Tyr Residues Research Articles

The relationship between the tyrosine residue 850–830 cm−1 Raman doublet intensity ratio and the aromatic side chain χ1 torsion angle

Tyrosine (Tyr) residue in a peptide chain is characterized by the presence of seven Raman markers, referred to as Yi (i = 1, …, 7), distributed over the middle wavenumber spectral region. Particularly, the changes observed in the relative intensity of Y5 and Y6 markers, appearing as a side by side doublet at ca. 850–830 cm−1, has received a great attention. Primarily assigned to a Fermi-resonance effect between phenol ring planar and nonplanar modes, former density functional theory calculations led us to affiliate the Y5–Y6 doublet to two distinct fundamental modes. Furthermore, despite the previous assumptions, it was evidenced that the reversal of the doublet intensity ratio cannot be solely explained by hydrogen bonding on the phenol hydroxyl group involved in Tyr. Herein, upon analyzing the observed and theoretical data collected from the cationic species of the tripeptide Gly-Tyr-Gly, the crucial effect of the aromatic side chain orientation, especially that of the χ1 torsion angle defined around the CαCβ bond, on the Tyr doublet intensity ratio has been evidenced.

Non-covalent interaction between hemp seed globulin and two hemp seed phenolic compounds: Mechanism and effects on protein structure, bioactivity, and in vitro simulated digestion

This study focused on elucidating the non-covalent interactions between hemp seed globulin (GLB) and two hemp seed phenolic compounds, Cannabisin A (CA) and Cannabisin B (CB), and to explore these interactions on the protein's structure, conformation, and functionality. Fluorescence quenching and thermodynamic analysis revealed that static quenching governed non-covalent interaction processes, with hydrogen bonds and van der Waals forces functioning as major forces. This was further substantiated by molecular docking studies. The binding affinity order was CA > CB, indicating that the specific phenolic compound had a notable impact on the binding affinity. Furthermore, when complexed with CA, Tyr and Trp residues were exposed to a more hydrophilic environment than when complexed with CB. It was noted that the complexation with either CA or CB consistently affects GLB's secondary structure, particle size, and ζ-potential. GLB treated with the phenolic compounds exhibited enhanced ABTS and DPPH scavenging activities and improved digestibility compared to untreated GLB. Furthermore, the non-covalent interactions significantly increased CA's water solubility, highlighting GLB as a promising natural carrier for hydrophobic bioactive components. These findings hold potential implications for enhancing hemp seed protein applications within the food industry by positively influencing its functional properties and bioactivity.

Interactions between phosvitin and aldehydes affect the release of flavor from Russian sturgeon caviar

The release mechanism of flavor during caviar storage was studied by the interaction between phosvitin and four aldehydes. Gas chromatography–mass spectrometry showed that the binding rate of phosvitin with 3-methylbutanal, nonanal, (E,Z)-2,6-nonadienal, and (E)-2-octenal decreased with an increase in the aldehyde concentrations. Among them, (E,Z)-2,6-Nonadienal (0.5 mM) had the highest binding rate (84.47%). The main quenching mechanism of (E,Z)-2,6-nonadienal with phosvitin was static quenching and the binding force comprised spontaneous hydrophobic interactions. An increase in the aldehyde concentrations reduced the α-helix content of phosvitin and led to aggregation of the microstructure of phosvitin. The results of molecular docking showed that tyr residue contributed the most to the binding of phosvitin to aldehydes. This study has elucidated the mechanism of the effect of caviar protein on changes in the caviar flavor during storage and provides effective strategies for regulation of caviar flavor during storage.

New strategies for evaluating imidacloprid-induced biological consequences targeted to Eisenia fetida species and the corresponding mechanisms of its toxicity

Imidacloprid (IMI), a neonicotinoid insecticide, has a wide variety of applications in both agriculture and horticulture. As a result of it massive and repeated use, its traces remained in soil pose severe damage to soil invertebrates, particularly earthworms. Limited information is available regarding the underlying mechanisms of IMI toxicity toward earthworms at the molecular, transcriptional, and cellular levels. Here, Eisenia fetida coelomocytes and key defensive proteins were selected as targeted receptors to explore the toxic mechanisms of oxidative stress-mediated cytotoxicity, genotoxicity, and antioxidant responses induced by IMI stress and the molecular mechanisms underlying the binding of IMI and superoxide dismutase (SOD)/catalase (CAT). Results showed that IMI exposure destroyed the cell membrane integrity of earthworm cells, causing cell damage and cytotoxicity. The intracellular levels of ROS, including ·O2− and H2O2 were induced by IMI exposure, thereby triggering oxidative stress and damage. Moreover, IMI exposure attenuated the antioxidative stress responses (reduced antioxidant capacity and CAT/SOD activities) and caused deleterious effects (enhanced DNA damage, lipid peroxidation (LPO), and protein carbonylation (PCO)) through ROS-mediated oxidative stress pathway. Aberrant gene expression associated with oxidative stress and defense regulation, including CAT, CRT, MT, SOD, GST, and Hsp70 were induced after IMI exposure. Concentration-dependent conformational and structural alterations of CAT/SOD were observed when IMI binding. Also, direct binding of IMI resulted in significant inhibition of CAT/SOD activities in vitro. Molecular simulation showed that IMI preferred to bind to CAT active center through its direct binding with the key residue Tyr 357, while IMI bound more easily to the connecting cavity of two subunits away from SOD active center. In addition, hydrogen bonds and hydrophobic force are the main driving force of IMI binding with CAT/SOD. These findings have implications for comprehensive evaluation of IMI toxicity to soil eco-safety and offer novel strategies to elucidate the toxic mechanisms and pathways of IMI stress.

ROR2 homodimerization is sufficient to activate a neuronal Wnt/calcium signaling pathway

Wnt signaling plays a key role in the mature CNS by regulating trafficking of NMDA-type glutamate receptors and intrinsic properties of neurons. The Wnt receptor ROR2 has been identified as a necessary component of the neuronal Wnt5a/Ca2+ signaling pathway that regulates synaptic and neuronal function. Since ROR2 is considered a pseudokinase, its mechanism for downstream signaling upon ligand binding has been controversial. It has been suggested that its role is to function as a coreceptor of a G-protein-coupled Wnt receptor of the Frizzled family. We show that chemically induced homodimerization of ROR2 is sufficient to recapitulate key signaling events downstream of receptor activation in neurons, including PKC and JNK kinases activation, elevation of somatic and dendritic Ca2+ levels, and increased trafficking of NMDARs to synapses. In addition, we show that homodimerization of ROR2 induces phosphorylation of the receptor on Tyr residues. Point mutations in the conserved but presumed nonfunctional ATP-binding site of the receptor prevent its phosphorylation, as well as downstream signaling. This suggests an active kinase domain. Our results indicate that ROR2 can signal independently of Frizzled receptors to regulate the trafficking of a key synaptic component. Additionally, they suggest that homodimerization can overcome structural conformations that render the tyrosine kinase inactive. A better understanding of ROR2 signaling is crucial for comprehending the regulation of synaptic and neuronal function in normal brain processes in mature animals.

The Molecular Basis of Catalysis by SDR Family Members Ketoacyl-ACP Reductase FabG and Enoyl-ACP Reductase FabI in Type-II Fatty Acid Biosynthesis.

The short-chain dehydrogenase/reductase (SDR) superfamily members acyl-ACP reductases FabG and FabI are indispensable core enzymatic modules and catalytic orientation controllers in type-II fatty acid biosynthesis. Herein, we report their distinct substrate allosteric recognition and enantioselective reduction mechanisms. FabG achieves allosteric regulation of ACP and NADPH through ACP binding across two adjacent FabG monomers, while FabI follows an irreversible compulsory order of substrate binding in that NADH binding must precede that of ACP on a discrete FabI monomer. Moreover, FabG and FabI utilize a backdoor residue Phe187 or a "rheostat" α8 helix for acyl chain length selection, and their corresponding triad residues Ser142 or Tyr145 recognize the keto- or enoyl-acyl substrates, respectively, facilitating initiation of nucleophilic attack by NAD(P)H. The other two triad residues (Tyr and Lys) mediate subsequent proton transfer and (R)-3-hydroxyacyl- or saturated acyl-ACP production.

Selective turn-on sensing of adenosine diphosphate and phosphate anions by ruthenium (II) polypyridine anchored p-tert-butylcalix[4]arene platform

BackgroundNucleoside polyphosphate (NPP) anions are important for enzymatic activity and should be monitored by scientists in industry and medicine. By elucidating enzyme kinetics and processes, it aids in the discovery of effective inhibitors and activators. Nucleoside polyphosphate (NPP) anions are used by kinases, GTPases, and glycosyltransferases (GTs). Phosphorylation of certain amino acid residues (Ser, Thr, and Tyr) on proteins requires the breakdown of ATP by protein kinases, which produces ADP. Protein kinases, breakdown of ATP, and NPP are the focus of oncology drug development because the aberrant control of kinase activity is a common cause of cancer. ResultsHowever, a discriminative turn-on fluorescent property is exhibited by non-fluorescent p-tertbutylcalix[4]arene modified 1,2,3-triazole containing bis-ruthenium polypyridyl complex (RL) upon the addition of phosphate anions such as (dihydrogen pyrophosphate (H2P2O72−) and dihydrogen phosphate (H2PO4−)) in CH3CN solvent and Adenosine Diphosphate (ADP) in CH3CN/HEPES (pH = 7.4) buffer (9/1, v/v). The probe RL shows a better-recognizing ability with pyrophosphate anion (H2P2O72−) than dihydrogen phosphate anion (H2PO4−). With H2P2O72− and H2PO4− anions, the RL detection limit was calculated to be as low as 83 nM and 198 nM, respectively. SignificanceThe calix[4]arene macrocycle's excellent size and binding cone conformation make it a good host–guest interface for the pyrophosphate anion and ADP. The bis-ruthenium polypyridyl complex's connection to the p-tertbutyl calix[4]arene moiety creates the ADP selectivity turn-on sensor. When moving from mono-nuclear to bi-nuclear ruthenium complex anchored on p-tertbutyl calix[4]arene, the probe can differentiate ADP, ATP, and AMP. Furthermore, this platform is a great resource for creating devices to simultaneously assess phosphate anions in environmental samples.

Insights into the catalytic mechanism of Grimontia hollisae collagenase through structural and mutational analyses.

Grimontia hollisae collagenase (Ghcol) consists of 767 amino acid residues with a single catalytic domain containing the zinc-binding motif H492 EYVH496 . The crystal structure of Ghcol in complex with its substrate (Gly-Pro-hydroxyproline-Gly-Pro-hydroxyproline) and site-directed mutagenesis of active-site Tyr residues revealed the catalytic mechanism: Glu493 functions as an acid and base catalyst while Tyr564 stabilizes the tetrahedral complex in the transition state.

The strategic involvement of IRS in cancer progression

Insulin Receptor Substrate (IRS), an intracellular molecule devoid of an intrinsic kinase activity, is activated upon binding to IR which thereby works as a scaffold, organizing all signaling complexes and initiating the signaling process downstream. The level of IRS proteins and their stability in the cell is mostly maintained through the phosphorylation status of their tyrosine and serine residues. IRS is positively regulated by phosphorylation of its Tyr residues whereas a Ser residue phosphorylation attenuates it, although there exist some exceptions as well. Other post-translational modifications like O-linked glycosylation, N-linked glycosylation and acetylation also play a prominent role in IRS regulation. Since the discovery of the Warburg effect, people have been curious to find out all possible signaling networks and molecules that could lead to cancer and no doubt, the insulin signaling pathway is identified as one such pathway, which is highly deregulated in cancers. Eminent studies reveal that IRS is a pertinent regulator of cancer and is highly overexpressed in the five most commonly occurring cancers namely- Prostate, Ovarian, Breast, Colon and Lung cancers. IRS1 and IRS2 family members are actively involved in the progression, invasion and metastasis of these cancers. Recently, less studied IRS4 has also emerged as a contributor in ovarian, breast, colorectal and lung cancer, but no such studies related to IRS4 are found in Prostate cancer. The involvement of other IRS family members in cancer is still undiscovered and so paves the way for further exploration. This review is a time-lapse study of IRSs in the context of cancer done over the past two decades and it highlights all the major discoveries made till date, in these cancers from the perspective of IRS.

AQcalc: A web server that identifies weak molecular interactions in protein structures.

Weak molecular interactions play an important role in protein structure and function. Computational tools that identify weak molecular interactions are, therefore, valuable for the study of proteins. Here, we present AQcalc, a web server (https://aqcalcbiocomputing.com/) that can be used to identify anion-quadrupole (AQ) interactions, which are weak interactions involving aromatic residue (Trp, Tyr, and Phe) ring edges and anions (Asp, Glu, and phosphate ion) both within proteins and at their interfaces (protein-protein, protein-nucleic acids, and protein-lipid bilayer). AQcalc identifies AQ interactions as well as clusters involving AQ, cation-π, and salt bridges, among others. Utilizing AQcalc we analyzed weak interactions in protein models, even in the absence of experimental structures, to understand the contributions of weak interactions to deleterious structural changes, including those associated with oncogenic and germline disease variants. We identified several deleterious variants with disrupted AQ interactions (comparable in frequency to cation-π disruptions). Amyloid fibrils utilize AQ to bury anions at frequencies that far exceed those observed for globular proteins. AQ interactions were detected three and five times more frequently than the hydrogen-bonded AQ (HBAQ) in fibril structures and protein-lipid bilayer interfaces, respectively. By contrast, AQ and HBAQ interactions were detected with similar frequencies in globular proteins. Collectively, these findings suggest AQcalc will be effective in facilitating fine structural analysis. As other web utilities designed to identify protein residue interaction networks do not report AQ interactions, wide use of AQcalc will enrich our understanding of residue interaction networks and facilitate hypothesis testing by identifying and experimentally characterizing these comparably weak but important interactions.

Molecular interaction mechanisms and cellular response of superoxide dismutase and catalase to fluoranthene.

As an important raw material and intermediate product of the petrochemical industry, fluoranthene (Fla) can be emitted with industrial activities and has become a typical polycyclic aromatic hydrocarbon enriched in the Chinese topsoil layer, posing a significant threat to sensitive soil biota. Here, multispectral tools and molecular simulation techniques were integrated to elucidate the molecular mechanism of Fla interaction with key antioxidant enzymes superoxide dismutase (SOD) and catalase (CAT) at the molecular level. Meanwhile, we further revealed the cellular responses of SOD and CAT and the associated redox states in earthworm (Eisenia fetida) coelomocytes based on the molecular-level results. Our results showed that the exposure to Fla affected the backbone structure of SOD and CAT molecules and resulted in the formation of Fla-SOD polymers as well as an overall reduction in the size of the Fla-CAT binding system. Fla altered the microenvironment around Tyr residues in the SOD molecule and quenched the endogenous fluorescence of Tyr within the CAT molecule. In earthworm coelomocytes, Fla at 60 and 80 μM resulted in a significant elevation of CAT and SOD activities by 114% (p = 0.032) and 6.09% (p = 0.013), respectively. Molecular simulation results suggested that Fla-induced changes in the structure and conformation of SOD and CAT may be the key reason for their altered activities. The related redox homeostasis detection in earthworm coelomocytes indicated that high concentrations (80 μM) of Fla led to a significant accumulation of intracellular ROS (p = 0.018) and resulted in the development of lipid peroxidation. Our work contributes to an in-depth understanding of the biological effect of Fla to sensitive soil fauna, thus providing new ideas for Fla ecological risk prevention and control.

Possible role of essential tyrosine on the protonation of isoalloxazine ring in the excited singlet state and the triplet state in photolyase from Escherichia coli. Molecular orbital study

Photolyases from Escherichia coli. (PLEC) function to repair UV-damaged DNA. Photolyases and cryptochromes (altogether 42 proteins) are found to contain at least one tyrosine (Tyr) residue near the isoalloxazine ring (Iso) of flavin adenine dinucleotide (FAD) within 1.2 nm, Tyr281 in PLEC. Iso in PLEC is surrounded by four Trp residues and one Tyr within 1.2 nm from Iso. Photoinduced charge transfer interactions (PCT) among these chromophores in the Iso-Tyr281-Trp277-Trp338-Trp382-Trp384 system were studied by means of a semi-empirical molecular orbital (MO) method. Structure of the system was extracted from crystal structure of PLEC. In the ground state the PCT interactions between any pairs were negligible. Upon photo-excitation almost one electron transferred from Trp382 to the excited Iso, to which an electron transport chain from Tyr residues at the protein - water interface to Iso is connected. Protonation at N1 or N5 of Iso from Tyr281 markedly stabilized the transition energy in the excited singlet state and triplet state, depending on the polarity of the medium, but not from a source other than Tyr281. In these states, nearly one electron migrates from Tyr281 to Trp382. Effects of the protonation from Tyr281 to the fully reduced Iso were also examined, where total charge of the system was −2. In the ground state the energy of the system was stabilized by the protonation, when the proton was bound to N5 of Iso, but not to N1. In the excited singlet state and triplet state of the fully reduced Iso, the transition energies of the system were also stabilized upon the protonation to N1 or N5 of Iso from Tyr281, but not from a source other than Tyr281. In the ground state almost two negative charges were located at Iso. In the excited singlet state one of two negative charges was mostly localized to Iso and another to Trp277 at the dielectric constant, 3, and to Trp384 at the dielectric constant, 10. In the triplet state without the protonation, one of two negative charges was localized to Iso and another to Trp384 at any dielectric constant. Upon protonation to N1 or N5 of Iso in the triplet state, one of the negative charges was localized to Iso and another to Tyr281 at any value of dielectric constant. Thus Tyr281 closely interacted with Iso in the excited singlet state and triplet state, and other Trp residues in the system through the proton transfer.

Nitrosylation of β2-Tubulin Promotes Microtubule Disassembly and Differentiated Cardiomyocyte Beating in Ischemic Mice.

Beating cardiomyocyte regeneration therapies have revealed as alternative therapeutics for heart transplantation. Nonetheless, the importance of nitric oxide (NO) in cardiomyocyte regeneration has been widely suggested, little has been reported concerning endogenous NO during cardiomyocyte differentiation. Here, we used P19CL6 cells and a Myocardiac infarction (MI) model to confirm NO-induced protein modification and its role in cardiac beating. Two tyrosine (Tyr) residues of β2-tubulin (Y106 and Y340) underwent nitrosylation (Tyr-NO) by endogenously generated NO during cardiomyocyte differentiation from pre-cardiomyocyte-like P19CL6 cells. Tyr-NO-β2-tubulin mediated the interaction with Stathmin, which promotes microtubule disassembly, and was prominently observed in spontaneously beating cell clusters and mouse embryonic heart (E11.5d). In myocardial infarction mice, Tyr-NO-β2-tubulin in transplanted cells was closely related with cardiac troponin-T expression with their functional recovery, reduced infarct size and thickened left ventricular wall. This is the first discovery of a new target molecule of NO, β2-tubulin, that can promote normal cardiac beating and cardiomyocyte regeneration. Taken together, we suggest therapeutic potential of Tyr-NO-β2-tubulin, for ischemic cardiomyocyte, which can reduce unexpected side effect of stem cell transplantation, arrhythmogenesis.

Pharmacophore derived 3D-QSAR, molecular docking, and simulation studies of quinoxaline derivatives as ALR2 inhibitors

Aldose Reductase 2 (ALR2), a key enzyme of the polyol pathway, plays a crucial role in the pathogenesis of diabetic complications. Quinoxaline scaffold-based compounds have been identified as potential ALR2 inhibitors for the management of diabetic complications. In the present work, molecular dynamic simulation studies in conjugation with pharmacophore mapping and atom-based 3D-QSAR were performed on a dataset of 99 molecules in comparison with Epalrestat (reference) to mark the desirable structural features of quinoxaline analogs to generate a probable template for designing novel and effective ALR2 inhibitors. The most potent compound 81 was subjected to MD simulation studies and found to be stable, with better interactions with the binding pocket as compared to Epalrestat. The MM-GBSA and MM-PBSA calculations showed that compound 81 possessed binding free energies of −35.96 and −4.92 kcal/mol, respectively. Atom-based 3D-QSAR yielded various pharmacophoric features with excellent statistical measures, such as correlation coefficient (R 2 value), F-value (Fischer ratio), Q 2 value (cross-validated correlation coefficient), and Pearson’s R-value for training and test sets. Furthermore, the pharmacophore mapping provided a five-point hypothesis (AADRR) and docking analysis revealed the active ligand-binding orientations on the active site’s amino acid residues TYR 48, HIE 110, TRP 111, and TRP 219. The results of this study will help in designing potent inhibitors of ALR2 for the management of diabetic complications. Communicated by Ramaswamy H. Sarma

Exploring the Landscape of the PP7 Virus-like Particle for Peptide Display.

Self-assembling virus-like particles (VLPs) can tolerate a wide degree of genetic and chemical manipulation to their capsid protein to display a foreign molecule polyvalently. We previously reported the successful incorporation of foreign peptide sequences in the junction loop and onto the C-terminus of PP7 dimer VLPs, as these regions are accessible for surface display on assembled capsids. Here, we report the implementation of a library-based approach to test the assembly tolerance of PP7 dimer capsid proteins to insertions or terminal extensions of randomized 15-mer peptide sequences. By performing two iterative rounds of assembly-based selection, we evaluated the degree of favorability of all 20 amino acids at each of the 15 randomized positions. Deep sequencing analysis revealed a distinct preference for the inclusion of hydrophilic peptides and negatively charged amino acids (Asp and Glu) and the exclusion of positively charged peptides and bulky and hydrophobic amino acid residues (Trp, Phe, Tyr, and Cys). Within the libraries tested here, we identified 4000 to 22,000 unique 15-mer peptide sequences that can successfully be displayed on the surface of the PP7 dimer capsid. Overall, the use of small initial libraries consisting of no more than a few million members yielded a significantly larger number of unique and assembly-competent VLP sequences than have been previously characterized for this class of nucleoprotein particle.

Amyloid Fibrils Formed by Short Prion-Inspired Peptides Are Metalloenzymes.

Enzymes typically fold into defined 3D protein structures exhibiting a high catalytic efficiency and selectivity. It has been proposed that the earliest enzymes may have arisen from the self-assembly of short peptides into supramolecular amyloid-like structures. Several artificial amyloids have been shown to display catalytic activity while offering advantages over natural enzymes in terms of modularity, flexibility, stability, and reusability. Hydrolases, especially esterases, are the most common artificial amyloid-like nanozymes with some reported to act as carbonic anhydrases (CA). Their hydrolytic activity is often dependent on the binding of metallic cofactors through a coordination triad composed of His residues in the β-strands, which mimic the arrangement found in natural metalloenzymes. Tyr residues contribute to the coordination of metal ions in the active center of metalloproteins; however, their use has been mostly neglected in the design of metal-containing amyloid-based nanozymes. We recently reported that four different polar prion-inspired heptapeptides spontaneously self-assembled into amyloid fibrils. Their sequences lack His but contain three alternate Tyr residues exposed to solvent. We combine experiments and simulations to demonstrate that the amyloid fibrils formed by these peptides can efficiently coordinate and retain different divalent metal cations, functioning as both metal scavengers and nanozymes. The metallized fibrils exhibit esterase and CA activities without the need for a histidine triad. These findings highlight the functional versatility of prion-inspired peptide assemblies and provide a new sequential context for the creation of artificial metalloenzymes. Furthermore, our data support amyloid-like structures acting as ancestral catalysts at the origin of life.

Flavonoids as potential reactivators of structural mutation p53Y220C by computational and cell-based studies

The p53 Y220C is one of the most frequently observed structural mutants in various human cancers. The substitution of residue Tyr to Cys makes the p53 DNA binding domain susceptible to solvent entry into the hydrophobic core of the domain thereby destabilizing p53, which results in loss of its tumor suppressor activity. The mutation creates a structural crevice at the region between S3/S4 and S7/S8 loops in the DNA binding domain which can be targeted by small molecules. Studies have shown that the synthetic and natural compounds could bind to this crevice and restore the structure and function of the mutant p53Y220C to the wild type. In our previous study, we have shown Curcumin could rescue the function of mutant p53Y220C in pancreatic cancer cell line BxPC-3 harboring genomic mutation. In this study, we explored six flavonoids structurally similar to Curcumin such as Apigenin, Isoliquiritigenin, Liquiritigenin, Luteolin, Methylophiopogonanone A (MPA), and Methylophiopogonanone B (MPB) to test their potency to restore p53Y220C by molecular docking, molecular dynamics simulations and cytotoxicity assay. The secondary structure analysis after the MD simulations suggested that these compounds could stabilize the mutant p53 DNA binding domain to the wild type. In the cell-based cytotoxicity studies using p53Y220C harbouring BxPC-3 cell lines, the compounds MPA and MPB showed 75% cell death at 100 µM concentration. We proposed that the flavonoids MPA and MPB have the therapeutic potential to restore p53Y220C and could be used as a combinatorial therapy to reduce the dosage burden. Communicated by Ramaswamy H. Sarma

Computational Prediction of 3,5-Diaryl-1H-Pyrazole and spiropyrazolines derivatives as potential acetylcholinesterase inhibitors for alzheimer disease treatment by 3D-QSAR, molecular docking, molecular dynamics simulation, and ADME-Tox

The efficacy of 40 synthesized variants of 3,5-diaryl-1H-pyrazole and spiropyrazoline’ derivatives as acetylcholinesterase inhibitors is verified using a quantitative three-dimensional structure-activity relationship (3D-QSAR) by comparative molecular field analysis (CoMFA) and molecular similarity index analysis (CoMSIA) models. In this research, different field models proved that CoMSIA/SE model is the best model with high predictive power compared to several models (Qved2 = O.65; R2 = 0.980; R2test = 0.727). Also, contour maps produced by CoMSIA/SE model have been employed to prove the key structural needs of the activity. Consequently, six new compounds have been generated. Among these compounds, M4 and M5 were the most active but remained toxic and had poor absorption capacities. While the M1, M2, M3 and M6 remained highly active while respecting ADMET's characteristics. Molecular docking results showed compound M2 better with acetylcholinesterase than compound 22. The interactions are classical hydrogen bonding with residues TYR:124, TYR:72, and SER:293, which play a critical role in the biological activity as AChE inhibitors. MD results confirmed the docking results and showed that compound M2 had satisfactory stability with (ΔGbinding = −151.225 KJ/mol) in the active site of AChE receptor compared with compound 22 (ΔGbinding = −133.375 KJ/mol). In addition, both compounds had good stability regarding RMSD, Rg, and RMSF. The previous results show that the newly designed compound M2 is more active in the active site of AChE receptor than compound 22. Communicated by Ramaswamy H. Sarma

Comprehending the intermolecular interaction of JAK inhibitor fedratinib with bovine serum albumin (BSA)/human alpha-1-acid glycoprotein (HAG): Multispectral methodologies and molecular simulation

The primary coverage of this paper is to investigate the molecular interaction of JAK2 inhibitor, fedratinib (FED) with BSA/HAG proteins through multispectral approaches and molecular docking as well as MD calculation. Arrival at a conclusion, the endogenous fluorescence of BSA/HAG protein was quenched separately in the form of static and mixed quenching. The FED-BSA and FED-HAG complexes with the stoichiometric ratio of 1:1 were formed in the interaction process. And, The Kb values of these complexes were of 104–105 M−1 and 105–106 M−1, respectively, representing that the FED-HAG complex exhibited a comparatively high affinity compared to the FED-BSA complex. It is confimed that FED inserted into the interface area between subdomain IIA and IIB of BSA (marked as site II') and the bucket-shaped hydrophobic cavity of HAG, respectively, resulting in the slight alteration in the secondary structure of BSA/HAG and the micro-environment round Tyr and Trp residues. The expetimental results also confirmed that van der Waals forces (VDW), hydrogen bonds and hydrophobic interaction played a dominant role in the formation of two stable complexes. The above experimental results were supplemented and verified through molecular docking and MD simulation. Meanwhile, the effects of common ions on affinity were explored. This study could shine a light on evaluating the pharmacological properties of the JAK inhibitor FED, understanding the distribution and operation of the drug in the body, and leading to the development of the creation of novel medication devise.

Human 2'-Deoxynucleoside 5'-Phosphate N-Hydrolase 1: Mechanism of 2'-Deoxyuridine 5'-Monophosphate Hydrolysis.

The enzyme 2'-deoxynucleoside 5'-phosphate N-hydrolase 1 (DNPH1) catalyzes the N-ribosidic bond cleavage of 5-hydroxymethyl-2'-deoxyuridine 5'-monophosphate to generate 2-deoxyribose 5-phosphate and 5-hydroxymethyluracil. DNPH1 accepts other 2'-deoxynucleoside 5'-monophosphates as slow-reacting substrates. DNPH1 inhibition is a promising strategy to overcome resistance to and potentiate anticancer poly(ADP-ribose) polymerase inhibitors. We solved the crystal structure of unliganded human DNPH1 and took advantage of the slow reactivity of 2'-deoxyuridine 5'-monophosphate (dUMP) as a substrate to obtain a crystal structure of the DNPH1:dUMP Michaelis complex. In both structures, the carboxylate group of the catalytic Glu residue, proposed to act as a nucleophile in covalent catalysis, forms an apparent low-barrier hydrogen bond with the hydroxyl group of a conserved Tyr residue. The crystal structures are supported by functional data, with liquid chromatography-mass spectrometry analysis showing that DNPH1 incubation with dUMP leads to slow yet complete hydrolysis of the substrate. A direct UV-vis absorbance-based assay allowed characterization of DNPH1 kinetics at low dUMP concentrations. A bell-shaped pH-rate profile indicated that acid-base catalysis is operational and that for maximum kcat/KM, two groups with an average pKa of 6.4 must be deprotonated, while two groups with an average pKa of 8.2 must be protonated. A modestly inverse solvent viscosity effect rules out diffusional processes involved in dUMP binding to and possibly uracil release from the enzyme as rate limiting to kcat/KM. Solvent deuterium isotope effects on kcat/KM and kcat were inverse and unity, respectively. A reaction mechanism for dUMP hydrolysis is proposed.