Phenylalanine Moiety Research Articles

A structure-based pharmacophore modelling approach to identify and design new neprilysin (NEP) inhibitors: An in silico-based investigation

Neutral endopeptidase or neprilysin (NEP) cleaves the natriuretic peptides, bradykinin, endothelin, angiotensin II, amyloid β protein, substance P, etc., thus modulating their effects on heart, kidney, and other organs. NEP has a proven role in hypertension, heart disease, renal disease, Alzheimer's, diabetes, and some cancers. NEP inhibitor development has been in focus since the US FDA approved a combination therapy of angiotensin II type 1 receptor inhibitor (valsartan) and NEP inhibitor (sacubitril) for use in heart failure. Considering the importance of NEP inhibitors the present work focuses on the designing of a potential lead for NEP inhibition. A structure-based pharmacophore modelling approach was employed to identify NEP inhibitors from the pool of 1140 chemical entities obtained from the ZINC database. Based on the docking score and pivotal interactions, ten molecules were selected and subjected to binding free energy calculations and ADMET predictions. The top two compounds were studied further by molecular dynamics simulations to determine the stability of the ligand-receptor complex. ZINC0000004684268, a phenylalanine derivative, showed affinity and complex stability comparable to sacubitril. However, in silico studies indicated that it may have poor pharmacokinetic parameters. Therefore, the molecule was optimized using bioisosteric replacements, keeping the phenylalanine moiety intact, to obtain five potential lead molecules with an acceptable pharmacokinetic profile. The works thus open up the scope to further corroborate the present in silico findings with the biological analysis.

Aptamer-Functionalized Interface Nanopores Enable Amino Acid-Specific Peptide Detection.

Single-molecule proteomics based on nanopore technology has made significant advances in recent years. However, to achieve nanopore sensing with single amino acid resolution, several bottlenecks must be tackled: controlling nanopore sizes with nanoscale precision and slowing molecular translocation events. Herein, we address these challenges by integrating amino acid-specific DNA aptamers into interface nanopores with dynamically tunable pore sizes. A phenylalanine aptamer was used as a proof-of-concept: aptamer recognition of phenylalanine moieties led to the retention of specific peptides, slowing translocation speeds. Importantly, while phenylalanine aptamers were isolated against the free amino acid, the aptamers were determined to recognize the combination of the benzyl or phenyl and the carbonyl group in the peptide backbone, enabling binding to specific phenylalanine-containing peptides. We decoupled specific binding between aptamers and phenylalanine-containing peptides from nonspecific interactions (e.g., electrostatics and hydrophobic interactions) using optical waveguide lightmode spectroscopy. Aptamer-modified interface nanopores differentiated peptides containing phenylalanine vs. control peptides with structurally similar amino acids (i.e., tyrosine and tryptophan). When the duration of aptamer-target interactions inside the nanopore were prolonged by lowering the applied voltage, discrete ionic current levels with repetitive motifs were observed. Such reoccurring signatures in the measured signal suggest that the proposed method has the possibility to resolve amino acid-specific aptamer recognition, a step toward single-molecule proteomics.

Ionizable Polymeric Micelles with Phenylalanine Moieties Enhance Intracellular Delivery of Self-Replicating RNA for Long-Lasting Protein Expression In Vivo.

mRNA-based therapeutics are revolutionizing the landscape of medical interventions. However, the short half-life of mRNA and transient protein expression often limits its therapeutic potential, demanding high treatment doses or repeated administrations. Self-replicating RNA (RepRNA)-based treatments could offer enhanced protein production and reduce the required dosage. Here, we developed polymeric micelles based on flexible poly(ethylene glycol)-poly(glycerol) (PEG-PG) block copolymers modified with phenylalanine (Phe) moieties via biodegradable ester bonds for the efficient delivery of RepRNA. These polymers successfully encapsulated RepRNA into sub-100 nm micelles assisted by the hydrophobicity of the Phe moieties and their ability to π-π stack with the bases in RepRNA. The micelles made from Phe-modified PEG-PG (PEG-PG(Phe)) effectively maintained the integrity of the loaded RepRNA in RNase-rich serum conditions. Once taken up by cells, the micelles triggered a pH-responsive membrane disruption, promoted by the strong protonation of the amino groups at endosomal pH, thereby delivering the RepRNA to the cytosol. The system induced strong protein expression in vitro and outperformed commercial transfecting reagents in vivo, where it resulted in enhanced and long-lasting protein expression.

Impact of Physicochemical Modifications in Casein Promoted by UV-C on the Peptide Profile of Gastric Digestion and the Transepithelial Transport of Peptides.

Caseins are the main proteins in milk, and their structure and spatial conformation are responsible for their slow digestion rate. The release of bioactive and β-casomorphin peptides from casein digestion may induce allergic responses during consumption. Spectroscopic techniques were used to observe the structural changes in casein conformation induced by Ultraviolet light irradiation (UV-C). Raman spectroscopy results showed more pronounced peaks at 618 and 640 cm-1 for phenylalanine and tyrosine moieties of the photolyzed micellar casein, respectively, suggesting changes in the micelle structure. The decrease in the intensity of Raman signals for tryptophan and tyrosine corroborates to the UV-C-induced modifications of the micelle structure. Particle size distribution showed a decrease in the average micelle size after 15 min of UV-C exposure, while low-temperature, long-time (LTLT) pasteurization led to the formation of large aggregates, as observed by atomic force microscopy. UV-C did not impact the formation or transport of peptides, as observed by using the Caco-2 cell as a model for peptide absorption. However, the absence of the opioid peptide SRYPSY from κ-casein and only 20% of the concentration of opioid peptide RYLGY were noted. This work demonstrated that UV-C can be utilized to induce the physicochemical modification of dairy products, promoting a higher digestion rate and reducing allergenicity.

Aceclofenac Derivatives: Synthesis, Characterization, and Determination of Anti‐oxidant and Anti‐inflammatory Activities by Chemiluminescence Assays and Molecular Docking Studies

AbstractAceclofenac (ACF) is a newer derivative of diclofenac, and one of the emerging NSAIDs for the treatment of various inflammatory diseases. In this research we have develop a set of 2‐(2‐(2‐((2,6‐dichlorophenyl)amino)phenyl)acetoxy)acetic acid derivatives (AR1‐AR12) using Fischer esterification in good yields and in an efficient manner. All the compounds were fully characterized physical (solubility and melting points) and chemical by spectral data analysis of FTIR, 1HNMR and 13CNMR and elemental analysis. In‐vitro anti‐inflammatory activity was performed by Chemiluminescence technique in which we found 2‐oxo‐1,2‐diphenylethyl2‐(2‐(2((2,6‐dichlorophenyl)amino)phenyl) acetoxy)acetate (AR2 71 %), 2‐(4‐formyl‐2‐methoxyphenoxy)‐2‐oxoethyl2‐(2‐((2,6 dichloro‐phenyl) amino)phenyl)acetate (AR3 74.7 %),2‐(2‐(2‐(2‐((2,6‐dichloropheny l)amino) phenyl) acetoxy) acetoxy)‐3‐(2‐(2‐(3‐((2,6‐dichlorophenyl) amino) phenyl) acetoxy)acetoxy)succinic acid (AR6 89.2 %), 2‐(4‐aminophenoxy)‐2‐oxoethyl2‐(2‐((2,6‐dichloro‐phenyl) amino) phenyl) acetate (AR8 71.1 %), 1,3‐dioxo‐2,3‐dihydro‐1H‐indene‐2,2‐diyl bis(2‐(2‐(2‐((2,6‐dichlorophenyl)amino)phenyl)acetoxy)acetate) (AR9 76.3 %) found more potent as compared to parent compound while AR3, AR6 and AR9 highly potent than standard reference ibuprofen (73.2 %). The current molecular docking study was performed In order to check the suitable method for the binding of target ligands and proteins Glide docking with extra precision (XP) mode. The hydrogen bonding interactions of Aceclofenac are prominent with Isoleucine moiety, those of compound AR‐6 shows hydrophobic interaction with active amino acid Leucine and Phenylalanine moieties. Anti‐oxidant activities were also performed, AR‐3 (79.30 %), AR‐5 (91.23 %), AR‐9 (83.43 %) AR‐12 (92.43 %) were found to be more anti‐oxidant as compared to aceclofenac (ACF) (66.46 %). These derivatives were synthesized with different aliphatic and aromatic alcohols and phenols.

A K+-selective channel with a record-high K+/Na+ selectivity of 20.1.

For compounds each containing a phenylalanine moiety with its two ends amidated to have a 15-crown-5 unit and an alkyl chain, a simple tuning of the alkyl chain length delivered a K+-selective channel with a record-high K+/Na+ selectivity of 20.1.

Crosslinked polymethacrylate absorbent with phenylalanine and stearate pendants

Herein, we report a new class of oil absorbents via conventional free radical polymerization method to prepare polymethacrylate gels with a range of crosslinking density having both phenylalanine and stearate moieties in the gel matrix. Analogue crosslinked gel was also synthesized with only stearate pendants without phenylalanine. Solvent absorbing capacity of gels was studied in various solvents with different dielectric constants. The mechanical property and morphology of the absorbents were studied by rheological method and field emission scanning electron microscopy, respectively. Modulation of porosity, absorption capacity and mechanical property of the absorbent were achieved with the variation of crosslinking density. The side chain pendants in the absorbent played an important role toward the solvent uptake capabilities. The absorbent readily can uptake 66 times chloroform and 14 times petrol of its dry weight at room temperature. Overall, the solvent uptake capacity of a new class of absorbents was well studied in this report.

Asperopiperazines A and B: Antimicrobial and Cytotoxic Dipeptides from a Tunicate-Derived Fungus Aspergillus sp. DY001.

Investigation of the cytotoxic fractions of the ethyl acetate extract of the fermentation broth of the tunicate-derived Aspergillus sp. DY001 afforded two new dipeptides, asperopiperazines A and B (1 and 2), along with the previously reported compounds (+)-citreoisocoumarin (3) and (−)-6,8-di-O-methylcitreoisocoumarin (4). Analyses of the 1D and 2D NMR spectroscopic data of the compounds supported their structural assignments. Asperopiperazine A (1) is a cyclic dipeptide of leucine and phenylalanine moieties, which are substituted with an N-methyl and an N-acetyl group, respectively. On the other hand, asperopiperazine B (2) is a cyclic dipeptide of proline and phenylalanine moieties with a hydroxyl group at C-2 of the proline part. The absolute configuration of the amino acid moieties in 1 and 2 were determined by Marfey’s analyses and DFT NMR chemical shift calculations, leading to their assignment as cyclo(l-NMe-Leu-l-NAc-Phe) and cyclo(d-6-OH-Pro-l-Phe), respectively. Asperopiperazines A and B displayed higher antimicrobial effects against Escherichia coli and Staphylococcus aureus than Candida albicans. Furthermore, compounds 1–4 displayed variable growth inhibitory effects towards HCT 116 and MDA-MB-231 cells, with asperopiperazine A as the most active one towards HCT 116.

Biphenyl-Induced Superhelix in l -Phenylalanine-Based Supramolecular Self-Assembly with Dynamic Morphology Transitions

Biphenyl-Induced Superhelix in <scp>l</scp> -Phenylalanine-Based Supramolecular Self-Assembly with Dynamic Morphology Transitions

"Thermal Peroxidation" of Dietary Pentapeptides Yields N-Terminal 1,2-Dicarbonyls.

In this contribution we investigate the thermal degradation of dietary-relevant pentapeptides. Most unsaturated lipids degrade by the well-known peroxidation mechanism. Here we show a degradation mechanism of peptides analogous to lipid peroxidation, forming a series of novel degradation products with possible toxicological relevance. At elevated temperatures above 180°C, pentapeptides with an N-terminal phenylalanine moiety react via a debenzylation to form 1,2-dicabonyl compounds, replacing the N-terminal primary amine. We propose a radical-based reaction mechanism that leads via a common peroxoaminal intermediate to two distinct types of reaction products with a terminal α-1,2 diamide or an α-amide-aldehyde functionality.

Self-Assembly of Angiotensin-Converting Enzyme Inhibitors Captopril and Lisinopril and Their Crystal Structures.

The peptide angiotensin-converting enzyme inhibitors captopril and lisinopril are unexpectedly shown to exhibit critical aggregation concentration (CAC) behavior through measurements of surface tension, electrical conductivity, and dye probe fluorescence. These three measurements provide similar values for the CAC, and there is also evidence from circular dichroism spectroscopy for a possible conformational change in the peptides at the same concentration. Cryogenic transmission electron microscopy indicates the formation of micelle-like aggregates above the CAC, which can thus be considered a critical micelle concentration, and the formation of aggregates with a hydrodynamic radius of ∼6–7 nm is also evidenced by dynamic light scattering. We also used synchrotron radiation X-ray diffraction to determine the single-crystal structure of captopril and lisinopril. Our results improve the accuracy of previous data reported in the literature, obtained using conventional X-ray sources. We also studied the structure of aqueous solutions containing captopril or lisinopril at high concentrations. The aggregation may be driven by intermolecular interactions between the proline moiety of captopril molecules or between the phenylalanine moiety of lisinopril molecules.

A Peptide-Based Nanocarrier for an Enhanced Delivery and Targeting of Flurbiprofen into the Brain for the Treatment of Alzheimer's Disease: An In Vitro Study.

Alzheimer’s disease (AD) is an age-related disease caused by abnormal accumulation of amyloid-β in the brain leading to progressive tissue degeneration. Flurbiprofen (FP), a drug used to mitigate the disease progression, has low efficacy due to its limited permeability across the blood–brain barrier (BBB). In a previous work, FP was coupled at the uppermost branching of an ε-lysine-based branched carrier, its root presenting a phenylalanine moiety able to increase the hydrophobicity of the complex and enhance the transport across the BBB by adsorptive-mediated transcytosis (AMT). The present study explores a different molecular design of the FP-peptide delivery system, whereby its root presents an ApoE-mimicking peptide, a targeting ligand that could enhance transport across the BBB by receptor-mediated transcytosis (RMT). The functionalised complex was synthesised using a solid-phase peptide synthesis and characterised by mass spectrometry and FTIR. Cytotoxicity and permeability of this complex across an in vitro BBB model were analysed. Moreover, its activity and degradation to release the drug were investigated. The results revealed successful synthesis and grafting of FP molecules at the uppermost molecular branches of the lysine terminal without observed cytotoxicity. When covalently linked to the nanocarrier, FP was still active on target cells, albeit with a reduced activity, and was released as a free drug upon hydrolysis in a lysosome-mimicking medium. Noticeably, this work shows the high efficiency of RMT-driven FP delivery over delivery systems relying on AMT.

Artificial Chloride-Selective Channel: Shape and Function Mimic of the ClC Channel Selective Pore.

An artificial channel molecule 1 that mimics the shape and function of the ClC channel selective pore was described. To facilitate the transport of chloride along a unimolecular pathway, anion-π interactions were introduced as the noncovalent driving force. The hourglass-like shape of 1 was constructed with 1,3-alternate tetraoxacalix[2]arene[2]triazine as the narrowest (central) unit. Two diglycolamine-linked imide arms were tethered as the extending part, and phenylalanine moieties were fixed as the terminal anchoring groups. The ion transport activity was examined by a combination of vesicle and planar bilayer conductance techniques (BLM). The fluorescence analysis on the vesicle indicated that 1 is an efficient chloride transporter with high activity (EC50 = 1.50 μM; 1/lipid = 1:89). The ion channel characteristics were confirmed by BLM measurements, showing an average conductance of 20.8 ± 1.0 pS in symmetric KCl solutions (cis/trans = 1.0 M/1.0 M). Anion/cation selectivity with a permeability ratio PCl-/PK+ = 1.90 in an asymmetric KCl solution (cis/trans = 1.0 M/0.25 M) and anion/anion selectivity with PCl-/PBr- = 22.83 in a KCl/KBr solution (cis/trans = 1.0 M KCl/1.0 M KBr) were demonstrated.

Supramolecular Assembly of Amino Acid Based Cationic Polymer for Efficient Gene Transfection Efficiency in Triple Negative Breast Cancer.

The success of gene therapy is enormously dependent on an efficient gene carrier, and in this context, cationic polymers still continue to play a major role particularly with respect to the safety issue compared to viral vectors. Developing an efficient gene carrier system having promising gene transfection efficiency with low toxicity is the foremost impediment associated with a nonviral carrier. Here, we explored amino acid based biocompatible polymers synthesized via reversible addition-fragmentation chain transfer (RAFT) polymerization where glycine (Gly), leucine (Leu), and phenyl alanine (Phe) amino acids were used as the pendent groups of the polymeric brushes. The presence of both a hydrophobic group (long chain aliphatic group associated with the RAFT agent) and hydrophilic amino groups was associated with the supramolecular assembly of the polymeric chain having hydrodynamic sizes within the range of 150-300 nm with a positive zeta potential of 30 ± 5 mV. All polymers showed very low toxicity and possessed >80% cell viability even at a very high concentration of 1000 μg/mL against both normal and cancerous cells. In addition to this, the polymers also showed excellent blood compatibility, and negligible hemolysis was observed at the concentration of 500 μg/mL. All polymers showed efficient DNA complexation capability as well as excellent protection of DNA against highly negatively charged surfactant and enzymatic digestion, although the efficiency was dependent on the N/P ratio of polymer/DNA complexes. Interestingly, the phenyl alanine moiety containing polymer brush P(HEMA-Phe-NH2) showed a hexagonal shaped nanoparticle after complexation with pDNA and consequently showed higher cellular uptake, resulting in a higher transfection efficiency in a triple negative breast cancer cell, the MDA-MB-231 cell. Therefore, the synthesized polymer containing an amino acid pendent group, especially the phenyl alanine moiety, may be a promising nonviral gene carrier system in gene therapy application in the future.

Using molecular dynamics simulation to explore the binding of the three potent anticancer drugs sorafenib, streptozotocin, and sunitinib to functionalized carbon nanotubes.

The adsorption of the anticancer drugs sorafenib (SF), streptozotocin (STZ), and sunitinib (STB) on pristine and functionalized carbon nanotubes (FCNTs, functionalized with valine or phenylalanine moieties) was investigated using molecular dynamics simulation. Descriptors such as the van der Waals (vdW) energy, the number of hydrogen bonds, and the radial distribution function were considered. It was found that the type of functional group on the nanotube is a key influence on the vdW interaction energy between a drug molecule and a nanotube. In addition, the positions of the functional groups on a nanotube are a key influence on the adsorption of drug molecules on its surface. Our study indicated that the adsorption of STZ on CNT/FCNTs involves a partial π-π interaction and hydrogen bonding, whereas SF and STB are adsorbed on CNT/FCNTs through π-π stacking and hydrogen bonding. Our results suggest that altering the functionalization of the nanotube surface can affect the drug-nanotube interaction. The results reported here should aid attempts to optimize the design of novel CNT-based drug carriers.

Dual-cross-linked dynamic hydrogels with cucurbit[8]uril and imine linkages.

The strategy of dual cross-linking was investigated by enhancing the performance of dynamic hydrogels. To this end, phenylalanine modified ε-polylysine was synthesized and employed as the polymer backbone of hydrogels. The phenylalanine moieties and amine groups of the polymer could be cross-linked with cucurbit[8]uril (CB[8]) and the dialdehyde cross-linker, respectively. Single CB[8] linkage with fast dynamics led to an increase in the viscosity of the polymer solution, and single imine linkage with slow dynamics led to the formation of weak and brittle hydrogels. However, the two linkages were combined together to form a dual-cross-linked hydrogel and the performance of the hydrogel could be well enhanced. Compared with the single imine cross-linked hydrogel, the dual-cross-linked hydrogel demonstrated a higher mechanical strength, better extensibility and faster self-healing rate. It is anticipated that this line of research could provide a useful method to enhance the performance of dynamic hydrogels.

Synthesis carbonic anhydrase enzyme inhibition and antioxidant activity of novel benzothiazole derivatives incorporating glycine, methionine, alanine, and phenylalanine moieties

Thirteen novel benzothiazole derivatives incorporating glycine, methionine, alanine, and phenylalanine were synthesised by facile acylation reactions through benzotriazole or DCC mediated reactions and their structures were identified by 1H-NMR, 13C-NMR, and FT-IR spectroscopic techniques and elemental analysis. The carbonic anhydrase (CA, EC 4.2.1.1) inhibitory activity of the new compounds was assessed against four human (h) isoforms, hCA I, hCA II, hCA V, and hCA XIII. Some of the synthesised compounds showed good in vitro carbonic anhydrase inhibitory properties, with inhibition constants in the micromolar level. The new amino acid benzothiazole conjugates found to be more effective against hCA V and hCA II inhibition. In vitro antioxidant activities of the novel compounds were determined by DPPH method. Most of the synthesised compounds showed moderate to low antioxidant activities compared to the control antioxidant compounds (BHA and α-tocopherol).

Clickable conjugates of bile acids and nucleosides: Synthesis, characterization, in vitro anticancer and antituberculosis studies

A series of clickable bile acid-nucleosides conjugates linked directly or via amino acid linker were synthesized, and characterized by spectroscopic techniques such as 1H NMR, 13C NMR, FT-IR, HRMS and HPLC. The synthesized compounds 6a–p were screened for their in vitro anticancer property against a panel of three cancer cell lines (PC-3, MCF-7, IMR-32). In addition, the synthesized derivatives were also tested for their antimycobacterial activity against Mycobacterium tuberculosis H37Rv (ATCC 27294 strain). Among the screened compounds, cholic acid-uridine clicked conjugate (6c), and cholic acid-uridine clicked conjugate liked via phenylalanine moiety (6m) were found to be most active against MCF-7 and IMR-32 exhibiting an IC50 value of 8.084 and 8.71 µM, respectively. The antimycobacterial study of the synthesized conjugates revealed all the conjugates to be active with MIC values in the range of 4.09–15.41 µM. Deoxycholic acid-adenosine clicked conjugate (6b) showed most promising antituberculosis property with MIC value of 4.09 µM. Most of the synthesized conjugates were found to be safe at 50 µM against normal human embryonic kidney (HEK 293 T) cell line.

Chemical space screening around Phe3 in opioid peptides: Modulating µ versus δ agonism by Suzuki-Miyaura cross-couplings

In this study, affinities and activities of derivatized analogues of Dmt-dermorphin[1–4] (i.e. Dmt-d-Ala-Phe-GlyNH2, Dmt = 2′,6′-dimethyl-(S)-tyrosine) for the µ opioid receptor (MOP) and δ opioid receptor (DOP) were evaluated using radioligand binding studies, functional cell-based assays and isolated organ bath experiments. By means of solid-phase or solution-phase Suzuki-Miyaura cross-couplings, various substituted regioisomers of the phenylalanine moiety in position 3 of the sequence were prepared. An 18-membered library of opioid tetrapeptides was generated via screening of the chemical space around the Phe3 side chain. These substitutions modulated bioactivity, receptor subtype selectivity and highly effective ligands with subnanomolar binding affinities, contributed to higher functional activities and potent analgesic actions. In search of selective peptidic ligands, we show here that the Suzuki-Miyaura reaction is a versatile and robust tool which could also be deployed elsewhere.

Pd-catalyzed intramolecular C(sp2)–H amination of phenylalanine moieties in dipeptides: synthesis of indoline-2-carboxylate-containing dipeptides

A palladium-catalyzed intramolecular C(sp2)-H amination of phenylalanine moieties in dipeptides is described. By this protocol, a series of indoline-2-carboxylate-containing dipeptides were synthesized from dipeptides. The N-protected amino acid moiety within the peptide is used as an intrinsic bidentate directing group. This intramolecular C-H amination reaction provides an appealing strategy for the post-synthetic modification of peptides.