Three approaches are being pursued to identify lead structures for the design of ZIKV protease inhibitors: 1) Based on fragment hits identified from the ECBL and the Molecule Archive (MA) and 47 recently published fragments, molecules were designed using fragment growing and linking strategies. Based on Hyde scores, LE and LLE, four compounds were selected, and synthesis strategies were elaborated and initiated. Additionally, easy-to-synthesize, close fragment hit analogues have been designed as backup strategies in case of synthesis failure or poor affinity. 2) The compounds of the MA were virtually screened. 18 virtual hit compounds were submitted for crystal soaking. By now, structural data for one of the virtual hits was obtained and its experimental binding pose closely resembled the highly ranked predicted poses. 3) Chemical space docking using the Enamine Real Space yielded two additional virtual hits that have been ordered from Enamine and will be subjected to crystal soaking.
After 3 months, Christoph has achieved the following milestones:
- Four compounds were designed based on CFS hits from the ECBL and Molecule Archive Library, showing improved HYDE scores, ligand efficiency (LE), and lipophilic ligand efficiency (LLE). Each originated from distinct fragment binders in the S1 pocket, the primary binding site of fragments. In two cases, the Inspirator tool was used for linking to S2 pocket fragments, with linkers later simplified for synthetic accessibility. A similar approach linked fragments in the S1 and S1′ pockets. The fourth compound resulted from fragment expansion and contains a pyrrolo[2,3-c]pyridine scaffold forming multiple hydrogen bonds and polar contacts in the S1 pocket and extending into the S2 pocket (HYDE: 0.43–4.3 µM, LE = 0.39, LLE = 9.711, rot. bonds = 8). As a backup strategy, a focused library resembling two S1 fragments was designed to improve polar interactions with only minimal structural changes. These fragments can be improved via quick iterative synthesis, soaking, and design cycles.
- Fragment-anchored Chemical Space Docking was initiated based on a fragment hit from the Molecule Archive (MA) as an anchor and using the Enamine Real Space. The anchor fragment was located in the S1 pocket of the active site. After anchoring, filtering was performed based on affinity, LE, LLE, and suitable exit vectors. The goal was to achieve further growth, especially towards the S2 and S3 pockets. Two highly ranked derivatives (CSD-1, CSD-2) were ordered from Enamine and will be submitted to crystal soaking. In the proposed binding mode, CSD-1 extends to the S2 and CSD-2 to the S3 pocket. Notably, CSD-2 features a centrally positioned amino group offering an additional exit vector to incorporate the substituent of CSD-1 in the S2 pocket. Depending on the structural data from crystal soaking, either a CSD-1/2 combination approach or individual optimization of the CSD hits will be pursued.
- A total of 16,934 molecules from the Molecule Archive were initially filtered by molecular weight (>2000 Da) and sLogP ( 0.205, LLE > 2.0, and rot. bonds < 10, resulting in 22 candidates. Seven were excluded due to undesired functionalities (e.g., azides, silicon, hydroquinones). The top three compounds by HYDE score were retained regardless of other parameters, yielding 18 compounds for crystal soaking. Five have been tested to date, with structural data obtained for one fragment-like binder, which resembles the top predicted poses. Unfortunately, the compound seems to interact with the neighbouring symmetry mate. Results for the remaining compounds are pending. Based on small molecule crystal soaking we hope to identify lead structures for optimization or further fragments for fragment-based design.