Incorporation of phenylcarbonyl groups in the sidechain: A tool to induce ordered assembly of peptides on surfaces.

The possibility of introducing various functionalities on peptides with relative ease allows them to be used for molecular applications. However, oligopeptides prepared entirely from proteinogenic amino acids seldom assemble as ordered structures on surfaces. Therefore, sidechain modifications of peptides that can increase the intermolecular interactions without altering the constitution of a given peptide become an attractive route to self-assembling them on surfaces. We find that replacing phenylalanine residues with unusual amino acids that have phenylcarbonyl sidechains in oligopeptides increases the formation of ordered self-assembly on a highly ordered pyrolytic graphite surface. Peptides containing the modified amino acids provided extended long-range ordered assemblies, while the analogous peptides containing phenylalanine residues failed to form long-range assemblies. X-ray crystallographic analysis of the bulk structures of these peptides and the analogous peptides containing phenylalanine residues reveal that such modifications do not alter the secondary structure in crystals. It also reveals that the secondary hydrogen bonding interaction through phenylcarbonyl sidechains facilitates extended growth of the peptides on graphite.

Amphiphilic conjugates of ferrocene with amino acids and peptides: Design, synthesis, and studies on their aggregation behavior.

A new class of ferrocenyl surfactants based on covalent linkage between amino acids or peptides and ferrocene was designed. Accordingly, five ferrocenyl amphiphiles, FcS1-5, were synthesized, and their aggregation behaviors in aqueous solutions were studied. Compared to the other surfactants containing ferrocenyl units, FcS have a relatively smaller size and low molecular weight and are easy to synthesize. The influences of the number of carboxylic acid head groups and the number of Fc group in the hydrophobic tail, on the stability and aggregation behavior of these amphiphiles in aqueous medium, were explored to deduce the structure property relationships. A combination of fluorescence and dynamic light scattering techniques was used to elucidate the behavior of these molecules. A good agreement between the results obtained using different techniques was observed.

d-Prolyl-2-(trifluoromethylsulfonamidopropyl)pyrrolidine: An Organocatalyst for Asymmetric Michael Addition of Aldehydes to ß-Nitroalkenes at Ambient Conditions.

Four 2-(trifluoromethylsulfonamidoalkyl)pyrrolidines and their d-prolinamides were prepared and screened as organocatalysts for the Michael addition reaction of aldehydes with ß-nitroalkenes at rt and without the use of additives. d-Prolyl-2-(trifluoromethylsulfonamidopropyl)pyrrolidine was found to be the best among the molecules studied, which yielded γ-nitro aldehydes in very high yields (up to 95%), with high diastereoselectivity (up to >99:1) and with up to 97% ee.

Synthesis of peptides containing oxo amino acids and their crystallographic analysis.

An isolated uncharged hydrogen bond acceptor such as the carbonyl functionality of an aldehyde or a keto group is absent in natural amino acids. Although glutamine and asparagine are known to hydrogen bond through the amide carbonyl group in their side chains, they also possess the amide NH2 group, which can act as a hydrogen bond donor. This makes the structural study of peptides containing an oxo residue, with an isolated carbonyl group in the side chain, interesting. Here, we report the synthesis of δ- and ε-oxo amino acids and their incorporation into oligopeptides as the N-terminal residue. The resultant oxo peptides were extensively studied using X-ray crystallography to understand the interactions offered by the oxo group in peptide crystals. We find that the oxo groups are capable of providing additional hydrogen bonding opportunities to the peptides, resulting in increased intermolecular interactions in crystals. The study thus offers avenues for the utilization of oxo residues to introduce intermolecular interactions in synthetic peptides.

Enantioselective Synthesis of 2-Aminomethyl and 3-Amino Pyrrolidines and Piperidines through 1,2-Diamination of Aldehydes.

An efficient method for the synthesis of 1,2-diamines from aldehydes through proline-catalyzed asymmetric α-amination followed by reductive amination is reported. The products resemble those obtained through direct asymmetric diamination of terminal alkenes. The methodology is used to synthesize 2-aminomethyl and 3-amino pyrrolidines and piperidines in high yields and with a good enantioselectivity. The usefulness of the method is demonstrated through the synthesis of a 2-aminomethyl iminocyclitol.

Click Chemistry Route to the Synthesis of Unusual Amino Acids, Peptides, Triazole-Fused Heterocycles and Pseudodisaccharides.

Conjugation of different molecular species using copper(I)-catalyzed click reaction between azides and terminal alkynes is among the best available methods to prepare multifunctional compounds. The effectiveness of this method has provided wider acceptance to the concept of click chemistry, which is now widely employed to synthesize densely functionalized organic molecules. This article summarizes the contributions from our group in the development of new methods for the synthesis of functional molecules using copper(I)-catalyzed click reactions. We have developed very efficient methods for the synthesis of peptides and amino acids conjugated with carbohydrates, thymidine and ferrocene. We have also developed an efficient strategy to synthesize triazole-fused heterocycles from primary amines, amino alochols and diols. Finally, an interesting method for the synthesis of pseudodisaccharides linked through triazoles, starting from carbohydrate-derived donor-acceptor cyclopropanes is discussed.

Diastereoselective Synthesis of 1-Deoxygalactonojirimycin, 1-Deoxyaltronojirimycin, and N-Boc-(2S,3S)-3-Hydroxypipecolic Acid via Proline Catalyzed α-Aminoxylation of Aldehydes.

An efficient synthesis of deoxygalactonojirimycin and deoxyaltronojirimycin through the use of proline catalyzed asymmetric α-aminoxylation of a higher homologue of Garner's aldehyde, derived from l-aspartic acid, is reported. The method is also used for a highly diastereoselective synthesis of the N-Boc derivative of (2S,3S)-3-hydroxypipecolic acid. The configuration of the proline catalyst used for the asymmetric aminoxylation step ultimately controls the absolute configuration of three adjacent stereogenic centers in the final products.

Divergent synthesis of various iminocyclitols from D-ribose.

A very efficient route to the diastereoselective synthesis of polyhydroxy pyrrolidines, piperidines and azepanes from an aldehyde derivative of ribose is reported. Asymmetric α-amination of aldehydes using proline catalysed hydrazination is the key step in the synthesis. The method utilizes the stereocenters present in ribose and the extra carbon atoms present in the target molecules are incorporated using Wittig reactions. The incorporation of the amino group is carried out asymmetrically to account for additional stereocenters. This synthetic route to iminocyclitols has the potential to be extended for the synthesis of a large class of such compounds starting from other sugar derived aldehydes.

Synthesis of stable C-linked ferrocenyl amino acids and their use in solution-phase peptide synthesis.

Incorporation of ferrocenyl group to peptides is an efficient method to alter their hydrophobicity. Ferrocenyl group can also act as an electrochemical probe when incorporated onto functional peptides. Most often, ferrocene is incorporated onto peptides post-synthesis via amide, ester or triazole linkages. Stable amino acids containing ferrocene as a C-linked side chain are potentially useful building units for the synthesis of ferrocene-containing peptides. We report here an efficient route to synthesize ferrocene-containing amino acids that are stable and can be used in peptide synthesis. Coupling of 2-ferrocenyl-1,3-dithiane and iodides derived from aspartic acid or glutamic acid using n-butyllithium leads to the incorporation of a ferrocenyl unit to the δ-position or ε-position of an α-amino acid. The reduction or hydrolysis of the dithiane group yields an alkyl or an oxo derivative. The usability of the synthesized amino acids is demonstrated by incorporating one of the amino acids in both C-terminus and N-terminus of tripeptides in solution phase.

A highly efficient catalyst for selective oxidative scission of olefins to aldehydes: abnormal-NHC-Ru(II) complex in oxidation chemistry.

The utility and selectivity of the catalyst [Ru(COD)(L(1))Br2] (1) bearing a fused π-conjugated imidazo[1,2-a][1,8]naphthyridine-based abnormal N-heterocyclic carbene ligand L(1) is demonstrated toward selective oxidation of C═C bonds to aldehydes and C≡C bonds to α-diketones in an EtOAc/CH3CN/H2O solvent mixture at room temperature using a wide range of substrates, including highly functionalized sugar- and amino acid-derived compounds.

Enhancing Photocatalytic Attributes of Perovskite Nanocrystals in Aqueous Media via Ligand Engineering.

The remarkable catalytic potential of perovskite nanocrystals (NCs) remains underutilized due to their limited stability in polar media, resulting from the vulnerability of their structure to disruption by polar solvents. In this study, we address this challenge by employing the bolaamphiphilic NKE-12 ligand, which features multiple denticities to effectively shield the surface of CsPbBr3 NCs from polar solvent interactions without compromising their light-harvesting properties. Our research, utilizing electrochemical impedance and photocurrent response measurements, highlights efficient charge separation and charge transfer enabled by NKE-12 ligands, which feature multiple ionic groups and peptide bonds, compared to conventional oleylamine/oleic acid ligands on CsPbBr3 NCs. Through the utilization of purely ligand-derived water-dispersed CsPbBr3/NKE-12 NCs, we successfully showcased their photocatalytic activity for acrylamide polymerization. A series of control experiments unveil a radical-based reaction pathway and suggest the synergistic involvement of photogenerated electrons and holes in producing the O2·- and OH· free radicals, respectively. Our findings emphasize the crucial role of ligand engineering in stabilizing perovskites in water and harnessing their exceptional photocatalytic attributes. This study opens new avenues for applying perovskite NCs in various catalytic processes in polar media.

Powerful binders for the D-dimer by conjugation of the GPRP peptide to polypeptides from a designed set--illustrating a general route to new binders for proteins.

The synthetic tetrapeptide GPRP based on the amino-terminal GPR sequence of the fibrin α-chain binds the D-dimer protein with a dissociation constant K(D) of 25 µM. The D-dimer protein, a well-known biomarker for thrombosis, contains two cross-linked D fragments from the fibrinogen protein formed upon degradation of the fibrin gel, the core component of blood clots. In order to develop a specific high-affinity binder for the D-dimer protein, GPRP was conjugated via an aliphatic spacer to each member of a set of sixteen polypeptides designed for the development of binder molecules for proteins in general. The binders were individually characterized and ranked using surface plasmon resonance (SPR) analysis. The dissociation constant of the complex formed from the D-dimer and 4-D15L8-GPRP labeled with fluorescein was determined by fluorescense titration and found to be 3 nM, an affinity 4 orders of magnitude higher than that of free GPRP. According to SPR analysis, binding was completely inhibited by free GPRP at mM concentrations and the polypeptide conjugate was therefore shown to bind specifically to the binding site of GPRP. Affinities were further enhanced by dimerization of the polypeptide conjugates via a bifunctional linker resulting in dissociation constants that were further decreased (affinities increased) by factors of 2-4. The results suggest an efficient route to specific binders for proteins based on short peptides with affinities that need only to be modest, thus shortening the time of binder development dramatically.

An improved procedure for the synthesis of dehydroamino acids and dehydropeptides from the carbonate derivatives of serine and threonine using tetrabutylammonium fluoride.

Dehydroamino acids are important precursors for the synthesis of a number of unnatural amino acids and are structural components in many biologically active peptide derivatives. However, efficient synthetic procedures for their production in large amounts and without side reactions are limited. We report here an improved procedure for the synthesis of dehydroalanine and dehydroamino butyric acid from the carbonate derivatives of serine and threonine using TBAF. The antiselective E(2) elimination of the carbonate derivatives of serine and threonine using TBAF is milder and more efficient than other available procedures. The elimination reaction is completed in less than 10 min with various carbonate derivatives studied and the methodology is very efficient for the synthesis of dehydroamino acids and dehydropeptides. The procedure thus provides an easy access to key synthetic precursors and can be used to introduce interesting structural elements to designed peptides.

Revealing the Limits of Intermolecular Interactions: Molecular Rings of Ferrocene Derivatives on Graphite Surface.

We report the formation of discrete molecular rings/spirals of small molecules (1,3-dithia derivatives of ferrocene) on a highly oriented pyrolytic graphite (HOPG) surface. On the basis of microscopy and theoretical calculations, molecular level arrangement within the molecular rings is understood. The molecular rings show a limiting inner diameter, and we interpret it to be related to the critical intermolecular interaction limit. This limiting value of the inner diameter is surprisingly correlated with that observed for molecular rings/disks of a few reported molecules. The correlation reveals that molecular rings formed typically by weak van der Waals interactions should always show a limiting inner diameter and should be independent of molecular structure, size, and chemical nature.

Development and characterization of lysine based tripeptide analogues as inhibitors of Sir2 activity.

Sirtuins are NAD(+) dependent deacetylases that modulate various essential cellular functions. Development of peptide based inhibitors of Sir2s would prove useful both as pharmaceutical agents and as effectors by which downstream cellular alterations can be monitored. Click chemistry that utilizes Huisgen's 1,3-dipolar cycloaddition permits attachment of novel modifications onto the side chain of lysine. Herein, we report the synthesis of peptide analogues prepared using click reactions on Nepsilon-propargyloxycarbonyl protected lysine residues and their characterization as inhibitors of Plasmodiumfalciparum Sir2 activity. The peptide based inhibitors exhibited parabolic competitive inhibition with respect to acetylated-peptide substrate and parabolic non-competitive inhibition with NAD(+) supporting the formation of EI(2) and E.NAD(+).I(2) complexes. Cross-competition inhibition analysis with the non-competitive inhibitor nicotinamide (NAM) ruled out the possibility of the NAM-binding site being the second inhibitor binding site, suggesting the presence of a unique alternate pocket accommodating the inhibitor. One of these compounds was also found to be a potent inhibitor of the intraerythrocytic growth of P.falciparum with 50% inhibitory concentration in the micromolar range.

One-pot protection and activation of amino acids using pentafluorophenyl carbonates.

Protection of the amino group and activation of the carboxylic acid groups are the most important steps associated with any peptide synthesis protocol; hence, a one-pot process to achieve these is highly desirable. A possible strategy is to use pentafluorophenyl carbonates to simultaneously protect the amino group as a carbamate derivative and activate the carboxylic acid group as a pentafluorophenyl ester. A detailed study is carried out to understand the scope and limitations of this method using five different pentaflurophenyl carbonates. The efficiency of these one-pot reactions depends largely on the nature of the pentafluorophenyl carbonates and also on the nature of the amino acids. Electron deficient and sterically less demanding carbonates reacted faster than the others, whereas amino acids with longer aliphatic side chains gave better yields than more polar amino acids.

A bromo-capped diruthenium(i,i) N-heterocyclic carbene compound for in situ bromine generation with NBS: catalytic olefin aziridination reactions.

A bromo-capped metal-metal bonded diruthenium(i,i) complex Ru2(CO)4(PIN)2Br2 (1) (PIN = 1-isopropyl-3-(5,7-dimethyl-1,8-naphthyrid-2-yl)imidazol-2-ylidene) generates bromine with N-bromosuccinimide (NBS) at room temperature. Cycloalkene and stilbene are readily brominated by stoichiometric reactions with 1 and NBS. An analysis of the dibrominated products suggests the formation of cyclic bromonium intermediates indicating in situ Br2 generation. Complex 2, an iodide analogue of 1, is also synthesized. The reaction of 2 with N-iodosuccinimide releases I2, which is confirmed by the starch-iodine test. The catalytic utility of 1 is examined for the bromination of phenol. Catalyst 1, in combination with NBS and base, exhibits regioselectivity towards monobrominated products. Furthermore, efficient olefin aziridination is demonstrated utilizing catalyst 1 in the presence of NBS, K2CO3 and TsNH2.

Diastereoselective synthesis of furanose and pyranose substituted glycine and alanine derivatives via proline-catalyzed asymmetric α-amination of aldehydes.

A concise organocatalytic route toward the synthesis of furanose and pyranose substituted glycine and alanine derivatives is reported. These compounds are core structural units of some of the naturally available antibiotics and antifungal agents. Proline-catalyzed asymmetric α-amination of aldehydes derived from sugars is used as the key reaction to synthesize twelve sugar amino acid derivatives. The asymmetric transformations proceeded in good yields and with good to excellent diastereoselectivity. The application of the synthesized amino acids is demonstrated by synthesizing a tripeptide containing one of them.

Applications of propargyl esters of amino acids in solution-phase Peptide synthesis.

Propargyl esters are employed as effective protecting groups for the carboxyl group during solution-phase peptide synthesis. The propargyl ester groups can be introduced onto free amino acids by treating them with propargyl alcohol saturated with HCl. The reaction between propargyl groups and tetrathiomolybdate is exploited to deblock the propargyl esters. The removal of the propargyl group with the neutral reagent tetrathiomolybdate ensures that most of the other protecting groups used in peptide synthesis are untouched. Both acid labile and base labile protecting groups can be removed in the presence of a propargyl ester. Amino acids protected as propargyl esters are employed to synthesize di- to tetrapeptides in solution-phase demonstrating the possible synthetic utilities of the methodology. The methodology described here could be a valuable addition to currently available strategies for peptide synthesis.