Improvement of COVID-19 clinical condition was seen in studies where combination of antiretroviral drugs, lopinavir and ritonavir, as well as immunomodulant antimalaric, chloroquine/hydroxychloroquine together with the macrolide-type antibiotic, azithromycin, was used for patient's treatment. Although these drugs are “old”, their pharmacological and toxicological profile in SARS-CoV-2 – infected patients are still unknown. Thus, by using
in silico
toxicogenomic data-mining approach, we aimed to assess both risks and benefits of the COVID-19 treatment with the most promising candidate drugs combinations: lopinavir/ritonavir and chloroquine/hydroxychloroquine + azithromycin. The Comparative Toxicogenomics Database (CTD;
http://CTD.mdibl.org
), Cytoscape software (
https://cytoscape.org
) and ToppGene Suite portal (
https://toppgene.cchmc.org
) served as a foundation in our research. Our results have demonstrated that lopinavir/ritonavir increased the expression of the genes involved in immune response and lipid metabolism (
IL6
,
ICAM1
,
CCL2
,
TNF
,
APOA1
,
etc.
). Chloroquine/hydroxychloroquine + azithromycin interacted with 6 genes (
CCL2
,
CTSB
,
CXCL8
,
IL1B
,
IL6
and
TNF
), whereas chloroquine and azithromycin affected two additional genes (
BCL2L1
and
CYP3A4
), which might be a reason behind a greater number of consequential diseases. In contrast to lopinavir/ritonavir, chloroquine/hydroxychloroquine + azithromycin downregulated the expression of
TNF
and
IL6
. As expected, inflammation, cardiotoxicity, and dyslipidaemias were revealed as the main risks of lopinavir/ritonavir treatment, while chloroquine/hydroxychloroquine + azithromycin therapy was additionally linked to gastrointestinal and skin diseases. According to our results, these drug combinations should be administrated with caution to patients suffering from cardiovascular problems, autoimmune diseases, or acquired and hereditary lipid disorders.