The G protein-coupled receptor (GPCR) CCR6 mediates the migration of pathogenic immune cells to the site of inflammation in response to the chemokine CCL20. CCR6 is an attractive target for the treatment of chronic autoimmune disease as antagonism of the receptor is expected to block CCL20-mediated immune cell recruitment. High-throughput-screening identified a squaramide-based, allosteric antagonist of CCR6 that potently inhibited CCL20-mediated T cell chemotaxis, but it also inhibited CXCL1-mediated neutrophil chemotaxis through CXCR2 antagonism. Lead optimization achieved differentiation from CXCR2 through identification of a methyl substituent-dependent selectivity switch or "magic methyl for selectivity". The mechanism for this effect is rooted in different antagonist-induced ligand-receptor behaviors, insurmountable for CCR6 and surmountable for CXCR2. Herein, we report the discovery and preclinical evaluation of the CCR6 antagonist PF-07054894 (18l) which has advanced to clinical trials as a first in class approach targeting the receptor.

Living matter shows an impressive architectural ability -starting from molecules that must react to their nanometer-scale local environment, structures are robustly generated on both the cellular scale (10's of µm) and the tissue scale (meters).To appreciate these scales, one may imagine that molecules assembling a cytokinetic ring at the center of a 10 µm cell is analogous to a group of people meeting at the precise center of New York City while walking with a blindfold on.This would rarely occur by chance, and instead information about instantaneous position relative to the city must be made available locally to each person.The concept of a positional information field permeating living cells and tissues has long been appreciated [1].

Epigenetic proteins containing YEATS domains (YD) are an emerging target class in drug discovery. Described herein are the discovery and characterization efforts associated with PFI-6, a new chemical probe for the YD of MLLT1 (ENL/YEATS1) and MLLT3 (AF9/YEATS3). For hit identification, fragment-like mimetics of endogenous YD ligands (crotonylated histone-containing proteins), were synthesized via parallel medicinal chemistry (PMC) and screened for MLLT1 binding. Subsequent SAR studies led to iterative MLLT1/3 binding and selectivity improvements, culminating in the discovery of PFI-6. PFI-6 demonstrates good affinity and selectivity for MLLT1/3 vs. other human YD proteins (YEATS2/4) and engages MLLT3 in cells. Small-molecule X-ray co-crystal structures of two molecules, including PFI-6, bound to the YD of MLLT1/3 are also described. PFI-6 may be a useful tool molecule to better understand the biological effects associated with modulation of MLLT1/3.

Force fields form the basis for classical molecular simulations and their accuracy is crucial for the quality of, for instance, protein-ligand binding simulations in drug discovery. The huge diversity of small molecule chemistry makes it a challenge to build and parameterize a suitable force field. The Open Force Field Initiative is a combined industry and academic consortium developing a state-of-the-art small molecule force field. In this report industry members of the consortium worked together to objectively evaluate the performance of the force fields (referred to here as OpenFF) produced by the initiative on a combined public and proprietary dataset of 19,653 relevant molecules selected from their internal research and compound collections. This evaluation was important because it was completely blind; at most partners, none of the molecules or data were used in force field development or testing prior to this work. We compare the Open Force Field "Sage" version 2.0.0 and "Parsley" version 1.3.0 with GAFF-2.11-AM1BCC, OPLS4 and SMIRNOFF99Frosst. We analyzed force field-optimized geometries and conformer energies compared to reference quantum mechanical data. We show that OPLS4 performs best, and the latest Open Force Field release shows a clear improvement compared to its predecessors. The performance of established force fields such as GAFF-2.11 was generally worse. While OpenFF researchers were involved in building the benchmarking infrastructure used in this work, benchmarking was done entirely in-house within industrial organizations and the resulting assessment is reported here. This work assesses the force field performance using separate benchmarking steps, external datasets, and involving external research groups. This effort may also be unique in terms of the number of different industrial partners involved, with 10 different companies participating in the benchmark efforts.

A key event at the onset of development is the activation of a contractile actomyosin cortex during the oocyte-to-embryo transition(1-3). Here we report on the discovery that, in Caenorhabditis elegans oocytes, actomyosin cortex activation is supported by the emergence of thousands of short-lived protein condensates rich in F-actin, N-WASP and the ARP2/3 complex(4-8) that form an active micro-emulsion. A phase portrait analysis of the dynamics of individual cortical condensates reveals that condensates initially grow and then transition to disassembly before dissolving completely. We find that, in contrast to condensate growth through diffusion(9), the growth dynamics of cortical condensates are chemically driven. Notably, the associated chemical reactions obey mass action kinetics that govern both composition and size. We suggest that the resultant condensate dynamic instability(10) suppresses coarsening of the active micro-emulsion(11), ensures reaction kinetics that are independent of condensate size and prevents runaway F-actin nucleation during the formation of the first cortical actin meshwork.

Biomolecular condensates grow in busy cellular environments. Statistical image analysis of heterogeneous structures now enables quantification of macromolecular interactions between condensates and cytoskeletal filaments.

Biomolecular condensation has emerged as a key organizing principle governing the formation of membraneless cellular assemblies. Revealing the mechanism of formation of biomolecular condensates requires the quantitative examination of their growth kinetics. Here, we introduce mass balance imaging (MBI) as a general method to study compositional growth dynamics based on fluorescent images of multicomponent clusters. MBI allows the visualization and measurement of composition-dependent growth rates of biomolecular condensates and other assemblies. We provide a computational pipeline and demonstrate the applicability of our method by investigating cortical assemblies containing N-WASP (WSP-1) and F-actin that appear during oocyte cortex activation in C. elegans. In general, the method can be broadly implemented to identify interactions that underlie growth kinetics of multicomponent assemblies in vivo and in vitro.

A series of small-molecule YEATS4 binders have been discovered as part of an ongoing research effort to generate high-quality probe molecules for emerging and/or challenging epigenetic targets. Analogues such as 4d and 4e demonstrate excellent potency and selectivity for YEATS4 binding versus YEATS1,2,3 and exhibit good physical properties and in vitro safety profiles. A new X-ray crystal structure confirms direct binding of this chemical series to YEATS4 at the lysine acetylation recognition site of the YEATS domain. Multiple analogues engage YEATS4 with nanomolar potency in a whole-cell nanoluciferase bioluminescent resonance energy transfer assay. Rodent pharmacokinetic studies demonstrate the competency of several analogues as in vivo-capable binders.

A direct, stereocontrolled synthesis of acyclic α-chloroenamides is presented. Our methodology showed good yields and substrate scope. Mechanistic insights are provided that account for the high levels of stereoselectivity reported. Subsequent synthetic manipulation of the α-chloroenamides provides direct entry to polyfunctionalized acyclic enamides, compounds of wide use in organic chemistry and the pharmaceutical industry.

Sickle cell disease (SCD) is a genetic disorder caused by a single point mutation (β6 Glu → Val) on the β-chain of adult hemoglobin (HbA) that results in sickled hemoglobin (HbS). In the deoxygenated state, polymerization of HbS leads to sickling of red blood cells (RBC). Several downstream consequences of polymerization and RBC sickling include vaso-occlusion, hemolytic anemia, and stroke. We report the design of a noncovalent modulator of HbS, clinical candidate PF-07059013 (23). The seminal hit molecule was discovered by virtual screening and confirmed through a series of biochemical and biophysical studies. After a significant optimization effort, we arrived at 23, a compound that specifically binds to Hb with nanomolar affinity and displays strong partitioning into RBCs. In a 2-week multiple dose study using Townes SCD mice, 23 showed a 37.8% (±9.0%) reduction in sickling compared to vehicle treated mice. 23 (PF-07059013) has advanced to phase 1 clinical trials.

A variety of long-lived carbocations containing the p(pentafluorosulfanyl)phenyl and m-(pentafluorosulfanyl)phenyl groups have been characterized by low-temperature NMR spectroscopy. In the case of potential nonclassical carbocations substituted with the p-(pentafluorosulfanyl)phenyl substituent, deviations from linearity when the Hammett parameter (sigma(C+)) is plotted versus C-13 NMR shifts of the carbocationic center were observed. Plotting the experimentally derived C-13 NMR shifts versus sigma(C+) or sigma(+) of classical 4-phenyl-X substituted carbocations also provides a means to accurately back-calculate the sigma(+)and sigma(C+) parameters of the -SF5 substituent.

The formation of misfolded protein aggregates is a hallmark of neurodegenerative diseases. The aggregate formation process exhibits an initial lag phase when precursor clusters spontaneously assemble. However, most experimental assays are blind to this lag phase. We develop a quantitative assay based on super-resolution imaging in fixed cells and light sheet imaging of living cells to study the early steps of aggregation in mammalian cells. We find that even under normal growth conditions mammalian cells have precursor clusters. The cluster size distribution is precisely that expected for a so-called super-saturated system in first order phase transition. This means there exists a nucleation barrier, and a critical size above which clusters grow and mature. Homeostasis is maintained through a Szilard model entailing the preferential clearance of super-critical clusters. We uncover a role for a putative chaperone (RuvBL) in this disassembly of large clusters. The results indicate early aggregates behave like condensates. Editorial note: This article has been through an editorial process in which the authors decide how to respond to the issues raised during peer review. The Reviewing Editor's assessment is that all the issues have been addressed (see decision letter).

Direct synthesis of triarylacetamides and 9-fluorenecarboxamides has been achieved. Phenylglyoxamides upon superelectrophilic activation in trifluoromethanesulfonic acid (triflic acid, TFSA) leads to Friedel–Crafts hydroxyalkylation or one-pot tandem hydroxyalkylation-4 π -electrocyclization of aromatics into triarylacetamides or 9-fluorenecarboxamides, respectively. Mechanistic investigation by DFT calculations suggests the intermediacy of diprotonated (or “protosolvated”) intermediates.

Protein abnormalities in cells are the cause of major pathologies, and a number of adaptive responses have evolved to relieve the toxicity of misfolded polypeptides. To trigger these responses, cells must detect the buildup of aberrant proteins which often associate with proteasome failure, but the sensing mechanism is poorly understood. Here we demonstrate that this mechanism involves the heat shock protein 70-Bcl-2-associated athanogene 3 (Hsp70-Bag3) complex, which upon proteasome suppression responds to the accumulation of defective ribosomal products, preferentially recognizing the stalled polypeptides. Components of the ribosome quality control system LTN1 and VCP and the ribosome-associated chaperone NAC are necessary for the interaction of these species with the Hsp70-Bag3 complex. This complex regulates important signaling pathways, including the Hippo pathway effectors LATS1/2 and the p38 and JNK stress kinases. Furthermore, under proteotoxic stress Hsp70-Bag3-LATS1/2 signaling regulates protein aggregation. We established that the regulated step was the emergence and growth of abnormal protein oligomers containing only a few molecules, indicating that aggregation is regulated at very early stages. The Hsp70-Bag3 complex therefore functions as an important signaling node that senses proteo-toxicity and triggers multiple pathways that control cell physiology, including activation of protein aggregation.

Failure in protein quality control can often lead to protein aggregation, yet in neuro-degenerative diseases, by the time aggregates can be seen, the cells have advanced well into the disease pathology. Here, we develop a quantitative imaging approach to study the protein aggregation process in living mammalian cells with unprecedented spatio-temporal resolution. We find that sub-diffractive precursor aggregates may form even in untreated cells, and their size distribution is exactly as predicted for a system undergoing a first order phase transition. Practically, this implies that as soon as aggregates reach a critical size (Rc = 162 ± 4 nm untreated cells), they will spontaneously grow into large inclusions. Our data suggest that a previously uncharacterized, RuvBL1 dependent mechanism clears aggregates above the critical size. Our study unveils the existence of sub-diffractive aggregates in living cells; and the strong agreement between cellular data and a nucleation theory, based on first order phase transition, provides insight into regulatory steps in the early stages of aggregate formation in vivo.

The C-5 substituted 2,4-diaminoquinazoline RG3039 (compound 1), a member of a chemical series that was identified and optimized using an SMN2 promoter screen, prolongs survival and improves motor function in a mouse model of spinal muscular atrophy (SMA). It is a potent inhibitor of the mRNA decapping scavenger enzyme (DcpS), but the mechanism whereby DcpS inhibition leads to therapeutic benefit is unclear. Compound 1 is a dibasic lipophilic molecule that is predicted to accumulate in lysosomes. To understand if the in vivo efficacy is due to DcpS inhibition or other effects resulting from the physicochemical properties of the chemotype, we undertook structure based molecular design to identify DcpS inhibitors with improved physicochemical properties. Herein we describe the design, synthesis, and in vitro pharmacological characterization of these DcpS inhibitors along with the in vivo mouse CNS PK profile of PF-DcpSi (compound 24), one of the analogs found to be efficacious in SMA mouse model.

Single-molecule based super-resolution microscopy ([Betzig et al., 2006][1]; [Hess et al., 2006][2]; [Rust et al., 2006][3]) provides insight into the spatiotemporal organization and dynamics of biomolecules at the length scale of ten to hundreds of nanometers, which is most relevant to protein