Carboxylic Acid Side Chain Research Articles

Protecting Groups in Peptide Synthesis.

The protection of amino acid reactive functionalities including the α-amino group, the side chain (amines, carboxylic acids, alcohols, and thiols), or the carboxylic acid terminus is an essential strategy in peptide chemistry. This is mandatory to prevent polymerization of the amino acids and to minimize undesirable side reactions during the synthetic process. Proper protecting group manipulation strategies can maximize the yield of the desired product or allow the construction of complex peptide-based structures. Thus, the compatibility and orthogonality of each protecting group are key to achieve the proper control of molecular structure. Herein, we describe some common protecting groups and their general unmasking methods, in order to mask and expose amine, carboxylic acid, alcohol, and thiol functionalities to achieve the synthesis of peptides and related molecules.

Synthesis and Self‐assembly of a Helical Polymer Grafted from a Foldable Polyurethane Scaffold

Herein a polyurethane graft poly-l-glutamate amphiphilic copolymer was synthesized from a polyurethane (PU)-based macro-initiator (containing pendant primary amine groups) through the ring opening polymerization of N-carboxy anhydride of γ-benzyl-l-glutamate (BLG-NCA). On average, twenty two l-glutamic acids were grafted from each amino group which was pendant on the polyurethane chain with 10 repeating units. The grafted polymer (PU-PP-1) exhibits self-assembly to produce a hydrogel in a wide pH window ranging from pH 5.0 to 8.0 with a critical gelation concentration (CGC) of 5.0 wt % (w/v) at pH 7.4. Furthermore, circular dichroism study revealed the transition of the α-helix to a random coil upon increasing the pH. Due to the protonation of side chains at pH 4.0, PU-PP-1 adopted an α-helical conformation whereas at pH >8.0 the side-chain carboxylic acid groups of the PLGAs were ionized, leading to the formation of an extended random coil conformation as a result of charge repulsion. Conformational switching was also supported by FTIR spectroscopy.

Abstract 2167: Antibody glycoengineering for drug delivery applications

Abstract Antibody-drug conjugates (ADC) hold considerable promise as anticancer agents. A critical determinant of the effectiveness of ADCs is the chemistry that is used to conjugate the payload. Currently used approaches include primarily conjugation to either side-chain amine or carboxylic acid groups or conjugation to thiols. Because these reactions are not site specific and not easily controlled, these chemistries can result in reduced affinity for the target antigen. Further, these conjugation reactions lack selectivity and can result in heterogeneous mixtures of products that differ in the sites and stoichiometry of modification. We investigated a glycoengineering strategy that enables the introduction of artificial azide groups in the antibody without affecting their antigen affinity. This is based on the observation that glycosyltransferases can incorporate non-natural sugars (e.g., azido mannose) at different sites on an IgG molecule. The azide groups in these artificial sugars are then available to react with alkynes through copper-catalyzed ‘click’ chemistry or with strained alkynes such as dibenzyl cyclooctyne (DBCO) allowing for biorthogonal, copper-free ‘click’ chemistry. Because the sugars are added reproducibly and at a site that does not affect antigen binding, the glycoengineering technology would overcome problems associated with traditional conjugation strategies. Using this approach, azide groups were introduced in anti-CD133 and anti-perlecan antibodies. Further, the azide groups were available to react with various DBCO conjugates including fluorophores, drug molecules and nanoparticles. Importantly, the addition of artificial sugar and subsequent azide-alkyne reaction did not affect the affinity of the antibody for the target antigen. Conjugation of a cytotoxin to the antibody resulted in enhanced cell kill in vitro and efficacy in vivo. We plan on further improving the effectiveness of this approach by investigating cleavable linker technology in combination with the glycoengineering strategy. We expect that this strategy will prove to be a unique platform technology that will have a significant impact on antibody-based therapeutics. Citation Format: Drishti Navin Sehgal, Stephen Kalscheuer, Jayanth Panyam. Antibody glycoengineering for drug delivery applications [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 2167.

Cyclization of N-Terminal Glutamic Acid to pyro-Glutamic Acid Impacts Monoclonal Antibody Charge Heterogeneity Despite Its Appearance as a Neutral Transformation

Pyroglutamic acid (pyroGlu) is commonly observed at the N-terminus of therapeutic monoclonal antibodies. Notably, the term “pyroGlu” refers to a single product that could originate from the cyclization of either an N-terminal glutamine or an N-terminal glutamic acid. This is an important and easily overlooked distinction that has major implications on the charge variant nature of a pyroGlu relative to its uncyclized form. Cyclization of an N-terminal glutamine for instance clearly produces an acidic variant with a lower isoelectric point owing to the loss of the positively charged N-terminal amine. In this report, we demonstrate that cyclization of an N-terminal glutamic acid on the other hand produces a basic variant with a higher isoelectric point contrary to the typical assumption that the simultaneous loss of the N-terminal amine and the carboxylic acid side-chain would negate the formation of a charge variant. The results of our investigation demonstrate the need to consider the relative strengths of the acidic and basic functional groups which are altered when assessing whether the product will be a charge variant. This study also adds new knowledge and experimental evidence to understand charge heterogeneity in monoclonal antibodies.

Deprotonation-Induced Conductivity Shift of Polyethylenedioxythiophenes in Aqueous Solutions: The Effects of Side-Chain Length and Polymer Composition.

Deprotonation-induced conductivity shift of poly(3,4-ethylenedixoythiophene)s (PEDOTs) in aqueous solutions is a promising platform for chemical or biological sensor due to its large signal output and minimum effect from material morphology. Carboxylic acid group functionalized poly(Cn-EDOT-COOH)s are synthesized and electrodeposited on microelectrodes. The microelectrodes are utilized to study the effect of carboxylic acid side-chain length on the conductivity curve profiles in aqueous buffer with different pH. The conductivity shifts due to the buffer pH are effected by the length of the carboxylic acid side-chains. The shifts can be explained by the carboxylic acid dissociation property (pKa) at the solid–liquid interface, self-doping effect, and effective conjugation length. Conductivity profiles of poly(EDOT-OH-co-C2-EDOT-COOH) copolymers are also studied. The shifts show linear relationship with the feed monomer composition used in electrochemical polymerization.

Gallate-induced nanoparticle uptake by tumor cells: Structure-activity relationships.

How nanoparticles interact with biological systems determines whether they can be used in theranostic applications. It has been demonstrated that tea catechins, may enhance interactions of magnetic nanoparticles (MNPs) with tumor cells and the subsequent cellular internalization of MNPs. As part of the chemical structure of the major tea catechins, gallates are found in a variety of plants and thus food components. We asked whether the structure of gallate might act as a pharmacophore in the enhancement of the effects of MNP-cell interactions. Uptake of dextran-coated MNPs by glioma cells and cell-associated MNPs (MNPcell) were respectively analyzed by confocal microscopy and a colorimetric iron assay. Co-incubation of MNPs and gallates, such as gallic acid and methyl gallate, induced a concentration-dependent increase in MNPcell, which was associated with co-localization of internalized MNPs and lysosomes. An analysis of the structure-activity relationship (SAR) revealed that the galloyl moiety exerted the most prominent enhancement effects on MNPcell which was further potentiated by the application of magnetic force; catechol coupled with a conjugated carboxylic acid side chain displayed comparable effects to gallate. Blockade or reduction in the number of hydroxyl groups rendered these compounds less effective, but without inducing cytotoxicity. The SAR results suggest that neighboring hydroxyl groups on the aromatic ring form an essential scaffold for the uptake effects; a similar SAR on antioxidant activities was also observed using a free radical-scavenging method. The results provide pivotal information for theranostic applications of gallates by facilitating nanoparticle-cell interactions and nanoparticle internalization by tumor cells.

NaBr-Induced Production of Brominated Azaphilones and Related Tricyclic Polyketides by the Marine-Derived Fungus Penicillium janthinellum HK1-6.

Cultivation of the mangrove rhizosphere soil-derived fungus Penicillium janthinellum HK1-6 with NaBr led to the isolation of two new brominated azaphilones, penicilones G and H (5, 6), two new tricyclic polyketides, penijanthinones A and B (7, 8), and two known azaphilones, penicilones A and B (1, 2). The planar structures and relative configurations of the new compounds were elucidated using comprehensive spectroscopic methods including 1D and 2D NOE spectra. Their absolute configurations were determined by chemical conversions, TDDFT ECD calculations, and comparisons of their ECD spectra. Interestingly, the NaBr-induced brominated azaphilones (5, 6) had the opposite configuration at C-7 compared to the chloro analogues (3, 4) produced by this fungus cultivated with sea salt. Ester hydrolysis of penicilone B (2) afforded the carboxylic acid side chain 2,4-dimethyldec-2-enoic acid (9), with a 4 S configuration assigned by its specific rotation. Penicilone H (6) showed antibacterial activity with MIC values ranging from 3.13 to 12.5 μg/mL.

Synthetic mimics of cyclic antimicrobial peptides via templated ring-opening metathesis (TROM)

We utilized a templated ring-opening metathesis (TROM) strategy to synthesize a series of precision macrocyclic olefins, each containing two, three or four repeating units of a cyclooctene with pendant carboxylic acid side chains.

Core-Shell-Corona Micelles from a Polyether-Based Triblock Terpolymer: Investigation of the pH-Dependent Micellar Structure.

Core-shell-corona micelles featuring a pH-responsive shell have been characterized in dilute aqueous solution at different pH values (4-8) by using dynamic light scattering (DLS), field-flow fractionation coupled with multiangle light scattering detector (FFF-MALS), steady-state fluorescence, small-angle X-ray scattering (SAXS), and cryogenic transmission electron microscopy (cryo-TEM). The micelles are formed by self-assembly of a polyether-based triblock terpolymer consisting of a hydrophobic poly( tert-butyl glycidyl ether) block (P tBGE), a pH-responsive modified poly(allyl glycidyl ether) segment (PAGECOOH), and a neutral hydrophilic poly(ethylene oxide) block (PEO). Because of the side-chain carboxylic acids in the middle block, the micellar structure and size depends on the solution pH. Hereby, we show that an increase in pH induces a decrease in the aggregation number ( Nagg). In addition, the combination of the above measurements revealed an unexpected morphological change from spherical to ellipsoidal micelles by increasing pH.

Experimental and Theoretical Investigations of Infrared Multiple Photon Dissociation Spectra of Aspartic Acid Complexes with Zn2+ and Cd2.

Complexes of aspartic acid (Asp) cationized with Zn2+: Zn(Asp-H)+, Zn(Asp-H)+(ACN) where ACN = acetonitrile, and Zn(Asp-H)+(Asp); as well as with Cd2+, CdCl+(Asp), were examined by infrared multiple photon dissociation (IRMPD) action spectroscopy using light generated from a free electron laser. A series of low-energy conformers for each complex was found using quantum chemical calculations to identify the structures formed experimentally. The main binding motif observed for the heavy-metal complex, CdCl+(Asp)[N,CO,COs], is a charge-solvated, tridentate structure, where the metal center binds to the backbone amino group and carbonyl oxygens of the backbone and side-chain carboxylic acids. Likewise, the deprotonated Zn(Asp-H)+(ACN) and Zn(Asp-H)+(Asp) complexes show comparable [N,CO-,COs](ACN) and [N,CO-,COs][N,CO,COs] coordinations, respectively. Interestingly, there was only minor spectral evidence for the analogous Zn(Asp-H)+[N,CO-,COs] binding motif, even though this species is predicted to be the lowest-energy conformer. Instead, rearrangement and partial dissociation of the amino acid are observed, as spectral features most consistent with the experimental spectrum are exhibited by a four-coordinate Zn(Asp-NH4)+[CO2-,COs](NH3) complex. Analysis of the mechanistic pathway leading from the predicted lowest-energy conformer to the isobaric deaminated complex is explored theoretically. Further, comparison of the current work to that of Zn2+ and Cd2+ complexes of asparagine (Asn) allows additional conclusions regarding populated conformers and effects of carboxamide versus carboxylic acid binding to be drawn.

Prerequisites of Isopeptide Bond Formation in Microcystin Biosynthesis.

The biosynthesis of the potent cyanobacterial hepatotoxin microcystin involves isopeptide bond formation through the carboxylic acid side chains of d-glutamate and β-methyl d-aspartate. Analysis of the in vitro activation profiles of the two corresponding adenylation domains, McyE-A and McyB-A2 , either in a didomain or a tridomain context with the cognate thiolation domain and the upstream condensation domain revealed that substrate activation of both domains strictly depended on the presence of the condensation domains. We further identified two key amino acids in the binding pockets of both adenylation domains that could serve as a bioinformatic signature of isopeptide bond-forming modules incorporating d-glutamate or d-aspartate. Our findings further contribute to the understanding of the multifaceted role of condensation domains in nonribosomal peptide synthetase assembly lines.

Abstract 4593: Glycoengineered antibodies for click chemistry applications

Abstract Antibody-drug conjugates (ADC) hold considerable promise as anticancer agents. A critical determinant of the effectiveness of ADCs is the chemistry that is used to conjugate the payload. Currently used approaches include primarily conjugation to either side-chain amine or carboxylic acid groups or conjugation to thiols. Because these reactions are not site specific and not easily controlled, these chemistries can result in reduced affinity for the target antigen. Further, these conjugation reactions lack selectivity and can result in heterogeneous mixtures of products that differ in the sites and stoichiometry of modification. We investigated a glycoengineering strategy that enables the introduction of artificial azide groups in the antibody without affecting their antigen affinity. This is based on the observation that glycosyltransferases can incorporate non-natural sugars (e.g., azido mannose) at different sites on an IgG molecule. The azide groups inthese artificial sugars are then available to react with alkynes through copper-catalyzed ‘click’ chemistry or with strained alkynes such as dibenzyl cyclooctyne (DBCO) allowing for biorthogonal, copper-free ‘click’ chemistry. Because the sugars are added reproducibly and at asite that does not affect antigen binding, the glycoengineering technology would overcome problems associated with traditional conjugation strategies. Using this approach, azide groups were introduced in anti-CD133 and anti-perlecan antibodies. Further, the azide groups were available to react with various DBCO conjugates including fluorophores, drug molecules and nanoparticles. Importantly, the addition of artificial sugar and subsequent azide-alkyne reactiondid not affect the affinity of the antibody for the target antigen. Conjugation of nanoparticles to antibodies using this approach resulted in enhanced cellular uptake of the nanoparticles. Similarly, conjugation of a cytotoxin to the antibody resulted in enhanced cell kill in vitro. Weexpect that this glycoengineering strategy will prove to be a unique platform technology that will have a significant impact on antibody-based therapeutics. Citation Format: Drishti Sehgal, Stephen Kalscheuer, Tanmoy Sadhukha, Jayanth Panyam. Glycoengineered antibodies for click chemistry applications [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 4593. doi:10.1158/1538-7445.AM2017-4593

Proteorhodopsin Photocycle Kinetics Between pH 5 and pH 9.

The retinal protein proteorhodopsin is a homolog of the well-characterized light-driven proton pump bacteriorhodopsin. Basic mechanisms of proton transport seem to be conserved, but there are noticeable differences in the pH ranges of proton transport. Proton transport and protonation state of a carboxylic acid side chain, the primary proton acceptor, are correlated. In case of proteorhodopsin, the pKa of the primary proton acceptor Asp-97 (pKa ≈7.5) is unexpectedly close to environmental pH (pH≈8). A significant fraction of proteorhodopsin is possibly inactive at natural pH, in contrast to bacteriorhodopsin. We investigated photoinduced kinetics of proteorhodopsin between pH 5 and pH 9 by time resolved UV/vis absorption spectroscopy. Kinetics is inhomogeneous within that pH region and can be considered as a superposition of two fractions. These fractions are correlated with the Asp-97 titration curve. Beside Asp-97, protonation equilibria of other groups influence kinetics, but the observations do not point toward major differences of primary proton acceptor function in proteorhodopsin and bacteriorhodopsin. The pKa of proteorhodopsin and some of its variants is suspected to be an example of molecular adaptation to the physiology of the original organisms.

Supramolecular frameworks based on [60]fullerene hexakisadducts.

[60]Fullerene hexakisadducts possessing 12 carboxylic acid side chains form crystalline hydrogen-bonding frameworks in the solid state. Depending on the length of the linker between the reactive sites and the malonate units, the distance of the [60]fullerene nodes and thereby the spacing of the frameworks can be controlled and for the most elongated derivative, continuous channels are obtained within the structure. Stability, structural integrity and porosity of the material were investigated by powder X-ray diffraction, thermogravimetry and sorption measurements.

Phosphonated superplasticizers synthesis: adsorption, dispersion and fluidification ability on calcium carbonate suspensions.

Superplasticizers are chemical admixtures used to fluidize cement pastes. Among them, polycarboxylate are comb-like copolymers with carboxylic acid and poly(ethylene glycol) side chains. We present here the synthesis of various polycarboxylate-like copolymers including phosphonic acid functions. Their adsorption, dispersion and fluidification efficiencies are evaluated on calcium carbonate suspensions, a mineral material commonly used to simulate early-age cement behaviour.

Synthetic study of cnicin: Synthesis of the side chain and its esterification

Cnicin is a germacranolide sesquiterpene lactone that possesses potent inhibitory activity against the protozoan parasite Trypanosoma brucei, which causes human African trypanosomiasis (HAT). Although cnicin has an interesting structure and attractive biological activity, synthetic studies of cnicin have not yet been reported. This report describes the synthesis of the protected side chain carboxylic acid moiety at C8 of cnicin via two routes starting from l-ascorbic acid. In addition, esterification between the synthetic side chain and salonitenolide derivative, which can be achieved via hydrolysis of cnicin and protection of the primary alcohol, was conducted. Thus, a semi-synthesis of cnicin was achieved.

Analyzing pH-induced changes in a myofibril model system with vibrational and fluorescence spectroscopy

The decline of pH and ultimate pH in meat postmortem greatly influences meat quality (e.g. water holding capacity). Four spectroscopic techniques, Raman, Fourier transform infrared (FT-IR), near infrared (NIR) and fluorescence spectroscopy, were used to study protein and amino acid modifications to determine pH-related changes in pork myofibril extracts at three different pH-levels, 5.3, 5.8 and 6.3. Protonation of side-chain carboxylic acids of aspartic and glutamic acid and changes in secondary structure, mainly the amide I–III peaks, were the most important features identified by Raman and FT-IR spectroscopy linked to changes in pH. Fluorescence spectroscopy identified tryptophan interaction with the molecular environment as the most important contributor to changes in the spectra. NIR spectroscopy gave no significant contributions to interpreting protein structure related to pH. Results from our study are useful for interpreting spectroscopic data from meat where pH is an important variable.

Thermal Unthreading of the Lasso Peptides Astexin-2 and Astexin-3.

Lasso peptides are a class of knot-like polypeptides in which the C-terminal tail of the peptide threads through a ring formed by an isopeptide bond between the N-terminal amine group and a side chain carboxylic acid. The small size (∼20 amino acids) and simple topology of lasso peptides make them a good model system for studying the unthreading of entangled polypeptides, both with experiments and atomistic simulation. Here, we present an in-depth study of the thermal unthreading behavior of two lasso peptides astexin-2 and astexin-3. Quantitative kinetics and energetics of the unthreading process were determined for variants of these peptides using a series of chromatography and mass spectrometry experiments and biased molecular dynamics (MD) simulations. In addition, we show that the Tyr15Phe variant of astexin-3 unthreads via an unprecedented "tail pulling" mechanism. MD simulations on a model ring-thread system coupled with machine learning approaches also led to the discovery of physicochemical descriptors most important for peptide unthreading.

Multifunctional co-poly(amic acid): A new binder for Si-based micro-composite anode of lithium-ion battery

Multifunctional co-poly(amic acid) (PAmA) containing pyrene and carboxylic acid side-chains is developed as a binder for the recycled kerf-loss Si-Ni-SiC composite anode. The capacity retention performance of the lithium-ion battery can be apparently enhanced. In a long-cycle test of 300 lithiation/delithiation cycles, 79% of capacity retention is achieved. In considering that the recycled kerf-loss Si sample contains 38 wt% inactive micro-sized SiC abrasive particles, the achieved capacity of 648 mAh g−1 is reasonably high in comparison to other reported values. Small anode thickness expansion of 43% is found in a 100 cycle test, reflecting that the use of the PAmA binder can create strong interconnection among the silicon particles, conductive carbons and copper electrode.

Development of Improved Vaccine Adjuvants Based on the Saponin Natural Product QS-21 through Chemical Synthesis.

ConspectusVaccines based on molecular subunit antigens are increasingly being investigated due to their improved safety and more precise targeting compared to classical whole-pathogen vaccines. However, subunit vaccines are inherently less immunogenic; thus, coadministration of an adjuvant to increase the immunogenicity of the antigen is often necessary to elicit a potent immune response. QS-21, an immunostimulatory saponin natural product, has been used as an adjuvant in conjunction with various vaccines in numerous clinical trials, but suffers from several inherent liabilities, including scarcity, chemical instability, and dose-limiting toxicity. Moreover, little is known about its mechanism of action. Over a decade-long effort, beginning at the University of Illinois at Urbana-Champaign and continuing at the Memorial Sloan Kettering Cancer Center (MSKCC), the group of Prof. David Y. Gin accomplished the total synthesis of QS-21 and developed a practical semisynthetic approach to novel variants that overcome the liabilities of the natural product. First, semisynthetic QS-21 variants were designed with stable amide linkages in the acyl chain domain that exhibited comparable in vivo adjuvant activity and lower toxicity than the natural product. Further modifications in the acyl chain domain and truncation of the linear tetrasaccharide domain led to identification of a trisaccharide variant with a simple carboxylic acid side chain that retained potent adjuvant activity, albeit with reemergence of toxicity. Conversely, an acyl chain analogue terminating in a free amine was inactive but enabled chemoselective functionalization with radiolabeled and fluorescent tags, yielding adjuvant-active saponin probes that, unlike inactive congeners, accumulated in the lymph nodes in vaccinated mice and internalized into dendritic cells. Subtle variations in length, stereochemistry, and conformational flexibility around the central glycosidic linkage provided QS-21 variants with adjuvant activities that correlated with specific conformations found in molecular dynamics simulations. Notably, deletion of the entire branched trisaccharide domain afforded potent, truncated saponin variants with negligible toxicity and improved synthetic access, facilitating subsequent investigation of the triterpene core. The triterpene C4-aldehyde substituent, previously proposed to be important for QS-21 adjuvant activity, proved to be dispensable in these truncated saponin variants, while the presence of the C16 hydroxyl group enhanced activity. Novel adjuvant conjugates incorporating the small-molecule immunopotentiator tucaresol at the acyl chain terminus afforded adjuvant-active variants but without significant synergistic enhancement of activity. Finally, a new divergent synthetic approach was developed to provide versatile and streamlined access to additional linear oligosaccharide domain variants with modified sugars and regiochemistries, opening the door to the rapid generation of diverse, synthetically accessible analogues. In this Account, we summarize these multidisciplinary studies at the interface of chemistry, immunology, and medicine, which have provided critical information on the structure–activity relationships (SAR) of this Quillaja saponin class; access to novel, potent, nontoxic adjuvants for use in subunit vaccines; and a powerful platform for investigations into the mechanisms of saponin immunopotentiation.