Using random forest to classify T-cell epitopes based on amino acid properties and molecular features

T-lymphocyte (T-cell) is a very important component in human immune system. T-cell epitopes can be used for the accurately monitoring the immune responses which activation by major histocompatibility complex (MHC), and rationally designing vaccines. Therefore, accurate prediction of T-cell epitopes is crucial for vaccine development and clinical immunology. In current study, two types peptide features, i.e., amino acid properties and chemical molecular features were used for the T-cell epitopes peptide representation. Based on these features, random forest (RF) algorithm, a powerful machine learning algorithm, was used to classify T-cell epitopes and non-T-cell epitopes. The classification accuracy, sensitivity, specificity, Matthews correlation coefficient (MCC), and area under the curve (AUC) values for proposed method are 97.54%, 97.22%, 97.60%, 0.9193, and 0.9868, respectively. These results indicate that current method based on the combined features and RF is effective for T-cell epitopes prediction.     

QSAR Study on Binding Affinity of PATs (Rodenticides) to the [3H]-Mepyramine-Labelled H1 Receptor In Rat and Guinea Pig Brain

Abstract

The binding of a series of PAT analogues (rodenticides) to the [³H]-mepyramine-labelled H₁ receptor in rat and guinea pig brain was investigated topologically using negentropy (N), molecular redundancy (MRI), first-order molecular connectivity (¹X _v ), Wiener (W), and Szeged (Sz) indices. Multiple regression analyses showed that MRI provided excellent results upon introduction of indicator parameters. Predictive ability of the proposed models was discussed using cross-validation parameters.     

Reversible Control over Molecular Recognition in Surface‐Bound Photoswitchable Hydrogen‐Bonding Receptors: Towards Read–Write–Erase Molecular Printboards

The synthesis of an anthracene‐bearing photoactive barbituric acid receptor and its subsequent grafting onto azide‐terminated alkanethiol/Au self‐assembled monolayers by using an Cu^I‐catalyzed azide–alkyne reaction is reported. Monolayer characterization using contact‐angle measurements, electrochemistry, and spectroscopic ellipsometry indicate that the monolayer conversion is fast and complete. Irradiation of the receptor leads to photodimerization of the anthracenes, which induces the open‐to‐closed gating of the receptor by blocking access to the binding site. The process is thermally reversible, and polarization‐modulated IR reflection–absorption spectroscopy indicates that photochemical closure and thermal opening of the surface‐bound receptors occur in 70 and 100 % conversion, respectively. Affinity of the open and closed surface‐bound receptor was characterized by using force spectroscopy with a barbituric‐acid‐modified atomic force microscope tip.     

Chirality Induction by Formation of Assembled Structures Based on Anion‐Responsive π‐Conjugated Molecules

Anion‐responsive π‐conjugated compounds having chiral alkyl chains were synthesized. Circular dichroism (CD) and circularly polarized luminescence (CPL) were observed in the solution‐state assemblies of the chiral anion receptors and those of their anion complexes as salts of a planar triazatriangulenium cation. The CD and CPL spectral patterns of the ion‐pair‐based assemblies were completely opposite to those of the anion‐free assemblies, and this suggests that anion binding and subsequent ion pairing change the chirality of the assembly modes.     

Pyrrolic Tripodal Receptors for the Molecular Recognition of Carbohydrates: Ditopic Receptors for Dimannosides

Synthetic ditopic receptors, designed for the molecular recognition of dimannosides, have been prepared by bridging two monotopic units effectively recognizing mannosides with linkers of the appropriate size and flexibility, endowed with hydrogen‐bonding groups. Affinities toward the α and β glycosides of the biologically relevant Manα(1–2)Man disaccharide were measured by NMR spectroscopy and isothermal titration calorimetry (ITC) in polar organic media (30–40 % DMF in chloroform). Significant selectivities and affinities in the micromolar range were observed in most cases, with two newly designed receptors being the most effective receptors of the set, together with a distinct preference of the dimannosides for the (S) enantiomer of the receptor in all cases. A 3D view of the recognition mode was elucidated by a combined NMR spectroscopic/molecular modeling approach, showing the dimannoside included in the cleft of the receptor. Compared to the monotopic precursors, the ditopic receptors showed markedly improved recognition properties, proving the efficacy of the modular receptor design for the recognition of disaccharides.     

Carbazole-Based Colorimetric Anion Sensors

Owing to their strong carbazole chromophore and fluorophore, as well as to their powerful and convergent hydrogen bond donors, 1,8-diaminocarbazoles are amongst the most attractive and synthetically versatile building blocks for the construction of anion receptors, sensors, and transporters. Aiming to develop carbazole-based colorimetric anion sensors, herein we describe the synthesis of 1,8-diaminocarbazoles substituted with strongly electron-withdrawing substituents, i.e., 3,6-dicyano and 3,6-dinitro. Both of these precursors were subsequently converted into model diamide receptors. Anion binding studies revealed that the new receptors exhibited significantly enhanced anion affinities, but also significantly increased acidities. We also found that rear substitution of 1,8-diamidocarbazole with two nitro groups shifted its absorption spectrum into the visible region and converted the receptor into a colorimetric anion sensor. The new sensor displayed vivid color and fluorescence changes upon addition of basic anions in wet dimethyl sulfoxide, but it was poorly selective; because of its enhanced acidity, the dominant receptor-anion interaction for most anions was proton transfer and, accordingly, similar changes in color were observed for all basic anions. The highly acidic and strongly binding receptors developed in this study may be applicable in organocatalysis or in pH-switchable anion transport through lipophilic membranes.     

Understanding the Chloride Affinity of Barbiturates for Anion Receptor Design

Due to their potential binding sites, barbituric acid (BA) and its derivatives have been used in metal coordination chemistry. Yet their abilities to recognize anions remain unexplored. In this work, we were able to identify four structural features of barbiturates that are responsible for a certain anion affinity. The set of coordination interactions can be finely tuned with covalent decorations at the methylene group. DFT-D computations at the BLYP-D3(BJ)/aug-cc-pVDZ level of theory show that the C−H bond is as effective as the N−H bond to coordinate chloride. An analysis of the electron charge density at the C−H⋅⋅⋅Cl⁻ and N−H⋅⋅⋅Cl⁻ bond critical points elucidates their similarities in covalent character. Our results reveal that the special acidity of the C−H bond shows up when the methylene group moves out of the ring plane and it is mainly governed by the orbital interaction energy. The amide and carboxyl groups are the best choices to coordinate the ion when they act together with the C−H bond. We finally show how can we use this information to rationally improve the recognition capability of a small cage-like complex that is able to coordinate NaCl.     

Tailoring Chimeric Ligands for Studying and Biasing ErbB Receptor Family Interactions

Described is the development and application of a versatile semisynthetic strategy, based on a combination of sortase‐mediated coupling and tetrazine ligation chemistry, which can be exploited for the efficient incorporation of tunable functionality into chimeric recombinant proteins. To demonstrate the scope of the method, the assembly of a set of bivalent ligands, which integrate members of the epidermal growth factor (EGF) ligand family, is described. By using a series of bivalent EGFs with variable intraligand spacing, the differences in structure were correlated with the ability to bias signaling in the ErbB receptor family in a cell motility assay. Biasing away from EGFR‐HER2 dimerization with a bivalent EGF was observed to reduce cell motility in an intraligand distance‐dependent fashion, thus demonstrating the utility of the approach for acutely perturbing receptor‐mediated cell signaling pathways.     

Discrimination between Olfactory Receptor Agonists and Non‐agonists

A joint approach combining free‐energy calculations and calcium‐imaging assays on the broadly tuned human 1G1 olfactory receptor is reported. The free energy of binding of ten odorants was computed by means of molecular‐dynamics simulations. This state function allows separating the experimentally determined eight agonists from the two non‐agonists. This study constitutes a proof‐of‐principle for the computational deorphanization of olfactory receptors.