Differential inhibitory effect of a pyrazolopyran compound on human serine hydroxymethyltransferase-amino acid complexes
Abstract
Serine hydroxymethyltransferase (SHMT) is a pivotal enzyme in one-carbon metabolism that catalyses the reversible conversion of serine and tetrahydrofolate into glycine and methylenetetrahydrofolate. It exists in cytosolic (SHMT1) and mitochondrial (SHMT2) isoforms. Research on one-carbon metabolism in cancer cell lines has shown that SHMT1 preferentially catalyses serine synthesis, whereas in mitochondria SHMT2 is involved in serine breakdown. Recent research has focused on the identification of inhibitors that bind at the folate pocket. We have previously found that a representative derivative of the pyrazolopyran scaffold, namely 2.12, inhibits both SHMT isoforms, with a preference for SHMT1, causing apoptosis in lung cancer cell lines. Here we show that the affinity of 2.12 for SHMT depends on the identity of the amino acid substrate bound to the enzyme. The dissociation constant of 2.12 is 50-fold lower when it binds to SHMT1 enzyme-serine complex, as compared to the enzyme-glycine complex. Evidence is presented for a similar behaviour of compound 2.12 in the cellular environment. These findings suggest that the presence and identity of the amino acid substrate should be considered when designing SHMT inhibitors. Moreover, our data provide the proof-of-concept that SHMT inhibitors selectively targeting the directionality of one-carbon metabolism flux could be designed.
Integrity signals
Registry
Cites
Statistics
Claims the paper makes
Claims other papers make about this one
Each is checked against this paper’s own text: does it say what the citing paper says it does?
Prior to Nonaka and co-worker's study, only marginal selectivity between the two SHMT isoforms had been achieved, with inhibitors being selective for SHMT1 by 2- to 3-fold.
“Prior to Nonaka and co-worker’s study, generally, only marginal selectivity between the two SHMT isoforms has been achieved, with the inhibitors being selective for SHMT1 by 2- to 3-fold.”
From A review of small-molecule inhibitors of one-carbon enzymes: SHMT2 and MTHFD2 in the spotlight (2021) · cites this paper as [155]
Cites
PRODRG: a tool for high-throughput crystallography of protein–ligand complexes
Schüttelkopf, A. W., & van Aalten, D. M. F. (2004) · Acta Crystallographica Section D Biological Crystallography · doi:10.1107/s0907444904011679 · Cited by 4,815 · see citing works
Metabolite profiling identifies a key role for glycine in rapid cancer cell proliferation
Jain, M., Nilsson, R., Sharma, S., Madhusudhan, N., Kitami, T., Souza, A. L., Kafri, R., Kirschner, M. W., Clish, C. B., & Mootha, V. K. (2012) · Science · doi:10.1126/science.1218595 · Cited by 1,403 · see citing works
Llopis, J. L., McCaffery, J. M., Miyawaki, A., Farquhar, M. G., & Tsien, R. Y. (1998) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.95.12.6803 · Cited by 1,133 · see citing works
Zhang, W. C., Shyh-Chang, N., Yang, H., Rai, A., Umashankar, S., Ma, S., Soh, B. S., Sun, L. L., Tai, B. C., Nga, M. E., et al. (2012) · Cell · doi:10.1016/j.cell.2011.11.050 · Cited by 660 · see citing works
Reversal of cytosolic one-carbon flux compensates for loss of the mitochondrial folate pathway
Ducker, G. S., Chen, L., Morscher, R. J., Ghergurovich, J. M., Esposito, M., Teng, X., Kang, Y., & Rabinowitz, J. D. (2016) · Cell Metabolism · doi:10.1016/j.cmet.2016.04.016 · Cited by 419 · see citing works
Ducker, G. S., Ghergurovich, J. M., Mainolfi, N., Suri, V., Jeong, S. K., Hsin-Jung Li, S., Friedman, A., Manfredi, M. G., Gitai, Z., Kim, H., et al. (2017) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1706617114 · Cited by 261 · see citing works
SHMT1 and SHMT2 Are Functionally Redundant in Nuclear De novo Thymidylate Biosynthesis
Anderson, D. D., & Stover, P. J. (2009) · PLoS ONE · doi:10.1371/journal.pone.0005839 · Cited by 199 · see citing works
Garrow, T. A., Brenner, A., Whitehead, V. M., Chen, X. N., Duncan, R., Korenberg, J. R., & Shane, B. (1993) · Journal of Biological Chemistry · doi:10.1016/s0021-9258(19)50286-1 · Cited by 179 · see citing works
Stover, P. J., & Schirch, V. (1991) · Journal of Biological Chemistry · doi:10.1016/s0021-9258(18)52328-0 · Cited by 132 · see citing works
SHMT1 knockdown induces apoptosis in lung cancer cells by causing uracil misincorporation
Paone, A., Marani, M., Fiascarelli, A., Rinaldo, S., Giardina, G., Contestabile, R., Paiardini, A., & Cutruzzolà, F. (2014) · Cell Death and Disease · doi:10.1038/cddis.2014.482 · Cited by 129 · see citing works
Self-citationMetformin regulates global DNA methylation via mitochondrial one-carbon metabolism
Cuyàs, E., Fernández‐Arroyo, S., Verdura, S., Garcia, R., Štursa, J., Werner, L., Blanco‐González, E., Montes‐Bayón, M., Joven, J., Viollet, B., et al. (2017) · Oncogene · doi:10.1038/onc.2017.367 · Cited by 120 · see citing works
Giardina, G., Brunotti, P., Fiascarelli, A., Cicalini, A., Costa, M. G. S., Buckle, A. M., di Salvo, M. L., Giorgi, A., Marani, M., Paone, A., et al. (2015) · FEBS Journal · doi:10.1111/febs.13211 · Cited by 104 · see citing works
Self-citationl ‐Threonine aldolase, serine hydroxymethyltransferase and fungal alanine racemase
Contestabile, R., Paiardini, A., Pascarella, S., di Salvo, M. L., D’Aguanno, S., & Bossa, F. (2001) · European Journal of Biochemistry · doi:10.1046/j.0014-2956.2001.02606.x · Cited by 99 · see citing works
Self-citationReversal of Cytosolic One-Carbon Flux Compensates for Loss of the Mitochondrial Folate Pathway
Ducker, G. S., Chen, L., Morscher, R. J., Ghergurovich, J. M., Esposito, M., Teng, X., Kang, Y., & Rabinowitz, J. D. (2016) · Cell Metabolism · doi:10.1016/j.cmet.2016.09.011 · Cited by 91 · see citing works
Schirch, L., & Ropp, M. (1967) · Biochemistry · doi:10.1021/bi00853a039 · Cited by 86 · see citing works
Fu, T.-F., Rife, J. P., & Schirch, V. (2001) · Archives of Biochemistry and Biophysics · doi:10.1006/abbi.2001.2471 · Cited by 72 · see citing works
Measurement of cytosolic and mitochondrial pH in living cells during reversible metabolic inhibition
Balut, C., vandeVen, M., Despa, S. I., Lambrichts, I., Ameloot, M. M., Steels, P., & Smets, I. (2007) · Kidney International · doi:10.1038/sj.ki.5002632 · Cited by 70 · see citing works
The origin of reaction specificity in serine hydroxymethyltransferase.
Schirch, V., Shostak, K., Zamora, M., & Guatam-Basak, M. (1991) · Journal of Biological Chemistry · doi:10.1016/s0021-9258(17)35237-7 · Cited by 66 · see citing works
Daidone, F., Florio, R., Rinaldo, S., Contestabile, R., di Salvo, M. L., Cutruzzolà, F., Bossa, F., & Paiardini, A. (2011) · European Journal of Medicinal Chemistry · doi:10.1016/j.ejmech.2011.02.009 · Cited by 64 · see citing works
Self-citationWitschel, M. C., Rottmann, M., Schwab, A., Leartsakulpanich, U., Chitnumsub, P., Seet, M., Tonazzi, S., Schwertz, G., Stelzer, F., Mietzner, T., et al. (2015) · Journal of Medicinal Chemistry · doi:10.1021/jm501987h · Cited by 63 · see citing works
Marani, M., Paone, A., Fiascarelli, A., Macone, A., Gargano, M., Rinaldo, S., Giardina, G., Pontecorvi, V., Koes, D. R., McDermott, L. A., et al. (2015) · Oncotarget · doi:10.18632/oncotarget.6726 · Cited by 57 · see citing works
Self-citationPaiardini, A., Tramonti, A., Schirch, D., Guiducci, G., di Salvo, M. L., Fiascarelli, A., Giorgi, A., Maras, B., Cutruzzolà, F., & Contestabile, R. (2016) · Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics · doi:10.1016/j.bbapap.2016.08.010 · Cited by 44 · see citing works
Self-citationSerine hydroxymethyltransferase activity and serine incorporation in leukocytes.
Thorndike, J., Pelliniemi, T., & Beck, W. S. (1979) · PubMed · Cited by 39 · see citing works
Paiardini, A., Fiascarelli, A., Rinaldo, S., Daidone, F., Giardina, G., Koes, D. R., Parroni, A., Montini, G., Marani, M., Paone, A., et al. (2015) · ChemMedChem · doi:10.1002/cmdc.201500028 · Cited by 37 · see citing works
Self-citationMalerba, F., Bellelli, A., Giorgi, A., Bossa, F., & Contestabile, R. (2007) · Biochemical Journal · doi:10.1042/bj20061681 · Cited by 30 · see citing works
Self-citationSchwertz, G., Witschel, M. C., Rottmann, M., Leartsakulpanich, U., Chitnumsub, P., Jaruwat, A., Amornwatcharapong, W., Ittarat, W., Schäfer, A., Aponte, R. A., et al. (2018) · ChemMedChem · doi:10.1002/cmdc.201800053 · Cited by 27 · see citing works
Amornwatcharapong, W., Maenpuen, S., Chitnumsub, P., Leartsakulpanich, U., & Chaiyen, P. (2017) · Archives of Biochemistry and Biophysics · doi:10.1016/j.abb.2017.07.017 · Cited by 15 · see citing works
Site-Directed Mutagenesis Techniques in the Study ofEscherichia coliSerine Hydroxymethyltransferase
Iurescia, S., Condò, I., Angelaccio, S., Fratte, S. D., & Bossa, F. (1996) · Protein Expression and Purification · doi:10.1006/prep.1996.0046 · Cited by 14 · see citing works
Flagged first, then by citations
1 of the 29 references couldn’t be matched to a known paper.
Cited by
Sorted by citations
A review of small-molecule inhibitors of one-carbon enzymes: SHMT2 and MTHFD2 in the spotlight
Cuthbertson, C. R., Arabzada, Z., Bankhead, A., Kyani, A., & Neamati, N. (2021) · ACS Pharmacology & Translational Science · doi:10.1021/acsptsci.0c00223 · Cited by 57 · see citing works
Guiducci, G., Paone, A., Tramonti, A., Giardina, G., Rinaldo, S., Bouzidi, A., Magnifico, M. C., Marani, M., Menéndez, J. A., Fatica, A., et al. (2019) · Nucleic Acids Research · doi:10.1093/nar/gkz129 · Cited by 56 · see citing works
Self-citationScaletti, E. R., Jemth, A., Helleday, T., & Stenmark, P. (2019) · FEBS Letters · doi:10.1002/1873-3468.13455 · Cited by 52 · see citing works
Tramonti, A., Nardella, C., di Salvo, M. L., Barile, A., Cutruzzolà, F., & Contestabile, R. (2018) · Biochemistry · doi:10.1021/acs.biochem.8b01074 · Cited by 37 · see citing works
Self-citationStudy of SHMT2 Inhibitors and Their Binding Mechanism by Computational Alanine Scanning
He, L., Bao, J., Yang, Y., Dong, S., Zhang, L., Qi, Y., & Zhang, J. Z. H. (2019) · Journal of Chemical Information and Modeling · doi:10.1021/acs.jcim.9b00370 · Cited by 33 · see citing works
Metformin Is a Pyridoxal-5′-phosphate (PLP)-Competitive Inhibitor of SHMT2
Tramonti, A., Cuyàs, E., Encinar, J. A., Pietzke, M., Paone, A., Verdura, S., Arbusà, A., Martı́n-Castillo, B., Giardina, G., Joven, J., et al. (2021) · Cancers · doi:10.3390/cancers13164009 · Cited by 31 · see citing works
Self-citationArabidopsis thaliana serine hydroxymethyltransferases: functions, structures, and perspectives
Nogués, I., Sekula, B., Angelaccio, S., Grzechowiak, M., Tramonti, A., Contestabile, R., & Ruszkowski, M. (2022) · Plant Physiology and Biochemistry · doi:10.1016/j.plaphy.2022.07.025 · Cited by 31 · see citing works
Self-citationXie, S.-Y., Shi, D., Ouyang, Y. Q., Cheng, X.-Y., Chen, X., Jiang, T., Xia, W., Guo, L., & Lin, H. (2021) · Research Square · doi:10.21203/rs.3.rs-1016628/v1 · Cited by 22 · see citing works
Maenpuen, S., Mee-udorn, P., Pinthong, C., Athipornchai, A., Phiwkaow, K., Watchasit, S., Pimviriyakul, P., Rungrotmongkol, T., Tinikul, R., Leartsakulpanich, U., et al. (2023) · Archives of Biochemistry and Biophysics · doi:10.1016/j.abb.2023.109712 · Cited by 22 · see citing works
Targeting Amino Acid Metabolic Vulnerabilities in Myeloid Malignancies
Fultang, L., Gneo, L., Santo, C. D., & Mussai, F. (2021) · Frontiers in Oncology · doi:10.3389/fonc.2021.674720 · Cited by 23 · see citing works
Transcriptomic and proteomic analysis of Staphylococcus aureus response to cuminaldehyde stress
Li, H., Huang, Y.-Y., Addo, K. A., Huang, Z.-X., Yu, Y.-G., & Xiao, X. (2022) · International Journal of Food Microbiology · doi:10.1016/j.ijfoodmicro.2022.109930 · Cited by 17 · see citing works
Cytosolic localization and in vitro assembly of human de novo thymidylate synthesis complex
Spizzichino, S., Boi, D., Boumis, G., Lucchi, R., Liberati, F. R., Capelli, D., Montanari, R., Pochetti, G., Piacentini, R., Parisi, G., et al. (2021) · FEBS Journal · doi:10.1111/febs.16248 · Cited by 15 · see citing works
Self-citationPhosphorylated SHMT2 Regulates Oncogenesis Through m6A Modification in Lung Adenocarcinoma
Han, T., Wang, Y., Cheng, M., Hu, Q., Wan, X., Huang, M.-L., Liu, Y., Xun, W., Xu, J., Wang, L., et al. (2024) · Advanced Science · doi:10.1002/advs.202307834 · Cited by 14 · see citing works
Identification of three new compounds that directly target human serine hydroxymethyltransferase 2
Han, Y., He, L., Qi, Y., Zhao, Y., Pan, Y., Fang, B., Li, S., Zhang, J. Z. H., & Zhang, L. (2020) · Chemical Biology & Drug Design · doi:10.1111/cbdd.13774 · Cited by 13 · see citing works
The Role of One‐Carbon Metabolism in Cancer and Its Therapeutic Significance
Jiang, Y., Zhou, G., Zhang, Q., & Zhou, S. (2026) · MedComm – Oncology · doi:10.1002/mog2.70062 · Cited by 1 · see citing works
Li, J.-Y., Zhang, X., & Sheng, R. (2026) · Journal of Translational Medicine · doi:10.1186/s12967-026-08044-x · Cited by 1 · see citing works
SHMT2 inhibition triggers mitochondrial apoptosis to suppress lung adenocarcinoma progression
Chen, Y., Zhang, X. H., Pang, X., Yang, Y., Lu, D., Zhao, J., Zhu, J., Du, W., Gu, C., Li, J., et al. (2026) · Journal of Translational Medicine · doi:10.1186/s12967-026-07975-9
Li, M., Xu, Y. N., Su, X., & Wen, J. (2026) · PeerJ · doi:10.7717/peerj.21570
- Authors
- Tramonti, A., Paiardini, A., Paone, A., Bouzidi, A., Giardina, G., Guiducci, G., Magnifico, M. C., Rinaldo, S., McDermott, L., Menendez, J. A., Contestabile, R., & Cutruzzolà, F.
- Affiliations
- Institute of Molecular Biology and Pathology (IT)
- Sapienza University of Rome (IT)
- University of Pittsburgh (US)
- Corresponding author
- Contestabile, Roberto
- Cutruzzolà, Francesca
- ORCID
- Venue
- Archives of Biochemistry and Biophysics
- Publisher
- Elsevier BV
- Published
- 2018-09
- Volume
- 653
- Pages
- 71-79
- ISSN
- 0003-9861 (ISSN-L)
- OpenAlex
- W2810955549
- Cited by
- 18
- References
- 29
- Citations by year
- 2026: 4 · 2024: 1 · 2023: 1 · 2022: 3 · 2021: 4 · 2020: 1 · 2019: 3 · 2018: 1
- FWCI
- 0.97
- Type
- journal article
- Language
- en
- Open access
- closed
- Locations
- Archives of Biochemistry and Biophysics (publishedVersion)
- PubMed (publishedVersion)
- IRIS Research product catalog (Sapienza University of Rome) (submittedVersion)
- Queen Mary Research Online (Queen Mary University of London) (submittedVersion)
- CINECA IRIS Institutional Research Information System (University of Bari Aldo Moro) (submittedVersion)
- Funders
- Associazione Italiana per la Ricerca sul Cancro (AIRC-IG2015 n. 16720)
- Sapienza University of Rome (RP11715C644A5CCE)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Biochemistry › Amino Acid Enzymes and Metabolism
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Biochemical and Molecular Research
- Health Sciences › Medicine › Rheumatology › Folate and B Vitamins Research
- Keywords
- serine hydroxymethyltransferase, SHMT1, SHMT2, one-carbon metabolism, enzyme-substrate complex, enzyme inhibition, lung cancer, inhibitor design, tetrahydrofolate
- MeSH terms
- Enzyme Inhibitors, Glycine, Humans, Hydrogen Bonding, Lung Neoplasms, Pyrans, Pyrazoles, Serine, Glycine Hydroxymethyltransferase, Spectrometry, Fluorescence, Substrate Specificity, Apoptosis, Cell Line, Tumor
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
Are you an author, or do you see a problem with this page? Request a review