L-Enantiomers of transition state analogue inhibitors bound to human purine nucleoside phosphorylase

Human purine nucleoside phosphorylase (PNP) was crystallized with transition-state analogue inhibitors Immucillin-H and DADMe-Immucillin-H synthesized with ribosyl mimics of l-stereochemistry. The inhibitors demonstrate that major driving forces for tight binding of these analogues are the leaving group interaction and the cationic mimicry of the transition state, even though large geometric changes occur with d-Immucillins and l-Immucillins bound to human PNP.     

Phosphate activation in the ground state of purine nucleoside phosphorylase

Phosphate and ribose 1-phosphate (R1P) bound to human purine nucleoside phosphorylase (PNP) have been studied by FTIR spectroscopy for comparison with phosphate bound with a transition state analogue. Bound phosphate is dianionic but exists in two distinct binding modes with similar binding affinities. The phosphate of bound R1P is also dianionic. Bound R1P slowly hydrolyzes to ribose and phosphate even in the absence of nucleobase. The C-OP bond is cleaved in bound R1P, the same as in the PNP-catalyzed reaction. Free R1P undergoes both C-OP and CO-P solvolysis. A hydrogen bond to one P-O group is stronger than those to the other two P-O groups in both the PNP.R1P complex and in one form of the PNP.PO4 complex. The average hydrogen bond strength to the PO bonds in the PNP.R1P complex is less than that in water but stronger than that in the PNP.PO4 complex. Hydrolysis of bound R1P may be initiated by distortion of the phosphate moiety in bound R1P. The unfavorable interactions on the phosphate moiety of bound R1P are relieved by dissociation of R1P from PNP or by hydrolysis to ribose and phosphate. The two forms of bound phosphate in the PNP.PO4 complex are interpreted to be phosphate positioned as the product in the nucleoside synthesis direction and as the reactant in the phosphorolysis reaction; their interconversion can occur by the transfer of a proton from one PO bond to another. The electronic structure of phosphate bound with a transition state analogue differs substantially from that in the Michaelis complexes.     

Transition state analogue discrimination by related purine nucleoside phosphorylases

Transition state analogues of PNP, the Immucillins and DADMe-Immucillins, were designed to match transition state features of bovine and human PNPs, respectively. The inhibitors with or without the hydroxyl and hydroxymethyl groups of the substrate demonstrate that inhibitor geometry mimicking that of the transition state confers binding affinity discrimination. This finding is remarkable since crystallographic analysis indicates complete conservation of active site residues and contacts to ligands in human and bovine PNPs.     

Syntheses and bio-activities of the L-enantiomers of two potent transition state analogue inhibitors of purine nucleoside phosphorylases

(1R)-1-(9-Deazahypoxanthin-9-yl)-1,4-dideoxy-1,4-imino-L-ribitol [(+)-5] and (3S,4S)-1-[(9-deazahypoxanthin-9-yl)methyl]-4-(hydroxymethyl)pyrrolidin-3-ol [(-)-6] are the L-enantiomers of immucillin-H (D-ImmH) and DADMe-immucillin-H (D-DADMe-ImmH), respectively, these D-isomers being high affinity transition state analogue inhibitors of purine nucleoside phosphorylases (PNPases) developed as potential pharmaceuticals against diseases involving irregular activation of T-cells. The C-nucleoside hydrochloride D-ImmH [(-)-5) x HCl], now "Fodosine" is in phase II clinical trials as an anti-T-cell leukaemia agent, while D-DADMe-ImmH is a second generation inhibitor with extreme binding to the target enzyme and has entered the clinic for phase I testing as an anti-psoriasis drug. Since the enantiomers of some pharmaceuticals have revealed surprising biological activities, the L-nucleoside analogues (+)-5 x HCl and (-)-6, respectively, of D-ImmH and D-DADMe-ImmH, were prepared and their PNPase binding properties were studied. For the synthesis of compound (-)-6 suitable enzyme-based routes to the enantiomerically pure starting material (3S,4S)-4-(hydroxymethyl)pyrrolidin-3-ol [(-)-6] and its enantiomer were developed. The L-enantiomers (+)-5 x HCl and (-)-6 bind to the PNPases approximately 5- to 600-times less well than do the D-compounds, but nevertheless remain powerful inhibitors with nanomolar dissociation constants.     

An efficient and large-scale enantioselective synthesis of PNP405: a purine nucleoside phosphorylase inhibitor

An efficient and large-scale enantioselective synthesis of PNP405 (1), a purine nucleoside phosphorylase inhibitor, is described. This synthesis of 1 involved eight steps starting from o-fluorophenylacetic acid with a 21.6% overall yield and >99.5% enantiopurity. The key stereogenic center with (R)-configuration was created using Evans' asymmetric alkylation methodology. This synthesis also features the racemization-free reductive removal of the chiral auxiliary in 5 using sodium borohydride, protection of the gamma-cyano alcohol 6 as the trityl ether by a new water-assisted tritylation with trityl chloride and triethylamine or with trityl alcohol and catalytic trifluoroacetic acid, and an efficient one-pot cyclo-guanidinylation of 10 using cyanamide as the guanidinylating agent.     

Synthesis of pentafluorophenylmethylamines via silicon Mannich reaction

[reaction: see text] The three-component coupling of aldehydes, secondary amines, and methoxytris(pentafluorophenyl)silane, MeOSi(C(6)F(5))(3), affording pentafluorophenylmethylamines has been described. The generation of the five-coordinate silicate intermediate is believed to be the key feature responsible for the efficiency of the reaction.     

Synthesis of Mannich type products via a three-component coupling reaction

The reactions of alkyl nitriles, acetyl chloride, aldehydes and β-ketoesters or simple ketones was studied for the one-pot synthesis of β-acetamido carbonyl compounds. It was observed that the reaction proceeds in the absence of Lewis acids. However, a Lewis acid catalyzes the reaction and several were tested. It was found that whereas Cu(OTf)₂ is suitable for the coupling of β-ketoesters with aldehydes, Sc(OTf)₃ is the best for ketones. A possible mechanism is proposed based on the isolation and characterization of an intermediate.     

A transition state analogue for an RNA-editing reaction

Deamination at C6 of adenosine in RNA catalyzed by the ADAR enzymes generates inosine at the corresponding position. Because inosine is decoded as guanosine during translation, this modification can lead to codon changes in messenger RNA. Hydration of 8-azanebularine across the C6-N1 double bond generates an excellent mimic of the transition state proposed for the hydrolytic deamination reaction catalyzed by ADARs. Here, we report the synthesis of a phosphoramidite of 8-azanebularine and its use in the preparation of RNAs mimicking the secondary structure found at a known editing site in the glutamate receptor B subunit pre-mRNA. The binding properties of analogue-containing RNAs indicate that a tight binding ligand for an ADAR can be generated by incorporation of 8-azanebularine. The observed high-affinity binding is dependent on a functional active site, the presence of one, but not the other, of ADAR2's two double-stranded RNA-binding motifs (dsRBMs), and the correct placement of the nucleoside analogue into the sequence/structural context of a known editing site. These results advance our understanding of substrate recognition during ADAR-catalyzed RNA editing and are important for structural studies of ADAR.RNA complexes.     

Synthesis of the first stable phosphonamide transition state analogue

Three methods were selected for the one-pot synthesis of the fully protected beta-fluoroaminophosphonic acids, using the readily accessible N-protected beta-fluoroaminals. These were activated by acylation leading, by beta-elimination, to a transient N-acylimine immediately trapped by reactive forms of dialkyl phosphites. Avoiding basic conditions, the complete or partial deprotection of these N-protected beta-fluoroaminophosphonic esters allowed the synthesis of the free amino acids, their esters, and a racemic beta-trifluorophosphonamidic acid. The latter, which represents a transition state analogue formed by the bacterial transpeptidase, is perfectly stable at pH 4.7, contrary to the nonfluorinated compounds.     

Structure-activity relationships for a collection of structurally diverse inhibitors of purine nucleoside phosphorylase

Values of inhibition constants, Ki, and concentrations required for 50% inhibition, IC50, for a collection of structurally diverse competitive inhibitors of calf spleen purine nucleoside phosphorylase have been determined employing inosine as substrate. These values have been employed to create predictive quantitative structure-activity relationships (QSAR) which link structure to values of Ki and IC50. These QSAR models have substantial power to predict values and the associated uncertainties for Ki and IC50 for unknown, structurally diverse inhibitors of purine nucleoside phosphorylase.     

Synthesis of a ketone analogue of biotin via the intramolecular Pauson-Khand reaction

We report an improved synthesis of 5-(5-oxohexahydrocyclopenta[c]thiophen-1-yl)pentanoic acid (ketone biotin, 1) based on the intramolecular Pauson-Khand cyclization. The synthesis proceeds in eight steps and in 2.7% overall yield from cyclohexene.     

Acyclic ribooxacarbenium ion mimics as transition state analogues of human and malarial purine nucleoside phosphorylases

Transition state analogues of PNP, the Immucillins and DADMe-Immucillins, were designed to match transition state features of bovine and human PNPs, respectively. A third generation of inhibitors has been designed that contain an acyclic iminoalcohol to replace the cyclic mimic of the ribooxacarbenium ion at the transition states of PNPs. The best third generation inhibitor is equivalent to the best inhibitors found in the previous transition state analogues.     

Alternative route towards the convergent synthesis of a human purine nucleoside phosphorylase inhibitor—forodesine HCl

Forodesine HCl is being investigated as a potential target for the control of T-cell proliferation. Herein we present an alternative route for the synthesis of the target molecule with addition of lactam to the lithiated deazahypoxanthine (generated in situ). The lactam was synthesized in five steps starting from l-pyroglutamic acid.     

Activating the phosphate nucleophile at the catalytic site of purine nucleoside phosphorylase: a vibrational spectroscopic study

Difference Raman and FTIR studies complemented by vibrational analysis based on ab initio calculations show that the dianionic phosphate in the PNP.ImmH.PO4 complex is forced into a unique bonding arrangement in which one of the PO bonds is greatly polarized by enzyme active site interactions, such that it resembles a PO bond that is about one-quarter of the way toward forming a bridging P-O-C single P-O bond.     

Synthesis of phosphinopeptides via the Mannich ligation

Phosphinopeptides are a class of unnatural peptides containing a tetrahedral phosphorus atom and have potential for use as enzyme inhibitors. A series of phosphinopeptides were synthesized via the Mannich-type reaction of aryldichlorophosphines, aldehydes, and N-protected amino amides or peptide amides and subsequent aminolysis with amino esters or peptide esters. The current method named the Mannich ligation is an efficient route to synthesis of phosphinopeptides through convergent condensation.     

Synthesis and evaluation of macrocyclic transition state analogue inhibitors for alpha-chymotrypsin

Lactams 1 and 2 are readily formed from acyclic precursors in the presence of trypsin and chymotrypsin, respectively, identifying the macrocyclic ring system as a potential motif for constrained transition state analogue inhibitors of the serine peptidases. Ketone 3 was synthesized and shown to be a modest inhibitor of chymotrypsin (Ki = 220 microM), albeit 4-fold more potent than the acyclic hydroxy acid 25 (Ki = 1.5 mM as a mixture of epimers). A precursor (31) to the amino boronic acid 4 was also prepared; although this derivative was a potent inhibitor of chymotrypsin (Ki = 130 nM) by virtue of the boronic acid moiety, it showed no advantage over the des-amino analogue 32 (Ki = 120 nM), which is not capable of cyclizing.     

Synthesis of alkoxymethyl derivatives of resorcinarene via the Mannich reaction catalysed with iminodiacetic acid

The conditions of a simple synthesis of tetra(alkoxymethyl) derivatives of resorcinarene via the Mannich reaction catalysed with iminodiacetic acid are described. A possibility of high yield synthesis of such derivatives for the selected straight-chain alcohols is shown. A possible mechanism of this reaction is suggested.     

新型类嘌呤脱氧核糖核苷类化合物的合成

以1,3,5-三-O-苯甲酰基-2-脱氧-2-β-氟-α-D-核糖为原料,通过溴代、与4-氯吡咯[2,3-d]嘧啶的钠盐偶合、4-氯的氨基化等反应,设计合成了一系列具有新型结构的4-取代-9-(2′-脱氧-2′-β-氟-β-D-呋喃糖基)吡咯[2,3-d]嘧啶类化合物,其化学结构经核磁共振、高分辨率质谱分析确证;并且初步探讨了反应条件和反应机理.结果表明,以无水四氢呋喃为溶剂,密闭高压回流反应,反应产率较高.     

Facile synthesis of 9-substituted 9-deazapurines as potential purine nucleoside phosphorylase inhibitors

A facile synthesis of 9-substituted 9-deazapurines as potential inhibitors of purine nucleoside phosphorylase has been achieved by the direct Friedel-Crafts aroylation or arylmethylation of 9-deazapurines using trifluoromethanesulfonic acid as catalyst. The aroylated 9-deazapurines could be transformed into the corresponding 9-aryimethyl derivatives by the Wolff-Kishner reaction. A novel synthesis of 9-deazahypoxanthine was also developed by treatment of 4-hydroxy-5-phenylazo-6-methylpyrimidin-2-thione with triethyl orthoformate in trifluoroacetic acid (TFA) to yield 8-oxo-7H-2-phenylpyrimido[5,4-c]pyridazin-6-thione followed by Raney nickel reduction.