Search results for "Hydrogen bonding"
showing 10 items of 290 documents
Comparative Study of the Mechanical Unfolding Pathways of α- and β-Peptides
2015
Using molecular simulations, we analyze the unfolding pathways of various peptides. We compare the mechanical unfolding of a β-alanine's octamer (β-HAla8) and an α-alanine's decamer (α-Ala10). Using force-probe molecular-dynamics simulations, to induce unfolding, we show that the 3(14)-helix formed by β-HAla8 is mechanically more stable than the α-helix formed by α-Ala10, although both structures are stabilized by six hydrogen bonds. Additionally, computations of the potential of mean force validate this result and show that also the thermal stability of the 3(14)-helix is higher. It is demonstrated that β-HAla8 unfolds in a two-step fashion with a stable intermediate. This is contrasted wi…
Synthesis and Structure-Activity Relationships of Amino Acid Conjugates of Cholanic Acid as Antagonists of the EphA2 Receptor
2013
The Eph–ephrin system plays a critical role in tumor growth and vascular functions during carcinogenesis. We had previously identified cholanic acid as a competitive and reversible EphA2 antagonist able to disrupt EphA2-ephrinA1 interaction and to inhibit EphA2 activation in prostate cancer cells. Herein, we report the synthesis and biological evaluation of a set of cholanic acid derivatives obtained by conjugation of its carboxyl group with a panel of naturally occurring amino acids with the aim to improve EphA2 receptor inhibition. Structure-activity relationships indicate that conjugation of cholanic acid with linear amino acids of small size leads to effective EphA2 antagonists whereas …
A cocrystal of two Mo(VI) complexes bearing different diastereomers of the 2,4-di-tert-butyl-6-{[(1-oxido-1-phenylpropan-2-yl)(methyl)amino]methyl}ph…
2013
The title cocrystal contains two chiral conformational diastereomers,viz.(1S,2R,RN)- and (1S,2R,SN)-, of [2,4-di-tert-butyl-6-{[(1-oxido-1-phenylpropan-2-yl)(methyl)amino]methyl}phenolato](methanol)-cis-dioxidomolybdenum(VI), [Mo(C25H35NO2)O2(CH3OH)], representing the first example of a structurally characterized molybdenum complex with enantiomerically pure ephedrine derivative ligands. The MoVIcations exhibit differently distorted octahedral coordination environments, with two oxide ligands positionedcisto each other. The remainder of the coordination comprises phenoxide, alkoxide and methanol O atoms, with an amine N atom completing the octahedron. The distinct complexes are linked by st…
Reactions at Interfaces: Oxygenation of n-Butyl Ligands Anchored on Silica Surfaces with Methyl(trifluoromethyl)dioxirane
2011
The oxygenation of n-butyl and n-butoxy chains bonded to silica with methyl(trifluoromethyl)dioxirane (1) revealed the ability of the silica matrix to release electron density toward the reacting C(2)-H σ-bond through the Si-C(1) and Si-O(1) σ-bonds connecting the alkyl chain to the surface (silicon β-effect). The silica surface impedes neither the alkyl chain adopting the conformation required for the silicon β-effect nor dioxirane 1 approaching the reactive C(2) methylene group. Reaction regioselectivity is insensitive to changes in the solvation of the reacting system, the location of organic ligands on the silica surface, and the H-bonding character of the silica surface. Reaction rates…
Analysis of Vibrational Circular Dichroism Spectra of Peptides
2020
Vibrational circular dichroism (VCD) is one of the major spectroscopic tools to study peptides. Nevertheless, a full understanding of what determines the signs and intensities of VCD bands of these compounds in the amide I and amide II spectral regions is still far from complete. In the present work, we study the origin of these VCD signals using the general coupled oscillator (GCO) analysis, a novel approach that has recently been developed. We apply this approach to the ForValNHMe model peptide in both α-helix and β-sheet configurations. We show that the intense VCD signals observed in the amide I and amide II spectral regions essentially have the same underlying mechanism, namely, the th…
Halogen and Hydrogen Bonded Complexes of 5-Iodouracil
2013
Three derivatives of 5-iodouracil were prepared, and their complexation properties, supplemented by 5-iodouracil under the same conditions, were studied with and without halogen bond acceptors in N,N-dimethylformamide, N,N-diethylformamide, N-methylformamide, formamide, dimethylsulfoxide, and water. The intermolecular halogen and hydrogen bonding interactions observed in the solid state were investigated using single crystal X-ray diffraction and quantum chemical calculations, and the acquired data were contrasted with bonding interactions previously reported for 5-iodouracil in the Cambridge Structural Database. It was found that the polarized iodine atom and the amidic NH functionality ac…
The mechanism of formamide hydrolysis in water from ab initio calculations and simulations.
2005
The neutral hydrolysis of formamide in water is a suitable reference to quantify the efficiency of proteolytic enzymes. However, experimental data for this reaction has only very recently been obtained and the kinetic constant determined experimentally is significantly higher than that predicted by previous theoretical estimations. In this work, we have investigated in detail the possible mechanisms of this reaction. Several solvent models have been considered that represent a considerable improvement on those used in previous studies. Density functional and ab initio calculations have been carried out on a system which explicitly includes the first solvation shell of the formamide molecule…
Molecular recognition of nucleotides in water by scorpiand-type receptors based on nucleobase discrimination.
2014
Abstract: The detection of nucleotides is of crucial impor-tance because they are the basic building blocks of nucleicacids. Scorpiand-based polyamine receptors functionalizedwith pyridine or anthracene units are able to form stablecomplexes with nucleotides in water, based on coulombic,p–p stacking, and hydrogen-bonding interactions. This be-havior has been rationalized by means of an explorationwith NMR spectroscopy and DFT calculations. Binding con-stants were determined by potentiometry. Fluorescencespectroscopy studies have revealed the potential of these re-ceptors as sensors to effectively and selectively distinguishguanosine-5’-triphosphate (GTP) from adenosine-5’-triphos-phate (ATP…
Experimental-Like Affinity Constants and Enantioselectivity Estimates from Flexible Docking
2012
Experimental-like affinity constants and enantioselectivity estimates, not predicted so far computationally, were obtained using a novel flexible modeling/docking combined strategy. The S- and R-warfarin-human serum albumin (HSA, site I) complexes were used as an interaction model. The process for a verified estimation includes the following: (i) ionized open chain forming at physiological pH (a recent focus); (ii) conformational search (molecular mechanics and Monte Carlo methods); (iii) rigid protein-flexible ligand docking (GlideXP) generating low energy paired S- and R-poses; (iv) graphical comparison against the X-ray crystal structure (unsatisfactory verification step); (v) quantum po…
In silico identification and experimental validation of hits active against KPC-2 β-lactamase
2018
Bacterial resistance has become a worldwide concern, particularly after the emergence of resistant strains overproducing carbapenemases. Among these, the KPC-2 carbapenemase represents a significant clinical challenge, being characterized by a broad substrate spectrum that includes aminothiazoleoxime and cephalosporins such as cefotaxime. Moreover, strains harboring KPC-type β-lactamases are often reported as resistant to available β-lactamase inhibitors (clavulanic acid, tazobactam and sulbactam). Therefore, the identification of novel non β-lactam KPC-2 inhibitors is strongly necessary to maintain treatment options. This study explored novel, non-covalent inhibitors active against KPC-2, …