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Biochemistry and Bioorganic Chemistry
Doctoral Programme,
Faculty of Food and Biochemical Technology
The aim of this programme is to prepare highly qualified professionals capable of independent scientific work, who will be involved in the implementation of new visions and methods in practice or will continue their scientific work at universities and scientific institutes and thus contribute to clarifying the functional principles of living organisms. The programme Biochemistry and Bioorganic Chemistry was created by merging two fields of chemistry. In this way, it will educate specialists preferentially oriented either to biochemistry or to bioorganic chemistry. The common denominator of both fields is to identify the chemical nature of important processes in living organisms, to study the relationship between the structure and biological activity of biopolymers, as well as natural organic compounds or their synthetic analogues. CareersGraduates of this programme are able to apply their knowledge in various fields such as biochemistry, cell biology and molecular genetics, microbiology, organic chemistry and chemistry of natural compounds (in relation to the dissertation topic). Based on the acquired knowledge, the student is able to plan the research project independently, critically assess the risks of the proposed procedures and apply innovative research methods. Another acquired competency of the graduate is the pedagogical and managerial experience due to involvment in teaching of bachelor and master programs, primarily in the role of assistants in laboratory courses and consultations of bachelor and master theses. Theoretical, experimental, pedagogical and managerial experience predispose the graduates to creative scientific and research activities, which is increasingly sought at various institutions of the institutes of the Academy of Sciences of the Czech Republic, universities, medical facilities, pharmaceutical companies and state and private research laboratories in the Czech Republic and abroad, dealing with problems in the field of biochemistry and bioorganic chemistry. Programme Details
Ph.D. topics for study year 2024/25Bioactivity of novel synthetic drugs and their enantiomers
AnnotationChemical modifications of illegal drugs lead to the formation of novel compounds, i.e. new synthetic drugs that circumvent legislation. While preserving the pharmacophore of such modified substances, they thus mimic the biological effects of the parent drug, but with unexplored pharmacological effects and toxicity that is often significantly higher than that of the parent drug. The main topic of the thesis will be the study of novel synthetic drugs, both synthesized de novo and retained at the black market. The toxicity of these substances will be examined in model cell lines, further, the metabolism of these compounds and the activity of selected metabolites will be studied. Furthermore, the mode of their action (agonist/antagonist) on selected G-protein-coupled receptors will be determined and we will focus in detail on the activity and mechanism of action of individual enantiomers of selected novel synthetic drugs.
Contact supervisor
Study place:
Department of Biochemistry and Microbiology, FFBT, VŠCHT Praha
Phages of phytopathogenic bacteria as a neglected factor in plant-microbiome interactions
AnnotationBacterial plant diseases cause losses of up to 10% of global food production each year. Unlike bacterial diseases in humans, antibiotics cannot be used to protect plants, and at the same time EU legislation still does not allow the modification of the plant genome to increase resistance through genetic manipulation. The search for alternative approaches to plant protection is therefore highly desirable. The proposed project focuses on an innovative method to utilise the potential of bacteriophages, which are still almost exclusively used in human medicine, for plant protection. The student will be involved in researching the role of phages in the plant phyllosphere (the microbiome associated with the above ground part of the plant) and their use for the protection and prevention of bacteriosis in plants of the Solanaceae and Brassicaceae families. The work combines approaches of molecular biology, microbiology, metagenomics, bioinformatics, advanced microscopy and plant physiology.
Contact supervisor
Study place:
Department of Biochemistry and Microbiology, FFBT, VŠCHT Praha
Rhomboid protease inhibitors
AnnotationThe proposed PhD project will be focused on the development of inhibitors and probes for rhomboid intramembrane proteases, which have been implicated in the regulation of mitophagy, malaria parasite invasion and epithelial homeostasis. Prior work in the thesis advisor’s lab has shown that peptidyl ketoamides are potent rhomboid protease inhibitors. The aim of the thesis will be to establish platforms to investigate and improve the potency and selectivity of this class of compounds for rhomboids and develop potent inhibitors and probes for specific rhomboid proteases implicated in Parkinson’s disease and epithelial homeostasis. These compounds will enable and facilitate biological studies of rhomboid proteins and serve as starting points for potential pharmacological applications.
Contact supervisor
Study place:
Institute of Organic Chemistry and Biochemistry of the CAS
Cryo-EM structural biology of diseases: Rationally designed viral-RNA based inhibitors of influenza RNA polymerase
AnnotationEffective treatment against influenza viruses (Flu) suffers from virus resistance. Therefore, there is a great demand for exploring new drug targets and developing effective novel antivirals. This is challenging, since there is only a limited number of antiviral targets for rational drug design. This project will tackle both; it will explore and verify a new target and develop inhibitors against it. Cutting edge results in structural biology of the influenza RNA-dependent RNA polymerase (FluPol), identified a common general mechanism of Flu RNA transcription and replication cycle. The mechanism is entirely dependent on binding of viral endogenous RNA molecules to specific sites on the FluPol. Aided by already existing cryo-EM structures of FluPol, we will design inhibitors based on the sequence, atomic structure and interactions with the protein, and add extensive chemical modification to these viral RNAs. We will then test whether they can inhibit FluPol by in vitro and in cell-based experiments. Targeting these RNA binding sites and using RNA-scaffold based molecules is an innovative concept and expected to be robust in respect to the development of viral resistance. Altogether, the approach has great potential to bring a new universal paradigm to the field of antiviral drug discovery.
Contact supervisor
Study place:
Institute of Organic Chemistry and Biochemistry of the CAS
Modified nucleotides for selection of functional nucleic acids and labelled probes for chemical biology
AnnotationWe will design and synthesize modified nucleoside triphosphates bearing diverse functional groups for enzymatic synthesis of modified oligonucleotides which will be applied in selection and construction of new functional nucleic acids, e.g. aptamers or aptazymes and for the construction of fluorescent or redox probes for applications in chemical biology. References: 1. Hocek, M.: "Enzymatic Synthesis of Base-Functionalized Nucleic Acids for Sensing, Cross-linking, and Modulation of Protein–DNA Binding and Transcription" Acc. Chem. Res. 2019, 52, 1730-1737. 2. Micura, R.; Höbartner, C. Fundamental studies of functional nucleic acids: aptamers, riboswitches, ribozymes and DNAzymes. Chem. Soc. Rev. 2020, 49, 7331–7353.
Contact supervisor
Study place:
Institute of Organic Chemistry and Biochemistry of the CAS
New cytostatic nucleosides and nucleotides with new mechanisms of action
AnnotationWe will design and synthesize new modified nucleosides and nucleotides as potential cytostatic agents with new mechanisms of action which includes modulation of receptors or activation of cytostatic proteins. Selected active compounds will be further optimized in order to identify preclinical drug candidates. References: 1. Jordheim, L. P.; Durantel, D.; Zoulim, F.; Dumontet, C. Advances in the development of nucleoside and nucleotide analogues for cancer and viral diseases. Nat. Rev. Drug Discov. 2013, 12, 447–464. 2. Perlíková, P.; Hocek, M. Pyrrolo[2,3-d]pyrimidine (7-deazapurine) as a privileged scaffold in design of antitumor and antiviral nucleosides. Med. Res. Rev. 2017, 37, 1429–1460.
Contact supervisor
Study place:
Institute of Organic Chemistry and Biochemistry of the CAS
Novel carbohydrate ligands for the diagnosis and therapy of galectin-related pathologies
AnnotationGalectins are animal lectins with affinity to beta-D-galactosides, which in vivo participate in, e.g., cancerogenesis, cardiopathologies, they are connected with the modulation of immune response and the course of allergic reaction. The concentration of extracellular galectins in vivo may be used as diagnostic markers in pathologies, such as colorectal carcinoma. A targeted inhibition of extracellular galectins is a prospective therapeutic approach to the treatment of pathologies associated with galectin overproduction. A range of recent structure-function studies is devoted to defining structural requirements for high-affinity and selective carbohydrate ligands of individual galectins. The avidity of specific carbohydrate inhibitors to selected galectins may also be increased by multivalent presentation. The aim of this work is to synthesize new carbohydrate ligands (glycomimetics) with a high afinity and possibly also selectivity for target galectins. Besides usually studied galectins Gal-1 and Gal-3, attention will be devoted to the group of tandem-repeat galectins (Gal-4, Gal-8, and Gal-9). The inhibitory and binding potential of these glycomimetics to galectins will be assayed by in vitro methods of ELISA and other biophysical methods. Structure-affinity relations will be discussed in relation to molecular modeling. Prepared ligands with a high affinity may be used in subsequent experiments with cell cultures, which are available at the supervisor workplace.
Contact supervisor
Study place:
Institute of Microbiology of the CAS
Dissecting molecular basis of nonhost resistance to <i>Leptoshaeria maculans</i>in plants of the Brassicaceae family
AnnotationOilseed rape (Brassica napus) is the second most important oilseed crop in the world. Its production is limited by pathogens and pests. Among the most serious of these is the ascomycete Leptosphaeria maculans, the causal agent of phoma stem canker. The project focuses on non-host resistance to this pathogen, which is based on basic mechanisms of plant immunity and is not easily overcome by virulent races of the pathogen selected from the population. Using the natural variability of the model plant Arabidopsis thaliana and approaches of molecular biology, microbiology, bioinformatics, advanced microscopy and plant physiology, the work will aim to unravel the nature of nonhost resistance in B. napus and other plants of the Brassicaceae family.
Contact supervisor
Study place:
Department of Biochemistry and Microbiology, FFBT, VŠCHT Praha
Preparation and applications of charged heterodienes in bioorthogonal reactions
AnnotationOur group recently described the development and first applications of N1-alkyl-1,2,4-triazinium salts in bioorthogonal reactions (Angew. Chem. Int. Ed., 2023, e202306828). In this project, we want to explore the chemistry of these charged heterodienes in more detail. In addition, we want to apply the developed reagents in applications ranging from selective modification of biomolecules to cellular applications (e.g. bioimaging). The project combines synthetic organic chemistry, reaction kinetics and stability studies with biological experiments that will be performed mainly in collaboration with biologists in the group.
Contact supervisor
Study place:
Institute of Organic Chemistry and Biochemistry of the CAS
Synthesis of defined chitosan oligomers as multivalent carriers for bioactive glycans
AnnotationChitin is the second most abundant polymer in nature. Partial deacetylation of chitin produces chitosan, a linear polymer composed mainly of glucosamine units (GlcN) and to a lesser extent of N-acetylglucosamine units (GlcNAc) linked ?(1?4) by glycosidic bonds. Chitosan is biocompatible and can therefore be advantageously used in a variety of biological and biomedical applications. For many biological applications, it is advantageous to work with shorter chains of chitosan, the so-called chitooligosaccharides (COS). COS have been intensively researched for decades in the fields of medicine, pharmaceuticals, textile industry, food industry and agriculture. Despite their tremendous potential use, poorly characterized heterogeneous mixtures are used in most studies due to the unavailability of well-defined COS. The thesis will focus on the preparation of authentic, pure and fully structurally characterized chitooligosaccharides and their analysis. Exoskeletons of crustaceans, insects (grasshoppers, bees, tarantulas) and fungi will be used as a source of chitin/chitosan. Subsequently, the defined COS chains will be used as carriers for multivalent presentation of bioactive carbohydrates, especially rutinose and galactosyl-carrying glycomimetics, for biological tests with lectins.
Contact supervisor
Study place:
Institute of Microbiology of the CAS
Preparation of a library of human milk oligosaccharides in a cell factory and their effect on food allergies
AnnotationHuman milk oligosaccharides (HMOs) are the third most important component of breast milk after lactose and fat. HMOs pass through the digestive tract without major changes and are partially absorbed into the bloodstream through the intestinal wall. They serve as prebiotics for the gut microbiome of infants, which is important for allergy susceptibility. HMOs prevent adhesion of pathogens to the intestinal epithelium and directly regulate the immune system, e.g. by altering cytokine production. HMOs have been found to prevent or alleviate allergy symptoms. Bacterial cell factories have been used for the high-yield enzymatic synthesis of HMOs without the need for purification of recombinant enzymes. Genetically modified strains of Escherichia coli are suitable for the production of breast milk oligosaccharides. To date, applications have mostly been limited to a basic selection of HMOs, while a broader spectrum of these structures is not available. The subject of this thesis is the development of the synthesis of selected complex HMOs, in particular fucosylated and/or sialylated, on the E. coli platform. These compounds will be further tested in biological experiments concerning their effect on processes related to the initiation and development of allergies, such as passage through the intestinal membrane, expression of relevant biomarkers in epithelial cells, etc.
Contact supervisor
Study place:
Institute of Microbiology of the CAS
Regulation of growth and metabolism
AnnotationWe have a long-standing interest in the regulation of growth and metabolism that stems from our early work on the pathway anchored by mTOR protein kinase. We now appreciate that it is a major regulator of growth and anabolism in animals and responds to diverse stimuli, including nutrients. Because our work revealed that lysosomes play a key role in the activation of mTORC1 by nutrients, we began to study lysosomes as well as other organelles. Available thesis projects: (1) Nutrient sensing by mTOR. We seek to: discover the glucose sensor for mTORC1 and nutrient sensors in animals beyond mammals; understand how the known nutrient sensors function in vivo; and elucidate the biochemical function of GATOR2. (2) Lysosomes in normal physiology and disease. Using the Lyso-IP methodology and CRISPR screening we seek to understand how neurodegenerative diseases impact lysosomes and identify the contents of lysosomes in specialized cells, like immune cells. (3) Methods to study small molecule metabolism in vivo. We seek to develop methods to study carbohydrate metabolism in cells in vivo in mice. (4) Development of drug-like molecules. In collaboration with chemists at IOCB and elsewhere, we seek to develop drug-like molecules that target mTOR pathway components as well lysosomal and mitochondrial proteins.
Contact supervisor
Study place:
Institute of Organic Chemistry and Biochemistry of the CAS
Sequence-specific enzymatic synthesis of base-modified RNA
AnnotationWe will design and synthesize modified ribonucleoside triphosphates bearing diverse functional groups at nucleobase. These nucleotides will be used for sequence-specific enzymatic synthesis of oligoribonucleotides (RNA) bearing labels or modifications at specific positions using engineered DNA polymerases. The applications will include tRNA, mRNA, sgRNA etc. References: 1. Micura, R.; Höbartner, C. Fundamental studies of functional nucleic acids: aptamers, riboswitches, ribozymes and DNAzymes. Chem. Soc. Rev. 2020, 49, 7331–7353. 2. Milisavljevic, N.; Perlíková, P.; Pohl, R.; Hocek, M. Enzymatic synthesis of base-modified RNA by T7 RNA polymerase. A systematic study and comparison of 5-substituted pyrimidine and 7-substituted 7-deazapurine nucleoside triphosphates as substrates. Org. Biomol. Chem. 2018, 16, 5800-5807.
Contact supervisor
Study place:
Institute of Organic Chemistry and Biochemistry of the CAS
Stops making sense - tRNA miscoding as a therapeutic tool? *
AnnotationImagine a gene is a sentence starting with a capital letter and ending with a period, and a genome as a book telling an entire story. In some protozoans, extra periods have infiltrated the sentences, replacing specific letters of arbitrary words (E and W). As a r.sult, readers are confus.d as to .here thes. sentences really .nd and th. story becom.s disjointed. In this issu. of Nature (https://www.nature.com/articles/s41586-022-05584-2), we describ. a molecular mechanism that thes. organisms must hav. developed to allo. the reader to navigat. the s.ntences as if there .ere no .xtra periods. Th. sentences are so specifically .ncrypted that read.rs of no other organisms but thos. very fe. can decipher the story in a prop.r .ay. The trick lies in the l.ngth of the tRNA molecul., and in the uniqu. modification of a prot.in that normally ensur.s dot recognition in c.lls - the precis. end of prot.in synthesis. By the intEraction of thesE tWo modified moleculEs, the ribosomE of this protozoan knoWs when to correctly terminatE, notWithstanding the many dots, and whEn to replace thE dots with the two original lettErs, which returns mEaning to the genetic information. LEt’s Explore hoW it is possible on thE molecular levEl and WhEther it could bE used for the benEfit of human hEalth! *This PhD thesis topic and the supervisor are subject to approval by the Faculty's Scientific Council.
Contact supervisor
Study place:
Institute of Microbiology of the CAS
Light upconversion paramagnetic nanoparticles for monitoring beta cell mass in pankreas and in vivo by magnetic resonance
AnnotationAccurate methods to detect pancreatic ?-cell mass and functionality in vivo are essential to better understand the pathogenesis of diabetes associated with pancreatic ?-cell deficiency and to develop new treatment options. Therefore, we will develop polymer-coated paramagnetic core-shell upconversion nanoparticles (UCNPs) conjugated with small GLP-1 receptor ligands (GLP-1 peptide, liraglutide or agonist 3) to target and monitor pancreatic ?-cell mass using magnetic resonance imaging (MRI) and luminescence. The newly developed UCNPs will be optimized in size to penetrate blood capillaries of the native and transplanted pancreatic islets and modified for long-term monitoring. Ultrasmall UCNPs (5 nm) will serve as a contrast agent for electron microscopy to visualize and count mtDNA nucleoids in ?-cells, which are typically reduced in diabetes. The specificity, safety and efficacy of all developed UCNPs will be validated in in vitro and in vivo models using multimodal imaging including luminescence, MRI and electron microscopy. See Ref. doi: 10.1021/acsami.2c04274.
Contact supervisor
Study place:
Institute of Physiology of the CAS
Multistep enzymatic synthesis of bioactive chitooligomers with varying degrees of acetylation
AnnotationThe project for this dissertation focuses on developing a three-step enzymatic synthesis of bioactive chitooligomers (COS) useful in organic crop protection. Chitooligomers are ?-1-4-linked oligosaccharides composed of N-acetylglucosamine and glucosamine units whose biological activity depends mainly on their degree of polymerization (DP) and degree of acetylation (DA). COS are known for their ability to induce an immune response in plants and can thus be used as natural crop protection agents against microbial pests. The project will prepare mutant variants of a novel fungal chitinase with enhanced hydrolytic activity to increase the efficiency of chitin cleavage, by which COS fractions with lower DP will be prepared. In the next step, mutant variants of chitinases and ?-N-acetylhexosaminidases with transglycosidase activity suitable for preparing COS with degrees of polymerization of 5-10 on a preparative scale will be used. These chitooligomers will be partially deacetylated with novel chitin deacetylases, yielding COS fractions with different degrees of polymerization and acetylation that are not yet available. The biological activity of the prepared well-defined COS will be tested in collaboration with the Institute of Experimental Botany of the CAS.
Contact supervisor
Study place:
Institute of Microbiology of the CAS
The influence of synthetic modifications on the biological activity of flavonoids
AnnotationFlavonoids, natural compounds found in various plants and foods, continue to attract great interest due to their known positive biological effects. However, these effects are compromised by their low bioavailability after oral administration. In the frame of this work new derivatives of flavonoids will be synthesized and the effect of various modifications on the bioavailability and biological activity of flavonoids will be evaluated. We will focus on the ability of the prepared derivatives to modulate drug resistance of bacteria, the chelatory activity and platelet aggregation inhibitory activity of flavonoids.
Contact supervisor
Study place:
Institute of Microbiology of the CAS
Selected biologically active substances and their derivatives with potential for cancer therapy
AnnotationThe main topic of the thesis is the study of substances isolated from natural sources as well as de novo synthesized with the potential to inhibit the proliferation of tumor cells and activate the immune system response. The work is mainly focused on cardiac glycosides, such as digitoxin or digoxin, and antimitotics, such as colchicine or paclitaxel. The biological effects of newly prepared derivatives of these substances on 2D and 3D cell models of cancerous and noncancerous cell lines will be studied. We will focus on the mechanism of action of these substances, a targeted increase in selectivity for cancer cells and induction of an immune response. Last, but not least, targeted nanosystem delivery will be developed, in cooperation, for the most potent derivatives of the studied compounds.
Contact supervisor
Study place:
Department of Biochemistry and Microbiology, FFBT, VŠCHT Praha
3D superresolution microscopy for accessing mitochondrial ultramorphology
Annotation3D nanoscopy has not yet assessed mitochondrial cristae morphology, nor the internal structure of mitochondrial DNA (mtDNA) & protein complexes, termed nucleoids. Hence, we’ll survey 3D-redistribution of cristae and their shaping proteins or nucleois employing our prototype Vutara 3D superresolution microscope for stochastic techniques such a PALM and dSTORM. We will conduct studies under physiological situations vs. pathology (type-2 diabetes, cancer) using dSTORM with nanobodies or FRET excited PALM/dSTORM. Thus nm changes will be reflected by novel 3D nanoscopy methods. Also mtDNA nucleoids will be studied at increased and diminished mitochondrial biogenesis, while applying own mitoFISH nanoscopy for D-loop counting. Artificial manipulations of nucleoid size and mtDNA content will be studied as well as nucleoid division. Results will be translated into specific protocols for 3D nanoscopy, specifically developing novel relevant 3D image analyses based upon the Ripley’s K-function and Delaunay algorithm. Molecular cell biology will thus be combined with up-to-date 3D nanoscopy. Note, the molecular biology techniques will be conducted and be ready for the applicants by the coworkers of the Department No.75. See Ref. doi: 10.1089/ars.2022.0173.
Contact supervisor
Study place:
Institute of Physiology of the CAS
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Updated: 20.1.2022 16:26, Author: Jan Kříž