Biological selection makes natural products promising scaffolds for drug development and the ever growing number of newly identified, structurally diverse molecules helps to fill the gaps in chemical space. Elucidating the function of a small molecule, such as identifying its protein binding partners, its on- and off-targets, is becoming increasingly important. Activity- and affinity-based protein profiling are modern strategies to acquire such molecular-level information. Introduction of a molecular handle (azide, alkyne, biotin) can shed light on the mode of action of small molecules. This Concept article covers central points on synthetic methodology for integrating a terminal alkyne into a molecule of interest.

Methicillin-resistant Staphylococcus aureus (MRSA) causes severe infections with only few effective antibiotic therapies currently available. To approach this challenge, chemical entities with a novel and resistance-free mode of action are desperately needed. Here, we introduce a new hydroxyamide compound that effectively reduces the expression of devastating toxins in various S. aureus and MRSA strains. The molecular mechanism was investigated by transcriptome analysis as well as by affinity-based protein profiling. Down-regulation of several pathogenesis associated genes suggested the inhibition of a central virulence-related pathway. Mass spectrometry-based chemical proteomics revealed putative molecular targets. Systemic treatment with the hydroxyamide showed significant reduction of abscess sizes in a MRSA mouse skin infection model. The absence of resistance development in vitro further underlines the finding that targeting virulence could lead to prolonged therapeutic options in comparison to antibiotics that directly address bacterial survival.

Vibrio is a model organism for the study of quorum sensing (QS) signaling and is used to identify QS-interfering drugs. Naturally occurring fimbrolides are important tool compounds known to affect QS in various organisms; however, their cellular targets have so far remained elusive. Here we identify the irreversible fimbrolide targets in the proteome of living V. harveyi and V. campbellii via quantitative mass spectrometry utilizing customized probes. Among the major hits are two protein targets with essential roles in Vibrio QS and bioluminescence. LuxS, responsible for autoinducer 2 biosynthesis, and LuxE, a subunit of the luciferase complex, were both covalently modified at their active-site cysteines leading to inhibition of activity. The identification of LuxE unifies previous reports suggesting inhibition of bioluminescence downstream of the signaling cascade and thus contributes to a better mechanistic understanding of these QS tool compounds.

Vibrio ist ein Modellorganismus zur molekularen Analyse des Quorum Sensings (QS) und zur Identifikation QS-interferierender Wirkstoffe. Die natürlichen Fimbrolide sind für die QS-inhibierenden Wirkungen in verschiedenen Organismen bekannt, allerdings waren die zellulären Angriffspunkte bisher verborgen. Nun ist es gelungen, die irreversiblen Zielstrukturen der Fimbrolide im Proteom von V. harveyi und V. campbellii mithilfe quantitativer Massenspektrometrie und chemisch modifizierter Fimbrolide aufzudecken. Hauptangriffspunkte sind zwei Proteine, die eine essenzielle Rolle für QS und Biolumineszenz in Vibrio spielen. LuxS, das für die Autoinduktor-2-Biosynthese verantwortlich ist, und LuxE, eine Untereinheit des Luziferasekomplexes, wurden beide kovalent an Cysteinresten im jeweiligen aktiven Zentrum modifiziert und dadurch inhibiert. Die Identifizierung von LuxE ist in Einklang mit früheren Studien, die die Inhibierung der Biolumineszenz ebenfalls downstream der Signalkaskade vermuteten.

Natural products represent a rich source of bioactive compounds that constitute a large fraction of approved drugs. Among those are molecules with electrophilic scaffolds, such as Michael acceptors, β-lactams, and epoxides that irreversibly inhibit essential enzymes based on their catalytic mechanism. In the search for novel bioactive molecules, current methods are challenged by the frequent rediscovery of known chemical entities. Herein small nucleophilic probes that attack electrophilic natural products and enhance their detection by HPLC-UV and HPLC-MS are introduced. A screen of diverse probe designs revealed one compound with a desired selectivity for epoxide- and maleimide-based antibiotics. Correspondingly, the natural products showdomycin and phosphomycin could be selectively targeted in extracts of their natural producing organism, in which the probe-modified molecules exhibited superior retention and MS detection relative to their unmodified counterparts. This method may thus help to discover small, electrophilic molecules that might otherwise easily elude detection in complex samples.

Trotz der strukturellen Ähnlichkeit der beiden Naturstoffe Omuralid und Vibralacton zeigen sich unerwartete Unterschiede in den Präferenzen ihrer jeweiligen Zielenzyme. Während Omuralid das Chymotrypsin-ähnliche aktive Zentrum des Proteasoms mit IC₅₀ = 47 nM inhibiert, hat Vibralacton auch bei Konzentrationen von bis zu 1 mM keinen Effekt auf diese Protease. Aktivitätsbasiertes Protein-Profiling in HeLa-Zellen identifizierte APT1 und APT2 als zelluläre Angriffsziele von Vibralacton.

Resistance to chemotherapeutic agents represents a major challenge in cancer research. One approach to this problem is combination therapy, the application of a toxic chemotherapeutic drug together with a sensitizing compound that addresses the vulnerability of cancer cells to induce apoptosis. Here we report the discovery of a new compound class (T8) that sensitizes various cancer cells towards etoposide treatment at subtoxic concentrations. Proteomic analysis revealed protein disulfide isomerase (PDI) as the target of the T8 class. In-depth chemical and biological studies such as the synthesis of optimized compounds, molecular docking analyses, cellular imaging, and apoptosis assays confirmed the unique mode of action through reversible PDI inhibition.

Die Entwicklung von Resistenzen gegen Chemotherapeutika stellt eine der größten Herausforderungen der Krebsforschung dar. Eine Möglichkeit dieses Problem zu umgehen ist, Chemotherapeutika zusammen mit Verbindungen zu verabreichen, die Zellen gegen die Medikamente sensibilisieren und Apoptose induzieren. Wir beschreiben die Entdeckung einer neuen Substanzklasse (T8), die verschiedene Krebszellen gegen subtoxische Konzentrationen von Etoposid sensibilisiert. Durch Proteomanalysen konnte gezeigt werden, dass die Proteindisulfidisomerase (PDI) das alleinige Ziel der T8-Verbindungen ist. Detaillierte biologische und chemische Studien wie die Optimierung der Molekülstrukturen, Docking-Analysen, Fluoreszenzmikroskopie und Apoptoseuntersuchungen belegen den Wirkmechanismus der reversiblen Inhibition der PDI und zeigen eine erhöhte Stressantwort im endoplasmatischen Retikulum durch T8.

Skin infections caused by Staphylococcus aureus are a major clinical concern, especially if they are caused by multi-resistant strains. In these cases, a spread into deeper soft tissues or the bloodstream results in life-threatening conditions that are difficult to treat by conventional antibiotics. Previous in vitro experiments with a small β-lactone-based molecule demonstrated that antibiotic-sensitive and -resistant S. aureus strains are effectively disarmed in their virulence and corresponding pathogenicity. In this work, in vivo mouse studies show that this methodology is effective for the treatment of skin abscesses in mice. A single dose of the β-lactone significantly decreased abscess size even when applied 6 h post-infection. Although the molecule requires pharmacological optimization (improved stability, for example), this study emphasizes the potential value of antivirulence therapies.

Despite their structural similarity, the natural products omuralide and vibralactone have different biological targets. While omuralide blocks the chymotryptic activity of the proteasome with an IC₅₀ value of 47 nM, vibralactone does not have any effect at this protease up to a concentration of 1 mM. Activity-based protein profiling in HeLa cells revealed that the major targets of vibralactone are APT1 and APT2.

Copper-catalysed alkyne–azide 1,3-dipolar cycloaddition (CuAAC) is the predominantly used bioconjugation method in the field of activity-based protein profiling (ABPP). Several limitations, however, including conversion efficiency, protein denaturation and buffer compatibility, restrict the scope of established procedures. We introduce an ABPP customised click methodology based on refined CuAAC conditions together with new accelerating copper ligands. A screen of several triazole compounds revealed the cationic quaternary {3-[4-({bis[(1-tert-butyl-1H-1,2,3-triazol-4-yl)methyl]amino}methyl)-1H-1,2,3-triazol-1-yl]propyl}trimethylammonium trifluoroacetate (TABTA) to be a superior ligand. TABTA exhibited excellent in vitro conjugation kinetics and optimal ABPP labelling activity while almost exclusively preserving the native protein fold. The application of this CuAAC-promoting system is amenable to existing protocols with minimal perturbations and is even compatible with previously unusable buffer systems such as Tris⋅HCl.

Rugulactone is a dihydro-α-pyrone isolated from the plant Cryptocarya rugulosa in 2009. It has been reported to display IkB kinase (IKK) inhibitory activity, as well as antibiotic activity in several strains of pathogenic bacteria. However, its biological targets and mode of action in bacteria have not yet been explored. Here we present enantioselective syntheses of rugulactone and of some corresponding activity-based protein profiling (ABPP) probes. We found that the ABPP probes in this study are more potent than rugulactone against Staphyloccocus aureus NCTC 8325, S. aureus Mu50, Listeria welshimeri SLCC 5334 and Listeria monocytogenes EGD-e, and that molecules of this class probably exert their antibacterial effect through a combination of targets. These targets include covalent inhibition of 4-amino-5-hydroxymethyl-2-methylpyrimidine phosphate (HMPP) kinase (ThiD), which is an essential component of the thiamine biosynthesis pathway in bacteria. This represents the first example of a small-molecule inhibitor of ThiD.

Bacterial infections of skin and soft tissue represent a major health threat, especially if they are caused by multidrug-resistant strains such as MRSA. Novel treatment options for topical application are urgently needed, and even if new drug candidates are identified, their properties must match the specific physical requirements of the skin in order to penetrate and reach the site of bacterial infection. β-Lactones have been shown to eliminate bacterial virulence, but knowledge about their potential in topical treatments had thus far been lacking. Herein we present the synthesis and in-depth investigations of skin permeation and skin distribution of a radioactive ¹⁴C-labeled tool compound that was formulated with various basic ointments and applied to pig skin samples. Our results show that skin penetration depends highly on the nature of the formulation base. Vaseline is the most efficient ointment and is best suited for effecting maximal drug delivery within and through the stratum corneum, an important entrance barrier, and meets the required quantities for eliciting anti-virulence effects. We are confident that the nature of these new β-lactone virulence inhibitors confers applicability and potency for topical treatment, and will translate into a new formulation of this highly potent drug candidate for the treatment of skin and soft tissue infections.

Das aktivitätsbasierte Protein-Profiling (ABPP) hat sich zu einer ausgereiften Standardmethode für die schnelle, empfindliche und selektive Identifizierung von Enzymaktivitäten und Inhibitoren in Proteomen entwickelt. Mit naturstoffbasierenden Sonden lassen sich die Angriffsziele (targets) vieler bislang uncharakterisierter Moleküle leicht in komplexen Proteomen aufklären und so ihre genaue Funktion und der Wirkmechanismus verstehen. Zum anderen dienen Naturstoffsonden und ihre Derivate als pharmakologische Leitstrukturen, die essenzielle Komponenten in der Zelle hemmen und in biologischen Assays ihre Wirksamkeit zeigen. Da die komplexen regulatorischen Prozesse einer Zelle mehr umfassen als nur Transkription, Translation und Aktivierung, ist es entscheidend, auch die Produkte des aktiven Proteoms – die Metaboliten und Bindungspartner einzelner Enzyme und Proteine – zu identifizieren. Dabei sind Methoden nötig, mit denen sich das chemisch komplexe Metabolom charakterisieren lässt. In den letzten Jahren gab es hierzu eine Reihe interessanter Ansätze, mit denen eine globale Untersuchung von Enzym-Metabolit-Paaren jetzt zum ersten Mal möglich ist.

Activity-based protein profiling (ABPP) has matured into a standard method for the fast, sensitive, and selective identification of enzyme activity and inhibitors in proteomes. By using natural product based probes, the targets of many uncharacterized molecules can be easily identified in complex proteomes, and their exact function and mechanism of action understood. Natural products and their derivatives can also serve as pharmaceutical lead structures that impede essential components in the cell and their effects can be studied in biological assays. Since the complex regulatory processes in a cell go beyond mere transcription, translation, and activation, it is imperative to also identify the products of the active proteome—the metabolites and binding partners of individual enzymes and proteins. Therefore, methods by which the chemically complex metabolome can be characterized are necessary. A series of interesting approaches have become available in recent years that enable the global investigation of enzyme–metabolite pairs.