grant:KP-06-H31/18/13.12.2019, Engineering functional nucleic acids for synthetic control of gene expression in prokaryotes and eukaryotes awarded to Prof. Robert Penchovsky by the Bulgarian National Science Fund (BNSF)

Goal: The proposed project aims to take advantage of well-established research on computational design and experimental validation of allosteric ribozymes started by the project leader Dr. Penchovsky at Yale University and continued by him with a very successful grant DDVU02/5/2010 awarded by the Bulgarian Science Fund. This grant funded with 83 000 leva and has just completed with 9 scientific publications with a total impact factor (IF) of 33, defense of 7 mater’s theses with honor, and one granted US patent.

In fact, the current project application is a direct application of ribozyme design methods developed by us. Our methods are very time and labor efficient because they can produce within a few minutes the desired sequences of high-speed allosteric ribozymes that can work in the cell. The ribozymes can sense the presence of any specific RNA or DNA sequences or small molecules. We intend to apply these ribozymes for exogenous control of gene expression in E. coli, S. cerevisiae, and mammalian cell lines. There are substantial preliminary research results concerning any of our goals, which makes our research proposal low risky.

Dr. Martina Traykovska won an award for first place for the work of a young microbiologist in a national contest by the Foundation in the name of Acad. Prof. Stephan Angeloff on March 7, 2023, for our paper Engineering antisense oligonucleotides as antibacterial agents that target FMN riboswitches and inhibit the growth of Staphylococcus aureus, Listeria monocytogenes, and Escherichia coli (see the image below). Bravo Martina!

Our highly respectable rector (at that time) Prof. Anastas Gerdzhikov together with my doctoral student Georgi Miloshev, the winner of the prize "doctoral student of the year 2022" of Sofia University, in the Aula of the SU, after the ceremony, May 26, 2022. Georgi works on several research projects, including DN13/14/20.12.2017, KP-06-H31/18/13.12.2019, and KP-06-M33/5/18.12.2019 awarded by the BNSF (for more information click here).

The research of the project is published in 15 publications with an impact factor of 56.51 points and Q1-4 of 274 points, two invited presentations on a congress and a festival and 12 pieces of software are made, and 4 doctoral students are graduated - see below. The first half and the completed project received the highest grades on evaluation.

Publications for the first half of the project:

1. Robert Penchovsky, Nikolet Pavlova and Dimitrios Kaloudas, ExBWS: Extended Bioinformatics Web Services for Sequence Analyses - International Journal of Bioinformatics Research and Applications (2021)…IF:0.5, (Q4, Scopus)

2. Lozena A. Otcheva, Nikolet Pavlova, Katya B Popova, Martina Traykovska and Robert Penchovsky, Why Some Riboswitches are Suitable Targets for Antibacterial Drug Discovery? - EC Microbiology (2020)…

3. Katya B. Popova and Robert Penchovsky, Why Some Functional RNAs Such as Bacterial Riboswitches are Versatile Targets for Antibacterial Drug Discovery? - EC Microbiology (2020)…

4. Robert Penchovsky, Georgi Miloshev, Nilolet Pavlova, Katya B. Popova, Lozena A. Otcheva and Martina Traykovska, Book chapter 8: Small RNA-based systems for sensing and therapeutic applications - New Frontiers and Applications of Synthetic Biology, Elsevier (2022), (Indexed in Scopus)

5. Georgi Miloshev, Martina Traykovska, Dimitrios Kaloudas and Robert Penchovsky, Engineering a plasmid as a reporter system for quantifying gene expression in Escherichia coli, Comptes rendus de l'Académie bulgare des Sciences, (2022)…IF:0.38, (Q2, Scopus). The sequence of our plasmid pRS414ge is given here.

6. Aikaterini Valsamatzi-Panagiotou, and Robert Penchovsky, Environmental factors influencing the transmission of the coronavirus 2019, Environmental Chemistry Letters, (2022)…IF:15.7, (Q1, Scopus)

7. Martina Traykovska, Katya B. Popova and Robert Penchovsky, Targeting glmS ribozyme with chimeric antisense oligonucleotides for antibacterial drug development, ACS Synthetic Biology (2021)… IF:4.8 (Q1, Scopus)

Publications so far for the second half of the project:

8. 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:4.8 (Q1, Scopus)

9. Dimitrios Kaloudas and Robert Penchovsky, An allosteric ribozyme generator and an inverse folding ribozyme generator: Two computer programs for automated computational design of oligonucleotide-sensing allosteric hammerhead ribozymes with YES Boolean logic function based on experimentally validated algorithms - Computers in Biology and Medicine (2022)… IF:7.7 (Q1, Socpus)

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

11. 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:4.2 (Q2, Scopus)

12. Nikolet Pavlova and Robert Penchovsky, Bioinformatics and Genomic Analyses of the Suitability of Eight Riboswitches for Antibacterial Drug Targets - Antibiotics (2022)…IF:4.8 (Q1, Scopus)

13. Martina Traykovska, Lozena A. Otcheva and Robert Penchovsky, Targeting TPP Riboswitches Using Chimeric Antisense Oligonucleotide Technology for Antibacterial Drug Development - ACS Applied Bio Materials (2022)…IF:4.7 (Q1, Scopus)

14. Martina Traykovska and Robert Penchovsky, Targeting SAM-I Riboswitch Using Antisense Oligonucleotide Technology for Inhibiting the Growth of Staphylococcus aureus and Listeria monocytogenes - Antibiotics (2022)…IF:4.8 (Q1, Scopus)

15. Dimitrios Kalouda, Nikolet Pavlova & Robert Penchovsky, GHOST-NOT and GHOST-YES: Two Programs for Generating high-speed Biosensors with Randomized Oligonucleotide Binding Sites with NOT or YES Boolean Logic Functions Based on Experimentally Validated Algorithms - Journal of Biotechnology (2023)…IF:4.1 (Q1, Scopus)

Conferences of the project:

1. 15^th Congress of Microbiologists in Bulgaria with International Participation invited lecture on "Targeting glmS and FMN riboswitches with antisense oligonucleotides for antibactеrial drug development" October 5-8, 2022 in Koprivshtitsa, Bulgaria.

2. Robert has been invited to give a talk on "The New Antibiotics" at the 13^th Sofia Science Festival, May 11^th-14^th, 2023 in Sofia, Bulgaria (watch the video of Robert's presentation in Bulgarian below).

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

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

Software produced within the first half of the project:

1. We have made two programs for computer design of high-speed allosteric ribozymes with YES or NOT Boolean logic functions.

2. DNA/RNA Translator: If you want to translate DNA or RNA sequence click here…

3. RandomOligoGenerator: If you want to change a protein sequence from one letter code to three letters and vice versa click here…

4. Virtual PCR: If you want to perform a PCR reaction click here…

5. HydropathyPlot-Proteins: If you want to perform a Hydropathy plot of an amino acid sequence click here…

6. Reverse Translator: If you want to perform a Reverse translation of a protein sequence click here…

7. Eukaryotic ORF finder: If you want to search for Open Reading Frames (ORFs) in Eukaryotic DNA sequences click here…

8. Oligonucleotide-sensing ribozyme generator: A generator of oligonucleotide-sensing ribozyme with YES Boolean logic function click here…

9. Inverse ribozyme generator: An inverse generator of oligonucleotide-sensing ribozyme with YES Boolean logic function click here…

Software produced within the secod half of the project:

10. Oligonucleotide-sensing ribozyme generators, Generators of fast oligonucleotide-sensing ribozyme with YES (GHOST-YES) or NOT (GHOST-NOT) Boolean logic function click here…

11.Oligonucleotide-sensing ribozyme generator, A generator of slow oligonucleotide-sensing ribozyme with YES Boolean logic function click here…

12. Inverse ribozyme generator, An inverse generator of slow oligonucleotide-sensing ribozyme with YES Boolean logic function click here…

Graduated Doctoral Students within the first half 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.

Graduated Doctoral Students within the second half of the project:

4. Dr. Georgi Miloshev, enrolled in year 2019 - the image below. Georgi holds a Bachelor's degree in Molecular Biology and a Master's degree in Genetics    and Genomics from Sofia University, Bulgaria. Georgi defended his Ph.D. thesis on October 20^th, 2023.