NMR-Based Structural Chemistry

To be able to develop new drugs against infectious diseases we need to uncover their molecular basis. Therefore it is essential to understand how pathogens replicate, how they interact with the host and how these processes are regulated. The research group NMR-based structural chemistry investigates RNA_protein complexes involved in various aspects of infection, from both the pathogens and hosts life cycle. 


Our Research

The research group has two objectives. First, we are investigating the structure and mechanism of action of protein and ribonucleoprotein (RNP) complexes involved in RNA processing and gene expression regulation. Secondly, we are developing methods to support structure-based drug design (SBDD).

These two areas reflect two sides of infection research: The mechanism of pathogen replication and interaction with the host (RNP complexes, molecular machines) and the development of small molecules as inhibitors of these processes (SBDD). In the field of protein-protein and protein-RNA complexes, our activities focus on four biological areas: RNA modifications, regulatory RNAs, chromatin-modifying enzymes and non-ribosomal peptide synthesis.

RNA Modifications

RNA editing and modification are post-transcriptional processes found in all organisms that contribute to numerous biological functions, including splicing, mRNA regulation, protein synthesis control and mRNA surveillance. More than hundred nucleotide types are modified in rRNA, mRNA and tRNA, suggesting an amazing variety of mechanisms to control RNA function through modification.

Defects in RNA modification patterns cause disease in humans and cell death in yeasts. In addition, the mRNA of some pathogens undergoes an extensive editing process in order to obtain a functioning protein expression machinery. Nevertheless, RNA-editing enzymes are still an unexplored class of drug targets. We are investigating tRNA and rRNA-editing enzymes in infectious agents.

Regulatory RNAs

One of the most important discoveries of the last twenty years in the field of RNA has revealed the presence of a large number of small, non-coding RNAs involved in the regulation of numerous cellular processes (siRNA, miRNA, lncRNA, crRNA, piRNA, etc.). We now know that these RNAs not only play a role in the life cycle of the cell by controlling gene expression, for example, but are also important in infection processes by regulating pathogenicity and immune response. We are investigating regulatory RNAs in infection- and immunity-relevant processes.

Chromatin-editing enzymes

We use NMR to elucidate the mechanisms of histone chaperone mediated processes such as histone processing and folding. By using special solution-state NMR techniques, we can gain insights into dynamic processes such as histone folding, histone chaperone and histone DNA interactions, even if they are only transient.

Of particular interest to us is the modulation of enzyme function by histone chaperones. In this context, we investigate the histone acetyltransferase or regulator of the Ty1 transposition protein 109 (Rtt109). Drugs targeting proteins involved in epigenetic regulation have recently proven to be promising candidates for cancer therapy, and Rtt109 in particular has been suggested as a possible therapeutic approach against opportunistic fungal infections. Detailed structural studies of these proteins will not only contribute to the understanding of the regulation and maintenance of chromatin structure, but also provide a new interface to target by drug discovery.

Non-ribosomal peptide synthesis

The rapid rise of drug-resistant bacterial strains has made it imperative to search for new antibacterial active substances and, above all, for cheaper methods to produce them. The current pipeline for the discovery of active chemical substances requires at least a decade of manpower and millions of euros in investment. However, nature has its own repertoire of highly effective therapeutics, the so-called non-ribosomal peptides (NRPs). These peptides have various pharmaceutical activities, for example they have an antibacterial and anti-tumor effect.

The diverse structures of the NRPs form promising frameworks for the development of new and potent therapeutics. As the name suggests, these peptides are not synthesized by the ribosomal machinery, but by elegant molecular factories called non-ribosomal peptide synthases or NRPS. We investigate the conformation and dynamics of NRPS, which are essential for catalytic activity. Our research will enable the development of NRPS enzymes that can provide structurally and chemically optimized therapeutics.

Integrative Structural Biology

Structural biology, biophysics and in silico modelling are established approaches to uncover the functional and regulatory mechanisms of enzymes consisting of both proteins and protein-nucleic acid complexes. Thanks to the latest hardware and software developments, electron microscopy (EM) promises to replace crystallization as the standard method for determining the structure of any stable biomolecular complex. Despite these advances, it remains a challenge to understand the dynamic biomolecular changes of a complex during its functional cycle and the nature of transient interactions. Dynamics and transient interactions are the foundations of both enzyme processing and regulation; in this context, structural biology techniques that can deal with heterogeneity of conformations, structural changes or dynamic processes are important. Among them, nuclear magnetic resonance spectroscopy (NMR), small angle scattering (SAS), electron paramagnetic resonance (EPR), mass spectrometric cross-linking and fluorescence (FRET) are the best known.

My group has first-class know-how in NMR spectroscopy and SAS and their combination with EPR and X-ray crystallography. Only recently have we begun to develop expertise in the analysis of EM data - data that we have gained with cooperation partners. The great potential of structural biology lies in the complementarity of all available techniques. According to this idea, my group develops integrative methods for structure determination (Fig. 1, Karaca et al., Nature Methods 2017).

Structure-based drug design

The second important goal of our research work is the development of methods to support structure-based drug design (SBDD) in the field of infection. This search for new active molecules begins with screening experiments to identify potential interaction partners. It continues with the development of small molecules into effective drugs that combine high affinity and specificity for the target molecule as well as good pharmacokinetic properties. At this level, structural information about the active ligands in the complex with the receptor is of crucial importance.

We are the developers of INPHARMA (Interligand NOEs for PHArmacophore Mapping), an NMR-based method that provides access to the relative binding mode of pairs of competitive ligands without requiring large amounts of protein, recombinant material or expensive labeling experiments. Currently, INPHARMA is being further developed in several directions and is used in collaboration with the pharmaceutical industry or scientific institutes in medically relevant systems.

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