Structural insights into selective small molecule activation of PKG1α.

cGMP-dependent protein kinase I-α (PKG1α) is a target for pulmonary arterial hypertension due to its role in the regulation of smooth muscle function. While most work has focused on regulation of cGMP turnover, we recently described several small molecule tool compounds which were capable of activating PKG1α via a cGMP independent pathway. Selected molecules were crystallized in the presence of PKG1α and were found to bind to an allosteric site proximal to the low-affinity nucleotide binding domain. These molecules act to displace the switch helix and cause activation of PKG1α representing a new mechanism for the activation and control of this critical therapeutic path. The described structures are vital to understanding the function and control of this key regulatory pathway.

Optimization and Mechanistic Investigations of Novel Allosteric Activators of PKG1α.

Activation of PKG1α is a compelling strategy for the treatment of cardiovascular diseases. As the main effector of cyclic guanosine monophosphate (cGMP), activation of PKG1α induces smooth muscle relaxation in blood vessels, lowers pulmonary blood pressure, prevents platelet aggregation, and protects against cardiac stress. The development of activators has been mostly limited to cGMP mimetics and synthetic peptides. Described herein is the optimization of a piperidine series of small molecules to yield activators that demonstrate in vitro phosphorylation of vasodilator-stimulated phosphoprotein as well as antiproliferative effects in human pulmonary arterial smooth muscle cells. Hydrogen/deuterium exchange mass spectrometry experiments with the small molecule activators revealed a mechanism of action consistent with cGMP-induced activation, and an X-ray co-crystal structure with a construct encompassing the regulatory domains illustrated a binding mode in an allosteric pocket proximal to the low-affinity cyclic nucleotide-binding domain.

Building a Culture of Medicinal Chemistry Knowledge Sharing.

Increasing the efficiency of the drug discovery process is a challenge faced by drug hunters everywhere. One strategy medicinal chemists employ to meet this challenge is learning from knowledge sources within and beyond their organization. In this Perspective, we discuss the evolution of mechanisms for medicinal chemistry knowledge capture and sharing at Merck & Co. over the past 15 years. We describe our approach to knowledge management and report on the multiple enduring and complementary teams and initiatives we have created to capture and share knowledge within a geographically diverse medicinal chemistry community. In addition, this Perspective will share the benefits we have observed and also reflect on what has allowed our efforts to be both successful and sustainable.

Using measures of metabolic flux to align screening and clinical development: Avoiding pitfalls to enable translational studies.

Screening campaigns, especially those aimed at modulating enzyme activity, often rely on measuring substrate→product conversions. Unfortunately, the presence of endogenous substrates and/or products can limit one's ability to measure conversions. As well, coupled detection systems, often used to facilitate optical readouts, are subject to interference. Stable isotope labeled substrates can overcome background contamination and yield a direct readout of enzyme activity. Not only can isotope kinetic assays enable early screening, but they can also be used to follow hit progression in translational (pre)clinical studies. Herein, we consider a case study surrounding lipid biology to exemplify how metabolic flux analyses can connect stages of drug development, caveats are highlighted to ensure reliable data interpretations. For example, when measuring enzyme activity in early biochemical screening it may be enough to quantify the formation of a labeled product. In contrast, cell-based and in vivo studies must account for variable exposure to a labeled substrate (or precursor) which occurs via tracer dilution and/or isotopic exchange. Strategies are discussed to correct for these complications. We believe that measures of metabolic flux can help connect structure-activity relationships with pharmacodynamic mechanisms of action and determine whether mechanistically differentiated biophysical interactions lead to physiologically relevant outcomes. Adoption of this logic may allow research programs to (i) build a critical bridge between primary screening and (pre)clinical development, (ii) elucidate biology in parallel with screening and (iii) suggest a strategy aimed at in vivo biomarker development.

Scalable Preparation of 4,4-Disubstituted Six-Membered Cyclic Sulfones.

We provide an account of synthetic strategies aimed at the efficient preparation of 4-amino-4-methyltetrahydro-2H-thiopyran 1,1-dioxide (3), an important cyclic sulfone building block for medicinal chemistry. A practical and scalable protocol has been developed that readily gives access to the title compound from commercially available and inexpensive starting materials. In addition, this novel approach has enabled the synthesis of various related 4,4-disubstituted cyclic sulfone derivatives that serve as valuable structural motifs for drug discovery.

Mercury concentration in shark meat from traditional markets of Gyeongsangbuk-do, South Korea.

BACKGROUND: Although unusually high levels of blood mercury have been reported in the North Gyeongsang Province (Gyeongsangbuk-do), mercury contents from shark meat distributed in this region have not been assessed yet. Thus, this study aims to identify the hazard by evaluating the mercury contents of the shark meat sold in the traditional market of Gyeongsangbuk-do. METHODS: The shark meat in the form of muscle meat was obtained from 15 traditional markets of Gyeongsangbuk-do in the summer and winter of 2013. Out of 105 samples in total, 49 were collected in the summer and 56 in the winter. The total mercury concentration was measured by the combustion-gold amalgamation method using an automatic mercury analyzer (Milestone DMA-80, Milestone). RESULTS: The average mercury concentration of shark meat was 2.29 ± 1.77 µg/g, ranging between 0.06-8.93 µg/g with a geometric mean of 1.44 µg/g, which is higher than those reported in many countries. The mercury concentration in 77 of 105 shark meat samples exceeded 1 µg/g. Mercury concentration ranged between 0.09-8.93 µg/g (geometric mean: 1.45) in the summer and 0.06-6.73 µg/g (geometric mean: 1.48) in the winter. CONCLUSIONS: Shark meat sold in the market contained a substantial amount of mercury. This suggests that it is difficult to reduce mercury intake by simply strengthening the standard level of mercury concentration in shark meat. Therefore, it is need to communication and awareness programs with consumers about hazardous effects of mercury inherent in shark meat.

Use of molecular modeling aided design to dial out hERG liability in adenosine A(2A) receptor antagonists.

Molecular modeling was performed on a triazolo quinazoline lead compound to help develop a series of adenosine A2A receptor antagonists with improved hERG profile. Superposition of the lead compound onto MK-499, a benchmark hERG inhibitor, combined with pKa calculations and measurement, identified terminal fluorobenzene to be responsible for hERG activity. Docking of the lead compound into an A2A crystal structure suggested that this group is located at a flexible, spacious, and solvent-exposed opening of the binding pocket, making it possible to tolerate various functional groups. Transformation analysis (MMP, matched molecular pair) of in-house available experimental data on hERG provided suggestions for modifications in order to mitigate this liability. This led to the synthesis of a series of compounds with significantly reduced hERG activity. The strategy used in the modeling work can be applied to other medicinal chemistry programs to help improve hERG profile.

Adenosine A2A receptor as a drug discovery target.

The adenosine A2A receptor is a G-protein-coupled receptor (GPCR) that has been extensively studied during the past few decades because it offers numerous possibilities for therapeutic applications. Herein we describe adenosine A2A receptor distribution, signaling pathways, pharmacology, and molecular structure, followed by a summary and SAR discussion of the most relevant series of adenosine A2A agonists and antagonists. This review also provides an update of the A2A ligands that are undergoing or have undergone clinical studies, including the two currently marketed agonists adenosine and regadenoson.

Steroidal C-21 heteroaryl thioethers. Part 3: pregn-4-eno-[3,2-c]pyrazole fused A ring modified steroids as selective glucocorticoid receptor modulators (dissociated steroids).

The introduction of A ring pyrazole modification to the hydrocortisone C-21 heteroaryl thioethers generated compounds with excellent transrepression potency (IL-8 inhibition) compared to their hydrocortisone analogs. However, the transcriptional transactivation activity of these compounds were considerably higher than the corresponding hydrocortisone analogs. Among all the compounds evaluated, a quinoxaline thioether modification demonstrated the best overall in vitro separation.

Core-clickable PEG-branch-azide bivalent-bottle-brush polymers by ROMP: grafting-through and clicking-to.

The combination of highly efficient polymerizations with modular "click" coupling reactions has enabled the synthesis of a wide variety of novel nanoscopic structures. Here we demonstrate the facile synthesis of a new class of clickable, branched nanostructures, polyethylene glycol (PEG)-branch-azide bivalent-brush polymers, facilitated by "graft-through" ring-opening metathesis polymerization of a branched norbornene-PEG-chloride macromonomer followed by halide-azide exchange. The resulting bivalent-brush polymers possess azide groups at the core near a polynorbornene backbone with PEG chains extended into solution; the structure resembles a unimolecular micelle. We demonstrate copper-catalyzed azide-alkyne cycloaddition (CuAAC) "click-to" coupling of a photocleavable doxorubicin (DOX)-alkyne derivative to the azide core. The CuAAC coupling was quantitative across a wide range of nanoscopic sizes (∼6-∼50 nm); UV photolysis of the resulting DOX-loaded materials yielded free DOX that was therapeutically effective against human cancer cells.

Effects of a novel arginine methyltransferase inhibitor on T-helper cell cytokine production.

The protein arginine methyltransferase (PRMT) family of enzymes catalyzes the transfer of methyl groups from S-adenosylmethionine to the guanidino nitrogen atom of peptidylarginine to form monomethylarginine or dimethylarginine. We created several less polar analogs of the specific PRMT inhibitor arginine methylation inhibitor-1, and one such compound was found to have improved PRMT inhibitory activity over the parent molecule. The newly identified PRMT inhibitor modulated T-helper-cell function and thus may serve as a lead for further inhibitors useful for the treatment of immune-mediated disease.

Benzimidazole and related ligands for Cu-catalyzed azide-alkyne cycloaddition.

Tris(2-benzimidazolylmethyl)amines have been found to be superior accelerating ligands for the copper(I)-catalyzed azide-alkyne cycloaddition reaction. Candidates bearing different benzimidazole N-substituents as well as benzothiazole and pyridyl ligand arms were evaluated by absolute rate measurements under relatively dilute conditions by aliquot quenching kinetics and by relative rate measurements under concentrated conditions by reaction calorimetry. Benzimidazole-based ligands with pendant alkylcarboxylate arms proved to be advantageous in the latter case. The catalyst system was shown to involve more than one active species, providing a complex response to changes in pH and buffer salts and the persistence of high catalytic rate in the presence of high concentrations of coordinating ligands. The water-soluble ligand (BimC4A)3 was found to be especially convenient for the rapid and high-yielding synthesis of several functionalized triazoles with 0.01-0.5 mol % Cu.

Asymmetry by electrophilic rearrangement of symmetric 2-pyridone photodimers.

[reaction: see text] Halogenation of achiral trans-2-pyridone photodimers results in 1,3-migration of an amide nitrogen and formation of a chiral structure with six stereogenic centers and well-differentiated functionality. The reactivity of this product toward nucleophiles, including the allylic halide, is dominated by participation by the amide nitrogen.

The total synthesis of (-)-SNF4435 C and (+)-SNF4435 D.

The size and positioning of substituents on a tetraene, along with the Woodward-Hoffmann rules, control the relative stereochemistry at the four adjacent chiral centers that are generated in the 8pi/6pi electrocyclization cascade. A biomimetic synthesis of (-)-SNF4435 C and (+)-SNF4435 D exploits these steric effects and allows confirmation of the predicted absolute stereochemistry of the natural products.

"Endo" and "exo" bicyclo[4.2.0]-octadiene isomers from the electrocyclization of fully substituted tetraene models for SNF 4435C and D. control of stereochemistry by choice of a functionalized substituent.

[reaction: see text] A tandem electrocyclic closure, perceived as the key step in a biomimetic approach to SNF 4435C and D, was tested with 1,1,8-trisubstituted tetraene substrates. The ratio of endo:exo products could be controlled by the choice of the RZ substituent at C-1. On the basis of these results, a short stereoselective route to an advanced SNF 4435 intermediate was devised.

Studies in bicyclo[3.1.0]hexane methanolysis. Ring opening of activated cyclopropanes under acidic and basic conditions.

A bicyclo[3.1.0]hexane, with one cyclopropane carbon flanked by a ketone and an ester or an aldehyde, undergoes methanolysis with cleavage of one of the two activated cyclopropane bonds, depending on the reaction conditions. Acidic conditions yield primarily or exclusively a 4-methoxycyclohexane, while basic conditions yield a 3-methoxymethylcyclopentanone.