Biosynthesis and Structure-Activity Relationship Studies of Okaramines That Target Insect Glutamate-Gated Chloride Channels

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.

Genomic and Comparative Transcriptomic Analyses Reveal Key Genes Associated with the Biosynthesis Regulation of Okaramine B in Penicillium daleae NBP-49626

Restricted production of fungal secondary metabolites hinders the ability to conduct comprehensive research and development of novel biopesticides. Okaramine B from Penicillium demonstrates remarkable insecticidal efficacy; however, its biosynthetic yield is low, and its regulatory mechanism remains unknown. The present study found that the yield difference was influenced by fermentation modes in okaramine-producing strains and performed genomic and comparative transcriptome analysis of P. daleae strain NBP-49626, which exhibits significant features. The NBP-49626 genome is 37.4 Mb, and it encodes 10,131 protein-encoding genes. Up to 5097 differentially expressed genes (DEGs) were identified during the submerged and semi-solid fermentation processes. The oka gene cluster, lacking regulatory and transport genes, displayed distinct transcriptional patterns in response to the fermentation modes and yield of Okaramine B. Although transcription trends of most known global regulatory genes are inconsistent with those of oka, this study identified five potential regulatory genes, including two novel Zn(II)2Cys6 transcription factors, Reg2 and Reg19. A significant correlation was also observed between tryptophan metabolism and Okaramine B yields. In addition, several transporter genes were identified as DEGs. These results were confirmed using real-time quantitative PCR. This study provides comprehensive information regarding the regulatory mechanism of Okaramine B biosynthesis in Penicillium and is critical to the further yield improvement for the development of insecticides.

Biosyntheses of azetidine-containing natural products

Azetidine is a four-membered polar heterocycle including a basic secondary amine, and is characterized by its high ring-strain energy, strong molecular rigidity and satisfactory stability. As a result, azetidine exhibits great challenges in its chemical synthesis and biosynthesis, which may explain the limited number of azetidine-containing natural products uncovered to date. In particular, the biosynthetic mechanisms of naturally occurring azetidines are poorly understood. Only some of them have been intensively investigated and few reviews have been published for the summarization of azetidine biosynthesis. In this review, we provide a comprehensive description of the biosyntheses of all the azetidine-containing natural products, especially the biosyntheses of azetidine moieties. We hope that this review will draw much attention to the biosynthetic research of the largely unexplored azetidine moieties as well as the discovery of novel azetidine-containing natural products in the near future.

Halogenated Indoles Decrease the Virulence of Vibrio campbellii in a Gnotobiotic Brine Shrimp Model

Indole signaling is viewed as a potential target for antivirulence therapy against antibiotic-resistant pathogens because of its link with the production of virulence factors. This study examined the antimicrobial and antivirulence properties of 44 indoles toward Vibrio campbellii. Based on the results, 17 halogenated indole analogues were selected, as they significantly improved the survival of brine shrimp larvae challenged with V. campbellii. Specifically, 6-bromoindole, 7-bromoindole, 4-fluoroindole, 5-iodoindole, and 7-iodoindole showed a high protective effect, improving the survival of brine shrimp to over 80% even at a low concentration of 10 μM. To explore the impact of selected indole analogues on bacterial virulence phenotypes, swimming motility, biofilm formation, protease activity, and hemolytic activity of V. campbellii were determined. The results showed that all of the 17 selected indole analogues decreased swimming motility at both 10 μM and 100 μM. Most of the indole analogues decreased biofilm formation at a concentration of 100 μM. In contrast, only a slightly decreased protease activity and no effect on hemolytic activity were observed at both concentrations. To our knowledge, this is the first study of the structure-activity relation of halogenated indole analogues with respect to virulence inhibition of a pathogenic bacterium in an in vivo host model system, and the results demonstrate the potential of these compounds in applications aiming at the protection of shrimp from vibriosis, a major disease in aquaculture. IMPORTANCE Bacterial diseases are a major problem in the aquaculture industry. In order to counter this problem, farmers have been using antibiotics, and this has led to the evolution and spread of antibiotic resistance. In order for the aquaculture industry to further grow in a sustainable way, novel and sustainable methods to control diseases are needed. We previously reported that indole signaling is a valid target for the development of novel therapies to control disease caused by Vibrio campbellii and related bacteria, which are among the major bacterial pathogens in aquaculture. In the present study, we identified indole analogues that are more potent in protecting brine shrimp (a model organism for shrimp) from V. campbellii. To our knowledge, this is the first study of the structure-activity relation of halogenated indole analogues with respect to virulence inhibition of a pathogenic bacterium in an in vivo host model system.

Data Science-Driven Analysis of Substrate-Permissive Diketopiperazine Reverse Prenyltransferase NotF: Applications in Protein Engineering and Cascade Biocatalytic Synthesis of (-)-Eurotiumin A

Prenyltransfer is an early-stage carbon-hydrogen bond (C-H) functionalization prevalent in the biosynthesis of a diverse array of biologically active bacterial, fungal, plant, and metazoan diketopiperazine (DKP) alkaloids. Toward the development of a unified strategy for biocatalytic construction of prenylated DKP indole alkaloids, we sought to identify and characterize a substrate-permissive C2 reverse prenyltransferase (PT). As the first tailoring event within the biosynthesis of cytotoxic notoamide metabolites, PT NotF catalyzes C2 reverse prenyltransfer of brevianamide F. Solving a crystal structure of NotF (in complex with native substrate and prenyl donor mimic dimethylallyl S-thiolodiphosphate (DMSPP)) revealed a large, solvent-exposed active site, intimating NotF may possess a significantly broad substrate scope. To assess the substrate selectivity of NotF, we synthesized a panel of 30 sterically and electronically differentiated tryptophanyl DKPs, the majority of which were selectively prenylated by NotF in synthetically useful conversions (2 to >99%). Quantitative representation of this substrate library and development of a descriptive statistical model provided insight into the molecular origins of NotF's substrate promiscuity. This approach enabled the identification of key substrate descriptors (electrophilicity, size, and flexibility) that govern the rate of NotF-catalyzed prenyltransfer, and the development of an "induced fit docking (IFD)-guided" engineering strategy for improved turnover of our largest substrates. We further demonstrated the utility of NotF in tandem with oxidative cyclization using flavin monooxygenase, BvnB. This one-pot, in vitro biocatalytic cascade enabled the first chemoenzymatic synthesis of the marine fungal natural product, (-)-eurotiumin A, in three steps and 60% overall yield.

Biosynthesis of pyrroloindoline-containing natural products

Covering: up to 2022Pyrroloindoline is a privileged tricyclic indoline motif widely present in many biologically active and medicinally valuable natural products. Thus, understanding the biosynthesis of this molecule is critical for developing convenient synthetic routes, which is highly challenging for its chemical synthesis due to the presence of rich chiral centers in this molecule, especially the fully substituted chiral carbon center at the C3-position of its rigid tricyclic structure. In recent years, progress has been made in elucidating the biosynthetic pathways and enzymatic mechanisms of pyrroloindoline-containing natural products (PiNPs). This article reviews the main advances in the past few decades based on the different substitutions on the C3 position of PiNPs, especially the various key enzymatic mechanisms involved in the biosynthesis of different types of PiNPs.

Natural products from mangrove sediments-derived microbes: Structural diversity, bioactivities, biosynthesis, and total synthesis

The mangrove forests are a complex ecosystem, and the microbial communities in mangrove sediments play a critical role in the biogeochemical cycles of mangrove ecosystems. Mangrove sediments-derived microbes (MSM), as a rich reservoir of natural product diversity, could be utilized in the exploration of new antibiotics or drugs. To understand the structural diversity and bioactivities of the metabolites of MSM, this review for the first time provides a comprehensive overview of 519 natural products isolated from MSM with their bioactivities, up to 2021. Most of the structural types of these compounds are alkaloids, lactones, xanthones, quinones, terpenoids, and steroids. Among them, 210 compounds are obtained from bacteria, most of which are from Streptomyces, while 309 compounds are from fungus, especially genus Aspergillus and Penicillium. The pharmacological mechanisms of some representative lead compounds are well studied, revealing that they have important medicinal potentials, such as piericidins with anti-renal cell cancer effects, azalomycins with anti-MRSA activities, and ophiobolins as antineoplastic agents. The biosynthetic pathways of representative natural products from MSM have also been summarized, especially ikarugamycin, piericidins, divergolides, and azalomycins. In addition, the total synthetic strategies of representative secondary metabolites from MSM are also reviewed, such as piericidin A and borrelidin. This review provides an important reference for the research status of natural products isolated from MSM and the lead compounds worthy of further development, and reveals that MSM have important medicinal values and are worthy of further development.

Azobenzene-Avermectin B1a Derivatives for Optical Modulation of Insect Behaviors

Naturally occurring avermectins are allosteric modulators of glutamate-gated chloride channels (GluCls) and possess exceptionally potent anthelmintic, acaricidal, and insecticidal activities. Here, we develop photoswitchable azobenzene-avermectin (ABAVM) derivatives, which can be photoactivated upon ultraviolet irradiation. After illumination, the best compound p-AB4″AVM had a 1.88-fold and 2.74-fold insecticidal activity enhancement toward Culex pipiens pallens and Mythimna separata larvae, respectively. p-AB4″AVM allows for optical regulation of dorsal unpaired median neuron membrane potential with a 2.15-fold fluorescence intensity decrease after illumination. p-AB4″AVM and p-AB5AVM enable optical modulation of the behavioral response of Culex pipiens pallens larvae with 1- and 4-fold reduced mobility upon irradiation, respectively. The ABAVMs could be used to reversibly manipulate GluCls with light and may be useful for the mechanistic study of macrocyclic lactone insecticides.

Chemical and biological studies of natural and synthetic products for the highly selective control of pest insect species

Tanacetum cinerariifolium was known to produce pyrethrins, but the mechanism of pyrethrin biosynthesis was largely unclear. The author showed that the nonmevalonate and oxylipin pathways underlie biosynthesis of the acid and alcohol moieties, respectively, and a GDSL lipase joins the products of these pathways. A blend of the green leaf volatiles and (E)-β-farnesene mediates the induction of wounding responses to neighboring intact conspecies by enhancing pyrethrin biosynthesis. Plants fight against herbivores underground as well as aboveground, and, in soy pulps, some fungi produce compounds selectively modulating ion channels in insect nervous system. The author proposed that indirect defense of plants occurs where microorganisms produce defense substances in the rhizosphere. Broad-spectrum pesticides, including neonicotinoids, may affect nontarget organisms. The author discovered cofactors enabling functional expression of insect nicotinic acetylcholine receptors (nAChRs). This led to understanding the mechanism of insect nAChR-neonicotinoid interactions, thus paving new avenues for controlling crop pests and disease vectors.

Divergent syntheses of okaramines C, J, L, and S-U

The total synthesis of six novel okaramines (C, J, L, and S-U) was accomplished with a precise synthesis scheme involving a few steps and a practical yield of 6.7%-23% was obtained. The significance of this study includes the design of a successful and convenient synthesis method for preparation of 3a-hydroxy-pyrrolo[2,3-b]-indole and C-7 prenylated l-tryptophan derivatives using a nucleophilic attack of cyclopropylazetoindoline and an aza-Claisen rearrangement of N-reverse-prenyl tryptophan, respectively.

Turning a Drug Target into a Drug Candidate: A New Paradigm for Neurological Drug Discovery?

The conventional paradigm for developing new treatments for disease mainly involves either the discovery of new drug targets, or finding new, improved drugs for old targets. However, an ion channel found only in invertebrates offers the potential of a completely new paradigm in which an established drug target can be re-engineered to serve as a new candidate therapeutic agent. The L-glutamate-gated chloride channels (GluCls) of invertebrates are absent from vertebrate genomes, offering the opportunity to introduce this exogenous, inhibitory, L-glutamate receptor into vertebrate neuronal circuits either as a tool with which to study neural networks, or a candidate therapy. Epileptic seizures can involve L-glutamate-induced hyper-excitation and toxicity. Variant GluCls, with their inhibitory responses to L-glutamate, when engineered into human neurons, might counter the excitotoxic effects of excess L-glutamate. In reviewing recent studies on model organisms, it appears that this approach might offer a new paradigm for the development of candidate therapeutics for epilepsy.

Metabolome Analysis Identified Okaramines in the Soybean Rhizosphere as a Legacy of Hairy Vetch

Inter-organismal communications below ground, such as plant-microbe interactions in the rhizosphere, affect plant growth. Metabolites are shown to play important roles in biological communication, but there still remain a large number of metabolites in soil to be uncovered. Metabolomics, a technique for the comprehensive analysis of metabolites in samples, may uncover the molecules that intermediate these interactions. We conducted a multivariate analysis using liquid chromatography (LC)-mass spectrometry (MS)-based untargeted metabolomics in several soil samples and also targeted metabolome analysis for the identification of the candidate compounds in soil. We identified okaramine A, B, and C in the rhizosphere soil of hairy vetch. Okaramines are indole alkaloids first identified in soybean pulp (okara) inoculated with Penicillium simplicissimum AK-40 and are insecticidal. Okaramine B was detected in the rhizosphere from an open field growing hairy vetch. Okaramine B was also detected in both bulk and rhizosphere soils of soybean grown following hairy vetch, but not detected in soils of soybean without hairy vetch growth. These results suggested that okaramines might be involved in indirect defense of plants against insects. To our knowledge, this is the first report of okaramines in the natural environment. Untargeted and targeted metabolomics would be useful to uncover the chemistry of the rhizosphere.

Bioorganic chemistry of signaling molecules in microbial communication

Microorganisms produce and secrete a variety of secondary metabolites including fatty acids, polyketides, terpenoids, alkaloids, and peptides. Among them, many molecules act as chemical signals that play important roles in inter-/intra-species microbial communication or the interaction with host organisms. In this review, I focus on our recent reports of the microbial signaling molecules involved in bacterium-fungus, bacterium-plant, and fungus-plant interactions. Their potential contribution to pest management is also discussed.

Non-lipopeptide fungi-derived peptide antibiotics developed since 2000

The 2,5-diketopiperazines (DKPs) are the smallest cyclopeptides and their basic structure includes a six-membered piperazine nucleus. Typical peptides lack a special functional group in the oligopeptide nucleus. Both are produced by at least 35 representative genera of fungi, and possess huge potential as pharmaceutical drugs and biocontrol agents. To date, only cyclosporin A has been developed into a commercial product. This review summarises 186 fungi-derived compounds reported since 2000. Antibiotic (antibacterial, antifungal, synergistic antifungal, antiviral, antimycobacterial, antimalarial, antileishmanial, insecticidal, antitrypanosomal, nematicidal and antimicroalgal) activities are discussed for 107 of them, including 66 DKPs (14 epipolythiodioxopiperazines, 20 polysulphide bridge-free thiodiketopiperazines, and 32 sulphur-free prenylated indole DKPs), 15 highly N-methylated, and 26 non-highly N-methylated typical peptides. Structure-activity relationships, mechanisms of action, and research methods are covered in detail. Additionally, biosynthases of tardioxopiperazines and neoechinulins are highlighted. These compounds have attracted considerable interest within the pharmaceutical and agrochemical industries.

Nematicidal and insecticidal activities of halogenated indoles

Parasite death via ion channel activations is the hallmark of anthelmintic and antiparasitic drugs. Glutamate gated chloride channel (GluCl) is a prominent targets for drug selection and design in parasitology. We report several iodine-fluorine based lead activators of GluCl by computational studies and structure-activity relationship analysis. 5-Fluoro-4-iodo-1H-pyrrolo [2, 3-b] pyridine and 5-iodoindole were bioactive hits that displayed in vitro anthelmintic and insecticidal activities against Bursaphelenchus xylophilus, Meloidogyne incognita, and Tenebrio molitor. Two important findings stood out: (i) 5F4IPP induced parasite death, and interacted proficiently with Gln²¹⁹ amino acid of pentameric GluCl in docking analysis, and (ii) 5-iodoindole appeared to act by forming giant vacuoles in nematodes, which led to a form of non-apoptotic death known as methuosis. The study suggests halogenated-indoles and 1H-pyrrolo [2, 3-b] pyridine derivatives be regarded potential biocides for plant-parasitic nematodes and insects, and warrants further research on the mode of actions, and field investigations.

Okaramines and other plant fungal products as new insecticide leads

Okaramine were indole alkaloids discovered from products of Penicillium simplicissimum AK-40 in soy bean pulp 'okara'. Okaramines exhibit insecticidal activity on a broad range of insects. Hence, more insecticide leads were explored by fermenting the other fungi with okara, resulting in the isolations of meroterpenes and cyclic peptides as well as indole alkaloids with distinct skeletons. Most okaramines activate l-glutamate-gated chloride channels found only in invertebrate nervous systems and muscle cells. Other fungal products selectively modulate other invertebrate ligand-gated chloride channels. Recently, the okaramine biosynthetic pathway has been elucidated, providing new insights in structural features important for activity. Enhanced production of okaramine in okara points to the involvement of plant mediators in the production of insect modulators by plant associated microorganisms in the rhizosphere as a novel defense strategy.

Anti-plant viral activity of peptaibols, trichorzins HA II, HA V, and HA VI, isolated from Trichoderma harzianum HK-61

Three peptaibols, trichorzins HA II (1), HA V (2), and HA VI (3), were isolated from okara fermented with Trichoderma harzianum HK-61 as anti-plant viral agents. Their structures were confirmed by spectroscopic and chemical methods. At micro molar concentrations, the trichorzins inhibited infections by Cucumber mosaic virus in the cowpea plant Vigna sesquipedalis.

Fungal Metabolite Antagonists of Plant Pests and Human Pathogens: Structure-Activity Relationship Studies

Fungi are able to produce many bioactive secondary metabolites that belong to different classes of natural compounds. Some of these compounds have been selected for their antagonism against pests and human pathogens and structure-activity relationship (SAR) studies have been performed to better understand which structural features are essential for the biological activity. In some cases, these studies allowed for the obtaining of hemisynthetic derivatives with increased selectivity and stability in respect to the natural products as well as reduced toxicity in view of their potential practical applications. This review deals with the SAR studies performed on fungal metabolites with potential fungicidal, bactericidal, insecticidal, and herbicidal activities from 1990 to the present (beginning of 2018).

Hot off the Press

A personal selection of 32 recent papers is presented covering various aspects of current developments in bioorganic chemistry and novel natural products such as mollebenzylanol A from Rhododendron molle.