CRM646-A and -B, novel fungal metabolites that inhibit heparinase

Discovery of a novel tetrahydroimidazo[1,2-a]pyridine-5-carboxylic acid derivative as a potent and selective heparanase-1 inhibitor utilizing an improved synthetic approach

Heparanase-1 (HPSE1) is an endo-β-d-glucuronidase that catalyzes degradation of heparan sulfate proteoglycans. Inhibition of HPSE1 appears to be a useful therapeutic target against cancer and proteinuric kidney diseases. We previously reported tetrahydroimidazo[1,2-a]pyridine 2 as a potent HPSE1 inhibitor after optimization of the synthetic reaction. However, synthesis of 2 involves a total of 19 steps, including a cyclization process that accompanies a strong odor due to the use of Lawesson's reagent and an epimerization reaction; furthermore, 2 exhibited insufficient selectivity for HPSE1 over exo-β-d-glucuronidase (GUSβ) and glucocerebrosidase (GBA), which also needed to be addressed. First, the cyclization reaction was optimized to synthesize tetrahydroimidazo[1,2-a]pyridine without using Lawesson's reagent or epimerization, with reference to previous reports. Next, 16 and 17 containing a bulkier substituent at position 6 than the 6-methoxyl group in 2 were designed and synthesized using the improved cyclization conditions, so that the synthetic route of 16 and 17 was shortened by five steps as compared with that of 2. The inhibitory activities of 16 and 17 against GUSβ and GBA were reduced as compared with those of 2, that is, the compounds showed improved selectivity for HPSE1 over GUSβ and GBA. In addition, 16 showed enhanced inhibitory activity against HPSE1 as compared with that of 2. Compound 16 appears promising as an HPSE1 inhibitor with therapeutic potential due to its highly potent inhibitory activity against HPSE1 with high selectivity for HPSE1.

Structure-based lead optimization to improve potency and selectivity of a novel tetrahydroimidazo[1,2-a]pyridine-5-carboxylic acid series of heparanase-1 inhibitor

Heparanase-1 (HPSE1) is an endo-β-d-glucuronidase that is the only mammalian enzyme known to cleave heparan sulfate (HS) of heparan sulfate proteoglycans (HSPG), a key component of the glycocalyx layer of the vascular endothelium matrix. Inhibition of HPSE1 has therapeutic potential for cancer and proteinuric kidney diseases. We previously reported that 2 showed a moderate potency as an HPSE1 inhibitor and an issue of selectivity against exo-β-d-glucuronidase (GUSβ) and glucocerebrosidase (GBA) remained. A structure-based lead optimization of 2 using X-ray co-crystal structure analysis and fragment molecular orbital calculation resulted in 4e, which showed a more than 7-fold increase in HPSE1 inhibitory activity. The subsequent introduction of a methyl group into the 6-hydroxy group of 4e resulted in 18 with reduced inhibitory activities against GUSβ and GBA while maintaining the inhibitory activity against HPSE1. The inhibitory activities of 18 against serum HPSE1 in mice were significant and lasted for 4 h at doses of 3, 30, and 100 mg/kg. Compound 18 could be a novel lead compound for HPSE1 inhibitors with improved inhibitory activity against HPSE1 and increased HPSE1 selectivity over GUSβ and GBA.

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.

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.

Arenicolins: C-Glycosylated Depsides from Penicillium arenicola

During investigation of the secondary metabolism of four strains of Penicillium arenicola, two new depsides, arenicolins A (1) and B (2), were isolated and characterized. Their structures were established mainly by analysis of NMR and HRMS data and by comparison with known compounds. These depsides incorporate intriguing structural features, including dual alkyl side chains and a C-glycosyl unit, with 1 also containing an acylated 2-hydroxymethyl-4,5,6-trihydroxycyclohexenone moiety. Although the arenicolins were produced by all strains tested, arenicolin A (1) was obtained using only one of five medium compositions employed, while arenicolin B (2) was produced in all media tested. Neither compound showed antibacterial or antifungal activity, but 1 exhibited cytotoxicity toward mammalian cell lines, including colorectal carcinoma (HCT-116), neuroblastoma (IMR-32), and ductal carcinoma (BT-474), with IC50 values of 7.3, 6.0, and 9.7 μM, respectively.

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.

Dual Role of a Fluorescent Peptidyl Probe Based on Self-Assembly for the Detection of Heparin and for the Inhibition of the Heparin-Digestive Enzyme Reaction

The detection of fluorescent probes for biomolecules and control of the function of a complex through a recognition process have not been investigated intensively. A fluorescent peptidyl probe (1) based on the self-assembly stimulated by heparin was synthesized. The fluorescent probe with an aggregation-induced emission fluorophore formed a self-assembling complex with heparin, resulting in a sensitive and selective turn-on response to heparin compared to its biological competitors. The detection limits for heparin were measured to be 138.0 pM (R² = 0.976) in aqueous solution and 2.6 nM (R² = 0.996) in aqueous solution containing human serum. Nanosized aggregates formed through the self-assembly of the complex showed potent resistance against the heparin-digestive enzyme. The dual role of the probe for the detection of heparin and the inhibition of heparinase-mediated digestion through the recognition process was used for the real-time monitoring of the enzyme activity of heparinase for the digestion of heparin. Furthermore, the dual role of the probe was applied for the detection of the oversulfated chondroitin sulfate contaminant in heparin.

Amphiphilic glycoconjugates as potential anti-cancer chemotherapeutics

Amphiphilicity is one of the desirable features in the process of drug development which improves the biological as well as the pharmacokinetics profile of bioactive molecule. Carbohydrate moieties present in anti-cancer natural products and synthetic molecules influence the amphiphilicity and hence their bioactivity. This review focuses on natural and synthetic amphiphilic anti-cancer glycoconjugates. Different classes of molecules with varying degree of amphiphilicity are covered with discussions on their structure-activity relationship and mechanism of action.

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.

Testing of potential glycan-based heparanase inhibitors in a fluorescence activity assay using either bacterial heparinase II or human heparanase

Heparanase, an endo-β-glucuronidase cleaving heparan sulfate (HS) chains at cell surfaces and in the extracellular matrix (ECM), is involved in angiogenesis, tumor progression and metastasis as well as in inflammation and kidney dysfunction. Therefore, heparanase is considered a promising therapeutic target and diagnostic marker. Recently, we have developed a simple, rapid, fully automatable fluorimetric activity assay using the synthetic sulfated pentasaccharide fondaparinux as substrate and bacterial heparinase II (HEP-II) instead of human heparanase (hHEP). The aim of this study was to evaluate this assay for inhibitor testing as well as to check whether the assay principle is applicable to measure the activity and inhibition, respectively, of the actual target enzyme hHEP. Besides the known hHEP inhibitor suramin and the antiinflammatory and antimetastatic PS3, two series of β-1,3-glucan sulfates differing in their chain length and degree of sulfation, further semisynthetic sulfated glycans, and two sulfated polysaccharides isolated from algae were included to examine structure-activity relationships. The inhibitory activity of sulfated glycans showed to be greatly dependent on both their degree of sulfation and their basic glycan structure, but independent of their molecular size. The β-1,3-glucan sulfates were superior to suramin as well as to the other glycans with similar degree of sulfations. The most active inhibitor was found to be the β-1,3-glucan sulfate PS3 (IC₅₀=0.017 μM). By using hHEP instead of HEP-II comparable results were obtained. With an IC₅₀ being about 160 times lower than that of suramin, PS3 exhibited again the strongest inhibitory effects. Inhibition of hHEP may therefore contribute to the potent antiinflammatory and antimetastatic activities of PS3 in vivo. In conclusion, the fluorimetric hHEP activity assay proved to be a simple, fully automatable tool for testing potential inhibitors. In case of HS mimetic inhibitors, the assay variant with HEP-II may provide a fast and inexpensive option for initial screening purposes.

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.

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.

Inhibition of telomerase activity by fungus metabolites, CRM646-A and thielavin B

We performed a screening program to identify telomerase inhibitors from our drug source obtained from fungus fermentations, and found that two compounds, CRM646-A and thielavin B, inhibited telomerase activity at doses of 3.2 and 32 microM, respectively. These compounds also inhibited the activity of viral reverse transcriptase at almost the same dose levels which inhibited telomerase activity.