Augmenting a training dataset of the generative diffusion model for molecular docking with artificial binding pockets.

This study introduces the PocketCFDM generative diffusion model, aimed at improving the prediction of small molecule poses in the protein binding pockets. The model utilizes a novel data augmentation technique, involving the creation of numerous artificial binding pockets that mimic the statistical patterns of non-bond interactions found in actual protein-ligand complexes. An algorithmic method was developed to assess and replicate these interaction patterns in the artificial binding pockets built around small molecule conformers.

3DProtDTA: a deep learning model for drug-target affinity prediction based on residue-level protein graphs.

Accurate prediction of the drug-target affinity (DTA) is of critical importance for modern drug discovery. Computational methods of DTA prediction, applied in the early stages of drug development, are able to speed it up and cut its cost significantly. A wide range of approaches based on machine learning were recently proposed for DTA assessment.

Organelle specific fluorescent phenomics and transcriptomic profiling to evaluate cellular response to tris(1,3 dichloro 2 propyl)phosphate.

Tris(1,3-dichloro-2-propyl)phosphate (TDCPP) has been suspected to cause toxicity invertebrates, but its phenotypic effects and the underlying regulatory mechanism have not been fully revealed. Generally, cellular responses tightly control and affect various phenotypes. The scope of the whole organism or cellular toxicological phenotyping, however, has been limited, and quantitative analysis methods using phenotype data have not been fully established.

Kidney-Targeted Cytosolic Delivery of siRNA Using a Small-Sized Mirror DNA Tetrahedron for Enhanced Potency.

A proper intracellular delivery method with target tissue specificity is critical to utilize the full potential of therapeutic molecules including siRNAs while minimizing their side effects. Herein, we prepare four small-sized DNA tetrahedrons (sTds) by self-assembly of different sugar backbone-modified oligonucleotides and screened them to develop a platform for kidney-targeted cytosolic delivery of siRNA. An biodistribution study revealed the kidney-specific accumulation of mirror DNA tetrahedron (L-sTd).

Expression of micro-RNA hsa-miR-30c-5p and hsa-miR-138-1 in renal cell carcinoma.

Aim: To analyze the expression levels of hsa-miR-30c-5p and hsa-miR-138-1 in tumors of patients with renal cell carcinoma to determine whether they could be used as diagnostic markers.

Materials And Methods: The relative expression of hsa-miR-30c-5p and hsa-miR-138-1 was compared in the paired samples of kidney tumor tissue and conventionally normal tissue adjacent to the tumor.

Results: We found a significant decrease in miR-30c-5p and miR-138-1 levels in tumor tissues even in the cases of early stage cancer.