In Silico Studies on DARC.

International audienceThe Duffy Antigen/Receptor for Chemokine (DARC) is a seven segment transmembrane protein. It was firstly discovered as a blood group antigen and was the first specific gene locus assigned to a specific autosome in man. It became more famous as an erythrocyte receptor for malaria parasites (Plasmodium vivax and Plasmodium knowlesi), and finally for chemokines. DARC is an unorthodox chemokine receptor as (i) it binds chemokines of both CC and CXC classes and (ii) it lacks the Asp-Arg-Tyr consensus motif in its second cytoplasmic loop hence cannot couple to G proteins and activate their signaling pathways. DARC had also been associated to cancer progression, numerous inflammatory diseases, and possibly to AIDS. In this review, we will summarize important biological data on DARC. Then we shall focus on recent development of the elaboration and analyzes of structural models of DARC. We underline the difficulty to propose pertinent structural models of transmembrane protein using comparative modeling process, and other dedicated approaches as the Protein Blocks. The chosen structural models encompass most of the biochemical data known to date. Finally, we present recent development of protein - protein docking between DARC structural models and CXCL-8 structures. We propose a hierarchal search based on separated rigid and flexible docking

Synthesis, In Silico Studies, Antiprotozoal and Cytotoxic Activities of Quinoline‐Biphenyl Hybrids

This is the pre-peer reviewed version of the following article: Synthesis, In Silico Studies, Antiprotozoal and Cytotoxic Activities of Quinoline‐Biphenyl Hybrids, which has been published in final form at https://doi.org/10.1002/slct.201903835. This article may be used for non-commercial purposes in accordance with Wiley Terms and Conditions for Use of Self-Archived VersionsThe synthesis, in silico studies, antiprotozoal and cytotoxic activities of eleven quinoline‐biphenyl hybrids are described herein. The structure of the synthesized products was elucidated by a combination of spectrometric analyses. The synthesized compounds were evaluated against Plasmodium falciparum, and amastigotes forms both Leishmania (V) panamensis and Trypanosoma cruzi. Cytotoxicity was evaluated against human U‐937 macrophages. 8‐phenylquinoline (4 a) showed similar activity than meglumine antimoniate and 4‐(quinolin‐8‐yl)phenol (4 b) exhibited an activity similar to that of benznidazole. 8‐(3,4‐dimethoxyphenyl) quinoline (4 k) showed the best activity against P. falciparum. Although these compounds were toxic for mammalian U‐937 cells, however they may still have potential to be considered as candidates for drug development because of their antiparasite activity. Molecular docking was used to determine the in silico inhibition of some of the designed compounds against PfLDH and cruzipain, two important pharmacological targets involved in antiparasitic diseases. All hybrids were docked to the three‐dimensional structures of PfLDH and T. cruzi cruzipain as enzymes using AutoDock Vina. Notably, the docking results showed that the most active compounds 4‐(quinolin‐8‐yl)phenol (4 b, CE50: 11.33 μg/mL for T. cruzi) and 8‐(3,4‐dimethoxyphenyl) quinoline (4 k, CE50: 8.84 μg/mL for P. falciparum) exhibited the highest scoring pose (−7.5 and −7.7 kcal/mol, respectively). This result shows a good correlation between the predicted scores with the experimental data profile, suggesting that these ligands could act as competitive inhibitors of PfLDH or T. cruzi cruzipain enzymes, respectively. Finally, in silico ADME studies of the quinoline hybrids showed that these novel compounds have suitable drug‐like properties, making them potentially promising agents for antiprotozoal therapy

Exploiting the CH-π interactions in supramolecular hydrogels of aromatic carbohydrate amphiphiles

A novel class of supramolecular hydrogels derived from amino sugars is reported, where the self-assembly of aromatic carbohydrate amphiphiles is driven by CH-π interactions, rather than π–π stacking and H-bonding associated with gelators based on aromatic peptide amphiphiles. Spectroscopic data is provided as evidence for this mode of self-assembly and in silico studies revealed that a combination of CH-π and T-stacking of the fluorenyl groups contribute to the formation of the aggregated structures

Molecular Level in Silico Studies for Oncology. Direct Models Review

The combination of therapy and diagnostics in one process "theranostics" is a trend in a modern medicine, especially in oncology. Such an approach requires development and usage of multifunctional hybrid nanoparticles with a hierarchical structure. Numerical methods and mathematical models play a significant role in the design of the hierarchical nanoparticles and allow looking inside the nanoscale mechanisms of agent-cell interactions. The current position of in silico approach in biomedicine and oncology is discussed. The review of the molecular level in silico studies in oncology, which are using the direct models, is presented

Molecular Level in Silico Studies for Oncology. Direct Models Review

The combination of therapy and diagnostics in one process "theranostics" is a trend in a modern medicine, especially in oncology. Such an approach requires development and usage of multifunctional hybrid nanoparticles with a hierarchical structure. Numerical methods and mathematical models play a significant role in the design of the hierarchical nanoparticles and allow looking inside the nanoscale mechanisms of agent-cell interactions. The current position of in silico approach in biomedicine and oncology is discussed. The review of the molecular level in silico studies in oncology, which are using the direct models, is presented

Modeling and Simulation of the Effects of Cyclic Loading on Articular Cartilage Lesion Formation

We present a model of articular cartilage lesion formation to simulate the effects of cyclic loading. This model extends and modifies the reaction-diffusion-delay model by Graham et al. 2012 for the spread of a lesion formed though a single traumatic event. Our model represents "implicitly" the effects of loading, meaning through a cyclic sink term in the equations for live cells. Our model forms the basis for in silico studies of cartilage damage relevant to questions in osteoarthritis, for example, that may not be easily answered through in vivo or in vitro studies. Computational results are presented that indicate the impact of differing levels of EPO on articular cartilage lesion abatement

In silico studies of OLED device architectures regarding their efficiency

Simulations have become increasingly important to understand and design organic optoelectronic devices, such as organic light emitting diodes (OLEDs) and to optimize their performance by selecting appropriate materials and layer arrangements. To achieve accurate device simulations, it is crucial to consider the interplay between material properties, device architecture, and operating conditions and to incorporate physical processes such as charge injection, transport, recombination, and exciton decay. Simulations can provide insights into device bottlenecks and streamline optimization cycles, eliminating the need for physical prototyping and rationalizing OLED design. In this study, we investigated three heuristic OLED architectures with a 3D kinetic Monte Carlo (kMC) model and compared their quantum efficiency at different operation voltages. Our investigation focused on examining the effects of various layer arrangements on charge and exciton dynamics in OLED devices and establishing design principles for achieving high efficiency, which are consistent with experimental observations. Notably, we find that increasing the thickness of the emissive layer (EML) led to higher luminance efficiency, and that an emitter concentration of approximately 5% results in optimal performance. By using this model, it is possible to rapidly study the influence of many device parameters and explore a broad range of parameter and architecture space within a reasonable time-frame

Potency Of Vigna Angularis Against Erα Through In Silico Studies

Vigna angularis, from the legume family, contains phytoestrogens. Phytoestrogens can activate estrogen receptors and are safer than estrogen. The study aims to analyze the potential of Vigna angularis as an activator of estrogen receptor-α (ERα) through in silico studies. The analysis of molecular docking used SAR (Structure Activity Relationship). A previous study has shown that Vigna angularis contains isoflavones such as Genestein (0.5%), daidzein (14.9%), glycitein (25.8%), formononetin (13%), and biochanin A (45.5%). The results of molecular docking to ERα show that genestein has a free energy binding value of -9.3 and the same amino acid structure, with a control level over estrogen of 66%. In conclusion, in silico studies have shown that genestein from Vigna angularis is the main component that activates the ERα.

Growth Cone Pathfinding: a competition between deterministic and stochastic events

BACKGROUND: Growth cone migratory patterns show evidence of both deterministic and stochastic search modes. RESULTS: We quantitatively examine how these two different migration modes affect the growth cone's pathfinding response, by simulating growth cone contact with a repulsive cue and measuring the resultant turn angle. We develop a dimensionless number, we call the determinism ratio Ψ, to define the ratio of deterministic to stochastic influences driving the growth cone's migration in response to an external guidance cue. We find that the growth cone can exhibit three distinct types of turning behaviors depending on the magnitude of Ψ. CONCLUSIONS: We conclude, within the context of these in silico studies, that only when deterministic and stochastic migration factors are in balance (i.e. Ψ ~ 1) can the growth cone respond constructively to guidance cues