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. 

Leader

Our Research

The structure of RNA methylated machinery box C/D RNP shows that always only one pair of proteins (blue) can add methyl groups to RNA (red) (Nature, Oct 2013).

RNA modifications

RNA editing and modification are post-transcriptional processes found in all organisms and involved in many biological functions such as splicing, miRNA regulation, control of protein synthesis and mRNA surveillance. More than 100 nucleotide types are modified in rRNA, mRNA and tRNA, suggesting an amazing diversity in the mechanisms of control of RNA function through modification. Defects in RNA modification patters have been shown to cause diseases in humans or cell death in yeast. Furthermore, some pathogens are subjected to extensive editing of their mRNA to yield functional protein expression machinery; nevertheless, RNA-editing enzymes are a still unexplored class of drug targets.

Regulatory RNAs

One of the most significant discoveries of the last 20 years in the RNA field revealed the existence of a plethora of small non-coding RNAs, which are involved in the regulation of a large number of cellular processes (siRNA, miRNA, lncRNA, crRNA, piRNA, etc.). Nowadays, it is recognized that these RNAs play a role not only in the cellular life cycle, regulating for example gene expression, but also in infection events, regulating pathogenicity and immune response. 

To study the structure of RNP complexes, my team uses a multidisciplinary approach combining Nuclear Magnetic Resonance spectroscopy (NMR), biochemical, biophysical and computational methods.

Our philosophy is to tackle the structure of high-molecular weight complexes, whose large size impedes a detailed structural description by NMR only, with an array of different complementary methodologies, such as:

  • segmental and specific labeling of both proteins and RNAs,
  • small angle scattering (SAS),
  • electron microscopy (EM),
  • Electron Paramagnetic Resonance (EPR),
  • Fluorescence Resonance Energy Transfer (FRET),
  • mutational analysis and biochemical experiments (e.g. cross-link).

With our complementary approach it is possible to examine RNP particles in solution, in their native environment, where they preserve both their structure and dynamic properties.

The second major aim of our research is the development of methodologies to support structure-based drug design (SBDD) in infection. The search of new active molecules starts with screening experiments for the identification of possible interaction partners and proceeds to the development of the small molecule leads into efficient drugs, with both high affinity and specificity to the target and good pharmacokinetic properties. At this stage, structural information on the active ligands in complex with the receptor is essential. We are the developers of INPHARMA (Interligand NOEs for PHArmacophore Mapping), a NMR-based methodology designed to access the relative binding mode of pairs of competitive ligands without need of large protein amounts, recombinant material or expensive labeling schemes.

Currently, we develop INPHARMA in new directions and apply the method, in collaboration with pharmaceutical industries or scientific institutes, on medically relevant systems.

Further information is also available at www.carlomagno-group.org.

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