Deoxy Analogues Research Articles

An Unusual Diterpene-Enhygromic Acid and Deoxyenhygrolides from a Marine Myxobacterium, Enhygromyxa sp.

Three new compounds, enhygromic acid (1) and deoxyenhygrolides A (2) and B (3), were isolated from a marine myxobacterium, Enhygromyxa sp. Compound 1 was found to be an acrylic acid derivative with a rare polycyclic carbon skeleton, decahydroacenaphthylene, by spectroscopic analyses. Compounds 2 and 3 were deoxy analogs of the known γ-alkylidenebutenolides, enhygrolides. Compound 1 exhibited cytotoxicity against B16 melanoma cells and anti-bacterial activity against Bacillus subtilis, and enhanced the NGF-induced neurite outgrowth of PC12 cells.

NMR studies on 4-thio-5-furan-modified and 4-thio-5-thiophene-modified nucleosides.

Systematic NMR characterization of 4-thio-5-furan-pyrimidine nucleosides or 4-thio-5-thiophene-pyrimidine nucleosides (ribonucleosides and 2'-deoxynucleosides) was performed. All proton and carbon signals of 4-thio-5-thiophene-ribouridine and related analogues were unambiguously assigned. The orientations of the base (4-thiouridine or its deoxy analogue) relative to the ring (furan or thiophene) are explored by a NMR approach and further supported by X-ray crystallographic studies. The procedures presented here would be applicable to other modified nucleosides and nucleotides. Copyright © 2016 John Wiley & Sons, Ltd.

Enzymatic synthesis of 2′-ara and 2′-deoxy analogues of c-di-GMP

The substrate specificity of recombinant full-length diguanylate cyclase (DGC) of Thermotoga maritima with mutant allosteric site was investigated. It has been originally shown that the enzyme could use GTP closest analogues – 2′-deoxyguanosine-5′-triphosphate (dGTP) and 9-β-D-arabinofuranosyl-guanine-5′-triphosphate (araGTP) as the substrates. The first demonstrations of an enzymatic synthesis of bis-(3′-5′)-cyclic dimeric deoxyguanosine monophosphate (c-di-dGMP) and the previously unknown bis-(3′-5′)-cyclic dimeric araguanosine monophosphate (c-di-araGMP) using DGC of T. maritima in the form of inclusion bodies have been provided.

Lead structures for new antibacterials: stereocontrolled synthesis of a bioactive muraymycin analogue.

Naturally occurring muraymycin nucleoside antibiotics represent a promising class of novel antibacterial agents. The structural complexity suggests the investigation of simplified analogues as potential lead structures, which can then be further optimized towards highly potent antimicrobials. Herein we report studies on muraymycin-derived potential lead structures lacking an aminoribose motif found in most naturally occurring muraymycins. We have identified a 5'-defunctionalized motif to be ideal in terms of stability and chemical accessibility and have synthesized a full-length muraymycin analogue based on this structure using a novel fully stereocontrolled route. The obtained 5'-deoxy analogue of the natural product muraymycin C4 showed good inhibitory properties towards the bacterial target protein MraY, sufficient pharmacokinetic stability and no cytotoxicity against human cells, thus making it a promising lead for antibacterial drug development.

Synthesis of diastereomeric, deoxy and ring-expanded sulfone analogues of aigialomycin D

Several analogues of the fungal natural product aigialomycin D (AmD) have been synthesised. These include the stereoisomer 5′R,6′S-AmD, 2,4-di-deoxyAmD, 1′,2′,7′,8′-tetrahydroAmD and a 15-membered macrocyclic sulfone. Growth inhibitory activities of these compounds against the HL-60 leukaemic cell line were measured. The ring-expanded sulfone and tetrahydro-analogue were found to have similar IC50 values to the natural product, whereas the 5′R,6′S-stereoisomer was inactive. Energy minimisation of AmD and the synthesised analogues resulted in a range of lowest energy conformers, from planar, open arrangements of the macrocycle in AmD and tetrahydroAmD to bent, L-shaped structures for the sulfone. The synthesis of methyl orsellinate was investigated and optimised as part of this work. A stereodivergent route to both enantiomers of the diol fragment from d-ribose was also achieved.

First Identification of 5,11-Dideoxytetrodotoxin in Marine Animals, and Characterization of Major Fragment Ions of Tetrodotoxin and Its Analogs by High Resolution ESI-MS/MS

Even though tetrodotoxin (TTX) is a widespread toxin in marine and terrestrial organisms, very little is known about the biosynthetic pathway used to produce it. By describing chemical structures of natural analogs of TTX, we can start to identify some of the precursors that might be important for TTX biosynthesis. In the present study, an analog of TTX, 5,11-dideoxyTTX, was identified for the first time in natural sources, the ovary of the pufferfish and the pharynx of a flatworm (planocerid sp. 1), by comparison with totally synthesized (−)-5,11-dideoxyTTX, using high resolution ESI-LC-MS. Based on the presence of 5,11-dideoxyTTX together with a series of known deoxy analogs, 5,6,11-trideoxyTTX, 6,11-dideoxyTTX, 11-deoxyTTX, and 5-deoxyTTX, in these animals, we predicted two routes of stepwise oxidation pathways in the late stages of biosynthesis of TTX. Furthermore, high resolution masses of the major fragment ions of TTX, 6,11-dideoxyTTX, and 5,6,11-trideoxyTTX were also measured, and their molecular formulas and structures were predicted to compare them with each other. Although both TTX and 5,6,11-trideoxyTTX give major fragment ions that are very close, m/z 162.0660 and 162.1020, respectively, they are distinguishable and predicted to be different molecular formulas. These data will be useful for identification of TTXs using high resolution LC-MS/MS.

Synthesis of New Furo[3,4‐b]quinolin‐1(3H)‐one Scaffolds Derived from γ‐Lactone‐Fused Quinolin‐4(1H)‐ones

AbstractIn the context of our aim of discovering new antitumor drugs among synthetic γ‐lactone‐ and γ‐lactam‐fused 1‐methylquinolin‐4(1H)‐ones, we developed a rapid access to 5‐methyl‐1,3‐dioxolo[4,5‐g]furo[3,4‐b]quinoline‐8,9(5H,6H)‐dione (9) exploiting the γ‐lactone‐fused chloroquinoline 10 previously synthesized in our laboratory (Scheme 1). We also elaborated efficient synthetic methods allowing for a rapid access to two nonclassical bioisosteres of 9, i.e., a deoxy and a carba analogue. The deoxy analogue 11 was prepared in two steps from the γ‐lactone‐fused quinoline 13 which was also the synthetic precursor of 10 (Scheme 1). The carba analogue 6,9‐dihydro‐5‐methyl‐9‐methylene‐1,3‐dioxolo[4,5‐g]furo[3,4‐b]quinolin‐8(5H)‐one (12) was easily prepared by HCl elimination from the 9‐(chloromethyl)dioxolofuroquinoline 15, which was obtained via a three‐component one‐pot reaction from N‐methyl‐3,4‐(methylenedioxy)aniline (=N‐methyl‐1,3‐benzodioxol‐5‐amine; 16), commercially available chloroacetaldehyde, and tetronic acid (17) (Scheme 2).

Synthesis and Biological Properties of C-2 Triazolylinosine Derivatives

O(6)-(Benzotriazol-1H-yl)guanosine and its 2'-deoxy analogue are readily converted to the O(6)-allyl derivatives that upon diazotization with t-BuONO and TMS-N(3) yield the C-2 azido derivatives. We have previously analyzed the solvent-dependent azide·tetrazole equilibrium of C-6 azidopurine nucleosides, and in contrast to these, the O(6)-allyl C-2 azido nucleosides appear to exist predominantly in the azido form, relatively independent of solvent polarity. In the presently described cases, the tetrazole appears to be very minor. Consistent with the presence of the azido functionality, each neat C-2 azide displayed a prominent IR band at 2126-2130 cm(-1). A screen of conditions for the ligation of the azido nucleosides with alkynes showed that CuCl in t-BuOH/H(2)O is optimal, yielding C-2 1,2,3-triazolyl nucleosides in 70-82% yields. Removal of the silyl groups with Et(3)N·3HF followed by deallylation with PhSO(2)Na/Pd(PPh(3))(4) gave the C-2 triazolylinosine nucleosides. In a continued demonstration of the versatility of O(6)-(benzotriazol-1H-yl)purine nucleosides, one C-2 triazolylinosine derivative was converted to two adenosine analogues via these intermediates, under mild conditions. Products were desilylated for biological assays. The two C-2 triazolyl adenosine analogues demonstrated pronounced antiproliferative activity in human ovarian and colorectal carcinoma cell cultures. When evaluated for antiviral activity against a broad spectrum of DNA and RNA viruses, some of the C-2 triazolylinosine derivatives showed modest inhibitory activity against cytomegalovirus.

Multi-enzymatic cascade synthesis of d-fructose 6-phosphate and deoxy analogs as substrates for high-throughput aldolase screening

We have evaluated different strategies for the one-pot synthesis of D-fructose 6-phosphate and its 1-deoxy and 3-deoxy analogs from readily available starting materials, by building up “artificial metabolisms” in vitro. The first consisted of an aldol cleavage–aldol formation cascade, in which glyceraldehyde 3-phosphate as the central intermediate is generated from fructose 1,6-bisphosphate and consumed in situ for a consecutive carboligation step catalyzed by fructose 6-phosphate aldolase (FSA). The second approach consisted of an aldolase–kinase coupling, in which the unphosphorylated ketose was produced in situ by FSA-catalyzed carboligation, followed by a hexokinase-catalyzed phosphorylation step. While both approaches profited from the high stereoselectivity and stability of the aldolases used, the first approach proved to be the most practical, effective and economical, whereas the second strongly depends on the substrate specificity of hexokinase, which shows inferior catalytic efficiency with the 1-deoxy substrate. Phosphorylation of 3-deoxyfructose failed because, contradictory to a literature report, this compound was found not to be acceptable as a substrate of yeast hexokinase.

Studies Directed toward the Elucidation of the Pharmacophore of Steroid-Based Sonic Hedgehog Signaling Inhibitors

Previous work from our laboratory has established that the readily available steroid-based analog 2 of cyclopamine 1 is, like 1, a highly potent inhibitor of Hedgehog signaling. The first structure-activity relationship studies on 2, i.e., the synthesis and biological evaluation of both the C-17 epi analog 4 and the C-3 deoxy analog 11, both of which are more potent than cyclopamine 1, are described. The implications of these results for the emerging pharmacophore of these Sonic Hedgehog signaling inhibitors are discussed.

Synthesis of phosphates and phosphates–acetates hybrids of green tea polyphenol (−)- epigallocatechine-3-gallate (EGCG) and its G ring deoxy analogs as potential anticancer prodrugs

A series of phosphate or phosphate–acetate hybrid modified EGCG or EGCG G ring deoxy analogs were synthesized by a convenient semi-synthesis strategy from the abundant natural compound EGCG.

Peculiarities of Homooligonucleotides Wrapping around Carbon Nanotubes: Molecular Dynamics Modeling

Spontaneous adsorption of homooligonucleotides dC(25), dT(25), dG(25), and dA(25) on the surface of the carbon nanotube (16,0) has been simulated by the molecular dynamics method. It was demonstrated that the rate of pyrimidine oligonucleotide wrapping around the nanotube is higher than that of purine ones which do not form a complete pitch even after the maximum simulation time (50 ns). This behavior can be explained by a stronger self-stacking between the purines than pyrimidines, which prevents the reorientation of the polymer required for the acquisition of a more energetically favored conformation on the nanotube. Estimations obtained from modeling allowed to establish the oligonucleotide row which demonstrates decreasing interaction energies between oligonucleotides and the carbon nanotube: d(T)(25) > d(C)(25) > d(A)(25) ≈ d(G)(25). It was shown that the temperature growth increases the rate of oligonucleotides to reach the maximum binding energy mainly due to the destruction of nitrogen base self-stacking. Ribonucleic oligonucleotides r(C)(25), r(A)(25), and r(G)(25) do not make a pitch around the nanotube for 50 ns. The presence of the additional hydroxyl group in ribose restricts the conformational flexibility of ribonucleic oligonucleotides in comparison with their deoxy analogues and this reduces the possibility of rapid occupation of the stable conformation on the nanotube surface.

Synthesis and biological evaluation of deoxy-hematoxylin derivatives as a novel class of anti-HIV-1 agents

SAR studies for the exploration a novel class of anti-human immunodeficiency virus type 1 (HIV-1) agents based on the hematoxylin structure (1) are described. The systematic deoxygenations of 1 including asymmetric synthesis were conducted to obtain a compound showing high potencies for inhibiting the nuclear import and viral replication as anti-HIV-1 agent. Among all, C-3-deoxygenated analog 16 exhibited most promising biological activities as anti-HIV-1 agent such as lower cytotoxicity (16:1; >80:40 μM), stronger inhibition of nuclear import (0.5:1.3 μM), and viral replication in HIV-1-infected TZM-bl cells (24.6:100 μM), human peripheral blood mononuclear cells (PMBCs) (30.1 μM: toxic). Different spectra of inhibitory activities against infected three healthy humans macrophages with high (donor A) and low (donor B and C) amounts of virus were also observed. Thus 16 showed 10-times stronger activity than 1 (16:1; 0.1:<1.0 μM) in the case of A, while 16 and 1 showed comparable activities in the cases of B and C (>0.01 and >0.00 1μM). The comparison of the inhibition of viral p24 antigen production was clearly indicated that compound 16 is at least twofold more potent anti-viral activity than 1. Thus, structures and actions of deoxy analogs particularly 16 could provide valuable information for the development of a novel class of anti-HIV-1 agents.

Synthesis of 3′‐S‐Phosphonomethyl‐Modified Nucleoside Phosphonates with a 3′‐Deoxy‐3′‐thio‐α‐L‐threosyl Sugar Moiety

AbstractThe synthesis and antiviral evaluation of 3′‐deoxy‐3′‐S‐phosphonomethyl‐3′‐thio‐α‐L‐threosyl nucleosides as well as the 2′‐deoxy analogues related to PMDTT are described. The key transformations involved the synthesis of the 3′‐deoxy‐3′‐thio‐L‐threosyl and the 2′,3′‐dideoxy‐3′‐thio‐L‐threosyl derivatives by the Mitsunobu reaction. The phosphonate function was introduced by nucleophilic substitution and the glycosylation was carried out under Vorbrüggen conditions. None of these synthesized compounds showed significant in vitro activity against HIV, HCV, and RSV, or cytotoxicity.

Kinase inhibition by deoxy analogues of the resorcylic lactone L-783277.

The natural product L-783277 is a resorcylic lactone type covalent kinase inhibitor. We have prepared the 5'-deoxy analogue of L-783277 (1) in a stereoselective fashion. Remarkably, this analogue retains almost the full kinase inhibitory potential of natural L-783277, with low nanomolar IC50 values against the most sensitive kinases, and it exhibits essentially the same selectivity profile (within the panel of 39 kinases investigated). In contrast, removal of both the 4'- and the 5'-hydroxyl groups leads to a more significant reduction in kinase inhibitory activity and so does a change in the geometry of the C7'-C8' double bond in 1 from Z to E. These findings offer new perspectives for the design of second generation resorcylic lactone-based kinase inhibitors.

Crystal molecular dynamics simulations to speed up MM/PB(GB)SA evaluation of binding free energies of di‐mannose deoxy analogs with P51G‐m4‐Cyanovirin‐N

Complexes of two Cyanovirin-N (CVN) mutants, m4-CVN and P51G-m4-CVN, with deoxy di-mannose analogs were employed as models to generate conformational ensembles using explicit water Molecular Dynamics (MD) simulations in solution and in crystal environment. The results were utilized for evaluation of binding free energies with the molecular mechanics Poisson-Boltzmann (or Generalized Born) surface area, MM/PB(GB)SA, methods. The calculations provided the ranking of deoxy di-mannose ligands affinity in agreement with available qualitative experimental evidences. This confirms the importance of the hydrogen-bond network between di-mannose 3'- and 4'-hydroxyl groups and the protein binding site B(M) as a basis of the CVN activity as an effective HIV fusion inhibitor. Comparison of binding free energies averaged over snapshots from the solution and crystal simulations showed high promises in the use of the crystal matrix for acceleration of the conformational ensemble generation, the most time consuming step in MM/PB(GB)SA approach. Correlation between energy values based on solution versus crystal ensembles is 0.95 for both MM/PBSA and MM/GBSA methods.

Equitoxic Doses of 5-Azacytidine and 5-Aza-2′Deoxycytidine Induce Diverse Immediate and Overlapping Heritable Changes in the Transcriptome

BackgroundThe hypomethylating agent 5-Azacytidine (5-Aza-CR) is the first drug to prolong overall survival in patients with myelodysplastic syndrome (MDS). Surprisingly, the deoxyribonucleoside analog 5-Aza-2′deoxycytidine (5-Aza-CdR) did not have a similar effect on survival in a large clinical trial. Both drugs are thought to exert their effects after incorporation into DNA by covalent binding of DNA methyltransferase (DNMT). While 5-Aza-CdR is incorporated into only DNA, 5-Aza-CR is also incorporated into RNA. Here, we have analyzed whether this difference in nucleic acid incorporation may influence the capacities of these drugs to regulate the expression of mRNA and microRNAs (miRNA), which may potentially affect the activities of the drugs in patients.Methodology/Principal FindingsA hematopoietic (HL-60; acute myeloid leukemia) and a solid (T24; transitional cell carcinoma) cancer cell line were treated with equitoxic doses of 5-Aza-CR and 5-Aza-CdR for 24 hrs, and the immediate (day 2) and lasting (day 8) effects on RNA expression examined. There was considerable overlap between the RNAs heritably upregulated by both drugs on day 8 but more RNAs were stably induced by the deoxy analog. Both drugs strongly induced expression of cancer testis antigens. On day 2 more RNAs were downregulated by 5-Aza-CR, particularly at higher doses. A remarkable downregulation of miRNAs and a significant upregulation of tRNA synthetases and other genes involved in amino acid metabolism was observed in T24 cells.Conclusions/SignificanceOverall, this suggests that significant differences exist in the immediate action of the two drugs, however the dominant pattern of the lasting, and possible heritable changes, is overlapping.

ChemInform Abstract: Synthesis and Antiviral Activity of Deoxy Analogs of 1-((2- Hydroxyethoxy)methyl)-6-(phenylthio)thymine (HEPT) as Potent and Selective Anti-HIV-1 Agents.

ChemInform Abstract: Synthesis and Antiviral Activity of Deoxy Analogs of 1-((2- Hydroxyethoxy)methyl)-6-(phenylthio)thymine (HEPT) as Potent and Selective Anti-HIV-1 Agents.

Intra‐ and Intermolecular Oxa‐Pictet–Spengler Cyclization Strategy for the Enantioselective Synthesis of Deoxy Analogues of (+)‐Nanomycin A Methyl Ester, (+)‐Eleutherin, (+)‐Allo‐Eleutherin, and (+)‐Thysanone

AbstractEnantioselective synthesis of deoxy analogues of pyranonaphthoquinone antibiotics (+)‐nanomycin A methyl ester, (+)‐eleutherin, (+)‐allo‐eleutherin, and (+)‐thysanone was achieved in good overall yield with high enantio‐ and diastereoselectivity from the common intermediate (R)‐3‐(2,5‐dimethoxyphenyl)propane‐1,2‐diol. The intramolecular oxa‐Pictet–Spengler cyclization of 6‐aryl‐1,3‐dioxolone was developed for the first time and utilized in the enantioselective synthesis of (+)‐deoxynanomycin A methyl ester, whereas the intermolecular oxa‐Pictet–Spengler cyclization strategy was applied to the enantioselective synthesis of deoxy analogues of (+)‐eleutherin, (+)‐allo‐eleutherin, and (+)‐thysanone.

Palladium‐Catalyzed Aryl Amination Reactions of 6‐Bromo‐ and 6‐Chloropurine Nucleosides

Palladium‐catalyzed C—N bond forming reactions of 6‐bromo‐ as well as 6‐chloropurine ribonucleosides and the 2′‐deoxy analogues with arylamines are described. Efficient conversions were observed with palladium(II) acetate/Xantphos/cesium carbonate, in toluene at 100 °C. Reactions of the bromonucleoside derivatives could be conducted at a lowered catalytic loading [5 mol% Pd(OAc)2/7.5 mol% Xantphos], whereas good product yields were obtained with a higher catalyst load [10 mol% Pd(OAc)2/15 mol% Xantphos] when the chloro analogue was employed. Among the examples evaluated, silyl protection for the hydroxy groups appears better as compared to acetyl. The methodology has been evaluated via reactions with a variety of arylamines and by synthesis of biologically relevant deoxyadenosine and adenosine dimers. This is the first detailed analysis of aryl amination reactions of 6‐chloropurine nucleosides, and comparison of the two halogenated nucleoside substrates.