Renal cancer would greatly benefit from new therapeutic strategies since, in advanced stages, it is refractory to classical chemotherapeutic approaches. In this context, lysosomal protease cysteine cathepsins may represent new pharmacological targets. In renal cancer, they are characterized by a higher expression, and they were shown to play a role in its aggressiveness and spreading. Traditional studies in the field were focused on understanding the therapeutic potentialities of cysteine cathepsin inhibition, while the direct impact of such therapeutics on the expression of these enzymes was often overlooked. In this work, we engineered two fluoromethyl ketone-based peptides with inhibitory activity against cathepsins to evaluate their potential anticancer activity and impact on the lysosomal compartment in human renal cancer. Molecular modeling and biochemical assays confirmed the inhibitory properties of the peptides against cysteine cathepsin B and L. Different cell biology experiments demonstrated that the peptides could affect renal cancer cell migration and organization in colonies and spheroids, while increasing their adhesion to biological substrates. Finally, these peptide inhibitors modulated the expression of LAMP1, enhanced the expression of E-cadherin, and altered cathepsin expression. In conclusion, the inhibition of cysteine cathepsins by the peptides was beneficial in terms of cancer aggressiveness; however, they could affect the overall expression of these proteases.

Significantly diverging results may be obtained while modeling the behavior of an enzyme–substrate complex with modern non-polarizable force fields.

An in silico approach was adopted to identify potential cyclooxygenase inhibitors through molecular docking studies. Four potentially active molecules were generated by fusion of dopamine with ibuprofen or ketorolac derivatives. The binding mode of the considered ligands to cyclooxygenase-1 and cyclooxygenase-2 isoforms was described using Autodock Vina. Preliminary docking to full cyclooxygenase isoforms’ structures was used to determine possible binding sites for the described dopamine-derived ligands. The following more accurate docking iteration to the described binding sites was used to achieve better conformational sampling. Among the studied molecules, IBU-GABA-DA showed preferable binding to cyclooxygenase active site of cyclooxygenase-1, while IBU-DA bound to peroxidase site of cyclooxygenase-1, making these ibuprofen-comprising ligands a base for further research and design of selective cyclooxygenase-1 inhibitors. Keterolac-derived ligands KET-DA and KET-GABA-DA demonstrated binding to both cyclooxygenase isoforms at a side pocket, which does not relate to any known functional site of cyclooxygenases and needs to be further investigated.