Symon Gathiaka

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 BRAFV600K 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 (BRAFL505H), 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 BRAFL505H, 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.

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  – (n+1)|) ≈ 1.7° (n = even) and Δθ(s|n – (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 40.4–49.4° (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°.

A Remodeled Protein Arginine Methyltransferase 1 (PRMT1) Generates Symmetric Dimethylarginine

Background: Asymmetric and symmetric dimethylarginine (ADMA and SDMA) residues are biologically distinct products of protein arginine methyltransferase (PRMT) isoforms. Results: Met-48 in PRMT1 regulates the regiochemistry of dimethylation, and SDMA formation is energetically costly. Conclusion: Steric changes in the PRMT1 active site can reprogram product formation. Significance: SDMA-forming PRMTs may require additional factors to overcome the energetic cost of SDMA. 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.

Design, development and evaluation of novel dual PPARδ/PPARγ agonists.

Type 2 diabetes is at epidemic proportions and thus development of novel pharmaceutical therapies for improving insulin sensitivity has become of paramount importance. The objectives of the current study were to develop novel dual PPARγ/δ agonists without the deleterious side effects associated with full PPARγ agonists. Docking simulations of 23 novel compounds within the ligand binding domain of PPARγ/δ were performed using AutoDock Vina which consistently reproduced experimental binding poses from known PPAR agonists. Comparisons were made and described with other docking programs AutoDock and Surflex-Dock (from SYBYL-X). Biological evaluation of compounds was accomplished by transcriptional promoter activity assays, quantitative PCR gene analysis for known PPARγ/δ targets as well as in vitro assays for lipid accumulation and mitochondrial biogenesis verses known PPAR agonists. We found one (compound 9) out of the 23 compounds evaluated, to be the most potent and selective dual PPARγ/δ agonist which did not display the deleterious side effects associated with full PPARγ agonists.

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.

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.

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.

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.

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.