Dysfunction of serotoninergic neurotransmission is known to be involved in the pathophysiology of major depression. The molecules that enhance the level of serotonin either via blocking serotonin reuptake or through inhibition of its metabolism are effective antidepressants. With this as the basis, a group of new molecules that supposedly effect serotoninergic neurotransmission were designed and tested. The new molecular entities (NME-2, NME-5, NME-16 and NME- 24) are active in animal models of behavioral despair. In the present study, the binding of these new NMEs to the serotonin transporter protein (SERT) has been modeled and their activity correlated with the behavioral pattern observed in the mouse forced swim test (FST) model. The putative binding orientations of the NMEs have been identified by docking the molecules into the active site of the SERT. A 3D model of the SERT active site was constructed using comparative protein modeling principles with the X-ray structure of the leucine transporter (LeuT) as template. 3D-QSAR models based on the CoRIA formalism were generated from the experimental data and docking scores for eight novel SERT inhibitors. The CoRIA models highlight the salient features for effective binding of NMEs to the serotonin transporter and are also able to predict pKd values. Based on the significant correlation between the anti-immobility effect seen in the mouse FST study and the binding energies obtained from the docking study along with insights from the interaction patterns with the receptor obtained from the docking, the CoRIA models can be used to suggest structural modifications that can help in optimization of the SERT inhibition. Experimental evidence shows that the NMEs are highly efficacious and could be developed into potential antidepressants.