Natural Amino Acids Research Articles

Characterization of a Molecularly Engineered Banlec-Type Lectin (rBTL).

Lectins are proteins that reversibly bind to carbohydrates and are commonly found across many species. The Banana Lectin (BanLec) is a member of the Jacalin-related Lectins, heavily studied for its immunomodulatory, antiproliferative, and antiviral activity. In this study, a novel sequence was generated in silico considering the native BanLec amino acid sequence and 9 other lectins belonging to JRL. Based on multiple alignment of these proteins, 11 amino acids of the BanLec sequence were modified because of their potential for interference in active binding site properties resulting in a new lectin named recombinant BanLec-type Lectin (rBTL). rBTL was expressed in E. coli and was able to keep biological activity in hemagglutination assay (rat erythrocytes), maintaining similar structure with the native lectin. Antiproliferative activity was demonstrated on human melanoma lineage (A375), evaluated by 3-(4,5-Dimethylthiazol-2-yl)-2,5-Diphenyltetrazolium Bromide (MTT). rBTL was able to inhibit cellular growth in a concentration-dependent manner, in an 8-h incubation, 12µg/mL of rBTL led to a 28.94% of cell survival compared to cell control with 100%. Through a nonlinear fit out log-concentration versus biological response, an IC50% of 3.649µg/mL of rBTL was determined. In conclusion, it is possible to state that the changes made to the rBTL sequence maintained the structure of the carbohydrate-binding site without changing specificity. The new lectin is biologically active, with an improved carbohydrate recognition spectrum compared to nBanLec, and can also be considered cytotoxic for A375 cells.

The chiral proteomic analysis applied to aging collagens by LC-MS: Amino acid racemization, post-translational modifications, and sequence degradations during the aging process

Collagen is the most abundant protein in the animal and human bodies, and it is not exempt from this aging phenomenon. Some age-related changes may appear on collagen sequences, such as increased surface hydrophobicity, the appearance of post-translational modifications, and amino acids racemization. This study has shown that the protein hydrolysis under deuterium conditions is privileged to limit the natural racemization during the hydrolysis. Indeed, under the deuterium condition, the homochirality of recent collagens is preserved whose amino acids are found in their L-form. However, in aging collagen, a natural amino acid racemization was observed. These results confirmed that the % d-amino acids are progressive according to age. The collagen sequence is degraded over time, and a fifth of the sequence information is lost during aging. Post-translational modifications (PTMs) in aging collagens can be a hypothesis to explain the modification of the hydrophobicity of the protein with the decrease of hydrophilic groups and the increase of hydrophobic groups. Finally, the exact positions of d-amino acids and PTMs have been correlated and elucidated.

New Approved Drugs Appearing in the Pharmaceutical Market in 2022 Featuring Fragments of Tailor-Made Amino Acids and Fluorine.

The strategic fluorination of oxidatively vulnerable sites in bioactive compounds is a relatively recent, widely used approach allowing us to modulate the stability, bio-absorption, and overall efficiency of pharmaceutical drugs. On the other hand, natural and tailor-made amino acids are traditionally used as basic scaffolds for the development of bioactive molecules. The main goal of this review article is to emphasize these general trends featured in recently approved pharmaceutical drugs.

Metabolomic Profiling of Asparagine Deprivation in Asparagine Synthetase Deficiency Patient-Derived Cells.

The natural amino acid asparagine (Asn) is required by cells to sustain function and proliferation. Healthy cells can synthesize Asn through asparagine synthetase (ASNS) activity, whereas specific cancer and genetically diseased cells are forced to obtain asparagine from the extracellular environment. ASNS catalyzes the ATP-dependent synthesis of Asn from aspartate by consuming glutamine as a nitrogen source. Asparagine Synthetase Deficiency (ASNSD) is a disease that results from biallelic mutations in the ASNS gene and presents with congenital microcephaly, intractable seizures, and progressive brain atrophy. ASNSD often leads to premature death. Although clinical and cellular studies have reported that Asn deprivation contributes to the disease symptoms, the global metabolic effects of Asn deprivation on ASNSD-derived cells have not been studied. We analyzed two previously characterized cell culture models, lymphoblastoids and fibroblasts, each carrying unique ASNS mutations from families with ASNSD. Metabolomics analysis demonstrated that Asn deprivation in ASNS-deficient cells led to disruptions across a wide range of metabolites. Moreover, we observed significant decrements in TCA cycle intermediates and anaplerotic substrates in ASNS-deficient cells challenged with Asn deprivation. We have identified pantothenate, phenylalanine, and aspartate as possible biomarkers of Asn deprivation in normal and ASNSD-derived cells. This work implies the possibility of a novel ASNSD diagnostic via targeted biomarker analysis of a blood draw.

Comparative genomic analysis of Halomonas campaniensis wild-type and ultraviolet radiation-mutated strains reveal genomic differences associated with increased ectoine production

Ectoine is a natural amino acid derivative and one of the most widely used compatible solutes produced by Halomonas species that affects both cellular growth and osmotic equilibrium. The positive effects of UV mutagenesis on both biomass and ectoine content production in ectoine-producing strains have yet to be reported. In this study, the wild-type H. campaniensis strain XH26 (CCTCCM2019776) was subjected to UV mutagenesis to increase ectoine production. Eight rounds of mutagenesis were used to generate mutated XH26 strains with different UV-irradiation exposure times. Ectoine extract concentrations were then evaluated among all strains using high-performance liquid chromatography analysis, alongside whole genome sequencing with the PacBio RS II platform and comparison of the wild-type strain XH26 and the mutant strain G8-52 genomes. The mutant strain G8-52 (CCTCCM2019777) exhibited the highest cell growth rate and ectoine yields among mutated strains in comparison with strain XH26. Further, ectoine levels in the aforementioned strain significantly increased to 1.51 ± 0.01 g L−1 (0.65 g g−1 of cell dry weight), representing a twofold increase compared to wild-type cells (0.51 ± 0.01 g L−1) when grown in culture medium for ectoine accumulation. Concomitantly, electron microscopy revealed that mutated strain G8-52 cells were obviously shorter than wild-type strain XH26 cells. Moreover, strain G8-52 produced a relatively stable ectoine yield (1.50 g L−1) after 40 days of continuous subculture. Comparative genomics analysis suggested that strain XH26 harbored 24 mutations, including 10 nucleotide insertions, 10 nucleotide deletions, and unique single nucleotide polymorphisms. Notably, the genes orf00723 and orf02403 (lipA) of the wild-type strain mutated to davT and gabD in strain G8-52 that encoded for 4-aminobutyrate-2-oxoglutarate transaminase and NAD-dependent succinate-semialdehyde dehydrogenase, respectively. Consequently, these genes may be involved in increased ectoine yields. These results suggest that continuous multiple rounds of UV mutation represent a successful strategy for increasing ectoine production, and that the mutant strain G8-52 is suitable for large-scale fermentation applications.

A Novel Fast Approach for Protein Classification and Evolutionary Analysis

In this paper, we propose a new fast alignment-free method for protein sequence similarity and evolutionary analysis. First 20 natural amino acids are clustered into 6 groups based on their physicochemical properties, then a 12-dimensional vector is constructed based on the frequency and the average position of occurrence of amino acids in each reduced amino acid sequences. Finally, the Euclidean distance is used to measure the similarity and evolutionary distance between protein sequences. The test on three datasets shows that our method can cluster each protein sequence accurately, which illustrates the effective of our method.

Macrocyclization of Maleimide-Decorated Peptides via Late-Stage Rh(III)-Catalyzed Trp(C7) Alkenylation.

Here, we report a novel strategy for constructing maleimide-containing peptides and cyclic peptides using Rh(III)-catalyzed tryptophan (Trp) (C7) alkenylation, which is challenging due to the inherent reactivity of the indole benzenoid ring. This method is scalable and exhibits broad substrate scope. The utility of this protocol could further be demonstrated by the synthesis of peptide conjugates with natural products and amino acids as well as the construction of maleimide-braced cyclic peptides.

Examining Interactions of Uranyl(VI) Ions with Amino Acids in the Gas Phase

Gas-phase experiments, using electrospray ionization quadrupole ion trap mass spectrometry (ESI-QIT/MS), were conducted to probe basic interactions of the uranyl(VI) ion, UO22+, with selected natural amino acids, namely, L-cysteine (Cys), L-histidine (His), and L-aspartic acid (Asp), which strongly bind to metal ions. The simplest amino acid, glycine (Gly), was also studied for comparison. Cys, His, and Asp have additional potentially coordinating groups beyond the amino and carboxylic acid functional groups, specifically thiol in Cys, imidazole in His, and a second carboxylate in Asp. Gas-phase experiments comprised collision-induced dissociation (CID) of uranyl–amino acid complexes and competitive CID to assess the relative binding strength of different amino acids in the same uranyl complex. Reactivity of selected uranyl–amino acid complexes with water provided further insights into relative stabilities. In positive ion mode, CID and ensuing reactions with water suggested that uranyl–neutral AA binding strength decreased in the order His > Asp > Cys > Gly, which is similar to amino acid proton affinities. In negative ion mode, CID revealed a decreasing dissociation tendency in the order Gly >> His ≈ Cys > Asp, presumably reflecting a reverse enhanced binding to uranyl of the doubly deprotonated amino acids formed in CID.

Copper-Catalyzed [3 + 2] Cycloaddition Reaction of N-Hydroxysuccinimide Ester with Isocyanoacetates for the Synthesis of 4,5-Disubstituted Oxazoles.

The cycloaddition reaction of N-hydroxysuccinimide ester and isocyanatoacetate catalyzed by copper was described. A series of 4,5-disubstituted oxazole compounds, including ones derived from natural fatty acids, drugs, amino acids, and peptides, were obtained in moderate to high yields. The derivatization reaction was explored. The reaction mechanism was discussed.

Acidic graphene organocatalyst for the superior transformation of wastes into high-added-value chemicals

Our dependence on finite fossil fuels and the insecure energy supply chains have stimulated intensive research for sustainable technologies. Upcycling glycerol, produced from biomass fermentation and as a biodiesel formation byproduct, can substantially contribute in circular carbon economy. Here, we report glycerol’s solvent-free and room-temperature conversion to high-added-value chemicals via a reusable graphene catalyst (G-ASA), functionalized with a natural amino acid (taurine). Theoretical studies unveil that the superior performance of the catalyst (surpassing even homogeneous, industrial catalysts) is associated with the dual role of the covalently linked taurine, boosting the catalyst’s acidity and affinity for the reactants. Unlike previous catalysts, G-ASA exhibits excellent activity (7508 mmol g−1 h−1) and selectivity (99.9%) for glycerol conversion to solketal, an additive for improving fuels’ quality and a precursor of commodity and fine chemicals. Notably, the catalyst is also particularly active in converting oils to biodiesel, demonstrating its general applicability.

Fluorescent Activity-Based Probe To Image and Inhibit Factor XIa Activity in Human Plasma.

Anticoagulation therapy is a mainstay of the treatment of thrombotic disorders; however, conventional anticoagulants trade antithrombotic benefits for bleeding risk. Factor (f) XI deficiency, known as hemophilia C, rarely causes spontaneous bleeding, suggesting that fXI plays a limited role in hemostasis. In contrast, individuals with congenital fXI deficiency display a reduced incidence of ischemic stroke and venous thromboembolism, indicating that fXI plays a role in thrombosis. For these reasons, there is intense interest in pursuing fXI/factor XIa (fXIa) as targets for achieving antithrombotic benefit with reduced bleeding risk. To obtain selective inhibitors of fXIa, we employed libraries of natural and unnatural amino acids to profile fXIa substrate preferences. We developed chemical tools for investigating fXIa activity, such as substrates, inhibitors, and activity-based probes (ABPs). Finally, we demonstrated that our ABP selectively labels fXIa in the human plasma, making this tool suitable for further studies on the role of fXIa in biological samples.

Expanding the Horizon of Bio-Inspired Catalyst Design with Tactical Incorporation of Drug Molecules.

The development of potent H2 production catalysts is a key aspect in our journey toward the establishment of a sustainable carbon-neutral power infrastructure. Hydrogenase enzymes provide the blueprint for designing efficient catalysts by the rational combination of central metal core and protein scaffold-based outer coordination sphere (OCS). Traditionally, a biomimetic catalyst is crafted by including natural amino acids as OCS features around a synthetic metal motif to functionally imitate the metalloenzyme activity. Here, we have pursued an unconventional approach and implanted two distinct drug molecules (isoniazid and nicotine hydrazide) at the axial position of a cobalt core to create a new genre of synthetic catalysts. The resultant cobalt complexes are active for both electrocatalytic and photocatalytic H2 production in near-neutral water, where they significantly enhance the catalytic performance of the unfunctionalized parent cobalt complex. The drug molecules showcased a dual effect as they influence the catalytic HER by improving the surrounding proton relay along and exerting subtle electronic effects. The isoniazid-ligated catalyst C1 outperformed the nicotine hydrazide-bound complex C2, as it produced H2 from water (pH 6.0) at a rate of 3960 s-1 while exhibiting Faradaic efficiency of about 90 %. This strategy opens up newer avenues of bio-inspired catalyst design beyond amino acid-based OCS features.

Monosodium Glutamate Perturbs Human Trophoblast Invasion and Differentiation through a Reactive Oxygen Species-Mediated Pathway: An In-Vitro Assessment.

The overproduction of reactive oxygen species (ROS) has been associated with various human diseases. ROS exert a multitude of biological effects with both physiological and pathological consequences. Monosodium glutamate (MSG), a sodium salt of the natural amino acid glutamate, is a flavor-enhancing food additive, which is widely used in Asian cuisine and is an ingredient that brings out the "umami" meat flavor. MSG consumption in rats is associated with ROS generation. Owing to its consumption as part of the fast-food culture and concerns about its possible effects on pregnancy, we aimed to study the impact of MSG on placental trophoblast cells. MSG exposure influenced trophoblast invasion and differentiation, two of the most critical functions during placentation through enhanced production of ROS. Similar findings were also observed on MSG-treated placental explants, as confirmed by elevated Nrf2 levels. Ultrastructural studies revealed signs of subcellular injury by MSG exposure. Mechanistically, MSG-induced oxidative stress with endoplasmic reticulum stress pathways involving Xbp1s and IRE1α was observed. The effect of MSG through an increased ROS production indicates that its long-term exposure might have adverse health effect by compromising key trophoblast functions.

Recent Advances in Asymmetric Synthesis of Pyrrolidine-Based Organocatalysts and Their Application: A 15-Year Update

In 1971, chemists from Hoffmann-La Roche and Schering AG independently discovered a new asymmetric intramolecular aldol reaction catalyzed by the natural amino acid proline, a transformation now known as the Hajos-Parrish-Eder-Sauer-Wiechert reaction. These remarkable results remained forgotten until List and Barbas reported in 2000 that L-proline was also able to catalyze intermolecular aldol reactions with non-negligible enantioselectivities. In the same year, MacMillan reported on asymmetric Diels-Alder cycloadditions which were efficiently catalyzed by imidazolidinones deriving from natural amino acids. These two seminal reports marked the birth of modern asymmetric organocatalysis. A further important breakthrough in this field happened in 2005, when Jørgensen and Hayashi independently proposed the use of diarylprolinol silyl ethers for the asymmetric functionalization of aldehydes. During the last 20 years, asymmetric organocatalysis has emerged as a very powerful tool for the facile construction of complex molecular architectures. Along the way, a deeper knowledge of organocatalytic reaction mechanisms has been acquired, allowing for the fine-tuning of the structures of privileged catalysts or proposing completely new molecular entities that are able to efficiently catalyze these transformations. This review highlights the most recent advances in the asymmetric synthesis of organocatalysts deriving from or related to proline, starting from 2008.

Managing iodine and tin based defects for efficient and stable mixed Sn-Pb perovskite solar cells

In recent hotly researched tin–lead (Sn-Pb) mix perovskite solar cells (PSCs), the oxidation of Sn2+ is not an isolated process but accompanied by the oxidation of I− to I2, which are both responsible for the severe p-doping and complex defect situation. Diffusion of interstitial I further severely corrodes the metal electrode to fail the PSC. Thereby, managing the I− oxidation and meanwhile neutralizing the movable I− together with suppressing Sn2+ oxidation is quite a challenge for efficient and stable Sn-Pb PSCs. In this work, a natural reductive amino acid (DOPA) is introduced into perovskite layer to successfully inhibit the oxidation of both Sn2+ and I−, at the same time, neutralize the diffusive I− to protect the Ag electrode from corrosion. Benefiting from the improved chemistry situation, the DOPA doped PSC shows significantly promoted photovoltage and efficiency at AM1.5, with enhanced light and shelf stability. This work highlights the importance of I defects management to achieve efficient and stable Sn-Pb PSCs.

Stereoretentive Post-Translational Protein Editing.

Chemical post-translational methods allow convergent side-chain editing of proteins without needing to resort to genetic intervention. Current approaches that allow the creation of constitutionally native side chains via C-C bond formation, using off-protein carbon-centered C· radicals added to unnatural amino acid radical acceptor (SOMOphile, singly occupied molecular orbital (SOMO)) "tags" such as dehydroalanine, are benign and wide-ranging. However, they also typically create epimeric mixtures of d/l-residues. Here, we describe a light-mediated desulfurative method that, through the creation and reaction of stereoretained on-proteinl-alanyl Cβ· radicals, allows Cβ-Hγ, Cβ-Oγ, Cβ-Seγ, Cβ-Bγ, and Cβ-Cγ bond formation to flexibly generate site-selectively edited proteins with full retention of native stereochemistry under mild conditions from a natural amino acid precursor. This methodology shows great potential to explore protein side-chain diversity and function and in the construction of useful bioconjugates.

Active Role Carbon by Adjoining Amino Acids in Protein Nature of Interaction

Active Role Carbon by Adjoining Amino Acids in Protein Nature of Interaction

Recent Advances on the Carboxylations of C(sp3)–H Bonds Using CO2 as the Carbon Source

AbstractCarbon dioxide (CO2) is widely known as being a sustainable C1 synthon for the synthesis of various carboxylic acid derivatives, including essential natural and unnatural amino acids. While it is sustainable, the high thermodynamic stability and kinetic inertness of the CO2 molecule is a major drawback to its wider use in organic synthesis. However, the reduction of this inert and highly stable CO2 molecule has been carried out successfully over the past few years using various stoichiometric as well as catalytic approaches. Initially, chemists employed transition-metal/transition-metal-free thermochemical methods for the incorporation of CO2 into organic compounds, however, gradually, the introduction of greener approaches such as visible-light-induced photoredox catalysis and electrocatalysis became revolutionary for the synthesis of carboxylic acids under mild reaction conditions. In this short review, we discuss the recent advances in carboxylation reactions via functionalization of the (sp3)C–H bonds of various organic molecules with CO2 using thermochemical, photochemical and electrochemical methods.1 Introduction2 Transition-Metal/Transition-Metal-Free Thermochemical Carbox ylations of C(sp3)–H Bonds2.1 C(sp3)–H Bond Carboxylation of Carbonyls2.2 Allylic, Benzylic and Alkyl C(sp3)–H Bond Carboxylation3 Photochemical C(sp3)–H Bond Carboxylation3.1 Allylic C(sp3)–H Bond Carboxylation3.2 Benzylic C(sp3)–H Bond Carboxylation4 Electrochemical Carboxylation of C(sp3)–H Bonds5 Conclusion and Outlook

Amphiphilic O(Phe-r-Glu) oligopeptides randomly polymerized via papain exhibiting a pH-insensitive emulsification property

Natural amino acid polymers have been wide-used as bio-compatible emulsion stabilizers. In this study, Amphiphilic O(Phe-r-Glu)s were synthesized through the papain-catalyzed random polymerization of L-phenylalanine and L-glutamate with the major degree of polymerization value of 6–7. The polymerization yield was increased by more than 35 % using choline to reduce the energy barrier for the amino substrates to form the tetrahedral intermediate with the catalytic triad. The squalene/water emulsions stabilized by O(Phe-r-Glu) nanoparticles were pH-insensitive at pH 1–12. The investigation of mechanism found the combined effects of steric hindrance, electrostatic repulsion and the viscosity of the emulsion contributed to the stability of the emulsion droplets. Under acidic condition, the layers of O(Pho-r-Glu)s particle aggregates formed around the emulsion droplets and the higher viscosity of emulsion mainly contributed to the stability of emulsions. At basic condition, the strong electrostatic repulsion between emulsion droplets covered by the negatively charged O(Pho-r-Glu) particles and the steric hindrance contributed mainly to the prevention of the coalescence of emulsion droplets. The application of enzymatically synthesized amphiphilic peptides in emulsion, along with tunable performance through the polymerization of amino substrates, is in line with the sustainable development requirements in fields such as pharmaceuticals, food and cosmetics.

Boosting the Piezoelectric Sensitivity of Amino Acid Crystals by Mechanical Annealing for the Engineering of Fully Degradable Force Sensors.

Biodegradable piezoelectric force sensors can be used as implantable medical devices for monitoring physiological pressures of impaired organs or providing essential stimuli for drug delivery and tissue regeneration without the need of additional invasive removal surgery or battery power. However, traditional piezoelectric materials, such as inorganic ceramics and organic polymers, show unsatisfactory degradability, and cytotoxicity. Amino acid crystals are biocompatible and exhibit outstanding piezoelectric properties, but their small crystal size makes it difficult to align the crystals for practical applications. Here, a mechanical-annealing strategy is reported for engineering all-organic biodegradable piezoelectric force sensors using natural amino acid crystals as piezoelectric materials. It is shown that the piezoelectric constant of the mechanical-annealed crystals can reach 12 times that of the single crystal powders. Moreover, mechanical annealing results in flat and smooth surfaces, thus improving the contact of the crystal films with the electrodes and leading to high output voltages of the devices. The packaged force sensors can be used to monitor dynamic motions, including muscle contraction and lung respiration, in vivo for 4weeks and then gradually degrade without causing obvious inflammation or systemic toxicity. This work provides a way to engineer all-organic and biodegradable force sensors for potential clinical applications.