Protein binding sites for drug design

BindingSiteDTI: differential-scale binding site modelling for drug-target interaction prediction

MOTIVATION

Enhanced by contemporary computational advances, the prediction of drug-target interactions (DTIs) has become crucial in developing de novo and effective drugs. Existing deep learning approaches to DTI prediction are frequently beleaguered by a tendency to overfit specific molecular representations, which significantly impedes their predictive reliability and utility in novel drug discovery contexts. Furthermore, existing DTI networks often disregard the molecular size variance between macro molecules (targets) and micro molecules (drugs) by treating them at an equivalent scale that undermines the accurate elucidation of their interaction.

RESULTS

We propose a novel DTI network with a differential-scale scheme to model the binding site for enhancing DTI prediction, which is named as BindingSiteDTI. It explicitly extracts multiscale substructures from targets with different scales of molecular size and fixed-scale substructures from drugs, facilitating the identification of structurally similar substructural tokens, and models the concealed relationships at the substructural level to construct interaction feature. Experiments conducted on popular benchmarks, including DUD-E, human, and BindingDB, shown that BindingSiteDTI contains significant improvements compared with recent DTI prediction methods.

AVAILABILITY AND IMPLEMENTATION

The source code of BindingSiteDTI can be accessed at https://github.com/MagicPF/BindingSiteDTI.

Probing the interaction of lysozyme with cardiac glycoside digitoxin: experimental and in silico analyses

Digitoxin is a cardiac glycoside used to treat heart failure and heart arrhythmia. However, its therapeutic concentration range is very narrow. High doses of digitoxin are associated with severe side effects; therefore, it is necessary to develop the delivery system which can control the plasma levels of it. In this context, the binding of lysozyme, an important protein having many applications, with digitoxin has been studied to see the ability of the former as a carrier. The studies were carried out using both experimental and computational methods. The intrinsic fluorescence of lysozyme increased on the addition of digitoxin. Fluorescence results suggested that there was a strong interaction between lysozyme and digitoxin which was favored, mainly, by hydrophobic forces. Further, digitoxin affected the secondary structure of lysozyme slightly by causing the partial unfolding of lysozyme. The preferred binding site of digitoxin within lysozyme was the large cavity of the protein. Molecular docking studies also established the principal role of hydrophobic forces in the binding with a significant support of hydrogen bonding. Frontier molecular orbitals of free digitoxin and in complexation with lysozyme were also computed and discussed. The findings from molecular dynamics simulation studies elucidate that, when contrasted with the first and third conformations of the digitoxin-bound lysozyme complex, the second conformation promotes structural stability, reduces flexibility, and enhances the compactness and folding properties of lysozyme. The overall study shows that lysozyme could act as a potential carrier for digitoxin in pharmaceutical formulations.

Computational biophysics and structural biology of proteins-a Special Issue in honor of Prof. Haruki Nakamura's 70th birthday

Receiving his initial training jointly in theoretical and applied physics at the University of Tokyo, Professor Haruki Nakamura has had a long and eventful scientific career, along the way helping to shape the way that biophysics is carried out in Japan. Concentrating his research efforts on the simulation of protein structure and function, he has, over his career arc, acted as director of the Institute for Protein Research (Osaka, Japan), director of the Protein Data Bank of Japan (PDBj), president of the Biophysical Society of Japan (BSJ), president of the Protein Science Society of Japan (PSSJ), and group leader and professor of Bioinformatics and Computational Structural Biology at Osaka University. In 2022, Prof. Haruki Nakamura turned 70 years old, and to mark this occasion, his scientific colleagues from around the world have combined their efforts to produce this Festschrift Issue of the IUPAB Biophysical Reviews journal around the theme of the computational biophysics and structural biology of proteins.