Structure-based design of bacterial hyaluronan lyase inhibitors

Hyaluronidases depolymerize hyaluronic acid, an important component of the extracellular matrix. Bacterial hyaluronan lyases (EC 4.2.2.1) contribute to the spreading of microorganisms in tissues. Potent and selective inhibitors are not known up to now, but would be interesting pharmacological tools and potential drugs for the treatment of bacterial infections. Starting from two crystal structures of streptococcal hyaluronan lyases, a homology model of the S. agalactiae strain 4755 enzyme hylB(4755) was generated and applied to structure-based inhibitor design with the de novo design program LUDI. The databases LeadQuest((R)) Vol. 1&2, Accelrys and ChemACX containing 228000 compounds were screened resulting in 1275 hits. Based on high LUDI scores, synthetic feasibility and commercial availability, 19 of these hits were investigated for inhibition of hylB(4755). 13 compounds were active in the milli- and submillimolar range. 1,3-diacetylbenz-imidazole-2-thione with IC50 values of 5 mu M and 160 mu M at physiological and optimum pH, respectively, is one of the two most potent inhibitors of hyaluronan lyases known to date. Depending on the LUDI sphere radius, it was docked in two different poses with similar scores. To analyze whether the hits represent (physico) chemical properties typical for drugability and optimal pharmacokinetics, the distributions of six descriptors within all hits from LeadQuest((R)) and ChemACX and within the original databases were compared. Generally, the hit distributions represent the type of the original ones, but are narrower with slightly different medians. More than 80% of the hits have molecular weights between 1,50 and 350, XLOGP values between 1 and 4, one H-donor, 1-3 H-acceptors, 0-3 rotatable bonds and 1-3 rings. In conclusion, the application of LUDI to both databases has led to the accumulation of relatively rigid, drug-like molecules.