The rapid spread of fatal diseases forces us to reconsider our position as researchers in the field of drug development assisted by computer. Alternatively, new drugs are constantly being developed from natural compounds using computer-aided methods. The virtual screening is carried out in accordance with protocols established by accredited organizations and is based on the structure of ligands or the structure of target proteins. The formation of a data base based on phytotherapy is the best option because Morocco is known for its wealth of plants and their traditional uses in medicine, which encourages us to better utilize our cultural heritage and the diversity of our country nature in the therapeutic field. The combination of these fields of CADD and Phytotherapy can yield positive results in terms of the development of molecules with the goal of using them as drugs capable of inhibiting a pathological protein. In the present study, deep research was done to collect a set of phytoconstituents extracted from Moroccan plants to evaluate their ability to limit the proliferation of SARS-CoV-2. Molecular docking was done in the active site of 6lu7 and 6m0j proteins to assess their binding affinity. The structural stability of the target protein was validated by redocking. The compounds with good values of binding affinity were further subjected to Lipinski’s rule of five, chemical absorption and toxicity analysis. The results revealed that only 2 compounds present good binding affinity towards target proteins and able to be oral available medication against SARS-CoV-2.