Modification Of Side Chains Research Articles

Thermal Responses and Cell Adhesive Properties of Glycosylated Jigsaw‐Shaped Self‐Assembling Peptides

ABSTRACTAs represented by the posttranslational modifications of proteins, the chemical modifications of side chains of peptide residues enable to regulate their physicochemical properties, conformation, and biological activities. Glycosylation is a main post‐translational modification, which allows for recognition by partner proteins to exert diverse function including increase in the conformational stability. Here, we studied the effects of glucose modification, which is a representative glycosylation sugar chains, to different positions of an amphiphilic peptide having a jigsaw‐shaped hydrophobic part (JigSAP). JigSAP forms a β‐sheet structure to self‐assemble into fibrous objects providing a hydrogel that can be used as a matrix for regenerative medicine. JigSAPs modified with glucose at the N‐terminus and middle portion were synthesized, and both of them self‐assemble in water to form hydrogels. The hydrogel composed of JigSAP containing the glucose group attached to the N‐terminus undergoes a gel‐to‐sol macroscopic phase transition upon heating, accompanied by a conformational change of JigSAP from the β‐sheet to an α‐helix structure. On the other hand, JigSAP with the glucose group in the middle, retained its β‐sheet structure even at high temperatures maintaining the gel state. Both glucose‐modified JigSAP fibers showed cell adhesion activity similar to that of non‐glycosylated JigSAP. This suggests that the glycosylation is effective in regulating the thermal stability of JigSAP fibers while maintaining their extracellular matrix properties depending on the modification site.

Modulating crystallinity and mixed ionic–electronic conduction properties via terminal side chain engineering of n-type small molecules

Via versatile terminal side chain modification in n-type small molecular mixed conductors, a superior figure of merit μC* of 14.1 F V−1 cm−1 s−1 in OECTs is achieved, along with robust synaptic tunability and excellent non-volatility in OENSs.

Improving voltage and quantum efficiency in blade-coated ITO-free organic solar cells processed with a non-halogenated solvent

ITO-free OSCs (PM6:Y6) blade-coated with o-xylene show enhanced donor–acceptor separation and trap density, leading to limited VOC. Acceptor side chain modification enhances the morphology and reduces traps, boosting photovoltaic performance.

The Furan-Thiol-Amine Reaction Facilitates DNA-Compatible Thiopyrrole-Grafted Macrocyclization and Late-Stage Amine Transformation.

We here report an efficient DNA-compatible furan-thiol-amine reaction for macrocyclization and late-stage amine transformation. This reaction, conducted under mild conditions, enables the facile cyclization of DNA-conjugated linear peptides into thiopyrrole-grafted macrocycles regardless of ring size or side-chain modification with good to excellent conversion yields. Additionally, this strategy was employed for the late-stage transformation of terminal amines, serving as critical intermediates in the construction of DNA-encoded peptide libraries. Diverse amines were successfully converted into their corresponding thiopyrrole scaffolds, thereby expanding the structural diversity that can be achieved within DNA-encoded libraries.

Fine Tuning the Glass Transition Temperature and Crystallinity by Varying the Thiophene-Quinoxaline Copolymer Composition.

In recent years, the design and synthesis of high-performing conjugated materials for the application in organic photovoltaics (OPVs) have achieved lab-scale devices with high power conversion efficiency. However, most of the high-performing materials are still synthesised using complex multistep procedures, resulting in high cost. For the upscaling of OPVs, it is also important to focus on conjugated polymers that can be made via fewer simple synthetic steps. Therefore, an easily synthesised amorphous thiophene-quinoxaline donor polymer, TQ1, has attracted our attention. An analogue, TQ-EH that has the same polymer backbone as TQ1 but with short branched side-chains, was previously reported as a donor polymer with increased crystallinity. We have synthesised copolymers with varied ratios between octyloxy and branched (2-ethylhexyl)oxy-substituted quinoxaline units having the same polymer backbone, with the aim to control the aggregation/crystallisation behaviour of the resulting copolymers. The optical properties, glass transition temperatures and degree of crystallinity of the new copolymers were systematically examined in relation to their copolymer composition, revealing that the composition can be used to fine-tune these properties of conjugated polymers. In addition, multiple sub-Tg transitions were found from some of the polymers, which are not commonly or clearly seen in other conjugated polymers. The new copolymers were tested in photovoltaic devices with a fullerene derivative as the acceptor, achieving slightly higher performances compared to the homopolymers. This work demonstrates that side-chain modification by copolymerisation can fine-tune the properties of conjugated polymers without requiring complex organic synthesis, thereby expanding the number of easily synthesised polymers for future upscaling of OPVs.

Synthesis and biological evaluation of lappaconitine analogues as potential anti-neuroinflammatory agents by side chain modification and scaffold hopping strategy

Neuroinflammation mediated by microglia is widely recognized as a key pathophysiological mechanism in neurodegenerative diseases. Lappaconitine (LA) is a natural C18-diterpenoid alkaloid isolated from Aconitum sinomontanum Nakai, and previous study showed that LA and its derivatives inhibited lipopolysaccharide (LPS)-induced nitric oxide (NO) production in RAW264.7 cells. However, the anti-neuroinflammatory effects of LA and its derivatives on microglia are still not clear. Here, LA analogues were designed and synthesized, and the anti-neuroinflammatory activity of the synthesized compounds was screened using LPS-induced overexpression of NO in BV-2 microglia. The screening results showed that compound 10 displayed the highest ability to inhibit NO production (IC50 = 9.98 ± 1.6 µM). Mechanistic investigations revealed that compound 10 attenuated LPS-activated neuroinflammation through suppression of TLR4/MyD88/NF-κB pathway in BV-2 microglia. Acute toxicity assays showed that compound 10 (LD50 = 508.1 mg/kg) was safer relative to LA (LD50 = 30.6 mg/kg). Collectively, our findings show that compound 10 could have potential as anti-neuroinflammatory agents.

Combination of Transfer Learning and Chemprop Interpreter with Support of Deep Learning for the Energy Levels of Organic Photovoltaic Materials Prediction and Regulation.

It is challenging to build a deep learning predictive model using traditional data mining methods due to the scarcity of available data, and the model's internal decision-making process is often nonintuitive and difficult to explain. In this work, a directed message passing neural network model with transfer learning (TL) and chemprop interpreter is proposed to improve energy levels prediction and visualization for organic photovoltaic materials. The established model shows the best performance, with coefficient of determination reaching 0.787 for HOMO and 0.822 for LUMO in a small testing set after TL, compared to the other four models. Then, the chemprop interpreter analyzes local and global effects of 12 molecular structures on the energy levels for organic materials. After a comprehensive analysis of the energy level effects of nonfullerene Y-series, IT-series, and other organic materials, 12 new IT-series derivatives are designed. 1,1-dicyano-methylene-3-indanone (IC) end group halogenation can reduce HOMO and LUMO energy levels to varying degrees, while IC end group modified by electron-withdrawing aromatic groups can increase HOMO and LUMO energy levels and obtain relatively smaller electrostatic potential (ESP) to reducing intermolecular interactions. The influence of side-chain modification on energy levels is limited. It is worth mentioning that the predicted results of IT-series derivatives match density functional theory calculations. The model also shows good generalization and transferability for predicting the energy levels of other organic electronic materials. This work not only provides a cost-effective model for predicting the energy levels of organic photovoltaic materials but also explains the potential bridge between molecular structure and electronic properties.

When more sugar is better-a GPI side chain modification results in a less virulent phenotype during a protozoan infection.

The assembly and function of side chain modifications of glycosylphosphatidylinositol (GPI) units (anchors or free forms) are poorly defined. In a recent study, two enzymes, PIGJ and PIGE, of the protozoan parasite Toxoplasma gondii were identified and shown to be involved in the assembly of such GPI side chains (J. A. Alvarez, E. Gas-Pascual, S. Malhi, J. C. Sánchez-Arcila, et al., mBio 15:e00527-24, 2024, https://doi.org/10.1128/mbio.00527-24). PIGJ adds N-acetylgalactosamine to the GPI core structure, while PIGE subsequently adds a terminal glucose. Deletion of PIGJ resulted in the loss of the side chain and, strikingly, increased mortality in infected mice, in contrast to PIGE knockouts. Absence of the side chain led to increased binding of the scavenger receptor CD36 to mutant parasites. In galectin-3 knockout mice, the virulent phenotype of side-chain-deficient parasites was largely lost. While the exact mechanisms remain to be elucidated by more experiments, these findings provide the first evidence for the importance of GPI side chains in parasite-host interactions in vivo.

Modifications of Prenyl Side Chains in Natural Product Biosynthesis.

In recent years, there has been a growing interest in understanding the enzymatic machinery responsible for the modifications of prenyl side chains and elucidating their roles in natural product biosynthesis. This interest stems from the pivotal role such modifications play in shaping the structural and functional diversity of natural products, as well as from their potential applications to synthetic biology and drug discovery. In addition to contributing to the diversity and complexity of natural products, unique modifications of prenyl side chains are represented by several novel biosynthetic mechanisms. Representative unique examples of epoxidation, dehydrogenation, oxidation of methyl groups to carboxyl groups, unusual C-C bond cleavage and oxidative cyclization are summarized and discussed. By revealing the intriguing chemistry and enzymology behind these transformations, this comprehensive and comparative review will guide future efforts in the discovery, characterization and application of modifications of prenyl side chains in natural product biosynthesis.

Modifications of Prenyl Side Chains in Natural Product Biosynthesis

AbstractIn recent years, there has been a growing interest in understanding the enzymatic machinery responsible for the modifications of prenyl side chains and elucidating their roles in natural product biosynthesis. This interest stems from the pivotal role such modifications play in shaping the structural and functional diversity of natural products, as well as from their potential applications to synthetic biology and drug discovery. In addition to contributing to the diversity and complexity of natural products, unique modifications of prenyl side chains are represented by several novel biosynthetic mechanisms. Representative unique examples of epoxidation, dehydrogenation, oxidation of methyl groups to carboxyl groups, unusual C−C bond cleavage and oxidative cyclization are summarized and discussed. By revealing the intriguing chemistry and enzymology behind these transformations, this comprehensive and comparative review will guide future efforts in the discovery, characterization and application of modifications of prenyl side chains in natural product biosynthesis.

Structural analysis of gum arabic side chains from Acacia seyal released by bifidobacterial β-arabino-oligosaccharide 3-O-β-l-arabinopyranosyl-α-l-arabinofuranosidase

Gum arabic is widely used in the food and beverage industries for its emulsifying, stabilizing, and prebiotic effects, which promote Bifidobacterium growth. The two commercially approved varieties of gum arabic, namely, Acacia senegal gum and A. seyal gum, predominantly consist of arabinogalactan protein (AGP), albeit with different side chain modifications. We previously characterized two enzymes belonging to glycoside hydrolase (GH) family 39 in bifidobacteria involved in the release of α-d-Gal-(1→3)-α-l-Ara and β-l-Arap-(1→3)-α-l-Ara from the side chains of A. senegal gum. Although the carbohydrate structure of A. senegal gum is being increasingly explored, limited information is available on A. seyal gum. In this study, we discovered a novel GH39 β-arabino-oligosaccharide 3-O-β-l-arabinopyranosyl-α-l-arabinofuranosidase from Bifidobacterium catenulatum and revealed the accurate structure of β-l-arabino-oligosaccharides released from A. seyal gum as [β-l-Araf-(1→2)-]n-β-l-Arap-(1→3)-α-l-Araf-(1→) (n = 0–3). Growth assays and intracellular enzyme activity assessments using B. catenulatum revealed that β-l-arabino-oligosaccharides were degraded to l-arabinose by GH127 β-l-arabinofuranosidase and GH36 β-l-arabinopyranosidase. This study provides new insights into the diversity of AGP structures and the utilization mechanisms of A. seyal gum in bifidobacteria.

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

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

How Can the Filler-Polymer Interaction in Mixed Matrix Membranes Be Enhanced?

Mixed matrix membranes (MMMs) constitute a type of molecular separation membranes in which a nanomaterial type filler is dispersed in a given polymer to enhance its selective permeation ability. The key issue in MMMs is the establishing of a proper filler-polymer interaction to avoid non-selective transport paths while increasing permeability but also to improve other membrane properties such as aging and plasticization. Along the pass years several strategies have been applied to enhance the physicochemical interaction between the fillers (e. g. silicas, zeolites, porous coordination polymers, carbonaceous materials, etc.) and the membrane polymers: increase of external surface area, priming, use of intrinsically more compatible fillers, in situ synthesis of filler, in situ polymerization, polymer side-chain modification and post-synthetic modification of filler.

Reprogramming the genetic code with flexizymes.

In the canonical genetic code, the 61 sense codons are assigned to the 20 proteinogenic amino acids. Advancements in genetic code manipulation techniques have enabled the ribosomal incorporation of nonproteinogenic amino acids (npAAs). The critical molecule for translating messenger RNA (mRNA) into peptide sequences is aminoacyl-transfer RNA (tRNA), which recognizes the mRNA codon through its anticodon. Because aminoacyl-tRNA synthetases (ARSs) are highly specific for their respective amino acid-tRNA pairs, it is not feasible to use natural ARSs to prepare npAA-tRNAs. However, flexizymes are adaptable aminoacylation ribozymes that can be used to prepare diverse aminoacyl-tRNAs at will using amino acids activated with suitable leaving groups. Regarding recognition elements, flexizymes require only an aromatic ring in either the leaving group or side chain of the activated amino acid, and the conserved 3'-end CCA of the tRNA. Therefore, flexizymes allow virtually any amino acid to be charged onto any tRNA. The flexizyme system can handle not only L-α-amino acids with side chain modifications but also various backbone-modified npAAs. This Review describes the development of flexizyme variants and discusses their structure and mechanism and their applications in genetic code reprogramming for the synthesis of unique peptides and proteins.

The GPI sidechain of Toxoplasma gondii inhibits parasite pathogenesis.

Glycosylphosphatidylinositols (GPIs) are highly conserved anchors for eukaryotic cell surface proteins. The apicomplexan parasite, Toxoplasma gondii, is a widespread intracellular parasite of warm-blooded animals whose plasma membrane is covered with GPI-anchored proteins, and free GPIs called GIPLs. While the glycan portion is conserved, species differ in sidechains added to the triple mannose core. The functional significance of the Glcα1,4GalNAcβ1- sidechain reported in Toxoplasma gondii has remained largely unknown without understanding its biosynthesis. Here we identify and disrupt two glycosyltransferase genes and confirm their respective roles by serology and mass spectrometry. Parasites lacking the sidechain on account of deletion of the first glycosyltransferase, PIGJ, exhibit increased virulence during primary and secondary infections, suggesting it is an important pathogenesis factor. Cytokine responses, antibody recognition of GPI-anchored SAGs, and complement binding to PIGJ mutants are intact. By contrast, the scavenger receptor CD36 shows enhanced binding to PIGJ mutants, potentially explaining a subtle tropism for macrophages detected early in infection. Galectin-3, which binds GIPLs, exhibits an enhancement of binding to PIGJ mutants, and the protection of galectin-3 knockout mice from lethality suggests that Δpigj parasite virulence in this context is sidechain dependent. Parasite numbers are not affected by Δpigj early in the infection in wild-type mice, suggesting a breakdown of tolerance. However, increased tissue cysts in the brains of mice infected with Δpigj parasites indicate an advantage over wild-type strains. Thus, the GPI sidechain of T. gondii plays a crucial and diverse role in regulating disease outcomes in the infected host.IMPORTANCEThe functional significance of sidechain modifications to the glycosylphosphatidylinositol (GPI) anchor in parasites has yet to be determined because the glycosyltransferases responsible for these modifications have not been identified. Here we present identification and characterization of both Toxoplasmsa gondii GPI sidechain-modifying glycosyltransferases. Removal of the glycosyltransferase that adds the first GalNAc to the sidechain results in parasites without a sidechain on the GPI, and increased host susceptibility to infection. Loss of the second glycosyltransferase results in a sidechain with GalNAc alone, and no glucose added, and has negligible effect on disease outcomes. This indicates GPI sidechains are fundamental to host-parasite interactions.

Renal-Clearable Organic Probes From D-A-D Type Aza-BODIPY Fluorophores for Multiphoton Deep-Brain Imaging.

Bright near-infrared (NIR) fluorescent probes play an important role in in vivo optical imaging. Here, renal-clearable nanodots prepared from Aza-BODIPY are reported fluorophores for multiphoton brain imaging. The design of donor-acceptor-donor (D-A-D) type conjugated structures endowed the fluorophores with large three-photon absorption cross-section for both 1620 and 2200nm excitation. The side chain modification and lipid encapsulation yield ultrasmall nanodots (≈4nm) and a high fluorescence quantum yield (≈0.35) at 720nm emission in the aqueous phase. The measured three-photon action cross-section of a single Aza-BODIPY fluorophore in the nanodots is ≈30 times higher than the commonly used Sulforhodamine 101 dye. Three-photon deep brain imaging of subcortical structures is demonstrated, reaching a depth of 1900µm below the brain surface in a live mouse study. The nanodots enabled blood flow measurement at a depth of 1617µm using line scanning three-photon microscopy (3PM). This work provides superior fluorescent probes for multiphoton deep-brain imaging.

Side-chain-induced changes in aminated chitosan: Insights from molecular dynamics simulations

Chitosan is a functional polymer with diverse applications in biomedicine, agriculture, water treatment, and beyond. Via derivatization of pristine chitosan, its functionality can be tailored to desired applications, e.g. immobilization of biomolecules. Here, we performed molecular dynamics simulations of three aminated chitosan polymers, where one, two, and three long-distanced side chains have been incorporated. These polymers have been previously synthesized and their properties were investigated experimentally, however, the observed dependencies could not be fully explained on the molecular level. Here, we develop a computational protocol for the simulation of functionalized chitosan polymers and perform advanced analysis of their conformational states, intramolecular interactions, and water binding. We demonstrate that intra- and intermolecular forces, especially hydrogen bonds induced by polymer side chain modifications, modulate dihedral angle conformational states of the polymer backbone and interactions with water. We explain the role of the chemical composition of the functionalized chitosans in their tendency to collapse and reveal the key role of the protonation of the amino group near the polymer backbone on the reduction of polymer collapse. We demonstrate that specific binding of water molecules, especially the intermediate water, is more pronounced in the polymer exhibiting such an amino group.

Inner Side Chain Modification of Small Molecule Acceptors Enables Lower Energy Loss and High Efficiency of Organic Solar Cells Processed with Non-halogenated Solvents.

Organic solar cells (OSCs) processed with non-halogenated solvents usually suffer from excessive self-aggregation of small molecule acceptors (SMAs), severe phase separation and higher energy loss (Eloss), leading to reduced open-circuit voltage (Voc) and power conversion efficiency (PCE). Regulating the intermolecular interaction to disperse the aggregation and further improve the molecular packing order of SMAs would be an effective strategy to solve this problem. Here, we designed and synthesized two SMAs L8-PhF and L8-PhMe by introducing different substituents (fluorine for L8-PhF and methyl for L8-PhMe) on the phenyl end group of the inner side chains of L8-Ph, and investigated the effect of the substituents on the intermolecular interaction of SMAs, Eloss and performance of OSCs processed with non-halogenated solvents. Through single crystal analysis and theoretical calculations, it is found that compared with L8-PhF, which possesses strong and abundant intermolecular interactions but downgraded molecular packing order, L8-PhMe with the methyl substituent possesses more effective non-covalent interactions, which improves the tightness and order of molecular packing. When blending the SMAs with polymer donor PM6, the differences in intermolecular interactions of the SMAs influenced the film formation process and phase separation of the blend films. The L8-PhMe based blend film exhibits shorten film formation and more homogeneous phase separation than those of the L8-PhF and L8-Ph based ones. Especially, the OSCs based on L8-PhMe show reduced non-radiative energy loss and enhanced Voc than the devices based on the other two SMAs. Consequently, the L8-PhMe based device processed with o-xylene (o-XY) and using 2PACz as the hole transport layer (HTL) shows an outstanding PCE of 19.27 %. This study highlights that the Eloss of OSCs processed with non-halogenated solvents could be decreased through regulating the intermolecular interactions of SMAs by inner side chain modification, and also emphasize the importance of effectivity rather than intensity of non-covalent interactions introduced in SMAs on the molecular packing, morphology and PCE of OSCs.

High-Performance Semiconducting Carbon Nanotube Transistors Using Naphthalene Diimide-Based Polymers with Biaxially Extended Conjugated Side Chains.

Polymer-wrapped single-walled carbon nanotubes (SWNTs) are a potential method for obtaining high-purity semiconducting (sc) SWNT solutions. Conjugated polymers (CPs) can selectively sort sc-SWNTs with different chiralities, and the structure of the polymer side chains influences this sorting capability. While extensive research has been conducted on modifying the physical, optical, and electrical properties of CPs through side-chain modifications, the impact of these modifications on the sorting efficiency of sc-SWNTs remains underexplored. This study investigates the introduction of various conjugated side chains into naphthalene diimide-based CPs to create a biaxially extended conjugation pattern. The CP with a branched conjugated side chain (P3) exhibits reduced aggregation, resulting in improved wrapping ability and the formation of larger bundles of high-purity sc-SWNTs. Grazing incidence X-ray diffraction analysis confirms that the potential interaction between sc-SWNTs and CPs occurs through π-π stacking. The field-effect transistor device fabricated with P3/sc-SWNTs demonstrates exceptional performance, with a significantly enhanced hole mobility of 4.72 cm2 V-1 s-1 and high endurance/bias stability. These findings suggest that biaxially extended side-chain modification is a promising strategy for improving the sorting efficiency and performance of sc-SWNTs by using CPs. This achievement can facilitate the development of more efficient and stable electronic devices.

3D Bioprinted Tissue-Engineered Bone with Enhanced Mechanical Strength and Bioactivities: Accelerating Bone Defect Repair through Sequential Immunomodulatory Properties.

In this study, a new-generation tissue-engineered bone capable of temporally regulating the immune response, balancing proinflammatory and anti-inflammatory activities, and facilitating bone regeneration and repair to address the challenges of delayed healing and nonunion in large-sized bone defects, is innovatively developed. Using the innovative techniques including multiphysics-assisted combined decellularization, side-chain biochemical modification, and sterile freeze-drying, a novel photocurable extracellular matrix hydrogel, methacrylated bone-derived decellularized extracellular matrix (bdECM-MA), is synthesized. After incorporating the bdECM-MA with silicon-substituted calcium phosphate and bone marrow mesenchymal stem cells, the tissue-engineered bone is fabricated through digital light processing 3D bioprinting. This study provides in vitro confirmation that the engineered bone maintains high cellular viability while achieving MPa-level mechanical strength. Moreover, this engineered bone exhibits excellent osteogenesis, angiogenesis, and immunomodulatory functions. One of the molecular mechanisms of the immunomodulatory function involves the inhibition of the p38-MAPK pathway. A pioneering in vivo discovery is that the natural biomaterial-based tissue-engineered bone demonstrates sequential immunomodulatory properties that activate proinflammatory and anti-inflammatory responses in succession, significantly accelerating the repair of bone defects. This study provides a new research basis and an effective method for developing autogenous bone substitute materials and treating large-sized bone defects.