Human SHMT inhibitors reveal defective glycine import as a targetable metabolic vulnerability of diffuse large B-cell lymphoma

Abstract

The enzyme serine hydroxymethyltransferse (SHMT) converts serine into glycine and a tetrahydrofolate-bound one-carbon unit. Folate one-carbon units support purine and thymidine synthesis, and thus cell growth. Mammals have both cytosolic SHMT1 and mitochondrial SHMT2, with the mitochondrial isozyme strongly up-regulated in cancer. Here we show genetically that dual SHMT1/2 knockout blocks HCT-116 colon cancer tumor xenograft formation. Building from a pyrazolopyran scaffold that inhibits plant SHMT, we identify small-molecule dual inhibitors of human SHMT1/2 (biochemical IC ∼ 10 nM). Metabolomics and isotope tracer studies demonstrate effective cellular target engagement. A cancer cell-line screen revealed that B-cell lines are particularly sensitive to SHMT inhibition. The one-carbon donor formate generally rescues cells from SHMT inhibition, but paradoxically increases the inhibitor's cytotoxicity in diffuse large B-cell lymphoma (DLBCL). We show that this effect is rooted in defective glycine uptake in DLBCL cell lines, rendering them uniquely dependent upon SHMT enzymatic activity to meet glycine demand. Thus, defective glycine import is a targetable metabolic deficiency of DLBCL.

Structural basis of inhibition of the human serine hydroxymethyltransferase SHMT2 by antifolate drugs

“…SHMT1 was consistently shown to be inhibited by antifolates to a greater extent than hSHMT2 in our competition assay. Such differences in inhibition between hSHMT isoforms has been observed in recent studies of pyrazolpyran derived inhibitors, which are more potent inhibitors of hSHMT1 than hSHMT2 . Interestingly, while MTX had very little effect on hSHMT2 activity it was the second best inhibitor of hSHMT1 of the antifolates tested.…”

“…There have also been studies aimed at utilizing selective serine analogues and amino acid derivatives as SHMT inhibitors, however this has not proven to be particularly successful . Recently, compounds derived from a pyrazolpyran scaffold have been explored as inhibitors of human SHMT . Pyrazolpyran derivatives had previously been shown inhibit plant SHMT1 and showed efficacy as herbicides .…”

The catalytic activity of serine hydroxymethyltransferase is essential for de novo nuclear dTMP synthesis in lung cancer cells

“…6 A, hexagonal and tetragonal, respectively. Crystals were cryo-protected by soaking in a mother liquor solution containing 25% glycerol before flash freezing in liquid nitrogen.…”

“…Tumour cells recycle one-carbon units from different amino acids within the folate and methionine cycles to produce the building blocks needed to sustain high proliferation rates [1][2][3]. Given its pivotal role in OCM, it is not surprising that SHMT is considered a potential drug target for cancer therapy [4][5][6][7]. Serine fuels the folate cycle through the reaction catalysed by serine hydroxymethyltransferase (SHMT) that reversibly interconverts serine and tetrahydrofolate (THF) to glycine and 5,10-methylene-THF (Fig.…”

Potent Inhibitors of Plasmodial Serine Hydroxymethyltransferase (SHMT) Featuring a Spirocyclic Scaffold

“…Human cytosolic SHMT1 and mitochondrial SHMT2 are of emerging interest as potential anticancer targets . We therefore tested the potent spiro‐dihydroindene analogues against h SHMT1 (Table ).…”