For our August Newsletter we featured a story on one of you RAPc projects submitted by Dr. Steve Almo’s group at the Albert Einstein College of Medicine. Dr. Almo was kind enough to answer a few questions for us, which can be read in their entirety below.
Tell me about yourself and your lab and your SARS-CoV-2 project with NCCAT.
Steven Almo: We are a lab using structure guided approaches to define molecular mechanisms in order to develop new therapeutic strategies. We have a particular interest in novel biologic strategies as well as small molecule discovery. All of our thinking begins with structural and mechanistic principles, with the ultimate goal of real clinical impact.
With NCCAT we have begun to work on the structural characterization of the SARS-CoV-2 Spike protein. Our first efforts were met with remarkable success; with the tremendous assistance of the NCCAT staff, we were able to reproduce (at 3.2 Angstrom resolution) the reported structure of the SARS-CoV-2 Spike protein; our first structure determination took shape in less than 48 hours. For us, this was absolutely remarkable, and a true testament to the phenomenal infrastructure that NCCAT has assembled. We are now using this structure as the foundation to determine the structures of the SARS-CoV-2 Spike protein bound to Fab fragments derived from broadly neutralizing antibodies cloned from the B cells of convalescent patients at Montefiore Medical Center (with Jon Lai and Kartik Chandran). These studies will define the mechanisms responsible for the clinical activity of these naturally occurring antibodies and may afford new therapeutic opportunities. As I write this, Anthony Fauci in his opening statement to the House of Representatives has just referenced the cryo-EM structure of the Spike protein, underscoring the importance of these studies.
What did you work on before COVID?
SA: For all of our projects, we take a biochemical/mechanistic approach, and leverage a variety of high-throughput technologies for protein production and a spectrum of tools for the discovery of new cell surface protein interactions and immunological profiles. We focus on two areas:
1) Structural, mechanistic and functional analysis of the cell surface proteins that regulate immunity, especially T cell immunity. We have determined a number of structures using X-ray crystallography of the central cell surface immune molecules and defined unique mechanistic features that have supported novel strategies for the rational control of the immune system to treat cancer, autoimmune diseases and infectious diseases. This work resulted in the founding of Cue Biopharma, a cutting-edge immunotherapy company located in Cambridge, MA (https://www.cuebiopharma.com/).
2) Discovery and annotation of enzyme function/mechanism and new metabolic pathways. This work takes advantage of our HTP gene-to-function platform capabilities. We have a particularly unique resource for the study of oxygen-sensitive proteins, which is the only infrastructure in existence supporting HTP structural (X-ray) and functional genomics capabilities in an anaerobic environment (i.e. oxygen-free) (http://www.nysgxrc.org/psi3/anaerobic.html). These capabilities have resulted in the discovery of a variety of new therapeutic opportunities, including new naturally occurring antiviral drugs and new targets for small molecule interventions to treat inflammation, gastric cancer and ulcers.
How has the pandemic affected your work?
SA: On a personal level, we have experienced the same surreal effects that have been shared nationally and globally. Ghost-like occupancy of Albert Einstein, nearly empty lab (due to CDC safety limits), the need to perform work in shifts and meetings by Zoom.
Scientifically, we have been fortunate, as many of the approaches, technologies and areas of scientific focus (e.g., controlling the human system for viral control, discovering/developing new small molecule targets to inhibit viral genome replication and general inflammatory processes, and microarray technologies for immune profiling, and our passion for structure) were immediately applicable to studying basic viral mechanisms and developing new therapeutic strategies to treat COVID-19. (I can provide specific examples if desired). Fortuitously, we were very well positioned to pivot to COVID-19 research, while maintaining the overall focus of our research program.
Immediately after the pandemic became apparent, members of my lab (Natalia Herrera, Nick Morano and Scott Garforth) began working on multiple fronts, the initial being a collaborative effort with Einstein colleague Jon Lai to develop enhanced expression systems for the two most commonly utilized expression constructs for the Spike protein. All of this work was deemed “essential” so my lab personnel were allowed access to the laboratories, of course with all of the proper social distancing, PPE and safety measures.
Tell me a bit about your life in lockdown (e.g. interesting coping mechanisms, new day to day).
SA: I am not sure that I needed to implement any new coping mechanisms, as much as I needed to emphasize my overall philosophy (adopted from Seinfeld) of “Serenity now, sanity later”. Increased patience and proper calibration of expectations are essential, as everyone is experiencing uncharted challenges.
Where there any roadblocks or bottlenecks you needed to overcome for this project?
SA: Most surprisingly, and most satisfyingly, my group, department and the entire Einstein administration were wholly successful in making Einstein a safe working environment (both physically and psychologically). Incredibly, we did not hit any real bottlenecks.
What assistance was provided by the group at NCCAT?
SA: NCCAT was absolutely remarkable in the assistance they provided, including taking possession of protein samples (Spike protein) early in the morning and performing all aspects of grid preparation, initial screening, data collection and processing and structure characterization and manuscript preparation. Ed, Laura, Alex, Clint and Bridget were always available for zooms, etc.
Ed and Laura in particular exhibited extreme patience in his tutelage, providing basic training, instruction, and guidance in the cryo-EM process, in addition to conducting processing and reconstructions. Jeff Bonanno in our lab is now self-sufficient in the data processing/structure determination process, aided in this evolution by the fact that he is a professional structural biologist/crystallographer.
In your opinion is this virus a sign of end of days?
SA: This is most definitely not the end of days, but it is an inflection point for a number of institutions and practices that are taken for granted. What will the future of higher education look like? Sea changes in higher education were evident with the enormous surge of on-line course work that is increasingly available (e.g., EDx; https://www.edx.org/). The work place will not be the same, as a considerable fraction of the meetings with which we are familiar, apparently can be easily performed on-line. I also think that recent events underscore the need to objectively evaluate the viability of a number of professions and begin to develop a realistic blueprint for the economy of the future. Perhaps most relevant to NCCAT, recent events will likely significantly impact the focus of biomedical research (i.e., infectious diseases), at least in the near to intermediate term.
So, these are not the end of days, and in fact, many unique opportunities are now at hand. However, while we can enthusiastically discuss all of the new scientific opportunities, we need to always temper our actions and responses with the understanding that real patients are suffering and that it is our responsibility to let this fact drive our daily work in the laboratory.
Is there anything you learned during your time in lockdown?
SA: I am not sure that I learned anything new, but these challenges highlighted how truly independent and committed my lab members are, and how expendable I am. I could not be more proud of my lab!
I also learned that my house is way too small. With me, my wife (Anne Bresnick, another Professor in the Department of Biochemistry) and (especially) two 16-year old daughters at home who were engaged in distance learning, there was never sufficient space for me to stay out of trouble – this gave new meaning tosocial distancing.
Can you think of any silver linings to come out of this pandemic?
SA: Scientifically, the pandemic gave me the first real opportunity to perform cryo-EM. All of our previous structural targets were well suited for crystallographic approaches and too small for cryo-EM. In contrast, the SARS-CoV-2 Spike protein is ideally suited for our introduction to cryo-EM. We are now sold on the remarkable power of cryo-EM.
Additionally, while Einstein has always been an enormously collaborative institution, the challenges of the pandemic resulted in even greater synergy and collaboration. Even more gratifying has been the remarkable interactions between the basic science investigators and the clinicians at Einstein and Montefiore Medical Center. These interactions have resulted in new clinical tests for SARS-CoV-2, new grant applications and new manuscript submissions, which required the participation of basic, translational and clinical investigators.