{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,22]],"date-time":"2026-09-22T09:04:02Z","timestamp":1790067842112,"version":"4.0.1"},"reference-count":45,"publisher":"MDPI AG","issue":"9","license":[{"start":{"date-parts":[[2026,9,17]],"date-time":"2026-09-17T00:00:00Z","timestamp":1789603200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Pharmaceuticals"],"abstract":"<jats:p>Background\/Objectives: Indoles and benzimidazoles are important nitrogen-containing heterocyclic scaffolds and are a cornerstone of synthetic drugs. In this study, benzamides of 2-aminophenylindoles and 2-aminophenylbenzimidazoles were synthesized and evaluated for their potential. Further, they were also subjected to computational studies for their ADMET profiling and binding with target proteins. Methods: The synthesized compounds were characterized by ATR-FTIR, 1H NMR, 13C NMR and electrospray ionization mass spectroscopy (ESI-MS). They were screened for their in vitro antibacterial activity by the Microplate Alamar Blue Assay (MABA) and for their anticancer potential by the MTT assay against the HeLa, PC3 and 3T3 cell lines. Further, the compounds were assessed for their ADMET profiles by the Deep-PK platform, and binding with selected kinases was assessed by AutoDock Vina v1.2.7, followed by MD simulations in GROMACS. Density functional theory (DFT) calculations were also performed to investigate the electronic properties of the synthesized compounds. Results: All synthesized compounds were inactive in antibacterial assays and mildly active against cancer cells. N-[4-(1H-benzimidazol-2-yl-phenyl]benzamide (4-APB-B) exhibited good activity against the HeLa cell line (IC50: 5.48 \u00b1 0.01 \u00b5M) while showing very low cytotoxicity against the 3T3 cell line (selectivity index: 10.7), against which doxorubicin was highly active, indicating selectivity towards specific cancer cells. Docking studies indicated favorable binding affinities towards the selected kinase targets. Further, ligands with the best binding affinities in docking studies were subjected to MD simulations of 100 ns, and DFT studies were also performed to assess the electronic properties of the synthesized compounds. Conclusions: Our study provides a pathway for the synthesis of 2-phenylbenzimidazoles and 2-phenylindoles and demonstrates that the synthetic compound 4-APB-B possesses remarkable selective cytotoxic activity and can serve as a lead molecule for further development into a successful anticancer agent.<\/jats:p>","DOI":"10.3390\/ph19091485","type":"journal-article","created":{"date-parts":[[2026,9,21]],"date-time":"2026-09-21T09:01:38Z","timestamp":1789981298000},"page":"1485","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Benzamides of 2-(aminophenyl)benzimidazoles and 2-(aminophenyl)indoles as Anticancer Scaffolds: Synthesis, In Silico and In Vitro Evaluation"],"prefix":"10.3390","volume":"19","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-1433-8574","authenticated-orcid":false,"given":"Adil","family":"Saeed","sequence":"first","affiliation":[{"name":"Riphah Institute of Pharmaceutical Sciences, Riphah International University, Islamabad 44000, Pakistan"}],"role":[{"vocabulary":"crossref","role":"author"},{"role":"methodology","vocabulary":"credit"},{"role":"conceptualization","vocabulary":"credit"},{"role":"software","vocabulary":"credit"},{"role":"validation","vocabulary":"credit"},{"role":"formal-analysis","vocabulary":"credit"},{"role":"investigation","vocabulary":"credit"},{"role":"resources","vocabulary":"credit"},{"role":"writing-original-draft","vocabulary":"credit"},{"role":"writing-review-editing","vocabulary":"credit"},{"role":"visualization","vocabulary":"credit"}]},{"given":"Humaira","family":"Nadeem","sequence":"additional","affiliation":[{"name":"Riphah Institute of Pharmaceutical Sciences, Riphah International University, Islamabad 44000, Pakistan"}],"role":[{"vocabulary":"crossref","role":"author"},{"role":"methodology","vocabulary":"credit"},{"role":"supervision","vocabulary":"credit"},{"role":"project-administration","vocabulary":"credit"},{"role":"formal-analysis","vocabulary":"credit"},{"role":"writing-review-editing","vocabulary":"credit"},{"role":"conceptualization","vocabulary":"credit"}]},{"given":"Fouzia Perveen","family":"Malik","sequence":"additional","affiliation":[{"name":"Materials Modelling Lab, School of Interdisciplinary Engineering & Sciences (SINES), NUST, Islamabad 44000, Pakistan"}],"role":[{"vocabulary":"crossref","role":"author"},{"role":"software","vocabulary":"credit"},{"role":"validation","vocabulary":"credit"},{"role":"formal-analysis","vocabulary":"credit"},{"role":"investigation","vocabulary":"credit"},{"role":"data-curation","vocabulary":"credit"}]},{"given":"Rehan Zafar","family":"Paracha","sequence":"additional","affiliation":[{"name":"Riphah Institute of Pharmaceutical Sciences, Riphah International University, Islamabad 44000, Pakistan"}],"role":[{"vocabulary":"crossref","role":"author"},{"role":"software","vocabulary":"credit"},{"role":"formal-analysis","vocabulary":"credit"},{"role":"investigation","vocabulary":"credit"},{"role":"resources","vocabulary":"credit"}]},{"given":"Sehrosh Naz","family":"Khan","sequence":"additional","affiliation":[{"name":"Panjwani Center for Molecular Medicine and Drug Research, International Center for Chemical & Biological Sciences (ICCBS), University of Karachi, Karachi 75270, Pakistan"}],"role":[{"vocabulary":"crossref","role":"author"},{"role":"resources","vocabulary":"credit"},{"role":"investigation","vocabulary":"credit"},{"role":"formal-analysis","vocabulary":"credit"},{"role":"data-curation","vocabulary":"credit"}]}],"member":"1968","published-online":{"date-parts":[[2026,9,17]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"1331","DOI":"10.1042\/BCJ20220217","article-title":"How many kinases are druggable? A review of our current understanding","volume":"480","author":"Anderson","year":"2023","journal-title":"Biochem. J."},{"key":"ref_2","doi-asserted-by":"crossref","unstructured":"Dr\u0103goi, C.M., Nicolae, A.-C., and Dumitrescu, I.-B. (2026). The indole scaffold in biochemistry and therapeutics: A privileged structure with diverse chemical, biological, and clinical significance. Targets, 4.","DOI":"10.3390\/targets4010004"},{"key":"ref_3","doi-asserted-by":"crossref","unstructured":"Zhang, H., He, F., Gao, G., Lu, S., Wei, Q., Hu, H., Wu, Z., Fang, M., and Wang, X. (2023). Approved small-molecule ATP-competitive kinases drugs containing indole\/azaindole\/oxindole scaffolds: R&D and binding patterns profiling. Molecules, 28.","DOI":"10.3390\/molecules28030943"},{"key":"ref_4","doi-asserted-by":"crossref","first-page":"24101","DOI":"10.1038\/s41598-024-73793-y","article-title":"Design, synthesis and mechanistic study of N-4-Piperazinyl Butyryl Thiazolidinedione derivatives of ciprofloxacin with Anticancer Activity via Topoisomerase I\/II inhibition","volume":"14","author":"Aziz","year":"2024","journal-title":"Sci. Rep."},{"key":"ref_5","doi-asserted-by":"crossref","first-page":"101139","DOI":"10.1016\/j.rechem.2023.101139","article-title":"Benzimidazole: A versatile scaffold for drug discovery and beyond\u2014A comprehensive review of synthetic approaches and recent advancements in medicinal chemistry","volume":"6","author":"Mahurkar","year":"2023","journal-title":"Results Chem."},{"key":"ref_6","doi-asserted-by":"crossref","first-page":"1421","DOI":"10.2174\/13895575113139990072","article-title":"Novel research strategies of benzimidazole derivatives: A review","volume":"13","author":"Barot","year":"2013","journal-title":"Mini Rev. Med. Chem."},{"key":"ref_7","doi-asserted-by":"crossref","first-page":"478","DOI":"10.1016\/j.apsb.2022.09.010","article-title":"Benzimidazole and its derivatives as cancer therapeutics: The potential role from traditional to precision medicine","volume":"13","author":"Lee","year":"2023","journal-title":"Acta Pharm. Sin. B"},{"key":"ref_8","doi-asserted-by":"crossref","first-page":"227","DOI":"10.1021\/cr60258a004","article-title":"Studies on the Fischer indole synthesis","volume":"69","author":"Robinson","year":"1969","journal-title":"Chem. Rev."},{"key":"ref_9","doi-asserted-by":"crossref","first-page":"2875","DOI":"10.1021\/cr0505270","article-title":"Practical methodologies for the synthesis of indoles","volume":"106","author":"Humphrey","year":"2006","journal-title":"Chem. Rev."},{"key":"ref_10","doi-asserted-by":"crossref","first-page":"2258","DOI":"10.1080\/00397911.2019.1620282","article-title":"2-Phenylindole derivatives as anticancer agents: Synthesis and screening against murine melanoma, human lung and breast cancer cell lines","volume":"49","author":"Gaikwad","year":"2019","journal-title":"Synth. Commun."},{"key":"ref_11","unstructured":"Joule, J.A., and Mills, K. (2008). Heterocyclic Chemistry, John Wiley & Sons."},{"key":"ref_12","doi-asserted-by":"crossref","first-page":"2491","DOI":"10.3390\/molecules15042491","article-title":"New 3 H-Indole Synthesis by Fischer\u2019s Method. Part I","volume":"15","author":"Sajjadifar","year":"2010","journal-title":"Molecules"},{"key":"ref_13","doi-asserted-by":"crossref","first-page":"1905","DOI":"10.2174\/138527212802651232","article-title":"Synthetic approaches to 2-arylbenzimidazoles: A review","volume":"16","author":"Panda","year":"2012","journal-title":"Curr. Org. Chem."},{"key":"ref_14","doi-asserted-by":"crossref","unstructured":"Alheety, N.F., Awad, S.A., Alheety, M.A., Darwesh, M.Y., Abbas, J.A., and Besbes, R. (2026). Benzimidazole Derivatives: A Review of Advances in Synthesis, Biological Potential, Computational Modelling, and Specialized Material Functions. Chemistry, 8.","DOI":"10.3390\/chemistry8010001"},{"key":"ref_15","doi-asserted-by":"crossref","first-page":"1255","DOI":"10.3109\/14756366.2012.729828","article-title":"Microwave-assisted synthesis of sec\/tert-butyl 2-arylbenzimidazoles and their unexpected antiproliferative activity towards ER negative breast cancer cells","volume":"28","author":"Arumugam","year":"2013","journal-title":"J. Enzym. Inhib. Med. Chem."},{"key":"ref_16","unstructured":"Furniss, B.S. (2004). Practical Organic Chemistry, Pearson Education India."},{"key":"ref_17","doi-asserted-by":"crossref","first-page":"118","DOI":"10.1016\/j.biopha.2018.03.174","article-title":"Novel compounds TAD-1822-7-F2 and F5 inhibited HeLa cells growth through the JAK\/Stat signaling pathway","volume":"103","author":"Yang","year":"2018","journal-title":"Biomed. Pharmacother."},{"key":"ref_18","doi-asserted-by":"crossref","first-page":"1346","DOI":"10.1158\/1078-0432.CCR-24-3028","article-title":"Targeting AXL inhibits the growth and metastasis of prostate cancer in bone","volume":"31","author":"Chiu","year":"2025","journal-title":"Clin. Cancer Res."},{"key":"ref_19","doi-asserted-by":"crossref","first-page":"4072","DOI":"10.1074\/jbc.272.7.4072","article-title":"Conventional PKC-\u03b1, novel PKC-\u03b5 and PKC-\u03b8, but not atypical PKC-\u03bb are MARCKS kinases in intact NIH 3T3 fibroblasts","volume":"272","author":"Giselbrecht","year":"1997","journal-title":"J. Biol. Chem."},{"key":"ref_20","doi-asserted-by":"crossref","unstructured":"Supino, R. (1995). MTT assays. In Vitro Toxicity Testing Protocols, Springer.","DOI":"10.1385\/0-89603-282-5:137"},{"key":"ref_21","doi-asserted-by":"crossref","first-page":"1005","DOI":"10.1021\/ol007056i","article-title":"Acylation of indole under friedel\u2013crafts conditions an improved method to obtain 3-acylindoles regioselectively","volume":"3","author":"Ottoni","year":"2001","journal-title":"Org. Lett."},{"key":"ref_22","doi-asserted-by":"crossref","first-page":"29","DOI":"10.1039\/C2SC21185H","article-title":"Indole synthesis\u2013something old, something new","volume":"4","author":"Inman","year":"2013","journal-title":"Chem. Sci."},{"key":"ref_23","doi-asserted-by":"crossref","first-page":"5587","DOI":"10.1007\/s11164-014-1683-9","article-title":"Room temperature synthesis of 2-benzimidazoles with hydrogen peroxide as oxidant and supported ammonium molybdate as catalyst","volume":"41","author":"Lan","year":"2015","journal-title":"Res. Chem. Intermed."},{"key":"ref_24","doi-asserted-by":"crossref","first-page":"1375","DOI":"10.1080\/00397910701230170","article-title":"One-pot synthesis of benzimidazoles from o-nitroanilines under microwaves via a reductive cyclization","volume":"37","author":"Surpur","year":"2007","journal-title":"Synth. Commun."},{"key":"ref_25","unstructured":"Vogel, A.I., and Furniss, B.S. (1989). Vogel\u2019s Textbook of Practical Organic Chemistry, Pearson."},{"key":"ref_26","doi-asserted-by":"crossref","first-page":"2320","DOI":"10.1007\/s11172-020-3036-8","article-title":"New possibilities for the synthesis of high-molecular weight poly (2,5(6)-benzimidazole) and studies of its solutions in DMSO-based complex organic solvent","volume":"69","author":"Ponomarev","year":"2020","journal-title":"Russ. Chem. Bull."},{"key":"ref_27","doi-asserted-by":"crossref","first-page":"101134","DOI":"10.1016\/j.rechem.2023.101134","article-title":"A facile synthesis and characterization of some novel benzimidazole derivatives","volume":"6","author":"Shinde","year":"2023","journal-title":"Results Chem."},{"key":"ref_28","doi-asserted-by":"crossref","first-page":"101","DOI":"10.1080\/00202967.1934.11871610","article-title":"The electrodeposition of tin from sodium stannate solutions with the use of insoluble anodes","volume":"9","author":"Hothersall","year":"1934","journal-title":"Trans. IMF"},{"key":"ref_29","doi-asserted-by":"crossref","first-page":"2612","DOI":"10.1128\/AAC.49.7.2612-2617.2005","article-title":"Microplate Alamar blue assay for Staphylococcus epidermidis biofilm susceptibility testing","volume":"49","author":"Pettit","year":"2005","journal-title":"Antimicrob. Agents Chemother."},{"key":"ref_30","doi-asserted-by":"crossref","unstructured":"El-Saghier, A.M., Hamed, A.M., Abosella, L., Br\u00e4se, S., and Aziz, H.A. (2026). Novel N-4-(5-Amino-7-substituted-triazolotriazinepiperazin-1-yl) Norfloxacin Analogues Exhibit Potent and Selective Anticancer Activity via Topoisomerase Inhibition, Cell-Cycle Arrest, and Apoptosis in A 431 Skin Carcinoma Cells. Pharmaceuticals, 19.","DOI":"10.3390\/ph19050657"},{"key":"ref_31","doi-asserted-by":"crossref","first-page":"2711875","DOI":"10.1080\/14756366.2026.2711875","article-title":"Exploration of novel hydroxamic acid-based candidates integrating chalcone scaffold cap as multitarget HDAC inhibitors: Design, anti-prostatic cancer assessment, in silico docking and molecular dynamic simulation","volume":"41","author":"Salem","year":"2026","journal-title":"J. Enzym. Inhib. Med. Chem."},{"key":"ref_32","doi-asserted-by":"crossref","first-page":"W469","DOI":"10.1093\/nar\/gkae254","article-title":"Deep-PK: Deep learning for small molecule pharmacokinetic and toxicity prediction","volume":"52","author":"Myung","year":"2024","journal-title":"Nucleic Acids Res."},{"key":"ref_33","doi-asserted-by":"crossref","first-page":"W486","DOI":"10.1093\/nar\/gkr320","article-title":"ChemMine tools: An online service for analyzing and clustering small molecules","volume":"39","author":"Backman","year":"2011","journal-title":"Nucleic Acids Res."},{"key":"ref_34","unstructured":"Frisch, M., Trucks, G., Schlegel, H., Scuseria, G., Robb, M., Cheeseman, J., Scalmani, G., Barone, V., Mennucci, B., and Petersson, G. (2009). Gaussian 09, Gaussian, Inc.. revision D. 01."},{"key":"ref_35","doi-asserted-by":"crossref","first-page":"5648","DOI":"10.1063\/1.464913","article-title":"Density-functional thermochemistry. III. The role of exact exchange","volume":"98","author":"Becke","year":"1993","journal-title":"J. Chem. Phys."},{"key":"ref_36","doi-asserted-by":"crossref","first-page":"785","DOI":"10.1103\/PhysRevB.37.785","article-title":"Development of the Colle-Salvetti correlation-energy formula into a functional of the electron density","volume":"37","author":"Lee","year":"1988","journal-title":"Phys. Rev. B"},{"key":"ref_37","doi-asserted-by":"crossref","first-page":"430","DOI":"10.1016\/j.molstruc.2015.11.010","article-title":"Click one pot synthesis, spectral analyses, crystal structures, DFT studies and brine shrimp cytotoxicity assay of two newly synthesized 1,4,5-trisubstituted 1,2,3-triazoles","volume":"1106","author":"Ahmed","year":"2016","journal-title":"J. Mol. Struct."},{"key":"ref_38","unstructured":"Pacheco, A.B., and Hpc, L. (2012). Introduction to AutoDock and AutoDock Tools, Louisiana State University."},{"key":"ref_39","doi-asserted-by":"crossref","first-page":"3891","DOI":"10.1021\/acs.jcim.1c00203","article-title":"AutoDock Vina 1.2. 0: New docking methods, expanded force field, and python bindings","volume":"61","author":"Eberhardt","year":"2021","journal-title":"J. Chem. Inf. Model."},{"key":"ref_40","first-page":"455","article-title":"Software news and update AutoDock Vina: Improving the speed and accuracy of docking with a new scoring function","volume":"31","author":"Trott","year":"2009","journal-title":"Effic. Optim. Multithreading"},{"key":"ref_41","first-page":"82","article-title":"Pymol: An open-source molecular graphics tool","volume":"40","author":"DeLano","year":"2002","journal-title":"CCP4 Newsl. Protein Crystallogr."},{"key":"ref_42","doi-asserted-by":"crossref","first-page":"1859","DOI":"10.1002\/jcc.20945","article-title":"CHARMM-GUI: A web-based graphical user interface for CHARMM","volume":"29","author":"Jo","year":"2008","journal-title":"J. Comput. Chem."},{"key":"ref_43","doi-asserted-by":"crossref","first-page":"5466","DOI":"10.1021\/acs.jpcb.7b11734","article-title":"Biomolecular simulations under realistic macroscopic salt conditions","volume":"122","author":"Ross","year":"2018","journal-title":"J. Phys. Chem. B"},{"key":"ref_44","doi-asserted-by":"crossref","first-page":"1545","DOI":"10.1002\/jcc.21287","article-title":"CHARMM: The biomolecular simulation program","volume":"30","author":"Brooks","year":"2009","journal-title":"J. Comput. Chem."},{"key":"ref_45","doi-asserted-by":"crossref","first-page":"405","DOI":"10.1021\/acs.jctc.5b00935","article-title":"CHARMM-GUI input generator for NAMD, GROMACS, AMBER, OpenMM, and CHARMM\/OpenMM simulations using the CHARMM36 additive force field","volume":"12","author":"Lee","year":"2016","journal-title":"J. Chem. Theory Comput."}],"container-title":["Pharmaceuticals"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/1424-8247\/19\/9\/1485\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,9,22]],"date-time":"2026-09-22T08:31:07Z","timestamp":1790065867000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/1424-8247\/19\/9\/1485"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,9,17]]},"references-count":45,"journal-issue":{"issue":"9","published-online":{"date-parts":[[2026,9]]}},"alternative-id":["ph19091485"],"URL":"https:\/\/doi.org\/10.3390\/ph19091485","relation":{},"ISSN":["1424-8247"],"issn-type":[{"value":"1424-8247","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,9,17]]}}}