inhibited by SB505124. Finally, mice treated with SB505124 had significantly lower tissue burdens following Toxoplasma infection. These data therefore identify SB505124 as a novel small molecule inhibitor that acts by inhibiting two distinct targets, host HIF-1 and TgMAPK1. Understanding how a compound blocks growth of an intracellular pathogen is important not only for developing these compounds into drugs that can be prescribed to patients, but also because these data will likely provide novel insight into the biology of these pathogens. Forward genetic screens are one established approach towards defining these mechanisms. But performing these screens with intracellular parasites has been limited not only because of technical limitations but also because the compounds may have off-target effects in either the host or parasite. Here, we report the first compound that kills a pathogen by simultaneously inhibiting distinct host- and parasite-encoded targets. Because developing drug resistance simultaneously to two targets is less likely, this work may highlight a new approach to antimicrobial drug discovery.
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Affiliation(s)
- Kevin M Brown
- Department of Microbiology and Immunology, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma, United States of America
| | - Elena Suvorova
- Departments of Molecular Medicine & Global Health, University of South Florida, Tampa, Florida, United States of America
| | - Andrew Farrell
- Department of Biology, Boston College, Chestnut Hill, Massachusetts, United States of America
| | - Aaron McLain
- Department of Microbiology and Immunology, University at Buffalo, Buffalo, New York, United States of America
| | - Ashley Dittmar
- Department of Microbiology and Immunology, University at Buffalo, Buffalo, New York, United States of America
| | - Graham B Wiley
- Arthritis and Clinical Immunology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, Oklahoma, United States of America
| | - Gabor Marth
- Department of Biology, Boston College, Chestnut Hill, Massachusetts, United States of America
| | - Patrick M Gaffney
- Arthritis and Clinical Immunology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, Oklahoma, United States of America
| | - Marc Jan Gubbels
- Department of Biology, Boston College, Chestnut Hill, Massachusetts, United States of America
| | - Michael White
- Departments of Molecular Medicine & Global Health, University of South Florida, Tampa, Florida, United States of America
| | - Ira J Blader
- Department of Microbiology and Immunology, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma, United States of America; Department of Microbiology and Immunology, University at Buffalo, Buffalo, New York, United States of America
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Shi H, Ruan L, Yan X, Yao D, Xu X. The role of Litopenaeus vannamei p38 in white spot syndrome virus infection. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2014; 44:180-185. [PMID: 24361691 DOI: 10.1016/j.dci.2013.12.005] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2013] [Revised: 11/29/2013] [Accepted: 12/02/2013] [Indexed: 06/03/2023]
Abstract
p38 as a member of MAPK family, has been conversed from yeast to mammals. It has been implicated in numerous biological processes, including the responses to stress and inflammation. In this study, three closely related p38 MAPK homologs, lvp38a, lvp38b and lvp38c, which differ only in an internal 25-amino acid sequence, have been cloned from Litopenaeus vannamei. Three isoforms shared p38 conserved TGY motif and catalytic center, as well as had maximum identities to human p38α and Drosophila p38b. Tissue distribution revealed that lvp38a and lvp38b were ubiquitously expressed in most tissues, while lvp38c showed at relatively low levels and in a tissue-specific manner. Western blotting analysis showed that lvp38 was activated by phosphorylation during WSSV infection. Furthermore, silencing lvp38 mediated by specific dsRNA in shrimps promoted white spot syndrome virus (WSSV) replication and viral gene transcription at the early stage. These results demonstrated that lvp38 was involved in WSSV infection and might participate in host defense at the early stage.
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Affiliation(s)
- Hong Shi
- Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography, State Oceanic Administration (SOA), No. 178 Daxue Road, Xiamen 361005, PR China.
| | - Lingwei Ruan
- Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography, State Oceanic Administration (SOA), No. 178 Daxue Road, Xiamen 361005, PR China
| | - Xinfu Yan
- Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography, State Oceanic Administration (SOA), No. 178 Daxue Road, Xiamen 361005, PR China
| | - Defu Yao
- Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography, State Oceanic Administration (SOA), No. 178 Daxue Road, Xiamen 361005, PR China; School of Life Science, Xiamen University, Xiamen 361005, PR China
| | - Xun Xu
- Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography, State Oceanic Administration (SOA), No. 178 Daxue Road, Xiamen 361005, PR China
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Baur B, Storch K, Martz KE, Goettert MI, Richters A, Rauh D, Laufer SA. Metabolically stable dibenzo[b,e]oxepin-11(6H)-ones as highly selective p38 MAP kinase inhibitors: optimizing anti-cytokine activity in human whole blood. J Med Chem 2013; 56:8561-78. [PMID: 24131218 DOI: 10.1021/jm401276h] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Five series of metabolically stable disubstituted dibenzo[b,e]oxepin-11(6H)-ones were synthesized and tested in a p38α enzyme assay for their inhibition of tumor necrosis factor-α (TNF-α) release in human whole blood. Compared to the monosubstituted dibenzo[b,e]oxepin-11(6H)-one derivatives, it has been shown that the additional introduction of hydrophilic residues at position 9 leads to a substantial improvement of the inhibitory potency and metabolic stability. Using protein X-ray crystallography, the binding mode of the disubstituted dibenzoxepinones and the induction of a glyince flip in the hinge region were confirmed. The most potent compound of this series, 32e, shows an outstanding biological activity on isolated p38α, with an IC50 value of 1.6 nM, extraordinary selectivity (by a factor >1000, Kinase WholePanelProfiler), and low ATP competitiveness. The ability to inhibit the release of TNF-α from human whole blood was optimized down to an IC50 value of 125 nM. With the promising dibenzoxepinone inhibitor 3i, a pharmacokinetic study in mice was conducted.
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Affiliation(s)
- Benjamin Baur
- Institute of Pharmacy , Department of Pharmaceutical and Medicinal Chemistry, Eberhard-Karls-University Tübingen , Auf der Morgenstelle 8, 72076 Tübingen, Germany
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He S, Qian Z, Yang J, Wang X, Mi X, Liu Y, Hou F, Liu Q, Liu X. Molecular characterization of a p38 MAPK from Litopenaeus vannamei and its expression during the molt cycle and following pathogen infection. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2013; 41:217-221. [PMID: 23707783 DOI: 10.1016/j.dci.2013.05.010] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2013] [Revised: 05/14/2013] [Accepted: 05/15/2013] [Indexed: 06/02/2023]
Abstract
The p38 mitogen-activated protein kinase (MAPK), a serine/threonine-specific protein kinase, has been reported to be involved in innate immunity, development and muscle differentiation. To explore the function of p38 in shrimp, partial cDNA sequence of p38 in Litopenaeus vannamei (designated as Lv-p38) was characterized and the expression of Lv-p38 in hepatopancreas of the shrimp after being infected with Vibrio parahaemolyticus and in muscle of the shrimp at different molt stages was detected by quantitative RT-PCR in this study. The results showed that the open reading frame of Lv-p38 was 1098 bp and encoded a protein of 365 amino acids. The protein of Lv-p38 which showed close phylogenetic relationship to Marsupenaeus japonicus p38 had a conserved TGY motif and serine/threonine protein kinase (S_TKc) domain. The expression of Lv-p38 was detected in all tested tissues, especially in the hepatopancreas and muscle. The expression of Lv-p38 in the hepatopancreas was different from that of the control at the 24th hour after the injection of V. parahaemolyticus and in the muscle significantly increased at stage C but decreased at other stages during molt, illustrating that Lv-p38 could be involved in pathogen infection and the molt cycle of shrimp. In conclusion, we identified Lv-p38 and studied its role in pathogen infection and molting, which might facilitate our understanding of the function of p38 in innate immunity and growth during molt of shrimp.
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Affiliation(s)
- Shulin He
- College of Animal Science and Technology, Northwest A&F University, Shaanxi Key Laboratory of Molecular Biology for Agriculture, Yangling, Shaanxi 712100, China
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Zhu S, Travis SM, Elcock AH. Accurate calculation of mutational effects on the thermodynamics of inhibitor binding to p38α MAP kinase: a combined computational and experimental study. J Chem Theory Comput 2013; 9:3151-3164. [PMID: 23914145 PMCID: PMC3731164 DOI: 10.1021/ct400104x] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
A major current challenge for drug design efforts focused on protein kinases is the development of drug resistance caused by spontaneous mutations in the kinase catalytic domain. The ubiquity of this problem means that it would be advantageous to develop fast, effective computational methods that could be used to determine the effects of potential resistance-causing mutations before they arise in a clinical setting. With this long-term goal in mind, we have conducted a combined experimental and computational study of the thermodynamic effects of active-site mutations on a well-characterized and high-affinity interaction between a protein kinase and a small-molecule inhibitor. Specifically, we developed a fluorescence-based assay to measure the binding free energy of the small-molecule inhibitor, SB203580, to the p38α MAP kinase and used it measure the inhibitor's affinity for five different kinase mutants involving two residues (Val38 and Ala51) that contact the inhibitor in the crystal structure of the inhibitor-kinase complex. We then conducted long, explicit-solvent thermodynamic integration (TI) simulations in an attempt to reproduce the experimental relative binding affinities of the inhibitor for the five mutants; in total, a combined simulation time of 18.5 μs was obtained. Two widely used force fields - OPLS-AA/L and Amber ff99SB-ILDN - were tested in the TI simulations. Both force fields produced excellent agreement with experiment for three of the five mutants; simulations performed with the OPLS-AA/L force field, however, produced qualitatively incorrect results for the constructs that contained an A51V mutation. Interestingly, the discrepancies with the OPLS-AA/L force field could be rectified by the imposition of position restraints on the atoms of the protein backbone and the inhibitor without destroying the agreement for other mutations; the ability to reproduce experiment depended, however, upon the strength of the restraints' force constant. Imposition of position restraints in corresponding simulations that used the Amber ff99SB-ILDN force field had little effect on their ability to match experiment. Overall, the study shows that both force fields can work well for predicting the effects of active-site mutations on small molecule binding affinities and demonstrates how a direct combination of experiment and computation can be a powerful strategy for developing an understanding of protein-inhibitor interactions.
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Affiliation(s)
- Shun Zhu
- Department of Biochemistry, University of Iowa, Iowa City, IA 52242
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Gill K, Singh AK, Kapoor V, Nigam L, Kumar R, Holla P, Das SN, Yadav S, Subbarao N, Mohanti BK, Dey S. Development of peptide inhibitor as a therapeutic agent against head and neck squamous cell carcinoma (HNSCC) targeting p38alpha MAP kinase. Biochim Biophys Acta Gen Subj 2013; 1830:2763-9. [PMID: 23238519 DOI: 10.1016/j.bbagen.2012.12.001] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2012] [Revised: 11/17/2012] [Accepted: 12/03/2012] [Indexed: 12/28/2022]
Abstract
BACKGROUND The p38alpha MAP kinase pathway is involved in inflammation, cell differentiation, growth, apoptosis and production of pro-inflammatory cytokines TNF-alpha and IL-1beta. The overproduction of these cytokines plays an important role in cancer. The aim of this work was to design a peptide inhibitor on the basis of structural information of the active site of p38alpha. METHODS A tetrapeptide, VWCS as p38alpha inhibitor was designed on the basis of structural information of the ATP binding site by molecular modeling. The inhibition study of peptide with p38alpha was performed by ELISA, binding study by Surface Plasmon Resonance and anti-proliferative assays by MTT and flow cytometry. RESULTS The percentage inhibition of designed VWCS against pure p38alpha protein and serum of HNSCC patients was 70.30 and 71.5%, respectively. The biochemical assay demonstrated the K(D) and IC50 of the selective peptide as 7.22 x 10(-9) M and 20.08 nM, respectively. The VWCS as inhibitor significantly reduced viability of oral cancer KB cell line with an IC50 value of 10 microM and induced apoptosis by activating Caspase 3 and 7. CONCLUSIONS VWCS efficiently interacted at the ATP binding pocket of p38alpha with high potency and can be used as a potent inhibitor in case of HNSCC. GENERAL SIGNIFICANCE VWCS can act as an anticancer agent as it potentially inhibits the cell growth and induces apoptosis in oral cancer cell-line in a dose as well as time dependent manner. Hence, p38alpha MAP kinase inhibitor can be a potential therapeutic agent for human oral cancer.
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Affiliation(s)
- Kamaldeep Gill
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi, India
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Lozano-Núñez A, Ikeda KN, Sauer T, de Graffenried CL. An analogue-sensitive approach identifies basal body rotation and flagellum attachment zone elongation as key functions of PLK in Trypanosoma brucei. Mol Biol Cell 2013; 24:1321-33. [PMID: 23447704 PMCID: PMC3639044 DOI: 10.1091/mbc.e12-12-0846] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
The Polo-like kinase homologue in Trypanosoma brucei (TbPLK) regulates the assembly of a series of organelles necessary for positioning the parasite's flagellum. An analogue-sensitive strategy is used to acutely and specifically inhibit the kinase with a small molecule, making it possible to identify novel TbPLK functions. Polo-like kinases are important regulators of cell division, playing diverse roles in mitosis and cytoskeletal inheritance. In the parasite Trypanosoma brucei, the single PLK homologue TbPLK is necessary for the assembly of a series of essential organelles that position and adhere the flagellum to the cell surface. Previous work relied on RNA interference or inhibitors of undefined specificity to inhibit TbPLK, both of which have significant experimental limitations. Here we use an analogue-sensitive approach to selectively and acutely inhibit TbPLK. T. brucei cells expressing only analogue-sensitive TbPLK (TbPLKas) grow normally, but upon treatment with inhibitor develop defects in flagellar attachment and cytokinesis. TbPLK cannot migrate effectively when inhibited and remains trapped in the posterior of the cell throughout the cell cycle. Using synchronized cells, we show that active TbPLK is a direct requirement for the assembly and extension of the flagellum attachment zone, which adheres the flagellum to the cell surface, and for the rotation of the duplicated basal bodies, which positions the new flagellum so that it can extend without impinging on the old flagellum. This approach should be applicable to the many kinases found in the T. brucei genome that lack an ascribed function.
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Affiliation(s)
- Ana Lozano-Núñez
- Max F. Perutz Laboratories, Center for Molecular Biology, University of Vienna, 1030 Vienna, Austria
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Ngoei KRW, Ng DCH, Gooley PR, Fairlie DP, Stoermer MJ, Bogoyevitch MA. Identification and characterization of bi-thiazole-2,2'-diamines as kinase inhibitory scaffolds. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2013; 1834:1077-88. [PMID: 23410953 DOI: 10.1016/j.bbapap.2013.02.001] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2012] [Revised: 01/30/2013] [Accepted: 02/03/2013] [Indexed: 11/18/2022]
Abstract
Based on bioinformatics interrogation of the genome, >500 mammalian protein kinases can be clustered within seven different groups. Of these kinases, the mitogen-activated protein kinase (MAPK) family forms part of the CMGC group of serine/threonine kinases that includes extracellular signal regulated kinases (ERKs), cJun N-terminal kinases (JNKs), and p38 MAPKs. With the JNKs considered attractive targets in the treatment of pathologies including diabetes and stroke, efforts have been directed to the discovery of new JNK inhibitory molecules that can be further developed as new therapeutics. Capitalizing on our biochemical understanding of JNK, we performed in silico screens of commercially available chemical databases to identify JNK1-interacting compounds and tested their in vitro JNK inhibitory activity. With in vitro and cell culture studies, we showed that the compound, 4'-methyl-N(2)-3-pyridinyl-4,5'-bi-1,3-thiazole-2,2'-diamine (JNK Docking (JD) compound 123, but not the related compound (4'-methyl-N~2~-(6-methyl-2-pyridinyl)-4,5'-bi-1,3-thiazole-2,2'-diamine (JD124), inhibited JNK1 activity towards a range of substrates. Molecular docking, saturation transfer difference NMR experiments and enzyme kinetic analyses revealed both ATP- and substrate-competitive inhibition of JNK by JD123. In characterizing JD123 further, we noted its ATP-competitive inhibition of the related p38-γ MAPK, but not ERK1, ERK2, or p38-α, p38-β or p38-δ. Further screening of a broad panel of kinases using 10μM JD123, identified inhibition of kinases including protein kinase Bβ (PKBβ/Aktβ). Appropriately modified thiazole diamines, as typified by JD123, thus provide a new chemical scaffold for development of inhibitors for the JNK and p38-γ MAPKs as well as other kinases that are also potential therapeutic targets such as PKBβ/Aktβ.
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Affiliation(s)
- Kevin R W Ngoei
- Department of Biochemistry and Molecular Biology, University of Melbourne, Victoria, Australia
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40
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Dimova D, Iyer P, Vogt M, Totzke F, Kubbutat MHG, Schächtele C, Laufer S, Bajorath J. Assessing the Target Differentiation Potential of Imidazole-Based Protein Kinase Inhibitors. J Med Chem 2012; 55:11067-71. [DOI: 10.1021/jm3014508] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Affiliation(s)
- Dilyana Dimova
- Department of Life Science Informatics,
B-IT, LIMES Program Unit Chemical Biology and Medicinal Chemistry, Rheinische Friedrich-Wilhelms-Universität, Dahlmannstrasse
2, D-53113 Bonn, Germany
| | - Preeti Iyer
- Department of Life Science Informatics,
B-IT, LIMES Program Unit Chemical Biology and Medicinal Chemistry, Rheinische Friedrich-Wilhelms-Universität, Dahlmannstrasse
2, D-53113 Bonn, Germany
| | - Martin Vogt
- Department of Life Science Informatics,
B-IT, LIMES Program Unit Chemical Biology and Medicinal Chemistry, Rheinische Friedrich-Wilhelms-Universität, Dahlmannstrasse
2, D-53113 Bonn, Germany
| | - Frank Totzke
- ProQinase GmbH, Breisacher Strasse 117, D-79106 Freiburg, Germany
| | | | | | - Stefan Laufer
- Department of Pharmacy and Biochemistry,
Pharmaceutical/Medicinal Chemistry, Eberhard-Karls-Universität Tübingen, Auf der Morgenstelle 8, D-72076 Tübingen,
Germany
| | - Jürgen Bajorath
- Department of Life Science Informatics,
B-IT, LIMES Program Unit Chemical Biology and Medicinal Chemistry, Rheinische Friedrich-Wilhelms-Universität, Dahlmannstrasse
2, D-53113 Bonn, Germany
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41
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He LS, Xu Y, Matsumura K, Zhang Y, Zhang G, Qi SH, Qian PY. Evidence for the involvement of p38 MAPK activation in barnacle larval settlement. PLoS One 2012; 7:e47195. [PMID: 23115639 PMCID: PMC3480373 DOI: 10.1371/journal.pone.0047195] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2012] [Accepted: 09/12/2012] [Indexed: 11/27/2022] Open
Abstract
The barnacle Balanus ( = Amphibalanus) amphitrite is a major marine fouling animal. Understanding the molecular mechanism of larval settlement in this species is critical for anti-fouling research. In this study, we cloned one isoform of p38 MAPK (Bar-p38 MAPK) from this species, which shares the significant characteristic of containing a TGY motif with other species such as yeast, Drosophila and humans. The activation of p38 MAPK was detected by an antibody that recognizes the conserved dual phosphorylation sites of TGY. The results showed that phospho-p38 MAPK (pp38 MAPK) was more highly expressed at the cyprid stage, particularly in aged cyprids, in comparison to other stages, including the nauplius and juvenile stages. Immunostaining showed that Bar-p38 MAPK and pp38 MAPK were mainly located at the cyprid antennules, and especially the third and fourth segments, which are responsible for substratum exploration during settlement. The expression and localization patterns of Bar-p38 MAPK suggest its involvement in larval settlement. This postulation was also supported by the larval settlement bioassay with the p38 MAPK inhibitor SB203580. Behavioral analysis by live imaging revealed that the larvae were still capable of exploring the surface of the substratum after SB203580 treatment. This shows that the effect of p38 MAPK on larval settlement might be by regulating the secretion of permanent proteinaceous substances. Furthermore, the level of pp38 MAPK dramatically decreased after full settlement, suggesting that Bar-p38 MAPK maybe plays a role in larval settlement rather than metamorphosis. Finally, we found that Bar-p38 MAPK was highly activated when larvae confronted extracts of adult barnacle containing settlement cues, whereas larvae pre-treated with SB203580 failed to respond to the crude adult extracts.
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Affiliation(s)
- Li-Sheng He
- KAUST Global Collaborative Research Program, Division of Life Science, Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong SAR, China
| | - Ying Xu
- KAUST Global Collaborative Research Program, Division of Life Science, Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong SAR, China
| | - Kiyotaka Matsumura
- KAUST Global Collaborative Research Program, Division of Life Science, Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong SAR, China
| | - Yu Zhang
- KAUST Global Collaborative Research Program, Division of Life Science, Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong SAR, China
| | - Gen Zhang
- KAUST Global Collaborative Research Program, Division of Life Science, Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong SAR, China
| | - Shu-Hua Qi
- South China Sea Institute of Oceanography, Chinese Academy of Science, Guangzhou, China
| | - Pei-Yuan Qian
- KAUST Global Collaborative Research Program, Division of Life Science, Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong SAR, China
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42
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Tzarum N, Eisenberg-Domovich Y, Gills JJ, Dennis PA, Livnah O. Lipid molecules induce p38α activation via a novel molecular switch. J Mol Biol 2012; 424:339-53. [PMID: 23079240 DOI: 10.1016/j.jmb.2012.10.007] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2012] [Revised: 10/05/2012] [Accepted: 10/09/2012] [Indexed: 11/19/2022]
Abstract
p38α mitogen-activated protein kinase (MAPK) is generally activated by dual phosphorylation but has also been shown to exhibit alternative activation modes. One of these modes included a direct interaction with phosphatidylinositol ether lipid analogues (PIA) inducing p38α autoactivation and apoptosis. Perifosine, an Akt inhibitor in phase II clinical trials, also showed p38α activation properties similarly to those of PIAs. The crystal structures of p38α in complex with PIA23, PIA24 and perifosine provide insights into this unique activation mode. The activating molecules bind a unique hydrophobic binding site in the kinase C'-lobe formed in part by the MAPK insert region. In addition, there are conformational changes in the short αEF/αF loop region that acts as an activation switch, inducing autophosphorylation. Structural and biochemical characterization of the αEF/αF loop identified Trp197 as a key residue in the lipid binding and in p38α catalytic activity. The lipid binding site also accommodates hydrophobic inhibitor molecules and, thus, can serve as a novel p38α-target for specific activation or inhibition, with novel therapeutic implications.
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Affiliation(s)
- Netanel Tzarum
- Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences and The Wolfson Centre for Applied Structural Biology, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
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43
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He J, Liu Z, Zheng Y, Qian J, Li H, Lu Y, Xu J, Hong B, Zhang M, Lin P, Cai Z, Orlowski RZ, Kwak LW, Yi Q, Yang J. p38 MAPK in myeloma cells regulates osteoclast and osteoblast activity and induces bone destruction. Cancer Res 2012; 72:6393-402. [PMID: 23066034 DOI: 10.1158/0008-5472.can-12-2664] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
p38 mitogen-activated protein kinase (MAPK), which is constitutively activated in human myeloma, has been implicated in bone destruction by this cancer, but the processes it recruits are obscure. In this study, we show that p38 activity in myeloma inhibits osteoblast differentiation and bone formation, but also enhances osteoclast maturation and bone resorption. p38 regulated the expression and secretion of the Wnt pathway antagonist DKK-1 and the monocyte chemoattractant MCP-1. Attenuating p38, DKK-1, or MCP-1 were each sufficient to reduce bone lesions in vivo. Although it is well known that DKK-1 inhibits osteoblast differentiation, we found that together with MCP-1, it could also promote osteoclast differentiation and bone resorption. The latter effects were mediated by enhancing expression of RANK in osteoclast progenitor cells and by upregulating secretion of its ligand RANKL from stromal cells and mature osteoblasts. In summary, our study defined the mechanisms by which p38 signaling in myeloma cells regulates osteoblastogenesis, osteoclastogenesis, and bone destruction. Our findings, which may have implications for bone invasion by other cancers where p38 is elevated, strongly suggests that targeting p38 for inhibition may offer an effective therapeutic approach to treat osteolytic bone lesions in patients with myeloma.
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Affiliation(s)
- Jin He
- Department of Lymphoma/Myeloma, Division of Cancer Medicine and Center for Cancer Immunology Research, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
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44
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Songtawee N, Gleeson MP, Choowongkomon K. Computational study of EGFR inhibition: molecular dynamics studies on the active and inactive protein conformations. J Mol Model 2012; 19:497-509. [PMID: 22955422 DOI: 10.1007/s00894-012-1559-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2011] [Accepted: 08/02/2012] [Indexed: 10/27/2022]
Abstract
The structural diversity observed across protein kinases, resulting in subtly different active site cavities, is highly desirable in the pursuit of selective inhibitors, yet it can also be a hindrance from a structure-based design perspective. An important challenge in structure-based design is to better understand the dynamic nature of protein kinases and the underlying reasons for specific conformational preferences in the presence of different inhibitors. To investigate this issue, we performed molecular dynamics simulation on both the active and inactive wild type epidermal growth factor receptor (EGFR) protein with both type-I and type-II inhibitors. Our goal is to better understand the origin of the two distinct EGFR protein conformations, their dynamic differences, and their relative preference for Type-I inhibitors such as gefitinib and Type-II inhibitors such as lapatinib. We discuss the implications of protein dynamics from a structure-based design perspective.
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Affiliation(s)
- Napat Songtawee
- Department of Biochemistry, Faculty of Science, Kasetsart University, 50 Phaholyothin Rd, Chatuchak, Bangkok, 10900, Thailand
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45
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Azevedo R, van Zeeland M, Raaijmakers H, Kazemier B, de Vlieg J, Oubrie A. X-ray structure of p38α bound to TAK-715: comparison with three classic inhibitors. ACTA CRYSTALLOGRAPHICA SECTION D: BIOLOGICAL CRYSTALLOGRAPHY 2012; 68:1041-50. [PMID: 22868770 DOI: 10.1107/s090744491201997x] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2012] [Accepted: 05/03/2012] [Indexed: 11/11/2022]
Abstract
The p38α mitogen-activated protein kinase regulates the synthesis of pro-inflammatory cytokines in response to stimulation by a diverse set of stress signals. Various different chemotypes and clinical candidates that inhibit p38α function have been reported over the years. In this publication, the novel structure of p38α cocrystallized with the clinical candidate TAK-715 is reported. Owing to the impact of crystallization conditions on the conformation of protein kinases (and in particular p38α), the structures of complexes of p38α with SB-203580, SCIO-469 and VX-745 have also been determined to enable in-depth comparison of ligand-induced protein conformations. The impact of experimental conditions on p38α-inhibitor complex structures, most importantly soaking versus cocrystallization, is discussed. Analysis of the structures and quantification of the protein-ligand interactions couples ligand-induced protein conformations to the number of interactions and to inhibitor selectivity against the human kinome. This shows that for the design of novel kinase inhibitors, selectivity is best obtained through maximization of the number of interactions throughout the ATP pocket and the exploitation of specific features in the active site.
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Affiliation(s)
- Rita Azevedo
- Merck Research Laboratories, MSD, PO Box 20, 5340 BH Oss, The Netherlands
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46
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Randhawa V, Bagler G. Identification of SRC as a potent drug target for asthma, using an integrative approach of protein interactome analysis and in silico drug discovery. OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY 2012; 16:513-26. [PMID: 22775150 DOI: 10.1089/omi.2011.0160] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Network-biology inspired modeling of interactome data and computational chemistry have the potential to revolutionize drug discovery by complementing conventional methods. We consider asthma, a complex disease characterized by intricate molecular mechanisms, for our study. We aim to integrate prediction of potent drug targets using graph-theoretical methods and subsequent identification of small molecules capable of modulating activity of the best target. In this work, we construct the protein interactome underlying this disease: Asthma Protein Interactome (API). Using a strategy based on network analysis of the interactome, we identify a set of potential drug targets for asthma. Topologically and dynamically, v-src sarcoma (Schmidt-Ruppin A-2) viral oncogene homolog (SRC) emerges as the most central target in API. SRC is known to play an important role in promoting airway smooth muscle cell growth and facilitating migration in airway remodeling. From interactome analysis, and with the reported role in respiratory mechanisms, SRC emerges as a promising drug target for asthma. Further, we proceed to identify leads for SRC from a public database of small molecules. We predict two potential leads for SRC using ligand-based virtual screening methodology.
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Affiliation(s)
- Vinay Randhawa
- Biotechnology Division, Institute of Himalayan Bioresource Technology, Council of Scientific and Industrial Research (CSIR-IHBT), Palampur, India
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47
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Getlik M, Simard JR, Termathe M, Grütter C, Rabiller M, van Otterlo WAL, Rauh D. Fluorophore labeled kinase detects ligands that bind within the MAPK insert of p38α kinase. PLoS One 2012; 7:e39713. [PMID: 22768308 PMCID: PMC3388095 DOI: 10.1371/journal.pone.0039713] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2012] [Accepted: 05/25/2012] [Indexed: 11/19/2022] Open
Abstract
The vast majority of small molecules known to modulate kinase activity, target the highly conserved ATP-pocket. Consequently, such ligands are often less specific and in case of inhibitors, this leads to the inhibition of multiple kinases. Thus, selective modulation of kinase function remains a major hurdle. One of the next great challenges in kinase research is the identification of ligands which bind to less conserved sites and target the non-catalytic functions of protein kinases. However, approaches that allow for the unambiguous identification of molecules that bind to these less conserved sites are few in number. We have previously reported the use of fluorescent labels in kinases (FLiK) to develop direct kinase binding assays that exclusively detect ligands which stabilize inactive (DFG-out) kinase conformations. Here, we present the successful application of the FLiK approach to develop a high-throughput binding assay capable of directly monitoring ligand binding to a remote site within the MAPK insert of p38α mitogen-activated protein kinase (MAPK). Guided by the crystal structure of an initially identified hit molecule in complex with p38α, we developed a tight binding ligand which may serve as an ideal starting point for further investigations of the biological function of the MAPK insert in regulating the p38α signaling pathway.
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Affiliation(s)
- Matthäus Getlik
- Chemical Genomics Centre of the Max Planck Society, Dortmund, Germany
- Max-Planck-Institute of Molecular Physiology, Dortmund, Germany
| | - Jeffrey R. Simard
- Chemical Genomics Centre of the Max Planck Society, Dortmund, Germany
- Max-Planck-Institute of Molecular Physiology, Dortmund, Germany
| | - Martin Termathe
- Chemical Genomics Centre of the Max Planck Society, Dortmund, Germany
- Max-Planck-Institute of Molecular Physiology, Dortmund, Germany
| | - Christian Grütter
- Chemical Genomics Centre of the Max Planck Society, Dortmund, Germany
- Fakultät Chemie, Chemische Biologie, Technische Universität Dortmund, Dortmund, Germany
- Max-Planck-Institute of Molecular Physiology, Dortmund, Germany
| | - Matthias Rabiller
- Chemical Genomics Centre of the Max Planck Society, Dortmund, Germany
- Max-Planck-Institute of Molecular Physiology, Dortmund, Germany
| | - Willem A. L. van Otterlo
- Department of Chemistry and Polymer Sciences, Stellenbosch University, Stellenbosch, South Africa
| | - Daniel Rauh
- Chemical Genomics Centre of the Max Planck Society, Dortmund, Germany
- Fakultät Chemie, Chemische Biologie, Technische Universität Dortmund, Dortmund, Germany
- Max-Planck-Institute of Molecular Physiology, Dortmund, Germany
- * E-mail:
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48
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Vinh NB, Simpson JS, Scammells PJ, Chalmers DK. Virtual screening using a conformationally flexible target protein: models for ligand binding to p38α MAPK. J Comput Aided Mol Des 2012; 26:409-23. [PMID: 22527960 DOI: 10.1007/s10822-012-9569-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2011] [Accepted: 03/26/2012] [Indexed: 12/25/2022]
Abstract
We have used virtual screening to develop models for the binding of aryl substituted heterocycles to p38α MAPK. Virtual screening was conducted on a number of p38α MAPK crystal structures using a library of 46 known p38α MAPK inhibitors containing a heterocyclic core substituted by pyridine and fluorophenyl rings (structurally related to SB203580) and a set of decoy compounds. Multiple protonation states and tautomers of active and decoy compounds were considered. Each docking model was evaluated using receiver operating characteristic (ROC) curves and enrichment factors. The two best performing single crystal structures were found to be 1BL7 and 2EWA, with enrichment factors of 14.1 and 13.0 at 2% of the virtual screen respectively. Ensembles of up to four receptors of similar conformations were generated, generally giving good or very good performances with high ROC AUCs and good enrichment. The 1BL7-2EWA ensemble was able to outperform each of its constituent receptors and gave high enrichment factors of 17.3, 12.0, 8.0 at 2, 5 and 10% respectively, of the virtual screen. A ROC AUC of 0.94 was obtained for this ensemble. This method may be applied to other proteins where there are a large number of inhibitor classes with different binding site conformations.
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Affiliation(s)
- Natalie B Vinh
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University (Parkville Campus), 381 Royal Parade, Parkville, VIC, 3052, Australia
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49
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Mouchlis VD, Melagraki G, Mavromoustakos T, Kollias G, Afantitis A. Molecular Modeling on Pyrimidine-Urea Inhibitors of TNF-α Production: An Integrated Approach Using a Combination of Molecular Docking, Classification Techniques, and 3D-QSAR CoMSIA. J Chem Inf Model 2012; 52:711-23. [DOI: 10.1021/ci200579f] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
| | - Georgia Melagraki
- Department
of Chemoinformatics, NovaMechanics, Ltd., Nicosia, Cyprus
| | - Thomas Mavromoustakos
- Laboratory
of Organic Chemistry,
Department of Chemistry, University of Athens, Athens 15771, Greece
| | - George Kollias
- Institute
of Immunology, Biomedical Sciences Research Center “Alexander Fleming”, Athens, Greece
| | - Antreas Afantitis
- Department
of Chemoinformatics, NovaMechanics, Ltd., Nicosia, Cyprus
- Institute
of Immunology, Biomedical Sciences Research Center “Alexander Fleming”, Athens, Greece
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50
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Swarbrick ME. The Learning and Evolution of Medicinal Chemistry against Kinase Targets. KINASE DRUG DISCOVERY 2011. [DOI: 10.1039/9781849733557-00079] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
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