Virtual screening of potential inhibitor against breast cancer-causing estrogen receptor alpha (ERα): molecular docking and dynamic simulations

References

• Sibuh BZ, Skhanna, et al. Molecular docking, synthesis and anticancer activity of thiosemicarbazone derivatives against MCF-7 human breast cancer cell line. Life Sci. 2021;273:119305.
   PubMed Web of Science ®Google Scholar
• Kalvala J, Parks RM, Green AR, et al. Concordance between core needle biopsy and surgical excision specimens for Ki-67 in breast cancer – a systematic review of the literature. Histopathology. 2021;80:468–484.
   PubMed Web of Science ®Google Scholar
• Liu Y, Ma H, Yao J. ERα, a key target for cancer therapy: a review. OncoTarget The. 2020;13:2183.
   Google Scholar
• Rana P, Shrama A, Mandal CC. Molecular insights into phytochemicals-driven break function in tumor microenvironment. J Food Biochem. 2021: e13824.
   PubMed Web of Science ®Google Scholar
• Balogun TA, Iqbal MN, Saibu OA, et al. Discovery of potential HER2 inhibitors from mangifera indica for the treatment of HER2-positive breast cancer: an integrated computational approach. J Biomol Struct Dyn. 2021: 1–13.
   Google Scholar
• Prabhavathi H, Dasegowda KR, Renukananda KH, et al. Exploration and evaluation of bioactive phytocompounds against BRCA proteins by in silico approach. J Biomol Struct Dyn. 2020: 1–15.
   PubMed Web of Science ®Google Scholar
• Agabio R, Clelia M, Paolo, et al. Alcohol consumption Is a modifiable risk factor for breast cancer: are women aware of this relationship? Alcohol Alcohol. 2021.
   PubMed Web of Science ®Google Scholar
• Rossini E, Giacopuzzi E, Gangemi F, et al. Estrogen-like effect of mitotane explained by its agonist activity on estrogen receptor-α. Biomedicines. 2021;9(6):681.
   PubMed Web of Science ®Google Scholar
• Rogger TM, De Marchi G, Brozzi L, et al. Immunoglobulin G4-related disease responder index correlates with the risk of 1-year relapse in type 1 autoimmune pancreatitis. Pancreas. 2021;50(6):879–881.
   PubMed Web of Science ®Google Scholar
• Badodekar N, Sharma A, Patil V, et al. Angiogenesis induction in breast cancer: a paracrine paradigm. Cell Biochem Funct. 2021;39:860–873.
   PubMed Web of Science ®Google Scholar
• Jerry DJ, Shull JD, Hadsell DL, et al. Genetic variation in sensitivity to estrogens and breast cancer risk. Mammal Genome. 2018;29(1):24–37.
   PubMed Web of Science ®Google Scholar
• Elengoe A, Sundramoorthy ND. Molecular docking of curcumin with breast cancer cell line proteins. Pharmaceut Biomed Res. 2020;6(1):27–36.
   Google Scholar
• Hatamipour M, Hadizadeh F, Jaafari MR, et al. Anti-proliferative potential of fluorinated curcumin analogues: experimental and computational analysis and review of the literature. Curr Med Chem. 2021;29:1459–1471.
   Web of Science ®Google Scholar
• Farghadani R, Naidu R. Curcumin: modulator of key molecular signaling pathways in hormone-independent breast cancer. Cancers. 2021;13(14):3427.
   PubMed Web of Science ®Google Scholar
• Novitasari D, Jenie RI, Utomoet RY, et al. CCA-1.1, a novel curcumin analog, exerts cytotoxic anti-migratory activity toward TNBC and HER2-enriched breast cancer cells. Asia Pac J Cancer Prevent. 2021;22(6):1827.
   PubMedGoogle Scholar
• Chikan NA, Bhavaniprasad V, Anbarasu K, et al. From natural products to drugs for epimutation computer-aided drug design. Appl Biochem Biotechnol. 2013;170(1):164–175.
   PubMed Web of Science ®Google Scholar
• Qaisar M, Muhammad S, Iqbal J, et al. Identification of marine fungi-based antiviral agents as potential inhibitors of SARS-CoV-2 by molecular docking. ADMET and molecular dynamic study. J Comput Biophys Chem. 2022;21:1–15.
   Google Scholar
• Mohammad T, Arif K, Alajmi MF, et al. Identification of high-affinity inhibitors of pyruvate dehydrogenase kinase-3: towards therapeutic management of cancer. J Biomol Struct Dyn. 2021;39(2):586–594.
   PubMed Web of Science ®Google Scholar
• Saba A, Muhammad S, Khera RA, et al. Identification of halogen-based derivatives as potent inhibitors of estrogen receptor alpha of breast cancer: an in-silico investigation. J Comput Biophys Chem. 2022;21:1–25.
   Google Scholar
• Muhammad S, Qaisar M, Iqbal J, et al. Exploring the inhibitory potential of novel bioactive compounds from mangrove actinomycetes against nsp10 the major activator of SARS-CoV-2 replication. Chem Paper. 2022;76:1–14.
   PubMed Web of Science ®Google Scholar
• Qaddir I, Rasool N, Hussain W, et al. Computer-aided analysis of phytochemicals as potential dengue virus inhibitors based on molecular docking, ADMET and DFT studies. J Vector Borne Dis. 2017;54(3):255.
   PubMed Web of Science ®Google Scholar
• Macalino SJY, Gosu V, Hong S, et al. Role of computer-aided drug design in modern drug discovery. Arch Pharm Res. 2015;38(9):1686–1701.
   PubMed Web of Science ®Google Scholar
• Wong SC, Kamarudin MNA, Naidu R. Anticancer mechanism of curcumin on human glioblastoma. Nutrients. 2021;13(3):950.
   PubMed Web of Science ®Google Scholar
• Rose Y, Duarte JM, Segura J, et al. RCSB protein data bank: architectural advances towards integrated searching and efficient access to macromolecular structure data from the PDB archive. J Mol Biol. 2021;433(11):166704.
   PubMed Web of Science ®Google Scholar
• Haroon M, Akhtar T, Khalid M, et al. Synthesis, antioxidant, antimicrobial and antiviral docking studies of ethyl 2-(2-(arylidene) hydrazinyl) thiazole-4-carboxylates. Zeitschrift für Naturforschung C. 2021;76(11–12):467–480.
   PubMed Web of Science ®Google Scholar
• Mahmud S, Uddin MAR, Paul GK, et al. Virtual screening and molecular dynamics simulation study of plant-derived compounds to identify potential inhibitors of main protease from SARS-CoV-2. Brief Bioinform. 2021;22(2):1402–1414.
   PubMed Web of Science ®Google Scholar
• Lim JPL, Mac Kevin EB, Nellas RB. The effect of ligand affinity to the contact dynamics of the ligand binding domain of thyroid hormone receptor-retinoid X receptor. J Mol Graph Model. 2021;104:107829.
   PubMed Web of Science ®Google Scholar
• Rasul HO, Aziz BK, Ghafour DD, et al. In silico molecular docking and dynamic simulation of eugenol compounds against breast cancer. J Mol Model. 2022;28(1):1–18.
   Web of Science ®Google Scholar
• Dariya B, Muppala S, Srivani G, et al. Targeting STAT proteins via computational analysis in colorectal cancer. Mol Cell Biochem. 2021;476(1):165–174.
   PubMed Web of Science ®Google Scholar
• Ma H, Zu F, Liu X, et al. Virtual screening methods as tools for drug lead discovery from large chemical libraries. Curr Med Chem. 2012;19(32):5562–5571.
   PubMed Web of Science ®Google Scholar
• Shah V, Bhaliya J, Patel GM. In silico docking and ADME study of deketene curcumin derivatives (DKC) as an aromatase inhibitor or antagonist to the estrogen-alpha positive receptor (Erα+): potent application of breast cancer. Struct Chem. 2022;33:1–30.
   Web of Science ®Google Scholar
• Kumari R, Rathi R, Pathak SR, et al. Structural-based virtual screening and identification of novel potent antimicrobial compounds against YsxC of staphylococcus aureus. J Mol Struct. 2022;1255:132476.
   PubMed Web of Science ®Google Scholar
• Prabhavathi H, Dasegowda KR, Renukananda KH, et al. Molecular docking and dynamic simulation to identify potential phytocompound inhibitors for EGFR and HER2 as anti-breast cancer agents. J Biomol Struct Dyn. 2020;40:1–12.
   Google Scholar
• Yousuf Z, lman K, Iftikhar N. et al. Structure-based virtual screening and molecular docking for the identification of potential multi-targeted inhibitors against breast cancer. Breast Cancer. 2017;9:447.
   PubMed Web of Science ®Google Scholar
• Trott O, Olson AJ. AutoDock Vina: improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading. J Computational Chem. 2010;31(2):455–461.
   Google Scholar
• Muhammad S, Hassan SH, Al-Sehemi AG, et al. Exploring the new potential antiviral constituents of moringa oliefera for SARS-COV-2 pathogenesis: An in silico molecular docking and dynamic studies. Chem Phys Lett. 2021;767:138379.
   PubMed Web of Science ®Google Scholar
• Majethia P, Mishra S, Rao L, et al. NAD (P) HX dehydratase (NAXD) deficiency due to a novel biallelic missense variant and review of literature. Europ J Med Genet. 2021;64:104266.
   Web of Science ®Google Scholar
• Preethi L, Ganamurali N, Dhanasekaran D, et al. Therapeutic use of guggulsterone in COVID-19 induced obesity (COVIBESITY) and significant role in immunomodulatory effect. Obes Med. 2021;24:100346.
   Google Scholar
• Chidambaram S, EI-sheikh MA, Alarhan AH, et al. Synthesis of novel coumarin analogues: investigation of molecular docking interaction of SARS-CoV-2 proteins with natural and synthetic coumarin analogues and their pharmacokinetics studies. Saudi J Biol Sci. 2021;28(1):1100–1108.
   PubMed Web of Science ®Google Scholar
• Anbarasu K, Jayanthi S. Identification of curcumin derivatives as human LMTK3 inhibitors for breast cancer: a docking, dynamics, and MM/PBSA approach. 3 Biotech. 2018;8(5):1–12.
   PubMedGoogle Scholar
• Jephthah S, Pesce F, Lindorff-Larsen K, et al. Force field effects in simulations of flexible peptides with varying polyproline II propensity. J Chem Theor Comput. 2021;17:5969-6670.
   PubMed Web of Science ®Google Scholar
• Phillips JC, Hardy DJ, Maia JDC, et al. Scalable molecular dynamics on CPU and GPU architectures with NAMD. J Chem Phys. 2020;153(4):044130.
   PubMed Web of Science ®Google Scholar
• Mahmoodi MH, Manteghian M, Naeiji P. Study the effect of Ag nanoparticles on the kinetics of CO2 hydrate growth by molecular dynamics simulation. J Mol Liq. 2021;153(4):044130.
   Google Scholar
• Ahmadi M, Chen Z. Emulsification of surfactants during bitumen recovery: molecular dynamics simulation). In 82nd EAGE annual conference & exhibition. 2021. European Association of Geoscientists & Engineers.
   Google Scholar
• Liu H, Hou T. CaFE: a tool for binding affinity prediction using end-point free energy methods. Bioinformatics. 2016;32(14):2216–2218.
   PubMed Web of Science ®Google Scholar
• Ray T, Ryusaki T, Ray PS. Therapeutically targeting cancers that overexpress FOXC1: A transcriptional driver of cell plasticity, partial EMT, and cancer metastasis. Front Oncol. 2021;11:721959.
   Web of Science ®Google Scholar
• Boni C, Sorio C. Current views on the interplay between tyrosine kinases and phosphatases in chronic myeloid leukemia. Cancers. 2021;13(10):2311.
   PubMed Web of Science ®Google Scholar
• Sarkar A, Sen D, Sharma A, et al. Structure-based virtual screening and molecular dynamics simulation to identify potential SARS-CoV-2 spike receptor inhibitors from natural compound database. Pharmaceut Chem J. 2021;55:1–13.
   PubMed Web of Science ®Google Scholar
• Taurin S, Nimick M, Larsen L, et al. A novel curcumin derivative increases the cytotoxicity of raloxifene in estrogen receptor-negative breast cancer cell lines. Int J Oncol. 2016;48(1):385–398.
   PubMed Web of Science ®Google Scholar
• Rodrigues FC, Kumar NV, Hari G, et al. The inhibitory potency of isoxazole-curcumin analogue for the management of breast cancer: a comparative in vitro and molecular modeling investigation. Chem Paper. 2021;75(11):5995–6008.
   Web of Science ®Google Scholar
• Mahajanakatti AB, Murthy G, Sharma N, et al. Exploring inhibitory potential of curcumin against various cancer targets by in silico virtual screening. Interdiscip Sci. 2014;6(1):13–24.
   PubMed Web of Science ®Google Scholar
• Chaudhary M, Kumar K, Baldi A, et al. 4-Bromo-4′-chloro pyrazoline analog of curcumin augmented anticancer activity against human cervical cancer, HeLa cells: in silico-guided analysis, synthesis, and in vitro cytotoxicity. J Biomol Struct Dyn. 2020;38(5):1335–1353.
   PubMed Web of Science ®Google Scholar
• Lai H-W, Chien S-Y, Kuo S-J, et al. The potential utility of curcumin in the treatment of HER-2-overexpressed breast cancer: an in vitro and in vivo comparison study with herceptin. Evidence-Based Complement Alternat Med. 2012;2012:486568–486580.
   Web of Science ®Google Scholar
• Hatamipour M, Hadizadeh F, Jaafari MR, et al. Anti-proliferative potential of fluorinated curcumin analogues: experimental and computational analysis and review of the literature. Curr Med Chem. 2022;29(13):1459–1471.
   PubMed Web of Science ®Google Scholar
• Labban L. Medicinal and pharmacological properties of turmeric (Curcuma longa): a review. Int J Pharm Biomed Sci. 2014;5(1):17–23.
   Google Scholar
• Geetha Rani Y, Lakshmi BS. Structural insight into the antagonistic action of diarylheptanoid on human estrogen receptor alpha. J Biomol Struct Dyn. 2019;37(5):1189–1203.
   PubMed Web of Science ®Google Scholar
• Lee HG, Kang S, Lee JS. Binding characteristics of staphylococcal protein A and streptococcal protein G for fragment crystallizable portion of human immunoglobulin G. Comput Struct Biotechnol J. 2021;19:3372–3383.
   PubMed Web of Science ®Google Scholar
• Ortiz CLD, Completo GC, Nacario RC, et al. Potential inhibitors of galactofuranosyltransferase 2 (GlfT2): molecular docking, 3D-QSAR, and in silico ADMETox studies. Sci Rep. 2019;9(1):1–28.
   PubMedGoogle Scholar
• Mohan B, Muhammad S, Al-Shemei AG, et al. Synthesis of copper (II) coordination complex, its molecular docking and computational exploration for novel functional properties: a dual approach. Chem Select. 2021;6(4):738–745.
   Google Scholar
• Sarkar P, Srivastava V. Molecular docking, drug likeliness and in silico ADMET study of bioactive compounds against DNA methyltransferase. Mater Today. 2021;52:2193–2200.
   Google Scholar
• Chen X, Li HL, Tian L, et al. Analysis of the physicochemical properties of acaricides based on lipinski’s rule of five. J Comput Biol. 2020;27(9):1397–1406.
   PubMed Web of Science ®Google Scholar
• Anjum F, Mohammad T, Almalki AA, et al. Phytoconstituents and Medicinal plants for anticancer drug discovery: computational identification of potent inhibitors of PIM1 kinase. OMICS. 2021;25(9):580–590.
   PubMed Web of Science ®Google Scholar
• Zia M, Muhammad S, Bibi S, et al. Exploring the potential of novel phenolic compounds as potential therapeutic candidates against SARS-CoV-2, using quantum chemistry, molecular docking and dynamic studies. Bioorg Med Chem Lett. 2021;43:128079.
   PubMed Web of Science ®Google Scholar
• Alghamdi HA, Attique SA, Yan W, et al. Repurposing the inhibitors of COVID-19 key proteins through molecular docking approach. Process Biochem. 2021;110:216–222.
   PubMed Web of Science ®Google Scholar
• Gupta S, Singh AK, Kushwaha PP, et al. Identification of potential natural inhibitors of SARS-CoV2 main protease by molecular docking and simulation studies. J Biomol Struct Dyn. 2021;39(12):4334–4345.
   PubMed Web of Science ®Google Scholar
• Jain, S. and D.J. Sen, Exploration of indolo-imidazo [1, 2-a] Pyridine compounds as anti-tubercular agents through docking. ADMET Drug Likeliness Stud. 2021;11:3350–3361.
   Google Scholar
• Ishola AA, Joshi T, Abdulai SI, et al. Molecular basis for the repurposing of histamine H2-receptor antagonist to treat COVID-19. J Biomol Struct Dyn. 2021;40:1–18.
   PubMed Web of Science ®Google Scholar
• Kufareva I, Abagyan R. Methods of protein structure comparison. In: Andrew JW Orry, Rubben Abagyan, editors. Homology modeling. Springer; 2011. p. 231–257.
   Google Scholar
• Tang Q-Y, Kaneko K. Dynamics-evolution correspondence in protein structures. Phys Rev Lett. 2021;127(9):098103.
   PubMed Web of Science ®Google Scholar
• Al-Karmalawy AA, Alnajjar R, Dahab M, et al. Molecular docking and dynamics simulations reveal the potential of anti-HCV drugs to inhibit COVID-19 main protease. Pharm Sci. 2021;10:S109–S121
   Google Scholar
• Avti P, Chauhan A, Shekhar N, et al. Computational basis of SARS-CoV 2 main protease inhibition: an insight from molecular dynamics simulation based findings. J Biomol Struct Dyn. 2021;40:1–11.
   Google Scholar
• Chatterjee SS, Malathesh BC, Das S, et al. Interactions of recommended COVID-19 drugs with commonly used psychotropics. Asia J Psychiat. 2020;52:102173.
   PubMed Web of Science ®Google Scholar
• Muralidharan N, Sakthivel R, Velmurugan D, et al. Computational studies of drug repurposing and synergism of lopinavir, oseltamivir and ritonavir binding with SARS-CoV-2 protease against COVID-19. J Biomol Struct Dyn. 2021;39(7):2673–2678.
   PubMed Web of Science ®Google Scholar
• Ahmad N, Rehman AU, Badshah SL, et al. Molecular dynamics simulation of Zika virus NS5 RNA dependent RNA polymerase with selected novel non-nucleoside inhibitors. J Mol Struct. 2020;1203:127428.
   Web of Science ®Google Scholar
• Khan RJ, Jha RK, Amera GM, et al. Targeting SARS-CoV-2: a systematic drug repurposing approach to identify promising inhibitors against 3C-like proteinase and 2′-O-ribose methyltransferase. J Biomol Struct Dyn. 2021;39(8):2679–2692.
   PubMed Web of Science ®Google Scholar
• Marsh JA, Teichmann SA. Relative solvent accessible surface area predicts protein conformational changes upon binding. Structure. 2011;19(6):859–867.
   PubMed Web of Science ®Google Scholar
• Sahu SN, Mishra B, Sahu R, et al. Molecular dynamics simulation perception study of the binding affinity performance for main protease of SARS-CoV-2. J Biomol Struct Dyn. 2020: 1–16.
   Web of Science ®Google Scholar
• Qaisar M, Muhammad S, Iqbal J, et al. Identification of marine fungi-based antiviral agents as potential inhibitors of SARS-CoV-2 by molecular docking, ADMET and molecular dynamic study. J Comput Biophys Chem. 2021;21:1–15.
   Google Scholar
• Elmezayen AD, Obaidi A-AL, Sahin AT, et al. Drug repurposing for coronavirus (COVID-19): in silico screening of known drugs against coronavirus 3CL hydrolase and protease enzymes. J Biomol Struct Dyn. 2021;39(8):2980–2992.
   PubMed Web of Science ®Google Scholar