Subtle Chemical Modifications Research Articles

Beyond N-Alkylation: Synthesis, Structure, and Function of N-Amino Peptides.

ConspectusThe growing list of physiologically important protein-protein interactions (PPIs) has amplified the need for compounds to target topologically complex biomolecular surfaces. In contrast to small molecules, peptide and protein mimics can exhibit three-dimensional shape complementarity across a large area and thus have the potential to significantly expand the "druggable" proteome. Strategies to stabilize canonical protein secondary structures without sacrificing side-chain content are particularly useful in the design of peptide-based chemical probes and therapeutics.Substitution of the backbone amide in peptides represents a subtle chemical modification with profound effects on conformation and stability. Studies focused on N-alkylation have already led to broad-ranging applications in peptidomimetic design. Inspired by nonribosomal peptide natural products harboring amide N-oxidations, we envisioned that main-chain hydrazide and hydroxamate bonds would impose distinct conformational preferences and offer unique opportunities for backbone diversification. This Account describes our exploration of peptide N-amination as a strategy for stabilizing canonical protein folds and for the structure-based design of soluble amyloid mimics.We developed a general synthetic protocol to access N-amino peptides (NAPs) on solid support. In an effort to stabilize β-strand conformation, we designed stitched peptidomimetics featuring covalent tethering of the backbone N-amino substituent to the preceding residue side chain. Using a combination of NMR, X-ray crystallography, and molecular dynamics simulations, we discovered that backbone N-amination alone could significantly stabilize β-hairpin conformation in multiple models of folding. Our studies revealed that the amide NH2 substituent in NAPs participates in cooperative noncovalent interactions that promote β-sheet secondary structure. In contrast to Cα-substituted α-hydrazino acids, we found that N-aminoglycine and its N'-alkylated derivatives instead stabilize polyproline II (PPII) conformation. The reactivity of hydrazides also allows for late-stage peptide macrocyclization, affording novel covalent surrogates of side-chain-backbone H-bonds.The pronounced β-sheet propensity of Cα-substituted α-hydrazino acids prompted us to target amyloidogenic proteins using NAP-based β-strand mimics. Backbone N-amination was found to render aggregation-prone lead sequences soluble and resistant to proteolysis. Inhibitors of Aβ and tau identified through N-amino scanning blocked protein aggregation and the formation of mature fibrils in vitro. We further identified NAP-based single-strand and cross-β tau mimics capable of inhibiting the prion-like cellular seeding activity of recombinant and patient-derived tau fibrils.Our studies establish backbone N-amination as a valuable addition to the peptido- and proteomimetic tool kit. α-Hydrazino acids show particular promise as minimalist β-strand mimics that retain side-chain information. Late-stage derivatization of hydrazides also provides facile entry into libraries of backbone-edited peptides. We anticipate that NAPs will thus find applications in the development of optimally constrained folds and modulators of PPIs.

Driving Triplet State Population in Benzothioxanthene Imide Dyes: Let's twist!

Controlling the formation of photoexcited triplet states is critical for many (photo)chemical and physical applications. Here, we demonstrate that a permanent out-of-plane distortion of the benzothioxanthene imide (BTI) dye promotes intersystem crossing by increasing spin-orbit coupling. This manipulation was achieved through a subtle chemical modification, specifically the bay-area methylation. Consequently, this simple yet efficient approach expands the catalog of known molecular engineering strategies for synthesizing heavy atom-free, dual redox-active, yet still emissive and synthetically accessible photosensitizers.

N‐Cyanopiperazines as Specific Covalent Inhibitors of the Deubiquitinating Enzyme UCHL1

AbstractCyanamides have emerged as privileged scaffolds in covalent inhibitors of deubiquitinating enzymes (DUBs). However, many compounds with a cyanopyrrolidine warhead show cross‐reactivity toward small subsets of DUBs or toward the protein deglycase PARK7/DJ‐1, hampering their use for the selective perturbation of a single DUB in living cells. Here, we disclose N’‐alkyl,N‐cyanopiperazines as structures for covalent enzyme inhibition with exceptional specificity for the DUB UCHL1 among 55 human deubiquitinases and with effective target engagement in cells. Notably, transitioning from 5‐membered pyrrolidines to 6‐membered heterocycles eliminated PARK7 binding and introduced context‐dependent reversibility of the isothiourea linkage to the catalytic cysteine of UCHL1. Compound potency and specificity were analysed by a range of biochemical assays and with a crystal structure of a cyanopiperazine in covalent complex with UCHL1. The structure revealed a compound‐induced conformational restriction of the cross‐over loop, which underlies the observed inhibitory potencies. Through the rationalization of specificities of different cyanamides, we introduce a framework for the investigation of protein reactivity of bioactive nitriles of this compound class. Our results represent an encouraging case study for the refining of electrophilic compounds into chemical probes, emphasizing the potential to engineer specificity through subtle chemical modifications around the warhead.

N-Cyanopiperazines as Specific Covalent Inhibitors of the Deubiquitinating Enzyme UCHL1.

Cyanamides have emerged as privileged scaffolds in covalent inhibitors of deubiquitinating enzymes (DUBs). However, many compounds with a cyanopyrrolidine warhead show cross-reactivity toward small subsets of DUBs or toward the protein deglycase PARK7/DJ-1, hampering their use for the selective perturbation of a single DUB in living cells. Here, we disclose N'-alkyl,N-cyanopiperazines as structures for covalent enzyme inhibition with exceptional specificity for the DUB UCHL1 among 55 human deubiquitinases and with effective target engagement in cells. Notably, transitioning from 5-membered pyrrolidines to 6-membered heterocycles eliminated PARK7 binding and introduced context-dependent reversibility of the isothiourea linkage to the catalytic cysteine of UCHL1. Compound potency and specificity were analysed by a range of biochemical assays and with a crystal structure of a cyanopiperazine in covalent complex with UCHL1. The structure revealed a compound-induced conformational restriction of the cross-over loop, which underlies the observed inhibitory potencies. Through the rationalization of specificities of different cyanamides, we introduce a framework for the investigation of protein reactivity of bioactive nitriles of this compound class. Our results represent an encouraging case study for the refining of electrophilic compounds into chemical probes, emphasizing the potential to engineer specificity through subtle chemical modifications around the warhead.

Pendent supported rare coordination for flavin: Structural, photophysical and morphological characterization of flavin-silver(I) complexes

The present manuscript discusses our effort in stabilizing the rare bidentate coordinate mode for the flavin entity, via pendent supported secondary coordination; thereby resulting in a polymeric structure. Subtle chemical modification around the flavin core structure incorporating allyl and picolyl functionality in proximity to the secondary coordinate site was envisaged and two novel flavin analogues allylflavin (AF) and picolylflavin (PiF) was synthesized and solid-state X-ray diffraction studies was performed to elucidate the structural features of their silver complexes. Interestingly, two crystallographically unique silver ions was found to be characteristic feature, with different geometry around silver ion is observed depending on its involvement in coordination at primary or secondary site of the flavin unit. Furthermore, complexation behavior has been probed via photophysical techniques and morphological studies were undertaken to ascertain the facile transfer of the coordination polymeric motif onto the surface.

Switching on/off aryl hydrocarbon receptor and pregnane X receptor activities by chemically modified tryptamines

Microbial indoles have been demonstrated as selective or dual agonists and ligands of the pregnane X receptor (PXR) and aryl hydrocarbon receptor (AhR). However, structural determinants of microbial indoles selectivity towards both receptors remain elusive. Here, we studied the effects of existing and newly synthesized derivatives of indole microbial metabolite tryptamine on the activity of AhR and PXR receptors. We show that the elongation of indolyl-3-alkaneamine chain, indole N-methylation and conversion of indolyl-3-alkaneamines to oleamides resulted in a major increase of PXR activity and in parallel loss of AhR activity. Using reporter gene assays, RT-PCR and TR-FRET techniques, we have characterized in detail the activation of PXR by novel indolyl-3-alkanyl-oleamides, 1-methyltryptamine and 1-methyltryptamine-acetamide. As a proof of concept, we demonstrated anti-inflammatory and epithelial barrier-protective activity of lead derivatives in intestinal Caco-2 cells, employing the measurement of expression of pro-inflammatory chemokines, tight junction genes, trans-epithelial electric resistance TEER, and dextran-FITC permeability assay. In conclusion, we show that a subtle chemical modifications of simple microbial indole metabolite tryptamine, leads to substantial changes in AhR and PXR agonist activities.

Aggregation‐Dependent Thermally Activated Delayed Fluorescence Emitters: AIE or ACQ?

AbstractThe understanding of the excited state dynamics of thermally activated delayed fluorescence (TADF) materials is crucial. In this study, two donor–acceptor‐type TADF emitters with highly twisted conformation are synthesized. The emitters with subtle chemical modification of donor unit exhibit opposite aggregation luminescent behaviors: aggregation‐induced emission (AIE) and aggregation‐caused quenching (ACQ). Through the photophysical properties study, crystallographic analysis, and theory simulations, it is discovered that X‐aggregation supports AIE behavior by restricting the intramolecular motions and preserving TADF emission via an efficient reverse intersystem crossing (RISC) process, but on the other hand, H‐aggregation leads to ACQ behavior due to inhibited RISC, disabled TADF channel, and weak phosphorescence from radiative low‐lying triplet state. The findings shed light on the excited‐state dynamic behaviors of TADF emitters, which are dependent on aggregation.

Coherent Vibronic Wavepackets Show Structure-Directed Charge Flow in Host-Guest Donor-Acceptor Complexes.

Designing and controlling charge transfer (CT) pathways in organic semiconductors are important for solar energy applications. To be useful, a photogenerated, Coulombically bound CT exciton must further separate into free charge carriers; direct observations of the detailed CT relaxation pathways, however, are lacking. Here, photoinduced CT and relaxation dynamics in three host-guest complexes, where a perylene (Per) electron donor guest is incorporated into two symmetric and one asymmetric extended viologen cyclophane acceptor hosts, are presented. The central ring in the extended viologen is either p-phenylene (ExV2+) or electron-rich 2,5-dimethoxy-p-phenylene (ExMeOV2+), resulting in two symmetric cyclophanes with unsubstituted or methoxy-substituted central rings, ExBox4+ and ExMeOBox4+, respectively, and an asymmetric cyclophane with one of the central viologen rings being methoxylated ExMeOVBox4+. Upon photoexcitation, the asymmetric host-guest ExMeOVBox4+ ⊃ Per complex exhibits directional CT toward the energetically unfavorable methoxylated side due to structural restrictions that facilitate strong interactions between the Per donor and the ExMeOV2+ side. The CT state relaxation pathways are probed using ultrafast optical spectroscopy by focusing on coherent vibronic wavepackets, which are used to identify CT relaxations along charge localization and vibronic decoherence coordinates. Specific low- and high-frequency nuclear motions are direct indicators of a delocalized CT state and the degree of CT character. Our results show that the CT pathway can be controlled by subtle chemical modifications of the acceptor host in addition to illustrating how coherent vibronic wavepackets can be used to probe the nature and time evolution of the CT states.

Mass Spectrometry Approaches Empowering Neuropeptide Discovery and Therapeutics.

The discovery of insulin in the early 1900s ushered in the era of research related to peptides acting as hormones and neuromodulators, among other regulatory roles. These essential gene products are found in all organisms, from the most primitive to the most evolved, and carry important biologic information that coordinates complex physiology and behavior; their misregulation has been implicated in a variety of diseases. The evolutionary origins of at least 30 neuropeptide signaling systems have been traced to the common ancestor of protostomes and deuterostomes. With the use of relevant animal models and modern technologies, we can gain mechanistic insight into orthologous and paralogous endogenous peptides and translate that knowledge into medically relevant insights and new treatments. Groundbreaking advances in medicine and basic science influence how signaling peptides are defined today. The precise mechanistic pathways for over 100 endogenous peptides in mammals are now known and have laid the foundation for multiple drug development pipelines. Peptide biologics have become valuable drugs due to their unique specificity and biologic activity, lack of toxic metabolites, and minimal undesirable interactions. This review outlines modern technologies that enable neuropeptide discovery and characterization, and highlights lessons from nature made possible by neuropeptide research in relevant animal models that is being adopted by the pharmaceutical industry. We conclude with a brief overview of approaches/strategies for effective development of peptides as drugs. SIGNIFICANCE STATEMENT: Neuropeptides, an important class of cell-cell signaling molecules, are involved in maintaining a range of physiological functions. Since the discovery of insulin's activity, over 100 bioactive peptides and peptide analogs have been used as therapeutics. Because these are complex molecules not easily predicted from a genome and their activity can change with subtle chemical modifications, mass spectrometry (MS) has significantly empowered peptide discovery and characterization. This review highlights contributions of MS-based research towards the development of therapeutic peptides.

Chalcone Scaffolds, Bioprecursors of Flavonoids: Chemistry, Bioactivities, and Pharmacokinetics.

Chalcones are secondary metabolites belonging to the flavonoid (C6-C3-C6 system) family that are ubiquitous in edible and medicinal plants, and they are bioprecursors of plant flavonoids. Chalcones and their natural derivatives are important intermediates of the flavonoid biosynthetic pathway. Plants containing chalcones have been used in traditional medicines since antiquity. Chalcones are basically α,β-unsaturated ketones that exert great diversity in pharmacological activities such as antioxidant, anticancer, antimicrobial, antiviral, antitubercular, antiplasmodial, antileishmanial, immunosuppressive, anti-inflammatory, and so on. This review provides an insight into the chemistry, biosynthesis, and occurrence of chalcones from natural sources, particularly dietary and medicinal plants. Furthermore, the pharmacological, pharmacokinetics, and toxicological aspects of naturally occurring chalcone derivatives are also discussed herein. In view of having tremendous pharmacological potential, chalcone scaffolds/chalcone derivatives and bioflavonoids after subtle chemical modification could serve as a reliable platform for natural products-based drug discovery toward promising drug lead molecules/drug candidates.

Subtle Chemical Changes Cross the Boundary between Agonist and Antagonist: New A3 Adenosine Receptor Homology Models and Structural Network Analysis Can Predict This Boundary.

Distinguishing compounds' agonistic or antagonistic behavior would be of great utility for the rational discovery of selective modulators. We synthesized truncated nucleoside derivatives and discovered 6c (Ki = 2.40 nM) as a potent human A3 adenosine receptor (hA3AR) agonist, and subtle chemical modification induced a shift from antagonist to agonist. We elucidated this shift by developing new hA3AR homology models that consider the pharmacological profiles of the ligands. Taken together with molecular dynamics (MD) simulation and three-dimensional (3D) structural network analysis of the receptor-ligand complex, the results indicated that the hydrogen bonding with Thr943.36 and His2727.43 could make a stable interaction between the 3'-amino group with TM3 and TM7, and the corresponding induced-fit effects may play important roles in rendering the agonistic effect. Our results provide a more precise understanding of the compounds' actions at the atomic level and a rationale for the design of new drugs with specific pharmacological profiles.

Chemistry-dependent Raman spectral features of glauconite and nontronite: Implications for mineral identification and provenance analysis

Abstract This study provides a comprehensive Raman spectral characterization of nontronite and glauconitenontronite mixed-layer phases from seafloor hydrothermal fields. These 2:1 phyllosilicates, which show isomorphous cation exchange between Mg2++Fe2+ and Fe3++Al3+ in the dioctahedral sheets, exhibit three diagnostic Raman peaks in the low wavenumber region (v1 ~241–257 cm−1; v2 ~600–606 cm−1; v3 ~690 cm−1), and one peak at ~3548–3570 cm−1 (v4). With increasing (Mg2++Fe2+)oct, the presumed stretching band of octahedral OH-O bonds (v1) is displaced to a higher wavenumber, whereas the stretching band of tetrahedral Si-O-Si bonds (v2) is shifted to a lower wavenumber. Peak v4, which relates to O-H bonds of hydroxyls linked to octahedral cations, shows a downshift with increasing (Mg2++Fe2+)oct. The band v4 can be mathematically fitted by three bands, two of which strongly correlate with the cation occupancy in the octahedral sheets; i.e., vibrations of hydroxyls linked to triva-lent cations (Fe3+ and Al3+) are mainly represented by a band at ~3560–3573 cm−1, whereas divalent cations (Mg2+ and Fe2+) mainly contribute to a band at ~3538–3540 cm−1. This result is consistent with theoretical considerations for dioctahedral phyllosilicates, which predict for the incorporation of Mg2+ and Fe2+ a weakening/lengthening of O-H bonds in the OH groups, accounting for a downshift of the O-H vibrations. Hence, this is one of the first studies that trace how even subtle chemical modifications in phyllosilicates influence Raman spectral features. The reported findings have implications for mineral identification and provenance analysis, such as during surface exploration on Mars, where compositionally diverse phyllosilicates occur.

Synergistic Effects of Chlorination and Branched Alkyl Side Chain on the Photovoltaic Properties of Simple Non‐Fullerene Acceptors with Quinoxaline as the Core

To date, the fused-ring electron acceptors show the best photovoltaic performances, and the development of simple non-fullerene acceptors via intramolecular noncovalent interactions can reduce synthetic costs. In this work, four simple non-fullerene acceptors with an A-D-A'-D-A configuration (QCIC1, QCIC2, QCIC3, and QCIC4) were synthesized. They contained the same conjugated backbone (A': quinoxaline; D: cyclopentadithiophene; A: dicyano-indanone) but different halogen atoms and alkyl side chains. Due to the chlorination on the end-groups and the most and/or longest branched alkyl side chains on the backbone, the blended film composed of QCIC3 and donor poly{[2,6'-4,8-di(5-ethylhexylthienyl)benzo [1,2-b : 4,5-b']dithiophene]-alt-[5,5-(1',3'-di-2-thienyl-5',7'-bis(2-ethylhexyl)benzo[1',2'-c : 4',5'-c']dithiophene-4,8-dione)]} (PBDB-T) exhibited the strongest π-π stacking and the most suitable phase-separation domains among the four blended films. Therefore, the QCIC3-based organic solar cells yielded the highest power conversion efficiency of 10.55 %. This work provides a pathway to optimize the molecular arrangements and enhance the photovoltaic property of simple electron acceptors through subtle chemical modifications.

Galectin-4 N-Terminal Domain: Binding Preferences Toward A and B Antigens With Different Peripheral Core Presentations.

The tandem-repeat Galectin-4 (Gal-4) contains two different domains covalently linked through a short flexible peptide. Both domains have been shown to bind preferentially to A and B histo blood group antigens with different affinities, although the binding details are not yet available. The biological relevance of these associations is unknown, although it could be related to its attributed role in pathogen recognition. The presentation of A and B histo blood group antigens in terms of peripheral core structures differs among tissues and from that of the antigen-mimicking structures produced by pathogens. Herein, the binding of the N-terminal domain of Gal-4 toward a group of differently presented A and B oligosaccharide antigens in solution has been studied through a combination of NMR, isothermal titration calorimetry (ITC), and molecular modeling. The data presented in this paper allow the identification of the specific effects that subtle chemical modifications within this antigenic family have in the binding to the N-terminal domain of Gal-4 in terms of affinity and intermolecular interactions, providing a structural-based rationale for the observed trend in the binding preferences.

Tailoring the nonlinear absorption of fluorescent dyes by substitution at a boron center

The tuning of the spectroscopic signatures of boron-carrying fluorescent dyes by subtle chemical modifications is achieved.

Self-Assembly of Nucleoside-Derived Low-Molecular-Weight Gelators: A Thermodynamics and Kinetics Study on Different Length Scales.

Biocompatible materials are of paramount importance in numerous fields. Unlike chemically bridge polymer-based hydrogels, low-molecular-weight gelators can form a reversible hydrogel as their structures rely on noncovalent interaction. Although many applications with this type of hydrogel can be envisioned, we still lack their understanding due to the complexity of their self-assembly process and the difficulty in predicting their behaviors (transition temperature, gelation kinetics, the impact of solvent, etc.). In this study, we extend the investigations of a series of nucleoside-derived gelators, which only differ by subtle chemical modifications. Using a multitechnique approach, we determined their thermodynamic and kinetic features on various scale (molecular to macro) in different conditions. Monitored at the supramolecular level by circular dichroism as well as macroscopic scales by rheology and turbidimetry, we found out that the sol-gel and gel-sol transitions are greatly dependent on the concentration and on the mechanisms that are probed. Self-assembly kinetics depends on hydrogel molecules and is modulated by temperature and solvent. This fundamental study provides insight on the impact of some parameters on the gelation process, such as concentration, cooling rate, and the nature of the solvent.

Fluorinated Carbohydrates as Lectin Ligands: Simultaneous Screening of a Monosaccharide Library and Chemical Mapping by 19F NMR Spectroscopy.

Molecular recognition of carbohydrates is a key step in essential biological processes. Carbohydrate receptors can distinguish monosaccharides even if they only differ in a single aspect of the orientation of the hydroxyl groups or harbor subtle chemical modifications. Hydroxyl-by-fluorine substitution has proven its merits for chemically mapping the importance of hydroxyl groups in carbohydrate–receptor interactions. 19F NMR spectroscopy could thus be adapted to allow contact mapping together with screening in compound mixtures. Using a library of fluorinated glucose (Glc), mannose (Man), and galactose (Gal) derived by systematically exchanging every hydroxyl group by a fluorine atom, we developed a strategy combining chemical mapping and 19F NMR T2 filtering-based screening. By testing this strategy on the proof-of-principle level with a library of 13 fluorinated monosaccharides to a set of three carbohydrate receptors of diverse origin, i.e. the human macrophage galactose-type lectin, a plant lectin, Pisum sativum agglutinin, and the bacterial Gal-/Glc-binding protein from Escherichia coli, it became possible to simultaneously define their monosaccharide selectivity and identify the essential hydroxyls for interaction.

The origin of the high stability of 3'-terminal uridine tetrads: contributions of hydrogen bonding, stacking interactions, and steric factors evaluated using modified oligonucleotide analogs.

RNA G-quadruplexes fold almost exclusively into parallel-stranded structures and thus display much less structural diversity than their DNA counterparts. However, also among RNA G-quadruplexes peculiar structural elements can be found which are capable of reshaping the physico-chemical properties of the folded structure. A striking example is provided by a uridine tetrad (U-tetrad) placed on the 3′-terminus of the tetramolecular G-quadruplex. In this context, the U-tetrad adopts a unique conformation involving chain reversal and is responsible for a tremendous stabilization of the G-quadruplex (ΔTm up to 30°C). In this report, we attempt to rationalize the origin of this stabilizing effect by concurrent structural, thermal stability, and molecular dynamics studies of a series of G-quadruplexes with subtle chemical modifications at their 3′-termini. Our results provide detailed insights into the energetics of the “reversed” U-tetrad motif and the requirements for its formation. They point to the importance of the 2′OH to phosphate hydrogen bond and preferential stacking interactions for the formation propensity and stability of the motif.

Plasma Amine Oxidase-Induced Nanoparticle-to-Nanofiber Geometric Transformation of an Amphiphilic Peptide for Drug Encapsulation and Enhanced Bactericidal Activity.

Patients with cancer have reduced immune function and are susceptible to bacterial infection after surgery, chemotherapy, or radiotherapy. Spherical nanoparticles formed by the self-assembled peptide V6K3 can be used as carriers for poorly soluble antitumor drugs to effectively deliver drugs into tumor cells. V6K3 was designed to achieve nanoparticle-to-nanofiber geometric transformation under induction by plasma amine oxidase (PAO). PAO is commercially available and functionally similar to lysyl oxidase (LO), which is widely present in serum. After the addition of fetal bovine serum (FBS) or PAO, the secondary structure of the peptide changed, while the spherical nanoparticles stretched and transformed into nanofibers. The conversion of the self-assembled morphology reveals the susceptibility of this amphiphilic peptide to subtle chemical modifications and may lead to promising strategies to control self-assembled architecture via enzyme induction. Enzymatically self-assembled V6K3 had bactericidal properties after PAO addition that were surprisingly superior to those before PAO addition, enabling this peptide to be used to prevent infection. The amphiphilic peptide V6K3 displayed antitumor properties and low toxicity in mammalian cells, demonstrating good biocompatibility, as well as bactericidal properties, to prevent bacterial contamination. These advantages indicate that enzymatically self-assembled V6K3 has great biomedical application potential in cancer therapy.

Synthesis, characterization and use of benzothioxanthene imide based dimers.

The synthesis of benzothioxanthene imide based dimers is reported herein. Subtle chemical modifications were carried out and their impact on the optical and electrochemical properties was investigated for a better structure-property relationship analysis. The icing on the cake was that these new structures were used as light emitting materials for the fabrication and demonstration of the first BTXI-based OLEDs.