Development of an analytical methodology using Fourier transform mass spectrometry to discover new structural analogs of wine natural sweeteners

Volatile and non-volatile molecules are directly responsible for the thrill and excitement provided by wine-tasting. Their elucidation requires powerful analytical techniques and innovative methodologies. In a recent work, two novel sweet compounds called quercotriterpenosides (QTT) were identified in oak wood used for wine-ageing. The aim of the present study is to discover structural analogs of such natural sweeteners in oak wood. For this purpose, an analytical approach was developed as an alternative to chemical synthesis. Orbitrap mass spectrometry proved to be a crucial technique both to demonstrate the presence of QTT analogs in oak wood by targeted screening and to guide the purification pathway of these molecules using complementary chromatographic tools. Four compounds were isolated and identified for the first time: two isomers, one glucosyl derivative and one galloyl derivative of QTT. Their tasting showed that only the two new isomers were sweet, thus demonstrating both the pertinence of the strategy and the influence of functional groups on gustatory properties. Finally, this paper presents some developments involving multistage Fourier transform mass spectrometry (FTMS) to provide solid structural information on these functional groups prior to any purification of compounds. Such analytical developments could be particularly useful for research on taste-active or bio-active products.     

Novel plastoquinone analogs containing benzocaine and its analogs: structure‐based design,synthesis, and structural characterization

Introducing new biologically active organic molecules or their analogs into the pharmaceutically important molecules significantly enables the discovery and development of the medicines that improve the health of patients. Chemical synthesis has a key role in pharmaceutical research and development, aiming to design and build molecules with the essential biological activity needed in drugs. For that reason, herein, three series of novel PQ analogs (the nonhalogenated (PQ1-6) and the halogenated PQ analogs (BrPQ1-6 and ClPQ1-6)) containing benzocaine and its analogs were designed and synthesized starting from the commercially available dimethylhydroquinone (1) with benzocaine and its analogs. The structures of all synthesized analogs were characterized by using spectroscopic methods. The in vitro antibacterial and antifungal activities were evaluated for the PQ analogs.

     

Recent Advances in the Chemistry and Therapeutic Evaluation of Naturally Occurring and Synthetic Withanolides

Natural products are a major source of biologically active compounds that make promising lead molecules for developing efficacious drug-like molecules. Natural withanolides are found in many flora and fauna, including plants, algae, and corals, that traditionally have shown multiple health benefits and are known for their anti-cancer, anti-inflammatory, anti-bacterial, anti-leishmaniasis, and many other medicinal properties. Structures of these withanolides possess a few reactive sites that can be exploited to design and synthesize more potent and safe analogs. In this review, we discuss the literature evidence related to the medicinal implications, particularly anticancer properties of natural withanolides and their synthetic analogs, and provide perspectives on the translational potential of these promising compounds.     

Application of an integrated cheminformatics-molecular docking approach for discovery for physicochemically similar analogs of fluoroquinolones as putative HCV inhibitors

BackgroundHepatitis C Virus (HCV) infection is a major public health concern across the globe. At present, direct-acting antivirals are the treatment of choice. However, the long-term effect of this therapy has yet to be ascertained. Previously, fluoroquinolones have been reported to inhibit HCV replication by targeting NS3 protein. Therefore, it is logical to hypothesize that the natural analogs of fluoroquinolones will exhibit NS3 inhibitory activity with substantially lesser side effects.MethodIn this study, we tested the application of a recently devised integrated in-silico Cheminformatics-Molecular Docking approach to identify physicochemically similar natural analogs of fluoroquinolones from the available databases (Ambinter, Analyticon, Indofines, Specs, and TimTec). Molecular docking and ROC curve analyses were performed, using PatchDock and Graphpad software, respectively, to compare and analyze drug-protein interactions between active natural analogs, Fluoroquinolones, and HCV NS3 protein.ResultIn our analysis, we were able to shortlist 18 active natural analogs, out of 10,399, that shared physicochemical properties with the template drugs (fluoroquinolones). These analogs showed comparable binding efficacy with fluoroquinolones in targeting 32 amino acids in the HCV NS3 active site that are crucial for NS3 activity. Our approach had around 80 % sensitivity and 70 % specificity in identifying physicochemically similar analogs of fluoroquinolones.ConclusionOur current data suggest that our approach can be efficiently applied to identify putative HCV drug inhibitors that can be taken for in vitro testing. This approach can be applied to discover physicochemically similar analogs of virtually any drug, thus providing a speedy and inexpensive approach to complement drug discovery and design, which can tremendously economize on time and money spent on the screening of putative drugs.     

Structural Aspects of Nucleic Acid Analogs and Antisense Oligonucleotides

Hybridization of complementary oligonucleotides is essential to highly valuable research tools in many fields including genetics, molecular biology, and cell biology. For example, an antisense molecule for a particular segment of sense messenger RNA allows gene expression to be selectively turned off, and the polymerase chain reaction requires complementary primers in order to proceed. It is hoped that the antisense approach may lead to therapeutics for treatment of various diseases including cancer. Areas of active research in the antisense field focus on the mechanisms of cellular uptake of antisense molecules and their delivery to specific cell sites, an improved understanding of how these molecules inhibit the production of proteins, as well as the optimization of the chemical stability of antisense molecules and the thermodynamic stability of the duplexes they form with the mRNA targets. The last two issues in particular have prompted chemists to launch an extensive search for oligonucleotide analogs with improved binding properties for hybridization with RNA and higher resistance toward nuclease degradation. During the last years this research has resulted in a flurry of new chemical analogs of DNA and RNA with modifications in the sugar–phosphate backbone as well as in the nucleobase sites. However, to date little effort has been directed toward uncovering the exact origins of the gain or loss in stability when nucleic acid analogs bind to RNA. Although large amounts of thermodynamic data have been collected, the structural perturbations induced by the modifications in hybrid duplexes are only poorly understood. For many modified oligonucleotides the compatibility of protection, coupling, and deprotection chemistry with standard DNA and RNA synthesis protocols makes it now possible to generate modified nucleic acid fragments or mixed oligonucleotides containing modifications at selected sites in quantities suitable for three-dimensional structure investigations. Such studies should reveal the structural origins of the observed changes in affinity and specificity of binding for particular modifications and may guide the development of second-and third-generation antisense molecules. In addition, the availability of a previously unimaginable variety of modified building blocks and the investigation of their structures provides the basis for a deeper understanding of the native DNA and RNA structures. This contribution will summarize the results of X-ray crystallographic structure determinations of modified nucleic acid fragments conducted in our laboratory during the last three years and the insights gained from them.     

Translating Planar Heterocycles into Three-Dimensional Analogs by Photoinduced Hydrocarboxylation**

The rapid preparation of complex three-dimensional (3D) heterocyclic scaffolds is a key challenge in modern medicinal chemistry. Despite the increased probability of clinical success for small molecule therapeutic candidates with increased 3D complexity, new drug targets remain dominated by flat molecules due to the abundance of coupling reactions available for their construction. In principle, heteroarene hydrofunctionalization reactions offer an opportunity to transform readily accessible planar molecules into more three-dimensionally complex analogs through the introduction of a single molecular vector. Unfortunately, dearomative hydrofunctionalization reactions remain limited. Herein, we report a new strategy to enable the dearomative hydrocarboxylation of indoles and related heterocycles. This reaction represents a rare example of a heteroarene hydrofunctionalization that meets the numerous requirements for broad implementation in drug discovery. The transformation is highly chemoselective, broad in scope, operationally simple, and readily amenable to high-throughput experimentation (HTE). Accordingly, this process will allow existing libraries of heteroaromatic compounds to be translated into diverse 3D analogs and enable exploration of new classes of medicinally relevant molecules.     

Acyl radical insertion for the direct formation of new seven-substituted pterin analogs

A variety of pterin molecules were synthesized via an under-utilized acyl radical insertion, using aldehydes and α-keto esters as the acyl source. These reactions gave complete regiospecificity for the 7-isomer, with reaction times ranging in minutes, often with instantaneous product precipitation. This approach led to the construction of new pterin analogs unaccessible via traditional Friedel-Crafts acylation. The compounds were characterized by NMR spectroscopy and high-resolution mass spectroscopy.     

A tetrafluorophenyl activated ester self-assembled monolayer for the immobilization of amine-modified oligonucleotides

A tetrafluorophenyl (TFP) ester-terminated self-assembled monolayer (SAM) for the fabrication of DNA arrays on gold surfaces is described. Activated ester SAMs are desirable for biomolecule array fabrication because they readily react with amine-containing molecules to form a stable amide linkage. N-Hydroxysuccinimide (NHS) ester SAMs are commonly used for this purpose but are subject to a competing hydrolysis side reaction, limiting their effectiveness under basic conditions. TFP was evaluated here as an alternative activated ester leaving group with a potentially greater stability under basic conditions. It is shown that TFP SAMs are much more stable to basic pH than their NHS analogs and are also more hydrophobic, which is an advantage in the fabrication of high-density spotted arrays. DNA arrays prepared on TFP SAMs at pH 10 have a 5-fold greater surface density of DNA molecules, reduced fluorescence background, and smaller spot radii than those prepared on NHS SAM analogs.     

Rational Design in Photopharmacology with Molecular Photoswitches

Photopharmacology is an attractive approach for achieving targeted drug action with the use of light. In photopharmacology, molecular photoswitches are introduced into the structure of biologically active small molecules to allow for the optical control of their potency. Going beyond trial and error, photopharmacology has progressively applied rational drug design methodologies to devise light-controlled bioactive ligands. In this review, we categorize photopharmacological efforts from the standpoint of medicinal chemistry strategies, focusing on diffusible photochromic ligands modified with photoswitches that operate through E-Z bond isomerization. In the vast majority of cases, photoswitchable ligands are designed as analogs of existing compounds, through a variety of approaches. By analyzing in detail a comprehensive list of instructive examples, we describe the state of the art and discuss future opportunities for rational design in photopharmacology.     

High-Throughput Diversification of Complex Bioactive Molecules by Accelerated Synthesis in Microdroplets

Late-stage diversification of drug molecules is an important strategy in drug discovery that can be facilitated by reaction screening using high-throughput experimentation. Here we present a rapid method for functionalizing bioactive molecules based on accelerated reactions in microdroplets. Reaction mixtures are nebulized at throughputs better than 1 reaction/second and the accelerated reactions occurring in the microdroplets are followed by desorption electrospray ionization mass spectrometry (DESI-MS). Because the accelerated reactions occur on the millisecond timescale, they allow an overall screening throughput of 1 Hz working at the low nanogram scale. Using this approach, an opioid agonist (PZM21) and an antagonist (naloxone) were diversified using three reactions important in medicinal chemistry: sulfur fluoride exchange (SuFEx) click reactions, imine formation reactions, and ene-type click reactions. Some 269 functionalized analogs of naloxone and PZM21 were generated and characterized by tandem mass spectrometry (MS/MS) after screening over 500 reactions.     

Exploring structural feature of aldose-reductase inhibition by 5-[[2-(omega-carboxyalkoxy)aryl]methylene]-4-oxo-2-thioxothiazolidine derivatives employing Fujita-Ban and Hansch approach

Designing of a highly selective, potent and safe inhibitor of aldose reductase (ALR) capable of potentially blocking the excess glucose flux through the polyol pathway that prevails under diabetic condition has been a long standing challenge. In our study, we did quantitative structure-activity relationship (QSAR) analysis, based on Fujita-Ban and classical Hansch approach, on 5-[[2-(omega-carboxyalkoxy)aryl]methylene]-4-oxo-2-thioxothiazolidine derivatives. Study gave structural insight into the binding mode of the molecules to the aldose reductase enzyme. The Fujita-Ban approach revealed that benzylidene thiazolidine nucleus is more potent as compare to naphthyl-methylene thiazolidine analogs. The bulkierness of naphthyl-methylene might be inquisitive with receptor. Hansch approach suggested that electron-withdrawing groups are conducive to aldose reductase inhibitory activity.     

Convergent Assembly of the Tricyclic Labdane Core Enables Synthesis of Diverse Forskolin-like Molecules

We report a new synthetic strategy for the flexible preparation of forskolin-like molecules. The approach is different from the previously published works and employs a convergent assembly of the tricyclic labdane-type core from pre-functionalized cyclic building blocks. Stereoselective Michael addition enabled the fragment coupling with excellent control over three newly created contiguous stereocenters, all-carbon quaternary centers included. Silyl enol ether-promoted ring-opening metathesis paired with ring closure were the other key steps enabling concise assembly of the tricyclic core. Late-stage functionalization sequences transformed the tricyclic intermediates into a set of different forskolin-like molecules. The modular nature of the synthetic scheme described herein has the potential to become a general platform for the preparation of analogs of forskolin and other complex tricyclic labdanes.     

Identification of a nanomolar affinity α-synuclein fibril imaging probe by ultra-high throughput in silico screening

Small molecules that bind with high affinity and specificity to fibrils of the α-synuclein (αS) protein have the potential to serve as positron emission tomography (PET) imaging probes to aid in the diagnosis of Parkinson''s disease and related synucleinopathies. To identify such molecules, we employed an ultra-high throughput in silico screening strategy using idealized pseudo-ligands termed exemplars to identify compounds for experimental binding studies. For the top hit from this screen, we used photo-crosslinking to confirm its binding site and studied the structure–activity relationship of its analogs to develop multiple molecules with nanomolar affinity for αS fibrils and moderate specificity for αS over Aβ fibrils. Lastly, we demonstrated the potential of the lead analog as an imaging probe by measuring binding to αS-enriched homogenates from mouse brain tissue using a radiolabeled analog of the identified molecule. This study demonstrates the validity of our powerful new approach to the discovery of PET probes for challenging molecular targets.     

The Effect of Vicinal Difluorination on the Conformation and Potency of Histone Deacetylase Inhibitors

Histone deacetylase enzymes (HDACs) are potential targets for the treatment of cancer and other diseases, but it is challenging to design isoform-selective agents. In this work, we created new analogs of two established but non-selective HDAC inhibitors. We decorated the central linker chains of the molecules with specifically positioned fluorine atoms in order to control the molecular conformations. The fluorinated analogs were screened against a panel of 11 HDAC isoforms, and minor differences in isoform selectivity patterns were observed.     

Green and catalyst-free synthesis of olsalazine analogs

A greener protocol for the synthesis of olsalazine analogs is reported. Olsalazine analogs are prepared in high yields by a one-pot reaction of two molecules of mesalazine with benzotriazole-activated aspartic acid and glutamic acid in water under microwave irradiation.     

Combining multi-catalysis and multi-component systems for the development of one-pot asymmetric reactions: stereoselective synthesis of highly functionalized bicyclo[4.4.0]decane-1,6-diones

We have developed a direct amine/acid-catalyzed stereoselective hydrogenation of a variety of Wieland-Miescher (W-M) ketones, Hajos-Parrish (H-P) ketones and their analogs with organic hydrides (Hantzsch esters) as the hydrogen source. This astonishingly simple and biomimetic approach was used to construct highly functionalized chiral bicyclo[4.4.0]decane-1,6-diones in a diastereoselective fashion. This is an example of the development of a new technology by the combination of multiple catalysts and components in one pot to deliver highly functionalized chiral molecules.     

Anion mediated activation of guanidine rich small molecules

Cell penetrating peptides (CPPs) and their synthetic analogs are of widespread interest. Here we report that guanidine rich small molecules can be potential membrane transporters in the presence of hydrophobic counteranion activators. To our knowledge, this is the first example of small molecules that mimic the anion-activated transport function of CPP.