1
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Li P, Xia C, Kong X, Zhang J. Enhancing nicotinamide N-methyltransferase bisubstrate inhibitor activity through 7-deazaadenosine and linker modifications. Bioorg Chem 2024; 143:106963. [PMID: 38048700 DOI: 10.1016/j.bioorg.2023.106963] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Revised: 11/06/2023] [Accepted: 11/08/2023] [Indexed: 12/06/2023]
Abstract
Nicotinamide N-methyltransferase (NNMT) catalyzes the transfer of a methyl group from S-adenosylmethionine (SAM) to nicotinamide (NAM) and other pyridine-related compounds and is involved in various metabolic processes in the human body. In addition, abnormal expression of NNMT occurs under various pathological conditions such as cancer, diabetes, metabolic disorders, and neurodegenerative diseases, making it a promising drug target worthy of in-depth research. Small-molecule NNMT inhibitors with high potency and selectivity are necessary chemical tools to test biological hypotheses and potential therapies. In this study, we developed a series of highly active NNMT inhibitors by modifying N7 position of adenine. Among them, compound 3-12 (IC50 = 47.9 ± 0.6 nM) exhibited potent inhibitory activity and also had an excellent selectivity profile over a panel of human methyltransferases. We showed that the N7 position of adenine in the NNMT bisubstrate inhibitor was a modifiable site, thus offering insights into the development of NNMT inhibitors.
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Affiliation(s)
- Pengyu Li
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Science, Guangzhou 510530, China; University of Chinese Academy of Sciences, No. 19 Yuquan Road, Beijing 100049, China
| | - Cuicui Xia
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Science, Guangzhou 510530, China; Division of Life Science and Medicine, University of Science and Technology of China, Hefei 230026, China
| | - Xiangqian Kong
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Science, Guangzhou 510530, China; University of Chinese Academy of Sciences, No. 19 Yuquan Road, Beijing 100049, China.
| | - Jiancun Zhang
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Science, Guangzhou 510530, China; University of Chinese Academy of Sciences, No. 19 Yuquan Road, Beijing 100049, China.
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2
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Meng Y, Iyamu ID, Ahmed NAM, Huang R. Comparative Analysis of Two NNMT Bisubstrate Inhibitors through Chemoproteomic Studies: Uncovering the Role of Unconventional SAM Analogue Moiety for Improved Selectivity. ACS Chem Biol 2024; 19:89-100. [PMID: 38181447 DOI: 10.1021/acschembio.3c00531] [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: 01/07/2024]
Abstract
Unconventional S-adenosyl-L-methionine (SAM) mimics with enhanced hydrophobicity are an adaptable building block to develop cell-potent inhibitors for SAM-dependent methyltransferases as targeted therapeutics. We recently discovered cell-potent bisubstrate inhibitors for nicotinamide N-methyltransferase (NNMT) by using an unconventional SAM mimic. To delve into the selectivity implications of the unconventional SAM mimic, we employed a chemoproteomic approach to assess two potent NNMT inhibitors LL320 (Ki, app = 6.8 nM) and II399 (containing an unconventional SAM mimic, Ki, app = 5.9 nM) within endogenous proteomes. Our work began with the rational design and synthesis of immobilized probes 1 and 2, utilizing LL320 and II399 as parent compounds. Systematic analysis of protein networks associated with these probes revealed a comprehensive landscape. Notably, NNMT emerged as the top-ranking hit, substantiating the high selectivity of both inhibitors. Meanwhile, we identified additional interacting proteins for LL320 (38) and II399 (17), showcasing the intricate selectivity profiles associated with these compounds. Subsequent experiments confirmed LL320's interactions with RNMT, DPH5, and SAHH, while II399 exhibited interactions with SHMT2 and MEPCE. Importantly, incorporating the unconventional SAM mimic in II399 led to improved selectivity compared to LL320. Our findings underscore the importance of selectivity profiling and validate the utilization of the unconventional SAM mimic as a viable strategy to create highly selective and cell-permeable inhibitors for SAM-dependent methyltransferases.
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Affiliation(s)
- Ying Meng
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue Institute for Drug Discovery, Purdue University, West Lafayette, Indiana 47907, United States
| | - Iredia D Iyamu
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue Institute for Drug Discovery, Purdue University, West Lafayette, Indiana 47907, United States
| | - Noha A M Ahmed
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue Institute for Drug Discovery, Purdue University, West Lafayette, Indiana 47907, United States
| | - Rong Huang
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue Institute for Drug Discovery, Purdue University, West Lafayette, Indiana 47907, United States
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3
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Lin B, Xiang L, Yuan Z, Hou Q, Ruan Y, Zhang J. ReACT (redox-activated chemical tagging) chemistry enables direct derivatization and fluorescence detection of S-adenosyl-L-homocysteine (SAH). Org Biomol Chem 2023; 21:7085-7089. [PMID: 37602780 DOI: 10.1039/d3ob01073b] [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: 08/22/2023]
Abstract
S-Adenosyl-L-homocysteine (SAH) is a universal byproduct and product inhibitor of the methyltransferase-catalyzed methylation reaction. Here based on ReACT (redox-activated chemical tagging) chemistry, direct derivatization and fluorescence measurement of SAH were achieved with features such as mild reaction conditions and simple operation.
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Affiliation(s)
- Bohong Lin
- Artemisinin Research Center and The First Affiliated Hospital, Guangzhou University of Chinese Medicine, 12 Jichang Road, Guangzhou 510405, China.
| | - Lingling Xiang
- Artemisinin Research Center and The First Affiliated Hospital, Guangzhou University of Chinese Medicine, 12 Jichang Road, Guangzhou 510405, China.
| | - Zhijun Yuan
- Artemisinin Research Center and The First Affiliated Hospital, Guangzhou University of Chinese Medicine, 12 Jichang Road, Guangzhou 510405, China.
| | - Qi Hou
- Artemisinin Research Center and The First Affiliated Hospital, Guangzhou University of Chinese Medicine, 12 Jichang Road, Guangzhou 510405, China.
| | - Yaoping Ruan
- Artemisinin Research Center and The First Affiliated Hospital, Guangzhou University of Chinese Medicine, 12 Jichang Road, Guangzhou 510405, China.
| | - Jing Zhang
- Artemisinin Research Center and The First Affiliated Hospital, Guangzhou University of Chinese Medicine, 12 Jichang Road, Guangzhou 510405, China.
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4
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Iyamu ID, Zhao T, Huang R. Structure-Activity Relationship Studies on Cell-Potent Nicotinamide N-Methyltransferase Bisubstrate Inhibitors. J Med Chem 2023; 66:10510-10527. [PMID: 37523719 DOI: 10.1021/acs.jmedchem.3c00632] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/02/2023]
Abstract
Nicotinamide N-methyltransferase (NNMT) is a metabolic enzyme implicated in multiple diseases, making it a promising therapeutic target. Building upon our recently reported NNMT inhibitor II399, we systematically investigate the structure-activity relationship by designing and synthesizing a series of analogues. Among them, two top inhibitors II559 (Ki = 1.2 nM) and II802 (Ki = 1.6 nM) displayed over 5000-fold selectivity for NNMT over closely related methyltransferases. Moreover, II559 and II802 showed enhanced cellular inhibition, with a cellular IC50 value of approximately 150 nM, making them the most cell-potent bisubstrate inhibitors reported to date. Furthermore, both inhibitors reduced the cell viability with a GI50 value of ∼10 μM and suppressed the migration of aggressive clear cell renal cancer cell carcinoma cell lines. Overall, II559 and II802 would serve as valuable probes to investigate the enzymatic function of NNMT in health and diseases.
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Affiliation(s)
- Iredia D Iyamu
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue Institute for Drug Discovery, Purdue University Center for Cancer Research, Purdue University, West Lafayette, Indiana 47907, United States
| | - Tianqi Zhao
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue Institute for Drug Discovery, Purdue University Center for Cancer Research, Purdue University, West Lafayette, Indiana 47907, United States
| | - Rong Huang
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue Institute for Drug Discovery, Purdue University Center for Cancer Research, Purdue University, West Lafayette, Indiana 47907, United States
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5
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Mahmoodi N, Minnow YVT, Harijan RK, Bedard GT, Schramm VL. Cell-Effective Transition-State Analogue of Phenylethanolamine N-Methyltransferase. Biochemistry 2023; 62:2257-2268. [PMID: 37467463 PMCID: PMC10646973 DOI: 10.1021/acs.biochem.3c00103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/21/2023]
Abstract
Phenylethanolamine N-methyltransferase (PNMT) catalyzes the S-adenosyl-l-methionine (SAM)-dependent methylation of norepinephrine to form epinephrine. Epinephrine is implicated in the regulation of blood pressure, respiration, Alzheimer's disease, and post-traumatic stress disorder (PTSD). Transition-state (TS) analogues bind their target enzymes orders of magnitude more tightly than their substrates. A synthetic strategy for first-generation TS analogues of human PNMT (hPNMT) permitted structural analysis of hPNMT and revealed potential for second-generation inhibitors [Mahmoodi, N.; J. Am. Chem. Soc. 2020, 142, 14222-14233]. A second-generation TS analogue inhibitor of PNMT was designed, synthesized, and characterized to yield a Ki value of 1.2 nM. PNMT isothermal titration calorimetry (ITC) measurements of inhibitor 4 indicated a negative cooperative binding mechanism driven by large favorable entropic contributions and smaller enthalpic contributions. Cell-based assays with HEK293T cells expressing PNMT revealed a cell permeable, intracellular PNMT inhibitor with an IC50 value of 81 nM. Structural analysis demonstrated inhibitor 4 filling catalytic site regions to recapitulate both norepinephrine and SAM interactions. Conformation of the second-generation inhibitor in the catalytic site of PNMT improves contacts relative to those from the first-generation inhibitors. Inhibitor 4 demonstrates up to 51,000-fold specificity for PNMT relative to DNA and protein methyltransferases. Inhibitor 4 also exhibits a 12,000-fold specificity for PNMT over the α2-adrenoceptor.
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Affiliation(s)
- Niusha Mahmoodi
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, New York 10461, United States
| | - Yacoba V T Minnow
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, New York 10461, United States
| | - Rajesh K Harijan
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, New York 10461, United States
| | - Gabriel T Bedard
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, New York 10461, United States
| | - Vern L Schramm
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, New York 10461, United States
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6
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Barrows RD, Jeffries DE, Vishe M, Tukachinsky H, Zheng SL, Li F, Ma Z, Li X, Jin S, Song H, Zhang R, Zhang S, Ni J, Luan H, Wen L, Rongshan Y, Ying C, Shair MD. Potent Uncompetitive Inhibitors of Nicotinamide N-Methyltransferase (NNMT) as In Vivo Chemical Probes. J Med Chem 2022; 65:14642-14654. [DOI: 10.1021/acs.jmedchem.2c01166] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Robert D. Barrows
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, Massachusetts 02138, United States
| | - Daniel E. Jeffries
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, Massachusetts 02138, United States
| | - Mahesh Vishe
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, Massachusetts 02138, United States
| | - Hanna Tukachinsky
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, Massachusetts 02138, United States
| | - Shao-Liang Zheng
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, Massachusetts 02138, United States
| | - Fanfan Li
- Pharmaron Beijing Co., Ltd., 6 Taihe Road, BDA, Beijing 100176, China
| | - Zhenjie Ma
- Pharmaron Beijing Co., Ltd., 6 Taihe Road, BDA, Beijing 100176, China
| | - Xiaolei Li
- Pharmaron Beijing Co., Ltd., 6 Taihe Road, BDA, Beijing 100176, China
| | - Shujuan Jin
- Pharmaron Beijing Co., Ltd., 6 Taihe Road, BDA, Beijing 100176, China
| | - Haobin Song
- Pharmaron Beijing Co., Ltd., 6 Taihe Road, BDA, Beijing 100176, China
| | - Ruonan Zhang
- Pharmaron Beijing Co., Ltd., 6 Taihe Road, BDA, Beijing 100176, China
| | - Shaofeng Zhang
- Pharmaron Beijing Co., Ltd., 6 Taihe Road, BDA, Beijing 100176, China
| | - Jing Ni
- Pharmaron Beijing Co., Ltd., 6 Taihe Road, BDA, Beijing 100176, China
| | - Haofei Luan
- Pharmaron Beijing Co., Ltd., 6 Taihe Road, BDA, Beijing 100176, China
| | - Lei Wen
- Pharmaron Beijing Co., Ltd., 6 Taihe Road, BDA, Beijing 100176, China
| | - Yan Rongshan
- WuXi AppTec Co., Ltd., #288 FuTe ZhongLu WaiGaoQiao Free Trade Zone, Shanghai 200131, China
| | - Chen Ying
- WuXi AppTec Co., Ltd., #288 FuTe ZhongLu WaiGaoQiao Free Trade Zone, Shanghai 200131, China
| | - Matthew D. Shair
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, Massachusetts 02138, United States
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7
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Ruf S, Rajagopal S, Kadnur SV, Hallur MS, Rani S, Kristam R, Swaminathan S, Zope BR, Gondrala PK, Swamy I, Putta VPRK, Kandan S, Zech G, Schreuder H, Rudolph C, Elvert R, Czech J, Birudukota S, Siddiqui MA, Anand NN, Mane VS, 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 2022; 12:15440. [PMID: 36104373 PMCID: PMC9474883 DOI: 10.1038/s41598-022-19634-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Accepted: 08/31/2022] [Indexed: 11/30/2022] Open
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.
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8
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Pozzi V, Campagna R, Sartini D, Emanuelli M. Nicotinamide N-Methyltransferase as Promising Tool for Management of Gastrointestinal Neoplasms. Biomolecules 2022; 12:biom12091173. [PMID: 36139012 PMCID: PMC9496617 DOI: 10.3390/biom12091173] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Revised: 08/21/2022] [Accepted: 08/23/2022] [Indexed: 12/24/2022] Open
Abstract
Gastrointestinal (GI) neoplasms include esophageal, gastric, colorectal, hepatic, and pancreatic cancers. They are characterized by asymptomatic behavior, being responsible for diagnostic delay. Substantial refractoriness to chemo- and radiotherapy, exhibited by late-stage tumors, contribute to determine poor patient outcome. Therefore, it is of outmost importance to identify new molecular targets for the development of effective therapeutic strategies. In this study, we focused on the enzyme nicotinamide N-methyltransferase (NNMT), which catalyzes the N-methylation reaction of nicotinamide and whose overexpression has been reported in numerous neoplasms, including GI cancers. The aim of this review was to report data illustrating NNMT involvement in these tumors, highlighting its contribution to tumor cell phenotype. Cited works clearly demonstrate the interesting potential use of enzyme level determination for both diagnostic and prognostic purposes. NNMT was also found to positively affect cell viability, proliferation, migration, and invasiveness, contributing to sustain in vitro and in vivo tumor growth and metastatic spread. Moreover, enzyme upregulation featuring tumor cells was significantly associated with enhancement of resistance to treatment with chemotherapeutic drugs. Taken together, these results strongly suggest the possibility to target NNMT for setup of molecular-based strategies to effectively treat GI cancers.
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Affiliation(s)
- Valentina Pozzi
- Department of Clinical Sciences, Polytechnic University of Marche, 60020 Ancona, Italy
| | - Roberto Campagna
- Department of Clinical Sciences, Polytechnic University of Marche, 60020 Ancona, Italy
| | - Davide Sartini
- Department of Clinical Sciences, Polytechnic University of Marche, 60020 Ancona, Italy
- Correspondence: ; Tel.: +39-071-2204673
| | - Monica Emanuelli
- Department of Clinical Sciences, Polytechnic University of Marche, 60020 Ancona, Italy
- New York-Marche Structural Biology Center (NY-MaSBiC), Polytechnic University of Marche, 60131 Ancona, Italy
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Yoshida S, Uehara S, Kondo N, Takahashi Y, Yamamoto S, Kameda A, Kawagoe S, Inoue N, Yamada M, Yoshimura N, Tachibana Y. Peptide-to-Small Molecule: A Pharmacophore-Guided Small Molecule Lead Generation Strategy from High-Affinity Macrocyclic Peptides. J Med Chem 2022; 65:10655-10673. [PMID: 35904556 DOI: 10.1021/acs.jmedchem.2c00919] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Recent technological innovations have led to the development of methods for the rapid identification of high-affinity macrocyclic peptides for a wide range of targets; however, it is still challenging to achieve the desired activity and membrane permeability at the same time. Here, we propose a novel small molecule lead discovery strategy, ″Peptide-to-Small Molecule″, which is a combination of rapid identification of high-affinity macrocyclic peptides via peptide display screening followed by pharmacophore-guided de novo design of small molecules, and demonstrate the applicability using nicotinamide N-methyltransferase (NNMT) as a target. Affinity selection by peptide display technology identified macrocyclic peptide 1 that exhibited good enzymatic inhibitory activity but no cell-based activity. Thereafter, a peptide pharmacophore-guided de novo design and further structure-based optimization resulted in highly potent and cell-active small molecule 14 (cell-free IC50 = 0.0011 μM, cell-based IC50 = 0.40 μM), indicating that this strategy could be a new option for drug discovery.
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Affiliation(s)
- Shuhei Yoshida
- Pharmaceutical Research Division, Shionogi Pharmaceutical Research Center, 3-1-1 Futaba-cho, Toyonaka, Osaka 561-0825, Japan
| | - Shota Uehara
- Pharmaceutical Research Division, Shionogi Pharmaceutical Research Center, 3-1-1 Futaba-cho, Toyonaka, Osaka 561-0825, Japan
| | - Noriyasu Kondo
- Pharmaceutical Research Division, Shionogi Pharmaceutical Research Center, 3-1-1 Futaba-cho, Toyonaka, Osaka 561-0825, Japan
| | - Yu Takahashi
- Pharmaceutical Research Division, Shionogi Pharmaceutical Research Center, 3-1-1 Futaba-cho, Toyonaka, Osaka 561-0825, Japan
| | - Shiho Yamamoto
- Pharmaceutical Research Division, Shionogi Pharmaceutical Research Center, 3-1-1 Futaba-cho, Toyonaka, Osaka 561-0825, Japan
| | - Atsushi Kameda
- Pharmaceutical Research Division, Shionogi Pharmaceutical Research Center, 3-1-1 Futaba-cho, Toyonaka, Osaka 561-0825, Japan
| | - Soichiro Kawagoe
- Pharmaceutical Research Division, Shionogi Pharmaceutical Research Center, 3-1-1 Futaba-cho, Toyonaka, Osaka 561-0825, Japan
| | - Naoko Inoue
- PeptiDream Inc. 3-25-23 Tonomachi, Kawasaki-ku, Kawasaki, Kanagawa 210-0821, Japan
| | - Masami Yamada
- PeptiDream Inc. 3-25-23 Tonomachi, Kawasaki-ku, Kawasaki, Kanagawa 210-0821, Japan
| | - Norito Yoshimura
- Pharmaceutical Research Division, Shionogi Pharmaceutical Research Center, 3-1-1 Futaba-cho, Toyonaka, Osaka 561-0825, Japan
| | - Yuki Tachibana
- Pharmaceutical Research Division, Shionogi Pharmaceutical Research Center, 3-1-1 Futaba-cho, Toyonaka, Osaka 561-0825, Japan
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10
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Li XY, Pi YN, Chen Y, Zhu Q, Xia BR. Nicotinamide N-Methyltransferase: A Promising Biomarker and Target for Human Cancer Therapy. Front Oncol 2022; 12:894744. [PMID: 35756670 PMCID: PMC9218565 DOI: 10.3389/fonc.2022.894744] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2022] [Accepted: 04/29/2022] [Indexed: 11/13/2022] Open
Abstract
Cancer cells typically exhibit a tightly regulated program of metabolic plasticity and epigenetic remodeling to meet the demand of uncontrolled cell proliferation. The metabolic-epigenetic axis has recently become an increasingly hot topic in carcinogenesis and offers new avenues for innovative and personalized cancer treatment strategies. Nicotinamide N-methyltransferase (NNMT) is a metabolic enzyme involved in controlling methylation potential, impacting DNA and histone epigenetic modification. NNMT overexpression has been described in various solid cancer tissues and even body fluids, including serum, urine, and saliva. Furthermore, accumulating evidence has shown that NNMT knockdown significantly decreases tumorigenesis and chemoresistance capacity. Most importantly, the natural NNMT inhibitor yuanhuadine can reverse epidermal growth factor receptor tyrosine kinase inhibitor resistance in lung cancer cells. In this review, we evaluate the possibility of NNMT as a diagnostic biomarker and molecular target for effective anticancer treatment. We also reveal the exact mechanisms of how NNMT affects epigenetics and the development of more potent and selective inhibitors.
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Affiliation(s)
- Xiao-Yu Li
- The First Affiliated Hospital of University of Science and Technology of China (USTC), Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
| | - Ya-Nan Pi
- Department of Gynecology, Harbin Medical University Cancer Hospital, Harbin, China
| | - Yao Chen
- Department of Gynecology, Bengbu Medical College Bengbu, Anhui, China
| | - Qi Zhu
- The First Affiliated Hospital of University of Science and Technology of China (USTC), Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
| | - Bai-Rong Xia
- The First Affiliated Hospital of University of Science and Technology of China (USTC), Division of Life Sciences and Medicine, University of Science and Technology of China, Anhui Provincial Cancer Hospital, Hefei, China
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11
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Iyamu ID, Vilseck JZ, Yadav R, Noinaj N, Huang R. Exploring Unconventional SAM Analogues To Build Cell-Potent Bisubstrate Inhibitors for Nicotinamide N-Methyltransferase. Angew Chem Int Ed Engl 2022; 61:e202114813. [PMID: 35134268 PMCID: PMC8983580 DOI: 10.1002/anie.202114813] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Indexed: 12/17/2022]
Abstract
Nicotinamide N-methyltransferase (NNMT) methylates nicotinamide and has been associated with various diseases. Herein, we report the first cell-potent NNMT bisubstrate inhibitor II399, demonstrating a Ki of 5.9 nM in a biochemical assay and a cellular IC50 value of 1.9 μM. The inhibition mechanism and cocrystal structure confirmed II399 engages both the substrate and cofactor binding pockets. Computational modeling and binding data reveal a balancing act between enthalpic and entropic components that lead to II399's low nM binding affinity. Notably, II399 is 1 000-fold more selective for NNMT than closely related methyltransferases. We expect that II399 would serve as a valuable probe to elucidate NNMT biology. Furthermore, this strategy provides the first case of introducing unconventional SAM mimics, which can be adopted to develop cell-potent inhibitors for other SAM-dependent methyltransferases.
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Affiliation(s)
- Iredia D. Iyamu
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue Institute for Drug Discovery, Purdue University Center for Cancer Research, Purdue University, West Lafayette, Indiana 47907, United States
| | - Jonah Z. Vilseck
- Department of Biochemistry and Molecular Biology, Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, Indiana 46202, United States
| | - Ravi Yadav
- Department of Biological Sciences, Markey Center for Structural Biology, and the Purdue Institute of Inflammation, Immunology and Infectious Disease, Purdue University, West Lafayette, IN 47907, United States
| | - Nicholas Noinaj
- Department of Biological Sciences, Markey Center for Structural Biology, and the Purdue Institute of Inflammation, Immunology and Infectious Disease, Purdue University, West Lafayette, IN 47907, United States
| | - Rong Huang
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue Institute for Drug Discovery, Purdue University Center for Cancer Research, Purdue University, West Lafayette, Indiana 47907, United States
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12
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Wang W, Yang C, Wang T, Deng H. Complex roles of nicotinamide N-methyltransferase in cancer progression. Cell Death Dis 2022; 13:267. [PMID: 35338115 PMCID: PMC8956669 DOI: 10.1038/s41419-022-04713-z] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Revised: 02/23/2022] [Accepted: 03/08/2022] [Indexed: 02/07/2023]
Abstract
Nicotinamide N-methyltransferase (NNMT) is an intracellular methyltransferase, catalyzing the N-methylation of nicotinamide (NAM) to form 1-methylnicotinamide (1-MNAM), in which S-adenosyl-l-methionine (SAM) is the methyl donor. High expression of NNMT can alter cellular NAM and SAM levels, which in turn, affects nicotinamide adenine dinucleotide (NAD+)-dependent redox reactions and signaling pathways, and remodels cellular epigenetic states. Studies have revealed that NNMT plays critical roles in the occurrence and development of various cancers, and analysis of NNMT expression levels in different cancers from The Cancer Genome Atlas (TCGA) dataset indicated that NNMT might be a potential biomarker and therapeutic target for tumor diagnosis and treatment. This review provides a comprehensive understanding of recent advances on NNMT functions in different tumors and deciphers the complex roles of NNMT in cancer progression.
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Affiliation(s)
- Weixuan Wang
- Institute of Chinese Medicine, Guangdong Pharmaceutical University, Guangzhou, People's Republic of China
| | - Changmei Yang
- MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systematic Biology, School of Life Sciences, Tsinghua University, Beijing, People's Republic of China
| | - Tianxiang Wang
- MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systematic Biology, School of Life Sciences, Tsinghua University, Beijing, People's Republic of China
| | - Haiteng Deng
- MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systematic Biology, School of Life Sciences, Tsinghua University, Beijing, People's Republic of China.
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13
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Iyamu ID, Vilseck JZ, Yadav R, Noinaj N, Huang R. Exploring Unconventional SAM Analogues To Build Cell‐Potent Bisubstrate Inhibitors for Nicotinamide
N
‐Methyltransferase. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202114813] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Iredia D. Iyamu
- Department of Medicinal Chemistry and Molecular Pharmacology Purdue Institute for Drug Discovery Purdue University Center for Cancer Research Purdue University West Lafayette IN 47907 USA
| | - Jonah Z. Vilseck
- Department of Biochemistry and Molecular Biology Center for Computational Biology and Bioinformatics Indiana University School of Medicine Indianapolis IN 46202 USA
| | - Ravi Yadav
- Department of Biological Sciences, Markey Center for Structural Biology and the Purdue Institute of Inflammation Immunology and Infectious Disease Purdue University West Lafayette IN 47907 USA
| | - Nicholas Noinaj
- Department of Biological Sciences, Markey Center for Structural Biology and the Purdue Institute of Inflammation Immunology and Infectious Disease Purdue University West Lafayette IN 47907 USA
| | - Rong Huang
- Department of Medicinal Chemistry and Molecular Pharmacology Purdue Institute for Drug Discovery Purdue University Center for Cancer Research Purdue University West Lafayette IN 47907 USA
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Ahmed‐Belkacem R, Debart F, Vasseur J. Bisubstrate Strategies to Target Methyltransferases. European J Org Chem 2022. [DOI: 10.1002/ejoc.202101481] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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15
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Gutiérrez JR, Salgadoa ARM, Arias MDÁ, Vergara HSJ, Rada WR, Gómez CMM. Epigenetic Modulators as Treatment Alternative to Diverse Types of Cancer. Curr Med Chem 2021; 29:1503-1542. [PMID: 34963430 DOI: 10.2174/0929867329666211228111036] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Revised: 08/17/2021] [Accepted: 10/21/2021] [Indexed: 01/10/2023]
Abstract
DNA is packaged in rolls in an octamer of histones forming a complex of DNA and proteins called chromatin. Chromatin as a structural matrix of a chromosome and its modifications are nowadays considered relevant aspects for regulating gene expression, which has become of high interest in understanding genetic mechanisms regulating various diseases, including cancer. In various types of cancer, the main modifications are found to be DNA methylation in the CpG dinucleotide as a silencing mechanism in transcription, post-translational histone modifications such as acetylation, methylation and others that affect the chromatin structure, the ATP-dependent chromatin remodeling and miRNA-mediated gene silencing. In this review we analyze the main alterations in gene expression, the epigenetic modification patterns that cancer cells present, as well as the main modulators and inhibitors of each epigenetic mechanism and the molecular evolution of the most representative inhibitors, which have opened a promising future in the study of HAT, HDAC, non-glycoside DNMT inhibitors and domain inhibitors.
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Affiliation(s)
- Jorseth Rodelo Gutiérrez
- Organic and Biomedical Chemistry Research Group, Faculty of Basic Sciences, Universidad del Atlántico, Barranquilla, Colombia
| | - Arturo René Mendoza Salgadoa
- Organic and Biomedical Chemistry Research Group, Faculty of Basic Sciences, Universidad del Atlántico, Barranquilla, Colombia
| | - Marcio De Ávila Arias
- Department of Medicine, Biotechnology Research Group, Health Sciences Division, Universidad del Norte, Barranquilla, Colombia
| | - Homero San- Juan- Vergara
- Department of Medicine, Biotechnology Research Group, Health Sciences Division, Universidad del Norte, Barranquilla, Colombia
| | - Wendy Rosales Rada
- Advanced Biomedicine Research Group. Faculty of Exact and Natural Sciences, Universidad Libre Seccional, Barranquilla, Colombia
- Advanced Biomedicine Research Group. Faculty of Exact and Natural Sciences, Universidad Libre Seccional, Barranquilla, Colombia
| | - Carlos Mario Meléndez Gómez
- Organic and Biomedical Chemistry Research Group, Faculty of Basic Sciences, Universidad del Atlántico, Barranquilla, Colombia
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16
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Nicotinamide N-Methyltransferase in Head and Neck Tumors: A Comprehensive Review. Biomolecules 2021; 11:biom11111594. [PMID: 34827592 PMCID: PMC8615955 DOI: 10.3390/biom11111594] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Revised: 10/19/2021] [Accepted: 10/26/2021] [Indexed: 12/31/2022] Open
Abstract
The head and neck tumors (HNT) are a heterogeneous group of diseases ranging from benign to malignant lesions, with distinctive molecular and clinical behaviors. Several studies have highlighted the presence of an altered metabolic phenotype in HNT, such as the upregulation of nicotinamide N-methyltransferase (NNMT). However, its biological effects have not been completely disclosed and the role of NNMT in cancer cell metabolism remains unclear. Therefore, this comprehensive review aims to evaluate the available literature regarding the biological, diagnostic, and prognostic role of NNMT in HNT. NNMT was shown to be significantly overexpressed in all of the evaluated HNT types. Moreover, its upregulation has been correlated with cancer cell migration and adverse clinical outcomes, such as high-pathological stage, lymph node metastasis, and locoregional recurrences. However, in oral squamous cell carcinoma (OSCC) these associations are still debated, and several studies have failed to demonstrate the prognostic significance of NNMT. The shRNA-mediated gene silencing efficiently suppressed the NNMT gene expression and exhibited a clear inhibitory effect on cell proliferation, promoting the expression of apoptosis-related proteins and modulating the cell cycle. NNMT could represent a new molecular biomarker and a new target of molecular-based therapy, although further studies on larger patient cohorts are needed to explore its biological role in HNT.
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van Haren MJ, Zhang Y, Thijssen V, Buijs N, Gao Y, Mateuszuk L, Fedak FA, Kij A, Campagna R, Sartini D, Emanuelli M, Chlopicki S, Jongkees SAK, Martin NI. Macrocyclic peptides as allosteric inhibitors of nicotinamide N-methyltransferase (NNMT). RSC Chem Biol 2021; 2:1546-1555. [PMID: 34704059 PMCID: PMC8496086 DOI: 10.1039/d1cb00134e] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2021] [Accepted: 08/18/2021] [Indexed: 12/27/2022] Open
Abstract
Nicotinamide N-methyltransferase (NNMT) methylates nicotinamide to form 1-methylnicotinamide (MNA) using S-adenosyl-l-methionine (SAM) as the methyl donor. The complexity of the role of NNMT in healthy and disease states is slowly being elucidated and provides an indication that NNMT may be an interesting therapeutic target for a variety of diseases including cancer, diabetes, and obesity. Most inhibitors of NNMT described to date are structurally related to one or both of its substrates. In the search for structurally diverse NNMT inhibitors, an mRNA display screening technique was used to identify macrocyclic peptides which bind to NNMT. Several of the cyclic peptides identified in this manner show potent inhibition of NNMT with IC50 values as low as 229 nM. The peptides were also found to downregulate MNA production in cellular assays. Interestingly, substrate competition experiments reveal that these cyclic peptide inhibitors are noncompetitive with either SAM or NA indicating they may be the first allosteric inhibitors reported for NNMT.
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Affiliation(s)
- Matthijs J van Haren
- Biological Chemistry Group, Institute of Biology Leiden, Leiden University Sylviusweg 72 2333 BE Leiden The Netherlands
| | - Yurui Zhang
- Biological Chemistry Group, Institute of Biology Leiden, Leiden University Sylviusweg 72 2333 BE Leiden The Netherlands
| | - Vito Thijssen
- Chemical Biology & Drug Discovery Group, Utrecht Institute for Pharmaceutical Sciences Universiteitsweg 99 3584 CG Utrecht The Netherlands
| | - Ned Buijs
- Biological Chemistry Group, Institute of Biology Leiden, Leiden University Sylviusweg 72 2333 BE Leiden The Netherlands
| | - Yongzhi Gao
- Biological Chemistry Group, Institute of Biology Leiden, Leiden University Sylviusweg 72 2333 BE Leiden The Netherlands
| | - Lukasz Mateuszuk
- Jagiellonian University, Jagiellonian Centre for Experimental Therapeutics (JCET) Bobrzynskiego 14 30-348 Krakow Poland
| | - Filip A Fedak
- Jagiellonian University, Jagiellonian Centre for Experimental Therapeutics (JCET) Bobrzynskiego 14 30-348 Krakow Poland
| | - Agnieszka Kij
- Jagiellonian University, Jagiellonian Centre for Experimental Therapeutics (JCET) Bobrzynskiego 14 30-348 Krakow Poland
| | - Roberto Campagna
- Department of Clinical Sciences, Universitá Politecnica delle Marche Via Ranieri 65 60131 Ancona Italy
| | - Davide Sartini
- Department of Clinical Sciences, Universitá Politecnica delle Marche Via Ranieri 65 60131 Ancona Italy
| | - Monica Emanuelli
- Department of Clinical Sciences, Universitá Politecnica delle Marche Via Ranieri 65 60131 Ancona Italy
| | - Stefan Chlopicki
- Jagiellonian University, Jagiellonian Centre for Experimental Therapeutics (JCET) Bobrzynskiego 14 30-348 Krakow Poland.,Jagiellonian University Medical College, Chair of Pharmacology Grzegorzecka 16 31-531 Krakow Poland
| | - Seino A K Jongkees
- Chemical Biology & Drug Discovery Group, Utrecht Institute for Pharmaceutical Sciences Universiteitsweg 99 3584 CG Utrecht The Netherlands .,Department of Chemistry and Pharmaceutical Sciences, Vrije Universiteit Amsterdam De Boelelaan 1108 1081 HZ Amsterdam The Netherlands
| | - Nathaniel I Martin
- Biological Chemistry Group, Institute of Biology Leiden, Leiden University Sylviusweg 72 2333 BE Leiden The Netherlands
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18
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Parsons RB, Facey PD. Nicotinamide N-Methyltransferase: An Emerging Protagonist in Cancer Macro(r)evolution. Biomolecules 2021; 11:1418. [PMID: 34680055 PMCID: PMC8533529 DOI: 10.3390/biom11101418] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Revised: 09/17/2021] [Accepted: 09/24/2021] [Indexed: 12/15/2022] Open
Abstract
Nicotinamide N-methyltransferase (NNMT) has progressed from being considered merely a Phase II metabolic enzyme to one with a central role in cell function and energy metabolism. Over the last three decades, a significant body of evidence has accumulated which clearly demonstrates a central role for NNMT in cancer survival, metastasis, and drug resistance. In this review, we discuss the evidence supporting a role for NNMT in the progression of the cancer phenotype and how it achieves this by driving the activity of pro-oncogenic NAD+-consuming enzymes. We also describe how increased NNMT activity supports the Warburg effect and how it promotes oncogenic changes in gene expression. We discuss the regulation of NNMT activity in cancer cells by both post-translational modification of the enzyme and transcription factor binding to the NNMT gene, and describe for the first time three long non-coding RNAs which may play a role in the regulation of NNMT transcription. We complete the review by discussing the development of novel anti-cancer therapeutics which target NNMT and provide insight into how NNMT-based therapies may be best employed clinically.
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Affiliation(s)
- Richard B. Parsons
- Institute of Pharmaceutical Science, King’s College London, 150 Stamford Street, London SE1 9NH, UK
| | - Paul D. Facey
- Singleton Park Campus, Swansea University Medical School, Swansea University, Swansea SA2 8PP, UK;
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19
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Esterase-Sensitive Prodrugs of a Potent Bisubstrate Inhibitor of Nicotinamide N-Methyltransferase (NNMT) Display Cellular Activity. Biomolecules 2021; 11:biom11091357. [PMID: 34572571 PMCID: PMC8466754 DOI: 10.3390/biom11091357] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Revised: 09/03/2021] [Accepted: 09/10/2021] [Indexed: 02/04/2023] Open
Abstract
A recently discovered bisubstrate inhibitor of Nicotinamide N-methyltransferase (NNMT) was found to be highly potent in biochemical assays with a single digit nanomolar IC50 value but lacking in cellular activity. We, here, report a prodrug strategy designed to translate the observed potent biochemical inhibitory activity of this inhibitor into strong cellular activity. This prodrug strategy relies on the temporary protection of the amine and carboxylic acid moieties of the highly polar amino acid side chain present in the bisubstrate inhibitor. The modification of the carboxylic acid into a range of esters in the absence or presence of a trimethyl-lock (TML) amine protecting group yielded a range of candidate prodrugs. Based on the stability in an aqueous buffer, and the confirmed esterase-dependent conversion to the parent compound, the isopropyl ester was selected as the preferred acid prodrug. The isopropyl ester and isopropyl ester-TML prodrugs exhibit improved cell permeability, which also translates to significantly enhanced cellular activity as established using assays designed to measure the enzymatic activity of NNMT in live cells.
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20
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Gao Y, van Haren MJ, Buijs N, Innocenti P, Zhang Y, Sartini D, Campagna R, Emanuelli M, Parsons RB, Jespers W, Gutiérrez-de-Terán H, van Westen GJP, Martin NI. Potent Inhibition of Nicotinamide N-Methyltransferase by Alkene-Linked Bisubstrate Mimics Bearing Electron Deficient Aromatics. J Med Chem 2021; 64:12938-12963. [PMID: 34424711 PMCID: PMC8436214 DOI: 10.1021/acs.jmedchem.1c01094] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
![]()
Nicotinamide N-methyltransferase (NNMT) methylates
nicotinamide (vitamin B3) to generate 1-methylnicotinamide (MNA).
NNMT overexpression has been linked to a variety of diseases, most
prominently human cancers, indicating its potential as a therapeutic
target. The development of small-molecule NNMT inhibitors has gained
interest in recent years, with the most potent inhibitors sharing
structural features based on elements of the nicotinamide substrate
and the S-adenosyl-l-methionine (SAM) cofactor.
We here report the development of new bisubstrate inhibitors that
include electron-deficient aromatic groups to mimic the nicotinamide
moiety. In addition, a trans-alkene linker was found
to be optimal for connecting the substrate and cofactor mimics in
these inhibitors. The most potent NNMT inhibitor identified exhibits
an IC50 value of 3.7 nM, placing it among the most active
NNMT inhibitors reported to date. Complementary analytical techniques,
modeling studies, and cell-based assays provide insights into the
binding mode, affinity, and selectivity of these inhibitors.
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Affiliation(s)
- Yongzhi Gao
- Biological Chemistry Group, Institute of Biology Leiden, Leiden University, Sylviusweg 72, 2333 BE Leiden, The Netherlands
| | - Matthijs J van Haren
- Biological Chemistry Group, Institute of Biology Leiden, Leiden University, Sylviusweg 72, 2333 BE Leiden, The Netherlands
| | - Ned Buijs
- Biological Chemistry Group, Institute of Biology Leiden, Leiden University, Sylviusweg 72, 2333 BE Leiden, The Netherlands
| | - Paolo Innocenti
- Biological Chemistry Group, Institute of Biology Leiden, Leiden University, Sylviusweg 72, 2333 BE Leiden, The Netherlands
| | - Yurui Zhang
- Biological Chemistry Group, Institute of Biology Leiden, Leiden University, Sylviusweg 72, 2333 BE Leiden, The Netherlands
| | - Davide Sartini
- Department of Clinical Sciences, Universitá Politecnica delle Marche, Via Ranieri 65, 60131 Ancona, Italy
| | - Roberto Campagna
- Department of Clinical Sciences, Universitá Politecnica delle Marche, Via Ranieri 65, 60131 Ancona, Italy
| | - Monica Emanuelli
- Department of Clinical Sciences, Universitá Politecnica delle Marche, Via Ranieri 65, 60131 Ancona, Italy
| | - Richard B Parsons
- Institute of Pharmaceutical Science, King's College London, London SE1 9NH, United Kingdom
| | - Willem Jespers
- Drug Discovery and Safety, Leiden Academic Center for Drug Research, Einsteinweg 55, 2333 CC Leiden, The Netherlands.,Department of Cell and Molecular Biology, Uppsala University, Uppsala 75124, Sweden
| | | | - Gerard J P van Westen
- Drug Discovery and Safety, Leiden Academic Center for Drug Research, Einsteinweg 55, 2333 CC Leiden, The Netherlands
| | - Nathaniel I Martin
- Biological Chemistry Group, Institute of Biology Leiden, Leiden University, Sylviusweg 72, 2333 BE Leiden, The Netherlands
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Al-Hamashi AA, Chen D, Deng Y, Dong G, Huang R. Discovery of a potent and dual-selective bisubstrate inhibitor for protein arginine methyltransferase 4/5. Acta Pharm Sin B 2021; 11:2709-2718. [PMID: 34589391 PMCID: PMC8463262 DOI: 10.1016/j.apsb.2020.10.013] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2020] [Revised: 09/27/2020] [Accepted: 10/13/2020] [Indexed: 02/06/2023] Open
Abstract
Protein arginine methyltransferases (PRMTs) have been implicated in the progression of many diseases. Understanding substrate recognition and specificity of individual PRMT would facilitate the discovery of selective inhibitors towards future drug discovery. Herein, we reported the design and synthesis of bisubstrate analogues for PRMTs that incorporate a S-adenosylmethionine (SAM) analogue moiety and a tripeptide through an alkyl substituted guanidino group. Compound AH237 is a potent and selective inhibitor for PRMT4 and PRMT5 with a half-maximal inhibition concentration (IC50) of 2.8 and 0.42 nmol/L, respectively. Computational studies provided a plausible explanation for the high potency and selectivity of AH237 for PRMT4/5 over other 40 methyltransferases. This proof-of-principle study outlines an applicable strategy to develop potent and selective bisubstrate inhibitors for PRMTs, providing valuable probes for future structural studies.
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Affiliation(s)
- Ayad A. Al-Hamashi
- Department of Medicinal Chemistry and Molecular Pharmacology, Center for Cancer Research, Institute for Drug Discovery, Purdue University, West Lafayette, IN 47907, USA
- Department of Pharmaceutical Chemistry, College of Pharmacy, University of Baghdad, Bab-almoadham, Baghdad 10047, Iraq
| | - Dongxing Chen
- Department of Medicinal Chemistry and Molecular Pharmacology, Center for Cancer Research, Institute for Drug Discovery, Purdue University, West Lafayette, IN 47907, USA
| | - Youchao Deng
- Department of Medicinal Chemistry and Molecular Pharmacology, Center for Cancer Research, Institute for Drug Discovery, Purdue University, West Lafayette, IN 47907, USA
| | - Guangping Dong
- Department of Medicinal Chemistry and Molecular Pharmacology, Center for Cancer Research, Institute for Drug Discovery, Purdue University, West Lafayette, IN 47907, USA
| | - Rong Huang
- Department of Medicinal Chemistry and Molecular Pharmacology, Center for Cancer Research, Institute for Drug Discovery, Purdue University, West Lafayette, IN 47907, USA
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22
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Iyamu ID, Huang R. Mechanisms and inhibitors of nicotinamide N-methyltransferase. RSC Med Chem 2021; 12:1254-1261. [PMID: 34458733 PMCID: PMC8372200 DOI: 10.1039/d1md00016k] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2021] [Accepted: 04/22/2021] [Indexed: 12/13/2022] Open
Abstract
Nicotinamide N-methyltransferase (NNMT) plays an important role in diverse biological processes by regulating methylation potential and the degradation of nicotinamide. Meanwhile, the aberrant expression of NNMT has been implicated in multiple cancers, metabolic and liver diseases. Therefore, there has been an emerging interest in assessing NNMT as a potential therapeutic target and discovering NNMT inhibitors over the past 5 years. Herein, we focus on the recognition, mechanism, and inhibitors of NNMT with emphasis on key advancements in the field. We also discuss future directions for the development of NNMT inhibitors.
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Affiliation(s)
- Iredia D Iyamu
- Department of Medicinal Chemistry and Molecular Pharmacology, Center for Cancer Research, Institute for Drug Discovery, Purdue University West Lafayette Indiana 47907 USA +1 765 494 3426
| | - Rong Huang
- Department of Medicinal Chemistry and Molecular Pharmacology, Center for Cancer Research, Institute for Drug Discovery, Purdue University West Lafayette Indiana 47907 USA +1 765 494 3426
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The Utility of Nicotinamide N-Methyltransferase as a Potential Biomarker to Predict the Oncological Outcomes for Urological Cancers: An Update. Biomolecules 2021; 11:biom11081214. [PMID: 34439880 PMCID: PMC8393883 DOI: 10.3390/biom11081214] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Revised: 08/06/2021] [Accepted: 08/09/2021] [Indexed: 01/03/2023] Open
Abstract
Nicotinamide N-methyltransferase (NNMT) catalyzes the N-methylation reaction of nicotinamide, using S-adenosyl-L-methionine as the methyl donor. Enzyme overexpression has been described in many non-neoplastic diseases, as well as in a wide range of solid malignancies. This review aims to report and discuss evidence available in scientific literature, dealing with NNMT expression and the potential involvement in main urologic neoplasms, namely, renal, bladder and prostate cancers. Data illustrated in the cited studies clearly demonstrated NNMT upregulation (pathological vs. normal tissue) in association with these aforementioned tumors. In addition to this, enzyme levels were also found to correlate with key prognostic parameters and patient survival. Interestingly, NNMT overexpression also emerged in peripheral body fluids, such as blood and urine, thus leading to candidate the enzyme as promising biomarker for the early and non-invasive detection of these cancers. Examined results undoubtedly showed NNMT as having the capacity to promote cell proliferation, migration and invasiveness, as well as its potential participation in fundamental events highlighting cancer progression, metastasis and resistance to chemo- and radiotherapy. In the light of this evidence, it is reasonable to attribute to NNMT a promising role as a potential biomarker for the diagnosis and prognosis of urologic neoplasms, as well as a molecular target for effective anti-cancer treatment.
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Griffiths A, Wang J, Song Q, Iyamu ID, Liu L, Park J, Jiang Y, Huang R, Song Z. Nicotinamide N-methyltransferase (NNMT) upregulation via the mTORC1-ATF4 pathway activation contributes to palmitate-induced lipotoxicity in hepatocytes. Am J Physiol Cell Physiol 2021; 321:C585-C595. [PMID: 34378991 DOI: 10.1152/ajpcell.00195.2021] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Defined as the dysfunction and/or cell death caused by toxic lipids accumulation in hepatocytes, hepatic lipotoxicity plays a pathological role in non-alcoholic fatty liver disease. The cellular and molecular mechanisms underlying lipotoxicity remain to be elucidated. In this study, using AML12 cells, a non-transformed murine hepatocyte cell line, exposed to palmitate (a 16-C saturated fatty acid) as an experimental model, we investigated the role and mechanisms of nicotinamide N-methyltransferase (NNMT), a methyltransferase catalyzing nicotinamide methylation and degradation, in hepatic lipotoxicity. We initially identified activating transcription factor 4 (ATF4) as a major transcription factor for hepatic NNMT expression. Here, we demonstrated that palmitate upregulates NNMT expression via activating ATF4 in a mechanistic target of rapamycin complex 1 (mTORC1)-dependent mechanism in that mTORC1 inhibition by both Torin1 and rapamycin attenuated ATF4 activation and NNMT upregulation. We further demonstrated that the mTORC1-dependent ATF4 activation is an integral signaling event of unfolded protein response (UPR) as both ATF4 activation and NNMT upregulation by tunicamycin, a well-documented endoplasmic reticulum (ER) stress inducer, are blunted when hepatocytes were pretreated with Torin1. Importantly, our data uncovered that NNMT upregulation contributes to palmitate-induced hepatotoxicity as NNMT inhibition, via either pharmacological (NNMT inhibitors) or genetic approach (siRNA transfection), provided protection against palmitate lipotoxicity. Our further mechanistic exploration identified protein kinase A (PKA) activation to contribute, at least, partially to the protective effect of NNMT inhibition against lipotoxicity. Collectively, our data demonstrated that NNMT upregulation by the mTORC1-ATF4 pathway activation contributes to the development of lipotoxicity in hepatocytes.
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Affiliation(s)
- Alexandra Griffiths
- Department of Kinesiology and Nutrition, University of Illinois at Chicago, Chicago, IL, United States
| | - Jun Wang
- Department of Kinesiology and Nutrition, University of Illinois at Chicago, Chicago, IL, United States.,Department of Gastroenterology, Tongji Medical College and The Central Hospital of Wuhan, Huazhong University of Science and Technology, Wuhan, China
| | - Qing Song
- Department of Kinesiology and Nutrition, University of Illinois at Chicago, Chicago, IL, United States
| | - Iredia D Iyamu
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, IN, United States
| | - Lifeng Liu
- Department of Physiology and Biophysics, University of Illinois at Chicago, Chicago, IL, United States
| | - Jooman Park
- Department of Physiology and Biophysics, University of Illinois at Chicago, Chicago, IL, United States
| | - Yuwei Jiang
- Department of Physiology and Biophysics, University of Illinois at Chicago, Chicago, IL, United States
| | - Rong Huang
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, IN, United States
| | - Zhenyuan Song
- Department of Kinesiology and Nutrition, University of Illinois at Chicago, Chicago, IL, United States
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25
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Chen D, Meng Y, Yu D, Noinaj N, Cheng X, Huang R. Chemoproteomic Study Uncovers HemK2/KMT9 As a New Target for NTMT1 Bisubstrate Inhibitors. ACS Chem Biol 2021; 16:1234-1242. [PMID: 34192867 DOI: 10.1021/acschembio.1c00279] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Understanding the selectivity of methyltransferase inhibitors is important to dissecting the functions of each methyltransferase target. From this perspective, we report a chemoproteomic study to profile the selectivity of a potent protein N-terminal methyltransferase 1 (NTMT1) bisubstrate inhibitor NAH-C3-GPKK (Ki, app = 7 ± 1 nM) in endogenous proteomes. First, we describe the rational design, synthesis, and biochemical characterization of a new chemical probe 6, a biotinylated analogue of NAH-C3-GPKK. Next, we systematically analyze protein networks that may selectively interact with the biotinylated probe 6 in concert with the competitor NAH-C3-GPKK. Besides NTMT1, the designated NTMT1 bisubstrate inhibitor NAH-C3-GPKK was found to also potently inhibit a methyltransferase complex HemK2-Trm112 (also known as KMT9-Trm112), highlighting the importance of systematic selectivity profiling. Furthermore, this is the first potent inhibitor for HemK2/KMT9 reported until now. Thus, our studies lay the foundation for future efforts to develop selective inhibitors for either methyltransferase.
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Affiliation(s)
- Dongxing Chen
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue Institute for Drug Discovery, Purdue University Center for Cancer Research, Purdue University, West Lafayette, Indiana 47907, United States
| | - Ying Meng
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue Institute for Drug Discovery, Purdue University Center for Cancer Research, Purdue University, West Lafayette, Indiana 47907, United States
| | - Dan Yu
- Department of Epigenetics and Molecular Carcinogenesis, University of Texas M.D. Anderson Cancer Center, Houston, Texas 77030, United States
| | - Nicholas Noinaj
- Department of Biological Sciences, Markey Center for Structural Biology, and the Purdue Institute of Inflammation, Immunology and Infectious Disease, Purdue University, West Lafayette, Indiana 47907, United States
| | - Xiaodong Cheng
- Department of Epigenetics and Molecular Carcinogenesis, University of Texas M.D. Anderson Cancer Center, Houston, Texas 77030, United States
| | - Rong Huang
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue Institute for Drug Discovery, Purdue University Center for Cancer Research, Purdue University, West Lafayette, Indiana 47907, United States
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García-Cañaveras JC, Lahoz A. Tumor Microenvironment-Derived Metabolites: A Guide to Find New Metabolic Therapeutic Targets and Biomarkers. Cancers (Basel) 2021; 13:3230. [PMID: 34203535 PMCID: PMC8268968 DOI: 10.3390/cancers13133230] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Revised: 06/17/2021] [Accepted: 06/23/2021] [Indexed: 12/11/2022] Open
Abstract
Metabolic reprogramming is a hallmark of cancer that enables cancer cells to grow, proliferate and survive. This metabolic rewiring is intrinsically regulated by mutations in oncogenes and tumor suppressors, but also extrinsically by tumor microenvironment factors (nutrient and oxygen availability, cell-to-cell interactions, cytokines, hormones, etc.). Intriguingly, only a few cancers are driven by mutations in metabolic genes, which lead metabolites with oncogenic properties (i.e., oncometabolites) to accumulate. In the last decade, there has been rekindled interest in understanding how dysregulated metabolism and its crosstalk with various cell types in the tumor microenvironment not only sustains biosynthesis and energy production for cancer cells, but also contributes to immune escape. An assessment of dysregulated intratumor metabolism has long since been exploited for cancer diagnosis, monitoring and therapy, as exemplified by 18F-2-deoxyglucose positron emission tomography imaging. However, the efficient delivery of precision medicine demands less invasive, cheaper and faster technologies to precisely predict and monitor therapy response. The metabolomic analysis of tumor and/or microenvironment-derived metabolites in readily accessible biological samples is likely to play an important role in this sense. Here, we review altered cancer metabolism and its crosstalk with the tumor microenvironment to focus on energy and biomass sources, oncometabolites and the production of immunosuppressive metabolites. We provide an overview of current pharmacological approaches targeting such dysregulated metabolic landscapes and noninvasive approaches to characterize cancer metabolism for diagnosis, therapy and efficacy assessment.
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Affiliation(s)
- Juan C. García-Cañaveras
- Biomarkers and Precision Medicine Unit, Medical Research Institute-Hospital La Fe, Av. Fernando Abril Martorell 106, 46026 Valencia, Spain
| | - Agustín Lahoz
- Biomarkers and Precision Medicine Unit, Medical Research Institute-Hospital La Fe, Av. Fernando Abril Martorell 106, 46026 Valencia, Spain
- Analytical Unit, Medical Research Institute-Hospital La Fe, Av. Fernando Abril Martorell 106, 46026 Valencia, Spain
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Nicotinamide N-methyl transferase (NNMT): An emerging therapeutic target. Drug Discov Today 2021; 26:2699-2706. [PMID: 34029690 DOI: 10.1016/j.drudis.2021.05.011] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Revised: 04/15/2021] [Accepted: 05/17/2021] [Indexed: 01/01/2023]
Abstract
Nicotinamide N-methyltransferase (NNMT) methylates nicotinamide (NA) to generate 1-methyl nicotinamide. Since its discovery 70 years ago, the appreciation of the role of NNMT in human health has evolved from serving only metabolic functions to also being a driving force in diseases, including a variety of cancers. Despite the increasing evidence indicating NNMT as a viable therapeutic target, the development of cell-active inhibitors against this enzyme is lacking. In this review, we provide an overview of the current status of NNMT inhibitor development, relevant in vitro and in vivo studies, and a discussion of the challenges faced in the development of NNMT inhibitors.
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Lewis CA, Wolfenden R. The Burden Borne by Protein Methyltransferases: Rates and Equilibria of Non-enzymatic Methylation of Amino Acid Side Chains by SAM in Water. Biochemistry 2021; 60:854-858. [PMID: 33667085 DOI: 10.1021/acs.biochem.1c00028] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
SAM is a powerful methylating agent, with a methyl group transfer potential matching the phosphoryl group transfer potential of ATP. SAM-dependent N-methyltransferases have evolved to catalyze the modification of specific lysine residues in histones and transcription factors, in addition to generating epinephrine, N-methylnicotinamide, and a quaternary amine (betaine) that is used to maintain osmotic pressure in plants and halophilic bacteria. To assess the catalytic power of these enzymes and their potential susceptibility to transition state and multisubstrate analogue inhibitors, we determined the rates and positions of the equilibrium of methyl transfer from the trimethylsulfonium ion to model amines in the absence of a catalyst. Unlike the methyl group transfer potential of SAM, which becomes more negative with an increase in pH throughout the normal pH range, equilibrium constants for the hydrolytic demethylation of secondary, tertiary, and quaternary amines are found to be insensitive to a change in pH and resemble each other in magnitude, with an average ΔG value of approximately -0.7 kcal/mol at pH 7. Thus, each of the three steps in the mono-, di-, and trimethylation of lysine by SAM is accompanied by a change in free energy of -7.5 kcal/mol in a neutral solution. Arrhenius analysis of the uncatalyzed reactions shows that the unprotonated form of glycine attacks the trimethylsulfonium ion (TMS+) with second-order rates constant of 1.8 × 10-7 M-1 s-1 at 25 °C (ΔH⧧ = 22 kcal/mol, and TΔS⧧ = -6 kcal/mol). Comparable values are observed for the methylation of secondary and tertiary amines, with k25 values of 1.1 × 10-7 M-1 s-1 for sarcosine and 4.3 × 10-8 M-1 s-1 for dimethylglycine. The non-enzymatic methylations of imidazole and methionine by TMS+, benchmarks for the methylation of histidine and methionine residues by SETD3, exhibit k25 values of 3.3 × 10-9 and 1.2 × 10-9 M-1 s-1, respectively. Lysine methylation by SAM, although slow under physiological conditions (t1/2 = 7 weeks at 25 °C), is accelerated 1.1 × 1012 -fold at the active site of a SET domain methyltransferase.
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Affiliation(s)
- Charles A Lewis
- Department of Biochemistry and Biophysics, The University of North Carolina, Chapel Hill, North Carolina 27514, United States
| | - Richard Wolfenden
- Department of Biochemistry and Biophysics, The University of North Carolina, Chapel Hill, North Carolina 27514, United States
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Kannt A, Rajagopal S, Hallur MS, Swamy I, Kristam R, Dhakshinamoorthy S, Czech J, Zech G, Schreuder H, Ruf S. Novel Inhibitors of Nicotinamide- N-Methyltransferase for the Treatment of Metabolic Disorders. Molecules 2021; 26:molecules26040991. [PMID: 33668468 PMCID: PMC7918612 DOI: 10.3390/molecules26040991] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Revised: 02/01/2021] [Accepted: 02/06/2021] [Indexed: 12/29/2022] Open
Abstract
Nicotinamide-N-methyltransferase (NNMT) is a cytosolic enzyme catalyzing the transfer of a methyl group from S-adenosyl-methionine (SAM) to nicotinamide (Nam). It is expressed in many tissues including the liver, adipose tissue, and skeletal muscle. Its expression in several cancer cell lines has been widely discussed in the literature, and recent work established a link between NNMT expression and metabolic diseases. Here we describe our approach to identify potent small molecule inhibitors of NNMT featuring different binding modes as elucidated by X-ray crystallographic studies.
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Affiliation(s)
- Aimo Kannt
- Fraunhofer Institute for Translational Medicine and Pharmacology-ITMP, Theodor-Stern-Kai 7, 60596 Frankfurt am Main, Germany;
| | - Sridharan Rajagopal
- Jubilant Biosys Limited, #96, Industrial Suburb, 2nd Stage Yeshwanthpur, Bangalore 560022, India; (S.R.); (M.S.H.); (I.S.); (R.K.); (S.D.)
| | - Mahanandeesha S. Hallur
- Jubilant Biosys Limited, #96, Industrial Suburb, 2nd Stage Yeshwanthpur, Bangalore 560022, India; (S.R.); (M.S.H.); (I.S.); (R.K.); (S.D.)
| | - Indu Swamy
- Jubilant Biosys Limited, #96, Industrial Suburb, 2nd Stage Yeshwanthpur, Bangalore 560022, India; (S.R.); (M.S.H.); (I.S.); (R.K.); (S.D.)
| | - Rajendra Kristam
- Jubilant Biosys Limited, #96, Industrial Suburb, 2nd Stage Yeshwanthpur, Bangalore 560022, India; (S.R.); (M.S.H.); (I.S.); (R.K.); (S.D.)
| | - Saravanakumar Dhakshinamoorthy
- Jubilant Biosys Limited, #96, Industrial Suburb, 2nd Stage Yeshwanthpur, Bangalore 560022, India; (S.R.); (M.S.H.); (I.S.); (R.K.); (S.D.)
| | - Joerg Czech
- Sanofi-Aventis Deutschland Gmbh, Industriepark Hoechst, 65926 Frankfurt am Main, Germany; (J.C.); (G.Z.); (H.S.)
| | - Gernot Zech
- Sanofi-Aventis Deutschland Gmbh, Industriepark Hoechst, 65926 Frankfurt am Main, Germany; (J.C.); (G.Z.); (H.S.)
| | - Herman Schreuder
- Sanofi-Aventis Deutschland Gmbh, Industriepark Hoechst, 65926 Frankfurt am Main, Germany; (J.C.); (G.Z.); (H.S.)
| | - Sven Ruf
- Sanofi-Aventis Deutschland Gmbh, Industriepark Hoechst, 65926 Frankfurt am Main, Germany; (J.C.); (G.Z.); (H.S.)
- Correspondence:
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30
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Poltronieri P, Celetti A, Palazzo L. Mono(ADP-ribosyl)ation Enzymes and NAD + Metabolism: A Focus on Diseases and Therapeutic Perspectives. Cells 2021; 10:cells10010128. [PMID: 33440786 PMCID: PMC7827148 DOI: 10.3390/cells10010128] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Revised: 01/05/2021] [Accepted: 01/05/2021] [Indexed: 12/19/2022] Open
Abstract
Mono(ADP-ribose) transferases and mono(ADP-ribosyl)ating sirtuins use NAD+ to perform the mono(ADP-ribosyl)ation, a simple form of post-translational modification of proteins and, in some cases, of nucleic acids. The availability of NAD+ is a limiting step and an essential requisite for NAD+ consuming enzymes. The synthesis and degradation of NAD+, as well as the transport of its key intermediates among cell compartments, play a vital role in the maintenance of optimal NAD+ levels, which are essential for the regulation of NAD+-utilizing enzymes. In this review, we provide an overview of the current knowledge of NAD+ metabolism, highlighting the functional liaison with mono(ADP-ribosyl)ating enzymes, such as the well-known ARTD10 (also named PARP10), SIRT6, and SIRT7. To this aim, we discuss the link of these enzymes with NAD+ metabolism and chronic diseases, such as cancer, degenerative disorders and aging.
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Affiliation(s)
- Palmiro Poltronieri
- Institute of Sciences of Food Productions, National Research Council of Italy, via Monteroni 7, 73100 Lecce, Italy
- Correspondence: (P.P.); (A.C.); (L.P.)
| | - Angela Celetti
- Institute for the Experimental Endocrinology and Oncology, National Research Council of Italy, Via Sergio Pansini 5, 80131 Naples, Italy
- Correspondence: (P.P.); (A.C.); (L.P.)
| | - Luca Palazzo
- Institute for the Experimental Endocrinology and Oncology, National Research Council of Italy, Via Tommaso de Amicis 95, 80145 Naples, Italy
- Correspondence: (P.P.); (A.C.); (L.P.)
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31
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Lu J, Bart AG, Wu Q, Criscione KR, McLeish MJ, Scott EE, Grunewald GL. Structure-Based Drug Design of Bisubstrate Inhibitors of Phenylethanolamine N-Methyltransferase Possessing Low Nanomolar Affinity at Both Substrate Binding Domains 1. J Med Chem 2020; 63:13878-13898. [PMID: 33147410 DOI: 10.1021/acs.jmedchem.0c01475] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
The enzyme phenylethanolamine N-methyltransferase (PNMT, EC 2.1.1.28) catalyzes the final step in the biosynthesis of epinephrine and is a potential drug target, primarily for the control of hypertension. Unfortunately, many potent PNMT inhibitors also possess significant affinity for the a2-adrenoceptor, which complicates the interpretation of their pharmacology. A bisubstrate analogue approach offers the potential for development of highly selective inhibitors of PNMT. This paper documents the design, synthesis, and evaluation of such analogues, several of which were found to possess human PNMT (hPNMT) inhibitory potency <5 nM versus AdoMet. Site-directed mutagenesis studies were consistent with bisubstrate binding. Two of these compounds (19 and 29) were co-crystallized with hPNMT and the resulting structures revealed both compounds bound as predicted, simultaneously occupying both substrate binding domains. This bisubstrate inhibitor approach has resulted in one of the most potent (20) and selective (vs the a2-adrenoceptor) inhibitors of hPNMT yet reported.
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Affiliation(s)
- Jian Lu
- Department of Medicinal Chemistry, University of Kansas, Lawrence, Kansas 66045, United States
| | - Aaron G Bart
- Department of Medicinal Chemistry, University of Kansas, Lawrence, Kansas 66045, United States
| | - Qian Wu
- Department of Chemistry and Chemical Biology, Purdue School of Science, IUPUI, Indianapolis, Indiana 46202, United States
| | - Kevin R Criscione
- Department of Medicinal Chemistry, University of Kansas, Lawrence, Kansas 66045, United States
| | - Michael J McLeish
- Department of Chemistry and Chemical Biology, Purdue School of Science, IUPUI, Indianapolis, Indiana 46202, United States
| | - Emily E Scott
- Department of Medicinal Chemistry, University of Kansas, Lawrence, Kansas 66045, United States
| | - Gary L Grunewald
- Department of Medicinal Chemistry, University of Kansas, Lawrence, Kansas 66045, United States
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32
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Chen D, Dong C, Dong G, Srinivasan K, Min J, Noinaj N, Huang R. Probing the Plasticity in the Active Site of Protein N-terminal Methyltransferase 1 Using Bisubstrate Analogues. J Med Chem 2020; 63:8419-8431. [PMID: 32605369 PMCID: PMC7429357 DOI: 10.1021/acs.jmedchem.0c00770] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
The bisubstrate analogue strategy is a promising approach to develop potent and selective inhibitors for protein methyltransferases. Herein, the interactions of a series of bisubstrate analogues with protein N-terminal methyltransferase 1 (NTMT1) were examined to probe the molecular properties of the active site of NTMT1. Our results indicate that a 2-C to 4-C atom linker enables its respective bisubstrate analogue to occupy both substrate- and cofactor-binding sites of NTMT1, but the bisubstrate analogue with a 5-C atom linker only interacts with the substrate-binding site and functions as a substrate. Furthermore, the 4-C atom linker is the optimal and produces the most potent inhibitor (Ki,app = 130 ± 40 pM) for NTMT1 to date, displaying more than 3000-fold selectivity for other methyltransferases and even for its homologue NTMT2. This study reveals the molecular basis for the plasticity of the active site of NTMT1. Additionally, our study outlines general guidance on the development of bisubstrate inhibitors for any methyltransferases.
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Affiliation(s)
- Dongxing Chen
- Department of Medicinal Chemistry and Molecular Pharmacology, Center for Cancer Research, Institute for Drug Discovery, Purdue University, West Lafayette, Indiana 47907, United States
| | - Cheng Dong
- Structural Genomics Consortium, Department of Physiology, University of Toronto, Toronto, Ontario M5G 1L7, Canada
| | - Guangping Dong
- Department of Medicinal Chemistry and Molecular Pharmacology, Center for Cancer Research, Institute for Drug Discovery, Purdue University, West Lafayette, Indiana 47907, United States
| | - Karthik Srinivasan
- Markey Center for Structural Biology, Department of Biological Sciences and the Purdue Institute of Inflammation, Immunology and Infectious Disease, Purdue University, West Lafayette, Indiana 47907, United States
| | - Jinrong Min
- Structural Genomics Consortium, Department of Physiology, University of Toronto, Toronto, Ontario M5G 1L7, Canada
| | - Nicholas Noinaj
- Markey Center for Structural Biology, Department of Biological Sciences and the Purdue Institute of Inflammation, Immunology and Infectious Disease, Purdue University, West Lafayette, Indiana 47907, United States
| | - Rong Huang
- Department of Medicinal Chemistry and Molecular Pharmacology, Center for Cancer Research, Institute for Drug Discovery, Purdue University, West Lafayette, Indiana 47907, United States
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33
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Mahmoodi N, Harijan RK, Schramm VL. Transition-State Analogues of Phenylethanolamine N-Methyltransferase. J Am Chem Soc 2020; 142:14222-14233. [PMID: 32702980 DOI: 10.1021/jacs.0c05446] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Phenylethanolamine N-methyltransferase (PNMT) is a critical enzyme in catecholamine synthesis. It transfers the methyl group of S-adenosylmethionine (SAM) to catalyze the synthesis of epinephrine from norepinephrine. Epinephrine has been associated with diverse human processes, including the regulation of blood pressure and respiration, as well as neurodegeneration found in Alzheimer's disease. Human PNMT (hPNMT) proceeds through an SN2 transition state (TS) in which the transfer of the methyl group is rate limiting. TS analogue enzyme inhibitors are specific for their target and bind orders of magnitude more tightly than their substrates. Molecules resembling the TS of hPNMT were designed, synthesized, and kinetically characterized. This new inhibitory scaffold was designed to mimic the geometry and electronic properties of the hPNMT TS. Synthetic efforts resulted in a tight-binding inhibitor with a Ki value of 12.0 nM. This is among the first of the TS analogue inhibitors of methyltransferase enzymes to show an affinity in the nanomolar range. Isothermal titration calorimetry (ITC) measurements indicated negative cooperative binding of inhibitor to the dimeric protein, driven by favorable entropic contributions. Structural analysis revealed that inhibitor 3 binds to hPNMT by filling the catalytic binding pockets for the cofactor (SAM) and the substrate (norepinephrine) binding sites.
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Affiliation(s)
- Niusha Mahmoodi
- Department of Biochemistry, Albert Einstein College of Medicine, New York, New York 10461, United States
| | - Rajesh K Harijan
- Department of Biochemistry, Albert Einstein College of Medicine, New York, New York 10461, United States
| | - Vern L Schramm
- Department of Biochemistry, Albert Einstein College of Medicine, New York, New York 10461, United States
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34
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Mackie BD, Chen D, Dong G, Dong C, Parker H, Schaner Tooley CE, Noinaj N, Min J, Huang R. Selective Peptidomimetic Inhibitors of NTMT1/2: Rational Design, Synthesis, Characterization, and Crystallographic Studies. J Med Chem 2020; 63:9512-9522. [PMID: 32689795 DOI: 10.1021/acs.jmedchem.0c00689] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Protein N-terminal methyltransferases (NTMTs) methylate the α-N-terminal amines of proteins starting with the canonical X-P-K/R motif. Genetic studies imply that NTMT1 regulates cell mitosis and DNA damage repair. Herein, we report the rational design and development of the first potent peptidomimetic inhibitor for NTMT1/2. Biochemical and cocrystallization studies manifest that BM30 (with a half-maximal inhibitory concentration of 0.89 ± 0.10 μM) is a competitive inhibitor to the peptide substrate and noncompetitive to the cofactor S-adenosylmethionine. BM30 exhibits over 100-fold selectivity to NTMT1/2 among a panel of 41 MTs, indicating its potential to achieve high selectivity when targeting the peptide substrate binding site of NTMT1/2. Its cell-permeable analogue DC432 (IC50 of 54 ± 4 nM) decreases the N-terminal methylation level of the regulator of chromosome condensation 1 and SET proteins in HCT116 cells. This proof-of principle study provides valuable probes for NTMT1/2 and highlights the opportunity to develop more cell-potent inhibitors to elucidate the function of NTMTs in the future.
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Affiliation(s)
- Brianna D Mackie
- Department of Medicinal Chemistry, Institute of Structural Biology, Drug Discovery and Development, School of Pharmacy, Virginia Commonwealth University, Richmond, Virginia 23298, United States
| | - Dongxing Chen
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue Institute for Drug Discovery, Purdue University Center for Cancer Research, Purdue University, West Lafayette, Indiana 47907, United States
| | - Guangping Dong
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue Institute for Drug Discovery, Purdue University Center for Cancer Research, Purdue University, West Lafayette, Indiana 47907, United States
| | - Cheng Dong
- Structural Genomics Consortium, Department of Physiology, University of Toronto, Toronto, Ontario M5G 1L7, Canada
| | - Haley Parker
- Department of Biochemistry, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, New York 14203, United States
| | - Christine E Schaner Tooley
- Department of Biochemistry, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, New York 14203, United States
| | - Nicholas Noinaj
- Department of Biological Sciences, Markey Center for Structural Biology, and the Purdue Institute of Inflammation, Immunology and Infectious Disease, Purdue University, West Lafayette, Indiana 47907, United States
| | - Jinrong Min
- Structural Genomics Consortium, Department of Physiology, University of Toronto, Toronto, Ontario M5G 1L7, Canada
| | - Rong Huang
- Department of Medicinal Chemistry, Institute of Structural Biology, Drug Discovery and Development, School of Pharmacy, Virginia Commonwealth University, Richmond, Virginia 23298, United States.,Department of Medicinal Chemistry and Molecular Pharmacology, Purdue Institute for Drug Discovery, Purdue University Center for Cancer Research, Purdue University, West Lafayette, Indiana 47907, United States
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35
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Iyamu ID, Huang R. Development of fluorescence polarization-based competition assay for nicotinamide N-methyltransferase. Anal Biochem 2020; 604:113833. [PMID: 32622979 DOI: 10.1016/j.ab.2020.113833] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2020] [Revised: 06/14/2020] [Accepted: 06/15/2020] [Indexed: 12/31/2022]
Abstract
Methylation-mediated pathways play important roles in the progression of various diseases. Thus, targeting methyltransferases has proven to be a promising strategy for developing novel therapies. Nicotinamide N-methyltransferase (NNMT) is a major metabolic enzyme involved in epigenetic regulation through catalysis of methyl transfer from the cofactor S-adenosyl-l-methionine onto nicotinamide and other pyridines. Accumulating evidence infers that NNMT is a novel therapeutic target for a variety of diseases such as cancer, diabetes, obesity, cardiovascular and neurodegenerative diseases. Therefore, there is an urgent need to discover potent and specific inhibitors for NNMT to assess its therapeutical potential. Herein, we reported the design and synthesis of a fluorescent probe II138, exhibiting a Kd value of 369 ± 14 nM for NNMT. We also established a fluorescence polarization (FP)-based competition assay for evaluation of NNMT inhibitors. Importantly, the unique feature of this FP competition assay is its capability to identify inhibitors that interfere with the interaction of the NNMT active site directly or allosterically. In addition, this assay performance is robust with a Z'factor of 0.76, indicating its applicability in high-throughput screening for NNMT inhibitors.
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Affiliation(s)
- Iredia D Iyamu
- Department of Medicinal Chemistry and Molecular Pharmacology, Center for Cancer Research, Institute for Drug Discovery, Purdue University, West Lafayette, IN, 47907, United States
| | - Rong Huang
- Department of Medicinal Chemistry and Molecular Pharmacology, Center for Cancer Research, Institute for Drug Discovery, Purdue University, West Lafayette, IN, 47907, United States.
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