Structure-based design of inhibitors of purine nucleoside phosphorylase. 1. 9-(Arylmethyl) derivatives of 9-deazaguanine

Abstract

Purine nucleoside phosphorylase (PNP, EC 2.4.2.1) is a salvage enzyme important to the T-cell-mediated part of the immune system and as such is an important therapeutic target. This paper describes the design, synthesis, and enzymatic evaluation of potent, competitive inhibitors of PNP. Potential inhibitors were designed using the three-dimensional structure of the enzyme in an iterative process that involved interactive computer graphics to model the native enzyme and complexes of it with the inhibitors, Monte Carlo-based conformational searching, and energy minimization. Studies of the enzyme/inhibitor complexes were used to determine priorities of the synthetic efforts. The resulting compounds were then evaluated by determination of their IC50 values and by X-ray diffraction analysis using difference Fourier maps. In this manner, we have developed a series of 9-(arylmethyl)-9-deazapurines (2-amino-7-(arylmethyl)-4H-pyrrolo[3,2-d]-pyrimidin-4-ones) that are potent, membrane-permeable inhibitors of the enzyme. The IC50 values of these compounds range from 17 to 270 nM (in 1 mM phosphate), with 9-(3,4-dichlorobenzyl)-9-deazaguanine being the most potent inhibitor. X-ray analysis explained the role of the aryl groups and revealed the rearrangement of hydrogen bonds in the binding of the 9-deazaguanines in the active site of PNP relative to the binding of the 8-aminoguanines that results in more potent inhibition of the enzyme.

A Novel Approach to the Design of Inhibitors of Human Secreted Phospholipase A2 Based on Native Peptide Inhibition

“…For some targets such as influenza virus neuraminidase (35), HIV protease (for a selected sample see Ref. 36), purine nucleoside phosphorylase (37), and thymidylate synthase (38), these approaches have led to the de novo design of compounds that show promising therapeutic benefit as well as being useful tools for probing the biological function of the proteins. Here we have successfully applied this approach to (i) gain further insight into the sites and mode of interaction of native peptide inhibitors of human sPLA 2 -IIA that were originally derived from the primary sequence of the enzyme itself (30) and (ii) improve the potency of specific inhibitors.…”

Calf spleen purine nucleoside phosphorylase: purification, sequence and crystal structure of its complex with an N(7)‐acycloguanosine inhibitor

“…Cocrystallization with various inhibitors, together with molecular modelling, were employed in attempts to develop more potent inhibitors [14][15][16]. These studies suggested that binding of guanine analogue inhibitors involves the purine ring N(7) as a hydrogen bond acceptor [15].…”

“…Cocrystallization with various inhibitors, together with molecular modelling, were employed in attempts to develop more potent inhibitors [14][15][16]. These studies suggested that binding of guanine analogue inhibitors involves the purine ring N(7) as a hydrogen bond acceptor [15]. This is in striking contrast to our finding that a variety of N(7)-alkylguanosines, in which the ring N (7) is blocked and the imidazole ring carries a positive charge, are good substrates, some even superior to the parent guanosine [17][18][19].…”

Identification of Novel Potent Inhibitors for ATP-Phosphoribosyl Transferase Using Three-Dimensional Structural Database Search Technique

“…These suggest that the simultaneous occupation of both substrate-binding sites enables PRibPP to have high affinity to the enzyme. This bi-substrate mimicking approach is reported in the study to design purine-nucleoside phosphorylase (PNP) inhibitor for the treatments of psoriasis and cultaneous T-cell lymphoma, which is one of the most famous and successful studies using the structure-based drug design technique [24][25][26][27][28]. PNP catalyzes the reversible conversion of purine nucleosides, (deoxy)guanosine or (deoxy)inosine, to the base and sugar-phosphate.…”