The Brazilian compound library (BraCoLi) database: a repository of chemical and biological information for drug design

Abstract

The Brazilian Compound Library (BraCoLi) is a novel open access and manually curated electronic library of compounds developed by Brazilian research groups to support further computer-aided drug design works. Herein, the first version of the database is described comprising 1,176 compounds. Also, the chemical diversity and drug-like profiles of BraCoLi were defined to analyze its chemical space. A significant amount of the compounds fitted Lipinski and Veber's rules, alongside other drug-likeness properties. A comparison using principal component analysis showed that BraCoLi is similar to other databases (FDA-approved drugs and NuBBEDB) regarding structural and physicochemical patterns. Furthermore, a scaffold analysis showed that BraCoLi presents several privileged chemical skeletons with great diversity. Despite the similar distribution in the structural and physicochemical spaces, similarity analysis indicated that compounds present in the BraCoLi are generally different from the two other databases showing an interesting innovative aspect, which is a desirable feature for novel drug design purposes.

Machine Learning-Based Virtual Screening of Antibacterial Agents against Methicillin-Susceptible and Resistant Staphylococcus aureus

“…After the training and validation step, the three most predictive models for the MRSA inhibitor subset, the MSSA inhibitor subset, and the SRI subset were selected for a virtual screening protocol, totaling nine distinct virtual screenings. Then, those models were employed to predict the activities of BraCoLi and NuBBE , databases. After the compounds were classified as active by most of the models, a concordance between each subset was made, and the selected compounds were experimentally validated according to the availability of samples.…”

“…Those models were generated using diverse methods such as distance-based, neural networks, and support vector machines and were validated according to QSAR literature standards. Validated models were used to virtually screen two relevant small molecule libraries BraCoLi and NuBBE. , Potential hits selected from this screening underwent biological evaluation against an S. aureus reference strain as well as a reference and two clinical isolates of MRSA strains.…”

Aminopyrimidine Derivatives as Multiflavivirus Antiviral Compounds Identified from a Consensus Virtual Screening Approach

“…The pharmacophore model was generated in UNITY (SYBYL-X 2.1.1), based on the binding site characterization and relevant residues identified from the MD simulations of known hits. Four chemical libraries were accessed, and the complete data set included the following: (i) the Brazilian Compounds Library (BraCoLi) ( n = 1,176 compounds); (ii) a subset ( n = 7.586 million) from the ZINC15 database (), available from MolPort; (iii) NuBBE, , a chemical library of natural products ( n = 2,712); and (iv) DrugBank ( n = 9,821 drugs). The data set summed up around 7.6 million compounds, the total amount available in each library at the time (March 2019).…”

Screening the Pathogen Box to Discover and Characterize New Cruzain and TbrCatL Inhibitors

“…Analogues of MMV688179 were searched in BraCoLi, a diverse database (containing 1176 molecules previously synthesized by Brazilian medicinal chemistry groups as of October 2022) [ 69 ] using DataWarrior. FragFP molecular fingerprints were generated for the entire library and then used to generate a similarity map.…”