Chemical biology & drug design 2016 12 09() doi 10.1111/cbdd.12917
Comparative molecular field analysis (CoMFA), topomer CoMFA and hologram QSAR (HQSAR) as three efficient methods of QSAR have been performed on 40 newly synthesized inhibitors against HIV-1 protease. Molecular alignment was done by aid of crystallographic structure of template inhibitor (indirectly alignment) and also by the molecular mechanic (MM) minimized structure. Both alignment methods produced satisfactory statistics for training set, but indirectly alignment had more predictive power. Generated counter maps, especially by topomer CoMFA, give comprehensive information about structural features affecting the inhibitory activities of studied chemicals. Based on the obtained information, some new inhibitors were suggested.