AI is a viable alternative to high throughput screening: a 318-target study
Wallach, Izhar; Bernard, Denzil; Nguyen, Kong; Ho, Gregory; Morrison, Adrian; Stecula, Adrian; Rosnik, Andreana; O"™Sullivan, Ann Marie; Davtyan, Aram; Samudio, Ben; Thomas, Bill; Worley, Brad; Butler, Brittany; Laggner, Christian; Thayer, Desiree; Moharreri, Ehsan; Friedland, Greg; Truong, Ha; van den Bedem, Henry; Ng, Ho Leung; Stafford, Kate; Sarangapani, Krishna; Giesler, Kyle; Ngo, Lien; Mysinger, Michael; Ahmed, Mostafa; Anthis, Nicholas J.; Henriksen, Niel; Gniewek, Pawel; Eckert, Sam; de Oliveira, Saulo; Suterwala, Shabbir; PrasadPrasad, Srimukh Veccham Krishna; Shek, Stefani; Contreras, Stephanie; Hare, Stephanie; Palazzo, Teresa; O"™Brien, Terrence E.; Van Grack, Tessa; Williams, Tiffany; Chern, Ting Rong; Kenyon, Victor; Lee, Andreia H.; Cann, Andrew B.; Bergman, Bastiaan; Anderson, Brandon M.; Cox, Bryan D.; Warrington, Jeffrey M.; Sorenson, Jon M.; Goldenberg, Joshua M.; Young, Matthew A.; DeHaan, Nicholas; Pemberton, Ryan P.; Schroedl, Stefan; Abramyan, Tigran M.; Gupta, Tushita; Mysore, Venkatesh; Presser, Adam G.; Ferrando, Adolfo A.; Andricopulo, Adriano D.; Ghosh, Agnidipta; Ayachi, Aicha Gharbi; Mushtaq, Aisha; Shaqra, Ala M.; Toh, Alan Kie Leong; Smrcka, Alan V.; Ciccia, Alberto; de Oliveira, Aldo Sena; Sverzhinsky, Aleksandr; de Sousa, Alessandra Mara; Agoulnik, Alexander I.; Kushnir, Alexander; Freiberg, Alexander N.; Statsyuk, Alexander V.; Gingras, Alexandre R.; Degterev, Alexei; Tomilov, Alexey; Vrielink, Alice; Garaeva, Alisa A.; Bryant-Friedrich, Amanda; Caflisch, Amedeo; Patel, Amit K.; Rangarajan, Amith Vikram; Matheeussen, An; Battistoni, Andrea; Caporali, Andrea; Chini, Andrea; Ilari, Andrea; Mattevi, Andrea; Foote, Andrea Talbot; Trabocchi, Andrea; Stahl, Andreas; Herr, Andrew B.; Berti, Andrew; Freywald, Andrew; Reidenbach, Andrew G.; Lam, Andrew; Cuddihy, Andrew R.; White, Andrew; Taglialatela, Angelo; Ojha, Anil K.; Cathcart, Ann M.; Motyl, Anna A.L.; Borowska, Anna; D"™Antuono, Anna; Hirsch, Anna K.H.; Porcelli, Anna Maria; Minakova, Anna; Montanaro, Anna; Müller, Anna; Fiorillo, Annarita; Virtanen, Anniina; O"™Donoghue, Anthony J.; Del Rio Flores, Antonio; Garmendia, Antonio E.; Pineda-Lucena, Antonio; Panganiban, Antonito T.; Samantha, Ariela; Chatterjee, Arnab K.; Haas, Arthur L.; Paparella, Ashleigh S.; John, Ashley L.St; Prince, Ashutosh; ElSheikh, Assmaa; Apfel, Athena Marie; Colomba, Audrey; O"™Dea, Austin; Diallo, Bakary N"™tji; Ribeiro, Beatriz Murta Rezende Moraes; Bailey-Elkin, Ben A.; Edelman, Benjamin L.; Liou, Benjamin; Perry, Benjamin; Chua, Benjamin Soon Kai; Kováts, Benjámin; Englinger, Bernhard; Balakrishnan, Bijina; Gong, Bin; Agianian, Bogos; Pressly, Brandon; Salas, Brenda P.Medellin; Duggan, Brendan M.; Geisbrecht, Brian V.; Dymock, Brian W.; Morten, Brianna C.; Hammock, Bruce D.; Mota, Bruno Eduardo Fernandes; Dickinson, Bryan C.; Fraser, Cameron; Lempicki, Camille; Novina, Carl D.; Torner, Carles; Ballatore, Carlo; Bon, Carlotta; Chapman, Carly J.; Partch, Carrie L.; Chaton, Catherine T.; Huang, Chang; Yang, Chao Yie; Kahler, Charlene M.; Karan, Charles; Keller, Charles; Dieck, Chelsea L.; Huimei, Chen; Liu, Chen; Peltier, Cheryl; Mantri, Chinmay Kumar; Kemet, Chinyere Maat; Müller, Christa E.; Weber, Christian; Zeina, Christina M.; Muli, Christine S.; Morisseau, Christophe; Alkan, Cigdem; Reglero, Clara; Loy, Cody A.; Wilson, Cornelia M.; Myhr, Courtney; Arrigoni, Cristina; Paulino, Cristina; Santiago, César; Luo, Dahai; Tumes, Damon J.; Keedy, Daniel A.; Lawrence, Daniel A.; Chen, Daniel; Manor, Danny; Trader, Darci J.; Hildeman, David A.; Drewry, David H.; Dowling, David J.; Hosfield, David J.; Smith, David M.; Moreira, David; Siderovski, David P.; Shum, David; Krist, David T.; Riches, David W.H.; Ferraris, Davide Maria; Anderson, Deborah H.; Coombe, Deirdre R.; Welsbie, Derek S.; Hu, Di; Ortiz, Diana; Alramadhani, Dina; Zhang, Dingqiang; Chaudhuri, Dipayan; Slotboom, Dirk J.; Ronning, Donald R.; Lee, Donghan; Dirksen, Dorian; Shoue, Douglas A.; Zochodne, Douglas William; Krishnamurthy, Durga; Duncan, Dustin; Glubb, Dylan M.; Gelardi, Edoardo Luigi Maria; Hsiao, Edward C.; Lynn, Edward G.; Silva, Elany Barbosa; Aguilera, Elena; Lenci, Elena; Abraham, Elena Theres; Lama, Eleonora; Mameli, Eleonora; Leung, Elisa; Christensen, Emily M.; Mason, Emily R.; Petretto, Enrico; Trakhtenberg, Ephraim F.; Rubin, Eric J.; Strauss, Erick; Thompson, Erik W.; Cione, Erika; Lisabeth, Erika Mathes; Fan, Erkang; Kroon, Erna Geessien; Jo, Eunji; Garcia-Cuesta, Eva M.; Glukhov, Evgenia; Gavathiotis, Evripidis; Yu, Fang; Xiang, Fei; Leng, Fenfei; Wang, Feng; Ingoglia, Filippo; van den Akker, Focco; Borriello, Francesco; Vizeacoumar, Franco J.; Luh, Frank; Buckner, Frederick S.; Vizeacoumar, Frederick S.; Bdira, Fredj Ben; Svensson, Fredrik; Rodriguez, G. Marcela; Bognár, Gabriella; Lembo, Gaia; Zhang, Gang; Dempsey, Garrett; Eitzen, Gary; Mayer, Gaétan; Greene, Geoffrey L.; Garcia, George A.; Lukacs, Gergely L.; Prikler, Gergely; Parico, Gian Carlo G.; Colotti, Gianni; De Keulenaer, Gilles; Cortopassi, Gino; Roti, Giovanni; Girolimetti, Giulia; Fiermonte, Giuseppe; Gasparre, Giuseppe; Leuzzi, Giuseppe; Dahal, Gopal; Michlewski, Gracjan; Conn, Graeme L.; Stuchbury, Grant David; Bowman, Gregory R.; Popowicz, Grzegorz Maria; Veit, Guido; de Souza, Guilherme Eduardo; Akk, Gustav; Caljon, Guy; Alvarez, Guzmán; Rucinski, Gwennan; Lee, Gyeongeun; Cildir, Gokhan; Li, Hai; Breton, Hairol E.; Jafar-Nejad, Hamed; Zhou, Han; Moore, Hannah P.; Tilford, Hannah; Yuan, Haynes; Shim, Heesung; Wulff, Heike; Hoppe, Heinrich; Chaytow, Helena; Tam, Heng Keat; Van Remmen, Holly; Xu, Hongyang; Debonsi, Hosana Maria; Lieberman, Howard B.; Jung, Hoyoung; Fan, Hua Ying; Feng, Hui; Zhou, Hui; Kim, Hyeong Jun; Greig, Iain R.; Caliandro, Ileana; Corvo, Ileana; Arozarena, Imanol; Mungrue, Imran N.; Verhamme, Ingrid M.; Qureshi, Insaf Ahmed; Lotsaris, Irina; Cakir, Isin; Perry, J. Jefferson P.; Kwiatkowski, Jacek; Boorman, Jacob; Ferreira, Jacob; Fries, Jacob; Kratz, Jadel Müller; Miner, Jaden; Siqueira-Neto, Jair L.; Granneman, James G.; Ng, James; Shorter, James; Voss, Jan Hendrik; Gebauer, Jan M.; Chuah, Janelle; Mousa, Jarrod J.; Maynes, Jason T.; Evans, Jay D.; Dickhout, Jeffrey; MacKeigan, Jeffrey P.; Jossart, Jennifer N.; Zhou, Jia; Lin, Jiabei; Xu, Jiake; Wang, Jianghai; Zhu, Jiaqi; Liao, Jiayu; Xu, Jingyi; Zhao, Jinshi; Lin, Jiusheng; Lee, Jiyoun; Reis, Joana; Stetefeld, Joerg; Bruning, John B.; , ; Coles, John G.; Tanner, John J.; Pascal, John M.; So, Jonathan; Pederick, Jordan L.; Costoya, Jose A.; Rayman, Joseph B.; Maciag, Joseph J.; Nasburg, Joshua Alexander; Gruber, Joshua J.; Finkelstein, Joshua M.; Watkins, Joshua; Rodriguez-Frade, José Miguel; Arias, Juan Antonio Sanchez; Lasarte, Juan José; Oyarzabal, Julen; Milosavljevic, Julian; Cools, Julie; Lescar, Julien; Bogomolovas, Julijus; Wang, Jun; Kee, Jung Min; Kee, Jung Min; Liao, Junzhuo; Sistla, Jyothi C.; Abrahão, Jônatas Santos; Sishtla, Kamakshi; Francisco, Karol R.; Hansen, Kasper B.; Molyneaux, Kathleen A.; Cunningham, Kathryn A.; Martin, Katie R.; Gadar, Kavita; Ojo, Kayode K.; Wong, Keith S.; Wentworth, Kelly L.; Lai, Kent; Lobb, Kevin A.; Hopkins, Kevin M.; Parang, Keykavous; Machaca, Khaled; Pham, Kien; Ghilarducci, Kim; Sugamori, Kim S.; McManus, Kirk James; Musta, Kirsikka; Faller, Kiterie M.E.; Nagamori, Kiyo; Mostert, Konrad J.; Korotkov, Konstantin V.; Liu, Koting; Smith, Kristiana S.; Sarosiek, Kristopher; Rohde, Kyle H.; Kim, Kyu Kwang; Lee, Kyung Hyeon; Pusztai, Lajos; Lehtio, Lari; Haupt, Larisa M.; Cowen, Leah E.; Byrne, Lee J.; Su, Leila; Wert-Lamas, Leon; Puchades-Carrasco, Leonor; Chen, Lifeng; Malkas, Linda H.; Zhuo, Ling; , ; Hedstrom, Lizbeth; Walensky, Loren D.; Antonelli, Lorenzo; Iommarini, Luisa; Whitesell, Luke; Randall, Lia M.; Fathallah, M. Dahmani; Nagai, Maira Harume; Kilkenny, Mairi Louise; Ben-Johny, Manu; Lussier, Marc P.; Windisch, Marc P.; Lolicato, Marco; Lolli, Marco Lucio; Vleminckx, Margot; Caroleo, Maria Cristina; Macias, Maria J.; Valli, Marilia; Barghash, Marim M.; Mellado, Mario; Tye, Mark A.; Wilson, Mark A.; Hannink, Mark; Ashton, Mark R.; Cerna, Mark Vincent C.dela; Giorgis, Marta; Safo, Martin K.; Maurice, Martin St; McDowell, Mary Ann; Pasquali, Marzia; Mehedi, Masfique; Serafim, Mateus Sá Magalhães; Soellner, Matthew B.; Alteen, Matthew G.; Champion, Matthew M.; Skorodinsky, Maxim; O"™Mara, Megan L.; Bedi, Mel; Rizzi, Menico; Levin, Michael; Mowat, Michael; Jackson, Michael R.; Paige, Mikell; Al-Yozbaki, Minnatallah; Giardini, Miriam A.; Maksimainen, Mirko M.; De Luise, Monica; Hussain, Muhammad Saddam; Christodoulides, Myron; Stec, Natalia; Zelinskaya, Natalia; Van Pelt, Natascha; Merrill, Nathan M.; Singh, Nathanael; Kootstra, Neeltje A.; Singh, Neeraj; Gandhi, Neha S.; Chan, Nei Li; Trinh, Nguyen Mai; Schneider, Nicholas O.; Matovic, Nick; Horstmann, Nicola; Longo, Nicola; Bharambe, Nikhil; Rouzbeh, Nirvan; Mahmoodi, Niusha; Gumede, Njabulo Joyfull; Anastasio, Noelle C.; Khalaf, Noureddine Ben; Rabal, Obdulia; Kandror, Olga; Escaffre, Olivier; Silvennoinen, Olli; Bishop, Ozlem Tastan; Iglesias, Pablo; Sobrado, Pablo; Chuong, Patrick; O"™Connell, Patrick; Martin-Malpartida, Pau; Mellor, Paul; Fish, Paul V.; Moreira, Paulo Otávio Lourenço; Zhou, Pei; , ; Liu, Pengda; Wu, Pengpeng; Agogo-Mawuli, Percy; Jones, Peter L.; Ngoi, Peter; Toogood, Peter; Ip, Philbert; von Hundelshausen, Philipp; Lee, Pil H.; Rowswell-Turner, Rachael B.; Balaña-Fouce, Rafael; Rocha, Rafael Eduardo Oliveira; Guido, Rafael V.C.; Ferreira, Rafaela Salgado; Agrawal, Rajendra K.; Harijan, Rajesh K.; Ramachandran, Rajesh; Verma, Rajkumar; Singh, Rakesh K.; Tiwari, Rakesh Kumar; Mazitschek, Ralph; Koppisetti, Rama K.; Dame, Remus T.; Douville, Renée N.; Austin, Richard C.; Taylor, Richard E.; Moore, Richard G.; Ebright, Richard H.; Angell, Richard M.; Yan, Riqiang; Kejriwal, Rishabh; Batey, Robert A.; Blelloch, Robert; Vandenberg, Robert J.; Hickey, Robert J.; Kelm, Robert J.; Lake, Robert J.; Bradley, Robert K.; Blumenthal, Robert M.; Solano, Roberto; Gierse, Robin Matthias; Viola, Ronald E.; McCarthy, Ronan R.; Reguera, Rosa Maria; Uribe, Ruben Vazquez; do Monte-Neto, Rubens Lima; Gorgoglione, Ruggiero; Cullinane, Ryan T.; Katyal, Sachin; Hossain, Sakib; Phadke, Sameer; Shelburne, Samuel A.; Geden, Sandra E.; Johannsen, Sandra; Wazir, Sarah; Legare, Scott; Landfear, Scott M.; Radhakrishnan, Senthil K.; Ammendola, Serena; Dzhumaev, Sergei; Seo, Seung Yong; Li, Shan; Zhou, Shan; Chu, Shaoyou; Chauhan, Shefali; Maruta, Shinsaku; Ashkar, Shireen R.; Shyng, Show Ling; Conticello, Silvestro G.; Buroni, Silvia; Garavaglia, Silvia; White, Simon J.; Zhu, Siran; Tsimbalyuk, Sofiya; Chadni, Somaia Haque; Byun, Soo Young; Park, Soonju; Xu, Sophia Q.; Banerjee, Sourav; Zahler, Stefan; Espinoza, Stefano; Gustincich, Stefano; Sainas, Stefano; Celano, Stephanie L.; Capuzzi, Stephen J.; Waggoner, Stephen N.; Poirier, Steve; Olson, Steven H.; Marx, Steven O.; Van Doren, Steven R.; Sarilla, Suryakala; Brady-Kalnay, Susann M.; Dallman, Sydney; Azeem, Syeda Maryam; Teramoto, Tadahisa; Mehlman, Tamar; Swart, Tarryn; Abaffy, Tatjana; Akopian, Tatos; Haikarainen, Teemu; Moreda, Teresa Lozano; Ikegami, Tetsuro; Teixeira, Thaiz Rodrigues; Jayasinghe, Thilina D.; Gillingwater, Thomas H.; Kampourakis, Thomas; Richardson, Timothy I.; Herdendorf, Timothy J.; Kotzé, Timothy J.; O"™Meara, Timothy R.; Corson, Timothy W.; Hermle, Tobias; Ogunwa, Tomisin Happy; Lan, Tong; Su, Tong; Banjo, Toshihiro; O"™Mara, Tracy A.; Chou, Tristan; Chou, Tsui Fen; Baumann, Ulrich; Desai, Umesh R.; Pai, Vaibhav P.; Thai, Van Chi; Tandon, Vasudha; Banerji, Versha; Robinson, Victoria L.; Gunasekharan, Vignesh; Namasivayam, Vigneshwaran; Segers, Vincent F.M.; Maranda, Vincent; Dolce, Vincenza; Maltarollo, Vinicius Gonçalves; Scoffone, Viola Camilla; Woods, Virgil A.; Ronchi, Virginia Paola; Van Hung Le, Vuong; Clayton, W. Brent; Lowther, W. Todd; Houry, Walid A.; Li, Wei; Tang, Weiping; Zhang, Wenjun; Van Voorhis, Wesley C.; Donaldson, William A.; Hahn, William C.; Kerr, William G.; Gerwick, William H.; Bradshaw, William J.; Foong, Wuen Ee; Blanchet, Xavier; Wu, Xiaoyang; Lu, Xin; Qi, Xin; Xu, Xin; Yu, Xinfang; Qin, Xingping; Wang, Xingyou; Yuan, Xinrui; Zhang, Xu; Zhang, Yan Jessie; Hu, Yanmei; Aldhamen, Yasser Ali; Chen, Yicheng; Li, Yihe; Sun, Ying; Zhu, Yini; Gupta, Yogesh K.; Pérez-Pertejo, Yolanda; Li, Yong; Tang, Young; He, Yuan; Tse-Dinh, Yuk Ching; Sidorova, Yulia A.; Yen, Yun; Li, Yunlong; Frangos, Zachary J.; Chung, Zara; Su, Zhengchen; Wang, Zhenghe; Zhang, Zhiguo; Liu, Zhongle; Inde, Zintis; Artia, Zoraima; Heifets, Abraham
High throughput screening (HTS) is routinely used to identify bioactive small molecules. This requires physical compounds, which limits coverage of accessible chemical space. Computational approaches combined with vast on-demand chemical libraries can access far greater chemical space, provided that the predictive accuracy is sufficient to identify useful molecules. Through the largest and most diverse virtual HTS campaign reported to date, comprising 318 individual projects, we demonstrate that our AtomNet® convolutional neural network successfully finds novel hits across every major therapeutic area and protein class. We address historical limitations of computational screening by demonstrating success for target proteins without known binders, high-quality X-ray crystal structures, or manual cherry-picking of compounds. We show that the molecules selected by the AtomNet® model are novel drug-like scaffolds rather than minor modifications to known bioactive compounds. Our empirical results suggest that computational methods can substantially replace HTS as the first step of small-molecule drug discovery.
SCOPUS:85191821387
ISSN: 2045-2322
CID: 5658952