6XRP

Crystal structure of GlpG in complex with peptide ketoamide inhibitor, Ac-RVWHA-ketoamide-phenylbutyl

Summary for 6XRP

• Entry DOI: 10.2210/pdb6xrp/pdb
• Descriptor: Rhomboid protease GlpG, peptide ketoamide inhibitor, N-(4-phenylbutyl)formamide, ... (4 entities in total)
• Functional Keywords: glpg, rhomboid protease, hydrolase-hydrolase inhibitor complex, membrane protein, hydrolase/hydrolase inhibitor
• Biological source: Escherichia coli; More
• Total number of polymer chains: 2
• Total formula weight: 24734.23

Authors

Urban, S.,Cho, S. (deposition date: 2020-07-13, release date: 2020-09-16, Last modification date: 2023-10-18)

Primary citation

Gandhi, S.,Baker, R.P.,Cho, S.,Stanchev, S.,Strisovsky, K.,Urban, S.
Designed Parasite-Selective Rhomboid Inhibitors Block Invasion and Clear Blood-Stage Malaria.
Cell Chem Biol, 27:1410-1424.e6, 2020

PubMed Abstract: Rhomboid intramembrane proteases regulate pathophysiological processes, but their targeting in a disease context has never been achieved. We decoded the atypical substrate specificity of malaria rhomboid PfROM4, but found, unexpectedly, that it results from "steric exclusion": PfROM4 and canonical rhomboid proteases cannot cleave each other's substrates due to reciprocal juxtamembrane steric clashes. Instead, we engineered an optimal sequence that enhanced proteolysis >10-fold, and solved high-resolution structures to discover that boronates enhance inhibition >100-fold. A peptide boronate modeled on our "super-substrate" carrying one "steric-excluding" residue inhibited PfROM4 but not human rhomboid proteolysis. We further screened a library to discover an orthogonal alpha-ketoamide that potently inhibited PfROM4 but not human rhomboid proteolysis. Despite the membrane-immersed target and rapid invasion, ultrastructural analysis revealed that single-dosing blood-stage malaria cultures blocked host-cell invasion and cleared parasitemia. These observations establish a strategy for designing parasite-selective rhomboid inhibitors and expose a druggable dependence on rhomboid proteolysis in non-motile parasites.

PubMed: 32888502
DOI: 10.1016/j.chembiol.2020.08.011

Experimental method

X-RAY DIFFRACTION (2.4 Å)