Multiple genetic modifications of the erythromycin polyketide synthase to produce a library of novel "unnatural" natural products

Homologation of Ketones: Direct Transformation of Alkyl Ketones to Aryl Ketones via Photoredox Catalyzed Deacylation-Aroylation Sequence

Ketones, as essential functional group skeletons, have garnered significant interest due to their diverse transformations. Herein, we describe a versatile photoredox catalyzed deacylation-aroylation strategy that enables the direct transformation of alkyl ketones to aryl ketones. This process involves photoredox deacylation of dihydroquinazolinones derived from alkyl ketones to generate alkyl radicals, followed by subsequent NHC-catalyzed or NHC-mediated radical aroylation.

Architecture of full-length type I modular polyketide synthases revealed by X-ray crystallography, cryo-electron microscopy, and AlphaFold2

Covering: up to the end of 2023Type I modular polyketide synthases construct polyketide natural products in an assembly line-like fashion, where the growing polyketide chain attached to an acyl carrier protein is passed from catalytic domain to catalytic domain. These enzymes have immense potential in drug development since they can be engineered to produce non-natural polyketides by strategically adding, exchanging, and deleting individual catalytic domains. In practice, however, this approach frequently results in complete failures or dramatically reduced product yields. A comprehensive understanding of modular polyketide synthase architecture is expected to resolve these issues. We summarize the three-dimensional structures and the proposed mechanisms of three full-length modular polyketide synthases, Lsd14, DEBS module 1, and PikAIII. We also describe the advantages and limitations of using X-ray crystallography, cryo-electron microscopy, and AlphaFold2 to study intact type I polyketide synthases.

Advances, opportunities, and challenges in methods for interrogating the structure activity relationships of natural products

Time span in literature: 1985-early 2024Natural products play a key role in drug discovery, both as a direct source of drugs and as a starting point for the development of synthetic compounds. Most natural products are not suitable to be used as drugs without further modification due to insufficient activity or poor pharmacokinetic properties. Choosing what modifications to make requires an understanding of the compound's structure-activity relationships. Use of structure-activity relationships is commonplace and essential in medicinal chemistry campaigns applied to human-designed synthetic compounds. Structure-activity relationships have also been used to improve the properties of natural products, but several challenges still limit these efforts. Here, we review methods for studying the structure-activity relationships of natural products and their limitations. Specifically, we will discuss how synthesis, including total synthesis, late-stage derivatization, chemoenzymatic synthetic pathways, and engineering and genome mining of biosynthetic pathways can be used to produce natural product analogs and discuss the challenges of each of these approaches. Finally, we will discuss computational methods including machine learning methods for analyzing the relationship between biosynthetic genes and product activity, computer aided drug design techniques, and interpretable artificial intelligence approaches towards elucidating structure-activity relationships from models trained to predict bioactivity from chemical structure. Our focus will be on these latter topics as their applications for natural products have not been extensively reviewed. We suggest that these methods are all complementary to each other, and that only collaborative efforts using a combination of these techniques will result in a full understanding of the structure-activity relationships of natural products.

Sustainable Electrochemical Benzylic C-H Oxidation Using MeOH as an Oxygen Source

New methods and strategies for the direct oxidation of benzylic C-H bonds are highly desirable, owing to the importance of ketone motifs in significant organic transformations and the synthesis of valuable molecules, including pharmaceuticals, pesticides, and fine chemicals. Herein, we describe an electrochemical benzylic C-H oxidation strategy for the synthesis of ketones using MeOH as an oxygen source. Inexpensive and safe KBr serves as both an electrolyte and a bromide radical precursor in the reaction. This transformation also offers several advantages such as mild conditions, broad functional group tolerance, and operational simplicity. Mechanistic investigations by control experiments, radical scavenging experiments, electron paramagnetic resonance (EPR), kinetic studies, cyclic voltammetry (CV), and in-situ Fourier transform infrared (FTIR) spectroscopy support a pathway involving the formation and transformation of benzyl methyl ether via hydrogen atom transfer (HAT) and single-electron transfer (SET). The practical application of our strategy is highlighted by the successful synthesis of five pharmaceuticals, namely lenperone, melperone, diphenhydramine, cinnarizine, and flunarizine.

Synthesis of Functionalized Organosilicon Compounds/Distal Ketones via Ring-Opening Giese Addition of Cycloalkanols under Organophotocatalytic Conditions

Visible-light-induced organophotocatalyzed ring-opening followed by remote Giese addition of tertiary cycloalkanols with β-silylmethylene malonates has been developed under mild reaction conditions for the synthesis of organosilicon compounds, bearing a ketone group distally substituted with a silyl group with an additional dialkyl malonate functional handle in moderate to good yields (34-72%). The protocol also worked well with diverse Michael acceptors, such as alkylidene/benzylidene malonates, trifluoro methylidene malonate, benzylidene malononitrile, α-cyano-enone, and α-cyano vinyl sulfone, and delivered desired valuable distally functionalized ketones. To showcase the potential of the method, various synthetic transformations of the obtained product were also demonstrated.

Cooperative Photoredox and N-Heterocyclic Carbene Catalysis Suzuki-Miyaura-Type Reaction: Radical Coupling of Aroyl Fluorides and Alkyl Boronic Acids

An intermolecular Suzuki-Miyaura-type reaction of benzoyl fluorides with alkyl boronic acids to synthetic ketone was revealed by cooperative N-heterocyclic carbene (NHC) and photoredox catalysis. Various alkyl boric acids can be converted into alkyl radicals without external oxidants or activators. Moreover, the catalytic system was feasible for the difunctionalization of styrenes via a radical relay process. Mechanistic experiments suggested that the benzoate anion intermediate might play a unique role in this reaction system.

Pro-aromatic Dihydroquinazolinones - From Multigram Synthesis to Reagents for Gram-scale Metallaphotoredox Reactions

Dihydroquinazolinone (DHQZ) has recently been harnessed as a ketone-derived pro-aromatic reagent extensively employed in (metalla)photoredox reactions as versatile group transfer agents. In this work, we outline a column chromatography-free protocol for the multigram-scale synthesis of pro-aromatic DHQZs as well as its use in a gram-scale nickel/photoredox dual-catalyzed cross-coupling in single-batch, photoflow, and simultaneous multiple smaller batches. While the single-batch approach leveraged moderate yields, a simple plug-flow photoreactor also exhibited amenable productivity (up to 45 % yield) despite the use of a heterogeneous base. Meanwhile, performing the metallaphotoredox-catalyzed reaction in multiple smaller batches in an improvised photoreactor facilitated high yields of up to 59 % and good reproducibility, implying a convenient alternative in the absence of photoflow setups.

Biosensor Guided Polyketide Synthases Engineering for Optimization of Domain Exchange Boundaries

Type I modular polyketide synthases (PKSs) are multi-domain enzymes functioning like assembly lines. Many engineering attempts have been made for the last three decades to replace, delete and insert new functional domains into PKSs to produce novel molecules. However, inserting heterologous domains often destabilize PKSs, causing loss of activity and protein misfolding. To address this challenge, here we develop a fluorescence-based solubility biosensor that can quickly identify engineered PKSs variants with minimal structural disruptions. Using this biosensor, we screen a library of acyltransferase (AT)-exchanged PKS hybrids with randomly assigned domain boundaries, and we identify variants that maintain wild type production levels. We then probe each position in the AT linker region to determine how domain boundaries influence structural integrity and identify a set of optimized domain boundaries. Overall, we have successfully developed an experimentally validated, high-throughput method for making hybrid PKSs that produce novel molecules.

Ketones from aldehydes via alkyl C(sp3)-H functionalization under photoredox cooperative NHC/palladium catalysis

Direct synthesis of ketones from aldehydes features high atom- and step-economy. Yet, the coupling of aldehydes with unactivated alkyl C(sp³)-H remains challenging. Herein, we develop the synthesis of ketones from aldehydes via alkyl C(sp³)-H functionalization under photoredox cooperative NHC/Pd catalysis. The two-component reaction of iodomethylsilyl alkyl ether with aldehydes gave a variety of β-, γ- and δ-silyloxylketones via 1,n-HAT (n = 5, 6, 7) of silylmethyl radicals to generate secondary or tertiary alkyl radicals and following coupling with ketyl radicals from aldehydes under photoredox NHC catalysis. The three-component reaction with the addition of styrenes gave the corresponding ε-hydroxylketones via the generation of benzylic radicals by the addition of alkyl radicals to styrenes and following coupling with ketyl radicals. This work demonstrates the generation of ketyl radical and alkyl radical under the photoredox cooperative NHC/Pd catalysis, and provides two and three component reactions for the synthesis of ketones from aldehydes with alkyl C(sp³)-H functionalization. The synthetic potential of this protocol was also further illustrated by the late-stage functionalization of natural products.

Ti-Catalyzed Modular Ketone Synthesis from Carboxylic Derivatives and gem-Dihaloalkanes

Ketones are ubiquitous in organic synthesis. However, the general method to convert widely available carboxylic acids, unactivated esters, and amides into ketones remains elusive. Herein, we describe the Ti-catalyzed modular ketone synthesis from carboxylic derivatives and easily accessed gem-dihaloalkanes. Notably, this protocol could achieve the direct catalytic olefination of carboxylic acids. This method features a sequence of olefination and electrophilic transformation and good functional group compatibility and allows rapid access to various functionalized ketones. Preliminary mechanistic studies provide insights into the reaction pathway and support the intermediacy of plausible alkylidene titanocene and gem-bimetallic complexes.

Acyltransferase Domain Exchange between Two Independent Type I Polyketide Synthases in the Same Producer Strain of Macrolide Antibiotics

Streptomyces graminofaciens A-8890 produces two macrolide antibiotics, FD-891 and virustomycin A, both of which show significant biological activity. In this study, we identified the virustomycin A biosynthetic gene cluster, which encodes type I polyketide synthases (PKSs), ethylmalonyl-CoA biosynthetic enzymes, methoxymalony-acyl carrier protein biosynthetic enzymes, and post-PKS modification enzymes. Next, we demonstrated that the acyltransferase domain can be exchanged between the Vsm PKSs and the PKSs involved in FD-891 biosynthesis (Gfs PKSs), without any supply problems of the unique extender units. We exchanged the malonyltransferase domain in the loading module of Gfs PKS with the ethylmalonyltransferase domain and the methoxymalonyltransferase domain of Vsm PKSs. Consequently, the expected two-carbon-elongated analog 26-ethyl-FD-891 was successfully produced with a titer comparable to FD-891 production by the wild type; however, exchange with the methoxymalonyltransferase domain did not produce any FD-891 analogs. Furthermore, 26-ethyl-FD-891 showed potent cytotoxic activity against HeLa cells, like natural FD-891.

Carbene and photocatalyst-catalyzed decarboxylative radical coupling of carboxylic acids and acyl imidazoles to form ketones

The carbene and photocatalyst co-catalyzed radical coupling of acyl electrophile and a radical precursor is emerging as attractive method for ketone synthesis. However, previous reports mainly limited to prefunctionalized radical precursors and two-component coupling. Herein, an N-heterocyclic carbene and photocatalyst catalyzed decarboxylative radical coupling of carboxylic acids and acyl imidazoles is disclosed, in which the carboxylic acids are directly used as radical precursors. The acyl imidazoles could also be generated in situ by reaction of a carboxylic acid with CDI thus furnishing a formally decarboxylative coupling of two carboxylic acids. In addition, the reaction is successfully extended to three-component coupling by using alkene as a third coupling partner via a radical relay process. The mild conditions, operational simplicity, and use of carboxylic acids as the reacting partners make our method a powerful strategy for construction of complex ketones from readily available starting materials, and late-stage modification of natural products and medicines.

The combination of carbene- and photocatalysis has enabled unorthodox routes to ketone syntheses, but usually requires engineered or activated substrates. Herein the authors present a carbene- and photocatalytic decarboxylative radical coupling of carboxylic acids and acyl imidazoles, in which the carboxylic acids are directly used as radical precursors.

Synthetic Biology Advanced Natural Product Discovery

A wide variety of bacteria, fungi and plants can produce bioactive secondary metabolites, which are often referred to as natural products. With the rapid development of DNA sequencing technology and bioinformatics, a large number of putative biosynthetic gene clusters have been reported. However, only a limited number of natural products have been discovered, as most biosynthetic gene clusters are not expressed or are expressed at extremely low levels under conventional laboratory conditions. With the rapid development of synthetic biology, advanced genome mining and engineering strategies have been reported and they provide new opportunities for discovery of natural products. This review discusses advances in recent years that can accelerate the design, build, test, and learn (DBTL) cycle of natural product discovery, and prospects trends and key challenges for future research directions.

From Esters to Ketones via a Photoredox-Assisted Reductive Acyl Cross-Coupling Strategy

A method was developed for ketone synthesis via a photoredox-assisted reductive acyl cross-coupling (PARAC) using a nickel/photoredox dual-catalyzed cross-electrophile coupling of two different carboxylic acid esters. A variety of aryl, 1°, 2°, 3°-alkyl 2-pyridyl esters can act as acyl electrophiles while N-(acyloxy)phthalimides (NHPI esters) act as 1°, 2°, 3°-radical precursors. Our PARAC strategy provides an alternative and reliable way to synthesize various sterically congested 3°-3°, 3°-2°, and aryl-3° ketones under mild and highly unified conditions, which have been otherwise difficult to access. The combined experimental and computational studies identified a Ni⁰ /Ni^I /Ni^III pathway for ketone formation.

Engineering biosynthetic enzymes for industrial natural product synthesis

Covering: 2000 to 2020 Natural products and their derivatives are commercially important medicines, agrochemicals, flavors, fragrances, and food ingredients. Industrial strategies to produce these structurally complex molecules encompass varied combinations of chemical synthesis, biocatalysis, and extraction from natural sources. Interest in engineering natural product biosynthesis began with the advent of genetic tools for pathway discovery. Genes and strains can now readily be synthesized, mutated, recombined, and sequenced. Enzyme engineering has succeeded commercially due to the development of genetic methods, analytical technologies, and machine learning algorithms. Today, engineered biosynthetic enzymes from organisms spanning the tree of life are used industrially to produce diverse molecules. These biocatalytic processes include single enzymatic steps, multienzyme cascades, and engineered native and heterologous microbial strains. This review will describe how biosynthetic enzymes have been engineered to enable commercial and near-commercial syntheses of natural products and their analogs.

Photoredox/nickel-catalyzed hydroacylation of ethylene with aromatic acids

We report a general, practical and scalable hydroacylation reaction of ethylene with aromatic carboxylic acids with the synergistic combination of nickel and photoredox catalysis. Under ambient temperature and pressure, feedstock chemicals such as ethylene can be converted into high-value-added aromatic ketones in moderate to good yields (up to 92%) with reaction time of 2-6 hours.

One Pot Conversion of Carboxylic Acid to Ketone Using Trimethylsilyl Chloride

Background:

Ketone is abundant in many natural products and in pharmaceuticals. It is believed to be one of the important functional groups in organic chemistry. Till date,several research approaches have been made to access ketone from a readily available starting materials. One such notable transformation consists of the conversion of carboxylic acid to the corresponding ketone in a one pot manner.

Objective:

We aimed to develop a simple one pot reaction for the conversion of carboxylic acid to ketone. This reaction could be useful to convert all types of carboxylic acid to ketone in a facile manner.

Methods:

In this procedure, a carboxylic acid has been converted to the corresponding trimethylsilyl ester using trimethylsilyl chloride in the presence of a base. A suitable organometallic reagent can interact with the ester formed at 20°C to produce the corresponding ketone.

Results:

Under the optimized reaction conditions, various aromatic, aliphatic and heteroaromatic carboxylic acids have been converted to the corresponding ketones using organolithium reagents, in a one pot manner. Moderate to good yields of the desired ketones were observed in most of the transformations.

Conclusion:

Conversion of carboxylic acid to ketone has been reported in a one pot fashion, where carboxylic acid has been transformed to its silyl ester. Organolithium reagents were used as nucleophile for our reaction purpose, whereas the organomagnesium reagents were not useful for this transformation. Aliphatic, aromatic and heteroaromatic carboxylic acids have been converted to the ketones following a simple process.

Transition Metal Catalyst-Free, Base-Promoted 1,2-Additions of Polyfluorophenylboronates to Aldehydes and Ketones

A novel protocol for the transition metal-free 1,2-addition of polyfluoroaryl boronate esters to aldehydes and ketones is reported, which provides secondary alcohols, tertiary alcohols, and ketones. Control experiments and DFT calculations indicate that both the ortho-F substituents on the polyfluorophenyl boronates and the counterion K+ in the carbonate base are critical. The distinguishing features of this procedure include the employment of commercially available starting materials and the broad scope of the reaction with a wide variety of carbonyl compounds giving moderate to excellent yields. Intriguing structural features involving O-H⋅⋅⋅O and O-H⋅⋅⋅N hydrogen bonding, as well as arene-perfluoroarene interactions, in this series of racemic polyfluoroaryl carbinols have also been addressed.

A Global Approach to Estimating the Abundance and Duplication of Polyketide Synthase Domains in Dinoflagellates

Many dinoflagellate species make toxins in a myriad of different molecular configurations but the underlying chemistry in all cases is presumably via modular synthases, primarily polyketide synthases. In many organisms modular synthases occur as discrete synthetic genes or domains within a gene that act in coordination thus forming a module that produces a particular fragment of a natural product. The modules usually occur in tandem as gene clusters with a syntenic arrangement that is often predictive of the resultant structure. Dinoflagellate genomes however are notoriously complex with individual genes present in many tandem repeats and very few synthetic modules occurring as gene clusters, unlike what has been seen in bacteria and fungi. However, modular synthesis in all organisms requires a free thiol group that acts as a carrier for sequential synthesis called a thiolation domain. We scanned 47 dinoflagellate transcriptomes for 23 modular synthase domain models and compared their abundance among 10 orders of dinoflagellates as well as their co-occurrence with thiolation domains. The total count of domain types was quite large with over thirty-thousand identified, 29 000 of which were in the core dinoflagellates. Although there were no specific trends in domain abundance associated with types of toxins, there were readily observable lineage specific differences. The Gymnodiniales, makers of long polyketide toxins such as brevetoxin and karlotoxin had a high relative abundance of thiolation domains as well as multiple thiolation domains within a single transcript. Orders such as the Gonyaulacales, makers of small polyketides such as spirolides, had fewer thiolation domains but a relative increase in the number of acyl transferases. Unique to the core dinoflagellates, however, were thiolation domains occurring alongside tetratricopeptide repeats that facilitate protein-protein interactions, especially hexa and hepta-repeats, that may explain the scaffolding required for synthetic complexes capable of making large toxins. Clustering analysis for each type of domain was also used to discern possible origins of duplication for the multitude of single domain transcripts. Single domain transcripts frequently clustered with synonymous domains from multi-domain transcripts such as the BurA and ZmaK like genes as well as the multi-ketosynthase genes, sometimes with a large degree of apparent gene duplication, while fatty acid synthesis genes formed distinct clusters. Surprisingly the acyl-transferases and ketoreductases involved in fatty acid synthesis (FabD and FabG, respectively) were found in very large clusters indicating an unprecedented degree of gene duplication for these genes. These results demonstrate a complex evolutionary history of core dinoflagellate modular synthases with domain specific duplications throughout the lineage as well as clues to how large protein complexes can be assembled to synthesize the largest natural products known.

Hemiacetal-less rapamycin derivatives designed and produced by genetic engineering of a type I polyketide synthase

Engineering polyketide synthases is one of the most promising ways of producing a variety of polyketide derivatives. Exploring the undiscovered chemical space of this medicinally important class of middle molecular weight natural products will aid in the development of improved drugs in the future. In previous work, we established methodology designated 'module editing' to precisely manipulate polyketide synthase genes cloned in a bacterial artificial chromosome. Here, in the course of investigating the engineering capacity of the rapamycin PKS, novel rapamycin derivatives 1-4, which lack the hemiacetal moiety, were produced through the heterologous expression of engineered variants of the rapamycin PKS. Three kinds of module deletions in the polyketide synthase RapC were designed, and the genetically engineered vectors were prepared by the in vitro module editing technique. Streptomyces avermitilis SUKA34 transformed with these edited PKSs produced new rapamycin derivatives. The planar structures of 1-4 established based on 1D and 2D NMR, ESI-TOF-MS and UV spectra revealed that 2 and 3 had skeletons well-matched to the designs, but 1 and 4 did not. The observations provide important insights into the mechanisms of the later steps of rapamycin skeletal formation as well as the ketone-forming oxygenase RapJ.

Engineering the acyltransferase domain of epothilone polyketide synthase to alter the substrate specificity

Background

Polyketide synthases (PKSs) include ketone synthase (KS), acyltransferase (AT) and acyl carrier protein (ACP) domains to catalyse the elongation of polyketide chains. Some PKSs also contain ketoreductase (KR), dehydratase (DH) and enoylreductase (ER) domains as modification domains. Insertion, deletion or substitution of the catalytic domains may lead to the production of novel polyketide derivatives or to the accumulation of desired products. Epothilones are 16-membered macrolides that have been used as anticancer drugs. The substrate promiscuity of the module 4 AT domain of the epothilone PKS (EPOAT4) results in production of epothilone mixtures; substitution of this domain may change the ratios of epothilones. In addition, there are two dormant domains in module 9 of the epothilone PKS. Removing these redundant domains to generate a simpler and more efficient assembly line is a desirable goal.

Results

The substitution of module 4 drastically diminished the activity of epothilone PKS. However, with careful design of the KS-AT linker and the post-AT linker, replacing EPOAT4 with EPOAT2, EPOAT6, EPOAT7 or EPOAT8 (specifically incorporating methylmalonyl-CoA (MMCoA)) significantly increased the ratio of epothilone D (4) to epothilone C (3) (the highest ratio of 4:3 = 4.6:1), whereas the ratio of 4:3 in the parental strain Schlegelella brevitalea 104-1 was 1.4:1. We also obtained three strains by swapping EPOAT4 with EPOAT3, EPOAT5, or EPOAT9, which specifically incorporate malonyl-CoA (MCoA). These strains produced only epothilone C, and the yield was increased by a factor of 1.8 compared to that of parental strain 104-1. Furthermore, mutations of five residues in the AT domain identified Ser310 as the critical factor for MMCoA recognition in EPOAT4. Then, the mutation of His308 to valine or tyrosine combined with the mutation of Phe310 to serine further altered the product ratios. At the same time, we successfully deleted the inactive module 9 DH and ER domains and fused the ΨKR domain with the KR domain through an ~ 25-residue linker to generate a productive and simplified epothilone PKS.

Conclusions

These results suggested that the substitution and deletion of catalytic domains effectively produces desirable compounds and that selection of the linkers between domains is crucial for maintaining intact PKS catalytic activity.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12934-021-01578-3.

Synthesis of Ketones by C-H Functionalization of Aldehydes with Boronic Acids under Transition-Metal-Free Conditions

A method for the synthesis of ketones from aldehydes and boronic acids via a transition-metal-free C-H functionalization reaction is reported. The method employs nitrosobenzene as a reagent to drive the simultaneous activation of the boronic acid as a boronate and the activation of the C-H bond of the aldehyde as an iminium species that triggers the key C-C bond-forming step via an intramolecular migration from boron to carbon. These findings constitute a practical, scalable, and operationally straightforward method for the synthesis of ketones.

Differential mass spectrometry-based proteome analyses unveil major regulatory hubs in rifamycin B production in Amycolatopsis mediterranei

Rifamycin B is produced by Amycolatopsis mediterranei S699 as a secondary metabolite. Its semi-synthetic derivatives have been used for curing tuberculosis caused by Mycobacterium tuberculosis. But the emergence of rifampicin-resistant strains required analogs of rifamycin B to be developed by rifamycin biosynthetic gene cluster manipulation. In 2014 genetic engineering of the rifamycin polyketide synthase gene cluster in S699 led to a mutant, A. mediterranei DCO#34, that produced 24-desmethylrifamycin B. Unfortunately, the productivity was strongly reduced to 20 mgL^-1 as compared to 50 mgL^-1 of rifamycin B. To understand the mechanisms leading to reduced productivity and rifamycin biosynthesis by A. mediterranei S699 during the early and late growth phase we performed a proteome study for wild type strain S699, mutant DCO#34, and the non-producer strain SCO2-2. Proteins identification and relative label-free quantification were performed by nLC-MS/MS. Data are available via ProteomeXchange with identifier PXD016416. Also, in-silico protein-protein interaction approach was used to determine the relationship between different structural and regulatory proteins involved in rifamycin biosynthesis. Our studies revealed RifA, RifK, RifL, Rif-Orf19 as the major regulatory hubs. Relative abundance expression values revealed that genes encoding RifC-RifI and the transporter RifP, down-regulated in DCO#34 and genes encoding RifR, RifZ, other regulatory proteins up-regulated. SIGNIFICANCE: The study is designed mainly to understand the underlying mechanisms of rifamycin biosynthesis in Amycolatopsis mediterranei. This resulted in the identification of regulatory hubs which play a crucial role in regulating secondary metabolism. It elucidates the complex mechanism of secondary metabolite biosynthesis and their conversion and extracellular transportation in temporal correlation with the different growth phases. The study also elucidated the mechanisms leading to reduced production of analog, 24-desmethylrifamycin B by the genetically modified strain DCO#34, derivatives of which have been found effective against rifampicin-resistant strains of Mycobacterium tuberculosis. These results can be useful while carrying out genetic manipulations to improve the strains of Amycolatopsis to produce better analogs/drugs and promote the eradication of TB. Thus, this study is contributing significantly to the growing knowledge in the field of the crucial drug, rifamycin B biosynthesis by an economically important bacterium Amycolatopsis mediterranei.

A General Approach to Intermolecular Olefin Hydroacylation through Light-Induced HAT Initiation: An Efficient Synthesis of Long-Chain Aliphatic Ketones and Functionalized Fatty Acids

Herein, an operationally simple, environmentally benign and effective method for intermolecular radical hydroacylation of unactivated substrates by employing photo-induced hydrogen atom transfer (HAT) initiation is described. The use of commercially available and inexpensive photoinitiators (Ph₂ CO and NHPI) makes the process attractive. The olefin hydroacylation protocol applies to a wide array of substrates bearing numerous functional groups and many complex structural units. The reaction proves to be scalable (up to 5 g). Different functionalized fatty acids, petrochemicals and naturally occurring alkanes can be synthesized with this protocol. A radical chain mechanism is implicated in the process.

RedEx: a method for seamless DNA insertion and deletion in large multimodular polyketide synthase gene clusters

Biosynthesis reprograming is an important way to diversify chemical structures. The large repetitive DNA sequences existing in polyketide synthase genes make seamless DNA manipulation of the polyketide biosynthetic gene clusters extremely challenging. In this study, to replace the ethyl group attached to the C-21 of the macrolide insecticide spinosad with a butenyl group by refactoring the 79-kb gene cluster, we developed a RedEx method by combining Redαβ mediated linear-circular homologous recombination, ccdB counterselection and exonuclease mediated in vitro annealing to insert an exogenous extension module in the polyketide synthase gene without any extra sequence. RedEx was also applied for seamless deletion of the rhamnose 3′-O-methyltransferase gene in the spinosad gene cluster to produce rhamnosyl-3′-desmethyl derivatives. The advantages of RedEx in seamless mutagenesis will facilitate rational design of complex DNA sequences for diverse purposes.

Complex natural product production methods and options

Natural products have had a major impact upon quality of life, with antibiotics as a classic example of having a transformative impact upon human health. In this contribution, we will highlight both historic and emerging methods of natural product bio-manufacturing. Traditional methods of natural product production relied upon native cellular host systems. In this context, pragmatic and effective methodologies were established to enable widespread access to natural products. In reviewing such strategies, we will also highlight the development of heterologous natural product biosynthesis, which relies instead on a surrogate host system theoretically capable of advanced production potential. In comparing native and heterologous systems, we will comment on the base organisms used for natural product biosynthesis and how the properties of such cellular hosts dictate scaled engineering practices to facilitate compound distribution. In concluding the article, we will examine novel efforts in production practices that entirely eliminate the constraints of cellular production hosts. That is, cell free production efforts will be introduced and reviewed for the purpose of complex natural product biosynthesis. Included in this final analysis will be research efforts made on our part to test the cell free biosynthesis of the complex polyketide antibiotic natural product erythromycin.

Organocatalytic Three-Component 1,2-Cyanoalkylacylation of Alkenes via Radical Relay

Here, we report an unprecedented regioselective, intermolecular 1,2-cyanoalkylacylation of feedstock alkenes with readily available oxime esters and aldehydes by N-heterocyclic carbene (NHC) organocatalysis. The crux of this success is the exquisite control over the radical relay process by an NHC organocatalyst. This protocol offers a general platform for diversity-oriented synthesis of valuable ketonitriles under mild, transition-metal-free, and redox-neutral conditions and highlights its potential in the late-stage functionalization of pharmaceutical architectures and natural products.

Exploration of Mesyl Chloride in a One Pot Conversion of Carboxylic Acids to Ketones

Background:

Due to the ubiquitous nature of the ketone functionality, it is considered an important functional group in organic chemistry. Hence, the synthesis of ketones from readily available starting materials is an important chemical transformation in organic synthesis. Consequently, several research efforts have been reported in the literature for the transformation of carboxylic acids to ketones in a one-pot synthesis. However, some of the procedures have limitations, such as long reaction times, harsh reaction conditions, and usage of expensive metal catalysts. Thus, a simple and convenient one-pot conversion of carboxylic acids to ketones remains desirable.

Objective:

We intended to develop a simple and convenient one-pot methodology for the synthesis of ketones from carboxylic acids. Our objective was to build up a carboxylic acid-based chemical template where various types of organometallic reagents can interact to produce the desired ketone.

Methods:

In this procedure, a carboxylic acid was converted to a mixed anhydride using mesyl chloride in the presence of a base. This mixed anhydride was then reacted with a suitable organometallic reagent at -20°C to obtain the desired ketone. The reaction was performed in a one-pot fashion.

Results:

Under the optimized reaction conditions, various aromatic and heteroaromatic carboxylic acids were converted to the corresponding ketones using organolithium and organomagnesium reagents with short reaction times. Moderate to good yields of the desired ketones were observed in many of these transformations.

Conclusion:

A simple and convenient one-pot method for the conversion of carboxylic acids to ketones has been reported. Specifically, various aromatic and `heteroaromatic carboxylic acids have been converted to the corresponding ketones in moderate to good yields. Organomagnesium and organolithium reagents were used as nucleophiles for this reaction.

In vitro Cas9-assisted editing of modular polyketide synthase genes to produce desired natural product derivatives

One major bottleneck in natural product drug development is derivatization, which is pivotal for fine tuning lead compounds. A promising solution is modifying the biosynthetic machineries of middle molecules such as macrolides. Although intense studies have established various methodologies for protein engineering of type I modular polyketide synthase(s) (PKSs), the accurate targeting of desired regions in the PKS gene is still challenging due to the high sequence similarity between its modules. Here, we report an innovative technique that adapts in vitro Cas9 reaction and Gibson assembly to edit a target region of the type I modular PKS gene. Proof-of-concept experiments using rapamycin PKS as a template show that heterologous expression of edited biosynthetic gene clusters produced almost all the desired derivatives. Our results are consistent with the promiscuity of modular PKS and thus, our technique will provide a platform to generate rationally designed natural product derivatives for future drug development.

Several different genetic strategies have been reported for the modification of polyketide synthases but the highly repetitive modular structure makes this difficult. Here the authors report on an adapted Cas9 reaction and Gibson assembly to edit a target region of the polyketide synthases gene in vitro.

Upgrading ketone synthesis direct from carboxylic acids and organohalides

The ketone functional group has a unique reactivity in organic chemistry and is associated with a number of useful reactions. Catalytic methods for ketone synthesis are continually being developed. Here, we report a photoredox, nickel and phosphoranyl radical synergistic cross-electrophile coupling of commercially available chemicals, aromatic acids and aryl/alkyl bromides. This allows for concise synthesis of highly functionalized ketones directly, without the preparation of activated carbonyl intermediates or organometallic compounds, and thus complements the conventional Weinreb ketone synthesis. Use of the appropriate photocatalyst, ligand amount and solvents can match the reaction rate required by any simple catalytic cycle. The practicality and synthetic robustness of the reaction are illustrated by the facile synthesis of complex ketones from readily available feedstock chemicals.

Due to their abundance and importance in organic chemistry, development of methods for ketone synthesis is essential. Here, the authors report a photoredox, nickel and phosphoranyl radical synergistic cross-electrophile coupling of aromatic acids and aryl/alkyl bromides to directly synthesise ketones.

Probing Selectivity and Creating Structural Diversity Through Hybrid Polyketide Synthases

Engineering polyketide synthases (PKS) to produce new metabolites requires an understanding of catalytic points of failure during substrate processing. Growing evidence indicates the thioesterase (TE) domain as a significant bottleneck within engineered PKS systems. We created a series of hybrid PKS modules bearing exchanged TE domains from heterologous pathways and challenged them with both native and non-native polyketide substrates. Reactions pairing wildtype PKS modules with non-native substrates primarily resulted in poor conversions to anticipated macrolactones. Likewise, product formation with native substrates and hybrid PKS modules bearing non-cognate TE domains was severely reduced. In contrast, non-native substrates were converted by most hybrid modules containing a substrate compatible TE, directly implicating this domain as the major catalytic gatekeeper and highlighting its value as a target for protein engineering to improve analog production in PKS pathways.

Bacteria as genetically programmable producers of bioactive natural products

Next to plants, bacteria account for most of the biomass on Earth. They are found everywhere, although certain species thrive only in specific ecological niches. These microorganisms biosynthesize a plethora of both primary and secondary metabolites, defined, respectively, as those required for the growth and maintenance of cellular functions and those not required for survival but offering a selective advantage for the producer under certain conditions. As a result, bacterial fermentation has long been used to manufacture valuable natural products of nutritional, agrochemical and pharmaceutical interest. The interactions of secondary metabolites with their biological targets have been optimized by millions of years of evolution and they are, thus, considered to be privileged chemical structures, not only for drug discovery. During the last two decades, functional genomics has allowed for an in-depth understanding of the underlying biosynthetic logic of secondary metabolites. This has, in turn, paved the way for the unprecedented use of bacteria as programmable biochemical workhorses. In this Review, we discuss the multifaceted use of bacteria as biological factories in diverse applications and highlight recent advances in targeted genetic engineering of bacteria for the production of valuable bioactive compounds. Emphasis is on current advances to access nature's abundance of natural products.

Evolution and Diversity of Assembly-Line Polyketide Synthases

Assembly-line polyketide synthases (PKSs) are among the most complex protein machineries known in nature, responsible for the biosynthesis of numerous compounds used in the clinic. Their present-day diversity is the result of an evolutionary path that has involved the emergence of a multimodular architecture and further diversification of assembly-line PKSs. In this review, we provide an overview of previous studies that investigated PKS evolution and propose a model that challenges the currently prevailing view that gene duplication has played a major role in the emergence of multimodularity. We also analyze the ensemble of orphan PKS clusters sequenced so far to evaluate how large the entire diversity of assembly-line PKS clusters and their chemical products could be. Finally, we examine the existing techniques to access the natural PKS diversity in natural and heterologous hosts and describe approaches to further expand this diversity through engineering.