Discovery of MK-1084: An Orally Bioavailable and Low-Dose KRASG12C Inhibitor.

Oncogenic mutations in the RAS gene account for 30% of all human tumors; more than 60% of which present as KRAS mutations at the hotspot codon 12. After decades of intense pursuit, a covalent inhibition strategy has enabled selective targeting of this previously "undruggable" target. Herein, we disclose our journey toward the discovery of MK-1084, an orally bioavailable and low-dose KRASG12C covalent inhibitor currently in phase I clinical trials (NCT05067283). We leveraged structure-based drug design to identify a macrocyclic core structure, and hypothesis-driven optimization of biopharmaceutical properties to further improve metabolic stability and tolerability.

Discovery of non-boronic acid Arginase 1 inhibitors through virtual screening and biophysical methods.

Inhibiting Arginase 1 (ARG1), a metalloenzyme that hydrolyzes l-arginine in the urea cycle, has been demonstrated as a promising therapeutic avenue in immuno-oncology through the restoration of suppressed immune response in several types of cancers. Most of the currently reported small molecule inhibitors are boronic acid based. Herein, we report the discovery of non-boronic acid ARG1 inhibitors through virtual screening. Biophysical and biochemical methods were used to experimentally profile the hits while X-ray crystallography confirmed a class of trisubstituted pyrrolidine derivatives as optimizable alternatives for the development of novel classes of immuno-oncology agents targeting this enzyme.

Comprehensive Strategies to Bicyclic Prolines: Applications in the Synthesis of Potent Arginase Inhibitors.

Comprehensive synthetic strategies afforded a diverse set of structurally unique bicyclic proline-containing arginase inhibitors with a high degree of three-dimensionality. The analogs that favored the Cγ-exo conformation of the proline improved the arginase potency over the initial lead. The novel synthetic strategies reported here not only enable access to previously unknown stereochemically complex proline derivatives but also provide a foundation for the future synthesis of bicyclic proline analogs, which incorporate inherent three-dimensional character into building blocks, medicine, and catalysts and could have a profound impact on the conformation of proline-containing peptides and macrocycles.

Structure-Based Discovery of Proline-Derived Arginase Inhibitors with Improved Oral Bioavailability for Immuno-Oncology.

Recent data suggest that the inhibition of arginase (ARG) has therapeutic potential for the treatment of a number of indications ranging from pulmonary and vascular disease to cancer. Thus, high demand exists for selective small molecule ARG inhibitors with favorable druglike properties and good oral bioavailability. In light of the significant challenges associated with the unique physicochemical properties of previously disclosed ARG inhibitors, we use structure-based drug design combined with a focused optimization strategy to discover a class of boronic acids featuring a privileged proline scaffold with superior potency and oral bioavailability. These compounds, exemplified by inhibitors 4a, 18, and 27, demonstrated a favorable overall profile, and 4a was well tolerated following multiple days of dosing at concentrations that exceed those required for serum arginase inhibition and concomitant arginine elevation in a syngeneic mouse carcinoma model.

Cryo-EM structures of inhibitory antibodies complexed with arginase 1 provide insight into mechanism of action.

Human Arginase 1 (hArg1) is a metalloenzyme that catalyzes the hydrolysis of L-arginine to L-ornithine and urea, and modulates T-cell-mediated immune response. Arginase-targeted therapies have been pursued across several disease areas including immunology, oncology, nervous system dysfunction, and cardiovascular dysfunction and diseases. Currently, all published hArg1 inhibitors are small molecules usually less than 350 Da in size. Here we report the cryo-electron microscopy structures of potent and inhibitory anti-hArg antibodies bound to hArg1 which form distinct macromolecular complexes that are greater than 650 kDa. With local resolutions of 3.5 Å or better we unambiguously mapped epitopes and paratopes for all five antibodies and determined that the antibodies act through orthosteric and allosteric mechanisms. These hArg1:antibody complexes present an alternative mechanism to inhibit hArg1 activity and highlight the ability to utilize antibodies as probes in the discovery and development of peptide and small molecule inhibitors for enzymes in general.

Discovery and Optimization of Rationally Designed Bicyclic Inhibitors of Human Arginase to Enhance Cancer Immunotherapy.

The action of arginase, a metalloenzyme responsible for the hydrolysis of arginine to urea and ornithine, is hypothesized to suppress immune-cell activity within the tumor microenvironment, and thus its inhibition may constitute a means by which to potentiate the efficacy of immunotherapeutics such as anti-PD-1 checkpoint inhibitors. Taking inspiration from reported enzyme-inhibitor cocrystal structures, we designed and synthesized novel inhibitors of human arginase possessing a fused 5,5-bicyclic ring system. The prototypical member of this class, 3, when dosed orally, successfully demonstrated serum arginase inhibition and concomitant arginine elevation in a syngeneic mouse carcinoma model, despite modest oral bioavailability. Structure-based design strategies to improve the bioavailability of this class, including scaffold modification, fluorination, and installation of active-transport recognition motifs were explored.

Understanding Keesom Interactions in Monolayer-Based Large-Area Tunneling Junctions.

Charge transport across self-assembled monolayers (SAMs) has been widely studied. Discrepancies of charge tunneling data that arise from various studies, however, call for efforts to develop new statistical analytical approaches to understand charge tunneling across SAMs. Structure-property studies on charge tunneling across SAM-based junctions have largely been through comparison of average tunneling rates and associated variance. These early moments (especially the average) are dominated by barrier width-a static property of the junction. In this work, we show that analysis of higher statistical moments (skewness and kurtosis) reveals the dynamic nature of the tunnel junction. Intramolecular Keesom (dipole-dipole) interactions dynamically fluctuate with bias as dictated by stereoelectronic limitations. Analyzing variance in the distribution of tunneling data instead of the first statistical moment (average), for a series of n-alkanethiols containing internal amide and aromatic terminal groups, we observe that the direction of dipole moments affects molecule-electrode coupling. An applied bias induces changes in the tunneling probability, affecting the distribution of tunneling paths in large-area molecular junctions.

D3R Grand Challenge 2: blind prediction of protein-ligand poses, affinity rankings, and relative binding free energies.

The Drug Design Data Resource (D3R) ran Grand Challenge 2 (GC2) from September 2016 through February 2017. This challenge was based on a dataset of structures and affinities for the nuclear receptor farnesoid X receptor (FXR), contributed by F. Hoffmann-La Roche. The dataset contained 102 IC50 values, spanning six orders of magnitude, and 36 high-resolution co-crystal structures with representatives of four major ligand classes. Strong global participation was evident, with 49 participants submitting 262 prediction submission packages in total. Procedurally, GC2 mimicked Grand Challenge 2015 (GC2015), with a Stage 1 subchallenge testing ligand pose prediction methods and ranking and scoring methods, and a Stage 2 subchallenge testing only ligand ranking and scoring methods after the release of all blinded co-crystal structures. Two smaller curated sets of 18 and 15 ligands were developed to test alchemical free energy methods. This overview summarizes all aspects of GC2, including the dataset details, challenge procedures, and participant results. We also consider implications for progress in the field, while highlighting methodological areas that merit continued development. Similar to GC2015, the outcome of GC2 underscores the pressing need for methods development in pose prediction, particularly for ligand scaffolds not currently represented in the Protein Data Bank ( http://www.pdb.org ), and in affinity ranking and scoring of bound ligands.

Revisiting OPLS Force Field Parameters for Ionic Liquid Simulations.

Our OPLS-2009IL force field parameters (J. Chem. Theory Comput. 2009, 5, 1038-1050) were originally developed and tested on 68 unique ionic liquids featuring the 1-alkyl-3-methylimidazolium [RMIM], N-alkylpyridinium [RPyr], and choline cations. Experimental validation was limited to densities and a few, largely conflicting, heat of vaporization (ΔHvap) values reported in the literature at the time. Owing to the use of Monte Carlo as our sampling technique, it was also not possible to investigate the reproduction of dynamics. The [RMIM] OPLS-2009IL parameters have been revisited in this work and adapted for use in molecular dynamics (MD) simulations. In addition, new OPLS-AA parameters have been developed for multiple anions, i.e., AlCl4-, BF4-, Br-, Cl-, NO3-, PF6-, acetate, benzoate bis(pentafluoroethylsulfonyl)amide, bis(trifluoroethylsulfonyl)amide, dicyanamide, formate, methylsulfate, perchlorate, propanoate, thiocyanate, tricyanomethanide, and trifluoromethanesulfonate. The computed solvent densities, heats of vaporization, viscosities, diffusion coefficients, heat capacities, surface tensions, and other relevant solvent data compared favorably with experiment. A charge scaling of ±0.8 e was also investigated as a means to mimic polarization and charge transfer effects. The 0.8-scaling led to significant improvements for ΔHvap, surface tension, and self-diffusivity; however, a concern when scaling charges is the potential degradation of local intermolecular interactions at short ranges. Radial distribution functions (RDFs) were used to examine cation-anion interactions when employing 0.8*OPLS-2009IL and the scaled force field accurately reproduced RDFs from ab initio MD simulations.

D3R grand challenge 2015: Evaluation of protein-ligand pose and affinity predictions.

The Drug Design Data Resource (D3R) ran Grand Challenge 2015 between September 2015 and February 2016. Two targets served as the framework to test community docking and scoring methods: (1) HSP90, donated by AbbVie and the Community Structure Activity Resource (CSAR), and (2) MAP4K4, donated by Genentech. The challenges for both target datasets were conducted in two stages, with the first stage testing pose predictions and the capacity to rank compounds by affinity with minimal structural data; and the second stage testing methods for ranking compounds with knowledge of at least a subset of the ligand-protein poses. An additional sub-challenge provided small groups of chemically similar HSP90 compounds amenable to alchemical calculations of relative binding free energy. Unlike previous blinded Challenges, we did not provide cognate receptors or receptors prepared with hydrogens and likewise did not require a specified crystal structure to be used for pose or affinity prediction in Stage 1. Given the freedom to select from over 200 crystal structures of HSP90 in the PDB, participants employed workflows that tested not only core docking and scoring technologies, but also methods for addressing water-mediated ligand-protein interactions, binding pocket flexibility, and the optimal selection of protein structures for use in docking calculations. Nearly 40 participating groups submitted over 350 prediction sets for Grand Challenge 2015. This overview describes the datasets and the organization of the challenge components, summarizes the results across all submitted predictions, and considers broad conclusions that may be drawn from this collaborative community endeavor.

Effect of Substrate Morphology on the Odd-Even Effect in Hydrophobicity of Self-Assembled Monolayers.

Surface roughness, often captured through root-mean-square roughness (Rrms), has been shown to impact the quality of self-assembled monolayers (SAMs) formed on coinage metals. Understanding the effect of roughness on hydrophobicity of SAMs, however, is complicated by the odd-even effect-a zigzag oscillation in contact angles with changes in molecular length. We recently showed that for surfaces with Rrms > 1 nm, the odd-even effect in hydrophobicity cannot be empirically observed. In this report, we compare wetting properties of SAMs on Ag and Au surfaces of different morphologies across the Rrms ∼ 1 nm limit. We prepared surfaces with comparable properties (grain sizes and Rrms) and assessed the wetting properties of resultant SAMs. Substrates with Rrms either below or above the odd-even limit were investigated. With smoother surfaces (lower Rrms), an inverted asymmetric odd-even zigzag oscillation in static contact angles (θs) was observed with change from Au to Ag. Asymmetry in odd-even oscillation in Au was attributed to a larger change in θs from odd to even number of carbons in the n-alkanethiol and vice versa for Ag. For rougher surfaces, no odd-even effect was observed; however, a gradual increase in the static contact angle was observed. Increase in the average grain sizes (>3 times larger) on rough surfaces did not lead to significant difference in the wetting properties, suggesting that surface roughness significantly dominated the nature of the SAMs. We therefore infer that the predicted roughness-dependent limit to the observation of the odd-even effect in wetting properties of n-alkanethiols cannot be overcome by creating surfaces with large grain sizes for surfaces with Rrms > 1 nm. We also observed that the differences between Au and Ag surfaces are dominated by differences in the even-numbered SAMs, but this difference vanishes with shorter molecular chain length (≤C3).

Understanding protein arginine methyltransferase 1 (PRMT1) product specificity from molecular dynamics.

Protein arginine methyltransferases (PRMTs) catalyze the post-translational methylation of specific arginyl groups within targeted proteins to regulate fundamental biological responses in eukaryotic cells. The major Type I PRMT enzyme, PRMT1, strictly generates monomethyl arginine (MMA) and asymmetric dimethylarginine (ADMA), but not symmetric dimethylarginine (SDMA). Multiple diseases can arise from the dysregulation of PRMT1, including heart disease and cancer, which underscores the need to elucidate the origin of product specificity. Molecular dynamics (MD) simulations were carried out for WT PRMT1 and its M48F, H293A, H293S, and H293S-M48F mutants bound with S-adenosylmethionine (AdoMet) and the arginine substrate in an unmethylated or methylated form. Experimental site-directed mutagenesis and analysis of the resultant products were also performed. Two specific PRMT1 active site residues, Met48 and His293, have been determined to play a key role in dictating product specificity, as: (1) the single mutation of Met48 to Phe enabled PRMT1 to generate MMA, ADMA, and a limited amount of SDMA; (2) the single mutation of His293 to Ser formed the expected MMA and ADMA products only; whereas (3) the double mutant H293S-M48F-PRMT1 produced SMDA as the major product with limited amounts of MMA and ADMA. Calculating the formation of near-attack conformers resembling SN2 transition states leading to either the ADMA or SDMA products finds that Met48 and His293 may enable WT PRMT1 to yield ADMA exclusively by precluding MMA from binding in an orientation more conducive to SDMA formation, i.e., the methyl group bound at the arginine Nη2 position.

Application of Ionic Liquids in Pot-in-Pot Reactions.

Pot-in-pot reactions are designed such that two reaction media (solvents, catalysts and reagents) are isolated from each other by a polymeric membrane similar to matryoshka dolls (Russian nesting dolls). The first reaction is allowed to progress to completion before triggering the second reaction in which all necessary solvents, reactants, or catalysts are placed except for the starting reagent for the target reaction. With the appropriate trigger, in most cases unidirectional flux, the product of the first reaction is introduced to the second medium allowing a second transformation in the same glass reaction pot--albeit separated by a polymeric membrane. The basis of these reaction systems is the controlled selective flux of one reagent over the other components of the first reaction while maintaining steady-state catalyst concentration in the first "pot". The use of ionic liquids as tools to control chemical potential across the polymeric membranes making the first pot is discussed based on standard diffusion models--Fickian and Payne's models. Besides chemical potential, use of ionic liquids as delivery agent for a small amount of a solvent that slightly swells the polymeric membrane, hence increasing flux, is highlighted. This review highlights the critical role ionic liquids play in site-isolation of multiple catalyzed reactions in a standard pot-in-pot reaction.

Limits to the Effect of Substrate Roughness or Smoothness on the Odd-Even Effect in Wetting Properties of n-Alkanethiolate Monolayers.

This study investigates the effect of roughness on interfacial properties of an n-alkanethiolate self-assembled monolayer (SAM) and uses hydrophobicity to demonstrate the existence of upper and lower limits. This article also sheds light on the origin of the previously unexplained gradual increase in contact angles with increases in the size of the molecule making the SAM. We prepared Au surfaces with a root-mean-square (RMS) roughness of ∼0.2-0.5 nm and compared the wetting properties of n-alkanethiolate (C10-C16) SAMs fabricated on these surfaces. Static contact angles, θ(s), formed between the SAM and water, diethylene glycol, and hexadecane showed an odd-even effect irrespective of the solvent properties. The average differences in subsequent SAM(E) and SAM(O) are Δθ(s|n  ­â€¯(n+1)|) ≈ 1.7° (n = even) and Δθ(s|n ­â€¯(n+1)|) ≈ 3.1° (n = odd). A gradual increase in θ(s) with increasing length of the molecule was observed, with values ranging from water 104.7-110.7° (overall Δθ(s) = 6.0° while for the evens Δθ(s)(E) = 4.4° and odds Δθ(s)(O) = 3.5°) to diethylene glycol 72.9-80.4° (overall Δθ(s) = 7.5° while for the evens Δθ(s)(E) = 2.9° and odds Δθ(s)(O) = 2.4°) and hexadecane 40.4­49.4° (overall Δθ(s) = 9.0° while for the evens Δθ(s)(E) = 3.7° and odds Δθ(s)(O) = 2.1°). This article establishes that the gradual increase in θ(s) with increasing molecular size in SAMs is due to asymmetry in the zigzag oscillation in the odd-even effect. Comparison of the magnitude and proportion differences in this asymmetry allows us to establish the reduction in interfacial dispersive forces, due to increasing SAM crystallinity with increasing molecular size, as the origin of this asymmetry. By comparing the dependence of θ(s) on surface roughness we infer that (i) RMS roughness ≈ 1 nm is a theoretical limit beyond which the odd-even effect cannot be observed and (ii) on a hypothetically flat surface the maximum difference in hydrophobicity, as expressed in θ(s), is ∼3°.

Odd-even effect in the hydrophobicity of n-alkanethiolate self-assembled monolayers depends upon the roughness of the substrate and the orientation of the terminal moiety.

The origin of the odd-even effect in properties of self-assembled monolayers (SAMs) and/or technologies derived from them is poorly understood. We report that hydrophobicity and, hence, surface wetting of SAMs are dominated by the nature of the substrate (surface roughness and identity) and SAM tilt angle, which influences surface dipoles/orientation of the terminal moiety. We measured static contact angles (θs) made by water droplets on n-alkanethiolate SAMs with an odd (SAM(O)) or even (SAM(E)) number of carbons (average θs range of 105.8-112.1°). When SAMs were fabricated on smooth "template-stripped" metal (M(TS)) surfaces [root-mean-square (rms) roughness = 0.36 ± 0.01 nm for Au(TS) and 0.60 ± 0.04 nm for Ag(TS)], the odd-even effect, characterized by a zigzag oscillation in values of θs, was observed. We, however, did not observe the same effect with rougher "as-deposited" (M(AD)) surfaces (rms roughness = 2.27 ± 0.16 nm for Au(AD) and 5.13 ± 0.22 nm for Ag(AD)). The odd-even effect in hydrophobicity inverts when the substrate changes from Au(TS) (higher θs for SAM(E) than SAM(O), with average Δθs |n - (n + 1)| ≈ 3°) to Ag(TS) (higher θs for SAM(O) than SAM(E), with average Δθs |n - (n + 1)| ≈ 2°). A comparison of hydrophobicity across Ag(TS) and Au(TS) showed a statistically significant difference (Student's t test) between SAM(E) (Δθs |Ag evens - Au evens| ≈ 5°; p < 0.01) but failed to show statistically significant differences on SAM(O) (Δθs |Ag odds - Au odds| ≈ 1°; p > 0.1). From these results, we deduce that the roughness of the metal substrate (from comparison of M(AD) versus M(TS)) and orientation of the terminal -CH2CH3 (by comparing SAM(E) and SAM(O) on Au(TS) versus Ag(TS)) play major roles in the hydrophobicity and, by extension, general wetting properties of n-alkanethiolate SAMs.

Exploring the catalytic mechanism of alkanesulfonate monooxygenase using molecular dynamics.

The complex mechanistic properties of alkanesulfonate monooxygenase (SsuD) provide a particular challenge for identifying catalytically relevant amino acids. In response, a joint computational and experimental study was conducted to further elucidate the SsuD mechanism. Extensive unbiased molecular dynamics (MD) simulations were performed for six SsuD systems: (1) substrate-free, (2) bound with FMNH2, (3) bound with a C4a-peroxyflavin intermediate (FMNOO(-)), (4) bound with octanesulfonate (OCS), (5) co-bound with FMNH2 and OCS, and (6) co-bound with FMNOO(-) and OCS. A previous theoretical study suggested that salt bridges between Arg297 and Glu20 or Asp111 initiated conformational changes critical for catalysis. However, our MD simulations and steady-state kinetic experiments did not corroborate this result. Similar kcat/Km values for both the E20A and D111A SsuD variants to wild-type SsuD suggest that the salt bridges are not critical to the desulfonation mechanism. Instead, the predicted role of Arg297 is to favorably interact with the phosphate group of the reduced flavin. Concomitantly, Arg226 functioned as a "protection" group shielding FMNOO(-) from bulk solvent and was more pronounced when both FMNOO(-) and OCS were bound. The stabilization of FMNOO(-) through electrostatic interactions with Arg226 would properly position the C4a peroxy group for the proposed nucleophilic attack on the sulfur of octanesulfonate.

A remodeled protein arginine methyltransferase 1 (PRMT1) generates symmetric dimethylarginine.

Protein arginine methylation is emerging as a significant post-translational modification involved in various cell processes and human diseases. As the major arginine methylation enzyme, protein arginine methyltransferase 1 (PRMT1) strictly generates monomethylarginine and asymmetric dimethylarginine (ADMA), but not symmetric dimethylarginine (SDMA). The two types of dimethylarginines can lead to distinct biological outputs, as highlighted in the PRMT-dependent epigenetic control of transcription. However, it remains unclear how PRMT1 product specificity is regulated. We discovered that a single amino acid mutation (Met-48 to Phe) in the PRMT1 active site enables PRMT1 to generate both ADMA and SDMA. Due to the limited amount of SDMA formed, we carried out quantum mechanical calculations to determine the free energies of activation of ADMA and SDMA synthesis. Our results indicate that the higher energy barrier of SDMA formation (ΔΔG(‡) = 3.2 kcal/mol as compared with ADMA) may explain the small amount of SDMA generated by M48F-PRMT1. Our study reveals unique energetic challenges for SDMA-forming methyltransferases and highlights the exquisite control of product formation by active site residues in the PRMTs.

Determination of antiplasmodial activity and binding affinity of curcumin and demethoxycurcumin towards PfTrxR.

In our study, the inhibitory activity of curcuminoids towards Plasmodium falciparum thioredoxin reductase (PfTrxR) was determined using LC-MS-based functional assay and showed that only demethoxycurcumin (DMC) inhibited PfTrxR (IC50: 2 µM). In silico molecular modelling was used to ascertain and further confirm that the binding affinities of curcumin and DMC are towards the dimer interface of PfTrxR. The in vitro antiplasmodial activities of curcumin and DMC were evaluated and shown to be active against chloroquine (CQ)-sensitive (D6 clone) and moderately active against CQ-resistant (W2 clone) strains of Plasmodium falciparum while no cytotoxicity was observed against Vero cells.

Identification of PLX4032-resistance mechanisms and implications for novel RAF inhibitors.

BRAF inhibitors improve melanoma patient survival, but resistance invariably develops. Here we report the discovery of a novel BRAF mutation that confers resistance to PLX4032 employing whole-exome sequencing of drug-resistant BRAF(V600K) melanoma cells. We further describe a new screening approach, a genome-wide piggyBac mutagenesis screen that revealed clinically relevant aberrations (N-terminal BRAF truncations and CRAF overexpression). The novel BRAF mutation, a Leu505 to His substitution (BRAF(L505H) ), is the first resistance-conferring second-site mutation identified in BRAF mutant cells. The mutation replaces a small nonpolar amino acid at the BRAF-PLX4032 interface with a larger polar residue. Moreover, we show that BRAF(L505H) , found in human prostate cancer, is itself a MAPK-activating, PLX4032-resistant oncogenic mutation. Lastly, we demonstrate that the PLX4032-resistant melanoma cells are sensitive to novel, next-generation BRAF inhibitors, especially the 'paradox-blocker' PLX8394, supporting its use in clinical trials for treatment of melanoma patients with BRAF-mutations.