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Objective: The current study's objective is to highlight the value of using plant resources to identify key bioactive molecules and implement green chemistry in research and development to meet market demand. Materials and Methods: The black cumin seeds (Saudi and Syria originated) were utilized to make silver nanoparticles (Ag-NPs), which were subsequently confirmed using a UV spectrophotometer and color analysis of reaction mixtures. The antibacterial activity of Ag-NPs was tested against E. coli, K. pneumoniae, and S. aureus, and antioxidant activity was measured using the DPPH assay. Swiss-ADME, pkCSM, and ProTox-II were also used to assess the pharmacokinetics, oral bioavailability, toxicity, and safety endpoints of molecules. Result: The antibacterial effect of Ag-NPs from Saudi-origin black cumin seeds was observed higher. In comparison to the standard, the Saudi and Syrian Ag-NPs combined displayed synergistic antibacterial effects and were found to be more susceptible to S. aureus. In comparison to the reference, the antioxidant activity of Ag-NPs indicated 60–85% radical scavenging. All molecules passed the Lipinski rule, the filter (Veber, Egan, and Muegge), PAINS, and the Brenk structural alert (zero violations), and the synthetic score was also found to be in the easy limit (1 to 2). The compounds were found to be non-substrate for p-glycoprotein, high GIA% (>90%), non-inhibitor for CYP3A4, CYP2C19, CYP2C9, CYP2D6 (except 5 and 10), Log Po/w (1.71 to 3.26), TPSA 150 2 and MR 155. The compounds likewise had high Caco2 values (log Papp >0.9) with the exception of 4 and 9 (log Papp 0.9), were non-inhibitors of P-gp-I and II and hERG I and II, and showed no AMES toxicity. Except for molecule 11, no organ damage (hepatotoxicity) or endpoint toxicity (mutagenicity, immunotoxicity, carcinogenicity, and cytotoxicity) was identified in ProTox-II. Conclusion: The current study sheds new light on the significance of bioactive molecules found in black cumin seeds, with molecules 3 and 6 identified as potential leads (highest GIA%, no AMES toxicity, oral rat acute and chronic toxicity, lack of renal OCT2 substrate, high total clearance, and lack of organ toxicity) for further research for a variety of medical applications.