In this issue of “Small Molecule Highlights” we bring you 5 new small molecules out of recent drug discovery journals. These molecules target a diverse selection of targets, including TRPA1, troponin, EBP, BRD4, and IRAK4. Enjoy!
GDC-6599
GDC-6599: Genentech has recently disclosed their lead optimization of a TRPA1 ion channel agonist for asthma and respiratory inflammatory disease. Their main goal was to mitigate associated anti-coagulation issues found in preclinical monkey models. In the model, repeat dosing of the parent compound was not tolerated, with signs of hemorrhage and blood loss being observed in multiple organs. The pre-clinical conundrum, what could be causing this coagulopathy? The drug development team identified two potential sites of untoward reactivity that might be responsible. The first was an oxadiazolone ring that was prone to ring opening. Such groups are present as covalent warheads for catalytic serine residues in several lipase inhibitors. The solution, deletion of the problematic carbonyl group and rearrangement of the heteroatoms to arrive at the 1,2,4-oxadiazole of GDC-6559. Further optimization of the pendant ether-linked 4-chlorophenyl group was required to dial in the required potency. The second site targeted for optimization was a metabolic soft spot located on the hypoxanthine substituent. Metabolite identification (MetID) in monkey hepatocytes revealed that this group was prone to oxidation. A key piece to the puzzle was found in MetID studies in dog hepatocytes where this metabolite was not observed, implicating aldehyde oxidase (AO) as the main culprit. An AO inhibitor (hydralazine) was added to monkey liver S9 fractions incubated with compound to confirm. Furthermore, the metabolite possessed similar structural features to a group of anticoagulant small molecules targeting VKOR (an enzyme in the vitamin K redox cycle). To mitigate AO mediated oxidation, the researchers surveyed a variety of blocking substituents, finally arriving at a methyl group to prevent formation of the undesired metabolite. In cells, a 4-fold increase in potency compared to the parent compound was achieved after lead optimization (hTRPA1 IC50 = 5.1 nM). GDC-6599 exhibited low clearance in human and moderate clearance in rat hepatocytes (CLHep = 4 and 27 mL/min/kg, respectively). Also, hepatocyte MetID across several species did not detect the problematic metabolite. Pharmacodynamic characterization in a guinea pig model of induced cough revealed dose-dependant inhibition of effect upon application of a TRPA1 agonist (cinnamaldehyde). Follow-up in vivo safety studies did not indicate any signs of significant toxicity in rats or monkey (100 mg/kg, 7-day, chronic dosing). The only finding was a mild prolongation of coagulations with none of the corresponding histological observations observed with the parent compound. The authors attribute this to the ever so slight overlap in structure, especially around the optimized methyl substituent, between GDC-6599 and vitamin K. Currently, GDC-6599 has completed a Phase I clinical trial in healthy volunteers and is currently recruiting for a Phase II study in patients with chronic cough (NCT05660850).
Reference: https://doi.org/10.1021/acs.jmedchem.3c02121
CK-963
CK-963: Scientists at Cytokinetics recently described the development of a novel cardiac troponin agonist for the treatment of physiological conditions related/contributing to heart failure. Specifically, the team was interested in selectively promoting contraction of heart muscle tissues without invoking calcium-dependant pathways. Currently, cardiac calcitrope drugs, such as dobutamine, milrinone, and digoxin, are used to treat acute heart contractility issues. However, significant cardiovascular issues, like cardiac arrythmia and systemic hypotension, have been associated with long-term use, especially with drugs modulating phosphodiesterase-3 (PDE-3). In search of a starting point, researchers screened their internal compound collection for a molecule that sensitizes cardiac troponin to calcium without inhibiting PDE-3. The HTS identified two molecules, one of which exhibited the desired selectivity for cardiac muscles without perturbing calcium homeostasis. SAR around the pyridyl-piperidine substituent was crucial to increasing potency. Modifications to the quinazolinone group were geared towards increasing solubility whilst maintaining selectivity over PDE-3. CK-936 was shown to directly interact with cardiac troponin using isothermal calorimetry (ITC; Ki = 11.5 μM). Sub-micromolar activity was observed in rat derived cardiac myofibrils (AC50 = 0.7 μM). Also, CK-936 was found to be a poor inhibitor of PDE-3 (IC50 > 40 μM). In pharmacokinetic studies, the compound exhibited moderate clearance in rats (CLrat = 7.1 mL/min/kg) and a low plasma half-life (T1/2 = 0.6 h). A pharmacodynamic study conducted in anesthetized rats indicated increased heart contractility upon i.v. administration of CK-963 (cumulative highest dose was 199 mg/kg). In the study, a 40% increase in left ventricle activity was observed at 32.8 μM plasma concentration. Given the underwhelming Phase III results of omecamtiv mecabril (Galactic-HF trial), Cytokinetics has offered a glimpse into the pharmacophores they are exploring next.
Reference: https://doi.org/10.1021/acs.jmedchem.3c02412
Compound 11
Compound 11: Multiple Sclerosis (MS) is a debilitating and chronic disease, characterized by progressive decline in cognitive and physical function. The cause, immune-mediated destruction of myelin and myelin-producing oligodendrocytes within the CNS. Recently, the development of “remyelinating” agents has garnered a significant amount of attention as a regenerative medicine approach for the treatment of MS, complementing existing immunomodulatory modalities that do little to halt the progression of the disease. Scientists at Genentech have targeted the emopamil binding protein (EBP) as it plays a role in the regulation of oligodendrocyte precursor cell (OPC) differentiation. A structurally enabled medicinal chemistry program commenced with a cryo-EM structure of an OPC enhancing literature compound bound to EBP. The structure revealed a linear conformation of the compound in the binding pocket, with the piperidine substituent, hypothesized to be protonated in the microenvironment, engaging in crucial long-range H-bonding interactions with Glu80, Glu122, and Asn193 residues of EBP TM4 (transmembrane 4) domain. SAR around the initial spiroindolinone group successfully dialed in selectivity for EBP and bestowed greater metabolic stability. The hydantoin substituent of compound 11 was found to be the optimal replacement for this group. Modifications to the pendant aryl group were used to optimize drug half-life. Working within a TPSA range permitting CNS access (<80 Å2), the research team identified the para-cyclopropylphenyl group as the best compromise between lipophilicity and drug clearance parameters. The spiro-piperidine had significant hERG liability concerns as lipophilic basic amines are prevalent hERG inhibitors. Strategies to sterically congest the area around the amine and decrease amine basicity had detrimental effects on activity. In the end, the original tetrahydropyran was maintained as it offered a sufficient therapeutic window (>100-fold). In mouse derived OPCs, compound 11 was found to potently inhibit EBP function (as assessed by EBP substrate accumulation; EC50 = 6 nM). Further studies in human cortical organoid corroborated results found in mouse OPCs (EC50 = 31 nM) and provided substantive support for de novo formation of oligodendrocytes in human cells. Pharmacokinetic evaluation in murine models revealed good oral bioavailability (F(%) = 68/42 in mouse/rat) and BBB penetration (Kp,uu = 0.77/0.74 in mouse/rat; i.v. dosing). In summary, compound 11 provides a therapeutic proof-of-concept to further support the development of remyelination therapies. It will be interesting to see whether Genentech continues to develop compound 11 as a clinical candidate.
Reference: https://doi.org/10.1021/acs.jmedchem.3c02396
BRD-SF2
BRD-SF2: This unoptimized BRD degrader was recently disclosed by scientists at GSK and the Molecular Sciences Research Hub at Imperial College to highlight their VHL-covalent PROTAC technology. The advantages of an E3 covalent PROTAC are obvious, binary vs ternary complex formation while maintaining the potential for catalytic degradation (dependant on coopted E3 ligase protein turnover). While a handful of cysteine-targeting covalent PROTACS have been reported previously, this technology targets Ser110 in the HIFα binding site of VHL. The challenge, balancing the reactivity profile of the warhead (WH) to modify serine while resisting hydrolysis under physiological conditions. Using a structure guided design approach, the team was able to pick out a viable WH attachment point that maintained critical non-covalent interactions between VH032 (VHL ligand) and its target. Sulfonyl fluoride was proposed as the best WH for modifying Ser110, however, incorporation was met with some difficulty. Specifically, preliminary conditions to generate the sulfonyl fluoride led to epimerization of the proline substituent of the VHL ligand. Fortunately, milder conditions using Selectfluor were developed to mitigate the observed racemization. With the WH in place, further optimization of the ligand, culminating in the introduction of the isoxazole, enhanced target engagement to a point where activity could be assessed. PROTACs targeting BRD4 and androgen receptor (AR) were prepared. For the sake of brevity, results for the BRD4 PROTAC (BRD-SF2) are discussed in detail. For BRD-SF2, dependence on the ubiquitin-proteosome system (UPS) was confirmed with inhibitors of proteosome activity (epoxomicin) and NEDDylation (MLN4924). A head-to-head comparison with MZ-1 (a non-covalent BRD4 PROTAC) revealed inferior degradation efficiency (compared to MZ-1). However, in wash-out experiments, the relative reduction in degradation was less for BRD-SF2 (27%) compared to MZ-1 (48%), indicating the persistence of a covalently modified degradation complex. This result highlights the therapeutic advantage of covalent E3 ligase recruiters. Taken together, initial results from these unoptimized covalent PROTACs look promising. Further optimization of the covalent VHL recruiting ligand will undoubtably furnish a useful tool for targeted protein degradation research.
Reference: https://doi.org/10.1021/acs.jmedchem.3c02123
BIO-7488
BIO-7488: Interleukin receptor-associated kinase 4 (IRAK4) plays a key role in the regulation of proinflammatory mediators in response to tissue injury. While numerous peripherally restricted inhibitors have been developed for arthritis indications, CNS penetrant drugs targeting IRAK4 have not received a lot of attention. Researchers at Biogen recognized the link between IRAK4 signalling and the progression of inflammation-mediated neurodegeneration post acute ischemic stroke (AIS). As such, they embarked to develop a brain-penetrant small molecule for the treatment of inflammation post stroke. Their medicinal chemistry campaign produced a molecule with interesting structural features. For instance, the terminal bridged-cyclic ether is a substituent that is rarely seen. It was incorporated to engage in solvent-facing interactions and shown to be less susceptible to oxidative metabolism compared to the other groups considered. Placement of the amide was crucial as its oxygen made a key H-bonding interaction with the hinge Met265. The isopropoxy substituent helped with initial amide hydrolysis issues and contributed, in part, to IRAK4 inhibition. The right-hand aromatic group was optimized to confer greater activity and target specificity. This was attributed to interactions between the pyrazolopyrimidine nitrogen and Val263 (water-bridged interaction), as well as π-stacking interactions with gatekeeper residue Tyr262. In biochemical assays, BIO-7488 inhibited IRAK4 function at sub-nanomolar concentrations (IC50 = 0.5 nM). Exquisite selectivity was demonstrated in a Kinomescan Assay (Eurofins) where MEK5 was the only other protein identified as a significant binder (>80% at 1 μM). Pharmacokinetic characterization revealed great oral bioavailability across species (F(%) = 91/98/95/96 in rat/mouse/monkey/dog). Follow-up safety studies did not identify any concerns related to genotoxicity (negative Ames and micronucleus tests) and cardiac safety ( hERG IC50 > 30 μM, Cav1.2/Nav1.5 IC50 > 10 μM). Pharmacodynamic efficacy was assessed in a mouse LPS challenge model. In the model, dose-dependent suppression of inflammatory cytokines IL-1β, TNFα, and IL-6 was observed with plasma cytokine concentration being reduced to levels comparable to control groups at the lowest dose tested (10 mg/kg, i.p.). Given its clean safety profile and favourable PD, it’s likely that BIO-7488 will undergo further preclinical evaluation to enable Phase I trials.
Reference: https://doi.org/10.1021/acs.jmedchem.3c02226
