Targeting human inosine 5’ monophosphate dehydrogenase type 2 for anti-dengue lead identification – a computational approach

References

• Alla, D., Alla, S. S., Vempati, R., Bhatt, H., Sultana, Q., Bhatt, S., Mohsin, T., Siddiqua, A., Bhatt, H. M., & Bhatt, S. G. (2022). Dengue & COVID-19: A comparison and the challenges at Hand. Cureus, 14(11), e31877. https://doi.org/10.7759/cureus.31877
   PubMed Web of Science ®Google Scholar
• Altamish, M., Khan, M., Baig, M. S., Pathak, B., Rani, V., Akhtar, J., Khan, A. A., Ahmad, S., & Krishnan, A. (2022). Therapeutic potential of medicinal plants against dengue infection: A mechanistic viewpoint. ACS Omega, 7(28), 24048–24065. https://doi.org/10.1021/acsomega.2c00625
   PubMed Web of Science ®Google Scholar
• Aziz, M., Ejaz, S. A., Tamam, N., Siddique, F., Riaz, N., Qais, F. A., Chtita, S., & Iqbal, J. (2022). Identification of potent inhibitors of NEK7 protein using a comprehensive computational approach. Scientific Reports, 12(1), 6404. https://doi.org/10.1038/s41598-022-10253-5
   PubMed Web of Science ®Google Scholar
• 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
   PubMed Web of Science ®Google Scholar
• Behnam, M. A., Nitsche, C., Boldescu, V., & Klein, C. D. (2016). The medicinal chemistry of dengue virus. Journal of Medicinal Chemistry, 59(12), 5622–5649. https://doi.org/10.1021/acs.jmedchem.5b01653
   PubMed Web of Science ®Google Scholar
• Bharadwaj, S., Dubey, A., Yadava, U., Mishra, S. K., Kang, S. G., & Dwivedi, V. D. (2021). Exploration of natural compounds with anti-SARS-CoV-2activity via inhibition of SARS-CoV-2 Mpro. Briefings in Bioinformatics, 22(2), 1361–1377. https://doi.org/10.1093/bib/bbaa382
   PubMed Web of Science ®Google Scholar
• Biju, C. K., Lekshmi, R., & Sreekumar, S. (2023). Anti-dengue leads from Caesalpiniabonduc – an in silico approach. International Journal of Pharmaceutical Sciences and Drug Research, 15(04), 445–454. https://doi.org/10.25004/IJPSDR.2023.150408
   Google Scholar
• Charuvil, K. B., Sivanandan, S., & Kesavan Lekshmi, R. (2022). Screening for anti-dengue leads from Euphorbia hirta L. through In Silico methods. Indian Journal of Pharmaceutical Sciences, 84(4), 950–958. https://doi.org/10.36468/pharmaceutical-sciences.989
   Web of Science ®Google Scholar
• Calderón-Peláez, M. A., Velandia-Romero, M. L., Bastidas-Legarda, L. Y., Beltrán, E. O., Camacho-Ortega, S. J., & Castellanos, J. E. (2019). Dengue virus infection of blood–brain barrier cells: Consequences of severe disease. Frontiers in Microbiology, 10, 1435. https://doi.org/10.3389/fmicb.2019.01435
   PubMed Web of Science ®Google Scholar
• Dallakyan, S., & Olson, A. J. (2015). Small-molecule library screening by docking with PyRx. InChemical biology (pp. 243–250). Humana Press.
   Google Scholar
• Dash, R., Ali, M. C., Dash, N., Azad, M. A. K., Hosen, S. M. Z., Hannan, M. A., & Moon, I. S. (2019). Structural and dynamic characterizations highlight the deleterious role of SULT1A1 R213H polymorphism in substrate binding. International Journal of Molecular Science, 20, 1–e22.
   Web of Science ®Google Scholar
• Dighe, S. N., Ekwudu, O., Dua, K., Chellappan, D. K., Katavic, P. L., & Collet, T. A. (2019). Recent update on anti-dengue drug discovery. European Journal of Medicinal Chemistry, 176, 431–455. https://doi.org/10.1016/j.ejmech.2019.05.010
   PubMed Web of Science ®Google Scholar
• Egan, W. J., Merz, K. M., & Baldwin, J. J. (2000). Prediction of drug absorption using multivariate statistics. Journal of Medicinal Chemistry, 43(21), 3867–3877. https://doi.org/10.1021/jm000292e
   PubMed Web of Science ®Google Scholar
• El Omari, N., Jaouadi, I., Lahyaoui, M., Benali, T., Taha, D., Bakrim, S., El Menyiy, N., El Kamari, F., Zengin, G., Bangar, S. P., Lorenzo, J. M., Gallo, M., Montesano, D., & Bouyahya, A. (2022). Natural sources, pharmacological properties, and health benefits of daucosterol: Versatility of actions. Applied Sciences, 12(12), 5779. https://doi.org/10.3390/app12125779
   Google Scholar
• Gadhwal, A. K., Ankit, B. S., Chahar, C., Tantia, P., Sirohi, P., & Agrawal, R. P. (2016). Effect of Carica papaya leaf extract capsule on platelet count in patients of dengue fever with thrombocytopenia. Journal of the Association of Physicians of India, 64(6), 22–26.
   PubMedGoogle Scholar
• Guzman, M. G., Gubler, D. J., Izquierdo, A., Martinez, E., & Halstead, S. B. (2016). Dengue infection. Nature Reviews Disease Primers, 2(1), 1–25.
   Google Scholar
• 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
   Web of Science ®Google Scholar
• Jang, J., Kim, S.-M., Yee, S.-M., Kim, E.-M., Lee, E.-H., Choi, H.-R., Lee, Y.-S., Yang, W.-K., Kim, H.-Y., Kim, K.-H., Kang, H.-S., & Kim, S.-H. (2019). Daucosterol suppresses dextran sulfate sodium (DSS)-induced colitis in mice. International Immunopharmacology, 72, 124–130. https://doi.org/10.1016/j.intimp.2019.03.062
   PubMed Web of Science ®Google Scholar
• Kasture, P. N., Nagabhushan, K. H., & Kumar, A. A. (2016). Multi-centric, double-blind, placebo-controlled, randomized, prospective study to evaluate the efficacy and safety of Carica papaya leaf extract, as empirical therapy for thrombocytopenia associated with dengue fever. Journal of the Association of Physicians of India, 64(6), 15–20.
   PubMedGoogle Scholar
• Kumari, R., Kumar, R., & Lynn, A. (2014). Open-source drug discovery consortium, Lynn A. g_mmpbsa. A GROMACS tool for high-throughput MM-PBSA calculations. Journal of Chemical Information and Modeling, 54(7), 1951–1962. https://doi.org/10.1021/ci500020m
   PubMed Web of Science ®Google Scholar
• Lee, J. H., Lee, J. Y., Park, J. H., Jung, H. S., Kim, J. S., Kang, S. S., Kim, Y. S., & Han, H. (2007). Immunoregulatory activity by daucosterol, a-sitosterol glycoside, induces protective Th1 immune response against disseminated candidiasis in mice. Vaccine, 25(19), 3834–3840. https://doi.org/10.1016/j.vaccine.2007.01.108
   PubMed Web of Science ®Google Scholar
• Lekshmi, R. K., Biju, C. K., & Sreekumar, S. (2021). Identification of potential anti-dengue lead from nilavembu through in silico study. International Journal of Pharmaceutical Sciences and Drug Research, 13(05), 581–588. https://doi.org/10.25004/IJPSDR.2021.130517
   Google Scholar
• Lemkul, J. A. (2018). From proteins to perturbed hamiltonians: A suite of tutorials for the GROMACS-2018 molecular simulation package, v1.0. Living Journal of Computational Molecular Science, 1(1), 5068.
   Google Scholar
• Lipinski, C. A., Lombardo, F., Dominy, B. W., & Feeney, P. J. (1997). Experimental and computational approaches to estimate solubility and permeability in drug discovery and development settings. Advanced Drug Delivery Reviews, 23(1-3), 3–25. https://doi.org/10.1016/S0169-409X(96)00423-1
   Web of Science ®Google Scholar
• Martyna, G. J., Tobias, D. J., & Klein, M. L. (1994). Constant pressure molecular dynamics algorithms. The Journal of Chemical Physics, 101(5), 4177–4189. https://doi.org/10.1063/1.467468
   Web of Science ®Google Scholar
• Morris, G. M., Huey, R., Lindstrom, W., Sanner, M. F., Belew, R. K., Goodsell, D. S., & Olson, A. J. (2019). AutoDock4 and AutoDockTools4: Automated docking with selective receptor flexibility. Journal of Computational Chemistry, 30(16), 2785–2791. https://doi.org/10.1002/jcc.21256
   Google Scholar
• Nair, V., & Shu, Q. (2007). Inosine monophosphate dehydrogenase as a probe in anti-viral drug discovery. Antiviral Chemistry & Chemotherapy, 18(5), 245–258. https://doi.org/10.1177/095632020701800501
   PubMedGoogle Scholar
• Nandini, C., Madhunapantula, S. V., Bovilla, V. R., Ali, M., Mruthunjaya, K., Santhepete, M. N., & Jayashree, K. (2021). Platelet enhancement by Carica papaya L. leaf fractions in cyclophosphamide induced thrombocytopenic rats is due to elevated expression of CD110 receptor on megakaryocytes. Journal of Ethnopharmacology, 275, 114074. https://doi.org/10.1016/j.jep.2021.114074
   PubMed Web of Science ®Google Scholar
• Naveed, M., Ali, U., Aziz, T., Naveed, R., Mahmood, S., Khan, M. M., Alharbi, M., Albekairi, T. H., & Alasmari, A. F. (2024). An Aedes–anopheles vaccine candidate supplemented with BCG epitopes against the aedes and anopheles genera to overcome hypersensitivity to mosquito bites. Acta Parasitologica, 69,1–22. https://doi.org/10.1007/s11686-023-00771-1
   Web of Science ®Google Scholar
• Naveed, M., Jabeen, K., Aziz, T., Mughual, M. S., Ul-Hassan, J., Sheraz, M., Rehman, H. M., Alharbi, M., Albekairi, T. H., & Alasmari, A. F. (2023). Whole proteome analysis of MDR Klebsiella pneumoniae to identify mRNA and multiple epitope based vaccine targets against emerging nosocomial and lungs associated infections. Journal of Biomolecular Structure & Dynamics, 13, 1–14. https://doi.org/10.1080/07391102.2023.2293266
   Google Scholar
• Naveed, M., Makhdoom, S. I., Ali, U., Jabeen, K., Aziz, T., Khan, A. A., Jamil, S., Shahzad, M., Alharbi, M., & Alshammari, A. (2022). Immunoinformatics approach to design multi-epitope-based vaccine against machupo virus taking viral nucleocapsid as a potential candidate. Vaccines, 10(10), 1732. https://doi.org/10.3390/vaccines10101732
   Web of Science ®Google Scholar
• Nguyen, N. M., Tran, C. N. B., Phung, L. K., Duong, K. T. H., Huynh, H. L A., Farrar, J., Nguyen, Q. T. H., Tran, H. T., Nguyen, C. V. V., Merson, L., Hoang, L. T., Hibberd, M. L., Aw, P. P. K., Wilm, A., Nagarajan, N., Nguyen, D. T., Pham, M. P., Nguyen, T. T., Javanbakht, H., … Simmons, C. P. (2013). A randomized, double-blind placebo controlled trial of balapiravir, a polymerase inhibitor, in adult dengue patients. The Journal of Infectious Diseases, 207(9), 1442–1450. https://doi.org/10.1093/infdis/jis470
   PubMed Web of Science ®Google Scholar
• Padmi, H., Ansori, A. N., Probojati, R. T., Murtadlo, A. A., Sunarwidhi, A. L., Hernawan, A., Sunarpi, H., Widyastuti, S., Nikmatullah, A., & Prasedya, E. S. (2021). Anti-inflammatory potential of λ-carrageenan by inhibition of IL-6 receptor: In silico study. InIOP Conference Series: Earth and Environmental Science, 913(1), 012106.
   Google Scholar
• Palanichamy Kala, M., St. John, A. L., & Rathore, A. P. (2023). Dengue: Update on clinically relevant therapeutic strategies and vaccines. Current Treatment Options in Infectious Diseases, 15(2), 27–52. https://doi.org/10.1007/s40506-023-00263-w
   PubMedGoogle Scholar
• Pirolli, D., Sciandra, F., Bozzi, M., Giardina, B., Brancaccio, A., & De Rosa, M. C. (2014). Insights from molecular dynamics simulations: Structural basis for the V567D mutation-induced instability of zebrafish alpha-dystroglycan and comparison with the murine model. PloS One, 9(7), e103866. https://doi.org/10.1371/journal.pone.0103866
   PubMed Web of Science ®Google Scholar
• Ren, J., Yuan, X., Li, J., Lin, S., Yang, B., Chen, C., Zhao, J., Zheng. (2020). Assessing the performance of the g_mmpbsa tools to simulate the inhibition of oseltamivir to influenza virus neuraminidase by molecular mechanics Poisson–Boltzmann surface area methods. Journal of the Chinese Chemical Society, 67(1), 46–53.
   Web of Science ®Google Scholar
• Sahoo, C. R., Paidesetty, S. K., Dehury, B., & Padhy, R. N. (2020). Moleculardynamics and computational study of Mannich-based coumarin derivatives: Potent tyrosine kinase inhibitor. Journal of Biomolecular Structure & Dynamics, 38(18), 5419–5428. https://doi.org/10.1080/07391102.2019.1701554
   PubMed Web of Science ®Google Scholar
• Tarek, M., & Tobias, D. J. (2008). The role of protein–solvent hydrogen bond dynamics in the structural relaxation of a protein in glycerol versus water. European Biophysics Journal: EBJ, 37(5), 701–709. https://doi.org/10.1007/s00249-008-0324-x
   PubMed Web of Science ®Google Scholar
• Tricou, V., Minh, N. N., Van, T. P., Lee, S. J., Farrar, J., Wills, B., Tran, H. T., & Simmons, C. P. (2010). A randomized controlled trial of chloroquine for the treatment of dengue in Vietnamese adults. PLoS Neglected Tropical Diseases, 4(8), e785. https://doi.org/10.1371/journal.pntd.0000785
   PubMed Web of Science ®Google Scholar
• Trott, O., & Olson, A. J. (2010). AutoDockVina: Improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading. Journal of Computational Chemistry, 31(2), 455–461. https://doi.org/10.1002/jcc.21334
   PubMed Web of Science ®Google Scholar
• Trujillo-Correa, A. I., Quintero-Gil, D. C., Diaz-Castillo, F., Quiñones, W., Robledo, S. M., & Martinez-Gutierrez, M. (2019). In vitro and in silico anti-dengue activity of compounds obtained from Psidiumguajava through bioprospecting. BMC Complementary Medicine and Therapies, 19, 1–6.
   Google Scholar
• Veber, D. F., Johnson, S. R., Cheng, H. Y., Smith, B. R., Ward, K. W., & Kopple, K. D. (2002). Molecular properties that influence the oral bioavailability of drug candidates. Journal of Medicinal Chemistry, 45(12), 2615–2623. https://doi.org/10.1021/jm020017n
   PubMed Web of Science ®Google Scholar
• Wang, S., Sun, H., Liu, H., Li, D., Li, Y., & Hou, T. (2016). ADMET evaluation in drug discovery. 16. Predicting hERG blockers by combining multiple pharmacophores and machine learning approaches. Molecular Pharmaceutics, 13(8), 2855–2866. https://doi.org/10.1021/acs.molpharmaceut.6b00471
   PubMed Web of Science ®Google Scholar
• Whitehorn, J., Nguyen, C. V. V., Khanh, L. P., Kien, D. T. H., Quyen, N. T. H., Tran, N. T. T., Hang, N. T., Truong, N. T., Hue Tai, L. T., Cam Huong, N. T., Nhon, V. T., Van Tram, T., Farrar, J., Wolbers, M., Simmons, C. P., & Wills, B. (2016). Lovastatin for the treatment of adult patients with dengue: A randomized, double-blind, placebo-controlled trial. Clinical Infectious Diseases: An Official Publication of the Infectious Diseases Society of America, 62(4), 468–476. https://doi.org/10.1093/cid/civ949
   PubMed Web of Science ®Google Scholar
• Xiong, G., Wu, Z., Yi, J., Fu, L., Yang, Z., Hsieh, C., Yin, M., Zeng, X., Wu, C., Lu, A., Chen, X., Hou, T., & Cao, D. (2021). ADMETlab 2.0: An integrated online platform for accurate and comprehensive predictions of ADMET properties. Nucleic Acids Research, 49(W1), W5–W14. https://doi.org/10.1093/nar/gkab255
   PubMed Web of Science ®Google Scholar
• Xu, S., Ding, D., Zhang, X., Sun, L., Kang, D., Huang, B., Liu, X., & Zhan, P. (2022). Newly emerging strategies in antiviral drug discovery: Dedicated to Prof. Dr. Erik De Clercq on occasion of His 80th anniversary. Molecules (Basel, Switzerland), 27(3), 850. https://doi.org/10.3390/molecules27030850
   PubMed Web of Science ®Google Scholar
• Yu, W., He, X., Vanommeslaeghe, K., & MacKerell, A. D. (2012). Extension of the CHARMM general force field to sulfonyl-containing compounds and its utility in biomolecular simulations. Journal of Computational Chemistry, 33(31), 2451–2468. https://doi.org/10.1002/jcc.23067
   PubMed Web of Science ®Google Scholar
• Zhang, D., & Lazim, R. (2017). Application of conventional molecular dynamics simulation in evaluating the stability of apomyoglobin in urea solution. Scientific Reports, 7, 44651. https://doi.org/10.1038/srep44651
   PubMed Web of Science ®Google Scholar