Institute of Organic Chemistry and Biochemistry of the CAS, v. v. i.

Granting Departments:	Department of Organic Chemistry Institute of Organic Chemistry and Biochemistry of the CAS, v. v. i.
Study Programme/Specialization:	Chemistry ( in English language )
Supervisor:	Dr. Paulo Paioti

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Atropisomers are conformational isomers arising from restricted rotation around a single bond. Our main goal is inducing conformational restriction to create pharmaceutical leads by developing catalytic stereoselective synthesis toward difficult-to-access drug-like atropisomers. Atropisomers are chiral, giving rise to two or more isomers that have different pharmacological properties. These attributes relate to a poorly understood fundamental question of how conformational changes, from achiral and flexible to chiral and more rigid impact a molecule’s ability to interact with biological receptors. But to study such concepts, one must first of all create and then synthesize this challenging class of compounds. The main challenge is that atropisomers are intrinsically sterically hindered and potentially configurationally unstable. Accordingly, we will develop new catalytic synthesis methods and strategies, hoping to deliver more efficient, practical and (atropo)selective methods.

Granting Departments:	Department of Biochemistry and Microbiology Institute of Organic Chemistry and Biochemistry of the CAS, v. v. i.
Study Programme/Specialization:	Biochemistry and Bioorganic Chemistry ( in English language )
Supervisor:	Mgr. Tomáš Kouba, Ph.D.

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Effective 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.

Granting Departments:	Department of Biochemistry and Microbiology Institute of Organic Chemistry and Biochemistry of the CAS, v. v. i.
Study Programme/Specialization:	Microbiology ( in English language )
Supervisor:	Mgr. Jan Weber, CSc.

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The entry of viruses into host cells is a crucial initial step, particularly for respiratory viruses with significant pandemic potential such as SARS-CoV-2 and influenza A virus. Analyzing the interactomes of coronaviruses and influenza A virus and comprehending the early interactions between viral and cellular proteins can provide valuable insights for developing targeted or broad-spectrum antiviral therapies. The main goal of this project is to understand the viral and cellular factors influencing the entry of respiratory viruses. We will employ several strains of coronaviruses and influenza A virus, known to exploit different entry routes into the host cell, and will compare their cellular interactome at the time of entry and during early post-entry events. From the identified cellular interacting partners, interesting candidates will be selected and their role in the virus life cycle analyzed. The student will learn how to work with cell cultures in biosafety level 3, perform proteomic and bioinformatic analyses, and conduct siRNA experiments for gene-knockdown in mammalian cells infected with various viruses. The proposed project will broaden our current knowledge about the early phase of infections of mammalian cells with respiratory viruses.

Granting Departments:	Department of Organic Chemistry Institute of Organic Chemistry and Biochemistry of the CAS, v. v. i.
Study Programme/Specialization:	Bioinformatics ( in English language )
Supervisor:	Mgr. Tomáš Pluskal, Ph.D.

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Our lab combines cutting-edge experimental (e.g., LC-MS, metabolomics, RNA-seq) and computational (e.g., bioinformatics, molecular networking, machine learning) approaches to develop rapid, generally applicable workflows for the discovery and utilization of bioactive molecules derived from plants. The successful candidate for this position will be developing machine learning models for the prediction of enzymatic activities of enzymes in specialized biosynthetic pathways.

Granting Departments:	Department of Organic Chemistry Institute of Organic Chemistry and Biochemistry of the CAS, v. v. i.
Study Programme/Specialization:	Chemistry ( in English language )
Supervisor:	Mgr. Radim Nencka, Ph.D.

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The thesis will focus on the research of new inhibitors of methyltransferases. These enzymes play an important role in the pathogenesis of many diseases and are essential for the life cycle of many infectious pathogens. In this thesis, the student will investigate the rational design and synthesis of novel methyltransferase inhibitors that use S-adenosylmethionine (SAM) as the methyl group donor. Both SAM derivatives and compounds obtained by screening will be studied. The student will use computational methods to design and optimize new derivatives.

Granting Departments:	Department of Chemistry of Natural Compounds Institute of Organic Chemistry and Biochemistry of the CAS, v. v. i.
Study Programme/Specialization:	Biochemistry and Bioorganic Chemistry ( in English language )
Supervisor:	prof. Ing. Michal Hocek, DSc.

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We 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.

Granting Departments:	Department of Organic Chemistry Institute of Organic Chemistry and Biochemistry of the CAS, v. v. i.
Study Programme/Specialization:	Chemistry ( in English language )
Supervisor:	Mgr. Jiří Kaleta, Ph.D.

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The multiphotochromic systems are made by interconnection of two or more photoswitches (molecules, whose geometry can be reversibly switched using light). Individual parts (photoswitches and unidirectional molecular motors) of these molecules will be selectively activated/switched by action of a light of defined wavelength. The goal of this Ph.D. project is design, synthesis and study of these unique molecules and their possible utilization for construction of first prototypes of molecular machines of this kind. Special attention will be dedicated to various combinations of individual photoswithes as well as the type of their mutual interconnection (orthogonal vs. non-orthogonal).

Granting Departments:	Department of Organic Chemistry Institute of Organic Chemistry and Biochemistry of the CAS, v. v. i.
Study Programme/Specialization:	Chemistry ( in English language )
Supervisor:	prof. Ing. Michal Hocek, DSc.

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We 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.

Granting Departments:	Department of Organic Chemistry Institute of Organic Chemistry and Biochemistry of the CAS, v. v. i.
Study Programme/Specialization:	Chemistry ( in English language )
Supervisor:	Ing. Zlatko Janeba, Ph.D.

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The project aims to design and synthesize novel inhibitors of nucleotide salvage pathway enzymes (phosphoribosyltransferase, phosphorylases) and evaluate their biological properties (in collaboration with biochemistry groups). Such inhibitors have the potential to treat various types of cancer.

Granting Departments:	Department of Organic Chemistry Institute of Organic Chemistry and Biochemistry of the CAS, v. v. i.
Study Programme/Specialization:	Chemistry ( in English language )
Supervisor:	RNDr. Tomáš Slanina, Ph.D.

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Stable radical cations and anions are unique molecules that have found numerous applications in photovoltaics, organic electronics, batteries, and catalysis. While electrochemical and redox preparation of radical ions has been studied in detail, little is known about their photochemistry. The candidate will synthesize radical ions based on triarylamines, hexaarylethanes, perylene diimides, quinones, and other motives, and will study their photochemical stability and reactivity in perspective of the application in photoredox and hydrogen atom transfer catalysis. The candidate will use steady state and time-resolved spectroscopy of stable radical ions to elucidate the mechanisms of photochemical redox reactions.

Granting Departments:	Department of Organic Chemistry Institute of Organic Chemistry and Biochemistry of the CAS, v. v. i.
Study Programme/Specialization:	Chemistry ( in English language )
Supervisor:	Ing. Milan Vrábel, Ph.D.

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Our 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.

Granting Departments:	Department of Biochemistry and Microbiology Institute of Organic Chemistry and Biochemistry of the CAS, v. v. i.
Study Programme/Specialization:	Biochemistry and Bioorganic Chemistry ( in English language )
Supervisor:	David Marcelo Sabatini, M.D., Ph.D.

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We 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.

Granting Departments:	Department of Biochemistry and Microbiology Institute of Organic Chemistry and Biochemistry of the CAS, v. v. i.
Study Programme/Specialization:	Biochemistry and Bioorganic Chemistry ( in English language )
Supervisor:	Ing. Kvido Stříšovský, Ph.D.

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The 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.

Granting Departments:	Department of Organic Chemistry Institute of Organic Chemistry and Biochemistry of the CAS, v. v. i.
Study Programme/Specialization:	Chemistry ( in English language )
Supervisor:	prof. Ing. Michal Hocek, DSc.

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We 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.

Granting Departments:	Department of Organic Chemistry Institute of Organic Chemistry and Biochemistry of the CAS, v. v. i.
Study Programme/Specialization:	Chemistry ( in English language )
Supervisor:	Dr. habil. Ullrich Jahn

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With the project, synthetic approaches to complex indoloterpene and their analogs displaying wide-ranging biological activity will be developed.