1
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Castellón JO, Ofori S, Burton NR, Julio AR, Turmon AC, Armenta E, Sandoval C, Boatner LM, Takayoshi EE, Faragalla M, Taylor C, Zhou AL, Tran K, Shek J, Yan T, Desai HS, Fregoso OI, Damoiseaux R, Backus KM. Chemoproteomics Identifies State-Dependent and Proteoform-Selective Caspase-2 Inhibitors. J Am Chem Soc 2024; 146:14972-14988. [PMID: 38787738 DOI: 10.1021/jacs.3c12240] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/26/2024]
Abstract
Caspases are a highly conserved family of cysteine-aspartyl proteases known for their essential roles in regulating apoptosis, inflammation, cell differentiation, and proliferation. Complementary to genetic approaches, small-molecule probes have emerged as useful tools for modulating caspase activity. However, due to the high sequence and structure homology of all 12 human caspases, achieving selectivity remains a central challenge for caspase-directed small-molecule inhibitor development efforts. Here, using mass spectrometry-based chemoproteomics, we first identify a highly reactive noncatalytic cysteine that is unique to caspase-2. By combining both gel-based activity-based protein profiling (ABPP) and a tobacco etch virus (TEV) protease activation assay, we then identify covalent lead compounds that react preferentially with this cysteine and afford a complete blockade of caspase-2 activity. Inhibitory activity is restricted to the zymogen or precursor form of monomeric caspase-2. Focused analogue synthesis combined with chemoproteomic target engagement analysis in cellular lysates and in cells yielded both pan-caspase-reactive molecules and caspase-2 selective lead compounds together with a structurally matched inactive control. Application of this focused set of tool compounds to stratify the functions of the zymogen and partially processed (p32) forms of caspase-2 provide evidence to support that caspase-2-mediated response to DNA damage is largely driven by the partially processed p32 form of the enzyme. More broadly, our study highlights future opportunities for the development of proteoform-selective caspase inhibitors that target nonconserved and noncatalytic cysteine residues.
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Affiliation(s)
- José O Castellón
- Biological Chemistry Department, David Geffen School of Medicine, UCLA, Los Angeles, California 90095, United States
| | - Samuel Ofori
- Biological Chemistry Department, David Geffen School of Medicine, UCLA, Los Angeles, California 90095, United States
| | - Nikolas R Burton
- Biological Chemistry Department, David Geffen School of Medicine, UCLA, Los Angeles, California 90095, United States
- Department of Chemistry and Biochemistry, UCLA, Los Angeles, California 90095, United States
| | - Ashley R Julio
- Biological Chemistry Department, David Geffen School of Medicine, UCLA, Los Angeles, California 90095, United States
- Department of Chemistry and Biochemistry, UCLA, Los Angeles, California 90095, United States
| | - Alexandra C Turmon
- Biological Chemistry Department, David Geffen School of Medicine, UCLA, Los Angeles, California 90095, United States
- Department of Chemistry and Biochemistry, UCLA, Los Angeles, California 90095, United States
| | - Ernest Armenta
- Biological Chemistry Department, David Geffen School of Medicine, UCLA, Los Angeles, California 90095, United States
- Department of Chemistry and Biochemistry, UCLA, Los Angeles, California 90095, United States
| | - Carina Sandoval
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, California 90095, United States
| | - Lisa M Boatner
- Biological Chemistry Department, David Geffen School of Medicine, UCLA, Los Angeles, California 90095, United States
- Department of Chemistry and Biochemistry, UCLA, Los Angeles, California 90095, United States
| | - Evan E Takayoshi
- Biological Chemistry Department, David Geffen School of Medicine, UCLA, Los Angeles, California 90095, United States
- Department of Chemistry and Biochemistry, UCLA, Los Angeles, California 90095, United States
| | - Marina Faragalla
- Biological Chemistry Department, David Geffen School of Medicine, UCLA, Los Angeles, California 90095, United States
- Department of Chemistry and Biochemistry, UCLA, Los Angeles, California 90095, United States
| | - Cameron Taylor
- California NanoSystems Institute (CNSI), UCLA, Los Angeles, California 90095, United States
| | - Ann L Zhou
- Biological Chemistry Department, David Geffen School of Medicine, UCLA, Los Angeles, California 90095, United States
- Department of Chemistry and Biochemistry, UCLA, Los Angeles, California 90095, United States
| | - Ky Tran
- Biological Chemistry Department, David Geffen School of Medicine, UCLA, Los Angeles, California 90095, United States
- Department of Chemistry and Biochemistry, UCLA, Los Angeles, California 90095, United States
| | - Jeremy Shek
- Biological Chemistry Department, David Geffen School of Medicine, UCLA, Los Angeles, California 90095, United States
- Department of Chemistry and Biochemistry, UCLA, Los Angeles, California 90095, United States
| | - Tianyang Yan
- Biological Chemistry Department, David Geffen School of Medicine, UCLA, Los Angeles, California 90095, United States
- Department of Chemistry and Biochemistry, UCLA, Los Angeles, California 90095, United States
| | - Heta S Desai
- Biological Chemistry Department, David Geffen School of Medicine, UCLA, Los Angeles, California 90095, United States
| | - Oliver I Fregoso
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, California 90095, United States
| | - Robert Damoiseaux
- Jonsson Comprehensive Cancer Center, UCLA, Los Angeles, California 90095, United States
- Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, UCLA, Los Angeles, California 90095, United States
- California NanoSystems Institute (CNSI), UCLA, Los Angeles, California 90095, United States
- Department of Molecular and Medical Pharmacology, UCLA, Los Angeles, California 90095, United States
- Department of Bioengineering, Samueli School of Engineering, UCLA, Los Angeles, California 90095, United States
| | - Keriann M Backus
- Biological Chemistry Department, David Geffen School of Medicine, UCLA, Los Angeles, California 90095, United States
- Department of Chemistry and Biochemistry, UCLA, Los Angeles, California 90095, United States
- DOE Institute for Genomics and Proteomics, UCLA, Los Angeles, California 90095, United States
- Jonsson Comprehensive Cancer Center, UCLA, Los Angeles, California 90095, United States
- Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, UCLA, Los Angeles, California 90095, United States
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2
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Anderson J, Grillo MJ, Harki DA. Development of Allosteric NIK Ligands from Fragment-Based NMR Screening. ACS Med Chem Lett 2023; 14:1815-1820. [PMID: 38116406 PMCID: PMC10726469 DOI: 10.1021/acsmedchemlett.3c00429] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Revised: 10/24/2023] [Accepted: 10/26/2023] [Indexed: 12/21/2023] Open
Abstract
NF-κB inducing kinase (NIK) is vital for the induction of many immune responses, and as such, NIK dysregulation has been implicated in various inflammatory diseases and cancers. NIK has been pursued as a potential therapeutic target, and small-molecule inhibitors that bind the orthosteric site on NIK have been reported. However, despite the established chemical matter, NIK inhibitors have not yet reached the clinic. With the goal of developing allosteric NIK ligands using a fragment-based NMR screening approach, we report the identification and development of a series of allosteric, fragment-sized NIK ligands that bind with micromolar potency and good ligand efficiency.
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Affiliation(s)
- Jared
J. Anderson
- Department
of Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Michael J. Grillo
- Department
of Medicinal Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Daniel A. Harki
- Department
of Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, United States
- Department
of Medicinal Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, United States
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3
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Di Fruscia P, Edfeldt F, Shamovsky I, Collie GW, Aagaard A, Barlind L, Börjesson U, Hansson EL, Lewis RJ, Nilsson MK, Öster L, Pemberton J, Ripa L, Storer RI, Käck H. Fragment-Based Discovery of Novel Allosteric MEK1 Binders. ACS Med Chem Lett 2021; 12:302-308. [PMID: 33603979 PMCID: PMC7883464 DOI: 10.1021/acsmedchemlett.0c00563] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Accepted: 01/25/2021] [Indexed: 01/02/2023] Open
Abstract
The MEK1 kinase plays a critical role in key cellular processes, and as such, its dysfunction is strongly linked to several human diseases, particularly cancer. MEK1 has consequently received considerable attention as a drug target, and a significant number of small-molecule inhibitors of this kinase have been reported. The majority of these inhibitors target an allosteric pocket proximal to the ATP binding site which has proven to be highly druggable, with four allosteric MEK1 inhibitors approved to date. Despite the significant attention that the MEK1 allosteric site has received, chemotypes which have been shown structurally to bind to this site are limited. With the aim of discovering novel allosteric MEK1 inhibitors using a fragment-based approach, we report here a screening method which resulted in the discovery of multiple allosteric MEK1 binders, one series of which was optimized to sub-μM affinity for MEK1 with promising physicochemical and ADMET properties.
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Affiliation(s)
- Paolo Di Fruscia
- Structure
Biophysics & Fragments, Discovery Sciences, R&D, AstraZeneca, Cambridge CB4 0WG, United Kingdom
| | - Fredrik Edfeldt
- Structure
Biophysics & Fragments, Discovery Sciences, R&D, AstraZeneca, Gothenburg 431 83, Sweden
| | - Igor Shamovsky
- Medicinal
Chemistry, Research & Early Development, Respiratory & Immunology,
BioPharmaceuticals R&D, AstraZeneca, Gothenburg 431 83, Sweden
| | - Gavin W. Collie
- Structure
Biophysics & Fragments, Discovery Sciences, R&D, AstraZeneca, Cambridge CB4 0WG, United Kingdom
| | - Anna Aagaard
- Structure
Biophysics & Fragments, Discovery Sciences, R&D, AstraZeneca, Gothenburg 431 83, Sweden
| | - Louise Barlind
- Discovery
Biology, Discovery Sciences, R&D, AstraZeneca, Gothenburg 431 83, Sweden
| | - Ulf Börjesson
- Structure
Biophysics & Fragments, Discovery Sciences, R&D, AstraZeneca, Gothenburg 431 83, Sweden
| | - Eva L. Hansson
- Mechanistic
Biology and Profiling, Discovery Sciences, R&D, AstraZeneca, Gothenburg 431 83, Sweden
| | - Richard J. Lewis
- Medicinal
Chemistry, Research & Early Development, Respiratory & Immunology,
BioPharmaceuticals R&D, AstraZeneca, Gothenburg 431 83, Sweden
| | - Magnus K. Nilsson
- Medicinal
Chemistry, Research & Early Development, Respiratory & Immunology,
BioPharmaceuticals R&D, AstraZeneca, Gothenburg 431 83, Sweden
| | - Linda Öster
- Structure
Biophysics & Fragments, Discovery Sciences, R&D, AstraZeneca, Gothenburg 431 83, Sweden
| | - Josefine Pemberton
- Structure
Biophysics & Fragments, Discovery Sciences, R&D, AstraZeneca, Gothenburg 431 83, Sweden
| | - Lena Ripa
- Medicinal
Chemistry, Research & Early Development, Respiratory & Immunology,
BioPharmaceuticals R&D, AstraZeneca, Gothenburg 431 83, Sweden
| | - R. Ian Storer
- Structure
Biophysics & Fragments, Discovery Sciences, R&D, AstraZeneca, Cambridge CB4 0WG, United Kingdom
| | - Helena Käck
- Structure
Biophysics & Fragments, Discovery Sciences, R&D, AstraZeneca, Gothenburg 431 83, Sweden
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4
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Synthesis, Characterization, and In Vivo Anti-Cancer Activity of New Metal Complexes Derived from Isatin- N(4)antipyrinethiosemicarbazone Ligand Against Ehrlich Ascites Carcinoma Cells. Molecules 2019; 24:molecules24183313. [PMID: 31514445 PMCID: PMC6766913 DOI: 10.3390/molecules24183313] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2019] [Revised: 09/07/2019] [Accepted: 09/09/2019] [Indexed: 12/15/2022] Open
Abstract
The current study aimed to synthesize new metal coordination complexes with potential biomedical applications. Metal complexes were prepared via the reaction of isatin-N(4)anti- pyrinethiosemicarbazone ligand 1 with Cu(II), Ni(II), Co(II), Zn(II), and Fe(III) ions. The obtained metal complexes 2-12 were characterized using elemental, spectral (1H-NMR, EPR, Mass, IR, UV-Vis) and thermal (TGA) techniques, as well as magnetic moment and molar conductance measurements. In addition, their geometries were studied using EPR and UV-Vis spectroscopy. To evaluate the in vivo anti-cancer activities of these complexes, the ligand 1 and its metal complexes 2, 7 and 9 were tested against solid tumors. The solid tumors were induced by subcutaneous (SC) injection of Ehrlich ascites carcinoma (EAC) cells in mice. The impact of the selected complexes on the reduction of tumor volume was determined. Also, the expression levels of vascular endothelial growth factor (VEGF) and cysteine aspartyl-specific protease-7 (caspase-7) in tumor and liver tissues of mice bearing EAC tumor were determined. Moreover, their effects on alanine transaminase (ALT), aspartate transaminase (AST), albumin, and glucose levels were measured. The results revealed that the tested compounds, especially complex 9, reduced tumor volume, inhibited the expression of VEGF, and induced the expression of caspase-7. Additionally, they restored the levels of ALT, AST, albumin, and glucose close to their normal levels. Taken together, our newly synthesized metal complexes are promising anti-cancer agents against solid tumors induced by EAC cells as supported by the inhibition of VEGF and induction of caspase-7.
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5
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Meyer-Almes FJ. Determination of the binding mechanism of histone deacetylase inhibitors. Chem Biol Drug Des 2019; 93:1214-1250. [PMID: 30480375 DOI: 10.1111/cbdd.13449] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2018] [Revised: 10/14/2018] [Accepted: 11/11/2018] [Indexed: 12/20/2022]
Abstract
This article places its focus on methods and tools enabling the elucidation of the mechanism by which ligands, small-molecule inhibitors, or substrates interact with zinc-containing bacterial or human members of the histone deacetylase family (HDACs). These methods include biochemical and biophysical approaches and can be subdivided into equilibrium and kinetic methods. More information about the exact mode of action can be obtained by combining these methods with specific mutant variants of the enzymes and/or series of structural similar ligands. All available equilibrium and kinetic data including additional information from 3D structures of HDAC-ligand complexes can be beneficially combined in a data analysis procedure called Integrated Global-Fit analysis eventually providing the most likely binding mechanism.
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Affiliation(s)
- Franz-Josef Meyer-Almes
- Department of Chemical Engineering and Biotechnology, University of Applied Sciences, Darmstadt, Germany
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6
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Abstract
Proteases drive the life cycle of all proteins, ensuring the transportation and activation of newly minted, would-be proteins into their functional form while recycling spent or unneeded proteins. Far from their image as engines of protein digestion, proteases play fundamental roles in basic physiology and regulation at multiple levels of systems biology. Proteases are intimately associated with disease and modulation of proteolytic activity is the presumed target for successful therapeutics. "Proteases: Pivot Points in Functional Proteomics" examines the crucial roles of proteolysis across a wide range of physiological processes and diseases. The existing and potential impacts of proteolysis-related activity on drug and biomarker development are presented in detail. All told the decisive roles of proteases in four major categories comprising 23 separate subcategories are addressed. Within this construct, 15 sets of subject-specific, tabulated data are presented that include identification of proteases, protease inhibitors, substrates, and their actions. Said data are derived from and confirmed by over 300 references. Cross comparison of datasets indicates that proteases, their inhibitors/promoters and substrates intersect over a range of physiological processes and diseases, both chronic and pathogenic. Indeed, "Proteases: Pivot Points …" closes by dramatizing this very point through association of (pro)Thrombin and Fibrin(ogen) with: hemostasis, innate immunity, cardiovascular and metabolic disease, cancer, neurodegeneration, and bacterial self-defense.
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Affiliation(s)
- Ingrid M Verhamme
- Department of Pathology, Microbiology and Immunology, Vanderbilt University School of Medicine, Nashville, TN, USA.
| | - Sarah E Leonard
- Chemical and Biomolecular Engineering, University of Illinois Champaign-Urbana School of Chemical Sciences, Champaign, IL, USA
| | - Ray C Perkins
- New Liberty Proteomics Corporation, New Liberty, KY, USA.
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7
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Krishna Deepak RNV, Abdullah A, Talwar P, Fan H, Ravanan P. Identification of FDA-approved drugs as novel allosteric inhibitors of human executioner caspases. Proteins 2018; 86:1202-1210. [PMID: 30194780 DOI: 10.1002/prot.25601] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2018] [Revised: 09/03/2018] [Accepted: 09/04/2018] [Indexed: 01/10/2023]
Abstract
The regulation of apoptosis is a tightly coordinated process and caspases are its chief regulators. Of special importance are the executioner caspases, caspase-3/7, the activation of which irreversibly sets the cell on the path of death. Dysregulation of apoptosis, particularly an increased rate of cell death lies at the root of numerous human diseases. Although several peptide-based inhibitors targeting the homologous active site region of caspases have been developed, owing to their non-specific activity and poor pharmacological properties their use has largely been restricted. Thus, we sought to identify FDA-approved drugs that could be repurposed as novel allosteric inhibitors of caspase-3/7. In this study, we virtually screened a catalog of FDA-approved drugs targeting an allosteric pocket located at the dimerization interface of caspase-3/7. From among the top-scoring hits we short-listed 5 compounds for experimental validation. Our enzymatic assays using recombinant caspase-3 suggested that 4 out of the 5 drugs effectively inhibited caspase-3 enzymatic activity in vitro with IC50 values ranging ~10-55 μM. Structural analysis of the docking poses show the 4 compounds forming specific non-covalent interactions at the allosteric pocket suggesting that these molecules could disrupt the adjacently-located active site. In summary, we report the identification of 4 novel non-peptide allosteric inhibitors of caspase-3/7 from among FDA-approved drugs.
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Affiliation(s)
- R N V Krishna Deepak
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), Singapore
| | - Ahmad Abdullah
- Apoptosis and Cell Survival Research Laboratory, School of Biosciences and Technology, VIT University, Vellore, Tamil Nadu, India
| | - Priti Talwar
- Apoptosis and Cell Survival Research Laboratory, School of Biosciences and Technology, VIT University, Vellore, Tamil Nadu, India
| | - Hao Fan
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), Singapore.,Department of Biological Sciences, National University of Singapore, Singapore.,Centre for Computational Biology, DUKE-NUS Medical School, Singapore
| | - Palaniyandi Ravanan
- Apoptosis and Cell Survival Research Laboratory, School of Biosciences and Technology, VIT University, Vellore, Tamil Nadu, India
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8
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Qi J, Yao Q, Qian K, Tian L, Cheng Z, Wang Y. Gallium(III) complexes of α- N -heterocyclic piperidylthiosemicarbazones: Synthesis, structure-activity relationship, cellular uptake and activation of caspases-3/7/9. J Inorg Biochem 2018; 186:42-50. [DOI: 10.1016/j.jinorgbio.2018.05.005] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2018] [Revised: 05/03/2018] [Accepted: 05/08/2018] [Indexed: 10/16/2022]
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9
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Vance NR, Gakhar L, Spies MA. Allosteric Tuning of Caspase-7: A Fragment-Based Drug Discovery Approach. Angew Chem Int Ed Engl 2017; 56:14443-14447. [PMID: 28940929 PMCID: PMC5698726 DOI: 10.1002/anie.201706959] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2017] [Revised: 08/28/2017] [Indexed: 11/12/2022]
Abstract
The caspase family of cysteine proteases are highly sought‐after drug targets owing to their essential roles in apoptosis, proliferation, and inflammation pathways. High‐throughput screening efforts to discover inhibitors have gained little traction. Fragment‐based screening has emerged as a powerful approach for the discovery of innovative drug leads. This method has become a central facet of drug discovery campaigns in the pharmaceutical industry and academia. A fragment‐based drug discovery campaign against human caspase‐7 resulted in the discovery of a novel series of allosteric inhibitors. An X‐ray crystal structure of caspase‐7 bound to a fragment hit and a thorough kinetic characterization of a zymogenic form of the enzyme were used to investigate the allosteric mechanism of inhibition. This work further advances our understanding of the mechanisms of allosteric control of this class of pharmaceutically relevant enzymes, and provides a new path forward for drug discovery efforts.
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Affiliation(s)
- Nicholas R Vance
- Division of Medicinal and Natural Products Chemistry, College of Pharmacy, University of Iowa, 115 S Grand Ave, Iowa City, IA, 52242, USA
| | - Lokesh Gakhar
- Department of Biochemistry, College of Medicine, University of Iowa, 51 Newton Road, Iowa City, IA, 52242, USA.,Protein Crystallography Facility, Roy J. and Lucille A. Carver College of Medicine, University of Iowa, 51 Newton Road, Iowa City, IA, 52242, USA
| | - M Ashley Spies
- Division of Medicinal and Natural Products Chemistry, College of Pharmacy, University of Iowa, 115 S Grand Ave, Iowa City, IA, 52242, USA.,Department of Biochemistry, College of Medicine, University of Iowa, 51 Newton Road, Iowa City, IA, 52242, USA
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