Amino Acid Monomers Research Articles

Synthesis of Three‐Dimensional Chiral Covalent Organic Frameworks Using Surfactant as Inducer in Water

Comprehensive SummaryChiral covalent organic frameworks (COFs) have shown promising applications in asymmetric catalysis, enantiomer separation and chiral recognition due to their tunable structures and permanent porosity. Currently, synthesis of chiral COFs mainly relies on direct‐ synthesis method which requires asymmetric monomers to polymerize and crystallize with symmetric monomers and post‐synthesis method which has been greatly limited to having complete reactions with the micro‐/meso‐sized pores of COFs. Recently, the synthesis of two‐dimensional COFs by covalent replacement of chiral competitor has been reported. Herein, we present the synthesis of three types of 3D COFs with tunable chirality using chiral amino acid derivative surfactant as inducer in water under ambient conditions. The hydrogen bonds and electrostatic interactions between amino acid derivative surfactant and monomers as well as their precursors facilitate the transfer of the chirality.

Poly(Glutamic Acid-Lysine) Hydrogels with Alternating Sequence Resist the Foreign Body Response in Rodents and Non-Human Primates.

The foreign body response (FBR) to implanted biomaterials and biomedical devices can severely impede their functionality and even lead to failure. The discovery of effective anti-FBR materials remains a formidable challenge. Inspire by the enrichment of glutamic acid (E) and lysine (K) residues on human protein surfaces, a class of zwitterionic polypeptide (ZIP) hydrogels with alternating E and K sequences to mitigate the FBR is prepared. When subcutaneously implanted, the ZIP hydrogels caused minimal inflammation after 2 weeks and no obvious collagen capsulation after 6 months in mice. Importantly, these hydrogels effectively resisted the FBR in non-human primate models for at least 2 months. In addition, the enzymatic degradability of the gel can be controlled by adjusting the crosslinking degree or the optical isomerism of amino acid monomers. The long-term FBR resistance and controlled degradability of ZIP hydrogels open up new possibilities for a broad range of biomedical applications.

Facile synthesis of N-phenoxycarbonyl amino acids by a two-phase reaction for direct polymerization

A facile method for synthesizing N-phenoxycarbonyl amino acid (NPC) monomers has been developed by a simple two-phase reaction without the necessity for column chromatography or recrystallization.

Tough and elastic hydrogels based on robust hydrophobicity-assisted metal ion coordination for flexible wearable devices.

Flexible wearable sensors that combine excellent flexibility, high elasticity, sensing capabilities, and outstanding biocompatibility are gaining increasing attention. In this study, we successfully develop a robust and elastic hydrogel-based flexible wearable sensor by modulating molecular structures combined with metal ion coordination. We leverage three N-acryloyl amino acid monomers, including N-acryloyl glycine (AG), N-acryloyl alanine (AA), and N-acryloyl valine (AV) with different hydrophobic groups adjacent to the carboxyl group, to copolymerize with acrylamide (AM) in the presence of Zr4+ for hydrogel preparation in one step (P(AM3-AG/AA/AV0.06)-Zr0.034+ hydrogels). Our investigation reveals that the P(AM3-AV0.06)-Zr0.034+ hydrogel with the most hydrophobic side group demonstrates superior mechanical properties (1.1 MPa tensile stress, 3566 kJ m-3 toughness and 1.3 kJ m-2 fracture energy) and resilience to multiple tensile (30% strain, 500 cycles) and compression cycling (50% strain, 500 cycles). Moreover, the P(AM3-AV0.06)-Zr0.034+ hydrogel exhibits good biocompatibility and high conductivity (1.1 S m-1) and responsivity (GF = 16.21), and is proved to be suitable as a flexible wearable sensor for comprehensive human activity monitoring.

Self-Assembled Nanostructures of Homo-Oligopeptide as a Potent Ice Growth Inhibitor.

This study reports the formation of self-assembled nanostructures with homo-oligopeptides consisting of amino acids (i.e., alanine, threonine, valine, and tyrosine), the resulting morphologies (i.e., spherical shape, layered structure, and wire structure) in aqueous solution, and their potential as ice growth inhibitors. Among the homo-oligopeptides investigated, an alanine homo-oligopeptide (n = 5) with a spherical nanostructure showed the highest ice recrystallization inhibition (IRI) activity without showing a burst ice growth property and with low ice nucleation activity. The presence of nanoscale self-assembled structures in the solution showed superior IRI activity compared to an amino acid monomer because of the higher binding affinity of structures on the growing ice crystal plane. Simulation results revealed that the presence of nanostructures induced a significant inhibition of ice growth and increased lifetime of hydrogen bonding compared with unassembled homo-oligopeptide. These results envision extraordinary performance for self-assembled nanostructures as a desirable and potent ice growth inhibitor.

Efficient separation of IgG from IgM antibodies via conjugated surfactant micelles

Immunoglobulin-G (IgG) (∼150 kDa) antibodies confer longer term immunity against bacterial or viral infections than the heavier IgM’s (∼900 kDa), which are generally detectable in blood circulation in response to more recently acquired infections. There may be, however, a time overlap, which is problematic for diagnostic purposes, in the interests of which it is essential to separate IgM's from IgG’s. We describe a purification platform, functioning at pH 6.5, containing Tween-20, or Brij-O20, non-ionic detergent micelles, mixed with the sugar-rich detergent dodecyl maltoside (DDM), amino acid monomer tyrosine (Tyr), and conjugated by the amphiphilic complex [(bathophenanthroline)3: Fe2+]. Using conjugated Brij-O20 micelles, with input molar ratio IgG: IgM 9:1, IgG is recovered at 10 °C with 85–90% yield, (by SDS-PAGE densitometry) and ≥95% purity (also by SDS-PAGE), while IgM's are recovered at lower yields (28–34%) and contain small amounts of co-extracted IgG's. Addition of E. coli lysate as an artificial contamination background does not reduce the yield or purity of the recovered IgG. Tween-20/DDM/Tyr micelles lead to IgG purity ≥95% similar to that of Brij-O20, but with lower process yields (64–70%, by densitometry). Chromatographic separation with Protein A or Protein G resins leads to yields comparable to those obtained with Brij-O20 micelles, but with lower purity.

Lysine-Derived Charge-Altering Releasable Transporters: Targeted Delivery of mRNA and siRNA to the Lungs.

Targeted delivery of nucleic acid therapeutics to the lungs could transform treatment options for pulmonary disease. We have previously developed oligomeric charge-altering releasable transporters (CARTs) for in vivo mRNA transfection and demonstrated their efficacy for use in mRNA-based cancer vaccination and local immunomodulatory therapies against murine tumors. While our previously reported glycine-based CART-mRNA complexes (G-CARTs/mRNA) show selective protein expression in the spleen (mouse, >99%), here, we report a new lysine-derived CART-mRNA complex (K-CART/mRNA) that, without additives or targeting ligands, shows selective protein expression in the lungs (mouse, >90%) following systemic IV administration. We further show that by delivering siRNA using the K-CART, we can significantly decrease expression of a lung-localized reporter protein. Blood chemistry and organ pathology studies demonstrate that K-CARTs are safe and well-tolerated. We report on the new step economical, organocatalytic synthesis (two steps) of functionalized polyesters and oligo-carbonate-co-α-aminoester K-CARTs from simple amino acid and lipid-based monomers. The ability to direct protein expression selectively in the spleen or lungs by simple, modular changes to the CART structure opens fundamentally new opportunities in research and gene therapy.

Evaluating Translational Efficiency of Noncanonical Amino Acids to Inform the Design of Druglike Peptide Libraries.

Advances in genetic code reprogramming have allowed the site-specific incorporation of noncanonical functionalities into polypeptides and proteins, providing access to wide swaths of chemical space via in vitro translation techniques like mRNA display. Prior efforts have established that the translation machinery can tolerate amino acids with modifications to both the peptide backbone and side chains, greatly broadening the chemical space that can be interrogated in ligand discovery efforts. However, existing methods for confirming the translation yield of new amino acid building blocks for these technologies necessitate multistep workups and, more importantly, are not relevant for measuring translation within the context of a combinatorial library consisting of multiple noncanonical amino acids. In this study, we developed a luminescence-based assay to rapidly assess the relative translation yield of any noncanonical amino acid in real time. Among the 59 amino acids tested here, we found that many translate with high efficiency, but translational yield is not necessarily correlated to whether the amino acid is proteinogenic or has high tRNA acylation efficiency. Interestingly, we found that single-template translation data can inform the library-scale translation yield and that shorter peptide libraries are more tolerant of lower-efficiency amino acid monomers. Together our data show that the luminescence-based assay described herein is an essential tool in evaluating new building blocks and codon table designs within mRNA display toward the goal of developing druglike peptide-based libraries for drug discovery campaigns.

Chemical Shifts of Artificial Monomers Used to Construct Heterogeneous-Backbone Protein Mimetics in Random Coil and Folded States.

The construction of protein-sized synthetic chains that blend natural amino acids with artificial monomers to create so-called heterogeneous-backbones is a powerful approach to generate complex folds and functions from bio-inspired agents. A variety of techniques from structural biology commonly used to study natural proteins have been adapted to investigate folding in these entities. In NMR characterization of proteins, proton chemical shift is a straightforward to acquire, information-rich metric that bears directly on a variety of properties related to folding. Leveraging chemical shift to gain insight into folding requires a set of reference chemical shift values corresponding to each building block type (i.e., the 20 canonical amino acids in the case of natural proteins) in a random coil state and knowledge of systematic changes in chemical shift associated with particular folded conformations. Although well documented for natural proteins, these issues remain unexplored in the context of protein mimetics. Here, we report random coil chemical shift values for a library of artificial amino acid monomers frequently used to construct heterogeneous-backbone protein analogues as well as a spectroscopic signature associated with one monomer class, β3-residues bearing proteinogenic side chains, adopting a helical folded conformation. Collectively, these results will facilitate the continued utilization of NMR for the study of structure and dynamics in protein-like artificial backbones.

Tyrosine, Phenylalanine, and Tryptophan Undergo Self-Aggregation in Similar and Different Manners

Phenylalanine, tyrosine, and tryptophan are aromatic amino acids, and they are of high interest in both health science and biotechnology. These amino acids form organized structures, like fibrils and nanotubes. Although these amino acids belong to the same family, they still differ from each other with respect to polarity, hydrophobicity as well as internal structures. In this work, we performed extensive molecular dynamics simulations to investigate the dynamics of the self-aggregations of these amino acids and studied the details of the formed structures. The amino acid monomers placed in water were simulated at a constant temperature. It has been observed that they compose nanostructures with similarities and differences.

Detergent micelle conjugates containing amino acid monomers allow purification of human IgG near neutral pH

Industrial scale production of therapeutic monoclonal antibodies (mAbs) is commonly achieved with Protein A chromatography, a process that requires exposure of the antibody to strongly acidic conditions during the eluting step. Exposure to acid inactivates virus contaminants but may, in parallel, lead to antibody aggregation that must be eliminated or kept at acceptably low levels. This report seeks to provide a practical method for overcoming a long-standing problem. We show how Brij-O20 detergent micelles, conjugated by the amphiphilic [(bathophenanthroline)3:Fe2+] complex in the presence of amino acid monomers: phenylalanine (Phe), tyrosine (Tyr), tryptophan (Trp), isoleucine (Ile) or valine (Val), efficiently capture polyclonal human IgG (hIgG) at neutral pH and allow its recovery by extraction either at pH 4 (85–97% yield) or at pH 6.3 (72–84% yield). Of the five amino acid monomers surveyed, Phe or Tyr produced the highest overall process yield at both pH 4 and 6.3. The monomeric state of the purified hIgG's was confirmed by dynamic light scattering (DLS). Potential advantages of the purification method are discussed.

Syntheses of Polypeptides and Their Biomedical Application for Anti-Tumor Drug Delivery.

Polypeptides have attracted considerable attention in recent decades due to their inherent biodegradability and biocompatibility. This mini-review focuses on various ways to synthesize polypeptides, as well as on their biomedical applications as anti-tumor drug carriers over the past five years. Various approaches to preparing polypeptides are summarized, including solid phase peptide synthesis, recombinant DNA techniques, and the polymerization of activated amino acid monomers. More details on the polymerization of specifically activated amino acid monomers, such as amino acid N-carboxyanhydrides (NCAs), amino acid N-thiocarboxyanhydrides (NTAs), and N-phenoxycarbonyl amino acids (NPCs), are introduced. Some stimuli-responsive polypeptide-based drug delivery systems that can undergo different transitions, including stability, surface, and size transition, to realize a better anti-tumor effect, are elaborated upon. Finally, the challenges and opportunities in this field are briefly discussed.

Conjugated detergent micelles as a platform for IgM purification.

Immunoglobulin M (IgM) antibodies hold promise as anticancer drugs and as agents for promoting immune homeostasis. This promise has not been realized due to low expression levels in mammalian cells producing IgM class antibodies, and the failure of protein A chromatography for IgM purification. Here, we describe a nonchromatographic platform for quantitatively capturing IgMs at neutral pH, which is then recovered with 86%–94% yield and >95% purity at pH 3. The platform contains micelles conjugated with the [(bathophenanthroline)3:Fe2+] amphiphilic complex. Inclusion of amino acid monomers, for example, phenylalanine or tyrosine, during conjugation of detergent micelles, allows subsequent extraction of IgMs at close to neutral pH. With the successful implementation of this purification platform for both polyclonal humans and bovine IgMs, we anticipate similar results for monoclonal IgMs, most relevant for the pharmaceutical industry.

Conjugates of Recombinant Protein‐Based Polymers: Combining Precision with Chemical Diversity

Inspired by nature, scientists have harnessed the natural protein translation machinery to produce intricate and precise protein‐based polymers (PBPs)—composed of natural amino acid monomers and assembled on the nano‐to‐macro scale—for drug and gene delivery, to sense the environment, to produce valuable molecules, and to grow cells and tissues. Beyond the chemical repertoire of natural amino acids, the conjugation of chemically diverse molecules to recombinant PBPs can increase the ability of the latter to mimic or modify the remarkable properties of natural biomaterials and to impart new functions. In this review, recent progress in the production and application of recombinant PBP‐conjugates is described. First, the various approaches for protein conjugation or crosslinking are briefly discussed and then the utility of this approach for imparting new or improved properties and functions onto PBPs composed of elastin‐, resilin‐, silk‐, or collagen‐based sequences is demonstrated. Finally, emerging knowledge of and technologies for PBP‐conjugate production with the potential to expand the use of such precise and chemically diverse polymers in biomedicine is discussed.

Vibrational Spectroscopy of Homo- and Heterochiral Amino Acid Dimers: Conformational Landscapes.

The homo- and heterochiral protonated dimers of asparagine with serine and with valine were investigated using infrared multiple-photon dissociation (IRMPD) spectroscopy. Extensive quantum-chemical calculations were used in a three-tiered strategy to screen the conformational spaces of all four dimer species. The resulting binary structures were further grouped into five different types based on their intermolecular binding topologies and subunit configurations. For each dimer species, there are eight to fourteen final conformational geometries within a 10 kJ mol−1 window of the global minimum structure for each species. The comparison between the experimental IRMPD spectra and the simulated harmonic IR features allowed us to clearly identify the types of structures responsible for the observation. The monomeric subunits of the observed homo- and heterochiral dimers are compared to the corresponding protonated/neutral amino acid monomers observed experimentally in previous IRMDP/rotational spectroscopic studies. Possible chirality and kinetic influences on the experimental IRMPD spectra are discussed.

Self-Assembled Nanosized Vehicles from Amino Acid-Based Amphiphilic Polymers with Pendent Carboxyl Groups for Efficient Drug Delivery.

Developing safe and efficient delivery vehicles for chemotherapeutic drugs has been a long-standing demanding. Amino acid-based polymers are promising candidates to address this challenge due to their excellent biocompatibility and biodegradation. Herein, a series of well-defined amphiphilic block copolymers were prepared by PET-RAFT polymerization of N-acryloyl amino acid monomers. By altering monomer types and the block ratio of the copolymers, the copolymers self-assembled into nanostructures with various morphologies, including spheres, rod-like, fibers, and lamellae via hydrophobic and hydrogen bonding interactions. Significantly, the nanoparticles (NPs) assembled from amphiphilic block copolymers poly(N-acryloyl-valine)-b-poly(N-acryloyl-aspartic acid) (PV-b-PD) displayed an appealing cargo loading efficiency (21.8-32.6%) for a broad range of drugs (paclitaxel, doxorubicin (DOX), cisplatin, etc.) due to strong interactions. The DOX-loaded PV-b-PD NPs exhibited rapid cellular uptake (within 1 min) and a great therapeutic performance. These drug delivery systems provide new insights for regulating the controlled morphologies and improving the efficiency of drug delivery.

Evaluation of Biological Degraded Keratin for Biogas Production Using Dry Anaerobic Digestion System

Anaerobic digestion is a methane gas production process that can be used as sustainable alternative energy. Anaerobic digestion utilized various types of organic waste as substrate for the reaction process. Keratin waste is an organic waste mainly produced from the poultry and farming industry. Pretreatment is usually required to hydrolyzed keratin protein complex as the amino acid is easily used as the substrate in anaerobic digestion reaction. Biological pretreatment was selected because it more energy saver and generating diverse types of amino acid monomers. Three types of keratins used in this research were feathers, wool, and hair. Culture of Bacillus sp. C4 were inoculated into keratins and incubated for 24 hours, 48 hours, and 72 hours. The chicken feathers produce the soluble protein as much as 7.23 mg/ml, 32.59 mg/ml and 45.99 mg/ml respectively, while the sheep wool produce 24.08 mg/ml, 36.73 mg/ml and 38.75 mg/ml respectively according to incubation time. Meanwhile, keratin hair cannot be degraded by Bacillus sp. C4 at all. Free ammonia formed by hydrolysis of proteins is suspected to be an inhibitor in the methanogenesis process, as total methane produced from degraded keratin only 256,6 ml C4/gr VS in 36 days retention time.

CAN: A new program to streamline preparation of molecular coordinate files for molecular dynamics simulations.

Preparing molecular coordinate files for molecular dynamics (MD) simulations can be a very time-consuming process. Herein we present the development of a user-friendly program that drastically reduces the time required to prepare these molecular coordinate files for MD software packages such as AmberTools. Our program, known as charge atomtype naming (CAN), creates and uses a library of structures such as amino acid monomers to update the charge, atom type, and name of atoms in any molecular structure (mol2) file. We demonstrate the utility of this new program by rapidly preparing structural files for MD simulations for polypeptides ranging from small molecules to large protein structures. Both native and non-native amino acid residues are easily handled by this new program.

Assembly of a Phenylalanine Nanotube by the use of Molecular Dynamics Manipulator

Studies of the processes of self-organization and self-assembly of various complexly organized (including spiral) structures based on amino acids intensively carried out in recent years. Various methods of molecular modeling, including molecular dynamics (MD) methods, are developed. In this paper, we propose a new approach for a relatively simple technique for conducting MD simulation (MDS) of various molecular nanostructures, determining the trajectory of the MD run and forming the final structure: a molecular dynamic manipulator (MD manipulator). It is an imitation of the operation of an existing or imaginary device or structure by applying force to the existing initial structure in order to obtain a new final structure, having the same chemical composition, but with a different geometry (topology). The PUMA-CUDA software package was applied as the main MD modeling program, which uses the physics of the PUMA software package, developed by the laboratory headed by N.K. Balabaev. Using this MDS tool, you can investigate the formation of helical structures from a linear sequence of any amino acids variation. As an example, the applicability of the developed algorithm for assembling nanotubes from linear phenylalanine (Phe) chains of different chirality (left L-Phe and right D-Phe) is considered by including additional force effects in the molecular dynamics simulation program for these structures. During the MD run, the applied actions, which are the same for the left and right helices of the formed nanotubes, lead the system to an α-helix structure. The work was carried out in an interactive mode using a number of additional programs, incl. trajectory analyzer program MD (TAMD). As a result, the modes that are most adequate for the formation of nanotubes of the right chirality D from the initial L-Phe monomer and nanotubes of the left chirality L from the D-Phe amino acid monomer were determined. The results obtained were compared with data from other works on modeling similar nanotubes of different chirality and experimental data. These are fully in line with the law of change in sign of chirality of molecular structures with complication of their hierarchical level of organization. The molecular animation of the assembly of a left-chiral nanotube from D-monomers is freely available at: http://lmd.impb.ru/Supplementary/PHE.avi.

Underlying Mechanisms for the Modulation of Self-Assembly and the Intrinsic Fluorescent Properties of Amino Acid-Functionalized Gold Nanoparticles.

The origin of the blue fluorescence of proteins and peptides in the visible region has been a subject of intense debate despite several efforts. Although aromatic amino acids, namely tryptophan (Trp), tyrosine (Tyr), and phenylalanine (Phe) are responsible for the intrinsic luminescence of proteins and peptides, the underlying mechanism and contributions of these amino acids to the unusual blue fluorescence are still not well resolved. In the present endeavor, we show that the clusterization of both aromatic and aliphatic amino acids on the surface of the gold nanoparticles (Au NPs) leads to clusteroluminescence, which could be linked to the unusual fluorescence properties of the proteins and peptides and have been ignored in the past. The amino acid monomers initially form small aggregates through clusterization, which provides the fundamental building blocks to establish the amyloid structure as well as the luminescence property. Because of the clusterization, these Au NPs/nano-aggregate systems are also found to exhibit remarkable stability against the freeze-thaw cycle and several other external stimuli, which can be useful for biological and biomedical applications.