2. Academic Validation
  3. Targeted design, synthesis, molecular simulation, ADME-T and in-vitro anticancer assessment of phenyl-substituted-thioxo-tetrahydro-pyrimidin-benzenesulfonamide derivatives as potential BRAFV600E/WT inhibitors

Targeted design, synthesis, molecular simulation, ADME-T and in-vitro anticancer assessment of phenyl-substituted-thioxo-tetrahydro-pyrimidin-benzenesulfonamide derivatives as potential BRAFV600E/WT inhibitors

  • Bioorg Med Chem Lett. 2025 Oct 8:130:130431. doi: 10.1016/j.bmcl.2025.130431.
Ankit Kumar Singh 1,  Vineet Prajapati 2,  Adarsh Kumar 2,  Vimlendu Kumar Sah 2,  Prateek Pathak 3,  Mashooq A Bhat 4,  Mohamed A Al-Omar 5,  Amita Verma 6,  Pradeep Kumar 7
Affiliations

Affiliations

  • 1 Department of Pharmaceutical Sciences and Natural Products, Central University of Punjab, Ghudda, Bathinda 151401, India; Bioorganic and Medicinal Chemistry Research Laboratory, Department of Pharmaceutical Sciences, Sam Higginbottom University of Agriculture, Technology and Sciences, Prayagraj 211007, India.
  • 2 Department of Pharmaceutical Sciences and Natural Products, Central University of Punjab, Ghudda, Bathinda 151401, India.
  • 3 Department of Pharmaceutical Analysis, Quality Assurance and Pharmaceutical Chemistry, School of Pharmacy, GITAM (Deemed to be University), Hyderabad Campus, India.
  • 4 Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University, Riyadh 11451, Saudi Arabia. Electronic address: mabhat@ksu.edu.sa.
  • 5 Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University, Riyadh 11451, Saudi Arabia. Electronic address: malomar1@ksu.edu.sa.
  • 6 Bioorganic and Medicinal Chemistry Research Laboratory, Department of Pharmaceutical Sciences, Sam Higginbottom University of Agriculture, Technology and Sciences, Prayagraj 211007, India. Electronic address: amita.verma@shiats.edu.in.
  • 7 Department of Pharmaceutical Sciences and Natural Products, Central University of Punjab, Ghudda, Bathinda 151401, India. Electronic address: pradeep.kumar@cup.edu.in.
PMID: 41072865 DOI: 10.1016/j.bmcl.2025.130431
Abstract

BRAF is one of the most commonly mutated oncogenes in human cancers, with more than 90 % of mutations occurring at codon 600. Among these, BRAFV600E is the most prevalent, accounting for nearly 90 % of all BRAF codon 600 mutations, while the less frequent variants are collectively referred to as BRAFV600WT. BRAF mutations are reported across several cancers, with the highest frequency in malignant melanoma (70-90 %). To target these mutations, a series of phenyl-substituted thioxo-tetrahydro-pyrimidine-benzenesulfonamide hybrids in the [αC-OUT/DFG-IN] conformation were designed. Fourteen derivatives were synthesized through multistep reactions and evaluated for ADME-T properties and in silico binding affinities using molecular docking, further validated by molecular dynamics (MD) simulations of the top-ranked compound. In addition, cytotoxic activity against melanoma cell lines was assessed, followed by kinase inhibition studies on the most potent derivatives against BRAFV600E/WT. All compounds exhibited favorable ADME-T and drug-like properties. Among them, AV05 demonstrated the highest binding affinity (-8.013 kcal/mol) and potent cytotoxic activity (IC₅₀ = 1.25 ± 0.57 μM), with BRAFV600E inhibition (0.89 ± 0.78 μM) comparable to sorafenib (-6.189 kcal/mol; IC₅₀ = 0.90 ± 0.21 μM; inhibition = 0.10 ± 0.01 μM). In contrast, AV01 showed the strongest affinity for BRAFV600WT (-4.954 kcal/mol) and kinase inhibition (0.93 ± 0.28 μM), relative to sorafenib (-12.241 kcal/mol; inhibition = 0.16 ± 0.01 μM). Collectively, computational and biological evaluations revealed that the synthesized hybrids exhibited higher selectivity and potency toward BRAFV600E than BRAFV600WT, with AV05 emerging as the most promising compound.

Keywords

ADME-T; BRAF(V600E/WT); Cancer; Melanoma; Molecular docking and MD simulation; αC-OUT/DFG-IN.

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