Document Type



Doctor of Philosophy (PhD)


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First Advisor's Name

Yuk-Ching Tse-Dinh

First Advisor's Committee Title

Committee chair

Second Advisor's Name

Watson Lees

Second Advisor's Committee Title

Committee member

Third Advisor's Name

Yuan Liu

Third Advisor's Committee Title

Committee member

Fourth Advisor's Name

Fenfei Leng

Fourth Advisor's Committee Title

Committee member

Fifth Advisor's Name

Manuel Barbieri

Fifth Advisor's Committee Title

Committee member


topoisomerases, DNA, drug discovery, antimicrobial resistance, antibiotic resistance, COVID-19, SARS-CoV-2, HTOP3B, bacterial topoisomerase I, HTOP1, inflammation, sepsis, septic shock, drug repurposing, in-silico screening, SAR

Date of Defense



DNA topoisomerases are universal enzymes that control the topological features of DNA in all forms of life. This study aims to find potential inhibitors of some of the DNA topoisomerases in bacteria and humans that can be developed into potential therapeutics.

The first aim of this study is to find potential inhibitors of bacterial topoisomerase I that can be developed into antibiotics. There is an urgent need to develop novel antibiotics to overcome the world-wide health crisis of antimicrobial resistance. Virtual screening and biochemical assays were combined to screen thousands of compounds for potential inhibitors of bacterial topoisomerase I. NSC76027 inhibits the topoisomerase I of Mycobacterium tuberculosis and Escherichia coli with IC50 values of 2-3 µM, and MIC values for growth inhibition of several mycobacteria including M. tuberculosis at 12.5 – 50 µM. The mechanism of action of this compound depends on the presence of the C-terminal region of the target enzyme. Structurally similar compounds were studied to understand the Structure-Activity-Relationship that governs the antibacterial activity of this compound.

The second aim of this study is to find potential inhibitors of human topoisomerase IIIβ, which is hijacked by positive-sense ssRNA viruses including SARS-CoV-2 for viral replication. In this study, several drugs that had been previously approved for other uses were identified as potential drug repurposing candidates against this enzyme. The anticancer agents venetoclax, dactinomycin, and Bemcentinib showed inhibition of this enzyme. Moreover, some polyamines belonging to the Torrey Pines Institute combinatorial libraries were found to inhibit HTOP3β. These drugs and molecules are candidates for evaluation of antiviral activity in follow up studies.

The third aim of this study is to find catalytic inhibitors of human topoisomerase I that can be useful in sepsis treatment. This enzyme facilitates the expression of the genes responsible for sepsis. A novel yeast-based screening system was developed and successfully used in this study to achieve this goal. NSC76028 was found to be a catalytic inhibitor of HTOP1 that can avoid the cytotoxic effect of poison inhibitors. Further investigations are required to determine the exact mechanism of action of NSC76028 and its impacts on human cells.




Previously Published In

Seddek, A.; Annamalai, T.; Tse-Dinh, Y.-C. Type IA Topoisomerases as Targets for Infectious Disease Treatments. Microorganisms 2021, 9, 86.



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