1
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Shendy NAM, Bikowitz M, Sigua LH, Zhang Y, Mercier A, Khashana Y, Nance S, Liu Q, Delahunty IM, Robinson S, Goel V, Rees MG, Ronan MA, Wang T, Kocak M, Roth JA, Wang Y, Freeman BB, Orr BA, Abraham BJ, Roussel MF, Schonbrunn E, Qi J, Durbin AD. Group 3 medulloblastoma transcriptional networks collapse under domain specific EP300/CBP inhibition. Nat Commun 2024; 15:3483. [PMID: 38664416 PMCID: PMC11045757 DOI: 10.1038/s41467-024-47102-0] [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: 06/05/2023] [Accepted: 03/14/2024] [Indexed: 04/28/2024] Open
Abstract
Chemical discovery efforts commonly target individual protein domains. Many proteins, including the EP300/CBP histone acetyltransferases (HATs), contain several targetable domains. EP300/CBP are critical gene-regulatory targets in cancer, with existing high potency inhibitors of either the catalytic HAT domain or protein-binding bromodomain (BRD). A domain-specific inhibitory approach to multidomain-containing proteins may identify exceptional-responding tumor types, thereby expanding a therapeutic index. Here, we discover that targeting EP300/CBP using the domain-specific inhibitors, A485 (HAT) or CCS1477 (BRD) have different effects in select tumor types. Group 3 medulloblastoma (G3MB) cells are especially sensitive to BRD, compared with HAT inhibition. Structurally, these effects are mediated by the difluorophenyl group in the catalytic core of CCS1477. Mechanistically, bromodomain inhibition causes rapid disruption of genetic dependency networks that are required for G3MB growth. These studies provide a domain-specific structural foundation for drug discovery efforts targeting EP300/CBP and identify a selective role for the EP300/CBP bromodomain in maintaining genetic dependency networks in G3MB.
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Affiliation(s)
- Noha A M Shendy
- Division of Molecular Oncology, Department of Oncology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Melissa Bikowitz
- Drug Discovery Department, Moffitt Cancer Center, Tampa, FL, USA
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL, USA
| | - Logan H Sigua
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Yang Zhang
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Audrey Mercier
- Tumor Cell Biology Department, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Yousef Khashana
- Division of Molecular Oncology, Department of Oncology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Stephanie Nance
- Division of Molecular Oncology, Department of Oncology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Qi Liu
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Ian M Delahunty
- Division of Molecular Oncology, Department of Oncology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Sarah Robinson
- Tumor Cell Biology Department, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Vanshita Goel
- Tumor Cell Biology Department, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Matthew G Rees
- The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | | | - Tingjian Wang
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Mustafa Kocak
- The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | | | - Yingzhe Wang
- Preclinical Pharmacokinetics Shared Resource, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Burgess B Freeman
- Preclinical Pharmacokinetics Shared Resource, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Brent A Orr
- Department of Pathology, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Brian J Abraham
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Martine F Roussel
- Tumor Cell Biology Department, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Ernst Schonbrunn
- Drug Discovery Department, Moffitt Cancer Center, Tampa, FL, USA.
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL, USA.
| | - Jun Qi
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA.
- Department of Medicine, Harvard Medical School, Boston, MA, USA.
| | - Adam D Durbin
- Division of Molecular Oncology, Department of Oncology, St. Jude Children's Research Hospital, Memphis, TN, USA.
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2
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Sato N, Suetaka S, Hayashi Y, Arai M. Rational peptide design for inhibition of the KIX-MLL interaction. Sci Rep 2023; 13:6330. [PMID: 37072438 PMCID: PMC10113271 DOI: 10.1038/s41598-023-32848-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Accepted: 04/03/2023] [Indexed: 05/03/2023] Open
Abstract
The kinase-inducible domain interacting (KIX) domain is an integral part of the general transcriptional coactivator CREB-binding protein, and has been associated with leukemia, cancer, and various viral diseases. Hence, the KIX domain has attracted considerable attention in drug discovery and development. Here, we rationally designed a KIX inhibitor using a peptide fragment corresponding to the transactivation domain (TAD) of the transcriptional activator, mixed-lineage leukemia protein (MLL). We performed theoretical saturation mutagenesis using the Rosetta software to search for mutants expected to bind KIX more tightly than the wild-type MLL TAD. Mutant peptides with higher helical propensities were selected for experimental characterization. We found that the T2857W mutant of the MLL TAD peptide had the highest binding affinity for KIX compared to the other 12 peptides designed in this study. Moreover, the peptide had a high inhibitory effect on the KIX-MLL interaction with a half-maximal inhibitory concentration close to the dissociation constant for this interaction. To our knowledge, this peptide has the highest affinity for KIX among all previously reported inhibitors that target the MLL site of KIX. Thus, our approach may be useful for rationally developing helical peptides that inhibit protein-protein interactions implicated in the progression of various diseases.
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Affiliation(s)
- Nao Sato
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, 3-8-1 Komaba, Meguro, Tokyo, 153-8902, Japan
| | - Shunji Suetaka
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, 3-8-1 Komaba, Meguro, Tokyo, 153-8902, Japan
| | - Yuuki Hayashi
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, 3-8-1 Komaba, Meguro, Tokyo, 153-8902, Japan
- Environmental Science Center, The University of Tokyo, 7-3-1 Hongo, Bunkyo, Tokyo, 113-0033, Japan
| | - Munehito Arai
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, 3-8-1 Komaba, Meguro, Tokyo, 153-8902, Japan.
- Department of Physics, Graduate School of Science, The University of Tokyo, 3-8-1 Komaba, Meguro, Tokyo, 153-8902, Japan.
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3
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Rooklin D, Modell AE, Li H, Berdan V, Arora PS, Zhang Y. Targeting Unoccupied Surfaces on Protein-Protein Interfaces. J Am Chem Soc 2017; 139:15560-15563. [PMID: 28759230 DOI: 10.1021/jacs.7b05960] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
The use of peptidomimetic scaffolds to target protein-protein interfaces is a promising strategy for inhibitor design. The strategy relies on mimicry of protein motifs that exhibit a concentration of native hot spot residues. To address this constraint, we present a pocket-centric computational design strategy guided by AlphaSpace to identify high-quality pockets near the peptidomimetic motif that are both targetable and unoccupied. Alpha-clusters serve as a spatial representation of pocket space and are used to guide the selection of natural and non-natural amino acid mutations to design inhibitors that optimize pocket occupation across the interface. We tested the strategy against a challenging protein-protein interaction target, KIX/MLL, by optimizing a single helical motif within MLL to compete against the full-length wild-type MLL sequence. Molecular dynamics simulation and experimental fluorescence polarization assays are used to verify the efficacy of the optimized peptide sequence.
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Affiliation(s)
- David Rooklin
- Department of Chemistry, New York University , New York, New York 10003, United States
| | - Ashley E Modell
- Department of Chemistry, New York University , New York, New York 10003, United States
| | - Haotian Li
- Department of Chemistry, New York University , New York, New York 10003, United States
| | - Viktoriya Berdan
- Department of Chemistry, New York University , New York, New York 10003, United States
| | - Paramjit S Arora
- Department of Chemistry, New York University , New York, New York 10003, United States
| | - Yingkai Zhang
- Department of Chemistry, New York University , New York, New York 10003, United States.,NYU-ECNU Center for Computational Chemistry, New York University-Shanghai , Shanghai 200122, China
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4
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Berthet M, Cheviet T, Dujardin G, Parrot I, Martinez J. Isoxazolidine: A Privileged Scaffold for Organic and Medicinal Chemistry. Chem Rev 2016; 116:15235-15283. [PMID: 27981833 DOI: 10.1021/acs.chemrev.6b00543] [Citation(s) in RCA: 171] [Impact Index Per Article: 21.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
The isoxazolidine ring represents one of the privileged structures in medicinal chemistry, and there have been an increasing number of studies on isoxazolidine and isoxazolidine-containing compounds. Optimization of the 1,3-dipolar cycloaddition (1,3-DC), original methods including electrophilic or palladium-mediated cyclization of unsaturated hydroxylamine, has been developed to obtain isoxazolidines. Novel reactions involving the isoxazolidine ring have been highlighted to accomplish total synthesis or to obtain bioactive compounds, one of the most significant examples being probably the thermic ring contraction applied to the total synthesis of (±)-Gelsemoxonine. The unique isoxazolidine scaffold also exhibits an impressive potential as a mimic of nucleosides, carbohydrates, PNA, amino acids, and steroid analogs. This review aims to be a comprehensive and general summary of the different isoxazolidine syntheses, their use as starting building blocks for the preparation of natural compounds, and their main biological activities.
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Affiliation(s)
- Mathéo Berthet
- Institut des Biomolécules Max Mousseron , IBMM UMR-5247 CNRS, Université de Montpellier, ENSCM, CC17-03, Pl. E. Bataillon, 34095 Montpellier Cedex 5, France
| | - Thomas Cheviet
- Institut des Biomolécules Max Mousseron , IBMM UMR-5247 CNRS, Université de Montpellier, ENSCM, CC17-03, Pl. E. Bataillon, 34095 Montpellier Cedex 5, France
| | - Gilles Dujardin
- Institut des Molécules et Matériaux du Mans , IMMM UMR 6283 CNRS, Université du Maine, UFR Sciences et Techniques, Avenue Olivier Messiaen, 72085 Le Mans, France
| | - Isabelle Parrot
- Institut des Biomolécules Max Mousseron , IBMM UMR-5247 CNRS, Université de Montpellier, ENSCM, CC17-03, Pl. E. Bataillon, 34095 Montpellier Cedex 5, France
| | - Jean Martinez
- Institut des Biomolécules Max Mousseron , IBMM UMR-5247 CNRS, Université de Montpellier, ENSCM, CC17-03, Pl. E. Bataillon, 34095 Montpellier Cedex 5, France
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5
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Piskacek M, Havelka M, Rezacova M, Knight A. The 9aaTAD Transactivation Domains: From Gal4 to p53. PLoS One 2016; 11:e0162842. [PMID: 27618436 PMCID: PMC5019370 DOI: 10.1371/journal.pone.0162842] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2016] [Accepted: 08/29/2016] [Indexed: 12/30/2022] Open
Abstract
The family of the Nine amino acid Transactivation Domain, 9aaTAD family, comprises currently over 40 members. The 9aaTAD domains are universally recognized by the transcriptional machinery from yeast to man. We had identified the 9aaTAD domains in the p53, Msn2, Pdr1 and B42 activators by our prediction algorithm. In this study, their competence to activate transcription as small peptides was proven. Not surprisingly, we elicited immense 9aaTAD divergence in hundreds of identified orthologs and numerous examples of the 9aaTAD species' convergence. We found unforeseen similarity of the mammalian p53 with yeast Gal4 9aaTAD domains. Furthermore, we identified artificial 9aaTAD domains generated accidentally by others. From an evolutionary perspective, the observed easiness to generate 9aaTAD transactivation domains indicates the natural advantage for spontaneous generation of transcription factors from DNA binding precursors.
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Affiliation(s)
- Martin Piskacek
- Laboratory of Cancer Biology and Genetics, Department of Pathological Physiology, Faculty of Medicine, Masaryk University Brno, Kamenice 5, 625 00, Brno, Czech Republic
| | - Marek Havelka
- Laboratory of Cancer Biology and Genetics, Department of Pathological Physiology, Faculty of Medicine, Masaryk University Brno, Kamenice 5, 625 00, Brno, Czech Republic
| | - Martina Rezacova
- Laboratory of Cancer Biology and Genetics, Department of Pathological Physiology, Faculty of Medicine, Masaryk University Brno, Kamenice 5, 625 00, Brno, Czech Republic
| | - Andrea Knight
- Gamma Delta T Cell Laboratory, Department of Pathological Physiology, Faculty of Medicine, Masaryk University Brno, Kamenice 5, 625 00, Brno, Czech Republic
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6
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Larsen MJ, Larsen SD, Fribley A, Grembecka J, Homan K, Mapp A, Haak A, Nikolovska-Coleska Z, Stuckey JA, Sun D, Sherman DH. The role of HTS in drug discovery at the University of Michigan. Comb Chem High Throughput Screen 2015; 17:210-30. [PMID: 24409957 DOI: 10.2174/1386207317666140109121546] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2013] [Revised: 11/05/2013] [Accepted: 01/07/2014] [Indexed: 12/17/2022]
Abstract
High throughput screening (HTS) is an integral part of a highly collaborative approach to drug discovery at the University of Michigan. The HTS lab is one of four core centers that provide services to identify, produce, screen and follow-up on biomedical targets for faculty. Key features of this system are: protein cloning and purification, protein crystallography, small molecule and siRNA HTS, medicinal chemistry and pharmacokinetics. Therapeutic areas that have been targeted include anti-bacterial, metabolic, neurodegenerative, cardiovascular, anti-cancer and anti-viral. The centers work in a coordinated, interactive environment to affordably provide academic investigators with the technology, informatics and expertise necessary for successful drug discovery. This review provides an overview of these centers at the University of Michigan, along with case examples of successful collaborations with faculty.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | - David H Sherman
- Center for Chemical Genomics, Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109, USA.
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7
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Cecioni S, Aouadi K, Guiard J, Parrot S, Strazielle N, Blondel S, Ghersi-Egea JF, Chapelle C, Denoroy L, Praly JP. Novel routes to either racemic or enantiopure α-amino-(4-hydroxy-pyrrolidin-3-yl)acetic acid derivatives and biological evaluation of a new promising pharmacological scaffold. Eur J Med Chem 2015; 98:237-49. [PMID: 26043161 DOI: 10.1016/j.ejmech.2015.05.017] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2015] [Revised: 04/23/2015] [Accepted: 05/11/2015] [Indexed: 12/20/2022]
Abstract
Cycloaddition between (+) or (-)-menthone-derived nitrones and N-benzyl-3-pyrroline afforded enantiopure spiro-fused heterocycles. The reaction occurred enantio- and diastereo-selectively on the less hindered side of the nitrone, the 3-pyrroline N-benzyl group being oriented outwards, thus controlling the configurations of three simultaneously created chiral centers. From either (+) or (-)-menthone, both enantiomeric cycloadducts were synthesized in excellent yield. Removing the chiral auxiliary and the N-benzyl group delivered a series of enantiopure 4-hydroxy-3-glycinyl-pyrrolidine derivatives in 3-5 steps and 36 to 81 overall yields. Using two other achiral nitrones, shorter routes to racemic analogues were developed. Two of the synthesized compounds markedly lowered extracellular glutamate level and modestly interacted with cannabinoid type-1 receptors. As these two neuroactive compounds were devoid of in vitro toxicity and did not cross the blood brain interface, they might represent potential pharmacological agents to target peripheral organs.
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Affiliation(s)
- Samy Cecioni
- CNRS UMR 5246, Université Lyon1, Institut de Chimie et Biochimie Moléculaires et Supramoléculaires (ICBMS), F-69622 Villeurbanne, France
| | - Kaïss Aouadi
- CNRS UMR 5246, Université Lyon1, Institut de Chimie et Biochimie Moléculaires et Supramoléculaires (ICBMS), F-69622 Villeurbanne, France
| | - Julie Guiard
- CNRS UMR 5246, Université Lyon1, Institut de Chimie et Biochimie Moléculaires et Supramoléculaires (ICBMS), F-69622 Villeurbanne, France
| | - Sandrine Parrot
- INSERM U1028, CNRS UMR5292, Université Lyon 1, Lyon Neuroscience Research Center, NeuroDialyTics Unit, Lyon F-69000, France
| | - Nathalie Strazielle
- INSERM U1028, CNRS UMR5292, Université Lyon 1, Lyon Neuroscience Research Center, Blood Brain Interfaces Exploratory Platform BIP, Lyon F-69000, France
| | - Sandrine Blondel
- INSERM U1028, CNRS UMR5292, Université Lyon 1, Lyon Neuroscience Research Center, Blood Brain Interfaces Exploratory Platform BIP, Lyon F-69000, France
| | - Jean-François Ghersi-Egea
- INSERM U1028, CNRS UMR5292, Université Lyon 1, Lyon Neuroscience Research Center, Blood Brain Interfaces Exploratory Platform BIP, Lyon F-69000, France
| | | | - Luc Denoroy
- INSERM U1028, CNRS UMR5292, Université Lyon 1, Lyon Neuroscience Research Center, NeuroDialyTics Unit, Lyon F-69000, France; INSERM U1028, CNRS UMR5292, Université Lyon 1, Lyon Neuroscience Research Center, BioRaN, Lyon F-69000, France.
| | - Jean-Pierre Praly
- CNRS UMR 5246, Université Lyon1, Institut de Chimie et Biochimie Moléculaires et Supramoléculaires (ICBMS), F-69622 Villeurbanne, France
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8
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Affiliation(s)
| | - Philip A. Cole
- Department
of Pharmacology
and Molecular Sciences, The Johns Hopkins
University School of Medicine, 725 North Wolfe Street, Hunterian 316, Baltimore, Maryland 21205, United States
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9
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Abstract
The kinase-inducible domain interacting (KIX) domain of the CREB binding protein (CBP) is capable of simultaneously binding two intrinsically disordered transcription factors, such as the mixed-lineage leukemia (MLL) and c-Myb peptides, at isolated interaction sites. In vitro, the affinity for binding c-Myb is approximately doubled when KIX is in complex with MLL, which suggests a positive cooperative binding mechanism, and the affinity for MLL is also slightly increased when KIX is first bound by c-Myb. Expanding the scope of recent NMR and computational studies, we explore the allosteric mechanism at a detailed molecular level that directly connects the microscopic structural dynamics to the macroscopic shift in binding affinities. To this end, we have performed molecular dynamics simulations of free KIX, KIX-c-Myb, MLL-KIX, and MLL-KIX-c-Myb using a topology-based Gō-like model. Our results capture an increase in affinity for the peptide in the allosteric site when KIX is prebound by a complementary effector and both peptides follow an effector-independent folding-and-binding mechanism. More importantly, we discover that MLL binding lowers the entropic cost for c-Myb binding, and vice versa, by stabilizing the L12-G2 loop and the C-terminal region of the α3 helix on KIX. This work demonstrates the importance of entropy in allosteric signaling between promiscuous molecular recognition sites and can inform the rational design of small molecule stabilizers to target important regions of conformationally dynamic proteins.
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10
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Sequence and expression analyses of KIX domain proteins suggest their importance in seed development and determination of seed size in rice, and genome stability in Arabidopsis. Mol Genet Genomics 2013; 288:329-46. [PMID: 23756993 DOI: 10.1007/s00438-013-0753-9] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2012] [Accepted: 05/17/2013] [Indexed: 12/26/2022]
Abstract
The KIX domain, which mediates protein-protein interactions, was first discovered as a motif in the large multidomain transcriptional activator histone acetyltransferase p300/CBP. Later, the domain was also found in Mediator subunit MED15, where it interacts with many transcription factors. In both proteins, the KIX domain is a target of activation domains of diverse transcription activators. It was found to be an essential component of several specific gene-activation pathways in fungi and metazoans. Not much is known about KIX domain proteins in plants. This study aims to characterize all the KIX domain proteins encoded by the genomes of Arabidopsis and rice. All identified KIX domain proteins are presented, together with their chromosomal locations, phylogenetic analysis, expression and SNP analyses. KIX domains were found not only in p300/CBP- and MED15-like plant proteins, but also in F-box proteins in rice and DNA helicase in Arabidopsis, suggesting roles of KIX domains in ubiquitin-mediated proteasomal degradation and genome stability. Expression analysis revealed overlapping expression of OsKIX_3, OsKIX_5 and OsKIX_7 in different stages of rice seeds development. Moreover, an association analysis of 136 in silico mined SNP loci in 23 different rice genotypes with grain-length information identified three non-synonymous SNP loci in these three rice genes showing strong association with long- and short-grain differentiation. Interestingly, these SNPs were located within KIX domain encoding sequences. Overall, this study lays a foundation for functional analysis of KIX domain proteins in plants.
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11
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Majmudar CY, Højfeldt JW, Arevang CJ, Pomerantz WC, Gagnon JK, Schultz PJ, Cesa LC, Doss CH, Rowe SP, Vásquez V, Tamayo-Castillo G, Cierpicki T, Brooks CL, Sherman DH, Mapp AK. Sekikaic Acid and Lobaric Acid Target a Dynamic Interface of the Coactivator CBP/p300. Angew Chem Int Ed Engl 2012. [DOI: 10.1002/ange.201206815] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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12
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Majmudar CY, Højfeldt JW, Arevang CJ, Pomerantz WC, Gagnon JK, Schultz PJ, Cesa LC, Doss CH, Rowe SP, Vásquez V, Tamayo-Castillo G, Cierpicki T, Brooks CL, Sherman DH, Mapp AK. Sekikaic acid and lobaric acid target a dynamic interface of the coactivator CBP/p300. Angew Chem Int Ed Engl 2012; 51:11258-62. [PMID: 23042634 DOI: 10.1002/anie.201206815] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2012] [Indexed: 12/25/2022]
Abstract
Capturing a coactivator, naturally: the natural products sekikaic acid and lobaric acid, isolated after a high-throughput screen of a structurally diverse extract collection, effectively target the dynamic binding interfaces of the GACKIX domain of the coactivator CBP/p300. These molecules are the most effective inhibitors of the GACKIX domain yet described and are uniquely selective for this domain.
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13
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Abstract
E-proteins are critical transcription factors in B-cell lymphopoiesis. E2A, 1 of 3 E-protein-encoding genes, is implicated in the induction of acute lymphoblastic leukemia through its involvement in the chromosomal translocation 1;19 and consequent expression of the E2A-PBX1 oncoprotein. An interaction involving a region within the N-terminal transcriptional activation domain of E2A-PBX1, termed the PCET motif, which has previously been implicated in E-protein silencing, and the KIX domain of the transcriptional coactivator CBP/p300, critical for leukemogenesis. However, the structural details of this interaction remain unknown. Here we report the structure of a 1:1 complex between PCET motif peptide and the KIX domain. Residues throughout the helical PCET motif that contact the KIX domain are important for both binding KIX and bone marrow immortalization by E2A-PBX1. These results provide molecular insights into E-protein-driven differentiation of B-cells and the mechanism of E-protein silencing, and reveal the PCET/KIX interaction as a therapeutic target for E2A-PBX1-induced leukemia.
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14
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Pomerantz WC, Wang N, Lipinski AK, Wang R, Cierpicki T, Mapp AK. Profiling the dynamic interfaces of fluorinated transcription complexes for ligand discovery and characterization. ACS Chem Biol 2012; 7:1345-50. [PMID: 22725662 DOI: 10.1021/cb3002733] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
The conformationally dynamic binding surfaces of transcription complexes present a particular challenge for ligand discovery and characterization. In the case of the KIX domain of the master coactivator CBP/p300, few small molecules have been reported that target its two allosterically regulated binding sites despite the important roles that KIX plays in processes ranging from memory formation to hematopoiesis. Taking advantage of the enrichment of aromatic amino acids at protein interfaces, here we show that the incorporation of six (19)F-labeled aromatic side chains within the KIX domain enables recapitulation of the differential binding footprints of three natural activator peptides (MLL, c-Myb, and pKID) in complex with KIX and effectively reports on allosteric changes upon binding using 1D NMR spectroscopy. Additionally, the examination of both the previously described KIX protein-protein interaction inhibitor Napthol-ASE-phosphate and newly discovered ligand 1-10 rapidly revealed both the binding sites and the affinities of these small molecules. Significantly, the utility of using fluorinated transcription factors for ligand discovery was demonstrated through a fragment screen leading to a new low molecular weight fragment ligand for CBP/p300, 1G7. Aromatic amino acids are enriched at protein-biomolecule interfaces; therefore, this quantitative and facile approach will be broadly useful for studying dynamic transcription complexes and screening campaigns complementing existing biophysical methods for studying these dynamic interfaces.
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Affiliation(s)
- William C. Pomerantz
- Department of Chemistry, ‡Program in Chemical
Biology and §Department of Pathology, University of Michigan, Ann Arbor Michigan 48109, United States
| | - Ningkun Wang
- Department of Chemistry, ‡Program in Chemical
Biology and §Department of Pathology, University of Michigan, Ann Arbor Michigan 48109, United States
| | - Ashley K. Lipinski
- Department of Chemistry, ‡Program in Chemical
Biology and §Department of Pathology, University of Michigan, Ann Arbor Michigan 48109, United States
| | - Rurun Wang
- Department of Chemistry, ‡Program in Chemical
Biology and §Department of Pathology, University of Michigan, Ann Arbor Michigan 48109, United States
| | - Tomasz Cierpicki
- Department of Chemistry, ‡Program in Chemical
Biology and §Department of Pathology, University of Michigan, Ann Arbor Michigan 48109, United States
| | - Anna K. Mapp
- Department of Chemistry, ‡Program in Chemical
Biology and §Department of Pathology, University of Michigan, Ann Arbor Michigan 48109, United States
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15
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Rajasekar Reddy A, Guo Z, Siu FM, Lok CN, Liu F, Yeung KC, Zhou CY, Che CM. Diastereoselective ruthenium porphyrin-catalyzed tandem nitrone formation/1,3-dipolar cycloaddition for isoxazolidines. Synthesis, in silico docking study and in vitro biological activities. Org Biomol Chem 2012; 10:9165-74. [DOI: 10.1039/c2ob26518d] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
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16
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Lee GM, Shahian T, Baharuddin A, Gable JE, Craik CS. Enzyme inhibition by allosteric capture of an inactive conformation. J Mol Biol 2011; 411:999-1016. [PMID: 21723875 DOI: 10.1016/j.jmb.2011.06.032] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2011] [Revised: 06/15/2011] [Accepted: 06/16/2011] [Indexed: 10/18/2022]
Abstract
All members of the human herpesvirus protease (HHV Pr) family are active as weakly associating dimers but inactive as monomers. A small-molecule allosteric inhibitor of Kaposi's sarcoma-associated herpesvirus protease (KSHV Pr) traps the enzyme in an inactive monomeric state where the C-terminal helices are unfolded and the hydrophobic dimer interface is exposed. NMR titration studies demonstrate that the inhibitor binds to KSHV Pr monomers with low micromolar affinity. A 2.0-Å-resolution X-ray crystal structure of a C-terminal truncated KSHV Pr-inhibitor complex locates the binding pocket at the dimer interface and displays significant conformational perturbations at the active site, 15 Å from the allosteric site. NMR and CD data suggest that the small molecule inhibits human cytomegalovirus protease via a similar mechanism. As all HHV Prs are functionally and structurally homologous, the inhibitor represents a class of compounds that may be developed into broad-spectrum therapeutics that allosterically regulate enzymatic activity by disrupting protein-protein interactions.
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Affiliation(s)
- Gregory M Lee
- Department of Pharmaceutical Chemistry, University of California, San Francisco, CA 94158-2280, USA
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