4RKX

Identification and characterization of a small molecule inhibitor of S. pyogenes SpeB.

Summary for 4RKX

• Entry DOI: 10.2210/pdb4rkx/pdb
• Related: 4D8e 4d8b 4d8i
• Descriptor: Streptopain, NITRATE ION, benzyl (cyanomethyl)carbamate, ... (4 entities in total)
• Functional Keywords: papain fold, cysteine protease, secreted, hydrolase-hydrolase inhibitor complex, hydrolase/hydrolase inhibitor
• Biological source: Streptococcus pyogenes
• Total number of polymer chains: 1
• Total formula weight: 28933.90

Authors

Wang, A.Y.,Gonzalez-Paez, G.E.,Wolan, D.W. (deposition date: 2014-10-14, release date: 2015-07-22, Last modification date: 2023-09-20)

Primary citation

Wang, A.Y.,Gonzalez-Paez, G.E.,Wolan, D.W.
Identification and Co-complex Structure of a New S. pyogenes SpeB Small Molecule Inhibitor.
Biochemistry, 54:4365-4373, 2015

PubMed Abstract: The secreted Streptococcus pyogenes cysteine protease SpeB is implicated in host immune system evasion and bacterial virulence. We present a small molecule inhibitor of SpeB 2477 identified from a high-throughput screen based on the hydrolysis of a fluorogenic peptide substrate Ac-AIK-AMC. 2477 inhibits other SpeB-related proteases but not human caspase-3, suggesting that the molecule targets proteases with the papain-like structural fold. A 1.59 Å X-ray crystal structure of 2477 bound to the SpeB active site reveals the mechanism of inhibition and the essential constituents of 2477 necessary for binding. An assessment against a panel of 2477 derivatives confirms our structural findings and shows that a carbamate and nitrile on 2477 are required for SpeB inhibition, as these moieties provide an extensive network of electrostatic and hydrogen-bonding interactions with SpeB active site residues. Surprisingly, despite 2477 having a reduced inhibitory potential against papain, the majority of 2477-related compounds inhibit papain to a much greater and broader extent than SpeB. These findings indicate that SpeB is more stringently selective than papain for this panel of small molecule inhibitors. On the basis of our structural and biochemical characterization, we propose modifications to 2477 for subsequent rounds of inhibitor design that will impart specificity to SpeB over other papain-like proteases, including alterations of the compound to exploit the differences in CA protease active site pocket sizes and electrostatics.

PubMed: 26132413
DOI: 10.1021/acs.biochem.5b00607

Experimental method

X-RAY DIFFRACTION (1.59 Å)