Bank RPD (n.d.) PDB Statistics. Retrieved December 9, 2024, from https://www.rcsb.org/stats

Baron R, Kneissel M (2013) WNT signaling in bone homeostasis and disease: from human mutations to treatments. Nat Med 19(2):179–192. https://doi.org/10.1038/nm.3074

Article  PubMed  CAS  Google Scholar 

CHARMM-GUI (n.d.) Retrieved December 9 (2024) from https://www.charmm-gui.org/

Choudhary G, Prajapat M, Kaur G, Singh H, Mahendiratta S, Prakash A, Medhi B (2024) Integrated in-silico and in-vitro assessments of HDAC6 inhibitor efficacy in mitigating amyloid beta pathology in alzheimer’s disease. J Biomol Struct Dyn 42(18):9720–9730. https://doi.org/10.1080/07391102.2023.2274518

Article  PubMed  CAS  Google Scholar 

Clevers H, Nusse R (2012) Wnt/β-catenin signaling and disease. Cell 149(6):1192–1205. https://doi.org/10.1016/j.cell.2012.05.012

Article  PubMed  CAS  Google Scholar 

dccm.pca. Bio3d 2.3-0 (n.d.) Retrieved December 9, (2024) from http://thegrantlab.org/bio3d_v2/html/dccm.pca.html

E F, Dl AA, Mc W, Sg A, Aj D, R.,E, S (2011) Analysis of β-amino alcohols as inhibitors of the potential anti-tubercular target N-acetyltransferase. Bioorg Med Chem Lett 21:1185–1190

Farmer J, Kanwal F, Nikulsin N, Tsilimigras MCB, Jacobs DJ (2017) Statistical measures to quantify similarity between molecular dynamics simulation trajectories. Entropy 19(12):646. https://doi.org/10.3390/e19120646

Article  PubMed  CAS  Google Scholar 

Galland F, Seady M, Taday J, Smaili SS, Gonçalves CA, Leite MC (2019) Astrocyte culture models: molecular and function characterization of primary culture, immortalized astrocytes and C6 glioma cells. Neurochem Int 131:104538. https://doi.org/10.1016/j.neuint.2019.104538

Article  PubMed  CAS  Google Scholar 

Glide | Schrödinger (n.d.) Retrieved December 9, (2024) from https://www.schrodinger.com/platform/products/glide/

Gutiérrez-Almeida CE, Santerre A, León-Moreno LC, Aguilar-García IG, Castañeda-Arellano R, Dueñas-Jiménez SH, Dueñas-Jiménez JM (2022) Proliferation and apoptosis regulation by G protein-coupled Estrogen receptor in glioblastoma C6 cells. Oncol Lett 24(1):217. https://doi.org/10.3892/ol.2022.13338

Article  PubMed  PubMed Central  CAS  Google Scholar 

Hatimuria M, Vishwakarma J, Takkella D, Chandran CN, Phukan P, Gavvala K, Pabbathi A (2025) Repurposing of approved drugs towards Nipah virus treatment: an in silico docking, molecular dynamics simulation and a MM/GBSA approach. In Silico Pharmacol 13(2):86. https://doi.org/10.1007/s40203-025-00371-z

Article  PubMed  Google Scholar 

Home (n.d.) Asinex.Com. Retrieved December 9, (2024) from https://www.asinex.com/

How do I calculate the binding energy of a bimolecular complex with Jaguar? (n.d.) Retrieved December 9, (2024) from https://support.schrodinger.com/s/article/1618

Knopman DS, Amieva H, Petersen RC, Chételat G, Holtzman DM, Hyman BT, Nixon RA, Jones DT (2021) Alzheimer disease. Nat Reviews Disease Primers 7(1):33. https://doi.org/10.1038/s41572-021-00269-y

Article  PubMed  Google Scholar 

Kortagere S, Mortensen OV, Xia J, Lester W, Fang Y, Srikanth Y, Salvino JM, Fontana ACK (2018) Identification of novel allosteric modulators of glutamate transporter EAAT2. ACS Chem Neurosci 9(3):522–534. https://doi.org/10.1021/acschemneuro.7b00308

Article  PubMed  CAS  Google Scholar 

Kumari R, Kumar R, Lynn A, Open Source Drug Discovery Consortium (2014) G_mmpbsa—a GROMACS tool for high-throughput MM-PBSA calculations. J Chem Inf Model 54(7):1951–1962. https://doi.org/10.1021/ci500020m

Article  PubMed  CAS  Google Scholar 

Manisha C, Selvaraj A, Jubie S, Moola Joghee Nanjan C, Moola Joghee N, Clement JP, Justin A (2020) Positive allosteric activation of glial EAAT-2 transporter protein: a novel strategy for alzheimer’s disease. Med Hypotheses 142:109794. https://doi.org/10.1016/j.mehy.2020.109794

Article  PubMed  CAS  Google Scholar 

Pajarillo E, Rizor A, Lee J, Aschner M, Lee E (2019) The role of astrocytic glutamate transporters GLT-1 and GLAST in neurological disorders: potential targets for neurotherapeutics. Neuropharmacology 161:107559. https://doi.org/10.1016/j.neuropharm.2019.03.002

Article  PubMed  PubMed Central  CAS  Google Scholar 

Parsekar SU, Singh M, Mishra DP, Antharjanam PKS, Koley AP, Kumar M (2019) Efficient hydrolytic cleavage of DNA and antiproliferative effect on human cancer cells by two dinuclear Cu(II) complexes containing a carbohydrazone ligand and 1,10-phenanthroline as a coligand. JBIC J Biol Inorg Chem 24(3):343–363. https://doi.org/10.1007/s00775-019-01651-8

Article  PubMed  CAS  Google Scholar 

Prajapat M, Singh H, Chaudhary G, Sarma P, Kaur G, Patel P, A., Medhi B (2023) A novel inhibitor of DKK1/LRP6 interactions against the alzheimer disease: an insilco approach. Bioinform Biol Insights 17:11779322231183762. https://doi.org/10.1177/11779322231183762

Article  PubMed  PubMed Central  Google Scholar 

Puntambekar SS, Moutinho M, Lin PB-C, Jadhav V, Tumbleson-Brink D, Balaji A, Benito MA, Xu G, Oblak A, Lasagna-Reeves CA, Landreth GE, Lamb BT (2022) CX3CR1 deficiency aggravates amyloid driven neuronal pathology and cognitive decline in alzheimer’s disease. Mol Neurodegeneration 17:47. https://doi.org/10.1186/s13024-022-00545-9

Article  CAS  Google Scholar 

QikProp | Schrödinger (n.d.) Retrieved December 9, (2024) from https://www.schrodinger.com/platform/products/qikprop/

Rajendran K, Krishnan UM (2024) Mechanistic insights and emerging therapeutic stratagems for Alzheimer’s disease. Ageing Res Rev 97:102309. https://doi.org/10.1016/j.arr.2024.102309

Article  PubMed  CAS  Google Scholar 

Revett TJ, Baker GB, Jhamandas J, Kar S (2013) Glutamate system, amyloid β peptides and Tau protein: functional interrelationships and relevance to alzheimer disease pathology. J Psychiatry Neuroscience: JPN 38(1):6–23. https://doi.org/10.1503/jpn.110190

Article  Google Scholar 

Sargazi ML, Juybari KB, Tarzi ME, Amirkhosravi A, Nematollahi MH, Mirzamohammdi S, Mehrbani M, Mehrabani M, Mehrabani M (2021) Naringenin attenuates cell viability and migration of C6 glioblastoma cell line: A possible role of Hedgehog signaling pathway. Mol Biol Rep 48(9):6413–6421. https://doi.org/10.1007/s11033-021-06641-1

Article  PubMed  CAS  Google Scholar 

SAVESv6.1—Structure Validation Server (n.d.) Retrieved December 9, (2024) from https://saves.mbi.ucla.edu/

Scott HA, Gebhardt FM, Mitrovic AD, Vandenberg RJ, Dodd PR (2011) Glutamate transporter variants reduce glutamate uptake in alzheimer’s disease. Neurobiol Aging 32(3):553e1–55311. https://doi.org/10.1016/j.neurobiolaging.2010.03.008

Article  CAS  Google Scholar 

Sharma A, Kazim SF, Larson CS, Ramakrishnan A, Gray JD, McEwen BS, Rosenberg PA, Shen L, Pereira AC (2019) Divergent roles of astrocytic versus neuronal EAAT2 deficiency on cognition and overlap with aging and alzheimer’s molecular signatures. Proc Natl Acad Sci U S A 116(43):21800–21811. https://doi.org/10.1073/pnas.1903566116

Article  PubMed  PubMed Central  CAS  Google Scholar 

Shukla R, Munjal NS, Singh TR (2019) Identification of novel small molecules against GSK3β for alzheimer’s disease using chemoinformatics approach. J Mol Graph Model 91:91–104. https://doi.org/10.1016/j.jmgm.2019.06.008

Article  PubMed  CAS  Google Scholar 

Shukla R, Kumar A, Kelvin DJ, Singh TR (2023) Disruption of DYRK1A-induced hyperphosphorylation of amyloid-beta and tau protein in Alzheimer’s disease: an integrative molecular modeling approach. Front Mol Biosci. https://doi.org/10.3389/fmolb.2022.1078987

Article  PubMed  PubMed Central  Google Scholar 

Singh H, Raja A, Prakash A, Medhi B (2023) Based on Gromacs and Zenity-Dependent GUI for Beginners in MD Simulation Study. J Chem Inf Model 63(9):2603–2608. https://doi.org/10.1021/acs.jcim.3c00341. Gmx_qk: An Automated Protein/Protein-Ligand Complex Simulation Workflow Bridged to MM/PBSA

Sk MF, Roy R, Jonniya NA, Poddar S, Kar P (2020) Elucidating biophysical basis of binding of inhibitors to SARS-CoV-2 main protease by using molecular dynamics simulations and free energy calculations. J Biomol Struct Dyn 39(10). https://doi.org/10.1080/07391102.2020.1768149

Article  PubMed  CAS  Google Scholar 

Vallée A, Vallée J-N, Guillevin R, Lecarpentier Y (2020) Riluzole: A therapeutic strategy in alzheimer’s disease by targeting the WNT/β-catenin pathway. Aging 12(3):3095–3113. https://doi.org/10.18632/aging.102830

Article  PubMed  PubMed Central  Google Scholar 

Vallée A, Vallée J-N, Lecarpentier Y (2022) WNT/β-catenin pathway: A possible link between hypertension and alzheimer’s disease. Curr Hypertens Rep 24(10):465–475. https://doi.org/10.1007/s11906-022-01209-1

Article  PubMed  CAS  Google Scholar