Stereocontrolled synthesis of peptide bond isosteres

Absolute stereochemical control is employed in the synthesis of isosteres for dipeptide subunits (1; see Fig. 1) in which the amide linkage has been replaced by a trans carbon-carbon double bond. The synthesis affords access to the four stereoisomers of 1 in which R and R' = CH3, including the isostere for D-alanine-D-alanine (D-Ala-D-Ala), 2.     

Towards Decoding the Sequence-Based Grammar Governing the Functions of Intrinsically Disordered Protein Regions

A substantial portion of the proteome consists of intrinsically disordered regions (IDRs) that do not fold into well-defined 3D structures yet perform numerous biological functions and are associated with a broad range of diseases. It has been a long-standing enigma how different IDRs successfully execute their specific functions. Further putting a spotlight on IDRs are recent discoveries of functionally relevant biomolecular assemblies, which in some cases form through liquid-liquid phase separation. At the molecular level, the formation of biomolecular assemblies is largely driven by weak, multivalent, but selective IDR-IDR interactions. Emerging experimental and computational studies suggest that the primary amino acid sequences of IDRs encode a variety of their interaction behaviors. In this review, we focus on findings and insights that connect sequence-derived features of IDRs to their conformations, propensities to form biomolecular assemblies, selectivity of interaction partners, functions in the context of physiology and disease, and regulation of function. We also discuss directions of future research to facilitate establishing a comprehensive sequence-function paradigm that will eventually allow prediction of selective interactions and specificity of function mediated by IDRs.     

Effect of a Dipeptide-Enriched Diet in an Adult Drosophila melanogaster Laboratory Strain

A novel ZMP analog 3 was synthesized from inosine in 10 steps, and exhibited small but significant inhibitory activity toward protein kinase C.     

Calculation of Solvation Free-Energy Differences for Large Solute Change from Computer Simulations with Quadrature-Based Nearly Linear Thermodynamic Integration

Abstract

The free-energy simulation methodology is reviewed from the point of view of calculating large free-energy differences. The advantages of the nearly linear thermodynamic integration based on Gaussian quadrature are highlighted and its performance is characterized on systems ranging from the Lennard-Jones fluid to the A to B transition of DNA oligomers. A technique for optimizing the runlength at each quadrature point is given. Examples for the sensitivity of the calculated free energy to the atomic charges used are also presented.     

Inhibitory Activities of Aromatic Amino Acid Esters and Peptides against Ovalbumin Permeation through Caco-2 Cell Monolayers

Trp, Phe, and Tyr ethyl esters and their dipeptides with Gly at the C-terminals inhibited ovalbumin (OVA) permeation through Caco-2 monolayers. The inhibitory activity of Trp ethyl ester was the highest at near the concentration of 10^-6 M. It was suggested that Trp ethyl ester inhibited transcellular permeation of OVA.     

Substrate Specificity of Thermostable D-Alanine-D-alanine ligase from Thermotoga maritima ATCC 43589

D-Alanine-D-alanine ligase (Ddl) and its mutants maintain the biosynthesis of peptidoglycan, and the substrate specificity of Ddls partially affects the resistance mechanism of vancomycin-resistant enterococci. Through investigation of Ddls, Ddl from Thermotoga maritima ATCC 43589 showed novel characteristics, vis. thermostability up to 90 °C and broad substrate specificity toward 15 D-amino acids, particularly D-alanine, D-cysteine, and D-serine, in that order.     

Phospholipid Composition of Gluconobacter cerinus

Phospholipids of Gluconobacter cerinus were investigated. The cells of this bacterium were found to have cardiolipin, phosphatidylglycerol, phosphatidylethanolamine and phosphatidylcholine together with three ornithine-containing lipids. Phosphatidylcholine was the most abundant of these phospholipids, and calculated at 31.0% of total phospholipids in the cells at the late logarithmic phase. The fatty acid of this lipid was composed of palmitate, stearate and vaccenate, and there were no remarkable differences in quality among fatty acids of these four phospholipids. The phosphatidylcholine was also found in other acetic acid bacteria.     

Metal ion-induced assembly of dipeptide-attached perylenediimide for fluorometric “turn on” detection of biologically important small molecule

A dipeptide-appended perylenediimide (PDI-CFF) fluorescent molecule was designed, synthesized, and characterized. Though the molecule does not dissolve in any individual solvent, it dissolves well in an organic/water mixed solvent system such as tetrahydrofuran/water. This new fluorescent molecule was self-assembled in a tetrahydrofuran/water mixture to form both nanofibrous network structures and a nano ring structure. It has shown nanofibril morphology by the interactions with ferric ions (PDI-CFF/Fe³⁺ system) with diminishing fluorescent property. Interestingly, L-ascorbic acid (LAA) interacts with the PDI-CFF/Fe³⁺ system, showing turn-on fluorescence. Another interesting feature is that the minimum detection limits for Fe³⁺ ions and LAA are at the submicromolar levels of 6.2 × 10⁻⁸ and 3 × 10⁻⁸ M, respectively. Moreover, the fluorescent (10 μM) signals can be monitored by the naked eye under handheld UV lamp irradiation at 365 nm, and this is very convenient for the real application. In this study, the molecule offers the opportunity for processing these sequential fluorescence responses in order to fabricate a implication logic gate that includes NOT, AND, and OR simple logic gates using chemical stimuli (ferric ions and LAA) as inputs and fluorescence emission at 536 nm as output. The detailed mechanism of interactions of Fe³⁺ with PDI-CFF and LAA with the PDI-CFF/Fe³⁺ system is vividly studied by using Fourier transform infrared (FT-IR) analysis and fluorescence. Moreover, this new molecule was reusable for several times without significant loss of its activity. The construction of logic gates using biologically important molecules/ions holds future promise for the design and development of new bio-logic gates.     

Dialkylmethyl β-glycosides of <Emphasis Type="Italic">N</Emphasis>-acetylmuramyl-<Emphasis Type="Italic">L</Emphasis>-alanyl-<Emphasis Type="Italic">D</Emphasis>-isoglutamine: Synthesis and protective antiinfection and cytotoxic activities

Symmetric secondary linear alcohols were proposed as aglycones for the synthesis of lipophilic glycosides of β-N-acetylmuramyl-L-alanyl-D-isoglutamine (MDP). Pentadecan-8-ol, nonadecan-10-ol, and tricosan-12-ol were glycosylated by the oxazoline method. Based on the corresponding glucosaminides, alkyl β-glycosides of 4,6-O-isopropylidene-N-acetylmuramic acid were synthesized and coupled with the dipeptide. Deprotection of isopropylidene groups by acidic hydrolysis and catalytic hydrogenolysis of benzyl esters resulted in the target muramyldipeptide glycosides. Nonadecan-10-yl and tricosan-12-yl β-MDPs at doses 2 μg/mice most effectively stimulated antibacterial resistance in mice against Staphylococcus aureus. In contrast to the previously synthesized undecan-6-yl β-MDP, pentadecan-8-yl, nonadecan-10-yl, and tricosan-12-yl β-MDPs demonstrated direct cytotoxicity toward tumor cells K-562 and blood mononuclear cells.     

Application of Dmb-Dipeptides in the Fmoc SPPS of Difficult and Aspartimide-Prone Sequences

Mutter’s pseudoproline dipeptides and Sheppard’s Hmb derivatives are powerful tools for enhancing synthetic efficiency in Fmoc SPPS. They work by exploiting the natural propensity of N-alkyl amino acids to disrupt the formation of the secondary structures during peptide assembly. Their use results in better and more predictable acylation and deprotection kinetics, enhanced reaction rates, and improved yields of crude products. However, these approaches have certain limitations: pseudoproline dipeptides can only be used for sequences containing serine or threonine, and the coupling of the amino acid following the Hmb residue can be extremely difficult. To alleviate some of these shortcomings, we have prepared a range of Fmoc-Aaa-(Dmb)Gly-OH dipeptides and tested their efficacy in the synthesis of a number of challenging hydrophobic peptides. We also compared the efficiency of N-Dmb against N-Hmb backbone protection in preventing aspartimide formation in the Fmoc SPPS of peptides containing the Asp-Gly sequence.