The ProBiS H2O MD approach for identification of conserved waters and water sites of interest in macromolecular systems, which is becoming a typical step in a structure-based drug design or macromolecular study in general, is described. This work explores an extension of the ProBiS H2O approach introduced by Jukicˇet al. Indeed, water molecules are key players in the interaction mechanisms of macromolecules and small molecules and play structural roles. Our earlier developed approach, ProBiS H2O, is a simple and transparent workflow for conserved water detection. Here we have considered generalizing the idea by supplementing the experimental data with data derived from molecular dynamics to facilitate work on less known systems. Newly developed ProBiS H2O MD workflow uses trajectory data, extracts and identifies interesting water sites, and visualizes the results. ProBiS H2O MD can thus robustly process molecular dynamic trajectory snapshots, perform local superpositions, collect water location data, and perform density-based clustering to identify discrete sites with high conservation of water molecules. This is a new approach that uses experimental data in silico to identify interesting water sites. Methodology is fast and water-model or molecular dynamics software independent. Trends in the conservation of water molecules can be followed over a variety of trajectories, and our approach has been successfully validated using reported protein systems with experimentally observed conserved water molecules. ProBiS H2O MD is freely available as PyMOL plugin at http://insilab.org.
COBISS.SI-ID: 23077142
In the context of antibacterial drug discovery resurgence, novel therapeutic targets and new compounds with alternative mechanisms of action are of paramount importance. We focused on UDP-N-acetylenolpyruvylglucosamine reductase (i.e. MurB), an underexploited target enzyme that is involved in early steps of bacterial peptidoglycan biosynthesis. On the basis of the recently reported crystal structure of MurB in complex with NADP+, a pharmacophore model was generated and used in a virtual screening campaign with combined structure-based and ligand-based approaches. To explore chemical space around hit compounds, further similarity search and organic synthesis were employed to obtain several compounds with micromolar IC50 values on MurB. The best inhibitors in the reported series of 5-substituted tetrazol-2-yl acetamides were compounds 13, 26 and 30 with IC50 values of 34, 28 and 25 microM, respectively. None of the reported compounds possessed in vitro antimicrobial activity against Staphylococcus aureus and Escherichia coli.
COBISS.SI-ID: 4478065
MurA is an intracellular bacterial enzyme that is essential for peptidoglycan biosynthesis, and is therefore an important target for antibacterial drug discovery. We report the synthesis, in silico studies and extensive structure-activity relationships of a series of quinazolinone-based inhibitors of MurA from Escherichia coli. 3-Benzyloxyphenylquinazolinones showed promising inhibitory potencies against MurA, in the low micromolar range, with an IC50 of 8 mM for the most potent derivative (58). Furthermore, furan-substituted quinazolinones (38, 46) showed promising antibacterial activities, with MICs from 1 mg/mL to 8 mg/mL, concomitant with their MurA inhibitory potencies. These data represent an important step towards the development of novel antimicrobial agents to combat increasing bacterial resistance.
COBISS.SI-ID: 4336241
Identification of conserved waters in protein structures is a challenging task with applications in molecular docking and protein stability prediction. As an alternative to computationally demanding simulations of proteins in water, experimental cocrystallized waters in the Protein Data Bank (PDB) in combination with a local structure alignment algorithm can be used for reliable prediction of conserved water sites. We developed the ProBiS H2O approach based on the previously developed ProBiS algorithm, which enables identification of conserved water sites in proteins using experimental protein structures from the PDB or a set of custom protein structures available to the user. With a protein structure, a binding site, or an individual water molecule as a query, ProBiS H2O collects similar proteins from the PDB and performs local or binding site-specific superimpositions of the query structure with similar proteins using the ProBiS algorithm. It collects the experimental water molecules from the similar proteins and transposes them to the query protein. Transposed waters are clustered by their mutual proximity, which enables identification of discrete sites in the query protein with high water conservation. ProBiS H2O is a robust and fast new approach that uses existing experimental structural data to identify conserved water sites on the interfaces of protein complexes, for example protein–small molecule interfaces, and elsewhere on the protein structures. It has been successfully validated in several reported proteins in which conserved water molecules were found to play an important role in ligand binding with applications in drug design.
COBISS.SI-ID: 6273306
The increase of antimicrobial resistance necessitates the renewal and strong research involvement in antibacterial drug design. In the following work, we comment on the key approaches used in development of new antibacterials, focusing on intracellular therapeutic targets that have been so far mostly underexplored: the enzymes of the Mur pathway MurA to MurF. We identify common obstacles observed during research on MurA, MurB, and Mur ligases inhibitors and their development into potential antibacterial compounds, and discern several approaches and solutions to tackle the whole%cell activity of designed compounds. Furthermore, we consolidate recent literature reports and encourage the further research on Mur enzymes.
COBISS.SI-ID: 4623217