Enamine Kinase Inhibitors (MurD MurE)
This project is a collaboration between Dr Joe Eyermann, The University of Cape Town H3D and Northeastern University, and Rebecca Steventon at Warwick University.
There is a large level of consensus within the ATP binding pocket of the Mur ligases, allowing for an inhibitor to be designed that can target multiple Mur ligases.
The way in which ATP binds to the Mur ligases is similar to the ATP binding seen to the ‘hinge’ of human kinases. See the figure of x-ray structure of ATP bound to the hinge of human kinase CDK2 (PDBID: 1HCK) and the comparison of 1HCK versus ATP bound to E. coli murD bound to ATP (PDBID:2UAG).
An issue of cross reactivity could arise due to this, but there is a difference in the way the phosphate groups of ATP bind to Mur ligases compared to protein kinases, which should allow for specific inhibitors to be designed.
The ATP binding site has been previously targeted with inhibitors such as pyrazolopyrimidines against MurC. The pyrazolopyrimidines were from a kinase scaffold but were selective for MurC against a panel of human kinases, showing that kinase scaffolds can be used to selectively target Mur ligases.
A virtual screen of 40,000 compounds from an Enamine kinase inhibitor library was carried out using the Maestro software from Schrodinger. The compounds were targeted towards binding to an Asn residue which hydrogen-bonds to the adenine ring of ADP, as well as the H-bond donors that interact with the ADP phosphate groups. The screen was run against Streptococcus Agalactiae MurD and Escherichia coli MurE. ~600 compounds were identified as being potential candidates. The figures below show fragment binding to the ATP binding pocket of MurD (A-B) and MurE (C). The potential candidates will be biochemically screened at Warwick and undergo an XChem fragment screen at Diamond Light Source.
Fragment screening against MurE:
- Number of compounds screened: 662
- Number of compounds in the repeat screen: 202
- Number of compounds for which we did not get any diffraction data: 45
- Number of compounds which melted crystals in both screens: 6
The compounds were screened against MurE and no hits were obtained from those successfully screened. The summary of the compounds screened can be found in https://github.com/opensourceantibiotics/murligase/blob/master/MurD%20and%20MurE%20fragments_Joe%20and%20Becca_summary%20of%20screening.xlsx
There has been some discussion of results in GH Issues #6 and #17