Graph Theory Network, Molecular Docking, Quantum Chemicals and Pharmacokinetics-Based Investigation on Phytochemicals from Sida rhombifolia against Alzheimer’s Disease

References

• K.D. Rainsford, and M.W. Whitehouse, “Anti-Inflammatory/anti-Pyretic Salicylic Acid Esters with Low Gastric Ulcerogenic Activity,” Agents and Actions 10, no. 5 (1980): 451–6. doi:10.1007/BF01968046
   PubMedGoogle Scholar
• M.R. Sulaiman, et al, “Antinociceptive and anti-Inflammatory Effects of Sida Rhombifolia L. in the Various Animal Models,” Res J Pharmacol 2 (2008): 13–6.
   Google Scholar
• Khalil, N. Maissar, J. Soares Sperotto, and M.P. Manfron, “Anti-Inflammatory Activity of the Hydroalcoholyc Extract of Leaves of Sida rhombifolia L.(Malvaceae),” Acta Farmaceutica Bonaerense 25.2 (2006): 260.
   Google Scholar
• D. J. Mabberley, The Plant-Book: A Portable Dictionary of the Vascular Plants (Cambridge: Cambridge university press, 1997).
   Google Scholar
• M.C. Thounaojam, R. N. Jadeja, U.V. Ramani, R.V. Devkar, and A.V. Ramachandran, “Sida rhomboidea. Roxb Leaf Extract down-Regulates Expression of PPARγ2 and Leptin Genes in High Fat Diet Fed C57BL/6J Mice and Retards in Vitro 3T3L1 Pre-Adipocyte Differentiation,” International Journal of Molecular Sciences 12, no. 7 (2011): 4661–77. doi:10.3390/ijms12074661
   PubMed Web of Science ®Google Scholar
• A.H.C. Merétika, N. Peroni, and N. Hanazaki, “Local Knowledge of Medicinal Plants in Three Artisanal Fishing Communities (Itapoá, Southern Brazil), according to Gender, Age, and Urbanization,” Acta Botanica Brasilica 24, no. 2 (2010): 386–94. doi:10.1590/S0102-33062010000200009
   Web of Science ®Google Scholar
• S. Archana, “An Ethnobotanical Study of Medicinal Plants in Sonebhadra District of Uttar, Pradesh, India with Reference to Their Infection by Foliar Fungi,” Journal of Medicinal Plants Research 6, no. 14 (2012): 2727–46.
   Google Scholar
• T.M. Viswanathan, K. Chitradevi, A. Zochedh, R. Vijayabhaskar, S. Sukumaran, S. Kunjiappan, N. S. Kumar, K. Sundar, E. Babkiewicz, P. Maszczyk, et al, “Guanidine–Curcumin Complex-Loaded Amine-Functionalised Hollow Mesoporous Silica Nanoparticles for Breast Cancer Therapy,” Cancers 14, no. 14 (2022): 3490. doi:10.3390/cancers14143490
   PubMed Web of Science ®Google Scholar
• B. Akendengue, “Medicinal Plants Used by the Fang Traditional Healers in Equatorial Guinea,” Journal of Ethnopharmacology 37, no. 2 (1992): 165–73. doi:10.1016/0378-8741(92)90075-3
   PubMed Web of Science ®Google Scholar
• A.J.P. Assam, J.P. Dzoyem, C.A. Pieme, and V.B. Penlap, “In Vitro Antibacterial Activity and Acute Toxicity Studies of Aqueous-Methanol Extract of Sida rhombifolia Linn.(Malvaceae),” BMC Complementary and Alternative Medicine 10.1 (2010): 40. doi:10.1186/1472-6882-10-40
   Web of Science ®Google Scholar
• S.H. Mishra, and S.C. Chaturvedi, “Antibacterial and Antifungal Activity of Alkaloid of Sida rhombifolia Linn,” Indian Drugs, 16, no. 3 (1978): 61–63.
   Google Scholar
• D.N. Muanza, B.W. Kim, K.L. Euler, and L. Williams, “Antibacterial and Antifungal Activities of Nine Medicinal Plants from Zaire,” International Journal of Pharmacognosy 32, no. 4 (1994): 337–45. doi:10.3109/13880209409083012
   Google Scholar
• S.R. Gupta, S.A. Nirmal, R.Y. Patil, and G.S. Asane, “Anti-Arthritic Activity of Various Extracts of Sida rhombifolia Aerial Parts,” Natural Product Research 23, no. 8 (2009): 689–95. doi:10.1080/14786410802242778
   PubMed Web of Science ®Google Scholar
• C.A. Dunstan, Y. Noreen, G. Serrano, P.A. Cox, P. Perera, and L. Bohlin, “Evaluation of Some Samoan and Peruvian Medicinal Plants by Prostaglandin Biosynthesis and Rat Ear Oedema Assays,” Journal of Ethnopharmacology 57, no. 1 (1997): 35–56. doi:10.1016/S0378-8741(97)00043-3
   PubMed Web of Science ®Google Scholar
• R.R. Sarangi, et al, “Evaluation of Antidiarrhoeal Activity of Sida rhombifolia Linn,” Root." Int Res J Pharm 2 (2011): 157–60.
   Google Scholar
• K. Dhalwal, V.M. Shinde, B. Singh, and K.R. Mahadik, “Hypoglycemic and Hypolipidemic Effect of Sida rhombifolia Ssp. retusa in Diabetic Induced Animals,” International Journal of Phytomedicine 2.2, no. 2 (2010): 160–5. doi:10.5138/ijpm.2010.0975.0185.02025
   Google Scholar
• K. Seshathri, and T. Thiyagarajan, “Antimicrobial Activity of Chewing Sticks of Jimma “Ethiopia against,” Journal of Phytology 3.8 (2011): 34–37.
   Google Scholar
• D. Debalke, M. Birhan, A. Kinubeh, and M. Yayeh, “Assessments of Antibacterial Effects of Aqueous-Ethanolic Extracts of Sida rhombifolia’s Aerial Part,” TheScientificWorldJournal 2018 (2018): 8429809. 2018). doi:10.1155/2018/8429809
   PubMedGoogle Scholar
• M.C. Thounaojam, R. N. Jadeja, D.K. Patel, R.V. Devkar, and A.V. Ramachandran, “Acute and Sub Chronic Oral Toxicity of Sida rhomboidea. Roxb Leaf Extract,” Journal of Complementary and Integrative Medicine 7, no. 1 (2010): 1–6. doi:10.2202/1553-3840.1312
   PubMedGoogle Scholar
• R. Valsaraj, P. Pushpangadan, U.W. Smitt, A. Adsersen, and U. Nyman, “Antimicrobial Screening of Selected Medicinal Plants from India,” Journal of Ethnopharmacology 58, no. 2 (1997): 75–83. doi:10.1016/S0378-8741(97)00085-8
   PubMed Web of Science ®Google Scholar
• T.C.J.Munasinghe, C.K. Seneviratne, M.I. Thabrew, and A.M. Abeysekera, “Antiradical and Antilipoperoxidative Effects of Some Plant Extracts Used by Sri Lankan Traditional Medical Practitioners for Cardioprotection,” Phytotherapy Research 15, no. 6 (2001): 519–23. doi:10.1002/ptr.994
   PubMed Web of Science ®Google Scholar
• R. Poojari, et al, “Sida rhombifolia Ssp. Retusa Seed Extract Inhibits DEN Induced Murine Hepatic Preneoplasia and Carbon Tetrachloride,” …" Asian Pacific Journal of Cancer Prevention 10 (2009): 1107–12.
   PubMedGoogle Scholar
• M. Ekramul Islam, M. Ekramul Haque, and M.A. Mosaddik, “Cytotoxicity and Antibacterial Activity of Sida rhombifolia (Malvaceae) Grown in Bangladesh,” Phytotherapy Research : PTR 17, no. 8 (2003): 973–5. doi:10.1002/ptr.1294
   PubMed Web of Science ®Google Scholar
• H.-J. Huang, H.-Y. Chen, C.-C. Lee, and C.Y.-C. Chen, “Computational Design of Apolipoprotein E4 Inhibitors for Alzheimer’s Disease Therapy from Traditional Chinese Medicine,” BioMed Research International 2014 (2014): 452625. 2014). doi:10.1155/2014/452625
   PubMed Web of Science ®Google Scholar
• K.J. Korshavn, C. Satriano, Y. Lin, R. Zhang, M. Dulchavsky, A. Bhunia, M.I. Ivanova, Y.-H. Lee, C. La Rosa, Mi.H. Lim, et al, “Reduced Lipid Bilayer Thickness Regulates the Aggregation and Cytotoxicity of Amyloid-β,” The Journal of Biological Chemistry 292, no. 11 (2017): 4638–50. doi:10.1074/jbc.M116.764092
   PubMed Web of Science ®Google Scholar
• K. Rajasekhar, N. Narayanaswamy, N.A. Murugan, G. Kuang, H. Ågren, and T. Govindaraju, “A High Affinity Red Fluorescence and Colorimetric Probe for Amyloid β Aggregates,” Scientific Reports 6, no. 1 (2016): 23668. doi:10.1038/srep23668
   PubMedGoogle Scholar
• G. Filiz, K.A. Price, A. Caragounis, T. Du, P.J. Crouch, and A.R. White, “The Role of Metals in Modulating Metalloprotease Activity in the AD Brain,” European Biophysics Journal : EBJ 37, no. 3 (2008): 315–21. doi:10.1007/s00249-007-0244-1
   PubMed Web of Science ®Google Scholar
• R. Vassar, “BACE1 Inhibitor Drugs in Clinical Trials for Alzheimer’s Disease,” Alzheimer’s Research & Therapy 6, no. 9 (2014): 89. doi:10.1186/s13195-014-0089-7
   PubMedGoogle Scholar
• A. Zochedh, M. Priya, A. Shunmuganarayanan, K. Thandavarayan, and A.B. Sultan, “Investigation on Structural, Spectroscopic, DFT, Biological Activity and Molecular Docking Simulation of Essential Oil Gamma-Terpinene,” Journal of Molecular Structure 1268 (2022): 133651. doi:10.1016/j.molstruc.2022.133651
   Web of Science ®Google Scholar
• C.S. Abraham, S. Muthu, J.C. Prasana, S. Armaković, S.J. Armaković, F. Rizwana B, B. Geoffrey, and H.A. David R, “Computational Evaluation of the Reactivity and Pharmaceutical Potential of an Organic Amine: A DFT, Molecular Dynamics Simulations and Molecular Docking Approach,” Spectrochimica Acta. Part A, Molecular and Biomolecular Spectroscopy 222 (2019): 117188. doi:10.1016/j.saa.2019.117188
   PubMed Web of Science ®Google Scholar
• S. Muthu, J.U.Maheswari, and T. Sundius, “Quantum Mechanical, Spectroscopic Studies (FT-IR, FT-Raman, NMR, UV) and Normal Coordinates Analysis on 3-([2-(Diaminomethyleneamino) Thiazol-4-yl] Methylthio)-N′-Sulfamoylpropanimidamide,” Spectrochimica Acta. Part A, Molecular and Biomolecular Spectroscopy 108 (2013): 307–18. doi:10.1016/j.saa.2013.02.022
   PubMed Web of Science ®Google Scholar
• Isac Paulraj, E., and S. Muthu, “Spectroscopic Studies (FTIR, FT-Raman and UV), Potential Energy Surface Scan, Normal Coordinate Analysis and NBO Analysis of (2R, 3R, 4R, 5S)-1-(2-Hydroxyethyl)-2-(Hydroxymethyl) Piperidine-3, 4, 5-Triol by DFT Methods,” Spectrochimica Acta. Part A, Molecular and Biomolecular Spectroscopy 108 (2013): 38–49. doi:10.1016/j.saa.2013.01.061
   PubMed Web of Science ®Google Scholar
• M.H. Rahuman, S. Muthu, B.R. Raajaraman, M. Raja, and H. Umamahesvari, “Investigations on 2-(4-Cyanophenylamino) Acetic Acid by FT-IR, FT-Raman, NMR and UV-Vis Spectroscopy, DFT (NBO, HOMO-LUMO, MEP and Fukui Function) and Molecular Docking Studies,” Heliyon 6, no. 9 (2020): e04976. doi:10.1016/j.heliyon.2020.e04976
   PubMed Web of Science ®Google Scholar
• S. Muthu, and A. Prabhakaran, “Vibrational Spectroscopic Study and NBO Analysis on Tranexamic Acid Using DFT Method,” Spectrochimica Acta. Part A, Molecular and Biomolecular Spectroscopy 129 (2014): 184–92. doi:10.1016/j.saa.2014.03.050
   PubMed Web of Science ®Google Scholar
• M. Priya, A. Zochedh, K. Arumugam, and A.B. Sultan, “Quantum Chemical Investigation, Drug-Likeness and Molecular Docking Studies on Galangin as Alpha-Synuclein Regulator for the Treatment of Parkinson’s Disease,” Chemistry Africa 6, no. 1 (2023): 287–309. doi:10.1007/s42250-022-00508-z
   Google Scholar
• M. Kohl, S. Wiese, and B. Warscheid, “Cytoscape: Software for Visualization and Analysis of Biological Networks,” Data Mining in Proteomics, 696 (2011): 291–303. doi:10.1007/978-1-60761-987-1_18
   Google Scholar
• G. Saravanan, T. Panneerselvam, S. Kunjiappan, P. Parasuraman, V. Alagarsamy, P. Udayakumar, M. Soundararajan, S.D. Joshi, S. Ramalingam, D.N. Ammunje, et al, “Graph Theoretical Analysis, in Silico Modeling, Prediction of Toxicity, Metabolism and Synthesis of Novel 2‐(Methyl/Phenyl)‐3‐(4‐(5‐Substituted‐1, 3, 4‐Oxadiazol‐2‐yl) Phenyl) Quinazolin‐4 (3H)‐Ones as NMDA Receptor Inhibitor,” Drug Development Research 80, no. 3 (2019): 368–85. doi:10.1002/ddr.21511
   PubMed Web of Science ®Google Scholar
• H.M. Berman, J. Westbrook, Z. Feng, G. Gilliland, T.N. Bhat, H. Weissig, I.N. Shindyalov, and P.E. Bourne, “The Protein Data Bank Nuclei c,” Nucleic Acids Research 28, no. 1 (2000): 235–42. " doi:10.1093/nar/28.1.235
   PubMed Web of Science ®Google Scholar
• L.I.G.A.N.D. Design, "Pharmacophore and ligand-based design with Biovia Discovery Studio®." BIOVIA. California, 2014.
   Google Scholar
• A. Zochedh, K. Chandran, M. Priya, A.B. Sultan, and T. Kathiresan, “Molecular Simulation of Naringin Combined with Experimental Elucidation–Pharmaceutical Activity and Molecular Docking against Breast Cancer,” Journal of Molecular Structure 1285 (2023): 135403. doi:10.1016/j.molstruc.2023.135403
   Web of Science ®Google Scholar
• K. Mohanraj, B.S. Karthikeyan, R.P. Vivek-Ananth, R.P.B. Chand, S.R. Aparna, P. Mangalapandi, and A. Samal, “IMPPAT: A Curated Database of Indian Medicinal Plants, Phytochemistry and Therapeutics,” Scientific Reports 8, no. 1 (2018): 1–17. doi:10.1038/s41598-018-22631-z
   PubMed Web of Science ®Google Scholar
• S. Kim, P.A. Thiessen, E.E. Bolton, J. Chen, G. Fu, A. Gindulyte, L. Han, J. He, S. He, B.A. Shoemaker, et al, “PubChem Substance and Compound Databases,” Nucleic Acids Research 44(2016): D1202–D1213. doi:10.1093/nar/gkv951
   PubMed Web of Science ®Google Scholar
• W. Tian, C. Chen, X. Lei, J. Zhao, and J. Liang, “CASTp 3.0: Computed Atlas of Surface Topography of Proteins,” Nucleic Acids Research 46(2018): W363–W367. doi:10.1093/nar/gky473
   PubMed Web of Science ®Google Scholar
• A. Zochedh, M. Priya, C.Chakaravarthy, A.B. Sultan, and T. Kathiresan, “Experimental and Computational Evaluation of Syringic Acid–Structural, Spectroscopic, Biological Activity and Docking Simulation,” Polycyclic Aromatic Compounds, 43 (2022): 1–33. doi:10.1080/10406638.2022.2118332
   Web of Science ®Google Scholar
• S. Dallakyan, and A.J. Olson, Small-Molecule Library Screening by Docking with PyRx." Chemical Biology. Humana Press, New York (NY), 2015. 243–50. doi:10.1007/978-1-4939-2269-7_19
   Google Scholar
• A. Zochedh, M. Priya, A. Shunmuganarayanan, A.B. Sultan, and T. Kathiresan, “Antitumor and Antimicrobial Effect of Syringic Acid Urea Cocrystal: Structural and Spectroscopic Characterization, DFT Calculation and Biological Evaluation,” Journal of Molecular Structure 1282 (2023): 135113. doi:10.1016/j.molstruc.2023.135113
   Web of Science ®Google Scholar
• M. J. Frisch, et al, GAUSSIAN 09 (Revision B. 01), Gaussian, Inc., Wallingford, CT: Gaussian." (2010).
   Google Scholar
• R. Premkumar, S. Hussain, S.-J. Koyambo-Konzapa, N.D. Jayram, M.R. Meera, T. Mathavan, and A. M. F. Benial, “SERS and DFT Studies of 2‐(Trichloroacetyl) Pyrrole Chemisorbed on the Surface of Silver and Gold Coated Thin Films: In Perspective of Biosensor Applications,” Journal of Molecular Recognition 34, no. 11 (2021): e2921. doi:10.1002/jmr.2921
   PubMed Web of Science ®Google Scholar
• R. Premkumar, S. Hussain, N.D. Jayram, S.-J. Koyambo-Konzapa, M.S. Revathy, T. Mathavan, and A. Milton Franklin Benial, “Adsorption and Orientation Characteristics of 1-Methylpyrrole-2-Carbonyl Chloride Using SERS and DFT Investigations,” Journal of Molecular Structure 1253 (2022): 132201. doi:10.1016/j.molstruc.2021.132201
   Web of Science ®Google Scholar
• R. Dennington, T. Keith, and J. Millam, "GaussView, version 5.", 2009.
   Google Scholar
• A. Zochedh, A. Shunmuganarayanan, and A. Bahadur Sultan, “Conformational Fidelity and Hydrogen Bond Associability of L-Histidine with Sulfamate Anion Studied through XRD, Quantum Chemical, Spectroscopic and Molecular Docking Simulation as a Cdk-4 Inhibitor against Retinoblastoma,” Journal of Molecular Structure 1274 (2023): 134402. doi:10.1016/j.molstruc.2022.134402
   Web of Science ®Google Scholar
• D.E.V. Pires, T.L. Blundell, and D.B. Ascher, “pkCSM: Predicting Small-Molecule Pharmacokinetic and Toxicity Properties Using Graph-Based Signatures,” Journal of Medicinal Chemistry 58, no. 9 (2015): 4066–72. doi:10.1021/acs.jmedchem.5b00104
   PubMed Web of Science ®Google Scholar
• A. Daina, O. Michielin, and V. Zoete, “SwissADME: A Free Web Tool to Evaluate Pharmacokinetics, Drug-Likeness and Medicinal Chemistry Friendliness of Small Molecules,” Scientific Reports 7, no. 7.1 (2017): 42717. doi:10.1038/srep42717
   PubMedGoogle Scholar
• A.A. Zochedh, S.A.Bahadur, and T. Kathiresan, “Quantum Chemical and Molecular Docking Studies of Naringin: A Potent anti-Cancer Drug,” Journal of Cardiovascular Disease Research no.12 (2021): 1140–8.
   Google Scholar
• A. Adlimoghaddam, M. Neuendorff, B. Roy, and B.C. Albensi, “A Review of Clinical Treatment Considerations of Donepezil in Severe Alzheimer’s Disease,” CNS Neuroscience & Therapeutics 24, no. 10 (2018): 876–88. doi:10.1111/cns.13035
   PubMed Web of Science ®Google Scholar
• A. Zochedh, K. Chandran, M. Priya, A.B. Sultan, and T. Kathiresan, “DFT Simulation of Berberine Chloride with Spectroscopic Characterization–Biological Activity and Molecular Docking against Breast Cancer,” Polycyclic Aromatic Compounds, 43 (2023): 1–25. doi:10.1080/10406638.2023.2201457
   Google Scholar
• M. Priya, et al, "Computer-Aided Analysis of Biochanin–A as a Potential Breast Cancer Drug Based on DFT, Molecular Docking, and Pharmacokinetic Studies.", 2022. doi:10.33263/LIANBS124.165
   Google Scholar
• N. Akram, A. Mansha, R. Premkumar, A.M. Franklin Benial, S. Asim, S.Z. Iqbal, and H.S. Ali, “Spectroscopic, Quantum Chemical and Molecular Docking Studies on 2, 4-Dimethoxy-1, 3, 5-Triazine: A Potent Inhibitor of Protein Kinase CK2 for the Development of Breast Cancer Drug,” Molecular Simulation 46, no. 17 (2020): 1340–53. doi:10.1080/08927022.2020.1822526
   Web of Science ®Google Scholar
• T. Valarmathi, R. Premkumar, M.R. Meera, and A. Milton Franklin Benial, “Spectroscopic, Quantum Chemical and Molecular Docking Studies on 1-Amino-5-Chloroanthraquinone: A Targeted Drug Therapy for Thyroid Cancer,” Spectrochimica Acta. Part A, Molecular and Biomolecular Spectroscopy 255 (2021): 119659. doi:10.1016/j.saa.2021.119659
   PubMed Web of Science ®Google Scholar
• S. Sukumaran, A. Zochedh, T.M. Viswanathan, A. B. Sultan, and T. Kathiresan, “Theoretical Investigation of 5-Fluorouracil and Tamoxifen Complex–Structural, Spectrum, DFT, ADMET and Docking Simulation,” Polycyclic Aromatic Compounds, 43 (2023): 1–18. doi:10.1080/10406638.2022.2164018
   Web of Science ®Google Scholar
• T.M. Viswanathan, et. al, “Investigation of Guanidine-Curcumin Complex Based on Quantum Chemicals, Pharmacokinetics and Molecular Docking Simulation against Breast Cancer: A Theoretical Approach,” Asian Journal of Chemistry, 35, no.5 (2023): 1189–1198. doi:10.14233/ajchem.2023.27805
   Google Scholar
• M.-Q. Zhang, and B. Wilkinson, “Drug Discovery beyond the ‘Rule-of-Five,” Current Opinion in Biotechnology 18, no. 6 (2007): 478–88. doi:10.1016/j.copbio.2007.10.005
   PubMed Web of Science ®Google Scholar
• S. Banu, K.R.I.M. Priya, and A.S. Azar Zochedh, “Identification of Novel Bioactive Compounds from Banana Fruit (Musa sapientum) as Antidepressant in Pregnant Women: Molecular Docking, Physiochemical and ADMET Evaluation,” Asian Journal of Biotechnology and Genetic Engineering 5.1 (2022): 9–24.
   Google Scholar
• K. Chandran, D.I. Shane, A. Zochedh, A.B. Sultan, and T. Kathiresan, “Docking Simulation and ADMET Prediction Based Investigation on the Phytochemical Constituents of Noni (Morinda citrifolia) Fruit as a Potential Anticancer Drug,” In Silico Pharmacology 10.1, no. 1 (2022): 14. doi:10.1007/s40203-022-00130-4
   Google Scholar