Caption: Modeling the PG9 and PG16 epitopes onto the HIV-1 trimer. The above model is adapted from a recent cryo-electron tomographic structure of the HIV-1 trimer. The crystal structure of the gp120 core (orange) has been fitted into the density map. The V1/V2 and V3 loops, which are not resolved in the crystal structure, are represented as green and yellow ovals, respectively. The approximate locations of gp41 and the viral membrane (not resolved in the structure) are shown in blue. The red structure located above the trimer is a human IgG molecule representative of PG9 and PG16. The PG9 and PG16 epitopes are believed to involve residues in the V1/V2 and V3 loops of gp120.
NEW YORK, NY, LA JOLLA and SAN FRANCISCO, CA, SEATTLE, WA, September 3, 2009—Researchers at and associated with the International AIDS Vaccine Initiative (IAVI), at The Scripps Research Institute, and at the biotechnology companies Theraclone Sciences and Monogram Biosciences have discovered two powerful new antibodies to HIV that reveal what may be an Achilles heel on the virus. They published their work in Science this week.
Researchers will now try to exploit the newfound vulnerability on the virus to craft novel approaches to designing an AIDS vaccine. Moreover, the global collaboration and process that led to the discovery of the two new broadly neutralizing antibodies (bNAbs) are likely to produce more such antibodies, which may in turn reveal additional vulnerabilities of HIV, adding still more vitality to the effort to develop a vaccine against AIDS.
“The findings themselves are an exciting advance toward the goal of an effective AIDS vaccine because now we’ve got a new, potentially better target on HIV to focus our efforts for vaccine design,” said Wayne Koff, senior vice president of research and development at IAVI. “And having identified this one, we’re set up to find more, which should further accelerate global efforts in AIDS vaccine development.”
Broadly neutralizing antibodies to HIV are produced by a minority of HIV-infected individuals and are distinct from other antibodies to HIV in that they neutralize a high percentage of the many types of HIV in circulation worldwide. It is widely believed that to prevent HIV infection an AIDS vaccine would need to teach the body to produce these powerful antibodies before exposure to the virus. Animal experiments suggest that conceptually such a vaccine would work. Before this finding only four antibodies to HIV had been discovered that were widely agreed to be broadly neutralizing.
The two newly discovered bNAbs, called PG9 and PG16, are the first to have been identified in more than a decade and are the first to have been isolated from donors in developing countries, where the majority of new HIV infections occur. Moreover, previously identified bNAbs against HIV have functioned by binding to places on HIV that have proven difficult to exploit by means of vaccine design.
“These new antibodies, which are more potent than other antibodies described to date while maintaining great breadth, attach to a novel, and potentially more accessible site on HIV to facilitate vaccine design,” said Dennis Burton, professor of immunology and microbial science and scientific director of the IAVI Neutralizing Antibody Center at The Scripps Research Institute in La Jolla, California. Professor Burton is also a member of the newly established Ragon Institute of MGH, MIT and Harvard. “So now we may have a better chance of designing a vaccine that will elicit such broadly neutralizing antibodies, which we think are key to successful vaccine development.”
Breadth of neutralization is important because any effective AIDS vaccine must provide protection from a diverse range of the most prevalent types of HIV circulating worldwide. High potency suggests that such antibodies will not have to be produced by the body in very large quantities to confer protection.
The two new antibodies target a region of the viral spike used by HIV to infect cells. The viral spike glycoproteins, termed gp120 and gp41, are highly variable and have evolved to thwart immune attack. But biochemical studies suggest that PG9 and PG16 target regions of gp120 that do not change, which probably accounts for their breadth of neutralization. Now researchers at the IAVI-organized Neutralizing Antibody Consortium (NAC), a scientific network focused on designing vaccines capable of eliciting broadly neutralizing antibodies, will turn their attention to studying the molecular structure of PG9 and PG16 and that of the region they target on the HIV spike. They will use this information to try to devise immunogens—the active ingredients of vaccines—that elicit similar antibodies.
How they were discovered
The methods by which PG9 and PG16 were isolated are themselves proving instructive. Their identification represents the first success of an ongoing global hunt launched by IAVI in 2006 to find new bNAbs to support the rational design of novel AIDS vaccine candidates. The effort, named Protocol G, is unprecedented in scale and distinguished by its emphasis on identifying antibodies that neutralize subtypes of HIV circulating primarily in developing countries. IAVI’s clinical research partners have collected blood specimens from upward of 1,800 HIV-infected volunteers from IAVI-supported clinical research centers in seven sub-Saharan countries as well as from centers in Thailand, Australia, the United Kingdom and the United States.
All samples were sent to Monogram Biosciences, which, working with researchers at IAVI’s AIDS Vaccine Design and Development Laboratory in New York City and the IAVI Neutralizing Antibody Center at The Scripps Research Institute, screened the sera for broadly neutralizing activity. Researchers historically have sought bNAbs in serum by testing whether antibodies from such samples bind to soluble versions of gp120 and gp41. It turns out that PG9 and PG16, however, bind to soluble forms of the proteins very weakly, if at all. The antibodies were detected only because a micro-neutralization assay developed by Monogram in partnership with IAVI measuring their ability to block HIV infection of target cells was run in parallel with the standard binding assays used for screening. This has significant implications for the future screening of bNAbs.
“If you think of it as a fishing expedition,” said Christos Petropoulos, chief scientific officer and vice president of virology research and development at Monogram Biosciences, “we and the rest of the field were previously using the wrong bait in the search for HIV-specific broadly neutralizing antibodies. Together with colleagues at IAVI, we reasoned that the best approach to identifying antibodies with the most potent and broad neutralizing activity was to screen directly for their ability to block HIV infection. To do this we developed a new, specialized test known as the micro-neutralization assay, which has opened up new avenues for exploration of additional donors for similar antibodies.”
Once the researchers had ranked the top 10% of serum samples in terms of breadth of neutralization, they needed to isolate the actual bNAbs. This can be painstaking work. But Theraclone Sciences, a company that had been working outside the HIV field, had a relevant and unique high-throughput process that it adapted to HIV work with financing from IAVI’s Innovation Fund, which is co-funded by the Bill & Melinda Gates Foundation. The Theraclone team used a system designed to expose the entire repertoire of antibodies from a blood sample obtained from an HIV-infected individual. Antibodies with broadly neutralizing potential were identified from this pool and traced to their corresponding antibody-forming cells. Using recombinant DNA technology, bNAb genes were then isolated from these cells to enable the production of unlimited quantities of the antibody clones for research.
“It is exciting that we were able to use our technology to identify and isolate these new bNAbs, which may offer important clues that could help create an effective AIDS vaccine. Through this strong scientific partnership, we have rapidly delivered promising results,” said Matthew Moyle, chief scientific officer and senior vice president of Theraclone Sciences. “This project has been a useful demonstration of Theraclone’s antibody discovery platform in infectious disease, and we highly value IAVI’s collaborative approach to solving the AIDS vaccine challenge,” said David Fanning, president and CEO of Theraclone Sciences.
With a large pool of HIV-positive donors from Protocol G now identified whose serum contains HIV-specific broadly neutralizing antibodies, it is likely that this global collaboration will generate more bNAbs that will benefit the vital enterprise of accelerating AIDS vaccine development.
“The story of the discovery of these two new antibodies demonstrates the challenges of AIDS vaccine research but also the power of the collaboration that formed to produce this advance. This is what can happen when you have researchers from the global North and South, from academia and industry, from within and outside the HIV field, working together in a framework to speed innovation,” said Seth Berkley, president and CEO of IAVI. “By working in this manner, I am confident we will continue to move toward solving the AIDS vaccine challenge, one of the greatest scientific and public health challenges of our time.”
The published study on the two new bNAbs is available online at www.sciencemag.org.
The International AIDS Vaccine Initiative (IAVI) is a global not-for-profit organization whose mission is to ensure the development of safe, effective, accessible, preventive HIV vaccines for use throughout the world. Founded in 1996 and operational in 24 countries, IAVI and its network of collaborators research and develop vaccine candidates. IAVI was founded with the generous support of the Alfred P. Sloan Foundation, The Rockefeller Foundation, The Starr Foundation and Until There’s A Cure Foundation. Other major supporters include the Bill & Melinda Gates Foundation, the Foundation for the National Institutes of Health, The John D. Evans Foundation, The New York Community Trust, the James B. Pendleton Charitable Trust; the Governments of Canada, Denmark, India, Ireland, The Netherlands, Norway, Spain, Sweden, the United Kingdom and the United States, the Basque Autonomous Government and the European Union, as well as The City of New York, Economic Development Corporation; multilateral organizations such as The World Bank; corporate donors including BD (Becton, Dickinson & Co.), Bristol-Myers Squibb, Continental Airlines, Google Inc., Henry Schein, Inc., Pfizer Inc, and Thermo Fisher Scientific Inc.; leading AIDS charities such as Broadway Cares/Equity Fights AIDS; other private donors such as The Haas Trusts; and many generous individuals from around the world. For more information, see www.iavi.org.
About The Scripps Rsearch Institute
The Scripps Research Institute is one of the world’s largest independent, non-profit biomedical research organizations, at the forefront of basic biomedical science that seeks to comprehend the most fundamental processes of life. Scripps Research is internationally recognized for its discoveries in immunology, molecular and cellular biology, chemistry, neurosciences, autoimmune, cardiovascular, and infectious diseases, and synthetic vaccine development. Established in its current configuration in 1961, it employs approximately 3,000 scientists, postdoctoral fellows, scientific and other technicians, doctoral degree graduate students, and administrative and technical support personnel. Scripps Research is headquartered in La Jolla, California. It also includes Scripps Florida, whose researchers focus on basic biomedical science, drug discovery, and technology development. Scripps Florida is located in Jupiter, Florida. For more information, see www.scripps.edu.
About Theraclone Science
Theraclone Sciences is a Seattle-based discovery-stage biotech focused on the development of novel therapeutic antibodies for the treatment of infectious disease and inflammation. The company’s technology harnesses the power of the human immune system to identify naturally evolved monoclonal antibodies from the blood cells of immunologically relevant human subjects. Recombinant human monoclonal antibodies can be rapidly obtained using our discovery platform and scaled for large-scale industrial production. Such antibody drug candidates may be uniquely important in combating disease and may have potential as therapeutic products that can be administered to a broad patient population. Theraclone is a privately held company with venture investment from ARCH Venture Partners, Canaan Partners, Healthcare Ventures, Amgen Ventures, MPM Capital, and Alexandria Real Estate Investment. For additional information, please visit www.theraclone-sciences.com.
About Monogram Bioscience
Monogram Biosciences, Inc. is advancing individualized medicine by discovering, developing and marketing innovative products to guide and improve treatment of serious infectious diseases and cancer. Monogram Biosciences, Inc.’s products are designed to help doctors optimize treatment regimens for their patients that lead to better outcomes and reduced costs. Monogram Biosciences, Inc.’s technology is also being used by numerous biopharmaceutical companies to develop new and improved anti-viral therapeutics and vaccines as well as targeted cancer therapeutics. More information about Monogram Biosciences, Inc. and its technology can be found on its web site at www.monogrambio.com.
Protocol G collaborating institutions include:
MRC/UVRI Uganda Research Unit on AIDS, Uganda Virus Research Institute, Entebbe, Uganda; St. Stephen’s AIDS Trust, Chelsea and Westminster NHS Foundation Trust, London UK; NRL, St. Vincent’s Institute, Melbourne, Victoria, Australia; Zambia Emory HIV Research Project, Lusaka, Zambia, and the Rwanda-Zambia HIV Research Group, Emory University, Atlanta, GA, USA; Projet San Francisco, Kigali, Rwanda and the Rwanda-Zambia HIV Research Group, Emory University, Atlanta, GA, USA; CeDReS/CHU Treichville, Abidjan, Côte d’Ivoire; Kenya AIDS Vaccine Initiative, College of Health Sciences, University of Nairobi, Nairobi, Kenya; SUNY Downstate Medical Center, Brooklyn, NY, USA; Desmond Tutu HIV Centre, University of Cape Town, Cape Town, South Africa; Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand; Department of Retrovirology, Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand; Rwanda-Zambia HIV Research Group, Emory University, Atlanta, GA, USA; Institute of Human Virology, Plateau State Human Virology Research Centre, Jos, Nigeria.
The Scripps Research Institute
AIDS Vaccine Research and Development:
The Role of Broadly Neutralizing Antibodies
What is a vaccine?
A preventive vaccine is a substance introduced into the human body that teaches the immune system to detect and destroy a pathogen—which is a particular virus, bacterium or parasite that causes a preventable disease. All vaccines contain some harmless form or part of the pathogen they target. They exert their effects through the adaptive immune response, an arm of the immune system that learns to recognize and neutralize specific pathogens (as opposed to pathogens in general).
What is an antibody?
Antibodies are infection-fighting protein molecules that tag, neutralize and help destroy toxins and invading pathogens. They are secreted by immune cells known as B lymphocytes (a kind of white blood cell) in response to stimulation by antigens, which are molecules found on the targeted pathogens. Each antibody binds only to the specific antigen that stimulated its production. More specifically, it homes in on an epitope, a patch of the antigen characterized by a relatively unique shape or surface. A neutralizing antibody against HIV latches onto the virus’s epitope and stops the virus from infecting its target cell—which is the CD4+ T lymphocyte, a central player in the adaptive immune response.
What is an immunogen?
An immunogen is a substance—an organism or an antigen—that consistently provokes an immune response. It is the active ingredient of a vaccine, the component that teaches the immune system how to detect and target the pathogen against which the vaccine is devised. Immunogens employed in vaccines might be a dead pathogen of interest, a pathogen that has been rendered harmless, molecules derived from that pathogen, or even isolated epitopes from antigens that are known to be responsible for eliciting antibodies of interest.
Why is it so hard to make a vaccine against HIV?
There are three major reasons HIV has proved such a formidable foe to vaccine designers and immune systems alike. First, it is by far the most mutable virus scientists have ever encountered. A number of different subtypes of the virus, known as clades, circulate in different regions of the world. Within those clades there is considerable variability, and, beyond that, the virus mutates furiously within the people it has infected. In fact, you will find more genetic variation in the HIV isolated from a single person who has been infected for a few years than you are likely to find globally in the dominant strain of influenza during flu season. As a consequence, researchers have not yet found a single, unchanging part of HIV that when used as an immunogen might teach the immune system to recognize and neutralize its countless naturally occurring variants. Second, because no one is known to have cleared an HIV infection, we do not know which elements of the immune response must be engaged to control the virus—and thus are uncertain how to replicate such responses. Finally, the immune system has a very narrow window of opportunity in which to neutralize HIV before the virus establishes a lifelong infection.
What is a broadly neutralizing antibody (bNAb)?
A bNAb is an antibody capable of blocking the ability of viruses from a number of types of HIV from infecting their target cells. Like other antibodies, they are produced by white blood cells known as B lymphocytes. Only a minority of people who are infected with HIV produce bNAbs.
Although HIV is a wildly mutable virus, certain parts of it are relatively resistant to change. These parts, for one reason or another, are essential to the virus’s ability to infect the CD4+ T lymphocyte and multiply. In general, these elements of HIV are what bNAbs target.
Only a handful of such antibodies have so far been isolated from HIV-positive people, and all of them until now were derived from individuals infected with the subtype of the virus that circulates primarily in the Americas, Europe and Australia. Researchers at the International AIDS Vaccine Initiative (IAVI) and The Scripps Research Institute, along with other partners, have been collaborating with a large network of clinical research centers around the world to find more bNAbs, with a special emphasis on varieties capable of neutralizing subtypes of HIV that predominate in developing countries. This work has resulted in the discovery and characterization of two novel bNAbs, the first to come from an HIV type that predominates in the developing world, where an AIDS vaccine is needed most.
Why are broadly neutralizing antibodies (bNAbs) important to the AIDS vaccine effort?
BNAbs provide very valuable clues to effective immunogen design. Careful study of their mechanisms of action reveals vulnerabilities that are shared by many different types of HIV. Most importantly, this research exposes the epitopes on HIV—those particular shapes recognized by bNAbs—that, if reproduced in a lab and delivered in a vaccine, might elicit similar antibodies in those who are vaccinated, conferring immunity to multiple types of HIV. The two recently identified bNAbs reveal a new target on HIV that is potentially a more accessible site on which to focus vaccine design efforts than the targets provided by previously identified bNAbs.
What do we know about existing bNAbs?
Researchers at labs around the world have charted, in atomic detail, the structure of a number of these antibodies and pieced together a pretty clear picture of how each latches on to its target epitope. Not surprisingly, given the difficulty of neutralizing HIV, the antibodies studied in detail so far display unique structural and mechanistic characteristics that complicate attempts to elicit them through a vaccine.
How is this information being used in AIDS vaccine research?
Researchers are using information generated from the close study of existing bnAbs to inform the design of what they hope will be a new class of AIDS vaccines. For example, members of the Neutralizing Antibody Consortium (NAC)—which was launched in 2002 by the International AIDS Vaccine Initiative and is directed by Dennis Burton, professor of immunology and microbial science at The Scripps Research Institute—are applying powerful computational and protein engineering techniques to
re-create the epitopes bnAbs latch onto and use them as immunogens for what might be called prototype HIV vaccine candidates. This work is still in its earliest stages, but when the researchers do construct an immunogen that elicits the desired antibody response in animal studies, it will be put through the steps required to turn it into a candidate vaccine for human trials.
IAVI, The Scripps Research Institute, Theraclone Sciences and Monogram Biosciences have just announced that they have found two new broadly neutralizing antibodies (bnAbs). What distinguishes them?
The two newly discovered bNAbs, called PG9 and PG16, are the first to have been identified in more than a decade and are the first to have been isolated from donors in developing countries, where the majority of new HIV infections occur. The bnAbs previously identified and studied by researchers in the NAC have all come from people infected with clade B HIV, which predominates in the Americas, Europe and Australia. Further, the newly isolated bnAbs neutralize a wider range of HIV subtypes than all but one of the existing bnAbs, and at low concentrations appear to outperform that antibody as well. They also seem to be far more potent than any of the previously isolated bnAbs.
What is the significance of these findings?
These antibodies are the first new bnAbs to have been isolated in more than a decade. They target a surface on the HIV spike, which the virus uses to infect cells, that none of the previously identified bnAbs targeted. This reveals a new and relatively unchanging spot on the highly mutable virus that vaccine designers may be able to exploit to generate immunogens (the active ingredients of vaccines). The breadth of neutralization of the new bnAbs makes them ideal candidates for study by AIDS vaccine designers, who must develop vaccines that protect people from subtypes of HIV circulating in developing countries if they hope to have a significant impact on the AIDS pandemic. The notable potency of these antibodies also holds promise: If they can be elicited via vaccination, they will not, in theory, have to be produced at very high levels in people to induce protection from HIV.
How will this discovery be exploited to support the design and development of novel vaccine candidates?
Like the previously discovered bnAbs, these new antibodies will now be closely studied by NAC researchers, who will work out their molecular structure and the precise mechanism by which they bind to their targets on the HIV spike. With this information in hand, they will begin trying to design novel immunogens to elicit these antibodies in all people. If they succeed, the immunogens will be put through the steps of preclinical development to produce an industrially viable vaccine candidate for further development. Similar efforts—albeit in the earliest of stages—are already underway within the NAC using the structural information derived from studies on previously discovered antibodies.
Will more bnAbs be found?
A number of collaborative efforts—including those of the NAC, the U.S. National Institutes of Health and the Collaboration for AIDS Vaccine Discovery—are currently engaged in a global hunt for more such antibodies. There is no doubt that more will be found and a fair chance that one or more of them will expose an Achilles heel on HIV that can be exploited by vaccine designers. Better yet, because these projects are global in scope they will yield antibodies that neutralize the types of HIV that predominate in developing countries, which is where 95% of new infections occur. All bnAbs identified until now have been derived from people infected with versions of HIV primarily found in Australia, the U.S. and Europe.
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