The paper presents a theoretical study on the similarities between some natural and synthetic HIV-1 non-nucleoside reverse transcriptase inhibitors. A lot of natural compounds from alkaloid, coumarin, flavonoid, lignan, phenolic, quinone, saponin, terpene, sterol, xanthone, carbohydrate, peptide, and protein classes reveal anti-HIV activity, some of them being with higher activity. Natural avarol and illimaquinone from the Red Sea sponges (Dysidea cinerea and Smenospongia, respectively), baicalin from Scutellariae radix, buchapine analogues from Euodia roxburghiana, depsidone from Lichens species, epiexcelsin from Litsea verticillata, magnoflorine from Toddalia asiatica, robustaflavone from Rhus succedanea, and especially 12-deoxyphorbol-13-(3E,5E-decadienoate) from Excoecaria agallocha, have anti-HIV activities and resembling to synthetic HIV-1 non-nucleoside reverse transcriptase inhibitors actually used to treat HIV infection: efavirenz, nevirapine, delavirdine, etravirine, and rilpivirine (the most recent approved by FDA, in May 2011). The most stable conformations of these compounds (obtained by molecular mechanics and conformational search analyses) are superimposed and similarities between them were identified. Furthermore, quantitative structure-activity relationships were obtained in the second generation of HIV-1 non-nucleoside reverse transcriptase inhibitors class, by using geometrical and BCUT descriptors (correlation coefficient of 0.96 for a bilinear model).
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