Total synthesis of CRM646-A and -B, two fungal glucuronides with potent heparinase inhibition activities

Characterization of Dichloroisoeverninic Acid Biosynthesis and Chemoenzymatic Synthesis of New Orthosomycins

The orthosomycins are highly modified oligosaccharide natural products with a broad spectrum and potent antimicrobial activities. These include everninomicins and avilamycins, which inhibit protein translation by binding a unique site on the bacterial ribosome. Notably, ribosomal bound structures reveal a network of interactions between the 50S subunit and dichloroisoeverninic acid (DCIE), the aromatic A1-ring conserved across orthosomycins, but the relationship of these interactions to their antimicrobial activity remains undetermined. Genetic functional analysis of three genes putatively associated with DCIE biosynthesis in the everninomicin producer Micromonospora carbonacea delineates the native biosynthetic pathway and provides previously unreported advanced biosynthetic intermediates. Subsequent in vitro biochemical analyses demonstrate the complete DCIE biosynthetic pathway and provide access to novel everninomicin analogs. In addition to the orsellinate synthase EvdD3 and a flavin-dependent halogenase EvdD2, our results identified a key acyltransferase, EvdD1, responsible for transferring orsellinate from the acyl carrier protein domain of EvdD3 to a heptasaccharide orthosomycin biosynthetic intermediate. We have also shown that EvdD1 is able to transfer unnatural aryl groups via their N-acyl cysteamine thioesters to the everninomicin scaffold and used this as a biocatalyst to generate a panel of unnatural aryl analogs. The impact of diverse aryl functional group substitution on both ribosome inhibition and antibacterial activities demonstrates the importance of the DCIE moiety in the pharmacology of orthosomycins, notably revealing an uncoupling between ribosomal engagement and antibiotic activity. Control of A1-ring functionality in this class of molecules provides a potential handle to explore and address pharmacological roles of the DCIE ring in this potent and unique class of antibiotics.

Lead identification of novel tetrahydroimidazo[1,2-a]pyridine-5-carboxylic acid derivative as a potent heparanase-1 inhibitor

Heparanase-1 (HPSE1) is an endo-β-d-glucuronidase that cleaves heparan sulfate proteoglycans into short-chain heparan sulfates (HS). The inhibition of HPSE1 has therapeutic potential for proteinuric diseases such as nephrotic syndrome because increased HPSE1 expression is associated with the loss of HS in the glomerular basement membrane, leading to the development of proteinuria. The present study examined the generation of a lead compound focusing on chemical structures with a sugar moiety, such as glycosides and sugar analogs, taking their physical properties into consideration. Compound 10, an exo-β-d-glucuronidase (GUSβ) inhibitor, was found to have a weak inhibitory activity against endo-β-d-glucuronidase HPSE1. A structure-activity relationship study using the X-ray co-crystal structure of 10 and HPSE1 resulted in 12a, which showed a more than 14-fold increase in HPSE1 inhibitory activity compared with that of 10. Compound 12a could be a novel lead compound for the development of a potent HPSE1 inhibitor.

Synthesis of barbacic acid

A new approach for the synthesis of the active barbatic acid has been achieved in eight steps with 22.3% total yield by using commercially available methyl atratate as starting material. This synthesis provides access to multi-gram quantities of barbatic acid with good purity for reference supplies and further analytical and toxicology investigations.

Identification of Novel Potential Heparanase Inhibitors Using Virtual Screening

Heparanase (HPSE) is a mammalian endo-β-D-glucuronidase that cleaves heparan sulphate (HS) side chains of heparin sulphate proteoglycans (HSPG), a class of molecules composed of repeating polysulfated disaccharide units of glucosamine and hexuronic acid residues. HPSE controls the availability of growth factors, chemokines, lipoproteins and other bioactive molecules by degrading HS into smaller fractions, allowing the release of saccharide fragments that activate a plethora of signaling processes. HPSE overexpression has been correlated with tumor survival and metastasis as well as several diseases associated with chronic inflammation, including the ongoing COVID-19 pandemic caused by SARS-CoV-2. Thus, the search for molecules that could potentially inhibit HPSE has become increasingly relevant in the clinic. In this study, we have integrated a strategy that combines virtual screening and molecular docking of publicly available chemical databases to identify small compounds that can be developed into novel HPSE inhibitors. Structural rationalization of the interactions previously reported compounds led us to identify promising unexplored chemotypes. Here we show that these novel potential HPSE inhibitors present optimized in silico druggability and docking properties and may serve as pharmacological tools for the treatment of chronic and infectious diseases associated with chronic inflammation.

Fungal Depsides-Naturally Inspiring Molecules: Biosynthesis, Structural Characterization, and Biological Activities

Fungi represent a huge reservoir of structurally diverse bio-metabolites. Although there has been a marked increase in the number of isolated fungal metabolites over the past years, many hidden metabolites still need to be discovered. Depsides are a group of polyketides consisting of two or more ester-linked hydroxybenzoic acid moieties. They possess valuable bioactive properties, such as anticancer, antidiabetic, antibacterial, antiviral, anti-inflammatory, antifungal, antifouling, and antioxidant qualities, as well as various human enzyme-inhibitory activities. This review provides an overview of the reported data on fungal depsides, including their sources, biosynthesis, physical and spectral data, and bioactivities in the period from 1975 to 2020. Overall, 110 metabolites and more than 122 references are confirmed. This is the first review of these multi-faceted metabolites from fungi.

Synthesis, biological, and photophysical studies of molecular rotor-based fluorescent inhibitors of the trypanosome alternative oxidase

We have recently reported on the development and trypanocidal activity of a class of inhibitors of Trypanosome Alternative Oxidase (TAO) that are targeted to the mitochondrial matrix by coupling to lipophilic cations via C14 linkers to enable optimal interaction with the enzyme's active site. This strategy resulted in a much-enhanced anti-parasite effect, which we ascribed to the greater accumulation of the compound at the location of the target protein, i.e. the mitochondrion, but to date this localization has not been formally established. We therefore synthesized a series of fluorescent analogues to visualize accumulation and distribution within the cell. The fluorophore chosen, julolidine, has the remarkable extra feature of being able to function as a viscosity sensor and might thus additionally act as a probe of the cellular glycerol that is expected to be produced when TAO is inhibited. Two series of fluorescent inhibitor conjugates incorporating a cationic julolidine-based viscosity sensor were synthesized and their photophysical and biological properties were studied. These probes display a red emission, with a high signal-to-noise ratio (SNR), using both single- and two-photon excitation. Upon incubation with T. brucei and mammalian cells, the fluorescent inhibitors 1a and 2a were taken up selectively in the mitochondria as shown by live-cell imaging. Efficient partition of 1a in functional isolated (rat liver) mitochondria was estimated to 66 ± 20% of the total. The compounds inhibited recombinant TAO enzyme in the submicromolar (1a, 2c, 2d) to low nanomolar range (2a) and were effective against WT and multidrug-resistant trypanosome strains (B48, AQP1-3 KO) in the submicromolar range. Good selectivity (SI > 29) over mammalian HEK cells was observed. However, no viscosity-related shift could be detected, presumably because the glycerol was produced cytosolically, and released through aquaglyceroporins, whereas the probe was located, virtually exclusively, in the trypanosome's mitochondrion.

Antitumor activity and structure-activity relationship of heparanase inhibitors: Recent advances

Heparanase (HPSE)-directed tumor progression plays a crucial role in mediating tumor-host crosstalk and priming the tumor microenvironment, leading to tumor growth, metastasis and chemo-resistance. HPSE-mediated breakdown of structural heparan sulfate (HS) networks in the extracellular matrix (ECM) and basement membranes (BM) directly facilitates tumor growth and metastasis. Lysosome HPSE also induces multi-drug resistance via enhanced autophagy. Therefore, HPSE inhibitors development has become an attractive topic to block tumor growth and metastasis or eliminate drug resistance. In this review, we summarize HPSE inhibitors applied experimentally and clinically according to interaction with the binding sites of HPSE and participation of growth factors. The antitumor activity and structure-activity relationship (SAR) are also emphasized.

CRM646-A, a Fungal Metabolite, Induces Nucleus Condensation by Increasing Ca2+ Levels in Rat 3Y1 Fibroblast Cells

We previously identified a new heparinase inhibitor fungal metabolite, named CRM646-A, which showed inhibition of heparinase and telomerase activities in an in vitro enzyme assay and antimetastatic activity in a cell-based assay. In this study, we elucidated the mechanism by which CRM646-A rapidly induced nucleus condensation, plasma membrane disruption and morphological changes by increasing intracellular Ca2+ levels. Furthermore, PD98059, a mitogen-activated protein kinase (MEK) inhibitor, inhibited CRM646-A-induced nucleus condensation through ERK1/2 activation in rat 3Y1 fibroblast cells. We identified CRM646-A as a Ca2+ ionophore-like agent with a distinctly different chemical structure from that of previously reported Ca2+ ionophores. These results indicate that CRM646-A has the potential to be used as a new and effective antimetastatic drug.

The Control of Heparanase Through the Use of Small Molecules

Despite the enormous progress made in recent years with antibodies, vaccines, antisense oligonucleotides, etc., the so-called "biological" approaches for tackling the control of various diseases, medicinal chemistry remains a bulwark to refer to for the development of new drugs. Also in the case of heparanase, medicinal chemistry has always been in the forefront to identify new inhibitors, through modification of natural macromolecules, e.g., sulfated polysaccharides like heparin, or of natural compounds isolated from bacteria or plants, or through rational design. In this chapter, the reader will find a detailed description of the most relevant small-molecule heparanase inhibitors reported so far in the scientific literature and in patent applications, with mention to the design strategy and to structure-activity relationships. Starting from heparanase inhibitors of natural origin and the attempts to improve their potency and selectivity, the reader will be guided through the major chemical classes of synthetic inhibitors, with representation of the structure of the most relevant compounds. The last paragraph is dedicated to a brief description of inhibitors that have reached clinical trials, highlighting their structure, mechanism, and improved derivatives.

Synthesis of some novel orsellinates and lecanoric acid related depsides as α-glucosidase inhibitors

Sixteen novel orsellinic esters (6a-l, 7a-d) along with four lecanoric acid related depsides (3a-c, 4) were synthesized and confirmed their structures by spectroscopic data (¹H, ¹³C & HRMS). The synthesized compounds were evaluated for their in vitro α-glucosidase (Saccharomyces cerevisiae) inhibitory potential. Among the tested compounds, 3c (IC₅₀: 140.9 μM) and 6c (IC₅₀: 203.9 μM) displayed potent α-glucosidase inhibitory activity and found more active than the standard drug acarbose (IC₅₀: 686.6 μM). Both the test compounds were subjected to in vivo antihyperglycemic activity using sucrose loaded model in Wistar rats and found compound 3c exhibited significant reduction in glucose levels.

Glucuronidated Flavonoids in Neurological Protection: Structural Analysis and Approaches for Chemical and Biological Synthesis

Both plant and mammalian cells express glucuronosyltransferases that catalyze glucuronidation of polyphenols such as flavonoids and other small molecules. Oral administration of select polyphenolic compounds leads to the accumulation of the corresponding glucuronidated metabolites at μM and sub-μM concentrations in the brain, associated with amelioration of a range of neurological symptoms. Determining the mechanisms whereby botanical extracts impact cognitive wellbeing and psychological resiliency will require investigation of the modes of action of the brain-targeted metabolites. Unfortunately, many of these compounds are not commercially available. This article describes the latest approaches for the analysis and synthesis of glucuronidated flavonoids. Synthetic schemes include both standard organic synthesis, semisynthesis, enzymatic synthesis and use of synthetic biology utilizing heterologous enzymes in microbial platform organisms.

First total synthesis of kipukasin A

In this paper, a practical approach for the total synthesis of kipukasin A is presented with 22% overall yield by using tetra-O-acetyl-β-D-ribose as starting material. An improved iodine-promoted acetonide-forming reaction was developed to access 1,2-O-isopropylidene-α-D-ribofuranose. For the first time, ortho-alkynylbenzoate was used as protecting group for the 5-hydoxy group. After subsequent Vorbrüggen glycosylation, the protecting group could be removed smoothly in the presence of 5 mol % Ph₃PAuOTf in dichloromethane to provide kipukasin A in high yield and regioselectivity.

Recent advances in the discovery of heparanase inhibitors as anti-cancer agents

Heparanase, an only endo-β-d-glucuronidase capable of cleaving heparan sulfate (HS) side chains at specific sites, contributes to remodeling of the extracellular matrix (ECM) and releasing of HS-linked growth factors, cytokines and signaling proteins. In addition, heparanase also plays an indispensable role in tumor angiogenesis, invasion and metastasis, indicating that it is a promising target for the development of antitumor drugs. Recent progress leads to three classes of heparanase inhibitors, including active analogs of endogenous substance, synthetic small molecule compounds and natural products. In this review, following an outline on the heparanase structure and function, an overview of the advancement of heparanase inhibitors as novel and potent anti-cancer agents will be given, especially introducing various existing heparanase inhibitors, as well as their inhibitory activities and mechanisms of action.

Ethynylbenzenoid metabolites of Antrodia camphorata: synthesis and inhibition of TNF expression

An improved synthesis of the anti-inflammatory natural product antrocamphin A (2), involving a key Castro-Stephens reaction, is presented, along with the first total synthesis of its congener antrocamphin B (3). Approaches towards the more complex co-metabolite antrodioxolanone (4) were unsuccessful, but a samarium diiodide-mediated pinacol coupling of antrocamphin B did provide the chiral epimers (51). Antrocamphin A (2) inhibits Tumour Necrosis Factor (TNF) reporter gene expression, but its development as an anti-inflammatory agent may be limited by cytotoxicity.

Synthesis and antibacterial evaluation of anziaic acid and analogues as topoisomerase I inhibitors

Naturally occurring anziaic acid was very recently reported as a topoisomerase I inhibitor with antibacterial activity. Herein total synthesis of anziaic acid and structural analogues is described and the preliminary structure-activity relationship (SAR) has been developed based on topoisomerase inhibition and whole cell antibacterial activity.

Assembly of naturally occurring glycosides, evolved tactics, and glycosylation methods

Glycosylation of proteins and lipids is critical to many life processes. Secondary metabolites (or natural products), such as flavonoids, steroids, triterpenes, and antibiotics, are also frequently modified with saccharides. The resulting glycosides include diverse structures and functions, and some of them have pharmacological significance. The saccharide portions of the glycosides often have specific structural characteristics that depend on the aglycones. These molecules also form heterogeneous "glycoform" mixtures where molecules have similar glycosidic linkages but the saccharides vary in the length and type of monosaccharide unit. Thus, it is difficult to purify homogeneous glycosides in appreciable amounts from natural sources. Chemical synthesis provides a feasible access to the homogeneous glycosides and their congeners. Synthesis of a glycoside involves the synthesis of the aglycone, the saccharide, the connection of these two parts, and the overall manipulation of protecting groups. However, most synthetic efforts to date have focused on the aglycones, treating the attachment of saccharides onto the aglycones as a dispensable topic. The synthesis of the aglycone and the synthesis of the saccharide belong to two independent categories of chemistry, and different types of the aglycones and saccharides pose as specific synthetic subjects in their own disciplines. The only reaction that integrates the broad chemistry of glycoside synthesis is the glycosidic bond formation between the saccharide and the aglycone. Focusing on this glycosylation reaction in this Account, we string together our experience with the synthesis of the naturally occurring glycosides. We briefly describe the synthesis of 18 glycosides, including glycolipids, phenolic glycosides, steroid glycosides, and triterpene glycosides. Each molecule represents a prototypical structure of a family of the natural glycosides with interesting biological activities, and we emphasize the general tactics for the synthesis of these diverse structures. We provide a rationale for four tactics for the synthesis of glycosides, based on the stage at which the glycosidic bond is formed between the saccharide and the aglycone. This choice of tactic determines the success or failure of a synthesis, and the flexibility and the overall efficiency of the synthesis as well. Toward the synthesis of heterogeneous glycoform mixtures, we discuss successive and random glycosylation reactions. Finally, we have developed two new glycosylation protocols that address the challenges in the glycosylation of aglycones that are poorly nucleophilic, extremely acid labile, or extremely electrophilic. One of these new protocols takes advantage of glycosyl trifluoroacetimidate donors, and a second protocol uses gold(I)-catalyzed glycosylation with glycosyl ortho-alkynylbenzoate donors.

Fast and reproducible chemical synthesis of zearalenone-14-β,D-glucuronide

The Fusarium mycotoxin zearalenone (ZEA) is mainly converted to the conjugate zearalenone-14-β,D-glucuronide (ZEA-14-GlcA) during phase II detoxification in humans and animals. This metabolite - previously described as zearalenone-4-O-β,D-glucuronide - is excreted via urine and could therefore serve as possible biomarker for ZEA exposure to estimate its intake. Direct determination of this substance is limited by the availability of a reference substance. So far, only the production of small amounts by enzymatic synthesis has been described. In this work, a fast and reproducible protocol for the chemical synthesis of ZEA-14-GlcA was developed, using substituted β-resorcylic acid esters as mycotoxin mimics and different glucuronyl donors for optimising the glycosylation (Königs-Knorr, trifluoroacetimidate method) and the deprotection step. This cost-effective procedure should be easily reproducible in other labs using standard equipment and common reagents.

Synthesis of Glycosides of Glucuronic, Galacturonic and Mannuronic Acids: An Overview

Uronic acids are carbohydrates present in relevant biologically active compounds. Most of the latter are glycosides or oligosaccharides linked by their anomeric carbon, so their synthesis requires glycoside-bond formation. The activation of this anomeric center remains difficult due to the presence of the electron-withdrawing C-5 carboxylic group. Herein we present an overview of glucuronidation, mannuronidation and galacturonidation reactions, including syntheses of prodrugs, oligosaccharides and stereochemical aspects.

Regio- and stereospecific synthesis of mono-beta-d-glucuronic acid derivatives of combretastatin A-1

Synthetic routes have been established for the preparation of regio- and stereoisomerically pure samples of the mono-beta-d-glucuronic acid derivatives of combretastatin A-1, referred to as CA1G1 (5a) and CA1G2 (6a). Judicious choice of protecting groups for the catechol ring was required for the regiospecific introduction of the glucuronic acid moiety. The tosyl group proved advantageous in this regard. The two monoglucuronic acid analogues demonstrate low cytotoxicity (compared to CA1, 2) against selected human cancer cell lines, with CA1G1 being slightly more potent than CA1G2.

Efficient synthesis of flavanone glucuronides

The first efficient synthesis of flavanone glucuronides as potential human metabolites is described. The synthetic strategy is based on acetyl protection, followed by a combination of chemical and enzymatic deprotection steps. As an example, the method is applied to a synthesis of 7,4'-di-O-methyleriodictyol 3'-O-beta-d-glucuronide. The aglycone is a flavanone naturally present in tarragon spice ( Artemisia dracunculus ) as well as in various Chinese, Brazilian, and Malaysian medicinal plants.

Synthesis and cytotoxicity of bidesmosidic betulin and betulinic acid saponins

The naturally occurring cytotoxic saponin 28-O-beta-d-glucopyranosylbetulinic acid 3beta-O-alpha-l-arabinopyranoside (3) was easily synthesized along with seven bidesmosidic saponins starting from the lupane-type triterpenoids betulin (1) and betulinic acid (2). As highlighted by the preliminary cytotoxicity evaluation against A549, DLD-1, MCF7, and PC-3 human cancer cell lines, the bidesmosidic betulin saponin 22a, bearing alpha-l-rhamnopyranoside moieties at both C-3 and C-28 positions, was determined to be a potent cytotoxic agent (IC(50) 1.8-1.9 microM).

Heparanase: a target for drug discovery in cancer and inflammation

The remodelling of the extracellular matrix (ECM) has been shown to be highly upregulated in cancer and inflammation and is critically linked to the processes of invasion and metastasis. One of the key enzymes involved in specifically degrading the heparan sulphate (HS) component of the ECM is the endo-beta-glucuronidase enzyme heparanase. Processing of HS by heparanase releases both a host of bioactive growth factors anchored within the mesh of the ECM as well as defined fragments of HS capable of promoting cellular proliferation. The finding that heparanase is elevated in a wide variety of tumor types and is subsequently linked to the development of pathological processes has led to an explosion of therapeutic strategies to inhibit its enzyme activity. So far only one compound, the sulphated oligosaccharide PI88, which both inhibits heparanase activity and has effects on growth factor binding has reached clinical trials where it has shown to have promising efficacy. The scene has clearly been set however for a new generation of compounds, either specific to the enzyme or with dual roles, to emerge from the lab and enter the clinic. The aim of this review is to describe the current drug discovery status of small molecule, sugar and neutralising antibody inhibitors of heparanase enzyme activity. Potential strategies will also be discussed on the selection of suitable biomarker strategies for specific monitoring of in vivo heparanase inhibition which will be crucial for both animal model and clinical trial testing.

Recent progress on the total synthesis of natural products in China

An overview of natural products synthesis in Mainland China during the past 10 years is provided. This review only emphasizes the first total synthesis of molecules of contemporary interest and syntheses that helped to correct structures. In addition, some significant results on the novel synthesis and structure-activity relationship (SAR) studies of several natural products are introduced.