Synthesis of novel analogs of aromatic peptide nucleic acids (APNAs) with modified conformational and electrostatic properties

Aromatic peptide nucleic acid analogs having an N-(2-aminobenzyl)glycine backbone (APNA 1) were previously identified as promising new leads for the design of polyaromatic DNA mimics. Structural modifications of 1, which lock the aromatic backbone into a unique conformation, while maintaining the same space distribution between the nucleobases as in 1, were investigated. The electrostatic potential of the aromatic backbone was also modified in an attempt to improve the solubility of these compounds in aqueous media and to evaluate how the quadrapole of the aromatic backbone may influence the biophysical properties of the APNA oligomers. PNA hexamers containing a single monomer insert of each new APNA monomer were used to explore the hybridization properties of these analogs with poly rA and poly dA. Preliminary results indicated that these modifications do not seriously alter the molecular recognition properties of APNAs towards DNA and RNA.     

A sequence and structural study of transmembrane helices

A comparison is made between the distribution of residue preferences, three dimensional nearest neighbour contacts, preferred rotamers, helix-helix crossover angles and peptide bond angles in three sets of proteins: a non-redundant set of accurately determined globular protein structures, a set of four-helix bundle structures and a set of membrane protein structures. Residue preferences for the latter two sets may reflect overall helix stabilising propensities but may also highlight differences arising out of the contrasting nature of the solvent environments in these two cases. The results bear out the expectation that there may be differences between residue type preferences in membrane proteins and in water soluble globular proteins. For example, the -branched residue types valine and isoleucine are considerably more frequently encountered in membrane helices. Likewise, glycine and proline, residue types normally associated with `helix-breaking' propensity are found to be relatively more common in membrane helices. Three dimensional nearest neighbour contacts along the helix, preferred rotamers, and peptide bond angles are very similar in the three sets of proteins as far as can be ascertained within the limits of the relatively low resolution of the membrane proteins dataset. Crossing angles for helices in the membrane protein set resemble the four helix bundle set more than the general non-redundant set, but in contrast to both sets they have smaller crossing angles consistent with the dual requirements for the helices to form a compact structure while having to span the membrane. In addition to the pairwise packing of helices we investigate their global packing and consider the question of helix supercoiling in helix bundle proteins.     

The use of glass capillary columns for the analysis of polar natural products

Two published procedures for glass capillary column production are applied to produce capillaries for chromatography of polar natural compounds. Soda lime glass capillaries, after leaching with aqueous HCL, are either treated with colloidal silicic acid or with barium carbonate and coated with either Silar 7CP or SE 52. A test mixture as well as polar carbohydrate and peptide mixtures are chromatographed on the different columns and their chromatographic properties are evaluated. Combined capillary gas chromatography-electron impact and chemical ionization mass spectrometry are used for identification of the peptide sequence.     

LyP-1 peptide-functionalized gold nanoprisms for SERRS imaging and tumor growth suppressing by PTT induced-hyperthermia

The gold nanoprisms (GNPs) have exhibited special plasmonic properties for biomedical applications because of their unique shapes and dimensions. Based on their optical performance, the NIR dye IR780 not only enabled the GNPs-based nanosystem as SERRS nanoparticles for Raman-encoded molecular imaging, but also enhanced the plasmonic photothermal property by laser irradiation. Meanwhile, the GNPs/IR780-Lyp-1 by introduction of tumor-homing peptide segment LyP-1, which presents high affinity to p32 protein, demonstrated the increased enrichment in tumor region and enhanced photothermal therapy efficacy.     

THPep: A machine learning-based approach for predicting tumor homing peptides

In the present era, a major drawback of current anti-cancer drugs is the lack of satisfactory specificity towards tumor cells. Despite the presence of several therapies against cancer, tumor homing peptides are gaining importance as therapeutic agents. In this regard, the huge number of therapeutic peptides generated in recent years, demands the need to develop an effective and interpretable computational model for rapidly, effectively and automatically predicting tumor homing peptides. Therefore, a sequence-based approach referred herein as THPep has been developed to predict and analyze tumor homing peptides by using an interpretable random forest classifier in concomitant with amino acid composition, dipeptide composition and pseudo amino acid composition. An overall accuracy and Matthews correlation coefficient of 90.13% and 0.76, respectively, were achieved from the independent test set on an objective benchmark dataset. Upon comparison, it was found that THPep was superior to the existing method and holds high potential as a useful tool for predicting tumor homing peptides. For the convenience of experimental scientists, a web server for this proposed method is provided publicly at http://codes.bio/thpep/.     

Synthesis and antiangiogenic activities of 5-amino-1,3-dihydro-1, 3-dioxo-2H-isoindole-2-propanoic acid derivatives

Based on the structure-activity relationships and antiangiogenic mechanism of RGD-containing peptides,a series of 5-amino- 1,3-dihydro-1,3-dioxo-2H-isoindole derivatives were synthesized.The structures were characterized by ~1H NMR,MS and elementary analysis.There ability to inhibit angiogenesis were evaluated by chick embryo chorioallantoic membrane assay at 10~(-5) mol/L.Compounds 7a and 7b displayed obvious antiangiogenic activity.     

Synthesis of protected peptides from the human IgG1 hinge region on PEG support using disulfide bond synthons and alkaline or enzymatic detachment

Peptides from the hinge region of human IgG1 are potential defined carriers of synthetic immunogens. Their synthesis was carried out on the soluble support—PEG-OMe 2000 using disulfide bond synthons. The loading capacity of the polymer was increased twofold by anchoring the lysine as a simple branching unit. The amino acid leucine was used as an enzymatically cleavable linker. Peptide detachment from the polymer was performed either by classical ester bond saponification or newly by peptide bond cleavage catalyzed by thermolysin in water.     

Molecule-Responsive Fluorescent Sensors of α-Helix Peptides Bearing α-Cyclodextrin, Pyrene and Nitrobenzene Units in Their Side Chains

-Helix peptides bearing one unit of -cyclodextrin (-CD), one unit of pyrene and one unit of nitrobenzene (NB) in their side chains have been designed and synthesized as novel molecule-responsive devices.In both the CD-peptides, -PR17 and -PL17, the NB unit is separated from the CD unit by two turns of the helix. Two reference peptides (PL17, and -P17,) have also been synthesized. The circular dichroism studies in the peptide absorption region (200–250 nm)of -PR17 and -PL17 suggestthat the CD-peptides form stable-helixstructures (83–77%), which was destabilized by accommodating guest molecules (e.g., n-pentanol) into the CD cavity. It suggests that formation of intramolecular host–guest(CD–NB) complex stabilized thehelical structure and exogenous guest molecule excluded the appending NB moiety from inside to outside of the CD cavity, thereby causing destabilization of the helical structure and increasing the random coil content. The ICD spectra of the peptides in the pyrene and nitrobenzene absorption region (250–40 nm) suggest that NB forms inclusion complex with CD. The fluorescence studies revealed that the fluorescence of the pyrene unit is quenched by the NB unit in -PR17 and -PL17. The fluorescence intensity increases with increasing guest concentration for the CD-peptides.This guest-responsiveenhancement in the fluorescence intensity can be explained in terms of increased distance between the pyrene and NB moieties, which is caused by exclusion of the NB moiety from the CD cavity by guest accommodation. Using the guest-responsive fluorescence quenching properties of the CD-peptides, we have obtained binding constants for various short chain alkanols. -PL17 has higher binding affinity to the guest molecules than its isomer, -PR17, indicating that the location of functional groups on the peptide scaffold is important in molecule detection.     

Solution conformation by NMR and molecular modeling of three sulfide-free somatostatin octapeptide analogs compared to angiopeptin

Summary The conformation in dimethylsulfoxide of the somatostatin derivative angiopeptin and of three disulfide-free analogs was estimated by two-dimensional nuclear magnetic resonance spectroscopy at room temperature. The resulting 3D molecular graphics were compared and shown to reflect the observed differences in the inhibition of restenosis after rat aorta balloon injury by these octapeptide inhibitors. Angiopeptin and its active analog 2 displayed a relatively rigid conformation of the cyclic hexapeptide backbone due to the presence of two well-defined hydrogen bonds, further stabilized by a third hydrogen bond outside the ring. No such constraints were detected for the two biologically inactive analogs, which, compared to 2, had a two-atom longer or shorter hexapeptide ring. The well-defined structure of compound 2 may serve as an improved pharmacophore for this new class of drugs.