Reductant-Induced Free Radical Fluoroalkylation of Nitrogen Heterocycles and Innate Aromatic Amino Acid Residues in Peptides and Proteins

A series of fluoroalkylated cyclic λ³-iodanes and their hydrochloride salts was prepared and used in a combination with sodium ascorbate in buffer or aqueous methanol mixtures for radical fluoroalkylation of a range of substituted indoles, pyrroles, tryptophan or its derivatives, and Trp residues in peptides. As demonstrated on several peptides, the aromatic amino acid residues of Trp, Tyr, Phe, and His are targeted with high selectivity to Trp. The functionalization method is biocompatible, mild, rapid, and transition-metal-free. The proteins myoglobin, ubiquitin, and human carbonic anhydrase I were also successfully functionalized.     

Harnessing Aromatic-Histidine Interactions through Synergistic Backbone Extension and Side Chain Modification

Peptide engineering efforts have delivered drugs for diverse human diseases. Side chain alteration is among the most common approaches to designing new peptides for specific applications. The peptide backbone can be modified as well, but this strategy has received relatively little attention. Here we show that new and favorable contacts between a His side chain on a target protein and an aromatic side chain on a synthetic peptide ligand can be engineered by rational and coordinated side chain modification and backbone extension. Side chain modification alone was unsuccessful. Binding measurements, high-resolution structural studies and pharmacological outcomes all support the synergy between backbone and side chain modification in engineered ligands of the parathyroid hormone receptor-1, which is targeted by osteoporosis drugs. These results should motivate other structure-based designs featuring coordinated side chain modification and backbone extension to enhance the engagement of peptide ligands with target proteins.     

Synthesis of Carbocycles via Intramolecular Conjugate Additions: Another Solution to the Terpenoid Side Chain Stereochemistry Problem

Intramolecular conjugate additions of keto esters 7-11, mediated by pyrrolidine-acetic acid, provide perhydroindans or bicyclo[6.3.0]undecanes with high levels of diastereoselectivity at the acyclic stereogenic center. Levels of acyclic diastereoselection depend on starting unsaturated ester olefin geometry.     

Characterization and Diagnostic Value of Amino Acid Side Chain Neutral Losses Following Electron-Transfer Dissociation

Using a large set of high mass accuracy and resolution ETD tandem mass spectra, we characterized ETD-induced neutral losses. From these data we deduced the chemical formula for 20 of these losses. Many of them have been previously observed in electron-capture dissociation (ECD) spectra, such as losses of the side chains of arginine, aspartic acid, glutamic acid, glutamine, asparagine, leucine, histidine, and carbamidomethylated cysteine residues. With this information, we examined the diagnostic value of these amino acid-specific losses. Among 1285 peptide–spectrum matches, 92.5% have agreement between neutral loss-derived peptide amino acid composition and the peptide sequences. Moreover, we show that peptides can be uniquely identified by using only the accurate precursor mass and amino acid composition based on neutral losses; the median number of sequence candidates from an accurate mass query is reduced from 21 to 8 by adding side chain loss information. Besides increasing confidence in peptide identification, our findings suggest the potential use of these diagnostic losses in ETD spectra to improve false discovery rate estimation and to enhance the performance of scoring functions in database search algorithms.     

The Impact of Amino Acid Side Chain Mutations in Conformational Design of Peptides and Proteins

Local energetic effects of amino acid replacements are often considered to have only a moderate influence on the backbone conformation of proteins or peptides. As these effects are difficult to determine experimentally, no comparison has yet been performed. However, knowledge of the influence of side chain mutations is essential in protein homology modeling and in optimizing biologically active peptide ligands in medicinal chemistry. Furthermore, the tool of N‐methylation of peptides is of increasing importance for the design of peptidic drugs to gain oral availability or receptor selectivity. However, N‐methylation is often accompanied by considerable population of cis‐peptide bond structures, resulting in completely different conformations compared with the parent peptide. To retain a favored structure, it might be important to understand the effect of different side chains on the backbone conformation and to enable the introduction of an N‐methylation at the right position without disturbing a biologically active conformation. In order to detect even small energetic effects due to side chain mutations, we employed a trick to investigate the structural equilibrium of a selected cyclic pentapeptide in which two conformations are equally populated. Very small energetic differences between both conformations could easily be determined experimentally by identifying shifts in the population of both isomers.     

Protonated Dipeptide Losses from b 5 and b 4 Ions of Side Chain Hydroxyl Group Containing Pentapeptides

In this study, C-terminal protonated dipeptide eliminations were reported for both b ₅ and b ₄ ions of side chain hydroxyl group (–OH) containing pentapeptides. The study utilized the model C-terminal amidated pentapeptides having sequences of XGGFL and AXVYI, where X represents serine (S), threonine (T), glutamic acid (E), aspartic acid (D), or tyrosine (Y) residue. Upon low-energy collision-induced dissociation (CID) of XGGFL (where X?=?S, T, E, D, and Y) model peptide series, the ions at m/z 279 and 223 were observed as common fragments in all b ₅ and b ₄ ion (except b ₄ ion of YGGFL) mass spectra, respectively. By contrast, peptides, namely S_MeGGFL-NH₂ and E_OMeGGFL-NH₂, did not show either the ion at m/z 279 or the ion at m/z 223. It is shown that the side chain hydroxyl group is required for the possible mechanism to take place that furnishes the protonated dipeptide loss from b ₅ and b ₄ ions. In addition, the ions at m/z 295 and 281 were detected as common fragments in all b ₅ and b ₄ ion (except b ₄ ion of AYVYI) mass spectra, respectively, for AXVYI model peptide series. The MS⁴ experiments exhibited that the fragment ions at m/z 279, 223, 295, and 281 entirely reflect the same fragmentation behavior of [M?+?H]⁺ ion generated from commercial dipeptides FL-OH, GF-OH, YI-OH, and VY-OH. These novel eliminations reported here for b ₅ and b ₄ ions can be useful in assigning the correct and reliable peptide sequences for high-throughput proteomic studies.

肽链体系中的长程电子转移: 多肽构象和旁链间距对电子转移矩阵元的影响

用AM1半经验方法,优化了吲哚和苯酚中性分子、正离子自由基和负离子自由基的几何构型。用线性反应坐标近似和溶剂效庆的类导体屏蔽模型（COSMO）构造吲哚正离子和苯酚中性分子间电子转移的双势阱,用以估算多肽链中色氨酸和酪氨酸之间的电子转移的反应热和内重组能。优化TrpH-(Pro)n-TyrOH(n=0-3)多肽模型分子的结构和构象,用能级分裂因子的极小值方法计算了这些多肽体系的电子转移矩阵元。     

Anchor Residues Guide Form and Function in Grafted Peptides

Loops at protein–protein interfaces are a rich source of peptide leads that have high specificity and low toxicity. Although such peptides typically need to be constrained to overcome thermodynamic and metabolic limitations, design guidelines to obtain a successfully constrained peptides, and thus facilitate the transition from loop to drug, are relatively poorly formulated. In this work, we surveyed the structures of interface loops and found the position of the terminal residues to be a key determinant of conformation. We used this knowledge to improve the process of molecular grafting, a valuable approach for constraining and stabilising peptides by fusing them to a suitable scaffold. We show that an informed choice of where a loop is “anchored” to a scaffold improves its form and function. This knowledge can help guide the choice of loop and its matching scaffold, and thus increase the success rate for designing stable and potent peptide drug leads.     

Ethynylation of Cysteine Residues: From Peptides to Proteins in Vitro and in Living Cells

Current approaches to introduce terminal alkynes for bioorthogonal reactions into biomolecules still present limitations in terms of either reactivity, selectivity, or adduct stability. We present a method for the ethynylation of cysteine residues based on the use of ethynylbenziodoxolone (EBX) reagents. The acetylene group is directly introduced onto the thiol group of cysteine and can be used for copper‐catalyzed alkyne‐azide cycloaddition (CuAAC) without further processing. Labeling proceeded with reaction rates comparable to or higher than the most often used iodoacetamide on peptides or maleimide on the antibody trastuzumab, and high cysteine selectivity was observed. The reagents were also used in living cells for cysteine proteomic profiling and displayed improved coverage of the cysteinome compared to previously reported iodoacetamide or hypervalent iodine reagents. Fine‐tuning of the EBX reagents allows optimization of their reactivity and physical properties.     

侧链含酞菁铜功能基的聚苯胺的制备与性能研究

以酞菁铜、氯磺酸和氯化亚砜为原料合成酞菁铜磺酰氯,并将其与本征态聚苯胺进行反应,合成了侧链悬挂酞菁铜功能基的聚苯胺(PAnCuPc).用元素分析、红外光谱和紫外-可见吸收光谱对产物和反应中间体进行了结构表征.PAnCuPc可溶于强极性非质子溶剂.如NMP,DMF,DMSO和DMAc,甚至在常用的低沸点溶剂如THF和三氯甲烷中也有一定的溶解性.红外光谱研究表明,与本征态聚苯胺相比,侧链含酞菁铜功能基的聚苯胺的吸收峰向低频方向移动.紫外-可见吸收光谱表明,侧链悬挂酞菁铜功能基的聚苯胺在可见光区和近红外区都具有较强的吸收.透射电镜和X射线衍射研究表明,该产物具有较强的结晶性能.     

螯合树脂研究——Ⅷ.以聚硫醚为主链的氧杂多乙烯多胺型螯合树脂的合成及其吸附性能

由聚[2′-氯乙基-2,3-环硫丙基醚]和多乙烯声胺反应,合成了四种以聚硫醚为主链的氧杂多乙烯多胺型螯合树脂,它们对贵金属离子Au(Ⅲ)、Pd(Ⅱ)、Pt(Ⅳ)、Ag~+等具有优良的吸附性能。     

Revisiting Chain Transfer to Polymer and Branching in Controlled Radical Polymerization of Butyl Acrylate

Acrylic monomers undergo chain transfer to polymer during polymerization leading to branched and even gelled polymers. It has been experimentally demonstrated that the extent of branching is higher for conventional free radical polymerization than for controlled radical polymerization (ATRP, RAFT, NMP) and this has been qualitatively explained in terms of the differences in the concentrations of highly reactive short‐chain radicals between controlled and conventional radical polymerizations. Contrary to this explanation, in this work, it is quantitatively demonstrated that the short transient lifetime of the radicals, i.e., the time between activation and deactivation of the radical in controlled radical polymerization, is the cause for the low level of branching in these polymerizations.

     

An Alkenyl Boronate as a Monomer for Radical Polymerizations: Boron as a Guide for Chain Growth and as a Replaceable Side Chain for Post‐Polymerization Transformation

The ability of isopropenyl boronate pinacol ester to serve as a monomer in radical polymerizations was established and exploited for the synthesis of polymers that are difficult to access using other polymerization techniques. Although the monomer exhibits an α‐methyl‐substituted unconjugated structure, which is usually unfavorable for radical propagation, both free and controlled radical polymerizations smoothly afford the corresponding polymers. A density‐functional‐theory‐based investigation revealed that the boron atom moderately stabilizes the radical species, which leads to the suppression of the degradative chain transfer to the α‐methyl groups, and thus guides the reaction towards the radical polymerization. The boronyl pendants, which are directly attached to the polymer backbone, can be replaced with ‐OH or ‐NH₂ to yield poly(α‐methyl vinyl amine) or poly(α‐methyl vinyl alcohol), which has been inaccessible by conventional synthetic methods.     

Calculations of Monomer Conversion and Radical Concentration in Reversible Addition‐Fragmentation Chain Transfer Radical Polymerization

Simple expressions are derived for the development of monomer conversion, as well as propagating radical, adduct radical, dormant chain, and dead chain concentrations in reverse addition‐fragmentation transfer polymerization (RAFT). The relations for the profiles of propagating radical concentration and conversion versus time are derived and depend on group parameters of rate constants and chemical recipe. The analytical equations are verified against numerical solutions of the mass‐balance differential equations. This derivation involves the steady‐state hypothesis for radical and RAFT agent concentrations. The errors introduced by these assumptions are negligible when the fragmentation rate constant, k_f, is higher than 10 s⁻¹ or when the cross‐termination rate constant, k_ct, is higher than 10⁵ L · mol⁻¹ s⁻¹.

Calculated concentration profiles (points: numerical, lines: analytical) of propagating radical R, adduct radical A, dormant T, and dead D (= P + P′) chains.