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Actinobacteria, which are one of the largest bacterial phyla and comprise between 13 and 30% of the soil microbiota, are the main source of antibiotic classes in clinical use 1 . During screens for antimicrobials, as many as 50% of actinomycete strains are discarded because they produce a known antibiotic (Supplementary Fig. 1 ) (ref. 2 ). Despite each strain likely having the capacity to produce many compounds, strains are abandoned because the already characterized antibiotic could interfere with screening for, or purification of, newly discovered compounds 3 . We applied CRISPR-Cas9 genome engineering to knockout genes encoding two of the most frequently rediscovered antibiotics, streptothricin or streptomycin, in 11 actinomycete strains. We report that this simple approach led to production of different antibiotics that were otherwise masked. We were able to rapidly discover rare and previously unknown variants of antibiotics including thiolactomycin, amicetin, phenanthroviridin and 5-chloro-3-formylindole. This strategy could be applied to existing strain collections to realize their biosynthetic potential. Dereplication by inactivation of antibiotic production clusters in actinomycetes enables antibiotic discovery.

Streptacidiphilus sp. PAMC 29251 represents the first member of its genus isolated from an Antarctic fruticose lichen Sphaerophorus globosus . To elucidate its ecological, metabolic, and biosynthetic features, we performed comparative genomic analyses in combination with physiological assays. PAMC 29251 exhibited distinct ecophysiological features compared with previously described Streptacidiphilus species, including the ability to grow at 4°C and across a broad alkaline range (pH 6.5–10.0). Genome sequencing revealed a 10.11 Mb linear chromosome containing 9,547 coding sequences, including 31 biosynthetic gene clusters (BGCs)—one of the richest repertoires within the genus. Several BGCs, including those putatively encoding lomofungin, maduralactomycin, and thiolactomycin, were detected only in PAMC 29251 among 14 Streptacidiphilus genomes investigated in this study. Consistent with these predictions, both cell and supernatant extracts showed antimicrobial activity against Escherichia coli , Staphylococcus aureus , and Candida albicans . Although PAMC 29251 lacked nitrogen fixation and phosphate solubilization, it possessed the capacity to hydrolyze multiple macromolecules and encoded diverse proteases and carbohydrate-degrading enzymes, suggesting a potential role in organic matter turnover within the lichen thallus. These results indicate that PAMC 29251 maintains the core genomic architecture of the genus Streptacidiphilus while exhibiting differentiated physiological traits and biosynthetic features, which may be relevant to its functional characteristics in lichen-associated environments.

Emergence of bacterial resistance is a major issue for all classes of antibiotics; therefore, the identification of new classes is critically needed. Recently we reported the discovery of platensimycin by screening natural product extracts using a target-based whole-cell strategy with antisense silencing technology in concert with cell free biochemical validations. Continued screening efforts led to the discovery of platencin, a novel natural product that is chemically and biologically related but different from platensimycin. Platencin exhibits a broad-spectrum Gram-positive antibacterial activity through inhibition of fatty acid biosynthesis. It does not exhibit cross-resistance to key antibiotic resistant strains tested, including methicillin-resistant Staphylococcus aureus, vancomycin-intermediate S. aureus, and vancomycin-resistant ENTEROCOCCI: Platencin shows potent in vivo efficacy without any observed toxicity. It targets two essential proteins, β-ketoacyl-[acyl carrier protein (ACP)] synthase II (FabF) and III (FabH) with IC₅₀ values of 1.95 and 3.91 μg/ml, respectively, whereas platensimycin targets only FabF (IC₅₀ = 0.13 μg/ml) in S. aureus, emphasizing the fact that more antibiotics with novel structures and new modes of action can be discovered by using this antisense differential sensitivity whole-cell screening paradigm.

The marine actinomycete genus Salinispora is a remarkably prolific source of structurally diverse and biologically active secondary metabolites. Herein, we select the model organism Salinispora tropica CNB-440 for development as a heterologous host for the expression of biosynthetic gene clusters (BGCs) to complement well-established Streptomyces host strains. In order to create an integratable host with a clean background of secondary metabolism, we replaced three genes (salA–C) essential for salinosporamide biosynthesis with a cassette containing the Streptomyces coelicolor ΦC31 phage attachment site attB to generate the mutant S. tropica CNB-4401 via double-crossover recombination. This mutagenesis not only knocks-in the attachment site attB in the genome of S. tropica CNB-440 but also abolishes production of the salinosporamides, thereby simplifying the strain’s chemical background. We validated this new heterologous host with the successful integration and expression of the thiolactomycin BGC that we recently identified in several S. pacifica strains. When compared to the extensively engineered superhost S. coelicolor M1152, the production of thiolactomycins from S. tropica CNB-4401 was approximately 3-fold higher. To the best of our knowledge, this is the first example of using a marine actinomycete as a heterologous host for natural product BGC expression. The established heterologous host may provide a useful platform to accelerate the discovery of novel natural products and engineer biosynthetic pathways.

Antimicrobial resistance (AMR) is the phenomenon developed by microorganism on exposure to antimicrobial agents, making them unresponsive. Development of microbial confrontation is a severe rising risk to global community well-being as treatment in addition, management of such resistant microbial infections is difficult and challenging. The situation requires action across all government sectors and society. The change in the molecular target on which antimicrobial drugs act is one of the key mechanisms behind AMR. One of the approaches to battle with AMR can be exploring newer molecular targets in microbes and discovering new molecules accordingly. There are various examples of novel targets such as biomolecules involving in biosynthesis of cell wall, biosynthesis of aromatic amino acid, cell disunion, biosynthesis of fatty acid, and isoprenoid biosynthesis and tRNA synthetases. Fatty acid biosynthesis (FAB) and their enzymes among all the above is the more appealing target for the advancement of new antimicrobial agents. Number of promising inhibitors have been developed for bacterial fatty acid synthesis (FAS) and also few of them are clinically used. Some of these potential inhibitors are found to be used in development of new antibacterial as a lead compound and have been discovered from high throughput screening processes like Platencimycin and their analogue, Platencin. The review majorly encompasses bacterial FAB in type II FAS system and potential inhibitors with respective targets of novel antibacterial.Antimicrobial resistance (AMR) is the phenomenon developed by microorganism on exposure to antimicrobial agents, making them unresponsive. Development of microbial confrontation is a severe rising risk to global community well-being as treatment in addition, management of such resistant microbial infections is difficult and challenging. The situation requires action across all government sectors and society. The change in the molecular target on which antimicrobial drugs act is one of the key mechanisms behind AMR. One of the approaches to battle with AMR can be exploring newer molecular targets in microbes and discovering new molecules accordingly. There are various examples of novel targets such as biomolecules involving in biosynthesis of cell wall, biosynthesis of aromatic amino acid, cell disunion, biosynthesis of fatty acid, and isoprenoid biosynthesis and tRNA synthetases. Fatty acid biosynthesis (FAB) and their enzymes among all the above is the more appealing target for the advancement of new antimicrobial agents. Number of promising inhibitors have been developed for bacterial fatty acid synthesis (FAS) and also few of them are clinically used. Some of these potential inhibitors are found to be used in development of new antibacterial as a lead compound and have been discovered from high throughput screening processes like Platencimycin and their analogue, Platencin. The review majorly encompasses bacterial FAB in type II FAS system and potential inhibitors with respective targets of novel antibacterial.

In the present investigation, the parent compound 4-amino-5-(4-fluoro-3-phenoxyphenyl)-4H-1,2,4-triazole-3-thiol (1) and its Schiff bases 2, 3, and 4 were subjected to whole-cell anti-TB against H37Rv and multi-drug-resistant (MDR) strains of Mycobacterium tuberculosis (MTB) by resazurin microtiter assay (REMA) plate method. Test compound 1 exhibited promising anti-TB activity against H37Rv and MDR strains of MTB at 5.5 µg/mL and 11 µg/mL, respectively. An attempt to identify the suitable molecular target for compound 1 was performed using a set of triazole thiol cellular targets, including β-ketoacyl carrier protein synthase III (FABH), β-ketoacyl ACP synthase I (KasA), CYP121, dihydrofolate reductase, enoyl-acyl carrier protein reductase, and N-acetylglucosamine-1-phosphate uridyltransferase. MTB β-ketoacyl ACP synthase I (KasA) was identified as the cellular target for the promising anti-TB parent compound 1 via docking and molecular dynamics simulation. MM(GB/PB)SA binding free energy calculation revealed stronger binding of compound 1 compared with KasA standard inhibitor thiolactomycin (TLM). The inhibitory mechanism of test compound 1 involves the formation of hydrogen bonding with the catalytic histidine residues, and it also impedes access of fatty-acid substrates to the active site through interference with α5–α6 helix movement. Test compound 1-specific structural changes at the ALA274–ALA281 loop might be the contributing factor underlying the stronger anti-TB effect of compound 1 when compared with TLM, as it tends to adopt a closed conformation for the access of malonyl substrate to its binding site.

In-depth botanical characterization was performed on Premna odorata Blanco (Lamiaceae) different organs for the first time. The leaves are opposite, hairy and green in color. Flowers possess fragrant aromatic odors and exist in inflorescences of 4–15 cm long corymbose cyme-type. In-depth morphological and anatomical characterization revealed the great resemblance to plants of the genus Premna and of the family Lamiaceae, such as the presence of glandular peltate trichomes and diacytic stomata. Additionally, most examined organs are characterized by non-glandular multicellular covering trichomes, acicular, and rhombic calcium oxalate crystals. P. odorata leaves n-hexane fraction revealed substantial anti-tuberculous potential versus Mycobacterium tuberculosis, showing a minimum inhibition concentration (MIC) of 100 μg/mL. Metabolic profiling of the n-hexane fraction using gas-chromatography coupled to mass spectrometry (GC/MS) analysis revealed 10 major compounds accounting for 93.01%, with trans-phytol constituting the major compound (24.06%). The virtual screening revealed that trans-phytol highly inhibited MTB C171Q receptor as M. tuberculosis KasA (β-ketoacyl synthases) with a high fitting score (∆G = −15.57 kcal/mol) approaching that of isoniazid and exceeding that of thiolactomycin, the co-crystallized ligand. Absorption, distribution, metabolism, excretion and toxicity predictions (ADME/TOPKAT) revealed that trans-phytol shows lower solubility and absorption levels when compared to thiolactomycin and isoniazid. Still, it is safer, causing no mutagenic or carcinogenic effects with higher lethal dose, which causes the death of 50% (LD50). Thus, it can be concluded that P. odorata can act as a source of lead entities to treat tuberculosis.

Fatty acids are among the major building blocks of living cells, making lipid biosynthesis a potent target for compounds with antibiotic or antineoplastic properties. We present the crystal structure of the 2.6-MDa Saccharomyces cerevisiae fatty acid synthase (FAS) multienzyme in complex with the antibiotic cerulenin, representing, to our knowledge, the first structure of an inhibited fatty acid megasynthase. Cerulenin attacks the FAS ketoacyl synthase (KS) domain, forming a covalent bond to the active site cysteine C1305. The inhibitor binding causes two significant conformational changes of the enzyme. First, phenylalanine F1646, shielding the active site, flips and allows access to the nucleophilic cysteine. Second, methionine M1251, placed in the center of the acyl-binding tunnel, rotates and unlocks the inner part of the fatty acid binding cavity. The importance of the rotational movement of the gatekeeping M1251 side chain is reflected by the cerulenin resistance and the changed product spectrum reported for S. cerevisiae strains mutated in the adjacent glycine G1250. Platensimycin and thiolactomycin are two other potent inhibitors of KSs. However, in contrast to cerulenin, they show selectivity toward the prokaryotic FAS system. Because the flipped F1646 characterizes the catalytic state accessible for platensimycin and thiolactomycin binding, we superimposed structures of inhibited bacterial enzymes onto the S. cerevisiae FAS model. Although almost all side chains involved in inhibitor binding are conserved in the FAS multienzyme, a different conformation of the loop K1413-K1423 of the KS domain might explain the observed low antifungal properties of platensimycin and thiolactomycin.

The increase in drug-resistant pathogenic bacteria has created an urgent demand for new antibiotics. Among the more attractive targets for the development of new antibacterial compounds are the enzymes of fatty acid biosynthesis. Although a number of potent inhibitors of microbial fatty acid biosynthesis have been discovered, few of these are clinically useful drugs. Several of these fatty acid biosynthesis inhibitors have potential as lead compounds in the development of new antibacterials. This review encompasses the known inhibitors and prospective targets for new antibacterials.

Tuberculosis (TB) is a leading infectious disease which kills a huge number of people every year over a decade, caused by Mycobacterium tuberculosis. The conventional drugs in the market are no longer effective due to the increasing mycobacterial resistance to antibiotics. Hence, the need of finding efficient drugs to solve this multiple drug resistant factor is becoming an immediate issue. The first-line drugs in current practice for the treatment of TB emphasize on mycolic acid, which protects the bacteria from an immune response generated by the host. A key enzyme involved in this mycolic acid biosynthesis, M. tuberculosis beta-ketoacyl-ACP synthase A (MTB-KasA) is a prime candidate in this study. Thiolactomycin is a natural product inhibitor has shown good inhibitory activity against MTB-KasA. Hence, several thiolactomycin derivatives collected from the literature were taken for absorption, distribution, metabolism, excretion and toxicity prediction, molecular docking and molecular dynamics simulation studies with MTB-KasA. The in silico drug designing methods used in this study suggests that the thiolactomycin derivatives are having a better binding activity against MTB-KasA and among them the ligand C14 is identified as a promising lead molecule to inhibit multidrug resistance of tuberculosis by showing a long time binding activity.