Computational identification and experimental validation of anti-filarial lead molecules targeting metal binding/substrate channel residues of Cu/Zn SOD1 from Wuchereria bancrofti

References

• Abraham, M. J., Murtola, T., Schulz, R., Páll, S., Smith, J. C., Hess, B., & Lindah, E. (2015). Gromacs: High performance molecular simulations through multi-level parallelism from laptops to supercomputers. SoftwareX, 1-2, 19–25. https://doi.org/10.1016/j.softx.2015.06.001
   Google Scholar
• Banci, L., Bertini, I., Durazo, A., Girotto, S., Gralla, E. B., Martinelli, M., Valentine, J. S., Vieru, M., & Whitelegge, J. P. (2007). Metal-free superoxide dismutase forms soluble oligomers under physiological conditions: A possible general mechanism for familial ALS. Proceedings of the National Academy of Sciences of the United States of America, 104(27), 11263–11267. https://doi.org/10.1073/pnas.0704307104
   PubMed Web of Science ®Google Scholar
• Berendsen, H. J. C., Postma, J. P. M., van Gunsteren, W. F., Dinola, A., & Haak, J. R. (1984). Molecular dynamics with coupling to an external bath. The Journal of Chemical Physics, 81(8), 3684–3690. https://doi.org/10.1063/1.448118
   Web of Science ®Google Scholar
• Bertini, I., Banci, L., Piccioli, M., & Luchinat, C. (1990). Spectroscopic studies on Cu2Zn2SOD: a continuous advancement of investigation tools. Coordination Chemistry Reviews, 100(C), 67–103. https://doi.org/10.1016/0010-8545(90)85005-D
   Google Scholar
• Boissinot, M., Karnas, S., Lepock, J. R., Cabelli, D. E., Tainer, J. A., Getzoff, E. D., & Hallewell, R. A. (1997). Function of the Greek key connection analysed using circular permutants of superoxide dismutase. The EMBO Journal, 16(9), 2171–2178. https://doi.org/10.1093/EMBOJ/16.9.2171
   PubMed Web of Science ®Google Scholar
• Brophy, P. M., & Pritchard, D. I. (1992). Immunity to helminths: Ready to tip the biochemical balance? Parasitology Today (Personal ed.), 8(12), 419–422. https://doi.org/10.1016/0169-4758(92)90195-8
   PubMedGoogle Scholar
• Callahan, H. L., Crouch, R. K., & James, E. R. (1988). Helminth anti-oxidant enzymes: a protective mechanism against host oxidants? Parasitology Today (Personal ed.), 4(8), 218–225. https://doi.org/10.1016/0169-4758(88)90162-7
   PubMedGoogle Scholar
• Chakraborty, S., Gurusamy, M., Zawieja, D. C., & Muthuchamy, M. (2013). Lymphatic filariasis: Perspectives on lymphatic remodeling and contractile dysfunction in filarial disease pathogenesis. Microcirculation (New York, N.Y.: 1994), 20(5), 349–364. https://doi.org/10.1111/MICC.12031
   PubMed Web of Science ®Google Scholar
• Cobo, F. (2016). Determinants of parasite drug resistance in human lymphatic filariasis. Revista Espanola de Quimioterapia: Publicacion Oficial de La Sociedad Espanola de Quimioterapia, 29(6), 288–295.
   PubMed Web of Science ®Google Scholar
• Daisy, P., Suveena, S., & Cecily Rosemary Latha, R. (2012). Target level analysis of antioxidant activity of costunolide and eremanthin isolated from Costus speciosus. Asian Journal of Pharmaceutical and Clinical Research, 5(4), 32–35.
   Google Scholar
• Darden, T., York, D., & Pedersen, L. (1993). Particle mesh Ewald: An N·log(N) method for Ewald sums in large systems. The Journal of Chemical Physics, 98(12), 10089–10092. https://doi.org/10.1063/1.464397
   Web of Science ®Google Scholar
• Davis, E. L., de Vlas, S. J., Fronterre, C., Hollingsworth, T. D., Kontoroupis, P., Michael, E., Prada, J. M., Smith, M. E., Stolk, W. A., & Touloupou, P. (2019). The roadmap towards elimination of lymphatic filariasis by 2030: Insights from quantitative and mathematical modelling. Gates Open Research, 3, 1–13. https://doi.org/10.12688/gatesopenres.13065.1
   PubMedGoogle Scholar
• Djinovic, K., Gatti, G., Coda, A., Antolini, L., Pelosi, G., Desideri, A., Falconi, M., Marmocchi, F., Rotilio, G., & Bolognesi, M. (1992). Crystal structure of yeast Cu, Zn Superoxide dismutase refinement at 2. 5 A resolution. Journal of Molecular Biology, 225(3), 791–809.
   PubMed Web of Science ®Google Scholar
• Dong, X., Zhang, Z., Zhao, J., Lei, J., Chen, Y., Li, X., Chen, H., Tian, J., Zhang, D., Liu, C., & Liu, C. (2016). The rational design of specific SOD1 inhibitors via copper coordination and their application in ROS signaling research. Chemical Science, 7(9), 6251–6262. https://doi.org/10.1039/C6SC01272H
   PubMed Web of Science ®Google Scholar
• Evans, D. B., Gelband, H., & Vlassoff, C. (1993). Social and economic factors and the control of lymphatic filariasis: A review. Acta Tropica, 53(1), 1–26. https://doi.org/10.1016/0001-706X(93)90002-S
   PubMed Web of Science ®Google Scholar
• Fielden, E. M., Roberts, P. B., Bray, R. C., Lowe, D. J., Mautner, G. N., Rotilio, G., & Calabrese, L. (1974). The mechanism of action of superoxide dismutase from pulse radiolysis and electron paramagnetic resonance. Evidence that only half the active sites function in catalysis. The Biochemical Journal, 139(1), 49–60. https://doi.org/10.1042/bj1390049
   PubMed Web of Science ®Google Scholar
• Ferraroni, M., Rypniewski, W., Wilson, K. S., Viezzoli, M. S., Banci, L., Bertini, I., & Mangani, S. (1999). The crystal structure of the monomeric human SOD mutant F50E/G51E/E133Q at atomic resolution. The enzyme mechanism revisited. Journal of Molecular Biology, 288(3), 413–426. https://doi.org/10.1006/jmbi.1999.2681
   PubMed Web of Science ®Google Scholar
• Freedman, D. O. (1998). Immune dynamics in the pathogenesis of human lymphatic filariasis. Parasitology Today (Personal ed.), 14(6), 229–234. https://doi.org/10.1016/S0169-4758(98)01244-7
   PubMedGoogle Scholar
• Fridovich, I. (1986). Superoxide dismutases. Advances in Enzymology and Related Areas of Molecular Biology, 58, 61–97. https://doi.org/10.1002/9780470123041.ch2
   PubMedGoogle Scholar
• Furukawa, Y., & O'Halloran, T. V. (2005). Amyotrophic lateral sclerosis mutations have the greatest destabilizing effect on the apo- and reduced form of SOD1, leading to unfolding and oxidative aggregation. The Journal of Biological Chemistry, 280(17), 17266–17274. https://doi.org/10.1074/jbc.M500482200
   PubMed Web of Science ®Google Scholar
• Getzoff, E. D., Cabelli, D. E., Fisher, C. L., Parge, H. E., Viezzoli, M. S., Banci, L., & Hallewell, R. A. (1992). Faster superoxide dismutase mutants designed by enhancing electrostatic guidance. Nature, 358(6384), 347–351. https://doi.org/10.1038/358347a0
   PubMed Web of Science ®Google Scholar
• Glide (2020). Schrödinger Release 2020-4. Schrödinger, LLC.
   Google Scholar
• Guru Raj, R., Biswal, J., Dhamodharan, P., Kanagarajan, S., & Jeyaraman, J. (2016). Identification of potential inhibitors for AIRS from de novo purine biosynthesis pathway through molecular modeling studies—A computational approach. Journal of Biomolecular Structure & Dynamics, 34(10), 2199–2213.
   PubMed Web of Science ®Google Scholar
• Hart, P. J., Balbirnie, M. M., Ogihara, N. L., Nersissian, A. M., Weiss, M. S., Valentine, J. S., & Eisenberg, D. (1999). A structure-based mechanism for copper-zinc superoxide dismutase. Biochemistry, 38(7), 2167–2178. https://doi.org/10.1021/bi982284u
   PubMed Web of Science ®Google Scholar
• Henkle-Dührsen, K., & Kampkötter, A. (2001). Antioxidant enzyme families in parasitic nematodes. Molecular and Biochemical Parasitology, 114(2), 129–142. https://doi.org/10.1016/S0166-6851(01)00252-3
   PubMed Web of Science ®Google Scholar
• Hess, B. (2008). P-LINCS: A parallel linear constraint solver for molecular simulation. Journal of Chemical Theory and Computation, 4(1), 116–122. https://doi.org/10.1021/ct700200b
   PubMed Web of Science ®Google Scholar
• Hough, M. A., & Hasnain, S. S. (2003). Structure of fully reduced bovine copper zinc superoxide dismutase at 1.15 Å. Structure (London, England: 1993), 11(8), 937–946. https://doi.org/10.1016/S0969-2126(03)00155-2
   PubMed Web of Science ®Google Scholar
• Humphrey, W., Dalke, A., & Schulten, K. (1996). VMD: Visual molecular dynamics. Journal of Molecular Graphics, 14(1), 33–38. https://doi.org/10.1016/0263-7855(96)00018-5
   PubMedGoogle Scholar
• James, E. R. (1994). Superoxide dismutase. Parasitology Today (Personal ed.), 10(12), 481–484. https://doi.org/10.1016/0169-4758(94)90161-9
   PubMedGoogle Scholar
• Kanagarajan, S., Mutharasappan, N., Dhamodharan, P., Jeyaraman, M., Ramadas, K., & Jeyaraman, J. (2014). Exploring the structural features of Aspartate Trans Carbamoylase (Tt ATCase) from Thermus thermophilus HB8 through in silico approaches: A potential drug target for inborn error of pyrimidine metabolism. Journal of Biomolecular Structure & Dynamics, 32(4), 591–601. https://doi.org/10.1080/07391102.2013.782825
   PubMed Web of Science ®Google Scholar
• Kiss, R., Sandor, M., & Szalai, F. A. (2012). A public web service for drug discovery. Journal of Cheminformatics, 4(S1), P17. https://doi.org/10.1186/1758-2946-4-S1-P17
   PubMed Web of Science ®Google Scholar
• 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
   Web of Science ®Google Scholar
• Leinartaite, L., Saraboji, K., Nordlund, A., Logan, D. T., & Oliveberg, M. (2010). Folding catalysis by transient coordination of Zn2+ to the Cu ligands of the ALS-associated enzyme Cu/Zn superoxide dismutase 1. Journal of the American Chemical Society, 132(38), 13495–13504. https://doi.org/10.1021/ja1057136.
   PubMed Web of Science ®Google Scholar
• Li, H. T., Jiao, M., Chen, J., & Liang, Y. (2010). Roles of zinc and copper in modulating the oxidative refolding of bovine copper, zinc superoxide dismutase. Acta Biochimica et Biophysica Sinica, 42(3), 183–194. https://doi.org/10.1093/abbs/gmq005
   PubMed Web of Science ®Google Scholar
• LigPrep. (2020). Schrödinger Release 2020-4. Schrödinger, LLC.
   Google Scholar
• Maddah, M., & Karami, L. (2021). An atomistic investigation on the interaction of distamycin A and its derivative with the telomeric G-Quadruplex as anticancer agents by molecular dynamics simulation. Archives of Biochemistry and Biophysics, 701, 108797. https://doi.org/10.1016/J.ABB.2021.108797
   PubMed Web of Science ®Google Scholar
• Madeira, F., Park, Y. M., Lee, J., Buso, N., Gur, T., Madhusoodanan, N., Basutkar, P., Tivey, A. R. N., Potter, S. C., Finn, R. D., & Lopez, R. (2019). The EMBL-EBI search and sequence analysis tools APIs in 2019. Nucleic Acids Research, 47(W1), W636–W641. https://doi.org/10.1093/nar/gkz268
   PubMed Web of Science ®Google Scholar
• Mathew, N., Karunan, T., Srinivasan, L., & Muthuswamy, K. (2009). Synthesis and screening of substituted 1,4-naphthoquinones (NPQs) as antifilarial agents. Drug Development Research, 71(3), n/a–n/a. https://doi.org/10.1002/ddr.20357
   Web of Science ®Google Scholar
• Mathew, N., Misra-Bhattacharya, S., Perumal, V., & Muthuswamy, K. (2008). Antifilarial lead molecules isolated from Trachyspermum ammi. Molecules (Basel, Switzerland), 13(9), 2156–2168. https://doi.org/10.3390/MOLECULES13092156
   PubMed Web of Science ®Google Scholar
• Michael, E., & Bundy, D. A. P. (1997). Global mapping of lymphatic filariasis. Parasitology Today (Personal ed.), 13(12), 472–476. https://doi.org/10.1016/S0169-4758(97)01151-4
   PubMedGoogle Scholar
• Michael, E., Bundy, D. A. P., & Grenfell, B. T. (1996). Re-assessing the global prevalence and distribution of lymphatic filariasis. Parasitology, 112(4), 409–428. https://doi.org/10.1017/S0031182000066646
   PubMedGoogle Scholar
• Misra, S., Singh, L. K., Gupta, J., Misra-Bhattacharya, S., D., Katiyar, & Priyanka. (2015). Synthesis and biological evaluation of 4-oxycoumarin derivatives as a new class of anti-filarial agents. European Journal of Medicinal Chemistry, 94, 211–217., https://doi.org/10.1016/J.EJMECH.2015.02.043
   PubMed Web of Science ®Google Scholar
• Nisha, M., Kalyanasundaram, M., Paily, K. P., Vanamail, P., K. Balaraman., & K. P. P., Abidha. (2007). In vitro screening of medicinal plant extracts for macrofilaricidal activity. Parasitology Research, 100(3), 575–579. https://doi.org/10.1007/S00436-006-0294-9
   PubMed Web of Science ®Google Scholar
• Nordlund, A., & Oliveberg, M. (2006). Folding of Cu/Zn superoxide dismutase suggests structural hotspots for gain of neurotoxic function in ALS: Parallels to precursors in amyloid disease. Proceedings of the National Academy of Sciences of the United States of America, 103(27), 10218–10223. https://doi.org/10.1073/pnas.0601696103.
   PubMed Web of Science ®Google Scholar
• Nordlund, A., & Oliveberg, M. (2008). SOD1‐associated ALS: a promising system for elucidating the origin of protein‐misfolding disease. HFSP Journal, 2(6), 354–364.
   PubMed Web of Science ®Google Scholar
• Nordlund, A., Leinartaite, L., Saraboji, K., Aisenbrey, C., Gröbner, G., Zetterström, P., Danielsson, J., Logan, D. T., & Oliveberg, M. (2009). Functional features cause misfolding of the ALS-provoking enzyme SOD1. Proceedings of the National Academy of Sciences of the United States of America, 106(24), 9667–9672.
   PubMed Web of Science ®Google Scholar
• Oostenbrink, C., Villa, A., Mark, A. E., & van Gunsteren, W. F. (2004). A biomolecular force field based on the free enthalpy of hydration and solvation: The GROMOS force-field parameter sets 53A5 and 53A6. Journal of Computational Chemistry, 25(13), 1656–1676. https://doi.org/10.1002/jcc.20090
   PubMed Web of Science ®Google Scholar
• Ottesen, E. A. (1985). Efficacy of diethylcarbamazine in eradicating infection with lymphatic-dwelling filariae in humans. Reviews of Infectious Diseases, 7(3), 341–356. https://doi.org/10.1093/clinids/7.3.341
   PubMedGoogle Scholar
• Ottesen, E. A., Duke, B. O. L., Karam, M., & Behbehani, K. (1997). Strategies and tools for the control/elimination of lymphatic filariasis. Bulletin of the World Health Organization, 75(6), 491–503.
   PubMed Web of Science ®Google Scholar
• Paily, K. P., Hoti, S. L., & Das, P. K. (2009). A review of the complexity of biology of lymphatic filarial parasites. Journal of Parasitic Diseases: Official Organ of the Indian Society for Parasitology, 33(1-2), 3–12. https://doi.org/10.1007/s12639-009-0005-4
   PubMedGoogle Scholar
• Parge, H. E., Hallewell, R. A., & Tainer, J. A. (1992). Atomic structures of wild-type and thermostable mutant recombinant human Cu,Zn superoxide dismutase. Proceedings of the National Academy of Sciences of the United States of America, 89(13), 6109–6113. https://doi.org/10.1073/PNAS.89.13.6109
   PubMed Web of Science ®Google Scholar
• Parrinello, M., & Rahman, A. (1981). Polymorphic transitions in single crystals: A new molecular dynamics method. Journal of Applied Physics, 52(12), 7182–7190. https://doi.org/10.1063/1.328693
   Web of Science ®Google Scholar
• Perumal, A. N. I., Gunawardene, Y. I. N. S., & Dassanayake, R. S. (2016). Setaria digitata in advancing our knowledge of human lymphatic filariasis. Journal of Helminthology, 90(2), 129–138. https://doi.org/10.1017/S0022149X15000309
   PubMed Web of Science ®Google Scholar
• Prabhu, D., Rajamanikandan, S., Saritha, P., & Jeyakanthan, J. (2020). Evolutionary significance and functional characterization of streptomycin adenylyltransferase from Serratia marcescens. Journal of Biomolecular Structure & Dynamics, 38(15), 4418–4431. https://doi.org/10.1080/07391102.2019.1682046
   PubMed Web of Science ®Google Scholar
• Prabhu, D., Rajamanikandan, S., Sureshan, M., Jeyakanthan, J., & Saraboji, K. (2021). Modelling studies reveal the importance of the C-terminal inter motif loop of NSP1 as a promising target site for drug discovery and screening of potential phytochemicals to combat SARS-CoV-2. Journal of Molecular Graphics & Modelling, 106, 107920. https://doi.org/10.1016/j.jmgm.2021.107920
   PubMed Web of Science ®Google Scholar
• Prime. (2020). Schrödinger Release 2020-4. Schrödinger, LLC.
   Google Scholar
• Protein Preparation Wizard. (2020). Epik. Schrödinger, LLC.
   Google Scholar
• QikProp. (2020). Schrödinger Release 2020-4. Schrödinger, LLC.
   Google Scholar
• Rajamanikandan, S., Soundarya, S., Paramasivam, A., Prabhu, D., Jeyakanthan, J., & Ramasamy, V. (2021). Computational identification of potential lead molecules targeting rho receptor of Neisseria gonorrhoeae. Journal of Biomolecular Structure & Dynamics, 40(14), 6415-6425. https://doi.org/10.1080/07391102.2021.1885491
   Google Scholar
• Rajamanikandan, S., & Srinivasan, P. (2017). Exploring the selectivity of auto-inducer complex with LuxR using molecular docking, mutational studies and molecular dynamics simulations. Journal of Molecular Structure, 1131, 281–293. https://doi.org/10.1016/j.molstruc.2016.11.056
   Web of Science ®Google Scholar
• Ramaiah, K. D., Das, P. K., Michael, E., & Guyatt, H. L. (2000). The economic burden of lymphatic filariasis in India. Parasitology Today (Personal ed.), 16(6), 251–253. https://doi.org/10.1016/S0169-4758(00)01643-4
   PubMedGoogle Scholar
• Routh, H. B., & Bhowmik, K. R. (1993). History of elephantiasis. International Journal of Dermatology, 32(12), 913–916. https://doi.org/10.1111/j.1365-4362.1993.tb01418.x
   PubMed Web of Science ®Google Scholar
• Schrödinger Release 2020-4: SiteMap. (2020). Schrödinger, LLC., NY.
   Google Scholar
• Schmidlin, T., Kennedy, B. K., & Daggett, V. (2009). Structural changes to monomeric CuZn superoxide dismutase caused by the familial amyotrophic lateral sclerosis-associated mutation A4V. Biophysical Journal, 97(6), 1709–1718. https://doi.org/10.1016/j.bpj.2009.06.043.
   PubMed Web of Science ®Google Scholar
• Schüttelkopf, A. W., & van Aalten, D. M. F. (2004). PRODRG: A tool for high-throughput crystallography of protein-ligand complexes. Acta Crystallographica. Section D, Biological Crystallography, 60(Pt 8), 1355–1363. https://doi.org/10.1107/S0907444904011679
   PubMedGoogle Scholar
• Schwab, A. E., Boakye, D. A., Kyelem, D., & Prichard, R. K. (2005). Detection of benzimidazole resistance-associated mutations in the filarial nematode Wuchereria bancrofti and evidence for selection by albendazole and ivermectin combination treatment. The American Journal of Tropical Medicine and Hygiene, 73(2), 234–238.
   PubMed Web of Science ®Google Scholar
• Selkirk, M. E., Smith, V. P., Thomas, G. R., & Gounaris, K. (1998). Resistance of filarial nematode parasites to oxidative stress. International Journal for Parasitology, 28(9), 1315–1332. https://doi.org/10.1016/S0020-7519(98)00107-6
   PubMed Web of Science ®Google Scholar
• Senanayake, K. S., Söderberg, J., Põlajev, A., Malmberg, M., Karunanayake, E. H., Tennekoon, K. H., Samarakoon, S. R., Bongcam-Rudloff, E., & Niazi, A. (2020). The genome of Setaria digitata: A cattle nematode closely related to human filarial parasites. Genome Biology and Evolution, 12(2), 3971–3976. https://doi.org/10.1093/GBE/EVAA017
   PubMed Web of Science ®Google Scholar
• Senathilake, K. S., Karunanayake, E. H., Samarakoon, S. R., Tennekoon, K. H., de Silva, E. D., & Adhikari, A. (2017). Oleanolic acid from antifilarial triterpene saponins of Dipterocarpus zeylanicus induces oxidative stress and apoptosis in filarial parasite Setaria digitata in vitro. Experimental Parasitology, 177, 13–21. https://doi.org/10.1016/J.EXPPARA.2017.03.007
   PubMed Web of Science ®Google Scholar
• Simonsen, P. E., & Mwakitalu, M. E. (2013). Urban lymphatic filariasis. Parasitology Research, 112(1), 35–44. https://doi.org/10.1007/s00436-012-3226-x
   PubMed Web of Science ®Google Scholar
• Sindhu, T., Venkatesan, T., Prabhu, D., Jeyakanthan, J., Gracy, G. R., Jalali, S. K., & Rai, A. (2018). Insecticide-resistance mechanism of Plutella xylostella (L.) associated with amino acid substitutions in acetylcholinesterase-1: A molecular docking and molecular dynamics investigation. Computational Biology and Chemistry, 77(August), 240–250. https://doi.org/10.1016/j.compbiolchem.2018.09.004
   PubMedGoogle Scholar
• Sirangelo, I., & Iannuzzi, C. (2017). The role of metal binding in the amyotrophic lateral sclerosis-related aggregation of copper-zinc superoxide dismutase. Molecules (Basel, Switzerland), 22(9), 1429. https://doi.org/10.3390/molecules22091429
   PubMed Web of Science ®Google Scholar
• Strange, R. W., Antonyuk, S., Hough, M. A., Doucette, P. A., Rodriguez, J. A., Hart, P. J., Hayward, L. J., Valentine, J. S., & Hasnain, S. S. (2003). The structure of holo and metal-deficient wild-type human Cu, Zn superoxide dismutase and its relevance to familial amyotrophic lateral sclerosis. Journal of Molecular Biology, 328(4), 877–891. https://doi.org/10.1016/S0022-2836(03)00355-3
   PubMed Web of Science ®Google Scholar
• Sureshan, M., Prabhu, D., Aruldoss, I., & Saraboji, K. (2022). Potential inhibitors for peroxiredoxin 6 of W. bancrofti: A combined study of modelling, structure-based drug design and MD simulation. Journal of Molecular Graphics & Modelling, 112, 108115. https://doi.org/10.1016/j.jmgm.2021.108115
   PubMed Web of Science ®Google Scholar
• Sureshan, M., Rajamanikandan, S., Srimari, S., Prabhu, D., Jeyakanthan, J., & Saraboji, K. (2022). Designing specific inhibitors against dihydrofolate reductase of W. bancrofti towards drug discovery for lymphatic filariasis. Structural Chemistry, 33(3), 935–947. https://doi.org/10.1007/s11224-022-01896-1
   Web of Science ®Google Scholar
• Tainer, J. A., Getzoff, E. D., Beem, K. M., Richardson, J. S., & Richardson, D. C. (1982). Determination and analysis of the 2 Å structure of copper, zinc superoxide dismutase. Journal of Molecular Biology, 160(2), 181–217. https://doi.org/10.1016/0022-2836(82)90174-7
   PubMed Web of Science ®Google Scholar
• The PyMOL Molecular Graphics System, Version 2.0 Schrödinger, LLC. (n.d).
   Google Scholar
• Tompa, D. R., & Kadhirvel, S. (2018). Molecular dynamics of a far positioned SOD1 mutant V14M reveals pathogenic misfolding behavior. Journal of Biomolecular Structure & Dynamics, 36(15), 4085–4098. https://doi.org/10.1080/07391102.2017.1407675.
   PubMed Web of Science ®Google Scholar
• Tompa, D. R., & Kadhirvel, S. (2020). Changes in hydrophobicity mainly promotes the aggregation tendency of ALS associated SOD1 mutants. International Journal of Biological Macromolecules, 145, 904–913. https://doi.org/10.1016/j.ijbiomac.2019.09.181.
   PubMed Web of Science ®Google Scholar
• Vrahatis, M. N., Androulakis, G. S., Lambrinos, J. N., & Magoulas, G. D. (2000). A class of gradient unconstrained minimization algorithms with adaptive stepsize. Journal of Computational and Applied Mathematics, 114(2), 367–386. https://doi.org/10.1016/S0377-0427(99)00276-9
   Web of Science ®Google Scholar
• Tiwari, A., Liba, A., Sohn, S. H., Seetharaman, S. V., Bilsel, O., Matthews, C. R., Hart, P. J., Valentine, J. S., & Hayward, L. J. (2009). Metal deficiency increases aberrant hydrophobicity of mutant superoxide dismutases that cause amyotrophic lateral sclerosis. The Journal of Biological Chemistry, 284(40), 27746–27758. https://doi.org/10.1074/JBC.M109.043729
   PubMed Web of Science ®Google Scholar