Evolution of novel antibiotic Scaffolds targeting the nucleic acid machineries RNA polymerase, DNA gyrase, and topoisomerase IV

The magic bullets for treating bacterial infection are getting less potent in face of the growing resistance. This warning situation urges for rapid development of new antibacterial weapons effective against resistant pathogens. In this thesis, novel antibiotic scaffolds with low resistance frequency were developed by two strategies. First, targeting a vital binding site (the switch region) of bacterial RNA polymerase: Following analog design approaches, six ureido-heterocycle-carboxylic acid classes were synthesized based on a previous class. The new compounds show potent activity against Gram-positive pathogens as well as the Gram-negative E. coli TolC strain. They are characterized by no crossresistance with the clinically used RNAP inhibitor rifampicin, lower rate of resistance development, and marginal cytotoxicity to human cells. These features were employed to target the closely related NNRTI binding site of HIV-1 reverse transcriptase. By structure-based optimization, the first small molecule dual antiinfectives were discovered exhibiting antibacterial and antiretroviral activities on HIV-1 wild type and resistant strains. Second, optimization of novel natural antibiotics (the cystobactamids) that target DNA gyrase and topoisomerase IV: Pursuing an interactive de novo design, both target and antibacterial activities of cystobactamid 507 were enhanced. The new congeners display an outstanding metabolic stability. Moreover, the synthetic route was markedly improved.Angesichts einer ständig wachsenden Resistenzentwicklung werden die therapeutischen Optionen zur Behandlung bakterieller Infektionen ständig schlechter. Deshalb sind neue Antibiotika gegen resistente Bakterien dringend notwendig. In dieser Doktorarbeit werden neue antibiotisch wirksame Scaffolds durch zwei Strategien entwickelt. Erstens Hemmstoffe der bakteriellen RNA Polymerase, die an die Switch Region binden: mittels Analog Design wurden Substanzen in sechs Klassen von Ureido-Heterocyclus-Carbonsäuren erhalten. Die Verbindungen zeigten eine starke antibakterielle Aktivität, keine Kreuzresistenz zu dem klinisch verwendeten Rifampicin, eine niedrigere Resistenz-Entwicklungsrate und eine nur geringfügige Toxizität gegenüber humanen Zellen. In einem weiteren Projekt wurde die Tatsache ausgenutzt, dass die NNRTI Bindestelle der HIV-1 Reversen Transkriptase strukturelle Ähnlichkeiten zur Switch Region hat. Geeignete, oben entwickelte Wirkstoffe wurden nun weiter strukturell optimiert und duale Hemmstoffe mit antibakterieller und antiretroviraler Aktivität an Wildtyp und resistenten Stämmen erhalten. Zweitens wurde eine Optimierung des natürlich vorkommenden Cystobactamids 507 hinsichtlich DNA Gyrase und Topoisomerase IV unternommen. Diese Ziele und eine Erhöhung der antibakteriellen Aktivität wurde durch interaktives de novo Design erreicht. Die neuen Derivate zeigten auch eine verbesserte metabolische Stabilität. Außerdem wurde der synthetische Zugang verbessert

Evolution of novel antibiotic Scaffolds targeting the nucleic acid machineries RNA polymerase, DNA gyrase, and topoisomerase IV

The magic bullets for treating bacterial infection are getting less potent in face of the growing resistance. This warning situation urges for rapid development of new antibacterial weapons effective against resistant pathogens. In this thesis, novel antibiotic scaffolds with low resistance frequency were developed by two strategies. First, targeting a vital binding site (the switch region) of bacterial RNA polymerase: Following analog design approaches, six ureido-heterocycle-carboxylic acid classes were synthesized based on a previous class. The new compounds show potent activity against Gram-positive pathogens as well as the Gram-negative E. coli TolC strain. They are characterized by no crossresistance with the clinically used RNAP inhibitor rifampicin, lower rate of resistance development, and marginal cytotoxicity to human cells. These features were employed to target the closely related NNRTI binding site of HIV-1 reverse transcriptase. By structure-based optimization, the first small molecule dual antiinfectives were discovered exhibiting antibacterial and antiretroviral activities on HIV-1 wild type and resistant strains. Second, optimization of novel natural antibiotics (the cystobactamids) that target DNA gyrase and topoisomerase IV: Pursuing an interactive de novo design, both target and antibacterial activities of cystobactamid 507 were enhanced. The new congeners display an outstanding metabolic stability. Moreover, the synthetic route was markedly improved.Angesichts einer ständig wachsenden Resistenzentwicklung werden die therapeutischen Optionen zur Behandlung bakterieller Infektionen ständig schlechter. Deshalb sind neue Antibiotika gegen resistente Bakterien dringend notwendig. In dieser Doktorarbeit werden neue antibiotisch wirksame Scaffolds durch zwei Strategien entwickelt. Erstens Hemmstoffe der bakteriellen RNA Polymerase, die an die Switch Region binden: mittels Analog Design wurden Substanzen in sechs Klassen von Ureido-Heterocyclus-Carbonsäuren erhalten. Die Verbindungen zeigten eine starke antibakterielle Aktivität, keine Kreuzresistenz zu dem klinisch verwendeten Rifampicin, eine niedrigere Resistenz-Entwicklungsrate und eine nur geringfügige Toxizität gegenüber humanen Zellen. In einem weiteren Projekt wurde die Tatsache ausgenutzt, dass die NNRTI Bindestelle der HIV-1 Reversen Transkriptase strukturelle Ähnlichkeiten zur Switch Region hat. Geeignete, oben entwickelte Wirkstoffe wurden nun weiter strukturell optimiert und duale Hemmstoffe mit antibakterieller und antiretroviraler Aktivität an Wildtyp und resistenten Stämmen erhalten. Zweitens wurde eine Optimierung des natürlich vorkommenden Cystobactamids 507 hinsichtlich DNA Gyrase und Topoisomerase IV unternommen. Diese Ziele und eine Erhöhung der antibakteriellen Aktivität wurde durch interaktives de novo Design erreicht. Die neuen Derivate zeigten auch eine verbesserte metabolische Stabilität. Außerdem wurde der synthetische Zugang verbessert

Potential Dental Biofilm Inhibitors: Dynamic Combinatorial Chemistry Affords Sugar-Based Molecules that Target Bacterial Glucosyltransferase

We applied dynamic combinatorial chemistry (DCC) to find novel ligands of the bacterial virulence factor glucosyltransferase (GTF) 180. GTFs are the major producers of extracellular polysaccharides, which are important factors in the initiation and development of cariogenic dental biofilms. Following a structure-based strategy, we designed a series of 36 glucose- and maltose-based acylhydrazones as substrate mimics. Synthesis of the required mono- and disaccharide-based aldehydes set the stage for DCC experiments. Analysis of the dynamic combinatorial libraries (DCLs) by UPLC-MS revealed major amplification of four compounds in the presence of GTF180. Moreover, we found that derivatives of the glucose-acceptor maltose at the C1-hydroxy group act as glucose-donors and are cleaved by GTF180. The synthesized hits display medium to low binding affinity (KD values of 0.4–10.0 mm) according to surface plasmon resonance. In addition, they were investigated for inhibitory activity in GTF-activity assays. The early-stage DCC study reveals that careful design of DCLs opens up easy access to a broad class of novel compounds that can be developed further as potential inhibitors

Discovery of Small-Molecule Stabilizers of 14-3-3 Protein-Protein Interactions via Dynamic Combinatorial Chemistry

Protein-protein interactions (PPIs) play an important role in numerous biological processes such as cell-cycle regulation and multiple diseases. The family of 14-3-3 proteins is an attractive target as they serve as binding partner to various proteins and are therefore capable of regulating their biological activities. Discovering small-molecule modulators, in particular stabilizers, of such complexes via traditional screening approaches is a challenging task. Herein, we pioneered the first application of dynamic combinatorial chemistry (DCC) to a PPI target, to find modulators of 14-3-3 proteins. Evaluation of the amplified hits from the DCC experiments for their binding affinity via surface plasmon resonance (SPR), revealed that the low-micromolar (KD 15-16 μM) acylhydrazones are 14-3-3/synaptopodin PPI stabilizers. Thus, DCC appears to be ideally suited for the discovery of not only modulators but even the more elusive stabilizers of notoriously challenging PPIs

Clean Synthetic Strategies to Biologically Active Molecules from Lignin:A Green Path to Drug Discovery**

Deriving active pharmaceutical agents from renewable resources is crucial to increasing the economic feasibility of modern biorefineries and promises to alleviate critical supply-chain dependencies in pharma manufacturing. Our multidisciplinary approach combines research in lignin-first biorefining, sustainable catalysis, and alternative solvents with bioactivity screening, an in vivo efficacy study, and a structural-similarity search. The resulting sustainable path to novel anti-infective, anti-inflammatory, and anticancer molecules enabled the rapid identification of frontrunners for key therapeutic indications, including an anti-infective against the priority pathogen Streptococcus pneumoniae with efficacy in vivo and promising plasma and metabolic stability. Our catalytic methods provided straightforward access, inspired by the innate structural features of lignin, to synthetically challenging biologically active molecules with the core structure of dopamine, namely, tetrahydroisoquinolines, quinazolinones, 3-arylindoles and the natural product tetrahydropapaveroline. Our diverse array of atom-economic transformations produces only harmless side products and uses benign reaction media, such as tunable deep eutectic solvents for modulating reactivity in challenging cyclization steps.</p

Clean Synthetic Strategies to Biologically Active Molecules from Lignin:A Green Path to Drug Discovery**

Deriving active pharmaceutical agents from renewable resources is crucial to increasing the economic feasibility of modern biorefineries and promises to alleviate critical supply-chain dependencies in pharma manufacturing. Our multidisciplinary approach combines research in lignin-first biorefining, sustainable catalysis, and alternative solvents with bioactivity screening, an in vivo efficacy study, and a structural-similarity search. The resulting sustainable path to novel anti-infective, anti-inflammatory, and anticancer molecules enabled the rapid identification of frontrunners for key therapeutic indications, including an anti-infective against the priority pathogen Streptococcus pneumoniae with efficacy in vivo and promising plasma and metabolic stability. Our catalytic methods provided straightforward access, inspired by the innate structural features of lignin, to synthetically challenging biologically active molecules with the core structure of dopamine, namely, tetrahydroisoquinolines, quinazolinones, 3-arylindoles and the natural product tetrahydropapaveroline. Our diverse array of atom-economic transformations produces only harmless side products and uses benign reaction media, such as tunable deep eutectic solvents for modulating reactivity in challenging cyclization steps.</p

Revision of the absolute configurations of chelocardin and amidochelocardin

Even with the aid of the available methods, the configurational assignment of natural products can be a challenging task that is prone to errors, and it sometimes needs to be corrected after total synthesis or single-crystal X-ray diffraction (XRD) analysis. Herein, the absolute configuration of amidochelocardin is revised using a combination of XRD, NMR spectroscopy, experimental ECD spectra, and time-dependent density-functional theory (TDDFT)-ECD calculations. As amidochelocardin was obtained via biosynthetic engineering of chelocardin, we propose the same absolute configuration for chelocardin based on the similar biosynthetic origins of the two compounds and result of TDDFT-ECD calculations. The evaluation of spectral data of two closely related analogues, 6-desmethyl-chelocardin and its semisynthetic derivative 1, also supports this conclusion

Octyl itaconate enhances VSVΔ51 oncolytic virotherapy by multitarget inhibition of antiviral and inflammatory pathways

The presence of heterogeneity in responses to oncolytic virotherapy poses a barrier to clinical effectiveness, as resistance to this treatment can occur through the inhibition of viral spread within the tumor, potentially leading to treatment failures. Here we show that 4-octyl itaconate (4-OI), a chemical derivative of the Krebs cycle-derived metabolite itaconate, enhances oncolytic virotherapy with VSVΔ51 in various models including human and murine resistant cancer cell lines, three-dimensional (3D) patient-derived colon tumoroids and organotypic brain tumor slices. Furthermore, 4-OI in combination with VSVΔ51 improves therapeutic outcomes in a resistant murine colon tumor model. Mechanistically, we find that 4-OI suppresses antiviral immunity in cancer cells through the modification of cysteine residues in MAVS and IKKβ independently of the NRF2/KEAP1 axis. We propose that the combination of a metabolite-derived drug with an oncolytic virus agent can greatly improve anticancer therapeutic outcomes by direct interference with the type I IFN and NF-κB-mediated antiviral responses.</p