Modification of Existing Inhibitors

OSA Series 1 project was focused on structural modifications of a potent MurC inhibitor AZ5595, developed by AstraZeneca through a lead modification campaign. Despite having single digit nanomolar activities against Eco and Pae MurC, it suffered from permeability issues and bacterial efflux mechanisms, and thereby failed to translate such potency to antibacterial activity against wild-types.

[Ref1] https://pubs.acs.org/doi/10.1021/cb500360c

Image from: Graphical abstract of the 2014 AZ paper. Compound 10 is the lead AZ5595.

Initially, we brought in the eNRTy rules from Hergenrother’s team: replacing the alcohol group in AZ5595 (and other potent derivatives) with amine, guanidinium or pyridinium groups as well as introducing strengthened rigidity (less rotational bonds) in pursuit of a better accumulation in bacteria.

[Ref 2] https://www.nature.com/articles/nature22308

[Ref 3] https://pubs.acs.org/doi/full/10.1021/acsinfecdis.0c00715

Additionally, considering Mur ligases share a highly conserved active site across enzyme types and bacterial species (also proven by latest crystallography data, see the following overlaying figures), further multi-targeting modifications (bioisostere replacement, ligand growing, and scaffold hopping) were implemented in hope of obtaining better binding interactions (especially targeting the active site helix which originally binds the ADP phosphate group) and improved binding pocket compatibility (reduce the potential steric clashes with Mur ligase C-terminus).

[Ref 4] https://onlinelibrary.wiley.com/doi/full/10.1111/mmi.12758

An overlay of different species of MurC crystal structures (Pae MurC 8DOF (yellow), 6X9F (pink), 6X9N (blue), Pae MurD 7U35 (white), Eco MurD 3UAG (green), Eco MurE 7B53 (magenta) with different AZ inhibitors (OSA_001044, AZ8074, AZ5595) in the ATP binding pocket, among which the residue ASN remains conserved in its binding position across different Mur ligases from different origins.

A structural overlay of ATP binding site from different Murs (A. baumannii, E. coli, and P. aeruginosa MurC–F ligase crystal structures with ADP bound) and a 2D illustration of their binding mode with ADP (with Pae MurD (PDB 7U35) as an example). The target helices are indicated by the yellow box.

@Yuhang-CADD's progress in the following routes for synthesizing AZ hits and further pyrazolopyrimidine analogues:

Latest collection of AZ series biodata: Find here