Aggregation of amyloid beta (A beta) is the hallmark of Alzheimer's disease (AD). Small molecules inhibiting A beta can be valuable therapeutics for AD. We have previously reported that 1,4-naphthoquinon-2-yk-tryptophan (NQTrp), reduces aggregation and oligomerization of A beta in vitro and in vivo. In silico analysis further showed that certain functional groups of NQTrp, not in the aromatic rings, are also involved in binding and inhibiting A beta. To better understand the exact mode of action and identify the groups crucial for NQTrp inhibitory activity, we conducted structure activity-analysis. Four derivatives of NQTrp were studied in silico: a D-isomer, two single-methylated and one double-methylated derivative. In silico results showed that the NQTrp groups involved in hydrogen bonds are the anilinic NH (i.e., the NH linker between the quinone and tryptophan moieties), the quinonic carbonyls, and the carboxylic acid. These predictions were supported by in vitro results. Our results should aid in designing improved small-molecule inhibitors of A beta aggregation for treating AD.