Unnatural Amino Acids: Strategies, Designs, and Applications in Medicinal Chemistry and Drug Discovery.

Peptides can operate as therapeutic agents that sit within a privileged space between small molecules and larger biologics. Despite examples of their potential to regulate receptors and modulate disease pathways, the development of peptides with drug-like properties remains a challenge. In the quest to optimize physicochemical parameters and improve target selectivity, unnatural amino acids (UAAs) have emerged as critical tools in peptide- and peptidomimetic-based drugs.

Hydrogen-bonding behavior of amidines in helical structure.

Amidines are an isostere of the amide bond and are completely unexplored in peptide secondary structure. This study marks the first investigation of the structural implications of amidines in folded helices. Amidines were found to engage in hydrogen-bonding interactions that are compatible with helical structure.

Facile Mechanochemical Functionalization of Hydrophobic Substrates for Single-Walled Carbon Nanotube Based Optical Reporters of Hydrolase Activity.

Single walled carbon nanotubes (SWCNT) have recently been demonstrated as modular, near-infrared (nIR) probes for reporting hydrolase activity; however, these have been limited to naturally amphipathic substrate targets used to noncovalently functionalize the hydrophobic nanoparticles. Many relevant substrate targets are hydrophobic (such as recalcitrant biomass) and pose a challenge for modular functionalization. In this work, a facile mechanochemistry approach was used to couple insoluble substrates, such as lignin, to SWCNT using l-lysine amino acid as a linker and tip sonication as the mechanochemical energy source.

Complementary Strategies for Installation of Thioimidates into Peptide Backbones.

Thioimidates are a precursor and synthetic branch point to access either thioamide or amidine isosteres of the native amide (peptide bond). Previous syntheses of thioimidate-containing peptides were prone to side reactivity and required slow, cumbersome steps that were difficult to monitor. We describe a more efficient approach to directly couple thioimidates onto the growing peptide chain.

Thioimidates provide general access to thioamide, amidine, and imidazolone peptide-bond isosteres.

Thioamides, amidines, and heterocycles are three classes of modifications that can act as peptide-bond isosteres to alter the peptide backbone. Thioimidate protecting groups can address many of the problematic synthetic issues surrounding installation of these groups. Historically, amidines have received little attention in peptides due to limitations in methods to access them.

General Installation of (4)-Imidazolone -Amide Bioisosteres Along the Peptide Backbone.

Imidazolones represent an important class of heterocycles present in a wide range of pharmaceuticals, metabolites, and bioactive natural products and serve as the active chromophore in green fluorescent protein. Recently, imidazolones have received attention for their ability to act as a nonaromatic amide bond bioisotere which improves pharmacological properties. Herein, we present a tandem amidine installation and cyclization with an adjacent ester to yield (4)-imidazolone products.

Thioimidate Solutions to Thioamide Problems during Thionopeptide Deprotection.

Thioamides have structural and chemical similarity to peptide bonds, offering valuable insights when probing peptide backbone interactions, but are prone to side reactions during solid-phase peptide synthesis (SPPS). Thioimidates have been demonstrated to be effective protecting groups for thioamides during peptide elongation. We further demonstrate how thioimidates can assist thioamides through the most yield-crippling step of thionopeptide deprotection, allowing for the first isolation of an important benchmark α-helical peptide that had previously eluded synthesis and isolation.

Anomeric Answer to Sulfenamide Stability and α-Nucleophilicity.

The S-N bond remains a synthetically challenging motif for organic chemists to access. The problem arises from instability in many sulfenamide derivatives, which has led to fewer S-N bond surrogate molecules compared to their hydroxylamine (NHOH) and hydrazine (NHNH) analogues. In turn, sulfenamides have often been omitted in studies regarding α-nucleophilicity.

Protein Conformational Dynamics Underlie Selective Recognition of Thermophilic over Mesophilic Enzyme I by a Substrate Analogue.

Substrate selectivity is an important preventive measure to decrease the possibility of cross interactions between enzymes and metabolites that share structural similarities. In addition, understanding the mechanisms that determine selectivity towards a particular substrate increases the knowledge base for designing specific inhibitors for target enzymes. Here, we combine NMR, molecular dynamics (MD) simulations, and protein engineering to investigate how two substrate analogues, allylicphosphonate (cPEP) and sulfoenolpyruvate (SEP), recognize the mesophilic (eEIC) and thermophilic (tEIC) homologues of the receptor domain of bacterial Enzyme I, which has been proposed as a target for antimicrobial research.

A General Strategy to Install Amidine Functional Groups Along the Peptide Backbone.

Amidines are a structural surrogate for peptide bonds, yet have received considerably little attention in peptides due to limitations in existing methods to access them. The synthetic strategy developed in this study represents the first robust and general procedure for the introduction of amidines into the peptide backbone. We exploit and further develop the utility and efficiency of thioimidate protecting groups as a means to side-step reactivity that ultimately renders existing methods unsuitable for the installation of amidines along the main-chain of peptides.

Attached Nitrogen Test by C-N Solid-State NMR Spectroscopy for the Structure Determination of Heterocyclic Isomers.

Differentiation of heterocyclic isomers by solution H, C, and N NMR spectroscopy is often challenging due to similarities in their spectroscopic signatures. Here, C{N} solid-state NMR spectroscopy experiments are shown to operate as an "attached nitrogen test", where heterocyclic isomers are easy to distinguish based on one-dimensional nitrogen-filtered C solid-state NMR. We anticipate that these NMR experiments will facilitate the assignment of heterocyclic isomers during synthesis and natural product discovery.

Hydrogen Bond and Geometry Effects of Thioamide Backbone Modifications.

Thioamide substitution of backbone peptide bonds can probe interactions along the main chain of proteins. Despite theoretical predictions of the enhanced hydrogen bonding propensities of thioamides, previous studies often do not consider the geometric constraints imposed by folded peptide secondary structure. This work addresses drawbacks in previous studies that ignored the geometry dependence and local dielectric properties of thioamide hydrogen bonding and identifies cases where thioamides may be either stronger or weaker hydrogen-bonding partners than amides.

Investigation of a Series of 2-(2'-Hydroxyaryl)benzazole Derivatives: Photophysical Properties, Excited-State Intramolecular Proton-Transfer Reactions, and Observation of Long-Lived Triplet Excited States.

Excited state intramolecular proton transfer (ESIPT) has drawn much attention for its important applications in a variety of areas. Here, the steady-state and time-resolved absorption spectroscopic experiments as well as DFT/TD-DFT calculations are employed to study the photophysical properties and photochemical reaction mechanisms of 2-(2'-hydroxyphenyl) benzoxazole () and selected derivatives (compounds -). Because of their larger π-conjugation framework, compounds - display red-shifted absorbance but blue-shifted fluorescence compared with .

Molecular Conformation in Charge Tunneling across Large-Area Junctions.

Self-assembled monolayers are predicated on thermodynamic equilibrium; hence, their properties project accessible relaxation pathways. Herein, we demonstrate that charge tunneling correlates with conformational degrees of freedom(s). Results from open chain and cyclic head groups show that, as expected, distribution in tunneling data correlates with the orientation of the head group, akin to the odd-even effect and more importantly the degree of conformational freedom, but fluctuates with applied bias.

Determination of Diffusion Kinetics of Ketamine in Brain Tissue: Implications for Mechanistic Studies of Drug Actions.

Ketamine has been in use for over 50 years as a general anesthetic, acting primarily through blockade of -methyl-D-aspartate receptors in the brain. Recent studies have demonstrated that ketamine also acts as a potent and rapid-acting antidepressant when administered at sub-anesthetic doses. However, the precise mechanism behind this effect remains unclear.

Detailed Visualization of Aromaticity Using Isotropic Magnetic Shielding.

For many years, Clar's aromatic sextet theory has served as a qualitative method for assessing the aromatic character of polycyclic aromatic hydrocarbons. A new approach, based on the calculation of isotropic magnetic shielding (IMS) contour plots, is shown to provide a feature-rich picture of aromaticity that is both quantitative yet still easily interpreted. Chemists are visual creatures who are adept at discerning reactivity and chemical behavior from molecular structures.

Fast Acquisition of Proton-Detected HETCOR Solid-State NMR Spectra of Quadrupolar Nuclei and Rapid Measurement of NH Bond Lengths by Frequency Selective HMQC and RESPDOR Pulse Sequences.

Fast magic-angle spinning (MAS), frequency selective (FS) heteronuclear multiple quantum coherence (HMQC) experiments which function in an analogous manner to solution SOFAST HMQC NMR experiments, are demonstrated. Fast MAS enables efficient FS excitation of H solid-state NMR signals. Selective excitation and observation preserves H magnetization, leading to a significant shortening of the optimal inter-scan delay.

Highly selective staining and quantification of intracellular lipid droplets with a compact push-pull fluorophore based on benzothiadiazole.

A robust lipophilic dye, based on the structures of the benzothiadiazole heterocycle, was shown to be a potent fluorescent stain for the selective imaging of lipid droplets (LDs) within both live and fixed human cells. Its small molecular framework, large Stokes shift, and vastly improved photostability over that of the current status quo, Nile Red, highlight its tremendous potential as a versatile chemical tool for facilitating LD imaging and research.

Blue-Light Photocleavable Protecting Groups Based on Benzothiadiazole Scaffolds.

An unexpected nucleophilic aromatic substitution lead to a novel benzothiadiazole scaffold that bore the functional group pattern associated with benzyl-type photocleavable protecting groups. The new molecules display efficient photochemical release of leaving groups with blue light. The performance of both ortho- and meta-substituted derivatives was probed through both structural manipulation and computational metrics to improve performance.

Deprotection Strategies for Thioimidates during Fmoc Solid-Phase Peptide Synthesis: A Safe Route to Thioamides.

Thioamides are important biophysical probes of peptide folding but are prone to α-C epimerization during Fmoc solid-phase peptide synthesis. The stereochemical integrity of thioamide-containing peptides can be dramatically improved by protecting the thioamide as a thioimidate during synthesis. A drawback of this approach, however, is that once synthesis of the peptide is complete, regeneration of the thioamide requires the toxic, corrosive, and flammable gas HS.

A Bottom-Up Approach To Preserve Thioamide Residue Stereochemistry during Fmoc Solid-Phase Peptide Synthesis.

Thioamides are useful biophysical probes for the study of peptide structure and folding. The α-C stereochemistry of thioamide amino acids, however, is easily epimerized during solid-phase peptide synthesis (SPPS), which limits the sequence space that is available to thioamide incorporation. This work demonstrates that the α-C stereochemistry of thioamides can be reversibly protected in a manner that is compatible with the standard methodology of SPPS to enable the facile implementation of thioamide probes.

Demonstration of Baird's rule complementarity in the singlet state with implications for excited-state intramolecular proton transfer.

The aromatic character of an arene is proposed to switch from aromatic in the ground state (S0) to antiaromatic in the S1 and T1 excited states. This behavior is known as Baird's rule and has been invoked to explain excited-state properties, primarily in the triplet state, whereas rationalization of antiaromaticity in the singlet state is less developed. This work demonstrates the first application of Baird's rule to rationalize previously unexplained experimental behavior of the singlet state process known as excited-state intramolecular proton transfer (ESIPT).