2. Academic Validation
  3. Discovery of thiadiazole-based small-molecule inhibitors of SARS-CoV-2 spike-ACE2 interaction through integrated computational prediction and experimental validation

Discovery of thiadiazole-based small-molecule inhibitors of SARS-CoV-2 spike-ACE2 interaction through integrated computational prediction and experimental validation

  • Sci Rep. 2026 Jan 2;16(1):1200. doi: 10.1038/s41598-025-30881-x.
Zakkia Gul 1,  Syed Ahsan Shahid 2 3,  Obaid-Ur-Rahman Abid 4,  Muhammad Waqas 1,  Shazia Rafique 5,  Ahmed E Al-Sabri 6,  Asma Sardar 7,  Afrah F Alkhuriji 8,  Nawal M Al-Malahi 8,  Muhammad Irfan 9,  Amjad Ali 10
Affiliations

Affiliations

  • 1 Department of Biotechnology and Genetic Engineering, Hazara University, Mansehra, 21300, Pakistan.
  • 2 Natural and Medical Sciences Research Center, University of Nizwa, Birkat Al-Mouz, Nizwa, 616, Oman.
  • 3 Department of Biotechnology, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, 45320, Pakistan.
  • 4 Department of Chemistry, Hazara University, Mansehra, 21300, Pakistan.
  • 5 National Centre of Excellence in Molecular Biology (CEMB), University of the Punjab, Lahore, 54590, Pakistan.
  • 6 Department of Botany and Microbiology, College of Science, King Saud University, P.O. Box 2455, Riyadh, 11451, Saudi Arabia. [email protected].
  • 7 Department of Chemistry, Fatima Jinnah Women University Rawalpindi, Rawalpindi, 46000, Pakistan.
  • 8 Department of Zoology, College of Science, King Saud University, P.O. Box 2455, Riyadh, 11451, Saudi Arabia.
  • 9 ASRT, Inc., Atlanta, Georgia, 30303, USA.
  • 10 Department of Biotechnology and Genetic Engineering, Hazara University, Mansehra, 21300, Pakistan. [email protected].
PMID: 41484143 DOI: 10.1038/s41598-025-30881-x
Abstract

The SARS-CoV-2 spike protein enables viral entry by binding to the human ACE2 receptor, making it a critical target for Antiviral intervention. In this study, five small molecules derived from 1,3,4-thiadiazole scaffolds were identified as potential inhibitors of the spike-ACE2 interaction using structure-based virtual screening and experimental validation. All five compounds were predicted to bind within the receptor-binding domain of the spike protein and disrupted ACE2 attachment. Simulations confirmed stable binding for all compounds without structural destabilization of the spike protein. Binding reduced the flexibility of key receptor-binding loops, maintained overall compactness of the spike structure, and restricted large-scale conformational shifts compared to the unbound protein. Energy analysis showed that hydrophobic contacts and electrostatic interactions contributed to stable complex formation. Of the five compounds, NS1 and NS2 demonstrated the strongest binding affinities (− 49.17 and − 47.74 kcal mol−¹), stable binding behavior over extended simulations, and consistent structural stabilization of the spike protein. In vitro, NS1 and NS2 inhibited the spike-ACE2 interaction with IC₅₀ values of 2162.77 nM and 2946.28 nM, respectively. Both compounds exhibited low cytotoxicity in human BJ fibroblast cells and predicted oral bioavailability based on pharmacokinetic modeling. We identified NS1 and NS2 as promising lead compounds capable of directly targeting the spike-ACE2 interface. Our results support small-molecule inhibition of spike-ACE2 binding as a viable Antiviral approach and highlight the identified thiadiazole scaffold as a starting point for future optimization and preclinical development.

Supplementary Information: The online version contains supplementary material available at 10.1038/s41598-025-30881-x.

Keywords

ACE2 interaction; Antiviral development; SARS-CoV-2 spike protein; Small-molecule inhibitors; Thiadiazole derivatives.

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