Modification Of Side Chains Research Articles

Enhancing lathyrane structural diversity and MDR activity by combinatorial modification of lathyrane nucleus and ester side chain: A case study of Euphorbia Factor L1 and Euphorbia Factor L3

The chemical transformation of lathyrane nucleus through reduction and oxidation reactions using Euphorbia Factor L1 (EFL1) and Euphorbia Factor L1 (EFL3) as examples were investigated, along with a co-modification strategy of lathyrane nucleus and its side ester chain. A total of 38 lathyrane derivatives (5–42) including 34 new compounds were obtained, which greatly enriched the structural diversity of the lathyrane-type diterpenoids. Cytotoxicity against drug-sensitive and drug (adriamycin, ADM) resistant MCF-7 cells showed that 23 out of 38 transformed derivatives possessed obvious cytotoxic activity with IC50 values ranging from 7.0 to 41.1 μM and 3.2 to 45.5 μM, respectively, against both cells, compared to the noncytotoxic EFL1 and EFL3. The multidrug resistance (MDR) reversing activities of these lathyrane derivatives were further evaluated in MCF-7/ADM. Three transformed compounds (reversal fold, RF = 151.33, 62.94 and 47.3 for 27, 37 and 42) showed markedly higher activity than EFL1 (RF = 32.92) and EFL3 (RF = 39.68). Structure-activity relationship study revealed an essential role of C-6/17 and C-12/13 double bonds on lathyrane nucleus for exerting MDR reversal activity. Western blotting analysis showed that 42 could reduce the expression level of P-glycoprotein (P-gp) in MCF-7/ADM cells; however, the most active compound 27 with an unnatural 5/7/7/4 fused-ring diterpenoid skeleton, had no inhibitory effect on P-gp expression.

Optimizing host–guest selectivity through side-chain modification of pillar[6]arenes for o-ethyltoluene/m-ethyltoluene separation

Separation of o-ethyltoluene (OET) and m-ethyltoluene (MET) poses a significant challenge in industrial applications due to their closely matched boiling points and similar chemical structures. In this study, we successfully achieve selective adsorptive separation of OET over MET by tuning the host–guest interactions of pillar[6]arenes with ethyltoluene isomers. Experimental results demonstrate that activated perbromoethylated pillar[6]arene (BrP6) can effectively separate OET and MET, yielding an impressive OET purity of 94.0 %. Unlike conventional alkyl chain-modified pillar[6]arenes such as perethylated pillar[6]arene (EtP6) and n-perpropylated pillar[6]arene (PrP6), the improved selectivity of BrP6 arises from the electron-withdrawing effect induced by the bromine atoms present on the side chain. The presence of bromine atoms enhances the electropositivity of the side chain in BrP6, amplifies the contrast in electron cloud density between the branched chains and the cavity of BrP6, and further facilitates the favorable binding of OET with BrP6 due to the concentrated electron density in OET's branched chain.

Ultrabright NIR-II Nanoprobe for Image-Guided Accurate Resection of Tiny Metastatic Lesions.

Fluorescence imaging is a vital way to delineate the tumor boundaries. Here, we achieve a NIR-II aggregation-induced emission luminogen (AIEgen) with a fluorescence quantum yield (QY) of 12.6% in water through straightforward alkyl side chain modification. After loading of NIR-II AIEgen into polystyrene (PS) nanospheres, the thermal deactivation pathway is extremely limited, thereby concentrating absorption excitation on fluorescence emission. The fluorescence intensity is further enhanced by 5.4 times, the QY increases to 21.1%, and the NIR-II imaging signal is accordingly enhanced by 8.7 times, surpassing conventional DSPE-PEG carriers. The NIR-II@PS nanoprobe showcases superior resolution and tissue penetration depth compared to indocyanine green (ICG) and short-range near-infrared AIEgens. In vivo investigations underscore its tumor-to-normal tissue ratio (3.9) at 24 h post intravenous injection, enabling complete resection of ≤1 mm metastases under NIR-II bioimaging guidance. Additionally, the PS carrier-nanoparticles exhibit low toxicity in vivo, laying a promising foundation for the future design of medical nanomaterials.

Cephalosporin C acylase: Important role, obstacles, and strategies to optimize expression in E. coli

Cephalosporins have gained popularity due to the increasing resistance to penicillin antibiotics. Since the first discovery of cephalosporin C in 1945, the development of cephalosporin-class antibiotics has continued. Cephalosporin C was converted into a 7-aminocephalosporanic acid (7-ACA) compound which became a precursor for producing cephalosporin class antibiotics through side chain modification. The conversion of cephalosporin C to 7-ACA is more beneficial when performed enzymatically using the enzyme cephalosporin C acylase (CA) compared to chemical methods. This article will present the importance of cephalosporin CA enzymes in the development of cephalosporin antibiotics, the obstacles, and strategies to optimize the expression of these enzymes in Escherichia coli hosts.

Intracellular delivery and deep tissue penetration of nucleoside triphosphates using photocleavable covalently bound dendritic polycations.

Nucleoside triphosphates (NTPs) are essential in various biological processes. Cellular or even organismal controlled delivery of NTPs would be highly desirable, yet in cellulo and in vivo applications are hampered owing to their negative charge leading to cell impermeability. NTP transporters or NTP prodrugs have been developed, but a spatial and temporal control of the release of the investigated molecules remains challenging with these strategies. Herein, we describe a general approach to enable intracellular delivery of NTPs using covalently bound dendritic polycations, which are derived from PAMAM dendrons and their guanidinium derivatives. By design, these modifications are fully removable through attachment on a photocage, ready to deliver the native NTP upon irradiation enabling spatiotemporal control over nucleotide release. We study the intracellular distribution of the compounds depending on the linker and dendron generation as well as side chain modifications. Importantly, as the polycation is bound covalently, these molecules can also penetrate deeply into the tissue of living organisms, such as zebrafish.

Assessing the immunogenicity risk of salmon calcitonin peptide impurities using in silico and in vitro methods.

Advances in synthetic peptide synthesis have enabled rapid and cost-effective peptide drug manufacturing. For this reason, peptide drugs that were first produced using recombinant DNA (rDNA) technology are now being produced using solid- and liquid-phase peptide synthesis. While peptide synthesis has some advantages over rDNA expression methods, new peptide-related impurities that differ from the active pharmaceutical ingredient (API) may be generated during synthesis. These impurity byproducts of the original peptide sequence feature amino acid insertions, deletions, and side-chain modifications that may alter the immunogenicity risk profile of the drug product. Impurities resulting from synthesis have become the special focus of regulatory review and approval for human use, as outlined in the FDA's Center for Drug Evaluation and Research guidance document, "ANDAs for Certain Highly Purified Synthetic Peptide Drug Products That Refer to Listed Drugs of rDNA Origin," published in 2021. This case study illustrates how in silico and in vitro methods can be applied to assess the immunogenicity risk of impurities that may be present in synthetic generic versions of the salmon calcitonin (SCT) drug product. Sponsors of generic drug abbreviated new drug applications (ANDAs) should consider careful control of these impurities (for example, keeping the concentration of the immunogenic impurities below the cut-off recommended by FDA regulators). Twenty example SCT impurities were analyzed using in silico tools and assessed as having slightly more or less immunogenic risk potential relative to the SCT API peptide. Class II human leukocyte antigen (HLA)-binding assays provided independent confirmation that a 9-mer sequence present in the C-terminus of SCT binds promiscuously to multiple HLA DR alleles, while T-cell assays confirmed the expected T-cell responses to SCT and selected impurities. In silico analysis combined with in vitro assays that directly compare the API to each individual impurity peptide may be a useful approach for assessing the potential immunogenic risk posed by peptide impurities that are present in generic drug products.

The backbone constitution drives passive permeability independent of side chains in depsipeptide and peptide macrocycles inspired by ent-verticilide.

The number of peptide-like scaffolds found in late-stage drug development is increasing, but a critical unanswered question in the field is whether substituents (side chains) or the backbone drive passive permeability. The backbone is scrutinized in this study. Five series of macrocyclic peptidic compounds were prepared, and their passive permeability was determined (PAMPA, Caco-2), to delineate structure-permeability relationships. Each series was based on the cell-permeable antiarrhythmic compound ent-verticilide, a cyclic oligomeric depsipeptide (COD) containing repeating ester/N-Me amide didepsipeptide monomers. One key finding is that native lipophilic ester functionality can impart a favorable level of permeability, but ester content alone is not the final determinant - the analog with highest P app was discovered by a single ester-to-N-H amide replacement. Furthermore, the relative composition of esters and N-Me amides in a series had more nuanced permeability behavior. Overall, a systematic approach to structure-permeability correlations suggests that a combinatorial-like investigation of functionality in peptidic or peptide-like compounds could better identify leads with optimal passive permeability, perhaps prior to modification of side chains.

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 modification of nisin with homocysteine thiolactone and its effect on antimicrobial activity.

The aim of the present study is to make an important contribution to the literature by focusing on the preparation of the N-homocysteine conjugate of nisin and evaluating the effect of the N-homocysteinylation reaction on its antimicriobial activity. The modification process was monitored using both acetic acid urea polyacrylamide gel electrophoresis (AAU-PAGE) and tricine sodium dodecyl sulphate polyacrylamide gel electrophoresis (tricine SDS-PAGE). The antibacterial effectiveness of modified nisin was assessed against Staphylococcus aureus ATCC 6538, Enterococcus faecium ATCC 9097, Bacillus subtilis ATCC 6633, Lactococcus lactis ssp. cremoris AÜ, Listeria monocytogenes NCTC 5348, and Escherichia coli RSKK. Optimal conditions for achieving the highest N-homocysteinylation degree (6.30%) were determined as 6 mg/mL nisin, 150 mM homocysteine thiolactone, 150 rpm shaking rate, pH of 3.0, and a reaction time of 6 h. The modified nisin obtained did not have a significant inhibitory effect on the strains tested except E. faecium. E. faecium was inhibited by the modified nisin and its antibacterial activity was determined as approximately 10% of the antibacterial activity of unmodified nisin. On the other hand, hydrolysis of nisin by trypsin and thermolysin resulted in significant specific side chain modifications induced by the homocysteine-thiolactone reaction, especially at Lys12 and Lys22. The results provide valuable insights into the potential of N-homocysteinylation to improve the antibacterial properties of nisin and also suggest that the effects of specific modifications identified during the modification process should be investigated.

Nanomolar Protein Thermal Profiling with Modified Cyanine Dyes.

Protein properties and interactions have been widely investigated by using external labels. However, the micromolar sensitivity of the current dyes limits their applicability due to the high material consumption and assay cost. In response to this challenge, we synthesized a series of cyanine5 (Cy5) dye-based quencher molecules to develop an external dye technique to probe proteins at the nanomolar protein level in a high-throughput one-step assay format. Several families of Cy5 dye-based quenchers with ring and/or side-chain modifications were designed and synthesized by introducing organic small molecules or peptides. Our results showed that steric hindrance and electrostatic interactions are more important than hydrophobicity in the interaction between the luminescent negatively charged europium-chelate-labeled peptide (Eu-probe) and the quencher molecules. The presence of substituents on the quencher indolenine rings reduces their quenching property, whereas the increased positive charge on the indolenine side chain improved the interaction between the quenchers and the luminescent compound. The designed quencher structures entirely altered the dynamics of the Eu-probe (protein-probe) for studying protein stability and interactions, as we were able to reduce the quencher concentration 100-fold. Moreover, the new quencher molecules allowed us to conduct the experiments using neutral buffer conditions, known as the peptide-probe assay. These improvements enabled us to apply the method in a one-step format for nanomolar protein-ligand interaction and protein profiling studies instead of the previously developed two-step protocol. These improvements provide a faster and simpler method with lower material consumption.

Oxidation and side-chain modifications decrease gastrointestinal digestibility and transport of proteins from salted bighead carp fillets after frozen storage.

This study examined the effects of protein oxidation on digestion behavior. The oxidation levels and in vitro digestibility of myofibrillar proteins from fresh-brined and frozen bighead carp fillets were investigated, and the intestinal transport property was characterized by comparing the peptides on both sides of the intestinal membrane. Frozen fillets showed high oxidation levels, low amino acid content and in vitro protein digestibility, which were further increased by brining. After storage, the number of modified peptides from myosin heavy chain (MHC) increased over 10-fold in NaCl-treated samples (2.0M). Various types of side-chain modifications in amino acids were identified, such as di-oxidation, α-aminoadipic semialdehyde (AAS), γ-glutamic semialdehyde (GGS), and protein-malondialdehyde (MDA) adducts, mainly originating from MHC. The Lysine/Arginine-MDA adducts, AAS, and GGS decreased protein digestibility and their intestinal transportation. These findings suggest that oxidation impacts protein digestion and should be considered in food processing and preservation strategies.

Side-Selective Solid-Phase Metallaphotoredox N(in)-Arylation of Peptides.

Postsynthetic diversification of peptides through selective modification of endogenous amino acid side chains has enabled significant advances in peptide drug discovery while expanding the biological and medical chemistry space. However, current tools have been focused on the modification of reactive polar and ionizable side chains, whereas the decoration of aromatic systems (e.g., the N(in) of the tryptophan) has been a long-standing challenge. Here, we introduce metallaphotocatalysis in solid-phase peptide synthesis for the on-resin orthogonal N-arylation of relevant tryptophan-containing peptides. The protocol allows the chemoselective introduction of a new C(sp2)-N bond at the N(in) of tryptophan in biologically active protected peptide sequences in the presence of native redox-sensitive side chains. The fusion of metallaphotocatalysis with solid-phase peptide synthesis opens new perspectives in diversifying native amino acid side chains.

Side chain modulated carbazole-based bifunctional hole-shuttle interlayer simultaneously improves interfacial energy level alignment and defect passivation in high-efficiency perovskite solar cells

Perovskite solar cells have reached a power conversion efficiency over 26.1 %, and the interface engineering between perovskite and hole transport layer (HTL) is crucial for achieving high performance. There exists a noticeable research gap when it comes to designing an interlayer layer that can both hold defect passivation and hole transportability. To bridge this gap, we have designed and synthesized two functional molecules with carbazole cores and side chain modifications, namely CVE-Br and CVE-DPA. Beyond the suitable energy levels of the carbazole group, CVE-Br can intercalate into perovskite lattice, create a low-dimensional perovskite, and further minimize defects. Instead of forming low dimensional structure, CVE-DPA molecule wraps around the perovskite. That makes it passivate perovskite defects and facilitate hole transport without the limitation of carrier transportation. As a result, the power conversion efficiency of perovskite solar cells with CVE-DPA can achieve 22.05 %. The hydrophobicity of CVE-DPA confers the corresponding devices to retain 87 % of the initial efficiency after 1000 h.

Amphiphilic PDMS-HEMA membrane surface for improved gas selectivity and blood compatibility

While extracorporeal oxygenation (ECMO) is regarded as the golden weapon for patients with cardiopulmonary failure in critical care, its clinical use is usually complicated by the blood coagulation on the hydrophobic surface of the artificial membrane for gas exchange. Herein, amphiphilic polydimethylsiloxane‐hydroxyethyl methacrylate (PDMS-HEMA) material was firstly synthesized from chemical reaction between HEMA and the vinyl group on the side chains of PDMS via a simple process, and then coated on the microporous polyethersulfone (PES) base membrane to obtain PDMS-HEMA/PES composite membrane. Structure characterizations demonstrated that HEMA and PDMS were successfully copolymerized, and PDMS-HEMA/PES composite membranes were well prepared with a flat dense PDMS-HEMA layer coated on the surface of microporous PES substrate. Surface property analyses confirmed much smoother membrane surface, phase-separated morphology, and significant decrement in water contact angles for PDMS-HEMA obtained. More importantly, the PDMS-HEMA/PES composite membrane exhibited a CO2/O2 gas selectivity of ∼6.5 in comparison to ∼5.5 of PDMS/PES, indicating improved gas exchange efficiency. Nevertheless, the PDMS-HEMA/PES composite membrane also displayed excellent and much improved performance in hemocompatibility and long-term stability for storage as well as against blood wetting. Therefore, side-chain modification of hydrophobic PDMS with hydrophilic HEMA through simple chemical copolymerization process is an easy and feasible method to make the membrane surface with long-term amphiphilicity less thrombogenic in contact with blood and more efficient in gas exchanges.

Controlling the Chameleonic Behavior and Membrane Permeability of Cyclosporine Derivatives via Backbone and Side Chain Modifications.

Some macrocycles exhibit enhanced membrane permeability through conformational switching in different environmental polarities, a trait known as chameleonic behavior. In this study, we demonstrate specific backbone and side chain modifications that can control chameleonic behavior and passive membrane permeability using a cyclosporin O (CsO) scaffold. To quantify chameleonic behavior, we used a ratio of the population of the closed conformation obtained in polar solvent and nonpolar solvent for each CsO derivative. We found that β-hydroxylation at position 1 (1 and 3) can encode chameleonicity and improve permeability. However, the conformational stabilization induced by adding an additional transannular H-bond (2 and 5) leads to a much slower rate of membrane permeation. Our CsO scaffold provides a platform for the systematic study of the relationship among conformation, membrane permeability, solubility, and protein binding. This knowledge contributes to the discovery of potent beyond the rule of five (bRo5) macrocycles capable of targeting undruggable targets.

Effect of Spacer Length Modification of the Cationic Side Chain on the Energetics of Antimicrobial Peptide Binding to Membrane-Mimetic Bilayers.

Understanding the mechanism of action of the antimicrobial peptide (AMP) in terms of its structure and energetics is the key to designing new potent and selective AMPs. Recently, we reported a membranolytic 14-residue-long lysine-rich cationic antimicrobial peptide (LL-14: NH3+-LKWLKKLLKWLKKL-CONH2) against Pseudomonas aeruginosa, Klebsiella pneumoniae, and Staphylococcus aureus, which is limited by cytotoxicity and expected to undergo facile protease degradation. Aliphatic side-chain-length modification of the cationic amino-acid residues (Lys and Arg) is a popular strategy for designing protease-resistant AMPs. However, the effect of the peptide side-chain length modifications on the membrane binding affinity and its relation to the atomic structure remain an unsolved problem. We report computer simulations that quantitatively calculated the difference in peptide binding affinity to membrane-mimetic-bilayer models (bacterial: 1-palmitoyl-2-oleoyl-phosphatidylethanolamine (POPE)/1-palmitoyl-2-oleoyl-phosphatidylglycerol (POPG) bilayer and mammalian: 1-palmitoyl-2-oleoyl-phosphatidylcholine (POPC) bilayer) upon decreasing or increasing the spacer length of the cationic lysine residues of LL-14 (as well as their arginine analogues). We show that the peptide/bilayer interaction energetics varies drastically in response to spacer length modification. The strength of peptide discrimination depends strongly on the nature of the bilayer (bacterial or mammalian mimetic model). An increase in the lysine spacer length by one carbon (i.e., homolysine analogue of LL-14) is weakly/strongly disfavored by the bacterial/mammalian-membrane-mimetic bilayer. Recently, we have demonstrated an excellent correlation between the antimicrobial activity of the membranolytic cationic peptides and their binding affinity to membrane-mimetic-bilayer models. Thus, the homolysine analogue of LL-14 is a promising noncytotoxic AMP with conserved activity. On the other hand, homoarginine analogue (arginine spacer length increment by a single carbon) was preferred by both the bacteria and the mammalian mimetic bilayers and displayed the strongest affinity for the former among the peptides studied in this work. Thus, the promising most potent homoarginine analogue is likely to be cytotoxic. Shortening the Lys/Arg side chain to a three-carbon spacer (Dab/Agb) improves the binding affinity to bacterial and mammalian-membrane-mimetic bilayers. Arginine and arginine-derivative peptides exhibited stronger binding affinity to the bilayers relative to the lysine analogue. The results provide a plausible explanation to the previous experimental observations, viz., superior antimicrobial activity of the arginine peptides relative to Lys peptides and the improvement of antimicrobial activity upon substitution of Lys with Dab in the cationic peptides. The simulations revealed that the small change in the peptide hydrophobicity by Lys/Arg spacer length modification could drastically alter the energetics of peptide/bilayer binding by fine-tuning the electrostatic interactions. The energetics underlying the peptide selectivity by simple membrane-mimetic bilayer models may be beneficial for designing new selective and protease-resistant AMPs.

Harnessing Aromatic-Histidine Interactions through Synergistic Backbone Extension and Side Chain Modification.

Peptide engineering efforts have delivered drugs for diverse human diseases. Side chain alteration is among the most common approaches to designing new peptides for specific applications. The peptide backbone can be modified as well, but this strategy has received relatively little attention. Here we show that new and favorable contacts between a His side chain on a target protein and an aromatic side chain on a synthetic peptide ligand can be engineered by rational and coordinated side chain modification and backbone extension. Side chain modification alone was unsuccessful. Binding measurements, high-resolution structural studies and pharmacological outcomes all support the synergy between backbone and side chain modification in engineered ligands of the parathyroid hormone receptor-1, which is targeted by osteoporosis drugs. These results should motivate other structure-based designs featuring coordinated side chain modification and backbone extension to enhance the engagement of peptide ligands with target proteins.

Harnessing Aromatic‐Histidine Interactions through Synergistic Backbone Extension and Side Chain Modification

AbstractPeptide engineering efforts have delivered drugs for diverse human diseases. Side chain alteration is among the most common approaches to designing new peptides for specific applications. The peptide backbone can be modified as well, but this strategy has received relatively little attention. Here we show that new and favorable contacts between a His side chain on a target protein and an aromatic side chain on a synthetic peptide ligand can be engineered by rational and coordinated side chain modification and backbone extension. Side chain modification alone was unsuccessful. Binding measurements, high‐resolution structural studies and pharmacological outcomes all support the synergy between backbone and side chain modification in engineered ligands of the parathyroid hormone receptor‐1, which is targeted by osteoporosis drugs. These results should motivate other structure‐based designs featuring coordinated side chain modification and backbone extension to enhance the engagement of peptide ligands with target proteins.

Pentasubstituted Phospholes with extended π-conjugated Arm – Synthesis, electrochemistry, spectra and quantum chemical calculations

λ3–1H-Phosphole is a unique heterocyclic compound characterized by low aromaticity with a limited number of cross-coupling reactions to allow side-chain modification. This severely limits the use of pentasubstituted phospholes in materials chemistry, including organic light-emitting diodes (OLEDs), organic solar cells (OSCs) or probes. Therefore, we developed a procedure for simple side-chain modification by Suzuki reactions. The synthesized pentasubstituted phospholes with a π-conjugated arm in position 2 of the phosphole ring were investigated electrochemically. In addition to the electrochemical study, we measured also the UV–VIS and fluorescence spectra for the prepared 1H-phospholes. The experimentally acquired data were correlated with quantum chemical calculations. The oxidation and reduction of all derivatives in acetonitrile at various electrodes is (quasi)reversible, the respective potentials as well as the extent of intramolecular electron communication and π-delocalization depend on the combination of electron withdrawing and donating substituents. The difference between the first oxidation and the first reduction potential (ΔE1) can be correlated with excitation energy.

A DFT Study on the Impact of Saturated and Conjugated Side Chains on the Optoelectronic Performance of Y-series Nonfullerene Acceptors

Organic photovoltaic (OPV) consisting of nonfullerene acceptors have been found to be excellent candidates for harnessing solar energy. Extensive studies are being carried out to modify structures in a number of ways to enhance their efficiency. These include modifications in the acceptor part, use of efficient backbones and insertion of pi spacers. One strategy is the attachment of donor side chains for better assembly of molecules. In this work, the effect of theoretically designed side chains on electrochemical and optical properties of OPVs was studied. A series of molecules consisting of saturated (SC1-4) and conjugated donor (CD1-2) were designed and studied computationally for their potential OPV properties. Parameters like Band gap, absorption spectrum, frontier molecular orbital distribution, binding energy, fill factor, open circuit voltage, excitation energies, density of states (DOS) and transition density matrix (TDM) were studied using DFT and TD-DFT methods. Unsaturated side chains although exhibit better performance in terms of open circuit voltage and hole mobility but reduce light harvesting efficiency. All saturated side chain modifications showed improvement in fill factor and open circuit voltage than reference molecule. SC3 modification with red shift and smaller band gap showed the best performance.