The antibiotic-resistant bacterial still remains a serious clinical trouble worldwide. Lately the isolation of resistant bacteria to drugs of therapeutic choice has become regular. Vancomycin has been the therapeutic answer to Staphylococcus aureus MRSA; but vancomycin-resistant strains have emerged clinically. Therefore new agents are urgently needed to counter the threats posed by antibiotic-resistant organisms. In this context, five pyrazolo-pyrimidine derivatives were recently tested in our laboratory as antibacterial agents against numerous resistant-bacteria strains isolated from Antônio Pedro University Hospital (HUAP) patients. These previous experimental results revealed only 4-(2’-metoxiphenyl)amino-1,3–diphenyl–1–H–pirazolo [3,4-B] pirimidine–5-carboxilic acid (1c) with antibacterial activity against S. aureus among the derivatives tested. As the target of pyrazolo-pyrimidines is still unknown, in this study we used a molecular modeling approach to evaluate these five compounds and determine important structural features for displaying this biological activity and a feasible structure-activity relationship (SAR). Conformational search for the minimal energy conformer of the five derivatives were done using Molecular Mechanics (MM) methods. Subsequently, a geometry optimization using AM1 semiempirical method was done and showed that all derivatives present different conformations. Molecular electrostatic potential maps (MEPs), HOMO and LUMO eigenvalues and orbital coefficients were calculated. In this work, the MEPs isoenergy contours were generated in a range from −25.000 to +40.000 kcal/mol and superimposed onto a surface of constant electron density of 0.002 e/au³. HOMO and LUMO isosurfaces were calculated at 0.0032 au. The constants employed in these isosurfaces calculations are default parameters in SPARTAN'04 program. Analogous to the experimental results, the SAR studies have demonstrated some important unique features in 1c such as the presence of an intramolecular hydrogen bond, which may be important for a better conformation and consequently interaction with the target-binding site. In addition 1c presented the highest HOMO and LUMO energies and GAP values, whereas MEP analyses demonstrated that the ortho substitution in 1c modifies its carboxylic acid moiety electronic density. Interestingly the replacement of the substituents of these five derivatives resulted in different spatial conformations, and 1c conformation could be related to an ortho effect recently described in literature as a feature of some biological active compounds. As receptors recognize stereoelectronic effects and not atom per se, our data suggest that the stereoelectronic parameters evaluated here are important for 1c antimicrobial activity against S. aureus resistant strains.