Coronavirus disease (COVID-19) pandemic has infected 630 million people and led to 6.59 million deaths worldwide since its outbreak. To control COVID-19 advance, finding new molecules with potential to inhibit viral spread is pivotal. Papain-like protease (PLpro) is one of the most interesting targets of pharmacological inhibition since it is implicated not only in viral replication but also in modulation of host immune response. Natural products are of great interest to the pharmaceutical industry due to their diverse structure and biological activities. The NuBBEDB (Nuclei of Bioassays, Biosynthesis and Ecophysiology of Natural Products Database) is an excellent source of natural products (NPs) from the Brazilian flora. In this study, we performed virtual screening, molecular dynamics, and binding energy analyses of the NuBBEDB library to target severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) papain-like protease (PLpro), the virus's protease essential for replication. Among the top-ranked molecules, the indole alkaloids raputindoles A, C, and D emerged as potential SARS-CoV-2 inhibitors, showing significant interactions with the pivotal Beta-Loop-2 (BL2) region, including the catalytic Y268 residue. Notably, raputindole D displayed enhanced stabilization of the BL2 region, while raputindole C exhibited superior overall stability. These in silico findings suggest that raputindoles, especially D, might offer therapeutic value against COVID-19, laying the groundwork for further experimental evaluations.