Approaches to Carbocyclic Sialidase Inhibitors

Summary.  The crucial role played by carbohydrates in many physiological processes has made this class of compounds an interesting target for drug design. Consequently mimicking carbohydrates has been one of the most rapidly growing fields in synthetic organic chemistry in recent years, and particularly intense focus has been devoted to sialic acids and sialic acid metabolizing enzymes, including sialidases. Inhibition of the latter enzyme from influenza virus can be regarded as one of the most successful examples of structure-based drug design and high affinity inhibitors based on neuraminic acid have been developed. There is an ongoing search for inhibitors with improved physicochemical properties and among them, carbocyclic systems, where the ring oxygen of the carbohydrate is replaced by carbon, have become the center of interest. This review intends to give a brief overview over the structures and synthetic approaches which surfaced in the last decade. E-mail: hansjoerg.streicher@uni-konstanz.de Received June 17, 2002; accepted June 21, 2002     

Derivatization of sialic acids for stabilization in matrix‐assisted laser desorption/ionization mass spectrometry and concomitant differentiation of α(2 → 3)‐ and α(2 → 6)‐isomers

Sialylated carbohydrates usually decompose by loss of sialic acid when ionized by matrix‐assisted laser desorption/ionization (MALDI) as the result of the labile carboxylic proton. Stabilization has previously been achieved by forming methyl esters with methyl iodide, a procedure that eliminates the labile proton. In this paper, we describe an alternative procedure for methyl ester formation that provides information on the sialic acid linkage directly from the MALDI spectrum. The sugars were desalted, dissolved in methanol, and treated with 4‐(4,6‐dimethoxy‐1,3,5‐triazin‐2‐yl)‐4‐methylmorpholinium chloride (DMT‐MM). After removal of the solvent, the products were transferred directly to the MALDI target and examined from 2,5‐dihydroxybenzoic acid. Small amounts of N‐glycans derived from biological sources benefited from an additional clean‐up stage involving Nafion 117. α(2 → 6)‐Linked sialic acid produced only methyl esters whereas α(2 → 3)‐linked sialic acids were converted into their lactones providing a 32 Da difference in mass. Negative ion collision‐induced decomposition (CID) mass spectra of these neutralized glycans provided information, in many cases, on the antenna of N‐linked glycans to which the variously linked sialic acids were attached. The method was applied to N‐linked glycans released from bovine fetuin and porcine thyroglobulin. Copyright © 2008 John Wiley & Sons, Ltd.     

Rational inhibitor design and iterative screening in the identification of selective plasmodial cyclin dependent kinase inhibitors

New chemical classes of compounds must be introduced into the malaria drug development pipeline in an effort to develop new chemotherapy options for the fight against malaria. In this review we describe an iterative approach designed to identify potent inhibitors of a kinase family that collectively functions as key regulators of the cell cycle. Cyclin-dependent protein kinases (CDKs) are attractive drug targets in numerous diseases and, most recently, they have become the focus of rational drug design programs for the development of new antimalarial agents. Our approach uses experimental and virtual screening methodologies to identify and refine chemical inhibitors and increase the success rate of discovering potent and selective inhibitors. The active pockets of the plasmodial CDKs are unique in terms of size, shape and amino acid composition compared with those of the mammalian orthologues. These differences exemplified through the use of screening assays, molecular modeling, and crystallography can be exploited for inhibitor design. To date, several classes of compounds including quinolines and oxindoles have been identified as selective inhibitors of the plasmodial CDK7 homologue, Pfmrk. From these initial studies and through the iterative rational drug design process, more potent, selective, and most importantly, chemically unique compound classes have been identified as effective inhibitors of the plasmodial CDKs and the malarial parasite.     

Carbohydrate chemistry in drug discovery

The multitude of roles that carbohydrates and their glyco-conjugates play in biological processes has stimulated great interest in determining the nature of their interactions in both normal and diseased states. Manipulating such interactions will provide leads for drug discovery. Of the major classes of biomolecule, carbohydrates are the most structurally diverse. This hetereogeneity makes isolation of pure samples, and in sufficient amounts, from biological sources extremely difficult. Chemical synthesis offers the advantage of producing pure and structurally defined oligosaccharides for biological investigations. Although the complex nature of carbohydrates means that this is challenging, recent advances in the field have facilitated access to these molecules. The synthesis and isolation of oligosaccharides combined with progress in glycoarray technology have aided the identification of new carbohydrate-binding drug targets. This review aims to provide an overview of the latest advancements in carbohydrate chemistry and the role of these complex molecules in drug discovery, focusing particularly on synthetic methodologies, glycosaminoglycans, glycoprotein synthesis and vaccine development over the last few years.     

The Total Synthesis of Starfish Ganglioside GP3 Bearing a Unique Sialyl Glycan Architecture

The total synthesis of ganglioside GP3, which is found in the starfish Asterina pectinifera, has been accomplished through stereoselective and effective glycosylation reactions. The sialic acid embedded octasaccharide moiety of the target compound was constructed by [4+4] convergent coupling. A tetrasaccharyl donor and acceptor that contained internal sialic acid residues were synthesized with an orthogonally protected N‐Troc sialic acid donor as the key common synthetic unit, and they underwent highly stereoselective glycosidation. The resulting sialosides were subsequently transformed into reactive glycosyl acceptors. [4+4] coupling furnished the octasaccharide framework in 91 % yield as a single stereoisomer. Final conjugation of the octasaccharyl donor and glucosyl ceramide acceptor produced the protected target compound in high yield, which underwent global deprotection to successfully deliver ganglioside GP3.     

Extending the possibility of an N-Troc-protected sialic acid donor toward variant sialo-glycoside synthesis

The potential of an N-Troc-protected sialic acid donor, equipped with phenylsulfenyl functionality as a leaving group, has been explored. As a result, the entitled donor was proven to be highly reactive and to have broad applicability toward the synthesis of variant sialo-glycans, which have N-glycolyl, de-N-acetyl, 1,5-lactam and 8-O-sulfo sialic acid analogs.     

BALLDock/SLICK: a new method for protein-carbohydrate docking

Protein-ligand docking is an essential technique in computer-aided drug design. While generally available docking programs work well for most drug classes, carbohydrates and carbohydrate-like compounds are often problematic for docking. We present a new docking method specifically designed to handle docking of carbohydrate-like compounds. BALLDock/SLICK combines an evolutionary docking algorithm for flexible ligands and flexible receptor side chains with carbohydrate-specific scoring and energy functions. The scoring function has been designed to identify accurate ligand poses, while the energy function yields accurate estimates of the binding free energies of these poses. On a test set of known protein-sugar complexes we demonstrate the ability of the approach to generate correct poses for almost all of the structures and achieve very low mean errors for the predicted binding free energies.     

Structural Insights in Mammalian Sialyltransferases and Fucosyltransferases: We Have Come a Long Way,but It Is Still a Long Way Down

Mammalian cell surfaces are modified with complex arrays of glycans that play major roles in health and disease. Abnormal glycosylation is a hallmark of cancer; terminal sialic acid and fucose in particular have high levels in tumor cells, with positive implications for malignancy. Increased sialylation and fucosylation are due to the upregulation of a set of sialyltransferases (STs) and fucosyltransferases (FUTs), which are potential drug targets in cancer. In the past, several advances in glycostructural biology have been made with the determination of crystal structures of several important STs and FUTs in mammals. Additionally, how the independent evolution of STs and FUTs occurred with a limited set of global folds and the diverse modular ability of catalytic domains toward substrates has been elucidated. This review highlights advances in the understanding of the structural architecture, substrate binding interactions, and catalysis of STs and FUTs in mammals. While this general understanding is emerging, use of this information to design inhibitors of STs and FUTs will be helpful in providing further insights into their role in the manifestation of cancer and developing targeted therapeutics in cancer.     

Preparation and evaluation of unimolecular pentavalent and hexavalent antigenic constructs targeting prostate and breast cancer: a synthetic route to anticancer vaccine candidates

Several novel, fully synthetic, carbohydrate-based antitumor vaccines have been assembled. Each construct consists of multiple cancer-related antigens displayed on a single polypeptide backbone. Recent advances in synthetic methodology have allowed for the incorporation of a complex oligosaccharide terminating in a sialic acid residue (i.e., GM2) as one of the carbohydrate antigens. Details of the vaccine synthesis as well as the results of preliminary immunological investigations are described herein.     

FeCl3‐Catalyzed Addition of 1,3‐Dicarbonyl Compounds to Aromatic Olefins

A direct, intermolecular addition of 1,3‐dicarbonyl compounds to styrenes in the presence of FeCl₃ as an inexpensive and disposable catalyst has been developed for the straightforward and practical synthesis of arylated diketones and ketoesters. The reactions proceed under mild conditions for most substrates (50–80 °C), and no strong acid or base is required. The synthetic value of the method is demonstrated by 15 examples, including the synthesis of the current pharmaceutical drug warfarin in one step and 42 % yield from commercially available substrates.     

PHA-L lectin and carbohydrate relationship: conjugation with CdSe/CdS nanoparticles, radiolabeling and in vitro affinities on MCF-7 cells

This research aims to investigate the interaction between phytohemagglutinin-L (PHA-L) and sialic acid, which is abundant on the breast cancer cell (MCF-7) surface and displays monosaccharide characteristics, by experimental and computational methods. Experimentally, CdSe/CdS nanoparticles (QDs) were synthesized; PHA-L was conjugated with QDs and labeled with ¹²⁵I. Radiolabeling yield was found to be 97 ± 1.2 %. Afterwards, in vitro bioaffinities of radiolabeled PHA-L conjugated QDs have been investigated on MCF-7 cells and it has been observed that the cell incorporation increased with time. The results indicated that ¹²⁵I labeled QD-PHA-L conjugates represent significant affinity on MCF-7 cells. In the second step of the study, the crystal structure of carbohydrate interaction surface of PHA-L was extracted from the crystal structure of PHA-L. The interactions between this surface and sialic acid were calculated by computational tools. These calculations revealed specific interactions between PHA-L and sialic acid. Semi-empirical methods, PM3 and AM1, were used in these calculations. Significant outcomes have been obtained from the experimental and computational studies and these results demonstrated that PHA-L may be an effective agent for imagining MCF-7 cells.     

A Diazido Mannose Analogue as a Chemoenzymatic Synthon for Synthesizing Di‐N‐acetyllegionaminic Acid‐Containing Glycosides

A chemoenzymatic synthon was designed to expand the scope of the chemoenzymatic synthesis of carbohydrates. The synthon was enzymatically converted into carbohydrate analogues, which were readily derivatized chemically to produce the desired targets. The strategy is demonstrated for the synthesis of glycosides containing 7,9‐di‐N‐acetyllegionaminic acid (Leg5,7Ac₂), a bacterial nonulosonic acid (NulO) analogue of sialic acid. A versatile library of α2‐3/6‐linked Leg5,7Ac₂‐glycosides was built by using chemically synthesized 2,4‐diazido‐2,4,6‐trideoxymannose as a chemoenzymatic synthon for highly efficient one‐pot multienzyme (OPME) sialylation followed by downstream chemical conversion of the azido groups into acetamido groups. The syntheses required 10 steps from commercially available d ‐fucose and had an overall yield of 34–52 %, thus representing a significant improvement over previous methods. Free Leg5,7Ac₂ monosaccharide was also synthesized by a sialic acid aldolase‐catalyzed reaction.     

Monomeric inhibitors of influenza neuraminidase enhance the hemagglutination inhibition activities of polyacrylamides presenting multiple C-sialoside groups

Background: Influenza viruses use hemagglutinin (HA) arrays to bind to sialic acid moieties on the surface of cells; crosslinking of erythrocytes by this mechanism leads to hemagglutination. A number of synthetic polymers containing multiple sialic acid (Neu5Ac) groups as side chains are potent inhibitors of this process. Inhibition may be due to two mechanisms: polyvalent binding of the inhibitor's multiple Neu5Ac side chains to multiple HA sites on the viral surface, or steric stabilization of the viral particle by a layer of the adsorbed, water-swollen polymer, which prevents adhesion to the erythrocyte. The balance between these two effects is not yet known.Results: Polyacrylamides with multiple C-sialosides (PA(Neu5Ac)) were 2–20 fold more effective as inhibitors of virally mediated hemagglutination when assayed in the presence of Neu2en-NH₂, a potent monomeric inhibitor of influenza neuraminidase (NA). The ability of monomeric inhibitors of NA to enhance the inhibition of hemagglutination in this assay correlated with the affinity of the monomer for NA.Conclusions: We propose that inhibitors of NA act by competing with the C-sialosides of PA(Neu5Ac) for binding to the active sites of the NA. Competitive displacement of Neu5Ac causes an expansion of the layer of polymeric gel adsorbed to the virus, enhancing its inhibitory effect. This study provides an example of synergy between two ligands directed toward the active sites of two different proteins, and reinforces the conclusion that steric stabilization is important for the activity of polyvalent inhibitors.     

Synthesis of a novel dioxan sialic acid analog

A preparative scale synthesis of a dioxan sialic acid analog was achieved from d-mannose. The conformation and the acidic character of this dioxan derivative, closely related to sialic acid, provides a scaffold for drug design.     

Probing the structural requirements of peptoids that inhibit HDM2-p53 interactions

Many cellular processes are controlled by protein-protein interactions, and selective inhibition of these interactions could lead to the development of new therapies for several diseases. In the area of cancer, overexpression of the protein, human double minute 2 (HDM2), which binds to and inactivates the protein p53, has been linked to tumor aggressiveness and drug resistance. In general, inhibition of protein-protein interactions with synthetic molecules is challenging and currently remains a largely uncharted area for drug development. One strategy to create inhibitors of protein-protein interactions is to recreate the three-dimensional arrangement of side chains that are involved in the binding of one protein to another, using a nonnatural scaffold as the attachment point for the side chains. In this study, we used oligomeric peptoids as the scaffold to begin to develop a general strategy in which we could rationally design synthetic molecules that can be optimized for inhibition of protein-protein interactions. Structural information on the HDM2-p53 complex was used to design our first class of peptoid inhibitors, and we provide here, in detail, the strategy to modify peptoids with the appropriate side chains that are effective inhibitors of HDM2-p53 binding. While we initially tried to develop rigid, helical peptoids as HDM2 binders, the best inhibitors were surprisingly peptoids that lacked any helix-promoting groups. These results indicate that starting with rigid peptoid scaffolds may not always be optimal to develop new inhibitors.     

Two procedures for the syntheses of labeled sialic acids and their 1,7-lactones

The synthesis of four deuterated sialic acids and their 1,7-lactones has been performed in two ways, one based on sialic acid classical chemistry, and the other involving a direct exchange of the unlabeled acyl group of N-acetylneuraminic acid with a labeled one mediated by a perfluorinated amide. The final lactonization is promoted by benzyloxycarbonyl chloride.     

A general, iterative, and modular approach toward carbohydrate libraries based on ruthenium-catalyzed oxidative cyclizations

Carbohydrates are an omnipresent class of highly oxygenated natural products. Due to their wide spectra of biological activities, they have been in the center of synthetic organic chemistry for more than 130 years. During the past 50 years non-natural carbohydrates attracted the interest of various chemists in the fields of organic, biological, and medical chemistry. Especially desoxygenated sugars proved to be an important class of compounds. Up to date, most non-natural analogues are synthesized starting from natural, enantiomerically pure carbohydrates in multistep synthesis. In this report, we present a synthetic strategy that allows the selective modular synthesis of natural and non-natural carbohydrates within five synthetic steps starting from readily available starting materials. Due to a sequential introduction of O- or N-functionalities, a regioselective protection of each new functional group is possible. The key step in the carbohydrate synthesis is a RuO4-catalyzed oxidative cyclization via a pH-dependent dehydrogenation-dihydroxylation-cyclization or an oxidative fragmentation-cyclization, leading to highly substituted new carbohydrates, in which each functional group is orthogonally protected and accessible for further synthetic operations.     

Advances in the Development of SARS-CoV-2 Mpro Inhibitors

Since the outbreak of COVID-19, one of the strategies used to search for new drugs has been to find inhibitors of the main protease (Mpro) of the virus SARS-CoV-2. Initially, previously reported inhibitors of related proteases such as the main proteases of SARS-CoV and MERS-CoV were tested. A huge effort was then carried out by the scientific community to design, synthesize and test new small molecules acting as inactivators of SARS-CoV-2 Mpro. From the chemical structure view, these compounds can be classified into two main groups: one corresponds to modified peptides displaying an adequate sequence for high affinity and a reactive warhead; and the second is a diverse group including chemical compounds that do not have a peptide framework. Although a drug including a SARS-CoV-2 main protease inhibitor has already been commercialized, denoting the importance of this field, more compounds have been demonstrated to be promising potent inhibitors as potential antiviral drugs.