94
Views
0
CrossRef citations to date
0
Altmetric
Research Articles

Understanding the impact of halogen functional group (Br, Cl, F, OH) in amprenavir ligand of the HIV protease

&
Pages 12157-12170 | Received 22 Mar 2022, Accepted 01 Jan 2023, Published online: 16 Jan 2023

References

  • Agniswamy, J., Shen, C.-H., Wang, Y.-F., Ghosh, A. K., Rao, K. V., Xu, C.-X., Sayer, J. M., Louis, J. M., & Weber, I. T. (2013). Extreme multidrug resistant HIV-1 protease with 20 mutations is resistant to novel protease inhibitors with P1′-pyrrolidinone or P2-tris-tetrahydrofuran. Journal of Medicinal Chemistry, 56(10), 4017–4027. https://doi.org/10.1021/jm400231
  • ALOGPS 2.1 home page. XXXX. Munich, Germany: Virtual Computational Chemistry Laboratory. http://www.vcclab.org/lab/alogps/.
  • Bader, R. (1990). Atoms in molecules: A quantum theory. Oxford University Press.
  • Berger, G., Frangville, P., & Meyer, F. (2020). Halogen bonding for molecular recognition: New developments in materials and biologicalsciences. Chemical Communications, 56(37), 4970–4981. https://doi.org/10.1039/D0CC00841A
  • Boys, S. F., & Bernardi, F. J. M. P. (1970). The calculation of small molecular interactions by the differences of separate total energies. Some procedures with reduced errors. Molecular Physics, 19(4), 553–566. https://doi.org/10.1080/00268977000101561
  • Brinck, T., Murray, J. S., & Politzer, P. (1992). Surface electrostatic potentials of halogenated methanes as indicators of directional intermolecular interactions. International Journal of Quantum Chemistry, 44(S19), 57–64. https://doi.org/10.1002/qua.560440709
  • Bulfield, D., & Huber, S. M. (2016). Halogen bonding in organic synthesis and organocatalysis. Chemistry (Weinheim an der Bergstrasse, Germany), 22(41), 14434–14450. https://doi.org/10.1002/chem.201601844
  • Carlsson, A.-C C., Scholfield, M. R., Rowe, R. K., Ford, M. C., Alexander, A. T., Mehl, R. A., & Ho, P. S. (2018). Increasing enzyme stability and activity through hydrogen bond-enhanced halogen bonds. Biochemistry, 57(28), 4135–4147. https://doi.org/10.1021/acs.biochem.8b00603
  • Cavallo, G., Metrangolo, P., Milani, R., Pilati, T., Priimagi, A., Resnati, G., & Terraneo, G. (2016). The halogen bond. Chemical Reviews, 116(4), 2478–2601. https://doi.org/10.1021/acs.chemrev.5b00484
  • Chen, J., Wang, X., Zhu, T., Zhang, Q., & Zhang, J. Z. (2015). A comparative insight into amprenavir resistance of mutations V32I, G48V, I50V, I54V, and I84V in HIV-1 protease based on thermodynamic integration and MM-PBSA methods. Journal of Chemical Information and Modeling, 55(9), 1903–1913. https://doi.org/10.1021/acs.jcim.5b00173
  • Clark, T., Hennemann, M., Murray, J. S., & Politzer, P. (2007). Halogen bonding: The Sigma-hole. proceedings of "modelling interactions in biomolecules II", Prague, september 5th-9th, 2005. Journal of Molecular Modeling, 13(2), 291–296. https://doi.org/10.1007/s00894-006-0130-2
  • Cohen, A. J., Mori-Sánchez, P., & Yang, W. (2012). Challenges for density functional theory. Chemical Reviews, 112(1), 289–320. https://doi.org/10.1021/cr200107z
  • Costa, P. J. (2017). The halogen bond: Nature and applications. Physical Sciences Reviews, 2(11), 20170136.
  • Deepa, P., Kolandaivel, P., & Senthilkumar, K. (2012). Theoretical investigation of interaction between psoralen and altretamine with stacked DNA base pairs. Materials Science and Engineering C, 32,3(1), 423–431. https://doi.org/10.1016/j.msec.2011.11.014
  • Deepa, P., & Thirumeignanam, D. (2020a). Understanding the impact of anticancer halogenated inhibitors and various functional groups (X = Cl, F, CF3, CH3, NH2, OH, H) of casein kinase 2 (CK2). Journal of Biomolecular Structure and Dynamics, 40(11),1–17. https://doi.org/10.1080/07391102.2020.1866075
  • Deepa, P., & Thirumeignanam, D. (2020b). Rising trend on the halogen and non-halogen derivatives (Br. Cl, CF3, F, CH3 and NH2) in Ruminal b-d-Xylopyranose – a quantum chemical perspective. Journal of Biomolecular Structure and Dynamics, 40(1), 449-467. https://doi.org/10.1080/07391102.2020.1815577
  • Deepa, P., Thirumeignanam, D., & Kolandaivel, P. (2019). An overview about the impact of hinge region towards the anticancer binding affinity of the Ck2 ligands: a quantum chemical analysis. Journal of Biomolecular Structure & Dynamics, 37(15), 3859–3876. https://doi.org/10.1080/07391102.2018.1533498
  • DeLano, W. (2002). The PyMOL molecular graphics system. San Carlos: Delano Scientific.
  • Deng, N. J., Zhang, P., Cieplak, P., & Lai, L. (2011). Elucidating the energetics of entropically driven protein–ligand association: calculations of absolute binding free energy and entropy. The Journal of Physical Chemistry. B, 115(41), 11902–11910. https://doi.org/10.1021/jp204047b
  • Frisch, M., Trucks, G., Schlegel, H., Scuseria, G., Robb, M., Cheeseman, J., Scalmani, G., Barone, V., Mennucci, B., & Petersson, G. A. (2009). G., 09, Revision D. 01. Gaussian. Inc.
  • Glendening, E. D., Reed, A. E., Carpenter, J. E., & Weinhold, F. (1990). NBO 3.0 program manual. Theoretical Chemistry Institute and Department of Chemistry, University of Wisconsin.
  • Hay, P. J., & Wadt, W. R. (1985). Ab initio effective core potentials for molecular calculations. Potentials for the transition metal atoms Sc to Hg. The Journal of Chemical Physics, 82(1), 270–283. https://doi.org/10.1063/1.448975
  • Heidrich, J., Exner, T. E., & Boeckler, F. M. (2019). Predicting the magnitude of σ-holes using VmaxPred, a fast and efficient tool supporting the application of halogen bonds in drug discovery. Journal of Chemical Information and Modeling, 59(2), 636–643. https://doi.org/10.1021/acs.jcim.8b00622
  • Hohenstein, E. G., Chill, S. T., & Sherrill, C. D. (2008). Assessment of the performance of the M05-2X and M06-2X exchange-correlation functionals for noncovalent interactions in biomolecules. Journal of Chemical Theory and Computation, 4(12), 1996–2000.https://doi.org/10.1021/ct800308k Epub 2008 Nov 19.
  • Hosseini, A., Alibés, A., Noguera-Julian, M., Gil, V., Paredes, R., Soliva, R., Orozco, M., & Guallar, V. (2016). Computational prediction of HIV-1 resistance to protease inhibitors. Journal of Chemical Information and Modeling, 56(5), 915–923. https://doi.org/10.1021/acs.jcim.5b00667
  • Kozuch, S., & Martin, J. M. (2013). Halogen bonds: Benchmarks and theoretical analysis. Journal of Chemical Theory and Computation, 9(4), 1918–1931. https://doi.org/10.1021/ct301064t
  • Leonis, G., Steinbrecher, T., & Papadopoulos, M. G. (2013). A contribution to the drug resistance mechanism of Darunavir, Amprenavir, Indinavir, and Saquinavir complexes with HIV-1 protease due to flap mutation I50V: A systematic MM–PBSA and thermodynamic integration study. Journal of Chemical Information and Modeling, 53(8), 2141–2153. https://doi.org/10.1021/ci4002102
  • Liu, F., Boross, P. I., Wang, Y. F., Tozser, J., Louis, J. M., Harrison, R. W., & Weber, I. T. (2005). Kinetic, stability, and structural changes in high-resolution crystal structures of HIV-1 protease with drug-resistant mutations L24I, I50V, and G73S. Journal of Molecular Biology, 354(4), 789–800. https://doi.org/10.1016/j.jmb.2005.09.095
  • Liu, F., Kovalevsky, A. Y., Tie, Y., Ghosh, A. K., Harrison, R. W., & Weber, I. T. (2008). Effect of flap mutations on structure of HIV-1 protease and inhibition by saquinavir and darunavir. Journal of Molecular Biology, 381(1), 102–115. https://doi.org/10.1016/j.jmb.2008.05.062
  • Margiotta, E., van der Lubbe, S. C., de Azevedo Santos, L., Paragi, G., Moro, S., Bickelhaupt, F. M., & Fonseca Guerra, C. (2020). Halogen bonds in ligand–protein systems: Molecular orbital theory for drug design. Journal of Chemical Information and Modeling, 60(3), 1317–1328. https://doi.org/10.1021/acs.jcim.9b00946
  • Margolis, D. M. (2011). Eradication therapies for HIV infection: Time to begin again. AIDS Research and Human Retroviruses, 27(4), 347–353.https://doi.org/10.1089/aid.2011.0017
  • Metrangolo, P., & Resnati, G. (2008). Halogen bonding: Fundamentals and applications. Springer.
  • Meyer, F., & Dubois, P. (2013). Halogen bonding at work: Recent applications in synthetic chemistry and materials science. CrystEngComm, 15(16), 3058–3071. https://doi.org/10.1039/C2CE26150B
  • Murphy, M. D., Marousek, G. I., & Chou, S. (2004). HIV protease mutations associated with amprenavir resistance during salvage therapy: importance of I54M. Journal of Clinical Virology: The Official Publication of the Pan American Society for Clinical Virology, 30(1), 62–67. https://doi.org/10.1016/j.jcv.2003.08.013
  • Navia, M. A., Fitzgerald, P. M. D., Mckeever, B. M., Leu, C. T., Heimbach, J. C., Herber, W. K., Sigal, I. S., Darke, P. L., & Springer, J. P. (1989). 3-dimensional structure of aspartyl protease from human immunodeficiency virus HIV-1. Nature, 337(6208), 615–620.
  • Nemec, V., Lisac, K., Bedeković, N., Fotović, L., Stilinović, V., & Cinčić, D. (2021). Crystal engineering strategies towards halogen-bonded metal–organic multi-component solids: salts, cocrystals and salt cocrystals. CrystEngComm, 23(17), 3063–3083. https://doi.org/10.1039/D1CE00158B
  • Politzer, P., Murray, J. S., & Clark, T. (2010). Halogen bonding: An electrostatically-driven highly directional noncovalent interaction. Physical Chemistry Chemical Physics: PCCP, 12(28), 7748–7757. https://doi.org/10.1039/c004189k
  • Rezac, J., & Lande, A. d. l. (2016). On the role of charge transfer in halogen bonding. Physical Chemistry Chemical Physics, 19(1), 791–803.
  • Riley, K. E., Murray, J. S., Fanfrlík, J., Řezáč, J., Solá, R. J., Concha, M. C., Ramos, F. M., & Politzer, P. (2013). Halogen bond tunability II: The varying roles of electrostatic and dispersion contributions to attraction in halogen bonds. Journal of Molecular Modeling, 19(11), 4651–4659. https://doi.org/10.1007/s00894-012-1428-x
  • Sahin, K., Zengin Kurt, B., Sonmez, F., & Durdagi, S. (2020). Investigation of novel indole-based HIV-1 protease inhibitors using virtual screening and text mining. Journal of Biomolecular Structure and Dynamics, 38(11), 3342–3358. https://doi.org/10.1080/07391102.2020.1775121
  • Schmider, H. L., & Becke, A. D. (1998). Optimized density functionals from the extended G2 test set. The Journal of Chemical Physics, 108(23), 9624–9631. https://doi.org/10.1063/1.476438
  • Sedlak, R., Kolář, M. H., & Hobza, P. (2015). Polar flattening and the strength of halogen bonding. Journal of Chemical Theory and Computation, 11(10), 4727–4732. https://doi.org/10.1021/acs.jctc.5b00687
  • Shen, C. H., Wang, Y. F., Kovalevsky, A. Y., Harrison, R. W., & Weber, I. T. (2010). Amprenavir complexes with HIV‐1 protease and its drug‐resistant mutants altering hydrophobic clusters. The FEBS Journal, 277(18), 3699–3714. doi: https://doi.org/10.1111/j.1742-4658.2010.07771.
  • Tingjun, H., & Ron, Y. (2007). Molecular dynamics and free energy studies on the wild-type and double mutant HIV-1 protease complexed with amprenavir and two amprenavir-related inhibitors: Mechanism for binding and drug resistance. Journal of Medicinal Chemistry, 50(6), 1177–1188. https://doi.org/10.1021/jm0609162
  • Tozser, J. (2001). HIV inhibitors: problems and reality. Annals of the New York Academy of Sciences, 946, 145–159.
  • Varadwaj, P. R., Varadwaj, A., & Marques, H. M. (2019). Halogen bonding: A halogen-centered noncovalent interaction yet to be understood. Inorganics, 7(3), 40. https://doi.org/10.3390/inorganics7030040a
  • Weber, I. T., Waltman, M. J., Mustyakimov, M., Blakeley, M. P., Keen, D. A., Ghosh, A. K., Langan, P., & Kovalevsky, A. Y. (2013). Joint X-ray/neutron crystallographic study of HIV-1 protease with clinical inhibitor amprenavir: insights for drug design. Journal of Medicinal Chemistry, 56(13), 5631–5635. https://doi.org/10.1021/jm400684f
  • Wilcken, R., Zimmermann, M. O., Lange, A., Joerger, A. C., & Boeckler, F. M. (2013). Principles and applications of halogen bonding in medicinal chemistry and chemical biology. Journal of Medicinal Chemistry, 56(4), 1363–1388. https://doi.org/10.1021/jm3012068
  • World health Organization. (XXXX). https://www.who.int/news-room/fact-sheets/detail/hiv-aids
  • Zhao, Y., Schultz, N. E., & Truhlar, D. G. (2005). Exchange-correlation functional with broad accuracy for metallic and nonmetallic compounds, kinetics, and noncovalent interactions. The Journal of Chemical Physics, 123(16), 161103. https://doi.org/10.1063/1.2126975
  • Zhao, Y., Schultz, N. E., & Truhlar, D. G. (2006). Design of density functionals by combining the method of constraint satisfaction with parametrization for thermochemistry, thermochemical kinetics, and noncovalent interactions. Journal of Chemical Theory and Computation, 2(2), 364–382. https://doi.org/10.1021/ct0502763

Reprints and Corporate Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

To request a reprint or corporate permissions for this article, please click on the relevant link below:

Academic Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

Obtain permissions instantly via Rightslink by clicking on the button below:

If you are unable to obtain permissions via Rightslink, please complete and submit this Permissions form. For more information, please visit our Permissions help page.