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

Abstract

Serine hydroxymethyltransferase (SHMT) is the major source of 1‐carbon units required for nucleotide synthesis. Humans have cytosolic (SHMT1) and mitochondrial (SHMT2) isoforms, which are upregulated in numerous cancers, making the enzyme an attractive drug target. Here, we show that the antifolates lometrexol and pemetrexed are inhibitors of SHMT2 and solve the first SHMT2‐antifolate structures. The antifolates display large differences in their hydrogen bond networks despite their similarity. Lometrexol was found to be the best hSHMT1/2 inhibitor from a panel antifolates. Comparison of apo hSHMT1 with antifolate bound hSHMT2 indicates a highly conserved active site architecture. This structural information offers insights as to how these compounds could be improved to produce more potent and specific inhibitors of this emerging anti‐cancer drug target.

Downregulating Serine Hydroxymethyltransferase 2 Deteriorates Hepatic Ischemia-Reperfusion Injury through ROS/JNK/P53 Signaling in Mice

“…Serine hydroxymethyl transferase (SHMT) is a pyridoxal-5′-phosphate-dependent enzyme functioning in the serine/glycine synthesis pathway and single-carbon metabolism, which provides essential precursors for protein and nucleic acid synthesis for cancer growth and metastasis [16]. Two types of SHMT (SHMT1 and SHMT2) genes have been discovered in the human genome [17]. In mammalian cells, SHMT1 and SHMT2 are encoded by different genes and are widely present in the cytoplasm and mitochondria, respectively.…”

Structural basis of methotrexate and pemetrexed action on serine hydroxymethyltransferases revealed using plant models

“…It is also very important to note that resolving positions of water molecules inside the antifolate-binding cavity was possible due to high resolution diffraction data obtained particularly for At SHMT2 structures. Lower resolution data from hmSHMT crystals 28 (2.3 Å, Protein Data Bank, PDB ID: 6qvl) allowed to trace only a very limited number of water molecules.

Figure 7Detailed binding mode of PTX to At SHMT2. PTX (orange bonds) interacts with the protein via an extensive network of hydrogen bonds (dashed, black lines; distances are given in Å), mostly mediated by water molecules (light blue circles).

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“…Importantly, computational drug design methods, which minimize the cost of development and increase the chance of finding a good candidate, are most successful if a crystal structure is known 27 . After completion of experiments for this article, structures of hmSHMT in complexes with PTX and lometrexol showed first structural insights into SHMT interactions with antifolates 28 . However, it has been impossible to obtain structures of MTX bound to human SHMT isoforms or any structure showing a cytosolic isoform complexed with antifolate.…”

Oncology Therapeutics Targeting the Metabolism of Amino Acids

“…Molecular docking studies and binding assays indicate that SHMT1 is the target of classical antifolates [ 108 ]. Lometrexol, an antifolate and the first GART inhibitor to be investigated clinically [ 109 , 110 ], has also been shown to inhibit SHMT2 [ 111 ] ( Figure 2 B). Lometrexol has undergone a Phase 2 clinical trial (NCT00033722) ( Table 1 ).…”

“…While SHIN1 is suitable for cell culture studies, it is not stable in vivo due to rapid clearance [ 99 ]. Issues with a high clearance were addressed with the dual SHMT inhibitor SHIN2 [ 111 ]. SHIN2 is the first SHMT1/2 inhibitor to demonstrate in vivo efficacy and synergizes with FDA approved antifolate methotrexate in mouse primary T cell acute lymphoblastic leukemia (T-ALL) and in PDXes ( Figure 2 B).…”