Dipeptidyl peptidase-IV inhibitors used in type-2 diabetes inhibit a phospholipase C: a case of promiscuous scaffolds in proteins

Abstract

The long term side effects of any newly introduced drug is a subject of intense research, and often raging controversies. One such example is the dipeptidyl peptidase-IV (DPP4) inhibitor used for treating type 2 diabetes, which is inconclusively implicated in increased susceptibility to acute pancreatitis. Previously, based on a computational analysis of the spatial and electrostatic properties of active site residues, we have demonstrated that phosphoinositide-specific phospholipase C (PI-PLC) from Bacillus cereus is a prolyl peptidase using in vivo experiments. In the current work, we first report the inhibition of the native activity of PI-PLC by two DPP4 inhibitors - vildagliptin (LAF-237) and K-579. While vildagliptin inhibited PI-PLC at micromolar concentrations, K-579 was a potent inhibitor even at nanomolar concentrations. Subsequently, we queried a comprehensive, non-redundant set of 5000 human proteins (50% similarity cutoff) with known structures using serine protease (SPASE) motifs derived from trypsin and DPP4. A pancreatic lipase and a gastric lipase are among the proteins that are identified as proteins having promiscuous SPASE scaffolds that could interact with DPP4 inhibitors. The presence of such scaffolds in human lipases is expected since they share the same catalytic mechanism with PI-PLC. However our methodology also detects other proteins, often with a completely different enzymatic mechanism, that have significantly congruent domains with the SPASE motifs. The reported elevated levels of serum lipase, although contested, could be rationalized by inhibition of lipases reported here. In an effort to further our understanding of the spatial and electrostatic basis of DPP4 inhibitors, we have also done a comprehensive analysis of all 76 known DPP4 structures liganded to inhibitors till date. Also, the methodology presented here can be easily adopted for other drugs, and provide the first line of filtering in the identification of pathways that might be inadvertently affected due to promiscuous scaffolds in proteins.

DOCLASP - Docking ligands to target proteins using spatial and electrostatic congruence extracted from a known holoenzyme and applying simple geometrical transformations

“…Previously, the conservation of spatial and electrostatic properties in cognate pairs of residues in the catalytic site of proteins with the same functionality has been used to develop a computational method (CLASP) for detecting binding and catalytic sites 12 – 15 . In the current work, this methodology has been extended by proposing a method for docking ligands into target proteins - DOCLASP ( Do cking using CLASP ).…”

“…The native activity of phosphoinositide-specific phospholipase C (PI-PLC) was previously shown to be inhibited by two dipeptidyl peptidase-IV (DPP4) inhibitors - vildagliptin (LAF-237) at micromolar concentrations, and K-579 at nanomolar concentrations using in vitro experiments based on CLASP analysis 15 . Since ‘comparing docking programs can be difficult’ 9 , the DOCLASP methodology is validated by docking vildagliptin to the PI-PLC structure in complex with myo-inositol 17 .…”

Directed evolution induces tributyrin hydrolysis in a virulence factor of Xylella fastidiosa using a duplicated gene as a template

“…However, most methods start with a template protein having the desired activity, known active site residues and 3D structure 23 – 25 . Previously, we have established a computational method (CLASP) based on spatial and electrostatic properties for the detection of active sites 26 – 29 , and a methodology to quantify promiscuity in proteins 30 . We also explored the prospect of promiscuous active sites to serve as the starting point for directed evolution (DECAAF) 31 , 32 .…”