Resistance gene-guided genome mining reveals the roseopurpurins as inhibitors of cyclin-dependent kinases

With the significant increase in the availability of microbial genome sequences in recent years, resistance gene-guided genome mining has emerged as a powerful approach for identifying natural products with specific bioactivities. Here, we present the use of this approach to reveal the roseopurpurins as potent inhibitors of cyclin-dependent kinases (CDKs), a class of cell cycle regulators implicated in multiple cancers. We identified a biosynthetic gene cluster (BGC) with a putative resistance gene with homology to human CDK2. Using targeted gene disruption and transcription factor overexpression in Aspergillus uvarum, and heterologous expression of the BGC in Aspergillus nidulans, we demonstrated that roseopurpurin C (1) is produced by this cluster and characterized its biosynthesis. We determined the potency, specificity, and mechanism of action of 1 as well as multiple intermediates and shunt products produced from the BGC. We show that 1 inhibits human CDK2 with a Kiapp of 44 nM, demonstrates selectivity for clinically relevant members of the CDK family, and induces G1 cell cycle arrest in HCT116 cells. Structural analysis of 1 complexed with CDK2 revealed the molecular basis of ATP-competitive inhibition.

Genome mining for unknown-unknown natural products

Genome mining of biosynthetic pathways with no identifiable core enzymes can lead to discovery of the so-called unknown (biosynthetic route)-unknown (molecular structure) natural products. Here we focused on a conserved fungal biosynthetic pathway that lacks a canonical core enzyme and used heterologous expression to identify the associated natural product, a highly modified cyclo-arginine-tyrosine dipeptide. Biochemical characterization of the pathway led to identification of a new arginine-containing cyclodipeptide synthase (RCDPS), which was previously annotated as a hypothetical protein and has no sequence homology to non-ribosomal peptide synthetase or bacterial cyclodipeptide synthase. RCDPS homologs are widely encoded in fungal genomes; other members of this family can synthesize diverse cyclo-arginine-Xaa dipeptides, and characterization of a cyclo-arginine-tryptophan RCDPS showed that the enzyme is aminoacyl-tRNA dependent. Further characterization of the biosynthetic pathway led to discovery of new compounds whose structures would not have been predicted without knowledge of RCDPS function.

Biosynthesis of AS2077715 and Funiculosin: Pathway Reconstitution and Identification of Enzymes that Form the All-cis Cyclopentanetetraol Moiety

The complete biosynthetic pathways of the potent antifungals AS2077715 (1) and funiculosin (2) are reconstituted and characterized. A five-enzyme cascade, including a multifunctional flavin-dependent monooxygenease and a repurposed O-methyltransferase, is involved to perform the dearomatization, stereoselective ring contraction, and redox transformations to morph a hydroxyphenyl-containing precursor into the unusual all-cis cyclopentanetetraol moiety.

Morphological and chemical plant traits associated with feeding non-preference to adult of Diabrotica speciosa (Coleoptera: Chrysomelidae) in soybean genotypes

Diabrotica speciosa is an important pest of several crops in South America, including soybeans. Adults cause severe defoliation in soybean plants, and damage is significant when cotyledons are attacked. This study evaluated feeding non-preference to D. speciosa adults using 10 soybean genotypes, testing (i) 15-day-old whole plants and (ii) leaf disks of 60-day-old plants, through assessments of soybean attractiveness and leaf area consumed (LAC). Foliar contents of flavonoids and nutrients, and leaf trichome density were quantified for potential correlations with soybean resistance to adult of D. speciosa. In the whole young-plant experiment, under free-choice conditions, the lowest LAC was observed in IAC 100 and PI 227687. In no-choice, PI 227687 and IGRA RA 626 RR showed lower LAC than the other genotypes. In the leaf disk test, in free-choice, the genotypes IAC 100, PI 274454, PI 227687, DM 339, and BR 16 were the least preferred by adult of D. speciosa. In no-choice, PI 274454 was one of the least preferred, similarly to IGRA RA 626 RR, Dowling, and PI 227687. In the whole plant experiment, a high rutin content and low amounts of zinc, calcium, sulfur and manganese were associated with less consumption of D. speciosa on leaves of resistant genotypes. In contrast, in the leaf disk test there was a significant influence of trichomes in soybean resistance to the pest. In conclusion, the PI lines herein assessed are also promising sources for developing cultivars resistant to D. speciosa.

Broomeanamides: Cyclic Octapeptides from an Isolate of the Fungicolous Ascomycete Sphaerostilbella broomeana from India

The genus Sphaerostilbella comprises fungi that colonize basidiomata of wood-inhabiting fungi, including important forest pathogens. Studies of fermentation cultures of an isolate (TFC201724) collected on the foothills of Himalayas, and closely related to S. broomeana isolates from Europe, led to the identification of a new cyclic octapeptide along with two closely related analogues (1-3) and four dioxopiperazines (4-7). The structure of the lead compound, broomeanamide A (1), was assigned mainly by analysis of 2D NMR and HRESIMS data. The structure consisted of one unit each of N-MeVal, Ala, N-MePhe, Pro, Val, and Ile and two N-MeLeu units. The amino acid sequence was determined on the basis of 2D NMR and HRESIMSMS data. NMR and HRMS data revealed that the other two new peptides have the same amino acid composition except that the Ile unit was replaced with Val in one instance (2) and the N-MeVal unit was replaced with Val in the other (3). The absolute configuration of 1 was assigned by analysis of the acid hydrolysate by application of Marfey's method using both C₁₈ and C₃ bonded-phase columns. Broomeanamide A (1) showed antifungal activity against Cryptococcus neoformans and Candida albicans, with MIC values of 8.0 and 64 μg/mL, respectively.

Design of experiments applied to stress testing of pharmaceutical products: A case study of Albendazole

Forced degradation tests are studies used to assess the stability of active pharmaceutical ingredients (APIs) and their formulations. These tests are performed submitting the API under extreme conditions in order to know the main degradation products in a short period of time. The results of these studies are used to assess the degradation susceptibility of APIs and to validate chromatographic analytical methods. However, most of degradation studies are performed using one-factor-at-the-time (OFAT) which does not consider the interactions between degradation variables. This work proposes the use of Design of Experiment (DoE) approach in forced degradation of albendazole (ABZ). It was used a central composite design (CCD) to evaluate the forced degradation in a multivariate way. Experiments were performed taking into account the variables pH, temperature, oxidizing agent (H₂O₂) and UV radiation. It was verified the influence of the variables and their interactions on the ABZ degradation. The ABZ oxidation showed to be the main degradation route for ABZ, which is strongly influenced by the temperature. The hydrolysis was relevant at alkaline medium and high temperature. LC-IT-MSⁿ was used to identify the degradation products. It was found three known degradation products (albendazole-2-amino, albendazole sulfoxide and albendazole sulfone) and a new derivate of albendazole molecule (albendazole sulfoxide with a chlorine). This last one was isolated and characterized by UPLC-QToF-MS and NMR analyses.

Abstract LB120: A novel peptide-drug conjugate induces DNA damage in SSTR2-expressing cells

Introductory statement: To overcome enzyme-mediated resistance mechanisms associated with the DNA alkylating agent, temozolomide (TMZ), we seek to develop a peptide-drug conjugate (PDC) for selective drug delivery in cells that express the somatostatin receptor subtype-2 (SSTR2). Material and methods: The clinically used somatostatin analog, 68Ga-DOTA-TOC, was used as a model for development of the SSTR2-targeted PDC. Synthesis was performed by (i) replacing DOTA with a multimodality chelator (MMC), (ii) attaching a modified TMZ analog to MMC, and (iii) conjugating the payload moiety to TOC on solid-phase. The resulting product, MMC(TMZ)-TOC, was radiolabeled with 67Ga using cation exchange chromatography methods optimized for 68Ga. Retention of SSTR2 binding was examined in cell lines with different expression level of SSTR2 with and without blocking doses of octreotide. A membrane acid wash was performed to evaluate internalization efficiency. The cytotoxicity of MMC(TMZ)-TOC was tested in IMR-32 cells that endogenously express SSTR2, and potency was compared to free-TMZ. An alkaline comet assay was then performed to assess the DNA-damaging properties of the PDC in the presence and absence of SSTR2 blocking. Unpublished results: MMC(TMZ)-TOC was efficiently produced with chemical purity >90% as shown by high-performance liquid chromatography (HPLC). Radiochemical purity following 67Ga labeling was >95% and indicates the feasibility of using the MMC to directly label the drug conjugates. Cell-based experiments showed that specific binding of the 67Ga-labeled PDC was similar to 67Ga-DOTA-TOC and correlated with SSTR2 expression. In HCT116-SSTR2 cells that overexpress SSTR2, 14.8±4.8% of 67Ga-MMC(TMZ)-TOC and 17.0±4.2% of 67Ga-DOTA-TOC were taken up by cells. Blocking the excess octreotide reduced binding to near background levels, illustrating receptor-mediated uptake of the PDC. Acid-washing demonstrated internalization of 67Ga-MMC(TMZ)-TOC after receptor-binding, indicating retention of the agonist properties of TOC after payload conjugation. Results from the cell cytotoxicity study demonstrated that the PDC inhibited cell growth in a dose-dependent manner that was similar to free-TMZ, with the IC50 values of 81.6 and 75.6 µM for free-TMZ and MMC(TMZ)-TOC, respectively. The comet assay revealed that MMC(TMZ)-TOC was effective in causing DNA damage in cells that express SSTR2, as shown by reduced cytotoxic effects when co-incubated with octreotide. Conclusions: We showed that a clinically used SSTR2-targeted radiopharmaceutical can be converted into a PDC that retains receptor-binding and internalization properties. We also showed that the cytotoxic effects of TMZ are maintained by the PDC. Based on these results, in vivo evaluation of MMC(TMZ)-TOC is warranted to assess its potential as a targeted therapy for NETs.

Citation Format: Solmaz AghaAmiri, Sukhen C. Ghosh, Lea Stitzlein, Servando Hernandez Vargas, Bruno Perlatti, Daniel M. Halperin, Ali Azhdarinia. A novel peptide-drug conjugate induces DNA damage in SSTR2-expressing cells [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr LB120.

Targeted Genome Mining Reveals the Biosynthetic Gene Clusters of Natural Product CYP51 Inhibitors

Lanosterol 14α-demethylase (CYP51) is an important target in the development of antifungal drugs. The fungal-derived restricticin 1 and related molecules are the only examples of natural products that inhibit CYP51. Here, using colocalizations of genes encoding self-resistant CYP51 as the query, we identified and validated the biosynthetic gene cluster (BGC) of 1. Additional genome mining of related BGCs with CYP51 led to production of the related lanomycin 2. The pathways for both 1 and 2 were identified from fungi not known to produce these compounds, highlighting the promise of the self-resistance enzyme (SRE) guided approach to bioactive natural product discovery.

Anti-cryptococcal activity of preussolides A and B, phosphoethanolamine-substituted 24-membered macrolides, and leptosin C from coprophilous isolates of Preussia typharum

Cryptococcus neoformans is a serious human pathogen with limited options for treatment. We have interrogated extracts from fungal fermentations to find Cryptococcus-inhibiting natural products using assays for growth inhibition and differential thermosensitivity. Extracts from fermentations of four fungal strains from wild and domestic animal dung from Arkansas and West Virginia, USA were identified as Preussia typharum. The extracts exhibited two antifungal regions. Purification of one region yielded new 24-carbon macrolides incorporating both a phosphoethanolamine unit and a bridging tetrahydrofuran ring. The structures of these metabolites were established mainly by analysis of high-resolution mass spectrometry and 2D NMR data. Relative configurations were assigned using NOESY data, and the structure assignments were supported by NMR comparison with similar compounds. These new metabolites are designated preussolides A and B. The second active region was caused by the cytotoxin, leptosin C. Genome sequencing of the four strains revealed biosynthetic gene clusters consistent with those known to encode phosphoethanolamine-bearing polyketide macrolides and the biosynthesis of dimeric epipolythiodioxopiperazines. All three compounds showed moderate to potent and selective antifungal activity toward the pathogenic yeast C. neoformans.

Campafungins: Inhibitors of Candida albicans and Cryptococcus neoformans Hyphal Growth

Campafungin A is a polyketide that was recognized in the Candida albicans fitness test due to its antiproliferative and antihyphal activity. Its mode of action was hypothesized to involve inhibition of a cAMP-dependent PKA pathway. The originally proposed structure appeared to require a polyketide assembled in a somewhat unusual fashion. However, structural characterization data were never formally published. This background stimulated a reinvestigation in which campafungin A and three closely related minor constituents were purified from fermentations of a strain of the ascomycete fungus Plenodomus enteroleucus. Labeling studies, along with extensive NMR analysis, enabled assignment of a revised structure consistent with conventional polyketide synthetic machinery. The structure elucidation of campafungin A and new analogues encountered in this study, designated here as campafungins B, C, and D, is presented, along with a proposed biosynthetic route. The antimicrobial spectrum was expanded to methicillin-resistant Staphylococcus aureus, Candida tropicalis, Candida glabrata, Cryptococcus neoformans, Aspergillus fumigatus, and Schizosaccharomyces pombe, with MICs ranging as low as 4-8 μg mL^-1 in C. neoformans. Mode-of-action studies employing libraries of C. neoformans mutants indicated that multiple pathways were affected, but mutants in PKA/cAMP pathways were unaffected, indicating that the mode of action was distinct from that observed in C. albicans.

Identification of the Antifungal Metabolite Chaetoglobosin P From Discosia rubi Using a Cryptococcus neoformans Inhibition Assay: Insights Into Mode of Action and Biosynthesis

Cryptococcus neoformans is an important human pathogen with limited options for treatments. We have interrogated extracts from fungal fermentations to find Cryptococcus-inhibiting natural products using assays for growth inhibition, differential thermosensitivity, and synergy with existing antifungal drugs. Extracts from fermentations of strains of Discosia rubi from eastern Texas showed anticryptococcal bioactivity with preferential activity in agar zone of inhibition assays against C. neoformans at 37°C versus 25°C. Assay-guided fractionation led to the purification and identification of chaetoglobosin P as the active component of these extracts. Genome sequencing of these strains revealed a biosynthetic gene cluster consistent with chaetoglobosin biosynthesis and β-methylation of the tryptophan residue. Proximity of genes of the actin-binding protein twinfilin-1 to the chaetoglobosin P and K gene clusters suggested a possible self-resistance mechanism involving twinfilin-1 which is consistent with the predicted mechanism of action involving interference with the polymerization of the capping process of filamentous actin. A C. neoformans mutant lacking twinfilin-1 was hypersensitive to chaetoglobosin P. Chaetoglobosins also potentiated the effects of amphotericin B and caspofungin on C. neoformans.

Acrophiarin (antibiotic S31794/F-1) from Penicillium arenicola shares biosynthetic features with both Aspergillus- and Leotiomycete-type echinocandins

The antifungal echinocandin lipopeptide, acrophiarin, was circumscribed in a patent in 1979. We confirmed that the producing strain NRRL 8095 is Penicillium arenicola and other strains of P. arenicola produced acrophiarin and acrophiarin analogues. Genome sequencing of NRRL 8095 identified the acrophiarin gene cluster. Penicillium arenicola and echinocandin-producing Aspergillus species belong to the family Aspergillaceae of the Eurotiomycetes, but several features of acrophiarin and its gene cluster suggest a closer relationship with echinocandins from Leotiomycete fungi. These features include hydroxy-glutamine in the peptide core instead of a serine or threonine residue, the inclusion of a non-heme iron, α-ketoglutarate-dependent oxygenase for hydroxylation of the C3 of the glutamine, and a thioesterase. In addition, P. arenicola bears similarity to Leotiomycete echinocandin-producing species because it exhibits self-resistance to exogenous echinocandins. Phylogenetic analysis of the genes of the echinocandin biosynthetic family indicated that most of the predicted proteins of acrophiarin gene cluster exhibited higher similarity to the predicted proteins of the pneumocandin gene cluster of the Leotiomycete Glarea lozoyensis than to those of the echinocandin B gene cluster from A. pachycristatus. The fellutamide gene cluster and related gene clusters are recognized as relatives of the echinocandins. Inclusion of the acrophiarin gene cluster into a comprehensive phylogenetic analysis of echinocandin gene clusters indicated the divergent evolutionary lineages of echinocandin gene clusters are descendants from a common ancestral progenitor. The minimal 10-gene cluster may have undergone multiple gene acquisitions or losses and possibly horizontal gene transfer after the ancestral separation of the two lineages.

Arenicolins: C-Glycosylated Depsides from Penicillium arenicola

During investigation of the secondary metabolism of four strains of Penicillium arenicola, two new depsides, arenicolins A (1) and B (2), were isolated and characterized. Their structures were established mainly by analysis of NMR and HRMS data and by comparison with known compounds. These depsides incorporate intriguing structural features, including dual alkyl side chains and a C-glycosyl unit, with 1 also containing an acylated 2-hydroxymethyl-4,5,6-trihydroxycyclohexenone moiety. Although the arenicolins were produced by all strains tested, arenicolin A (1) was obtained using only one of five medium compositions employed, while arenicolin B (2) was produced in all media tested. Neither compound showed antibacterial or antifungal activity, but 1 exhibited cytotoxicity toward mammalian cell lines, including colorectal carcinoma (HCT-116), neuroblastoma (IMR-32), and ductal carcinoma (BT-474), with IC50 values of 7.3, 6.0, and 9.7 μM, respectively.

Identification of Secondary Metabolites from Aspergillus pachycristatus by Untargeted UPLC-ESI-HRMS/MS and Genome Mining

Aspergillus pachycristatus is an industrially important fungus for the production of the antifungal echinocandin B and is closely related to model organism A. nidulans. Its secondary metabolism is largely unknown except for the production of echinocandin B and sterigmatocystin. We constructed mutants for three genes that regulate secondary metabolism in A. pachycristatus NRRL 11440, and evaluated the secondary metabolites produced by wild type and mutants strains. The secondary metabolism was explored by metabolic networking of UPLC-HRMS/MS data. The genes and metabolites of A. pachycristatus were compared to those of A.nidulans FGSC A4 as a reference to identify compounds and link them to their encoding genes. Major differences in chromatographic profiles were observable among the mutants. At least 28 molecules were identified in crude extracts that corresponded to nine characterized gene clusters. Moreover, metabolic networking revealed the presence of a yet unexplored array of secondary metabolites, including several undescribed fellutamides derivatives. Comparative reference to its sister species, A. nidulans, was an efficient way to dereplicate known compounds, whereas metabolic networking provided information that allowed prioritization of unknown compounds for further metabolic exploration. The mutation of global regulator genes proved to be a useful tool for expanding the expression of metabolic diversity in A. pachycristatus.

Stability of di-butyl-dichalcogenide-capped gold nanoparticles: experimental data and theoretical insights

Metals capped with organochalcogenides have attracted considerable interest due to their practical applications, which include catalysis, sensing, and biosensing, due to their optical, magnetic, electrochemical, adhesive, lubrication, and antibacterial properties. There are numerous reports of metals capped with organothiol molecules; however, there are few studies on metals capped with organoselenium or organotellurium. Thus, there is a gap to be filled regarding the properties of organochalcogenide systems which can be improved by replacing sulfur with selenium or tellurium. In the last decade, there has been significant development in the synthesis of selenium and tellurium compounds; however, it is difficult to find commercial applications of these compounds because there are few studies showing the feasibility of their synthesis and their advantages compared to organothiol compounds. Stability against oxidation by molecular oxygen under ambient conditions is one of the properties which can be improved by choosing the correct organochalcogenide; this can confer important advantages for many more suitable applications. This paper reports the successful synthesis and characterization of gold nanoparticles functionalized with organochalcogenide molecules (dibutyl-disulfide, dibutyl-diselenide and dibutyl-ditelluride) and evaluates the oxidation stability of the organochalcogenides. Spherical gold nanoparticles with diameters of 24 nm were capped with organochalcogenides and were investigated using X-ray photoelectron spectroscopy (XPS) to show the improved stability of organoselenium compared with organothiol and organotellurium. The results suggest that the organoselenium is a promising candidate to replace organothiol because of its enhanced stability towards oxidation by molecular oxygen under ambient conditions and its slow oxidation rate. The observed difference in the oxidation processes, as discussed, is also in agreement with theoretical calculations.

This study presents the improved stability against oxidation by molecular oxygen under ambient conditions of organoselenium compared with organothiol, and organotellurium.

Identification of Meliatoxins in Melia azedarach Extracts Using Mass Spectrometry for Quality Control

Indiscriminate use of synthetic pesticides can be hazardous to both humans and the environment, but the use of natural products as a source of bio-based products, such as Melia azedarach extracts, is an interesting approach to overcome these hazards. Unfortunately, the limonoids found in M. azedarach with desired insecticidal properties (e.g. azadirachtin) may also be present with limonoids toxic to mammals. The goal of this report was to develop a fast and reliable MS-based experiment to characterize meliatoxins in crude extracts of M. azedarach, in order to provide unequivocal assessment of the safety for extracts for application in the field. MS and MS/MS experiments using MALDI ionization were evaluated as tools for the assignment of characteristic ions produced by each meliatoxin in crude extracts.The use of different experiments in combination, such as the analysis of fragment m/z 557 and [M + Na]⁺ (adducts ions m/z 681 and m/z 667), MALDI-MS can be used for detection of meliatoxins A₁/B₁ or A₂/B₂ in a crude extract and may be used to discriminate meliatoxins A from B, respectively. Subsequent MS/MS experiments can distinguish between the presence of group 1 and/or 2 in each class of meliatoxins classifying the proposed approach as a quick and efficient quality control method of meliatoxins in real M. azedarach samples.

Biodegradation of 1,2,3,4-tetrachlorodibenzo-p-dioxin in liquid broth by brown-rot fungi

Dioxins are a class of extremely hazardous molecules that might pose a threat to the environment. This work evaluated the microbial degradation of 1,2,3,4-tetrachlorodibenzo-p-dioxin (1,2,3,4-TCDD), in liquid broth using three brown-rot fungi and one white-rot fungi as control. A fast and reliable extraction method with recoveries of over 98% together with a validated GC-MS method was developed, and applied to quantify 1,2,3,4-TCDD in liquid broth, mycelia and reaction flask, with detection limits of 10 ppb. Among the four strains tested, brown-rot fungus Aspergillus aculeatus showed best results, removing up to 21% of dioxin after 30-day incubation. The results open both a path for biotechnological interest in bioremediation purposes and environmental behavior studies by using brown-rot fungus.

Validation and application of HPLC-ESI-MS/MS method for the quantification of RBBR decolorization, a model for highly toxic molecules, using several fungi strains

A novel analytical method using HPLC-MS/MS operating in selected reaction monitoring (SRM) for evaluation of fungi efficacy to decolorize Remazol Brilliant Blue R (RBBR) dye solution was developed, validated and applied. The method shows high sensibility allowing the detection of 4.6 pM of RBBR. Four fungal strains were tested in liquid medium, three strains of Aspergillus (Aspergillus aculeatus, Aspergillus flavus and Aspergillus fumigatus) and Phanerochaete chrysosporium. All fungi were able to degrade the dye, with efficiencies ranging from 40% for P. chrysosporium up to 99% for A. flavus during a 30-day incubation period. During the experiment, increased accumulation of degradation products was observed in A. flavus cultures containing RBBR. Through the use of full scan HPLC-MS technique it was possible to propose the biogenesis of the microbial metabolic degradation pathway. Screening using microorganisms and RBBR may be hereafter used to investigate microbial biodegradation of high toxicity molecules such as dioxins.