grant:KP-06-M33/5/18.12.2019, Design and experimental validation of antisense oligonucleotides that specifically inhibit the bacterial growth of Helicobacter pylori and Porphyromonas gingivalis awarded to Assit. Prof. Martina Traykovska, Ph.D.by the Bulgarian National Science Fund (BNSF)

The main goal of this project is to continue a very successful research in the field of RNA synthetic and computational biology, medicine and pharmacy started by the project leader Assit. Prof. Martina Traykovska, Ph.D., Faculty of Biology. Since 2015 she has published articles with results related to this research in high impact factor journals like Expert Opinion On Drug Discovery. The main idea for this Project is to design antisense oligonucleotides (ASOs), which directly bind with the bacterial riboswitches, TPP riboswitch and the riboswitch for cobalamin that are part of the genome of the two pathogenic bacteria, Helicobacter pylori and Porphyromonas gingivalis, The riboswitch binding is targeted by the ASOs. 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 idea of the Project is very important nowadays because of the enormously growing number of resistant and multi-resistant pathogens. Multi-resistant strains of Helicobacter pylori and Porphyromonas gingivalis have also been detected. These bacteria cause severe diseases like gastritis, ulcer, stomach cancer, duodenal cancer and paradental disease. In recent studies the scientists correlate the presence of Porphyromonas gingivalis with the Alzheimer disease. The DNA of this bacteria has been isolated in every patient with Alzheimer disease. These two pathogenic bacteria has been detected to have resistance to the following antibiotics: amoxicillin, clindamycin, levofloxacin, clarithromycin and metronidazole. Antibiotic resistance has been detected in other pathogenic bacteria. In 2010, it is estimated about 14% of all pathogenic bacteria are resistant to penicillin, 16% to tetracycline and 10% to fluoroquinolone. 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 from which one of the most commonly found riboswitch, the TPP riboswitch is present in the genome of Helicobacter pylori and Porphyromonas gingivalis. Porphyromonas gingivalis also contains the riboswitch for cobalamin. 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 Staphylococcus 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.

Our doctoral student Georgi Miloshev won the prize doctoral student of the year 2022 of Sofia University! Georgi works on several research projects, including this one (for more information click here).

The research of the project funded with 15 345 EUR, is published in three publications. Papers have a common impact factor of 10 points with Scopus's Q1, Q2 and Q4 making 57 points, and three doctoral students are graduated - see below.

Publications of the project:

1. Martina Traykovska and Robert Penchovsky, Engineering antisense oligonucleotides as antibacterial agents that target FMN riboswitches and inhibit the growth of Staphylococcus aureus, Listeria monocytogenes, and Escherichia coli - ACS Synthetic Biology (2022)…IF:5.11 (Q1, Scopus)

2. Aikaterini Valsamatzi, Martina Traykovska and Robert Penchovsky, Coronavirus SARS-CoV-2: Where do we stand? - Acta Microbiologica Bulgarica (2022)…IF:0.115 (Q4, Scopus)

3. Nikolet Pavlova, Georgi Y Miloshev, Antoniya V. Georgieva, Martina Traykovska and Robert Penchovsky, Versatile Tools of Synthetic Biology applied for Drug Discovery and Production - Future Medicinal Chemistry (2022)…IF:4.8 (Q2, Scopus)

Our recent paper is an editors' choice of the American Chemical Society!

Our recent paper is an editors' choice of the ACS Synthetic Biology!

Our recent paper is among the most popular in the ACS Synthetic Biology!

Graduated Doctoral Students of the project:

1. Dr. Lozena Otcheva,  from Bulgaria, a former Doctoral student. Lozena holds Master's degree in Pharmacy and Industrial Pharmacy from the University  of Rome, Italy. She has graduated her doctoral study on February 10^th, 2021.

2. Dr. Katya Popova, from Bulgaria, a former Doctoral student. Katya holds a Bachelor's degree in Biology and a Master's degree in Genetics and Genomics from Sofia University, Bulgaria. She has graduated her doctoral study on April 16^th, 2021.

3. Dr. Aikaterini Valsamatzi, from Greece, a former Doctoral student. Aikaterini holds a Master's degree in Medicine from Medical University-Plovdiv, Bulgaria. She has graduated her doctoral study on April 14^th, 2021.