Hydroxylation of Oleanolic Acid to Queretaroic Acid by Cytochrome P450 fromNonomuraea recticatena

Structural determination and characterisation of the CYP105Q4 cytochrome P450 enzyme from Mycobacterium marinum

The cytochrome P450 family of heme metalloenzymes (CYPs) catalyse important biological monooxygenation reactions. Mycobacterium marinum contains a gene encoding a CYP105Q4 enzyme of unknown function. Other members of the CYP105 CYP family have key roles in bacterial metabolism including the synthesis of secondary metabolites. We produced and purified the cytochrome P450 enzyme CYP105Q4 to enable its characterization. Several nitrogen-donor atom-containing ligands were found to bind to CYP105Q4 generating type II changes in the UV-vis absorbance spectrum. Based on the UV-vis absorbance spectra none of the potential substrate ligands we tested with CYP105Q4 were able to displace the sixth distal aqua ligand from the heme, though there was evidence for binding of oleic acid and amphotericin B. The crystal structure of CYP105Q4 in the substrate-free form was determined in an open conformation. A computational structural similarity search (Dali) was used to find the most closely related characterized relatives within the CYP105 family. The structure of CYP105Q4 enzyme was compared to the GfsF CYP enzyme from Streptomyces graminofaciens which is involved in the biosynthesis of a macrolide polyketide. This structural comparison to GfsF revealed conformational changes in the helices and loops near the entrance to the substrate access channel. A disordered B/C loop region, usually involved in substrate recognition, was also observed.

Regioselective Hydroxylation of Oleanolic Acid Catalyzed by Human CYP3A4 to Produce Hederagenenin, a Chiral Metabolite

Oleanolic acid (OA) is a pentacyclic triterpenoid widely found in plants and foods as an aglycone of triterpenoid saponins or as a free acid. OA exhibits beneficial activities for humans, including antitumor, antivirus, and hepatoprotection properties without apparent toxicity. The metabolites produced by the cytochrome P450 (P450) enzymes are critical for the evaluation of the efficacy and safety of drugs. In this study, the potential metabolites of OA were investigated by P450-catalyzed oxidation reactions. Among the various tested human P450s, only human CYP3A4 was active for the hydroxylation of OA. The major metabolite was characterized by a set of analyses using HPLC, LC–MS, and NMR. It was found to be 4-epi-hederagenenin, a chiral product, by regioselective hydroxylation of the methyl group at the C-23 position. These results indicated that CYP3A4 can hydroxylate an OA substrate to make 4-epi-hederagenenin. Possible drug–food interactions are discussed.

Biological Activities and Chemistry of Triterpene Saponins from Medicago Species: An Update Review

Plants are known to be a great source of phytochemicals for centuries. Medicago, belonging to the Family Fabaceae, is a large and well spread genus comprising about 83 cosmopolitan species, of which one-third are annuals and span diverse ecological niches. Medicago species are rich in saponins mainly classified into three classes, namely, steroid alkaloid glycosides, triterpene glycosides, and steroid glycosides. These saponins are important compounds having diverse pharmacological and biological activities. As a whole, 95 of saponins are reported to date occurring in Medicago species using various latest extraction/isolation techniques. Considering the multiple biological and pharmacological potential of Medicago species due to saponins along with structural diversity, we compiled this review article to sum up the recent reports for the pharmacological potential of the Medicago's derived saponins in modern as well as traditional medication systems. The current manuscript produces data of chemical structures and molecular masses of all Medicago species saponins simultaneously. The toxicity of certain pure saponins (aglycones) has been reported in vitro; hederagenin appeared highly toxic in comparison to medicagenic acid and bayogenin against X. index, while soyasaponin I, containing soyasapogenol B as a glycone, appeared as the least toxic saponin. The diversity in the structural forms shows a close relationship for its biological and pharmacological actions. Moreover, saponins showed antioxidant properties and the mechanism behind antimicrobial potential also elaborated in this review article is mainly because of the side sugar groups on these compounds. The collected data presented herein include chemical structures and molecular masses of all saponins so far. Their biological activity and therapeutic potential are also discussed. This information can be the starting point for future research on this important genus.

Biotransformation of Oleanane and Ursane Triterpenic Acids

Oleanane and ursane pentacyclic triterpenoids are secondary metabolites of plants found in various climatic zones and regions. This group of compounds is highly attractive due to their diverse biological properties and possible use as intermediates in the synthesis of new pharmacologically promising substances. By now, their antiviral, anti-inflammatory, antimicrobial, antitumor, and other activities have been confirmed. In the last decade, methods of microbial synthesis of these compounds and their further biotransformation using microorganisms are gaining much popularity. The present review provides clear evidence that industrial microbiology can be a promising way to obtain valuable pharmacologically active compounds in environmentally friendly conditions without processing huge amounts of plant biomass and using hazardous and expensive chemicals. This review summarizes data on distribution, microbial synthesis, and biological activities of native oleanane and ursane triterpenoids. Much emphasis is put on the processes of microbial transformation of selected oleanane and ursane pentacyclic triterpenoids and on the bioactivity assessment of the obtained derivatives.

Exploring the molecular basis for substrate specificity in homologous macrolide biosynthetic cytochromes P450

Cytochromes P450 (P450s) are nature's catalysts of choice for performing demanding and physiologically vital oxidation reactions. Biochemical characterization of these enzymes over the past decades has provided detailed mechanistic insight and highlighted the diversity of substrates P450s accommodate and the spectrum of oxidative transformations they catalyze. Previously, we discovered that the bacterial P450 MycCI from the mycinamicin biosynthetic pathway in Micromonospora griseorubida possesses an unusually broad substrate scope, whereas the homologous P450 from tylosin-producing Streptomyces fradiae (TylHI) exhibits a high degree of specificity for its native substrate. Here, using biochemical, structural, and computational approaches, we aimed to understand the molecular basis for the disparate reactivity profiles of these two P450s. Turnover and equilibrium binding experiments with substrate analogs revealed that TylHI strictly prefers 16-membered ring macrolides bearing the deoxyamino sugar mycaminose. To help rationalize these results, we solved the X-ray crystal structure of TylHI in complex with its native substrate at 1.99-Å resolution and assayed several site-directed mutants. We also conducted molecular dynamics simulations of TylHI and MycCI and biochemically characterized a third P450 homolog from the chalcomycin biosynthetic pathway in Streptomyces bikiniensis These studies provided a basis for constructing P450 chimeras to gain further insight into the features dictating the differences in reaction profile among these structurally and functionally related enzymes, ultimately unveiling the central roles of key loop regions in influencing substrate binding and turnover. Our work highlights the complex nature of P450/substrate interactions and raises interesting questions regarding the evolution of functional diversity among biosynthetic enzymes.

Protein engineering of CYP105s for their industrial uses

Cytochrome P450 enzymes belonging to the CYP105 family are predominantly found in bacteria belonging to the phylum Actinobacteria and the order Actinomycetales. In this review, we focused on the protein engineering of P450s belonging to the CYP105 family for industrial use. Two Arg substitutions to Ala of CYP105A1 enhanced its vitamin D₃ 25- and 1α-hydroxylation activities by 400 and 100-fold, respectively. The coupling efficiency between product formation and NADPH oxidation was largely improved by the R84A mutation. The quintuple mutant Q87W/T115A/H132L/R194W/G294D of CYP105AB3 showed a 20-fold higher activity than the wild-type enzyme. Amino acids at positions 87 and 191 were located at the substrate entrance channel, and that at position 294 was located close to the heme group. Semi-rational engineering of CYP105A3 selected the best performing mutant, T85F/T119S/V194N/N363Y, for producing pravastatin. The T119S and N363Y mutations synergistically had remarkable effects on the interaction between CYP105A3 and putidaredoxin. Although wild-type CYP105AS1 hydroxylated compactin to 6-epi-pravastatin, the quintuple mutant I95T/Q127R/A180V/L236I/A265N converted almost all compactin to pravastatin. Five amino acid substitutions by two rounds of mutagenesis almost completely changed the stereo-selectivity of CYP105AS1. These results strongly suggest that the protein engineering of CYP105 enzymes greatly increase their industrial utility. This article is part of a Special Issue entitled: Cytochrome P450 biodiversity and biotechnology, edited by Erika Plettner, Gianfranco Gilardi, Luet Wong, Vlada Urlacher, Jared Goldstone.

Directed evolution of cytochrome P450 enzymes for biocatalysis: exploiting the catalytic versatility of enzymes with relaxed substrate specificity

Cytochrome P450 enzymes are renowned for their ability to insert oxygen into an enormous variety of compounds with a high degree of chemo- and regio-selectivity under mild conditions. This property has been exploited in Nature for an enormous variety of physiological functions, and representatives of this ancient enzyme family have been identified in all kingdoms of life. The catalytic versatility of P450s makes them well suited for repurposing for the synthesis of fine chemicals such as drugs. Although these enzymes have not evolved in Nature to perform the reactions required for modern chemical industries, many P450s show relaxed substrate specificity and exhibit some degree of activity towards non-natural substrates of relevance to applications such as drug development. Directed evolution and other protein engineering methods can be used to improve upon this low level of activity and convert these promiscuous generalist enzymes into specialists capable of mediating reactions of interest with exquisite regio- and stereo-selectivity. Although there are some notable successes in exploiting P450s from natural sources in metabolic engineering, and P450s have been proven repeatedly to be excellent material for engineering, there are few examples to date of practical application of engineered P450s. The purpose of the present review is to illustrate the progress that has been made in altering properties of P450s such as substrate range, cofactor preference and stability, and outline some of the remaining challenges that must be overcome for industrial application of these powerful biocatalysts.

Terpene hydroxylation with microbial cytochrome P450 monooxygenases

Terpenoids comprise a highly diverse group of natural products. In addition to their basic carbon skeleton, they differ from one another in their functional groups. Functional groups attached to the carbon skeleton are the basis of the terpenoids' diverse properties. Further modifications of terpene olefins include the introduction of acyl-, aryl-, or sugar moieties and usually start with oxidations catalyzed by cytochrome P450 monooxygenases (P450s, CYPs). P450s are ubiquitously distributed throughout nature, involved in essential biological pathways such as terpenoid biosynthesis as well as the tailoring of terpenoids and other natural products. Their ability to introduce oxygen into nonactivated C-H bonds is unique and makes P450s very attractive for applications in biotechnology. Especially in the field of terpene oxidation, biotransformation methods emerge as an attractive alternative to classical chemical synthesis. For this reason, microbial P450s depict a highly interesting target for protein engineering approaches in order to increase selectivity and activity, respectively. Microbial P450s have been described to convert industrial and pharmaceutically interesting terpenoids such as ionones, limone, valencene, resin acids, and triterpenes (including steroids) as well as vitamin D3. Highly selective and active mutants have been evolved by applying classical site-directed mutagenesis as well as directed evolution of proteins. As P450s usually depend on electron transfer proteins, mutagenesis has also been applied to improve the interactions between P450s and their respective redox partners. This chapter provides an overview of terpenoid hydroxylation reactions catalyzed by bacterial P450s and highlights the achievements made by protein engineering to establish productive hydroxylation processes.

The genus Nonomuraea: A review of a rare actinomycete taxon for novel metabolites

The genus Nonomuraea is a rare actinomycete taxon with a long taxonomic history, while its generic description was recently emended. The genus is less known among the rare actinomycete genera as its taxonomic position was revised several times. It can be found in diverse ecological niches, while most of its member species were isolated from soil samples. However, new trends to discover the genus in other habitats are increasing. Generic abundance of the genus was found to be dependent on geographical changes. Novel sources together with selective and invented isolation techniques might increase a chance to explore the genus and its novel candidates. Interestingly, some of its members have been revealed as a valuable source of novel metabolites for medical and industrial purposes. Broad-range of potent bioactive compounds including antimicrobial, anticancer, and antipsychotic substances, broad-spectrum antibiotics and biocatalysts can be synthesized by the genus. In order to investigate biosynthetic pathways of the bioactive compounds and self-resistant mechanisms to these compounds, the links from genes to metabolites have yet been needed for further discovery and biotechnological development of the genus Nonomuraea.

Biotransformation of oleanolic and maslinic acids by Rhizomucor miehei

Microbial transformation of oleanolic acid by Rhizomucor miehei produced three metabolites. A known compound, a 30-hydroxyl derivative (queretaroic acid), and two 7β,30- and 1β,30-dihydroxylated metabolites, respectively. The action of the same fungus (R. miehei) on maslinic acid produced an olean-11-en-28,13β-olide derivative, a metabolite hydroxylated at C-30, an 11-oxo derivative, and two metabolites with an 11α,12α-epoxy group, hydroxylated or not at C-30. Their structures were elucidated by extensive analyses of their spectroscopic data, and also by chemical correlations.

Efficient bioconversion of compactin to pravastatin by the quinoline-degrading microorganism Pseudonocardia carboxydivorans isolated from petroleum-contaminated soil

Pravastatin is one of the first available statins on the market. The purpose of this study was to isolate and identify the quinoline-degrading microorganism from petroleum-contaminated soil that could bioconvert compactin to pravastatin. There were 10,011 microorganism colonies isolated; five strains showed a higher capability for quinoline biodegradation. These five strains were evaluated for their pravastatin bioconversion ability; Pseudonocardia sp. had the highest efficiency for conversion of compactin to pravastatin. The strain was further identified as Pseudonocardia carboxydivorans PAH4. The bioconversion rates were studied under difference incubation conditions. Pre-incubation in medium containing 0.005% compactin sodium, resulted in the compactin utilization rate of almost 100% in a 1mg/ml compactin-containing medium. The rate of conversion of pravastatin was up to 68% after 6 days of incubation. In conclusion, the results of this study suggest that P. carboxydivorans PAH4 could be considered a candidate for the production of pravastatin on an industrial scale.

Cloning and characterization of the biosynthetic gene cluster of 16-membered macrolide antibiotic FD-891: involvement of a dual functional cytochrome P450 monooxygenase catalyzing epoxidation and hydroxylation

FD-891 is a 16-membered cytotoxic antibiotic macrolide that is especially active against human leukemia such as HL-60 and Jurkat cells. We identified the FD-891 biosynthetic (gfs) gene cluster from the producer Streptomyces graminofaciens A-8890 by using typical modular type I polyketide synthase (PKS) genes as probes. The gfs gene cluster contained five typical modular type I PKS genes (gfsA, B, C, D, and E), a cytochrome P450 gene (gfsF), a methyltransferase gene (gfsG), and a regulator gene (gfsR). The gene organization of PKSs agreed well with the basic polyketide skeleton of FD-891 including the oxidation states and alpha-alkyl substituent determined by the substrate specificities of the acyltransferase (AT) domains. To clarify the involvement of the gfs genes in the FD-891 biosynthesis, the P450 gfsF gene was inactivated; this resulted in the loss of FD-891 production. Instead, the gfsF gene-disrupted mutant accumulated a novel FD-891 analogue 25-O-methyl-FD-892, which lacked the epoxide and the hydroxyl group of FD-891. Furthermore, the recombinant GfsF enzyme coexpressed with putidaredoxin and putidaredoxin reductase converted 25-O-methyl-FD-892 into FD-891. In the course of the GfsF reaction, 10-deoxy-FD-891 was isolated as an enzymatic reaction intermediate, which was also converted into FD-891 by GfsF. Therefore, it was clearly found that the cytochrome P450 GfsF catalyzes epoxidation and hydroxylation in a stepwise manner in the FD-891 biosynthesis. These results clearly confirmed that the identified gfs genes are responsible for the biosynthesis of FD-891 in S. graminofaciens.

Identification and characterization of a bacterial cytochrome P450 for the metabolism of diclofenac

The bacterium Actinoplanes sp. ATCC 53771 is known to perform drug metabolism of several xenobiotics similarly to humans. We identified a cytochrome P450 enzyme from this strain, CYP107E4, and expressed it in Escherichia coli using the pET101 vector. The purified enzyme showed the characteristic reduced-CO difference spectra with a peak at 450 nm, indicating the protein is produced in the active form with proper heme incorporation. The CYP107E4 enzyme was found to bind the drug diclofenac. Using redox enzymes from spinach, the reconstituted system is able to produce hydroxylated metabolites of diclofenac. Production of the human 4'-hydroxydiclofenac metabolite by CYP107E4 was confirmed, and a second hydroxylated metabolite was also produced.

New triterpenic saponins from the aerial parts of Medicago arabica (L.) huds

The reinvestigation of saponin composition from Medicago arabica from Italy allowed the detection of nineteen (1-19) saponins. All of them were purified by reverse-phase chromatography and their structures elucidated by spectroscopic and spectrometric (1D and 2D NMR; ESI-MS/MS) and chemical methods. Fourteen were known saponins, previously found in other plants including other Medicago species. They have been identified as glycosides of oleanolic acid, 2beta,3beta-dihydroxyolean-12-en-28-oic acid, hederagenin, bayogenin and soyasapogenol B. Five saponins, identified as 3-O-[-alpha-L-arabinopyranosyl(1-->2)-beta-D-glucuronopyranosyl]-30-O-beta-D-glucopyranosyl 2beta,3beta,30-trihydroxyolean-12-en-28-oic acid (1), 3-O-[alpha-L-arabinopyranosyl(1-->2)-beta-D-glucuronopyranosyl]-30-O-[beta-D-glucopyranosyl] 3beta,30-dihydroxyolean-12-en-28-oic acid (2), 3-O-[beta-D-glucuronopyranosyl]-30-O-[alpha-L-arabinopyranosyl(1-->2)-beta-d-glucopyranosyl] 2beta,3beta,30-trihydroxyolean-12-en-28-oic acid (3), 3-O-[beta-D-glucuronopyranosyl]-30-O-[alpha-L-arabinopyranosyl(1-->2)-beta-D-glucopyranosyl] 3beta,30-dihydroxyolean-12-en-28-oic acid (4) and 3-O-[beta-D-glucuronopyranosyl]-30-O-[beta-D-glucopyranosyl] 2beta,3beta,30-trihydroxyolean-12-en-28-oic acid (5), are reported here as new natural compounds. These new saponins, possessing a hydroxy group at the 30-methyl position of the triterpenic skeleton, have never been previously found in the genus Medicago.

Crystal structure of cytochrome P450 MoxA from Nonomuraea recticatena (CYP105)

Cytochrome P450 MoxA (P450moxA) from a rare actinomycete Nonomuraea recticatena belongs to the CYP105 family and exhibits remarkably broad substrate specificity. Here, we demonstrate that P450moxA acts on several luciferin derivatives, which were originally identified as substrates of the human microsomal P450s. We also describe the crystal structure of P450moxA in substrate-free form. Structural comparison with various bacterial and human microsomal P450s reveals that the P450moxA structure is most closely related to that of the fungal nitric oxide reductase P450nor (CYP55A1). Final refined model of P450moxA comprises almost all the residues, including the "BC-loop" and "FG-loop" regions pivotal for substrate recognition, and the current structure thus defines a well-ordered substrate-binding pocket. Clear electron density map reveals that the MES molecule is bound to the substrate-binding site, and the sixth coordination position of the heme iron is not occupied by a water molecule, probably due to the presence of MES molecule in the vicinity of the heme. The unexpected binding of the MES molecule might reflect the ability of P450moxA to accommodate a broad range of structurally diverse compounds.