Predicting crystal form stability under real-world conditions.

The physicochemical properties of molecular crystals, such as solubility, stability, compactability, melting behaviour and bioavailability, depend on their crystal form1. In silico crystal form selection has recently come much closer to realization because of the development of accurate and affordable free-energy calculations2-4. Here we redefine the state of the art, primarily by improving the accuracy of free-energy calculations, constructing a reliable experimental benchmark for solid-solid free-energy differences, quantifying statistical errors for the computed free energies and placing both hydrate crystal structures of different stoichiometries and anhydrate crystal structures on the same energy landscape, with defined error bars, as a function of temperature and relative humidity. The calculated free energies have standard errors of 1-2 kJ mol-1 for industrially relevant compounds, and the method to place crystal structures with different hydrate stoichiometries on the same energy landscape can be extended to other multi-component systems, including solvates. These contributions reduce the gap between the needs of the experimentalist and the capabilities of modern computational tools, transforming crystal structure prediction into a more reliable and actionable procedure that can be used in combination with experimental evidence to direct crystal form selection and establish control5.

Challenges in the structure determination of a dimeric impurity found during development of GDC-0326.

While developing a synthetic route for GDC-0326, a PI3Kα selective inhibitor, a side product was identified which was adversely impacting process chemistry development. To aid in optimization of a viable synthetic pathway for the drug, it was decided to characterize this impurity. Initial efforts using typical high-resolution mass spectrometry data coupled with NMR analysis were unable to unambiguously identify the structure. The NMR analysis was hampered by a severe lack of protons in the core of the structure. While efforts were being made to produce suitable crystals for definitive x-ray analysis, Raman analysis was undertaken. The vibrational data were compared to DFT calculations for the two most likely structures. This data, along with chemical reasoning, eventually led to successful prediction of structure 2, which was ultimately confirmed by single crystal x-ray diffractometry data.

Two crystallographic forms and the absolute structure of 5α,14α-androstane.

5α,14α-Androstane (C19H32) crystallizes in two different polymorphic forms in the same vapor diffusion experiment. The major form (Form I) crystallizes as thin plates in the space group P21, with Z = 4. These plates are twinned along a long c axis of length 43 Šand readily suffer from radiation damage when diffracted. The minor form (Form II) crystallizes as fine needles in the space group P212121, Z = 3. In the minor form, 5α,14α-androstane cocrystallizes with 5α,14α-androstan-17-one, an oxidation product of 5α,14α-androstane. The presence of 5α,14α-androstan-17-one in the minor form of the crystals was confirmed by HR-MS. Form II can be crystallized as a pure form without the ketone impurity using a different solvent system. High level density functional theory (DFT) lattice free energy calculations were performed and show that both pure forms are isoergic within the estimated error of the calculations.

GDC-9545 (Giredestrant): A Potent and Orally Bioavailable Selective Estrogen Receptor Antagonist and Degrader with an Exceptional Preclinical Profile for ER+ Breast Cancer.

Breast cancer remains a leading cause of cancer death in women, representing a significant unmet medical need. Here, we disclose our discovery efforts culminating in a clinical candidate, 35 (GDC-9545 or giredestrant). 35 is an efficient and potent selective estrogen receptor degrader (SERD) and a full antagonist, which translates into better antiproliferation activity than known SERDs (1, 6, 7, and 9) across multiple cell lines. Fine-tuning the physiochemical properties enabled once daily oral dosing of 35 in preclinical species and humans. 35 exhibits low drug-drug interaction liability and demonstrates excellent in vitro and in vivo safety profiles. At low doses, 35 induces tumor regressions either as a single agent or in combination with a CDK4/6 inhibitor in an ESR1Y537S mutant PDX or a wild-type ERα tumor model. Currently, 35 is being evaluated in Phase III clinical trials.

Targeting KRAS Mutant Cancers via Combination Treatment: Discovery of a 5-Fluoro-4-(3H)-quinazolinone Aryl Urea pan-RAF Kinase Inhibitor.

Optimization of a series of aryl urea RAF inhibitors led to the identification of type II pan-RAF inhibitor GNE-0749 (7), which features a fluoroquinazolinone hinge-binding motif. By minimizing reliance on common polar hinge contacts, this hinge binder allows for a greater contribution of RAF-specific residue interactions, resulting in exquisite kinase selectivity. Strategic substitution of fluorine at the C5 position efficiently masked the adjacent polar NH functionality and increased solubility by impeding a solid-state conformation associated with stronger crystal packing of the molecule. The resulting improvements in permeability and solubility enabled oral dosing of 7. In vivo evaluation of 7 in combination with the MEK inhibitor cobimetinib demonstrated synergistic pathway inhibition and significant tumor growth inhibition in a KRAS mutant xenograft mouse model.

cis-Selective synthesis of 1,3-disubstituted tetrahydro-ß-carbolines from N-sulfonyl N,S-acetals.

Nucleophilic addition of Grignard reagents to tetrahydro-ß-carboline (THC) N-sulfonyl N,S-acetal generates exclusively cis-1,3-disubstituted THCs with a unique 1,3-diaxial conformation. The stereochemical relationship of the 1,3-substituents was confirmed by 2-dimensional NMR spectroscopy and X-ray crystallography. The mechanism of the reaction is proposed based on crystal structures and molecular orbital calculations.

Sodium-coupled electron transfer reactivity of metal-organic frameworks containing titanium clusters: the importance of cations in redox chemistry.

Stoichiometric reduction reactions of two metal-organic frameworks (MOFs) by the solution reagents (M = Cr, Co) are described. The two MOFs contain clusters with Ti8O8 rings: Ti8O8(OH)4(bdc)6; bdc = terephthalate (MIL-125) and Ti8O8(OH)4(bdc-NH2)6; bdc-NH2 = 2-aminoterephthalate (NH2-MIL-125). The stoichiometry of the redox reactions was probed using solution NMR methods. The extent of reduction is greatly enhanced by the presence of Na+, which is incorporated into the bulk of the material. The roughly 1 : 1 stoichiometry of electrons and cations indicates that the storage of e- in the MOF is tightly coupled to a cation within the architecture, for charge balance.

Identification of Selective Acyl Sulfonamide-Cycloalkylether Inhibitors of the Voltage-Gated Sodium Channel (NaV) 1.7 with Potent Analgesic Activity.

Herein, we report the discovery and optimization of a series of orally bioavailable acyl sulfonamide NaV1.7 inhibitors that are selective for NaV1.7 over NaV1.5 and highly efficacious in in vivo models of pain and hNaV1.7 target engagement. An analysis of the physicochemical properties of literature NaV1.7 inhibitors suggested that acyl sulfonamides with high fsp3 could overcome some of the pharmacokinetic (PK) and efficacy challenges seen with existing series. Parallel library syntheses lead to the identification of analogue 7, which exhibited moderate potency against NaV1.7 and an acceptable PK profile in rodents, but relatively poor stability in human liver microsomes. Further, design strategy then focused on the optimization of potency against hNaV1.7 and improvement of human metabolic stability, utilizing induced fit docking in our previously disclosed X-ray cocrystal of the NaV1.7 voltage sensing domain. These investigations culminated in the discovery of tool compound 33, one of the most potent and efficacious NaV1.7 inhibitors reported to date.

Understanding Phase Behavior of Nearly Energetically Equivalent Polymorphs To Achieve Controlled Crystallization for a Nav1.7 Pain Inhibitor Compound.

GENE-A, a Nav1.7 inhibitor compound with analgesic activity, was developed as a crystalline anhydrate, for which two polymorphic forms, I and II, were discovered. The two forms were found to possess very similar free energies as determined experimentally with Form II being thermodynamically stable above 25 °C based on solubility measurements. A detailed solid-state characterization was conducted to determine the relative stability of these solid forms, and both thermodynamic and kinetic pathways (slurry bridging and crystallization) were evaluated. Form II was obtained as the final form in competitive slurries at RT. The outcome of crystallization experiments in terms of the solid form obtained was complicated and yielded variable results depending on the form of the starting material and that of the seeds. Form II was reproducibly obtained as the end product in unseeded experiments and in those with Form II as seeds and starting material, while Form I was obtained in all other seeded experiments. On the basis of the experimental data, a controlled crystallization strategy was developed, wherein Form II was used both as starting material and seeds to reproducibly obtain the desired form upon scale-up.

Cell Active Hydroxylactam Inhibitors of Human Lactate Dehydrogenase with Oral Bioavailability in Mice.

A series of trisubstituted hydroxylactams was identified as potent enzymatic and cellular inhibitors of human lactate dehydrogenase A. Utilizing structure-based design and physical property optimization, multiple inhibitors were discovered with <10 µM lactate IC50 in a MiaPaca2 cell line. Optimization of the series led to 29, a potent cell active molecule (MiaPaca2 IC50 = 0.67 µM) that also possessed good exposure when dosed orally to mice.

Syntheses of Denudatine Diterpenoid Alkaloids: Cochlearenine, N-Ethyl-1α-hydroxy-17-veratroyldictyzine, and Paniculamine.

The denudatine-type diterpenoid alkaloids cochlearenine, N-ethyl-1α-hydroxy-17-veratroyldictyzine, and paniculamine have been synthesized for the first time (25, 26, and 26 steps from 16, respectively). These syntheses take advantage of a common intermediate (8) that we have previously employed in preparing aconitine-type natural products. The syntheses reported herein complete the realization of a unified strategy for the preparation of C20, C19, and C18 diterpenoid alkaloids.

Phosphonium Formation by Facile Carbon-Phosphorus Reductive Elimination from Gold(III).

A recent trend in homogeneous gold catalysis has been the development of oxidative transformations relying on Au(I)/Au(III) redox cycling. Typically, phosphine-supported Au(I) precatalysts are used in the presence of strong oxidants to presumably generate phosphine Au(III) intermediates. Herein, we disclose that such Au(III) complexes can undergo facile C(aryl)-P reductive elimination to afford phosphonium salts, which have been spectroscopically and crystallographically characterized. Mechanistic studies indicate that this process occurs from cationic species at temperatures as low as -20 °C but can be accelerated in the presence of nucleophiles, such as acetonitrile and phosphines, via a five-coordinate intermediate. Importantly, this study highlights that irreversible C(aryl)-P reductive elimination is a feasible decomposition or activation pathway for phosphine-supported Au(III) catalysts and should not be ignored in future reaction development.

Efficient and stereocontrolled synthesis of 1,2,4-trioxolanes useful for ferrous iron-dependent drug delivery.

Ferrous iron-promoted reduction of a hindered peroxide bond underlies the antimalarial action of the 1,2,4-trioxane artemisinin and the 1,2,4-trioxolane arterolane. In appropriately designed systems, a 1,2,4-trioxolane ring can serve as a trigger to realize ferrous iron-dependent and parasite-selective drug delivery, both in vitro and in vivo. A stereocontrolled, expeditious (three steps), and efficient (67-71% overall yield) synthesis of 1,2,4-trioxolanes possessing the requisite 3″ substitution pattern that enables ferrous iron-dependent drug delivery is reported. The key synthetic step involves a diastereoselective Griesbaum co-ozonolysis reaction to afford primarily products with a trans relationship between the 3″ substituent and the peroxide bridge, as confirmed by X-ray structural analysis of a 3″-substituted 4-nitrobenzoate analogue.

Synthesis of Stable Gold(III) Pincer Complexes with Anionic Heteroatom Donors.

A series of gold(III) complexes supported by pyridine-based bis(amidate), bis(carboxylate), and bis(iminothiolate) substituents is reported. These compounds represent rare examples of pincer-ligated gold(III) centers with multiple anionic heteroaom donors. Reactivity and electrochemical studies demonstrate the stability of these compounds and the marked difference in reduction potentials with varying ligand scaffolds.

Back pocket flexibility provides group II p21-activated kinase (PAK) selectivity for type I 1/2 kinase inhibitors.

Structure-based methods were used to design a potent and highly selective group II p21-activated kinase (PAK) inhibitor with a novel binding mode, compound 17. Hydrophobic interactions within a lipophilic pocket past the methionine gatekeeper of group II PAKs approached by these type I 1/2 binders were found to be important for improving potency. A structure-based hypothesis and strategy for achieving selectivity over group I PAKs, and the broad kinome, based on unique flexibility of this lipophilic pocket, is presented. A concentration-dependent decrease in tumor cell migration and invasion in two triple-negative breast cancer cell lines was observed with compound 17.

Napyradiomycin derivatives, produced by a marine-derived actinomycete, illustrate cytotoxicity by induction of apoptosis.

The microbial production, isolation, and structure elucidation of four new napyradiomycin congeners (1-4) is reported. The structures of these compounds, which are new additions to the marine-derived meroterpenoids, were defined by comprehensive spectroscopic analysis and by X-ray crystallography. Using fluorescence-activated cell sorting (FACS) analysis, napyradiomycins 1-4 were observed to induce apoptosis in the colon adenocarcinoma cell line HCT-116, indicating the possibility of a specific biochemical target for this class of cytotoxins.

Chiral amide directed assembly of a diastereo- and enantiopure supramolecular host and its application to enantioselective catalysis of neutral substrates.

The synthesis of a novel supramolecular tetrahedral assembly of K12Ga4L6 stoichiometry is reported. The newly designed chiral ligand exhibits high diastereoselective control during cluster formation, leading exclusively to a single diastereomer of the desired host. This new assembly also exhibits high stability toward oxidation or a low pH environment and is a more robust and efficient catalyst for asymmetric organic transformations of neutral substrates.

Accessible gold clusters using calix[4]arene N-heterocyclic carbene and phosphine ligands.

We investigate the synthesis of accessible calix[4]arene-bound gold clusters consisting of open "coordinatively unsaturated" active sites, using a comparative approach that relies on calix[4]arene ligands with various upper- and lower-rim substituents. In contrast with a reported Au(I)-tert-butyl-calixarene phosphine complex, which exhibits a single cone conformer in solution, the H upper-rim analog exhibits multiple conformers in solution. This contrasts with observations of the tert-butyl upper-rim analog, which exhibits a single cone conformer in solution under similar conditions. In the solid state, as determined by single-crystal X-ray diffraction, both H and tert-butyl upper-rim analogs exhibit exclusively cone conformer. A detailed structural analysis of these two solid-state structures highlights a CH-π interaction involving a methoxy lower-rim substituent and phenyl substituent on P as the key feature that enforces a tight configuration of Au(I) atoms on the same side of the calix[4]arene lower-rim plane. We hypothesize that such a configuration promotes chelation of the ligand to a gold surface and facilitates the synthesis of small Au11-sized clusters after reduction of both complexes. The new cluster, like the one reported with the tert-butyl analog, has an extraordinary 25% of surface atoms that are open and accessible to a 2-NT (2-naphthalenethiol) probe in solution. We also investigated the effect of calix[4]arene lower-rim substituents that coordinate to the metal, by using N-heterocyclic carbene (NHC) functional groups rather than phosphines. Four small (<1.6 nm diameter) calix[4]arene NHC-bound gold clusters were synthesized, including three using novel calix[4]arene NHC ligands. The smallest calix[4]arene NHC-bound Au cluster consisted of a 1.2 nm gold core, and its number density of accessible and open surface sites was measured. This required development of a new titration method for open sites on gold clusters, using a SAMSA fluorescein dye molecule, which excites and emits at lower energy relative to the previously used 2-NT probe. The number density of open sites on the new calix[4]arene NHC-bound gold cluster measured by the SAMSA fluorescein probe strongly supports the generality of a mechanical model of accessibility, which does not depend on the functional group involved in binding to the gold surface and rather depends on the relative radii of curvature of bound ligands and the gold cluster core.

Pyrimidoaminotropanes as potent, selective, and efficacious small molecule kinase inhibitors of the mammalian target of rapamycin (mTOR).

We have recently reported a series of tetrahydroquinazoline (THQ) mTOR inhibitors that produced a clinical candidate 1 (GDC-0349). Through insightful design, we hoped to discover and synthesize a new series of small molecule inhibitors that could attenuate CYP3A4 time-dependent inhibition commonly observed with the THQ scaffold, maintain or improve aqueous solubility and oral absorption, reduce free drug clearance, and selectively increase mTOR potency. Through key in vitro and in vivo studies, we demonstrate that a pyrimidoaminotropane based core was able to address each of these goals. This effort culminated in the discovery of 20 (GNE-555), a highly potent, selective, metabolically stable, and efficacious mTOR inhibitor.

Effect of basic site substituents on concerted proton-electron transfer in hydrogen-bonded pyridyl-phenols.

Separated concerted proton-electron transfer (sCPET) reactions of two series of phenols with pendent substituted pyridyl moieties are described. The pyridine is either attached directly to the phenol (HOAr-pyX) or connected through a methylene linker (HOArCH(2)pyX) (X = 4-NO(2), 5-CF(3), 4-CH(3), and 4-NMe(2)). Electron-donating and -withdrawing substituents have a substantial effect on the chemical environment of the transferring proton, as indicated by IR and (1)H NMR spectra, X-ray structures, and computational studies. One-electron oxidation of the phenols occurs concomitantly with proton transfer from the phenolic oxygen to the pyridyl nitrogen. The oxidation potentials vary linearly with the pK(a) of the free pyridine (pyX), with slopes slightly below the Nerstian value of 59 mV/pK(a). For the HOArCH(2)pyX series, the rate constants k(sCPET) for oxidation by NAr(3)(•+) or [Fe(diimine)(3)](3+) vary primarily with the thermodynamic driving force (ΔG°(sCPET)), whether ΔG° is changed by varying the potential of the oxidant or the substituent on the pyridine, indicating a constant intrinsic barrier λ. In contrast, the substituents in the HOAr-pyX series affect λ as well as ΔG°(sCPET), and compounds with electron-withdrawing substituents have significantly lower reactivity. The relationship between the structural and spectroscopic properties of the phenols and their CPET reactivity is discussed.