Structure-Based Drug Design in Medicinal Chemistry I. Development of Translesion Synthesis Inhibitors II. Synthesis and Biological Evaluation of Sulfonyl Piperazine Derivatives for LpxH Inhibition

Abstract

The identification of a promising lead compound is a crucial step for the drug development. Despite of a number of approaches, the optimization of promising hit compounds is still challenging. Structure-based drug design approach is a well established and widely used strategy based on the 3D atomic structure of proteins. The combined use of screening and computational method boost the search for lead compounds and optimization.The first part of the dissertation details studies of the development of translesion synthesis (TLS) inhibitors. Translesion synthesis is a major mechanism to enable bypass replication over DNA lesions. Lesion bypass is carried out by specialized TLS polymerases that use damaged DNA as templates and insert nucleotides opposite lesions, promoting mutagenic DNA synthesis. Since Rev1/Pol ζ-mediated translesion synthesis plays an important role in cisplatin-induced mutations, Rev1/Pol ζ interface is an attracted target for inhibition of TLS by small molecules. An ELISA assay has identified two promising hits for inhibition of Rev1/Rev7 interaction: quinolone scaffold RE01 and perhexiline maleate RE02. Our efforts for design, synthesis, and biological evaluation of analogs have led to the establishment of structure-activity relationships. Also, we have been developing novel synthetic approaches to extend a diversity of analogs and improve the activity. As an important step toward our goal of sensitizing cancer cells to cisplatin, additional in vitro studies reveal that RE01 sensitizes cancer cells to cisplatin and shows less mutation frequency than RE02, suggesting that RE01 is highly potent inhibitor of Rev1-mediated translesion synthesis. Moreover, the crystal structure of RE01-bound Rev1 along with modeling studies would facilitate the structural optimization of hit compound to improve the potency.The second part describes the synthesis and biological evaluation of LpxH inhibitors. Lipid A has a critical role in host response to bacterial infection and thus is required for the growth and survival of most Gram-negative bacteria. An effective therapeutic targeting lipid A biosynthesis can cure Gram-negative bacterial infections and sensitize infectious bacteria to other antibiotics. Essential and most widespread lipid A enzyme LpxH is an attractive target for the development of novel antibiotics. The AstraZeneca compound LH01 has been identified as an EcLpxH inhibitor. Based on the LH01 structure, we have prepared and evaluated a series of analogs for HiLpxH inhibition and the development of co-crystal structure. LpxH activity assays result in the identification of more potent inhibitors against EcLpxH, not HiLpxH. In addition, we have developed the photo-induced crosslinking probe to elucidate the binding mode of analogs. With the potential of analogs, we hope our analogs show good potency against different LpxH orthologs.The development process of lead compounds shown in this dissertationhighlights accomplishments as well as challenges, along with the value of structure-based lead optimization.