Screening methods for acinetobacter baumannii spot enzyme modulators

An in vitro method for identifying a compound which specifically modulates A. baumannii SpoT hydrolase activity, comprising the steps of:

• a) providing a candidate compound;
• b) providing an A. baumannii SpoT polypeptide or SpoT-ppGpp complex;
• c) contacting said candidate compound with said A. baumannii SpoT polypeptide or SpoT-ppGpp complex;
• d) determining the hydrolase activity of A. baumannii SpoT in the presence and absence of said candidate compound;
• and
• e) identifying said candidate compound as a compound which modulates A. baumannii SpoT if a change in hydrolase activity is detected.

A computer system, intended to generate three dimensional structural representations of an A. baumannii SpoT protein and/or SpoT-ppGpp complex, complexes of A. pbaumannii SpoT protein with binding compounds or modulators for analyzing or optimizing binding of compounds or modulators to said A. baumannii SpoT protein and/or SpoT-ppGpp complex, the system containing computer-readable data comprising one or more of:

• (a) the coordinates of the A. baumannii SpoT protein structure listed in Table 1, optionally varied by a root mean square deviation of residue backbone atoms of not more than 3 Å, or selected coordinates thereof,
• (b) the coordinates of the A. baumannii SpoT-ppGpp complex structure listed in Table 1, optionally varied by a root mean square deviation of residue backbone atoms of not more than 3 Å, or selected coordinates thereof;
• (c) the coordinates of a candidate binding compound or modulator generated by interpreting X-ray crystallographic data, cryo-EM or NMR data by reference to the coordinates of the A. baumannii SpoT protein structure and/or SpoT-ppGpp complex structure, listed in Table 1, optionally varied by a root mean square deviation of residue backbone atoms of not more than 3 Å, or selected coordinates thereof, and
• (d) structure factor data derivable from the coordinates of (a), (b) or (c).