{"id":2975,"date":"2023-10-19T09:38:17","date_gmt":"2023-10-19T08:38:17","guid":{"rendered":"https:\/\/springerhealthcare.nl\/france\/?p=2975"},"modified":"2023-10-20T10:11:02","modified_gmt":"2023-10-20T09:11:02","slug":"how-alphafold-and-other-ai-tools-could-help-us-prepare-for-the-next-pandemic","status":"publish","type":"post","link":"https:\/\/springerhealthplus.nl\/shmigrate\/how-alphafold-and-other-ai-tools-could-help-us-prepare-for-the-next-pandemic\/","title":{"rendered":"How AlphaFold and other AI tools could help us prepare for the next pandemic"},"content":{"rendered":"

[vc_row full_width=”stretch_row” content_placement=”middle” css=”.vc_custom_1663187695627{padding-bottom: 37px !important;background-image: url(http:\/\/springerhealthcare.nl\/wp-content\/uploads\/sites\/24\/2022\/09\/science_connect_back.png?id=2486) !important;background-position: center !important;background-repeat: no-repeat !important;background-size: cover !important;}” el_class=”sciencetitle”][vc_column][vc_custom_heading text=”Science Connect” font_container=”tag:h2|text_align:left|color:%23ffffff” use_theme_fonts=”yes” link=”url:https%3A%2F%2Fspringerhealthcare.nl%2Ffrance%2Fscience-connect-october-2023%2F”][vc_column_text css=”.vc_custom_1663186747780{margin-bottom: 40px !important;}”]A Springer Healthcare Initiative For Pharma Professionals<\/span>[\/vc_column_text][vc_column_text]OCTOBER 2023
\n<\/span>[\/vc_column_text][\/vc_column][\/vc_row][vc_row css=”.vc_custom_1538651642953{padding-top: 75px !important;}”][vc_column width=”3\/4″ css=”.vc_custom_1538657061395{border-right-width: 1px !important;padding-top: 0px !important;border-right-color: #8faec1 !important;border-right-style: solid !important;}”][vc_custom_heading source=”post_title” font_container=”tag:h1|font_size:40px|text_align:left|line_height:60px” google_fonts=”font_family:Merriweather%3Aregular%2Citalic|font_style:700%20regular%3A700%3Anormal” el_class=”title” css=”.vc_custom_1664358136969{margin-bottom: 30px !important;}”][vc_column_text css=”.vc_custom_1686833173052{padding-bottom: 0px !important;}”]Researchers are using machine-learning programs to predict the evolution of viruses and design vaccines.<\/strong><\/span>[\/vc_column_text][vc_column_text el_class=”intro-box”]By Ewen Callaway<\/span>[\/vc_column_text][vc_single_image image=”2995″ img_size=”full” el_class=”hero-img”][vc_column_text css=”.vc_custom_1695902816200{margin-bottom: 30px !important;}” el_class=”sc-img-caption”]The rare Langya virus (computer-generated image) is related to some deadly pathogens. Credit: Kateryna Kon\/Science Photo Library[\/vc_column_text][vc_column_text]

In the third year of the COVID-19 pandemic, researchers\u00a0reported another worrying virus<\/a>. Identified in 35 people in eastern China since 2018, Langya henipavirus causes breathing problems, fever and other troubling symptoms.<\/p>\n

Langya hasn\u2019t been linked to any deaths yet. But it is related to some deadly viruses, so researchers were keen to develop vaccines. There was just one problem: a viral protein that could form the basis of a jab seemed impossible to make in the lab.<\/p>\n

\u201cIf we can\u2019t even study the protein, how are we going to understand how it works, and how are we going to make a vaccine?\u201d says David Veesler, a structural virologist at the University of Washington (UW) in Seattle.<\/p>\n

Now, thanks to artificial intelligence (AI), biologists have cracked Langya\u2019s nut. In work posted on the bioRxiv preprint server in August, Veesler\u2019s team describes using the\u00a0prediction tool AlphaFold<\/a>\u00a0to map the structure of a protein with which Langya invades cells1<\/sup>. Another AI tool identified mutations that transformed the unruly molecule into a suitable vaccine candidate.<\/p>\n

The research, which has not yet been peer reviewed, is part of nascent efforts to use groundbreaking advances in AI, such as AlphaFold and large language models, to\u00a0prepare for future pandemics<\/a>. Funders are pouring money into this approach, which is already bearing fruit. In a\u00a0Nature<\/em>\u00a0paper published on 11 October, researchers report a machine-learning tool that can predict the evolution of viruses with the potential to cause a pandemic2<\/sup>. This information could improve the resilience of vaccines, including those against COVID-19, and could give the world a head start when the next pandemic threat appears.<\/p>\n

\u201cDoes machine learning give us new arrows in our quivers? Yes, absolutely,\u201d says Neil King, a biochemist at UW. \u201cBut it\u2019s still early days.\u201d<\/p>\n

\u2018We got lucky\u2019<\/h2>\n

During the COVID-19 pandemic, a stroke of luck meant that\u00a0researchers were well prepared to develop vaccines<\/a>. Previous research on other coronaviruses, including the one that causes Middle East respiratory syndrome (MERS), gave them a good idea of how to turn SARS-CoV-2\u2019s genetic sequence into a vaccine. \u201cWe got totally lucky, hugely lucky,\u201d says King.<\/p>\n

But there are no such insights for many other\u00a0viruses with pandemic potential<\/a>. That\u2019s where machine learning is, increasingly, playing a part.<\/p>\n

Langya virus is part of a family called henipaviruses. These include the\u00a0highly lethal Nipah virus<\/a>\u00a0and Hendra virus, which causes deadly outbreaks in horses and can be fatal to people. But Langya is sufficiently genetically distinct that countermeasures against its relatives \u2014 including a Hendra vaccine approved for horses and trialled in humans \u2014 are unlikely to work, says Veesler.<\/p>\n

His team set out to map the structure of Langya\u2019s version of the \u2018G protein\u2019 that is the target of infection-blocking antibodies in other henipaviruses, and the basis of the Hendra vaccine.<\/p>\n

Initial efforts to coax human cells to make Langya\u2019s G protein for study failed, so the researchers used AlphaFold to predict what the protein looks like. Another AI tool identified mutations that made the protein stable enough to investigate in the lab. The AI-tweaked viral protein is now the basis of a prototype vaccine for Langya, says Veesler. Machine learning, he says, \u201cenabled something that would not have been possible otherwise\u201d.<\/p>\n

Faster vaccine design<\/h2>\n

Jason McLellan, a structural biologist at the University of Texas at Austin, has started using some of the same AI tools to study viral proteins and modify them for vaccine design. In some cases, they\u2019ve identified changes that he would have missed otherwise.<\/p>\n

\u201cThese new techniques are changing our everyday life, making things so much faster,\u201d says Clara Schoeder, who works on computational design of therapies at Leipzig University in Germany.<\/p>\n

She is part of an effort, funded by the Coalition for Epidemic Preparedness Innovations (CEPI) in Oslo, to use machine-learning tools to help create a library of potential vaccines for a set of worrying viruses. Earlier this year, the US National Institute of Allergy and Infectious Diseases announced US$100 million in funding for similar work on vaccine libraries.<\/p>\n

\"A
COVID-19 vaccines were developed with the help of previous work on coronaviruses related to SARS-CoV-2. Credit: Koen Van Weel\/EPA-EFE\/Shutterstock<\/span><\/figcaption><\/figure>\n

 <\/p>\n

Schoeder and her colleagues are exploring whether a type of neural network called a protein language model can help with vaccine design. These networks, inspired by large language models such as ChatGPT, are\u00a0trained on vast troves of protein sequences<\/a>. This could help the networks identify evolutionarily plausible changes that could be used to make better vaccines, says Brian Hie, a computational biologist at Stanford University in California. \u201cIt\u2019s a very promising area,\u201d he says.<\/p>\n

Other researchers are\u00a0using AI to make vaccines based on designer proteins<\/a>. King\u2019s team is leaning heavily on machine-learning tools based on image-generating AIs such as Midjourney. One creation that the group has not yet published is a designer protein that holds a snippet of a malaria molecule, forcing it into a shape that attracts a powerful antibody response. \u201cThese methods have totally changed the game in terms of what is possible to design,\u201d King says.<\/p>\n

Staying ahead<\/h2>\n

Researchers are also beginning to use machine learning to design vaccines that are one or two steps ahead of the most troubling viruses. COVID-19 vaccines were wildly successful at protecting against the disease at first. But the\u00a0emergence of the immune-evading Omicron variant<\/a>\u00a0and its descendants has sapped the vaccines\u2019 strength and durability.\u00a0Updated vaccines<\/a>\u00a0\u2014 the most recent ones based on the\u00a0XBB.1.5 lineage<\/a>, which emerged in late 2022 \u2014 still lag months behind viral evolution.<\/p>\n

Debora Marks at Harvard Medical School in Boston, Massachusetts, applies AI to biological problems. In today\u2019s\u00a0Nature<\/em>\u00a0paper2<\/a><\/sup>, she and her team describe developing a deep-learning network able to predict mutations that help SARS-CoV-2 to spread and overcome immunity. They trained the model, called EVEscape, on coronavirus sequences generated before January 2020, when SARS-CoV-2 was first identified in Wuhan, China.<\/p>\n

EVEscape is an impressive SARS-CoV-2 soothsayer. Half of the mutations the model predicted in a region of the cell-invading spike protein most prone to change have already been observed in real-world SARS-CoV-2 variants, a figure that should grow as the virus continues to evolve2<\/sup>.<\/p>\n

In work posted on bioRxiv this week3<\/sup>, the team used the model to create a set of potential sequences for the SARS-CoV-2 spike protein, some containing as many as 46 mutations from the ancestral strain, with the hope of anticipating the virus\u2019s future evolution and contributing to the development of experimental vaccines.<\/p>\n

The model isn\u2019t limited to SARS-CoV-2. Marks and her colleagues found that it could also predict the evolution of HIV, influenza, Nipah and the virus that causes Lassa haemorrhagic fever. When a new virus with pandemic potential pops up, the team hopes to be ready with predictions for its evolution \u2014 and perhaps even vaccines based on those predictions.<\/p>\n

Melanie Saville, CEPI\u2019s executive director of vaccine research and development, says that machine learning has the potential to vastly increase the number of vaccine designs that can be used quickly to identify the most promising candidates. \u201cWe just need to be cautious not to say this computational design is going to be the solution to everything,\u201d she says. \u201cBut it\u2019s a great starting point.\u201d<\/p>\n

Nature<\/em>\u00a0622<\/strong>, 440-441 (2023)<\/p>\n

doi: https:\/\/doi.org\/10.1038\/d41586-023-03201-4<\/em><\/p>\n

References<\/h2>\n
    \n
  1. \n
      \n
    1. Wang, Z. et al<\/em>. Preprint at bioRxiv https:\/\/doi.org\/10.1101\/2023.08.20.554025<\/a> (2023).<\/li>\n
    2. Thadani, N. N. et al<\/em>. Nature<\/em> https:\/\/doi.org\/10.1038\/s41586-023-06617-0<\/a> (2023).<\/li>\n
    3. Youssef, N. A. et al<\/em>. Preprint at bioRxiv https:\/\/doi.org\/10.1101\/2023.10.08.561389<\/a> (2023).<\/li>\n<\/ol>\n<\/li>\n<\/ol>\n[\/vc_column_text][vc_column_text]\u00a9 2023 Springer Nature Limited.[\/vc_column_text][\/vc_column][vc_column width=”1\/4″ css=”.vc_custom_1538657003956{padding-top: 0px !important;padding-bottom: 0px !important;}”][vc_custom_heading text=”ISSUES” font_container=”tag:h3|font_size:12px|text_align:left|color:%23333333|line_height:18px” use_theme_fonts=”yes” el_class=”titlewidget”][vc_column_text el_class=”columnflex” css=”.vc_custom_1664404002021{margin-bottom: 40px !important;}”]

      October 2023<\/a><\/p>\r\n

      September 2023<\/a><\/p>\r\n

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