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Papasavvas E, Azzoni L, Ross BN, Fair M, Yuan Z, Gyampoh K, Mackiewicz A, Sciorillo AC, Pagliuzza A, Lada SM, Wu G, Goh SL, Bahnck-Teets C, Holder DJ, Zuck PD, Damra M, Lynn KM, Tebas P, Mounzer K, Kostman JR, Abdel-Mohsen M, Richman D, Chomont N, Howell BJ, Montaner LJ. Intact Human Immunodeficiency Virus (HIV) Reservoir Estimated by the Intact Proviral DNA Assay Correlates With Levels of Total and Integrated DNA in the Blood During Suppressive Antiretroviral Therapy. Clin Infect Dis 2021; 72:495-498. [PMID: 33527127 DOI: 10.1093/cid/ciaa809] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Accepted: 06/12/2020] [Indexed: 02/06/2023] Open
Abstract
Accurate characterization of the human immunodeficiency virus (HIV) reservoir is imperative to develop an effective cure. HIV was measured in antiretroviral therapy-suppressed individuals using the intact proviral DNA assay (IPDA), along with assays for total or integrated HIV DNA, and inducible HIV RNA or p24. Intact provirus correlated with total and integrated HIV.
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Affiliation(s)
| | - Livio Azzoni
- Wistar Institute, Philadelphia, Pennsylvania, USA
| | - Brian N Ross
- Wistar Institute, Philadelphia, Pennsylvania, USA
| | - Matthew Fair
- Wistar Institute, Philadelphia, Pennsylvania, USA
| | - Zhe Yuan
- Wistar Institute, Philadelphia, Pennsylvania, USA
| | | | | | | | | | - Steven M Lada
- Veterans Affairs San Diego Healthcare System and the University of California, San Diego, California, USA
| | - Guoxin Wu
- Merck & Co., Inc., Kenilworth, New Jersey, USA
| | | | | | | | - Paul D Zuck
- Merck & Co., Inc., Kenilworth, New Jersey, USA
| | | | - Kenneth M Lynn
- Presbyterian Hospital, University of Pennsylvania hospital, Philadelphia, Pennsylvania, USA
| | - Pablo Tebas
- Department of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Karam Mounzer
- Jonathan Lax Immune Disorders Treatment Center, Philadelphia Field Initiating Group for HIV-1 Trials, Philadelphia, Pennsylvania, USA
| | - Jay R Kostman
- John Bell Health Center, Philadelphia Field Initiating Group for HIV-1 Trials, Philadelphia, Pennsylvania, USA
| | | | - Douglas Richman
- Veterans Affairs San Diego Healthcare System and the University of California, San Diego, California, USA
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2
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Pertusi DA, O’Donnell G, Homsher MF, Solly K, Patel A, Stahler SL, Riley D, Finley MF, Finger EN, Adam GC, Meng J, Bell DJ, Zuck PD, Hudak EM, Weber MJ, Nothstein JE, Locco L, Quinn C, Amoss A, Squadroni B, Hartnett M, Heo MR, White T, May SA, Boots E, Roberts K, Cocchiarella P, Wolicki A, Kreamer A, Kutchukian PS, Wassermann AM, Uebele VN, Glick M, Rusinko A, Culberson JC. Prospective Assessment of Virtual Screening Heuristics Derived Using a Novel Fusion Score. SLAS DISCOVERY: Advancing the Science of Drug Discovery 2017; 22:995-1006. [DOI: 10.1177/2472555217706058] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
High-throughput screening (HTS) is a widespread method in early drug discovery for identifying promising chemical matter that modulates a target or phenotype of interest. Because HTS campaigns involve screening millions of compounds, it is often desirable to initiate screening with a subset of the full collection. Subsequently, virtual screening methods prioritize likely active compounds in the remaining collection in an iterative process. With this approach, orthogonal virtual screening methods are often applied, necessitating the prioritization of hits from different approaches. Here, we introduce a novel method of fusing these prioritizations and benchmark it prospectively on 17 screening campaigns using virtual screening methods in three descriptor spaces. We found that the fusion approach retrieves 15% to 65% more active chemical series than any single machine-learning method and that appropriately weighting contributions of similarity and machine-learning scoring techniques can increase enrichment by 1% to 19%. We also use fusion scoring to evaluate the tradeoff between screening more chemical matter initially in lieu of replicate samples to prevent false-positives and find that the former option leads to the retrieval of more active chemical series. These results represent guidelines that can increase the rate of identification of promising active compounds in future iterative screens.
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Affiliation(s)
- Dante A. Pertusi
- Modeling and Informatics, Merck & Co., Inc., West Point, PA, USA
| | - Gregory O’Donnell
- Screening and Protein Sciences, Merck & Co., Inc., North Wales, PA, USA
- Merck & Co., Inc., West Point, PA, USA
| | - Michelle F. Homsher
- Screening and Protein Sciences, Merck & Co., Inc., North Wales, PA, USA
- Merck & Co., Inc., West Point, PA, USA
| | - Kelli Solly
- Screening and Protein Sciences, Merck & Co., Inc., North Wales, PA, USA
- Merck & Co., Inc., West Point, PA, USA
| | - Amita Patel
- Screening and Protein Sciences, Merck & Co., Inc., North Wales, PA, USA
- Merck & Co., Inc., West Point, PA, USA
| | - Shannon L. Stahler
- Screening and Protein Sciences, Merck & Co., Inc., North Wales, PA, USA
- Merck & Co., Inc., West Point, PA, USA
| | - Daniel Riley
- Screening and Protein Sciences, Merck & Co., Inc., North Wales, PA, USA
- Merck & Co., Inc., West Point, PA, USA
| | - Michael F. Finley
- Screening and Protein Sciences, Merck & Co., Inc., North Wales, PA, USA
- Discovery Sciences, Janssen Research and Development LLC, Spring House, PA, USA
| | - Eleftheria N. Finger
- Screening and Protein Sciences, Merck & Co., Inc., North Wales, PA, USA
- Discovery & Preclinical Development, GlaxoSmithKline, Collegeville, PA, USA
| | - Gregory C. Adam
- Screening and Protein Sciences, Merck & Co., Inc., North Wales, PA, USA
- Merck & Co., Inc., West Point, PA, USA
| | - Juncai Meng
- Screening and Protein Sciences, Merck & Co., Inc., North Wales, PA, USA
| | - David J. Bell
- Screening and Protein Sciences, Merck & Co., Inc., North Wales, PA, USA
- Merck & Co., Inc., North Wales, PA, USA
| | - Paul D. Zuck
- Merck & Co., Inc., North Wales, PA, USA
- Automation and Engineering, Merck & Co., Inc., North Wales, PA, USA
| | - Edward M. Hudak
- Discovery Sample Management, Merck & Co., Inc., North Wales, PA, USA
| | - Michael J. Weber
- Automation and Engineering, Merck & Co., Inc., North Wales, PA, USA
| | - Jennifer E. Nothstein
- Merck & Co., Inc., West Point, PA, USA
- Automation and Engineering, Merck & Co., Inc., North Wales, PA, USA
| | - Louis Locco
- Automation and Engineering, Merck & Co., Inc., North Wales, PA, USA
| | - Carissa Quinn
- Discovery Sciences, Janssen Research and Development LLC, Spring House, PA, USA
- Automation and Engineering, Merck & Co., Inc., North Wales, PA, USA
| | - Adam Amoss
- Automation and Engineering, Merck & Co., Inc., North Wales, PA, USA
| | - Brian Squadroni
- Merck & Co., Inc., West Point, PA, USA
- Automation and Engineering, Merck & Co., Inc., North Wales, PA, USA
| | - Michelle Hartnett
- Discovery Sciences, Janssen Research and Development LLC, Spring House, PA, USA
- Automation and Engineering, Merck & Co., Inc., North Wales, PA, USA
| | - Mee Ra Heo
- Screening and Protein Sciences, Merck & Co., Inc., North Wales, PA, USA
- Merck & Co., Inc., North Wales, PA, USA
| | - Tara White
- Discovery Sample Management, Merck & Co., Inc., North Wales, PA, USA
| | - S. Alex May
- Automation and Engineering, Merck & Co., Inc., North Wales, PA, USA
| | - Evelyn Boots
- Screening and Protein Sciences, Merck & Co., Inc., North Wales, PA, USA
| | - Kenneth Roberts
- Automation and Engineering, Merck & Co., Inc., North Wales, PA, USA
| | | | - Alex Wolicki
- Screening and Protein Sciences, Merck & Co., Inc., North Wales, PA, USA
| | - Anthony Kreamer
- Screening and Protein Sciences, Merck & Co., Inc., North Wales, PA, USA
- Merck & Co., Inc., Kenilworth, NJ, USA
| | | | | | - Victor N. Uebele
- Screening and Protein Sciences, Merck & Co., Inc., North Wales, PA, USA
- Merck & Co., Inc., North Wales, PA, USA
| | - Meir Glick
- Modeling and Informatics, Merck & Co., Inc., Boston, MA, USA
| | - Andrew Rusinko
- Modeling and Informatics, Merck & Co., Inc., West Point, PA, USA
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