Discovery of novel phosphonate derivatives as hepatitis C virus NS3 protease inhibitors

A novel class of phosphonate derivatives was designed to mimic the interaction of product-like carboxylate based inhibitors of HCV NS3 protease. A phosphonic acid (compound 2) was demonstrated to be a potent HCV NS3 protease inhibitor, and a potential candidate for treating HCV infection. The syntheses and preliminary biological evaluation of this phosphonate class of inhibitor are described.     

EFFECT OF PHOSPHONIC ACID ANALOGS OF ACYCLOVIR AND GANCICLOVIR ON IN VITRO CYTOMEGALOVIRUS INFECTIONS

Abstract

Eight phosphonic acid analogs of acyclovir (ACV) or ganciclovir (DHPG) inhibited human cytomegalovirus in vitro. Therapeutic indices were: phosphonate diacid of DHPG: 500; DHPG: 500; phosphonate monoethylester of DHPG: 258; phosphonate monoethylester of ACV: 94; cyclic phosphonate of DHPG: 64; ACV: 60; phosphonate monobutylester of ACV: 1.5; phosphonate monoethylester of deoxy DHPG: 4.6; 8-bromo ACV phosphonate monoethylester: >2; phosphonate monoethylester heptyl of ACV: 1. Types 1 and 2 herpesvirus (HSV-1, HSV-2) and varicella zoster virus (VZV) were poorly inhibited by these new compounds, suggesting highly specific anti-HCMV activity. None exhibited significant cytotoxic effects as measured by uptake of [³H]thymidine, [³H]uridine and [³H]leucine.     

Phosphonoformate Esters of Anti-HIV Nucleosides: 3′-Azido-3′-deoxythymidine and 2′,3′-Dideoxycytidine Derivatives Containing a Small 5′-(0-Alkoxycarbon-ylphosphinyl) or 5′-(O-Cholesterylcarbonylphosphinyl) Substituent

Abstract

A convenient general method of synthesis of 5′-O-(alkoxycarbonyl)phosphonate esters of 2′,3′-dideoxyribonucleosides is presented, using the 5′-O-(methoxycarbonyl)phosphinyl, 5′-0-(ethoxycarbonyl)phosphinyl, and 5′-O-(cholesterylcarbonyl)phosphinyl derivatives of 3′-azido-3′-deoxythymidine (AZT) and the 5′-0-(ethoxycarbonyl)phosphinyl derivative of 2′,3′-dideoxycytidine (ddC) as examples. Reaction of trimethyl phosphonoformate, methyl phosphonoformate, or dimethyl cholesterylcarbonylphosphonate with phosphorus pentachloride in carbon tetrachloride, followed by direct condensation of the resulting phosphonyl chloride with the nucleoside, gave the fully esterified phosphonoformate derivatives, which on treatment with sodium iodide in tetrahydrofuran underwent selective cleavage of the P-OMe or P-OEt groups, leaving the carboxylate esters intact. The resulting products were converted from sodium salts to ammonium salts by ion-exchange chromatography.     

Studies Towards Synthesis of Dinucleoside Arylphosphonates with Metal Complexing Properties

Abstract

An efficient and stereospecific synthesis of dinucleoside 4′-(2,2′:6′,2″-terpyridyl)phosphonate 2 and 5-(2,2′-bipyridyl)phosphonate 3 via a palladium(0) cross coupling strategy has been developed.     

Structure of a reaction intermediate mimic in t6A biosynthesis bound in the active site of the TsaBD heterodimer from Escherichia coli

The tRNA modification N6-threonylcarbamoyladenosine (t⁶A) is universally conserved in all organisms. In bacteria, the biosynthesis of t⁶A requires four proteins (TsaBCDE) that catalyze the formation of t⁶A via the unstable intermediate l-threonylcarbamoyl-adenylate (TC-AMP). While the formation and stability of this intermediate has been studied in detail, the mechanism of its transfer to A37 in tRNA is poorly understood. To investigate this step, the structure of the TsaBD heterodimer from Escherichia coli has been solved bound to a stable phosphonate isosteric mimic of TC-AMP. The phosphonate inhibits t⁶A synthesis in vitro with an IC₅₀ value of 1.3 μM in the presence of millimolar ATP and L-threonine. The inhibitor binds to TsaBD by coordination to the active site Zn atom via an oxygen atom from both the phosphonate and the carboxylate moieties. The bound conformation of the inhibitor suggests that the catalysis exploits a putative oxyanion hole created by a conserved active site loop of TsaD and that the metal essentially serves as a binding scaffold for the intermediate. The phosphonate bound crystal structure should be useful for the rational design of potent, drug-like small molecule inhibitors as mechanistic probes or potentially novel antibiotics.     

Inhibition of Purine Nucleoside Phosphorylase by Phosphonoalkylpurines 1

Abstract

Optimum inhibition of human erythrocyte purine nucleoside phosphorylase by 9-(phosphonoalkyl)hypoxanthines required an alkyl chain of five carbons or longer. Appropriate modifications of either the base or phosphonate side chain resulted in increased inhibitory activity.     

OLigonucleotide (Cyanomethyl) Phosphonates

Abstract

A dinucleoside (cyanomethyl) phosphonate has been prepared, and its properties have been studied. This compound was converted into an oligonucleotide possessing alternating (cyanomethyl) phosphonate and phosphodiester backbone groups and its hybridization to complementary DNA and RNA sequences was studied versus methylphosphonate and phosphodiester controls.     

Synthesis of Oligodeoxyribonucleotide Analogues by Use of Deoxyribonucleoside-3′-yl O-bis(1,1,1,3,3,3-Hexafluoro-2-Propyl) Phosphites as New Key Intermediates

Abstract

The deoxyribonucleoside-3′-yl O-bis(1,1,1,3,3,3-hexafluoro-2-propyl) phosphite units (3) could be converted into the O-nucleosidyl phosphonate, O-2-cyanoethyl O-nucleosidyl phosphonate, and O-1,1,1,3,3,3-hexafluoro-2-propyl O-nucleosidyl phosphonothioate. Compound 3a was activated by methylimidazole to give the dithymidylate derivatives (8). The appropriately protected nucleosidyl phosphonates (3) were applied to the synthesis of oligodeoxyribonucleotides used as antisense oligonucleotides.     

ACYCLIC NUCLEOSIDE/NUCLEOTIDE ANALOGUES WITH AN IMIDAZOLE RING SKELETON

Syntheses of a few acyclic nucleoside and acyclic nucleoside phosphonate analogues containing an imidazole ring have been reported. These analogues include methyl 1-(2-hydroxyethoxymethyl)imidazole-4,5-dicarbo-xylate (1), 4,5-dicarbamoyl-1-(2-hydroxyethoxymethyl)imidazole (2), 4,5-dicya-no-1-(2-hydroxyethoxymethyl)imidazole (4), Methyl 1-(2-bromoethoxymethyl)- imidazole-4,5-dicarboxylate (7), 4,5-dicyano-(2-bromoethoxymethyl)imidazole (8), and Methyl 1-(2-phosphonomethoxyethyl)imidazole (10). Also reported are a few potential prodrugs of the above compounds, including the acetyl derivatives 5 and 6 (of 1 and 4, respectively), and the diethyl phosphonate ester 9 (of 10). In addition, the corresponding benzyl-protected precursors 11 and 12 (of 1 and 4, respectively), along with their common hydrolysis product, 1-(2-benzyloxy-ethoxymethyl)-4,5-imidazoledicarboxylic acid (3), are reported. Another potential prodrug included in the list is 1-(2-acetoxyethyl)-4,5-dicyanoimidazole (15). The compounds were screened for in vitro antiviral activity against a wide variety of herpes and respiratory viruses. The most active compound was the phosphonate analogue 9 which exhibited an anti-measles virus activity with an EC₅₀ of <2.5 μg/mL and an SI value of > 176.     

Synthesis of 2′-Deoxynucleoside 5′-Methylenebis-(phosphonate)s Using 2-(4-Nitrophenyl)ethyl Methylenebis(phosphonate) as the Phosphonylating Agent.

Abstract

2-(4-Nitrophenylethyl) methylenebis(phosphonate) (1) has been prepared by reaction of 2-(4-nitrophenyl)ethyl alcohol with methylenebis(phosphonyl) tetrachloride. Compound 1 was treated with diisopropylcarbodiimide (DIC) to give bicyclic intermediate 2, which in reaction with suitably protected 2′-deoxynucleosides 3 gave P¹,P²-disubstituted methylenebis(phosphonate)s 4. Removal of the nitrophenylethyl group by β-elimination with DBU afforded the corresponding 2′-deoxynucleoside 5′-methylenebis(phosphonate) analogues 5.

     

A NEW CLASS OF ACYCLIC NUCLEOSIDE PHOSPHONATES: SYNTHESIS AND BIOLOGICAL ACTIVITY OF 9-{[(PHOSPHONOMETHYL)AZIRIDIN-1-YL]METHYL}GUANINE (PMAMG) AND ANALOGUES

ABSTRACT

A new class of acyclic nucleoside phosphonates PMAMG, PMAMA, PMAMC, and PMAMT (compounds 1, 2, 3 and4) have been synthesized and tested in vitro against a wide variety of viruses, fungi and bacteria. PMAMG (1) was synthesized by the alkylation reaction of acetylguanine with the phosphonate side-chain, diisopropyl {[2-(bromomethyl)aziridin-1-yl]methyl}phosphonate (9), followed by deesterification reaction in the presence of TMSBr. In similar way, PMAMA, PMAMC, and PMAMT were prepared.     

Phosphonylalkoxyalkyl and Phosphonylalkyl Derivatives of Heterocyclic Bases

Abstract

This review describes chemical syntheses of acyclic nucleotide analogs containing various types of phosphonate grouping, with an emphasis on preparative methods for N-(3-hydroxy-2-phosphonylmethoxypropyl) and N-(2-phosphonylmethoxyethyl) derivatives of purine and pyrimidine bases.     

Dimeric Oligonucleotide Synthons Containing 2-Deoxy-3-O-Phosphonomethyl-α-D-erythro-pentofuranosyl Nucleosides

Abstract

The synthesis of 2′-deoxy-3′-O-phosphonomethyl-α-D-erythro-pentofuranosyl-thymine and -adenine (1, B is Thy or Ade) is described. Dimeric oligonucleotide synthons such as 2 containing isosteric phosphonate internucleoside linkage were prepared.     

Design and Synthesis of Novel Threosyl-5′- Deoxyphosphonic Acid Purine Analogues as Potent Anti-Hiv Agents

The discovery of threosyl phosphonate nucleoside (PMDTA, EC₅₀ = 2.53 μM) as a potent anti-HIV agent has led to the synthesis and biological evaluation of 5 ′-deoxyversions of threosyl phosphonate nucleosides from 1,4-dihydroxy-2-butene. The synthesized nucleoside phosphonic acid analogues 14 and 19 were tested for anti-HIV activity as well as cytotoxicity. The adenine analogue 14 exhibits moderate in vitro anti-HIV-1 activity (EC₅₀ = 12.6 μM).     

Synthesis of Novel 3′-Hydroxymethyl 5′-Deoxythreosyl Phosphonic Acid Nucleoside Analogues as Potent Antiviral Agents

A very efficient synthetic route to novel 3′-hydroxymethyl 5′-deoxythreosyl phosphonic acid nucleosides was described. The discovery of threosyl phosphonate nucleoside (PMDTA, EC₅₀ = 2.53 μM) as a potent antihuman immunodeficiency virus (anti-HIV) agent has led to the synthesis and biological evaluation of 3′-modified 5′-deoxy versions of the threosyl phosphonate nucleosides. 3′-Hydroxymethyl 5 ′-deoxythreosyl phosphonic acid nucleoside analogues 15, 19, 24, and 28 were synthesized from 1,3-dihydroxyacetone and tested for anti-HIV activity as well as cytotoxicity. The adenine analogue 19 exhibits moderate in vitro anti-HIV-1 activity (EC₅₀ = 10.2 μM).     

Synthesis of New PMEA Diphosphate Mimics

Abstract

We synthesized and characterized new diphosphate mimics of the acyclic nucleoside phosphonate PMEA [Adefovir, 9-(2-phosphonylmethoxyethyl)adenine].     

Studies Towards the Synthesis of the Saturated and Unsaturated Carbocyclic Methylene Phosphonate Analogs of Dideoxyadenosine

Abstract

The synthesis of the saturated carbocyclic methylene phosphonate analog of ddAMP is described by two different methods (epoxyde opening and “purinoselenylation”). Studies towards the formation of 2′,3′ unsaturated analogs by selenoxyde or mesylate elimination are also reported.     

Inhibition of adamalysin II and MMPs by phosphonate analogues of snake venom peptides

Phosphonate analogues of the peptidomimetic N-(Furan-2-yl)carbonyl-Leu-Trp-OH were prepared with the goal of evaluating the effect of phosphonate for carboxylate replacement on binding with snake venom metalloproteinases and MMPs. N-(Furan-2-yl)carbonyl-Leu-L-Trp(P)-(OH)2 showed a 75-fold increase of the inhibiting activity against adamalysin II, a snake venom metalloproteinase structurally related to MMPs and TACE. Both the phosphonate and carboxylate peptidomimetics fit into the active site adopting a retrobinding mode and provide the structural base for a new class of metalloproteinases inhibitors.     

Synthesis and Antiherpesvirus Activity of (S)-1-((3-Hydroxy-2-Phosphon-Ylmethoxy)Propyi.)Cytosine (HPMPC) and Related Nucleotide Analogues

Abstract

Of a series of phosphonate nucleotide analogues, HPMPC (2) showed the greatest in vivo therapeutic index against herpes simplex viruses.     

Synthesis of Novel 2′-Fluoro-3′-Hydroxymethyl-5′-Deoxythreosyl Phosphonic Acid Nucleoside Analogues As Antiviral Agents

A series of purine 5′-deoxyphosphonate analogues were designed and synthesized to mimic naturally occurring purine monophosphate from 1,3-dihydroxyacetone as starting material. The discovery of threosyl phosphonate nucleoside (PMDTA, EC₅₀ = 2.53 μM) as a potent anti-HIV agent has led to the synthesis and biological evaluation of 2′,3′-modified 5′-deoxyversions of the threosyl phosphonate nucleosides. The synthesized 2′-fluoro-3′-hydroxymethyl 5′-deoxythreosyl phosphonic acid nucleoside analogues 14, 18, 23, and 27 were tested for anti-HIV activity as well as cytotoxicity. The adenine analogue 18 exhibits weak in vitro anti-HIV-1 activity (EC₅₀ = 19.2 μM).