The present invention relates to a method for identifying target regions existing in the interface of monomers constituting the PilT protein with the view to design molecules potentially applicable in impairing the activity of this protein, thus controlling infectious processes. The method is characterized in (i) selecting at least one amino acid sequence constituting the PilT monomer; (ii) developing a three-dimensional computational model of the PilT homo-hexameric structure; (iii) analyzing and determining, with computer aid, the interface-forming residues (IFR) and their physicochemical and structural characteristics for all the chains of the models of hexameric complexes generated; (iv) selecting the regions to be used as therapeutic targets (and preferred therapeutic targets) in the interface between the monomers based on the intensity of determined parameters; (v) computer-aided design of molecules potentially capable of effecting bindings and/or interactions between target regions of the monomers. Markedly, some of the main applications of this technology consist in combating the bacteria Xylella fastidiosa, an etiologic agent of the Citrus Variegated Chlorosis (CVC or “Amarelinho”), and Pierce's disease.