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

Catalytic Stereoselective Synthesis of Elusive Atropisomers for Drug Discovery

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

Annotation

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.

Contact supervisor

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

Machine learning in biochemistry

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.

Annotation

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.

Contact supervisor

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

Methyltransferase inhibitors

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.

Annotation

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.

Contact supervisor

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

Modified nucleotides for selection of functional nucleic acids and labelled probes for chemical biology

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.

Annotation

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.

Contact supervisor

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

Multiphotochromic Molecular Machines

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.

Annotation

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).

Contact supervisor

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

New cytostatic nucleosides and nucleotides with new mechanisms of action

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.

Annotation

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.

Contact supervisor

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

Novel inhibitors of nucleotide salvage pathway enzymes with potential anticancer properties

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.

Annotation

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.

Contact supervisor

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

Photochemistry and Spectroscopy of Organic Radical Ions

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.

Annotation

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.

Contact supervisor

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

Preparation and applications of charged heterodienes in bioorthogonal 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.

Annotation

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.

Contact supervisor

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

Sequence-specific enzymatic synthesis of base-modified RNA

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.

Annotation

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.

Contact supervisor

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

Total Syntheses of Complex Indoloterpene Alkaloids and Their Analogs

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

Annotation

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

Contact supervisor

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

)

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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

We offer studies in interesting and promising directions of advanced chemistry

Research and Development

We offer advanced studies into interesting and promising directions of advanced chemistry

Research and Development

Chemistry and Technology of Materials

Chemistry and Chemical Technology

DATA

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

Catalytic Stereoselective Synthesis of Elusive Atropisomers for Drug Discovery

Annotation

Machine learning in biochemistry

Annotation

Methyltransferase inhibitors

Annotation

Modified nucleotides for selection of functional nucleic acids and labelled probes for chemical biology

Annotation

Multiphotochromic Molecular Machines

Annotation

New cytostatic nucleosides and nucleotides with new mechanisms of action

Annotation

Novel inhibitors of nucleotide salvage pathway enzymes with potential anticancer properties

Annotation

Photochemistry and Spectroscopy of Organic Radical Ions

Annotation

Preparation and applications of charged heterodienes in bioorthogonal reactions

Annotation

Sequence-specific enzymatic synthesis of base-modified RNA

Annotation

Total Syntheses of Complex Indoloterpene Alkaloids and Their Analogs

Annotation