Robert Penchovsky

Sofia University "St. Kliment Ohridski" · Department of Genetics

grant:KP-06-H63/1/13.12.2022 funded by BNSF

This grant was very successfully completed with many research publications with a common impact factor of 34 for only 42 000 EUR in July 2014 as detailed below: 1. Penchovsky, R. Computational design of allosteric ribozymes as Molecular Biosensors, Biotechnology Advances, 32, 1015-1027 (2014). – (IF:11.88). 2. Penchovsky, R. Chapter 16: Nucleic Acids-based Nanotechnology; Engineering Principals and Applications, Handbook of Research on Nanoscience, Nanotechnology, and Advanced Materials; Engineering Sciences Reference: An Imprint of IGI Global DOI: 10.4018/978-1-4666-5824-0.ch016, 414-430 (2014). 3. Penchovsky, R & Kostova, G. Computational selection and experimental validation of allosteric ribozymes that sense a specific sequence of human telomerase reverse transcriptase mRNAs as universal anticancer therapy agents. Nucleic Acid Therapeutics, 23, 408-431 (2013). - (IF:2.91). 4. Penchovsky, R. Present and Future RNA-based Approaches to Medical Genomics, International Journal of Genomic Medicine, 10.4172/2332-0672.1000110, 1(2), 1-7 (2013). 5. Penchovsky, R. Programmable and automated bead-based microfluidics for versatile DNA microarrays under isothermal conditions. Lab on a chip;13, 2370-80 (2013) - (IF:6.41). 6. Penchovsky, R. Computational design and biosensor applications of small molecule-sensing allosteric ribozymes. ACS Biomacromolecules, 14, 1240–1249 (2013). – (IF:5.77). 7. Penchovsky, R. & Stoilova C.C. Riboswitch-based antibacterial drug discovery using high-throughput screening methods. Expert Opinion on Drug Discovery, 8, 65-82. (2013).- (IF:3.5). 8. Penchovsky, R. Engineering integrated digital circuits with allosteric ribozymes for scaling up molecular computation and diagnostics. ACS Synthetic Biology, 1, 471-482 (2012). – (IF: 3.95). 9. Penchovsky, R. Chapter 5: Engineering Gene Control Circuits with Allosteric Ribozymes in Human Cells as a Medicine of the Future, in the book “Quality Assurance in Healthcare Service Delivery, Nursing and Personalized Medicine: Technologies and Processes”, Publisher IGI Global, DOI: 10.4018/978-1-120-7, 71-96 (2012).

The main goal of this project is to continue a very successful research in the field of RNA synthetic and computational biology, medicine and pharmaceutical started by the project leader Dr. rer. nat. Robert Penchovsky several years ago as a postdoctoral fellow at Yale University. Since 2005 he has published articles with results related to this research in high impact factor journals with more than 420 citations. His main background research is based on computer engineering of oligonucleotides. Our idea for this Project is to design antisense oligonucleotides, which are directly binding and regulating the target bacterial pathogen’s riboswitches. The riboswitches are structured RNA domains usually residing at the 5’ untranslated region of messenger RNAs that directly bind specific metabolites. They serve as logic gates regulating gene expression. As a result, riboswitches enable mRNAs to regulate their own expression without the need of any regulatory proteins. This way, the essential metabolites for the bacteria will not be synthesized by the cell or transported into the cell from the extracellular matrix. The result is the death of Staphylococcus aureus for instance. Antisense oligonucleotides show bacteriostatic effect and can be tested as novel antibacterial agents in bacterial isolates and human embryonic kidney cell lines (HEK 293) for toxicity. The Dean of the Medical Faculty of Medical University, Sofia – prof. md Ivan Mitov and his collective will provide the bacterial strains isolates from human samples and collection of modeling bacteria. The idea of the Project is very important nowadays because of the enormously growing number of resistant and multi-resistant pathogens. Examples of human bacterial pathogens are Staphylococcus aureus, Neisseria gonorrhoeae, Escherichia coli, Mycobacterium tuberculosis and 55 more. Most of these bacteria cause serious diseases like meningitis, listeriosis, botulism, pneumonia, gonorrhea, etc. In 2010, it is estimated about 14% of all pathogenic bacteria are resistant to penicillin, 16% to tetracycline and 10% to fluoroquinolone. Taking this into account, the Centers for Disease Control and Prevention at the U.S. Department of Health and Human Services expect over 2, 000, 000 illnesses and 23 000 deaths caused by antibiotic resistance in the USA alone. All of these facts demonstrate the need of developing and discovering new strategies for novel antibacterial agents. Bacterial riboswitches are discovered in 59 human bacterial pathogens. These findings indicate that bacteria widely use RNA switches to sense changes in cell physiology and to regulate metabolic pathways. Most of the riboswitches do not control the essential metabolites in human as in bacteria, so they can be used without harmful effect for the human. The whole group of methods and technologies (bioinformatics, microbiology, antisense oligonucleotide technology, etc.) are tested and proved. There are, also, laboratory validated results for the bacteriostatic effect of two of the tested antisense oligonucleotides (ASOs), targeting riboswitches like FMN resulting in the death of Staphyloccus aureus, for instance. All of these reasons are treated as facts, which demonstrate that the Project will achieve results with important social significance for the World’s health care system.