Byeang Hyean Kim

Heterocyclic nucleoside analogues: Design and synthesis of antiviral, modified nucleosides containing isoxazole heterocycles

We have designed and synthesized novel antiviral nucleoside analogues, which consist of isoxazole rings as modified sugars and nucleobases (thymine, uracil, and 5-fluorouracil) with a methylene linker between them. These compounds represent a new class of modified nucleoside analogues and some of them show potent antiviral activities against Polio virus (Coxsackie B type 3 and Vesicular Stomatitis).

Synthesis of 5-isoxazol-5-yl-2'-deoxyuridines exhibiting antiviral activity against HSV and several RNA viruses.

Abstract This paper describes a simple method for synthesizing a small library of 5-isoxazol-5-yl-2′-deoxyuridines from 5-iodo-2′-deoxyuridine. Nitrile oxides were generated in situ from oximes using a commercial bleaching agent; their cycloaddition with 5-ethynyl-2′-deoxyuridine yielded isoxazoles possessing activity against herpes simplex viruses 1 and 2, Encephalomyocarditis virus, Coxsackie B3, and vesicular stomatitis virus; these isoxazoles were, however, inactive against corona virus, influenza virus, and HIV.

Novel phosphoramidite building blocks in synthesis and applications toward modified oligonucleotides.

In recent years modified oligonucleotides (oligos) have become an area of increased research activity. These synthetic biopolymers have long been used as molecular probes to understand better the interaction between proteins and nucleic acids at molecular level, which in fact is responsible for all aspects of cellular or viral gene expression. Modified oligos have also been used as therapeutic and diagnostic agents. For example, the antisense oligos are used to block gene expression by binding especially with complimentary sequences of target mRNA. Also, over the past decade efforts are made to modify the native phosphodiester linkages to improve nuclease resistance and membrane permeation of naturally occurring oligonucleotide for therapeutic applications. Therefore, design and synthesis of modified oligonucleotides for a wide range of applications are of interest for bioorganic chemists and biologists. The advent of the phosphoramidite chemistry has accelerated the development of oligos with modified nucleobases, phosphate-protecting groups and modified sugars. In this review, we have presented the recently reported nucleoside based phosphoramidites with modified base, sugar or backbone units and their subsequent conversion into modified DNA and RNA analogs. The effect of such modification on structural, thermodynamic, and hybridization properties of the modified oligos and their duplex with natural complementary oligos have also been discussed for some cases. Similarly, we have highlighted the role of modified nucleoside phosphoramidite building blocks in synthesis of oligos modified with optically or electrochemically active molecules. Nucleoside phosphoramidites or small oligos immobilized over solid supports through different linkages or groups and their biological applications has also been mentioned.

Probing the B-to-Z-DNA duplex transition using terminally stacking ethynyl pyrene-modified adenosine and uridine bases

Pyrene-modified adenosine and uridine bases located in the dangling positions of G,C-alternating oligodeoxynucleotides undergo pi-stacking in their B-DNA duplexes, but not in their Z-DNA duplexes; fluorescence quenching in the former, through photoinduced electron transfer, but not in the latter, allows the state of the B-to-Z-DNA transition to be characterized visually.

Synthesis and characterization of new polyimides containing calix[4]arenes in the polymer backbone

Two diaminocalix[4]arene monomers were synthesized from p-tert-butylcalix[4]arene through a 4-step reaction sequence. New copoly(amic acid)s containing calix[4]arene moieties on the polymer backbone were successfully synthesized in N-methyl-2-pyrrolidone by polycondensations of 4,4′-oxydiphthalic anhydride (ODPA) with the diaminocalix[4]arene monomers using 4,4′-oxydiphenylene diamine (ODA) as a comonomer. These copoly(amic acid)s were soluble in aprotic polar solvents, so that they can be processed in various ways. The copoly(amic acid) precursors were thermally converted to the corresponding copolyimides in films. The copolyimide films are amorphous, but insoluble in common solvents. They are thermally stable up to 366°C. The copolyimides exhibit relatively high TECs, low Tgs, low refractive index, low dielectric constant, low optical anisotropy, low dielectric anisotropy, and low water uptake, compared to those of conventional ODPA-ODA polyimide. These property characteristics were interpreted in regard to bulky, cone-like calix[4]arene moieties and their effects on the chain conformation and morphological structure. The processability and property characteristics support that both of the copolyimides containing calix[4]arene moieties are potential candidate materials suitable for membranes, antioxidant additives, chemical sensor devices, and microelectronic devices.

Probing the stable G-quadruplex transition using quencher-free end-stacking ethynyl pyrene–adenosine

Pyrene-modified adenosines in the dangling positions of G-rich oligodeoxynucleotides undergo pi-stacking in their G-quadruplex formation, but not in their single strands, which can be characterized by fluorescence lambda(max) changes that occur on stacking.

Synthesis and enzyme inhibitory activities of novel peptide isosteres

Design and synthesis of metabolically stable peptide analogs that can either mimic or block the bioactivity of natural peptides or enzymes is an important constituent of bioorganic and medicinal chemistry research. Isosteric replacement of a scissile peptide bond represents a viable and popular approach in the rational design of peptidomimetics. Peptidomimetics find applications as drugs, in protein engineering and so on. This is evident from the wealth of therapeutically useful peptidomimetic leads incorporating any of the peptide isosteres that are currently available. In this review, we have given a brief account of the types of peptide isosteres widely known till date. With this background, we have described some of the recent developments in synthetic approaches. This includes methods involving a common intermediate to synthesize different possible isosteres and their peptide analogs, solid phase synthesis and combinatorial approach. One such method involving stereoselective nitrile oxide cycloaddition as the key step has been studied extensively in our research laboratory. Finally, we have also discussed about some of the recent reports on the design and inhibitory activities of peptidic or non-peptidic analogs against aspartic proteases (HIV-1, renin, ACE and pepsin) and peptide analogs of an immunomodulating hexapeptide.

Label-free detection of antibody-antigen interactions on (R)-lipo-diaza-18-crown-6 self-assembled monolayer modified gold electrodes.

Novel (R)-diaza-18-crown-6 has been prepared by a simple two-step synthetic method and characterized for its ability to form a uniform self-assembled monolayer (SAM) on gold as well as to immobilize proteins using atomic force microscopy, quartz crystal microbalance, and electrochemical impedance spectroscopy (EIS) experiments. The (R)-lipo-diaza-18-crown-6 was shown to form a well-defined SAM on gold, which subsequently captures the antibody (Ab) molecules that in turn capture the antigen (Ag) molecules. The Ab molecules studied include antibody C-reactive protein (Ab-CRP) and antibody ferritin (Ab-ferritin) along with their Ags, i.e., CRP and ferritin. Quantitative detection of the Ab-Ag interactions was accomplished by EIS experiments with a Fe(CN)6(3-/4-) redox probe present. The ratios of the charge-transfer resistances for the redox probe on the SAM-antibody-covered electrode to those with the antigen molecules attached show an excellent linearity for log[Ag] with lower detection limits than those of other SAMs for the electrochemical sensing of proteins.

Label-free impedimetric sensor for a ribonucleic acid oligomer specific to hepatitis C virus at a self-assembled monolayer-covered electrode.

A ribonucleic acid (RNA) sensor based on hybridization of its peptide nucleic acid (PNA) molecule with a target RNA oligomer of the internal ribosome entry site sequence specific to the hepatitis C virus (HCV) and the electrochemical impedance detection is described. This RNA is one of the most conservative molecules of the whole HCV RNA genome. The ammonium ion terminated PNA molecule was immobilized via its host-guest interactions with the diaza crown ring of 3-thiophene-acetamide-diaza-18-crown-6 synthesized by a simple two-step method, which forms a well-defined self-assembled monolayer (SAM) on gold. Hybridization events of the probe PNA with the target RNA were monitored by measuring charge-transfer resistances for the Fe(CN)(6)(3-/4-) redox probe using Fourier transform electrochemical impedance spectroscopy. The ratio of the resistances of the SAM-covered electrode measured before and after hybridization increased linearly with log[RNA] in the rat liver lysate with a detection limit of about 23 pM.

Reversible sol-gel signaling system with epMB for the study of enzyme- and pH-triggered oligonucleotide release from a biotin hydrogel

The biotin-based low molecular weight hydrogel (G1) is able to entrap the epMB and as a consequence, the color of the epMB changes from green to blue; the color change depends on the state of the gelator, i.e. upon proceeding from sol to gel and vice versa.