Drug discovery

Drug discovery

 

 Drug discovery is a whole process from the identification of compound synthesis, candidates, charact-erization, and assays for therapeutic efficacy to identify a compound as a potential drug. It needs the convergence of various scientific research areas, including biology, chemistry, and pharmacology.

 Our lab is working for finding the novel drug candidate. In addition to the kinase inhibitors, we are trying to discover the promising candidate molecules based on the PPI (protein-protein interaction) inhibition, PROTAC (Proteolysis-targeting chimera) technology.

Our research areas include:

Discovery of mutant FLT3 inhibitor as AML drug candidate

  • Acute Myeloid Leukemia(AML), which is the most common carcinoma of adult blood cancer, has the highest medical unmet needs among all types of leukemia. As 30% of AML patients have FLT3 mutations such as FLT3-ITD, FLT3-D835Y, kinase inhibitors targeting FLT3 are used for the AML patients who have FLT3 mutations.

  • However, current FLT3 kinase inhibitors revealed their limitation in terms of acquired resistance (ITD-F691L/D835Y) and poor kinase selectivity. Thus there is an emerging need for developing a new type of FLT3 drug that can broadly endure all kinds of FLT3 mutations.

  • To overcome FLT3 inhibitors induced mutation (ITD-F691L/D835Y), we designed over 300 kinds of novel derivatives, synthesized them, and analyzed SAR.

  • Our lead candidate DN200953 which is superior to the front runner drug gilteritinib (2018 FDA approved) in terms of in vivo potency against FLT3 ITD-F691L/D835Y Ba/F3 mouse model is now under clinical study (phase I).

First SAR Study for Overriding NRAS Mutant Driven Acute Myeloid Leukemia

(J. Med. Chem. 2018, 61, 18, 8353–8373.)

  • GNF-7, a multi-targeted kinase inhibitor selectively suppresses proliferation of AML patients driven cancer cells as well as AML cell lines bearing NRAS mutant by inhibiting ACK1 and GCK.

  • In our previous study, we identified GNF-7 derivatives which are superior to GNF-7 in terms of in vitro potency and differential cytotoxicity.

  • Among 29 GNF-7 derivatives, 10k shows favorable in vivo efficacy in Ba/F3-NRAS-G12D injected mice model and OCI-AML3 xenograft model without causing the prominent toxicity.

Reprinted with permission from (J. Med. Chem. 2018, 61, 18, 8353-8373). Copyright (2018) American Chemical Society.

   

   

Identification of KRAS inhibitors using novel strategies

  • KRAS is a small GTPase that converts GTP into GDP. KRAS transmit signals within cells (e.g. MAPK pathway), and KRAS overexpression/mutation can lead to cancer. Permanently activated KRAS mutants are found in 20 - 25% of all human tumors [up to 90% in certain types of cancer (e.g., pancreatic cancer)].

  • Although the KRAS mutants are attractive anti-cancer targets, they have been considered ‘undruggable’ targets in cancer research. The reason why the KRAS are considered undruggable targets is (1) strong binding affinity of RAS/GTP; (2) highly intracellular concentrations of GTP and GDP; (3) lack of drug-binding pockets.

  • Our KRAS targeting strategies are including: ​​

(1) Inhibiting the protein-protein interaction of KRAS and GEF (guanine nucleotide exchange factor)

(2) KRAS mutant degradation by the PROTAC platform.

Identification of kinase degraders based on the PROTAC technology

  • A PROTAC (Proteolysis-targeting chimera) is an emerging drug discovery platform that degrades disease-causing proteins through ubiquitin-proteasome system in cells. PROTACs are heterobifunctional molecules consisted of three parts: an E3 ligase binder, a warhead recognizing target proteins, and a linker. Once PROTACs form stable ternary complex (Target:PROTAC:E3 ligase) in cells, E2/E3 complex transfers a ubiquitin to target proteins. Subsequently, the ubiquitinated targets are recognized by proteasome where they are subjected to proteasomal degradation.

  • Owing to initial success of PROTACs to target key disease proteins including FLT3, androgen receptor (AR), and BRD4, a rapid growth in researches regarding PROTACs has been achieved.

  • With the help of PROTACs as a drug discovery platform, we have set our goals to surmount current limits of conventional kinase inhibitors particularly: a) acquiring high target selectivity, b) overcoming foregoing drug resistance, and c) targeting undruggable proteins.

  • Our current interests in PROTAC research program are namely:

                 1) Rational design and development of PROTACs aiming at undruggable targets such as Myc, 

                     RAS, and Tau protein.

                 2) Overcoming drug resistance arising from kinase mutations by using PROTACs.   

                 3) Identification of novel E3 ligase binders forming a stable ternary complex.

Medicinal Chemistry

 Medicinal chemistry deals with the design, optimization, and development of chemical compounds for their use as drugs. It is a multidisciplinary field of science, which is comprised of the synthesis of potential drugs and the investigation of their interactions with corresponding biological targets in order to grasp the knowledge of those medicinal effects of drugs, its metabolism, and possible adverse effects. In particular, medicinal chemistry, in common practice, encompasses synthetic organic chemistry focusing on small organic molecules, aspects of natural products, and computational chemistry in close combination with chemical biology, enzymology, and structural biology.

 

 Our researches concentrate on the development of kinase inhibitors, which are front runners in the signaling pathway because of their protein kinase inhibitory effect. Protein kinases comprise a major fraction of the signaling elements on whose activities the survival of cancer is dependent.

 

   Our recent accomplishments include:

  Identification of Novel Resorcinol Amide Derivatives as Potent and Specific PDHK Inhibitors

  (J. Med. Chem. 2019. 26;62(18):8461-8479.)

  • Pyruvate dehydrogenase kinases (PDHKs) promote abnormal respiration in cancer cells.

  • Among the resorcinol amide derivatives, we identified compound 19t which has highly potent and selective on PDHKs.

  • Also, 19n Induces OCR, ROS production, and mitochondrial depolarization by PDHK inhibition.

Reprinted with permission from (J. Med. Chem. 2019, 26, 62, 8461-8479). Copyright (2019) American Chemical Society.

  Development of a Selective and Potent Inhibitor of RET Gatekeeper Mutants

  (J . Med. Chem. 2016. 14;59(1):358-73.)

  • Aberrant RET kinase signaling plays critical roles in several human cancers such as thyroid carcinoma.

  • The gatekeeper mutants (V804L or V804M) of RET are resistant to currently approved RET inhibitors such as cabozantinib and vandetanib.

  • In our lab, for the first time, we reported a highly selective and extremely potent RET inhibitor(6i).

Reprinted with permission from (J. Med. Chem. 2016, 14, 59, 358-373). Copyright (2016) American Chemical Society.

   Discovery of a RET kinase inhibitor exhibiting enhanced metabolic stability

  (Eur. J. Med. Chem. 2017. 5;125:1145-1155.)

  • By hopping the scaffold of compound 6g, a novel and specific RET inhibitor was designed to enhance the metabolic stability.

  • Based on its exceptional kinase selectivity, great potency, and metabolic stability, 15l should be a key tool in studies aimed at understanding RET biology.

Identification of 1H-pyrazolo[3,4-b]pyridine derivatives as potent ALK-L1196M inhibitors

(J. Enzyme. Inhib. Med. Chem​. 2019. 34(1):1426-1438.)

  • ALK has received a great deal of attention as a promising therapeutic target for targeted cancer therapy for NSCLC pateints and, as a result, enormous efforts have been devoted to developing ALK inhibitors.

  • However, drug resistance caused by acquired secondary mutations in the ALK kinase domain still remained to be the major hurdle to overcome. The most frequent secondary mutation is the ALK gate keeper mutation L1196M.

  • Our SAR investigation led to identification of 10 g as a novel and potent inhibitior against ALK-L1196M (IC50 < 0.5 nM) as well as against ALK-wt (IC50 < 0.5 nM). The investigation has provided insight into new strategies to design novel and potent ALK-L1196M inhibitors that circumvent crizotinib resistance.

Ba/F3 panel

   

 Ba/F3 cells were originally isolated from murine bone marrow. The survival of Ba/F3 cells is entirely dependent on the presence of interleukin 3 (IL-3). (Ba/F3 cells without IL-3 are not able to survive in the culture media.) In 1988, Daley and Baltimore introduced Bcr-AbI gene which is main cause of chronic myeloid leukemia (CML), by using retroviral infection. This resulted in the transformation into Ba/F3 cells that could survive in the absence of IL-3. In addition, a number of studies demonstrated that the ectopic expression of constitutively activated kinase (e.g. NPM-ALK, FLT3-ITD, TEL-PDGFR and TEL-JAK2) is able to addict Ba/F3 cells.

 

 Thereafter, Ba/F3 cells have become a commonly-used model system not only for evaluating kinase inhibitor activity in drug discovery but also for exploring tumorigenesis of novel oncogenes. In our lab, we have more than 50 kinds of Ba/F3 cells harboring different kinases and utilize them to assess a cellular potency of novel kinase inhibitor for drug discovery.

Copyright © 2020 Chemical Kinomics & Innovative Drug Discovery lab.