Identification of Promising CD8 and CD4 T-cell Epitopes for Peptide Vaccine Formulation Against SARS-CoV-2

The novel virus “Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)” has been responsible for the worldwide pandemic causing huge devastation and deaths since December 2019. The disease caused by this virus is known as COVID-19. The present study is based on immunoinformatics approach to develop a multi-epitope loaded peptide vaccine to combat the COVID-19 menace. Here, we have reported the 9-mer CD8 T-cell epitopes and 15-mer CD4 T-cell epitopes, free from glycosylation sites, belonging to three proteins, viz. surface glycoprotein, membrane glycoprotein and envelope protein of this virus. Immunogenicity, aliphatic amino acid, antigenicity and hydrophilicity scores of the predicted epitopes were estimated. In addition, other physicochemical parameters namely net charge, Boman index and amino acid contents were also accounted. Out of all the epitopes, three CD8 T-cell epitopes viz. PDPSKPSKR, DPSKPSKRS and QTQTNSPRR and three CD4 T-cell epitopes viz. ASYQTQTNSPRRARS, RIGNYKLNTDHSSSS and RYRIGNYKLNTDHSS were found to be efficient targets for raising immunity in human against this virus. With the help of our identified potent epitopes, various pharma industries might initiate efforts to incorporate those epitopes with carrier protein or adjuvant to develop a multi-epitope-loaded peptide vaccine against SARS-CoV-2. The peptide vaccines are usually cost effective and therefore, could be administered as a preventive measure to combat the spread of this disease. Proper clinical trials must be conducted prior to the use of identified epitopes as vaccine candidates.

Structural Evidence of Active Site Adaptability towards Different Sized Substrates of Aromatic Amino Acid Aminotransferase from Psychrobacter Sp. B6

Aromatic amino acid aminotransferases present a special potential in the production of drugs and synthons, thanks to their ability to accommodate a wider range of substrates in their active site, in contrast to aliphatic amino acid aminotransferases. The mechanism of active site adjustment toward substrates of psychrophilic aromatic amino acid aminotransferase (PsyArAT) from Psychrobacter sp. B6 is discussed based on crystal structures of complexes with four hydroxy-analogs of substrates: phenylalanine, tyrosine, tryptophan and aspartic acid. These competitive inhibitors are bound in the active center of PsyArAT but do not undergo transamination reaction, which makes them an outstanding tool for examination of the enzyme catalytic center. The use of hydroxy-acids enabled insight into substrate binding by native PsyArAT, without mutating the catalytic lysine and modifying cofactor interactions. Thus, the binding mode of substrates and the resulting analysis of the volume of the catalytic site is close to a native condition. Observation of these inhibitors’ binding allows for explanation of the enzyme’s adaptability to process various sizes of substrates and to gain knowledge about its potential biotechnological application. Depending on the character and size of the used inhibitors, the enzyme crystallized in different space groups and showed conformational changes of the active site upon ligand binding.

Structural, Thermal, and Vibrational Properties of N,N-Dimethylglycine–Chloranilic Acid—A New Co-Crystal Based on an Aliphatic Amino Acid

The new complex of N,N-Dimethylglycine (DMG) with chloranilic acid (CLA) was synthesized and examined for thermal, structural, and dynamical properties. The structure of the reaction product between DMG and CLA was investigated in a deuterated dimethyl sulfoxide (DMSO-d6) solution and in the solid state by Nuclear Magnetic Resonance (NMR) (Cross Polarization Magic Angle Spinning-CPMAS NMR). The formation of the 1:1 complex of CLA and DMG in the DMSO solution was also confirmed by diffusion measurement. X-ray single crystal diffraction results revealed that the N,N-dimethylglycine–chloranilic acid (DMG+–CLA−) complex crystallizes in the centrosymmetric triclinic P-1 space group. The X-ray diffraction and NMR spectroscopy show the presence of the protonated form of N,N-dimethylglycine and the deprotonated form of chloranilic acid molecules. The vibrational properties of the co-crystal were investigated by the use of neutron (INS), infrared (IR), and Raman (RS) spectroscopies, as well as the density functional theory (DFT) with periodic boundary conditions. From the band shape analysis of the N–CH3 bending vibration, we can conclude that the CH3 groups perform fast (τR ≈ 10−11 to 10‒13 s) reorientational motions down to a temperature of 140 K, with activation energy at ca. 6.7 kJmol–1. X-ray diffraction and IR investigations confirm the presence of a strong N+–H···O− hydrogen bond in the studied co-crystal.

L-Type Amino Acid Transporter 1-Utilizing Prodrugs of Ketoprofen Can Efficiently Reduce Brain Prostaglandin Levels

In order to efficiently combat neuroinflammation, it is essential to deliver the anti-inflammatory drugs to their target sites in the brain. Pro-drugs utilizing the L-type amino acid transporter 1 (LAT1) can be transported across the blood-brain barrier (BBB) and the cellular barriers of the brain’s parenchymal cells. In this study, we evaluated, for the first time, the efficacy of LAT1-utilizing prodrugs of ketoprofen (KPF) on cyclooxygenase (COX) enzymes in vitro and prostaglandin E2 production in vivo by using an enzymatic assay and liquid chromatography- tandem mass spectrometry method, respectively. Aliphatic amino acid-conjugated pro-drugs inhibited the peroxidase activity of COX in vitro in their intact form (85% inhibition, IC50 ≈ 1.1 µM and 79%, IC50 ≈ 2.3 µM), which was comparable to KPF (90%, IC50 ≈ 0.9). Thus, these compounds acted more as KPF derivatives rather than pro-drugs. In turn, aromatic amino acid-conjugated pro-drugs behaved differently. The ester pro-drug inhibited the COX peroxidase activity in vitro (90%, IC50 ≈ 0.6 µM) due to its bioconversion to KPF, whereas the amide pro-drug was inactive toward COX enzymes in vitro. However, the amide pro-drug released KPF in the mouse brain in sufficient and effective amounts measured as reduced PGE2 levels.

Computational Analysis of the Primary and Secondary Structure of Amidases in Relation to their pH Adaptation

Background: Amidases are ubiquitous enzymes and biological functions of these enzymes vary widely. They are considered to be synergistically involved in the synthesis of a wide variety of carboxylic acids, hydroxamic acids and hydrazides, which find applications in commodity chemicals synthesis, pharmaceuticals agrochemicals and wastewater treatments. Methods: They hydrolyse a wide variety of amides (short-chain aliphatic amides, mid-chain amides, arylamides, α-aminoamides and α-hydroxyamides) and can be grouped on the basis of their catalytic site and preferred substrate. Despite their economic importance, we lack knowledge as to how these amidases withstand elevated pH and temperature whereas others cannot. Results: The present study focuses on the statistical comparison between the acid-tolerant, alkali tolerant and neutrophilic organisms. In silico analysis of amidases of acid-tolerant, alkali tolerant and neutrophilic organisms revealed some striking trends as to how amino acid composition varies significantly. Statistical analysis of primary and secondary structure revealed amino acid trends in amidases of these three groups of bacteria. The abundance of isoleucine (Ile, I) in acid-tolerant and leucine (Leu, L) in alkali tolerant showed the aliphatic amino acid dominance in extreme conditions of pH in acidtolerant and alkali tolerant amidases. Conclusion: The present investigation insights physiochemical properties and dominance of some crucial amino acid residues in the primary and secondary structure of some amidases from acid-tolerant, alkali tolerant and neutrophilic microorganisms.

Effective separation of aromatic and aliphatic amino acid mixtures using ionic-liquid-based aqueous biphasic systems

Ionic-liquid-based aqueous biphasic systems allow an efficient and selective separation of aliphatic and aromatic amino acid mixtures usually present in protein hydrolysates or fermentation broths.

DFT investigation on the selective complexation of ionic liquids based on α-amino acid anion and N7,N9-dimethyladeninium cation with CO2

A series of aliphatic amino acid ionic liquids (AAILs) composed of N7,N9-dimethyladeninium cation with an amino acid anion as the functionalized ILs, with dual amine group, have been designed for CO2 capture.