Biocatalytic modification of natural products

Late-stage diversification of bacterial natural products through biocatalysis

Bacterial natural products (BNPs) are very important sources of leads for drug development and chemical novelty. The possibility to perform late-stage diversification of BNPs using biocatalysis is an attractive alternative route other than total chemical synthesis or metal complexation reactions. Although biocatalysis is gaining popularity as a green chemistry methodology, a vast majority of orphan sequenced genomic data related to metabolic pathways for BNP biosynthesis and its tailoring enzymes are underexplored. In this review, we report a systematic overview of biotransformations of 21 molecules, which include derivatization by halogenation, esterification, reduction, oxidation, alkylation and nitration reactions, as well as degradation products as their sub-derivatives. These BNPs were grouped based on their biological activities into antibacterial (5), antifungal (5), anticancer (5), immunosuppressive (2) and quorum sensing modulating (4) compounds. This study summarized 73 derivatives and 16 degradation sub-derivatives originating from 12 BNPs. The highest number of biocatalytic reactions was observed for drugs that are already in clinical use: 28 reactions for the antibacterial drug vancomycin, followed by 18 reactions reported for the immunosuppressive drug rapamycin. The most common biocatalysts include oxidoreductases, transferases, lipases, isomerases and haloperoxidases. This review highlights biocatalytic routes for the late-stage diversification reactions of BNPs, which potentially help to recognize the structural optimizations of bioactive scaffolds for the generation of new biomolecules, eventually leading to drug development.

CRISPR-Cas9 driven structural elucidation of the heteroexopolysaccharides from Paenibacillus polymyxa DSM 365

Paenibacillus polymyxa is a Gram-positive soil bacterium known for producing a wide range of exopolysaccharides. However, due to the biopolymer's complexity, structural elucidation has so far been inconclusive. Combinatorial knock-outs of glycosyltransferases were generated in order to separate distinct polysaccharides produced by P. polymyxa. Using a complementary analytical approach consisting of carbohydrate fingerprints, sequence analysis, methylation analysis as well as NMR spectroscopy, the structure of the repeating units of two additional heteroexopolysaccharides termed paenan I and paenan III were elucidated. Results for paenan I identified a trisaccharide backbone consisting of 1➔4-β-d-Glc, 1➔4-β-d-Man and a 1,3,4-branching β-d-Gal residue with a sidechain comprising of a terminal β-d-Gal^3,4-Pyr and 1➔3-β-d-Glc. For paenan III, results indicated a backbone consisting of 1➔3-β-d-Glc, 1,3,4-linked α-d-Man and 1,3,4-linked α-d-GlcA. NMR analysis indicated monomeric β-d-Glc and α-d-Man sidechains for the branching Man and GlcA residues respectively.

Production of Taxifolin from Astilbin by Fungal Biotransformation

Taxifolin is known to have multiple biological functions. It has been widely used as a multifunctional food additive, and consequently, the global demand for taxifolin is increasing. The main method for taxifolin production is an extraction from larch wood, but the global resources of larch are limited. Astilbin, taxifolin-3-o-rhamnoside, is abundant in many plants and much more readily available, meaning taxifolin can be obtained by deglycosylation of astilbin. In this study, a fungal strain, Aspergillus fumigatus SQH4, was isolated from an enrichment culture of Smilax glabra rhizome to achieve the deglycosylation reaction. A culture of SQH4, adjusted to pH 6.5, with 5 g/L astilbin achieved a yield of taxifolin of 91.3% after biotransformation for 14 h at 35 °C. These findings offer an alternative method for the production of taxifolin.

Microbial Glycosylation of Phenanthrene and Bibenzyls by Mucor hiemalis

Microbial transformation of denthyrsinin (1), gigantol (2), and batatasin III (3), the major constituents of Dendrobium species (Orchidaceae), was performed using the filamentous fungus Mucor hiemalis KCTC 26779. Three glycosylated metabolites were obtained in the biotransformation of 1-3, and their structures were identified as denthyrsinin-6- O-β-d-glucoside (4), gigantol-5- O-β-d-glucoside (5), and batatasin III-3- O-β-d-glucoside (6) by analyzing 1-dimensional and 2-dimensional-nuclear magnetic resonance spectra, as well as high-resolution electrospray ionization mass spectral data. Among them, metabolite 4 has not been previously reported. Mucor hiemalis was revealed to catalyze enzymatically glucosylation of the hydroxyl group of phenanthrenes and bibenzyls. This research provides an efficient approach for the glycosylation of phenanthrenes and bibenzyls and can expand the library of available phenanthrene and bibenzyl derivatives for further biological evaluations.

Production of biologically active oxidized derivatives of finasteride through metabolism by Aspergillus niger culture

CONTEXT

Among the 4-azasteroids, finasteride is biologically the most important compound having preventive effect against male pattern baldness (MPH) and benign prostatic hyperplasia commonly called enlargement of prostate gland.

OBJECTIVE

The microbial transformation of finasteride by fungus Aspergillus niger (ATCC 10549) has been investigated to obtain biologically more potent derivatives.

MATERIALS AND METHODS

Fermentation of finasteride was performed with filamentous fungus Aspergillus niger (ATCC 10549). This transformation resulted in the production of two transformed products, which were purified through column chromatography. In vitro lipoxygenase inhibitory potential was determined by incubating 20 mL of the enzyme with 10 mL of test sample (100 μM) in 0.1 mM (pH 7.0) phosphate buffer for 5 min at 258 °C followed by addition of 10 μL of substrate (linolenic acid) to reaction mixture and measuring the formation of complex spectrophotometrically.

RESULTS

Structure elucidation of biotransformed metabolites was ascertained through extensive 1D and 2D spectroscopic techniques. This study established the fact that A. niger promoted stereospecific dihydroxylation at C-11 and C-15 of finasteride. The resulting biotransformed metabolites were characterized as 11α-hydroxyfinasteride and 15β-hydroxyfinasteride, respectively. Finasteride along with transformed metabolites were analyzed for their in vitro lipoxygenase (LOX) inhibition assay. Among the tested compounds 15β-hydroxyfinasteride showed good activity with IC₅₀ value 112.56 ± 2.23 μM while inhibitory effect in case of 11α-hydroxyfinasteride was low with IC₅₀ value 186.05 ± 1.34 μM. Standard compound baicalein revealed IC₅₀ value being 22.0 ± 0.05 μM.

CONCLUSION

The present investigation highlighted the fact that potentially active compound can be produced through the technology of biotransformation.

Microbial Transformation of 14-Anhydrodigoxigenin by Alternaria alternata

The microbial transformation of 14-anhydrodigoxigenin (1) by Alternaria alternata CGMCC 3.577 led to the production of seven new metabolites, 2-8. Their structures were determined by extensive spectroscopic (CD, IR, 1D- and 2D-NMR, and HR-ESI-MS) data analyses. The reactions in the bioprocess exhibited diversity, including specific oxidation, hydroxylation, reduction, epoxidation, and dehydration. In addition, a hypothetical biocatalytic pathway is proposed.

Biotransformation, a promising technology for anti-cancer drug development

With the high morbidity and mortality caused by cancer, finding new and more effective anti-cancer drugs is very urgent. In current research, biotransformation plays a vital role in the research and development of cancer drugs and has obtained some achievements. In this review, we have summarized four applications as follows: to exploit novel anti-cancer drugs, to improve existing anti-cancer drugs, to broaden limited anti-cancer drug resources and to investigate correlative mechanisms. Three different groups of important anti-cancer compounds were assessed to clarify the current practical applications of biotransformation in the development of anti-cancer drugs.

Influence of organic solvents on catalytic behaviors and cell morphology of whole-cell biocatalysts for synthesis of 5'-arabinocytosine laurate

A whole-cell based method was developed for the regioselective synthesis of arabinocytosine laurate. Among the seven kinds of bacteria strains tested in the acylation reaction, Pseudomonas fluorescens gave the highest productivity and a higher 5′-regioselectivity than 99%. Compared with pure organic solvents, the use of organic solvent mixtures greatly promoted the yield of the whole-cell catalyzed reaction, but showed little influence on the 5′-regioselectivity. Of all the tested solvent mixtures, the best reaction result was found in isopropyl ether/pyridine followed by isopentanol/pyridine. However, the whole-cells showed much lower thermostability in isopropyl ether/pyridine than in THF-pyridine. To better understand the toxic effects of the organic solvents on P. fluorescens whole-cells and growing cells were further examined. Significant influences of organic solvents on the biomass of the cells were found, which differed depending on the type of solvents used. SEM analysis visually revealed the changes in the surface morphology of whole-cells and growing cells cultured in media containing various organic solvents, in terms of surface smoothness, bulges and changed cell sizes. Results demonstrated that organic toxicity to cell structure played an important role in whole-cell mediated catalysis.

Biotransformation of resibufogenin by Actinomucor elegans

Resibufogenin (RB), a major bioactive bufadienolide, has the potential anticancer activity. In the present work, biotransformation of RB by Actinomucor elegans AS 3.2778 yielded five products, namely 3-oxo-resibufogenin (1), 3-epi-resibufogenin (2), 3-epi-12-oxo-hydroxylresibufogenin (3), 3α-acetoxy-15α-hydroxylbufalin (4), and 3-epi-12α-hydroxylresibufogenin (5), respectively. Among them, metabolites 3 and 4 are previously unreported. The chemical structures of metabolites 1-5 were fully elucidated on the basis of 2D NMR and HR-MS. The highly stereo- and regio-specific isomerization, hydroxylation, and esterification reactions were observed in the biotransformation process of RB by A. elegans. Their cytotoxicities against A549 and H1299 cells were evaluated.

Asymmetric catalysis at a distance: catalytic, site-selective phosphorylation of teicoplanin

We report three distinct, peptide-based catalysts that enable site-selective phosphorylation of three distinct hydroxyl groups within the complex glycopeptide antibiotic teicoplanin A2-2. Two of the catalysts are based on a design that capitalizes on a catalyst-substrate interaction that mimics the biological mechanism of action for teicoplanin. These catalysts are based on a DXaa-DXaa peptide motif that is known to target the teicoplanin structure in a specific manner. The third was identified through evaluation of a set of catalysts that had been developed for historically distinct projects. Each catalyst contains additional functionality designed to dispose a catalytic moiety (a nucleophilic alkylimidazole) at a different region of the glycopeptide structure. A combination of mass spectrometry and 2D-NMR spectroscopy allowed structural assignment of the distinct phosphorylated teicoplanin derivatives. Mechanistic studies are also reported that support the hypotheses that led to the discovery of the catalysts. In this manner, small molecule catalysts have been achieved that allow rational, catalytic control over reactions at sites that are separated by 11.6, 16.5, and nearly 17.7 Å, based on the X-ray crystal structure of teicoplanin A2-2. Finally, we report the biological activity of the new phosphorylated teicoplanin analogs and compare the results to the natural product itself.

Microbiological transformation of the triterpene nigranoic acid by the freshwater fungus Dictyosporium heptasporum

The microbiological transformation of the triterpene nigranoic acid (3,4-secocycloarta-4(28),24(Z)-diene-3,26-dioic acid) (1) to 3,4-secocycloarta-4(28),17(20),24(Z)-triene-7β-hydroxy-16β,26-lactone-3-oic acid (2) and 3,4-secocycloarta-4(28),17(20)(Z),24(Z)-triene-7β-hydroxy-16β-methoxy-3,26-dioic acid (3) by the freshwater fungus Dictyosporium heptasporum YMF1.01213 has been demonstrated. The structures of the biotransformation products were determined by spectroscopic and MS analyses. Compound 2, characterized by the presence of a formed C-16/C-26 ester bridge, provided a novel nine-membered lactone ring structural skeleton for 3,4-secocycloartane triterpenoid derivatives. In addition, Compounds 1-3 exhibited weak anti-HIV activity in vitro. Compounds 2 and 3 were reported for the first time as natural product derivatives.

Microbial Transformation of Curcumol by Aspergillus niger

Curcumol is a representative index component for the quality control of the essential oil of Curcuma wenyujin Y.H. Chen et C. Ling, an antivirus and anticancer drug in China. Microbial transformation of curcumol (1) by Aspergillus niger AS 3.739 yielded two products. Their structures were elucidated as 3α-hydroxycurcumol (2) and 3α-(4′-methoxy-succinyloxy)-curcumol (3) by extensive spectroscopic methods including 2D-NMR and HRESI-MS. Among them, 3 is a new compound. Esterification of the substrate with succinic acid is a novel reaction in the field of microbial transformation of natural products. Compound 2, the major transformation product of 1, was a high regio- and stereo-specific hydroxylation product and showed significant antiviral effects.

Microbial transformation of ursolic acid by Syncephalastrum racemosum (Cohn) Schroter AS 3.264

Biotransformation of ursolic acid by the filamentous fungus Syncephalastrum racemosum (Cohn) Schroter AS 3.264 yielded five metabolites. Their structures were identified as 3β,21β-dihydroxy-urs-11-en-28-oic acid-13-lactone, 3β,7β,21β-trihydroxy-urs-11-en-28-oic acid-13-lactone, 1β,3β-dihydroxy-urs-12-en-21-one-28-oic acid, 1β,3β,21β-trihydroxy-urs-12-en-28-oic acid and 11,26-epoxy-3β,21β-dihydroxy-urs-12-en-28-oic acid based on NMR and MS spectroscopic analyses. The condensation reactions to form 28-oic acid-13-lactone ring and 11,26-epoxy ring are not frequently seen for the biotransformation of triterpenoids. One compound showed moderate inhibitory activity against protein tyrosine phosphatase 1B (PTP1B).

Valuable chemicals by the enzymatic modification of molecules of natural origin: terpenoids, steroids, phenolics and related compounds

A renewed interest for using natural organic molecules for the production of valuable chemicals is observed in current organic processes. Natural compounds provide the access to natural grade chemicals when submitted to physical treatments or biotechnological processes. Dealing with structurally complex molecules, they can provide complex core structures for hemisynthesis purposes, and in many instances they offer the advantage of providing sustainable processes when using renewable resources. These assets could be synergistic with the assets of biocatalytic processes, to end-up with efficient and sustainable processes in the organic synthesis of valuable products. In this review, we have gathered a selection of examples on the use of enzymes for the modification of molecules of natural origin being either purified compounds (terpenoids, steroids, phenolics) or mixtures (essential oils, natural extracts) to access fine chemicals or organic polymers.

Biotransformation of sophoricoside in Fructus sophorae by the fungus Schizophyllum commune

Biotransformation of sophoricoside in Fructus sophorae was performed with Schizophyllum commune. Sophoricoside was firstly metabolized to 4',5,7-trihydroxyisoflavone (2), and then to 4',7-dihydroxy-5-methoxyisoflavone (3) and 5,7-dihydroxy-4'-methoxyisoflavone (4) as determined by NMR and MS analyzes. The content of compound (2) was increased by more than 30-fold, and compound (3) is a new product that showed good cytotoxic activity with an IC(50) of 12.1 nmol/ml against MCF-7 cells.

Novel microbial transformation of resibufogenin by Fusarium solani

In this paper, microbial transformation of resibufogenin by Fusarium solani AS 3.1829 was investigated, and five transformed products were isolated and identified as 3-ketone-resibufogenin (2), 3-one-cyclic 3-(1,2-dimethyl-1,2-ethanediylacetal)-resibufogenin (3), 3-dimethoxyl-resibufogenin (4), 3-epi-resibufogenin (5), and 3-epi-15α-hydroxy-7βH-bufalin (6), respectively. Among them, 3, 4, and 6 are new compounds, and the rare double oxidization of C-3 was reported. In addition, the cytotoxicities of transformed products were also investigated.

Transformation of isosteviol lactam by fungi and the suppressive effects of its transformed products on LPS-induced iNOS expression in macrophages

From the screening of 21 microbial strains, Absidia pseudocylindrospora ATCC 24169 and Aspergillus niger BCRC 32720 were found to reproducibly transform isosteviol lactam (4α-carboxy-13α-amino-13,16-seco-ent-19-norbeyeran-16-oic acid 13,16-lactam) (3) into various compounds. Preparative-scale transformation of 3 with Abs. pseudocylindrospora yielded two new hydroxylated compounds (4 and 5), with conservation of the lactam ring. Preparative-scale transformation of 3 with Asp. niger afforded seven new compounds, 6 and 9-14, together with the known compounds 7 and 8. A single-crystal X-ray diffraction experiment confirmed the structure of 14. The suppressive effects of compounds 1-14 on the lipopolysaccharide-induced expression of the inducible nitric oxide synthase gene in RAW 264.7 macrophages were examined by a reverse-transcription real-time PCR analysis. With the exception of 7, all other compounds significantly reduced levels of iNOS mRNA relative to control cells, which were induced by LPS alone. Compounds 2, 3, and 5 were similar in activity to dexamethasone, while 9 was more potent.

Microbial Transformation of Deoxyandrographolide by Alternaria Alternata AS 3.4578

Biotransformation of deoxyandrographolide (1) by Alternaria alternata AS 3.4578 gave five derivatives identified by spectral methods including 2D NMR as the known dehydroandrographolide (2) and 9β-hydroxy-dehydroandrographolide (3) and the new compounds 9β-hydroxy-deoxyandrographolide (4), 3α,17,19-trihydroxy-8,13-ent-labdadien-15,16-olide (5) and 3-oxo-9β-hydroxy-deoxyandrographolide (6).

Microbial Transformation of Marine Halogenated Sesquiterpenes

The sesquiterpene pacifenol is one of the main constituents of the red alga Laurencia claviformis. Earlier work on the semisynthetic derivatives of pacifenol afforded a series of halogenated sesquiterpenes. The aim of the present work was to obtain new hydroxylated derivatives of halogenated sesquiterpenes by means of microbial transformation using Aspergillus níger, Gibberella fujikuroi and Mucor plumbeus. The best results were obtained with M. plumbeus. The microbiological transformation by M. plumbeus of pacifenol, and two semisynthetic derivatives, is described. The structures of the new compounds obtained were determined by spectroscopic means.

An approach to the site-selective diversification of apoptolidin A with peptide-based catalysts

We report the application of peptide-based catalysts to the site-selective modification of apoptolidin A (1), an agent that displays remarkable selectivity for inducing apoptosis in E1A-transformed cell lines. Key to the approach was the development of an assay suitable for the screening of dozens of catalysts in parallel reactions that could be conducted using only microgram quantities of the starting material. Employing this assay, catalysts (e.g., 11 and ent-11) were identified that afforded unique product distributions, distinct from the product mixtures produced when a simple catalyst (N,N-dimethyl-4-aminopyridine (10)) was employed. Preparative reactions were then carried out with the preferred catalysts so that unique, homogeneous apoptolidin analogues could be isolated and characterized. From these studies, three new apoptolidin analogues were obtained (12-14), each differing from the other in either the location of acyl group substituents or the number of acetate groups appended to the natural product scaffold. Biological evaluation of the new apoptolidin analogues was then conducted using growth inhibition assays based on the H292 human lung carcinoma cell line. The new analogues exhibited activities comparable to apoptolidin A.

A novel biotransformation process of 4'-demethylepipodophyllotoxin to 4'-demethylepipodophyllic acid by Bacillus fusiformis CICC 20463, Part II: process optimization

This work optimized the novel biotransformation process of 4'-demethylepipodophyllotoxin (DMEP) into 4'-demethylepipodophyllic acid (DMEPA) by Bacillus fusiformis CICC 20463. Firstly, the biotransformation process was significantly affected by medium composition. 5 g/L of yeast extract and 10 g/L of peptone were optimal for DMEPA production (i.e., 2.81 + or - 0.21 mg/L), while not beneficial for the cell growth of B. fusiformis. This indicated that the biosynthesis of DMEPA was not corresponded well to the cell growth of B. fusiformis. 40 g/L of sucrose was optimal for DMEPA production (i.e., 2.94 + or - 0.17 mg/L), and 3 g/L of NaCl was the best for DMEPA production (i.e., 4.10 + or - 0.18 mg/L). Secondly, the production of DMEPA was significantly enhanced by the control of substrate concentration and culture pH. 100 mg/L of substrate was optimal for DMEPA production (i.e., 6.47 + or - 0.35 mg/L), and DMEPA concentration was enhanced to 38.78 mg/L by controlling culture pH at 9.0 in the stirred-tank bioreactors. The fundamental information obtained in this study provides a simple and efficient way to produce DMEPA by biotransformation.

Improvement of steroid biotransformation with hydroxypropyl-beta-cyclodextrin induced complexation

The inclusion complexes induced by cyclodextrins and its derivates have been shown previously to enhance the biotransformation of hydrophobic compounds. Using hydroxypropyl-beta-cyclodextrin (HP-beta-CD; 20% w/v), the water solubility of cortisone acetate increased from 0.039 to 7.382 g L(-1) at 32 degrees C. The solubilization effect of HP-beta-CD was far superior to dimethylformamide (DMF) and ethanol. The dissolution rate also significantly increased in the presence of HP-beta-CD. The enzymatic stability of Delta(1)-dehydrogenase from Arthrobacter simplex TCCC 11037 was not influenced by the increasing concentrations of HP-beta-CD contrary to the organic cosolvents which negatively influenced in the order DMF > ethanol. The activity inhibition effect caused by HP-beta-CD was not so conspicuous as ethanol and DMF. Inactivation constants of ethanol, DMF, and HP-beta-CD were 5.832, 4.541, and 1.216, respectively. The inactivation energy (E (a)) was in the order of HP-beta-CD (55.1 kJ mol(-1)) > ethanol (39.9 kJ mol(-1)) > DMF (37.1 kJ mol(-1)).

Synthesis and SAR of vinca alkaloid analogues

Versatile intermediates 12'-iodovinblastine, 12'-iodovincristine and 11'-iodovinorelbine were utilized as substrates for transition metal based chemistry which led to the preparation of novel analogues of the vinca alkaloids. The synthesis of key iodo intermediates, their transformation into final products, and the SAR based upon HeLa and MCF-7 cell toxicity assays is presented. Selected analogues 27 and 36 show promising anticancer activity in the P388 murine leukemia model.

Assembly of a three-dimensional array of glycoconjugates by combinatorial biocatalysis in nonaqueous media

Glycoconjugates can be artificially synthesized by combinatorial biocatalysis. An example is given in this paper describing the construction of glycoconjugates array by using glycosidase and lipase in nonaqueous media. This array was started from glucose, with three aryl alcohols as the aglycone moiety of glycosides and five acids or esters as acyl donors for combinatorial acylation of glycosides, affording a three-dimensional array containing about 30 members with diverse structures. The array would be more abundant if more aglycones and acyl donors with other structures were filled in. Indeed, diverse classes of carbohydrates besides glucose can also be employed for generating diverse glycoconjugates due to their different roles in numerous physiological responses. The composition and distribution of the demonstration glycoconjugates array was detected and evaluated by HPLC-MS with electrospray ionization. And also, the distribution of the artificial array can be adjusted by changing the molar ratio of the auxiliary materials.

Microbial transformation of three bufadienolides by Nocardia sp. and some insight for the cytotoxic structure–activity relationship (SAR)

Resibufogenin, cinobufagin, and bufalin are cytotoxic steroids isolated from the Chinese drug Chan'su. Biotransformation of these three bufadienolides by Nocardia sp. NRRL 5646 was investigated. Notably, resibufogenin was converted to 3-acetyl 15beta-hydroxyl bufotalin, via an unprecedented 14beta,15beta-epoxy ring cleavage and a regio-selective acetoxylation. This product showed significantly increased cytotoxic activity. The regio-selective acetylation of the 3-OH was also involved in the other reactions. The structures of metabolites were established by ESI-LC/MS and 2D NMR techniques. The in vitro cytotoxic activities against human cancer cell lines of the substrates and the transformed products were determined by the MTT method and their structure-activity relationship (SAR) was discussed. This investigation provided a useful approach to prepare new bufadienolides and the SAR research.