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An Allosteric PGAM1 Inhibitor Effectively Suppresses Pancreatic Ductal Adenocarcinoma

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An Allosteric PGAM1 Inhibitor Effectively Suppresses Pancreatic Ductal Adenocarcinoma An allosteric PGAM1 inhibitor effectively suppresses pancreatic ductal adenocarcinoma Chen-Lei Wena,b,1, Ke Huangc,1, Lu-Lu Jiangc,1, Xiong-Xiong Lua,b,1, Yu-Ting Daid,e,f, Min-Min Shia,b, Xiao-Mei Tanga,b, Qing-Bing Wangg, Xiao-Dan Zhangc, Peng-Hui Wangc, Hui-Ti Lic, Xiao-Xue Ruanc, Li-Wen Wanga,b, Xin-Jing Wanga,b, Qian Wangh, Wei Luc, Xiao-Qiang Xiangc, Xun Sunc, Yan-Hui Xuh, Lu-Hua Laii, Qian Zhana,b, Hong-Wei Lia, Cheng-Hong Penga,b, Jing Chenj, Jin-Yan Huangd,e, De-Yong Yec, Sai-Juan Chend,e, Zhu Chend,e,2, Min Lik,2, Yuan Fanga,b,2, Bai-Yong Shena,b,2, and Lu Zhouc,2 aResearch Institute of Pancreatic Disease, Ruijin Hospital, School of Medicine, Shanghai Jiao Tong University, 200025 Shanghai, China; bShanghai Institute of Digestive Surgery, Ruijin Hospital, School of Medicine, Shanghai Jiao Tong University, 200025 Shanghai, China; cSchool of Pharmacy, Fudan University, 201203 Shanghai, China; dNational Research Center for Translational Medicine, Ruijin Hospital, 200025 Shanghai, China; eState Key Laboratory of Medical Genomics, Shanghai Institute of Hematology, Ruijin Hospital, School of Medicine, Shanghai Jiao Tong University, 200025 Shanghai, China; fSchool of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 200240 Shanghai, China; gDepartment of Interventional Radiology, Ruijin Hospital, School of Medicine, Shanghai Jiao Tong University, 200025 Shanghai, China; hFudan University Shanghai Cancer Center, Institute of Biomedical Sciences, Shanghai Medical College of Fudan University, 200032 Shanghai, China; iCollege of Chemistry and Molecular Engineering, Peking University, 100871 Beijing, China; jDepartment of Hematology and Medical Oncology, Winship Cancer Institute, Emory University School of Medicine, Atlanta, GA 30322; and kDepartment of Surgery, The University of Oklahoma Health Sciences Center, Oklahoma City, OK 73101 Contributed by Zhu Chen, September 30, 2019 (sent for review August 21, 2019; reviewed by Surinder K. Batra and Ajay P. Singh) Glycolytic enzyme phosphoglycerate mutase 1 (PGAM1) plays a processes with a single drug, as a way of “killing two birds with critical role in cancer metabolism by coordinating glycolysis and one stone” (13). biosynthesis. A well-validated PGAM1 inhibitor, however, has not Pancreatic ductal adenocarcinoma (PDAC) is one of the most been reported for treating pancreatic ductal adenocarcinoma lethal malignancies, with 5-y survival rates about 6% (14). Sur- (PDAC), which is one of the deadliest malignancies worldwide. gery is the major therapy for treating early patients with PDAC; By uncovering the elevated PGAM1 expressions were statistically the 5-y survival rate of resected patients is about 20% (15, 16). related to worse prognosis of PDAC in a cohort of 50 patients, we MEDICAL SCIENCES developed a series of allosteric PGAM1 inhibitors by structure- Significance guided optimization. The compound KH3 significantly suppressed proliferation of various PDAC cells by down-regulating the levels of glycolysis and mitochondrial respiration in correlation with Dysregulated metabolism is one of the hallmarks of pancreatic PGAM1 expression. Similar to PGAM1 depletion, KH3 dramatically ductal adenocarcinoma, which is the major subtype of pan- hampered the canonic pathways highly involved in cancer metab- creatic cancer considered as the deadliest malignancy world- olism and development. Additionally, we observed the shared wide. This led us to search the potent therapeutic target for expression profiles of several signature pathways at 12 h after regulating cancer metabolism in treatment. By uncovering that treatment in multiple PDAC primary cells of which the matched phosphoglycerate mutase 1 (PGAM1), a critical metabolic en- patient-derived xenograft (PDX) models responded similarly to zyme involved in glycolysis and biosynthesis, was frequently KH3 in the 2 wk treatment. The better responses to KH3 in PDXs up-regulated in patients with pancreatic ductal adenocarci- were associated with higher expression of PGAM1 and longer/ noma (PDAC), we developed a series of allosteric PGAM1 in- stronger suppressions of cancer metabolic pathways. Taken to- hibitors which showed efficacious in multiple preclinical gether, our findings demonstrate a strategy of targeting cancer models of PDAC, especially with high PGAM1 expression. Of metabolism by PGAM1 inhibition in PDAC. Also, this work pro- note, PGAM1 inhibition cosuppressed several metabolic and vided “proof of concept” for the potential application of metabolic cancerous pathways, of which the suppression level was cor- treatment in clinical practice. related with efficacy. This work strongly suggests that in- hibition of cancer metabolism would be a strategy for treating PGAM1 inhibitor | PDAC | glycolysis | cancer metabolism pancreatic cancer. Author contributions: C.-L.W., K.H., X.-M.T., W.L., L.-H.L., H.-W.L., C.-H.P., J.C., D.-Y.Y., n recent years, research interest in tumor-specific altered me- S.-J.C., M.L., Y.F., B.-Y.S., and L.Z. designed research; C.-L.W., K.H., L.-L.J., X.-X.L., Y.-T.D., Itabolism, discovered by Otto Warburg about a century ago, has M.-M.S., X.-M.T., Q.-B.W., X.-D.Z., P.-H.W., H.-T.L., X.-X.R., L.-W.W., X.-J.W., W.L., X.-Q.X., been growing worldwide (1). Targeting cancer metabolism has X.S., Q.Z., C.-H.P., J.C., D.-Y.Y., S.-J.C., M.L., Y.F., B.-Y.S., and L.Z. performed research; C.-L.W., K.H., L.-L.J., X.-X.L., Y.-T.D., M.-M.S., X.-M.T., Q.W., W.L., Y.-H.X., L.-H.L., Q.Z., emerged during the past decade as a promising strategy for the J.C., J.-Y.H., D.-Y.Y., S.-J.C., Y.F., and L.Z. contributed new reagents/analytic tools; development of anticancer agents by aiming at a tumor’s sweet C.-L.W., K.H., L.-L.J., X.-X.L., Y.-T.D., M.-M.S., X.-M.T., W.L., X.-Q.X., J.-Y.H., D.-Y.Y., Z.C., spot during the past decade (2). It has been proposed that Y.F., and L.Z. analyzed data; and C.-L.W., K.H., L.-L.J., X.-X.L., Y.F., and L.Z. wrote accelerated aerobic glycolysis is capable of incorporating nutri- the paper. ents into the biomass (e.g., nucleotides, amino acids, and lipids) Reviewers: S.K.B., University of Nebraska Medical Center; and A.P.S., University of South Alabama. for rapidly growing tumor cells (3). Thus glycolysis and sub- The authors declare no competing interest. sequent biosynthesis pathways have not only been considered as an integral part of cancer biology, but have also become a Published under the PNAS license. promising target of cancer therapy (1, 3–12). Among all meta- Data deposition: All data can be viewed in NODE (http://www.biosino.org/node) by past- ing the accession OEP000515 into the text search box or through the URL: http://www. bolic enzymes involved in cancer metabolism, our previous study biosino.org/node/project/detail/OEP000515. has shown that phosphoglycerate mutase 1 (PGAM1) plays an 1C.-L.W., K.H., L.-L.J. and X.-X.L. contributed equally to this work. important role in coordinating glycolysis and biosynthesis in- 2To whom correspondence may be addressed. Email: [email protected], Min-Li@OUHSC. cluding pentose phosphate pathway and serine synthesis pathway edu, [email protected], [email protected], or [email protected]. to promote tumor growth (4). Furthermore, it has been sug- This article contains supporting information online at www.pnas.org/lookup/suppl/doi:10. gested that blocking of PGAM1 has potential for controlling 1073/pnas.1914557116/-/DCSupplemental. cancer cell growth by targeting both energetic and anabolic www.pnas.org/cgi/doi/10.1073/pnas.1914557116 PNAS Latest Articles | 1of10 Downloaded by guest on September 30, 2021 Unfortunately, most patients with PDAC have late-stage disease bond with Lys100. Additionally, the phenyl ring of KH2 interacts and are unable to have resection when they are diagnosed. with Phe22 through hydrophobic interaction (Fig. 1G), leading Combination chemotherapies have been used as first-line regi- to better binding affinity with a 15-fold improvement of in vitro mens for treating patients with late-stage PDAC, including a potency over Alizarin Red S. Compared with apo-form, residues combination therapy of gemcitabine with nab-paclitaxel (17) and 109 to 117 of PGAM1 in PGAM1-KH2 complex change its FOLFIRINOX, which is a 4-drug combination consisting of conformation, implying that KH2 is an allosteric inhibitor (SI leucovorin, fluorouracil, irinotecan, and oxaliplatin (18). The Appendix, Fig. S2). With further modification on phenyl ring by median overall survival of these regimens is only 8.5 and 11.1 mo, N-substituted pyrrolidine derivative compound, KH3 showed a respectively (17, 18). Hence, there is a strong demand to identify dramatic enhancement in both enzymatic (50-fold) and cell new therapeutic targets since PDAC is resistant to most of the proliferation assay (>100-fold) over Alizarin Red S, probably currently used therapies (14, 15). In PDAC, it has been shown due to its bigger N-substituted group for better binding and cell that reprogramming of cell metabolism is driven by frequently permeability. For cell-based assay, KH3 is the most potent mutated genes (16, 19), which make cancer cells more dependent PGAM1 inhibitor reported to date. on key metabolites (20) and more vulnerable to inhibition of metabolite-related enzymes. This is due to the strategy of col- Structural and Biochemical Analysis of PGAM1 Inhibitors. By de- lateral lethality which occurs when deletion of tumor suppressor veloping a series of PGAM1 inhibitors, we next moved to analyze genes results in codeletion of a large number of genes commonly their stuctural and chemical charateristics. Comparison of cocrystal known without direct role in cancer development, due to prox- structures containing 3PG (PDB:2F90) and KH2 (PDB:5Y65) imity of chromosome.
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