Jessica M. Grandner

Targeting HR-positive breast cancer via the inhibition of CDK4 and CDK6 has become the standard of care. However, progression inevitably occurs, and emerging data suggest the implication of CDK2 in this resistance mechanism. As part of our efforts to target this resistance, we embarked on a medicinal chemistry campaign to selectively inhibit CDK2 over the broadly essential CDK1. In order to obtain selectivity against CDK1, we utilized a molecular dynamics approach focused on interaction with a conserved lysine in the active site. Additionally, we uncovered a unique mechanism of clearance driven by both metabolism and efflux in rats and demonstrated that we could counter efflux-driven clearance with high permeability. Our efforts resulted in compound 19, which was potent against CDK2, exhibited good selectivity vs CDK4 and CDK1, and had pharmacokinetic properties that enabled evaluation in a CDK2 xenograft model of cancer, where it achieved nearly 80% tumor growth inhibition.

Despite recent interest in N-trifluoromethyl azoles, N-α,α-difluoroalkyl azoles [(azole)N–CF₂R] remain understudied and underutilized in medicinal chemistry. To address this deficiency, we have conducted a comparative study of medicinally-relevant properties for a series of (azole)N–CF₂R and their nonfluorinated matched molecular pairs (MMPs) that revealed fluorine-induced reductions in azole pK_a, hydrophilicity, experimental polar surface area, and metabolic oxidation of a labile vicinal position. Additionally, computational analysis supports the fluorine-induced suppression of metabolic aliphatic oxidation but suggests a limited impact of fluorination on conformational preferences within MMPs. Along with a newly-provided synthetic method to install such a substructure, this information will facilitate rational incorporation of (azole)N–CF₂R groups in drug optimization campaigns.

SARM1 (sterile alpha and Toll/interleukin-1 receptor motif-containing 1) has recently emerged as a promising therapeutic target for several neurodegenerative diseases. Herein, we detail our optimization of SARM1 orthosteric base exchange inhibitors. Early chemical matter was found to be substrates for either Pgp/MDR1 or breast cancer resistant protein (BCRP), resulting in compounds with poor overall brain exposure in rodents. Using structure-based drug design, we identified the crucial interactions for driving adduct formation and subsequently optimized the molecules to eliminate the MDR1 and BCRP efflux, yielding tool compounds with sufficient brain penetration to have a pharmacodynamic (PD) effect. Ultimately, we found these compounds activated SARM1 at low doses, leading to serious adverse events in vivo. These preclinical findings highlight the liability for these base exchange inhibitors for further progression.

Cyclin-dependent kinases (CDKs) are key regulators of the cell cycle and are frequently altered in cancer cells, thereby leading to uncontrolled proliferation. In this context, CDK2 has emerged as an appealing target for anticancer drug development. Herein, we describe the discovery of a series of selective small molecule inhibitors of CDK2 beginning with historical compounds from our ERK2 program (e.g., compound 6). Structure-based drug design led to the potent and selective tool compound 32, where excellent selectivity against ERK2 and CDK4 was achieved by filling the lipophilic DFG-1 pocket and targeting interactions with CDK2-specific lower hinge binding residues, respectively. Compound 32 demonstrated 112% tumor growth inhibition in mice bearing OVCAR3 tumors with 50 mg/kg bis in die (BID) oral dosing.

MycG is a cytochrome P450 that performs two sequential oxidation reactions on the 16-membered ring macrolide M-IV. The enzyme evolved to oxidize M-IV preferentially over M-III and M-VI, which differ only by the presence of methoxy vs free hydroxyl groups on one of the macrolide sugar moieties. We utilized a two-pronged computational approach to study both the chemoselective reactivity and substrate specificity of MycG. Density functional theory computations determined that epoxidation of the substrate hampers its ability to undergo C–H abstraction, primarily due to a loss of hyperconjugation in the transition state. Metadynamics and molecular dynamics simulations revealed a hydrophobic sugar-binding pocket that is responsible for substrate recognition/specificity and was not apparent in crystal structures of the enzyme/substrate complex. Computational results also led to the identification of other interactions between the enzyme and its substrates that had not previously been observed in the cocrystal structures. Site-directed mutagenesis was then employed to test the effects of mutations hypothesized to broaden the substrate scope and alter the product profile of MycG. The results of these experiments validated this complementary effort to engineer MycG variants with improved catalytic activity toward earlier stage mycinamicin substrates.

Melatonin receptors MT₁ and MT₂ are involved in synchronizing circadian rhythms and are important targets for treating sleep and mood disorders, type-2 diabetes and cancer. Here, we performed large scale structure-based virtual screening for new ligand chemotypes using recently solved high-resolution 3D crystal structures of agonist-bound MT receptors. Experimental testing of 62 screening candidates yielded the discovery of 10 new agonist chemotypes with sub-micromolar potency at MT receptors, with compound 21 reaching EC₅₀ of 0.36 nM. Six of these molecules displayed selectivity for MT₂ over MT₁. Moreover, two most potent agonists, including 21 and a close derivative of melatonin, 28, had dramatically reduced arrestin recruitment at MT₂, while compound 37 was devoid of G_i signaling at MT₁, implying biased signaling. This study validates the suitability of the agonist-bound orthosteric pocket in the MT receptor structures for the structure-based discovery of selective agonists.

Melatonin (N-acetyl-5-methoxytryptamine) is a neurohormone that maintains circadian rhythms¹ by synchronization to environmental cues and is involved in diverse physiological processes² such as the regulation of blood pressure and core body temperature, oncogenesis, and immune function³. Melatonin is formed in the pineal gland in a light-regulated manner⁴ by enzymatic conversion from 5-hydroxytryptamine (5-HT or serotonin), and modulates sleep and wakefulness⁵ by activating two high-affinity G-protein-coupled receptors, type 1A (MT₁) and type 1B (MT₂)^3,6. Shift work, travel, and ubiquitous artificial lighting can disrupt natural circadian rhythms; as a result, sleep disorders affect a substantial population in modern society and pose a considerable economic burden⁷. Over-the-counter melatonin is widely used to alleviate jet lag and as a safer alternative to benzodiazepines and other sleeping aids^8,9, and is one of the most popular supplements in the United States¹⁰. Here, we present high-resolution room-temperature X-ray free electron laser (XFEL) structures of MT₁ in complex with four agonists: the insomnia drug ramelteon¹¹, two melatonin analogues, and the mixed melatonin–serotonin antidepressant agomelatine^12,13. The structure of MT₂ is described in an accompanying paper¹⁴. Although the MT₁ and 5-HT receptors have similar endogenous ligands, and agomelatine acts on both receptors, the receptors differ markedly in the structure and composition of their ligand pockets; in MT₁, access to the ligand pocket is tightly sealed from solvent by extracellular loop 2, leaving only a narrow channel between transmembrane helices IV and V that connects it to the lipid bilayer. The binding site is extremely compact, and ligands interact with MT₁ mainly by strong aromatic stacking with Phe179 and auxiliary hydrogen bonds with Asn162 and Gln181. Our structures provide an unexpected example of atypical ligand entry for a non-lipid receptor, lay the molecular foundation of ligand recognition by melatonin receptors, and will facilitate the design of future tool compounds and therapeutic agents, while their comparison to 5-HT receptors yields insights into the evolution and polypharmacology of G-protein-coupled receptors.

The human MT₁ and MT₂ melatonin receptors^1,2 are G-protein-coupled receptors (GPCRs) that help to regulate circadian rhythm and sleep patterns³. Drug development efforts have targeted both receptors for the treatment of insomnia, circadian rhythm and mood disorders, and cancer³, and MT₂ has also been implicated in type 2 diabetes^4,5. Here we report X-ray free electron laser (XFEL) structures of the human MT₂ receptor in complex with the agonists 2-phenylmelatonin (2-PMT) and ramelteon⁶ at resolutions of 2.8 Å and 3.3 Å, respectively, along with two structures of function-related mutants: H208^5.46A (superscripts represent the Ballesteros–Weinstein residue numbering nomenclature⁷) and N86^2.50D, obtained in complex with 2-PMT. Comparison of the structures of MT₂ with a published structure⁸ of MT₁ reveals that, despite conservation of the orthosteric ligand-binding site residues, there are notable conformational variations as well as differences in [³H]melatonin dissociation kinetics that provide insights into the selectivity between melatonin receptor subtypes. A membrane-buried lateral ligand entry channel is observed in both MT₁ and MT₂, but in addition the MT₂ structures reveal a narrow opening towards the solvent in the extracellular part of the receptor. We provide functional and kinetic data that support a prominent role for intramembrane ligand entry in both receptors, and suggest that there might also be an extracellular entry path in MT₂. Our findings contribute to a molecular understanding of melatonin receptor subtype selectivity and ligand access modes, which are essential for the design of highly selective melatonin tool compounds and therapeutic agents.

The mechanism of permanganate-mediated dual C–H oxidation of complex diketopiperazines has been examined with density functional theory computations. The products of these oxidations are enabling intermediates in the synthesis of structurally diverse ETP natural products. We evaluated, for the first time, the impact of ion-pairing and aggregation states of the permanganate ion and counter-cations, such as bis(pyridine)-silver(I) (Ag⁺) and tetra-n-butylammonium (TBA⁺), on the C–H oxidation mechanism. The C–H abstraction occurs through an open shell singlet species, as noted previously, followed by O-rebound and a competing OH-rebound pathway. The second C–H oxidation proceeds with a second equivalent of oxidant with lower free energy barriers than the first C–H oxidation due to directing effects and the generation of a more reactive oxidant species after the first C–H oxidation. The success and efficiency of the second C−H oxidation are found to be critically dependent on the presence of an ion-paired oxidant. We used the developed mechanistic knowledge to rationalize an experimentally observed oxidation pattern for C³-indole-substituted diketopiperazine (+)-5 under optimal oxidation conditions: namely, the formation of diol (−)-6 as a single diastereomer and lack of the ketone products. We proposed two factors that may impede the ketone formation: (i) the conformational flexibility of the diketopiperazine ring, and (ii) hindrance of this site, making it less accessible to the ion-paired oxidant species.