The B-rapidly accelerated
fibrosarcoma (BRAF) is a proto-oncogene
that plays a vital role in cell signaling and growth regulation. Identifying
a potent BRAF inhibitor can enhance therapeutic success in high-stage
cancers, particularly metastatic melanoma. In this study, we proposed
a stacking ensemble learning framework for the accurate prediction
of BRAF inhibitors. We obtained 3857 curated molecules with BRAF inhibitory
activity expressed as a predicted half-maximal inhibitory concentration
value (pIC50) from the ChEMBL database. Twelve molecular
fingerprints from PaDeL-Descriptor were calculated for model training.
Three machine learning algorithms including extreme gradient boosting,
support vector regression, and multilayer perceptron were utilized
for constructing new predictive features (PFs). The meta-ensemble
random forest regression, called StackBRAF, was created based on the
36 PFs. The StackBRAF model achieves lower mean absolute error (MAE)
and higher coefficient of determination (R
2 and Q
2) than the individual baseline
models. The stacking ensemble learning model provides good y-randomization results, indicating a strong correlation
between molecular features and pIC50. An applicability
domain of the model with an acceptable Tanimoto similarity score was
also defined. Moreover, a large-scale high-throughput screening of
2123 FDA-approved drugs against the BRAF protein was successfully
demonstrated using the StackBRAF algorithm. Thus, the StackBRAF model
proved beneficial as a drug design algorithm for BRAF inhibitor drug
discovery and drug development.