Discovery of Bisubstrate Inhibitors of Nicotinamide N-Methyltransferase (NNMT)

Babault, Nicolas; Allali-Hassani, Abdellah; Li, Fengling; Fan, Jie; Yue, Alex; Ju, Kevin; Liu, Feng; Vedadi, Masoud; Liu, Jing; Jin, Jian

doi:10.1021/acs.jmedchem.7b01422

Title: Discovery of Bisubstrate Inhibitors of Nicotinamide N-Methyltransferase (NNMT)

Journal Article · Wed Jan 10 00:00:00 EST 2018 · Journal of Medicinal Chemistry

DOI:https://doi.org/10.1021/acs.jmedchem.7b01422· OSTI ID:1431360

Babault, Nicolas ^[1]; Allali-Hassani, Abdellah ^[2]; Li, Fengling ^[2]; Fan, Jie ^[3]; Yue, Alex ^[1]; Ju, Kevin ^[1];

^[4]; Vedadi, Masoud ^[2]; Liu, Jing ^[1];

^[1]

Icahn School of Medicine at Mount Sinai, New York, NY (United States)
Univ. of Toronto, ON (Canada)
Accutar Biotechnology, Brooklyn, NY (United States)
Soochow Univ., Jiangsu (People’s Republic of China)

Nicotinamide N-methyltransferase (NNMT) catalyzes the N-methylation of pyridine-containing compounds using the cofactor S-5'-adenosyl-l-methionine (SAM) as the methyl group donor. Through the regulation of the levels of its substrates, cofactor, and products, NNMT plays an important role in physiology and pathophysiology. Overexpression of NNMT has been implicated in various human diseases. Potent and selective small-molecule NNMT inhibitors are valuable chemical tools for testing biological and therapeutic hypotheses. However, very few NNMT inhibitors have been reported. Here, we describe the discovery of a bisubstrate NNMT inhibitor MS2734 (6) and characterization of this inhibitor in biochemical, biophysical, kinetic, and structural studies. Importantly, we obtained the first crystal structure of human NNMT in complex with a small-molecule inhibitor. The structure of the NNMT–6 complex has unambiguously demonstrated that 6 occupied both substrate and cofactor binding sites. Here, the findings paved the way for developing more potent and selective NNMT inhibitors in the future.

View Accepted Manuscript (DOE)

Cite

Export

Save

Research Organization:: Argonne National Lab. (ANL), Argonne, IL (United States)

Sponsoring Organization:: USDOE Office of Science (SC), Basic Energy Sciences (BES). Scientific User Facilities Division; U.S. National Inst. of Health; National Natural Science Foundation of China (NSFC); NIH-ORIP HEI

Grant/Contract Number:: AC02-06CH11357; R01GM122749; R01CA218600; R01HD088626; 21302134; P41 GM103403; S10OD021527

OSTI ID:: 1431360

Journal Information:: Journal of Medicinal Chemistry, Vol. 61, Issue 4; ISSN 0022-2623

Publisher:: American Chemical Society (ACS)Copyright Statement

Country of Publication:: United States

Language:: ENGLISH

Citation Metrics:

Cited by: 43 works

Citation information provided by
Web of Science

References (52)

Substrate specificity of nicotinamide methyltransferase isolated from porcine liver Alston, Theodore A.; Abeles, Robert H. Archives of Biochemistry and Biophysics, Vol. 260, Issue 2 https://doi.org/10.1016/0003-9861(88)90487-0	journal	February 1988
Solving structures of protein complexes by molecular replacement with Phaser McCoy, Airlie J. Acta Crystallographica Section D Biological Crystallography, Vol. 63, Issue 1 https://doi.org/10.1107/S0907444906045975	journal	December 2006
Refinement of Macromolecular Structures by the Maximum-Likelihood Method Murshudov, G. N.; Vagin, A. A.; Dodson, E. J. Acta Crystallographica Section D Biological Crystallography, Vol. 53, Issue 3 https://doi.org/10.1107/S0907444996012255	journal	May 1997
Fluorescence-Based Methods for Screening Writers and Readers of Histone Methyl Marks Allali-Hassani, Abdellah; Wasney, Gregory A.; Siarheyeva, Alena Journal of Biomolecular Screening, Vol. 17, Issue 1 https://doi.org/10.1177/1087057111422256	journal	October 2011
Enhanced Expression of Nicotinamide N -Methyltransferase in Human Papillary Thyroid Carcinoma Cells Xu, Jimin; Moatamed, Farhad; Caldwell, Jeremy S. The Journal of Clinical Endocrinology & Metabolism, Vol. 88, Issue 10 https://doi.org/10.1210/jc.2002-021843	journal	October 2003
Chemogenetic Analysis of Human Protein Methyltransferases: Chemogenetic Analysis of Human Protein Methyltransferases Richon, Victoria M.; Johnston, Danielle; Sneeringer, Christopher J. Chemical Biology & Drug Design, Vol. 78, Issue 2 https://doi.org/10.1111/j.1747-0285.2011.01135.x	journal	June 2011
Identification of Nicotinamide N -Methyltransferase as a Novel Serum Tumor Marker for Colorectal Cancer Roeßler, Markus; Rollinger, Wolfgang; Palme, Stefan Clinical Cancer Research, Vol. 11, Issue 18 https://doi.org/10.1158/1078-0432.CCR-05-0983	journal	September 2005
1-Methylnicotinamide (MNA), a primary metabolite of nicotinamide, exerts anti-thrombotic activity mediated by a cyclooxygenase-2/prostacyclin pathway: Anti-thrombotic activity of 1-methylnicotinamide Chlopicki, S.; Swies, J.; Mogielnicki, A. British Journal of Pharmacology, Vol. 152, Issue 2 https://doi.org/10.1038/sj.bjp.0707383	journal	September 2007
Nicotinamide N-Methyltransferase Upregulation Inversely Correlates with Lymph Node Metastasis in Oral Squamous Cell Carcinoma Sartini, Davide; Santarelli, Andrea; Rossi, Valentina Molecular Medicine, Vol. 13, Issue 7-8 https://doi.org/10.2119/2007-00035.Sartini	journal	July 2007
Towards automated crystallographic structure refinement with phenix.refine Afonine, Pavel V.; Grosse-Kunstleve, Ralf W.; Echols, Nathaniel Acta Crystallographica Section D Biological Crystallography, Vol. 68, Issue 4 https://doi.org/10.1107/S0907444912001308	journal	March 2012
Overlapping gene expression profiles of cell migration and tumor invasion in human bladder cancer identify metallothionein 1E and nicotinamide N-methyltransferase as novel regulators of cell migration Wu, Y.; Siadaty, M. S.; Berens, M. E. Oncogene, Vol. 27, Issue 52 https://doi.org/10.1038/onc.2008.264	journal	August 2008
Nicotinamide N -methyltransferase induces cellular invasion through activating matrix metalloproteinase-2 expression in clear cell renal cell carcinoma cells Tang, Sai-Wen; Yang, Tsung-Cheng; Lin, Wei-Chou Carcinogenesis, Vol. 32, Issue 2 https://doi.org/10.1093/carcin/bgq225	journal	November 2010
Expression of Nicotinamide N-Methyltransferase (E.C. 2.1.1.1) in the Parkinsonian Brain Parsons, Richard B.; Smith, Marie-Louise; Williams, Adrian C. Journal of Neuropathology & Experimental Neurology, Vol. 61, Issue 2 https://doi.org/10.1093/jnen/61.2.111	journal	February 2002
Aspartyl Phosphonates and Phosphoramidates: The First Synthetic Inhibitors of Bacterial Aspartate-Semialdehyde Dehydrogenase Cox, Russell J.; Gibson, Jennifer S.; Mayo Martín, María Belén ChemBioChem, Vol. 3, Issue 9 https://doi.org/10.1002/1439-7633(20020902)3:9<874::AID-CBIC874>3.0.CO;2-V	journal	September 2002
The CCP4 suite programs for protein crystallography Acta Crystallographica Section D Biological Crystallography, Vol. 50, Issue 5, p. 760-763 https://doi.org/10.1107/S0907444994003112	journal	September 1994
Gene expression analysis of renal carcinoma: adipose differentiation-related protein as a potential diagnostic and prognostic biomarker for clear-cell renal carcinoma Yao, Masahiro; Tabuchi, Hisahiro; Nagashima, Yoji The Journal of Pathology, Vol. 205, Issue 3 https://doi.org/10.1002/path.1693	journal	January 2005
Bisubstrate Inhibitors of Protein Kinases: from Principle to Practical Applications Lavogina, Darja; Enkvist, Erki; Uri, Asko ChemMedChem, Vol. 5, Issue 1 https://doi.org/10.1002/cmdc.200900252	journal	January 2010
The Differential Proteome Profile of Stomach Cancer: Identification of the Biomarker Candidates Jang, Joung S. Jang; Cho, Hee Y.; Lee, Young J. Oncology Research Featuring Preclinical and Clinical Cancer Therapeutics, Vol. 14, Issue 10 https://doi.org/10.3727/0965040042380441	journal	January 2004
Effects of Nicotinamide N-Methyltransferase on PANC-1 Cells Proliferation, Metastatic Potential and Survival Under Metabolic Stress Yu, Tao; Wang, Yong-Tao; Chen, Pan Cellular Physiology and Biochemistry, Vol. 35, Issue 2 https://doi.org/10.1159/000369731	journal	January 2015
Autotoxicity, methylation and a road to the prevention of Parkinson’s disease Williams, Adrian C.; Ramsden, David B. Journal of Clinical Neuroscience, Vol. 12, Issue 1 https://doi.org/10.1016/j.jocn.2004.10.002	journal	January 2005
Nicotinamide N-methyltransferase regulates hepatic nutrient metabolism through Sirt1 protein stabilization Hong, Shangyu; Moreno-Navarrete, Jose M.; Wei, Xiaojing Nature Medicine, Vol. 21, Issue 8 https://doi.org/10.1038/nm.3882	journal	July 2015
Melatonin Is a Potent Inhibitor for Myeloperoxidase Galijasevic, Semira; Abdulhamid, Ibrahim; Abu-Soud, Husam M. Biochemistry, Vol. 47, Issue 8 https://doi.org/10.1021/bi702016q	journal	February 2008
A Rapid and Efficient Assay for the Characterization of Substrates and Inhibitors of Nicotinamide N -Methyltransferase van Haren, Matthijs J.; Sastre Toraño, Javier; Sartini, Davide Biochemistry, Vol. 55, Issue 37 https://doi.org/10.1021/acs.biochem.6b00733	journal	September 2016
Role of sirtuins in lifespan regulation is linked to methylation of nicotinamide Schmeisser, Kathrin; Mansfeld, Johannes; Kuhlow, Doreen Nature Chemical Biology, Vol. 9, Issue 11 https://doi.org/10.1038/nchembio.1352	journal	September 2013
Overexpression of nicotinamide N-methyltransferase in gastric cancer tissues and its potential post-translational modification Lim, Bo-Hyun; Cho, Bok-Im; Kim, Yu Na Experimental & Molecular Medicine, Vol. 38, Issue 5 https://doi.org/10.1038/emm.2006.54	journal	October 2006
A coupled fluorescent assay for histone methyltransferases Collazo, Evys; Couture, Jean-François; Bulfer, Stacie Analytical Biochemistry, Vol. 342, Issue 1 https://doi.org/10.1016/j.ab.2005.04.007	journal	July 2005
Chemical Proteomic Profiling of Human Methyltransferases Horning, Benjamin D.; Suciu, Radu M.; Ghadiri, Darian A. Journal of the American Chemical Society, Vol. 138, Issue 40 https://doi.org/10.1021/jacs.6b07830	journal	September 2016
(R)-PFI-2 is a potent and selective inhibitor of SETD7 methyltransferase activity in cells Barsyte-Lovejoy, D.; Li, F.; Oudhoff, M. J. Proceedings of the National Academy of Sciences, Vol. 111, Issue 35 https://doi.org/10.1073/pnas.1407358111	journal	August 2014
The SUV4-20 inhibitor A-196 verifies a role for epigenetics in genomic integrity Bromberg, Kenneth D.; Mitchell, Taylor R. H.; Upadhyay, Anup K. Nature Chemical Biology, Vol. 13, Issue 3 https://doi.org/10.1038/nchembio.2282	journal	January 2017
Serum levels of nicotinamide N-methyltransferase in patients with lung cancer Tomida, Mikio; Mikami, Iwao; Takeuchi, Shingo Journal of Cancer Research and Clinical Oncology, Vol. 135, Issue 9 https://doi.org/10.1007/s00432-009-0563-y	journal	February 2009
Structure of Human SMYD2 Protein Reveals the Basis of p53 Tumor Suppressor Methylation Wang, Li; Li, Ling; Zhang, Hailong Journal of Biological Chemistry, Vol. 286, Issue 44 https://doi.org/10.1074/jbc.M111.262410	journal	August 2011
Expression of nicotinamide N-methyltransferase in hepatocellular carcinoma is associated with poor prognosis Kim, Jongmin; Hong, Seok Joo; Lim, Eun Kyung Journal of Experimental & Clinical Cancer Research, Vol. 28, Issue 1 https://doi.org/10.1186/1756-9966-28-20	journal	February 2009
Inhibitors of nicotinamide N-methyltransferase designed to mimic the methylation reaction transition state van Haren, Matthijs J.; Taig, Rebecca; Kuppens, Jilles Organic & Biomolecular Chemistry, Vol. 15, Issue 31 https://doi.org/10.1039/C7OB01357D	journal	January 2017
Adipose tissue as a source of nicotinamide N-methyltransferase and homocysteine Riederer, Monika; Erwa, Wolfgang; Zimmermann, Robert Atherosclerosis, Vol. 204, Issue 2 https://doi.org/10.1016/j.atherosclerosis.2008.09.015	journal	June 2009
Nicotinamide N-methyltransferase knockdown protects against diet-induced obesity Kraus, Daniel; Yang, Qin; Kong, Dong Nature, Vol. 508, Issue 7495 https://doi.org/10.1038/nature13198	journal	April 2014
MolProbity : all-atom structure validation for macromolecular crystallography Chen, Vincent B.; Arendall, W. Bryan; Headd, Jeffrey J. Acta Crystallographica Section D Biological Crystallography, Vol. 66, Issue 1 https://doi.org/10.1107/S0907444909042073	journal	December 2009
Biomimetic Chichibabin Pyridine Synthesis of the COPD Biomarkers and Elastin Cross-Linkers Isodesmosine and Desmosine Usuki, Toyonobu; Sugimura, Takanori; Komatsu, Akira Organic Letters, Vol. 16, Issue 6 https://doi.org/10.1021/ol500333t	journal	March 2014
Coot model-building tools for molecular graphics Emsley, Paul; Cowtan, Kevin Acta Crystallographica Section D Biological Crystallography, Vol. 60, Issue 12, p. 2126-2132 https://doi.org/10.1107/S0907444904019158	journal	November 2004
Structural Basis of Substrate Recognition in Human Nicotinamide N -Methyltransferase Peng, Yi; Sartini, Davide; Pozzi, Valentina Biochemistry, Vol. 50, Issue 36 https://doi.org/10.1021/bi2007614	journal	September 2011
Nitric Oxide Production and Endothelium-Dependent Vasorelaxation Ameliorated by N ¹ -Methylnicotinamide in Human Blood Vessels Domagala, Teresa B.; Szeffler, Agata; Dobrucki, Lawrence W. Hypertension, Vol. 59, Issue 4 https://doi.org/10.1161/HYPERTENSIONAHA.111.183210	journal	April 2012
Noncoupled Fluorescent Assay for Direct Real-Time Monitoring of Nicotinamide N -Methyltransferase Activity Neelakantan, Harshini; Vance, Virginia; Wang, Hua-Yu Leo Biochemistry, Vol. 56, Issue 6 https://doi.org/10.1021/acs.biochem.6b01215	journal	January 2017
PHENIX: a comprehensive Python-based system for macromolecular structure solution Adams, Paul D.; Afonine, Pavel V.; Bunkóczi, Gábor Acta Crystallographica Section D Biological Crystallography, Vol. 66, Issue 2, p. 213-221 https://doi.org/10.1107/S0907444909052925	journal	January 2010
Synthesis and evaluation of N6-substituted azide- and alkyne-bearing N-mustard analogs of S-adenosyl-l-methionine Ramadan, Mohamed; Bremner-Hay, Natalie K.; Carlson, Steig A. Tetrahedron, Vol. 70, Issue 34 https://doi.org/10.1016/j.tet.2014.05.055	journal	August 2014
NNMT promotes epigenetic remodeling in cancer by creating a metabolic methylation sink Ulanovskaya, Olesya A.; Zuhl, Andrea M.; Cravatt, Benjamin F. Nature Chemical Biology, Vol. 9, Issue 5 https://doi.org/10.1038/nchembio.1204	journal	March 2013
Nicotinamide N -Methyltransferase: More Than a Vitamin B3 Clearance Enzyme Pissios, Pavlos Trends in Endocrinology & Metabolism, Vol. 28, Issue 5 https://doi.org/10.1016/j.tem.2017.02.004	journal	May 2017
RNA-Mediated Gene Silencing of Nicotinamide N-Methyltransferase Is Associated with Decreased Tumorigenicity in Human Oral Carcinoma Cells Pozzi, Valentina; Sartini, Davide; Morganti, Stefano PLoS ONE, Vol. 8, Issue 8 https://doi.org/10.1371/journal.pone.0071272	journal	August 2013
Structure–Activity Relationship for Small Molecule Inhibitors of Nicotinamide N -Methyltransferase Neelakantan, Harshini; Wang, Hua-Yu; Vance, Virginia Journal of Medicinal Chemistry, Vol. 60, Issue 12 https://doi.org/10.1021/acs.jmedchem.7b00389	journal	June 2017
Crystal structures of monkey and mouse nicotinamide N-methyltransferase (NNMT) bound with end product, 1-methyl nicotinamide Swaminathan, Srinivasan; Birudukota, Swarnakumari; Thakur, Manish Kumar Biochemical and Biophysical Research Communications, Vol. 491, Issue 2 https://doi.org/10.1016/j.bbrc.2017.07.087	journal	September 2017
Differential gene expression profiling in human brain tumors Markert, James M.; Fuller, Catherine M.; Gillespie, G. Yancey Physiological Genomics, Vol. 5, Issue 1 https://doi.org/10.1152/physiolgenomics.2001.5.1.21	journal	February 2001
Selective Inhibitors of Histone Methyltransferase DOT1L: Design, Synthesis, and Crystallographic Studies Yao, Yuan; Chen, Pinhong; Diao, Jiasheng Journal of the American Chemical Society, Vol. 133, Issue 42 https://doi.org/10.1021/ja206312b	journal	October 2011
Bisubstrate Inhibition: Theory and Application to N -Acetyltransferases ^† Yu, Michael; Magalhães, Maria L. B.; Cook, Paul F. Biochemistry, Vol. 45, Issue 49 https://doi.org/10.1021/bi061621t	journal	December 2006
Human liver nicotinamide N-methyltransferase. cDNA cloning, expression, and biochemical characterization. Aksoy, S.; Szumlanski, C. L.; Weinshilboum, R. M. Journal of Biological Chemistry, Vol. 269, Issue 20 https://doi.org/10.1016/S0021-9258(17)36700-5	journal	May 1994

Cited By (4)

Synthesis of Adenine Dinucleosides 2′,5′-Bridged by Sulfur-Containing Linkers as Bisubstrate SAM Analogues for Viral RNA 2′- O -Methyltransferases: Synthesis of Adenine Dinucleosides 2′,5′-Bridged by Sulfur-Containing Linkers as Bisubstrate SAM Analogues for Viral RNA 2′- O -Methyltransferases Ahmed-Belkacem, Rostom; Sutto-Ortiz, Priscila; Decroly, Etienne European Journal of Organic Chemistry, Vol. 2019, Issue 38 https://doi.org/10.1002/ejoc.201901120	journal	September 2019
Synthesis, bioactivity, and enzymatic modification of antibacterial thiotetromycin derivatives Rothe, Marlene L.; Li, Jie; Garibay, Ernesto Organic & Biomolecular Chemistry, Vol. 17, Issue 13 https://doi.org/10.1039/c8ob03109f	journal	January 2019
Synthesis of SAM-Adenosine Conjugates for the Study of m ⁶ A-RNA Methyltransferases: Synthesis of SAM-Adenosine Conjugates for the Study of m ⁶ A-RNA Methyltransferases Atdjian, Colette; Iannazzo, Laura; Braud, Emmanuelle European Journal of Organic Chemistry, Vol. 2018, Issue 32 https://doi.org/10.1002/ejoc.201800798	journal	August 2018
Integrative -omics and HLA-ligandomics analysis to identify novel drug targets for ccRCC immunotherapy Reustle, Anna; Di Marco, Moreno; Meyerhoff, Carolin Genome Medicine, Vol. 12, Issue 1 https://doi.org/10.1186/s13073-020-00731-8	journal	March 2020

Similar Records

Structural Basis of Substrate Recognition in Human Nicotinamide N-Methyltransferase

Journal Article · Wed May 02 00:00:00 EDT 2012 · Biochemistry-US · OSTI ID:1431360

Peng, Yi; Sartini, Davide; Pozzi, Valentina; +3 more

Structural Biology of Human H3K9 Methyltransferases

Journal Article · Fri Jan 01 00:00:00 EST 2010 · PLoS One · OSTI ID:1431360

Wu, H; Min, J; Lunin, V; +6 more

S-adenosyl methionine is necessary for inhibition of the methyltransferase G9a by the lysine 9 to methionine mutation on histone H3

Journal Article · Mon May 16 00:00:00 EDT 2016 · Proceedings of the National Academy of Sciences of the United States of America · OSTI ID:1431360

Jayaram, Hariharan; Hoelper, Dominik; Jain, Siddhant U.; +7 more

Related Subjects

59 BASIC BIOLOGICAL SCIENCES
Crystal structure
Assays
Inhibitors
Nicotinamide
Screening assays

Title: Discovery of Bisubstrate Inhibitors of Nicotinamide N-Methyltransferase (NNMT)

Citation Formats

References (52)

Cited By (4)

Similar Records

Related Subjects