3-D QSAR Investigations of the Inhibition ofLeishmaniamajorFarnesyl Pyrophosphate Synthase by Bisphosphonates

Abstract

We report the activities of 62 bisphosphonates as inhibitors of the Leishmania major mevalonate/isoprene biosynthesis pathway enzyme, farnesyl pyrophosphate synthase. The compounds investigated exhibit activities (IC(50) values) ranging from approximately 100 nM to approximately 80 microM (corresponding to K(i) values as low as 10 nM). The most active compounds were found to be zoledronate (whose single-crystal X-ray structure is reported), pyridinyl-ethane-1-hydroxy-1,1-bisphosphonates or picolyl aminomethylene bisphosphonates. However, N-alicyclic aminomethylene bisphosphonates, such as incadronate (N-cycloheptyl aminomethylene bisphosphonate), as well as aliphatic aminomethylene bisphosphonates containing short (n = 4, 5) alkyl chains, were also active, with IC(50) values in the 200-1700 nM range (corresponding to K(i) values of approximately 20-170 nM). Bisphosphonates containing longer or multiple (N,N-) alkyl substitutions were inactive, as were aromatic species lacking an o- or m-nitrogen atom in the ring, or possessing multiple halogen substitutions or a p-amino group. To put these observations on a more quantitative structural basis, we used three-dimensional quantitative structure-activity relationship techniques: comparative molecular field analysis (CoMFA) and comparative molecular similarity index analysis (CoMSIA), to investigate which structural features correlated with high activity. Training set results (N = 62 compounds) yielded good correlations with each technique (R(2) = 0.87 and 0.88, respectively), and were further validated by using a training/test set approach. Test set results (N = 24 compounds) indicated that IC(50) values could be predicted within factors of 2.9 and 2.7 for the CoMFA and CoMSIA methods, respectively. The CoMSIA fields indicated that a positive charge in the bisphosphonate side chain and a hydrophobic feature contributed significantly to activity. Overall, these results are of general interest since they represent the first detailed quantitative structure-activity relationship study of the inhibition of an expressed farnesyl pyrophosphate synthase enzyme by bisphosphonate inhibitors and that the activity of these inhibitors can be predicted within about a factor of 3 by using 3D-QSAR techniques.

A Quantitative Structure−Activity Relationship and Pharmacophore Modeling Investigation of Aryl-X and Heterocyclic Bisphosphonates as Bone Resorption Agents

“…Their structures are shown below: For example, the drugs minodronate (3), olpadronate (31), and risedronate (8) (top row) are all potent γδ T cell activators ( Figure 3B-D), bone resorption drugs, 35,39,45,46 and FPPS inhibitors. 25,45 However, moving the position of ring alkylation in 3 (to 51), replacing the OH group by an NH 2 in 31 (to 49), or adding a CH 2 group to 8 (to 47) (bottom row) results in the loss of essentially all activity in γδ T cell activation ( Figure 3B-D), bone resorption, 39,45,46 or FPPS inhibition. 25,45 While these observations do not, in and of themselves, prove a causal link between FPPS inhibition and γδ T cell activation (as suggested by Thompson et al 19 ), the effects of minor structural changes are very pronounced and do suggest the possibility of such a relationship.…”

“…and is particularly useful in examining the spatial arrangements of these features. Both approaches have recently been successfully applied by us to analyze the inhibitory activity of bisphosphonates with an FPPS from Leishmania major, 25 a geranylgeranyl pyrophosphate synthase, 26 in Trypanosoma brucei growth inhibition 27 and in bone resorption. Figure 1.…”

“…Figure 1. The IC50 values for 16, 43, and 49 (11,154, and 371 µM) were not included in the CoMSIA analysis, due to the uncertainties in the side chain protonation state described previously (ref 25), but were included in the FPPS inhibition activity correlations (Figure 4). b Correlation coefficient.…”

“…The syntheses of the bisphosphonates investigated (3-51, 53-67; Figures 1 and 2) used methods which are described in more detail elsewhere. 25,26,[35][36][37][38][39][40][41][42] 52 was prepared using the following route: 31 and 49 were from Gador S.A. (Buenos Aires) and were a gift from Teresita Bellido at the University of Arkansas for Medical Sciences. Most compounds investigated were available from previous work.…”

Synthetic Procedures Leading towards Aminobisphosphonates

“…Because this compound was previously prepared by acid hydrolysis of N-benzhydrylaminomethylenebisphosphonic acid [83,100], it may be that it is formed upon hydrolysis of N-aryl derivatives. The three-component reaction was applied to synthesize a large series of physiologically active compounds, in some cases of very complex chemical structures, including bone antiresorptive drug candidates [75][76][77][78][79][80][81][82]; bone imaging [83,84], antiprotozoal [85][86][87][88], antibacterial [72,[89][90][91][92], anti-HIV [93] and anti-inflammatory [94] agents; herbicides [95][96][97]; and complex ones for various metals [10,98].…”