Discovery of PF-07265028, A Selective Small Molecule Inhibitor of Hematopoietic Progenitor Kinase 1 (HPK1) for the Treatment of Cancer.

Hematopoietic progenitor kinase 1 (HPK1/MAP4K1) represents a high interest target for the treatment of cancer through an immune-mediated mechanism. Herein we present highlights of the drug discovery campaign within the lactam/azalactam series of inhibitors that yielded a small molecule (, PF-07265028), which was advanced to a phase 1 clinical trial (NCT05233436). Key components of the discovery effort included optimization of potency through mitigation of ligand strain as guided by the use of cocrystal structures, mitigation of ADME liabilities (plasma instability and fraction metabolism by CYP2D6), and optimization of kinase selectivity, particularly over immune-modulating kinases with high homology to HPK1.

Simple Fluctuations in Simple Glass Formers.

Critical single-particle fluctuations associated with particle displacements are inherent to simple glass-forming liquids in the limit of large dimensions and leave a pseudocritical trace across all finite dimensions. This characteristic could serve as a crucial test for distinguishing between theories of glass formation. We here examine these critical fluctuations, as captured by the well-established non-Gaussian parameter, within both mode-coupling theory (MCT) and dynamical mean-field theory (DMFT) across dimensions for hard sphere fluids and for the minimally structured Mari-Kurchan model.

Critical-like slowdown in thermal soft-sphere glasses via energy minimization.

Using hybrid molecular dynamics/SWAP Monte Carlo (MD/SMC) simulations, we show that while the terminal relaxation times τ(ϕ) for FIRE energy minimization of soft-sphere glasses can decrease by orders of magnitude as sample equilibration proceeds and the jamming density ϕ_{J} increases, they always scale as τ(ϕ)∼(ϕ_{J}-ϕ)^{-2}∼[Z_{iso}-Z_{ms}(τ)]^{-2}, where Z_{iso}=2d and Z_{ms}(τ) is the average coordination number of particles satisfying a minimal local mechanical stability criterion (Z≥d+1) at the top of the final potential-energy-landscape (PEL) sub-basin the system encounters. This scaling allows us to collapse τ datasets that look very different when plotted as a function of ϕ, and to address a closely related question: how does the character of the PEL basins that dense thermal glasses most typically occupy evolve as the glasses age at constant ϕ and T?

Dynamics and fluctuations of minimally structured glass formers.

The mean-field theory (MFT) of simple structural glasses, which is exact in the limit of infinite spatial dimensions, d→∞, offers theoretical insight as well as quantitative predictions about certain features of d=3 systems. In order to more systematically relate the behavior of physical systems to MFT, however, various finite-d effects need to be accounted for. Although some efforts along this direction have already been undertaken, theoretical and technical challenges hinder progress.

Local stability of spheres via the convex hull and the radical Voronoi diagram.

Jamming is an emergent phenomenon wherein the local stability of individual particles percolates to form a globally rigid structure. However, the onset of rigidity does not imply that every particle becomes rigid, and indeed some remain locally unstable. These particles, if they become unmoored from their neighbors, are called rattlers, and their identification is critical to understanding the rigid backbone of a packing, as these particles cannot bear stress.

Nitro-sulfinate Reductive Coupling to Access (Hetero)aryl Sulfonamides.

A method to assemble (hetero)aryl sulfonamides via the reductive coupling of aryl sulfinates and nitroarenes is reported. Various reducing conditions with sodium bisulfite and with or without tin(II) chloride in DMSO were developed using an ultrasound bath to improve reaction homogeneity and mixing. A range of (hetero)aryl sulfonamides bearing a selection of functional groups were prepared, and the mechanism of the transformation was investigated.

Jamming, relaxation, and memory in a minimally structured glass former.

Structural glasses form through various out-of-equilibrium processes, including temperature quenches, rapid compression (crunches), and shear. Although each of these processes should be formally understandable within the recently formulated dynamical mean-field theory (DMFT) of glasses, the numerical tools needed to solve the DMFT equations up to the relevant physical regime do not yet exist. In this context, numerical simulations of minimally structured (and therefore mean-field-like) model glass formers can aid the search for and understanding of such solutions, thanks to their ability to disentangle structural from dimensional effects.

Parallel multi-droplet platform for reaction kinetics and optimization.

We present an automated droplet reactor platform possessing parallel reactor channels and a scheduling algorithm that orchestrates all of the parallel hardware operations and ensures droplet integrity as well as overall efficiency. We design and incorporate all of the necessary hardware and software to enable the platform to be used to study both thermal and photochemical reactions. We incorporate a Bayesian optimization algorithm into the control software to enable reaction optimization over both categorical and continuous variables.

Early Clinical Development of Lufotrelvir as a Potential Therapy for COVID-19.

Lufotrelvir was designed as a first in class 3CL protease inhibitor to treat COVID-19. Development of lufotrelvir was challenged by its relatively poor stability due to its propensity to epimerize and degrade. Key elements of process development included improvement of the supply routes to the indole and lactam fragments, a Claisen addition to homologate the lactam, and a subsequent phosphorylation reaction to prepare the prodrug as well as identification of a DMSO solvated form of lufotrelvir to enable long-term storage.

The dimensional evolution of structure and dynamics in hard sphere liquids.

The formulation of the mean-field infinite-dimensional solution of hard sphere glasses is a significant milestone for theoretical physics. How relevant this description might be for understanding low-dimensional glass-forming liquids, however, remains unclear. These liquids indeed exhibit a complex interplay between structure and dynamics, and the importance of this interplay might only slowly diminish as dimension d increases.

Three simple scenarios for high-dimensional sphere packings.

Based on results from the physics and mathematics literature which suggest a series of clearly defined conjectures, we formulate three simple scenarios for the fate of hard sphere crystallization in high dimension: in scenario A, crystallization is impeded and the glass phase constitutes the densest packing; in scenario B, crystallization from the liquid is possible, but takes place much beyond the dynamical glass transition and is thus dynamically implausible; and in scenario C, crystallization is possible and takes place before (or just after) dynamical arrest, thus making it plausibly accessible from the liquid state. In order to assess the underlying conjectures and thus obtain insight into which scenario is most likely to be realized, we investigate the densest sphere packings for dimension d=3-10 using cell-cluster expansions as well as numerical simulations. These resulting estimates of the crystal entropy near close packing tend to support scenario C.

Photoredox-Catalyzed Dehydrogenative Csp-Csp Cross-Coupling of Alkylarenes to Aldehydes in Flow.

Executing photoredox reactions in flow offers solutions to frequently encountered issues regarding reproducibility, reaction time, and scale-up. Here, we report the transfer of a photoredox-catalyzed benzylic coupling of alkylarenes to aldehydes to a flow chemistry setting leading to improvements in terms of higher concentration, shorter residence times, better yields, ease of catalyst preparation, and enhanced substrate scope. Its applicability has been demonstrated by a multi-gram-scale reaction using high-power light-emitting diodes (LEDs), late-stage functionalization of selected active pharmaceutical ingredients (APIs), and also a photocatalyst recycling method.

Thermodynamic stability of hard sphere crystals in dimensions 3 through 10.

Although much is known about the metastable liquid branch of hard spheres-from low dimension d up to [Formula: see text]-its crystal counterpart remains largely unexplored for [Formula: see text]. In particular, it is unclear whether the crystal phase is thermodynamically stable in high dimensions and thus whether a mean-field theory of crystals can ever be exact. In order to determine the stability range of hard sphere crystals, their equation of state is here estimated from numerical simulations, and fluid-crystal coexistence conditions are determined using a generalized Frenkel-Ladd scheme to compute absolute crystal free energies.

A direct link between active matter and sheared granular systems.

The similarity in mechanical properties of dense active matter and sheared amorphous solids has been noted in recent years without a rigorous examination of the underlying mechanism. We develop a mean-field model that predicts that their critical behavior-as measured by their avalanche statistics-should be equivalent in infinite dimensions up to a rescaling factor that depends on the correlation length of the applied field. We test these predictions in two dimensions using a numerical protocol, termed "athermal quasistatic random displacement," and find that these mean-field predictions are surprisingly accurate in low dimensions.

Memory Formation in Jammed Hard Spheres.

Liquids equilibrated below an onset condition share similar inherent states, while those above that onset have inherent states that markedly differ. Although this type of materials memory was first reported in simulations over 20 years ago, its physical origin remains controversial. Its absence from mean-field descriptions, in particular, has long cast doubt on its thermodynamic relevance.

Exploratory Volumetric Deep Earth Visualization by 2.5D Interactive Compositing.

In this contribution we consider the visualization of global, deep Earth volume datasets for display and researcher interaction. While the algorithms and data analysis techniques that produce such volumetric results have become more sophisticated, the manner of visualizing these findings can be improved. We address the challenge of making an illustrative, exploratory visualization of a global geoscience dataset using a combined seismic tomography result, the primary means by which geoscientists infer structure and process in the deep Earth.

Synthetic Approaches to New Drugs Approved during 2018.

New drugs introduced to the market every year represent privileged structures for particular biological targets. These new chemical entities (NCEs) provide insight into molecular recognition while serving as leads for designing future new drugs. This annual review describes the most likely process-scale synthetic approaches to 39 new chemical entities approved for the first time globally in 2018.

Tactical Tentacles: New Insights on the Processes of Sexual Selection Among the Cephalopoda.

The cephalopods (Mollusca: Cephalopoda) are an exceptional class among the invertebrates, characterised by the advanced development of their conditional learning abilities, long-term memories, capacity for rapid colour change and extremely adaptable hydrostatic skeletons. These traits enable cephalopods to occupy diverse marine ecological niches, become successful predators, employ sophisticated predator avoidance behaviours and have complex intraspecific interactions. Where studied, observations of cephalopod mating systems have revealed detailed insights to the life histories and behavioural ecologies of these animals.

Enantioselective counter-anions in photoredox catalysis: the asymmetric cation radical Diels-Alder reaction.

Control of absolute stereochemistry in radical and ion radical transformations is a major challenge in synthetic chemistry. Herein, we report the design of a photoredox catalyst system comprised of an oxidizing pyrilium salt bearing a chiral triflyl phosphoramide anion. This class of chiral organic photoredox catalysts is able to catalyze the formation of cation radical-mediated Diels-Alder transformations in up to 75:25 e.

Genome-wide comparisons reveal a clinal species pattern within a holobenthic octopod-the Australian Southern blue-ringed octopus, (Cephalopoda: Octopodidae).

The southern blue-ringed octopus, (Hoyle, 1883) lacks a planktonic dispersal phase, yet ranges across Australia's southern coastline. This species' brief and holobenthic life history suggests gene flow might be limited, leaving distant populations prone to strong genetic divergence. This study used 17,523 genome-wide SNP loci to investigate genetic structuring and local adaptation patterns of among eight sampling sites along its reported range.

Echoes of the Glass Transition in Athermal Soft Spheres.

Recent theoretical advances have led to the creation of a unified phase diagram for the thermal glass and athermal jamming transitions. This diagram makes clear that, while related, the mode-coupling-or dynamic-glass transition is distinct from the jamming transition, occurring at a finite temperature and significantly lower density than the jamming transition. Nonetheless, we demonstrate a prejamming transition in athermal frictionless spheres which occurs at the same density as the mode-coupling transition and is marked by percolating clusters of locally rigid particles.

Synthesis and Utilization of Nitroalkyne Equivalents in Batch and Continuous Flow.

We report a method for overcoming the low stability of nitroalkynes through the development of nitrated vinyl silyltriflate equivalents. Because of their instability, nitroalkynes have only rarely been utilized in synthesis. The reactivity of these silyltriflates, which are prepared in situ, is exemplified by dipolar cycloaddition reactions with nitrones to give highly substituted 4-nitro-4-isoxazolines in high yields.

Towards More Efficient, Greener Syntheses through Flow Chemistry.

Technological advances have an important role in the design of greener synthetic processes. In this Personal Account, we describe a wide range of thermal, photochemical, catalytic, and biphasic chemical transformations examined by our group. Each of these demonstrate how the merits of a continuous flow synthesis platform can align with some of the goals put forth by the Twelve Principles of Green Chemistry.