Laboratory of Protein Engineering
A new laboratory for SARS-CoV-2 research is being established at BIOCEV
Starting from January 1, 2023, a new laboratory dealing with host-pathogen interactions and protein engineering will be established in the BIOCEV center under the 1st Medical Faculty of the Charles University. As the first subject of study, the laboratory will focus on SARS-CoV-2 virus and its interaction with human cells, which has been studied intensively by Dr. Jiří Zahradník since the beginning of the pandemic. The SARS-CoV-2 coronavirus has affected lives of all of us. In the following lines, the junior PI of the laboratory will present the main findings from his research and outlines of the future directions.
How did you get involved in SARS-CoV-2 research?
At the beginning of spring 2020, we met in the laboratory of prof. Schreiber at the Weizmann Institute in Israel and discussed whether we would join the global effort to study SARS-CoV-2. As a biochemist specializing in protein-protein interactions and working in interferon* research for almost ten years, I saw this as a good opportunity to put my knowledge into practice. Prof. Schreiber initiated the formation of a group of scientists planning to research various aspects of SARS-CoV-2. Thanks to this group, the Weizmann Institute obtained all the necessary resources for research in very short time. The Israeli government and other entities also quickly supported the coronavirus research. Thanks to both, we had all necessary samples and the funding in less than two months. I would like to thank everyone involved for an unprecedented effort.
What was your initial idea for SARS-CoV-2 virus research?
My idea was pretty simple, yet unconventional. The point was to use virus’s own weapon against it. By the weapon, I mean the so-called RBD – receptor binding domain, which together with other domains is forming the Spike** protein. This domain is responsible for binding to the ACE2 receptor protein on the surface of human airway epithelia cells. The purified domain by itself can compete for the binding site on the ACE2 receptor with the virus, thus representing a competitive inhibitor of virus entry into cells. To make the whole system work better, I proposed to apply protein engineering method that I was developing at the time (1) and create a modified RBD with tighter binding to ACE2. This will increase the competition potency of the modified molecules to inhibit binding. The acceptance of my idea among colleagues and collaborators at the Weizmann Institute was rather restrained. Their main argument was the notion that host-virus interactions are honed to perfection by evolution and that it will be very difficult to improve such an interaction. Fortunately, I was stubborn and remained undeterred.
Against all expectations and after two months of intensive work, I created RBD variants (RBD-62) with up to 600x stronger binding to the ACE2 receptor, which inhibited virus infection exceptionally well in tissue culture. What was unexpected, and why my research is so significant, was not the strength of the engineered interaction. It was a shocking similarity between the mutations found in the high-affinity RBD variants I obtained and those found in circulating viral variants including Omicron. The result of my research goes against the majority of previous research, which tried to dominantly attribute the emergence of these mutations to so-called immune evasion. However, my experiments took place strictly in a test tube, in vitro, and the immune system could not participate. Analysis of the molecular details of the RBD-62 in complex with ACE2 using cryo-electron microscopy explained why we observe a high prevalence of mutations to positively charged amino acids – lysine and arginine. These mutations increase electrocompatibility of the interaction between RBD and ACE2 and thus the interaction affinity. At the same time, such changes can also lead to evasion of antibodies, and the virus gains two advantages at once. It is therefore not surprising that we observe convergent evolution*** of these mutations in different regions and lineages of the virus (2). To some extent, it is possible to predict mutations that will become dominant over time, as we did with the pair Q498R and N501Y(3).
What are you doing now? What will you and your lab focus in the future?
I am focused on possibilities and improvement of mapping future mutations of the RBD domain and monitoring the changes that are currently taking place. My goal is to transform this knowledge into a tool for development of advanced vaccines and drugs that will be resistant to the emergence of new variants. The established laboratory will take these topics even further and focus on other similar systems. For example, we will be interested in the evolutionary processes behind changing the viral receptor that has been described, but details and the likelihood of such an event are unknown.
What will you deal with besides the SARS-CoV-2 virus?
We will deal with the development and application of protein engineering techniques for the sake of studying various biological phenomena. We will be especially interested in those that are very difficult to study by classical methods of structural biology, such as unstructured proteins. Another area of our interest will be proteins of the immune system and their targeted modulation. For example, stronger target cell response can be achieved by altering the binding properties of cytokine.
In conclusion, I just want to mention that I am looking for motivated students, from bachelors to postdocs.
*Interferons are small proteins. The name interferons refers to their ability to interfere (prevent) viral infection. During my doctoral thesis, I dealt with type II (so-called gamma interferon) under the supervision of prof. Bohdan Schneider. Prof. Gideon Schreiber at the Weizmann Institute specializes in type I interferons (alpha and beta interferons).
** Spike is the largest protein structure found on the surface of the coronavirus particle. Its name is derived from the characteristic shape of virus particles in electron microscope images. The main role of the Spike protein is to mediate the entry of the coronavirus into host cells.
*** Convergent evolution is a phenomenon where unrelated species evolve similarly. A simple example is the shape similarity between fish and cetaceans. In the case of SARS-CoV-2 we talk about convergent evolution at the molecular level. Unrelated virus lineages acquire the same mutations that give them an adaptive advantage. The same selection pressure acting on them is responsible for this phenomenon.