IDEAS home Printed from https://ideas.repec.org/a/nat/natcom/v14y2023i1d10.1038_s41467-023-38952-1.html
   My bibliography  Save this article

Systematic literature review reveals suboptimal use of chemical probes in cell-based biomedical research

Author

Listed:
  • Jayden Sterling

    (The University of Sydney)

  • Jennifer R. Baker

    (The University of Newcastle)

  • Adam McCluskey

    (The University of Newcastle)

  • Lenka Munoz

    (The University of Sydney)

Abstract

Chemical probes have reached a prominent role in biomedical research, but their impact is governed by experimental design. To gain insight into the use of chemical probes, we conducted a systematic review of 662 publications, understood here as primary research articles, employing eight different chemical probes in cell-based research. We summarised (i) concentration(s) at which chemical probes were used in cell-based assays, (ii) inclusion of structurally matched target-inactive control compounds and (iii) orthogonal chemical probes. Here, we show that only 4% of analysed eligible publications used chemical probes within the recommended concentration range and included inactive compounds as well as orthogonal chemical probes. These findings indicate that the best practice with chemical probes is yet to be implemented in biomedical research. To achieve this, we propose ‘the rule of two’: At least two chemical probes (either orthogonal target-engaging probes, and/or a pair of a chemical probe and matched target-inactive compound) to be employed at recommended concentrations in every study.

Suggested Citation

  • Jayden Sterling & Jennifer R. Baker & Adam McCluskey & Lenka Munoz, 2023. "Systematic literature review reveals suboptimal use of chemical probes in cell-based biomedical research," Nature Communications, Nature, vol. 14(1), pages 1-12, December.
    • Handle: RePEc:nat:natcom:v:14:y:2023:i:1:d:10.1038_s41467-023-38952-1
    DOI: 10.1038/s41467-023-38952-1
    as

    Download full text from publisher

    File URL: https://www.nature.com/articles/s41467-023-38952-1
    File Function: Abstract
    Download Restriction: no
    File URL: https://libkey.io/10.1038/s41467-023-38952-1?utm_source=ideas
    LibKey link: if access is restricted and if your library uses this service, LibKey will redirect you to where you can use your library subscription to access this item
    ---><---

    References listed on IDEAS

    as
    1. Laurens Kruidenier & Chun-wa Chung & Zhongjun Cheng & John Liddle & KaHing Che & Gerard Joberty & Marcus Bantscheff & Chas Bountra & Angela Bridges & Hawa Diallo & Dirk Eberhard & Sue Hutchinson & Emm, 2012. "A selective jumonji H3K27 demethylase inhibitor modulates the proinflammatory macrophage response," Nature, Nature, vol. 488(7411), pages 404-408, August.
    2. Jeannine Diesch & Marguerite-Marie Le Pannérer & René Winkler & Raquel Casquero & Matthias Muhar & Mark van der Garde & Michael Maher & Carolina Martínez Herráez & Joan J. Bech-Serra & Michaela Fellne, 2021. "Inhibition of CBP synergizes with the RNA-dependent mechanisms of Azacitidine by limiting protein synthesis," Nature Communications, Nature, vol. 12(1), pages 1-13, December.
    3. Matthew J Page & Joanne E McKenzie & Patrick M Bossuyt & Isabelle Boutron & Tammy C Hoffmann & Cynthia D Mulrow & Larissa Shamseer & Jennifer M Tetzlaff & Elie A Akl & Sue E Brennan & Roger Chou & Jul, 2021. "The PRISMA 2020 statement: An updated guideline for reporting systematic reviews," PLOS Medicine, Public Library of Science, vol. 18(3), pages 1-15, March.
    4. Nicholas Kwiatkowski & Tinghu Zhang & Peter B. Rahl & Brian J. Abraham & Jessica Reddy & Scott B. Ficarro & Anahita Dastur & Arnaud Amzallag & Sridhar Ramaswamy & Bethany Tesar & Catherine E. Jenkins , 2014. "Targeting transcription regulation in cancer with a covalent CDK7 inhibitor," Nature, Nature, vol. 511(7511), pages 616-620, July.
    5. Jonathan Baell & Michael A. Walters, 2014. "Chemistry: Chemical con artists foil drug discovery," Nature, Nature, vol. 513(7519), pages 481-483, September.
    Full references (including those not matched with items on IDEAS)

    Most related items

    These are the items that most often cite the same works as this one and are cited by the same works as this one.
    1. Rizkiana Sidqiyatul Hamdani & Sudharto Prawata Hadi & Iwan Rudiarto, 2021. "Progress or Regress? A Systematic Review on Two Decades of Monitoring and Addressing Land Subsidence Hazards in Semarang City," Sustainability, MDPI, vol. 13(24), pages 1-26, December.
    2. Boglárka Anna Éliás & Attila Jámbor, 2021. "Food Security and COVID-19: A Systematic Review of the First-Year Experience," Sustainability, MDPI, vol. 13(9), pages 1-18, May.
    3. Omoyele, Olalekan & Hoffmann, Maximilian & Koivisto, Matti & Larrañeta, Miguel & Weinand, Jann Michael & Linßen, Jochen & Stolten, Detlef, 2024. "Increasing the resolution of solar and wind time series for energy system modeling: A review," Renewable and Sustainable Energy Reviews, Elsevier, vol. 189(PB).
    4. Cala, Anggie & Maturana-Córdoba, Aymer & Soto-Verjel, Joseph, 2023. "Exploring the pretreatments' influence on pressure reverse osmosis: PRISMA review," Renewable and Sustainable Energy Reviews, Elsevier, vol. 188(C).
    5. Ming Shan & Yu-Shan Li & Bon-Gang Hwang & Jia-En Chua, 2021. "Productivity Metrics and Its Implementations in Construction Projects: A Case Study of Singapore," Sustainability, MDPI, vol. 13(21), pages 1-19, November.
    6. Susca, T. & Zanghirella, F. & Colasuonno, L. & Del Fatto, V., 2022. "Effect of green wall installation on urban heat island and building energy use: A climate-informed systematic literature review," Renewable and Sustainable Energy Reviews, Elsevier, vol. 159(C).
    7. Alexander P. L. Martindale & Carrie D. Llewellyn & Richard O. Visser & Benjamin Ng & Victoria Ngai & Aditya U. Kale & Lavinia Ferrante Ruffano & Robert M. Golub & Gary S. Collins & David Moher & Melis, 2024. "Concordance of randomised controlled trials for artificial intelligence interventions with the CONSORT-AI reporting guidelines," Nature Communications, Nature, vol. 15(1), pages 1-11, December.
    8. Gizéh Rangel-de Lázaro & Josep M. Duart, 2023. "You Can Handle, You Can Teach It: Systematic Review on the Use of Extended Reality and Artificial Intelligence Technologies for Online Higher Education," Sustainability, MDPI, vol. 15(4), pages 1-23, February.
    9. Thaddeus J. Kunkel & Alice Townsend & Kyle A. Sullivan & Jean Merlet & Edward H. Schuchman & Daniel A. Jacobson & Andrew P. Lieberman, 2023. "The cholesterol transporter NPC1 is essential for epigenetic regulation and maturation of oligodendrocyte lineage cells," Nature Communications, Nature, vol. 14(1), pages 1-17, December.
    10. Kim, Hyunil & Kim, Yun Young & Song, Eun-Jee & Windsor, Liliane, 2024. "Policies to reduce child poverty and child maltreatment: A scoping review and preliminary estimates of indirect effects," Children and Youth Services Review, Elsevier, vol. 156(C).
    11. Austin Hsu & Qiming Duan & Daniel S. Day & Xin Luo & Sarah McMahon & Yu Huang & Zachary B. Feldman & Zhen Jiang & Tinghu Zhang & Yanke Liang & Michael Alexanian & Arun Padmanabhan & Jonathan D. Brown , 2022. "Targeting transcription in heart failure via CDK7/12/13 inhibition," Nature Communications, Nature, vol. 13(1), pages 1-11, December.
    12. Lee, Kuan-Ting & Chen, Yen-Chin & Yang, Yi-Ching & Wang, Wei-Li, 2024. "On practicing magicine, from wonder to care: A systematic review of studies that apply magic in healthcare," Social Science & Medicine, Elsevier, vol. 341(C).
    13. Deniz Dutz & Ingrid Huitfeldt & Santiago Lacouture & Magne Mogstad & Alexander Torgovitsky & Winnie van Dijk, 2021. "Selection in Surveys," NBER Working Papers 29549, National Bureau of Economic Research, Inc.
      • Deniz Dutz & Ingrid Huitfeldt & Santiago Lacouture & Magne Mogstad & Alexander Torgovitsky & Winnie van Dijk, 2021. "Selection in Surveys," Discussion Papers 971, Statistics Norway, Research Department.
    14. Lemesa Hirpe & Chunho Yeom, 2021. "Municipal Solid Waste Management Policies, Practices, and Challenges in Ethiopia: A Systematic Review," Sustainability, MDPI, vol. 13(20), pages 1-16, October.
    15. Simmons, Cassandra & Pot, Mirjam & Lorenz-Dant, Klara & Leichsenring, Kai, 2024. "Disentangling the impact of alternative payment models and associated service delivery models on quality of chronic care: A scoping review," Health Policy, Elsevier, vol. 143(C).
    16. Ellen Busink & Dana Kendzia & Fatih Kircelli & Sophie Boeger & Jovana Petrovic & Helen Smethurst & Stephen Mitchell & Christian Apel, 2023. "A systematic review of the cost-effectiveness of renal replacement therapies, and consequences for decision-making in the end-stage renal disease treatment pathway," The European Journal of Health Economics, Springer;Deutsche Gesellschaft für Gesundheitsökonomie (DGGÖ), vol. 24(3), pages 377-392, April.
    17. Ooms, Tahnee & Klaser, Klaudijo & Ishkanian, Armine, 2023. "The role of academia practice partnerships in the well-being economy: Retracing synergies between health and social sciences using bibliometric analysis," Health Policy, Elsevier, vol. 138(C).
    18. Wang, Nan & Wang, Julian & Feng, Yanxiao, 2022. "Systematic review: Acute thermal effects of artificial light in the daytime," Renewable and Sustainable Energy Reviews, Elsevier, vol. 165(C).
    19. Tania Mateos-Blanco & Encarnación Sánchez‐Lissen & Inés Gil‐Jaurena & Clara Romero‐Pérez, 2022. "Child‐Led Participation: A Scoping Review of Empirical Studies," Social Inclusion, Cogitatio Press, vol. 10(2), pages 32-42.
    20. Julian Packheiser & Helena Hartmann & Kelly Fredriksen & Valeria Gazzola & Christian Keysers & Frédéric Michon, 2024. "A systematic review and multivariate meta-analysis of the physical and mental health benefits of touch interventions," Nature Human Behaviour, Nature, vol. 8(6), pages 1088-1107, June.

    More about this item

    Statistics

    Access and download statistics

    Corrections

    All material on this site has been provided by the respective publishers and authors. You can help correct errors and omissions. When requesting a correction, please mention this item's handle: RePEc:nat:natcom:v:14:y:2023:i:1:d:10.1038_s41467-023-38952-1. See general information about how to correct material in RePEc.

    If you have authored this item and are not yet registered with RePEc, we encourage you to do it here. This allows to link your profile to this item. It also allows you to accept potential citations to this item that we are uncertain about.

    If CitEc recognized a bibliographic reference but did not link an item in RePEc to it, you can help with this form .

    If you know of missing items citing this one, you can help us creating those links by adding the relevant references in the same way as above, for each refering item. If you are a registered author of this item, you may also want to check the "citations" tab in your RePEc Author Service profile, as there may be some citations waiting for confirmation.

    For technical questions regarding this item, or to correct its authors, title, abstract, bibliographic or download information, contact: Sonal Shukla or Springer Nature Abstracting and Indexing (email available below). General contact details of provider: http://www.nature.com .

    Please note that corrections may take a couple of weeks to filter through the various RePEc services.

    IDEAS is a RePEc service. RePEc uses bibliographic data supplied by the respective publishers.