Vathan Kumar

α-(l)-(3′–2′)-Threofuranosyl nucleic acid (TNA) cross-pairs with DNA and RNA and is not degraded by nucleases and thus has potential for use in diagnostics and therapeutics based on nucleic acids. Here, we describe the synthesis of 15 building blocks of chiral 4′-(R)- and 15 building blocks of chiral (S)-methyl-α-(l)-threofuranosyl nucleic acid (4′-Me-TNA) monomers and their incorporation into oligonucleotides. Crystallographic studies of RNAs containing 4′-Me-TNA modifications revealed the impact of the methyl substituent on the sugar pucker and duplex conformation. Biostability studies showed that a terminal 4′-Me-TNA modification on a deoxyoligonucleotide imparted resistance to nuclease digestion equivalent to unmethylated TNA, which is markedly superior to that of more conventional 2′-ribo and 2′-deoxy modifications. A single nucleotide incorporation of the 4′-(R)-Me-TNA destabilized an otherwise all-RNA 12-mer duplex by 6.5 to 12 °C, depending on the base, relative to the unmodified RNA control duplex; the (S) isomer was less destabilizing than the (R) isomer. Computational models were used to rationalize the high levels of nuclease resistance and the thermal destabilization. The 4′-Me-TNA triphosphates are poorly recognized by an engineered TNA polymerase making it unlikely that the 4′-Me-TNA triphosphates will be recognized by natural polymerases. Together, these properties warrant the evaluation of 4′-Me-TNA in nucleic acid-based therapeutics.

Inspired by the uncommon furanose configuration of 3'-deoxyapio-containing nucleic acids (apioNAs), we developed a facile and convenient synthesis of 24 building blocks of this modified nucleic acid monomer, including phosphoramidites, H-phosphonates, solid supports, and nucleoside triphosphates. The building blocks included those containing the four canonical RNA bases A, G, U, and C as well as T and 5-methyl-C and were synthesized starting from a single common sugar intermediate derived from d-(+)-xylose. DNA and RNA duplexes with a single apioNA modification in one strand were less thermodynamically stable than unmodified DNA or RNA. The crystal structure of apioNA-modified RNA octamer showed that the apioNA residue adopts an RNA-like structure but local reorientation of the apioNA sugar and 2'-phosphate and the difference in helical rise on the 5' side of the apioNA T relative to RNA likely contribute to the destabilizing effect of apioNA residues. At the terminus of a DNA strand, this modification provides extremely high resistance against both 3'- and 5'-exonucleases even when linked to the adjacent residue by a phosphodiester moiety. Molecular modeling of a DNA duplex containing apioNA was used to rationalize the DNA duplex destabilization and the exonuclease resistance resulting from incorporation of the apioNA residue. Use of apioNA NTPs as substrates for previously engineered α-l-threofuranosyl polymerases depends on both the enzyme and the nucleobase. These data indicate that apioNAs warrant further evaluation, and the building blocks synthesized will allow incorporation of apioNA into therapeutic oligonucleotides.

Background: A growing body of evidence suggests that Hsp70, which is overexpressed in human breast tumors, plays a role in tumorigenesis and tumor progression in breast cancer as well as in its aggressive phenotypes. Hsp70 constitutes a potential therapeutic target in the treatment of this disease. Methods: We developed a new series of rhodacyanine-based Hsp70 inhibitors, represented by compounds 1 and 6, in which the cationic pyridin-1-ium or thiazol-3-ium ring of existing Hsp70 inhibitors (e.g., JG-40 and JG-98) was replaced by a corresponding benzo- fused N-heterocycle. Results: Several lines of evidence suggest that these benzo-fused derivatives may exert their antitumor activities, in part, by targeting Hsp70. These putative inhibitors displayed differential antiproliferative efficacy against breast cancer cells (IC₅₀ as low as 0.25 μM) versus nontumorigenic MCF-10A breast epithelial cells (IC₅₀ ≥ 5 μM). This was correlated with the corresponding Hsp70 expression levels. Using a protein refolding assay, we confirmed that these agents effectively inhibited the chaperone activity of Hsp70. Moreover, these inhibitors effectively suppressed the expression of well-known oncogenic client proteins of Hsp70’s, including FoxM1, HuR, and Akt, which paralleled their antiproliferative efficacy. Supporting the established role of Hsp70 in regulating protein refolding, these derivatives induced autophagy, as manifested by the conversion of LC3B-I to LC3B-II. Notably, these putative Hsp70 inhibitors did not cause a compensatory elevation in Hsp90 expression, contrasting with the previously reported effects of Hsp90 inhibitors on Hsp70 upregulation. Conclusion: Together with the finding that compounds 1 and 6 showed improved microsomal stability, these results suggest the translational potential of these putative Hsp70 inhibitors to foster new strategies for cancer therapy. However, whether these benzo-fused rhodacyanines act on kinases or other targets remains unclear. It is currently under investigation.

We have previously demonstrated the ability of I-Trp to disrupt the protein–protein interaction of β-tubulin with chaperonin-containing TCP-1β (CCT-β). This caused more severe apoptosis in multidrug-resistant MES-SA/Dx5, compared to MES-SA, due to its higher CCT-β overexpression. In this study, we screened a panel of cancer cell lines, finding CCT-β overexpression in the triple-negative breast cancer cell line MDA-MB-231, colorectal cancer cell lines Colo205 and HCT116, and a gastric cancer cell line MKN-45. Thus, I-Trp killed these cancers with sub- to low-μM EC₅₀, whereas it was non-toxic to MCF-10A. We then synthesized analogs of I-Trp and evaluated their cytotoxicity. Furthermore, apoptotic mechanism investigations revealed the activation of both protein ubiquitination/degradation and ER-associated protein degradation pathways. These pathways proceeded through activation of MAPKs at the onset of CCT-β : β-tubulin complex disruption. We thus establish an effective strategy to treat CCT-β overexpressed cancers by disrupting the CCT-β : β-tubulin complex.

High-throughput screening was performed on ∼6800 compounds to identify KR-72039 as an inhibitor of H1N1 and H5N1 neuraminidases (NAs). Structure–activity relationship studies led to 3e, which inhibited H5N1 NA with an IC₅₀ of 2.8 μM and blocked viral replication. Docking analysis shows that compounds bind to loop-430 around the NA active site. Compound 3l additionally inhibited H7N9 NA, making it a dual inhibitor of N1- and N2-type NAs.

Introduction: A novel coronavirus (CoV), unlike previous typical human coronaviruses (HCoVs), was identified as causative agent for severe acute respiratory syndrome (SARS). SARS first surfaced as a pandemic in late 2002 and originated in southern China. SARS-CoV rapidly spread to > 30 countries by 2003, infecting nearly 8,000 people and causing around 800 fatalities. After 10 years of silence, a 2012 report alarmed researchers about the emergence of a new strain of CoV causing SARS-like disease. Areas covered: To combat SARS, scientists applied for patents on various therapeutic agents, including small-molecule inhibitors targeting the essential proteases, helicase and other proteins of the virus, natural products, approved drugs, molecules binding to the virus, neutralizing antibodies, vaccines, anti-sense RNA, siRNA and ribozyme against SARS-CoV. In this article, the patents published from 2008 to the present for the new therapeutics that could potentially be used in the prophylaxis and treatment of SA...