Professional guarantor

Mgr. Radim Nencka, Ph.D., IOCB

Viral and bacterial diseases pose a significant health risk to the entire human population. And, as the COVID-19 pandemic has shown, they can also paralyse global society. Underdeveloped areas of research into new diagnostic and therapeutic methodologies impede the ability of society to adequately respond to current and future challenges posed by pathogens.

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Professional Goals

3_MUNI_02_Vácha: Antimicrobial Peptides at Viruses and Bacteria

We need to develop new antibiotics because bacterial resistance against available antibiotics is growing, and the resistant bacteria are already responsible for more than 700,000 deaths per year, with a forecast to reach 10 million in 2050. One of the promising candidates for new antibiotics is antimicrobial peptides. However, the further development of these peptides is hindered by the missing relationship between the peptide sequence and its antimicrobial activity. We will use computer simulations to determine peptide crucial features/sequence motives which are responsible for the disruption of bacterial membranes. Based on the obtained knowledge, we will design experimentally verify new antimicrobial peptides. The provided peptides could be the initial hits for the optimization and development of new antimicrobial compounds. Principal investigator Robert Vácha uses computer simulations to determine molecular mechanism of action for antimicrobial peptides magainin 2 and PGLa.

14_CUNI_03_Šašková: Discovery of new antiviral defense mechanisms

One of the approaches to achieve functional HBV cure is to target the interface between the viral and cellular proteins or HBV cccDNA. The goal is to identify the host proteins affecting viral replication and select new target candidates for possible therapeutic intervention. Among the viral targets suitable for preclinical investigation belong HBV core protein HBc. We will use the proximity-dependent biotinylation proteomic technique (BioID2) to identify novel proteins interacting with HBc and cccDNA. The in vitro high-throughput screening assays to identify small compounds affecting the respective protein-protein interaction will be designed and validated. Furthermore, we aim to validate whether the small molecules modulating the NRF1 (NFE2L1) pathway responsible for proteasome synthesis and heat shock proteins expression discovered by us affect HBV replication. Principal investigator Klára Grantz Šašková is an expert in drug discovery targeting viral proteins (HIV protease, capsid) and human proteins (DDI2, NRF1 modulators) with experience in translational research (discovery of novel LNPs)..

22_CUNI_08_Roh: Development of antimicrobial agents with activity against drug-resistant bacteria

Mortality associated with antimicrobial drug resistance is expected to reach 10 million deaths/year by 2050. Therefore, the main objective of this project is to develop novel (pre)clinical antimicrobial candidate(s) with the activity against drug-resistant (myco)bacteria. First, elucidation of the structure-activity-toxicity relationships of several unique in-house structural types of potential antimicrobial compounds with activity against drug-resistant (myco)bacterial strains will be conducted and the mechanisms of action of the most potent compounds will be evaluated. Based on the obtained results and in silico prediction, the design and synthesis of new analogues with improved activity and an ADMETox profile will be performed. Finally, their pharmacokinetic properties and the ability to tackle (myco)bacterial infections will be evaluated using in vivo models of (myco)bacterial infections. Principal investigator Jaroslav Roh has a strong expertise in the medicinal chemistry of antimycobacterial compounds, especially in the group of DprE1 inhibitors and prodrugs activated by Ddn.

23_UCT_01_Rumlová: Characterization of allosteric modulation of RNA-dependent RNA polymerase SARS-CoV-2

The SARS-CoV-2 infection has had an extraordinary impact on humanity and alerted the scientific community to the lack of effective treatment. We will study the modulation of SARS-CoV-2 RNA-dependent RNA polymerase activity, which is essential for virus replication. Using molecular modelling, we have preselected putative binding sites for allosteric modulators of the polymerase activity. We will use a combination of molecular docking, commercial libraries and organic compounds synthesis to test novel allosteric non-nucleoside inhibitors. We will characterise and verify the binding capacity of the compounds to the recombinant polymerase complex and evaluate their inhibitory activity. To determine the applicability of allosteric inhibitors in combination therapy, we will measure their ability to increase the efficiency of existing active site binding inhibitors, such as Remdesivir. Principal investigator Michaela Rumlová is an expert on the development of biochemical assays aimed at the screening of antiviral compounds.

26_UCT_01_Rumlová: multidrug-resistant bacteria

Antibiotic resistance has become one of the main problems in today’s healthcare system. Common mechanisms of bacterial resistance are antibiotic efflux; altered membrane permeability reduction of the antibiotic’s uptake; antibiotic inactivation by enzymatic modification, or mutation of the target site. We plan to search for inhibitors of transmembrane efflux pumps, which are the major cause of bacterial resistance. By using qPCR, we will determine the mechanisms of antibiotic resistance in clinical isolates. The search for new efflux pumps inhibitors will be based on, but not limited to, synthetic derivatives of known inhibitors and natural substances isolated from medicinal plants. Our aim is to verify the capability of the identified inhibitors to restore the sensitivity to antibiotics in drug-resistant bacterial strains. Principal investigator Michaela Rumlová is an expert in microbiology focused on the retroviral life cycle, antimicrobial therapy including phototherapy and biofilm inhibition and will be advisor for this project.

27_UP_01_Petřík: Radiolabelled siderophores for microbial infection imaging

Despite the success of antibiotics, microbial infections in hospitals are on the rise. Current diagnostic methods have major limitations in specificity and/or sensitivity. Molecular imaging has the potential for specific and sensitive detection of infections. The siderophore-based iron acquisition system, represents one of few fundamental differences between microbial and mammalian cells. Siderophores are low-molecular mass, iron specific chelators secreted by bacteria or fungi. Microorganisms possess dedicated transporters for the uptake of siderophores. Siderophores can be radiolabelled, replacing iron without the loss of bioactivity and allowing molecular imaging of microbial infections. Our goal is to open new diagnostic imaging strategies for microbial infections with improved sensitivity and specificity, which could provide the basis for a novel class of diagnostics for infectious diseases. Principal investigator Miloš Petřík is an expert in the field of nuclear medicine and molecular imaging focused on the development of novel radiotracers for infection imaging.

28_UP_02_Kolář: Antimicrobial resistance (AMR)

The increasing prevalence of bacteria resistant to antibacterial drugs opens the possibility of a new non-antibiotic era in which antibiotics will be unavailable to treat infections caused by multidrug-resistant (MDR) bacteria. Increasing bacterial resistance to antibiotics is a serious problem not only in human but also in veterinary medicine, which is commonly referred to as a global threat. The main goal of this task is to analyse the development of AMR at the phenotypic and genotypic levels, to evaluate the effect of antibiotic selection pressure on AMR and to define measures to maintain the effectiveness of antibacterial agents. The specific objectives can be characterized as follows, (1) detection of MDR bacteria, including phenotypic and genotypic analysis of the extent of resistance, (2) development of the primers for PCR amplification assay for identification of most extensive genes that confer β-lactams-, vancomycin and polymyxin resistance, and (3) implementation of appropriate infection control measures to prevent the further spread of AMR. Principal investigator Milan Kolář has a strong background in AMR analysis and the evaluation of antibiotic application effect on AMR.

29_UP_02_Kolář: Testing the antimicrobial activity of new compounds

The accelerating emergence of bacterial resistance to current antibiotics poses an increasing threat to public health, and this consequently results in an urgent need for novel effective antimicrobial compounds. A promising way to solve the problems of bacterial resistance are lipophosphonoxins (LPPOs) and silver nanoparticles (AgNPs). The solution in this area will be to test the antimicrobial effect of new substances, such as LPPOs and AgNPs, using the following methodologies, (1) determination of MIC and MBC values, (2) determination of antimicrobial activity in the presence of 4% BSA, (3), evaluation of bactericidal effect in time (kill-time assay), (4) persister killing assay, and (5) testing of possible selection of resistant bacterial cells to new substances. Principal investigator Milan Kolář has extensive experience in the complex testing of the antimicrobial effect of new substances.

30_UP_02_Kolář: Determination of bacterial pathogens in clinically important infections, especially nosocomial, and antibiotic treatment options, application of Antibiotic stewardship

Antibiotic stewardship may be defined as a set of measures leading to rational antibiotic therapy based on the adequate selection of antibacterial agents, appropriate duration of their administration and a suitable route of administration. The need for antibiotic stewardship implementation stems from the likely prospect of antibiotics losing their effectiveness and thus their ability to treat bacterial infections. These activities may be described as follows, (1) analysing the routes of spread of multidrug-resistant bacteria using modern molecular methods, (2) providing antibiotic consultant service for clinical physicians and deciding on antibiotic administration based on microbiological results and the knowledge of bacterial pathogens resistance in patients with bacterial infections, (3) assessing the clinical efficacy of antibiotics in the relevant epidemiological units and, if needed, introducing necessary regulatory measures. Principal investigator Milan Kolář has extensive experience with the full implementation of the Antibiotic stewardship, including the detection of bacterial pathogens and antibiotic treatment of bacterial infections.

35_IOCB_03_Nencka: Viral methyltransferase inhibitors – from bench to clinical candidates Viruses with pandemic potential pose a threat to our globalized society

The main objective of this project is to design and prepare new inhibitors of viruses from groups that have pandemic potential, e.g., pathogens from the families Coronaviridae, Flaviviridae, and Paramyxoviridae that have caused serious problems in the present and recent past. In particular, the project will use structure-based drug discovery approaches to identify novel inhibitors targeting viral methyltransferases (MTases). Our goal is to demonstrate that these compounds can effectively interfere with the life cycle of these viruses in vitro and in vivo and to deliver compounds that will be able to enter human clinical trials in near future. Principal investigator Radim Nencka is an expert in the medicinal chemistry of antiviral compounds. Recently, he has been using structure-based approaches to the identification of novel MTase inhibitors of SARS-CoV-2.

36_IOCB_04_Kožíšek: Identification and characterization of inhibitors of the influenza A polymerase and L-protein of Rift Valley Fever virus

The influenza virus causes severe infectious diseases that represents a serious threat to public health. There is an urgent need for the development of new anti-influenza drugs effective against resistant viral strains and different viral subtypes. In this project we plan to study endonuclease and cap-binding small molecule inhibitors, as well as peptide inhibitors targeting protein-protein interaction in viral polymerase. Furthermore, due to the functional and presumed structural similarity between the influenza A polymerase and L-protein of the emerging Rift Valley Fever virus (RVFV), we plan to utilize our prior experience to develop and identify novel inhibitors of the endonuclease and polymerase activity of RVFV. This project will thus allow the development of active compounds against these important pathogens. Principal investigator Milan Kožíšek has experience with the research of retroviruses and the influenza virus.

37_IOCB_04_Kožíšek: Viral proteases as therapeutic targets and pathogenic factors

Viral proteases are key enzymes in virion maturation that contribute to viral pathogenesis. Targeting viral proteases represents a viable strategy of antiviral therapy. The main focus of this research objective involves proteases of HIV, SARS-CoV-2, Zika and Dengue viruses. A detailed understanding of the regulatory steps during the autoactivation of these enzymes, their role in virion maturation and pathogenesis is still lacking. We plan to combine biological, chemical and biophysical approaches to study proteases activation, the regulation of maturation, intra and their interactions with low-molecular-weight ligands or other viral and host proteins. Principal investigator Milan Kožíšek has experience with targeting retroviral and influenza virus enzymes.

39_IOCB_05_Weber: Identification and targeting coronavirus attachment and entry

Viral attachment and entry to the host cell as initial steps for establishing a new infection are attractive targets for intervention. Many viruses use abundant adhesion molecules such as heparan sulphate proteoglycan at the surface for initial attachment to the cells. We plan to characterize and target this interaction with sulphated nanoparticles that mimic heparan sulphate. Our results will broaden the knowledge about the coronavirus usage of heparan sulphate for attachment to the cells and characterize complex host cell network in coronavirus entry pathways. Furthermore, it can lead to the development of heparan sulphate mimicking nanoparticles with virucidal activity and their application as a preventive measure to curb the coronavirus infection. Principal investigator Jan Weber besides to his interest in finding new antiviral compounds is also involved in the search for nanoparticles and nanomaterials with antiviral and virucidal activity.

40_IOCB_06_Rejman: Antimicrobials targeting cellular membranes

Bacterial diseases resistant to currently available drugs are among the most serious problems our society currently faces. The main objective of this project is to design, synthesize, and evaluate a novel membrane targeting antimicrobial compounds. Our goal is to develop novel, potent, and safe antimicrobials that will be difficult for bacteria to develop resistance to. Moreover, since the bacterial cellular membrane will be the target of these molecules, we also expect activity against dormant bacteria and persisters. Principal investigator Dominik Rejman is an expert in organic and medicinal chemistry. He has developed several generations of membrane targeting antimicrobial compounds termed lipophosphonoxins.

41_IOCB_06_Rejman: Nucleoside and non-nucleoside molecular tools for antimicrobial discovery

To overcome the increasing problem with antibiotic resistance, the mechanisms of resistance towards existing antibiotics need to be well understood and new antibacterial compounds aimed at new molecular targets need to be discovered. The objective of this project is to develop new molecular tools that will help a) study and understand the resistance mechanism (e. g. against Rifampicin) and b) uncover and study novel potential targets for future antibiotics (e. g., nucleotide metabolism or bacterial stringent response). Principal investigator Dominik Rejman is an expert in organic and medicinal chemistry particularly in the chemistry of nucleic acid components. He has developed several potent inhibitors of nucleotide metabolizing enzymes as well as novel molecular tools for studying biological processes.

48_IMIC_02_Janata: Antibiotics: Molecular principles of the resistance, action and (bio)synthesis

There is an urgent need of novel antimicrobials against strains that are resistant to currently used antimicrobial treatments. One of the approaches is to modify existing natural antibiotic scaffolds to overcome existing resistance mechanisms. Using our expertise in the molecular principles of the biosynthesis of lincomycin and celeticetin, new hybrid lincosamide derivatives will be designed in order to achieve more efficient and safer antibiotics, if compared to the macrolides and lincosamides currently available on the market (clarithromycin, azithromycin, clindamycin). The improved lincosamides may provide solutions for difficult-to-treat multidrug-resistant and pandrug-resistant infections caused by pathogens such as methicillin-resistant S. aureus (MRSA) or vancomycin-resistant enterococci (VRE) and have a potential to overcome the risk of pseudomembranous colitis. Principal investigator Jiri Janata is an expert in the biosynthesis of bacterial natural products, including antibiotics. His team has used its own expertise to design improved hybrid antibiotics, currently in preclinical testing.

50_IMIC_03_Krásný: Characterization of novel antimicrobials

Bacterial diseases resistant to currently available drugs already cause at least 700,000 deaths globally a year, including 230,000 deaths from multidrug-resistant tuberculosis. The world is already feeling the economic and health consequences as crucial medicines become ineffective. A highly attractive target for the development of antibacterial compounds is the cytoplasmic membrane as it is possible to design and prepare compounds that selectively attack the bacterial but not the eukaryotic membrane. In this research objective, we will characterize the properties and mechanistic functioning of novel compounds (developed by Dr. D. Rejman) targeting the bacterial membrane as well as compounds with off-target modes of action. This research will help develop novel antibacterial compounds. Principal investigator Libor Krásný is an expert in bacterial physiology, antibiotic resistance, gene expression at the transcription level and its regulation.

52_BC_01_Růžek: Human antibodies and antivirals to prevent and/or treat (re)emerging viral infections

The search for effective antivirals is one of the global research priorities. Today, only a few small-molecule antiviral drugs are available for the treatment of viral infections. Using already established platforms, we will screen libraries of known or newly synthesized chemical compounds for their antiviral activity against a panel of RNA and DNA viruses, including flaviviruses, coronaviruses, rhabdoviruses and herpesviruses, to identify novel antivirals active against these medically important viruses. The hit compounds will be characterized in more detail. The antiviral properties will be tested in vitro as well as in vivo using animal models. We will also generate virus escape mutants resistant to the drug to reveal the mechanisms involved in virus escape and the mechanisms of the action of antivirals. Principal investigator Daniel Růžek is well experienced with testing potential antivirals under in vitro and in vivo conditions.

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