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Lee CM, Hwang Y, Kim M, Park YC, Kim H, Fang S. PHGDH: a novel therapeutic target in cancer. Exp Mol Med 2024; 56:1513-1522. [PMID: 38945960 PMCID: PMC11297271 DOI: 10.1038/s12276-024-01268-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2023] [Revised: 03/18/2024] [Accepted: 04/01/2024] [Indexed: 07/02/2024] Open
Abstract
Serine is a key contributor to the generation of one-carbon units for DNA synthesis during cellular proliferation. In addition, it plays a crucial role in the production of antioxidants that prevent abnormal proliferation and stress in cancer cells. In recent studies, the relationship between cancer metabolism and the serine biosynthesis pathway has been highlighted. In this context, 3-phosphoglycerate dehydrogenase (PHGDH) is notable as a key enzyme that functions as the primary rate-limiting enzyme in the serine biosynthesis pathway, facilitating the conversion of 3-phosphoglycerate to 3-phosphohydroxypyruvate. Elevated PHGDH activity in diverse cancer cells is mediated through genetic amplification, posttranslational modification, increased transcription, and allosteric regulation. Ultimately, these characteristics allow PHGDH to not only influence the growth and progression of cancer but also play an important role in metastasis and drug resistance. Consequently, PHGDH has emerged as a crucial focal point in cancer research. In this review, the structural aspects of PHGDH and its involvement in one-carbon metabolism are investigated, and PHGDH is proposed as a potential therapeutic target in diverse cancers. By elucidating how PHGDH expression promotes cancer growth, the goal of this review is to provide insight into innovative treatment strategies. This paper aims to reveal how PHGDH inhibitors can overcome resistance mechanisms, contributing to the development of effective cancer treatments.
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Affiliation(s)
- Chae Min Lee
- Graduate School of Medical Science, Brain Korea 21 Project, Yonsei University College of Medicine, Seoul, Republic of Korea
- Department of Biomedical Sciences, Gangnam Severance Hospital, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Yeseong Hwang
- Graduate School of Medical Science, Brain Korea 21 Project, Yonsei University College of Medicine, Seoul, Republic of Korea
- Department of Biomedical Sciences, Gangnam Severance Hospital, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Minki Kim
- Graduate School of Medical Science, Brain Korea 21 Project, Yonsei University College of Medicine, Seoul, Republic of Korea
- Department of Biomedical Sciences, Gangnam Severance Hospital, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Ye-Chan Park
- Graduate School of Medical Science, Brain Korea 21 Project, Yonsei University College of Medicine, Seoul, Republic of Korea
- Department of Biomedical Sciences, Gangnam Severance Hospital, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Hyeonhui Kim
- Graduate School of Medical Science, Brain Korea 21 Project, Yonsei University College of Medicine, Seoul, Republic of Korea
- Department of Biomedical Sciences, Gangnam Severance Hospital, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Sungsoon Fang
- Graduate School of Medical Science, Brain Korea 21 Project, Yonsei University College of Medicine, Seoul, Republic of Korea.
- Department of Biomedical Sciences, Gangnam Severance Hospital, Yonsei University College of Medicine, Seoul, Republic of Korea.
- Chronic Intractable Disease for Systems Medicine Research Center, Yonsei University College of Medicine, Seoul, Republic of Korea.
- Severance Institute for Vascular and Metabolic Research, Yonsei University College of Medicine, Seoul, Republic of Korea.
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2
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Noom A, Sawitzki B, Knaus P, Duda GN. A two-way street - cellular metabolism and myofibroblast contraction. NPJ Regen Med 2024; 9:15. [PMID: 38570493 PMCID: PMC10991391 DOI: 10.1038/s41536-024-00359-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Accepted: 03/20/2024] [Indexed: 04/05/2024] Open
Abstract
Tissue fibrosis is characterised by the high-energy consumption associated with myofibroblast contraction. Although myofibroblast contraction relies on ATP production, the role of cellular metabolism in myofibroblast contraction has not yet been elucidated. Studies have so far only focused on myofibroblast contraction regulators, such as integrin receptors, TGF-β and their shared transcription factor YAP/TAZ, in a fibroblast-myofibroblast transition setting. Additionally, the influence of the regulators on metabolism and vice versa have been described in this context. However, this has so far not yet been connected to myofibroblast contraction. This review focuses on the known and unknown of how cellular metabolism influences the processes leading to myofibroblast contraction and vice versa. We elucidate the signalling cascades responsible for myofibroblast contraction by looking at FMT regulators, mechanical cues, biochemical signalling, ECM properties and how they can influence and be influenced by cellular metabolism. By reviewing the existing knowledge on the link between cellular metabolism and the regulation of myofibroblast contraction, we aim to pinpoint gaps of knowledge and eventually help identify potential research targets to identify strategies that would allow switching tissue fibrosis towards tissue regeneration.
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Affiliation(s)
- Anne Noom
- Julius Wolff Institute (JWI), Berlin Institute of Health and Center for Musculoskeletal Surgery at Charité - Universitätsmedizin Berlin, 13353, Berlin, Germany
- BIH Center for Regenerative Therapies (BCRT), Berlin Institute of Health at Charité - Universitätsmedizin Berlin, 13353, Berlin, Germany
| | - Birgit Sawitzki
- Department of Infectious Diseases and Respiratory Medicine, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt University of Berlin, 13353, Berlin, Germany
- Center of Immunomics, Berlin Institute of Health at Charité - Universitätsmedizin Berlin, 13353, Berlin, Germany
| | - Petra Knaus
- Institute of Chemistry and Biochemistry - Biochemistry, Freie Universität Berlin, 14195, Berlin, Germany
| | - Georg N Duda
- Julius Wolff Institute (JWI), Berlin Institute of Health and Center for Musculoskeletal Surgery at Charité - Universitätsmedizin Berlin, 13353, Berlin, Germany.
- BIH Center for Regenerative Therapies (BCRT), Berlin Institute of Health at Charité - Universitätsmedizin Berlin, 13353, Berlin, Germany.
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Lee SE, Park S, Yi S, Choi NR, Lim MA, Chang JW, Won HR, Kim JR, Ko HM, Chung EJ, Park YJ, Cho SW, Yu HW, Choi JY, Yeo MK, Yi B, Yi K, Lim J, Koh JY, Lee MJ, Heo JY, Yoon SJ, Kwon SW, Park JL, Chu IS, Kim JM, Kim SY, Shan Y, Liu L, Hong SA, Choi DW, Park JO, Ju YS, Shong M, Kim SK, Koo BS, Kang YE. Unraveling the role of the mitochondrial one-carbon pathway in undifferentiated thyroid cancer by multi-omics analyses. Nat Commun 2024; 15:1163. [PMID: 38331894 PMCID: PMC10853200 DOI: 10.1038/s41467-024-45366-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Accepted: 01/18/2024] [Indexed: 02/10/2024] Open
Abstract
The role of the serine/glycine metabolic pathway (SGP) has recently been demonstrated in tumors; however, the pathological relevance of the SGP in thyroid cancer remains unexplored. Here, we perform metabolomic profiling of 17 tumor-normal pairs; bulk transcriptomics of 263 normal thyroid, 348 papillary, and 21 undifferentiated thyroid cancer samples; and single-cell transcriptomes from 15 cases, showing the impact of mitochondrial one-carbon metabolism in thyroid tumors. High expression of serine hydroxymethyltransferase-2 (SHMT2) and methylenetetrahydrofolate dehydrogenase 2 (MTHFD2) is associated with low thyroid differentiation scores and poor clinical features. A subpopulation of tumor cells with high mitochondrial one-carbon pathway activity is observed in the single-cell dataset. SHMT2 inhibition significantly compromises mitochondrial respiration and decreases cell proliferation and tumor size in vitro and in vivo. Collectively, our results highlight the importance of the mitochondrial one-carbon pathway in undifferentiated thyroid cancer and suggest that SHMT2 is a potent therapeutic target.
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Affiliation(s)
- Seong Eun Lee
- Research Center for Endocrine and Metabolic Disease, College of Medicine, Chungnam National University, Daejeon, Republic of Korea
- Research Institute for Medical Sciences, College of Medicine, Chungnam National University, Daejeon, Republic of Korea
| | - Seongyeol Park
- GENOME INSIGHT TECHNOLOGY Inc, Daejeon, Republic of Korea
- Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA, USA
| | - Shinae Yi
- Research Center for Endocrine and Metabolic Disease, College of Medicine, Chungnam National University, Daejeon, Republic of Korea
- Research Institute for Medical Sciences, College of Medicine, Chungnam National University, Daejeon, Republic of Korea
| | - Na Rae Choi
- Research Center for Endocrine and Metabolic Disease, College of Medicine, Chungnam National University, Daejeon, Republic of Korea
- Research Institute for Medical Sciences, College of Medicine, Chungnam National University, Daejeon, Republic of Korea
| | - Mi Ae Lim
- Research Institute for Medical Sciences, College of Medicine, Chungnam National University, Daejeon, Republic of Korea
- Department of Otolaryngology-Head and Neck Surgery, College of Medicine, Chungnam National University, Daejeon, Republic of Korea
| | - Jae Won Chang
- Department of Otolaryngology-Head and Neck Surgery, College of Medicine, Chungnam National University, Daejeon, Republic of Korea
| | - Ho-Ryun Won
- Department of Otolaryngology-Head and Neck Surgery, College of Medicine, Chungnam National University, Daejeon, Republic of Korea
| | - Je Ryong Kim
- Department of Surgery, College of Medicine, Chungnam National University, Daejeon, Republic of Korea
| | - Hye Mi Ko
- Department of Surgery, College of Medicine, Chungnam National University, Daejeon, Republic of Korea
| | - Eun-Jae Chung
- Department of Otolaryngology-Head and Neck Surgery, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Young Joo Park
- Department of Internal Medicine, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Sun Wook Cho
- Department of Internal Medicine, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Hyeong Won Yu
- Department of Surgery, Seoul National University Bundang Hospital, Seongnam-si, Republic of Korea
| | - June Young Choi
- Department of Surgery, Seoul National University Bundang Hospital, Seongnam-si, Republic of Korea
| | - Min-Kyung Yeo
- Department of Pathology, College of Medicine, Chungnam National University, Daejeon, Republic of Korea
| | - Boram Yi
- GENOME INSIGHT TECHNOLOGY Inc, Daejeon, Republic of Korea
| | - Kijong Yi
- GENOME INSIGHT TECHNOLOGY Inc, Daejeon, Republic of Korea
| | - Joonoh Lim
- GENOME INSIGHT TECHNOLOGY Inc, Daejeon, Republic of Korea
| | - Jun-Young Koh
- GENOME INSIGHT TECHNOLOGY Inc, Daejeon, Republic of Korea
| | - Min Jeong Lee
- Department of Biochemistry, College of Medicine, Chungnam National University, Daejeon, Republic of Korea
| | - Jun Young Heo
- Department of Biochemistry, College of Medicine, Chungnam National University, Daejeon, Republic of Korea
| | - Sang Jun Yoon
- College of Pharmacy, Seoul National University, Seoul, Republic of Korea
| | - Sung Won Kwon
- College of Pharmacy, Seoul National University, Seoul, Republic of Korea
| | - Jong-Lyul Park
- Korea Research Institute of Bioscience and Biotechnology, Deajeon, Republic of Korea
| | - In Sun Chu
- Korea Research Institute of Bioscience and Biotechnology, Deajeon, Republic of Korea
- Department of Bioscience, University of Science and Technology (UST), Deajeon, Republic of Korea
| | - Jin Man Kim
- Department of Pathology, College of Medicine, Chungnam National University, Daejeon, Republic of Korea
| | - Seon-Young Kim
- Korea Research Institute of Bioscience and Biotechnology, Deajeon, Republic of Korea
- Department of Bioscience, University of Science and Technology (UST), Deajeon, Republic of Korea
- Korea Bioinformation Center (KOBIC), Korea Research Institute of Bioscience and Biotechnology, Daejeon, Republic of Korea
| | - Yujuan Shan
- Department of Nutrition, School of Public Health and Management, Wenzhou Medical University, Wenzhou, 325035, China
| | - Lihua Liu
- Department of Nutrition, School of Public Health and Management, Wenzhou Medical University, Wenzhou, 325035, China
| | - Sung-A Hong
- Department of Biochemistry, Chungnam National University, Daejeon, Republic of Korea
| | - Dong Wook Choi
- Department of Biotechnology, College of Life Sciences and Biotechnology, Korea University, Seoul, Republic of Korea
| | - Junyoung O Park
- Department of Chemical and Biomolecular Engineering, University of California, Los Angeles, Los Angeles, USA
| | - Young Seok Ju
- GENOME INSIGHT TECHNOLOGY Inc, Daejeon, Republic of Korea
- Graduate School of Medical Science and Engineering, Korea Advanced Institute of Science and Technology, Daejeon, Republic of Korea
| | - Minho Shong
- Graduate School of Medical Science and Engineering, Korea Advanced Institute of Science and Technology, Daejeon, Republic of Korea
| | - Seon-Kyu Kim
- Korea Research Institute of Bioscience and Biotechnology, Deajeon, Republic of Korea.
| | - Bon Seok Koo
- Research Institute for Medical Sciences, College of Medicine, Chungnam National University, Daejeon, Republic of Korea.
- Department of Otolaryngology-Head and Neck Surgery, College of Medicine, Chungnam National University, Daejeon, Republic of Korea.
| | - Yea Eun Kang
- Research Center for Endocrine and Metabolic Disease, College of Medicine, Chungnam National University, Daejeon, Republic of Korea.
- Research Institute for Medical Sciences, College of Medicine, Chungnam National University, Daejeon, Republic of Korea.
- Division of Endocrinology and Metabolism, Department of Internal Medicine, College of Medicine, Chungnam National University, Daejeon, Republic of Korea.
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Ma Y, Cai G, Chen J, Yang X, Hua G, Han D, Li X, Feng D, Deng X. Combined transcriptome and metabolome analysis reveals breed-specific regulatory mechanisms in Dorper and Tan sheep. BMC Genomics 2024; 25:70. [PMID: 38233814 PMCID: PMC10795462 DOI: 10.1186/s12864-023-09870-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Accepted: 12/04/2023] [Indexed: 01/19/2024] Open
Abstract
BACKGROUND Dorper and Tan sheep are renowned for their rapid growth and exceptional meat quality, respectively. Previous research has provided evidence of the impact of gut microbiota on breed characteristics. The precise correlation between the gastrointestinal tract and peripheral organs in each breed is still unclear. Investigating the metabolic network of the intestinal organ has the potential to improve animal growth performance and enhance economic benefits through the regulation of intestinal metabolites. RESULTS In this study, we identified the growth advantage of Dorper sheep and the high fat content of Tan sheep. A transcriptome study of the brain, liver, skeletal muscle, and intestinal tissues of both breeds revealed 3,750 differentially expressed genes (DEGs). The genes PPARGC1A, LPL, and PHGDH were found to be highly expressed in Doper, resulting in the up-regulation of pathways related to lipid oxidation, glycerophospholipid metabolism, and amino acid anabolism. Tan sheep highly express the BSEP, LDLR, and ACHE genes, which up-regulate the pathways involved in bile transport and cholesterol homeostasis. Hindgut content analysis identified 200 differentially accumulated metabolites (DAMs). Purines, pyrimidines, bile acids, and fatty acid substances were more abundant in Dorper sheep. Based on combined gene and metabolite analyses, we have identified glycine, serine, and threonine metabolism, tryptophan metabolism, bile secretion, cholesterol metabolism, and neuroactive ligand-receptor interaction as key factors contributing to the differences among the breeds. CONCLUSIONS This study indicates that different breeds of sheep exhibit unique breed characteristics through various physiological regulatory methods. Dorper sheep upregulate metabolic signals related to glycine, serine, and threonine, resulting in an increase in purine and pyrimidine substances. This, in turn, promotes the synthesis of amino acids and facilitates body development, resulting in a faster rate of weight gain. Tan sheep accelerate bile transport, reduce bile accumulation in the intestine, and upregulate cholesterol homeostasis signals in skeletal muscles. This promotes the accumulation of peripheral and intramuscular fat, resulting in improved meat quality. This work adopts a joint analysis method of multi-tissue transcriptome and gut metabolome, providing a successful case for analyzing the mechanisms underlying the formation of various traits.
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Affiliation(s)
- Yuhao Ma
- Key Laboratory of Animal Genetics, Breeding, and Reproduction of the Ministry of Agriculture and Beijing Key Laboratory of Animal Genetic Improvement, China Agricultural University, Beijing, 100193, China
| | - Ganxian Cai
- Key Laboratory of Animal Genetics, Breeding, and Reproduction of the Ministry of Agriculture and Beijing Key Laboratory of Animal Genetic Improvement, China Agricultural University, Beijing, 100193, China
| | - Jianfei Chen
- Key Laboratory of Animal Genetics, Breeding, and Reproduction of the Ministry of Agriculture and Beijing Key Laboratory of Animal Genetic Improvement, China Agricultural University, Beijing, 100193, China
| | - Xue Yang
- Key Laboratory of Animal Genetics, Breeding, and Reproduction of the Ministry of Agriculture and Beijing Key Laboratory of Animal Genetic Improvement, China Agricultural University, Beijing, 100193, China
| | - Guoying Hua
- Key Laboratory of Animal Genetics, Breeding, and Reproduction of the Ministry of Agriculture and Beijing Key Laboratory of Animal Genetic Improvement, China Agricultural University, Beijing, 100193, China
| | - Deping Han
- Key Laboratory of Animal Genetics, Breeding, and Reproduction of the Ministry of Agriculture and Beijing Key Laboratory of Animal Genetic Improvement, China Agricultural University, Beijing, 100193, China
| | - Xinhai Li
- Department of Animal Science and college of Agriculture, Ningxia University, Yinchuan, 750021, China
| | - Dengzhen Feng
- Department of Animal Science and college of Agriculture, Ningxia University, Yinchuan, 750021, China
| | - Xuemei Deng
- Key Laboratory of Animal Genetics, Breeding, and Reproduction of the Ministry of Agriculture and Beijing Key Laboratory of Animal Genetic Improvement, China Agricultural University, Beijing, 100193, China.
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Minchenko OH, Sliusar MY, Khita OO, Minchenko DO, Viletska YM, Halkin OV, Levadna LO, Cherednychenko AA, Khikhlo YP. Inhibition of signaling protein ERN1 increases the sensitivity of serine synthesis gene expressions to glucose and glutamine deprivations in U87MG glioblastoma cells. Endocr Regul 2024; 58:91-100. [PMID: 38656254 DOI: 10.2478/enr-2024-0010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 04/26/2024] Open
Abstract
Objective. Glucose and glutamine supply as well as serine synthesis and endoplasmic reticulum (ER) stress are important factors of glioblastoma growth. Previous studies showed that the knockdown of ERN1 (ER to nucleus signaling 1) suppressed glioblastoma cell proliferation and modified the sensitivity of numerous gene expressions to nutrient deprivations. The present study is aimed to investigate the impact of glucose and glutamine deprivations on the expression of serine synthesis genes in U87MG glioblastoma cells in relation to ERN1 knockdown with the intent to reveal the role of ERN1 signaling pathway on the ER stress-dependent regulation of these gene expressions. Clarification of the regulatory mechanisms of serine synthesis is a great significance for glioblastoma therapy. Methods. The control U87MG glioblastoma cells (transfected by empty vector) and ERN1 knockdown cells (transfected by dominant-negative ERN1) were exposed under glucose and glutamine deprivation conditions for 16 h. RNA was extracted from cells and reverse transcribed. The expression level of PHGDH (phosphoglycerate dehydrogenase), PSAT1 (phosphoserine amino-transferase 1), PSPH (phosphoserine phosphatase), ATF4 (activating transcription factor 4), and SHMT1 (serine hydroxymethyltransferase 1) genes was studied by real-time qPCR and normalized to ACTB. Results. It was found that the expression level of genes responsible for serine synthesis such as PHGDH, PSAT1, PSPH, and transcription factor ATF4 was up-regulated in U87MG glioblastoma cells under glucose and glutamine deprivations. Furthermore, inhibition of ERN1 significantly enhances the impact of glucose and especially glutamine deprivations on these gene expressions. At the same time, the expression of the SHMT1 gene, which is responsible for serine conversion to glycine, was down-regulated in both nutrient deprivation conditions with more significant changes in ERN1 knockdown glioblastoma cells. Conclusion. Taken together, the results of present study indicate that the expression of genes responsible for serine synthesis is sensitive to glucose and glutamine deprivations in gene-specific manner and that suppression of ERN1 signaling significantly modifies the impact of both glucose and glutamine deprivations on PHGDH, PSAT1, PSPH, ATF4, and SHMT1 gene expressions and reflects the ERN1-mediated genome reprograming introduced by nutrient deprivation condition.
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Affiliation(s)
- Oleksandr H Minchenko
- Department of Molecular Biology, Palladin Institute of Biochemistry, National Academy of Sciences of Ukraine, Kyiv, Ukraine
| | - Myroslava Y Sliusar
- Department of Molecular Biology, Palladin Institute of Biochemistry, National Academy of Sciences of Ukraine, Kyiv, Ukraine
| | - Olena O Khita
- Department of Molecular Biology, Palladin Institute of Biochemistry, National Academy of Sciences of Ukraine, Kyiv, Ukraine
| | - Dmytro O Minchenko
- Department of Molecular Biology, Palladin Institute of Biochemistry, National Academy of Sciences of Ukraine, Kyiv, Ukraine
- Department of Pediatrics, National Bohomolets Medical University, Kyiv, Ukraine
| | - Yuliia M Viletska
- Department of Molecular Biology, Palladin Institute of Biochemistry, National Academy of Sciences of Ukraine, Kyiv, Ukraine
| | - Oleh V Halkin
- Department of Molecular Biology, Palladin Institute of Biochemistry, National Academy of Sciences of Ukraine, Kyiv, Ukraine
| | - Liudmyla O Levadna
- Department of Pediatrics, National Bohomolets Medical University, Kyiv, Ukraine
| | - Anastasiia A Cherednychenko
- Department of Molecular Biology, Palladin Institute of Biochemistry, National Academy of Sciences of Ukraine, Kyiv, Ukraine
| | - Yevgen P Khikhlo
- Department of Molecular Biology, Palladin Institute of Biochemistry, National Academy of Sciences of Ukraine, Kyiv, Ukraine
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Murtas G, Zerbini E, Rabattoni V, Motta Z, Caldinelli L, Orlando M, Marchesani F, Campanini B, Sacchi S, Pollegioni L. Biochemical and cellular studies of three human 3-phosphoglycerate dehydrogenase variants responsible for pathological reduced L-serine levels. Biofactors 2024; 50:181-200. [PMID: 37650587 DOI: 10.1002/biof.2002] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Accepted: 08/12/2023] [Indexed: 09/01/2023]
Abstract
In the brain, the non-essential amino acid L-serine is produced through the phosphorylated pathway (PP) starting from the glycolytic intermediate 3-phosphoglycerate: among the different roles played by this amino acid, it can be converted into D-serine and glycine, the two main co-agonists of NMDA receptors. In humans, the enzymes of the PP, namely phosphoglycerate dehydrogenase (hPHGDH, which catalyzes the first and rate-limiting step of this pathway), 3-phosphoserine aminotransferase, and 3-phosphoserine phosphatase are likely organized in the cytosol as a metabolic assembly (a "serinosome"). The hPHGDH deficiency is a pathological condition biochemically characterized by reduced levels of L-serine in plasma and cerebrospinal fluid and clinically identified by severe neurological impairment. Here, three single-point variants responsible for hPHGDH deficiency and Neu-Laxova syndrome have been studied. Their biochemical characterization shows that V261M, V425M, and V490M substitutions alter either the kinetic (both maximal activity and Km for 3-phosphoglycerate in the physiological direction) and the structural properties (secondary, tertiary, and quaternary structure, favoring aggregation) of hPHGDH. All the three variants have been successfully ectopically expressed in U251 cells, thus the pathological effect is not due to hindered expression level. At the cellular level, mistargeting and aggregation phenomena have been observed in cells transiently expressing the pathological protein variants, as well as a reduced L-serine cellular level. Previous studies demonstrated that the pharmacological supplementation of L-serine in hPHGDH deficiencies could ameliorate some of the related symptoms: our results now suggest the use of additional and alternative therapeutic approaches.
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Affiliation(s)
- Giulia Murtas
- Department of Biotechnology and Life Sciences, University of Insubria, Varese, Italy
| | - Elena Zerbini
- Department of Biotechnology and Life Sciences, University of Insubria, Varese, Italy
| | - Valentina Rabattoni
- Department of Biotechnology and Life Sciences, University of Insubria, Varese, Italy
| | - Zoraide Motta
- Department of Biotechnology and Life Sciences, University of Insubria, Varese, Italy
| | - Laura Caldinelli
- Department of Biotechnology and Life Sciences, University of Insubria, Varese, Italy
| | - Marco Orlando
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Milan, Italy
| | | | | | - Silvia Sacchi
- Department of Biotechnology and Life Sciences, University of Insubria, Varese, Italy
| | - Loredano Pollegioni
- Department of Biotechnology and Life Sciences, University of Insubria, Varese, Italy
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7
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Cappello A, Tosetti G, Smirnov A, Ganini C, Yang X, Shi Y, Wang Y, Melino G, Bernassola F, Candi E. p63 orchestrates serine and one carbon metabolism enzymes expression in head and neck cancer. Biol Direct 2023; 18:73. [PMID: 37946250 PMCID: PMC10636826 DOI: 10.1186/s13062-023-00426-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Accepted: 10/12/2023] [Indexed: 11/12/2023] Open
Abstract
BACKGROUND Head and neck squamous cell carcinoma (HNSCC) is characterized by high proliferation and limited differentiation. The altered expression of the p53 family members, and specifically of p63, represents a pivotal event in the pathogenesis of HNSCC. Physiologically, p63 affects metabolism through the direct transactivation of the enzyme hexokinase 2, and subsequently controls the proliferation of epithelial cells; nonetheless, its role in cancer metabolism is still largely unclear. The high energetic demand of cancer and the consequent needs of a metabolic reshape, also involve the serine and glycine catabolic and anabolic pathways, including the one carbon metabolism (OCM), to produce energetic compounds (purines) and to maintain cellular homeostasis (glutathione and S-adenosylmethionine). RESULTS The involvement in serine/glycine starvation by other p53 family members has been reported, including HNSCC. Here, we show that in HNSCC p63 controls the expression of the enzymes regulating the serine biosynthesis and one carbon metabolism. p63 binds the promoter region of genes involved in the serine biosynthesis as well as in the one carbon metabolism. p63 silencing in a HNSCC cell line affects the mRNA and protein levels of these selected enzymes. Moreover, the higher expression of TP63 and its target enzymes, negatively impacts on the overall survival of HNSCC patients. CONCLUSION These data indicate a direct role of p63 in the metabolic regulation of HNSCC with significant clinical effects.
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Affiliation(s)
- Angela Cappello
- Department of Experimental Medicine, University of Rome "Tor Vergata", 00133, Rome, Italy
- Interdisciplinary Department of Medicine, University of Bari "Aldo Moro", 70121, Bari, Italy
| | - Giulia Tosetti
- Department of Experimental Medicine, University of Rome "Tor Vergata", 00133, Rome, Italy
| | - Artem Smirnov
- Department of Experimental Medicine, University of Rome "Tor Vergata", 00133, Rome, Italy
- Istituto Dermopatico dell'Immacolata, IDI-IRCCS, 00167, Rome, Italy
| | - Carlo Ganini
- Interdisciplinary Department of Medicine, University of Bari "Aldo Moro", 70121, Bari, Italy
- Division of Medical Oncology, A.O.U. Policlinico di Bari, 70124, Bari, Italy
| | - Xue Yang
- Department of Experimental Medicine, University of Rome "Tor Vergata", 00133, Rome, Italy
- Department of Tumor Immunology and Gene Therapy Center, Third Affiliated Hospital of Naval Medical University, Shanghai, 200438, China
- National Center for Liver Cancer, Shanghai, 201805, China
| | - Yufang Shi
- The Third Affiliated Hospital of Soochow University and State Key Laboratory of Radiation Medicine and Protection, Institute for Translational Medicine, Soochow University, Suzhou, China
| | - Ying Wang
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Gerry Melino
- Department of Experimental Medicine, University of Rome "Tor Vergata", 00133, Rome, Italy
| | - Francesca Bernassola
- Department of Experimental Medicine, University of Rome "Tor Vergata", 00133, Rome, Italy
| | - Eleonora Candi
- Department of Experimental Medicine, University of Rome "Tor Vergata", 00133, Rome, Italy.
- Istituto Dermopatico dell'Immacolata, IDI-IRCCS, 00167, Rome, Italy.
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8
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Franczak M, Toenshoff I, Jansen G, Smolenski RT, Giovannetti E, Peters GJ. The Influence of Mitochondrial Energy and 1C Metabolism on the Efficacy of Anticancer Drugs: Exploring Potential Mechanisms of Resistance. Curr Med Chem 2023; 30:1209-1231. [PMID: 35366764 DOI: 10.2174/0929867329666220401110418] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Revised: 01/06/2022] [Accepted: 01/24/2022] [Indexed: 11/22/2022]
Abstract
Mitochondria are the main energy factory in living cells. To rapidly proliferate and metastasize, neoplastic cells increase their energy requirements. Thus, mitochondria become one of the most important organelles for them. Indeed, much research shows the interplay between cancer chemoresistance and altered mitochondrial function. In this review, we focus on the differences in energy metabolism between cancer and normal cells to better understand their resistance and how to develop drugs targeting energy metabolism and nucleotide synthesis. One of the differences between cancer and normal cells is the higher nicotinamide adenine dinucleotide (NAD+) level, a cofactor for the tricarboxylic acid cycle (TCA), which enhances their proliferation and helps cancer cells survive under hypoxic conditions. An important change is a metabolic switch called the Warburg effect. This effect is based on the change of energy harvesting from oxygen-dependent transformation to oxidative phosphorylation (OXPHOS), adapting them to the tumor environment. Another mechanism is the high expression of one-carbon (1C) metabolism enzymes. Again, this allows cancer cells to increase proliferation by producing precursors for the synthesis of nucleotides and amino acids. We reviewed drugs in clinical practice and development targeting NAD+, OXPHOS, and 1C metabolism. Combining novel drugs with conventional antineoplastic agents may prove to be a promising new way of anticancer treatment.
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Affiliation(s)
- Marika Franczak
- Department of Biochemistry, Medical University of Gdansk, Gdansk, Poland
| | - Isabel Toenshoff
- Department of Medical Oncology, Cancer Center Amsterdam, Amsterdam UMC, VU University Medical Center (VUMC), Vrije Universiteit Amsterdam, The Netherlands.,Amsterdam University College, Amsterdam, The Netherlands
| | - Gerrit Jansen
- Amsterdam Rheumatology and Immunology Center, Amsterdam UMC, VU University Medical Center (VUMC), Amsterdam, The Netherlands
| | | | - Elisa Giovannetti
- Department of Medical Oncology, Cancer Center Amsterdam, Amsterdam UMC, VU University Medical Center (VUMC), Vrije Universiteit Amsterdam, The Netherlands.,Cancer Pharmacology Lab, Fondazione Pisana per la Scienza, Pisa, Italy
| | - Godefridus J Peters
- Department of Biochemistry, Medical University of Gdansk, Gdansk, Poland.,Department of Medical Oncology, Cancer Center Amsterdam, Amsterdam UMC, VU University Medical Center (VUMC), Vrije Universiteit Amsterdam, The Netherlands
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9
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Sliusar MY, Minchenko DO, Khita OO, Tsymbal DO, Viletska YM, Luzina OY, Danilovskyi SV, Ratushna OO, Minchenko OH. Hypoxia controls the expression of genes responsible for serine synthesis in U87MG cells on ERN1-dependent manner. Endocr Regul 2023; 57:252-261. [PMID: 37823569 DOI: 10.2478/enr-2023-0028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/13/2023] Open
Abstract
Objective. Serine synthesis as well as endoplasmic reticulum stress and hypoxia are important factors of malignant tumor growth including glioblastoma. Previous studies have shown that the knockdown of ERN1 (endoplasmic reticulum to nucleus signaling) significantly suppressed the glioblastoma cell proliferation and modified the hypoxia regulation. The present study is aimed to investigate the impact of hypoxia on the expression of PHGDH (phosphoglycerate dehydrogenase), PSAT1 (phosphoserine aminotransferase 1), PSPH (phosphoserine phosphatase), ATF4 (activating transcription factor 4), and SHMT1 (serine hydroxymethyltransferase 1) in U87MG glioblastoma cells in relation to knockdown of ERN1 with the intent to reveal the role of ERN1 signaling pathway on the endoplasmic reticulum stress-dependent regulation of expression of these genes. Methods. The control U87MG glioblastoma cells (transfected by empty vector) and ERN1 knockdown cells (transfected by dominant-negative ERN1) were exposed to hypoxia introduced by dimethyloxalylglycine for 4 h. RNA was extracted from cells and reverse transcribed. The expression level of PHGDH, PSAT1, PDPH, SHMT1, and ATF4 genes was studied by real-time qPCR and normalized to ACTB. Results. It was found that hypoxia up-regulated the expression level of PHGDH, PSAT1, and ATF4 genes in control U87MG cells, but PSPH and SHMT1 genes expression was down-regulated. The expression of PHGDH, PSAT1, and ATF4 genes in glioblastoma cells with knockdown of ERN1 signaling protein was more sensitive to hypoxia, especially PSAT1 gene. At the same time, the expression of PSPH gene in ERN1 knockdown cells was resistant to hypoxia. The expression of SHMT1 gene, encoding the enzyme responsible for conversion of serine to glycine, showed similar negative sensitivity to hypoxia in both control and ERN1 knockdown glioblastoma cells. Conclusion. The results of the present study demonstrate that the expression of genes responsible for serine synthesis is sensitive to hypoxia in gene-specific manner and that ERN1 knockdown significantly modifies the impact of hypoxia on the expression of PHGDH, PSAT1, PSPH, and ATF4 genes in glioblastoma cells and reflects the ERN1-mediated reprograming of hypoxic regulation at gene expression level.
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Affiliation(s)
- Myroslava Y Sliusar
- 1Department of Molecular Biology, Palladin Institute of Biochemistry, National Academy of Sciences of Ukraine, Kyiv, Ukraine
| | - Dmytro O Minchenko
- 1Department of Molecular Biology, Palladin Institute of Biochemistry, National Academy of Sciences of Ukraine, Kyiv, Ukraine
| | - Olena O Khita
- 1Department of Molecular Biology, Palladin Institute of Biochemistry, National Academy of Sciences of Ukraine, Kyiv, Ukraine
| | - Dariia O Tsymbal
- 1Department of Molecular Biology, Palladin Institute of Biochemistry, National Academy of Sciences of Ukraine, Kyiv, Ukraine
| | - Yuliia M Viletska
- 1Department of Molecular Biology, Palladin Institute of Biochemistry, National Academy of Sciences of Ukraine, Kyiv, Ukraine
| | - Olha Y Luzina
- 1Department of Molecular Biology, Palladin Institute of Biochemistry, National Academy of Sciences of Ukraine, Kyiv, Ukraine
| | - Serhij V Danilovskyi
- 1Department of Molecular Biology, Palladin Institute of Biochemistry, National Academy of Sciences of Ukraine, Kyiv, Ukraine
| | - Oksana O Ratushna
- 1Department of Molecular Biology, Palladin Institute of Biochemistry, National Academy of Sciences of Ukraine, Kyiv, Ukraine
| | - Oleksandr H Minchenko
- 1Department of Molecular Biology, Palladin Institute of Biochemistry, National Academy of Sciences of Ukraine, Kyiv, Ukraine
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10
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Marabitti V, Giansanti M, De Mitri F, Gatto F, Mastronuzzi A, Nazio F. Pathological implications of metabolic reprogramming and its therapeutic potential in medulloblastoma. Front Cell Dev Biol 2022; 10:1007641. [PMID: 36340043 PMCID: PMC9627342 DOI: 10.3389/fcell.2022.1007641] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2022] [Accepted: 10/05/2022] [Indexed: 07/30/2023] Open
Abstract
Tumor-specific alterations in metabolism have been recognized to sustain the production of ATP and macromolecules needed for cell growth, division and survival in many cancer types. However, metabolic heterogeneity poses a challenge for the establishment of effective anticancer therapies that exploit metabolic vulnerabilities. Medulloblastoma (MB) is one of the most heterogeneous malignant pediatric brain tumors, divided into four molecular subgroups (Wingless, Sonic Hedgehog, Group 3 and Group 4). Recent progresses in genomics, single-cell sequencing, and novel tumor models have updated the classification and stratification of MB, highlighting the complex intratumoral cellular diversity of this cancer. In this review, we emphasize the mechanisms through which MB cells rewire their metabolism and energy production networks to support and empower rapid growth, survival under stressful conditions, invasion, metastasis, and resistance to therapy. Additionally, we discuss the potential clinical benefits of currently available drugs that could target energy metabolism to suppress MB progression and increase the efficacy of the current MB therapies.
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Affiliation(s)
- Veronica Marabitti
- Department of Hematology/Oncology and Cell and Gene Therapy, Bambino Gesù Children’s Hospital, IRCCS, Rome, Italy
| | - Manuela Giansanti
- Department of Hematology/Oncology and Cell and Gene Therapy, Bambino Gesù Children’s Hospital, IRCCS, Rome, Italy
| | - Francesca De Mitri
- Department of Hematology/Oncology and Cell and Gene Therapy, Bambino Gesù Children’s Hospital, IRCCS, Rome, Italy
| | - Francesca Gatto
- Department of Laboratory Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Angela Mastronuzzi
- Department of Hematology/Oncology and Cell and Gene Therapy, Bambino Gesù Children’s Hospital, IRCCS, Rome, Italy
| | - Francesca Nazio
- Department of Hematology/Oncology and Cell and Gene Therapy, Bambino Gesù Children’s Hospital, IRCCS, Rome, Italy
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11
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Identification of Novel Natural Inhibitors to Human 3-Phosphoglycerate Dehydrogenase (PHGDH) for Cancer Treatment. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27186108. [PMID: 36144843 PMCID: PMC9501931 DOI: 10.3390/molecules27186108] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Revised: 09/07/2022] [Accepted: 09/10/2022] [Indexed: 11/17/2022]
Abstract
Targeting the serine biosynthesis pathway enzymes has turned up as a novel strategy for anti-cancer therapeutics. 3- Phosphoglycerate dehydrogenase (PHGDH) is the rate-limiting enzyme that catalyzes the conversion of 3-Phosphoglyceric acid (3-PG) into 3-Phosphohydroxy pyruvate (3-PPyr) in the first step of serine synthesis pathway and perform a critical role in cancer progression. PHGDH has been reported to be overexpressed in different types of cancers and emerged as a novel target for cancer therapeutics. During this study, virtual screening tools were used for the identification of inhibitors of PHGDH. A library of phenolic compounds was docked against two binding sites of PHGDH using Molegro Virtual Docker (MVD) software. Out of 169 virtually tested compounds, Salvianolic acid C and Schizotenuin F possess good binding potential to co-factor binding site of PHGDH while Salvianolic acid I and Chicoric acid were identified as the best binding compounds toward the substrate binding site of PHGDH. The top selected compounds were evaluated for different physiochemical and ADMET properties, the obtained results showed that none of these hit compounds violated the Pfizer Rule and they possess acceptable ADMET profiles. Further, a commercially available hit compound, Chicoric acid, was evaluated for its anti-cancer potential against PHGDH-expressing gastric cancer cell lines (MGC-803 and SGC-7901) as well as cell lines with low expression of PHGDH (MCF-7 and MDA-MB2-31), which demonstrated that Chicoric acid possesses selective cytotoxicity toward PHGDH expressing cancer cell lines. Thus, this study has unveiled the potential of phenolic compounds, which could serve as novel candidates for the development of PHGDH inhibitors as anti-cancer agents.
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12
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Lai HT, Naumova N, Marchais A, Gaspar N, Geoerger B, Brenner C. Insight into the interplay between mitochondria-regulated cell death and energetic metabolism in osteosarcoma. Front Cell Dev Biol 2022; 10:948097. [PMID: 36072341 PMCID: PMC9441498 DOI: 10.3389/fcell.2022.948097] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Accepted: 07/04/2022] [Indexed: 11/13/2022] Open
Abstract
Osteosarcoma (OS) is a pediatric malignant bone tumor that predominantly affects adolescent and young adults. It has high risk for relapse and over the last four decades no improvement of prognosis was achieved. It is therefore crucial to identify new drug candidates for OS treatment to combat drug resistance, limit relapse, and stop metastatic spread. Two acquired hallmarks of cancer cells, mitochondria-related regulated cell death (RCD) and metabolism are intimately connected. Both have been shown to be dysregulated in OS, making them attractive targets for novel treatment. Promising OS treatment strategies focus on promoting RCD by targeting key molecular actors in metabolic reprogramming. The exact interplay in OS, however, has not been systematically analyzed. We therefore review these aspects by synthesizing current knowledge in apoptosis, ferroptosis, necroptosis, pyroptosis, and autophagy in OS. Additionally, we outline an overview of mitochondrial function and metabolic profiles in different preclinical OS models. Finally, we discuss the mechanism of action of two novel molecule combinations currently investigated in active clinical trials: metformin and the combination of ADI-PEG20, Docetaxel and Gemcitabine.
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Affiliation(s)
- Hong Toan Lai
- CNRS, Institut Gustave Roussy, Aspects métaboliques et systémiques de l’oncogénèse pour de nouvelles approches thérapeutiques, Université Paris-Saclay, Villejuif, France
| | - Nataliia Naumova
- CNRS, Institut Gustave Roussy, Aspects métaboliques et systémiques de l’oncogénèse pour de nouvelles approches thérapeutiques, Université Paris-Saclay, Villejuif, France
| | - Antonin Marchais
- INSERM U1015, Gustave Roussy Cancer Campus, Université Paris-Saclay, Villejuif, France
- Department of Pediatric and Adolescent Oncology, Gustave Roussy Cancer Campus, Villejuif, France
| | - Nathalie Gaspar
- INSERM U1015, Gustave Roussy Cancer Campus, Université Paris-Saclay, Villejuif, France
- Department of Pediatric and Adolescent Oncology, Gustave Roussy Cancer Campus, Villejuif, France
| | - Birgit Geoerger
- INSERM U1015, Gustave Roussy Cancer Campus, Université Paris-Saclay, Villejuif, France
- Department of Pediatric and Adolescent Oncology, Gustave Roussy Cancer Campus, Villejuif, France
| | - Catherine Brenner
- CNRS, Institut Gustave Roussy, Aspects métaboliques et systémiques de l’oncogénèse pour de nouvelles approches thérapeutiques, Université Paris-Saclay, Villejuif, France
- *Correspondence: Catherine Brenner,
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13
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Lv L, Yang S, Zhu Y, Zhai X, Li S, Tao X, Dong D. Relationship between metabolic reprogramming and drug resistance in breast cancer. Front Oncol 2022; 12:942064. [PMID: 36059650 PMCID: PMC9434120 DOI: 10.3389/fonc.2022.942064] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Accepted: 08/01/2022] [Indexed: 11/13/2022] Open
Abstract
Breast cancer is the leading cause of cancer death in women. At present, chemotherapy is the main method to treat breast cancer in addition to surgery and radiotherapy, but the process of chemotherapy is often accompanied by the development of drug resistance, which leads to a reduction in drug efficacy. Furthermore, mounting evidence indicates that drug resistance is caused by dysregulated cellular metabolism, and metabolic reprogramming, including enhanced glucose metabolism, fatty acid synthesis and glutamine metabolic rates, is one of the hallmarks of cancer. Changes in metabolism have been considered one of the most important causes of resistance to treatment, and knowledge of the mechanisms involved will help in identifying potential treatment deficiencies. To improve women's survival outcomes, it is vital to elucidate the relationship between metabolic reprogramming and drug resistance in breast cancer. This review analyzes and investigates the reprogramming of metabolism and resistance to breast cancer therapy, and the results offer promise for novel targeted and cell-based therapies.
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Affiliation(s)
- Linlin Lv
- Department of Pharmacy, First Affiliated Hospital of Dalian Medical University, Dalian, China
- School of Life Science and Biotechnology, Dalian University of Technology, Dalian, China
| | - Shilei Yang
- Department of Pharmacy, First Affiliated Hospital of Dalian Medical University, Dalian, China
| | - Yanna Zhu
- Department of Pharmacy, First Affiliated Hospital of Dalian Medical University, Dalian, China
| | - Xiaohan Zhai
- Department of Pharmacy, First Affiliated Hospital of Dalian Medical University, Dalian, China
| | - Shuai Li
- Department of Pharmacy, First Affiliated Hospital of Dalian Medical University, Dalian, China
| | - Xufeng Tao
- Department of Pharmacy, First Affiliated Hospital of Dalian Medical University, Dalian, China
| | - Deshi Dong
- Department of Pharmacy, First Affiliated Hospital of Dalian Medical University, Dalian, China
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14
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Lu C, Liu S, Shi W, Yu J, Zhou Z, Zhang X, Lu X, Cai F, Xia N, Wang Y. Systemic evolutionary chemical space exploration for drug discovery. J Cheminform 2022; 14:19. [PMID: 35365231 PMCID: PMC8973791 DOI: 10.1186/s13321-022-00598-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Accepted: 03/11/2022] [Indexed: 11/29/2022] Open
Abstract
Chemical space exploration is a major task of the hit-finding process during the pursuit of novel chemical entities. Compared with other screening technologies, computational de novo design has become a popular approach to overcome the limitation of current chemical libraries. Here, we reported a de novo design platform named systemic evolutionary chemical space explorer (SECSE). The platform was conceptually inspired by fragment-based drug design, that miniaturized a “lego-building” process within the pocket of a certain target. The key to virtual hits generation was then turned into a computational search problem. To enhance search and optimization, human intelligence and deep learning were integrated. Application of SECSE against phosphoglycerate dehydrogenase (PHGDH), proved its potential in finding novel and diverse small molecules that are attractive starting points for further validation. This platform is open-sourced and the code is available at http://github.com/KeenThera/SECSE.
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Affiliation(s)
- Chong Lu
- Keen Therapeutics Co., Ltd., Shanghai, China
| | - Shien Liu
- Keen Therapeutics Co., Ltd., Shanghai, China
| | - Weihua Shi
- Keen Therapeutics Co., Ltd., Shanghai, China
| | - Jun Yu
- Keen Therapeutics Co., Ltd., Shanghai, China
| | - Zhou Zhou
- Keen Therapeutics Co., Ltd., Shanghai, China
| | | | - Xiaoli Lu
- Keen Therapeutics Co., Ltd., Shanghai, China
| | - Faji Cai
- Keen Therapeutics Co., Ltd., Shanghai, China
| | | | - Yikai Wang
- Keen Therapeutics Co., Ltd., Shanghai, China.
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15
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Rathore R, Van Tine B. Targeting one-carbon metabolism requires mTOR inhibition: a new therapeutic approach in osteosarcoma. Mol Cell Oncol 2021; 8:1902250. [PMID: 34027041 PMCID: PMC8128185 DOI: 10.1080/23723556.2021.1902250] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
The rate-limiting enzyme of serine biosynthesis, 3-phosphoglycerate dehydrogenase (PHGDH), contributes to rapid growth and proliferation when it is overexpressed in cancer. We recently described the metabolic adaptations that occur upon PHGDH inhibition in osteosarcoma. PHGDH inhibition causes metabolite accumulation that activates the mechanistic target of rapamycin (mTOR) signaling, sensitizing osteosarcoma to non-rapalog mTOR inhibition.
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Affiliation(s)
- Richa Rathore
- Division of Medical Oncology, Washington University in St. Louis, St. Louis, Missouri, USA
| | - Brian Van Tine
- Division of Medical Oncology, Washington University in St. Louis, St. Louis, Missouri, USA.,Division of Pediatric Hematology and Oncology, Children's Hospital, St. Louis, Missouri, USA.,Siteman Cancer Center, St. Louis, Missouri, USA
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16
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Xu H, Qing X, Wang Q, Li C, Lai L. Dimerization of PHGDH via the catalytic unit is essential for its enzymatic function. J Biol Chem 2021; 296:100572. [PMID: 33753166 PMCID: PMC8081924 DOI: 10.1016/j.jbc.2021.100572] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Revised: 03/12/2021] [Accepted: 03/18/2021] [Indexed: 11/25/2022] Open
Abstract
Human D-3-phosphoglycerate dehydrogenase (PHGDH), a key enzyme in de novo serine biosynthesis, is amplified in various cancers and serves as a potential target for anticancer drug development. To facilitate this process, more information is needed on the basic biochemistry of this enzyme. For example, PHGDH was found to form tetramers in solution and the structure of its catalytic unit (sPHGDH) was solved as a dimer. However, how the oligomeric states affect PHGDH enzyme activity remains elusive. We studied the dependence of PHGDH enzymatic activity on its oligomeric states. We found that sPHGDH forms a mixture of monomers and dimers in solution with a dimer dissociation constant of ∼0.58 μM, with the enzyme activity depending on the dimer content. We computationally identified hotspot residues at the sPHGDH dimer interface. Single-point mutants at these sites disrupt dimer formation and abolish enzyme activity. Molecular dynamics simulations showed that dimer formation facilitates substrate binding and maintains the correct conformation required for enzyme catalysis. We further showed that the full-length PHGDH exists as a dynamic mixture of monomers, dimers, and tetramers in solution with enzyme concentration-dependent activity. Mutations that can completely disrupt the sPHGDH dimer show different abilities to interrupt the full-length PHGDH tetramer. Among them, E108A and I121A can also disrupt the oligomeric structures of the full-length PHGDH and abolish its enzyme activity. Our study indicates that disrupting the oligomeric structure of PHGDH serves as a novel strategy for PHGDH drug design and the hotspot residues identified can guide the design process.
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Affiliation(s)
- Hanyu Xu
- BNLMS, Peking-Tsinghua Center for Life Sciences at College of Chemistry and Molecular Engineering, Peking University, Beijing, China
| | - Xiaoyu Qing
- BNLMS, Peking-Tsinghua Center for Life Sciences at College of Chemistry and Molecular Engineering, Peking University, Beijing, China
| | - Qian Wang
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing, China
| | - Chunmei Li
- Center for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
| | - Luhua Lai
- BNLMS, Peking-Tsinghua Center for Life Sciences at College of Chemistry and Molecular Engineering, Peking University, Beijing, China; Center for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China.
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