Robert Penchovsky

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Sofia University "St. Kliment Ohridski" · Faculty of Biology

In vitro selection of allosteric ribozymes has many challenges, such as complex and time-consuming experimental procedures, uncertain results, and the unwanted functionality of the enriched sequences. The precise computational design of allosteric ribozymes is achievable using RNA secondary structure folding principles. The computational design of...

This review is focused on antisense and functional nucleic acid used for completely rational drug design and drug target assessment, aiming to reduce the time and money spent and increase the successful rate of drug development. Nucleic acids have unique properties that play two essential roles in drug development as drug targets and as drugs. Drug...

In the last two decades, antisense oligonucleotide technology has emerged as a promising approach to tackling various healthcare issues and diseases, such as antimicrobial resistance, cancer, and neurodegenerative diseases. Despite the numerous improvements in the structure and modifications of the antisense oligonucleotides (ASOs), there are still...

Antimicrobial drug resistance has emerged as a significant challenge in contemporary medicine due to the proliferation of numerous bacterial strains resistant to all existing antibiotics. Meanwhile, riboswitches have emerged as promising targets for discovering antibacterial drugs. Ri-boswitches are regulatory elements in certain bacterial mRNAs th...

High-speed allosteric hammerhead ribozymes can be engineered to distinguish well between a perfectly matching effector and the nucleic acid sequences with a few mismatches under physiologically relevant conditions. Such ribozymes can be designed to control the expression of exogenous mRNAs and can be used to develop new gene therapies, including an...

An outbreak of coronavirus SARS-CoV-2 infection in December 2019 in Wuhan, a province of Chi¬na, has caused a worldwide pandemic that led to devastating effects on healthcare systems and the econ¬omy worldwide. The contagiousness of the infection and the consequences of the disease in everyday life highlighted the great need for a suitable treatmen...

With the discovery of antibiotics, a productive period of antibacterial drug innovation and application in healthcare systems and agriculture resulted in saving millions of lives. Unfortunately, the misusage of antibiotics led to the emergence of many resistant pathogenic strains. Some ri-boswitches have risen as promising targets for developing an...

As the tomato fruit grows, it goes through different developmental stages until it acquires its full size. This size is achieved with the completion οf the Μature Green stage of tomato development, after which the fruit enters the Turning stage, signifying the passage from growth to ripening, where it gradually loses its green color in favor of red...

Nowadays, the emergence and the transmission of multidrug-resistant pathogenic bacteria are a severe menace mounting a lot of pressure on the healthcare systems worldwide. Many severe outbreaks of bacterial infections have been reported worldwide in recent years. Thus, there is an immediate demand to develop antibiotics. Some riboswitches are poten...

Antibiotic resistance (AR) is an acute problem that results in prolonged and debilitating illnesses. AR mortality worldwide is growing and causes a pressing need to research novel mechanisms of action and untested target molecules. This article presents in silico analyses of eight bacterial riboswitches for their suitability for antibacterial drug...

Although synthetic biology is an emerging research field, which has come to prominence within the last decade, it already has many practical applications. Its applications cover the areas of pharmaceutical biotechnology and drug discovery, bringing essential novel methods and strategies such as metabolic engineering, reprogramming the cell fate, dr...

In the past several decades, antibiotic drug resistance has emerged as a significant challenge in modern medicine due to the rise of many bacterial pathogenic strains resistant to all known antibiotics. At the same time, riboswitches have emerged as novel targets for antibacterial drug discovery. Here for the first time, we describe the design and...

Designing oligonucleotide-sensing ribozymes using computational approaches is advantageous to in vitro selection methods for efficiency and accuracy. Allosteric ribozymes can be computationally designed for various applications in gene therapy, designer gene control systems, biosensors, and molecular computation. Here we present two programs, the a...

The coronavirus 2019 pandemic, induced by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has strongly altered healthcare systems and the economy worldwide. The lack of knowledge on this virus has led to the implementation of uncertain strategies and measures to fight the pandemic. Here, we review environmental factors that contro...

Different gene reporter assays are used for quantifying various methods for synthetic control of gene expression. The activity of a reporter protein, fluorescence or chemical stain, is usually proportional to the level of mRNA produced in the cell and can be utilized for monitoring the activity of a promoter or enhancer. Such a reporter gene is the...

This article describes how with the development of biotechnology, plants have gained again a prominent place as a relatively inexpensive source for the creation of recombinant pharmaceuticals. Plant-derived compounds have started playing a major role in the pharmaceutical industry with many plant-based products to have found their way in drugs and...

It is well established that RNA is a particularly suitable medium for engineering molecular sensors such as RNA aptamers and allosteric ribozymes. They can be employed for various biosensing applications such as synthetic control of gene expression, molecule detection, drug discovery, and RNA computing. Besides, RNA sensors are proposed to be used...

An outbreak of coronavirus infection named SARS-CoV-2 emerged in December 2019 in Wuhan, a province of China. It caused a worldwide pandemic that led to devastating effects on healthcare systems and the economy. The contagiousness of the infection and the consequences of the disease in everyday life highlighted the great need for a suitable treatme...

Wastewater treatment requires the removal of contaminants, solids, nutrients, coliforms, and pathogenic bacteria. Classical treatments require high energy and induce secondary pollution by disinfectants. Alternatively, phycoremediation, which involves the use of algae to clean water, appears smarter and more sustainable because compounds such as ni...

The high rate of depletion of fossil fuels and the negative effects caused by their use in industries and combustion engines are calling for biofuels. Alternatively, plant, algae and microbes are renewable biomasses for the generation of biofuels. Choosing a suitable biomass is of great importance for biofuel generation in good quantity and quality...

The rise of multidrug-resistant human pathogenic bacteria is calling for alternative approaches to design antibacterial drugs. Here, we review new approaches based on antisense oligonucleotides as antibacterial agents, fecal microbiota transplantation, and antimicrobial peptides and cell-penetrating peptides with antibacterial activity.

A variety of multidrug-resistant bacteria is blamed for severe infections worldwide. The emergence of antimicrobial resistance constitutes a serious problem for healthcare systems around the world. Here we review techniques for the prevention and constraint of antimicrobial resistance, the risk factors, and the ways by which antimicrobial resistanc...

The World Health Organization believes that there were about 480,000 cases of multi drug resistant tuberculosis in 2014 only. In addition, extensively drug resistant tuberculosis was identified in 105 countries during the same year. The methicillin resistant Staphylococcus aureus is a widespread cause of severe infections in health facilities and t...

The alternative approaches for antibacterial drug discovery have a huge potential to develop novel antibacterial agents against multi drug resistant human pathogenic bacteria that are much needed to tackle the urgent threats of multi drug resistant human pathogenic bacteria. We may be able to develop much faster novel antibiotics against multi drug...

It is universally known that antibiotics are one of the most important drugs against infectious diseases over the past 100 years. The father of modern chemotherapy is believed to be Paul Ehrlich who discovered the first antibiotic named Salvarsan in 1909. It was the first drug to be used for the treatment of syphilis, a sexually transmitted disease...

The RSwitch is a MySQL database implemented on a PHP-based server, which also provides various useful tools for analyses of DNA, RNA, and protein sequences applying a user-friendly interface. The RSwitch database currently contains information and annotations of 215 bacterial riboswitches from 16 different types found in 50 human pathogenic bacteri...

Objectives: A constantly growing number of antibiotic-resistant strains of human pathogenic bacteria is an acute problem. Prolonged illnesses and increasing mortality worldwide mean that there is an urgent need to develop novel antibacterial drugs based on new targets and mechanisms of action. We present in silico analyses of bacterial riboswitches...

Riboswitches are gene control elements that directly bind to specific ligands to regulate gene expression without the need for proteins. They are found in all three domains of life, including Bacteria, Archaea, and Eukaryota. Riboswitches are mostly spread in bacteria and archaea. In this paper, we discuss the general distribution, structure, and f...

An automated DNA hybridization transfer in a microflow reactor is demonstrated by moving paramagnetic beads between two spatially separate solutions with different pH values. The microbeads-based microfluidic platform is fully automated and programmable. It employs a robust chemical procedure for specific DNA hybridization transfer in microfluidic...

Since the early years of bioinformatics, computer programs were designed to help researchers with analyzing and comparing biological sequences. In this poster, we present Essential Bioinformatics Web Services (EBWS) implemented on a new PHP-based server that provide user-friendly interface and useful tools for analyses of DNA, RNA, and protein sequ...

This chapter describes how functional nucleic acids, such as aptamers, antisense oligonucleotides (ASOs), small interfering (si) RNAs, and ribozymes are considered by some researchers as valuable tools to develop therapeutic agents. They have not been particularly fast in reaching the market as medicines, due to endogenous barriers to extracellular...

The Essential Bioinformatics Web Services (EBWS) are implemented on a new PHP-based server that provides useful tools for analyses of DNA, RNA, and protein sequences applying a user-friendly interface. Nine Web-based applets are currently available on the Web server. They include reverse complementary DNA and random DNA/RNA/peptide oligomer generat...

This article describes how with the development of biotechnology, plants have gained again a prominent place as a relatively inexpensive source for the creation of recombinant pharmaceuticals. Plant-derived compounds have started playing a major role in the pharmaceutical industry with many plant-based products to have found their way in drugs and...

This article describes how an NC gene family has been identified in the genome of the Arabidopsis thaliana (Arabidopsis) by homology to the human Lecithin Retinal Acyl Transferase (LRAT) and the picornavirus 2A protein. The Arabidopsis proteins contain two motifs identified in a vast variety of organisms, an H-Box and an NC. Among related proteins...

Nanobiotechnology is emerging as a valuable field that integrates research from science and technology to create novel nanodevices and nanostructures with various applications in modern nanotechnology. Applications of nanobiotechnology are employed in biomedical and pharmaceutical research, biosensoring, nanofluidics, self-assembly of nanostructure...

Nanobiotechnology and synthetic biology are emerging as novel fields that integrate research from science and technology to create novel organisms with new desired properties. We present here the new revolutionary methods of synthetic biology that enable us to engineer gene control circuits, edit genomes, and create de novo whole genomes. The creat...

Introduction: In recent years, infections caused by multidrug-resistant bacterial pathogens have become a huge issue to public healthcare systems. Indeed, the misuse of antibiotics has led to, over the past 30 years, the emergence of a number of resistant bacterial strains including Staphylococcus aureus, Neisseria gonorrhoeae, Escherichia coli an...

Nucleic acids have proven to be a very suitable medium for engineering various nanostructures and devices. While synthetic DNAs are commonly used for self-assembly of nanostructures and devices in vitro, functional RNAs, such as ribozymes, are employed both in vitro and in vivo. Allosteric ribozymes have applications in molecular computing, biosens...

Nanobiotechnology is emerging as a valuable field that integrates research from science and technology to create novel nanodevices and nanostructures with various applications in modern nanotechnology. Applications of nanobiotechnology are employed in biomedical and pharmaceutical research, biosensoring, nanofluidics, self-assembly of nanostructure...

High expression levels of telomerase reverse transcriptase messenger RNAs in differentiated cells can be used as a common marker for cancer development. In this paper, we describe a novel computational method for selection of allosteric ribozymes that sense a specific sequence of human telomerase reverse transcriptase mRNAs. The in silico selection...

Advances in modern genomic research depend heavily on applications of various devices for automated high- or ultra-throughput arrays. Micro- and nanofluidics offer possibilities for miniaturization and integration of many different arrays onto a single device. Therefore, such devices are becoming a platform of choice for developing analytical instr...

Here I describe accurate and time-efficient computational methods for designing small molecule-sensing allosteric ribozymes that serve as logic gates with NOT or YES Boolean logic functions. Theophylline-sensing ribozymes are engineered to have a high cleavage rate of 1.3 min-1 under physiologically relevant conditions. They are highly specific to...

Nucleic acids-based technology is emerging as a valuable field that integrates research from science and technology to create novel nanodevices and nanostructures with various applicationsin modern nanotechnology. Nowadays, applicationsof RNA-based technologyare employed in biomedical and pharmaceutical research, biosensoring, nanopharmaceutics and...

Systems and synthetic biology promise to develop new approaches for analysis and design of complex gene expression regulatory networks in living cells with many practical applications to the pharmaceutical and biotech industries. In this chapter the development of novel universal strategies for exogenous control of gene expression is discussed. The...

Introduction: Bacterial riboswitches are structured RNA domains usually residing at the 5' untranslated region of messenger RNAs that can 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 for any regulatory proteins. The...

Here we describe molecular implementations of integrated digital circuits, including a three-input AND logic gate, a two-input multiplexer, and 1-to-2 decoder using allosteric ribozymes. Furthermore, we demonstrate a multiplexer-decoder circuit. The ribozymes are designed to seek-and-destroy specific RNAs with a certain length by a fully computeriz...

Systems and synthetic biology promise to develop new approaches for analysis and design of complex gene expression regulatory networks in living cells with many practical applications to the pharmaceutical and biotech industries. In this chapter the development of novel universal strategies for exogenous control of gene expression is discussed. The...

Systems and synthetic biology promise to develop new approaches for analysis and design of complex gene expression regulatory networks in living cells with many practical applications to the pharmaceutical and biotech industries. In this chapter the development of novel universal strategies for exogenous control of gene expression is discussed. The...

Riboswitches are newly-discovered gene control elements that are promising targets for antibacterial drug development. To facilitate the rapid discovery and development of riboswitch-targeted compounds, modern drug discovery techniques such as structure-based design and high-throughput screening will need to be applied. One promising riboswitch dru...

Allosteric RNAs operate as molecular switches that alter folding and function in response to ligand binding. A common type of natural allosteric RNAs is the riboswitch; designer RNAs with similar properties can be created by RNA engineering. We describe a computational approach for designing allosteric ribozymes triggered by binding oligonucleotide...

A novel approach to designing a DNA library for molecular computation is presented. The method is employed for encoding binary information in DNA molecules. It aims to achieve a practical discrimination between perfectly matched DNA oligomers and those with mismatches in a large pool of different molecules. The approach takes into account the abili...

Microfiov reactors provide a means of implementing DNA Computing as a vhole, not just individual steps. Contrary to surface based DNA Chips [1], lnicrofiov reactors vith active components in closed fiov systems can be used to integrate complete DNA computa- tions [2]. Microreactors allow complicated flow topologies to be realized which can implemen...

The paper demonstrates experimentally the basic principle of DNA transfer between magnetic bead based selection stages, which can be used in steady flow microreactors for DNA Computing [McCaskill, J.S.: Biosystems, 59 (2001) 125–138] and molecular diagnostics. Short DNA oligomers, which can be attached covalently to magnetic beads by a light progra...

A novel approach for light-dependent covalent immobilisation of synthetic DNA oligomers to amino-coated paramagnetic beads is described. A hetero-bifunctional photo-reactive cross-linking chemical, 4-nitrophenyl 3-diazopyruvate, is applied to attach 5' amino-modified DNA to both silica and polystyrene paramagnetic beads. The coupling yields are com...

A novel approach for light-dependent covalent immobilisation of synthetic DNA oligomers to amino-coated paramagnetic beads is described. A hetero-bifunctional photo-reactive cross-linking chemical, 4-nitrophenyl 3-diazopyruvate, is applied to attach 5′ amino-modified DNA to both silica and polystyrene paramagnetic beads. The coupling yields are com...

Microfiov reactors provide a means of implementing DNA Computing as a vhole, not just individual steps. Contrary to surface based DNA Chips [1], lnicrofiov reactors vith active components in closed fiov systems can be used to integrate complete DNA computa- tions [2]. Microreactors allow complicated flow topologies to be realized which can implemen...