Simone Kosol

First total synthesis of cortinarins A–C, cryptic cyclic peptides exhibiting non-classical atropisomerism. They mimic vasopressin-induced aquaporin-2 membrane localization through a distinct mode of action, offering leads for diabetes insipidus.

The peptide albicidin represents a highly promising lead structure which is a first‐in‐class antibiotic with remarkable potency against gram‐negative bacteria. Past efforts in the synthesis of albicidin analogs focused on increasing hydrophilicity, broadening of the antibacterial profile and overcoming resistance. Herein, we present synthetic albicidin derivatives with variations in the N‐terminal building block and characterize their antibacterial activity and DNA gyrase inhibition. Furthermore, we show that the N‐terminus of albicidin greatly affects binding to the resistance factor AlbAL. This transcription regulator senses albicidin and triggers the biosynthesis of the binding protein AlbAS, thus reducing the free concentration of the antibiotic. Here we demonstrate uncoupling of the binding event from transcription activation for some derivatives, and even a few derivatives seemed insensitive to sequestration by AlbA. This approach could be a strategy to develop albicidin analogs escaping AlbA resistance.

Im Kampf gegen bakterielle Infektionen, insbesondere gegen solche die von multiresistenten Pathogenen verursacht werden, die auch als “Superbugs” bekannt sind, ist der Bedarf an neuen antibakteriellen Wirkstoffen in der wissenschaftlichen Gemeinschaft unbestritten und wird mittlerweile auch in der Bevölkerung vermehrt wahrgenommen. Die Wissenschaftslandschaft hat sich jedoch in den vergangenen Jahren erheblich verändert. Mit wenigen Ausnahmen hat die Mehrheit der pharmazeutischen Unternehmen das Forschungsfeld verlassen und der Rückgang der F&E‐Aktivitäten zu antibakteriellen Wirkstoffen beeinträchtigt erheblich die Wirkstoffpipeline. In den vergangenen Jahren hat sich die antibakterielle Forschung zunehmend auf kleinere Firmen und akademische Forschungseinheiten verlagert, deren finanzielle Ressourcen zu begrenzt sind, um nach der Wirkstoffentdeckung ein Entwicklungsprogramm von Beginn an bis durch die klinische Phasen zu führen. Dieser Übersichtsartikel formuliert die Anforderungen an einen antibakteriellen Wirkstoff im Hinblick auf bakterielle Pathogene, Resistenzmechanismen und den Prozess der Wirkstofffindung. Strategien zur Entdeckung neuer antibakterieller Strukturen aus Quellen verschiedenen Ursprungs wie der Natur, der chemischen Synthese und kürzlich auch der künstlichen Intelligenz werden aufgezeigt. Dies wird ergänzt durch Prinzipien des Computer‐unterstützen Designs und der Verfeinerung von Leitstrukturen. Der zweite Teil des Artikels enthält eine Zusammenstellung von antibakteriellen Wirkstoffmolekülen, die gemäß ihrer Targetstrukturen klassifiziert werden, z. B. der Zellwandsynthese oder der Proteinsynthese, und tendenziell neueren Targetklassen wie Proteine der Fettsäuresynthese, Proteasen und Membranproteine. Aspekte der Herkunft, des antibakteriellen Wirkspektrums, der Resistenz und dem aktuellen Entwicklungsstatus der präsentierten Wirkstoffmoleküle werden beleuchtet.

In the fight against bacterial infections, particularly those caused by multi‐resistant pathogens known as “superbugs”, the need for new antibacterials is undoubted in scientific communities and is by now also widely perceived by the general population. However, the antibacterial research landscape has changed considerably over the past years. With few exceptions, the majority of big pharma companies has left the field and thus, the decline in R&D on antibacterials severely impacts the drug pipeline. In recent years, antibacterial research has increasingly relied on smaller companies or academic research institutions, which mostly have only limited financial resources, to carry a drug discovery and development process from the beginning and through to the beginning of clinical phases. This review formulates the requirements for an antibacterial in regard of targeted pathogens, resistance mechanisms and drug discovery. Strategies are shown for the discovery of new antibacterial structures originating from natural sources, by chemical synthesis and more recently from artificial intelligence approaches. This is complemented by principles for the computer‐aided design of antibacterials and the refinement of a lead structure. The second part of the article comprises a compilation of antibacterial molecules classified according to bacterial target structures, e.g. cell wall synthesis, protein synthesis, as well as more recently emerging target classes, e.g. fatty acid synthesis, proteases and membrane proteins. Aspects of the origin, the antibacterial spectrum, resistance and the current development status of the presented drug molecules are highlighted.

Lanthipeptides are ribosomally‐synthesized natural products from bacteria featuring stable thioether‐crosslinks and various bioactivities. Herein, we report on a new clade of tricyclic class‐IV lanthipeptides with curvocidin from Thermomonospora curvata as its first representative. We obtained crystal structures of the corresponding lanthipeptide synthetase CuvL that showed a circular arrangement of its kinase, lyase and cyclase domains, forming a central reaction chamber for the iterative substrate processing involving nine catalytic steps. The combination of experimental data and artificial intelligence‐based structural models identified the N‐terminal subdomain of the kinase domain as the primary site of substrate recruitment. The ribosomal precursor peptide of curvocidin employs an amphipathic α‐helix in its leader region as an anchor to CuvL, while its substrate core shuttles within the central reaction chamber. Our study thus reveals general principles of domain organization and substrate recruitment of class‐IV and class‐III lanthipeptide synthetases.

Lanthipeptides are ribosomally‐synthesized natural products from bacteria featuring stable thioether‐crosslinks and various bioactivities. Herein, we report on a new clade of tricyclic class‐IV lanthipeptides with curvocidin from Thermomonospora curvata as its first representative. We obtained crystal structures of the corresponding lanthipeptide synthetase CuvL that showed a circular arrangement of its kinase, lyase and cyclase domains, forming a central reaction chamber for the iterative substrate processing involving nine catalytic steps. The combination of experimental data and artificial intelligence‐based structural models identified the N‐terminal subdomain of the kinase domain as the primary site of substrate recruitment. The ribosomal precursor peptide of curvocidin employs an amphipathic α‐helix in its leader region as an anchor to CuvL, while its substrate core shuttles within the central reaction chamber. Our study thus reveals general principles of domain organization and substrate recruitment of class‐IV and class‐III lanthipeptide synthetases.

Amatoxins are strong inhibitors of RNA polymerase II, and cause cell death. Because of their cytotoxicity they are candidates for anti-cancer drugs, and understanding their structure-activity relationship is crucial. Amatoxins have a rigid bicyclic scaffold which consists of a cyclic octapeptide bridged by cysteine and tryptophan side chain forming a tryptathionine bridge. Here we show the influence of the N-methylation on the amatoxin scaffold by studying Gly5Sar-amanullin with MD simulations and NMR experiments. Since we have shown recently that the amatoxin scaffold allows for two isomeric forms (ansamers), we studied both isomers of Gly5Sar-amanullin. We found that both isomers of Gly5Sar-amanullin form two long-living conformations which is unusual for amatoxins, and that they are differently affected by the N-methylation. The natural Gly5Sar-amanullin forfeits the hydrogen bonds to Gly5 due to the N-methylation, which is expected from existing crystal structures for alpha-amanitin. Our results however indicate that this does not cause more flexibility due to a shift in the hydrogen bond pattern. In the unnatural isomer, we observe an interesting cis-trans-isomerisation of the backbone angles in Trp4 and Gly7, which is enabled by the N-methylation. We expect that our perspective on the effect of N-methylation in amatoxins could be a starting point for further SAR-studies which are urgently needed for the design of better anti-cancer agents.

α-Amanitin is a bicyclic octapeptide composed of a macrolactam with a tryptathionine cross-link forming a handle. Previously, the occurrence of isomers of amanitin, termed atropisomers has been postulated. Although the total synthesis of α-amanitin has been accomplished this aspect still remains unsolved. We perform the synthesis of amanitin analogs, accompanied by in-depth spectroscopic, crystallographic and molecular dynamics studies. The data unambiguously confirms the synthesis of two amatoxin-type isomers, for which we propose the term ansamers. The natural structure of the P-ansamer can be ansa-selectively synthesized using an optimized synthetic strategy. We believe that the here described terminology does also have implications for many other peptide structures, e.g. norbornapeptides, lasso peptides, tryptorubins and others, and helps to unambiguously describe conformational isomerism of cyclic peptides.

Crosstalk between cellular pathways is often mediated through scaffold proteins that function as platforms for the assembly of signaling complexes. Based on yeast two-hybrid analysis, we report here the interaction between two complex scaffold proteins, CREB-binding protein (CBP) and the Ras GTPase-activating-like protein 1 (IQGAP1). Dissection of the interaction between the two proteins reveals that the central, thus far uncharacterized, region of IQGAP1 interacts with the HAT domain and the C-terminal intrinsically disordered region of CBP (termed ID5). Structural analysis of ID5 by solution NMR spectroscopy and SAXS reveals the presence of two regions with pronounced helical propensity. The ID5 region(s) involved in the interaction of nanomolar affinity were delineated by solution NMR titrations and pull-down assays. Moreover, we found that IQGAP1 acts as an inhibitor of the histone acetyltransferase (HAT) activity of CBP. In in vitro assays, the CBP-binding region of IQGAP1 positively and negatively regulates the function of HAT proteins of different families including CBP, KAT5 and PCAF. As many signaling pathways converge on CBP and IQGAP1, their interaction provides an interface between transcription regulation and the coordination of cytoskeleton. Disruption or alteration of the interaction between these scaffold proteins may lead to cancer development or metastatic processes, highlighting the importance of this interaction.

The enoyl‐acyl carrier protein reductase enzyme FabI is essential for fatty acid biosynthesis in Staphylococcus aureus and represents a promising target for the development of novel, urgently needed anti‐staphylococcal agents. Here, we elucidate the mode of action of the kalimantacin antibiotics, a novel class of FabI inhibitors with clinically‐relevant activity against multidrug‐resistant S. aureus. By combining X‐ray crystallography with molecular dynamics simulations, in vitro kinetic studies and chemical derivatization experiments, we characterize the interaction between the antibiotics and their target, and we demonstrate that the kalimantacins bind in a unique conformation that differs significantly from the binding mode of other known FabI inhibitors. We also investigate mechanisms of acquired resistance in S. aureus and identify key residues in FabI that stabilize the binding of the antibiotics. Our findings provide intriguing insights into the mode of action of a novel class of FabI inhibitors that will inspire future anti‐staphylococcal drug development.