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Use of surrogate X-ray crystallographic structures to support drug discovery against a challenging kinase

The structure-based discovery of inhibitors of protein kinase activity for many different proteins has led to treatments of many diseases and conditions. A surrogate approach to determine crystal structures has led to the discovery of inhibitors of a challenging kinase that could lead to a potential treatment for Parkinson s disease.

Inhibition of the kinase domain of the multi-domain leucine-rich repeat kinase 2 (LRRK2) protein has long been identified as a potential treatment for Parkinson s disease. Although many have tried, however, it has proven impossible to determine an X-ray crystal structure of the LRRK2 kinase domain. A research collaboration between Vernalis and Lundbeck established a surrogate approach to

determine crystal structures, which informed the discovery of multiple series of potent, selective inhibitors.

An analysis of the ATP-binding pocket of available structures of kinase domains bound to the generic kinase inhibitor, staurosporine, identified checkpoint kinase 1 (CHK1) as having close similarity. Vernalis had previously established routine insect cell expression and crystallisation of CHK1 protein. After exploring different mutational strategies, a 10-point mutation of CHK1 was demonstrated to be an effective surrogate for wild-type LRRK2 [1], providing a structural rationale for the selectivity profile of published inhibitors.

The structures of compounds bound to the CHK1 10-pt mutant kinase have been effectively used to generate several series of LRRK2 inhibitors (Figure 146). A medicinal chemistry programme identified one series of inhibitors with high potency and exquisite selectivity for LRRK2. Underpinning the structure-based design was routine determination of crystal structures derived from quality data obtained at macromolecular crystallography beamline ID29, and at the Soleil and Diamond synchrotrons.

PRINCIPAL PUBLICATION AND AUTHORS

Design and Synthesis of Pyrrolo[2,3-d]pyrimidine-Derived Leucine-Rich Repeat Kinase 2 (LRRK2) Inhibitors Using a Checkpoint Kinase 1 (CHK1)-Derived Crystallographic Surrogate, D.S. Williamson (a), G.P Smith (b), G.K Mikkelsen (b), T. Jensen (b), P. Acheson-Dossang (a), L. Badolo (b), S.T. Bedford (a), V. Chell (a), I-J. Chen (a), P. Dokurno (a), M. Hentzer (b), S. Newland (a), S.C. Ray (a), T. Shaw (a), A.E. Surgenor (a), L. Terry (a), Y. Wang (a), K.V. Christensen (b), J. Med. Chem. 64, 14, 10312-10332 (2021); https:/doi.org/10.1021/acs.jmedchem.1c00720. (a) Vernalis (R&D) Ltd., Great Abington, Cambridge (UK) (b) H. Lundbeck A/S, Valby (Denmark)

REFERENCE [1] D.S. Williamson et al., J. Med. Chem. 60, 8945-8962 (2017).

Fig. 146: X-ray crystal structure of highly selective compound 45 in complex with LRRK2 surrogate (CHK1 10pt-mutant).