Patent Application
20200299671
The instant application contains a Sequence Listing which has been submitted in ASCII format via EFS-Web and is hereby incorporated by reference in its entirety. The ASCII copy of the Sequence Listing, which was created on Mar. 19, 2020, is named 13177N-2357US.txt, and is 14.6 kilobytes in size.
The present disclosure is directed to a halogenation system. In particular, the disclosure is directed to an immobilized multi-enzymatic halogenation system, methods of use thereof, and modified compounds produced therewith.
Halogenation is an important chemical modification with a potential to increase biological activity and bioavailability of molecules. Moreover, halogen groups can be further synthetically elaborated by transition metal-catalyzed coupling reactions. Halogenase enzymes are attractive potential halogenating tools, because, unlike synthetic halogenation, these enzymes ensure both regiospecificity and green chemistry.
Flavin adenine dinucleotide (FAD)-dependent tryptophan (Trp) halogenases have been the focus of development as halogenation tools. Mutagenesis of Trp halogenase RebH increased its stability, catalytic efficiency, and substrate scope, to halogenate natural products and drug-like molecules. Furthermore, halogenation on a gram scale by this enzyme was achieved by cross-linking it to coupled enzymes. A recent study of the detailed substrate profile of several bacterial Trp halogenases (including RebH) and two fungal phenolic halogenases (Rdc2 and GsfI) indicated that Trp halogenases displayed preference towards indole, phenyl piperidine, phenyl pyrrole, and phenoxyaniline derivatives as substrates, while phenolic halogenases had a narrow substrate profile of some anilines, phenol derivatives, and natural products such as macrolactones and curcumin. While the substrate profiles of some FAD-dependent Trp halogenases appear to be quite broad, the halide spectrum of characterized Trp and phenolic halogenases has been limited to at most two halides: most commonly chloride (Cl—) and bromide (Br—) ions, and for a phenolic halogenase Bmp5, bromide (Br—), and iodide (I—).
In these enzymes, the enzyme-FAD complex catalyzes conversion of a halide ion into a highly reactive hypohalous acid HOX, which diffuses through a protein channel protected from solvent to the substrate binding site, where it is proposed to react with a catalytic lysine residue to form a haloamine adduct, or to form hydrogen bonds with catalytic lysine and glutamic acid residues to act as an active oxidant, with subsequent halogenation of the substrate. FAD is usually a prosthetic group that is tightly and, in some cases, covalently bound to the enzyme, co-purifying with it. Some FAD-dependent halogenases use FAD that can dissociate from the enzyme for reduction (Table 1).
How FAD can dissociate and rebind into the confines of its binding site remains unclear though. Accordingly, there remains a need for an efficient and reusable enzymatic halogenation tool is highly desirable.
The presently-disclosed subject matter meets some or all of the above-identified needs, as will become evident to those of ordinary skill in the art after a study of information provided in this document.
This summary describes several embodiments of the presently-disclosed subject matter, and in many cases lists variations and permutations of these embodiments. This summary is merely exemplary of the numerous and varied embodiments. Mention of one or more representative features of a given embodiment is likewise exemplary. Such an embodiment can typically exist with or without the feature(s) mentioned; likewise, those features can be applied to other embodiments of the presently-disclosed subject matter, whether listed in this summary or not. To avoid excessive repetition, this summary does not list or suggest all possible combinations of such features.
In some embodiments, the presently-disclosed subject matter includes a halogenation system comprising PltM and a solid support, wherein the PltM is immobilized on the solid support. In some embodiments, the solid support is a resin. In one embodiments, the resin is an agarose resin. In one embodiment, the resin is packed into a spin column. In some embodiments, the halogenation system further includes one or more enzymes immobilized on the solid support. In one embodiment, the one or more enzymes includes a flavin adenine dinucleotide (FAD) reductase. In another embodiment, the FAD reductase includes SsuE. In one embodiment, the one or more enzymes include a NADPH regenerator. In another embodiment, the NADPH regenerator includes glucose dehydrogenase (GDH).
In some embodiments, the halogenation system includes PltM, a flavin adenine dinucleotide (FAD) reductase, a NADPH regenerator, and a solid support, wherein the PltM, the FAD reductase, and the NADPH regenerator are immobilized on the solid support. In some embodiments, the FAD reductase is SsuE. In some embodiments, the NADPH regenerator is glucose dehydrogenase (GDH). In some embodiments, the PltM, SsuE, and GDH are packed into a spin column.
Also provided herein, in some embodiments, is a method of halogenating a substrate, the method comprising running a substrate and reaction solution through the halogenation system including PltM immobilized on a solid support. In some embodiments, halogenation system further comprises SsuE and glucose dehydrogenase (GDH). In some embodiments, the substrate is a phenyl compound with one or more electron donating groups. In one embodiment, the phenyl compound is selected from the group consisting of phenolic derivatives, aniline derivatives, short-acting b2 adrenoreceptor agonists, natural products, and a combination thereof. In some embodiments, the substrate is mono-halogenated. In some embodiments, the substrate is di-halogenated.
Further provided herein, in some embodiments, is a halogenated compound such as 4,6-diCl-3, 4,6-diCl-8, 2,4-diCl-9, 2,6-diCl-11, 3,5-diCl-15, 4,6-diCl-16, 4,6-diCl-18, 4-Cl-23, and/or 4,6-diBr-3.
Further features and advantages of the presently-disclosed subject matter will become evident to those of ordinary skill in the art after a study of the description, figures, and non-limiting examples in this document.
The presently-disclosed subject matter will be better understood, and features, aspects and advantages other than those set forth above will become apparent when consideration is given to the following detailed description thereof. Such detailed description makes reference to the following drawings, wherein:
While the disclosure is susceptible to various modifications and alternative forms, specific embodiments thereof have been shown by way of example in the drawings and are herein described below in detail. It should be understood, however, that the description of specific embodiments is not intended to limit the disclosure to cover all modifications, equivalents and alternatives falling within the spirit and scope of the disclosure as defined by the appended claims.
The details of one or more embodiments of the presently-disclosed subject matter are set forth in this document. Modifications to embodiments described in this document, and other embodiments, will be evident to those of ordinary skill in the art after a study of the information provided in this document. The information provided in this document, and particularly the specific details of the described exemplary embodiments, is provided primarily for clearness of understanding and no unnecessary limitations are to be understood therefrom. In case of conflict, the specification of this document, including definitions, will control.
Unless defined otherwise, all technical and scientific terms used herein have the same meaning as is commonly understood by one of skill in the art to which the invention(s) belong. All patents, patent applications, published applications and publications, GenBank sequences, databases, websites and other published materials referred to throughout the entire disclosure herein, unless noted otherwise, are incorporated by reference in their entirety. In the event that there are a plurality of definitions for terms herein, those in this section prevail. Where reference is made to a URL or other such identifier or address, it understood that such identifiers can change and particular information on the internet can come and go, but equivalent information can be found by searching the internet. Reference thereto evidences the availability and public dissemination of such information.
Following long-standing patent law convention, the terms “a”, “an”, and “the” refer to “one or more” when used in this application, including the claims. Thus, for example, reference to “a cell” includes a plurality of such cells, and so forth.
The terms “comprising,” “including,” and “having” are intended to be inclusive and mean that there may be additional elements other than the listed elements.
Unless otherwise indicated, all numbers expressing quantities of ingredients, properties such as reaction conditions, and so forth used in the specification and claims are to be understood as being modified in all instances by the term “about”. Accordingly, unless indicated to the contrary, the numerical parameters set forth in this specification and claims are approximations that can vary depending upon the desired properties sought to be obtained by the presently-disclosed subject matter.
As used herein, ranges can be expressed as from “about” one particular value, and/or to “about” another particular value. It is also understood that there are a number of values disclosed herein, and that each value is also herein disclosed as “about” that particular value in addition to the value itself. For example, if the value “10” is disclosed, then “about 10” is also disclosed. It is also understood that each unit between two particular units are also disclosed. For example, if 10 and 15 are disclosed, then 11, 12, 13, and 14 are also disclosed.
As used herein, the term “about,” when referring to a value or to an amount of mass, weight, time, volume, concentration, percentage, or the like is meant to encompass variations of in some embodiments ±50%, in some embodiments ±40%, in some embodiments ±30%, in some embodiments ±20%, in some embodiments ±10%, in some embodiments ±5%, in some embodiments ±1%, in some embodiments ±0.5%, and in some embodiments ±0.1% from the specified amount, as such variations are appropriate to perform the disclosed method.
All combinations of method or process steps as used herein can be performed in any order, unless otherwise specified or clearly implied to the contrary by the context in which the referenced combination is made.
As used herein, nomenclature for compounds, including organic compounds, can be given using common names, IUPAC, IUBMB, or CAS recommendations for nomenclature. When one or more stereochemical features are present, Cahn-Ingold-Prelog rules for stereochemistry can be employed to designate stereochemical priority, ElZ specification, and the like. One of skill in the art can readily ascertain the structure of a compound if given a name, either by systemic reduction of the compound structure using naming conventions, or by commercially available software, such as CHEMDRAW™ (Cambridgesoft Corporation, U.S.A.).
As used herein, the terms “optional” or “optionally” means that the subsequently described event or circumstance can or cannot occur, and that the description includes instances where said event or circumstance occurs and instances where it does not.
As used herein, the term “subject” can be a vertebrate, such as a mammal, a fish, a bird, a reptile, or an amphibian. Thus, the subject of the herein disclosed methods can be a human, non-human primate, horse, pig, rabbit, dog, sheep, goat, cow, cat, guinea pig or rodent. The term does not denote a particular age or sex. Thus, adult and newborn subjects, as well as fetuses, whether male or female, are intended to be covered. In one aspect, the subject is a mammal. A patient refers to a subject afflicted with a disease or disorder. The term “patient” includes human and veterinary subjects.
As used herein, the term “derivative” refers to a compound having a structure derived from the structure of a parent compound (e.g., a compound disclosed herein) and whose structure is sufficiently similar to those disclosed herein and based upon that similarity, would be expected by one skilled in the art to exhibit the same or similar activities and utilities as the claimed compounds, or to induce, as a precursor, the same or similar activities and utilities as the claimed compounds. Exemplary derivatives include salts, esters, amides, salts of esters or amides, and N-oxides of a parent compound.
Although any methods, devices, and materials similar or equivalent to those described herein can be used in the practice or testing of the presently-disclosed subject matter, representative methods, devices, and materials are now described.
The presently-disclosed subject matter relates to a halogenation system. In some embodiments, the halogenation system includes a bacterial halogenase. Suitable bacterial halogenases include, but are not limited to, PltM. PltM is encoded in the biosynthetic gene cluster of pyoluteorin, an antifungal compound containing a dichloropyrrole moiety. In some embodiments, PltM halogenates substrates with one or more halides, such as, but not limited to, Cl−, Br−, I−, or a combination thereof. This halogenation of the substrate by PltM may include mono-halogenation or di-halogenation with the same or different halogens. For example, in one embodiment, as illustrated in
Although discussed above with regard to chlorination of phloroglucinol, the disclosure is not so limited and includes halogenation of other substrates with the same or different halides. In some embodiments, the substrate includes phenyl compounds with electron donating groups. In one embodiment, such compounds include, but are not limited to, phenolic derivatives (e.g.,
In some embodiments, the halogenation system includes multiple enzymes. In one embodiment, the system includes PltM and at least one other enzyme. In another embodiment, the at least one other enzyme includes one or more of a NADPH regenerator, such as glucose dehydrogenase (GDH), or a flavin adenine dinucleotide (FAD) reductase, such as SsuE. In some embodiments, the enzymes are immobilized on a solid support. Suitable solid supports include, but are not limited to, resins, such as the agarose resin Affi-Gel® 15. For example, in one embodiment, the halogenation system includes PltM, SsuE, and GDH immobilized on agarose resin (Affi-Gel® 15). In some embodiments, the immobilized enzymes are packed into a spin column, which may be used as a resin conjugate for halogenation. This protein bound resin provides a high halogenation yield for some compounds, which could not be efficiently halogenated by free enzymes in solution. Additionally or alternatively, the enzyme-resin conjugate may be reused 5-6 times without significant loss of efficiency. Without wishing to be bound by theory, this reusability is believed to be the result of a unique recycling mechanism of FAD provided by the combination of immobilized enzymes.
Also provided herein are methods of using the halogenation system. In some embodiments, the methods include running a substrate and reaction solution through the halogenation system disclosed herein. Any suitable substrate may be used based upon the one or more enzymes within the halogenation system. Suitable substrates include, but are not limited to, phenolic derivatives (e.g.,
Also provided herein are halogenated compounds formed with the halogenation system. The compounds include mono- and di-halogenated derivatives of any suitable PltM substrate. In one embodiment, the mono-halogenated derivatives include mono-chlorinated derivatives such as, but not limited to, 4-Cl-23 (
The presently-disclosed subject matter is further illustrated by the following specific but non-limiting examples. The following examples may include compilations of data that are representative of data gathered at various times during the course of development and experimentation related to the presently-disclosed subject matter. Those skilled in the art will recognize, or be able to ascertain, using no more than routine experimentation, numerous equivalents to the specific substances and procedures described herein.
This Example describes the characterization PltM and exploration of its ability to halogenate various compounds.
Results
Halide Versatility of PltM
To explore the halide profile of PltM, halogenation of 1 by PltM with NaF, NaCl, NaBr, and NaI used individually in a reaction mixture was tested first. Chlorinated, brominated, and iodinated, but not fluorinated 1, were identified as products (
Substrate Profile of PltM
Having established the halide versatility of PltM, its substrate profile was investigated next. A set of 20 structurally diverse small molecules was tested first, most, but not all of which were, like 1, phenolic (phenolic derivatives, anilines, nitrobenzene derivative) and included L-Trp (
PltM catalyzed halogenation of 18 of the 20 compounds tested, exhibiting remarkable substrate versatility for phenolic compounds (
Since the reaction with compound 11 showed very clear signals of chlorinated and iodinated 11, it was also tested for bromination and fluorination (
Crystal Structure of PltM and its Complex with Phloroglucinol
In addition to its remarkable halide versatility and a very broad substrate profile for a phenolic halogenase, PltM is at most ˜15% identical in sequence to other structurally characterized FAD-dependent halogenases, and it contains a unique C-terminal region (residues 390-502) (
A monomer of PltM (
The binding site of compound 1 is analogous to that of L-Trp in the crystal structure of RebH and PrnA (
/Rfree
aNumbers in parentheses indicate the values in the highest-resolution shell.
bIndicates Rampage statistics.
cNumber of ligands in the asymmetric unit.
indicates data missing or illegible when filed
Crystal Structures of PltM with FAD Bound in Different States
PltM represents a type of FAD-dependent enzyme, where FAD dissociates out of its binding site for reduction. To gain structural insight into this enigmatic process, a crystal structure of PltM-FAD complex was determined by soaking the crystals of apo PltM with FAD. Two different crystal forms of PltM-FAD complexes were obtained, where a molecule of FAD was bound to PltM in two different states (
A short nonconserved loop containing three Ala, a Gly and a Ser (residues 172-178) and the side chain of Gln321 are in two different conformations in these two structures (
Halogenation Assays in Fermentation Culture
As a preliminary assessment of potential use of PltM in a fermentation setting, the ability to halogenate phloroglucinol (1) upon addition to the culture of E. coli BL21(DE3) overexpressing PltM was tested. The substrate binding cavity observed in the crystal structures was also validated by testing halogenation by two PltM point mutants of PltM, L111Y and S404Y, in this setting. These two residues (one from the FAD binding fold and one from the C-terminal region) line the substrate binding cavity, and their bulkier substitutions are predicted to block binding of 1 (
A crystal structure of PltM L111Y was determined, which showed that the overall protein structure is unperturbed and the only effect of the mutation was to obstruct the access to the substrate binding pocket, as predicted (
Kinetics and Regiospecificity of PltM in Optimized Reactions
For quantitative analysis of enzyme kinetics and detailed structural characterization of reaction products, as well as for potential future biotechnological use, in vitro enzymatic reaction conditions were extensively optimized and enzymes were coupled to maximize product yield. The critical factors of the optimized conditions were introducing glucose dehydrogenase (GDH) for NADPH regeneration and lowering the concentrations of NADPH and halide salts. This optimization significantly improved reaction yields, resulting in full conversion of several substrates (Table 8). This additional information corroborated the preference for substrates containing electron-withdrawing groups and showed preference of PltM for substrates with 1- and 3-hydroxyl or amino groups.
a% overall conversion is the sum of all chlorinated products.
bYields of two independent reactions are reported.
The halide preference was determined and the kinetics of chlorination and bromination of substrates 3, 11, and 16 was evaluated quantitatively, which showed 100% conversion upon overnight reaction (
aThe values of all mono-halogenation and dihalogenation rate constants kcat, 1 and kcat, 2 respectively, and Km for mono-halogenation and dihalogenation (defined as (kd, 1 + kcat, 1)/ka, 1 and (kd, 2 + kcat, 2)/ka, 2, respectively) were determined by nonlinear regression using Dynafit, as described in Methods.
bTwo distinct mono-halogenation products of the same reaction are denoted by labels a and b.
The high yield of chlorination and bromination of these and several other compounds allowed the present inventors to establish the regiospecificity of the halogenation by PltM. However, some substrates or products were insufficiently stable during halogenation reactions precluding their quantitative structural analysis. The structures of the final dichlorinated products of 3, 8, 9, 11, 15, 16, 18, as well as the monochlorinated product of 23 and the dibrominated product of 3 were determined by NMR spectroscopy. The resulting products were 4,6-diCl-3, 4,6-diCl-8, 2,4-diCl-9, 2,6-diCl-11, 3,5-diCl-15, 4,6-diCl-16, 4,6-diCl-18, 4-Cl-23, and 4,6-diBr-3, respectively (
These results show that for mono- or di-hydroxylated or aminated substrates, PltM halogenates almost exclusively in ortho to these polar groups, but not between them. However, when a methyl or a styrene moiety was found in meta to two hydroxyls, as in compound 9 (which was dichlorinated) and resveratrol (23; which was monochlorinated), respectively, a chlorination event occurred between the two hydroxyls.
Development of an Immobilized Halogenating System
The halogenation yield is limited by stability of proteins, with PltM being the limiting factor. To achieve a more efficient and scalable halogenation reaction, the present inventors developed a method where all three proteins were immobilized on agarose resin (Affi-Gel® 15), packed into a spin column, and then used as a resin conjugate for halogenation. The halogenation reactions were performed by adding substrate and reagents into the column. This protein bound resin showed a high halogenation yield for some compounds, which could not be efficiently halogenated by free enzymes in solution (
The remarkable halide versatility for any FAD-dependent halogenase and very broad substrate profile for a phenolic halogenase call for future exploration of PltM as a halogenation tool. The structures discussed herein revealed a unique architecture of this enzyme, and an FAD orientation that may be relevant to the FAD recycling mechanism shared by FAD binding enzymes.
Methods
Materials and Instrumentation
The PltM, SsuE, and PltA (used as a control in this study) proteins were overexpressed and purified based on our previously described protocols. DNA primers for PCR were purchased from Integrated DNA Technologies (IDT; Coralville, Iowa, USA). Restriction enzymes, Phusion DNA polymerase, and T4 DNA ligase were purchased from New England BioLabs (NEB; Ipswich, Mass., USA). All chemicals and buffer components were purchased from Sigma-Aldrich or VWR (Radnor, Pa., USA) and used without any further purification. Size-exclusion chromatography was performed on a fast protein liquid chromatography (FPLC) system BioLogic DuoFlow (Bio-Rad; Hercules, Calif., USA) by using a HiPrep 26/60 S-200 HR column (GE Healthcare, Piscataway, N.J., USA). Liquid chromatography-mass spectrometry (LC-MS) was performed on a Shimadzu high-performance liquid chromatography (HPLC) system equipped with a DGU-20A/3R degasser, LC-20AD binary pumps, a CBM-20A controller, a SIL-20A/HT autosampler (Shimadzu, Kyoto, Japan), and Vydac HPLC DENALI™ Column (C18, 250×4.6 mm, 5∝cm particle size) from Grace (Columbia, Md., USA) and an AB SCIEX TripleTOF 5600 (AB SCIEX, Redwood City, Calif.) mass spectrometer recording in negative or positive mode between 80 and 600 m/z. HPLC was performed on an Agilent Technologies 1260 Infinity system equipped with a Vydac HPLC DENALI™ column (C18, 250×4.6 mm, 5∝cm particle size) and an Alltech Econosil HPLC column (C18, 250×10 mm, 10∝cm particle size; Grace) for analytical and semi-preparative experiments, respectively. 1H and 13C NMR spectra were recorded at 400 and 500 (for 1H) as well as 100 MHz (for 13C) on a Varian 400 MHz spectrometer, using deuterated solvents as specified. Chemical shifts (d) are given in parts per million (ppm). Coupling constants (J) are given in Hertz (Hz), and conventional abbreviations used for signal shape are as follows: s, singlet; d, doublet; t, triplet; m, multiplet; dd, doublet of doublets; ddd, doublet of doublet of doublets; br s, broad singlet; dt, doublet of triplets.
Synthesis of Compound 15
Aluminum chloride (1.3 g, 9.99 mmol) was slowly added to a solution of phloroglucinol (1, 315 mg, 2.50 mmol) in 1:1/1,2-dichloroethane:nitrobenzene (10 mL) at 0° C. After stirring this mixture at this temperature for 10 min under a nitrogen atmosphere, acetyl chloride (0.21 mL, 3.00 mmol) was added. Then the ice bath was removed, and the mixture stirred at 80° C. for 2 h. The reaction progress was monitored by TLC (1:2/EtOAc:Hexanes, Rf 0.35). The reaction mixture was quenched with H2O (60 mL), extracted with EtOAc (2×100 mL), washed with brine (20 mL), and then dried over MgSO4. The organic layer was removed under reduced pressure and the residue was purified by flash column chromatography (SiO2, 1:2/EtOAc:Hexanes) to afford the known compound 1530 (223 mg, 53%) as a yellow solid: 1H NMR (400 MHz, CD3OD) δ 5.78 (s, 2H), 2.58 (s, 3H); 13C NMR (100 MHz, (CD3)2SO) δ 203.1, 164.9, 164.5, 104.2, 94.1, 31.3.
PltM Mutagenesis
PltM mutants K87A, L111Y, and S404Y were constructed by splicing-by-overlap-extension method. The sequences downstream and upstream of the mutation site were amplified first individually from ppltM-pET28a(NHis). For PltM K87A mutant the primer pairs were: 5′-CGCCTGCGGGATCgcgCTGGGCTTCAGTTTTG-3′ (SEQ ID NO: 1) with 5′-CATACTCGAGCTAGACTTTGAGGATGAAACGATTG-3′(SEQ ID NO: 2); and 5′-CAAAACTGAAGCCCAGcgcGATCCCGCAGGCG-3′ (SEQ ID NO: 3) with 5′-GCAGCTCTCATATGAATCAGTACGACGTCATTATC-3′ (SEQ ID NO: 4). For PltM L111Y mutant the primers were: 5′-CTTGTGGCCCCGCCGtatAAGGTGCCGGAAGCC-3′ (SEQ ID NO: 5) with SEQ ID NO: 2; and 5′-GGCTTCCGGCACCTTataCGGCGGGGCCACAAG-3′ (SEQ ID NO: 6) with SEQ ID NO: 4. For PltM S404Y mutant, the primer pairs were: 5′-CTGGCTCAGCGGCtatAACCTGGGCAGTGC-3′ (SEQ ID NO: 7) with SEQ ID NO: 2; and 5′-GCACTGCCCAGGTTataGCCGCTGAGCCAG-3′ (SEQ ID NO: 8) with SEQ ID NO: 4. The PCR products of the above primer pairs were used as templates for another round of PCR using primers SEQ ID NO: 2 and SEQ ID NO: 4. The products from the second round of PCR were digested with restriction enzymes NdeI and XhoI and ligated into NdeI/XhoI-linearized pET28a, yielding ppltMK87A-pET28a, ppltML111Y-pET28a, and ppltMS404Y-pET28a. The mutations were verified by DNA sequencing (Eurofins Genomics).
Preparation of Pgdh-pET28a Overexpression Construct
The glucose dehydrogenase (gdh) gene was amplified from genomic DNA of Bacillus subtilis subsp. subtilis 168 by PCR with the forward and reverse primers: 5′-AGGATGCATATGTATCCGGATTTAAAAGGAAAAG-3′ (SEQ ID NO: 9) and 5′-CGCTTTCTCGAGTTAACCGCGGCCTGCCTGGAAT-3′ (SEQ ID NO: 10), respectively. The PCR product was purified by agarose gel extraction and digested by restriction enzymes NdeI and XhoI, which was subsequently ligated into NdeI/XhoI-linearized pET28a. The resulting plasmid pgdh-pET28a was transformed into a chemically competent E. coli TOP10 strain, and the cloning was verified by sequencing of the purified plasmids.
Preparation of PltM and Coupled Enzymes for In Vitro Assays
Open reading frames encoding PltM and FAD reductase SsuE were cloned into E. coli expression vectors as previously reported. For production of PltM, SsuE, and GDH, the expression vectors were transformed into E. coli BL21 (DE3) (ATCC; Manassas, Va.). In each case, a colony was grown overnight at 37° C. with shaking at 200 rpm in LB medium (5 mL) supplemented with 50 μg/mL kanamycin. These overnight cultures were inoculated into LB medium (1 L) supplemented with 50 μg/mL kanamycin. Cultures were grown (37° C., 200 rpm) until an attenuance at 600 nm of 0.6 was reached. At this time, protein expression was induced by adding isopropyl-β-
Preparation of PltM for Crystallography
Wild-type PltM and PltM L111Y mutant were purified as described above with an additional size-exclusion chromatography step. Wild-type PltM and PltM L111Y eluted from NiII resin were loaded onto an S-200 column equilibrated in 40 mM Tris-HCl pH 8.0, 100 mM NaCl, 2 mM βME. Fractions containing NHis6-PltM were pooled and concentrated to 40 mg/mL by using an Amicon Ultra-15 Centrifugal Filter Unit with 10 kDa MWCO. Purified PltM proteins were kept on ice for crystallization studies.
In Vitro Assays of PltM with Various Substrates and Halides
The halogenation assays were carried out similarly to a recently described procedure. The substrates that have been tested are given in
To establish if hetero-dihalogenation by PltM could be observed, halogenating competition assays in 1:1 or 10:1 mixtures of two different halide salts were performed (Assay 2). The reactions contained the same components as above except single halide salts were replaced with either a 1:1/NaCl:NaBr (Assay 2a), 1:1/NaCl:NaI (Assay 2b), or 1:1/NaBr:NaI (Assay 2c) mixtures (100 mM of each halide). The reactions were initiated by adding NADPH under N2. A 1:1/NaCl:NaBr reaction was also performed with 200 mM of each halide to test occurrence of homo-di- or hetero-chlorination/bromination, and 10:1/NaCl:NaI (Assay 2d) and 10:1/NaBr:NaI (Assay 2e) mixtures with 200 mM of NaCl or NaBr and 20 mM of NaI were tested to check whether chlorination or bromination could occur in the presence of iodide and whether iodination can occur with chlorination or bromination to yield a C1,I-substrate or Br,I-substrate. The reactions were incubated and processed as described above in Assay 1.
Optimized In Vitro PltM Halogenation Assay
To increase production of halogenated molecules and decrease the amount of NADPH required, the above in vitro assay was optimized by using an additional enzyme, glucose dehydrogenase (GDH). The optimized reaction mixture contained substrate (0.5 mM for chlorination and bromination; 0.25 mM for iodination; prepared from 50 mM stock in DMSO), FAD (5 μM), NADPH (5 μM), PltM (6 μM), SsuE (5 μM), GDH (0.5 μM), glucose (20 mM), NaX (10 mM for chlorination and bromination; 0.5 mM for iodination), and sodium phosphate (30 mM, pH 7.4), and was incubated at room temperature. The overall yield of halogenation products was determined for reactions run overnight for several substrates (Table 8). Conversion of the substrate to halogenated products was monitored by HPLC at λ=275-320 nm, where the absorbance of molecules is not affected by halogenation, and quantified as fraction of reaction species (%).
The time course experiments for kinetic analysis were performed in 100 μL reaction mixtures by quenching the reactions at 0, 5, 15, 30, 60, 120, 240, and 360 min (for 3 and 16), and an additional 720 min (for 11) for chlorination and bromination, and at 0, 30, 60, 120, 240, and 480 min (for 3 and 16), or an additional 720 min (for 11) for iodination. The time course experiments were performed in duplicate. Compound 1 was unstable under these optimized conditions, and it was not tested. The in vitro analysis of K87A mutant was performed overnight in 100 μL reaction mixture by using the compound 11 as a substrate. Wild-type PltM was used as a positive control, and no enzyme reaction was used as a negative control. In all above reactions, the compounds were extracted with EtOAc (4×100 μL) and dried under gentle air flow. The products were dissolved in MeOH (30 μL for chlorination and bromination; 15 μL for iodination) for HPLC analysis.
The scale-up experiments were performed overnight in 25 mL for compound 23, in 50 mL for compounds 3, 8, 9, 11, 15, and 18, or 100 mL for 16. PltM concentration was 25 μM with compounds 15 and 250 μM with compound 23. To process the chlorination reaction of compound 23, ice-cold MeOH (50 mL) was added to precipitate the proteins. This mixture was incubated for 2 h at −20° C., and the protein precipitate was removed by centrifugation (40,000×g, 30 min, 4° C.). The pellet was washed by ice-cold MeOH (50 mL) and centrifuged down again (40,000×g, 15 min, 4° C.). The supernatant was combined in a round bottomed flask, and MeOH was removed by in vacuo. The products were extracted with EtOAc (4× reaction volume) and dried in vacuo. These were dissolved in MeOH (0.5-1 mL) for purification by semi-preparative HPLC.
Halogenation Assay Using Immobilized Enzymes
To increase the yield of halogenation reaction and make the enzymes reusable, PltM, SsuE, and GDH, we immobilized these proteins on Affi-Gel® 15 resin (Bio-Rad, Hercules, Calif.). To increase the stability of the coupled enzymes, GDH from Bacillus amyloliquefaciens SB5 (GDH-BA) was used in this assay. This enzyme was expressed and purified, as described above, from a pET23a vector (ampR) containing a synthetic gene encoding this enzyme (NCBI accession # JQ305165) with an NHis6 tag, purchased from GenScript (Piscataway, N.J.). The enzymes were dialyzed into buffer C, which contains HEPES (50 mM, pH 7.5), βME (2 mM), and glycerol (10%). Suspended Affi-Gel® resin (250 pL) was transferred into a QIAquick spin column (Qiagen), and the resin was washed three times with 500 μL of H2O and buffer D (30 mM HEPES, pH 7.5). For each time, the wash solution was removed by centrifugation (400×g, for 15-30 s, 4° C.). The washed resin was incubated with SsuE (˜50 μM, 300 μL) for 4 h at 4° C. The beads were washed with buffer D twice and subsequently incubated with a mixture of GDH-BA (˜200 μM, 50 μL) and PltM (˜500 μM, 250 μL) overnight at 4° C. This resin-enzyme conjugate was washed twice with buffer D and preserved in 4° C. in buffer D until needed. For each 250 μL resin, 300 μL of reaction solution, which contained substrate (0.5 mM), FAD (5 μM), NADPH (5 μM), glucose (20 mM), NaCl (10 mM), and HEPES (30 mM, pH 7.5), was used. The reaction with resveratrol (23) was performed overnight at room temperature. The reaction solution was collected by centrifugation (400×g, every 15-30 s until the solution was removed, 4° C.), and the resin-enzyme conjugate in the column was washed with buffer D (300 μL) three times. These solutions were extracted with EtOAc (4×300 μL) and dried in vacuo. The solid material was dissolved in MeOH (200 μL) and analyzed by HPLC (
Kinetic Analysis of PltM Halogenation
To determine the halogenation preference, the kinetic parameters were obtained by the global nonlinear regression analysis of all reaction species using DynaFit software for the following halogenation mechanism:
where E, S, P1, P2 are enzyme, substrate, mono- and dihalogenated product, respectively.
Cell-Based Activity Assay of PltM
E. coli BL21 (DE3) cells were transformed with ppltM-pET28a, ppltMK87A-pET28a, ppltML111Y-pET28a, ppltMS404Y-pET28a, and ppltA-pET28a. The ppltA-pET28a plasmid overexpressing the halogenase PltA whose substrate is pyrrolyl-S-PltL (a peptidyl carrier protein-linked pyrrole) was used as a negative control. Five colonies from each transformant were cultured in 2×500 mL of LB medium (for ppltM-pET28a, ppltML111Y-pET28a, and ppltMS404Y-pET28a) and 1×500 mL of LB medium (for ppltMK87A-pET28a and ppltA-pET28a) with 50 μg/mL kanamycin at 37° C. and 200 rpm until attenuance of 0.2 at 600 nm. The cultures were then moved to 25° C. until attenuance of 0.5. Protein expression was induced by adding 0.2 mM IPTG to all seven flasks, and the cultures were incubated with shaking for 1 h. 12.5 μg/mL of compound 1 was added to 1×500 mL of LB medium containing ppltM-pET28a, ppltMK87A-pET28a, ppltML111Y-pET28a, ppltMS404Y-pET28a, and ppltA-pET28a. Compound 1 was not added to the three remaining flasks (negative controls). After additional incubation for 20 h, the cells were pelleted at 5,000 g for 10 min, and the supernatant was collected. The supernatant was extracted with EtOAc (3×330 mL), which was dried in vacuo. This was then dissolved in MeOH (100 μL) prior to addition of H2O (800 μL) followed by centrifugation at 20,000×g for 10 min to remove the precipitate. The supernatant was collected and 1 μL was diluted into 199 μL of MeOH for LC-MS analysis (Table 7).
HPLC and LC-MS Analysis of Halogenated Products
The halogenation reaction products were analyzed by HPLC or LC-MS by injecting 10 μL of each sample. The compounds were separated by Reversed-phase HPLC at the flow rate of 0.2 mL/min by using the following program: eluent A=H2O; eluent B=MeCN; gradient=2% B for 5 min, increase to 100% B over a 30 min period, stay at 100% B for 9 min, decrease to 2% B over a 1 min period, and re-equilibrate the column at 2% B for 30 min.
For HPLC analysis, the molecules were observed by absorbance at λ=275 nm as described above. As necessary, the following mass spectrometer was operated in negative and positive modes with the following parameters: For negative mode, mass range, 80-600 m/z in profile mode; temperature, 550° C. and ion spray voltage floating, −4500 V, and for positive mode, mass range, 80-600 m/z in profile mode; temperature, 550° C. and ion spray voltage floating, 4500 V. The presence of each compound was analyzed by extracted ion chromatograph (XIC) with the expected mass ±0.05 Da for Assay 1 and Assay 2 and ±0.005 Da for Assay 3 (
The LC-MS was operated by Analyt TF Software (SCIEX, Framingham, Mass.), and the data was analyzed by PeakView (SCIEX). To purify 4 selected scaled-up halogenated products, semi-preparative HPLC was performed by injecting 100 μL per injection at 1 mL/min by using the following gradient program with eluent A as H2O (with 0.1% TFA) (for compounds 3 and 11) or 10 mM ammonium bicarbonate (for 16) and eluent B as MeCN: 2% B for 10 min, increase to 100% B over a 40 min period, stay at 100% B for 5 min, decrease to 2% B over a 1 min period, followed by re-equilibration in 2% B for 9 min. The collected peak fractions were dried under reduced pressure and lyophilized for NMR analysis.
NMR analysis of products of large-scale halogenation
The exact position for the various halogenations were determined either by comparison with commercially available standards (4,6-dichlororesorcinol) or by a combination of HMBC and HSQC experiments.
The analysis of halogenation products is presented as follows:
Analysis of 4,6-dichlororesorcinol (4,6-diCl-3): 1H NMR (500 MHz, CD3OD,
Analysis of 4,6-dibromoresorcinol (4,6-diBr-3): 1H NMR (500 MHz, CD3OD,
Analysis of 2,4,6-trichlororesorcinol (4,6-diCl-8): 1H NMR (500 MHz, CD3OD,
Analysis of 2,4-dichloro-5-methylresorcinol (2,4-diCl-9): 1H NMR (500 MHz, CD3OD,
Analysis of 2,6-dichloro-3,5-dihydroxybenzyl alcohol (2,6-diCl-11): 1H NMR (500 MHz, CD3OD,
Analysis of 3,5-dichloro-2,4,6-trihydroxyacetophenone (3,5-diCl-15): 1H NMR (500 MHz, CD3OD,
Analysis of 5-amino-2,4-dichlorophenol (2,4-diCl-16): 1H NMR (400 MHz, CD3OD,
Analysis of 2,4-dichloro-1,5-diaminobenzene (2,4-diCl-18): 1H NMR (500 MHz, CD3OD,
Analysis of 4-chloro-resveratrol (4-Cl-23): 1H NMR (400 MHz, CD3OD,
Analysis of resveratrol (23): 1H NMR (400 MHz, CD3OD,
Crystallization of PltM
PltM crystals were obtained by the hanging drop method with drops containing 0.5 μL of PltM (40 mg/mL) and 0.5 μL of the reservoir solution (0.1 M Tris pH 8, 0.2 M NaCl, 0.1 M CaCl2) and 12-17% PEG 8000). The drops were equilibrated against 0.5 mL of reservoir solution at 21° C. Long rod-shaped crystals appeared after 1-3 days. The crystals were cryoprotected by a gradual transfer to the solution with the same composition as the reservoir solution, additionally containing 20% glycerol. The crystals were then frozen by a rapid immersion into liquid nitrogen.
Determination of the Crystal Structure of PltM
PltM does not contain a sufficient number of Met residues for structure determination by using anomalous signal from selenium atoms in Se-Met PltM. However, PltM contains eight Cys residues, which, if accessible, would react with Hg salts. Hg derivative crystals of PltM were prepared by transferring native crystals from its mother liquor to the reservoir solution containing 1 mM ethyl mercury phosphate (EMP) and incubated overnight. These crystals were cryoprotected similarly to the native crystals. X-ray diffraction data for this and other crystals of PltM were collected at 100 K at the wavelength of 1 Å at synchrotron beamline 22-ID at the Advanced Photon Source at the Argonne National Laboratory (Argonne, Ill.). All datasets were indexed, integrated and scaled using HKL2000. The structure was determined by the single anomalous dispersion (SAD) method from the EMP derivative data set (using the wavelength of 1.0 Å), as follows. A heavy atom search by using direct method-based SHELXD program initially yielded a substructure of 22 Hg atoms in the asymmetric unit. This Hg substructure was used as an input in Autosolve in PHENIX suite to obtain initial phases, which were bootstrapped by difference Fourier analysis to yield the total of 33 Hg atoms and a readily interpretable electron density map, with the figure of merit of 0.71 after density modification. The structure of the Hg-derivatized PltM was then iteratively built by using COOT and refined by using REFMAC5 (Table 5).
The refined structure contained four monomers of PltM and 33 Hg atoms coordinated to Cys residues per asymmetric unit. A monomer of PltM from this structure was then used as a search model to determine the structure of native PltM by molecular replacement with Phaser in CCP4i suite. The native crystal structure of PltM was then iteratively adjusted and refined by using COOT and REFMAC5, respectively. Table 5 contains data collection and structure refinement statistics for this and other crystal structures in this study. The crystal structure coordinates and structure factor amplitudes for all crystal structures were deposited in the Protein Data Bank under accession codes specified in Tables 5 and 6.
/
aNumbers in parentheses indicate the values in the highest-resolution shell.
bIndicates Rampage statistics.
cNumber of ligands in the asymmetric unit.
indicates data missing or illegible when filed
Structure Determination for the PltM-FAD Intermediate
PltM crystals were soaked in the reservoir solution used to obtained native PltM crystals, with additional 0.5 mM of FAD. The crystals were then gradually transferred to the reservoir solution with 20% v/v PEG 400 and 0.5 mM FAD, prior to quick immersion in liquid nitrogen. The diffraction data were collected and processed as described above. Rigid body refinement followed by restrained refinement were performed starting from the structure of apo PltM. FAD was readily discernable in the omit Fo-Fc map. Refinement and model building was carried out as described above.
Structure Determination for the Holo PltM-FAD Complex
Wild-type PltM and the L111Y mutant (each at 40 mg/mL) were crystallized by using the reservoir solution composed of 0.1 M Tris pH 8, 0.2 M NaBr, 0.1 M CaCl2) and 14% PEG 8000 (10% PEG 8000 in case of the PltM L111Y mutant). The crystals were gradually transferred to the cryoprotectant solution (0.1 M Tris pH 8, 0.2 M NaBr, 1 mM FAD, 16% PEG 8000 (14% PEG 8000 for the PltM L111Y mutant), 20% PEG 400 and 1 mM FAD) and incubated overnight. Prior to rapid freezing via liquid nitrogen, crystals were briefly transferred to the cryoprotectant solution containing additionally 0.2 M sodium dithionite. The crystal structures were determined by a procedure analogous to that described above.
Structure Determination for PltM-FAD-Phloroglucinol Complex
Native crystals of PltM were transferred to reservoir solution with 0.5 mM FAD either without or with 1 mM of phloroglucinol for 10 min, then to the cryoprotectant with the same composition, additionally containing 20% v/v PEG 400. After an overnight incubation, the crystals were rapidly frozen in liquid nitrogen. Compounds 1, 2, 3, 8, 21, 23 and 24 were tested. Data collection, processing, and the structure determination were carried out as described above. FAD was clearly discernable in the omit Fo-Fc electron density map. Out of all substrates tested, only compound 1 (phloroglucinol) yielded omit Fo-Fc electron density. Phloroglucinol was built into a very strong and featureful polder omit mFo-DFc electron density in three out of four substrate binding sites in the asymmetric unit (
Data Availability
The crystal structure coordinates and structure factor amplitudes for all crystal structures were deposited in the Protein Data Bank under accession codes 6BZN, 6BZI, 6BZA, 6BZQ, 6BZT and 6BZZ, as described in Tables 5 and 6. NMR spectra, LC-MS, and other chromatographic data are included in the raw format herein.
All publications, patents, and patent applications mentioned in this specification are herein incorporated by reference to the same extent as if each individual publication, patent, or patent application was specifically and individually indicated to be incorporated by reference, including the references set forth in the following list:
While the disclosure is susceptible to various modifications and alternative forms, specific embodiments thereof have been shown by way of example in the drawings and are herein described below in detail. It should be understood, however, that the description of specific embodiments is not intended to limit the disclosure to cover all modifications, equivalents and alternatives falling within the spirit and scope of the disclosure as defined by the appended claims.
This application claims the benefit of U.S. Provisional Application Ser. No. 62/820,780, filed Mar. 19, 2019, the entire disclosure of which is incorporated herein by this reference.
This invention was made with government support under grant numbers MCB-1149427, awarded by the National Science Foundation (NSF), and UL1TR000117, awarded by the National Institutes of Health (NIH). The Government has certain rights in the invention.
| Number | Date | Country | |
|---|---|---|---|
| 62820780 | Mar 2019 | US |
