Comprehensive analysis of acetylcholinesterase inhibitor and reactivator complexes: implications for drug design and antidote development.

The main function of acetylcholinesterase (AChE) is to regulate the levels of one of the most important neurotransmitters: acetylcholine. This makes AChE an ideal molecular target for the treatment of neurodegenerative diseases and dementia (such as Alzheimer's disease), as well as for the neutralisation of natural toxins (e.g.

Recent Advances in Studying Toll-like Receptors with the Use of Computational Methods.

Toll-like receptors (TLRs) are transmembrane proteins that recognize various molecular patterns and activate signaling that triggers the immune response. In this review, our goal is to summarize how, in recent years, various computational solutions have contributed to a better understanding of TLRs, regarding both their function and mechanism of action. We update the recent information about small-molecule modulators and expanded the topic toward next-generation vaccine design, as well as studies of the dynamic nature of TLRs.

Corrigendum to "Structure-function relationship between soluble epoxide hydrolases structure and their tunnel network" [Comput. Struct. Biotechnol. J. 20 (2022) 193-205].

[This corrects the article DOI: 10.1016/j.csbj.

Evolution of tunnels in α/β-hydrolase fold proteins-What can we learn from studying epoxide hydrolases?

The evolutionary variability of a protein's residues is highly dependent on protein region and function. Solvent-exposed residues, excluding those at interaction interfaces, are more variable than buried residues whereas active site residues are considered to be conserved. The abovementioned rules apply also to α/β-hydrolase fold proteins-one of the oldest and the biggest superfamily of enzymes with buried active sites equipped with tunnels linking the reaction site with the exterior.

Structure-function relationship between soluble epoxide hydrolases structure and their tunnel network.

Enzymes with buried active sites maintain their catalytic function a single tunnel or tunnel network. In this study we analyzed the functionality of soluble epoxide hydrolases (sEHs) tunnel network, by comparing the overall enzyme structure with the tunnel's shape and size. sEHs were divided into three groups based on their structure and the tunnel usage.

Investigation of Thiocarbamates as Potential Inhibitors of the SARS-CoV-2 Mpro.

In the present study we tested, using the microscale thermophoresis technique, a small library of thionocarbamates, thiolocarbamates, sulfide and disulfide as potential lead compounds for SARS-CoV-2 Mpro drug design. The successfully identified binder is a representative of the thionocarbamates group with a high potential for future modifications aiming for higher affinity and solubility. The experimental analysis was extended by computational studies that show insufficient accuracy of the simplest and widely applied approaches and underline the necessity of applying more advanced methods to properly evaluate the affinity of potential SARS-CoV-2 Mpro binders.

Applications of water molecules for analysis of macromolecule properties.

Water molecules maintain proteins' structures, functions, stabilities and dynamics. They can occupy certain positions or pass quickly a protein's interior. Regardless of their behaviour, water molecules can be used for the analysis of proteins' structural features and biochemical properties.