Reviews in Computational Chemistry Volume 18

74 The Use of Scoring Functions in Drug Discovery Applications
Therefore, a new rational approach was developed to generate lead structures
by using the detailed 3D structural information of the ATP binding site located
on subunit B. At the time of project initiation, the X-ray structures of the DNA
gyrase subunit B complexed with a nonhydrolyzable ATP analogue, with
novobiocin, and with cyclothialidine were available. In the inner part of the
pocket they all share a common binding motif: each donates a hydrogenbond
to an aspartic acid side chain (Asp 73) and accepts a hydrogen bond
from a conserved water molecule. It was reasoned that a novel inhibitor
should have the ability to form these two key hydrogen bonds and a lipophilic
part to pick up some lipophilic interactions with the enzyme.
A computational search of the ACD 209 and the Roche Compound Inventory,
employing the SCORE1 function also implemented in LUDI, was carried
out to identify molecules with a low molecular weight meeting the above criteria.
Relying on the results of the in silico screening, just 600 compounds were
tested initially. Then, analogues similar to the first hits were assayed. Overall,
assay results for 3000 compounds gave rise to 150 hits clustered into 14
chemical classes. Seven of those classes could be validated as true, novel
DNA gyrase inhibitors that act by binding to the ATP binding site located
on the B subunit. The maximum noneffective concentration (MNEC) was in
the 5–64 mg/mL range, that is, two to three orders of magnitude higher than
the MNEC of novobiocin or cyclothialidine. Subsequent structure-based optimization
of the hits led to compounds with potencies equal or up to 10 times
better than novobiocin. Compound 11 (Figure 11; MNEC < 0.03 mg/mL) is an
example of a novel potent inhibitor of DNA gyrase B resulting from structurebased
virtual screening.
An important factor contributing to the success of the project was a new
assay that allowed detecting not only highly potent inhibitors but also weak
ones, so as to allow testing compounds at high concentrations. Instead of a
supercoiling assay usually used to test DNA gyrase inhibitory activity, a
coupled spectrophotometric ATPase assay was employed. Compounds could
be assayed in concentrations up to 0.5 mM due to a higher tolerance of the
solubilizing agent DMSO in this assay.
Figure 11 An inhibitor of DNA gyrase B, discovered at
Roche by means of virtual screening and subsequent
structure-based optimization.
H
N
N
O S
11
O
O