Interaction targeting CoV therapeutics

I am a senior postdoctoral scientist at Dana-Farber Cancer Institute and Harvard Medical School interested in developing new therapeutic molecules for COVID-19. While pursuing my Ph.D., I have done extensive research in Pharmacology, utilizing a variety of chemical and genetic tools to specifically modulate molecular pathways and to monitor their cellular responses. During my postdoctoral training, I began to work on technology developments to quantitatively measure the formation and disruption of protein-protein interactions (PPIs) and to enable a high-throughput drug discovery against PPIs. Given the COVID-19 pandemic severely threatening human life, I want to contribute to the solution of this unprecedented public health challenge by developing new molecules that target viral PPIs of SARS-CoV-2. With new experimental approaches I developed, I will identify novel drug molecules that current mainstream drug discovery efforts are blinded to. PPI targeting drugs will offer higher selectivity and persistent efficacy in continually evolving coronaviruses. 

The COVID-19 pandemic poses an unprecedented, ongoing threat to humanity; claiming over a half million lives globally in last five months. Given no cure or vaccines are currently available despite decades of research on coronaviruses, developing an effective therapeutic is a daunting challenge, but is the only remaining option. One of the major difficulties is our narrow focus on only a small subset of viral proteins such as enzymes and receptors for antiviral drug development. To address this limitation, I developed a new approach enabling the discovery of novel molecules in any functional proteins within a protein complex. By focusing on a protein complex with multiple subunits, a deeper and wider chemical screening against essential viral proteins can be performed unbiasedly. I am focusing on discovering drugs inhibiting the Replication Transcription Complex (RTC) of SARS-CoV-2. If successful, this project will lead to development of effective therapeutics complementary to traditional drugs.

We are aiming for the preclinical development of COVID-19 therapeutics based on targeting PPIs of the RTC of SARS-CoV-2. It is a global problem currently with 13 million infected people and 0.5 million casualties. The United States is the epicenter of this pandemic currently with 3.4 million infections and 137,000 casualties. Since no cure or vaccines are available, these numbers are trending upwards, and the pandemic will not end unless 60% of the population are infected to gain a population level immunity, which would result in 10 ~ 60 times more deaths. PPIs between subunits of the RTC are crucial in the viral life cycle, evolutionally well-conserved among coronaviruses. Thus, PPI targeting therapeutics would be highly effective under the rapid evolution of SARS-CoV-2, yet mainstream drug developments have neglected PPIs. While incompletely understood, main constituents of the RTC are viral non-structural proteins, which collectively carry out multiple essential functions such as RNA-dependent RNA transcription, 5’ capping, and 3’-5’ proofreading activities all requiring PPIs. I developed a strategy to successfully identify highly potent PPI targeting molecules based on phenotypic screening. As successfully demonstrated this concept with a HDAC complex, this project will result in effective therapeutic molecules complementary to traditional approaches.

The goal of this project is to develop effective COVID-19 drugs by inhibiting the function of a viral protein complex involving genome replication of SARS-CoV-2. In traditional drug discovery approaches, it requires prior settings such as a well-defined biochemical activity of individual proteins in isolation, pre-determined protein or co-complex structures, or live coronaviruses for phenotypic screening. Our approach directly measures the activity of a protein complex allowing a high-throughput drug screening without an extensive optimization for individual proteins, biosafety level-3 containment, or pre-determined protein structures. Briefly, we use a reporter where structural and accessory proteins of SARS-CoV-2 are all deleted in the genome, but are replaced with a reporter, either nanoluciferase or URA3. The expression of the reporter requires a full activity of the RTC including RNA-dependent-RNA transcription and 5’ capping functionally unique to the viral RTC that any host proteins cannot induce the reporter expression. Compounds inhibitory to the RTC can be identified by significantly reduced reporter expression. Once inhibitory compounds are identified, they are tested for the disruption of individual PPIs of the RTC using highly quantitative, reversible PPI assays. Highly potent PPI-disrupting compounds are then tested with live viruses in animal models to move toward clinical developments.

This project serves all humankind, but it would likely help most the economically disadvantaged who lack access to medical facilities for COVID-19 treatment. There is an urgent need to develop therapeutics for the COVID-19 pandemic, yet at this stage, no clear outlook is presented with neither highly effective small molecule drugs nor functioning vaccines. Orally administrable, small molecule drugs are highly effective for mass production, and are more easily transported to rural areas than biologics such as vaccines, thus offering complementary advantages to cope with the pandemic and to support venerable populations. Since the continuous evolution of SARS-CoV-2 presents an unprecedented challenge to maintain the efficacy of drugs and vaccines, PPI targeting small molecule drugs which are resistant to viral evolution in coronaviruses. Such targeting would remain effective, not only for this pandemic, but also future outbreaks. 

My project most closely addresses “Elevating issues by driving action to solve the most difficult problems of our world”, as it tackles developing new types of therapeutics for the COVID-19 pandemic. The current situation is characterized by an uncontrolled spread of viral infection and mortality far beyond initial expectations. Thus, it is devastating numerous countries and communities, but hitting hardest the economically disadvantaged, ethnic minorities, and indigenous populations. It is truly worrisome that this pandemic may lead to the extinction of those unprotected communities and indigenous groups without quick access to medical care. We may not have enough time. 

The idea was originally conceived three months ago, when I discussed it with Professor Sam Kunes at Harvard who is familiar with my research targeting PPIs of a protein complex for drug discovery. In my own research, I demonstrated a strategy to discover small molecules that inhibit the function of an HDAC complex using high-throughput phenotypic screening in yeasts and mammalian cells. By building a transcriptional reporter whose expression is strongly suppressed by the HDAC complex, compounds inhibitory to the HDAC activity could be rapidly identified by increased reporter activity. PPI disruptive compounds were then identified when a combination of high-performance binary PPI assays was applied, which can quantitatively measure both inhibited or stabilized PPIs upon treatment of compounds. Identified PPI-disrupting molecules showed a far superior target specificity and tolerance in animals than traditional HDAC enzymatic inhibitors. This strategy is essentially adapted to discover highly potent and specific molecules that disrupt PPIs of the RTC of SARS-CoV-2. RTC is essential in viral replication enriched with PPIs between subunits. Since Professor Kunes is an expert in regulatory RNA structures with his prior work with David Botstein, we first made a core team for this project which is expanding with other collaborators. 

Reflecting the severity of the public health crisis caused by the COVID-19 pandemic, numerous people I know personally have been affected by this pandemic, losing their parents, close friends, and livelihoods. Unless effective vaccines and therapies become widely available, it is inevitable that this pandemic will last for many years and the number of deaths will grow much larger than the current 550,000. It is not only a public health crisis, but is also harming the fundamental values of our society, education, and economy. Nobody remains safe, and semi-permanent confinement adversely affects our lives. As an expert in drug discovery and technology development, and with experience successfully discovering drugs for specific PPIs of a protein complex, I recognize that I can contribute to making new types of highly effective drugs that target PPIs of SARS-CoV-2.  Working with prominent scientists and in leading research environments in greater Boston, I would like to contribute to developing effective COVID-19 therapeutics based on targeting viral PPIs. Given the complementarity of drug targets and biological functions with traditional drugs, my PPI-based drugs will provide orthogonal solutions to pre-existing concepts and technologies.  

I have a unique combination of research skills and experiences that well equip me to spearhead drug discovery against PPIs of SARS-CoV-2. PPIs are emerging drug targets expanding traditional druggable proteins such as enzymes, kinases, and receptors, as new technologies and concepts are being actively developed. While they are attractive drug targets, PPIs have not been widely considered for drug discovery in industry. I recently demonstrated the successful identification of PPI-disrupting small molecules for an HDAC complex involving epigenetic gene regulation. The success of the discovery of PPI-targeting molecules is represented by a series of innovations including 1) markedly increased detection efficiency of PPIs within a protein complex, 2) a high-throughput phenotypic screening strategy to robustly monitor the activity of the target protein complex, and 3) the integration of robust validation steps to identify “on-target” PPI-disrupting molecules. For SARS-CoV-2, I already began to build a robust screening pipeline to identify specific inhibitory molecules for the RTC activity, and interactome mapping is underway to identify specific PPIs between RTC subunits using high-performance PPI assays. I am perhaps one of only a few people worldwide capable of conducting this type of research, as I am an original investigator who developed a novel drug discovery paradigm to bridge fast and efficient drug discovery against PPIs in “protein complexes” and performed benchmarking experiments with multiple complementary PPI assays to efficiently identify compounds disrupting PPIs. Furthermore, the Consortium for COVID-19 therapeutics provides a mechanism to deliver the initial discovery of promising compounds to clinical developments. 

I have a very strong desire to excel in my profession. While I have always worked very hard, I lacked the energy. My mental and physical capabilities were not strong; I exhausted quickly, compromised my goals, and performed at a suboptimal level. This struggle led me to join the Republic of Korea Marine Corps, one of the most formidable, elite military forces in the world. Only a few pass muster and complete training to become Marines. Like our blood brothers, USMC, we share core values for realizing a free world. Three years of training in the Marines consistently challenged me to surpass the limit of my mental and physical capacities. There was no single easy day; I spent months in the wilderness, endured tough physical training such as “Hell Week”, and performed high-quality operations in constantly changing situations. The training transformed me into a capable person who can work as a team and overcome numerous difficulties. I now have the attitude that simply will not give up unless I die, and I exert all efforts to actualize goals. I believe that my team has the capability to deliver this project and yield new molecules potentially highly effective for treating COVID-19.

As a postdoctoral fellow in Marc Vidal’s lab, I became interested in developing drugs that target PPIs. Given that there are ~60,000 PPIs in the human proteome, while lacking effective chemical tools to target them, my research addresses this challenge. I first secured research funding from the Claudia Adams Barr Award to initiate this project. This allowed me serving as a principal investigator and recruiting research collaborators. With three PPI inhibitory molecules identified from the screening against the HDAC complex, I connected with experts in structural biology, chemistry, and disease models. Collaborating with Arthanari and Dhe-Paganon labs at DFCI, we identified how molecules bind to the target protein and disrupt PPIs at atomic resolution. Chemistry expert Sara Buhrlage at DFCI tested structural analogs and identified core-scaffolds for efficient molecule design. With Kimberly Stegmaier, an expert in oncology at DFCI, we identified how our compounds are selective to target genes in neuroblastoma. With Javier Gonzalez-Maeso, an expert in neurological disorders at Virginia Commonwealth University, we tested how selected compounds are functional in the brains of animals. By coordinating the project with diverse experts, I demonstrated how I can lead many people and groups to make timely progresses and generate important discoveries.

My project team and collaborators are located at Harvard University and Harvard Medical School. I work as a co-principal investigator of the project with professor Sam Kunes and will collaborate with other core researchers. As a leading academic institution, Harvard has abundant resources that can maximize the success of the drug discovery against the RTC of SARS-CoV-2. Discoveries and technological innovations from this work will be shared with the host institution.

My project is disruptive, as I am aiming to discover COVID-19 therapeutics encompassing outside of traditional druggable proteins by targeting protein-protein interactions (PPIs) of SARS-CoV-2. While the project is challenging, I think that it offers unique advantages over traditional approaches by examining viral proteins and biological mechanisms outside of the current mainstream approach which are somewhat confined to "known knowns" also described as a phenomenon called “looking under the lamppost”. As a scientist developed new methods for highly sensitive PPI detection (Choi et al, Nature Communications, 2019) and discovered PPI-targeting molecules based on high-throughput phenotypic screening (Choi et al, provisional patent submitted, 2020), I see that this innovative approach can be used to facilitate the development of new types of highly effective COVID-19 therapeutics the current approaches have not been successful thus far.

In one year, limited numbers of people such as hundreds can be clinically tested with the therapeutic candidate molecules from this study. In five years, if the compound(s) is found to be effective in human patients, it will be administered to millions of patients to treat their COVID-19 symptoms. 

Within the next year, I will identify top one or two molecules that display highly potent and specific PPI inhibitory activity for SARS-CoV-2. After animal tests of the top compounds using live SARS-CoV-2, we will begin to work with the pharmaceutical industry and other research labs at Massachusetts Consortium on Pathogen Readiness to optimize the efficacy of the molecules and to coordinate clinical trials of the finalized candidate molecule in human patients. Within the next five years, if successful, we will continue to work on developing PPI targeting drugs not only for coronaviruses but also other deadly pathogens such as cholera and zika virus affecting lives of vulnerable populations and indigenous communities in rural areas. 

The first barrier would be securing a funding for research, as the study cannot properly progress without financial supports regardless of innovation or importance of the research subject. Thus, elevate prize is quite important for us to provide an initial vital support. Once highly potent, specific PPI inhibitory compounds are identified for the RTC of SARS-CoV-2 within the first year, next challenge will be making the compounds highly effective in humans. At this stage, this type of works can be the best performed in pharmaceutical industry who can invest ample resources to optimize the chemical structure of molecules to improve in vivo efficacy. Through the Consortium of COVID-19 therapeutics and the intellectual property office of the home institution, we will find industry and academic collaborators to move this project towards clinical applications.

As an academic researcher who has new ideas and emerging technologies for COVID-19 therapeutics, yet we don’t currently have dedicated resources to adequately pursue this project. My team needs the prize, which can provide vital supports to purchase reagents and laboratory consumables for conducting a high-throughput screening and the interactome mapping of the viral complex and to hire a research scientist to experimentally support various drug discovery assays. The prize will greatly boost the research project and chances of successfully identifying new types of molecules effective to cope with the COVID-19 pandemic.