Quantitative Structure–Activity Relationship Study of 5-Iodo- and Diaryl-analogues of Tubercidin: Inhibitors of Adenosine Kinase

The adenosine kinase inhibitory (AKI) activity of 5-iodo and diaryl analogues of tubercidin is quantitatively analyzed using Fujita-Ban and Hansch type analyses. The Fujita-Ban analysis being a non-parametric approach assigned the highest contribution to Cl at the X-position, C6H4-4-Cl, C6H5, 2-furanyl and I at the Y-position and CH2NH2 and CH3 at the Z-position. In addition, a OH substituent at the C-position also emerged as a better choice possibly due to its engagement in hydrogen bonding with some active site function. Thus a compound having Cl, C6H4-4-Cl, CH2NH2 and OH respectively at X-, Y-, Z- and C-positions is predicted to have a potency nearly 1.5 orders of magnitude higher than the most potent compound of the parent data set. The Hansch type analysis, on the other hand, is a parametric approach and is carried out on two sub-sets of original compounds. This sub-division is based on size and nature of the substituents present at the X- and Y-positions. For the compounds in the first sub-set the derived significant correlation equation suggested that the substituent at the Y-position exhibiting a higher field effect and a substituent such as Cl and CH2NH2 at X- and Z-positions, respectively, are important for a compound to show increased AKI activity. Thio/alkylthio at X and CH2OCH3 at Z, on the other hand, lead to a detrimental effect. Similarly for the compounds in the second sub-set, the derived significant correlation equation showed that a substituent at the X-position having a higher negative field effect, a substituent at the Y-position having bulky groups and the C-position occupied by a OH group are essential for enhancement of the activity of a compound.     

The Critical Aggregation Concentration of β-Lactoglobulin-Based Fibril Formation

The critical aggregation concentration (CAC) for fibril formation of β-lactoglobulin (β-lg) at pH 2 was determined at 343, 353, 358, 363, and 383 K using a Thioflavin T assay and was approximately 0.16 wt%. The accuracy of the CAC was increased by measuring the conversion into fibrils at different stirring speeds. The corresponding binding energy per mol, as determined from the CAC, was 13 RT (∼40 kJ mol⁻¹) for the measured temperature range. The fact that the CAC was independent of temperature within the experimental error indicates that the fibril formation of β-lg at pH 2 and the measured temperature range is an entropy-driven process.     

Identification of Small Molecule Inhibitors of PTPσ through an Integrative Virtual and Biochemical Approach

PTPσ is a dual-domain receptor type protein tyrosine phosphatase (PTP) with physiologically important functions which render this enzyme an attractive biological target. Specifically, loss of PTPσ has been shown to elicit a number of cellular phenotypes including enhanced nerve regeneration following spinal cord injury (SCI), chemoresistance in cultured cancer cells, and hyperactive autophagy, a process critical to cell survival and the clearance of pathological aggregates in neurodegenerative diseases. Owing to these functions, modulation of PTPσ may provide therapeutic value in a variety of contexts. Furthermore, a small molecule inhibitor would provide utility in discerning the cellular functions and substrates of PTPσ. To develop such molecules, we combined in silico modeling with in vitro phosphatase assays to identify compounds which effectively inhibit the enzymatic activity of PTPσ. Importantly, we observed that PTPσ inhibition was frequently mediated by oxidative species generated by compounds in solution, and we further optimized screening conditions to eliminate this effect. We identified a compound that inhibits PTPσ with an IC₅₀ of 10 µM in a manner that is primarily oxidation-independent. This compound favorably binds the D1 active site of PTPσ in silico, suggesting it functions as a competitive inhibitor. This compound will serve as a scaffold structure for future studies designed to build selectivity for PTPσ over related PTPs.     

Synthesis,Antioxidant Activity,and Structure–Activity Relationship of SCAP1 Analogues

Nine analogues of antioxidant peptide SCAP1 were successfully synthesised using a solid-phase method on a 2-chlorotrytil resin. The compounds were obtained in a range of yields of 7.0–57.8%. The occurrence of aggregation during the synthesis is suspected to be responsible for the poor yields. All peptides were characterized by high-resolution time-of-flight mass spectrometry (HR-TOFMS) and nuclear magnetic resonance (NMR). The antioxidant activities of the SCAP1 analogues as well as SCAP1 were analysed utilising the 2,2-diphenyl-1-picryl-hydrazyl-hydrate (DPPH) assay. The results revealed that all of the analysed peptides exhibited moderate antioxidant properties. Moreover, the evaluation of the structure–activity relationship showed that the Asn residue is an important requirement for the antioxidant activity of SCAP1. The replacement of Asn with other amino acid residues (Thr, Pro, Tyr, Trp and Phe) resulted in a decrease in the IC₅₀ values of the peptides. Notably, however, the replacement of the Lys residue with Val marginally increased the activity.

     

A Quantitative Structure–Activity Relationship Study on a Series of Na+, K+-ATPase Inhibitors

A quantitative structure–activity relationship (QSAR) study has been made on a new series of digitalis-like Na⁺,K⁺-ATPase inhibitors in which the guanylhydrazone group has been replaced by an aminoalkyloxime group. The correlations obtained have shown that the oxime moiety, primary amine group, overall size, and polarizability of the new type of substituents are higly beneficial to the Na⁺,K⁺-ATPase inhibition potency of the compounds and that their effect can be quantitatively assessed. The study also showed that the inotropic activity of the compounds is very well correlated with their Na⁺,K⁺-ATPase inhibition potency.     

Structure–Activity Relationship of novel phenylacetic CXCR1 inhibitors

We reported recently the Structure–Activity Relationship (SAR) of a class of CXCL8 allosteric modulators. They invariably share a 2-arylpropionic moiety so far considered a key structural determinant of the biological activity. We show the results of recent SAR studies on a novel series of phenylacetic derivatives supported by a combined approach of mutagenesis experiments and conformational analysis. The results suggest novel insights on the fine role of the propionic/acetic chain in the modulation of CXCL8 receptors.     

Chromone-Fused Cytosine Analogues: Synthesis,Biological Activity,and Structure–Activity Relationship

The preparation of a series of novel chromone-fused cytosine analogues, i.e., chromeno[2,3-d]pyrimidines has been carried out from substituted 2-amino-4-oxo-4H-chromene-3-carbonitriles with urea, thiourea, and guanidine under different reaction conditions. These chromone-fused cytosine analogues were evaluated for their in vitro activity against Mycobacterium tuberculosis H₃₇Rv strain and different microbial pathogenic strains in cell culture for their structure–activity relationships, respectively. Among the synthesized compounds, 2d, 3a, and 4e showed better results against Mycobacterium tuberculosis H₃₇Rv. The compounds 2a, 2b, and 3a showed potential antibacterial activity against E. coli and P. aeruginosa, while the majority of compounds were found to be active against S. aureus as compared to ampicillin. The synthesized cytosine analogues having an imine (–C&dbnd;NH) have been less sensitive to the bacterial and fungal strains but have a more beneficial effect on Mycobacterium tuberculosis H₃₇Rv.     

l-Ala Modified Analogues of Amyloid β-Peptide Residue 17-20: Self-Association and Amyloid-like Fibril Formation

l-Ala modified analogues of amyloid β-peptide residue 17-20 LVFF (-l-Leu-l-Val-l-Phe-l-Phe-) have been designed and synthesized to study their self-assembling propensity, the nature of intermolecular interactions and rationalize with short hydrophobic sequences in the middle of Aβ that have important role in the neuropathology of Alzheimer’s disease. The peptides sequences LVFA and LAFA have been adopted from the β-sheet region of non-amyloidogenic proteins (hemoglobin-like falvoprotein and ATP synthase C chain, respectively). All the reported peptides self-associate into amyloid-like fibrils which are readily stained with a physiological dye Congo red and exhibits green gold birefringence under polarized light. The solid state FTIR studies of the fibrils reveal that the reported peptides self-associate through intermolecular hydrogen bonds to form antiparallel β-sheet structure, which is also supported by molecular modeling studies. This result suggests that l-Ala analogous of Aβ17-20, LVFA and LAFA also have virtually identical aggregation behavior.     

Structure Activity Relationship amongst Some Fungitoxic α-Naphthoquinones of Angiosperm Origin

Rubusoside, the β-D-glucosyl ester of 13-O-D-glucosyl-steviol which was isolated from leaves of Rubus suavissimus collected in China as the major sweet principle (yield: 5.4%), was subjected to α-1 4 transglucosylation with the cyclodextrin glucosyltransferase produced by Bacillus megaterium Strain No. 5 using soluble starch as a donor. A significant improvement in the quality of sweetness was observed for the crude reaction mixture, which was separated into mono-, di-, tri-, tetra-, penta-, and hexa-glucosylated products. All isomers of the mono- and di-glucosylated products were further separated. Evaluation of the sweetness of these products compared with stevioside, rebaudioside A, etc. disclosed that the ratio of the number of glucose units at the 13-hydroxyl group to that at 19-carboxyl group seems to have a significant relationship with the sweetness as well as the quality of taste for glucosides of this type.     

Investigation of the Relationship between the Lectin Activity of Azospirilla and Their α-Glucosidase, β-Glucosidase,and β-Galactosidase

The activities of -glucosidase, -glucosidase, and -galactosidase were studied during the isolation and purification of lectins from Azospirillum brasilenseSp7 and Azospirillum lipoferum59b cells. These enzymatic activities were revealed in crude extracts of surface proteins, protein fraction precipitated with ammonium sulfate or ethanol–acetone mixture, and protein fraction obtained by gel filtration on Sephadex G-75. The distribution of the enzymes between different protein fractions varied for the azospirilla studied. The cofunction of the A. brasilenseSp7 lectin and -galactosidase on the cell surface is assumed. A strong interaction between the A. lipoferum59b lectin and glucosidases was revealed. The lectin from A. lipoferum59b may possess saccharolytic activity.     

Activity of plasma membrane β-galactosidase and β-glucosidase

Human fibroblasts produce ceramide from sialyllactosylceramide on the plasma membranes. Sialidase Neu3 is known to be plasma membrane associated, while only indirect data suggest the plasma membrane association of β-galactosidase and β-glucosidase. To determine the presence of β-galactosidase and β-glucosidase on plasma membrane, cells were submitted to cell surface biotinylation. Biotinylated proteins were purified by affinity column and analyzed for enzymatic activities on artificial substrates. Both enzyme activities were found associated with the cell surface and were up-regulated in Neu3 overexpressing cells. These enzymes were capable to act on both artificial and natural substrates without any addition of activator proteins or detergents and displayed a trans activity in living cells.     

Amyloid-Like Fibril Formation by Tachykinin Neuropeptides and Its Relevance to Amyloid β-Protein Aggregation and Toxicity

Protein aggregation and amyloid formation are associated with both pathological conditions in humans such as Alzheimer's disease and native functions such as peptide hormone storage in the pituitary secretory granules in mammals. Here, we studied amyloid fibrils formation by three neuropeptides namely physalaemin, kassinin and substance P of tachykinin family using biophysical techniques including circular dichroism, thioflavin T, congo red binding and microscopy. All these neuropeptides under study have significant sequence similarity with Aβ(25-35) that is known to form neurotoxic amyloids. We found that all these peptides formed amyloid-like fibrils in vitro in the presence of heparin, and these amyloids were found to be nontoxic in neuronal cells. However, the extent of amyloid formation, structural transition, and morphology were different depending on the primary sequences of peptide. When Aβ(25-35) and Aβ40 were incubated with each of these neuropeptides in 1:1 ratio, a drastic increase in amyloid growths were observed compared to that of individual peptides suggesting that co-aggregation of Aβ and these neuropeptides. The electron micrographs of these co-aggregates were dissimilar when compared with individual peptide fibrils further supporting the possible incorporation of these neuropeptides in Aβ amyloid fibrils. Further, the fibrils of these neuropeptides can seed the fibrils formation of Aβ40 and reduced the toxicity of preformed Aβ fibrils. The present study of amyloid formation by tachykinin neuropeptides is not only providing an understanding of the mechanism of amyloid fibril formation in general, but also offering plausible explanation that why these neuropeptide might reduce the cytotoxicity associated with Alzheimer's disease related amyloids.     

Inhibition of Aggregation of Amyloid β42 by Arginine-Containing Small Compounds

Aggregations of proteins are in many cases associated with neurodegenerative diseases such as Alzheimer’s (AD). Small compounds capable of inhibiting protein aggregation are expected to be useful for not only in the treatment of disease but also in probing the structures of aggregated proteins. In previous studies using phage display, we found that arginine-rich short peptides consisting of four or seven amino acids bound to soluble 42-residue amyloid β (Aβ42) and inhibited globulomer (37/48 kDa oligomer) formation. In the present study, we searched for arginine-containing small molecules using the SciFinder searching service and tested their inhibitory activities against Aβ42 aggregation, by sodium dodecyl sulfate (SDS)-PAGE and thioflavine T binding assay. Commercially available Arg-Arg-7-amino-4-trifluoromethylcoumarin was found to exhibit remarkable inhibitory activities to the formation of the globulomer and the fibril of Aβ42. This chimera-type tri-peptide is expected to serve as the seed molecule of a potent inhibitor of the Aβ aggregation process.     

Anti-Barnacle Activities of Isothiocyanates Derived from β-Citronellol and Their Structure–Activity Relationships

Antifouling agents with low toxicity are in high demand for sustaining marine industries and the environment. This study aimed to synthesize 15 isothiocyanates derived from β-citronellol and evaluate their antifouling activities and toxicities against cypris larvae of the barnacle Amphibalanus amphitrite. The synthesized isothiocyanates exhibited effective antifouling activities (EC₅₀=0.10–3.33 μg mL⁻¹) with high therapeutic ratios (LC₅₀/EC₅₀ >30). Four isothiocyanates with an amide or isocyano group showed great potential as effective antifouling agents (EC₅₀=0.10–0.32 μg mL⁻¹, LC₅₀/EC₅₀=104–833). The enantiomers of the isothiocyanates only slightly differed in their antifouling activities. These results may serve as a basis for further research and development of β-citronellol-derived isothiocyanates as effective low-toxic antifouling agents. To the best of our knowledge, this study is the first to report the antifouling activities of isothiocyanates derived from accessible natural products.     

Polymorphic C-terminal β-Sheet Interactions Determine the Formation of Fibril or Amyloid β-derived Diffusible Ligand-like Globulomer for the Alzheimer Aβ42 Dodecamer

The relationship between amyloid deposition and cellular toxicity is still controversial. In addition to fibril-forming oligomers, other soluble Aβ forms (amyloid β-derived diffusible ligands (ADDLs)) were also suggested to form and to present different morphologies and mechanisms of toxicity. One ADDL type, the “globulomer,” apparently forms independently of the fibril aggregation pathway. Even though many studies argue that such soluble Aβ oligomers are off fibril formation pathways, they may nonetheless share some structural similarity with protofibrils. NMR data of globulomer intermediates, “preglobulomers,” suggested parallel in-register C-terminal β-sheets, with different N-terminal conformations. Based on experimental data, we computationally investigate four classes of Aβ dodecamers: fibril, fibril oligomer, prefibril/preglobulomer cluster, and globulomer models. Our simulations of the solvent protection of double-layered fibril and globulomer models reproduce experimental observations. Using a single layer Aβ fibril oligomer β-sheet model, we found that the C-terminal β-sheet in the fibril oligomer is mostly curved, preventing it from quickly forming a fibril and leading to its breaking into shorter pieces. The simulations also indicate that β-sheets packed orthogonally could be the most stable species for Aβ dodecamers. The major difference between fibril-forming oligomers and ADDL-like oligomers (globulomers) could be the exposure of Met-35 patches. Although the Met-35 patches are necessarily exposed in fibril-forming oligomers to allow their maturation into fibrils, the Met-35 patches in the globulomer are covered by other residues in the orthogonally packed Aβ peptides. Our results call attention to the possible existence of certain “critical intermediates” that can lead to both seeds and other soluble ADDL-like oligomers.     

IgE-Suppressive Activity of (−)-Matairesinol and Its Structure-Activity Relationship

The IgE-suppressive activity of (?)-matairesinol is demonstrated, and the structure-activity relationship of (?)-matairesinol clarified. 3′,4-Dihydroxy-3,4′-dimethoxylignano-9,9′-lactone showed higher IgE-suppressive activity than (?)-matairesinol without any cytotoxic activity. Some derivatives bearing a longer and more bulky alkoxy group at the 3 or 4 position showed IgE-accelerative activity.     

Discovery of a Small Molecule Agonist of Phosphatidylinositol 3-Kinase p110α That Reactivates Latent HIV-1

Combination antiretroviral therapy (cART) can effectively suppress HIV-1 replication, but the latent viral reservoir in resting memory CD4⁺ T cells is impervious to cART and represents a major barrier to curing HIV-1 infection. Reactivation of latent HIV-1 represents a possible strategy for elimination of this reservoir. In this study we describe the discovery of 1,2,9,10-tetramethoxy-7H-dibenzo[de,g]quinolin-7-one (57704) which reactivates latent HIV-1 in several cell-line models of latency (J89GFP, U1 and ACH-2). 57704 also increased HIV-1 expression in 3 of 4 CD8⁺-depleted blood mononuclear cell preparations isolated from HIV-1-infected individuals on suppressive cART. In contrast, vorinostat increased HIV-1 expression in only 1 of the 4 donors tested. Importantly, 57704 does not induce global T cell activation. Mechanistic studies revealed that 57704 reactivates latent HIV-1 via the phosphatidylinositol 3-kinase (PI3K)/protein kinase B (Akt) signaling pathway. 57704 was found to be an agonist of PI3K with specificity to the p110α isoform, but not the p110β, δ or γ isoforms. Taken together, our work suggests that 57704 could serve as a scaffold for the development of more potent activators of latent HIV-1. Furthermore, it highlights the involvement of the PI3K/Akt pathway in the maintenance of HIV-1 latency.     

Effect of Zn（Ⅱ） on the Structure and Biological Activity of Natural β-NGF

Only β-NGF, the subunit of the 7S NGF complex, exhibits NGF activity, but the function ofthe zinc ion in native β-NGF has received little attention. Flameless atomic absorption spectroscopy (FAAS)measurements reveal that native β-NGF contains Zn(Ⅱ) with a Zn(Ⅱ)/β-NGF stoichiometry of 1 : 14.6.The presence of Zn(Ⅱ) in the native molecule results in significant changes of the secondary structure andlocal tertiary structure around Trp(s) with respect to those of apo β-NGF, as suggested by spectra offluorescence and circular dichrosim. Stopped-flow studies show that there are at least two steps during theinteraction of Zn(Ⅱ) with the apo form. In comparison with its apo form, the native β-NGF shows a higherability to trigger the proliferation of TF1 cells and mediate the survival of PC 12. Thus it is most likely that thestructural changes caused by the presence of Zn(II) directly lead to the increase in the biological activity of β-NGE All results indicate that Zn(Ⅱ) in native β-NGF plays an important role in the structure and thebiological activity of the protein.     

Effect of Oil Type on Formation,Structure and Thermal Properties of γ-oryzanol and β-sitosterol-Based Organogels

Oil sources characterized of increasing viscosity and polarity (flax-seed oil, sunflower oil, extra virgin olive oil, triolein, castor oil) were gelled by using mixtures of β-sitosterol and γ-oryzanol (5, 10 and 20 % w/w). The gelling time, thermal properties as well as structure characteristics were determined. As the oil viscosity increased the gelling time increased. The effect of oil type resulted more evident as the structurant concentration decreased. Samples containing 5 % of the most viscous and polar castor oil did not gelled over the entire experiment. When gels were formed, the firmness of samples decreased in concomitance with modifications of thermal data as the oil viscosity increased. During storage at 20 °C the gels became stronger as consequence of the progression of the aggregation among sterol-sterol ester assemblages. Once again, less structurants were in the mixture more evident was the influence of oil type. These results were attributed to the increase of the difficulty of β-sitosterol and γ-oryzanol molecules to pack together as the oil viscosity increased.