Evidence map›Paper›PMID 40640184›Full record

ArticleNature communications2025

PIP4K2C inhibition reverses autophagic flux impairment induced by SARS-CoV-2.

Marwah Karim, Manjari Mishra, Chieh-Wen Lo, Sirle Saul, Halise Busra Cagirici, Manon Gourdelier, Luca Ghita, Amrita Ojha, Do Hoang Nhu Tran, Aditi Agrawal and 24 more

Abstract read
In one paragraph

Article in Nature communications, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 papers.

0numbers the graph read from it
0cells of the map it votes in
11citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

11 citing papers in PubMed.

  1. Article
  2. Article
  3. Review
  4. Review
  5. Targeting the senescence‒autophagy axis via p16Signal transduction and targeted therapy · 2026
    Article
  6. Review
  7. Article
  8. Organoids for disease modeling and treatment: state-of-the-art.Experimental hematology & oncology · 2026
    Review
  9. Article
  10. Article
  11. Review
4 · The record

Corrections and comments

5 · Who and what money

Authors and funding

34 authors.

Marwah Karim *Department of Medicine, Division of Infectious Diseases and Geographic Medicine, Stanford University, Stanford, CA, USA.ORCID http://orcid.org/0000-0003-0990-3962
Manjari Mishra *Department of Medicine, Division of Infectious Diseases and Geographic Medicine, Stanford University, Stanford, CA, USA.
Chieh-Wen LoDepartment of Medicine, Division of Infectious Diseases and Geographic Medicine, Stanford University, Stanford, CA, USA.
Sirle SaulDepartment of Medicine, Division of Infectious Diseases and Geographic Medicine, Stanford University, Stanford, CA, USA.
Halise Busra CagiriciDepartment of Medicine, Division of Infectious Diseases and Geographic Medicine, Stanford University, Stanford, CA, USA.ORCID http://orcid.org/0000-0002-0784-9803
Manon GourdelierDepartment of Medicine, Division of Infectious Diseases and Geographic Medicine, Stanford University, Stanford, CA, USA.
Luca GhitaDepartment of Medicine, Division of Infectious Diseases and Geographic Medicine, Stanford University, Stanford, CA, USA.ORCID http://orcid.org/0000-0001-6736-6355
Amrita OjhaDepartment of Medicine, Division of Infectious Diseases and Geographic Medicine, Stanford University, Stanford, CA, USA.ORCID http://orcid.org/0000-0001-9594-9195
Do Hoang Nhu TranDepartment of Medicine, Division of Infectious Diseases and Geographic Medicine, Stanford University, Stanford, CA, USA.ORCID http://orcid.org/0009-0006-3316-4812
Aditi AgrawalDepartment of Medicine, Division of Infectious Diseases and Geographic Medicine, Stanford University, Stanford, CA, USA.
Connor McGrawDepartment of Medicine, Division of Infectious Diseases and Geographic Medicine, Stanford University, Stanford, CA, USA.
Michael P EastDepartment of Pharmacology, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
Karen Anbro GammeltoftDepartment of Infectious Diseases, University of Copenhagen, Copenhagen, Denmark.ORCID http://orcid.org/0000-0003-0469-767X
Malaya Kumar SahooDepartment of Pathology, Stanford University School of Medicine, Stanford, CA, USA.ORCID http://orcid.org/0000-0001-9837-4032
Nancie A MooneyBaxter Laboratory, Department of Microbiology & Immunology. Stanford University School of Medicine, Stanford, CA, USA.
Gary L JohnsonDepartment of Pharmacology, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
Soumita DasBiomedical & Nutritional Science, Center for Pathogen Research & Training (CPRT), University of Massachusetts-Lowell, Lowell, USA.ORCID http://orcid.org/0000-0003-3895-3643
Pieter LeyssenKU Leuven, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Laboratory of Virology and Chemotherapy, Leuven, Belgium.ORCID http://orcid.org/0000-0002-7537-1688
Johan NeytsKU Leuven, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Laboratory of Virology and Chemotherapy, Leuven, Belgium.ORCID http://orcid.org/0000-0002-0033-7514
Winston ChiuKU Leuven, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Laboratory of Virology and Chemotherapy, Leuven, Belgium.ORCID http://orcid.org/0000-0001-5236-623X
Courtney A CohenUS Army Medical Research Institute of Infectious Diseases, Viral Immunology Branch, Frederick, MD, USA.
Jens BukhDepartment of Infectious Diseases, University of Copenhagen, Copenhagen, Denmark.ORCID http://orcid.org/0000-0002-7815-4806
Judith GottweinDepartment of Infectious Diseases, University of Copenhagen, Copenhagen, Denmark.ORCID http://orcid.org/0000-0003-2805-0256
John M DyeUS Army Medical Research Institute of Infectious Diseases, Viral Immunology Branch, Frederick, MD, USA.
Norma NeffChan Zuckerberg Biohub, San Francisco, CA, USA.ORCID http://orcid.org/0000-0001-7141-5420
Peter K JacksonBaxter Laboratory, Department of Microbiology & Immunology. Stanford University School of Medicine, Stanford, CA, USA.ORCID http://orcid.org/0000-0002-1742-2539
Benjamin A PinskyDepartment of Medicine, Division of Infectious Diseases and Geographic Medicine, Stanford University, Stanford, CA, USA.ORCID http://orcid.org/0000-0001-8751-4810
Tuomo LaitinenSchool of Pharmacy, Faculty of Health Sciences, University of Eastern Finland, Kuopio, Finland.ORCID http://orcid.org/0000-0003-1539-2142
Tatu PantsarSchool of Pharmacy, Faculty of Health Sciences, University of Eastern Finland, Kuopio, Finland.ORCID http://orcid.org/0000-0002-0369-2909
Antti PosoSchool of Pharmacy, Faculty of Health Sciences, University of Eastern Finland, Kuopio, Finland.ORCID http://orcid.org/0000-0003-4196-4204
Fabio ZaniniSchool of Clinical Medicine, UNSW Sydney, Sydney, NSW, Australia.
Steven De JongheKU Leuven, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Laboratory of Virology and Chemotherapy, Leuven, Belgium.ORCID http://orcid.org/0000-0002-3872-6558
Christopher R M AsquithSchool of Pharmacy, Faculty of Health Sciences, University of Eastern Finland, Kuopio, Finland.ORCID http://orcid.org/0000-0001-5871-3458
Shirit EinavDepartment of Medicine, Division of Infectious Diseases and Geographic Medicine, Stanford University, Stanford, CA, USA. seinav@stanford.edu.ORCID http://orcid.org/0000-0001-6441-4171

Funding

Illuminating Function of the Understudied Druggable KinomeU24DK116204 · NIDDK · UNIV OF NORTH CAROLINA CHAPEL HILL · PI JOHNSON, GARY L. · 2017 to 2022
$13.6M
EMERGING INFECTIOUS DISEASEST32AI007502 · NIAID · STANFORD UNIVERSITY · PI Prasanna Jagannathan, DAVID A. RELMAN · 1995 to 2026
$6.8M
Advancing the development of a novel class of small molecules for treating pan-coronavirus infectionsR01AI158569 · NIAID · STANFORD UNIVERSITY · PI EINAV, SHIRIT · 2021 to 2025
$3.7M
Innate responses following infection with enteric microbesR01DK107585 · NIDDK · UNIVERSITY OF CALIFORNIA, SAN DIEGO · PI DAS, SOUMITA · 2016 to 2020
$2.2M
NIAID NIH HHS R01 AI158569NIAID NIH HHS T32 AI007502NIDDK NIH HHS R01 DK107585NIDDK NIH HHS U24 DK116204United States Department of Defense | Defense Threat Reduction Agency (DTRA) HDTRA11810039U.S. Department of Defense (United States Department of Defense) W81XWH-16-1-0691U.S. Department of Defense (United States Department of Defense) W81XWH2210283
6 · The paper itself

Abstract

In search for broad-spectrum antivirals, we discover a small molecule inhibitor, RMC-113, that potently suppresses the replication of multiple RNA viruses including SARS-CoV-2 in human lung organoids. We demonstrate selective inhibition of the lipid kinases PIP4K2C and PIKfyve by RMC-113 and target engagement by its clickable analog. Lipidomics analysis reveals alteration of SARS-CoV-2-induced phosphoinositide signature by RMC-113 and links its antiviral effect with functional PIP4K2C and PIKfyve inhibition. We identify PIP4K2C's roles in SARS-CoV-2 entry, RNA replication, and assembly/egress, validating it as a druggable antiviral target. Integrating proteomics, single-cell transcriptomics, and functional assays, reveals that PIP4K2C binds SARS-CoV-2 nonstructural protein 6 and regulates virus-induced autophagic flux impairment. Promoting viral protein degradation by reversing autophagic flux impairment is a mechanism of antiviral action of RMC-113. These findings reveal virus-induced autophagy regulation via PIP4K2C, an understudied kinase, and propose dual PIP4K2C and PIKfyve inhibition as a candidate strategy to combat emerging viruses.

Indexed as

Antiviral AgentsAutophagyPhosphotransferases (Alcohol Group Acceptor)SARS-CoV-2COVID-19COVID-19 Drug TreatmentHumansLungOrganoidsPhosphatidylinositol 3-KinasesViral Nonstructural ProteinsVirus ReplicationAntiviral AgentsPhosphatidylinositol 3-KinasesPhosphotransferases (Alcohol Group Acceptor)PIKFYVE protein, humanViral Nonstructural Proteins

Identifiers

PMID40640184
PMCPMC12246422

What OpenQuestion holds

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LicenceCC BY-NC-ND
Read underepoch 390

Registered trials

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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.