Discovery of 1H-Pyrazole Biaryl Sulfonamides as Novel G2019S-LRRK2 Kinase Inhibitors.

pubs.acs.org/acsmedchemlett Letter Discovery of 1H-Pyrazole Biaryl Sulfonamides as Novel G2019SLRRK2 Kinase Inhibitors Robert K. Leśniak,* R. Jeremy Nichols,* Marcus Schonemann, Jing Zhao, Chandresh R. Gajera, Grace Lam, Khanh C. Nguyen, J. William Langston, Mark Smith,* and Thomas J. Montine* Cite This: ACS Med. Chem. Lett. 2022, 13, 981−988 ACCESS Metrics & More Read Online Article Recommendations sı Supporting Information * ABSTRACT: G2019S (GS) is the most prevalent mutation in the leucine rich repeat protein kinase 2 gene (LRRK2), a genetic predisposition that is common for Parkinson’s disease, as well as for some forms of cancer, and is a shared risk allele for Crohn’s disease. GS-LRRK2 has a hyperactive kinase, and although numerous drug discovery programs have targeted LRRK2 kinase, few have reached clinical development. We report the discovery and preliminary development of an entirely novel structural class of potent and selective GS-LRRK2 kinase inhibitors: biaryl-1Hpyrazoles. KEYWORDS: kinase inhibitors, selectivity, LRRK2, peptides and proteins in the LRRK2 field alone,9−12 most notably MLi-2 (1, Figure 1)9 developed by Merck. On the basis of our work developing GSLRRK2 selectivity in an indazole pharmacophore (2), we hypothesized that truncation to a 1H-pyrazole could provide a second structural series which maintains essential hinge-binding interactions present in the indazole core but with a lower molecular weight. A 1H-pyrazole could also enable access to novel chemical space directed at GS-LRRK2 selectivity, specifically targeting molecular interactions revealed in the development of 2. Here, we report the discovery and synthesis of substituted 1H-pyrazoles as potent and selective GS-LRRK2 kinase inhibitors. Our discovery of indazole 2 (Figure 1) highlighted that a hydrogen bond acceptor (HBA) motif attached to the phenyl ring of the tetrahydronapthalene provided a significant boost in potency (>10-fold) and selectivity (10-fold) toward GSLRRK2.8 Our structural model of the LRRK2 kinase active site, together with inhibition data, suggest that this nitrile makes a hydrogen bonding interaction with a lysine residue (Lys132) present at the boundary of the active site. Thus, we hoped also to incorporate this interaction in our new 1H-pyrazole series. To test our hypothesis, we designed and synthesized a series of molecules containing 3,4-substituted biaryl 1H-pyrazoles containing various HBA motifs (Figure 1). Out of our initial A utosomal dominant, missense mutations in the leucine rich repeat protein kinase 2 (LRRK2) gene are the most common genetic predisposition to Parkinson’s disease (PD).1 LRRK2 mutations account for approximately 1−5% of familial and sporadic PD.2 The most common LRRK2 mutation leads to a serine substitution of Gly2019 (GS) in the kinase domain,3 which increases kinase activity 2−4-fold.4 Following its discovery as a common genetic cause of PD, GS-LRRK2 carriers have been shown repeatedly to also be at increased risk for hormone-related cancers, especially breast cancer in women.5,6 Other mutations in LRRK2 have been shown to increase the risk of Crohn’s disease.7 As a highly validated therapeutic target for PD, multiple drug discovery programs have yielded potent LRRK2 inhibitors with some currently in clinical trials. To date, advanced LRRK2 kinase inhibitors inhibit both wild-type (WT) LRRK2 and GS-LRRK2, and many have shown significant unwanted side effects. Such side effects have not been definitively proven to arise from a lack of LRRK2 variant selectivity; however, selectively inhibiting the pathogenic G2019S-LRRK2 mutant kinase over WT would provide a more precise therapeutic, which may help alleviate such effects by sparing otherwise essential LRRK2 cellular functions. We recently reported a series of highly potent, selective, and brain-penetrant GS-LRRK2 inhibitors utilizing a 5-amino substituted indazole pharmacophore.8 The lead 5-amino indazole (2, Figure 1)8 possessed single-digit nanomolar in vitro potency for full-length GS-LRRK2 and >2000-fold mutant selectivity in human cells; dose-dependent GS-LRRK2-selective engagement in the brain also was observed in a G2019S knock-in mouse-model following I.P. administration. Indazoles are common kinase inhibitor pharmacophores, with >70 examples © 2022 American Chemical Society Received: March 16, 2022 Accepted: May 18, 2022 Published: May 23, 2022 981 https://doi.org/10.1021/acsmedchemlett.2c00116 ACS Med. Chem. Lett. 2022, 13, 981−988 ACS Medicinal Chemistry Letters pubs.acs.org/acsmedchemlett Letter Figure 1. Chemical structure representations of the nonselective LRRK2 kinase inhibitor MLi-2 (1), indazole 38 (2) from our previous work, and our subsequent hypothesis for a novel LRRK2 kinase inhibitor scaffold, biaryl 1H-pyrazoles. arise from incorporation of a 5-methyl substituent on substituted pyrazole scaffolds with highly substituted phenyl fragments at the R3 position. Modifications to the R3 region such as moving the methyl of 8 to give 14 and moving the sulfonamide of 9 to give 15, produced no significant improvements in potency (Table 1). We previously noted that selectivity and potency toward GS-LRRK can be enhanced through HBA interaction with Lys132. Indeed, a conserved interaction was predicted between sulfonamide oxygens and Lys132, in both 3and 4-subtituted phenylsulfonamides at R3. The sulfonamide moiety also was predicted to interact as a hydrogen bond donor (HBD) through its sulfonamide N−H bond to either Asp148 in the case of 3-sulfonamides 3 and 7 or Asp130 for 4-sulfonamides 4 and 9. In light of our discoveries thus far, we envisioned that sulfonamide 7 may be more favorable toward further investigation, and our efforts in this campaign are presented in Table 2. We initially focused on modifications in the R2 region and observed significant boosts in potency with modifications to the pyridine group, in contrast to analogous modifications to 9 presented in Table 1. As observed with our indazole series,8 the addition of a methyl group adjacent to the R2-pyridine nitrogen (16) gave a 3-fold boost in GS-LRRK2 kinase inhibition in IC50 and cellular assays compared to 7. Interestingly, this boost in potency was observed with (16) or without (17) the presence of a methyl at R1. We hoped to explore the R1 region; however, we discontinued these efforts given that CF3 analogue 18 significantly reduced potency. Incorporation of a morpholine group made 19 and 20 very potent GS-LRRK2 inhibitors in both IC50 and cellular assays. Methoxy pyridyl derivatives 21 and 22 did not improve potency, while dimethyl substituted pyridines 23 and 24 gave comparable inhibition as 16 and 17. We next focused our attention on the “central” ring (R3, Table 2) that links the pyrazole core to the benzenesulfonamide (R4) moiety. Modeling suggested structural modifications could be accommodated in this region of the active site. Indeed, incorporation of a methyl group at the R3 2-position (...truncated)