Database of Peptides with Potential for Pharmacological Intervention in Human Pathogen Molecular Targets

Description

Peptides are polymeric chains used as research objects in the search for new drugs with greater efficacy and fewer side effects. Therefore, we created three databases of antimicrobial peptides using PubChem and ChEMBL. First we acquired the Simplified Molecular-Input Line-Entry System (SMILES) of several peptides belonging to different types of pathogens, namely bacteria, viruses, parasites, and fungi. Using the OpenBabel software, these SMILES had their file formats and structures converted to create: one database in one dimension SMI format, and two with three-dimensional MOL2 and PDB file formats. In total the three databases consists of 718 peptides that have been shown to possess inhibitory activity on molecular targets of clinically important pathogens.

Steps to reproduce

Collection of compounds using databases Once the sources referring to the target compounds were gathered, started to search for each of the peptides found in the databases linked to the servers of the National Institutes of Health (NIH) or in ChEMBL (https://www.ebi.ac.uk/chembl/), so that it could have access to the desired data. The collected items were grouped in a Microsoft Office Excel (2019) spreadsheet with the names of the peptides, their SMILES notation and their International Union of Pure and Applied Chemistry (IUPAC) nomenclatures allowing for different ways for identification. Additional information such as organisms which the peptides demonstrated activity and the molecular targets were also included to help future users of the worksheet. Finally, one cannot fail to mention the insertion of all the references where it is possible to find the reports of the use of the peptide. The research has a total of found 718 peptides. Data Transformation The first database, called “antivirals.smi”, is made up of files in SMI format, generated through manual collection in the PubChem and ChEMBL databases. The second database “antivirals.mol2” is composed of files in MOL2 format. Data conversion was performed by accessing the OpenBabel software version 2.3.1 (O'BOYLE et al., 2011) via a Linux terminal using the command “obabel *. smi -O *.mol2 –gen3d”. This step is responsible for originating three-dimensional structure files. The last conversion step consisted of creating a database called “antivirals.pdb”. Still in three-dimensional form, it was transformed directly from MOL2 format to PDB format using the command “obabel *.mol 2 -O *.pdb” via Linux terminal. In the same way, following the steps (figure 1), all four databases were produced: antiviral, antibacterial, antifungal and antiparasitic. In case it is desirable to conduct the steps we did, all the structures were available in formats with X coordinates (1D format), and XYZ coordinates (3D formats), together with an Excel spreadsheet containing information about the peptides. Both SYBYL MOL2 and PDB formats are capable of recording atoms, bonds, vectors, 3D coordinates etc., as well as storing information about flexibility, which is important for in silico simulations, depending on the programs used and the context in which they are tested (CHEOHEN, ANDRIOLO, SILVA, 2022; DALBY et al, 1992).

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