7EU5

Co-crystal structure of Human Nicotinamide N-methyltransferase (NNMT) with tricyclic small molecule inhibitor JBSNF-000107

Summary for 7EU5

• Entry DOI: 10.2210/pdb7eu5/pdb
• Descriptor: Nicotinamide N-methyltransferase, S-ADENOSYL-L-HOMOCYSTEINE, 6-fluoranyl-10-methyl-1,10-diazatricyclo[6.3.1.0^{4,12}]dodeca-4,6,8(12)-trien-11-imine, ... (4 entities in total)
• Functional Keywords: nnmt, transferase
• Biological source: Homo sapiens (Human)
• Total number of polymer chains: 4
• Total formula weight: 127305.44

Authors

Swaminathan, S.,Gosu, R.,Birudukota, S.,Kandan, S.,Vaithilingam, K. (deposition date: 2021-05-16, release date: 2022-05-18, Last modification date: 2023-11-29)

Primary citation

Ruf, S.,Rajagopal, S.,Kadnur, S.V.,Hallur, M.S.,Rani, S.,Kristam, R.,Swaminathan, S.,Zope, B.R.,Gondrala, P.K.,Swamy, I.,Putta, V.P.R.K.,Kandan, S.,Zech, G.,Schreuder, H.,Rudolph, C.,Elvert, R.,Czech, J.,Birudukota, S.,Siddiqui, M.A.,Anand, N.N.,Mane, V.S.,Dittakavi, S.,Suresh, J.,Gosu, R.,Ramesh, M.,Yura, T.,Dhakshinamoorthy, S.,Kannt, A.
Novel tricyclic small molecule inhibitors of Nicotinamide N-methyltransferase for the treatment of metabolic disorders.
Sci Rep, 12:15440-15440, 2022

PubMed Abstract: Nicotinamide N-methyltransferase (NNMT) is a metabolic regulator that catalyzes the methylation of nicotinamide (Nam) using the co-factor S-adenosyl-L-methionine to form 1-methyl-nicotinamide (MNA). Overexpression of NNMT and the presence of the active metabolite MNA is associated with a number of diseases including metabolic disorders. We conducted a high-throughput screening campaign that led to the identification of a tricyclic core as a potential NNMT small molecule inhibitor series. Elaborate medicinal chemistry efforts were undertaken and hundreds of analogs were synthesized to understand the structure activity relationship and structure property relationship of this tricyclic series. A lead molecule, JBSNF-000028, was identified that inhibits human and mouse NNMT activity, reduces MNA levels in mouse plasma, liver and adipose tissue, and drives insulin sensitization, glucose modulation and body weight reduction in a diet-induced obese mouse model of diabetes. The co-crystal structure showed that JBSNF-000028 binds below a hairpin structural motif at the nicotinamide pocket and stacks between Tyr-204 (from Hairpin) and Leu-164 (from central domain). JBSNF-000028 was inactive against a broad panel of targets related to metabolism and safety. Interestingly, the improvement in glucose tolerance upon treatment with JBSNF-000028 was also observed in NNMT knockout mice with diet-induced obesity, pointing towards the glucose-normalizing effect that may go beyond NNMT inhibition. JBSNF-000028 can be a potential therapeutic option for metabolic disorders and developmental studies are warranted.

PubMed: 36104373
DOI: 10.1038/s41598-022-19634-2

Experimental method

X-RAY DIFFRACTION (2.731 Å)