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Alpha-Ketoamide Inhibitors of the SARS-CoV-2 Main Protease

Rolf Hilgenfeld, PhD, Professor, Institute of Molecular Medicine, University of Luebeck, Germany

At the forefront of battling coronaviruses since 1998, Dr. Rolf Hilgenfeld is focused on determining the mechanism of alpha-ketoamide inhibitors against the novel coronavirus main protease. He recently shared with Emily Le, conference producer of Therapeutic Pipeline for COVID-19, his current efforts to develop a COVID-19 therapy, which brought him out of retirement from research.

EL: Dr. Hilgenfeld, tell us why you are honing in on developing this class of compounds called alpha-ketoamide inhibitors against the novel coronavirus protease. What hypothesis led you to this path?

RH: We determined the crystal structure of the SARS-CoV-2 main protease by early February 2020 (Zhang et al., 2020a, Science 368, 409-412), and used this structural information to optimize the peptidomimetic alpha-ketoamide inhibitors that we had previously designed for other coronavirus main proteases such as those of SARS-CoV-1, MERS-CoV, HCoV NL63, and the bat-CoVs HKU4 and HKU9 (Zhang et al., 2020b, J. Med. Chem. 63, 4562-4578). Our current lead inhibitor, compound 13b, has an extended half-life and can be administered to mice by subcutaneous injection or by inhalation. Twice-daily inhalation at 20 mg/kg results in good levels of the compound in the lung epithelial lining fluid. Systemic application at 50 mg/kg leads to good compound levels in several organs after 24 hours. Further developments will be discussed during my talk.

EL: Can you please tell us about your background and current role.

RH: I was trained as a chemist and later turned biochemist and structural biologist. After obtaining a PhD in macromolecular crystallography at the Free University of Berlin in 1986, I moved to the pharmaceutical giant Hoechst AG (now Sanofi) in Frankfurt. It was here that I built a macromolecular crystallography lab. After my post-doc at the Biocenter in Basel, Switzerland, I returned to Hoechst in 1988 to help design the long-acting insulin Lantus, which reached annual sales of $7 billion in the years after 2000. I also worked on designing inhibitors for HIV-1 protease. In 1995, I accepted a professorship in Structural Biochemistry at the University of Jena and since 2003, I have been at the University of Luebeck as a Professor of Biochemistry and Director of the Institute of Biochemistry. I officially retired in March this year and currently hold a Senior Professorship at the Institute of Molecular Medicine.

EL: The world has been turned upside-down by the novel coronavirus and scientists have been scrambling to figure out potential treatments. A lot of companies and labs have just started working on COVID-19 this year. However, you have an incredibly unique experience of working on coronaviruses for many years. What triggered your interest in studying the novel coronavirus and when did you start your career as a researcher in this field?

RH: Indeed, I have been working on coronaviruses since 1998 — even before the outbreak of SARS-CoV-1 in 2003. I was always interested in proteases; and having worked on the HIV-1 protease during my time in the pharmaceutical industry, I was wondering why the coronavirus main protease is so much bigger than the retroviral protease. So I decided to determine crystal structures of these enzymes. We first determined the structure of the main protease of Transmissible Gastroenteritis Virus (TGEV), a coronavirus that infects pigs and kills young piglets with a very high fatality rate. Then we turned to Human Coronavirus 229E and determined the three-dimensional structure of its main protease and also designed some inhibitors. This was published during the peak of the SARS-1 outbreak in 2003. Subsequently, we determined the structures of many inhibitor complexes of the SARS-CoV-1 main protease; and also, those of several other components of the coronavirus replication complex, including several domains of non-structural protein 3 (Nsp3), and then Nsp7-8 and Nsp9). 

Since the MERS outbreak of 2012, we intensified our efforts to find useful inhibitors of the coronavirus main protease and started designing and developing alpha-ketoamides. We just had started developing our second generation of this compound class when COVID-19 arrived. Within two weeks after the publication of the genomic sequence of the new virus, we had determined the crystal structure of its main protease, as a free enzyme and as complex with our current alpha-ketoamide lead compound (compound 13b).

EL: What makes your approach different?

RH: Our main technology is structure-based drug design. Many people think that virtual screening and drug repurposing is easier and faster, but this view is not supported by the current successes, at least as long the target is the viral main protease.

EL: What stage are you now at with your candidate?

RH: We just entered testing in small-animal models for COVID-19, i.e., a mouse model and a hamster model. We do these experiments in collaboration with groups in Marburg, Germany, and in Leuven, Belgium.

EL: What is the future of research in coronaviruses? 

RH: The future should be bright if the funding exists. Here is my big worry: funding levels may well decline when the pandemic is over. That is exactly what happened after the SARS-1 outbreak. From about 2006 onwards, it was getting more difficult to obtain sufficient funding.

EL: There are two major types of therapy that people are pursuing for COVID treatment at the moment: either antibody or small molecule. In your opinion, which has more potential? 

RH: Both have their justifications and merits. Of course, an efficacious small-molecule therapy will be much more affordable than an antibody therapy.

EL: What do you personally think — can we expect a successful COVID-19 therapy in the market, say, by the end of this year?

EL: If an existing drug is discovered that has already been approved for another indication, then this could be before the end of the year. But apart from Gilead Science’s remdesivir, which has been proven to have limited efficacy against COVID-19, and, for severe cases, perhaps dexamethasone, nothing much has been discovered so far. This is not good news as the expectations are so high. I believe that successful drugs specifically designed for COVID-19 will not be in the market before 2025 or so.

EL: What talk(s) are you looking forward to the most at this Therapeutic Pipeline for COVID-19 meeting?

RH: I look forward to the whole meeting, I am sure I will be able to learn a lot!

If you would like to hear Dr. Rolf Hilgenfeld live at the Therapeutic Pipeline for COVID-19 Virtual Meeting, register today with a 30% Discount Promo Code: interview30 (Apply before checkout).

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