{"651841":{"#nid":"651841","#data":{"type":"news","title":"AI Tool Pairs Protein Pathways with Clinical Side Effects, Patient Comorbidities to Suggest Targeted Covid-19 Treatments","body":[{"value":"\u003Cp\u003EThe symptoms and side effects of Covid-19 are scattered across a diagnostic spectrum. Some patients are asymptomatic or experience a mild immune response, while others report significant long-term illnesses, lasting complications, or suffer fatal outcomes.\u003C\/p\u003E\r\n\r\n\u003Cp\u003EThree researchers from the Georgia Institute of Technology and one from Emory University are trying to help clinicians sort through these factors and spectrum of patient outcomes by equipping healthcare professionals with a new \u0026ldquo;decision prioritization tool.\u0026rdquo;\u003C\/p\u003E\r\n\r\n\u003Cp\u003EThe team\u0026rsquo;s new artificial intelligence-based tool helps clinicians understand and better predict which adverse effects their Covid-19 patients could experience, based on comorbidities and current side effects \u0026mdash; and, in turn, also helps suggest specific Food and Drug Administration-approved (FDA) drugs that could help treat the disease and improve patient health outcomes. The researcher\u0026#39;s latest findings are the focus of \u003Ca href=\u0022http:\/\/nature.com\/articles\/s41598-021-00368-6\u0022\u003Ea new study published October 21\u003C\/a\u003E in \u003Ca href=\u0022https:\/\/www.nature.com\/srep\/\u0022\u003E\u003Cem\u003ENature Scientific Reports\u003C\/em\u003E\u003C\/a\u003E.\u003C\/p\u003E\r\n\r\n\u003Cp\u003E\u003Cstrong\u003EArtificial intelligence, protein drivers, and \u0026lsquo;24 out of 26 clinical manifestations\u0026rsquo; of Covid-19\u003C\/strong\u003E\u003C\/p\u003E\r\n\r\n\u003Cp\u003EThe team\u0026rsquo;s new methodology, or tool, is called MOATAI-VIR (\u003Cstrong\u003EM\u003C\/strong\u003Eode \u003Cstrong\u003EO\u003C\/strong\u003Ef \u003Cstrong\u003EA\u003C\/strong\u003Ection proteins \u0026amp; \u003Cstrong\u003ET\u003C\/strong\u003Eargeted therapeutic discovery driven by \u003Cstrong\u003EA\u003C\/strong\u003Ertificial \u003Cstrong\u003EI\u003C\/strong\u003Entelligence for \u003Cstrong\u003EVIR\u003C\/strong\u003Euses. Researchers report it predicts 24 out of 26 major clinical manifestations of Covid-19 and their underlying disease-protein-pathway relationships.\u003C\/p\u003E\r\n\r\n\u003Cp\u003EThose clinical manifestations cover a \u003Ca href=\u0022https:\/\/jamanetwork.com\/journals\/jamainternalmedicine\/fullarticle\/2763184\u0022\u003Erange of issues\u003C\/a\u003E including \u003Ca href=\u0022https:\/\/www.nejm.org\/doi\/full\/10.1056\/nejmoa2020283\u0022\u003Eacute respiratory distress\u003C\/a\u003E, blood clotting issues, \u003Ca href=\u0022\/\/\/R.%20J.%20Jose,%20A.%20Manuel,%20COVID-19%20cytokine%20storm\/%20the%20interplay%20between%20inflammation%20and%20coagulation.%20The%20Lancet%20Respiratory%20Medicine%208,%20e46-e47%20(2020).\u0022\u003Ecytokine storms\u003C\/a\u003E, low blood oxygen and white blood cell counts, and even bone marrow failure. The commonly reported loss of smell or taste, along with \u003Ca href=\u0022https:\/\/www.cidrap.umn.edu\/news-perspective\/2021\/06\/neurologic-psychiatric-conditions-common-covid-19\u0022\u003Eunusual neurological symptoms\u003C\/a\u003E such as \u0026ldquo;brain fog\u0026rdquo; have received widespread attention \u0026mdash; as have considerations for patients who have previous health problems, or comorbidities, that could place them in higher risk categories related to Covid-19.\u003C\/p\u003E\r\n\r\n\u003Cp\u003E\u0026ldquo;It\u0026rsquo;s still the question of, what\u0026rsquo;s causing the side effects?\u0026rdquo; says \u003Ca href=\u0022https:\/\/biosciences.gatech.edu\/people\/jeffrey-skolnick\u0022\u003EJeffrey Skolnick\u003C\/a\u003E, professor and Mary and Maisie Gibson Chair in the \u003Ca href=\u0022https:\/\/biosciences.gatech.edu\/\u0022\u003ESchool of Biological Sciences\u003C\/a\u003E, and corresponding author for the study. \u0026ldquo;So, you lost sense of smell and got brain fog \u0026mdash; and another (patient) had respiratory distress, and another can\u0026rsquo;t remember the day of the week. What we\u0026rsquo;ve identified are the possible mode of action drivers for these various conditions, which is now setting the stage for who\u0026rsquo;s getting what side effects.\u0026rdquo;\u003C\/p\u003E\r\n\r\n\u003Cp\u003ESkolnick, also Georgia Research Alliance Eminent Scholar in Computational Systems Biology, notes that it makes sense to predict the side effects based on protein interactions.\u003C\/p\u003E\r\n\r\n\u003Cp\u003E\u0026ldquo;Humans are molecular machines, and presumably there are biological and physical rules to dictate our responses,\u0026rdquo; Skolnick says\u0026nbsp;. \u0026ldquo;We basically built an AI-based approach which was designed given the interactive set of proteins in humans which interact with the [novel] coronavirus,\u0026rdquo; he adds. \u0026ldquo;We then asked ourselves, \u0026lsquo;Could we predict, based on biochemical pathways, which interactive proteins are associated with side effects?\u0026rsquo;\u0026rdquo;\u003C\/p\u003E\r\n\r\n\u003Cp\u003EJoining Skolnick from the School of Biological Sciences are Ph.D. student \u003Ca href=\u0022https:\/\/bioinformatics.gatech.edu\/people\/Courtney-Astore\u0022\u003ECourtney Astore\u003C\/a\u003E and senior research scientist \u003Ca href=\u0022https:\/\/biosciences.gatech.edu\/people\/hongyi-zhou\u0022\u003EHongyi Zhou\u003C\/a\u003E, both from the \u003Ca href=\u0022http:\/\/cssb.biology.gatech.edu\/index.html\u0022\u003ECenter for the Study of Systems Biology\u003C\/a\u003E. Joshy Jacob of the Department of Microbiology and Immunology in the Emory Vaccine Center at the Emory School of Medicine also worked on the study.\u003C\/p\u003E\r\n\r\n\u003Cp\u003E\u003Cstrong\u003EMOATAI-VIR methodology\u003C\/strong\u003E\u003C\/p\u003E\r\n\r\n\u003Cp\u003ESkolnick explains that most known diseases are due to the \u0026ldquo;malfunction and interaction of many proteins,\u0026rdquo; and notes that it\u0026rsquo;s a collective effect \u0026mdash; a \u0026ldquo;many-targeted protein effect.\u0026rdquo; His team\u0026rsquo;s new AI methodology is identifying as many targets as possible of an interacting nature to predict a complex response from a complex set of interactions.\u003C\/p\u003E\r\n\r\n\u003Cp\u003EIt\u0026rsquo;s also well-understood in the medical community that comorbidities \u0026mdash; existing and chronic health factors such as diabetes, obesity, autoimmune disorders, and other conditions that affect the immune system \u0026mdash; can play an outsized a role in risk factors related to Covid-19. Skolnick says those comorbidities can be plugged into the team\u0026rsquo;s algorithm, too.\u003C\/p\u003E\r\n\r\n\u003Cp\u003E\u0026nbsp;\u0026ldquo;Alzheimer\u0026rsquo;s and hyperthyroidism are strongly correlated \u0026mdash; as is diabetes. There are six to eight (Covid-19) comorbidities with a patient that has Alzheimer\u0026rsquo;s,\u0026rdquo; Skolnick explains. \u0026ldquo;It\u0026rsquo;s not just old age \u0026mdash; it\u0026rsquo;s much more complicated.\u0026rdquo;\u003C\/p\u003E\r\n\r\n\u003Cp\u003EThe MOATAI-VIR methodology helps identify the common proteins of the comorbidities in relation to the parent disease. A clinician can then target the diseases with drugs. Researchers report that this specific methodology had 72% success in 123,146 drug-indication pair predictions found by Skolnick\u0026rsquo;s team.\u003C\/p\u003E\r\n\r\n\u003Cp\u003E\u0026ldquo;For a given disease, we prioritize them by the proteins that are most in common with the comorbid diseases to the given disease, giving rise to the particular complication, such as respiratory failure. This identifies the putative (assumed) driver proteins for the given complication,\u0026rdquo; he says. \u0026ldquo;Then we select repurposed drugs in two ways \u0026mdash; we screen the most common comorbid proteins for their most frequent binding to repurposed drugs. For the set of comorbid diseases to a given complication, choose the drugs that treat the most complications.\u0026rdquo;\u003C\/p\u003E\r\n\r\n\u003Cp\u003EIt\u0026rsquo;s critical to find the right drugs for those complications and side effects \u0026mdash; and using the new \u0026ldquo;decision tool\u0026rdquo; can help do that, Skolnick says.\u003C\/p\u003E\r\n\r\n\u003Cp\u003EHe cautions that researchers and clinicians must approach this objectively because \u0026ldquo;there are deep reasons why you have these \u0026lsquo;off-target\u0026rsquo; interactions, where a drug binds to another protein that is not its original intended target \u0026mdash; and that\u0026rsquo;s what these algorithms take in to counter them. It\u0026rsquo;s not magic\u0026rdquo; to run this methodology, Skolnick explains. \u0026ldquo;It\u0026rsquo;s fractional assistance in a decision-making process \u0026mdash; which comes with probabilities [that] it might work. If there\u0026rsquo;s an 80 percent probability, you probably ought to try it.\u0026rdquo;\u003C\/p\u003E\r\n\r\n\u003Cp\u003E\u003Cstrong\u003EThe MOATAI-VIR methodology algorithms (decision prioritization tool) can be downloaded at: \u003Ca href=\u0022https:\/\/sites.gatech.edu\/cssb\/moatai-vir\/\u0022\u003Ehttps:\/\/sites.gatech.edu\/cssb\/moatai-vir\/\u003C\/a\u003E\u003C\/strong\u003E\u003C\/p\u003E\r\n\r\n\u003Cp\u003E\u003Cem\u003EThis project was funded by R35GM118039 of the Division of General Medical Sciences of the National Institutes of Health. \u003C\/em\u003E \u003Cem\u003EDOI: www.nature.com\/articles\/s41598-021-00368-6\u003C\/em\u003E\u003C\/p\u003E\r\n\r\n\u003Cp\u003E\u0026nbsp;\u003C\/p\u003E\r\n\r\n\u003Cp\u003E\u003Cem\u003E\u003Cstrong\u003ERelated News\u003C\/strong\u003E\u003C\/em\u003E\u003C\/p\u003E\r\n\r\n\u003Cp\u003E\u003Cstrong\u003ESkolnick and Team Win Next Stage of NCATS Competition\u003C\/strong\u003E\u003C\/p\u003E\r\n\r\n\u003Cp\u003EJeffrey Skolnick is also part of an award-winning \u003Ca href=\u0022https:\/\/www.nih.gov\/\u0022\u003ENational Institutes of Health\u003C\/a\u003E effort to create innovative, AI-powered platforms for discovering new pain management drugs, and for identifying immediate solutions. The competition staged by NIH\u0026rsquo;s \u003Ca href=\u0022https:\/\/ncats.nih.gov\/\u0022\u003ENCATS (National Center for Advancing Translational Sciences\u003C\/a\u003E) addresses the national opioid public health crisis.\u003C\/p\u003E\r\n\r\n\u003Cp\u003EIn September, a team with Skolnick, \u003Ca href=\u0022https:\/\/biosciences.gatech.edu\/people\/hongyi-zhou\u0022\u003EHongyi Zhou\u003C\/a\u003E, senior research scientist in the School of Biological Sciences, Andre Ghetti with\u0026nbsp;\u003Ca href=\u0022https:\/\/anabios.com\/\u0022\u003EANABIOS Corporation\u003C\/a\u003E, and Nicole Jung with\u0026nbsp;\u003Ca href=\u0022https:\/\/www.kit.edu\/english\/index.php\u0022\u003EKarlsruhe Institute of Technology\u003C\/a\u003E\u0026nbsp;in Germany, was one of four winning the \u003Ca href=\u0022https:\/\/ncats.nih.gov\/aspire\/funding\/2020ChallengeWinners#c4\u0022\u003E2020 (NCATS) ASPIRE\u0026nbsp;(A Specialized Platform for Innovative Research Exploration) Challenge, Stage 2, Milestone 1 Award\u003C\/a\u003E. Skolnick and Zhou won the previous stage in \u003Ca href=\u0022https:\/\/cos.gatech.edu\/news\/aspire-ing-find-fast-solutions-opioid-health-crisis\u0022\u003EMay\u003C\/a\u003E.\u003C\/p\u003E\r\n\r\n\u003Cp\u003ETheir platform, Development of a Comprehensive Integrated Platform for Translational Innovation in Pain, Opioid Abuse Disorder and Overdose, will face the final stage, Prototype Delivery, Independent Validation and Testing in 2022.\u003C\/p\u003E\r\n","summary":null,"format":"limited_html"}],"field_subtitle":"","field_summary":[{"value":"\u003Cp\u003EResearchers led by Jeffrey Skolnick have designed a new AI-based \u0026ldquo;decision prioritization tool\u0026rdquo; that combines data on protein pathways with common Covid-19 side effects and known patient comorbidities. The tool offers possible targeted treatment options with existing FDA-approved drugs to foster better health outcomes for individuals fighting Covid-19.\u003C\/p\u003E\r\n","format":"limited_html"}],"field_summary_sentence":[{"value":"A new AI-based \u201cdecision prioritization tool\u201d combines data on protein pathways with common Covid-19 side effects and known patient comorbidities to offer possible targeted patient treatment options with existing FDA-approved drugs to help fight Covid-19."}],"uid":"34434","created_gmt":"2021-10-20 14:13:20","changed_gmt":"2021-10-21 16:15:04","author":"Renay San Miguel","boilerplate_text":"","field_publication":"","field_article_url":"","dateline":{"date":"2021-10-21T00:00:00-04:00","iso_date":"2021-10-21T00:00:00-04:00","tz":"America\/New_York"},"extras":[],"hg_media":{"651900":{"id":"651900","type":"image","title":"This colorized transmission electron micrograph shows SARS-CoV-2 virus particles (orange), isolated from a patient. Credit: NIAID via NIH","body":null,"created":"1634824300","gmt_created":"2021-10-21 13:51:40","changed":"1634824300","gmt_changed":"2021-10-21 13:51:40","alt":"","file":{"fid":"247334","name":"20200804-covid-moderate.jpg","image_path":"\/sites\/default\/files\/images\/20200804-covid-moderate.jpg","image_full_path":"http:\/\/hg.gatech.edu\/\/sites\/default\/files\/images\/20200804-covid-moderate.jpg","mime":"image\/jpeg","size":279299,"path_740":"http:\/\/hg.gatech.edu\/sites\/default\/files\/styles\/740xx_scale\/public\/images\/20200804-covid-moderate.jpg?itok=t9-66Ig1"}},"604486":{"id":"604486","type":"image","title":"Jeffrey Skolnick","body":null,"created":"1522353871","gmt_created":"2018-03-29 20:04:31","changed":"1522353871","gmt_changed":"2018-03-29 20:04:31","alt":"","file":{"fid":"230441","name":"Jeffrey Skolnick.tall250.jpg","image_path":"\/sites\/default\/files\/images\/Jeffrey%20Skolnick.tall250.jpg","image_full_path":"http:\/\/hg.gatech.edu\/\/sites\/default\/files\/images\/Jeffrey%20Skolnick.tall250.jpg","mime":"image\/jpeg","size":82212,"path_740":"http:\/\/hg.gatech.edu\/sites\/default\/files\/styles\/740xx_scale\/public\/images\/Jeffrey%20Skolnick.tall250.jpg?itok=axvvAkRI"}}},"media_ids":["651900","604486"],"related_links":[{"url":"https:\/\/cos.gatech.edu\/news\/aspire-ing-find-fast-solutions-opioid-health-crisis","title":"ASPIRE-ing to Find Fast Solutions to the Opioid Health Crisis"},{"url":"https:\/\/cos.gatech.edu\/news\/jeffrey-skolnick-2018-sigma-xi-sustained-research-award","title":"Jeffrey Skolnick: 2018 Sigma Xi Sustained Research Award"},{"url":"https:\/\/cos.gatech.edu\/news\/origin-lifes-handedness-and-protein-biochemistry","title":"Origin of Life\u2019s Handedness and Protein Biochemistry"}],"groups":[{"id":"1278","name":"College of Sciences"},{"id":"1275","name":"School of Biological Sciences"},{"id":"1188","name":"Research Horizons"},{"id":"1214","name":"News Room"}],"categories":[{"id":"135","name":"Research"},{"id":"138","name":"Biotechnology, Health, Bioengineering, Genetics"},{"id":"146","name":"Life Sciences and Biology"}],"keywords":[{"id":"4896","name":"College of Sciences"},{"id":"166882","name":"School of Biological Sciences"},{"id":"11937","name":"Jeffrey Skolnick"},{"id":"184289","name":"covid-19"},{"id":"189104","name":"Covid complications"},{"id":"2556","name":"artificial intelligence"},{"id":"189106","name":"comorbidities"},{"id":"189107","name":"clinical support"},{"id":"187915","name":"go-researchnews"},{"id":"187423","name":"go-bio"}],"core_research_areas":[{"id":"39441","name":"Bioengineering and Bioscience"},{"id":"39501","name":"People and Technology"},{"id":"39511","name":"Public Service, Leadership, and Policy"}],"news_room_topics":[],"event_categories":[],"invited_audience":[],"affiliations":[],"classification":[],"areas_of_expertise":[],"news_and_recent_appearances":[],"phone":[],"contact":[{"value":"\u003Cp\u003E\u003Cstrong\u003ERenay San Miguel\u003C\/strong\u003E\u003Cbr \/\u003E\r\nCommunications Officer II\/Science Writer\u003Cbr \/\u003E\r\nCollege of Sciences\u003Cbr \/\u003E\r\n404-894-5209\u003C\/p\u003E\r\n\r\n\u003Cp\u003E\u003Cstrong\u003EMedia Relations Contacts:\u003C\/strong\u003E\u003C\/p\u003E\r\n\r\n\u003Cp\u003E\u003Cstrong\u003EJess Hunt-Ralston\u003C\/strong\u003E\u003Cbr \/\u003E\r\nGeorgia Institute of Technology\u003Cbr \/\u003E\r\njess@cos.gatech.edu\u003Cbr \/\u003E\r\nOffice: 404-385-5207\u003C\/p\u003E\r\n\r\n\u003Cp\u003E\u003Cstrong\u003EGeorgia Parmelee\u003C\/strong\u003E\u003Cbr \/\u003E\r\nGeorgia Institute of Technology\u003Cbr \/\u003E\r\ngeorgia.parmelee@gatech.edu\u003Cbr \/\u003E\r\nOffice: 404-281-7818\u003C\/p\u003E\r\n\r\n\u003Cp\u003E\u003Cem\u003EBy: Renay San Miguel\u003Cbr \/\u003E\r\nEditors: Jess Hunt-Ralston and Georgia Parmelee\u003C\/em\u003E\u003C\/p\u003E\r\n","format":"limited_html"}],"email":["renay.san@cos.gatech.edu"],"slides":[],"orientation":[],"userdata":""}}}