In Silico Database of In Vitro Tested Antiviral Compounds

Published: 15 February 2023| Version 2 | DOI: 10.17632/jxgf4n3y6s.2
Nicolas Porto,
Caio Cheohen,
Maria Eduarda Alves Esteves


Antivirals are drugs used to treat viral diseases by inhibiting the infection or replication of viruses. With the wide variety of viruses, it is crucial to constantly find new antiviral options. One approach is to reposition existing drugs, which is a more cost-effective and faster method than traditional research and development. The problem is that there is a lack of organized and standardized data on these drugs. This work aims to address this issue by creating a database of in vitro-tested antivirals. The information and compounds were collected from published in vitro antiviral studies. The database includes six different file formats (SMILES, MOL, SDF 2D, MOL2, PDB, and PDBQT) and categorizes the compounds based on their antiviral activity.


Steps to reproduce

From canonic SMILES obtained by PubChem (, the 325 compounds were separated from a single file into individual files by the OpenBabel software via the Linux terminal command “obabel *.smi –O *.smi –m”, beingwith "-m" as the option responsible for generating multiple files generation (OPENBABEL,2011), generating the first one-dimensional database, called “antiviral_smi”. After splitting into multiple files, the SMI had hydrogen added to some structures(CHEOHEN, 2022; O’BOYLE, 2011). The second database, called “antiviral_mol” originated by the OpenBabel software via the Linux terminal command “obabel *.smi -O *.mol -d --gen2d”, contains files with two-dimensional structures of the molecules based on information from the SMILES present in the “antiviral_smi” with the option “-d” to remove hydrogens from compounds that were added after splitting into several files and the option “--gen2d” for creating 2D coordinates (OPENBABEL,2011).The “antiviral_mol” DB was used as a template for all other two-dimensional and three-dimensional antiviral DBs (Figure 1). The third database contains two-dimensional files in SDF format, called “antiviral_sdf2d” generated from the OpenBabel program, via the Linux terminal command “obabel *.mol -O *.sdf”. The fourth DB, called “antiviral_pdb” contains files in three dimensions in pdb format, formed by the OpenBabel program via the Linux terminal command “obabel *.mol -O *.pdb --gen3d”, with the option “--gen3d” for creating 3D coordinates (OPENBABEL,2011). The calculations of physicochemical and pharmacokinetic properties were originated by the Datawarrior program using the "antiviral_sdf2d" database, which contains 56 properties calculated and described for each compound available in the supplementary material (SANDER,2015). The fifth and sixth databases in MOL2 and PDBQT formats respectively are named “antiviral_mol2” and “antiviral_pdbqt”. These two DBs contain three-dimensional files with the addition of hydrogen, being in the DB “antiviral_pdbqt” with the addition of hydrogens at physiological pH (7.4). Using the OpenBabel program via the Linux terminal commands “obabel *.mol -O *. mol2 –h --gen3d” and “obabel *.mol -O *. pdbqt -p 7.4 --gen3d” were made databases “antiviral_mol” and “antiviral_pdbqt” respectively, with the option “-p” together with the value of “7.4” to generate hydrogens at pH 7.4 and the option “-h” to add the hydrogens in the compounds (OPENBABEL,2011).


Instituto Nacional de Metrologia Qualidade e Tecnologia, Universidade Federal do Rio de Janeiro, Fundacao Oswaldo Cruz


Biochemistry, Pharmacology, Bioinformatics, Antiviral


Fundação Carlos Chagas Filho de Amparo à Pesquisa do Estado do Rio de Janeiro

Conselho Nacional de Desenvolvimento Científico e Tecnológico

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior