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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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2
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Perry J, Harris RM, Moiani D, Olson AJ, Tainer J. p38alpha MAP kinase C-terminal domain binding pocket characterized by crystallographic and computational analyses. J Mol Biol 2009; 391:1-11. [PMID: 19501598 PMCID: PMC2724755 DOI: 10.1016/j.jmb.2009.06.005] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2009] [Revised: 05/28/2009] [Accepted: 06/01/2009] [Indexed: 01/07/2023]
Abstract
The mitogen-activated protein (MAP) kinase protein family has a critical role in cellular signaling events, with MAP kinase p38alpha acting in inflammatory processes and being an important drug discovery target. MAP kinase drug design efforts have focused on small-molecule inhibitors of the ATP catalytic site, which exhibit dose-limiting adverse effects. Therefore, characterizing other potential sites that bind substrates, inhibitors, or allosteric effectors is of great interest. Here, we present the crystal structure of human p38alpha MAP kinase, which has a lead compound bound both in the active site and in the lipid-binding site of the C-terminal cap. This C-terminal cap is formed from an extension to the kinase fold, unique to the MAP kinase and cyclin-dependent kinase families and glycogen synthase kinase 3. Binding of this lead, 4-[3-(4-fluorophenyl)-1H-pyrazol-4-yl]pyridine, to wild-type p38alpha induces movement of the C-terminal cap region, creating a hydrophobic pocket centered around residue Trp197. Computational analysis of this C-terminal domain pocket indicates notable flexibility for potentially binding different-shaped compounds, including lipids, oxidized arachidonic acid species such as leukotrienes, and small-molecule effectors. Furthermore, our structural results defining the open p38alpha C-lobe pocket provide a detailed framework for the design of novel small molecules with affinities comparable to active-site binders: to bind and potentially modulate the shape and activity of p38alpha in predetermined ways. Moreover, these results and analyses of p38alpha suggest strategies for designing specific binding compounds applicable to other MAP kinases, as well as the cyclin-dependent kinase family and glycogen synthase kinase 3beta that also utilize the C-terminal insert in their interactions.
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Affiliation(s)
- J.J.P. Perry
- Department of Molecular Biology, The Scripps Research Institute, La Jolla, CA 92037, USA.,The School of Biotechnology, Amrita University, Kollam, Kerala 690525, India
| | - R. M Harris
- Department of Molecular Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - D. Moiani
- Department of Molecular Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - A. J. Olson
- Department of Molecular Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - J.A. Tainer
- Department of Molecular Biology, The Scripps Research Institute, La Jolla, CA 92037, USA.,Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.,Correspondence sent to John A. Tainer, , Tel: (858) 784-8119, Fax: (858) 784-2277
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3
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Bukhtiyarova M, Karpusas M, Northrop K, Namboodiri HVM, Springman EB. Mutagenesis of p38alpha MAP kinase establishes key roles of Phe169 in function and structural dynamics and reveals a novel DFG-OUT state. Biochemistry 2007; 46:5687-96. [PMID: 17441692 DOI: 10.1021/bi0622221] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
In order to study the role of Phe169 in p38alpha MAP kinase structure and function, wild-type p38alpha and five p38alpha DFG motif mutants were examined in vitro for phosphorylation by MKK6, kinase activity toward ATF2 substrate, thermal stability, and X-ray crystal structure. All six p38alpha variants were efficiently phosphorylated by MKK6. However, only one activated p38alpha mutant (F169Y) possessed measurable kinase activity (1% compared to wild-type). The loss of kinase activity among the DFG mutants may result from an inability to correctly position Asp168 in the activated form of p38alpha. Two mutations significantly increased the thermal stability of p38alpha (F169A DeltaTm = 1.3 degrees C and D168G DeltaTm = 3.8 degrees C), and two mutations significantly decreased the stability of p38alpha (F169R DeltaTm = -3.2 degrees C and F169G DeltaTm = -4.7 degrees C). Interestingly, X-ray crystal structures of two thermally destabilized p38alpha-F169R and p38alpha-F169G mutants revealed a DFG-OUT conformation in the absence of an inhibitor molecule. This DFG-OUT conformation, termed alpha-DFG-OUT, is different from the ones previously identified in p38alpha crystal structures with bound inhibitors and postulated from high-temperature molecular dynamics simulations. Taken together, these results indicate that Phe169 is optimized for p38alpha functional activity and structural dynamics, rather than for structural stability. The alpha-DFG-OUT conformation observed for p38alpha-F169R and p38alpha-F169G may represent a naturally occurring intermediate state of p38alpha that provides access for binding of allosteric inhibitors. A model of the local forces driving the DFG IN-OUT transition in p38alpha is proposed.
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Affiliation(s)
- Marina Bukhtiyarova
- Department of Biology, Locus Pharmaceuticals, Inc., Four Valley Square, 512 Township Line Road, Blue Bell, Pennsylvania 19422, USA
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4
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Sabat M, Vanrens JC, Clark MP, Brugel TA, Maier J, Bookland RG, Laufersweiler MJ, Laughlin SK, Golebiowski A, De B, Hsieh LC, Walter RL, Mekel MJ, Janusz MJ. The development of novel C-2, C-8, and N-9 trisubstituted purines as inhibitors of TNF-α production. Bioorg Med Chem Lett 2006; 16:4360-5. [PMID: 16750367 DOI: 10.1016/j.bmcl.2006.05.050] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2006] [Revised: 05/15/2006] [Accepted: 05/16/2006] [Indexed: 10/24/2022]
Abstract
A series of C-2, C-8, and N-9 trisubstituted purine based inhibitors of TNF-alpha production are described. The most potent analogs showed low nanomolar activity against LPS-induced TNF-alpha production in a THP-1 cell based assay. The SAR of the series was optimized with the aid of X-ray co-crystal structures of these inhibitors bound with mutated p38 (mp38).
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Affiliation(s)
- Mark Sabat
- Procter and Gamble Pharmaceuticals, Health Care Research Center, Mason, OH 45040, USA.
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5
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Brugel TA, Maier JA, Clark MP, Sabat M, Golebiowski A, Bookland RG, Laufersweiler MJ, Laughlin SK, Vanrens JC, De B, Hsieh LC, Mekel MJ, Janusz MJ. Development of N-2,4-pyrimidine-N-phenyl-N'-phenyl ureas as inhibitors of tumor necrosis factor alpha (TNF-alpha) synthesis. Part 1. Bioorg Med Chem Lett 2006; 16:3510-3. [PMID: 16632356 DOI: 10.1016/j.bmcl.2006.03.095] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2006] [Revised: 03/27/2006] [Accepted: 03/28/2006] [Indexed: 11/25/2022]
Abstract
A new class of tumor necrosis factor alpha (TNF-alpha) synthesis inhibitors based on an N-2,4-pyrimidine-N-phenyl-N'-phenyl urea scaffold is described. Many of these compounds showed low-nanomolar activity against lipopolysaccharide stimulated TNF-alpha production. X-ray co-crystallization studies with mutated p38alpha showed that these trisubstituted ureas interact with the ATP-binding pocket in a pseudo-bicyclic conformation brought about by the presence of an intramolecular hydrogen bonding interaction.
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Affiliation(s)
- Todd A Brugel
- Procter and Gamble Pharmaceuticals, Health Care Research Center, 8700 Mason-Montgomery Rd., Mason, OH 45040, USA.
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6
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Maier JA, Brugel TA, Clark MP, Sabat M, Golebiowski A, Bookland RG, Laufersweiler MJ, Laughlin SK, Vanrens JC, De B, Hsieh LC, Brown KK, Juergens K, Walter RL, Janusz MJ. Development of N-2,4-pyrimidine-N-phenyl-N'-alkyl ureas as orally active inhibitors of tumor necrosis factor alpha (TNF-alpha) synthesis. Part 2. Bioorg Med Chem Lett 2006; 16:3514-8. [PMID: 16632350 DOI: 10.1016/j.bmcl.2006.03.096] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2006] [Revised: 03/27/2006] [Accepted: 03/28/2006] [Indexed: 10/24/2022]
Abstract
A new class of tumor necrosis factor alpha (TNF-alpha) synthesis inhibitors based on a N-2,4-pyrimidine-N-phenyl-N'-alkyl urea scaffold is described. Many of these compounds showed low-nanomolar activity against lipopolysaccharide stimulated TNF-alpha production. Two analogs were tested in an in vivo rat iodoacetate model of osteoarthritis and shown to be orally efficacious. X-ray co-crystallization studies with mutated p38alpha showed that these trisubstituted ureas interact with the ATP-binding pocket in a pseudo-bicyclic conformation brought about by the presence of an intramolecular hydrogen bonding interaction.
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Affiliation(s)
- Jennifer A Maier
- Procter & Gamble Pharmaceuticals, Health Care Research Center, 8700 Mason-Montgomery Rd., Mason, OH 45040, USA
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7
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Laufersweiler MJ, Brugel TA, Clark MP, Golebiowski A, Bookland RG, Laughlin SK, Sabat MP, Townes JA, VanRens JC, De B, Hsieh LC, Heitmeyer SA, Juergens K, Brown KK, Mekel MJ, Walter RL, Janusz MJ. The development of novel inhibitors of tumor necrosis factor-alpha (TNF-alpha) production based on substituted [5,5]-bicyclic pyrazolones. Bioorg Med Chem Lett 2005; 14:4267-72. [PMID: 15261284 DOI: 10.1016/j.bmcl.2004.06.001] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2004] [Revised: 06/02/2004] [Accepted: 06/02/2004] [Indexed: 11/29/2022]
Abstract
Novel substituted [5,5]-bicyclic pyrzazolones are presented as inhibitors of tumor necrosis factor-alpha (TNF-alpha) production. Many of these compounds show low nanomolar activity against lipopolysaccaride (LPS)-induced TNF-alpha production in THP-1 cells. This class of molecules was co-crystallized with mutated p38, and several analogs showed good oral bioavailability in the rat. Oral activity of these compounds in the rat iodoacetate model for osteoarthritis is discussed.
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Affiliation(s)
- Matthew J Laufersweiler
- Procter and Gamble Pharmaceuticals, Health Care Research Center, 8700 Mason-Montgomery Rd, Mason, OH 45040, USA.
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8
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Abstract
p38 is a mitogen-activated protein (MAP) kinase with structural and functional characteristics that distinguish it from JNK and ERK MAP kinases. p38 activity is upregulated when cells are exposed to a variety of stimuli including bacterial pathogens, proinflammatory cytokines, certain growth factors, and other forms of environmental stress. By regulating downstream substrates that include protein kinases and transcription factors, p38 participates in transmission, amplification, and diversification of the extracellular signal, initiating several different cellular responses. Studies have revealed that activation of p38 pathway is related to many pathological changes that occur in the course of inflammatory/immunologic and cardiovascular diseases.
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Affiliation(s)
- L New
- Department of Immunology, The Scripps Research Institute, La Jolla, California 92037, USA
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9
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Townes JA, Golebiowski A, Clark MP, Laufersweiler MJ, Brugel TA, Sabat M, Bookland RG, Laughlin SK, VanRens JC, De B, Hsieh LC, Xu SC, Janusz MJ, Walter RL. The development of new bicyclic pyrazole-based cytokine synthesis inhibitors. Bioorg Med Chem Lett 2004; 14:4945-8. [PMID: 15341957 DOI: 10.1016/j.bmcl.2004.07.024] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2004] [Revised: 07/12/2004] [Accepted: 07/12/2004] [Indexed: 10/26/2022]
Abstract
4-Aryl-5-pyrimidyl-based cytokine synthesis inhibitors of TNF-alpha production, which contain a novel bicyclic pyrazole heterocyclic core, are described. Many of these inhibitors showed low nanomolar activity against LPS-induced TNF-alpha production in a THP-1 cell-based assay and against human p38 alpha MAP kinase in an isolated enzyme assay. The X-ray crystal structure of a bicyclic pyrazole inhibitor co-crystallized with mutated p38 (mp38) is presented.
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Affiliation(s)
- Jennifer A Townes
- Procter and Gamble Pharmaceuticals, Health Care Research Center, 8700 Mason-Montgomery Rd, Mason, OH 45040, USA.
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10
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Patel SB, Cameron PM, Frantz-Wattley B, O'Neill E, Becker JW, Scapin G. Lattice stabilization and enhanced diffraction in human p38α crystals by protein engineering. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2004; 1696:67-73. [PMID: 14726206 DOI: 10.1016/j.bbapap.2003.09.009] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Mitogen-activated protein (MAP) kinase p38 alpha is activated in response to environmental stress and cytokines, and plays a significant role in inflammatory responses. For these reasons, it is an important target for the treatment of a wide range of inflammatory and autoimmune diseases. The crystals of p38 alpha that we obtained by published procedures were usually small, quite mosaic, and difficult to reproduce and thus posed a difficulty for the intensive high-resolution studies required for a structure-guided drug discovery approach. Based on crystallographic and biochemical evidences, we prepared a single point mutation of a surface cysteine (C162S) and found that it prevents aggregation and improves the homogeneity and stability of the enzyme. This mutation also facilitates the crystallization process and increases the diffracting power of p38 alpha crystals. Surprisingly, we found that the mutation induces a change in the conformation of a nearby surface loop resulting in stronger lattice interactions, consistent with the improved crystal quality. The mutant protein, because of its improved stability and strengthened lattice interactions, thus provides a significantly improved reagent for use in structure-based drug design for this important disease target.
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Affiliation(s)
- Sangita B Patel
- Department of Medicinal Chemistry, Merck Research Laboratory, PO Box 2000 RY50-105, Rahway, NJ 07065, USA
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11
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12
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Abstract
The p38 signalling transduction pathway, a Mitogen-activated protein (MAP) kinase pathway, plays an essential role in regulating many cellular processes including inflammation, cell differentiation, cell growth and death. Activation of p38 often through extracellular stimuli such as bacterial pathogens and cytokines, mediates signal transduction into the nucleus to turn on the responsive genes. p38 also transduces signals to other cellular components to execute different cellular responses. In this review, we summarize the characteristics of the major components of the p38 signalling transduction pathway and highlight the targets of this pathway and the physiological function of the p38 activation.
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Affiliation(s)
- K Ono
- Department of Immunology, The Scripps Research Institute, La Jolla, CA 92037, USA
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Tong L, Pav S, White DM, Rogers S, Crane KM, Cywin CL, Brown ML, Pargellis CA. A highly specific inhibitor of human p38 MAP kinase binds in the ATP pocket. NATURE STRUCTURAL BIOLOGY 1997; 4:311-6. [PMID: 9095200 DOI: 10.1038/nsb0497-311] [Citation(s) in RCA: 324] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
The crystal structure of human p38 mitogen-activated protein (MAP) kinase in complex with a potent and highly specific pyridinyl-imidazole inhibitor has been determined at 2.0 A resolution. The structure of the kinase, which is in its unphosphorylated state, is similar to that of the closely-related ERK2. The inhibitor molecule is bound in the ATP pocket. A hydrogen bond is made between the pyridyl nitrogen of the inhibitor and the main chain amido nitrogen of residue 109, analogous to the interaction from the N1 atom of ATP. The crystal structure provides possible explanations for the specificity of this class of inhibitors. Other protein kinase inhibitors may achieve their specificity through a similar mechanism. The structure also reveals a possible second binding site for this inhibitor, with currently unknown function.
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Affiliation(s)
- L Tong
- Boehringer Ingelheim Pharmaceuticals, Inc., Ridgefield, Connecticut 06877, USA
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