Carboxylic Acid Side Chain Research Articles

A switchable stapled peptide.

The O-N acyl transfer reaction has gained significant popularity in peptide and medicinal chemistry. This reaction has been successfully applied to the synthesis of difficult sequence-containing peptides, cyclic peptides, epimerization-free fragment coupling and more recently, to switchable peptide polymers. Herein, we describe a related strategy to facilitate the synthesis and purification of a hydrophobic stapled peptide. The staple consists of a serine linked through an amide bond formed from its carboxylic acid function and the side chain amino group of diaminopropionic acid and through an ester bond formed from its amino group and the side chain carboxylic acid function of aspartic acid. The α-amino group of serine was protonated during purification. Interestingly, when the peptide was placed at physiological pH, the free amino group initiated the O-N shift reducing the staple length by one atom, leading to a more hydrophobic stapled peptide.

Molecular dynamics simulation study of carboxylated and sulfonated poly(arylene ether sulfone) membranes for fuel cell applications

The performance of poly(arylene ether sulfone) as a proton exchange membrane, for application in a fuel cell, such as carboxylic acid side chain effects on the structural and dynamical properties have been studied by molecular dynamics simulation at 353 K. Different percentage of carboxylated monomer were simulated and the radial distribution function, water cluster size and mean square displacement were evaluated. The results showed that monomer carboxylation up to 10%, decreased the conductivity according to vehicular mechanism and then at 15% of monomer carboxylation the conductivity increased. Also, the greatest water clusters were formed at 15% carboxylated monomer and the increase in acidic sites made the polymer more hydrophilic. In addition, the diffusion and solubility of the gases, O2 and H2, into the membrane were studied and the results indicated that H2 has a higher diffusion coefficient than O2 and the diffusion phenomenon has a determining effect on the performance of proton exchange membrane.

Zanamivir Amidoxime- and N-Hydroxyguanidine-Based Prodrug Approaches to Tackle Poor Oral Bioavailability

The neuraminidase (NA) inhibitor zanamivir (1) is potently active against a broad panel of influenza A and B strains, including mutant viruses, but suffers from pharmacokinetic (PK) shortcomings. Here, distinct prodrug approaches are described that aimed at overcoming zanamivir's lack of oral bioavailability. Lowering the high basicity of the 4-guanidino group in zanamivir and of a bioisosteric 4-acetamidine analog (5) by N-hydroxylation was deemed to be a plausible tactic. The carboxylic acid and glycerol side chain were also masked with different ester groups. The bioisosteric amidine 5 turned out to be potently active against a panel of H1N1 (IC50 = 2-10 nM) and H3N2 (IC50 = 5-10 nM) influenza A viruses (NA inhibition assay). In vitro PK studies showed that all prodrugs were highly soluble, exhibited low protein binding, and were bioactivated by N-reduction to the respective guanidines and amidines. The most promising prodrug candidates, amidoxime ester 7 and N-hydroxyguanidine ester 8, were subjected to in vivo bioavailability studies. Unfortunately, both prodrugs were not orally bioavailable to a convincing degree (F ≤ 3.7%, rats). This finding questions the general feasibility of improving the oral bioavailability of 1 by lipophilicity-increasing prodrug strategies, and suggests that intrinsic structural features represent key hurdles.

An efficient strategy for the synthesis of syn 1,3-diols via iterative acetate aldol reactions and synthesis of atorvastatin lactone

An efficient strategy for the synthesis of syn 1,3-diol has been developed, employing an imidazolidinone based chiral auxiliary via stereoselective and sequential double acetate aldol reactions. The syn 1,3-diol subunit was modified to obtain the C-7 carboxylic acid side chain and further subjected to reaction with a suitable 1,4-diketone under Paal-Knorr conditions to obtain atorvastatin lactone.

Lasso peptides: an intriguing class of bacterial natural products.

Natural products of peptidic origin often represent a rich source of medically relevant compounds. The synthesis of such polypeptides in nature is either initiated by deciphering the genetic code on the ribosome during the translation process or driven by ribosome-independent processes. In the latter case, highly modified bioactive peptides are assembled by multimodular enzymes designated as nonribosomal peptide synthetases (NRPS) that act as a protein-template to generate chemically diverse peptides. On the other hand, the ribosome-dependent strategy, although relying strictly on the 20-22 proteinogenic amino acids, generates structural diversity by extensive post-translational-modification. This strategy seems to be highly distributed in all kingdoms of life. One example for this is the lasso peptides, which are an emerging class of ribosomally assembled and post-translationally modified peptides (RiPPs) from bacteria that were first described in 1991. A wide range of interesting biological activities are known for these compounds, including antimicrobial, enzyme inhibitory, and receptor antagonistic activities. Since 2008, genome mining approaches allowed the targeted isolation and characterization of such molecules and helped to better understand this compound class and their biosynthesis. Their defining structural feature is a macrolactam ring that is threaded by the C-terminal tail and held in position by sterically demanding residues above and below the ring, resulting in a unique topology that is reminiscent of a lariat knot. The ring closure is achieved by an isopeptide bond formed between the N-terminal α-amino group of a glycine, alanine, serine, or cysteine and the carboxylic acid side chain of an aspartate or glutamate, which can be located at positions 7, 8, or 9 of the amino acid sequence. In this Account, we discuss the newest findings about these compounds, their biosynthesis, and their physicochemical properties. This includes the suggested mechanism through which the precursor peptide is enzymatically processed into a mature lasso peptide and crucial residues for enzymatic recognition. Furthermore, we highlight new insights considering the protease and thermal stability of lasso peptides and discuss why seven amino acid residue rings are likely to be the lower limit feasible for this compound class. To elucidate their fascinating three-dimensional structures, NMR spectroscopy is commonly employed. Therefore, the general methodology to elucidate these structures by NMR will be discussed and pitfalls for these approaches are highlighted. In addition, new tools provided by recent investigations to assess and prove the lasso topology without a complete structure elucidation will be summarized. These include techniques like ion mobility-mass spectrometry and a combined approach of thermal and carboxypeptidase treatment with subsequent LC-MS analysis. Nevertheless, even though much was learned about these compounds in recent years, their true native function and the exact enzymatic mechanism of their maturation remain elusive.

TRNA acceptor stem and anticodon bases form independent codes related to protein folding

Aminoacyl-tRNA synthetases recognize tRNA anticodon and 3' acceptor stem bases. Synthetase Urzymes acylate cognate tRNAs even without anticodon-binding domains, in keeping with the possibility that acceptor stem recognition preceded anticodon recognition. Representing tRNA identity elements with two bits per base, we show that the anticodon encodes the hydrophobicity of each amino acid side-chain as represented by its water-to-cyclohexane distribution coefficient, and this relationship holds true over the entire temperature range of liquid water. The acceptor stem codes preferentially for the surface area or size of each side-chain, as represented by its vapor-to-cyclohexane distribution coefficient. These orthogonal experimental properties are both necessary to account satisfactorily for the exposed surface area of amino acids in folded proteins. Moreover, the acceptor stem codes correctly for β-branched and carboxylic acid side-chains, whereas the anticodon codes for a wider range of such properties, but not for size or β-branching. These and other results suggest that genetic coding of 3D protein structures evolved in distinct stages, based initially on the size of the amino acid and later on its compatibility with globular folding in water.

Chemical Synthesis of O-Glycosylated Human Interleukin-2 by the Reverse Polarity Protection Strategy.

The chemical synthesis of human interleukin-2 (IL-2) , having a core 1 sugar, by a ligation method is reported. Although IL-2 is a globular glycoprotein, its C-terminal region, in particular (99-133), is extremely insoluble when synthesized by solid-phase method. To overcome this problem, the side-chain carboxylic acid of the Glu residues was protected by a picolyl ester, thus reversing its polarity from negative to positive. This reverse polarity protection significantly increased the isoelectric point of the peptide segment and made it positive under acidic conditions and facilitated the purification. An efficient method to prepare the prolyl peptide thioester required for the synthesis of the (28-65) segment was also developed. These efforts resulted in the total synthesis of the glycosylated IL-2 having full biological activity.

The Hypothesis that the Genetic Code Originated in Coupled Synthesis of Proteins and the Evolutionary Predecessors of Nucleic Acids in Primitive Cells.

Although analysis of the genetic code has allowed explanations for its evolution to be proposed, little evidence exists in biochemistry and molecular biology to offer an explanation for the origin of the genetic code. In particular, two features of biology make the origin of the genetic code difficult to understand. First, nucleic acids are highly complicated polymers requiring numerous enzymes for biosynthesis. Secondly, proteins have a simple backbone with a set of 20 different amino acid side chains synthesized by a highly complicated ribosomal process in which mRNA sequences are read in triplets. Apparently, both nucleic acid and protein syntheses have extensive evolutionary histories. Supporting these processes is a complex metabolism and at the hub of metabolism are the carboxylic acid cycles. This paper advances the hypothesis that the earliest predecessor of the nucleic acids was a β-linked polyester made from malic acid, a highly conserved metabolite in the carboxylic acid cycles. In the β-linked polyester, the side chains are carboxylic acid groups capable of forming interstrand double hydrogen bonds. Evolution of the nucleic acids involved changes to the backbone and side chain of poly(β-d-malic acid). Conversion of the side chain carboxylic acid into a carboxamide or a longer side chain bearing a carboxamide group, allowed information polymers to form amide pairs between polyester chains. Aminoacylation of the hydroxyl groups of malic acid and its derivatives with simple amino acids such as glycine and alanine allowed coupling of polyester synthesis and protein synthesis. Use of polypeptides containing glycine and l-alanine for activation of two different monomers with either glycine or l-alanine allowed simple coded autocatalytic synthesis of polyesters and polypeptides and established the first genetic code. A primitive cell capable of supporting electron transport, thioester synthesis, reduction reactions, and synthesis of polyesters and polypeptides is proposed. The cell consists of an iron-sulfide particle enclosed by tholin, a heterogeneous organic material that is produced by Miller-Urey type experiments that simulate conditions on the early Earth. As the synthesis of nucleic acids evolved from β-linked polyesters, the singlet coding system for replication evolved into a four nucleotide/four amino acid process (AMP = aspartic acid, GMP = glycine, UMP = valine, CMP = alanine) and then into the triplet ribosomal process that permitted multiple copies of protein to be synthesized independent of replication. This hypothesis reconciles the “genetics first” and “metabolism first” approaches to the origin of life and explains why there are four bases in the genetic alphabet.

Temporary Conversion of Protein Amino Groups to Azides: A Synthetic Strategy for Glycoconjugate Vaccines.

Conjugation of synthetic oligosaccharides and native polysaccharides to proteins is an important tool in glycobiology to create vaccines and antigens to screen lectins, toxins, and antibodies. A novel approach to potentiate and profile the immune response to vaccines involves targeting antigens directly to dendritic cells (DCs), the key cells engaged in the immunization process. Inclusion of a carbohydrate ligand recognized by C-type lectins expressed on their cell surface ensures targeting of vaccines to DCs and improved immunological responses. Here we describe a strategy that permits three sequential orthogonal conjugation reactions to prepare glycoconjugates and apply them to the synthesis of a conjugate vaccine that is targeted for uptake by DCs. The carrier protein is treated with an azo-transfer reagent to convert accessible amino groups to azide and then amide bond formation via reaction with carboxylic acid side chains is used to attach amino tether groups of a ligand to the protein. Azide-alkyne Huisgen cycloaddition conjugation, "click chemistry" is used to attach a second ligand equipped with a propargyl group or an analogous terminal alkyne, and following reduction of protein azide groups back to amine, these amino acid side chains can be subjected to amide formation such as reaction with succinimide esters or homobifunctional coupling reagents such as dialkyl squarate.

Crystal structure of 3-(3-oxo-2,3,4,4a,5,6-hexa-hydro-benzo[h]cinnolin-2-yl)propionic acid.

The asymmetric unit of the title compound, C15H16N2O3, contains two independent mol­ecules, which present a different conformation of the carb­oxy­lic acid side chain [C—C—C—OH torsion angles = 65.3 (7) and −170.1 (5)°]. In both mol­ecules, the di­hydro­pyridazinone ring adopts a geometry inter­mediate between a twisted-boat and a half-chair conformation, while the central six-membered ring is almost in a half-boat conformation. In the crystal, mol­ecules are linked by O—H⋯Ok (k = ketone) hydrogen bonds, generating [01-1] chains. Aromatic π–π stacking contacts between the benzene and the di­hydro­pyridazinone rings [centroid–centroid distance [3.879 (9) Å] are also observed.

Screen-based analysis of magnetic nanoparticle libraries formed using peptidic iron oxide ligands.

The identification of effective polypeptide ligands for magnetic iron oxide nanoparticles (IONPs) could considerably accelerate the high-throughput analysis of IONP-based reagents for imaging and cell labeling. We developed a procedure for screening IONP ligands and applied it to compare candidate peptides that incorporated carboxylic acid side chains, catechols, and sequences derived from phage display selection. We found that only l-3,4-dihydroxyphenylalanine (DOPA)-containing peptides were sufficient to maintain particles in solution. We used a DOPA-containing sequence motif as the starting point for generation of a further library of over 30 peptides, each of which was complexed with IONPs and evaluated for colloidal stability and magnetic resonance imaging (MRI) contrast properties. Optimal properties were conferred by sequences within a narrow range of biophysical parameters, suggesting that these sequences could serve as generalizable anchors for formation of polypeptide–IONP complexes. Differences in the amino acid sequence affected T1- and T2-weighted MRI contrast without substantially altering particle size, indicating that the microstructure of peptide-based IONP coatings exerts a substantial influence and could be manipulated to tune properties of targeted or responsive contrast agents. A representative peptide–IONP complex displayed stability in biological buffer and induced persistent MRI contrast in mice, indicating suitability of these species for in vivo molecular imaging applications.

The detection of iron protoporphyrin (heme b) in phytoplankton and marine particulate material by electrospray ionisation mass spectrometry – comparison with diode array detection

A mass spectrometric (MS) method for the identification of iron protoporphyrin (IX) (FePTP, heme b) in marine particulate material and phytoplankton is described. Electrospray ionisation of FePTP produced the molecular Fe(III)PTP+ ion (m/z=616) or the pseudomolecular [Fe(II)PTP + H]+ ion (m/z=617), depending on the oxidation state of the central iron ion. Collision induced dissociation (CID) in the ion trap mass spectrometer resulted in a single detected product ion (m/z=557) indicative of loss of ethanoic acid from a carboxylic acid side chain. Widening the isolation width to 616±3 resulted in production of a mass spectrum demonstrating the distinctive isotopic ratio of the iron containing fragment, further increasing the specificity of the analysis. Selective reactant monitoring (SRM) of the fragment ion (m/z=557) was applied to the detection of FePTP after chromatography of ammoniacal OGP extracts of marine samples. The detection limit for FePTP analysed by SRM after chromatography was 1.2±0.5fmol. For phytoplankton samples, reasonably good agreement was achieved between results obtained with SRM and those obtained by monitoring absorbance at λ=400nm using a diode array detector (DAD). Use of SRM for analysis of particulate material obtained from the high latitude North Atlantic allowed for the analysis of FePTP in the presence of a co-eluting compound that interfered with detection by DAD. Simultaneous collection of mass spectra from m/z=300 to 1500 resulted in identification of the pseudomolecular ion for the interfering compound. The CID fragmentation pattern and UV–visible mass spectra indicated that the interfering compound was a previously unidentified chlorin type compound. Comparison of FePTP determined by SRM and DAD on samples where this compound could not be detected showed that results collected using the two methods correlated. The use of both MS and DAD results in a powerful tool for quantifying this important biogenic component of the particulate iron pool.

Electronic and Cationic Spectroscopy of 9-Hydroxy-9-fluorene Carboxylic Acid

Resonance-enhanced multiphoton ionization spectroscopy of supersonically cooled gas-phase 9-hydroxy-9-fluorene carboxylic acid (9HFCA) is reported for its first electronic excited state, S1. The UV-UV hole-burning experiment identifies a single conformer in the molecular beam, stabilized by an intramolecular hydrogen bond. For this Cs symmetric conformer, two low frequencies in the S1 spectrum are assigned: an in-plane rocking mode of the carboxylic acid side chain lies at 58 cm(-1), and an in-plane fluorene bending mode appears at 183 cm(-1). The corresponding mode frequencies in the cation, 58 and 196 cm(-1), are measured by zero electron kinetic energy (ZEKE) spectroscopy upon pumping the S1 vibronic states. The adiabatic ionization potential is measured to be 64 923 ± 5 cm(-1). In addition, a feature established by ZEKE spectroscopy upon pumping the hot band is found at 67 cm(-1). This is assigned as a hot band of the HO-C9-COOH rocking mode in the neutral ground state.

Corrigendum: Exocyclic Control of Turn Induction in Macrocyclic Peptide Scaffolds

In Figure 5 of this Communication, the chemical structure of the macrocycle in a) was incorrectly drawn. The correct Figure 5 is provided below. The author apologizes for the oversight. a) Bicycle formation with Lys side chain and isocyanide-derived carboxylic acid. b) NMR solution structure of 5 showing twenty lowest energy conformations in [D6]DMSO. The bicycle side chains and lactam bridge have been omitted for clarity. c) The average solution phase conformer of 5 shown with an electrostatic surface potential.

Adduct formation of ionic and nanoparticular silver with amino acids and glutathione

To investigate the interaction of ionic and nanoparticular silver with amino acids and small peptides, an electrospray ionization time-of-flight mass spectrometry method was developed. Monomeric and oligomeric silver adducts were formed with amino acids including cysteine (Cys), methionine, histidine, lysine, or the tripeptide glutathione (GSH). The obtained spectra for ionic silver show clusters in different ratios between Ag+ and the reaction partners (X) including [Ag n X m − (n + 1)H]− (n = 1–4, m = 1–3). Regarding Cys, adduct clusters up to n = 5 and m = 4 were observed as well. Considering silver–GSH interactions, even doubly charged oligomers occur generating [Ag(a + 1)GSH a − (a + 3)H]2− (a = 5–7) and [Ag b GSH b − (b + 2)H]2− (b = 4–8) ions. 1H NMR data of free GSH compared to that after treatment with Ag+ confirm sulfur–metal interactions due to changing chemical shifts for the protons located adjacent to the thiol group. Density functional theory calculations for silver–GSH clusters may explain the formation of experimentally recorded large clusters due to cooperative effects between silver and carboxylic acid side chains. Both sets of experiments indicate the presence of these adducts in the liquid phase. For silver nanoparticles, the respective data confirm the release of silver ions and the subsequent adduct formation.

Elemental and spectroscopic characterization of fractions of an acidic extract of oil sands process water

‘Naphthenic acids’ (NAs) in petroleum produced water and oil sands process water (OSPW), have been implicated in toxicological effects. However, many are not well characterized. A method for fractionation of NAs of an OSPW was used herein and a multi-method characterization of the fractions conducted.The unfractionated OSPW acidic extract was characterized by elemental analysis, electrospray ionization-Orbitrap-mass spectrometry (ESI-MS), and an esterified extract by Fourier Transform infrared (FTIR) and ultraviolet–visible (UV) absorption spectroscopy and by comprehensive multidimensional gas chromatography–MS (GCxGC–MS). Methyl esters were fractionated by argentation solid phase extraction (Ag+ SPE) and fractions eluting with: hexane; diethyl ether: hexane and diethyl ether, examined. Each was weighed, examined by elemental analysis, FTIR, UV, GC–MS and GCxGC–MS (both nominal and high resolution MS). The ether fraction, containing sulfur, was also examined by GCxGC–sulfur chemiluminescence detection (GCxGC–SCD).The major ions detected by ESI-MS in the OSPW extract were assigned to alicyclic and aromatic ‘O2’ acids; sulfur was also present. Components recovered by Ag+ SPE were also methyl esters of alicyclic and aromatic acids; these contained little sulfur or nitrogen. FTIR spectra showed that hydroxy acids and sulfoxides were absent or minor. UV spectra, along with the C/H ratio, further confirmed the aromaticity of the hexane:ether eluate.The more minor ether eluate contained further aromatics and 1.5% sulfur. FTIR spectra indicated free carboxylic acids, in addition to esters. Four major sulfur compounds were detected by GCxGC–SCD. GCxGC–high resolution MS indicated these were methyl esters of C18 S-containing, diaromatics with ⩾C3 carboxylic acid side chains.

Metalphthalocyanines Anchored Poly(1,3,4-oxadiazole arylene ether)s: Optical and Electrical Studies

New phenolphthalein based poly(1,3,4-oxadiazole aryl ether) (PHOP) containing side chain carboxylic acid groups derived from 2,5-bis(4-fluorophenyl)-1,3,4-oxadiazole and 2-(bis(4-hydroxyphenyl)methyl)benzoic acid have been synthesized from typical aromatic nucleophilic substitution reaction. The PHOP seizes high dielectric constant (300 at 50 Hz) by the assistance of polar pendants and its findness in advance studies needs some structure modification with high dielectric constant metalphthalocyanine (MPc, M=Co, Ni & Cu) macrocycle to come out as further enhancement of dielectric constant and become photoactive polymer embedded metalphthalocyanine (PPEMP1–9). The molecular weight of PHOP was determined by gel permeation chromatography and is found to be 33375 (M w/M n = 2.48). All the tailor-made polymers were well characterized by Solid State UV–Vis, thermogravimetric analysis and XRD analysis. FTIR and NMR spectroscopic techniques confirms MPc units are grafted into the polymer matrix and act as a utmost light catching materials in the visible to near IR region (400–900 nm) with remarkable drop off in optical band gap and exhibited impressive thermal properties. The variation in the AC conductivity was explained by electron hopping model and values are in the range of 3.16 × 10−5–4.78 × 10−5 (S/m) at 5 MHz measured at 20 °C.

2-Substituted-2-amino-6-boronohexanoic acids as arginase inhibitors

Substitution at the alpha center of the known human arginase inhibitor 2-amino-6-boronohexanoic acid (ABH) is acceptable in the active site pockets of both human arginase I and arginase II. In particular, substituents with a tertiary amine linked via a two carbon chain show improved inhibitory potency for both enzyme isoforms. This potency improvement can be rationalized by X-ray crystallography, which shows a water-mediated contact between the basic nitrogen and the carboxylic acid side chain of Asp200, which is situated at the mouth of the active site pocket of arginase II (Asp181 in arginase I). We believe that this is the first literature report of compounds with improved arginase inhibitory activity, relative to ABH, and represents a promising starting point for further optimization of in vitro potency and the identification of better tool molecules for in vivo investigations of the potential pathophysiological roles of arginases.

Tobacco mosaic virus rods and spheres as supramolecular high-relaxivity MRI contrast agents

To compensate for the low sensitivity of magnetic resonance imaging (MRI), nanoparticles have been developed to deliver high payloads of contrast agents to sites of disease. Here, we report the development of supramolecular MRI contrast agents using the plant viral nanoparticle tobacco mosaic virus (TMV). Rod-shaped TMV nanoparticles measuring 300×18 nm were loaded with up to 3,500 or 2,000 chelated paramagnetic gadolinium (III) ions selectively at the interior (iGd-TMV) or exterior (eGd-TMV) surface, respectively. Spatial control is achieved through targeting either tyrosine or carboxylic acid side chains on the solvent exposed exterior or interior TMV surface. The ionic T1 relaxivity per Gd ion (at 60 MHz) increases from 4.9 mM-1s-1 for free Gd(DOTA) to 18.4 mM-1s-1 for eGd-TMV and 10.7 mM-1s-1 for iGd-TMV. This equates to T1 values of ~ 30,000 mM-1s-1 and ~ 35,000 mM-1s-1 per eGd-TMV and iGd-TMV nanoparticle. Further, we show that interior-labeled TMV rods can undergo thermal transition to form 170 nm-sized spherical nanoparticles containing ~ 25,000 Gd chelates and a per particle relaxivity of almost 400,000 mM-1s-1 (15.2 mM-1s-1 per Gd). This work lays the foundation for the use of TMV as a contrast agent for MRI.

One-dimensional self-assembly of a water soluble perylene diimide molecule by pH triggered hydrogelation

A water soluble perylene diimide molecule has been fabricated into nanofibers via a pH triggered hydrogelation route. The one-dimensional self-assembly is dominated by the intermolecular π-π stacking interactions in concert with the hydrogen bonding between the carboxylic acid side chains. The anisotropic electronic and optical properties observed for the nanofibers are consistent with the one-dimensional intermolecular π-π arrangement.