Synthetic and computer-assisted analyses of the pharmacophore for the benzodiazepine receptor inverse agonist site

Abstract

The structural requirements for ligand binding to the benzodiazepine receptor (BzR) inverse agonist site were probed through the synthesis and in vitro evaluation of 3-substituted beta-carbolines 6, 7, 11, 12, gamma-carboline 13, and diindoles 18-21, 23-25, 27, 28, and 34. On the basis of the apparent binding affinities of these and other analogues, a hydrogen bond acceptor site (A2) on the receptor is proposed to interact with the N(9) hydrogen atom of the beta-carbolines or the N(7) hydrogen nuclei of the diindoles. Likewise, a proposed hydrogen bond donating site (H1) interacts with the N(2) nitrogen atom of the beta-carbolines or the N(5) nitrogen atom of the diindoles. It appears that interaction with both sites is a prerequisite for high affinity since analogues which have either one or both of these positions blocked exhibit substantial reduction in affinity. Moreover, H1 appears to be capable of engaging in a three-centered hydrogen bond with appropriately functionalized ligands, which explains the increase in potency observed in the following series of 3-substituted beta-carbolines: the n-butyl (12, IC50 = 245 nM), n-propoxy (9, IC50 = 11 nM), and propyl ketone (11, IC50 = 2.8 nM) congeners. In addition to H1 and A2, there appears to be a relatively narrow hydrophobic pocket in the binding cleft that can accommodate substituents at the 3-position of the beta-carbolines which have chain lengths less than or equal to C5. There is a 1 order of magnitude decrease in affinity between n-propoxy analogue 9 (IC50 = 11 nM, chain length = 4) and n-butoxy derivative 7 (IC50 = 98 nM, chain length = 5). Furthermore, alpha- and gamma-branching [e.g. ethoxycarbonyl (2), IC50 = 5 nM and tert-butoxycarbonyl (31) IC50 = 10 nM] but not beta- and delta-branching [e.g. isopropoxy (6), IC50 = 500 nM and (neopentyloxy) carbonyl (48), IC50 = 750 nM] at position 3 are tolerated. Occupation of this hydrophobic pocket is clearly important for high affinity as evidenced by the relatively low affinity of 30, a beta-carboline which possesses a hydrogen atom at the 3-position. This same hydrophobic pocket is partially filled by the D and E rings of the diindoles, which accounts for the high affinity of several members of this series. An excluded volume analysis using selected 3-substituted beta-carbolines and ring-E substituted pyridodiindoles is consistent with the presence of this hydrophobic pocket (see Figure 1).(ABSTRACT TRUNCATED AT 400 WORDS)

Synthesis and Evaluation of Analogues of the Partial Agonist 6-(Propyloxy)-4-(methoxymethyl)-β-carboline-3-carboxylic Acid Ethyl Ester (6-PBC) and the Full Agonist 6-(Benzyloxy)-4-(methoxymethyl)-β- carboline-3-carboxylic Acid Ethyl Ester (Zk 93423) at Wild Type and Recombinant GABAA Receptors

“…13,14 Initially, it was believed that an ester moiety at the 3-position was required for a compound to exhibit high-affinity binding at Bz binding sites. [34][35][36][37] However, the high affinity of the partial inverse agonist 3-ethoxy--carboline 54 (Table 3) demonstrated this was not the case.…”

2D-QSAR of non-benzodiazepines to benzodiazepines receptor (BZR)

“…Series A: This series contains 17 b-carbolines with their observed affinities (Allen et al, 1990;Good et al, 1993;Sharma et al, 1992;So et al, 1997) as reported in Table 1.…”

3D molecular similarity indices and their application in QSAR studies

“…Similarly, the Rl group of 7 is aligned in the same way as all other type a structures. It may be, however, that Rl groups containing other oxygens need to be realigned to a position closer to a postulated pharmacophore hydrogen bond (Allen et al, 1990). One way to alter alignments, of course, would be to apply similarity optimisation to the system, since at the moment only a simple least-squares fit of the central skeletons has been undertaken.…”

“…Allen et al (1990) were the first to study the benzodiazepine system using 3D QSAR techniques, employing CoMF A in order to characterize a pharmacophore for the site. This ligand set provides a good example of a system where 3D QSAR has significant advantages over more traditional methods.…”