Hormaomycins B and C: New Antibiotic Cyclic Depsipeptides from a Marine Mudflat-Derived Streptomyces sp

Proline Analogues

Within the canonical repertoire of the amino acid involved in protein biogenesis, proline plays a unique role as an amino acid presenting a modified backbone rather than a side-chain. Chemical structures that mimic proline but introduce changes into its specific molecular features are defined as proline analogues. This review article summarizes the existing chemical, physicochemical, and biochemical knowledge about this peculiar family of structures. We group proline analogues from the following compounds: substituted prolines, unsaturated and fused structures, ring size homologues, heterocyclic, e.g., pseudoproline, and bridged proline-resembling structures. We overview (1) the occurrence of proline analogues in nature and their chemical synthesis, (2) physicochemical properties including ring conformation and cis/trans amide isomerization, (3) use in commercial drugs such as nirmatrelvir recently approved against COVID-19, (4) peptide and protein synthesis involving proline analogues, (5) specific opportunities created in peptide engineering, and (6) cases of protein engineering with the analogues. The review aims to provide a summary to anyone interested in using proline analogues in systems ranging from specific biochemical setups to complex biological systems.

Unusual Enzymatic C-C Bond Formation and Cleavage Reactions during Natural Product Biosynthesis

Natural products from plants and microorganisms provide a valuable reservoir of pharmaceutical compounds. C-C bond formation and cleavage are crucial events during natural product biosynthesis, playing pivotal roles in generating diverse and intricate chemical structures that are essential for biological functions. This review summarizes our recent findings regarding biosynthetic enzymes that catalyze unconventional C-C bond formation and cleavage reactions during natural product biosynthesis.

Potentiality of Actinomycetia Prevalent in Selected Forest Ecosystems in Assam, India to Combat Multi-Drug-Resistant Microbial Pathogens

Actinomycetia are known for their ability to produce a wide range of bioactive secondary metabolites having significant therapeutic importance. This study aimed to explore the potential of actinomycetia as a source of bioactive compounds with antimicrobial properties against multi-drug-resistant (MDR) clinical pathogens. A total of 65 actinomycetia were isolated from two unexplored forest ecosystems, namely the Pobitora Wildlife Sanctuary (PWS) and the Deepor Beel Wildlife Sanctuary (DBWS), located in the Indo-Burma mega-biodiversity hotspots of northeast India, out of which 19 isolates exhibited significant antimicrobial activity. 16S rRNA gene sequencing was used for the identification and phylogenetic analysis of the 19 potent actinomycetia isolates. The results reveal that the most dominant genus among the isolates was Streptomyces (84.21%), followed by rare actinomycetia genera such as Nocardia, Actinomadura, and Nonomuraea. Furthermore, seventeen of the isolates tested positive for at least one antibiotic biosynthetic gene, specifically type II polyketide synthase (PKS-II) and nonribosomal peptide synthetases (NRPSs). These genes are associated with the production of bioactive compounds with antimicrobial properties. Among the isolated strains, three actinomycetia strains, namely Streptomyces sp. PBR1, Streptomyces sp. PBR36, and Streptomyces sp. DBR11, demonstrated the most potent antimicrobial activity against seven test pathogens. This was determined through in vitro antimicrobial bioassays and the minimum inhibitory concentration (MIC) values of ethyl acetate extracts. Gas chromatography-mass spectrometry (GS-MS) and whole-genome sequencing (WGS) of the three strains revealed a diverse group of bioactive compounds and secondary metabolite biosynthetic gene clusters (smBGCs), respectively, indicating their high therapeutic potential. These findings highlight the potential of these microorganisms to serve as a valuable resource for the discovery and development of novel antibiotics and other therapeutics with high therapeutic potential.

Naturally Occurring Organohalogen Compounds-A Comprehensive Review

The present volume is the third in a trilogy that documents naturally occurring organohalogen compounds, bringing the total number-from fewer than 25 in 1968-to approximately 8000 compounds to date. Nearly all of these natural products contain chlorine or bromine, with a few containing iodine and, fewer still, fluorine. Produced by ubiquitous marine (algae, sponges, corals, bryozoa, nudibranchs, fungi, bacteria) and terrestrial organisms (plants, fungi, bacteria, insects, higher animals) and universal abiotic processes (volcanos, forest fires, geothermal events), organohalogens pervade the global ecosystem. Newly identified extraterrestrial sources are also documented. In addition to chemical structures, biological activity, biohalogenation, biodegradation, natural function, and future outlook are presented.

Solonamides, a Group of Cyclodepsipeptides, Influence Motility in the Native Producer Photobacterium galatheae S2753

The marine bacterium Photobacterium galatheae S2753 produces a group of cyclodepsipeptides, called solonamides, which impede the virulence but not the survival of Staphylococcus aureus. In addition to their invaluable antivirulence activity, little is known about the biosynthesis and physiological function of solonamides in the native producer. This study generated a solonamide-deficient (Δsol) mutant by in-frame deletion of the sol gene, thereby identifying the core gene for solonamide biosynthesis. By annotation from antiSMASH, the biosynthetic pathway of solonamides in S2753 was also proposed. Mass spectrometry analysis of cell extracts found that deficiency of solonamide production influenced the production of a group of unknown compounds but otherwise did not alter the overall secondary metabolite profile. Physiological comparison between Δsol and wild-type S2753 demonstrated that growth dynamics and biofilm formation of both strains were similar; however, the Δsol mutant displayed reduced motility rings compared to the wild type. Reintroduction of sol restored solonamide production and motility to the mutant, indicating that solonamides influence the motility behavior of P. galatheae S2753. Proteomic analysis of the Δsol and wild-type strains found that eliminating solonamides influenced many cellular processes, including swimming-related proteins and proteins adjusting the cellular cyclic di-GMP concentration. In conclusion, our results revealed the biosynthetic pathway of solonamides and their ecological benefits to P. galatheae S2753 by enhancing motility, likely by altering the motile physiology. IMPORTANCE The broad range of bioactive potentials of cyclodepsipeptides makes these compounds invaluable in the pharmaceutical industry. Recently, a few novel cyclodepsipeptides have been discovered in marine Proteobacteria; however, their biosynthetic pathways remain to be revealed. Here, we demonstrated the biosynthetic genetic basis and pathway of the antivirulence compounds known as solonamides in P. galatheae S2753. This can pave the way for the biological overproduction of solonamides on an industrial scale. Moreover, the comparison of a solonamide-deficient mutant and wild-type S2753 demonstrated that solonamides stimulate the swimming behavior of S2753 and also influence a few key physiological processes of the native producers. These results evidenced that, in addition to their importance as novel drug candidates, these compounds play a pivotal role in the physiology of the producing microorganisms and potentially provide the native producer competitive benefits for their survival in nature.

Cystargamides C and D, New Cyclic Lipopeptides From a Tidal Mudflat-Derived Streptomyces sp. JMS132

Cystargamides C and D (2 and 3) were isolated from a marine actinomycete strain collected at Beolgyo, South Korea. The planar structures of the cystargamides were elucidated by 1/2D NMR, UV, and MS spectroscopic analyses. The absolute configurations of 2 and 3 were determined based on ROESY correlations and the advanced Marfey’s methods. The structures of the compounds were elucidated as new lipodepsipeptides bearing six amino acids with an epoxy fatty acid side chain. For the first time, the nonribosomal peptide synthetase biosynthetic pathway of the cystargamides has been proposed using whole genome sequence analysis. The cystargamides displayed antioxidant effect in the DPPH and ABTS assay. The discovery of new cyclic lipopeptides, cystargamides C and D, from a tidal mudflat-derived Streptomyces sp. supported that marine bacteria have potential as source of bioactive natural products.

Stereodivergent Nitrocyclopropane Formation during Biosynthesis of Belactosins and Hormaomycins

Belactosins and hormaomycins are peptide natural products containing 3-(2-aminocyclopropyl)alanine and 3-(2-nitrocyclopropyl)alanine residues, respectively, with opposite stereoconfigurations of the cyclopropane ring. Herein we demonstrate that the heme oxygenase-like enzymes BelK and HrmI catalyze the N-oxygenation of l-lysine to generate 6-nitronorleucine. The nonheme iron enzymes BelL and HrmJ then cyclize the nitroalkane moiety to the nitrocyclopropane ring with the desired stereochemistry found in the corresponding natural products. We also show that both cyclopropanases remove the 4-proS-H of 6-nitronorleucine during the cyclization, establishing the inversion and retention of the configuration at C4 during the BelL and HrmJ reactions, respectively. This study reveals the unique strategy for stereocontrolled cyclopropane synthesis in nature.

Marine Pyrrole Alkaloids

Nitrogen heterocycles are essential parts of the chemical machinery of life and often reveal intriguing structures. They are not only widespread in terrestrial habitats but can also frequently be found as natural products in the marine environment. This review highlights the important class of marine pyrrole alkaloids, well-known for their diverse biological activities. A broad overview of the marine pyrrole alkaloids with a focus on their isolation, biological activities, chemical synthesis, and derivatization covering the decade from 2010 to 2020 is provided. With relevant structural subclasses categorized, this review shall provide a clear and timely synopsis of this area.

Bacterial Endophytes: The Hidden Actor in Plant Immune Responses against Biotic Stress

Bacterial endophytes constitute an essential part of the plant microbiome and are described to promote plant health by different mechanisms. The close interaction with the host leads to important changes in the physiology of the plant. Although beneficial bacteria use the same entrance strategies as bacterial pathogens to colonize and enter the inner plant tissues, the host develops strategies to select and allow the entrance to specific genera of bacteria. In addition, endophytes may modify their own genome to adapt or avoid the defense machinery of the host. The present review gives an overview about bacterial endophytes inhabiting the phytosphere, their diversity, and the interaction with the host. Direct and indirect defenses promoted by the plant-endophyte symbiont exert an important role in controlling plant defenses against different stresses, and here, more specifically, is discussed the role against biotic stress. Defenses that should be considered are the emission of volatiles or antibiotic compounds, but also the induction of basal defenses and boosting plant immunity by priming defenses. The primed defenses may encompass pathogenesis-related protein genes (PR family), antioxidant enzymes, or changes in the secondary metabolism.

A Review: Halogenated Compounds from Marine Actinomycetes

Marine actinomycetes, Streptomyces species, produce a variety of halogenated compounds with diverse structures and a range of biological activities owing to their unique metabolic pathways. These halogenated compounds could be classified as polyketides, alkaloids (nitrogen-containing compounds) and terpenoids. Halogenated compounds from marine actinomycetes possess important biological properties such as antibacterial and anticancer activities. This review reports the sources, chemical structures and biological activities of 127 new halogenated compounds originated mainly from Streptomyces reported from 1992 to 2020.

Diverse endophytic Streptomyces species with dynamic metabolites and their meritorious applications: a critical review

The strains of actinobacteria are unique as they lie between true fungi and bacteria and several of them were reported as endophytic actinobacteria as they were isolated from the inner regions of various plant parts and will enhance uptake of nutrients and improve defense against pathogens. Literature and scientific communications reported the relationship between the endophytes and plants, most of them concluded the association as commensalism. Remarkably, bioactive compounds from endophytic Streptomyces sp. were confirmed with various applications. A retrospective consolidation on the endophytic Streptomyces sp. and their metabolite application in day to day life is presented here. It was deduced that this group of the organism are a source for a wide range of bioactive compounds including anticancer agents, immune suppressor, plant growth promoters, anti-inflammatory agents, anti-tumor agents, enzymes and antimicrobial substances. These antimicrobial metabolites show broad-spectrum activity and are effective against bacteria and fungi. The mechanism of action of secondary metabolites from endophytes and its positive influence on the host plants are noted as involvement in deterrence, antifeedant activity, toxicity against common pests, and as enhancers for physical mechanisms such as water uptake and sunlight absorption, thus supporting the growth of host plants.

Antimicrobial compounds from marine actinomycetes

Marine actinomycetes were the main origin of marine natural products in the past 40 years. This review was to present the sources, structures and antimicrobial activities of 313 new natural products from marine actinomycetes reported from 1976 to 2019.

Elucidating Mechanisms of Endophytes Used in Plant Protection and Other Bioactivities With Multifunctional Prospects

Endophytes are abundant in plants and studies are continuously emanating on their ability to protect plants from pathogens that cause diseases especially in the field of agriculture. The advantage that endophytes have over other biocontrol agents is the ability to colonize plant's internal tissues. Despite this attributes, a deep understanding of the mechanism employed by endophytes in protecting the plant from diseases is still required for both effectiveness and commercialization. Also, there are increasing cases of antibiotics resistance among most causative agents of diseases in human beings, which calls for an alternative drug discovery using natural sources. Endophytes present themselves as a storehouse of many bioactive metabolites such as phenolic acids, alkaloids, quinones, steroids, saponins, tannins, and terpenoids which makes them a promising candidate for anticancer, antimalarial, antituberculosis, antiviral, antidiabetic, anti-inflammatory, antiarthritis, and immunosuppressive properties among many others, even though the primary function of bioactive compounds from endophytes is to make the host plants resistant to both abiotic and biotic stresses. Endophytes still present themselves as a peculiar source of possible drugs. This study elucidates the mechanisms employed by endophytes in protecting the plant from diseases and different bioactivities of importance to humans with a focus on endophytic bacteria and fungi.

Marine Pharmacology in 2014-2015: Marine Compounds with Antibacterial, Antidiabetic, Antifungal, Anti-Inflammatory, Antiprotozoal, Antituberculosis, Antiviral, and Anthelmintic Activities; Affecting the Immune and Nervous Systems, and Other Miscellaneous Mechanisms of Action

The systematic review of the marine pharmacology literature from 2014 to 2015 was completed in a manner consistent with the 1998-2013 reviews of this series. Research in marine pharmacology during 2014-2015, which was reported by investigators in 43 countries, described novel findings on the preclinical pharmacology of 301 marine compounds. These observations included antibacterial, antifungal, antiprotozoal, antituberculosis, antiviral, and anthelmintic pharmacological activities for 133 marine natural products, 85 marine compounds with antidiabetic, and anti-inflammatory activities, as well as those that affected the immune and nervous system, and 83 marine compounds that displayed miscellaneous mechanisms of action, and may probably contribute to novel pharmacological classes upon further research. Thus, in 2014-2015, the preclinical marine natural product pharmacology pipeline provided novel pharmacology as well as new lead compounds for the clinical marine pharmaceutical pipeline, and thus continued to contribute to ongoing global research for alternative therapeutic approaches to many disease categories.

Metagenomics Approaches in Discovery and Development of New Bioactive Compounds from Marine Actinomycetes

Marine actinomycetes are prolific sources of marine drug discovery system contributing for several bioactive compounds of biomedical prominence. Metagenomics, a culture-independent technique through its sequence- and function-based screening has led to the discovery and synthesis of numerous biologically significant compounds like polyketide synthase, Non-ribosomal peptide synthetase, antibiotics, and biocatalyst. While metagenomics offers different advantages over conventional sequencing techniques, they also have certain limitations including bias classification, non-availability of quality DNA samples, heterologous expression, and host selection. The assimilation of advanced amplification and screening methods such as φ29 DNA polymerase, Next-Generation Sequencing, Cosmids, and recent bioinformatics tools like automated genome mining, anti-SMASH have shown promising results to overcome these constrains. Consequently, functional genomics and bioinformatics along with synthetic biology will be crucial for the success of the metagenomic approach and indeed for exploring new possibilities among the microbial consortia for the future drug discovery process.

Actinobacteria-Derived peptide antibiotics since 2000

Members of the Actinobacteria, including Streptomyces spp., Kutzneria sp. Actinoplanes spp., Actinomycete sp., Nocardia sp., Brevibacteriumsp.,Actinomadura spp., Micromonospora sp., Amycolatopsis spp., Nonomuraea spp., Nocardiopsis spp., Marinactinospora sp., Rhodococcus sp., Lentzea sp., Actinokineospora sp., Planomonospora sp., Streptomonospora sp., and Microbacterium sp., are an important source of structurally diverse classes of short peptides of ∼30 residues or fewer that will likely play an important role in new antibiotic development and discovery. Additionally, many have unique structures that make them recalcitrant to traditional modes of drug resistance via novel mechanisms, and these are ideal therapeutic tools and potential alternatives to current antibiotics. The need for novel antibiotic is urgent, and this review summarizes 199 Actinobacteria compounds published since 2000, including 35 cyclic lipopeptides containing piperazic or pipecolic acids, eight aromatic peptides, five glycopeptides, 21 bicyclic peptides, 44 other cyclic lipopeptides, five linear lipopeptides, six 2,5-diketopiperazines, one dimeric peptide, four nucleosidyl peptides, two thioamide-containing peptides, 25 thiopeptides, nine lasso peptides, and 34 typical cyclic peptides. The current and potential therapeutic applications of these peptides, including their structure, antituberculotic, antibacterial, antifungal, antiviral, anti-brugia, anti-plasmodial, and anti-trypanosomal activities, are discussed.

Biosynthesis and incorporation of an alkylproline-derivative (APD) precursor into complex natural products

This review covers the biosynthetic and evolutionary aspects of lincosamide antibiotics, antitumour pyrrolobenzodiazepines (PBDs) and the quorum-sensing molecule hormaomycin.

Actinomycetes: still a source of novel antibiotics

Covering: 2006 to 2017Actinomycetes have been, for decades, one of the most important sources for the discovery of new antibiotics with an important number of drugs and analogs successfully introduced in the market and still used today in clinical practice. The intensive antibacterial discovery effort that generated the large number of highly potent broad-spectrum antibiotics, has seen a dramatic decline in the large pharma industry in the last two decades resulting in a lack of new classes of antibiotics with novel mechanisms of action reaching the clinic. Whereas the decline in the number of new chemical scaffolds and the rediscovery problem of old known molecules has become a hurdle for industrial natural products discovery programs, new actinomycetes compounds and leads have continued to be discovered and developed to the preclinical stages. Actinomycetes are still one of the most important sources of chemical diversity and a reservoir to mine for novel structures that is requiring the integration of diverse disciplines. These can range from novel strategies to isolate species previously not cultivated, innovative whole cell screening approaches and on-site analytical detection and dereplication tools for novel compounds, to in silico biosynthetic predictions from whole gene sequences and novel engineered heterologous expression, that have inspired the isolation of new NPs and shown their potential application in the discovery of novel antibiotics. This review will address the discovery of antibiotics from actinomycetes from two different perspectives including: (1) an update of the most important antibiotics that have only reached the clinical development in the recent years despite their early discovery, and (2) an overview of the most recent classes of antibiotics described from 2006 to 2017 in the framework of the different strategies employed to untap novel compounds previously overlooked with traditional approaches.

Endophytic bacteria: a new source of bioactive compounds

In recent years, bioactive compounds are in high demand in the pharmaceuticals and naturopathy, due to their health benefits to human and plants. Microorganisms synthesize these compounds and some enzymes either alone or in association with plants. Microbes residing inside the plant tissues, known as endophytes, also produce an array of these compounds. Endophytic actinomycetes act as a promising resource of biotechnologically valuable bioactive compounds and secondary metabolites. Endophytic Streptomyces sp. produced some novel antibiotics which are effective against multi-drug-resistant bacteria Antimicrobial agents produced by endophytes are eco-friendly, toxic to pathogens and do not harm the human. Endophytic inoculation of the plants modulates the synthesis of bioactive compounds with high pharmaceutical properties besides promoting growth of the plants. Hydrolases, the extracellular enzymes, produced by endophytic bacteria, help the plants to establish systemic resistance against pathogens invasion. Phytohormones produced by endophytes play an essential role in plant development and drought resistance management. The high diversity of endophytes and their adaptation to various environmental stresses seem to be an untapped source of new secondary metabolites. The present review summarizes the role of endophytic bacteria in synthesis and modulation of bioactive compounds.

Marine natural products

Covering: 2015. Previous review: Nat. Prod. Rep., 2016, 33, 382-431This review covers the literature published in 2015 for marine natural products (MNPs), with 1220 citations (792 for the period January to December 2015) referring to compounds isolated from marine microorganisms and phytoplankton, green, brown and red algae, sponges, cnidarians, bryozoans, molluscs, tunicates, echinoderms, mangroves and other intertidal plants and microorganisms. The emphasis is on new compounds (1340 in 429 papers for 2015), together with the relevant biological activities, source organisms and country of origin. Reviews, biosynthetic studies, first syntheses, and syntheses that lead to the revision of structures or stereochemistries, have been included.

Peptides, Peptidomimetics, and Polypeptides from Marine Sources: A Wealth of Natural Sources for Pharmaceutical Applications

Nature provides a variety of peptides that are expressed in most living species. Evolutionary pressure and natural selection have created and optimized these peptides to bind to receptors with high affinity. Hence, natural resources provide an abundant chemical space to be explored in peptide-based drug discovery. Marine peptides can be extracted by simple solvent extraction techniques. The advancement of analytical techniques has made it possible to obtain pure peptides from natural resources. Extracted peptides have been evaluated as possible therapeutic agents for a wide range of diseases, including antibacterial, antifungal, antidiabetic and anticancer activity as well as cardiovascular and neurotoxin activity. Although marine resources provide thousands of possible peptides, only a few peptides derived from marine sources have reached the pharmaceutical market. This review focuses on some of the peptides derived from marine sources in the past ten years and gives a brief review of those that are currently in clinical trials or on the market.

QM-HiFSA-Aided Structure Determination of Succinilenes A-D, New Triene Polyols from a Marine-Derived Streptomyces sp

Based on profiles of secondary metabolites produced by marine bacteria obtained using LC/MS, succinilenes A-D (1-4), new triene polyols, were discovered from a culture of a Streptomyces strain SAK1, which was collected in the southern area of Jeju Island, Republic of Korea. The gross structures of 1-4 were primarily determined through analysis of NMR spectra. The double bond geometries of the succinilenes, which could not be established from conventional ¹H NMR spectra because of the highly overlapped olefinic signals, were successfully deciphered using the recently developed quantum-mechanics-driven ¹H iterative full spin analysis (QM-HiFSA). Succinilenes A-C (1-3) displayed inhibitory effects against lipopolysaccharide (LPS)-induced nitric oxide (NO) production, indicating their anti-inflammatory significance. These three compounds (1-3) commonly bear a succinic acid moiety, although succinilene D (4), which did not inhibit NO production, does not have this moiety in its structure. The absolute configurations of succinilenes A-D (1-4) were established through J-based configuration analysis, the modified Mosher's method following methanolysis, and CD spectral analysis.

Production of Enzymes from Marine Actinobacteria

Marine actinobacteria are well recognized for their capabilities to produce valuable natural products, which have great potential for applications in medical, agricultural, and fine chemical industries. In addition to producing unique enzymes responsible for biosynthesis of natural products, many marine actinobacteria also produce hydrolytic enzymes which are able to degrade various biopolymers, such as cellulose, xylan, and chitin. These enzymes are important to produce biofuels and biochemicals of interest from renewable biomass. In this chapter, the recent reports of novel enzymes produced by marine actinobacteria are reviewed, and advanced technologies that can be applied to search for novel marine enzymes as well as for improved enzyme production by marine actinobacteria are summarized, which include ribosome engineering, genome mining, as well as synthetic biology studies.

Mohangic Acids A-E, p-Aminoacetophenonic Acids from a Marine-Mudflat-Derived Streptomyces sp

Mohangic acids A-E (1-5) were isolated from a marine Streptomyces sp. collected from a mudflat in Buan, Republic of Korea. Comprehensive spectroscopic analysis revealed that the mohangic acids are new members of the p-aminoacetophenonic acid class. The relative and absolute configurations of the mohangic acids were determined by J-based configuration analysis and by the application of bidentate chiral NMR solvents followed by (13)C NMR analysis, chemical derivatization, and circular dichroism spectroscopy. Mohangic acid E (5), which is the first glycosylated compound in the p-aminoacetophenonic acid family, displayed significant quinone reductase induction activity.