Synthesis and Biological Evaluation of the Antimicrobial Natural Product Lipoxazolidinone A

1,1,1,3,3,3-Hexafluoroisopropanol-Promoted Synthesis of Structurally Diverse Alkylidene-4-thiazolidinones/selenazolidinones Involving an Azaoxyallyl Cation

A one-pot process involving cycloaddition of the azaoxyallyl cation with thioamide and a synchronous E1-type elimination of the C2 amino group from the cycloadduct is disclosed, leading to diverse alkylidene-4-thiazolidinones. Amine elimination under acid-free conditions or without quaternization and forging a stereoselective olefin formation were among the interesting reactivity traits revealed through the present work. Conjugated thioamide permitted side-chain branching through a three-component process. Access to spirooxindolyl thiazolidinones and selenazolidinones adds further value to the process.

The Pan-Canadian Chemical Library: A Mechanism to Open Academic Chemistry to High-Throughput Virtual Screening

Computationally screening chemical libraries to discover molecules with desired properties is a common technique used in early-stage drug discovery. Recent progress in the field now enables the efficient exploration of billions of molecules within days or hours, but this exploration remains confined within the boundaries of the accessible chemistry space. While the number of commercially available compounds grows rapidly, it remains a limited subset of all druglike small molecules that could be synthesized. Here, we present a workflow where chemical reactions typically developed in academia and unconventional in drug discovery are exploited to dramatically expand the chemistry space accessible to virtual screening. We use this process to generate a first version of the Pan-Canadian Chemical Library, a collection of nearly 150 billion diverse compounds that does not overlap with other ultra-large libraries such as Enamine REAL or SAVI and could be a resource of choice for protein targets where other libraries have failed to deliver bioactive molecules.

Ir(tri-N-heterocyclic carbene)-catalyzed upgrading of glycerol: C-C bond formation for the synthesis of α-hydroxy acids

Ir(triNHC) complexes catalyzed glycerol and alcohol dehydrogenative coupling, yielding diverse α-hydroxy acids. Unlike conventional conditions, Ir(triNHC) facilitated additional C-C bond formation after lactic acid production from glycerol, exhibiting high TOFs. This protocol successfully converted 1,2-propanediol and sorbitol into α-hydroxy acids, highlighting biomass-derived sources' potential as valuable platform chemicals.

Expanded library of novel 2,3-pyrrolidinedione analogues exhibit anti-biofilm activity

Herein we report a new library of 2,3-pyrrolidinedione analogues that expands on our previous report on the antimicrobial studies of this heterocyclic scaffold. The novel 2,3-pyrrolidinediones reported herein have been evaluated against S. aureus and methicillin-resistant S. aureus (MRSA) biofilms, and this work constitutes our first report on the antibiofilm properties of this class of compounds. The antibiofilm activity of these 2,3-pyrrolidinediones has been assessed through minimum biofilm eradication concentration (MBEC) and minimum biofilm inhibition concentration (MBIC) assays. The compounds displayed antibiofilm properties and represent intriguing scaffolds for further optimization and development.

Total Synthesis of the 2,5-Disubstituted γ-Pyrone E1 UAE Inhibitor Himeic Acid A

The first total synthesis of the E1 ubiquitin-activating enzyme inhibitor, himeic acid A, is reported. A McCombie reaction was used to form the core γ-pyrone via a 6π-electrocyclization. A dioxenone ring-opening/acyl ketene trapping reaction with a primary amide provided the unusual unsymmetrical imide functionality. Other key steps include the use of an Evans auxiliary alkylation (d.r. ≥ 95:5) to install the (S)-2-methyl succinic acid fragment and a cross-metathesis to install the unsaturated side-chain.

β-Lactams from the Ocean

The title of this essay is as much a question as it is a statement. The discovery of the β-lactam antibiotics-including penicillins, cephalosporins, and carbapenems-as largely (if not exclusively) secondary metabolites of terrestrial fungi and bacteria, transformed modern medicine. The antibiotic β-lactams inactivate essential enzymes of bacterial cell-wall biosynthesis. Moreover, the ability of the β-lactams to function as enzyme inhibitors is of such great medical value, that inhibitors of the enzymes which degrade hydrolytically the β-lactams, the β-lactamases, have equal value. Given this privileged status for the β-lactam ring, it is therefore a disappointment that the exemplification of this ring in marine secondary metabolites is sparse. It may be that biologically active marine β-lactams are there, and simply have yet to be encountered. In this report, we posit a second explanation: that the value of the β-lactam to secure an ecological advantage in the marine environment might be compromised by its close structural similarity to the β-lactones of quorum sensing. The steric and reactivity similarities between the β-lactams and the β-lactones represent an outside-of-the-box opportunity for correlating new structures and new enzyme targets for the discovery of compelling biological activities.

Synthesis of α-Hydroxy Acids via Dehydrogenative Cross-Coupling of a Sustainable C2 Chemical (Ethylene Glycol) with Alcohols

Ir(NHC) (NHC, N-heterocyclic carbene)-catalyzed dehydrogenative coupling of sustainable ethylene glycol and various bioalcohols can produce industrially valuable α-hydroxy acids (AHAs). This study is the first to report the sustainable synthesis of higher C_n AHAs, in addition to glycolic acid (C₂ AHA) and lactic acid (C₃ AHA). This catalytic system can be recycled to the seventh cycle while maintaining good yields. A reaction mechanism, including facile dehydrogenation of each alcohol and fast cross-coupling of dehydrogenated aldehydes forming products, was proposed based on ¹⁸O- and ²H-labeling experiments and electron spray ionization-mass spectrometry (ESI-MS) and NMR spectral analyses.

Fragmentation and transferability in Hirshfeld atom refinement

Hirshfeld atom refinement (HAR) is one of the most effective methods for obtaining accurate structural parameters for hydrogen atoms from X-ray diffraction data. Unfortunately, it is also relatively computationally expensive, especially for larger molecules due to wavefunction calculations. Here, a fragmentation approach has been tested as a remedy for this problem. It gives an order of magnitude improvement in computation time for larger organic systems and is a few times faster for metal-organic systems at the cost of only minor differences in the calculated structural parameters when compared with the original HAR calculations. Fragmentation was also applied to polymeric and disordered systems where it provides a natural solution to problems that arise when HAR is applied. The concept of fragmentation is closely related to the transferable aspherical atom model (TAAM) and allows insight into possible ways to improve TAAM. Hybrid approaches combining fragmentation with the transfer of atomic densities between chemically similar atoms have been tested. An efficient handling of intermolecular interactions was also introduced for calculations involving fragmentation. When applied in fragHAR (a fragmentation approach for polypeptides) as a replacement for the original approach, it allowed for more efficient calculations. All of the calculations were performed with a locally modified version of Olex2 combined with a development version of discamb2tsc and ORCA. Care was taken to efficiently use the power of multicore processors by simple implementation of load-balancing, which was found to be very important for lowering computational time.

A Novel Nano-Antimicrobial Polymer Engineered with Chitosan Nanoparticles and Bioactive Peptides as Promising Food Biopreservative Effective against Foodborne Pathogen E. coli O157-Caused Epithelial Barrier Dysfunction and Inflammatory Responses

For food quality and safety issues, the emergence of foodborne pathogenic bacteria has further accelerated the spread of antibiotic residues and drug resistance genes. To alleviate the harm caused by bacterial infections, it is necessary to seek novel antimicrobial agents as biopreservatives to prevent microbial spoilage. Nanoantimicrobials have been widely used in the direct treatment of bacterial infections. CNMs, formed by chitosan nanoparticles and peptides, are promising antibiotic alternatives for use as excellent new antibacterial drugs against pathogenic bacteria. Herein, the current study evaluated the function of CNMs in the protection of foodborne pathogen Escherichia coli (E. coli) O157 infection using an intestinal epithelial cell model. Antibacterial activity assays indicated that CNMs exerted excellent bactericidal activity against E. coli O157. Assessment of the cytotoxicity risks toward cells demonstrated that 0.0125–0.02% of CNMs did not cause toxicity, but 0.4% of CNMs caused cytotoxicity. Additionally, CNMs did not induced genotoxicity either. CNMs protected against E. coli O157-induced barrier dysfunction by increasing transepithelial electrical resistance, decreasing lactate dehydrogenase and promoting the protein expression of occludin. CNMs were further found to ameliorate inflammation via modulation of tumor factor α, toll-like receptor 4 and nuclear factor κB (NF-κB) expression via inhibition of mitogen-activated protein kinase and NF-κB activation and improved antioxidant activity. Taken together, CNMs could protect the host against E. coli O157-induced intestinal barrier damage and inflammation, showing that CNMs have great advantages and potential application as novel antimicrobial polymers in the food industry as food biopreservatives, bringing new hope for the treatment of bacterial infections.

Leveraging Marine Natural Products as a Platform to Tackle Bacterial Resistance and Persistence

Antimicrobial resistance to existing antibiotics represents one of the greatest threats to human health and is growing at an alarming rate. To further complicate treatment of bacterial infections, many chronic infections are the result of bacterial biofilms that are tolerant to treatment with antibiotics because of the presence of metabolically dormant persister cell populations. Together these threats are creating an increasing burden on the healthcare system, and a "preantibiotic" age is on the horizon if significant action is not taken by the scientific and medical communities. While the golden era of antibiotic discovery (1940s-1960s) produced most of the antibiotic classes in clinical use today, followed by several decades of limited development, there has been a resurgence in antibiotic drug discovery in recent years fueled by the academic and biotech sectors. Historically, great success has been achieved by developing next-generation variants of existing classes of antibiotics, but there remains a dire need for the identification of novel scaffolds and/or antimicrobial targets to drive future efforts to overcome resistance and tolerance. In this regard, there has been no more valuable source for the identification of antibiotics than natural products, with 69-77% of approved antibiotics either being such compounds or being derived from them.Our group has developed a program centered on the chemical synthesis and chemical microbiology of marine natural products with unusual structures and promising levels of activity against multidrug-resistant (MDR) bacterial pathogens. As we are motivated by preparing and studying the biological effects of these molecules, we are not initially pursuing a biological question but instead are allowing the observed phenotypes and activities to guide the ultimate project direction. In this Account, our recent efforts on the synoxazolidinone, lipoxazolidinone, and batzelladine natural products will be discussed and placed in the context of the field's greatest challenges and opportunities. Specifically, the synoxazolidinone family of 4-oxazolidinone-containing natural products has led to the development of several chemical methods to prepare antimicrobial scaffolds and has revealed compounds with potent activity as adjuvants to treat bacterial biofilms. Bearing the same 4-oxazolidinone core, the lipoxazolidinones have proven to be potent single-agent antibiotics. Finally, our synthetic efforts toward the batzelladines revealed analogues with activity against a number of MDR pathogens, highlighted by non-natural stereochemical isomers with superior activity and simplified synthetic access. Taken together, these studies provide several distinct platforms for the development of novel therapeutics that can add to our arsenal of scaffolds for preclinical development and can provide insight into the biochemical processes and pathways that can be targeted by small molecules in the fight against antimicrobial-resistant and -tolerant infections. We hope that this work will serve as inspiration for increased efforts by the scientific community to leverage synthetic chemistry and chemical microbiology toward novel antibiotics that can combat the growing crisis of MDR and tolerant bacterial infections.

Marine natural products

This review covers the literature published between January and December in 2018 for marine natural products (MNPs), with 717 citations (706 for the period January to December 2018) 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 (1554 in 469 papers for 2018), together with the relevant biological activities, source organisms and country of origin. Reviews, biosynthetic studies, first syntheses, and syntheses that led to the revision of structures or stereochemistries, have been included. The proportion of MNPs assigned absolute configuration over the last decade is also surveyed.

Landscape of Lankacidin Biomimetic Synthesis: Structural Revisions and Biogenetic Implications

In this report, a unified biomimetic approach to all known macrocyclic lankacidins is presented. By taking advantage of the thermolysis of N,O-acetal to generate the requisite N-acyl-1-azahexatriene species, we eventually realized the biomimetic Mannich macrocyclization, from which all of the macrocyclic lankacidins can be conquered by orchestrated desilylation. The reassignments of the reported structures of isolankacidinol (7 to 10) and the discovery of a recently isolated "lankacyclinol" found to be in fact 2,18-bis-epi-lankacyclinol (72) unraveled the previously underappreciated chemical diversity exhibited by the enzymatic macrocyclization. In addition, the facile elimination/decarboxylation/protonation process for the depletion of C1 under basic conditions resembling a physiological environment may implicate more undiscovered natural products with variable C2/C18 stereochemistries (i.e., 62, 73, and 75). The notable aspect provided by a biomimetic strategy is significantly reducing the step count compared with the two previous entries to macrocyclic lankacidins.

Genetic Determinants of Salmonella Resistance to the Biofilm-Inhibitory Effects of a Synthetic 4-Oxazolidinone Analog

Biofilms formed by Salmonella enterica are a frequent source of food supply contamination. Since biofilms are inherently resistant to disinfection, new agents capable of preventing biofilm formation are needed. Synthetic analogs of 4-oxazolidinone containing natural products have shown promise as antibiofilm compounds against Gram-positive bacteria. The purpose of our study was 2-fold: to establish the antibiofilm effects and mechanism of action of a synthetic 4-oxazolidinone analog (JJM-ox-3-70) and to establish mechanisms of resistance to this compound in Salmonella enterica serovar Typhimurium (S Typhimurium). JJM-ox-3-70 inhibited biofilm formation but had no effect on cell growth. The antibiofilm effects were linked to disruption of curli fimbriae and flagellar gene expression and alteration in swimming motility, suggesting an effect on multiple cellular processes. Using a 2-step screening approach of defined multigene and single-gene deletion mutant libraries, we identified 3 mutants that produced less biofilm in the presence of JJM-ox-3-70 than the isogenic WT, with phenotypes reversed by complementation in trans Genes responsible for S Typhimurium resistance to the compound included acrB, a component of the major drug efflux pump AcrAB-TolC, and two genes of unknown function (STM0437 and STM1292). The results of this study suggest that JJM-ox-3-70 inhibits biofilm formation by indirect inhibition of extracellular matrix production that may be linked to disruption of flagellar motility. Further work is needed to establish the role of the newly characterized genes as potential mechanisms of biofilm intrinsic antimicrobial resistance.IMPORTANCE Biofilms are resistant to killing by disinfectants and antimicrobials. S. enterica biofilms facilitate long-term host colonization and persistence in food processing environments. Synthetic analogs of 4-oxazolidinone natural products show promise as antibiofilm agents. Here, we show that a synthetic 4-oxazolidinone analog inhibits Salmonella biofilm through effects on both motility and biofilm matrix gene expression. Furthermore, we identify three genes that promote Salmonella resistance to the antibiofilm effects of the compound. This work provides insight into the mechanism of antibiofilm effects of a synthetic 4-oxazolidinone analog in Gram-negative bacteria and demonstrates new mechanisms of intrinsic antimicrobial resistance in Salmonella biofilms.

Synthesis of Dicarboxylic Acids from Aqueous Solutions of Diols with Hydrogen Evolution Catalyzed by an Iridium Complex

A catalytic system for the synthesis of dicarboxylic acids from aqueous solutions of diols accompanied by the evolution of hydrogen was developed. An iridium complex bearing a functional bipyridonate ligand with N,N-dimethylamino substituents exhibited a high catalytic performance for this type of dehydrogenative reaction. For example, adipic acid was synthesized from an aqueous solution of 1,6-hexanediol in 97 % yield accompanied by the evolution of four equivalents of hydrogen by the present catalytic system. It should be noted that the simultaneous production of industrially important dicarboxylic acids and hydrogen, which is useful as an energy carrier, was achieved. In addition, the selective dehydrogenative oxidation of vicinal diols to give α-hydroxycarboxylic acids was also accomplished.

5-Benzylidene-4-Oxazolidinones Are Synergistic with Antibiotics for the Treatment of Staphylococcus aureus Biofilms

The failure of frontline antibiotics in the clinic is one of the most serious threats to human health and requires a multitude of novel therapeutics and innovative approaches to treatment so as to curtail the growing crisis. In addition to traditional resistance mechanisms resulting in the lack of efficacy of many antibiotics, most chronic and recurring infections are further made tolerant to antibiotic action by the presence of biofilms. Herein, we report an expanded set of 5-benzylidene-4-oxazolidinones that are able to inhibit the formation of Staphylococcus aureus biofilms, disperse preformed biofilms, and, in combination with common antibiotics, are able to significantly reduce the bacterial load in a robust collagen-matrix model of biofilm infection.

Antibacterial Small Molecules That Potently Inhibit Staphylococcus aureus Lipoteichoic Acid Biosynthesis

The rise of antibiotic resistance, especially in Staphylococcus aureus, and the increasing death rate due to multiresistant bacteria have been well documented. The need for new chemical entities and/or the identification of novel targets for antibacterial drug development is high. Lipoteichoic acid (LTA), a membrane-attached anionic polymer, is important for the growth and virulence of many Gram-positive bacteria, and interest has been high in the discovery of LTA biosynthesis inhibitors. Thus far, only a handful of LTA biosynthesis inhibitors have been described with moderate (MIC=5.34 μg mL^-1 ) to low (MIC=1024 μg mL^-1 ) activities against S. aureus. Herein we describe the identification of novel compounds that potently inhibit LTA biosynthesis in S. aureus, displaying impressive antibacterial activities (MIC as low as 0.25 μg mL^-1 ) against methicillin-resistant S. aureus (MRSA). Under similar in vitro assay conditions, these compounds are 4-fold more potent than vancomycin and 8-fold more potent than linezolid against MRSA.

Expanded Structure-Activity Studies of Lipoxazolidinone Antibiotics

The lipoxazolidinone family of marine natural products, which contains an unusual 4-oxazolidinone core, was found to possess potent antimicrobial activity against methicillin resistant Staphylococcus aureus (MRSA). Herein, we expanded our previous synthetic efforts by preparing selected aryl derivatives of the lipoxazolidinones and further evaluating the potential to expand the activity of this class of molecules to Gram-negative pathogens. With these analogs, we explored the effect of varying the substitution pattern around the aromatic ring, increasing the chain length between the oxazolidinone core and the aryl system, and how altering the position of more polar functional groups affected the antimicrobial activity. Finally, we utilized a TolC knockout strain of E. coli to demonstrate that our compounds are subject to efflux in Gram-negative pathogens, and activity is restored in these knockouts. Together these results provide additional data for the further development of 4-oxazolidinone analogs 5, 20, and 21 for the treatment of infectious disease.