July 28 is World Hepatitis Day. We spoke with Biophysical Society members whose research focuses on viruses, including hepatitis B. Hepatitis B is a potentially life-threatening liver infection caused by the hepatitis B virus (HBV). It can cause chronic infection and puts people at high risk of death from cirrhosis and liver cancer. According to the World Health Organization, an estimated 257 million people are living with hepatitis B virus infection.
In recognition of World Hepatitis Day, Jodi A. Hadden and Juan R. Perilla, both University of Delaware, and JC Gumbart, Georgia Tech, filled us in on their research related to HBV.
Jodi A. Hadden and Juan R. Perilla
What is the connection between your research and hepatitis?
We employ all-atom molecular dynamics simulations to study fundamental cellular processes, such as viral infection. Hepatitis B is one of several viruses we are currently investigating (Hadden et al. eLife 2018; Perilla et al. Journal of Physical Chemistry Letters 2016). Thus far, our research has focused on the capsid of hepatitis B, a protein shell that encloses the viral genome and drives its delivery to the host cell nucleus. We have performed simulations of the empty hepatitis B capsid in its native environment and in the presence of assembly inhibitors, both on the microsecond timescale. The results of our simulations have enabled us to characterize the capsid’s biophysical properties and reveal insights into its dynamical structure and function.
Why is your research important to those concerned about hepatitis?
The hepatitis B capsid plays a critical role in viral infection and represents a promising therapeutic target. The capsid assembles to package viral RNA, serves as a container for reverse transcription of RNA to DNA, displays signals for intracellular trafficking, and dissociates at the correct place and time to deliver the viral DNA to the host cell nucleus. Drugs designed to disrupt the capsid or interfere with any of the viral processes it participates in could serve as new treatments for hepatitis B. Our research reveals important atomistic details regarding the capsid’s function in hepatitis B infection, which can be exploited in the design of new antiviral treatments.
How did you get into this area of research?
We began working on virus capsids with Professor Klaus Schulten in 2011, as part of close experimental collaborations that we have continued into our independent research careers at University of Delaware. The hepatitis B capsid project came about when Adam Zlotnick at Indiana University invited us to the FASEB meeting in Physical Virology. Adam has been studying hepatitis B since the 1990s and is an expert on the virus.
How long have you been working on it?
Combined, we have more than 20 years of experience using all-atom molecular dynamics simulations to study biomolecular systems. We started applying the method to investigate the structures and biophysical properties of virus capsids in 2011 and have been working on the hepatitis B capsid since 2013. To simulate the hepatitis B capsid for only one microsecond required more than six months on the Blue Waters supercomputer.
Do you receive public funding for this work? If so, from what agency?
Our hepatitis B capsid work receives support through the NIH-COBRE Center “Molecular Design of Responsive Biomaterials” and a research fellowship from the University of Delaware. We are seeking funding for development of therapeutics through the renewal of the NIH-COBRE Center “Discovery of Chemical Probes and Therapeutic Leads”. Also, our work is supported by allocations for hepatitis B research on the Blue Waters supercomputer, which is funded by the NSF and the State of Illinois.
Have you had any surprise findings thus far?
We were most surprised to learn how flexible the hepatitis B capsid is. Experimental structures of icosahedral virus capsids commonly impose icosahedral symmetry to improve resolution, but our simulations were performed on the complete capsid without any structural constraints. When the capsid was allowed free movement within its native environment, its spikes began to sway back and forth and it demonstrated the ability to distort asymmetrically. Experiments have suggested that capsid flexibility and asymmetry may be essential for function, and our simulations have enabled characterization of these features for the first time. We also discovered that drugs are able to alter the global structure of the capsid, as well as its physical properties.
What is particularly interesting about the work from the perspective of other researchers?
We used conformations of the hepatitis B capsid sampled during our simulations to perform a theoretical single-particle image reconstruction, mimicking the data post-processing that enables structure determination by cryo-EM. We found that the flexibility and asymmetry of the capsid led to a significant loss of resolution upon structural averaging, particularly icosahedral averaging, which is commonly employed when solving the structures of icosahedral capsids. It is an important observation that, despite ever advancing cryo-EM technology, protein flexibility may represent a major limiting factor to achieving true atomic (1-2 Å) resolution for virus capsids and other large biomolecular structures.
What is particularly interesting about the work from the perspective of the public?
Beyond the fact that the results of our work could one day guide the design of new treatments for hepatitis B, we have also gained important new insights into the inner workings of the hepatitis B capsid as a complex molecular machine. Basic science research into viral structures and their functions in infection processes will allow us to gradually unravel the mystery of viruses, ultimately bringing us closer to answering the fundamental question of how life arises from the interactions of biomolecules. Altogether, we are now in a position to start our large-scale drug discovery campaign.
Read more about their research.
JC Gumbart
What is the connection between your research and hepatitis?
We are studying Hepatitis B Virus (HBV), one of the most infectious and prevalent viruses in the world today. Like all viruses, HBV has a protein shell or “capsid” surrounding its genetic material. In the case of HBV, the capsid is composed of 240 copies of the same protein, simply called Cp (core protein). We are using molecular dynamics simulations in my lab to better characterize the dynamics of intermediate assemblies of Cp, including dimers, tetramers, and hexamers, as well as how small molecules interact with them to influence their conformation and, ultimately, their assembly pathway into capsids. Small molecules that can alter this pathway are known as “capsid assembly modifiers” (CAMs) and a few have already been discovered, albeit none approved for use yet. Thus, we are also searching for new lead candidates through so-called “ensemble docking” ( https://www.cell.com/biophysj/abstract/S0006-3495(18)30324-2 ), in which simulations are used to generate more protein conformations than provided by just a single crystal structure. These conformations are then used for docking, in which tens to hundreds of thousands of small molecules are tested virtually for their ability to bind to the protein.
Why is your research important to those concerned about hepatitis?
Roughly 250 million people worldwide suffer from chronic HBV infection and of those, approximately 20-30% will develop serious liver problems, including cirrhosis and/or cancer. Nearly 800,000 die yearly from these complications or from the infection itself. While some treatments exist, they do not eliminate the virus completely, allowing for recurrence of infection and requiring continued treatments. CAMs, on the other hand, have the potential to eliminate the virus completely, making them a true cure; however, further development is needed.
How did you get into this area of research?
A few years ago, I was approached by a Bioinformatics MS student and Fulbright fellow, Maksym Korablyov, who said he was very interested in finding ways to address HBV infection using computational approaches. While I didn’t have any direct experience with drug design at the time, my postdoc, Anna Pavlova, and I were both interested in learning more about the process and this seemed like a perfect project with which to get started. Therefore, I was happy for Maksym to join my lab and start on studying HBV protein dynamics and its interactions with small molecules. Although he has moved on to a PhD in the MIT Media Lab, Anna and I are continuing with the project.
How long have you been working on it?
We only started in early 2015, just over three years ago.
Do you receive public funding for this work? If so, from what agency?
Most of my lab’s funding is for studying a different kind of infectious agent - bacteria. HBV is our first foray into studying viruses; we have recently applied for funding from NIH for it and anxiously await the results.
Have you had any surprise findings thus far?
Our simulations have shown us that even with just a few hundred nanoseconds of dynamics, we can already begin to classify whether a particular Cp intermediate has the capability to form a capsid or not. Furthermore, a few of the lead candidates that we selected from our MD and docking studies have been tested experimentally by our collaborators Leda Bassit and Bryan Cox in the lab of Raymond Schinazi at Emory University just across town. These showed promising activity against HBV; we are now looking at ways to improve them. So despite our lack of experience in this area of research, we were able to make progress by following the established approaches of our colleagues.
What is particularly interesting about the work from the perspective of other researchers?
MD simulations can be a powerful complement to traditional drug design approaches. Beyond just giving us more conformations to dock small molecules to, they provide a way to rationalize the action of these small molecules against HBV in experiments, e.g., distorting the capsid or misdirecting its assembly, as well as calculate the energetics of their binding. Finally, they can reveal information about intermediates that are too transient to be studied experimentally.
What is particularly interesting about the work from the perspective of the public?
Drug design and development is not solely in the purview of pharmaceutical companies. In fact, studies consistently find that NIH funds basic science that contributes to the vast majority of new drugs brought to market. While most of it is focused on improving our understanding of drug targets, some NIH-funded research also leads to drug design itself, as we hope to do with HBV. Thus, public investment through NIH is critical for maintaining (or accelerating!) the pace of drug discovery. For more information, see: http://www.pnas.org/content/115/10/2329.