We've updated our Privacy Policy to make it clearer how we use your personal data. We use cookies to provide you with a better experience. You can read our Cookie Policy here.

Advertisement

How Broadly Neutralizing Antibodies Are Driving Next-Gen Vaccines

Illustration of a syringe dispersing broadly neutralizing antibodies targeting viral structures.
Credit: Technology Networks
Listen with
Speechify
0:00
Register for free to listen to this article
Thank you. Listen to this article using the player above.

Want to listen to this article for FREE?

Complete the form below to unlock access to ALL audio articles.

Read time: 8 minutes

Antibodies have become an integral part of research and medicine. Therapeutic applications of antibodies began to emerge following the publication of Köhler and Milstein’s groundbreaking 1975 paper in Nature describing the hybridoma technique to produce monoclonal antibodies (mAbs).


Introducing mAb technology enabled researchers to produce a single antibody to a specific antigen and replicate it in culture. In 1986, the Food and Drug Administration (FDA) approved the first therapeutic mAb designed to prevent transplant rejection. Since then, more than 100 mAbs have been approved for treating a range of diseases including cancer, autoimmune and chronic inflammatory diseases.


mAbs synthesized in the laboratory mimic natural antibodies produced by the body and are designed to target and neutralize pathogenic proteins or antigens selectively. A specific class of mAb, capable of broad neutralization, has become highly valued in vaccine development for its ability to neutralize multiple virus strains.


Broadly neutralizing antibodies (bNAbs) were first discovered in the '90s when it was observed that HIV-infected individuals possessed antibodies that could recognize and neutralize different subtypes of HIV. bNAbs are now being heavily researched, not only for their potential in the prevention of HIV, but also for other rapidly mutating viruses such as influenza and SARS-CoV-2.

Developing vaccines against an evolving threat

During replication, the nucleic acid of many viruses will mutate, reducing the protective ability of vaccines. Combating the ability of mutated viruses to escape the immune system remains one of the most pressing challenges faced by vaccine developers.


“Viruses are constantly under selective pressure from the human immune response,” Dr. William Voss, a postdoctoral fellow at The University of Texas at Austin told Technology Networks. “A particular virion that is neutralized by an antibody during infection cannot enter its host cell and replicate. This drives the process of immune escape, where viral variants that mutate the epitope targeted by a given neutralizing antibody, such that it no longer binds or neutralizes, survive and pass on their genetic material.”


The development of broad-spectrum vaccines that can induce bNAbs against various virus strains has been identified as one of the most promising ways to combat these mutations.


“When it comes to bNAbs potential in vaccines, two approaches are the subject of investigation. The first involves the concept of passively transferring vaccine-like antibodies into an individual. This would only be possible if you can extend the half-life of said antibodies,” Dr. Michael Diamond, the Herbert S. Gasser Professor in the department of medicine, molecular microbiology, pathology and immunology at Washington University School of Medicine told Technology Networks.


“This approach was taken by AstraZeneca when it produced Evusheld® (tixagevimab/cilgavimab), a long half-life mAb combination that could be administered prophylactically to combat emerging waves of SARS-CoV-2. The problem with Evusheld, and most other therapeutic anti-SARS-CoV-2 mAbs, was that it lost its effectiveness against newer variants and resistance emerged.”


Another concept is to induce bNAbs by providing a tailored antigen designed to focus the immune response on conserved epitopes of a virus. “There are vaccines that are trying to do this, and although they've been able to generate broadly neutralizing responses there hasn’t been much success generating bNAbs consistently,” explained Diamond.

What are conserved epitopes?

Conserved epitopes are portions of a foreign protein or antigen retained by multiple strains of a virus that binds with a complementary site of an antibody – such as the S2 domain of SARS-CoV-2.

Unraveling the mechanism of these antibody “heroes”

Like most antibodies, bNAbs are Y-shaped proteins (Figure 1) generated by a type of white blood cell called B cells. The exact mechanism of action of bNAbs has been an ongoing area of investigation. However, research has shown that most bNAbs target conserved epitopes.

Diagram of antibody structure showing variable regions, heavy and light chains and antigen binding sites.

Figure 1: Structure of an antibody. Credit: Technology Networks.


In 2022, researchers from The Pasteur Institute’s Virus and Immunity Unit described how anti-HIV bNAbs bind to viral particles to form aggregates at the surface of immune cells. These aggregates effectively block cell-to-cell transmission by preventing the release of viral particles and the formation of synapses used by viruses to move from one cell to another.


Producing bNAbs naturally in the human body is a long process in an antibody–virus race for dominance. For example, potent bNAbs develop in people living with HIV, but only rarely and after many months or even years after transmission.


Dr. Dennis Burton's group and others have shown that you require a substantial amount of somatic hypermutation over the context of many exposures to evolve these bNAbs. Work from Dr. Michel Nussenzweig has also shown this elegantly at the single B-cell level,” said Diamond.


As you could expect, identifying and characterizing bNAbs is no easy task; scientists have to comb through thousands of antibodies to identify those likely to be active against most viral strains.


Typical approaches for the high-throughput screening of antibodies include phage display, whereby high-affinity interactions between antibodies and antigens are identified by displaying proteins on the surface of bacteriophages. Techniques such as enzyme-linked immunosorbent assays (ELISAs) are often employed in hybridoma screening to identify monoclonal antibodies with high antigen affinity.


Diamond explained how antibody screening can also be done at a single B-cell level: “You can identify specific B cells that interact with a viral protein, and then make the antibody that single B cell encodes. Now you have a single antibody from a single B cell that binds to your protein of interest. Depending upon the sophistication of your screen, you may even be able to know right away if that's a neutralizing anybody.”


More recently, artificial intelligence (AI) and machine learning approaches have been suggested. AI could be useful for screening methods such as epitope/paratope mapping to predict the areas of the antibody (the paratope) and antigen (the epitope) involved in binding. However, AI methods can lack accuracy and still require experimental input.


In the context of mutating viruses, researchers have used machine learning to computationally redesign an existing antibody against an emerging strain of SARS-CoV-2 while maintaining efficacy against the dominant variant. The study's findings suggest that computational approaches can be used to optimize an antibody to target multiple escape variants.


Identifying bNAbs and utilizing them in vaccine technology has proven challenging, however, researchers have made multiple strides this year alone in disease areas such as COVID-19 and HIV.

Towards a preventative HIV vaccine

Today, infection with HIV is manageable using antiretroviral medications, however, a successful vaccine has alluded developers since the ‘80s. A critical roadblock in developing a preventative vaccine has been the inability to induce B-cell lineages of bNAbs that target the rapidly evolving virus.


A vaccine candidate developed at the Duke Human Vaccine Institute has now reportedly triggered low levels of HIV bNAbs among a small group of people in a clinical trial.


The vaccine targets an area on the HIV-1 outer envelope called the membrane-proximal external region (MPER), which remains stable even as the virus mutates. In the study, the researchers analyzed data from the HVTN 133 Phase 1 clinical trial, which involved 20 healthy, HIV-negative individuals.


“One of the questions we have worried about for many years is if it will take years to induce bNAbs with a vaccine like it takes for bNAbs to develop in people living with HIV,” Dr. Barton Haynes, director of the Duke Human Vaccine Institute previously told Technology Networks. “Here we found that bNAb lineages developed after the second immunization.”


This work shows the feasibility of inducing antibodies that neutralize the most difficult strains of HIV, however, the researchers stress that there is still more work to be done to create a more robust response.


A separate study, conducted by the Scripps Consortium for HIV/AIDS Vaccine Development, utilized germline targeting to stimulate animals’ immune systems to induce rare precursor B cells of a class of HIV-targeting bNAbs called 10E8.


The 10E8 bNAb binds to a conserved region of the glycoprotein gp41 on HIV’s surface. Designing an immunogen to stimulate the production of 10E8 bNAbs has been challenging because the binding region of gp41 is hidden in a recessed crevice on the virus’ surface.


To address this challenge, the researchers engineered immunogens on nanoparticles that mimic a specific part of gp41. Vaccinations in rhesus macaque monkeys and mice with these immunogens elicited responses from the 10E8 B cell precursors, and induced antibodies that showed signs of maturing into bNAbs that could reach the gp41 region.


The research forms part of the group's larger work to develop a germline-targeting strategy for priming the immune system to elicit a bNAb called VRC01, which was discovered by NIAID researchers almost 15 years ago.

bNAbs presence in COVID-19 research

The first vaccine a person receives promotes a strong primary immune response that shapes future interactions with the virus, a process known as imprinting.


Diamond and colleagues at Washington University School of Medicine in St. Louis recently detailed how imprinting affects subsequent COVID-19 vaccinations. Unlike the influenza virus, where immunity elicited by one year’s flu shot can interfere with subsequent immune responses, the researchers found that repeat vaccinations resulted in the production of bNAbs capable of neutralizing a wide range of SARS-CoV-2 variants.


The researchers concluded that these cross-reactive antibodies may confer substantial protection against future pandemics caused by a related coronavirus.

One bNAb to neutralize all variants

Researchers at The University of Texas at Austin recently discovered and isolated a particular bNAb, called SC27, which appears effective at neutralizing the numerous variants of SARS-CoV-2. “This research – including understanding how SC27 achieves its broadly neutralizing activity – helps inform vaccine development,” explained Voss. “Future vaccines that can trigger the production of such antibodies could protect us more broadly against emerging viral variants as SARS-CoV-2 continues to evolve. Additionally, SC27 itself could potentially be used as a therapeutic antibody.”

“Antibodies such as SC27 that may retain neutralizing activity despite future viral evolution represent a promising area of drug development,” said Voss.

SC27 recognized the different characteristics of the spike proteins in the many COVID variants. “A technique called deep mutational scanning quantified the potential for an array of spike mutations to escape SC27 and demonstrated that such mutations are rarely observed in circulating SARS-CoV-2,” described Voss.


“Several key amino acid residues within the epitope targeted by SC27 show minimal natural variation across SARS-CoV-2 variants, suggesting that SC27 may remain potently neutralizing moving forward.”


To isolate and identify the antibody the researchers developed a novel technique combining single-B cell sequencing and immunoglobulin proteomics, a method they named Ig-Seq.


Beyond COVID-19 research, Voss believes this approach could be used to study other rapidly mutating viruses: “As a high-throughput method for characterizing the plasma antibody repertoire and facilitating the cloning and characterization of specific antibodies of interest, Ig-Seq could be used to identify broadly neutralizing epitopes on a variety of pathogens, including influenza.”


Voss continued, “Identifying such regions of viral proteins and understanding the mechanism of antibodies that target them could inform the development of vaccines that aim to elicit bNAbs.”

How close are we to “one shot” vaccines?

Advancements in structural biology and immunologic technologies have brought researchers closer than ever to understanding bNAbs and the mechanisms that drive their production.


“To get a single shot vaccine to prevent infection in a sustained way, we also need to accelerate the development of mucosal vaccines. The emerging consensus is that most vaccines administered by an intramuscular route don’t induce enough upper airway immunity, especially in the setting of evolving variants that compromise neutralizing activity,” Diamond said of the possibility of a “one shot” vaccine for respiratory viruses.

“Alongside targeting specific epitopes with bNAbs, a successful ‘one shot’ vaccine will also need to induce ancillary immune responses such as T-cell responses and Fc effector responses,” said Diamond.

Diamond envisions two approaches could translate bNAbs to the clinic in the next few years. The first involves the concept of vaccine-like antibodies with an extended half-life. Instead of vaccinating and inducing an immune response, this would involve giving a patient a bNAb.


“The advantage of this approach is that elderly and immune-compromised people wouldn’t have to rely on a dysfunctional immune system making an antibody,” explained Diamond. “The downside is that you run the risk that if a virus is highly evolving you could generate escape in a population relatively quickly, as was the case with Evushield.”


The second approach would involve using vaccines to induce the production of bNAbs in a patient.


“Work still needs to be done to improve our understanding of how to focus and display epitopes recognized by bNAbs to be able to induce antibodies specifically and with high precision. We are still struggling as a field in the best way to do that. The rules that may work for flu may not be the same for HIV because the epitopes are different and must be displayed differently. Unfortunately, the lessons we continue to learn from one virus might not translate across different viruses,” Diamond concluded.