Comparative receptor mapping of serotoninergic 5-HT₃ and 5-HT₄ binding sites*

Abstract

The clinical use of currently available drugs acting at the5-HT₄ receptor has been hampered by their lack of selectivityover 5-HT₃ binding sites. For this reason, there is considerableinterest in the medicinal chemistry of these serotonin receptor subtypes, andsignificant effort has been made towards the discovery of potent and selectiveligands. Computer-aided conformational analysis was used to characterizeserotoninergic 5-HT₃ and 5-HT₄ receptorrecognition. On the basis of the generally accepted model of the5-HT₃ antagonist pharmacophore, we have performed a receptormapping of this receptor binding site, following the active analog approach(AAA) defined by Marshall. The receptor excluded volume was calculated as theunion of the van der Waals density maps of nine active ligands(pK_i ≥ 8.9), superimposed in pharmacophoric conformations.Six inactive analogs (pK_i < 7.0) were subsequently used todefine the essential volume, which in its turn can be used to define theregions of steric intolerance of the 5-HT₃ receptor. Five activeligands (pK_i ≥ 9.3) at 5-HT₄ receptors wereused to construct an antagonist pharmacophore for this receptor, and todetermine its excluded volume by superimposition of pharmacophoricconformations. The volume defined by the superimposition of five inactive5-HT₄ receptor analogs that possess the pharmacophoric elements(pK_i ≤ 6.6) did not exceed the excluded volume calculated forthis receptor. In this case, the inactivity may be due to the lack of positiveinteraction of the amino moiety with a hypothetical hydrophobic pocket, whichwould interact with the voluminous substituents of the basic nitrogen ofactive ligands. The difference between the excluded volumes of both receptorshas confirmed that the main difference is indeed in the basic moiety. Thus,the 5-HT₃ receptor can only accommodate small substituents inthe position of the nitrogen atom, whereas the 5-HT₄ receptorrequires more voluminous groups. Also, the basic nitrogen is located at ca.8.0 Å from the aromatic moiety in the 5-HT₄ antagonistpharmacophore, whereas this distance is ca. 7.5 Å in the5-HT₃ antagonist model. The comparative mapping of bothserotoninergic receptors has allowed us to confirm the three-componentpharmacophore accepted for the 5-HT₃ receptor, as well as topropose a steric model for the 5-HT₄ receptor binding site. Thisstudy offers structural insights to aid the design of new selective ligands,and the resulting models have received some support from the synthesis of twonew active and selective ligands: 24 (K_i(5-HT₃)= 3.7 nM; K_i(5-HT₄) > 1000 nM) and 25(K_i(5-HT₄) = 13.7 nM;K_i(5-HT₃) > 10 000 nM).