2. Academic Validation
  3. Electrophilic warhead engagement and structure-activity relationship of Benzothiazole-based putative covalent inhibitors targeting SARS-CoV-2 Main protease

Electrophilic warhead engagement and structure-activity relationship of Benzothiazole-based putative covalent inhibitors targeting SARS-CoV-2 Main protease

  • Bioorg Chem. 2026 Jun 5:173:109664. doi: 10.1016/j.bioorg.2026.109664.
Sofia Kanwal 1,  Anees Saeed 1,  Ayesha Tahir 1,  Muhammad Shah 1,  Fahad Hussain 1,  Muhammad Yaqoob 2,  Huaiji Zheng 3,  Muhammad Ikram 4,  Abbas Hassan 5,  Umer Rashid 6
Affiliations

Affiliations

  • 1 Department of Chemistry, COMSATS University Islamabad, Abbottabad Campus, 22060 Abbottabad, Pakistan.
  • 2 Department of Chemistry, COMSATS University Islamabad, Abbottabad Campus, 22060 Abbottabad, Pakistan; Shaanxi Key Laboratory of Natural Products & Chemical Biology, College of Chemistry & Pharmacy, Northwest Agriculture & Forestry University, Yangling 712100, China.
  • 3 Shaanxi Key Laboratory of Natural Products & Chemical Biology, College of Chemistry & Pharmacy, Northwest Agriculture & Forestry University, Yangling 712100, China. Electronic address: [email protected].
  • 4 Department of Pharmacy, COMSATS University Islamabad, Abbottabad Campus, 22060 Abbottabad, Pakistan.
  • 5 Department of Chemistry, College of Science, United Arab Emirates University, Al Ain, 15551, Abu Dhabi, United Arab Emirates. Electronic address: [email protected].
  • 6 Department of Chemistry, COMSATS University Islamabad, Abbottabad Campus, 22060 Abbottabad, Pakistan. Electronic address: [email protected].
PMID: 41722375 DOI: 10.1016/j.bioorg.2026.109664
Abstract

SARS-CoV-2 has precipitated a global health crisis. The Main Protease (Mpro) represents a validated pharmacological target. A series of benzothiazole-based derivatives was designed, synthesized, and evaluated as Mpro inhibitors. The synthesized 5-nitro benzothiazole intermediates (26-29) displayed moderate Mpro inhibition with low to moderate cytotoxicity (CC₅₀ = 16-83 μM in HEK-293 cells). These compounds were subsequently optimized through SAR studies guided by binding site analyses. Lead optimization afforded highly potent derivatives, notably compound 35 (IC50 = 0.026 μM), exhibiting superior potency compared to GC376 and an exceptionally high selectivity index (10,653.8), indicating a favorable potency and safety profile. Acute oral toxicity studies classified compound 35 (LD50 = 947.6 mg/kg BW) and 48 (LD50 = 274.6 mg/kg BW) as Category IV and III toxicants, indicating low acute oral toxicity. Histopathological analysis revealed that the intermediate compound 28 induced hepatic alterations, whereas the final SAR-optimized compound 35 exhibited preserved liver architecture with no apparent pathological changes. Molecular Docking analyses revealed that these benzothiazole derivatives effectively occupied the Mpro active site sub-pocket through stable H-bonding and hydrophobic interactions, thereby facilitating catalytic dyad engagement and pocket adaptability. Covalent docking of compound 35 indicated favorable binding and putative covalent interaction with Cys145. MD simulations confirmed that compound 35 stabilized the protein structure with enhanced compactness, stable interactions, and reduced conformational fluctuations compared to the apo protein. Collectively, these findings highlight benzothiazole-based scaffolds as promising SARS-CoV-2 Mpro inhibitors.

Keywords

Benzothiazole; Covalent docking; Main protease; Putative covalent inhibitors; SARS-CoV-2.

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