Fragment-Based Discovery of Novel MUS81 Inhibitors.

MUS81 is a structure-selective endonuclease that cleaves various branched DNA structures arising from natural physiological processes such as homologous recombination and mitosis. Due to this, MUS81 is able to relieve replication stress, and its function has been reported to be critical to the survival of many cancers, particularly those with dysfunctional DNA-repair machinery. There is therefore interest in MUS81 as a cancer drug target, yet there are currently few small molecule inhibitors of this enzyme reported, and no liganded crystal structures are available to guide hit optimization. Here we report the fragment-based discovery of novel small molecule MUS81 inhibitors with sub-µM biochemical activity. These inhibitors were used to develop a novel crystal system, providing the first structural insight into the inhibition of MUS81 with small molecules.

Identification of Novel, Selective Ataxia-Telangiectasia Mutated Kinase Inhibitors with the Ability to Penetrate the Blood-Brain Barrier: The Discovery of AZD1390.

The inhibition of ataxia-telangiectasia mutated (ATM) has been shown to chemo- and radio-sensitize human glioma cells in vitro and therefore might provide an exciting new paradigm in the treatment of glioblastoma multiforme (GBM). The effective treatment of GBM will likely require a compound with the potential to efficiently cross the blood-brain barrier (BBB). Starting from clinical candidate AZD0156, 4, we investigated the imidazoquinolin-2-one scaffold with the goal of improving likely CNS exposure in humans. Strategies aimed at reducing hydrogen bonding, basicity, and flexibility of the molecule were explored alongside modulating lipophilicity. These studies identified compound 24 (AZD1390) as an exceptionally potent and selective inhibitor of ATM with a good preclinical pharmacokinetic profile. 24 showed an absence of human transporter efflux in MDCKII-MDR1-BCRP studies (efflux ratio <2), significant BBB penetrance in nonhuman primate PET studies (Kp,uu 0.33) and was deemed suitable for development as a clinical candidate to explore the radiosensitizing effects of ATM in intracranial malignancies.

Discovery of a Potent and Orally Bioavailable Zwitterionic Series of Selective Estrogen Receptor Degrader-Antagonists.

Herein, we report the optimization of a meta-substituted series of selective estrogen receptor degrader (SERD) antagonists for the treatment of ER+ breast cancer. Structure-based design together with the use of modeling and NMR to favor the bioactive conformation led to a highly potent series of basic SERDs with promising physicochemical properties. Issues with hERG activity resulted in a strategy of zwitterion formation and ultimately in the identification of 38. This compound was shown to be a highly potent SERD capable of effectively degrading ERα in both MCF-7 and CAMA-1 cell lines. The low lipophilicity and zwitterionic nature led to a SERD with a clean secondary pharmacology profile and no hERG activity. Favorable physicochemical properties resulted in good oral bioavailability in preclinical species and potent in vivo activity in a mouse xenograft model.

B-N/B-H Transborylation: borane-catalysed nitrile hydroboration.

The reduction of nitriles to primary amines is a useful transformation in organic synthesis, however, it often relies upon stoichiometric reagents or transition-metal catalysis. Herein, a borane-catalysed hydroboration of nitriles to give primary amines is reported. Good yields (48-95%) and chemoselectivity (e.g., ester, nitro, sulfone) were observed. DFT calculations and mechanistic studies support the proposal of a double B-N/B-H transborylation mechanism.

Discovery of AZD9833, a Potent and Orally Bioavailable Selective Estrogen Receptor Degrader and Antagonist.

Herein we report the optimization of a series of tricyclic indazoles as selective estrogen receptor degraders (SERD) and antagonists for the treatment of ER+ breast cancer. Structure based design together with systematic investigation of each region of the molecular architecture led to the identification of N-[1-(3-fluoropropyl)azetidin-3-yl]-6-[(6S,8R)-8-methyl-7-(2,2,2-trifluoroethyl)-6,7,8,9-tetrahydro-3H-pyrazolo[4,3-f]isoquinolin-6-yl]pyridin-3-amine (28). This compound was demonstrated to be a highly potent SERD that showed a pharmacological profile comparable to fulvestrant in its ability to degrade ERα in both MCF-7 and CAMA-1 cell lines. A stringent control of lipophilicity ensured that 28 had favorable physicochemical and preclinical pharmacokinetic properties for oral administration. This, combined with demonstration of potent in vivo activity in mouse xenograft models, resulted in progression of this compound, also known as AZD9833, into clinical trials.

Hidden Boron Catalysis: Nucleophile-Promoted Decomposition of HBpin.

Simple nucleophiles with structural similarities to known hydroboration catalysts can readily mediate the formation of BH3 and borohydride species from pinacolborane (HBpin). Alkyne and alkene hydroboration reactions were successfully mediated by nucleophiles through BH3 generation, with BH3-catalyzed hydroboration found to dominate catalysis. NMR spectroscopy and kinetic analyses showed that the nucleophiles NaOtBu, Na[N(SiMe3)2], nBu2Mg, and nBuLi only promoted the formation of BH3 and were not "true" hydroboration catalysts.

Kinetics and Mechanism of the Arase-Hoshi R2BH-Catalyzed Alkyne Hydroboration: Alkenylboronate Generation via B-H/C-B Metathesis.

The mechanism of R2BH-catalyzed hydroboration of alkynes by 1,3,2-dioxaborolanes has been investigated by in situ 19F NMR spectroscopy, kinetic simulation, isotope entrainment, single-turnover labeling (10B/2H), and density functional theory (DFT) calculations. For the Cy2BH-catalyzed hydroboration 4-fluorophenylacetylene by pinacolborane, the resting state is the anti-Markovnikov addition product ArCH = CHBCy2. Irreversible and turnover-rate limiting reaction with pinacolborane (k ≈ 7 × 10-3 M-1 s-1) regenerates Cy2BH and releases E-Ar-CH═CHBpin. Two irreversible events proceed in concert with turnover. The first is a Markovnikov hydroboration leading to regioisomeric Ar-C(Bpin)═CH2. This is unreactive to pinacolborane at ambient temperature, resulting in catalyst inhibition every ∼102 turnovers. The second is hydroboration of the alkenylboronate to give ArCH2CH(BCy2)Bpin, again leading to catalyst inhibition. 9-BBN behaves analogously to Cy2BH, but with higher anti-Markovnikov selectivity, a lower barrier to secondary hydroboration, and overall lower efficiency. The key process for turnover is B-H/C-B metathesis, proceeding by stereospecific transfer of the E-alkenyl group within a transient, µ-B-H-B bridged, 2-electron-3-center bonded B-C-B intermediate.

Orally Bioavailable and Blood-Brain Barrier-Penetrating ATM Inhibitor (AZ32) Radiosensitizes Intracranial Gliomas in Mice.

Inhibition of ataxia-telangiectasia mutated (ATM) during radiotherapy of glioblastoma multiforme (GBM) may improve tumor control by short-circuiting the response to radiation-induced DNA damage. A major impediment for clinical implementation is that current inhibitors have limited central nervous system (CNS) bioavailability; thus, the goal was to identify ATM inhibitors (ATMi) with improved CNS penetration. Drug screens and refinement of lead compounds identified AZ31 and AZ32. The compounds were then tested in vivo for efficacy and impact on tumor and healthy brain. Both AZ31 and AZ32 blocked the DNA damage response and radiosensitized GBM cells in vitro AZ32, with enhanced blood-brain barrier (BBB) penetration, was highly efficient in vivo as radiosensitizer in syngeneic and human, orthotopic mouse glioma model compared with AZ31. Furthermore, human glioma cell lines expressing mutant p53 or having checkpoint-defective mutations were particularly sensitive to ATMi radiosensitization. The mechanism for this p53 effect involves a propensity to undergo mitotic catastrophe relative to cells with wild-type p53. In vivo, apoptosis was >6-fold higher in tumor relative to healthy brain after exposure to AZ32 and low-dose radiation. AZ32 is the first ATMi with oral bioavailability shown to radiosensitize glioma and improve survival in orthotopic mouse models. These findings support the development of a clinical-grade, BBB-penetrating ATMi for the treatment of GBM. Importantly, because many GBMs have defective p53 signaling, the use of an ATMi concurrent with standard radiotherapy is expected to be cancer-specific, increase the therapeutic ratio, and maintain full therapeutic effect at lower radiation doses. Mol Cancer Ther; 17(8); 1637-47. ©2018 AACR.

Particle-Based Modeling of Living Actin Filaments in an Optical Trap.

We report a coarse-grained molecular dynamics simulation study of a bundle of parallel actin filaments under supercritical conditions pressing against a loaded mobile wall using a particle-based approach where each particle represents an actin unit. The filaments are grafted to a fixed wall at one end and are reactive at the other end, where they can perform single monomer (de)polymerization steps and push on a mobile obstacle. We simulate a reactive grand canonical ensemble in a box of fixed transverse area A, with a fixed number of grafted filaments N f , at temperature T and monomer chemical potential µ 1 . For a single filament case ( N f = 1 ) and for a bundle of N f = 8 filaments, we analyze the structural and dynamical properties at equilibrium where the external load compensates the average force exerted by the bundle. The dynamics of the bundle-moving-wall unit are characteristic of an over-damped Brownian oscillator in agreement with recent in vitro experiments by an optical trap setup. We analyze the influence of the pressing wall on the kinetic rates of (de)polymerization events for the filaments. Both static and dynamic results compare reasonably well with recent theoretical treatments of the same system. Thus, we consider the proposed model as a good tool to investigate the properties of a bundle of living filaments.

A new algorithm for extended nonequilibrium molecular dynamics simulations of mixed flow.

In this work, we develop a new algorithm for nonequilibrium molecular dynamics of fluids under planar mixed flow, a linear combination of planar elongational flow and planar Couette flow. To date, the only way of simulating mixed flow using nonequilibrium molecular dynamics techniques was to impose onto the simulation box irreversible transformations. This would bring the simulation to an end as soon as the minimum lattice space requirements were violated. In practical terms, this meant repeating the short simulations to improve statistics and extending the box dimensions to increase the total simulation time. Our method, similar to what has already been done for pure elongational flow, allows a cuboid box to deform in time following the streamlines of the mixed flow and, after a period of time determined by the elongational field, to be mapped back and recover its initial shape. No discontinuity in physical properties is present during the mapping and the simulation can, in this way, be extended indefinitely. We also show that the most general form of mixed flow, in which the angle between the expanding (or contracting) direction and the velocity gradient axis varies, can be cast in a so-called canonical form, in which the angle assumes values that are multiples of π (when a mixed flow exists), by an appropriate choice of the field parameters.

Diffusion of linear polymer melts in shear and extensional flows.

We present results from molecular dynamics simulations for the anisotropic self-diffusion tensor and the velocity autocorrelation functions of monodisperse systems of dense linear chain molecules under flow. Two molecular models are used in these simulations: The finitely extensible nonlinear elastic chain and the freely jointed tangent sphere chain. Nonequilibrium molecular dynamics is used to simulate these systems under planar Couette flow and planar extensional flow. Under planar extensional flow, results presented here are the first, from simulation, for diffusion and velocity autocorrelation functions of molecules, while for planar Couette flow, we compare the broadest range of conditions. An explicit derivation is provided of the Green-Kubo expression for the diffusion tensor. This expression is then used to derive the relation involving the mean-squared displacement-an often used alternative method to calculate diffusion coefficients. Velocity autocorrelation functions have been used, in combination with results on the alignment of molecules from a previous paper, to provide some details of the molecular scale dynamics that influence diffusive transport under flow.

A diastereoselective radical cyclization approach to substituted quinuclidines.

A new, concise, and flexible approach to novel quinuclidines has been developed, which employs a phosphorus hydride mediated radical addition/cyclization reaction in the key step. 1,7-Diene 5 reacts with diethyl thiophosphite in an efficient and diastereoselective radical addition/cyclization reaction to give trisubstituted piperidines 4ab. Piperidines 4ab are subsequently converted into 2,5-disubstituted quinuclidines using S(N)2-type cyclizations. Finally, the resulting quinuclidines are shown to undergo novel Horner-Wadsworth-Emmons-type (HWE-type) reactions to give unsaturated quinuclidines 21a and 21b, which have structures similar to that of (-)-quinine 1.