Site-specific incorporation of 5'-methyl DNA enhances the therapeutic profile of gapmer ASOs.

We recently showed that site-specific incorporation of 2'-modifications or neutral linkages in the oligo-deoxynucleotide gap region of toxic phosphorothioate (PS) gapmer ASOs can enhance therapeutic index and safety. In this manuscript, we determined if introducing substitution at the 5'-position of deoxynucleotide monomers in the gap can also enhance therapeutic index. Introducing R- or S-configured 5'-Me DNA at positions 3 and 4 in the oligodeoxynucleotide gap enhanced the therapeutic profile of the modified ASOs suggesting a different positional preference as compared to the 2'-OMe gap modification strategy. The generality of these observations was demonstrated by evaluating R-5'-Me and R-5'-Ethyl DNA modifications in multiple ASOs targeting HDAC2, FXI and Dynamin2 mRNA in the liver. The current work adds to a growing body of evidence that small structural changes can modulate the therapeutic properties of PS ASOs and ushers a new era of chemical optimization with a focus on enhancing the therapeutic profile as opposed to nuclease stability, RNA-affinity and pharmacokinetic properties. The 5'-methyl DNA modified ASOs exhibited excellent safety and antisense activity in mice highlighting the therapeutic potential of this class of nucleic acid analogs for next generation ASO designs.

Understanding the effect of controlling phosphorothioate chirality in the DNA gap on the potency and safety of gapmer antisense oligonucleotides.

Therapeutic oligonucleotides are often modified using the phosphorothioate (PS) backbone modification which enhances stability from nuclease mediated degradation. However, substituting oxygen in the phosphodiester backbone with sulfur introduce chirality into the backbone such that a full PS 16-mer oligonucleotide is comprised of 215 distinct stereoisomers. As a result, the role of PS chirality on the performance of antisense oligonucleotides (ASOs) has been a subject of debate for over two decades. We carried out a systematic analysis to determine if controlling PS chirality in the DNA gap region can enhance the potency and safety of gapmer ASOs modified with high-affinity constrained Ethyl (cEt) nucleotides in the flanks. As part of this effort, we examined the effect of systematically controlling PS chirality on RNase H1 cleavage patterns, protein mislocalization phenotypes, activity and toxicity in cells and in mice. We found that while controlling PS chirality can dramatically modulate interactions with RNase H1 as evidenced by changes in RNA cleavage patterns, these were insufficient to improve the overall therapeutic profile. We also found that controlling PS chirality of only two PS linkages in the DNA gap was sufficient to modulate RNase H1 cleavage patterns and combining these designs with simple modifications such as 2'-OMe to the DNA gap resulted in dramatic improvements in therapeutic index. However, we were unable to demonstrate improved potency relative to the stereorandom parent ASO or improved safety over the 2'-OMe gap-modified stereorandom parent ASO. Overall, our work shows that while controlling PS chirality can modulate RNase H1 cleavage patterns, ASO sequence and design are the primary drivers which determine the pharmacological and toxicological properties of gapmer ASOs.

Site-specific replacement of phosphorothioate with alkyl phosphonate linkages enhances the therapeutic profile of gapmer ASOs by modulating interactions with cellular proteins.

Phosphorothioate-modified antisense oligonucleotides (PS-ASOs) interact with a host of plasma, cell-surface and intracellular proteins which govern their therapeutic properties. Given the importance of PS backbone for interaction with proteins, we systematically replaced anionic PS-linkages in toxic ASOs with charge-neutral alkylphosphonate linkages. Site-specific incorporation of alkyl phosphonates altered the RNaseH1 cleavage patterns but overall rates of cleavage and activity versus the on-target gene in cells and in mice were only minimally affected. However, replacing even one PS-linkage at position 2 or 3 from the 5'-side of the DNA-gap with alkylphosphonates reduced or eliminated toxicity of several hepatotoxic gapmer ASOs. The reduction in toxicity was accompanied by the absence of nucleolar mislocalization of paraspeckle protein P54nrb, ablation of P21 mRNA elevation and caspase activation in cells, and hepatotoxicity in mice. The generality of these observations was further demonstrated for several ASOs versus multiple gene targets. Our results add to the types of structural modifications that can be used in the gap-region to enhance ASO safety and provide insights into understanding the biochemistry of PS ASO protein interactions.

Flux Synthesis of a Metal Carbide Hydride Using Anthracene As a Reactant.

La15(FeC6)4H was synthesized from the reaction of iron and anthracene in La/Ni eutectic flux. Anthracene was the source of both the carbon and hydrogen in the product. The structure of this metal carbide hydride features hydride ions in tetrahedral interstitial sites surrounded by lanthanum ions, which was confirmed by single-crystal neutron diffraction studies. The trigonal planar FeC6 units in which the central iron atom is coordinated by three ethylenide groups are similar to those found in La3.67FeC6, a previously reported compound that is formed in the absence of a hydride source. Magnetic susceptibility data confirm that the iron sites do not have magnetic moments. Density of states calculations indicate that La15(FeC6)4H is metallic and is stabilized by the incorporation of hydride anions.

In Situ Neutron Diffraction Studies of the Metal Flux Growth of Ba/Yb/Mg/Si Intermetallics.

The Ba/Yb/Mg/Si intermetallic system is extremely complex, with four competing structurally related compounds forming from reactions of barium, ytterbium, and silicon in magnesium-rich Mg/Al flux. In addition to the previously reported Ba2Yb0.9Mg11.1Si7, Ba5Yb2Mg17Si12, and Ba20Yb5Mg61Si43, a new compound has been found. Ba6Yb1.84Mg18.16Si13 crystallizes in the P6̅ space group, with the Zr6Ni20P13 structure type. Quenching experiments and in situ neutron powder diffraction studies were carried out to determine the reaction parameters that favor particular products. Under slow-cooling conditions, Ba5Yb2Mg17Si12 precipitates from the flux at 800 °C. A faster cooling rate of an identical reaction results in the formation of single crystals of Ba20Yb5Mg61Si43 in the flux at 640 °C. This indicates that the crystallization of products in this metal flux reaction does not involve precipitation and interconversion of different phases but instead depends on the rate of cooling across the supersaturated metastable zone in this system.

Synthesis and Antitumor Activity Evaluation of Compounds Based on Toluquinol.

Encouraged by the promising antitumoral, antiangiogenic, and antilymphangiogenic properties of toluquinol, a set of analogues of this natural product of marine origin was synthesized to explore and evaluate the effects of structural modifications on their cytotoxic activity. We decided to investigate the effects of the substitution of the methyl group by other groups, the introduction of a second substituent, the relative position of the substituents, and the oxidation state. A set of analogues of 2-substituted, 2,3-disubstituted, and 2,6-disubstituted derived from hydroquinone were synthesized. The results revealed that the cytotoxic activity of this family of compounds could rely on the hydroquinone/benzoquinone part of the molecule, whereas the substituents might modulate the interaction of the molecule with their targets, changing either its activity or its selectivity. The methyl group is relevant for the cytotoxicity of toluquinol, since its replacement by other groups resulted in a significant loss of activity, and in general the introduction of a second substituent, preferentially in the para position with respect to the methyl group, was well tolerated. These findings provide guidance for the design of new toluquinol analogues with potentially better pharmacological properties.

An Olefin Cross-Metathesis Approach to Depudecin and Stereoisomeric Analogues.

A new total synthesis of the natural product (-)-depudecin, a unique and unexplored histone deacetylase (HDAC) inhibitor, is reported. A key feature of the synthesis is the utilization of an olefin cross-metathesis strategy, which provides for an efficient and improved access to natural depudecin, compared with our previous linear synthesis. Featured by its brevity and convergency, our developed synthetic strategy was applied to the preparation of the 10-epi derivative and the enantiomer of depudecin, which represent interesting stereoisomeric analogues for structure-activity relationship studies.

Conjugation of mono and di-GalNAc sugars enhances the potency of antisense oligonucleotides via ASGR mediated delivery to hepatocytes.

Antisense oligonucleotides (ASOs) conjugated to trivalent GalNAc ligands show 10-fold enhanced potency for suppressing gene targets expressed in hepatocytes. Trivalent GalNAc is a high affinity ligand for the asialoglycoprotein receptor (ASGR)-a C-type lectin expressed almost exclusively on hepatocytes in the liver. In this communication, we show that conjugation of two and even one GalNAc sugar to single stranded chemically modified ASOs can enhance potency 5-10 fold in mice. Evaluation of the mono- and di-GalNAc ASO conjugates in an ASGR binding assay suggested that chemical features of the ASO enhance binding to the receptor and provide a rationale for the enhanced potency.

A convenient synthesis of 5'-triantennary N-acetyl-galactosamine clusters based on nitromethanetrispropionic acid.

A convenient method for the synthesis of several triantennary GalNAc clusters based on a nitromethanetrispropionic acid core was developed. The synthetic approach involves pentafluorophenolic ester intermediates which can be used in a one-pot, seven reaction procedure to quickly prepare a variety of triantennary GalNAc conjugated ASOs. The GalNAc clusters were conjugated to the 5'-end of an antisense oligonucleotide and evaluated for activity in primary mouse hepatocytes where they showed ∼10-fold improvement in activity.

Synthesis, biophysical properties and biological activity of second generation antisense oligonucleotides containing chiral phosphorothioate linkages.

Bicyclic oxazaphospholidine monomers were used to prepare a series of phosphorothioate (PS)-modified gapmer antisense oligonucleotides (ASOs) with control of the chirality of each of the PS linkages within the 10-base gap. The stereoselectivity was determined to be 98% for each coupling. The objective of this work was to study how PS chirality influences biophysical and biological properties of the ASO including binding affinity (Tm), nuclease stability, activity in vitro and in vivo, RNase H activation and cleavage patterns (both human and E. coli) in a gapmer context. Compounds that had nine or more Sp-linkages in the gap were found to be poorly active in vitro, while compounds with uniform Rp-gaps exhibited activity very similar to that of the stereo-random parent ASOs. Conversely, when tested in vivo, the full Rp-gap compound was found to be quickly metabolized resulting in low activity. A total of 31 ASOs were prepared with control of the PS chirally of each linkage within the gap in an attempt to identify favorable Rp/Sp positions. We conclude that a mix of Rp and Sp is required to achieve a balance between good activity and nuclease stability.

Efficient Synthesis and Biological Evaluation of 5'-GalNAc Conjugated Antisense Oligonucleotides.

Conjugation of triantennary N-acetyl galactosamine (GalNAc) to oligonucleotide therapeutics results in marked improvement in potency for reducing gene targets expressed in hepatocytes. In this report we describe a robust and efficient solution-phase conjugation strategy to attach triantennary GalNAc clusters (mol. wt. ∼2000) activated as PFP (pentafluorophenyl) esters onto 5'-hexylamino modified antisense oligonucleotides (5'-HA ASOs, mol. wt. ∼8000 Da). The conjugation reaction is efficient and was used to prepare GalNAc conjugated ASOs from milligram to multigram scale. The solution phase method avoids loading of GalNAc clusters onto solid-support for automated synthesis and will facilitate evaluation of GalNAc clusters for structure activity relationship (SAR) studies. Furthermore, we show that transfer of the GalNAc cluster from the 3'-end of an ASO to the 5'-end results in improved potency in cells and animals.

Synthesis of bioactive speciosins G and P from Hexagonia speciosa.

The first total synthesis of speciosins P and G, previously isolated from Hexagonia speciosa, is reported. These compounds have been synthesized by Sonogashira coupling from readily available starting materials. Siccayne was also synthesized from the same starting material in two steps along with a number of other derivatives. The compounds were tested in the wheat coleoptile bioassay. The most active compound was the intermediate 18, followed by 29 and 17. The structural requirements for activity in these compounds are the presence of methoxy groups in the aromatic ring and a formyl or hydroxy group in the side chain.

Metabolomics during the spontaneous fermentation in cocoa (Theobroma cacao L.): An exploraty review.

Spontaneous fermentation is a process that depends on substrates' physical characteristics, crop variety, and postharvest practices; it induces variations in the metabolites that are responsible for the taste, aroma, and quality. Metabolomics makes it possible to detect key metabolites using chemometrics and makes it possible to establish patterns or identify biomarker behaviors under certain conditions at a given time. Therefore, sensitive and highly efficient analytical techniques allow for studying the metabolomic fingerprint changes during fermentation; which identify and quantify metabolites related to taste and aroma formation of an adequate processing time. This review shows that studying metabolomics in spontaneous fermentation permits the characterization of spontaneous fermentation in different stages. Also, it demonstrates the possibility of modulating the quality of cocoa by improving the spontaneous fermentation time (because of volatile aromatic compounds formation), thus standardizing the process to obtain attributes and quality that will later impact the chocolate quality.

Evaluation of Phosphorus and Non-Phosphorus Neutral Oligonucleotide Backbones for Enhancing Therapeutic Index of Gapmer Antisense Oligonucleotides.

The phosphorothioate (PS) linkage in an essential component of therapeutic oligonucleotides. PS in the DNA region of gapmer antisense oligonucleotides (ASOs) supports RNaseH1 activity and enhances nuclease stability. PS also promotes binding to plasma, cell surface, and intracellular proteins, which facilitates tissue distribution, cellular uptake, and endosomal escape of PS ASOs. We recently showed that site-specific replacement of PS in the DNA gap with methoxylpropyl phosphonate (MOP) linkages can enhance the therapeutic index of gapmer ASOs. In this article, we explored 18 phosphorus- and non-phosphorus-based neutral backbone modifications to determine the structure-activity relationship of neutral linkages for enhancing therapeutic index. Replacing MOP with other alkyl phosphonate and phosphotriester linkages enhanced therapeutic index, but these linkages were susceptible to chemical degradation during oligonucleotide deprotection from solid supports following synthesis. Replacing MOP with non-phosphorus linkages resulted in improved chemical stability, but these linkages were introduced into ASOs as nucleotide dimers, which limits their versatility. Overall, linkages such as isopropyl and isobutyl phosphonates and O-isopropyl and O-tetrahydrofuranosyl phosphotriesters, formacetal, and C3-amide showed improved activity in mice relative to MOP. Our data suggest that site-specific incorporation of any neutral backbone linkage can improve therapeutic index, but the size, hydrophobicity, and RNA-binding affinity of the linkage influence ASO activity.

Rheological, bioactive properties and sensory preferences of dark chocolates with partial incorporation of Sacha Inchi (Plukenetia volubilis L.) oil.

We studied the effect of substituting partially, cocoa butter (CB) with Sacha Inchi (Plukenetia volubilis L.) oil (SIO) on rheology, bioactive properties, and sensory preferences in potentially functional chocolate. For this 70% dark chocolates were prepared and the CB was substituted with 1.5%, 3%, and 4.5% of SIO. Hardness and viscosity of the SIO-chocolates were significantly reduced compared to the control (5451 ± 658 g; 17.01 ± 0.94 Pa s, respectively). Total phenolic content remained constant while the antioxidant capacity increased up to IC50 of 2.48 ± 0.10 as the content of SIO increased. The Casson yield stress and Casson plastic viscosity decreased as the amount of SIO increased. Chocolates with 4.5% SIO had a similar color, better glossiness, preferable snap attributes, and were more accepted (7.50 ± 0.08) compared to the control (p < 0.05), measured with a hedonic scale. Then, SIO can improve the bioactive properties of dark chocolates obtaining a potentially functional food with acceptable physicochemical characteristics. SIO can be considered as a new cocoa butter equivalent.

Synthesis and biophysical evaluation of 2',4'-constrained 2'O-methoxyethyl and 2',4'-constrained 2'O-ethyl nucleic acid analogues.

We have recently shown that combining the structural elements of 2'O-methoxyethyl (MOE) and locked nucleic acid (LNA) nucleosides yielded a series of nucleoside modifications (cMOE, 2',4'-constrained MOE; cEt, 2',4'-constrained ethyl) that display improved potency over MOE and an improved therapeutic index relative to that of LNA antisense oligonucleotides. In this report we present details regarding the synthesis of the cMOE and cEt nucleoside phosphoramidites and the biophysical evaluation of oligonucleotides containing these nucleoside modifications. The synthesis of the cMOE and cEt nucleoside phosphoramidites was efficiently accomplished starting from inexpensive commercially available diacetone allofuranose. The synthesis features the use of a seldom used 2-naphthylmethyl protecting group that provides crystalline intermediates during the synthesis and can be cleanly deprotected under mild conditions. The synthesis was greatly facilitated by the crystallinity of a key mono-TBDPS-protected diol intermediate. In the case of the cEt nucleosides, the introduction of the methyl group in either configuration was accomplished in a stereoselective manner. Ring closure of the 2'-hydroxyl group onto a secondary mesylate leaving group with clean inversion of stereochemistry was achieved under surprisingly mild conditions. For the S-cEt modification, the synthesis of all four (thymine, 5-methylcytosine, adenine, and guanine) nucleobase-modified phosphoramidites was accomplished on a multigram scale. Biophysical evaluation of the cMOE- and cEt-containing oligonucleotides revealed that they possess hybridization and mismatch discrimination attributes similar to those of LNA but greatly improved resistance to exonuclease digestion.

Formation of aromatic compounds precursors during fermentation of Criollo and Forastero cocoa.

There are three main genetic varieties of cocoa (Theobroma cacao L) used in chocolate making: Forastero, Trinitario and Criollo, which are distinguished by their aroma, an attribute that determines their quality. Criollo cocoa is of the highest quality and is used in the manufacture of fine chocolates because of its fruity aroma. The aroma of Criollo cocoa is defined by volatile compounds such as pyrazines and aldehydes, which are formed during roasting of the bean, from aroma precursors (reducing sugars and free amino acids) that are generated inside the bean via enzymatic reactions during fermentation; for this reason, fermentation is the most important process in the value chain. This review discusses the production of aroma precursors of Criollo and Forastero cocoa by studying the kinetics of spontaneous fermentation and the role of starter cultures to produce aroma precursors. Fine aroma precursors produced in the pulp during the fermentation phase will migrate into the bean when it's permeability is improved and then retained during the drying phase. Diffusion of aroma precursors into the cocoa bean may be possible, this process is mathematically characterized by the coefficient of molecular diffusion D, which describe the process of mass transfer via Fick's Second Law. The current state of knowledge is analyzed based on existing research and reports some gaps in the literature, suggesting future research that will be necessary for a better understanding of cocoa fermentation.

Structure-based design, synthesis, and A-site rRNA cocrystal complexes of functionally novel aminoglycoside antibiotics: C2" ether analogues of paromomycin.

A series of 2"-O-substituted ether analogues of paromomycin were prepared based on new site-selective functionalizations. X-ray cocrystal complexes of several such analogues revealed a new mode of binding in the A-site rRNA, whereby rings I and II adopted the familiar orientation and position previously observed with paromomycin, but rings III and IV were oriented differently. With few exceptions, all of the new analogues showed potent inhibitory activity equal or better than paromomycin against a sensitive strain of S. aureus. Single digit microM MIC values were obtained against E. coli, with some of the ether appendages containing polar or basic end groups. Two analogues showed excellent survival rate in a mouse septicemia protection assay. Preliminary histopathological analysis of the kidney showed no overt signs of toxicity, while controls with neomycin and kanamycin were toxic at lower doses.

Comprehensive Structure-Activity Relationship of Triantennary N-Acetylgalactosamine Conjugated Antisense Oligonucleotides for Targeted Delivery to Hepatocytes.

The comprehensive structure-activity relationships of triantennary GalNAc conjugated ASOs for enhancing potency via ASGR mediated delivery to hepatocytes is reported. Seventeen GalNAc clusters were assembled from six distinct scaffolds and attached to ASOs. The resulting ASO conjugates were evaluated in ASGR binding assays, in primary hepatocytes, and in mice. Five structurally distinct GalNAc clusters were chosen for more extensive evaluation using ASOs targeting SRB-1, A1AT, FXI, TTR, and ApoC III mRNAs. GalNAc-ASO conjugates exhibited excellent potencies (ED50 0.5-2 mg/kg) for reducing the targeted mRNAs and proteins. This work culminated in the identification of a simplified tris-based GalNAc cluster (THA-GN3), which can be efficiently assembled using readily available starting materials and conjugated to ASOs using a solution phase conjugation strategy. GalNAc-ASO conjugates thus represent a viable approach for enhancing potency of ASO drugs in the clinic without adding significant complexity or cost to existing protocols for manufacturing oligonucleotide drugs.

Evaluación del efecto antibacteriano del látex de Jatropha curcas "piñón" frente a Staphylococcus aureus / Evaluation of the antibacterial effect of latex Jatropha curcas "piñón" in front of Staphylococcus aureus

La presente investigación tuvo como objetivo evaluar el efecto antibacteriano del látex de Jatropha Curcas "Piñón" frente a Staphylococcus aureus. El método de difusión en disco, de Kirby Bauer, fue usado en la investigación; las concentraciones del látex de Jatropha Curcas "Piñón" fueron las siguientes: 10%, 20%, 30%, 40% y 100% usando agua destilada como solvente. Se realizó análisis fitoquímico y prueba de solubilidad al látex de la planta en estudio. El látex de Jatropha Curcas "Piñón" fue muy soluble en agua destilada, etanol y metanol; además, según el análisis fitoquímico, el látex presentó flavonoides, taninos, compuestos fenólicos, alcaloides y esteroides. La concentración del látex al 40% presentó el mayor efecto antibacteriano a un nivel de confianza del 95%, y un error relativo del 5%.

The present research aims to evaluate the antibacterial effect of Jatropha Curcas latex "Piñón" against Staphylococcus aureus. The disc diffusion method of Kirby Bauer was used in the research, the concentrations of Jatropha Curcas "Piñón" latex were as follows: 10%, 20%, 30%, 40% and 100% using distilled water as solvent. Phytochemical analysis and solubility test were performed on the latex of the plant under study. Jatropha Curcas "Piñón" latex was very soluble in distilled water, ethanol and methanol. According to the phytochemical analysis the latex presented flavonoids, tannins, phenolic compounds, alkaloids and steroids. The concentration of latex at 40% had the highest antibacterial effect at a 95% confidence level and a relative error of 5%.