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.     

Neutral loss of amino acid residues from protonated peptides in collision-induced dissociation generates N- or C-terminal sequence ladders

The widespread occurrence of the neutral loss of one to six amino acid residues as neutral fragments from doubly protonated tryptic peptides is documented for 23 peptides with individual sequences. Neutral loss of amino acids from the N-terminus of doubly charged tryptic peptides results in doubly charged y-ions, forming a ladder-like series with the ions [M + 2H](2+) = y(max) (2+), y(max - 1) (2+), y(max - 2) (2+), etc. An internal residue such as histidine, proline, lysine or arginine appears to favor this type of fragmentation, although it was sometimes also observed for peptides without this structure. For doubly protonated non-tryptic peptides with one of these residues at or near the N-terminus, we observed neutral loss from the C-terminus, resulting in a doubly charged b-type ion ladder. The analyses were performed by Q-TOF tandem mass spectrometry, facilitating the recognition of neutral loss ladders by their 2+ charge state and the conversion of the observed mass differences into reliable sequence information. It is shown that the neutral loss of amino acid residues requires low collision offset values, a simple mechanistic explanation based on established fragmentation rules is proposed and the utility of this neutral loss fragmentation pathway as an additional source for dependable peptide sequence information is documented.     

Distance distributions and dynamics of a zinc finger peptide from fluorescence resonance energy transfer measurements

Time-resolved fluorescence resonance energy transfer (FRET) measurements were used to measure distance distributions and intramolecular dynamics (site-to-site diffusion) of a 28-residue single-domain zinc finger peptide in the absence and presence of zinc ion. Energy transfer was measured between TRP₁₄ and a N-terminal DNS group. As expected, the TRP-to-DNS distance distribution for zinc-bound peptide is shorter and narrower (R _av=11.2 Å,hw=2.8 Å) than the metal-free peptide (R _av=20.1 Å,hw=14.5 Å). The degree of mutual donor-to-acceptor diffusion (D) was also determined for these distributions. For zinc-bound peptide there is no detectible diffusion (D0.2 Ų/ns), whereas for metal-free peptide a considerable amount of motion is occurring between the donor and the acceptor (D=12 Ų/ns). These results indicate that the zinc-bound peptide folds into a unique, well-defined conformation, whereas the metal-free conformation is flexible and rapidly changing. The absence of detectible mutual site-to-site diffusion between the donor and the acceptor in the metal-bound zinc finger peptide indicates that intramolecular motion is essentially frozen out, on the FRET time scale, as a consequence of zinc coordination.Dedicated to the memory of Barbara D. Wells.     

Antihypertensive Effect of Angiotensin‐Converting Enzyme Inhibitory Peptide Obtained from Hen Ovotransferrin

Angiotensin I‐converting enzyme (ACE) inhibitory peptide was isolated from the hen ovotransferrin hydrolysate using chymotryptic hydrolysis by two steps of reverse‐phase high‐performance liquid chromatography. The amino sequence of this novel peptide was identified as Lys‐Val‐Arg‐Glu‐Gly‐Thr‐Thr‐Tyr that inhibited ACE activity in vitro in a concentration‐dependent manner with an effective concentration (IC₅₀) of 102.8 μM. Also, this inhibition was identified as noncompetitive using the Lineweaver‐Burk plot. Moreover, the antihypertensive action of this novel peptide was investigated by an intravenous injection into spontaneously hypertensive rats (SHR). A dose‐dependent reduction of systolic blood pressure by this peptide was observed after 40 min of treatment and it decreased the blood pressure markedly at the maximal dose (1 nmol/mL/kg). The maximal blood pressure lowering activity of this peptide was calculated as 163% of captopril (10 pmol/mL/kg) that was used as positive control. In conclusion, the obtained data suggests that Lys‐Val‐Arg‐Glu‐Gly‐Thr‐Thr‐Tyr has an ability to inhibit ACE activity and decrease the systolic blood pressure in hypertensive animals.     

Application of AM SURE™ resin to solid-phase peptide synthesis

A core-shell structure was found in AM SURE™ resin, in which most amino groups were located at the skin layer. The AM SURE™ resin revealed better synthetic efficiency, compared to the noncore-shell type resin in the synthesis of the fragment 65-74 of acyl carrier protein, the fragment 27-35 of HIV (human immunodeficiency virus) fusion inhibitor (T-20) and the Jung-Redemann 10-mer.     

Purification and properties of a β-galactosidase with potential application as a digestive supplement

Functional-based screening of crude β-galactosidase activities from 42 yeast strains resulted in the selection of a single enzyme of potential interest as a digestive supplement. β-Galactosidase produced by Kluyveromyces marxianus DSM5418 was purified to homogeneity by a combination of gel filtration, ion-exchange, and hydroxylapatite chromatographies. The denatured (123 kDa) and native molecular masses (251 kDa) suggest that the enzyme is a homodimer. The optimum pH and temperature of the purified enzyme were 6.8 and 37°C, respectively. The unpurified β-galactosidase in particular displayed a high level of stability when exposed to simulated intestinal conditions in vitro for 4 h. Matrix-assisted laser desorption ionization mass sectrometry analysis revealed that the enzyme's trypsin-generated peptide mass fingerprint shares several peptide fragment hits with β-galactosidases from Kluyveromyces lactis. This confirms the enzyme's identity and indicates that significant sequence homology exists between these enzymes.