In vivo directed enzyme evolution in nanoliter reactors with antimetabolite selection.

Scoring changes in enzyme or pathway performance by their effect on growth behavior is a widely applied strategy for identifying improved biocatalysts. While in directed evolution this strategy is powerful in removing non-functional catalysts in selections, measuring subtle differences in growth behavior remains difficult at high throughput, as it is difficult to focus metabolic control on only one or a few enzymatic steps over the entire process of growth-based discrimination. Here, we demonstrate successful miniaturization of a growth-based directed enzyme evolution process. For cultivation of library clones we employed optically clear gel-like microcarriers of nanoliter volume (NLRs) as reaction vessels and used fluorescence-assisted particle sorting to estimate the growth behavior of each of the gel-embedded clones in a highly parallelized fashion. We demonstrate that the growth behavior correlates with the desired improvements in enzyme performance and that we can fine-tune selection stringency by including an antimetabolite in the assay. As a model enzyme reaction, we improve the racemization of ornithine, a possible starting block for the large-scale synthesis of sulphostin, by a broad-spectrum amino acid racemase and confirm the discriminatory power by showing that even moderately improved enzyme variants can be readily identified.

Synthesis and biological applications of phosphinates and derivatives.

This review first outlines general considerations on phosphinic acids and derivatives as bioisosteric groups. The next sections present key aspects of phosphinic acid-based molecules and include a brief description of the biological pathways involved for their activities. The synthetic aspects and the biological activities of such compounds reported in the literature between 2008 and 2013 are also described.

Sulfa and trimethoprim-like drugs - antimetabolites acting as carbonic anhydrase, dihydropteroate synthase and dihydrofolate reductase inhibitors.

Recent advances in microbial genomics, synthetic organic chemistry and X-ray crystallography provided opportunities to identify novel antibacterial targets for the development of new classes of antibiotics and to design more potent antimicrobial compounds derived from existing antibiotics in clinical use for decades. The antimetabolites, sulfa drugs and trimethoprim (TMP)-like agents, are inhibitors of three families of enzymes. One family belongs to the carbonic anhydrases, which catalyze a simple but physiologically relevant reaction in all life kingdoms, carbon dioxide hydration to bicarbonate and protons. The other two enzyme families are involved in the synthesis of tetrahydrofolate (THF), i.e. dihydropteroate synthase (DHPS) and dihydrofolate reductase. The antibacterial agents belonging to the THF and DHPS inhibitors were developed decades ago and present significant bacterial resistance problems. However, the molecular mechanisms of drug resistance both to sulfa drugs and TMP-like inhibitors were understood in detail only recently, when several X-ray crystal structures of such enzymes in complex with their inhibitors were reported. Here, we revue the state of the art in the field of antibacterials based on inhibitors of these three enzyme families.

Coarse grained molecular dynamics of engineered macromolecules for the inhibition of oxidized low-density lipoprotein uptake by macrophage scavenger receptors.

Atherosclerosis is a condition resulting from the accumulation of oxidized low-density lipoproteins (oxLDLs) in arterial walls. Previously developed macromolecules consisting of alkyl chains and polyethylene glycol (PEG) on a mucic acid backbone, termed nanolipoblockers (NLBs) are hypothesized to mitigate the uptake of oxLDL by macrophage scavenger receptors. In this work, we developed a coarse grained model to characterize the interactions between NLBs with a segment of human scavenger receptor A (SR-A), a key receptor domain that regulates cholesterol uptake and foam cell conversion of macrophages, and studied NLB ability to block oxLDL uptake in PBMC macrophages. We focused on four different NLB configurations with variable molecular charge, charge location, and degree of NLB micellization. Kinetic studies showed that three of the four NLBs form micelles within 300 ns and of sizes comparable to literature results. In the presence of SR-A, micelle-forming NLBs interacted with the receptor primarily in an aggregated state rather than as single unimers. The model showed that incorporation of an anionic charge near the NLB mucic acid head resulted in enhanced interaction with the proposed binding pocket of SR-A compared to uncharged NLBs. By contrast, NLBs with an anionic charge located at the PEG tail showed no interaction increase as NLB aggregates were predominately observed to interact away from the oxLDL binding site. Additionally, using two different methods to assess the number of contacts that each NLB type formed with SR-A, we found that the rank order of contacts coincided with our experimental flow cytometry results evaluating the ability of the different NLBs to block the uptake of oxLDL.

Antimetabolites: A First Synthesis of a New Class of Cytosine Thioglycoside Analogs.

A first synthesis of a new class of novel cytosine thioglycoside analogs from readily available starting materials has been described. The key step of this protocol is the formation of sodium pyrimidine-4-thiolate via condensation of N'-arylidene-2-cyanoacetohydrazides with sodium cyanocarbonimidodithioate salt, followed by coupling with halo sugars to give the corresponding cytosine thioglycoside analogs. Ammonolysis of the latter compounds afforded the free thioglycosides.

New trends in synthesis of pyrazole nucleosides as new antimetabolites.

Pyrazole nucleosides and condensed pyrazole nucleosides exhibit various biological activities. This article describes recent synthetic approaches to their preparation, chemical properties, biological activities, and structure-activity relationships, with emphasis to selected drugs or drug candidates. Two pyrazole C-nucleoside compounds pyrazofurin (pyrazomycin) and its alpha-epimer pyrazofurin B are active components of potent antivirals approved for therapeutic use in human medicine aimed against various diseases caused by DNA viruses.

Ring opening reactions: synthesis of AICAR analogs as potential antimetabolite agents.

In an attempt to improve the AzA selectivity of the 2-(aryl)alkylthio derivatives of adenosine, we planned the synthesis of the corresponding derivatives of the 5-N-ethylcarboxamidoadenosine (NECA). For this purpose, we designed the synthesis of 2-mercapto-NECA to be pursued by means of an opening-closure method We obtained the open AICAR analog; however, ring closure efforts failed to give the desired compound. The newly synthesized AICAR derivative could potentially be endowed with antiviral or antitumoral activity.

Synthesis and biological activity of potential antimetabolites of L-fucose.

6-Substituted 6-deoxy-L-galactose (L-fucose) derivatives were synthesized as potential antimetabolites of L-fucose. The cytotoxic effects of these compounds were evaluated on P388 leukemia cells in culture. The L-fucose analogues which showed the most potent growth inhibition were the sulfonyl ester, bromo, and iodo derivatives; since these compounds were all capable of alkylation, it is conceivable that their cytotoxic action is a consequence of this property. In agreement with this interpretation, none of the agents synthesized showed specific inhibition of the incorporation of L-[3H]fucose into glycoprotein.

Synthesis and antiviral activity of novel N-substituted derivatives of acyclovir.

Novel N-substituted derivatives of acyclovir (1a) were synthesized and evaluated for their antiviral, antimetabolic, and antitumor cell properties in vitro. Monomethylation of 1a at positions 1, 7, and N-2 gave compounds 2-4, respectively. When positions 1 and N-2 were linked together by an isopropeno group, the tricyclic 9-[(2-hydroxyethoxy)methyl]-1,N-2-isopropenoguanine (5) was obtained. Compound 5 was then further methylated at positions N-2 and 7 to give 6 and 7, respectively. None of the new acyclovir derivatives showed any appreciable antimetabolic or antitumor cell activity. However, compounds 2 and 5 exhibited a marked antiherpetic activity. Their activity spectrum was similar to that of acyclovir, and their selectivity as inhibitors of herpes simplex virus type 1 (HSV-1) and type 2 (HSV-2) was at least as great as, if not greater than, that of acyclovir.

Synthesis, antiretrovirus effects, and phosphorylation kinetics of 3'-isocyano-3'-deoxythymidine and 3'-isocyano-2',3'-dideoxyuridine.

The silylated AzddThd 5 and AzddUrd 6 prepared from 2,3'-anhydronucleoside derivatives 3 and 4 were transformed to formamides 7 and 8 by using the sequence RN3----RN = P(C6H5)----RNHCHO. Formamides 7 and 8 were dehydrated to the protected 3'-isocyano derivatives 9 and 10; deblocking gave 11 and 12. Neither 3'-isocyano-3'-deoxythymidine (11) nor 3'-isocyano-2',3'-dideoxyuridine (12) showed anti-HIV activity at noncytotoxic concentrations. ddThd derivative 11 was considerably more toxic to MT-4 cells than ddUrd derivative 12; it also had a much greater affinity (Ki) for MT-4 cell dThd kinase than ddUrd derivative 12. Both compounds appear to be linear mixed-type inhibitors of MT-4 cell dThd kinase.

Purine and 8-substituted purine arabinofuranosyl and ribofuranosyl nucleoside derivatives as potential inducers of the differentiation of the Friend erythroleukemia.

Several antimetabolites have been demonstrated to have the capacity to initiate differentiation in vitro of a variety of leukemic cell lines. To explore the structural requirements for this activity, a series of purine and 8-substituted purine arabinofuranosyl and ribofuranosyl nucleoside derivatives were synthesized and tested as inducers of the differentiation of Friend murine erythroleukemia cells. 9-(beta-D-Arabinofuranosyl)hypoxanthine and 6-(hydroxyamino)-9-(beta-D-arabinofuranosyl)purine were effective inducers of maturation, producing 82% and 74% benzidine-positive cells, a measure of the number of cells synthesizing hemoglobin. 6-Mercapto-9-(beta-D-ribofuranosyl)purine and 6-(methylmercapto)-9-(beta-D-ribofuranosyl)purine and their corresponding beta-D-arabinofuranosyl derivatives were also effective initiators of maturation, causing approximately 50% of the cell population to assume a differentiated phenotype.

An efficient synthesis of new fluorinated uracil derivatives.

A series of potentially biologically active fluorinated uracil derivatives has been prepared in three steps from oxazolines and fluorinated nitriles with good chemical yields.

Synthesis and evaluation of N-acyl-2-(5-fluorouracil-1-yl)-D,L-glycine as a colon-specific prodrug of 5-fluorouracil.

N-nicotinyl-2-(5-fluorouracil-1-yl)-D,L-glycine (NFG) and N-isonicotinyl-2-(5-fluorouracil-1-yl)-D,L-glycine (INFG) were synthesized as colon-specific prodrugs of 5-fluorouracil (5-FU). As N-aromatic acyl amides of glycine, they are expected to be stable in the upper intestine and delivered to the colon as an intact form if they are nonabsorbable. Microbial hydrolysis of amide bond in the colon will give 2-(5-fluorouracil)-D,L-glycine, which releases 5-FU by spontaneous decomposition. NFG and INFG were soluble in water and stable in pH 1.2 and 7.4 buffer solutions. The apparent partition coefficient of NFG or INFG in 1-octanol/pH 7.4 phosphate buffer solution at 37 degrees was 0.025 or 0.024, respectively. On incubation with cecal contents of rats, conversion of NFG or INFG proceeded only 9 or 5% in 8 h, respectively, producing 5-FU and a metabolite. The metabolite formation was inhibited in the presence of diazouracil, a dihydrouracil dehydrogenase inhibitor. The HPLC retention time of the metabolite from the incubation of 5-FU, NFG, or INFG with cecal contents was identical to dihydro-5-fluorouracil (dihydro-5FU). When N-nicotinyl-2-hydroxy-D,L-glycine methyl ester (NHGM) was incubated with the cecal contents, the extent of amide bond hydrolysis was 85% in 24 h. The result suggested that steric hindrance imposed by 5-FU at 2-position of glycine retarded the hydrolysis of the amide bond in NFG or INFG and suppressed the prodrug conversion.

Antiviral activity, antimetabolic activity, and cytotoxicity of 3'-substituted deoxypyrimidine nucleosides.

The antiviral activity, effect on cellular DNA and RNA synthesis, and cytotoxicity toward mammalian cells of 5-fluoro-2'-deoxyuridine, 5-methoxymethyl-2'-deoxyuridine, 2'-deoxythymidine, and their corresponding 3'-p-nitrophenylphosphate and 3'-p-aminophenylphosphate derivatives were determined. The 3'-p-aminophenylphosphate-2'-deoxy-5-methoxymethyluridine derivative was as potent as 5-methoxy-methyl-2'-deoxyuridine in inhibiting herpes simplex viruses; however, 3'-p-aminophenylphosphate-2'-deoxy-5-fluorouridine was less potent than 5-fluoro-2'-deoxyuridine in inhibiting viral replication. The results suggest that the deoxypyrimidine ribonucleoside kinase has bulk tolerance for substituents at the 3-position of the ribofuranose moiety. The effect on cellular DNA and RNA synthesis and cytotoxicity toward mammalian cells were monitored by studying the incorporation of radioactive precursors. 5-Methoxymethyl-2'-deoxyuridine and 3'-p-aminophenylphosphate-2'-deoxy-5-methoxymethyluridine failed to inhibit DNA or RNA synthesis. 5-Fluoro-2'-deoxyuridine and 3'-p-aminophenylphosphate-2'-deoxy-5-fluorouridine decreased incorporation of [3H]deoxyuridine by 50% at 1.0 and 40 microM, respectively. Cytotoxicity (microscopic lesions using monolayer cells) on exposure to 5-methoxymethyl-2'-deoxyuridine, 3'-p-aminophenylphosphate-2'-deoxy-5-methoxymethyluridine, 5-fluoro-2'-deoxyuridine, and 3'-p-aminophenylphosphate-2'-deoxy-5-fluorouridine was observed at 3800, 1600, 1.6, and 110 microM, respectively.

Antimetabolites produced by microorganisms XVI. Synthesis of N5-hydroxy-2-methylarginine and N5-hydroxy-2-methylornithine.

N5-Hydroxy-2-methylornithine and N5-hydroxy-2-methylarginine were synthesized. 2-Amino-5-hydroxy-2-methylpentanoic acid was prepared from 5-hydroxy-2-pentanone and converted to N-(tetrahydro-3-methyl-2-oxo-2H-pyran-3-yl) acetamide which was treated with hydrogen bromide affording 2-(acetylamino)-5-bromo-2-methylpentanoic acid. This acid was esterified with methanol and used to alkylate anti-benzaldoxime yielding methyl 2-(acetylamino)-2-methyl-5-[(phenylmethylene)amino]-pentanoate N5-oxide which, upon hydrolysis, yielded N5-hydroxy-2-methylornithine, and, upon aminolysis and short acid-treatment, gave N2-acetyl-N5-hydroxy-2-methylornithinamide. Carbamimidoylation and hydrolysis of the latter compound furnished N5-hydroxy-2-methylarginine.

Selective transport of a new class of purine antimetabolites by the protozoan parasite Trypanosoma brucei.

Purine antimetabolites have been very successful therapeutic agents against a host of infectious diseases and malignancies. Success of the treatment relies as much on the efficient accumulation by the target cell or organism as it does on selective action on a vital biochemical pathway of the target cell. Here we compare the ability of a new class of tricyclic purine antimetabolites to interact with transporters from human erythrocytes or Trypanosoma brucei. We show that these compounds display a remarkable selectivity for the parasite's transporters. The adenine analogue showed greater trypanocidal activity than the hypoxanthine or guanine analogues in vitro.

[Synthesis and antitumor action of N,N-di(2-chlorethyl)-hydrazines of alpha-aminocarboxylic acid antimetabolites]. / Synthese und geschwulsthemmende Wirkung von N,N-Di(2-chlorethyl)-hydrazinen der alpha-Aminocarbonsäureantimetabolite.

The N,N-di(2-chlorethyl)hydrazides of the following alpha-aminocarboxylic acid antimetabolites: methioninsulphoxide, ethionine, 2-, 3- and 4-fluorophenylalanine, 4-nitrophenylalanine and 2,2-dimethyl-thiazolidine-4-carboxylic acid were synthesized. Preliminary studies of the activity on experimental tumour models were carried out. It was shown that these compounds have a high antitumour effect (80-100%) on sarcoma Yoshida and carcinosarcoma Walker.

[Synthesis and antimetabolite properties of 5-substituted 2'-deoxyuridines. Anomeric 5-(2-aminohexafluoroprop-2-yl)- and 5-(2-trifluoroacetylaminohexafluoroprop-2-yl)-2'-deoxyuridine]. / Sintez i antimetabolitnye svoistva 5-zameshchennykh 2'-dezoksiuridinov. Anomernye 5-(2-aminogeksaftorprop-2-il)- i 5-(2-triftoratsetilaminogeksaftorprop-2-il)-2'-dezoksiuridiny.

Alkylation of 2,4-bis-O-(trimethylsilyl)uracil with hexafluoroacetone trifluoroacetylimine gave 5-(2-trifluoroacelylaminohexafluoroprop-2-yl)uracil, which was transformed by alkaline hydrolysis to 5-(2-aminohexafluoroprop-2-yl)uracil. The latter was glycosytated with 2-deoxy-3,5-di-O-p-toluoyl-alpha-D-ribofyranosyl chloride by means of various modifications of the silyl method leading to the predominant formation of beta-deoxynucleoside; after deacylation 1-(2-deoxy-beta-D-ribofuranosyl)-5-(2-aminohexafluoroprop-2-yl)ura cil was obtained. Interaction of silylated 5-(2-trifluoroacetylaminohexafluoroprop-2-yl)uracil with acylgalogenose gave anomeric O-substitutet deoxynucleosides, which were deblocked to give 5-(2-trifluoroacetylaminohexafluoroprop-2-yl)-2'-deoxyuridine and corresponding alpha-anomer. Alkaline hydrolysis of N-trifluoroacetyl group in both individual anomers produced 1-(2-deoxy-alpha-D-ribofuranosyl)-5-(2-aminohexafluoroprop-2-yl)ur acil and the abovementioned beta-anomer. Of all compounds synthesised only 1-(2-deoxy-beta-D-ribofuranosyl)-5-(2-aminohexafluoroprop-2-yl)ura cil has a moderate inhibitory effect on replication of vaccinia virus in vitro.

Assessment of drug candidates for broad-spectrum antiviral therapy targeting cellular pyrimidine biosynthesis.

Currently available antiviral drugs frequently induce side-effects or selection of drug-resistant viruses. We describe a novel antiviral principle based on targeting the cellular enzyme dihydroorotate dehydrogenase (DHODH). In silico drug design and biochemical evaluation identified Compound 1 (Cmp1) as a selective inhibitor of human DHODH in vitro (IC50 1.5±0.2nM). Crystallization data specified the mode of drug-target interaction. Importantly, Cmp1 displayed a very potent antiviral activity that could be reversed by co-application of uridine or other pyrimidine precursors, underlining the postulated DHODH-directed mode of activity. Human and animal cytomegaloviruses as well as adenoviruses showed strong sensitivity towards Cmp1 in cell culture-based infection systems with IC50 values in the low micromolar to nanomolar range. Particularly, broad inhibitory activity was demonstrated for various types of laboratory and clinically relevant adenoviruses. For replication of human cytomegalovirus in primary fibroblasts, antiviral mode of activity was attributed to the early stage of gene expression. A mouse in vivo model proved reduced replication of murine cytomegalovirus in various organs upon Cmp1 treatment. These findings suggested Cmp1 as drug candidate and validated DHODH as a promising cellular target for antiviral therapy.

Synthesis and evaluation of a dipeptide-drug conjugate library as substrates for PEPT1.

The oligopeptide transporter PEPT1 is considered as a valuable target for prodrug design, but its 3D structure and substrate specificity of PEPT1 are not fully understood. In this study, we designed a focused dipeptide conjugated azidothymidine (AZT) library and described a convenient and efficient solid phase synthesis scheme based on click chemistry. Over 60 candidate structures containing various dipeptide sequences were obtained with high purity, and screened in a PEPT1 overexpressing cell model for their abilities to compete with the known ligand cephalexin. Some of the compounds selected to have medium or high affinity were tested for their in vivo transport in a single-pass intestinal perfusion experiment. Results showed that the designed library contained some new structure features that have high affinities toward PEPT1 and could be further explored for their application in prodrug design and development.