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DIY Projects with SAnDReS for Beta-Lactamase (EC 3.5.2.6)

The figure on the left shows the electrostatic molecular surface for Beta-Lactamase (EC 3.5.2.6) after it has broken down a highly advanced carbapenem antibiotic. The surface in red color indicates the concentration of negative charge and blue color indicates positive charge. Neutral regions are indicated with white surface The atomic coordinates from 4EYL were used to generate this figure in the program Molegro Virtual Docker (MVD). The crystallographic position of the ligand is shown in light grey and the pose is shown in red. Beta-Lactamase has been studied as a target protein due to its role in breaking down the antibiotics into its component parts. Inhibition of Beta-Lactamase may improve the antibiotic action.

Here we have information for Beta-Lactamase that can be used to design drugs in your garage, the true "DIY drug design". For this system, we can find both, structural and ligand-binding information. You also find publications related to docking for this specific biological system. There are also links to DUD-E, Molecule of the Month site (MOTM), and ClinicalTrials.gov. DUD-E has information about decoys and benchmark results. For Beta-Lactamase we have an area under curve AUC = 78.92 % and an enrichment factor EF = 8.3. In addition, DUD-E provides a free online system to generate decoy ligands for your active compounds, to do so, you need SMILES structures for the active ligands. The ClinicalTrials.gov site brings information related to clinical trials focused on this target protein.     

To use SAnDReS in your DIY project, download the program clicking here and then follow the tutorial 1. For Beta-Lactamase, we have crystallographic structures for which ligand binding information is available for maximal inhibitory concentration (IC50) and inhibition constant (Ki). Application of machine learning techniques for regression analysis makes possible to generate scoring function specific for Beta-Lactamase. 

Clicking on IC50 or Ki below you download the zipped folder to be used as project directory in the SAnDReS session. Unzip the folder and move it to wherever you want to run your SAnDReS session. Inside each folder, you have the pdbCodes.csv file, with PDB access codes for Beta-Lactamase. For instance, if you click on IC50, you download the zipped folder with the pdbCodes.csv file. In this CSV file, you find the PDB access for all crystallographic structures for which IC50 information is available. The same is true for Ki. The idea is to have structures and binding affinity information, which allows to apply supervised machine learning techniques for regression analysis and to build a scoring function targeting Beta-Lactamase and the type of binding affinity. 

     

Beta-Lactamase (or Cephalosporinase):   ClinicalTrials.gov   DUD-E   IC50   Ki    MOTM   PubMed      


After finding and validating the docking protocol, you can use ligand libraries to carry out virtual screening focused on Beta-Lactamase. Among small-molecules libraries available for VS studies, we indicate ZINC natural products, available here.

For PDF version click here.