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Research Article

Unraveling the crystal structure, stability and drug likeness of 1,3,4-oxadiazole derivatives against Myelofibrosis: a combined experimental and computational investigation

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Received 03 Oct 2023, Accepted 20 Jan 2024, Published online: 31 Mar 2024

References

  • Acar Çevik, U., Celik, I., Işık, A., Ahmad, I., Patel, H., Özkay, Y., & Kaplancıklı, Z. A. (2023). Design, synthesis, molecular modeling, DFT, ADME and biological evaluation studies of some new 1, 3, 4-oxadiazole linked benzimidazoles as anticancer agents and aromatase inhibitors. Journal of Biomolecular Structure & Dynamics, 41(5), 1944–1958. https://doi.org/10.1080/07391102.2022.2025906
  • Ahmad, F., Sachdeva, P., Sachdeva, B., Singh, G., Soni, H., Tandon, S., Rafeeq, M. M., Alam, M. Z., Baeissa, H. M., & Khalid, M. (2022). Dioxinodehydroeckol: A potential neuroprotective marine compound identified by in silico screening for the treatment and management of multiple brain disorders. Molecular Biotechnology, 1–24. https://doi.org/10.1007/s12033-022-00629-3
  • Al-Otaibi, J. S., Almuqrin, A. H., Sheena Mary, Y., & Shyma Mary, Y. (2022). Utilization of O/S-doped graphene nanoclusters for ultrasensitive detection of flurane derivatives-DFT investigations. Journal of Biomolecular Structure & Dynamics, 40(12), 5320–5327. https://doi.org/10.1080/07391102.2020.1870155
  • B, M., Bodke, Y. D., O, N., N, L. T., G, N., & Ma, S. (2021). Coumarin-benzothiazole based azo dyes: synthesis, characterization, computational, photophysical and biological studies. Journal of Molecular Structure, 1246, 131170. https://doi.org/10.1016/j.molstruc.2021.131170
  • Carbone, M., Li, Y., Irace, C., Mollo, E., Castelluccio, F., Di Pascale, A., Cimino, G., Santamaria, R., Guo, Y.-W., & Gavagnin, M. (2011). Structure and cytotoxicity of phidianidines A and B: First finding of 1, 2, 4-oxadiazole system in a marine natural product. Organic Letters, 13(10), 2516–2519. https://doi.org/10.1021/ol200234r
  • Chaitra, K., Singh, K. R., Raghu, M. S., Sadashiva, M. P., & Prashanth, K. N. (2022). Mucic acid cross-linked chitosan nanoparticles as a dual drug delivery system for treatment of colorectal cancer-insilico and invitro studies. Chemical Data Collections, 41, 100928. https://doi.org/10.1016/j.cdc.2022.100928
  • Hage-Melim, L. I. D S., Federico, L. B., de Oliveira, N. K. S., Francisco, V. C. C., Correia, L. C., de Lima, H. B., Gomes, S. Q., Barcelos, M. P., Francischini, I. A. G., & da Silva, C. H. T. D P. (2020). Virtual screening, ADME/Tox predictions and the drug repurposing concept for future use of old drugs against the COVID-19. Life Sciences, 256, 117963. https://doi.org/10.1016/j.lfs.2020.117963
  • Dennington, R., Keith, T. A., & Millam, J. M. (2016). GaussView, version 6.0. 16. Semichem Inc Shawnee Mission KS.
  • Dhanalakshmi, B., Anil Kumar, B. M., Srinivasa Murthy, V., Srinivasa, S. M., Vivek, H. K., Sennappan, M., & Rangappa, S. (2023). Design, synthesis and docking studies of novel 4-aminophenol-1, 2, 4-oxadiazole hybrids as apoptosis inducers against triple negative breast cancer cells targeting MAP kinase. Journal of Biomolecular Structure & Dynamics, 1–17. https://doi.org/10.1080/07391102.2023.2239912
  • Frisch, M. J., & Clemente, F. R. (2009). Gaussian 09.
  • Genheden, S., & Ryde, U. (2015). The MM/PBSA and MM/GBSA methods to estimate ligand-binding affinities. Expert Opinion on Drug Discovery, 10(5), 449–461. https://doi.org/10.1517/17460441.2015.1032936
  • Greenidge, P. A., Kramer, C., Mozziconacci, J.-C., & Wolf, R. M. (2013). MM/GBSA binding energy prediction on the PDBbind data set: Successes, failures, and directions for further improvement. Journal of Chemical Information and Modeling, 53(1), 201–209. https://doi.org/10.1021/ci300425v
  • 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
  • Isamura, B. K., Patouossa, I., Muya, J. T., & . Lobb, K. A. (2022). Unveiling the reactivity of truxillic and truxinic acids (TXAs): Deprotonation, anion… H–O, cation… O and cation… π interactions in TXA0… Y + and TXA0… Z − complexes (Y = Li, Na, K; Z = F, Cl, Br). Structural Chemistry.
  • Kumar, D. V., Chethan, B. S., Gowda, D., Rangappa, K. S., & Lokanath, N. K. (2023). Investigation of the crystal structure, supramolecular architecture and in-silico myelofibrosis inhibition of a triazole derivative: A structural and theoretical approach. Journal of Molecular Structure, 1288, 135770. https://doi.org/10.1016/j.molstruc.2023.135770
  • Lamb, Y. N. (2022). Pacritinib: First approval. Drugs, 82(7), 831–838. https://doi.org/10.1007/s40265-022-01718-y
  • Lohith, T. N., Hema, M. K., Karthik, C. S., Sandeep, S., Mallesha, L., Alsaiari, N. S., Sridhar, M. A., Katubi, K. M., Abualnaja, K. M., Lokanath, N. K., Mallu, P., & Kumaraswamy, S. R. (2022). Persistent prevalence of non-covalent interaction in pyrimidine containing sulfonamide derivative: A quantum computational analysis. Journal of Molecular Structure, 1266, 133378. https://doi.org/10.1016/j.molstruc.2022.133378
  • Lohith, T. N., Hema, M. K., Karthik, C. S., Sandeep, S., Mallesha, L., Mallu, P., Jothi Ramalingam, R., Sridhar, M. A., Karnan, M., & Lokanath, N. K. (2022). N-[2-(5-bromo-2-chloro-pyrimidin-4-yl)thio)-4-methoxy-phenyl]-4-chlorobenzenesulfonamide: The existence of H-bond and halogen bond interactions assisted supramolecular architecture – A quantum chemical investigation. Journal of Molecular Structure, 1267, 133476. https://doi.org/10.1016/j.molstruc.2022.133476
  • Lohith, T. N., Hema, M. K., Karthik, C. S., Sandeep, S., Rajabathar, J. R., Karnan, M., Lokanath, N. K., Mallesha, L., Mallu, P., & Sridhar, M. A. (2023). Probing the hydrogen bond network in the crystal structure of a sulfonamide derivative: A quantum chemical approach. Journal of Molecular Structure, 1289, 135841. https://doi.org/10.1016/j.molstruc.2023.135841
  • Lohith, T. N., Shamanth, S., Sridhar, M. A., Mantelingu, K., & Lokanath, N. K. (2022). Synthesis, molecular structure, Hirshfeld surface, energy framework and DFT studies of 1,3,4 oxadiazole derivative. Journal of Molecular Structure, 1252, 132203. https://doi.org/10.1016/j.molstruc.2021.132203
  • Lu, T., & Chen, F. (2012). Multiwfn: A multifunctional wavefunction analyzer. Journal of Computational Chemistry, 33(5), 580–592. https://doi.org/10.1002/jcc.22885
  • Macrae, C. F., Sovago, I., Cottrell, S. J., Galek, P. T. A., McCabe, P., Pidcock, E., Platings, M., Shields, G. P., Stevens, J. S., Towler, M., & Wood, P. A. (2020). Mercury 4.0: From visualization to analysis, design and prediction. Journal of Applied Crystallography, 53(Pt 1), 226–235. https://doi.org/10.1107/S1600576719014092
  • Mangala, K., Vinayak, W., Aasiya, C., Chandrakant, B., Amol, M., Kumar, D., & Kulkarni, R. (2014). Reconnoitering imidazopyridazines as anticancer agents based on virtual modelling approach: quantitative structure activity relationship, molecular docking and molecular dynamics. Journal of Biomolecular Structure and Dynamics, 1–18.
  • Matondo, A., Dendera, W., Isamura, B. K., Mambo, H. V., Muzomwe, M., & Mudogo, V. (2022). In silico drug repurposing of anticancer drug 5-FU and analogues against SARS-CoV-2 main protease: Molecular docking, pharmacokinetics and chemical reactivity
  • Parthasarathi, R., Subramanian, V., & Grabowski, S. J. (2006). Hydrogen bonding-new insights. 1–50.
  • Piggot, T. J., Holdbrook, D. A., & Khalid, S. (2013). Conformational dynamics and membrane interactions of the E. coli outer membrane protein FecA: A molecular dynamics simulation study. Biochimica et Biophysica Acta, 1828(2), 284–293. https://doi.org/10.1016/j.bbamem.2012.08.021
  • Rodrigues-Vendramini, F. A. V., Faria, D. R., Arita, G. S., Capoci, I. R. G., Sakita, K. M., Caparroz-Assef, S. M., Becker, T. C. A., de Souza Bonfim-Mendonça, P., Felipe, M. S., Svidzinski, T. I. E., Maigret, B., & Kioshima, É. S. (2019). Antifungal activity of two oxadiazole compounds for the paracoccidioidomycosis treatment. PLoS Neglected Tropical Diseases, 13(6), e0007441. https://doi.org/10.1371/journal.pntd.0007441
  • Rohand, T., Ben EL Ayouchia, H., Achtak, H., Ghaleb, A., Derin, Y., Tutar, A., & Tanemura, K. (2022). Design, synthesis, DFT calculations, molecular docking and antimicrobial activities of novel cobalt, chromium metal complexes of heterocyclic moiety-based 1, 3, 4-oxadiazole derivatives. Journal of Biomolecular Structure & Dynamics, 40(22), 11837–11850. https://doi.org/10.1080/07391102.2021.1965031
  • Santhosh, C., Singh, K. R., Sheela, K., Swaroop, T. R., & Sadashiva, M. P. (2023). Regioselective synthesis of 2, 5-disubstituted-1, 3, 4-thiadiazoles and 1, 3, 4-oxadiazoles via alkyl 2-(methylthio)-2-thioxoacetates and alkyl 2-amino-2-thioxoacetates. The Journal of Organic Chemistry, 88(16), 11486–11496. https://doi.org/10.1021/acs.joc.3c00589
  • Sheldrick, G. M. (2015). Crystal structure refinement with SHELXL. Acta Crystallographica. Section C, Structural Chemistry, 71(Pt 1), 3–8. https://doi.org/10.1107/S2053229614024218
  • Singh, K. R., Santhosh, C., Swaroop, T. R., & Sadashiva, M. P. (2022). Regioselective synthesis of 2,5- and 4,5-disubstituted thiazoles via cyclization of 2-oxo-2-(amino)ethanedithioates with isocyanides. Organic & Biomolecular Chemistry, 20(29), 5771–5778. https://doi.org/10.1039/D2OB00837H
  • Soniat, M., Rogers, D. M., & Rempe, S. B. (2015). Dispersion-and exchange-corrected density functional theory for sodium ion hydration. Journal of Chemical Theory and Computation, 11(7), 2958–2967. https://doi.org/10.1021/acs.jctc.5b00357
  • Spackman, M. A., & Jayatilaka, D. (2009). Hirshfeld surface analysis. CrystEngComm, 11(1), 19–32. https://doi.org/10.1039/B818330A
  • Spackman, P. R., Turner, M. J., McKinnon, J. J., Wolff, S. K., Grimwood, D. J., Jayatilaka, D., & Spackman, M. A. (2021). CrystalExplorer: A program for Hirshfeld surface analysis, visualization and quantitative analysis of molecular crystals. Journal of Applied Crystallography, 54(Pt 3), 1006–1011. https://doi.org/10.1107/S1600576721002910
  • Spek, A. L. (2003). Single-crystal structure validation with the program PLATON. Journal of Applied Crystallography, 36(1), 7–13. https://doi.org/10.1107/S0021889802022112
  • Tumakuru Nagarajappa, L., Ravi Singh, K., Kabuyaya Isamura, B., Vinay Kumar, K. S., Mandayam Anandalwar, S., & Sadashiva, M. P. (2022). SARS-CoV-2 Mpro binding profile and drug-likeness of two novel thiazole derivatives: Structural elucidation, DFT studies, ADME-T and molecular docking simulations. Journal of Biomolecular Structure & Dynamics, 41(20), 11122–11136. https://doi.org/10.1080/07391102.2022.2159880
  • Turner, M. J., Thomas, S. P., Shi, M. W., Jayatilaka, D., & Spackman, M. A. (2015). Energy frameworks: Insights into interaction anisotropy and the mechanical properties of molecular crystals. Chemical Communications (Cambridge, England), 51(18), 3735–3738. https://doi.org/10.1039/C4CC09074H
  • Udoikono, A. D., Agwamba, E. C., Louis, H., Benjamin, I., Ahmad, I., Ejiofor, E. U., Ahuekwe, E. F., Chukwuemeka, K., Adeyinka, A. S., Patel, H. M., Manicum, A.-L., & Edim, M. (2022). Anti-inflammatory biomolecular activity of chlorinated-phenyldiazenyl-naphthalene-2-sulfonic acid derivatives: Perception from DFT, molecular docking, and molecular dynamic simulation. Journal of Biomolecular Structure & Dynamics, 41(19), 10136–10160. https://doi.org/10.1080/07391102.2022.2153414
  • Vinnarasi, S., Radhika, R., Vijayakumar, S., & Shankar, R. (2020). Structural insights into the anti-cancer activity of quercetin on G-tetrad, mixed G-tetrad, and G-quadruplex DNA using quantum chemical and molecular dynamics simulations. Journal of Biomolecular Structure & Dynamics, 38(2), 317–339. https://doi.org/10.1080/07391102.2019.1574239
  • Zhou, Y., Wang, J., Gu, Z., Wang, S., Zhu, W., Aceña, J. L., Soloshonok, V. A., Izawa, K., & Liu, H. (2016). Next generation of fluorine-containing pharmaceuticals, compounds currently in phase II–III clinical trials of major pharmaceutical companies: New structural trends and therapeutic areas. Chemical Reviews, 116(2), 422–518. https://doi.org/10.1021/acs.chemrev.5b00392

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