Structure-guided design of AMP mimics that inhibit fructose-1,6-bisphosphatase with high affinity and specificity

AMP binding sites are commonly used by nature for allosteric regulation of enzymes controlling the production and metabolism of carbohydrates and lipids. Since many of these enzymes represent potential drug targets for metabolic diseases, efforts were initiated to discover AMP mimics that bind to AMP-binding sites with high affinity and high enzyme specificity. Herein we report the structure-guided design of potent fructose 1,6-bisphosphatase (FBPase) inhibitors that interact with the AMP binding site on FBPase despite their structural dissimilarity to AMP. Molecular modeling, free-energy perturbation calculations, X-ray crystallography, and enzyme kinetic data guided our redesign of AMP, which began by replacing the 5'-phosphate with a phosphonic acid attached to C8 of the adenine base via a 3-atom spacer. Additional binding affinity was gained by replacing the ribose with an alkyl group that formed van der Waals interactions with a hydrophobic region within the AMP binding site and by replacing the purine nitrogens N1 and N3 with carbons to minimize desolvation energy expenditures. The resulting benzimidazole phosphonic acid, 16, inhibited human FBPase (IC50 = 90 nM) 11-fold more potently than AMP and exhibited high specificity for the AMP binding site on FBPase. 16 also inhibited FBPase in primary rat hepatocytes and correspondingly resulted in concentration-dependent inhibition of the gluconeogenesis pathway. Accordingly, these results suggest that the AMP site of FBPase may represent a potential drug target for reducing the excessive glucose produced by the gluconeogenesis pathway in patients with type 2 diabetes.     

P and H NMR studies of the transesterification polymerization of polyphosphonate oligomers

Polymeric phosphonate esters are an interesting class of organophosphorus polymers because both the polymer backbone and phosphorus substituents can be modified. These polymers have been prepared by ring-opening polymerizations of cyclic phosphites, stoichiometric polycondensations of dimethyl phosphonate with diols in conjunction with diazomethane treatment and by transesterification of polyphosphonate oligomers. Our initial attempts to prepare high molecular weight polymeric phosphonate esters by the transesterification methods were unsuccessful. Results indicate that the reactions of dimethyl phosphonate with diols to form polyphosphonate oligomers with only methyl phosphonate end groups are plagued by a serious side reaction that forms phosphonic acid end groups. These end groups do not participate in the transesterification reaction and limit the molecular weights of the polymers that can be obtained. The phosphonic acid end groups can be converted into reactive methyl phosphonate end groups by treatment with diazomethane, however diazomethane is explosive and the polymerization is slow. An alternative route for the production of high molecular weight polymers is the transesterification of the 1,12-bis(methyl phosphonato)dodecane, formed by the reaction of excess dimethyl phosphonate and 1,12-dodecanediol, with a Na₂CO₃ promoter. This allows polymers with molecular weights of up to 4.5×10⁴ to be prepared, and no phosphonic acid end groups are observed in these polymers. Thermal analyses of the poly(1,12-dodecamethylene phosphonate) have shown that this polymer has reasonable thermal stability (onset of thermal decomposition at 273 °C). This polymer also undergoes a cold crystallization process at 15 °C similar to that which has been observed in some polyesters, polyamides and elastomers.     

Phosphonate mediated surface reaction and reorganization: implications for the mechanism controlling cement hydration inhibition

Vertical scanning interferometry and XPS show the reaction of CaCO3 with the hydration retarder nitrilo-tris-(methylene)phosphonic acid follows a pathway of dissolution of the calcium followed by precipitation of a calcium phosphonate; subsequent surface reorganization/restructuring of the calcium phosphonate exposes the underlying CaCO3 for further hydration.     

Adsorption and precipitation of an aminoalkylphosphonate onto calcite

The mechanism of nitrilotris(methylenephosphonic acid) (H6NTMP)/calcite reaction was studied with a large number of batch experiments where phosphonic acid was neutralized with 0 to 5 equivalents of NaOH per phosphonic acid and the concentration ranged from about 10 nmol/L to 1 mol/L. It is proposed that the phosphonate/calcite reactions are characterized in three steps. At low phosphonate concentration (<1 micromol/L NTMP concentration), the phosphonate/calcite reaction can be characterized as a Langmuir isotherm. At saturation, only approximately 7% of the calcite surface is covered with phosphonate; presumably these are the kinks, step edges, or other imperfect sites. At higher phosphonate concentrations, the attachment is characterized by calcium phosphonate crystal growth to a maximum of four to five surface layer thick, with solid phase stoichiometry of Ca(2.5)HNTMP and a constant solubility product of 10(-24.11). After multiple layers of phosphonate are formed on the calcite surface, the solution is no longer at equilibrium with calcite. Further phosphonate retention is probably due to mixed calcium phosphonate solid phase formation at lower pH and depleted solution phase Ca conditions. The proposed mechanism is consistent with phosphate/calcite reaction and can be used to explain the fate of phosphonate in brines from oil producing wells and the results are compared with two oil wells.     

Calculation of relative binding affinities of fructose 1,6-bisphosphatase mutants with adenosine monophosphate using free energy perturbation method

The free energy perturbation (FEP) methodology is the most accurate means of estimating relative binding affinities between inhibitors and protein variants. In this article, the importance of hydrophobic and hydrophilic residues to the binding of adenosine monophosphate (AMP) to the fructose 1,6-bisphosphatase (FBPase), a target enzyme for type-II diabetes, was examined by FEP method. Five mutations were made to the FBPase enzyme with AMP inhibitor bound: 113Tyr --> 113Phe, 31Thr --> 31Ala, 31Thr --> 31Ser, 177Met --> 177Ala, and 30Leu --> 30Phe. These mutations test the strength of hydrogen bonds and van der Waals interactions between the ligand and enzyme. The calculated relative free energies indicated that: 113Tyr and 31Thr play an important role, each via two hydrogen bonds affecting the binding affinity of inhibitor AMP to FBPase, and any changes in these hydrogen bonds due to mutations on the protein will have significant effect on the binding affinity of AMP to FBPase, consistent to experimental results. Also, the free energy calculations clearly show that the hydrophilic interactions are more important than the hydrophobic interactions of the binding pocket of FBPase.     

Crystal Structures of 2-Aminobenzothiazole-based Inhibitors in Complexes with Urokinase-type Plasminogen Activator

Urokinase-type plasminogen activator （uPA） plays a crucial role in the regulation of plasminogen activation, tumor cell adhesion and migration. The inhibition of uPA activity is a promising mechanism for anti-cancer therapy. Most current uPA inhibitors employ a highly basic group （either amidine or guanidine group） to target the S1 pocket of uPA active site, which leads to poor oral bioavailability. Here we study the possibility of using less basic 2-aminobenzothiazole （ABT） as S1 pocket binding group. We report the crystal structures of uPA complexes with ABT or 2-amino-benzothiazole-6-carboxylic acid ethyl ester （ABTCE）. The inhibitory constants of these two inhibitors were measured by a chromogenic competitive assay, and it was found that ABTCE is a better inhibitor for uPA （Ki = 656 μM） than ABT （Ki = 5.03 mM）. This work shows that 2-amniobenzothiazole can be used as P1 group which may have better oral bioavailability than the commonly used amidine or guanidine group. We also found the ethyl ester group occupies the characteristic oxyanion hole and contacts to uPA 37- and 60-loops. Such work provides structural information for further improvements of potency and selectivity of this new class of uPA inhibitor.     

Glucose-lowering A ivity of Amino Acid- phosphonic Acid Oxovanadium Complexes and Its Interaction with DNA

Vanadium has well-documented lowering glucose properties both in vitro and in vivo. The design of new oxovanadium（IV） coordination compounds, intended for use as insulin-enhancing agents in the treatment of diabetes mellitus, can potentially benefit from a synergistic approach, in which the whole complex has more than an additive effect from its component parts. Biological testing with oxovanadium（IV） organic phosphonic acid, for insulin-enhancing potential included acute administration, by oral gavage in streptozotocin （STZ） diabetic rats. The complexes of oxovanadium（IV） amino acid-N-phosphonic acid exhibit higher lowering glucose activity in vivo. The interaction of the complexes of oxovanadium（IV） amino acid-N-phosphonic acid with DNA was investigated by agarose gel electrophoresis. The results indicated that these complexes have strong interaction with DNA.     

Novel and Convenient Method for the Preparation of Phosphonate Peptides and Phosphonamidate Peptides

Phosphonate and phosphonamidate peptides are phosphorus analogues of natural peptides. They have been great used as stable mimetics of tetrahedral transition states as enzyme inhibitors and as haptens for catalytic antibody research in recent years. Although several methods are available for the preparation of phosphonate peptides and phosphonamidate peptides, all of them use phosphonic acid derivatives as starting materials. The overall yields from the synthesis of phosphonic acid derivatives to desired peptides are not satisfactory in most cases.     

Calculation of relative binding free energy differences for fructose 1,6-bisphosphatase inhibitors using the thermodynamic cycle perturbation approach.

An iterative, computer-assisted, drug design strategy that combines molecular design, molecular mechanics, molecular dynamics (MD), and free energy perturbation (FEP) calculations with compound synthesis, biochemical testing of inhibitors, and crystallographic structure determination of protein-inhibitor complexes was successfully used to predict the rank order of a series of nucleoside monophosphate analogues as fructose 1,6-bisphosphatase (FBPase) inhibitors. The X-ray structure of FBPase complexed with 5-aminoimidazole-4-carboxamide-1-beta-D-ribofuranosyl 5'-monophosphate (ZMP) provided structural information used for subsequent analogue design and free energy calculations. The FEP protocol was validated by calculating the free energy differences for the mutation of ZMP (1) to AMP (2). The calculated results showed a net gain of 1.7 kcal/mol, which agreed with the experimental result of 1.3 kcal/mol. FEP calculations were performed for 18 other AMP analogues. Inhibition constants were determined for over half of these analogues, usually after completion of the calculation, and were consistent with the predictions. Solvation free energy differences between AMP and various AMP analogues proved to be an important factor in binding free energies, suggesting that increased desolvation costs associated with the addition of polar groups to an inhibitor must be overcome by stronger ligand-protein interactions if the structural modification is to enhance inhibitor potency. The results indicate that FEP calculations predict relative binding affinities with high accuracy and provide valuable insight into the factors that influence inhibitor binding and therefore should greatly aid efforts to optimize initial lead compounds and reduce the time required for the discovery of new drug candidates.     

Improved cyclic urea inhibitors of the HIV-1 protease: synthesis,potency, resistance profile,human pharmacokinetics and X-ray crystal structure of DMP 450

Background: Effective HIV protease inhibitors must combine potency towards wild-type and mutant variants of HIV with oral bioavailability such that drug levels in relevant tissues continuously exceed that required for inhibition of virus replication. Computer-aided design led to the discovery of cyclic urea inhibitors of the HIV protease. We set out to improve the physical properties and oral bioavailability of these compounds.Results: We have synthesized DMP 450 (bis-methanesulfonic acid salt), a water-soluble cyclic urea compound and a potent inhibitor of HIV replication in cell culture that also inhibits variants of HIV with single amino acid substitutions in the protease. DMP 450 is highly selective for HIV protease, consistent with displacement of the retrovirus-specific structural water molecule. Single doses of 10 mg kg⁻¹ DMP 450 result in plasma levels in man in excess of that required to inhibit wild-type and several mutant HIVs. A plasmid-based, in vivo assay model suggests that maintenance of plasma levels of DMP 450 near the antiviral IC₉₀ suppresses HIV protease activity in the animal. We did identify mutants that are resistant to DMP 450, however; multiple mutations within the protease gene caused a significant reduction in the antiviral response.Conclusions: DMP 450 is a significant advance within the cyclic urea class of HIV protease inhibitors due to its exceptional oral bioavailability. The data presented here suggest that an optimal cyclic urea will provide clinical benefit in treating AIDS if it combines favorable pharmacokinetics with potent activity against not only single mutants of HIV, but also multiply-mutant variants.     

Stafia-1: a STAT5a-Selective Inhibitor Developed via Docking-Based Screening of in Silico O-Phosphorylated Fragments

We present a new approach for the identification of inhibitors of phosphorylation-dependent protein–protein interaction domains, in which phenolic fragments are adapted by in silico O-phosphorylation before docking-based screening. From a database of 10 369 180 compounds, we identified 85 021 natural product-derived phenolic fragments, which were virtually O-phosphorylated and screened for in silico binding to the STAT3 SH2 domain. Nine screening hits were then synthesized, eight of which showed a degree of in vitro inhibition of STAT3. After analysis of its selectivity profile, the most potent inhibitor was then developed to Stafia-1, the first small molecule shown to preferentially inhibit the STAT family member STAT5a over the close homologue STAT5b. A phosphonate prodrug based on Stafia-1 inhibited STAT5a with selectivity over STAT5b in human leukemia cells, providing the first demonstration of selective in vitro and intracellular inhibition of STAT5a by a small-molecule inhibitor.     

Tailored control and optimisation of the number of phosphonic acid termini on phosphorus-containing dendrimers for the ex-vivo activation of human monocytes

The syntheses of a series of phosphonic acid-capped dendrimers is described. This collection is based on a unique set of dendritic structural parameters-cyclo(triphosphazene) core, benzylhydrazone branches and phosphonic acid surface-and was designed to study the influence of phosphonate (phosphonic acid) surface loading towards the activation of human monocytes ex vivo. Starting from the versatile hexachloro-cyclo(triphosphazene) N(3)P(3)Cl(6), six first-generation dendrimers were obtained, bearing one to six full branches, that lead to 4, 8, 12, 16, 20 and 24 phosphonate termini, respectively. The surface loading was also explored at the limit of dense packing by means of a first-generation dendrimer having a cyclo(tetraphosphazene) core and bearing 32 termini, and with a first-generation dendrimer based on a AB(2)/CD(5) growing pattern and bearing 60 termini. Human monocyte activation by these dendrimers confirms the requirement of the whole dendritic structure for bioactivity and identifies the dendrimer bearing four branches, thus 16 phosphonate termini, as the most bioactive.     

Properties of polyethylene modified with phosphonate side groups. I. Thermal and mechanical properties

Low-density polyethylene was modified by the inclusion of phosphonate ester pendent groups by using an oxidative chlorophosphonylation reaction followed by esterification of the polyethylene poly(phosphonyl chloride) with an alcohol. Two different types of phosphonate esters were prepared: dimethyl phosphonate from the reaction with methanol and a phosphonate graft copolymer from the reaction with hydroxy-terminated poly(ethylene oxide) (PEO). For the latter, oligomers with molecular weights of 350 and 750 were used. For each type of phosphonate, a series of polymers were prepared with pendent group concentrations ranging from 0 to 9.1 substituents per 100 carbon atoms. The modified polymers were characterized by infrared spectroscopy, differential scanning calorimetry, and by measurement of the tensile modulus. Infrared spectroscopy proved to be useful for determining if the polymer modification reaction resulted in entirely phosphonate ester pendent group substitutions or if unesterified phosphonic acid groups were also present. The polymers prepared in this investigation exhibited no infrared absorbances arising from phosphonic acid groups. The presence of phosphonate ester groups resulted in a decrease of crystallinity with increasing phosphonate concentration and with the exception of the polymers containing 9.1 PEO–phosphonate grafts per 100 carbon atoms, the effect of phosphonylation on the melting temperature of the polymers was consistent with Flory's theory for the melting point depression of random copolymers. The tensile modulus measured from a constant uniaxial elongation experiment decreased with increasing phosphonylation. The behavior of all three phosphonate series was identical and could be attributed to the effect of decreasing polymer crystallinity.     

An Analysis of the Enzyme-Inhibitor Binding Interactions for Phosphonic Acid Transition State Analogs of Thermolys in

Abstract

Potent inhibitors of the zinc endopeptidase thermolysin are produced on replacement of the scissile peptide linkage with phosphonamidate or phosphonate ester moieties. These inhibitors have been shown to be transition state analogs, and a comparison between the esters and amidates reveals the intrinsic binding energy due to a specific hydrogen bonding interaction. Incorporation of an α-substituted phosphonic acid analog leads to slow-binding behavior on the part of the inhibitors, which is attributed to expulsion of a specific water molecule from the active site.     

Synthesis and α-amylase inhibitory activity of glucose-deoxynojirimycin conjugates

Inhibitors of α-amylase have attracted attention for their putative effects against diabetes mellitus. Although numerous studies have explored natural small molecule inhibitors, acarbose is currently the only compound with sufficient inhibitory potency and drug-like characteristics to be considered as a potential therapeutic agent. We have synthesized conjugates of the potent glucosidase inhibitor, 1-deoxynojirimycin, and glucose, with the aim of enhancing inhibitory activity against α-amylase. This synthetic conjugate showed increased inhibition of α-amylase compared to 1-deoxynojirimycin alone, suggesting that similar modifications of existing glucosidase inhibitors may yield more potent α-amylase inhibitors.     

Design, synthesis, and characterization of a series of cytochrome P(450) 3A-activated prodrugs (HepDirect prodrugs) useful for targeting phosph(on)ate-based drugs to the liver

A new class of phosphate and phosphonate prodrugs, called HepDirect prodrugs, is described that combines properties of rapid liver cleavage with high plasma and tissue stability to achieve increased drug levels in the liver. The prodrugs are substituted cyclic 1,3-propanyl esters designed to undergo an oxidative cleavage reaction catalyzed by a cytochrome P(450) (CYP) expressed predominantly in the liver. Reported herein is the discovery of a prodrug series containing an aryl substituent at C4 and its use for the delivery of nucleoside-based drugs to the liver. Prodrugs of 5'-monophosphates of vidarabine, lamivudine (3TC), and cytarabine as well as the phosphonic acid adefovir were shown to cleave following exposure to liver homogenates and exhibit good stability in blood and other tissues. Prodrug cleavage required the presence of the aryl group in the cis-configuration, but was relatively independent of the nucleoside and absolute stereochemistry at C4. Mechanistic studies suggested that prodrug cleavage proceeded via an initial CYP3A-catalyzed oxidation to an intermediate ring-opened monoacid, which subsequently was converted to the phosph(on)ate and an aryl vinyl ketone by a beta-elimination reaction. Studies in primary rat hepatocytes and normal rats comparing 3TC and the corresponding HepDirect prodrug demonstrated the ability of these prodrugs to effectively bypass the rate-limiting nucleoside kinase step and produce higher levels of the biologically active nucleoside triphosphate.     

Luminescent ruthenium(II) bipyridyl-phosphonic acid complexes: pH dependent photophysical behavior and quenching with divalent metal ions

The synthesis, redox behavior, and photophysical properties of a series of Ru(II) bipyridyl complexes having diimine ligands with phosphonate and phosphonic acid substituents are presented. The phosphonate-containing ligands examined include diethyl 4-(2,2'-bipyrid-4-yl)benzylphosphonate (bpbzp), diethyl 4-(2,2'-bipyrid-4-yl)-phenylphosphonate (bppp), and 4,4'-(diethyl phosphonato)-2,2'-bipyridine (bpdp), and the [(bpy)2Ru(L)](PF6)2 complexes of both the diethyl phosphonate and the phosphonic acid were prepared. The Ru(III/II) potentials are more positive for the phosphonate complexes than for the phosphonic acids, and the first reduction is localized on the phosphonate-containing ligand for the bppp and bpdp complexes. The first reduction of the phosphonic acid complexes is at more negative potentials and cannot be distinguished from bpy reduction. For the bppp and bpdp complexes luminescence arises from a Ru(d pi)-->bpy-phosphonate (pi*) MLCT state; the phosphonic acid complexes luminescence at higher energies from a MLCT state not clearly isolated on one ligand. Iron(III) and copper(II) complex with and very efficiently quench the luminescence of all the phosphonic acid complexes in nonaqueous solvents. The quenching mechanism is discussed on the basis of luminescence decay and picosecond transient absorption measurements.     

Cloning, expression, and biochemical characterization of Streptomyces rubellomurinus genes required for biosynthesis of antimalarial compound FR900098

The antibiotics fosmidomycin and FR900098 are members of a unique class of phosphonic acid natural products that inhibit the nonmevalonate pathway for isoprenoid biosynthesis. Both are potent antibacterial and antimalarial compounds, but despite their efficacy, little is known regarding their biosynthesis. Here we report the identification of the Streptomyces rubellomurinus genes required for the biosynthesis of FR900098. Expression of these genes in Streptomyces lividans results in production of FR900098, demonstrating their role in synthesis of the antibiotic. Analysis of the putative gene products suggests that FR900098 is synthesized by metabolic reactions analogous to portions of the tricarboxylic acid cycle. These data greatly expand our knowledge of phosphonate biosynthesis and enable efforts to overproduce this highly useful therapeutic agent.     

New mixed phosphonate esters by transesterification of pinacol phosphonates and their use in aldehyde and ketone coupling reactions with nonstabilized phosphonates

Alkylpinacol phosphonates were prepared by rhodium-catalyzed olefin hydrophosphorylation, and attempted alpha-deprotonation of the pinacol derived alkyl phosphonates resulted in ring cleavage. The propensity of the alkylpinacol phosphonates to undergo ring opening was exploited to prepare phosphonic acid monomethyl esters in high yield by transesterification in acidulated methanol. Esterification and alkylation with aldehydes or ketones gave beta-hydroxy mixed phosphonate esters. tert-Butyl and benzylic phosphonate ester protective groups were introduced to improve the efficiency and functional group compatibility of beta-hydroxy phosphonate saponification. The beta-hydroxy phosphonic acid monomethyl esters were dehydrated with diisopropylcarbodiimide, which gave oxaphosphetane intermediates that collapse to an olefin. The overall reaction sequence complements the arsenal of Horner-Wadsworth-Emmons-type coupling reactions.