Search results for "molecular model"
showing 10 items of 274 documents
New potential DNA intercalators of the carbazole series from indole-2,3-quinodimethanes: Synthesis, crystal structure, and molecular modeling with a …
1993
1-Alkylpyrano[3,4-b]indol-3-ones3 react via a Diels-Alder step with an aryne or N-phenylmaleimide to furnish the new [b]annellated carbazoles4–10 in a one-pot process. In an analogous procedure, the in situ generated N-benzoylindole-2,3-quinodimethane (13) reacted with quinones to furnish the dioxocarbazoles14–16. Compounds4–8 and14–16 with a coplanar skeleton are members of a class of potential DNA intercalators, as has been shown for5 and8 by X-ray structural analysis. On the basis of the geometries determined by X-ray crystallography, the intercalative binding of these molecules with a Watson-Crick mini-helix was predicted by molecular modeling methods.
Synthesis and in Vitro Evaluation of Biotinylated RG108: A High Affinity Compound for Studying Binding Interactions with Human DNA Methyltransferases
2006
Small-molecule inhibitors of DNA methyltransferases such as RG108 represent promising candidates for cancer drug development. We report the synthesis and in vitro analysis of a biotinylated RG108 conjugate, 2-(1,3-dioxo-1,3-dihydro-isoindol-2-yl)-3-(5-[3-[5-(2-oxo-hexahydro-thieno[3,4-d]imidazol-4-yl)pentanoylamino]propoxy]-1H-indol-3-yl)propionic acid (bio-RG108), for the evaluation of interactions with DNA methyltransferase enzymes. The structural design of the chemically modified inhibitor was aided by molecular modeling, which suggested the possibility for extensive chemical modifications at the 5-position of the tryptophan moiety in RG108. The inhibitory activity of the corresponding d…
Molecular modeling approaches in the discovery of new drugs for anti-cancer therapy: the investigation of p53-MDM2 interaction and its inhibition by …
2010
The mdm2 oncogene product, MDM2, is an ubiquitin protein ligase that inhibits the transcriptional activity of the tumor suppressor p53 and promotes its degradation. About 50% of all human cancers present mutations or deletions in the TP53 gene. In the remaining half of all human neoplasias that express the wild-type protein, aberrations of p53 regula- tors, such as MDM2, account for p53 inhibition. For this reason, designing small-molecule inhibitors of the p53-MDM2 protein-protein interaction is a promising strategy for the treatment of cancers retaining wild-type p53. The development of inhibitors has been challenging. Although many small-molecule MDM2 inhibitors have shown potent in vitr…
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…
Leptin and the OB-receptor as anti-obesity target: recent in silico advances in the comprehension of the protein-protein interaction and rational dru…
2014
The OB-receptor or leptin receptor (LR) is crucial for energy homeostasis and regulation of food uptake. Leptin is a 16 kDa hormone that is mainly secreted by fat cells into the bloodstream. Under normal circumstances, circulating leptin levels are proportionate to the fat body mass. Sensing of elevated leptin levels by the hypothalamic neuro-circuitry activates a negative feedback loop resulting in reduced food intake and increased energy expenditure. Decreased leptin concentrations lead to opposite effects. Therefore, rational design of leptin agonists/antagonists could be an appealing challenge in the battle against obesity. The Leptin/LR interactions have been studied in several works b…
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.