301
|
Bueno AB, Showalter AD, Wainscott DB, Stutsman C, Marín A, Ficorilli J, Cabrera O, Willard FS, Sloop KW. Positive Allosteric Modulation of the Glucagon-like Peptide-1 Receptor by Diverse Electrophiles. J Biol Chem 2016; 291:10700-15. [PMID: 26975372 PMCID: PMC4865917 DOI: 10.1074/jbc.m115.696039] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2015] [Indexed: 11/25/2022] Open
Abstract
Therapeutic intervention to activate the glucagon-like peptide-1 receptor (GLP-1R) enhances glucose-dependent insulin secretion and improves energy balance in patients with type 2 diabetes mellitus. Studies investigating mechanisms whereby peptide ligands activate GLP-1R have utilized mutagenesis, receptor chimeras, photo-affinity labeling, hydrogen-deuterium exchange, and crystallography of the ligand-binding ectodomain to establish receptor homology models. However, this has not enabled the design or discovery of drug-like non-peptide GLP-1R activators. Recently, studies investigating 4-(3-benzyloxyphenyl)-2-ethylsulfinyl-6-(trifluoromethyl)pyrimidine (BETP), a GLP-1R-positive allosteric modulator, determined that Cys-347 in the GLP-1R is required for positive allosteric modulator activity via covalent modification. To advance small molecule activation of the GLP-1R, we characterized the insulinotropic mechanism of BETP. In guanosine 5′-3-O-(thio)triphosphate binding and INS1 832-3 insulinoma cell cAMP assays, BETP enhanced GLP-1(9–36)-NH2-stimulated cAMP signaling. Using isolated pancreatic islets, BETP potentiated insulin secretion in a glucose-dependent manner that requires both the peptide ligand and GLP-1R. In studies of the covalent mechanism, PAGE fluorography showed labeling of GLP-1R in immunoprecipitation experiments from GLP-1R-expressing cells incubated with [3H]BETP. Furthermore, we investigated whether other reported GLP-1R activators and compounds identified from screening campaigns modulate GLP-1R by covalent modification. Similar to BETP, several molecules were found to enhance GLP-1R signaling in a Cys-347-dependent manner. These chemotypes are electrophiles that react with GSH, and LC/MS determined the cysteine adducts formed upon conjugation. Together, our results suggest covalent modification may be used to stabilize the GLP-1R in an active conformation. Moreover, the findings provide pharmacological guidance for the discovery and characterization of small molecule GLP-1R ligands as possible therapeutics.
Collapse
Affiliation(s)
- Ana B Bueno
- From the Centro de Investigación Lilly, Eli Lilly and Co., Alcobendas 28108, Spain and
| | | | - David B Wainscott
- Quantitative Biology, Lilly Research Laboratories, Eli Lilly and Co., Indianapolis, Indiana 46285
| | | | - Aranzazu Marín
- From the Centro de Investigación Lilly, Eli Lilly and Co., Alcobendas 28108, Spain and
| | | | | | - Francis S Willard
- Quantitative Biology, Lilly Research Laboratories, Eli Lilly and Co., Indianapolis, Indiana 46285
| | | |
Collapse
|
302
|
Korczynska M, Le DD, Younger N, Gregori-Puigjané E, Tumber A, Krojer T, Velupillai S, Gileadi C, Nowak RP, Iwasa E, Pollock SB, Torres IO, Oppermann U, Shoichet BK, Fujimori DG. Docking and Linking of Fragments To Discover Jumonji Histone Demethylase Inhibitors. J Med Chem 2016; 59:1580-98. [PMID: 26699912 PMCID: PMC5080985 DOI: 10.1021/acs.jmedchem.5b01527] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Development of tool molecules that inhibit Jumonji demethylases allows for the investigation of cancer-associated transcription. While scaffolds such as 2,4-pyridinedicarboxylic acid (2,4-PDCA) are potent inhibitors, they exhibit limited selectivity. To discover new inhibitors for the KDM4 demethylases, enzymes overexpressed in several cancers, we docked a library of 600,000 fragments into the high-resolution structure of KDM4A. Among the most interesting chemotypes were the 5-aminosalicylates, which docked in two distinct but overlapping orientations. Docking poses informed the design of covalently linked fragment compounds, which were further derivatized. This combined approach improved affinity by ∼ 3 log-orders to yield compound 35 (Ki = 43 nM). Several hybrid inhibitors were selective for KDM4C over the related enzymes FIH, KDM2A, and KDM6B while lacking selectivity against the KDM3 and KDM5 subfamilies. Cocrystal structures corroborated the docking predictions. This study extends the use of structure-based docking from fragment discovery to fragment linking optimization, yielding novel KDM4 inhibitors.
Collapse
Affiliation(s)
- Magdalena Korczynska
- Department of Pharmaceutical Chemistry, University of California, San Francisco, Genentech Hall, 600 16th Street, MC2280, San Francisco, California 94158-2280, United States
| | - Daniel D. Le
- Chemistry and Chemical Biology Graduate Program, University of California, San Francisco, Genentech Hall, 600 16th Street, MC2280, San Francisco, California 94158-2280, United States
| | - Noah Younger
- Chemistry and Chemical Biology Graduate Program, University of California, San Francisco, Genentech Hall, 600 16th Street, MC2280, San Francisco, California 94158-2280, United States
| | - Elisabet Gregori-Puigjané
- Department of Pharmaceutical Chemistry, University of California, San Francisco, Genentech Hall, 600 16th Street, MC2280, San Francisco, California 94158-2280, United States
| | - Anthony Tumber
- Structural Genomics Consortium, University of Oxford, Oxford OX3 7DQ, U.K
- Nuffield Department of Clinical Medicine, Target Discovery Institute (TDI), University of Oxford, Oxford OX3 7BN, U.K
| | - Tobias Krojer
- Structural Genomics Consortium, University of Oxford, Oxford OX3 7DQ, U.K
| | | | - Carina Gileadi
- Structural Genomics Consortium, University of Oxford, Oxford OX3 7DQ, U.K
| | - Radosław P. Nowak
- Structural Genomics Consortium, University of Oxford, Oxford OX3 7DQ, U.K
| | - Eriko Iwasa
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, Genentech Hall, 600 16th Street, MC2280, San Francisco, California 94158-2280, United States
| | - Samuel B. Pollock
- Chemistry and Chemical Biology Graduate Program, University of California, San Francisco, Genentech Hall, 600 16th Street, MC2280, San Francisco, California 94158-2280, United States
| | - Idelisse Ortiz Torres
- Chemistry and Chemical Biology Graduate Program, University of California, San Francisco, Genentech Hall, 600 16th Street, MC2280, San Francisco, California 94158-2280, United States
| | - Udo Oppermann
- Structural Genomics Consortium, University of Oxford, Oxford OX3 7DQ, U.K
- Botnar Research Center, University of Oxford, Oxford OX3 7LD, U.K
| | - Brian K. Shoichet
- Department of Pharmaceutical Chemistry, University of California, San Francisco, Genentech Hall, 600 16th Street, MC2280, San Francisco, California 94158-2280, United States
| | - Danica Galonić Fujimori
- Department of Pharmaceutical Chemistry, University of California, San Francisco, Genentech Hall, 600 16th Street, MC2280, San Francisco, California 94158-2280, United States
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, Genentech Hall, 600 16th Street, MC2280, San Francisco, California 94158-2280, United States
| |
Collapse
|
306
|
Choi J, Choi KE, Park SJ, Kim SY, Jee JG. Ensemble-Based Virtual Screening Led to the Discovery of New Classes of Potent Tyrosinase Inhibitors. J Chem Inf Model 2016; 56:354-67. [DOI: 10.1021/acs.jcim.5b00484] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Joonhyeok Choi
- Research
Institute of Pharmaceutical Sciences, College of Pharmacy, Kyungpook National University, 80 Daehak-ro, Buk-gu, Daegu 702-701, Republic of Korea
| | - Kwang-Eun Choi
- Research
Institute of Pharmaceutical Sciences, College of Pharmacy, Kyungpook National University, 80 Daehak-ro, Buk-gu, Daegu 702-701, Republic of Korea
| | - Sung Jean Park
- College
of Pharmacy, Gachon University, Incheon 406-799, Republic of Korea
| | - Sun Yeou Kim
- College
of Pharmacy, Gachon University, Incheon 406-799, Republic of Korea
| | - Jun-Goo Jee
- Research
Institute of Pharmaceutical Sciences, College of Pharmacy, Kyungpook National University, 80 Daehak-ro, Buk-gu, Daegu 702-701, Republic of Korea
| |
Collapse
|
307
|
Huang L, Liao M, Yang X, Gong H, Ma L, Zhao Y, Huang K. Bisphenol analogues differently affect human islet polypeptide amyloid formation. RSC Adv 2016. [DOI: 10.1039/c5ra21792j] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Bisphenols (BPs) are widely used in the production of plastic material, misfolded human islet amyloid polypeptide (hIAPP) is a causal factor in diabetes. We demonstrated BPs analogues show different effects on hIAPP amyloid formation.
Collapse
Affiliation(s)
- Lizi Huang
- Tongji School of Pharmacy
- Huazhong University of Science and Technology
- Wuhan
- China
| | - Mingyan Liao
- Tongji School of Pharmacy
- Huazhong University of Science and Technology
- Wuhan
- China
| | - Xin Yang
- Tongji School of Pharmacy
- Huazhong University of Science and Technology
- Wuhan
- China
| | - Hao Gong
- Tongji School of Pharmacy
- Huazhong University of Science and Technology
- Wuhan
- China
| | - Liang Ma
- Tongji School of Pharmacy
- Huazhong University of Science and Technology
- Wuhan
- China
| | - Yudan Zhao
- Tongji School of Pharmacy
- Huazhong University of Science and Technology
- Wuhan
- China
| | - Kun Huang
- Tongji School of Pharmacy
- Huazhong University of Science and Technology
- Wuhan
- China
- Center for Biomedicine Research
| |
Collapse
|
308
|
Klumpp M. Non-stoichiometric inhibition in integrated lead finding - a literature review. Expert Opin Drug Discov 2015; 11:149-62. [PMID: 26653534 DOI: 10.1517/17460441.2016.1128892] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
INTRODUCTION Non-stoichiometric inhibition summarizes different mechanisms by which low-molecular weight compounds can reproducibly inhibit high-throughput screening (HTS) and other lead finding assays without binding to a structurally defined site on their molecular target. This disqualifies such molecules from optimization by medicinal chemistry, and therefore their rapid elimination from screening hit lists is essential for productive and effective drug discovery. AREAS COVERED This review covers recent literature that either investigates the various mechanisms behind non-stoichiometric inhibition or suggests assays and readouts to identify them. In addition, combination of the various methods to distill promising molecules out of raw primary hit lists step-by-step is considered. Emerging technologies to demonstrate target engagement in cells are also discussed. EXPERT OPINION Over the last few years, awareness of non-stoichiometric inhibitors within screening libraries and HTS hit lists has considerably increased, not only in the pharmaceutical industry but also in the academic drug discovery community. This has resulted in a variety of methods to detect and handle such compounds. These range from in silico approaches to flag suspicious compounds, and counterassays to measure non-stoichiometric inhibition, to biophysical methods that positively demonstrate stoichiometric binding. In addition, novel technologies to verify target engagement within cells are becoming available. While still a time- and resource-consuming nuisance, non-stoichiometric inhibitors therefore do not fundamentally jeopardize the discovery of low molecular weight lead and drug candidates. Rather, they should be viewed as a manageable issue that with appropriate expertise can be overcome through integration of the above-mentioned approaches.
Collapse
Affiliation(s)
- Martin Klumpp
- a Novartis Institute of Biomedical Research Basel, Novartis Pharma AG , Basel , Switzerland
| |
Collapse
|
309
|
Abstract
![]()
Many
questions about the biological activity and availability of
small molecules remain inaccessible to investigators who could most
benefit from their answers. To narrow the gap between chemoinformatics
and biology, we have developed a suite of ligand annotation, purchasability,
target, and biology association tools, incorporated into ZINC and
meant for investigators who are not computer specialists. The new
version contains over 120 million purchasable “drug-like”
compounds – effectively all organic molecules that are for
sale – a quarter of which are available for immediate delivery.
ZINC connects purchasable compounds to high-value ones such as metabolites,
drugs, natural products, and annotated compounds from the literature.
Compounds may be accessed by the genes for which they are annotated
as well as the major and minor target classes to which those genes
belong. It offers new analysis tools that are easy for nonspecialists
yet with few limitations for experts. ZINC retains its original 3D
roots – all molecules are available in biologically relevant,
ready-to-dock formats. ZINC is freely available at http://zinc15.docking.org.
Collapse
Affiliation(s)
- Teague Sterling
- Department of Pharmaceutical Chemistry, University of California, San Francisco , Byers Hall, 1700 4th Street, San Francisco, California 94158-2330, United States
| | - John J Irwin
- Department of Pharmaceutical Chemistry, University of California, San Francisco , Byers Hall, 1700 4th Street, San Francisco, California 94158-2330, United States
| |
Collapse
|