Search results for "MOLECULAR MODELING"
showing 10 items of 136 documents
Computational methodologies applied to Protein-Protein Interactions for molecular insights in Medicinal Chemistry
2021
In living systems, proteins usually team up into “molecular machinery” implementing several protein-to-protein physical contacts – or protein-protein interactions (PPIs) – to exert biological effects at both cellular and systems levels. Deregulations of protein-protein contacts have been associated with a huge number of diseases in a wide range of medical areas, such as oncology, cancer immunotherapy, infectious diseases, neurological disorders, heart failure, inflammation and oxidative stress. PPIs are very complex and usually characterised by specific shape, size and complementarity. The protein interfaces are generally large, broad and shallow, and frequently protein-protein contacts are…
Development of novel dipeptide-like rhodesain inhibitors containing the 3-bromoisoxazoline warhead in a constrained conformation.
2015
Novel dipeptide-like rhodesain inhibitors containing the 3-bromoisoxazoline warhead in a constrained conformation were developed; some of them possess K(i) values in the micromolar range. We studied the structure-activity relationship of these derivatives and we performed docking studies, which allowed us to find out the key interactions established by the inhibitors with the target enzyme. Biological results indicate that the nature of the P2 and P3 substituents and their binding to the S2/S3 pockets is strictly interdependent.
Conformational Analysis of beta-Lactam-Containing Ferrocene Peptides
2009
The homochiral 3-amino-1-(4-methoxyphenyl)-4-phenyl-beta-lactam (≡ Alm) was conjugated with Boc-Ala giving Ala-Alm (9) after Boc-deprotection (Boc = tert-butoxycarbonyl, Ala = alanine). Coupling of FcCOOH (1) and Boc-Fca (10) with “ dipeptide” 9 resulted in the formation of FcCO-Ala-Alm (12) and the trisamide Boc-Fca-Ala-Alm (13), respectively (Fc = ferrocenyl, Fca = 1’ -aminoferrocene-1-carboxylic acid). The reactions were accomplished by the HOBt/EDC procedure and the products were obtained in good yields (HOBt = 1-hydroxybenzotriazole, EDC = N-(3-dimethylaminopropyl)-N’ -ethylcarbodiimide hydrochloride). Symmetrically 1, 1’ -disubstituted “ tetrapeptide” Fn(CO-Ala-Alm)2 (14) was prepared…
Inhibition Mechanism of SARS‐CoV‐2 Main Protease with Ketone‐Based Inhibitors Unveiled by Multiscale Simulations: Insights for Improved Designs**
2021
Abstract We present the results of classical and QM/MM simulations for the inhibition of SARS‐CoV‐2 3CL protease by a hydroxymethylketone inhibitor, PF‐00835231. In the noncovalent complex the carbonyl oxygen atom of the warhead is placed in the oxyanion hole formed by residues 143 to 145, while P1–P3 groups are accommodated in the active site with interactions similar to those observed for the peptide substrate. According to alchemical free energy calculations, the P1′ hydroxymethyl group also contributes to the binding free energy. Covalent inhibition of the enzyme is triggered by the proton transfer from Cys145 to His41. This step is followed by the nucleophilic attack of the Sγ atom on …
Monte Carlo simulation in phylogenies: an application to test the constancy of evolutionary rates.
1994
Monte Carlo simulation has commonly been used in phylogenetic studies to test different tree-reconstruction methods, and consequently, its application for testing evolutionary models can be considered as a natural extension of this usage. Repetitive simulation of a given evolutionary process, under the restrictions imposed by the model to be tested, along a determinate tree topology allow the estimate of probability distributions for the desired parameters. Next, the phylogenetic tree can be reconstructed again without the constraints of the model, and the parameter of interest, derived from this tree, can be compared to the corresponding probability distribution derived from the restricted…
Guide to Practical Work with the Monte Carlo Method
2002
The guide is structured such that we proceed from the “easy” simulation methods and algorithms to the more sophisticated. For each method the algorithms are presented by the technique of stepwise refinement. We first present the idea and the basic outline. From then on we proceed by breaking up the larger logical and algorithmic structures into smaller ones, until we have reached the level of single basic statements. Sometimes we may elect not to go to such a depth and the reader is asked to fill in the gaps.
Induction of 2-hydroxycatecholestrogens O-methylation: A missing puzzle piece in diagnostics and treatment of lung cancer
2022
Lung cancer is one of the most common cancers worldwide, causing nearly one million deaths each year. Herein, we present the effect of 2-methoxyestradiol (2-ME), the endogenous metabolite of 17β-estradiol (E2), on non-small cell lung cancer (NSCLC) cells. We observed that 2-ME reduced the viability of lung adenocarcinoma in two-dimensional (2D) and three-dimensional (3D) spheroidal A549 cell culture models. Molecular modeling was carried out aiming to visualize amino acid residues within binding pockets of the acyl-protein thioesterases, namely 1 (APT1) and 2 (APT2), and thus to identify which ones were more likely involved in the interaction with 2-ME. Our findings suggest that 2-ME acts a…
On Complex Formation between 5-Fluorouracil and β-Cyclodextrin in Solution and in the Solid State: IR Markers and Detection of Short-Lived Complexes …
2020
In this work, the nuclear magnetic resonance (NMR) and IR spectroscopic markers of the complexation between 5-fluorouracil (5-FU) and &beta
Indicaxanthin from Opuntia ficus-indica Crosses the Blood–Brain Barrier and Modulates Neuronal Bioelectric Activity in Rat Hippocampus at Dietary-Con…
2015
Indicaxanthin is a bioactive and bioavailable betalain pigment from the Opuntia ficus-indica fruits. In this in vivo study, kinetic measurements showed that indicaxanthin is revealed in the rat brain within 1 h from oral administration of 2 μmol/ kg, an amount compatible with a dietary consumption of cactus pear fruits in humans. A peak (20 ± 2.4 ng of indicaxanthin per whole brain) was measured after 2.5 h; thereafter the molecule disappeared with first order kinetics within 4 h. The potential of indicaxanthin to affect neural activities was in vivo investigated by a microiontophoretic approach. Indicaxanthin, administered in a range between 0.085 ng and 0.34 ng per neuron, dose-dependentl…
Non-reversible Monte Carlo simulations of spin models
2011
Abstract Monte Carlo simulations are used to study simple systems where the underlying Markov chain satisfies the necessary condition of global balance but does not obey the more restrictive condition of detailed balance. Here, we show that non-reversible Markov chains can be set up that generate correct stationary distributions, but reduce or eliminate the diffusive motion in phase space typical of the usual Monte Carlo dynamics. Our approach is based on splitting the dynamics into a set of replicas with each replica representing a biased movement in reaction-coordinate space. This introduction of an additional bias in a given replica is compensated for by choosing an appropriate dynamics …