Technology
The need for new antibiotics that can combat the existing and also the constantly new occurring Multi-Resistant Bacteria are enormous. Bioimics develops innovative low-molecular weight antibiotics targeting a new therapeutic target, namely bacterial RNase P – an RNA enzyme (ribozyme).
RNase P is essential for cell survival, without functional RNase P protein synthesis is blocked and the bacteria will die. Bioimics has developed the required molecular biology tools and established a technology platform for fast evaluation of small molecules’ potential to block RNase P activity and to inhibit cell growth in a variety of bacteria

Quick links:
RNA as a drug target
RNase P – a ribozyme essential for protein synthesis
The concept of “Metal Mimics”
Strategy for identifying new antibiotics targeting RNase P
References

RNA as a drug target
Ribonucleic acid – RNA - is essential for cell survival and is, because of its central role, a suitable target for the development of new drugs, including new antibiotics. Bioimics has chosen bacterial RNase P as its primary target for the development of new antibiotics since RNase P is essential for bacterial cell growth and contains unique structural RNA elements that distinguish it from its human counterpart or even between various bacterial species


RNase P – a ribozyme essential for protein synthesis
RNase P is an essential enzyme involved in RNA processing and is critical for the generation of functional tRNA molecules, which roles are to bring the correct amino acids to the protein synthesis machinery (Figure 1).

Antibioitcs targeting RNase P will therefore kill bacteria by blocking protein synthesis. Bacterial RNase P consists of two subunits, one RNA molecule and one protein (Figure 2) while in humans RNase P is composed of one RNA molecule and at least nine different proteins. The RNA subunit of RNase P harbors the catalytic site of the RNase P enzyme and this discovery by Professor Sidney Altman was awarded the Nobel Prize in chemistry 1989 .

The striking differences between bacterial and human RNase P and the essential requirement for RNase P make bacterial RNase P a suitable target for the development of new antibiotics. Moreover, given that the structure of the RNA component of bacterial RNase P differs between various bacteria makes it possible to develop bacterial specific bullets, i.e. antibiotics targeting one bacteria while others are not affected (Figure 3).

The concept of “Metal Mimics"
The RNA component of RNase P, like other large RNAs and ribozymes, depends on divalent metal ions such as Mg2+ for proper function. The founders of Bioimics, Professors Leif A. Kirsebom and Anders Virtanen, discovered in the late 90's that antibiotics belonging to the aminoglycoside family, e.g. neomycin, bind to and interact with structured RNA molecules at positions were divalent metal ions bind to RNA. Binding of an aminoglycoside displaces functionally essential divalent metal ions and thereby inhibits RNA function.

The molecular mechanism of inhibition was referred to by Kirsebom and Virtanen as the “concept of metal mimics” (Figure 4; Mikkelsen et al., 1999; Mikkelsen et al., 2001) and laid the foundation for establishment of a unique and patented screening procedure for the identification of new antibiotics.

Strategy for identifying new antibiotics targeting RNase P
Bioimics has selected RNase P as a prime target for the development of new low molecular candidate drugs with antibacterial activities. Conceptually, the catalytic activity of RNase P depends on divalent metal ions positioned in specific binding pockets. Displacement of the metal ions by a small ligand (drug candidate) perturbs the catalytic activity of RNase P that leads to a lethal inhibition of tRNA processing and subsequently protein synthesis. In summary

(i) RNase P RNA structure is species specific - the binding pocket of bacterial RNase P RNA is not structurally related to the human counterpart. The human RNase P RNA lacks several structural motifs and consists of more protein subunits as compared to bacterial RNase P. This allows the identification of drug candidates that specifically interacts with bacterial RNase P and avoids undesired inhibition of human RNase P.

(ii) RNase P RNA structure is specific for different classes of bacteria - the overall structure of the catalytic center of the RNA differ considerably among Gram-negative and Gram-positive bacteria. This fact will allow the development of antibiotics specific for a specific class of bacteria, or even specific strains or species.

(iii) Resistance development expected to be lower or delayed – today bacterial RNase P is not targeted by any commercial antibiotics. Thus, selection for the appearance of resistant bacteria, escaping inhibition of RNase P, has not occurred due to usage of antibiotics targeting RNase P.

Furthermore, the targeted RNA domain is essential for bacterial life. Resistance development due to mutations reducing the capability of Bioimics compounds to affect the activity/ function would be disadvantageous for the bacteria. Consequently, targeting a unique and functionally essential RNA domain will most likely prolong the appearance of resistance against the drug.

tRNA
RNase P

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Figure 4. The “Metal Mimics” concept.
Two divalent metal ions located in a binding pocket of RNA (left side) are displaced by a small ligand (right side). Displacement of divalent metal ions inhibits RNA function. Bioimics identifies divalent metal binding sites in RNA and develops novel small molecules (ligands) with the ability to displace metal ions and thereby attenuates RNA functions and ultimately protein biosynthesis.




Finally, the difference in RNase P structure among different classes of bacteria allows the elucidation of structural-activity relationships (SAR) and the potential to develop antibiotics for specific infectious diseases.

The usage of the new antibiotic drugs with a novel mode of action is likely to be more specific and restricted, thus reducing the human exposure to the drug and thereby the development of resistance.


References
Kirsebom, L.A. and Virtanen, A. (2001). Inhibition of RNase P processing. Chapter published in RNA-Binding Antibiotics (edited by R. Schroeder and M. G. Wallis). Molecular Biology Intellegence Unit 13, p. 56-72. Eurekah.com, Austin, TX, USA and Landes Biosciences, Georgetown, TX USA

Kirsebom, L. A., Virtanen, A. and Mikkelsen, N. E. (2006) Aminoglycoside interactions with RNAs and nucleases. In: HEP, Springer-Verlag Berlin Heidelberg. 173 p. 73-96

Mikkelsen, N. E., Brännvall, M., Virtanen, A., and Kirsebom, L. A. (1999). Inhibition of RNase P RNA cleavage by aminoglycosides. Proc. Natl. Acad. Sci. USA, 96, 6155-6160

Mikkelsen, N.E., Johansson, K., Virtanen, A., and Kirsebom, L.A. (2001). Aminoglycoside binding displaces a divalent metal ion in a tRNA-neomycin B complex. Nature Struct. Biol.  8, 510-514


Ren, Y., Martinez, J., Kirsebom, L. A. and Virtanen, A. (2002). Inhibition of Klenow DNA polymerase and poly(A)-specific ribonuclease by aminoglycosides. RNA, 8, 1393-1400

Thuresson, A-C., Kirsebom, L.A. and Virtanen, A. (2007) Inhibition of poly(A) polymerase by aminoglycosides. Biochimie 89, 1221-1227