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Polishchuk Pavlo Ph.D., M.Sc.

Journals

NOWIKOW, C., R. FUERST, M. KAUDERER, C. DANK, W. SCHMID, M. HAJDÚCH, J. ŘEHULKA, S. GURSKÁ, O. MOKSHYNA, P. POLISHCHUK, I. ZUPKO, P. DŽUBÁK, U. RINNER
Synthesis and biological evaluation of cis-restrained carbocyclic combretastatin A-4 analogs: Influence of the ring size and saturation on cytotoxic properties. Bioorganic & Medicinal Chemistry. 2019, 27(19), 115032, ISSN: 0968-0896, PMID: 31401010,
KUTLUSHINA, A., A. KHAKIMOVA, T. MADZHIDOV, P. POLISHCHUK
Ligand-Based Pharmacophore Modeling Using Novel 3D Pharmacophore Signatures. Molecules. 2019, 23(12), pii: E3094, ISSN: 1420-3049, PMID: 30486389,  PDF.
GIMADIEV, T., T. MADZHIDOV, I. TETKO, R. NUGMANOV, I. CASCIUS, O. KLIMCHUK, A. BODROV, P. POLISHCHUK, I. ANTIPIN, A. VARNEK
Bimolecular Nucleophilic Substitution Reactions: Predictive Models for Rate Constants and Molecular Reaction Pairs Analysis. Molecular Informatics. 2018, 38(4), e1800104, ISSN: 1868-1743, PMID: 30468317,

Open positions

Projekt: Postdoctoral fellow/Researcher
Vedoucí: Polishchuk Pavlo Ph.D., M.Sc.
K dispozici: 1
Určeno pro: Postdoktorandské studium
Souhrn: The group of chemoinformatics and drug design at the Institute of
Molecular and Translational Medicine, Faculty of Medicine and
Dentistry, Palacky University in Olomouc, Czech Republic
(https://imtm.cz/laboratories/chemoinformatics-and-drug-design) seeks
for a postdoctoral fellow with experience in chemoinformatics and
programming.

The primary objective of the group is development of new computational
approaches and software tools in drug design and their application in
medicinal chemistry projects on hit/lead identification/optimization
and target identification.

The successful candidate will be mainly involved into the project on
de novo fragment-based drug design and optimization. He/she will
implement new and improve existing tools and approaches, validate them
retrospectively and apply those tools in ongoing medicinal chemistry
projects conducting at our institution in close collaboration with
medicinal chemists and biologists. The candidate can be involved in
other research projects depending on his/her experience and skills.

The formal requirements:
PhD in chemistry, chemoinformatics, computer science or related
fields or 3 years of experience in relevant fields
experience with molecular docking/pharmacophore modeling/machine
learning
knowledge of RDKit
good Python programming skills and experience in software
development
data analysis skills
basic medicinal chemistry knowledge is a plus
good publication record
excellent writing and spoken English

The position will be opened for 2-3 years with a possibility of
extension.

Informal inquiries as well as applications, including curriculum vitae
and bibliography, cover letter describing candidate research interests
and past accomplishments should be sent via email to
pavlo.polishchuk@upol.cz.
Projekt: Development of 3D pharmacophore signatures and their application in the design of anticancer drugs
Vedoucí: Polishchuk Pavlo Ph.D., M.Sc.
K dispozici: 1
Určeno pro: Doktorské studium
Souhrn: 1 place in the face-to-face form of study
Projekt: In silico design of compounds with desired properties
Vedoucí: Polishchuk Pavlo Ph.D., M.Sc.
K dispozici: 2
Určeno pro: Doktorské studium
Souhrn: One of the main goals of chemoinformatics is development of new compounds with desired properties or activities. Many de novo design approaches were suggested so far. The designed compounds should satisfy multiple criteria, e.g. synthetic accessibility, novelty, diversity, selectivity, etc. Generators of chemical structures satisfying these criteria are a core of all de novo design approaches. Available approaches often result in synthetically hardly accessible structures or limit their diversity and novelty. Within this study a new fragment-based approach for structure generation will be implemented which will result in chemically valid structures and will provide flexible control over their diversity, novelty and synthetic accessibility. This will be used for development of de novo design approaches based on molecular docking, pharmacophore modeling to generate compounds which will be able to fit to a binding site of a given protein. This can be used for development of novel compounds and for optimization of structures of available ligands. Developed approaches should be implemented in open-source software tools.
Projekt: Development of 3D pharmacophore signatures and their applications to drug design
Vedoucí: Polishchuk Pavlo Ph.D., M.Sc.
K dispozici: 1
Určeno pro: Doktorské studium
Souhrn: Pharmacophore modeling is a powerful approach to encode possible protein-ligand interactions and searching of new promising compounds in large libraries. So far, almost all available software for pharmacophore modeling is proprietary and implemented approaches have some limitations to efficiently work with big data. Within this study a new approach to represent 3D pharmacophores as hashes will be implemented. This representation will make it possible to quickly identify similar pharmacophores in large data sets. This property can be used to develop a new alignment free approach to ligand-based pharmacophore modeling. The developed 3D pharmacophore hashes will help to identify representative pharmacophores retrieved from molecular dynamic simulation of protein-ligand complexes. These developments will increase success rates of future screening campaigns and should be implemented in open-source software.
Projekt: Modifications of biologically active molecules leading to improvement of their pharmacological properties
Vedoucí: Urban Milan Ph.D., Ranc Václav Ph.D., Polishchuk Pavlo Ph.D., M.Sc.
K dispozici: 3
Určeno pro: Doktorské studium
Projekt: Ligand- and structure-based modeling of biologically active compounds
Vedoucí: Polishchuk Pavlo Ph.D., M.Sc.
K dispozici: 1
Určeno pro: Doktorské studium
Projekt: New chemoinformatics approaches to fragment-based drug discovery
Vedoucí: Polishchuk Pavlo Ph.D., M.Sc.
K dispozici: 1
Určeno pro: Doktorské studium
Projekt: Development of 3D pharmacophore signatures and their application in anticancer drug design
Vedoucí: Polishchuk Pavlo Ph.D., M.Sc.
K dispozici: 1
Určeno pro: Doktorské studium
Projekt: Fragment-based de novo design using pharmacophore models
Vedoucí: Polishchuk Pavlo Ph.D., M.Sc.
K dispozici: 1
Určeno pro: Magisterské studium
Projekt: Computationally guided optimization of compound properties
Vedoucí: Polishchuk Pavlo Ph.D., M.Sc.
K dispozici: 1
Určeno pro: Magisterské studium
Projekt: Applicability domains in machine learning modeling
Vedoucí: Polishchuk Pavlo Ph.D., M.Sc.
K dispozici: 1
Určeno pro: Magisterské studium
Projekt: Novel 3D pharmacophore representation for machine learning
Vedoucí: Polishchuk Pavlo Ph.D., M.Sc.
K dispozici: 1
Určeno pro: Magisterské studium