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  3. Identification of novel TMEM16A blockers through integrated virtual screening, molecular dynamics, and experimental studies

Identification of novel TMEM16A blockers through integrated virtual screening, molecular dynamics, and experimental studies

  • Sci Rep. 2025 Apr 29;15(1):15065. doi: 10.1038/s41598-025-99751-w.
Mattanun Sangkhawasi 1,  Wichuda Pitaktrakul 2 3,  Rungtiwa Khumjiang 2,  Yasuteru Shigeta 4,  Chatchai Muanprasat 5,  Kowit Hengphasatporn 6,  Thanyada Rungrotmongkol 7 8
Affiliations

Affiliations

  • 1 Center of Excellence in Biocatalyst and Sustainable Biotechnology, Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok, 10330, Thailand.
  • 2 Chakri Naruebodindra Medical Institute, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bang Pla, Bang Pli, Samut Prakan, 10540, Thailand.
  • 3 Division of Biochemistry, Department of Preclinical Science, Faculty of Medicine, Thammasat University, Pathumthani, 12120, Thailand.
  • 4 Center for Computational Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, 305-8577, Ibaraki, Japan.
  • 5 Chakri Naruebodindra Medical Institute, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bang Pla, Bang Pli, Samut Prakan, 10540, Thailand. chatchai.mua@mahidol.ac.th.
  • 6 Center for Computational Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, 305-8577, Ibaraki, Japan. kowith@ccs.tsukuba.ac.jp.
  • 7 Center of Excellence in Biocatalyst and Sustainable Biotechnology, Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok, 10330, Thailand. thanyada.r@chula.ac.th.
  • 8 Program in Bioinformatics and Computational Biology, Graduate School, Chulalongkorn University, Bangkok, 10330, Thailand. thanyada.r@chula.ac.th.
PMID: 40301508 DOI: 10.1038/s41598-025-99751-w
Abstract

The calcium-activated Chloride Channel TMEM16A is a promising drug target for treating hypertension, secretory diarrheas, and various cancers, including head and neck Cancer. Despite its potential, no FDA-approved drugs have provided the structural basis for directly inhibiting TMEM16A. This study aims to identify a novel pore-blocker of TMEM16A by integrating virtual screening, molecular dynamics simulations, and in vitro studies. Using the calcium-bound structure of TMEM16A with and without the pore-blocker 1PBC, we performed virtual screening on nearly 90,000 compounds from the ChemDiv database. Approximately 67% of these compounds demonstrated better binding affinity than 1PBC. Among the top 20 compounds selected for short-circuit current assays using human lung adenocarcinoma cells (Calu-3), compounds N066-0059, N066-0060, and N066-0067 inhibited TMEM16A activity with IC50 values of 0.24 µM, 0.41 µM, and 0.48 µM, respectively, which was lower than that of a positive control Ani9 (9 µM). Due to its highest potency in electrophysiological assays, N066-0059 was subjected to mechanistic studies. Molecular dynamics simulations elucidated its binding stability and strength, showing superior performance to 1PBC over 500 ns with 3 replicates. This study advances TMEM16A-targeted drug development, offering new insights for Anticancer therapies.

Keywords

And electrophysiological assays; Cytotoxicity; Molecular dynamics; Pore-blocker inhibitor; TMEM16A; Virtual screening.

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