References
- Ahmad Mir, S., Meher, R. K., Baitharu, I., & Nayak, B. (2022a). Molecular dynamic simulation, free binding energy calculation of Thiazolo-[2, 3-b] quinazolinone derivatives against EGFR-TKD and their anticancer activity. Results in Chemistry, 4, 100418. https://doi.org/10.1016/j.rechem.2022.100418
- Ahmad Mir, S., Paramita Mohanta, P., Kumar Meher, R., Baitharu, I., Kumar Raval, M., Kumar Behera, A., & Nayak, B. (2022b). Structural insights into conformational stability and binding of thiazolo-[2,3-b] quinazolinone derivatives with EGFR-TKD and in-vitro study. Saudi Journal of Biological Sciences, 29(12), 103478. https://doi.org/10.1016/j.sjbs.2022.103478
- Allred, D. R. (2019). Variable and variant protein multigene families in Babesia bovis persistence. Pathogens (Basel, Switzerland), 8(2), 76. https://doi.org/10.3390/pathogens8020076
- Anand, P., & Singh, B. (2013). A review on cholinesterase inhibitors for Alzheimer’s disease. Archives of Pharmacal Research, 36(4), 375–399. https://doi.org/10.1007/s12272-013-0036-3
- Banerjee, P., Eckert, A. O., Schrey, A. K., & Preissner, R. (2018). ProTox-II: A webserver for the prediction of toxicity of chemicals. Nucleic Acids Research, 46(W1), W257–W263. https://doi.org/10.1093/nar/gky318
- Borkotoky, S., & Murali, A. A. (2018). Computational assessment of pH-dependent differential interaction of T7 lysozyme with T7 RNA polymerase. BMC Structural Biology. 17(1), 1.
- Brooks, B. R., Brooks, C. L., Mackerell, A. D., Nilsson, L., Petrella, R. J., Roux, B., Won, Y., Archontis, G., Bartels, C., Boresch, S., Caflisch, A., Caves, L., Cui, Q., Dinner, A. R., Feig, M., Fischer, S., Gao, J., Hodoscek, M., Im, W., … Karplus, M. (2009). CHARMM: The biomolecular simulation program. Journal of Computational Chemistry, 30(10), 1545–1614. https://doi.org/10.1002/jcc.21287
- Cavdar, H., Senturk, M., Guney, M., Durdagi, S., Kayik, G., Supuran, C. T., & Ekinci, D. (2019). Inhibition of acetylcholinesterase and butyrylcholinesterase with uracil derivatives: Kinetic and computational studies. Journal of Enzyme Inhibition and Medicinal Chemistry, 34(1), 429–437. https://doi.org/10.1080/14756366.2018.1543288
- Cheung, J., Gary, E. N., Shiomi, K., & Rosenberry, T. L. (2013). Structures of human acetylcholinesterase bound to dihydrotanshinone I and territrem B show peripheral site flexibility. ACS Medicinal Chemistry Letters, 4(11), 1091–1096. https://doi.org/10.1021/ml400304w
- Haake, A., Nguyen, K., Friedman, L., Chakkamparambil, B., & Grossberg, G. T. (2020). An update on the utility and safety of cholinesterase inhibitors for the treatment of Alzheimer’s disease. Expert Opinion on Drug Safety, 19(2), 147–157. https://doi.org/10.1080/14740338.2020.1721456
- Halgren, T. A. (1999). MMFF VI. MMFF94s option for energy minimization studies. Journal of Computational Chemistry, 20(7), 720–729. https://doi.org/10.1002/(SICI)1096-987X(199905)20:7<720::AID-JCC7>3.0.CO;2-X
- Hess, B., Bekker, H., Berendsen, H. J., & Fraaije, J. G. (1997). LINCS: A linear constraint solver for molecular simulations. Journal of Computational Chemistry, 18(12), 1463–1472. https://doi.org/10.1002/(SICI)1096-987X(199709)18:12<1463::AID-JCC4>3.0.CO;2-H
- Kauzmann, W. (1959). Some factors in the interpretation of protein denaturation. Advances in Protein Chemistry, 14, 1–63. https://doi.org/10.1016/s0065-3233(08)60608-7
- Kleywegt, G. J., & Jones, T. A. (1996). Phi/psi-chology: Ramachandran revisited. Structure (London, England: 1993), 4(12), 1395–1400. https://doi.org/10.1016/s0969-2126(96)00147-5
- Košak, U., Brus, B., Knez, D., Šink, R., Žakelj, S., Trontelj, J., Pišlar, A., Šlenc, J., Gobec, M., Živin, M., Tratnjek, L., Perše, M., Sałat, K., Podkowa, A., Filipek, B., Nachon, F., Brazzolotto, X., Więckowska, A., Malawska, B., … Gobec, S. (2016). Development of an in-vivo active reversible butyrylcholinesterase inhibitor. Scientific Reports, 6(1), 39495. https://doi.org/10.1038/srep39495
- Laskowski, R. A., MacArthur, M. W., Moss, D. S., & Thornton, J. M. (1993). PROCHECK: A program to check the stereochemical quality of protein structures. Journal of Applied Crystallography, 26(2), 283–291. https://doi.org/10.1107/S0021889892009944
- Lee, B., & Richards, F. M. (1971). The interpretation of protein structures: Estimation of static accessibility. Journal of Molecular Biology, 55(3), 379–400. https://doi.org/10.1016/0022-2836(71)90324-x
- Lobanov, M. I., Bogatyreva, N. S., & Galzitskaia, O. V. (2008). Radius of gyration as an indicator of compactness of protein structure. Molekuliarnaia Biologiia, 42(4), 701–706.
- Mark, P., & Nilsson, L. (2001). Structure and dynamics of the TIP3P, SPC, and SPC/E water models at 298 K. The Journal of Physical Chemistry A, 105(43), 9954–9960. https://doi.org/10.1021/jp003020w
- Marucci, G., Buccioni, M., Ben, D. D., Lambertucci, C., Volpini, R., & Amenta, F. (2021). Efficacy of acetylcholinesterase inhibitors in Alzheimer’s disease. Neuropharmacology, 190, 108352. https://doi.org/10.1016/j.neuropharm.2020.108352
- Mir, S. A., & Nayak, B. (2022). In silico analysis of binding stability of quercetin with CmpA and in vitro growth inhibition study of cyanobacterial species using Azadirachta indica extracts. Chemistry Africa, 5(3), 691–701. https://doi.org/10.1007/s42250-022-00335-2
- Mir, S. A., & Nayak, B. (2023). Exploring binding stability of hydroxy-3-(4-hydroxyphenyl)-5-(4-nitrophenyl)-5,5a,7,8,9,9a-hexahydrothiazolo[2,3-b] quinazolin-6-one with T790M/L858R EGFR-TKD. Journal of Biomolecular Structure & Dynamics, 41(8), 3702–3716. https://doi.org/10.1080/07391102.2022.2053748
- Mir, S. A., Dash, G. C., Meher, R. K., Mohanta, P. P., Chopdar, K. S., Mohapatra, P. K., Baitharu, I., Behera, A. K., Raval, M. K., & Nayak, B. (2022). In silico and in vitro evaluations of fluorophoric thiazolo-[2,3-b]quinazolinones as anti-cancer agents targeting EGFR-TKD. Applied Biochemistry and Biotechnology, 194(10), 4292–4318. https://doi.org/10.1007/s12010-022-03893-w
- Mir, S. A., Meher, R. K., & Nayak, B. (2023a). Molecular modeling and simulations of some antiviral drugs, benzylisoquinoline alkaloid, and coumarin molecules to investigate the effects on Mpro main viral protease inhibition. Biochemistry and Biophysics Reports, 34, 101459. https://doi.org/10.1016/j.bbrep.2023.101459
- Mir, S. A., Muhammad, A., Padhiary, A., Ekka, N. J., Baitharu, I., Naik, P. K., & Nayak, B. (2023b). Identification of potent EGFR-TKD inhibitors from NPACT database through combined computational approaches. Journal of Biomolecular Structure & Dynamics, 1–14. https://doi.org/10.1080/07391102.2023.2171133
- O'Boyle, N. M., Banck, M., James, C. A., Morley, C., Vandermeersch, T., & Hutchison, G. R. (2011). Open Babel: An open chemical toolbox. Journal of Cheminformatics, 3(1), 33. https://doi.org/10.1186/1758-2946-3-33
- Onufriev, A., Bashford, D., & Case, D. A. (2000). Modification of the generalized born model suitable for macromolecules. The Journal of Physical Chemistry B, 104(15), 3712–3720. https://doi.org/10.1021/jp994072s
- Pereira, G. R., Da Silva, A. N., Do Nascimento, S. S., & De Mesquita, J. F. (2019). In silico analysis and molecular dynamics simulation of human superoxide dismutase 3 (SOD3) genetic variants. Journal of Cellular Biochemistry, 120(3), 3583–3598. https://doi.org/10.1002/jcb.27636
- Rather, M. A., Dutta, S., Guttula, P. K., Dhandare, B. C., Yusufzai, S. I., & Zafar, M. I. (2020). Structural analysis, molecular docking and molecular dynamics simulations of G-protein-coupled receptor (kisspeptin) in fish. Journal of Biomolecular Structure & Dynamics, 38(8), 2422–2439. https://doi.org/10.1080/07391102.2019.1633407
- Reitz, C., Brayne, C., & Mayeux, R. (2011). Epidemiology of Alzheimer disease. Nature Reviews. Neurology, 7(3), 137–152. https://doi.org/10.1038/nrneurol.2011.2
- Ricketts, R. E. (1982). Practical optimization, Philip E. Gill, Walter Murray and Margret H. Wright, Academic Press Inc.(London) Limited, 1981. No. of pages: 401. ISBN: 0.12. 283950.1. International Journal for Numerical Methods in Engineering, 18(6), 954–954. https://doi.org/10.1002/nme.1620180612
- Sarkar, B., Alam, S., Rajib, T. K., Islam, S. S., Araf, Y., & Ullah, M. A. (2021). Identification of the most potent acetylcholinesterase inhibitors from plants for possible treatment of Alzheimer’s disease: A computational approach. Egyptian Journal of Medical Human Genetics, 22(1), 1–20. https://doi.org/10.1186/s43042-020-00127-8
- Schmidt, U., Struck, S., Gruening, B., Hossbach, J., Jaeger, I. S., Parol, R., … Preissner, R. (2009). SuperToxic: A comprehensive database of toxic compounds. Nucleic Acids Research, 37, 295–299.
- Seniya, C., Khan, G. J., & Uchadia, K. (2014). Identification of potential herbal inhibitor of acetylcholinesterase associated Alzheimer’s disorders using molecular docking and molecular dynamics simulation. Biochemistry Research International, 2014, 705451–705457. https://doi.org/10.1155/2014/705451
- Showkat, A. M., & Nayak, B. (2022). Exploring binding stability of hydroxy-3-(4- hydroxyphenyl)-5-(4-nitrophenyl)-5, 5a, 7, 8, 9, 9a-hexahydrothiazolo [2, 3-b] quinazolin-6-one with T790M/L858R EGFR-TKD. Journal of Biomolecular Structure and Dynamics, 41(8), 3702-3716. https://doi.org/10.1080/07391102.2022.2053748. Epub 2022 Mar 28..
- Spezia, R., Aschi, M., Nola, A. D., Valentin, M. D., Carbonera, D., & Amadei, A. (2003). The effect of protein conformational flexibility on the electronic properties of a chromophore. Biophysical Journal, 84(5), 2805–2813. https://doi.org/10.1016/s0006-3495(03)70010-1
- Vecchio, I., Sorrentino, L., Paoletti, A., Marra, R., & Arbitrio, M. (2021). The state of the art on acetylcholinesterase inhibitors in the treatment of Alzheimer’s disease. Journal of Central Nervous System Disease, 13, 11795735211029113. https://doi.org/10.1177/11795735211029113
- Verma, N., Puri, A., Essuman, E., Skelton, R., Anantharaman, V., Zheng, H., White, S., Gunalan, K., Takeda, K., Bajpai, S., Lepore, T. J., Krause, P. J., Aravind, L., & Kumar, S. (2020). Antigen discovery, bioinformatics and biological characterization of novel immunodominant Babesia microti antigens. Scientific Reports, 10(1), 9598. https://doi.org/10.1038/s41598-020-66273-6
- Wiederstein, M., & Sippl, M. J. (2007). ProSA-web: Interactive web service for the recognition of errors in three-dimensional structures of proteins. Nucleic Acids Research, 35(Web Server issue), W407–W410. https://doi.org/10.1093/nar/gkm290
- Yaacob, N., Ahmad Kamarudin, N. H., Leow, A. T., Salleh, A. B., Rahman, R. A. R. N., & Mohamad Ali, M. S. (2017). The role of solvent-accessible Leu-208 of cold-active Pseudomonas fluorescens strain AMS8 lipase in interfacial activation, substrate accessibility and low-molecular weight esterification in the presence of toluene. Molecules (Basel, Switzerland), 22(8), 1312. https://doi.org/10.3390/molecules22081312
- Yan, X., Chen, T., Zhang, L., & Du, H. (2018). Study of the interactions of forsythiaside and rutin with acetylcholinesterase (AChE). International Journal of Biological Macromolecules, 119, 1344–1352. https://doi.org/10.1016/j.ijbiomac.2018.07.144
- Zhou, Y., Lu, X., Yang, H., Chen, Y., Wang, F., Li, J., Tang, Z., Cheng, X., Yang, Y., Xu, L., & Xia, Q. (2019). Discovery of selective butyrylcholinesterase (BChE) inhibitors through a combination of computational studies and biological evaluations. Molecules (Basel, Switzerland), 24(23), 4217. https://doi.org/10.3390/molecules24234217
- Zoete, V., Cuendet, M. A., Grosdidier, A., & Michielin, O. (2011). SwissParam, a fast force field generation tool for small organic molecules. Journal of Computational Chemistry, 32(11), 2359–2368. https://doi.org/10.1002/jcc.21816