Published August 26, 2025
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In silico and in vitro studies of gemcitabine derivatives as anticancer agents
Authors/Creators
- 1. University of Al-Kafeel, Najaf, Iraq|lKafeel Center for Medical and Pharmaceutical Sciences, Najaf, Iraq
- 2. Al-Furat Al-Awsat Technical University, Kufa, Iraq
- 3. Jabir Ibn Hayyan University of Medical and Pharmaceutical Sciences, Najaf, Iraq
- 4. Government College Women University, Faisalabd, Pakistan
Description
Cancer remains one of the leading causes of death globally and is expected to increase in incidence. The present investigation aimed to evaluate the anticancer efficacy of gemcitabine derivatives on MCF7, A549, and PC3 cell lines. Compounds Com. 10 and Com. 16 were the most potent, with IC₅₀ values of 9.45, 6.93, and 12.09 µM (Com. 10) and 12.23, 6.60, and 21.57 µM (Com. 16) for the three cell lines, showing a better response compared to the reference drug gemcitabine. Com. 9 and Com. 14 were also moderately active, preferentially on A549 and PC3. Com. 16 showed strong binding with the active residues as determined by molecular docking. Com. 16 bound to key cancer targets Vav1 (6NEW), ERK2 (4ZXT), and CYP3A4 (7LXL), with docking scores of −191.72, −187.66, and −221.08 kcal/mol, respectively. These interactions were electrostatic, hydrophobic, and π-type, similar to those induced by gemcitabine. Several other compounds also demonstrated good docking scores (−160 to −180 kcal/mol), and eight protein–ligand complexes emerged as leads. Moreover, ADME and physicochemical analyses of the top six active compounds indicated good drug-likeness and a favorable PK profile compared to gemcitabine.
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References
- Aslan JE (2019) Platelet Rho GTPase regulation in physiology and disease. Platelets 30: 17–22. https://doi.org/10.1080/09537104.2018.1475632
- Azmal M, Paul JK, Prima FS, Talukder OF, Ghosh A (2024) An in silico molecular docking and simulation study to identify potential anticancer phytochemicals targeting the RAS signaling pathway. PLOS ONE 19: e0310637. https://doi.org/10.1371/journal.pone.0310637
- Bender DM, Bao J, Dantzig AH, Diseroad WD, Law KL, Magnus NA, Peterson JA, Perkins EJ, Pu YJ, Reutzel-Edens SM, Remick DM, Starling JJ, Stephenson GA, Vaid RK, Zhang D, McCarthy JR (2009) Synthesis, crystallization, and biological evaluation of an orally active prodrug of gemcitabine. Journal of Medicinal Chemistry 52: 6958–6961. https://doi.org/10.1021/jm901181h
- Ali FN, Ammar KM, Dheyaa H M, Ehab KO, Ali JR (2020) Synthesis of new gemcitabine derivatives linked tetrazole ring as antibacterial activity. International Journal of Psychosocial Rehabilitation 20: 1806–1813. https://doi.org/10.37200/IJPR/V24I5/PR201852
- Cappuzzo F (2009) Gemcitabine for the treatment of advanced nonsmall cell lung cancer. OncoTargets and Therapy 2: 209. https://doi.org/10.2147/OTT.S4645
- Carmichael J, Fink U, Russell R, Spittle M, Harris A, Spiessi G, Blatter J (1996) Phase II study of gemcitabine in patients with advanced pancreatic cancer. British Journal of Cancer 73: 101–105. https://doi.org/10.1038/bjc.1996.18
- Dhillon AS, Hagan S, Rath O, Kolch W (2007) MAP kinase signalling pathways in cancer. Oncogene 26: 3279–3290. https://doi.org/10.1038/sj.onc.1210421
- Ewald B, Sampath D, Plunkett W (2008) Nucleoside analogs: molecular mechanisms signaling cell death. Oncogene 27: 6522–6537. https://doi.org/10.1038/onc.2008.316
- Farrell JJ, Elsaleh H, Garcia M, Lai R, Ammar A, Regine WF, Abrams R, Benson AB, Macdonald J, Cass CE, Dicker AP, Mackey JR (2009) Human equilibrative nucleoside transporter 1 levels predict response to gemcitabine in patients with pancreatic cancer. Gastroenterology 136: 187–195. https://doi.org/10.1053/j.gastro.2008.09.067
- Ferrazzi E, Stievano L (2006) Gemcitabine: monochemotherapy of breast cancer. Annals of Oncology 17: v169–v172. https://doi.org/10.1093/annonc/mdj975
- Ghasemi M, Liang S, Luu QM, Kempson I (2023) The MTT Assay: A Method for Error Minimization and Interpretation in Measuring Cytotoxicity and Estimating Cell Viability. In: Friedrich O, Gilbert DF (Eds) Cell Viability Assays. Methods in Molecular Biology, vol 2644. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-3052-5_2
- Hoang T, Kim K, Jaslowski A, Koch P, Beatty P, McGovern J, Quisumbing M, Shapiro G, Witte R, Schiller JH (2003) Phase II study of second-line gemcitabine in sensitive or refractory small cell lung cancer. Lung Cancer 42: 97–102. https://doi.org/10.1016/S0169-5002(03)00273-3
- Immordino ML, Brusa P, Rocco F, Arpicco S, Ceruti M, Cattel L (2004) Preparation, characterization, cytotoxicity and pharmacokinetics of liposomes containing lipophilic gemcitabine prodrugs. Journal of Controlled Release 100: 331–346. https://doi.org/10.1016/j.jconrel.2004.09.001
- Itoi T, Sofuni A, Fukushima N, Itokawa F, Tsuchiya T, Kurihara T, Moriyasu F, Tsuchida A, Kasuya K (2007) Ribonucleotide reductase subunit M2 mRNA expression in pretreatment biopsies obtained from unresectable pancreatic carcinomas. Journal of Gastroenterology 42: 389–394. https://doi.org/10.1007/s00535-007-2017-0
- Iwakiri S, Sonobe M, Nagai S, Hirata T, Wada H, Miyahara R (2008) Expression status of folate receptor α is significantly correlated with prognosis in non-small-cell lung cancers. Annals of Surgical Oncology 15: 889–899. https://doi.org/10.1245/s10434-007-9755-3
- Kaaki K, Hervé-Aubert K, Chiper M, Shkilnyy A, Soucé M, Benoit R, Paillard A, Dubois P, Saboungi M-L, Chourpa I (2012) Magnetic nanocarriers of doxorubicin coated with poly(ethylene glycol) and folic acid: relation between coating structure, surface properties, colloidal stability, and cancer cell targeting. Langmuir 28: 1496–1505. https://doi.org/10.1021/la2037845
- Kalli KR, Oberg AL, Keeney GL, Christianson TJH, Low PS, Knutson KL, Hartmann LC (2008) Folate receptor alpha as a tumor target in epithelial ovarian cancer. Gynecologic Oncology 108: 619–626. https://doi.org/10.1016/j.ygyno.2007.11.020
- Koolen SLW, Witteveen PO, Jansen RS, Langenberg MHG, Kronemeijer RH, Nol A, Garcia-Ribas I, Callies S, Benhadji KA, Slapak CA, Beijnen JH, Voest EE, Schellens JHM (2011) Phase i study of oral gemcitabine prodrug (LY2334737) alone and in combination with erlotinib in patients with advanced solid tumors. Clinical Cancer Research 17: 6071–6082. https://doi.org/10.1158/1078-0432.CCR-11-0353
- Krzywik J, Mozga W, Aminpour M, Janczak J, Maj E, Wietrzyk J, Tuszyński JA, Huczyński A (2020) Synthesis, antiproliferative activity and molecular docking studies of novel doubly modified colchicine amides and sulfonamides as anticancer agents. Molecules 25: 1789. https://doi.org/10.3390/molecules25081789
- Leskelä S, Honrado E, Montero-Conde C, Landa I, Cascón A, Letón R, Talavera P, Cózar JM, Concha A, Robledo M, Rodríguez-Antona C (2007) Cytochrome P450 3A5 is highly expressed in normal prostate cells but absent in prostate cancer. Endocrine-Related Cancer 14: 645–654. https://doi.org/10.1677/ERC-07-0078
- Lipinski CA, Lombardo F, Dominy BW, Feeney PJ (2001) 46 Advanced Drug Delivery Reviews Experimental and computational approaches to estimate solubility and permeability in drug discovery and development q settings. www.elsevier.com/locate/drugdeliv.
- Liu Y, Tarsounas M, O'Regan P, West SC (2007) Role of RAD51C and XRCC3 in Genetic Recombination and DNA Repair. Journal of Biological Chemistry 282: 1973–1979. https://doi.org/10.1074/jbc.M609066200
- Mohammed MJ, Oleiwi ZK, Al-Hilo MAH, Mubarak AKH, Obaid EK, Radhi AJ (2020) Synthesis and study biological activity of gemcitabine linked heterocyclic hybrids. Research Journal of Pharmacy and Technology 13: 3257. https://doi.org/10.5958/0974-360X.2020.00577.6
- Nakano Y, Tanno S, Koizumi K, Nishikawa T, Nakamura K, Minoguchi M, Izawa T, Mizukami Y, Okumura T, Kohgo Y (2007) Gemcitabine chemoresistance and molecular markers associated with gemcitabine transport and metabolism in human pancreatic cancer cells. British Journal of Cancer 96: 457–463. https://doi.org/10.1038/sj.bjc.6603559
- Naser AF, Madlool AK, Mohsin DH, Obaid EK, Radhi AJ (2020) Synthesis of new gemcitabine derivatives linked tetrazole ring as antibacterial activity. International Journal of Psychosocial Rehabilitation 20: 1806–1813. https://doi.org/10.37200/IJPR/V24I5/PR201852
- Ozols R (2005) Gemcitabine and carboplatin in second-line ovarian cancer. Seminars in Oncology 32: 4–8. https://doi.org/10.1053/j.seminoncol.2005.06.023
- Pace E, Melis M, Siena L, Bucchieri F, Vignola AM, Profita M, Gjomarkaj M, Bonsignore G (2000) Effects of gemcitabine on cell proliferation and apoptosis in non-small-cell lung cancer (NSCLC) cell lines. Cancer Chemotherapy and Pharmacology 46: 467–476. https://doi.org/10.1007/s002800000183
- Pasut G, Veronese FM (2009) PEG conjugates in clinical development or use as anticancer agents: An overview. Advanced Drug Delivery Reviews 61: 1177–1188. https://doi.org/10.1016/j.addr.2009.02.010
- Pasut G, Veronese FM (2012) State of the art in PEGylation: The great versatility achieved after forty years of research. Journal of Controlled Release 161: 461–472. https://doi.org/10.1016/j.jconrel.2011.10.037
- Radhi AW, AL-Yasiry ANT, Radhi AJ (2021) Synthesis of new tetrazole derivatives as potential antibacterial agents. International Journal of Pharmaceutical Research 13: 2931–2935. https://doi.org/10.31838/ijpr/2021.13.01.330
- Robinson BW, Ostruszka L, Im MM, Shewach DS (2004) Promising combination therapies with gemcitabine. Seminars in Oncology 31: 2–12. https://doi.org/10.1053/j.seminoncol.2004.03.021
- Salman FW, Twayej AJ, Shaheed HA, Radhi AJ (2019) New Gemcitabine Derivatives as Potent in vitro α-Glucosidase Inhibitors. Nano Biomedicine and Engineering 11(1): 84–90. https://doi.org/10.5101/nbe.v11i1.p84-90
- Seyedi S, Teo R, Foster L, Saha D, Mina L, Northfelt D, Anderson KS, Shibata D, Gatenby R, Cisneros L, Troan B, Anderson ARA, Maley CC (2023) Testing adaptive therapy protocols using gemcitabine and capecitabine on a mouse model of endocrine-resistant breast cancer. https://doi.org/10.1101/2023.09.18.558136
- Shmeeda H, Amitay Y, Gorin J, Tzemach D, Mak L, Ogorka J, Kumar S, Zhang JA, Gabizon A (2010) Delivery of zoledronic acid encapsulated in folate-targeted liposome results in potent in vitro cytotoxic activity on tumor cells. Journal of Controlled Release 146: 76–83. https://doi.org/10.1016/j.jconrel.2010.04.028
- Subhani S, Jamil K (2015) Molecular docking of chemotherapeutic agents to CYP3A4 in non-small cell lung cancer. Biomedicine & Pharmacotherapy 73: 65–74. https://doi.org/10.1016/j.biopha.2015.05.018
- Sung H, Ferlay J, Siegel RL, Laversanne M, Soerjomataram I, Jemal A, Bray F (2021) Global cancer statistics 2020: GLOBOCAN Estimates of incidence and mortality worldwide for 36 cancers in 185 countries. CA: A Cancer Journal for Clinicians 71: 209–249. https://doi.org/10.3322/caac.21660
- Thakkar S, Hutson T, Garcia J, Rothaermal J, Bart M, Dreicer R (2006) A phase II trial of gemcitabine and docetaxel in hormone-refractory metastatic prostate cancer. Journal of Clinical Oncology 24: 14501–14501. https://doi.org/10.1200/jco.2006.24.18_suppl.14501
- Thomsen R, Christensen MH (2006) MolDock: A new technique for high-accuracy molecular docking. Journal of Medicinal Chemistry 49: 3315–3321. https://doi.org/10.1021/jm051197e
- Torres Robles J, Stiegler AL, Boggon TJ, Turk BE (2025) Cancer hotspot mutations rewire ERK2 specificity by selective exclusion of docking interactions. Journal of Biological Chemistry 301: 108348. https://doi.org/10.1016/j.jbc.2025.108348
- Tsume Y, Borras Bermejo B, Amidon G (2014a) The dipeptide monoester prodrugs of floxuridine and gemcitabine—feasibility of orally administrable nucleoside analogs. Pharmaceuticals 7: 169–191. https://doi.org/10.3390/ph7020169
- Tsume Y, Incecayir T, Song X, Hilfinger JM, Amidon GL (2014b) The development of orally administrable gemcitabine prodrugs with d-enantiomer amino acids: Enhanced membrane permeability and enzymatic stability. European Journal of Pharmaceutics and Biopharmaceutics 86: 514–523. https://doi.org/10.1016/j.ejpb.2013.12.009
- Vandana M, Sahoo SK (2010) Long circulation and cytotoxicity of PEGylated gemcitabine and its potential for the treatment of pancreatic cancer. Biomaterials 31: 9340–9356. https://doi.org/10.1016/j.biomaterials.2010.08.010
- Varani K, Gessi S, Merighi S, Iannotta V, Cattabriga E, Pancaldi C, Cadossi R, Borea PA (2003) Alteration of A3 adenosine receptors in human neutrophils and low frequency electromagnetic fields. Biochemical Pharmacology 66: 1897–1906. https://doi.org/10.1016/S0006-2952(03)00454-4
- Ventura S, Serrano L (2004) Designing proteins from the inside out. Proteins: Structure, Function, and Bioinformatics 56: 1–10. https://doi.org/10.1002/prot.20142
- Wu Z, Xia F, Lin R (2024) Global burden of cancer and associated risk factors in 204 countries and territories, 1980–2021: a systematic analysis for the GBD 2021. Journal of Hematology & Oncology 17: 119. https://doi.org/10.1186/s13045-024-01640-8
- Xiong G, Wu Z, Yi J, Fu L, Yang Z, Hsieh C, Yin M, Zeng X, Wu C, Lu A, Chen X, Hou T, Cao D (2021) ADMETlab 2.0: an integrated online platform for accurate and comprehensive predictions of ADMET properties. Nucleic Acids Research 49: W5–W14. https://doi.org/10.1093/nar/gkab255
- Yang S-J, Lin F-H, Tsai K-C, Wei M-F, Tsai H-M, Wong J-M, Shieh M-J (2010) Folic Acid-Conjugated Chitosan Nanoparticles Enhanced Protoporphyrin IX Accumulation in Colorectal Cancer Cells. Bioconjugate Chemistry 21: 679–689. https://doi.org/10.1021/bc9004798
- Yardley D (2005) Gemcitabine Plus Paclitaxel in Breast Cancer. Seminars in Oncology 32: 14–21. https://doi.org/10.1053/j.seminoncol.2005.06.025
- Zhang J, Wan L, Dai X, Sun Y, Wei W (2014) Functional characterization of Anaphase Promoting Complex/Cyclosome (APC/C) E3 ubiquitin ligases in tumorigenesis. Biochimica et Biophysica Acta (BBA) - Reviews on Cancer 1845: 277–293. https://doi.org/10.1016/j.bbcan.2014.02.001
- Zhu C, Hu H, Ma Y, Xiong S, Zhu D (2023) Vav1‐dependent Rac1 activation mediates hypoxia‐induced gemcitabine resistance in pancreatic ductal adenocarcinoma cells through upregulation of HIF‐1α expression. Cell Biology International 47: 1835–1842. https://doi.org/10.1002/cbin.12074