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Alexey R, Dariya S, Liudmyla I, Lilia V, Valeriy M, Dmytro L, Oleksandr B, Svitlana S, Sergii O, Elijah B, Mariia S, Yaroslav B, Pavel K. Structure-based virtual screening and biological evaluation of novel inhibitors of mycobacterium Z-ring formation. J Cell Biochem 2022; 123:852-862. [PMID: 35297088 DOI: 10.1002/jcb.30232] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Revised: 02/04/2022] [Accepted: 02/08/2022] [Indexed: 11/07/2022]
Abstract
The major part of commercial prodrugs against Mycobacterium tuberculosis (Mtb) demonstrated a significant inhibitory effect on cell division and inhibition of bacterial growth in vitro. However, further implementation often failed to overcome the compensatory system of interchangeable cascades. This is the most common situation for the compounds, which hit the key enzymes activities involved in all basic stages of the cell cycle. We decided to find more compounds, which could affect a cytoskeleton complex playing important role in sensing the external signals, intracellular transport, and cell division. In general, the bacterial cytoskeleton is crucial for response to the environment and participates in cell-to-cell communication. In turn, filamentous temperature-sensitive Z (FtsZ) protein, a mycobacterial tubulin homolog, is essential for Z-ring formation and further bacteria cell division. We predicted the most preferable binding-sites and conducted a high-throughput virtual screening. Modeling results suggest that some compounds bind in a specific region on the surface Mtb FtsZ, which is absent in human, and other could hit GTPase activity of the FtsZ. Further in vitro studies confirmed that these novel molecules can efficiently bind to these pockets, demonstrating an effect on the polymerization state and kinetics mechanisms. The rescaling of the experiment on the cell line revealed that reported compounds are able to alter the polymerization level of the filamentous and, therefore, prevent mycobacteria reproduction.
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Affiliation(s)
- Rayevsky Alexey
- Institute of Food Biotechnology and Genomics, National Academy of Sciences of Ukraine, Кyiv, Ukraine
- Department of Molecular Modeling, Enamine Ltd., Kyiv, Ukraine
| | - Samofalova Dariya
- Institute of Food Biotechnology and Genomics, National Academy of Sciences of Ukraine, Кyiv, Ukraine
- R&D Department, Life Chemicals Inc., Niagara-on-the-Lake, Ontario, Canada
| | - Ishchenko Liudmyla
- Ukrainian Laboratory of Quality and Safety of Agricultural Products, National University of Life and Environmental Sciences of Ukraine, Kyiv, Ukraine
| | - Vygovska Lilia
- Ukrainian Laboratory of Quality and Safety of Agricultural Products, National University of Life and Environmental Sciences of Ukraine, Kyiv, Ukraine
| | - Mazur Valeriy
- Ukrainian Laboratory of Quality and Safety of Agricultural Products, National University of Life and Environmental Sciences of Ukraine, Kyiv, Ukraine
| | - Labudzynskyi Dmytro
- Palladin Institute of Biochemistry, National Academy of Sciences of Ukraine, Kyiv, Ukraine
| | - Borysov Oleksandr
- Department of Molecular Modeling, Enamine Ltd., Kyiv, Ukraine
- Institute of Organic Chemistry, National Academy of Sciences of Ukraine, Kyiv, Ukraine
| | - Spivak Svitlana
- Institute of Food Biotechnology and Genomics, National Academy of Sciences of Ukraine, Кyiv, Ukraine
| | - Ozheredov Sergii
- Institute of Food Biotechnology and Genomics, National Academy of Sciences of Ukraine, Кyiv, Ukraine
| | - Bulgakov Elijah
- Institute of Food Biotechnology and Genomics, National Academy of Sciences of Ukraine, Кyiv, Ukraine
| | - Stykhylias Mariia
- Institute of High Technologies, Taras Shevchenko National University of Kyiv, Kyiv, Ukraine
| | - Blume Yaroslav
- Institute of Food Biotechnology and Genomics, National Academy of Sciences of Ukraine, Кyiv, Ukraine
| | - Karpov Pavel
- Institute of Food Biotechnology and Genomics, National Academy of Sciences of Ukraine, Кyiv, Ukraine
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