Discovery of WRN deconjugase inhibitor HRO761

Background

Mismatch repair (MMR)-deficient cancers, particularly those characterized by microsatellite instability (MSI), pose unique challenges due to their heterogeneous nature and resistance to conventional treatments. The emergence of synthetic lethality as a strategy to selectively target DNA repair pathways offers a new avenue for precision oncology. In this context, the discovery of HRO761 as a Werner syndrome ATP-dependent helicase (WRN) inhibitor with synthetic lethality in MSI cancers represents a paradigm shift in the pursuit of tailored therapies for these aggressive malignancies.

Method and Disscussions

Novartis has published a major article in the journal nature reporting the structural, biochemical, cellular and pharmacological characterisation of the clinical-stage WRN deconjugate enzyme inhibitor HRO761, which was identified through an innovative strategy of Hit discovery and lead compound optimisation.HRO761 is a potent, selective, metastable WRN inhibitor, which binds to WRN at the D1 and D2 binding at the interface of the D1 and D2 deconjugase structural domains, locking WRN in an inactive conformation. A non-covalent compound 1 was obtained from an ATP binding screen of 150,000 compounds. As shown for compound 2, potency was improved in a manner that improved molecular mass and poorer physicochemical properties and based on structure-based design guided by lipophilic efficiency (lipE). The medicinal chemistry strategy is to use physics-based property prediction (logP) to systematically improve permeability and lipid solubility, two properties that are usually unrelated.

The eutectic structure of the complex formed by HRO761 with the WRN core deconjugate (consisting of two RecA-like deconjugate structural domains, D1 and D2) showed that HRO761 binds to a non-conserved variable site at the D1-D2 interface, rationalising the high selectivity of the related RecQ deconjugate. Although both HRO761 and the ATP analogue bind at the D1-D2 interface with overlapping D2 residues, the relative orientations are rotated by ~180°. The flexible conformation of the hinge between the D1 and D2 structural domains is due to a conformational change in residues 728-732 (Thr-Gly-Phe-Asp-Arg). Most of the hinge residues bind to HRO761, and almost every heavy atom of HRO761 interacts polarly with WRN.

The involvement of ATP-binding residues makes the pocket unusually polar and rich in arginine residues. This structure also explains the mechanism of action of ATP and DNA.HRO761-induced structural domain rotation bisects the ATP-binding site and replaces the Walker motif, resulting in a mixture of "competitive inhibition & uncompetitive inhibition of ATP" due to altered binding of HRO761, and competitive inhibition of orthosteric sites due to allozyme inhibition. competitive inhibition & uncompetitive inhibition, i.e., anti-competitive inhibition due to allosteric inhibition, and competitive inhibition of orthosteric sites, which is more specific).

Figure 2. HRO761 and related WRN inhibitors are selective WRN inhibitors mixed competitive with ATP and uncompetitive with DNA.

Conclusions

The discovery of HRO761 as a WRN inhibitor capable of inducing synthetic lethality in MSI cancers holds significant implications for precision oncology. By exploiting the genetic vulnerabilities of MMR-deficient tumors, HRO761 offers a novel therapeutic approach that selectively targets cancer cells while sparing normal tissues. The insights gained from this study not only advance our understanding of synthetic lethal interactions in cancer but also highlight the therapeutic potential of WRN inhibition in a subset of highly challenging malignancies. Moving forward, further investigations into the clinical applicability and safety profile of HRO761 in MSI cancer patients are warranted, with the ultimate goal of translating these preclinical discoveries into impactful treatments that could revolutionize the management of MSI cancers.

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