References
- A.S. Perelson, A.U. Neumann, M. Markowitz, J.M. Leonard, and D.D. Ho, HIV-1 dynamics in vivo: Virion clearance rate, infected cell life-span, and viral generation time, Science 271 (1996), pp. 1582–1586. doi:https://doi.org/10.1126/science.271.5255.1582.
- E.O. Freed, HIV-1 gag proteins: Diverse functions in the virus life cycle, Virology 251 (1998), pp. 1–15. doi:https://doi.org/10.1006/viro.1998.9398.
- T.W. Whitfield, D.A. Ragland, K.B. Zeldovich, and C.A. Schiffer, Characterizing protein–ligand binding using atomistic simulation and machine learning: Application to drug resistance in HIV-1 protease, J. Chem. Theory Comput. 16 (2020), pp. 1284–1299. doi:https://doi.org/10.1021/acs.jctc.9b00781.
- L.H. Pearl and W.R. Taylor, A structural model for the retroviral proteases, Nature 329 (1987), pp. 351–354. doi:https://doi.org/10.1038/329351a0.
- H. Toh, M. Ono, K. Saigo, and T. Miyata, Retroviral protease-like sequence in the yeast transposon Ty 1, Nature 315 (1985), pp. 691. doi:https://doi.org/10.1038/315691a0.
- M.A. Navia, P.M.D. Fitzgerald, B.M. McKeever, C.-T. Leu, J.C. Heimbach, W.K. Herber, I.S. Sigal, P.L. Darke, and J.P. Springer, Three-dimensional structure of aspartyl protease from human immunodeficiency virus HIV-1, Nature 337 (1989), pp. 615–620. doi:https://doi.org/10.1038/337615a0.
- T.D. Wu, C.A. Schiffer, M.J. Gonzales, J. Taylor, R. Kantor, S. Chou, D. Israelski, A.R. Zolopa, W.J. Fessel, and R.W. Shafer, Mutation patterns and structural correlates in human immunodeficiency virus type 1 protease following different protease inhibitor treatments, J. Virol. 77 (2003), pp. 4836–4847. doi:https://doi.org/10.1128/JVI.77.8.4836-4847.2003.
- H. Ohashi, K. Watashi, W. Saso, K. Shionoya, S. Iwanami, T. Hirokawa, T. Shirai, S. Kanaya, Y. Ito, K.S. Kim, T. Nomura, T. Suzuki, K. Nishioka, S. Ando, K. Ejima, Y. Koizumi, T. Tanaka, S. Aoki, K. Kuramochi, T. Suzuki, T. Hashiguchi, K. Maenaka, T. Matano, M. Muramatsu, M. Saijo, K. Aihara, S. Iwami, M. Takeda, J.A. McKeating, and T. Wakita, Potential anti-COVID-19 agents, cepharanthine and nelfinavir, and their usage for combination treatment, iScience 24 (2021), pp. 102367. doi:https://doi.org/10.1016/j.isci.2021.102367.
- P. Barragan and D. Podzamczer, Lopinavir/ritonavir: A protease inhibitor for HIV-1 treatment, Expert Opin. Pharm. 9 (2008), pp. 2363–2375. doi:https://doi.org/10.1517/14656566.9.13.2363.
- J.D. Croxtall and C.M. Perry, Lopinavir/Ritonavir: A review of its use in the management of HIV-1 infection, Drugs 70 (2010), pp. 1885–1915. doi:https://doi.org/10.2165/11204950-000000000-00000.
- K.F. Croom, S. Dhillon, and S.J. Keam, Atazanavir: A review of its use in the management of HIV-1 infection, Drugs 69 (2009), pp. 1107–1140. doi:https://doi.org/10.2165/00003495-200969080-00009.
- S. Becker and L. Thornton, Fosamprenavir: Advancing HIV protease inhibitor treatment options, Expert Opin. Pharm. 5 (2004), pp. 1995–2005. doi:https://doi.org/10.1517/14656566.5.9.1995.
- Z. Liu, Y. Wang, J. Brunzelle, I.A. Kovari, and L.C. Kovari, Nine crystal structures determine the substrate envelope of the MDR HIV-1 protease, Protein J. 30 (2011), pp. 173–183. doi:https://doi.org/10.1007/s10930-011-9316-2.
- M. Sanches, S. Krauchenco, N.H. Martins, A. Gustchina, A. Wlodawer, and I. Polikarpov, Structural characterization of B and non-B subtypes of HIV-protease: Insights into the natural susceptibility to drug resistance development, J. Mol. Biol. 369 (2007), pp. 1029–1040. doi:https://doi.org/10.1016/j.jmb.2007.03.049.
- M. Amano, P. Miguel Salcedo-Gómez, R.S. Yedidi, N.S. Delino, H. Nakata, K. Venkateswara Rao, A.K. Ghosh, and H. Mitsuya, GRL-09510, a unique P2-crown-tetrahydrofuranylurethane -containing HIV-1 protease inhibitor, maintains its favorable antiviral activity against highly-drug-resistant HIV-1 variants in vitro, Sci. Rep. 7 (2017), pp. 12235. doi:https://doi.org/10.1038/s41598-017-12052-9.
- M. Aoki, H. Hayashi, R.S. Yedidi, C.D. Martyr, Y. Takamatsu, H. Aoki-Ogata, T. Nakamura, H. Nakata, D. Das, Y. Yamagata, A.K. Ghosh, H. Mitsuya, and F. Kirchhoff, C-5-modified tetrahydropyrano-tetrahydofuran-derived protease inhibitors (PIs) exert potent inhibition of the replication of HIV-1 variants highly resistant to various PIs, including Darunavir, J. Virol. 90 (2016), pp. 2180–2194. doi:https://doi.org/10.1128/JVI.01829-15.
- A. Özen, K.-H. Lin, N. Kurt Yilmaz, and C.A. Schiffer, Structural basis and distal effects of Gag substrate coevolution in drug resistance to HIV-1 protease, Proc. Natl. Acad. Sci. U. S. A. 111 (2014), pp. 15993–15998. doi:https://doi.org/10.1073/pnas.1414063111.
- N.M. King, M. Prabu-Jeyabalan, R.M. Bandaranayake, M.N.L. Nalam, E.A. Nalivaika, A. Özen, T. Haliloǧlu, N.K. Yılmaz, and C.A. Schiffer, Extreme entropy–enthalpy compensation in a drug-resistant variant of HIV-1 protease, ACS Chem. Biol. 7 (2012), pp. 1536–1546. doi:https://doi.org/10.1021/cb300191k.
- G.-D. Hu, T. Zhu, S.-L. Zhang, D. Wang, and Q.-G. Zhang, Some insights into mechanism for binding and drug resistance of wild type and I50V V82A and I84V mutations in HIV-1 protease with GRL-98065 inhibitor from molecular dynamic simulations, Eur. J. Med. Chem. 45 (2010), pp. 227–235. doi:https://doi.org/10.1016/j.ejmech.2009.09.048.
- G. Hu, A. Ma, X. Dou, L. Zhao, and J. Wang, Computational studies of a mechanism for binding and drug resistance in the wild type and four mutations of HIV-1 protease with a GRL-0519 inhibitor, Int. J. Mol. Sci. 17 (2016), pp. 819. doi:https://doi.org/10.3390/ijms17060819.
- T. Hou, W.A. McLaughlin, and W. Wang, Evaluating the potency of HIV-1 protease drugs to combat resistance, Proteins 71 (2008), pp. 1163–1174. doi:https://doi.org/10.1002/prot.21808.
- G. Leonis, T. Steinbrecher, and M.G. Papadopoulos, 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, J. Chem. Inf. Model. 53 (2013), pp. 2141–2153. doi:https://doi.org/10.1021/ci4002102.
- F. Liu, A.Y. Kovalevsky, J.M. Louis, P.I. Boross, Y.-F. Wang, R.W. Harrison, and I.T. Weber, Mechanism of drug resistance revealed by the crystal structure of the unliganded HIV-1 Protease with F53L mutation, J. Mol. Biol. 358 (2006), pp. 1191–1199. doi:https://doi.org/10.1016/j.jmb.2006.02.076.
- Y.X. Yu, W. Wang, H.B. Sun, L.L. Zhang, S.L. Wu, and W.T. Liu, Insights into effect of the Asp25/Asp25ʹ protonation states on binding of inhibitors Amprenavir and MKP97 to HIV-1 protease using molecular dynamics simulations and MM-GBSA calculations, SAR QSAR Environ. Res. 32 (2021), pp. 615–641. doi:https://doi.org/10.1080/1062936X.2021.1939149.
- M.D. Altman, A. Ali, G.S.K. Kumar Reddy, M.N.L. Nalam, S.G. Anjum, H. Cao, S. Chellappan, V. Kairys, M.X. Fernandes, M.K. Gilson, C.A. Schiffer, T.M. Rana, and B. Tidor, HIV-1 protease inhibitors from inverse design in the substrate envelope exhibit subnanomolar binding to drug-resistant variants, J. Am. Chem. Soc. 130 (2008), pp. 6099–6113. doi:https://doi.org/10.1021/ja076558p.
- L.N. Rusere, G.J. Lockbaum, S.-K. Lee, M. Henes, K. Kosovrasti, E. Spielvogel, E.A. Nalivaika, R. Swanstrom, N.K. Yilmaz, C.A. Schiffer, and A. Ali, HIV-1 protease inhibitors incorporating stereochemically defined P2′ ligands to optimize hydrogen bonding in the substrate envelope, J. Med. Chem. 62 (2019), pp. 8062–8079. doi:https://doi.org/10.1021/acs.jmedchem.9b00838.
- Z. Liu, X. Huang, L. Hu, L. Pham, K.M. Poole, Y. Tang, B.P. Mahon, W. Tang, K. Li, N.E. Goldfarb, B.M. Dunn, R. McKenna, and G.E. Fanucci, Effects of hinge-region natural polymorphisms on human immunodeficiency virus-type 1 protease structure, dynamics, and drug pressure evolution, J. Biol. Chem. 291 (2016), pp. 22741–22756. doi:https://doi.org/10.1074/jbc.M116.747568.
- P. Lam, P. Jadhav, C. Eyermann, C. Hodge, Y. Ru, L. Bacheler, J. Meek, M. Otto, M. Rayner, and Y. Wong, Rational design of potent, bioavailable, nonpeptide cyclic ureas as HIV protease inhibitors, Science 263 (1994), pp. 380–384. doi:https://doi.org/10.1126/science.8278812.
- M.K. Parai, D.J. Huggins, H. Cao, M.N.L. Nalam, A. Ali, C.A. Schiffer, B. Tidor, and T.M. Rana, Design, synthesis, and biological and structural evaluations of novel HIV-1 protease inhibitors to combat drug resistance, J. Med. Chem. 55 (2012), pp. 6328–6341. doi:https://doi.org/10.1021/jm300238h.
- G.J. Lockbaum, F. Leidner, L.N. Rusere, M. Henes, K. Kosovrasti, G.S. Nachum, E.A. Nalivaika, A. Ali, N. Kurt Yilmaz, and C.A. Schiffer, Structural adaptation of Darunavir analogues against primary mutations in HIV-1 protease, ACS Infect. Dis. 5 (2019), pp. 316–325. doi:https://doi.org/10.1021/acsinfecdis.8b00336.
- A.K. Ghosh, J.N. Williams, R.Y. Ho, H.M. Simpson, S.-I. Hattori, H. Hayashi, J. Agniswamy, Y.-F. Wang, I.T. Weber, and H. Mitsuya, Design and synthesis of potent HIV-1 protease inhibitors containing bicyclic oxazolidinone scaffold as the P2 ligands: Structure–activity studies and biological and X-ray structural studies, J. Med. Chem. 61 (2018), pp. 9722–9737. doi:https://doi.org/10.1021/acs.jmedchem.8b01227.
- M. Henes, G.J. Lockbaum, K. Kosovrasti, F. Leidner, G.S. Nachum, E.A. Nalivaika, S.-K. Lee, E. Spielvogel, S. Zhou, R. Swanstrom, D.N.A. Bolon, N. Kurt Yilmaz, and C.A. Schiffer, Picomolar to micromolar: Elucidating the role of distal mutations in HIV-1 protease in conferring drug resistance, ACS Chem. Biol. 14 (2019), pp. 2441–2452. doi:https://doi.org/10.1021/acschembio.9b00370.
- J. Chen, X. Wang, T. Zhu, Q. Zhang, and J.Z.H. Zhang, 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, J. Chem. Inf. Model. 55 (2015), pp. 1903–1913. doi:https://doi.org/10.1021/acs.jcim.5b00173.
- J. Chen, C. Peng, J. Wang, and W. Zhu, Exploring molecular mechanism of allosteric inhibitor to relieve drug resistance of multiple mutations in HIV-1 protease by enhanced conformational sampling, Proteins 86 (2018), pp. 1294–1305. doi:https://doi.org/10.1002/prot.25610.
- R. Wang and Q. Zheng, Multiple molecular dynamics simulations of the inhibitor GRL-02031 complex with wild type and mutant HIV-1 protease reveal the binding and drug-resistance mechanism, Langmuir 36 (2020), pp. 13817–13832. doi:https://doi.org/10.1021/acs.langmuir.0c02151.
- R.-G. Wang, H.-X. Zhang, and Q.-C. Zheng, Revealing the binding and drug resistance mechanism of amprenavir, indinavir, ritonavir, and nelfinavir complexed with HIV-1 protease due to double mutations G48T/L89M by molecular dynamics simulations and free energy analyses, Phys. Chem. Chem. Phys. 22 (2020), pp. 4464–4480. doi:https://doi.org/10.1039/C9CP06657H.
- G.J. Lockbaum, F. Leidner, W.E. Royer, N. Kurt Yilmaz, and C.A. Schiffer, Optimizing the refinement of merohedrally twinned P61 HIV-1 protease–inhibitor cocrystal structures, Acta Crystallog. D 76 (2020), pp. 302–310. doi:https://doi.org/10.1107/S2059798320001989.
- F. Leidner, N. Kurt Yilmaz, J. Paulsen, Y.A. Muller, and C.A. Schiffer, Hydration structure and dynamics of inhibitor-bound HIV-1 protease, J. Chem. Theory Comput. 14 (2018), pp. 2784–2796. doi:https://doi.org/10.1021/acs.jctc.8b00097.
- Y. Yu, J. Wang, Q. Shao, J. Shi, and W. Zhu, Effects of drug-resistant mutations on the dynamic properties of HIV-1 protease and inhibition by Amprenavir and Darunavir, Sci. Rep. 5 (2015), pp. 10517. doi:https://doi.org/10.1038/srep10517.
- A.Y. Kovalevsky, J.M. Louis, A. Aniana, A.K. Ghosh, and I.T. Weber, Structural evidence for effectiveness of Darunavir and two related antiviral inhibitors against HIV-2 protease, J. Mol. Biol. 384 (2008), pp. 178–192. doi:https://doi.org/10.1016/j.jmb.2008.09.031.
- J. Chen, Z. Liang, W. Wang, C. Yi, S. Zhang, and Q. Zhang, Revealing origin of decrease in potency of Darunavir and Amprenavir against HIV-2 relative to HIV-1 protease by molecular dynamics simulations, Sci. Rep. 4 (2014), pp. 6872. doi:https://doi.org/10.1038/srep06872.
- P. Kar and V. Knecht, Origin of decrease in potency of Darunavir and two related antiviral inhibitors against HIV-2 compared to HIV-1 protease, J. Phys. Chem. B 116 (2012), pp. 2605–2614. doi:https://doi.org/10.1021/jp211768n.
- Y. Cong, Y. Li, K. Jin, S. Zhong, J.Z.H. Zhang, H. Li, and L. Duan, Exploring the reasons for decrease in binding affinity of HIV-2 against HIV-1 protease complex using interaction entropy under polarized force field, Front. Chem. 6 (2018). doi:https://doi.org/10.3389/fchem.2018.00380.
- M.F. Sk, N.A. Jonniya, and P. Kar, Exploring the energetic basis of binding of currently used drugs against HIV-1 subtype CRF01_AE protease via molecular dynamics simulations, J. Biomol. Struct. Dyn. (2020), pp. 1–18. doi:https://doi.org/10.1080/07391102.07392020.01794965.
- J. Chen, X. Wang, L. Pang, J.Z.H. Zhang, and T. Zhu, Effect of mutations on binding of ligands to guanine riboswitch probed by free energy perturbation and molecular dynamics simulations, Nucleic Acids Res. 47 (2019), pp. 6618–6631. doi:https://doi.org/10.1093/nar/gkz499.
- J. Wang, P.R. Arantes, A. Bhattarai, R.V. Hsu, S. Pawnikar, Y.-M.-M. Huang, G. Palermo, and Y. Miao, Gaussian accelerated molecular dynamics: Principles and applications, WIREs Comput. Mol. Sci. 11 (2021), pp. 1521. doi:https://doi.org/10.1002/wcms.1521.
- J. Wang and Y. Miao, Peptide Gaussian accelerated molecular dynamics (Pep-GaMD): Enhanced sampling and free energy and kinetics calculations of peptide binding, J. Chem. Phys. 153 (2020), pp. 154109. doi:https://doi.org/10.1063/5.0021399.
- W. Xue, F. Yang, P. Wang, G. Zheng, Y. Chen, X. Yao, and F. Zhu, What contributes to serotonin–norepinephrine reuptake inhibitors’ dual-targeting mechanism? The key role of transmembrane domain 6 in human serotonin and norepinephrine transporters revealed by molecular dynamics simulation, ACS Chem. Neurosci. 9 (2018), pp. 1128–1140. doi:https://doi.org/10.1021/acschemneuro.7b00490.
- M.-J. Yang, X.-Q. Pang, X. Zhang, and K.-L. Han, Molecular dynamics simulation reveals preorganization of the chloroplast FtsY towards complex formation induced by GTP binding, J. Struct. Biol. 173 (2011), pp. 57–66. doi:https://doi.org/10.1016/j.jsb.2010.07.013.
- Q. Shao and W. Zhu, Exploring the ligand binding/unbinding pathway by selectively enhanced sampling of ligand in a protein–ligand complex, J. Phys. Chem. B 123 (2019), pp. 7974–7983. doi:https://doi.org/10.1021/acs.jpcb.9b05226.
- J. Chen, L. Wang, W. Wang, H. Sun, L. Pang, and H. Bao, Conformational transformation of switch domains in GDP/K-Ras induced by G13 mutants: An investigation through Gaussian accelerated molecular dynamics simulations and principal component analysis, Comput. Biol. Med. 135 (2021), pp. 104639. doi:https://doi.org/10.1016/j.compbiomed.2021.104639.
- J. Devillers, Computational Design of Chemicals for the Control of Mosquitoes and Their Diseases, CRC Press, Boca Raton, 2018.
- S.S. Liang, X.G. Liu, Y.X. Cui, S.L. Zhang, Q.G. Zhang, and J.Z. Chen, Molecular mechanism concerning conformational changes of CDK2 mediated by binding of inhibitors using molecular dynamics simulations and principal component analysis, SAR QSAR Environ. Res. 32 (2021), pp. 573–594. doi:https://doi.org/10.1080/1062936X.2021.1934896.
- J. Devillers, C. Lagneau, A. Lattes, J.C. Garrigues, M.M. Clémenté, and A. Yébakima, In silico models for predicting vector control chemicals targeting Aedes aegypti, SAR QSAR Environ. Res. 25 (2014), pp. 805–835. doi:https://doi.org/10.1080/1062936X.2014.958291.
- W. Xue, P. Wang, G. Tu, F. Yang, G. Zheng, X. Li, X. Li, Y. Chen, X. Yao, and F. Zhu, Computational identification of the binding mechanism of a triple reuptake inhibitor amitifadine for the treatment of major depressive disorder, Phys. Chem. Chem. Phys. 20 (2018), pp. 6606–6616.
- E.L. Wu, K. Han, and J.Z.H. Zhang, Selectivity of neutral/weakly basic P1 group inhibitors of thrombin and trypsin by a molecular dynamics study, Chem. Eur. J. 14 (2008), pp. 8704–8714. doi:https://doi.org/10.1002/chem.200800277.
- F. Yan, X. Liu, S. Zhang, J. Su, Q. Zhang, and J. Chen, Molecular dynamics exploration of selectivity of dual inhibitors 5M7, 65X, and 65Z toward fatty acid binding proteins 4 and 5, Int. J. Mol. Sci. 19 (2018), pp. 2496. doi:https://doi.org/10.3390/ijms19092496.
- J. Chen, B. Yin, W. Wang, and H. Sun, Effects of disulfide bonds on binding of inhibitors to β-amyloid cleaving enzyme 1 decoded by multiple replica accelerated molecular dynamics simulations, ACS Chem. Neurosci. 11 (2020), pp. 1811–1826. doi:https://doi.org/10.1021/acschemneuro.0c00234.
- S.L. Wu, L.F. Wang, H.B. Sun, W. Wang, and Y.X. Yu, Probing molecular mechanism of inhibitor bindings to bromodomain-containing protein 4 based on molecular dynamics simulations and principal component analysis, SAR QSAR Environ. Res. 31 (2020), pp. 547–570. doi:https://doi.org/10.1080/1062936X.2020.1777584.
- J. Chen, W. Wang, H. Sun, L. Pang, and H. Bao, Binding mechanism of inhibitors to p38α MAP kinase deciphered by using multiple replica Gaussian accelerated molecular dynamics and calculations of binding free energies, Comput. Biol. Med. 134 (2021), pp. 104485. doi:https://doi.org/10.1016/j.compbiomed.2021.104485.
- L.L. Duan, T. Zhu, Y.C. Li, Q.G. Zhang, and J.Z.H. Zhang, Effect of polarization on HIV-1protease and fluoro-substituted inhibitors binding energies by large scale molecular dynamics simulations, Sci. Rep. 7 (2017), pp. 42223. doi:https://doi.org/10.1038/srep42223.
- Y. Gao, T. Zhu, and J. Chen, Exploring drug-resistant mechanisms of I84V mutation in HIV-1 protease toward different inhibitors by thermodynamics integration and solvated interaction energy method, Chem. Phys. Lett. 706 (2018), pp. 400–408. doi:https://doi.org/10.1016/j.cplett.2018.06.040.
- P. Kar and V. Knecht, Energetic basis for drug resistance of HIV-1 protease mutants against amprenavir, J. Comput.-Aided Mol. Des. 26 (2012), pp. 215–232. doi:https://doi.org/10.1007/s10822-012-9550-5.
- H. Tzoupis, G. Leonis, T. Mavromoustakos, and M.G. Papadopoulos, A comparative molecular dynamics, MM–PBSA and thermodynamic integration study of Saquinavir complexes with Wild-Type HIV-1 PR and L10I, G48V, L63P, A71V, G73S, V82A and I84V single mutants, J. Chem. Theory Comput. 9 (2013), pp. 1754–1764. doi:https://doi.org/10.1021/ct301063k.
- W. Wang and P.A. Kollman, Free energy calculations on dimer stability of the HIV protease using molecular dynamics and a continuum solvent model edited by B. Honig, J. Mol. Biol. 303 (2000), pp. 567–582. doi:https://doi.org/10.1006/jmbi.2000.4057.
- W. Wang and P.A. Kollman, Computational study of protein specificity: The molecular basis of HIV-1 protease drug resistance, Proc. Natl. Acad. Sci. U. S. A. 98 (2001), pp. 14937–14942. doi:https://doi.org/10.1073/pnas.251265598.
- C. Wang, D.A. Greene, L. Xiao, R. Qi, and R. Luo, Recent developments and applications of the MMPBSA Method, Front. Mol. Biosci. 4 (2018), pp. 87.
- J. Chen, W. Wang, H. Sun, L. Pang, and B. Yin, Mutation-mediated influences on binding of anaplastic lymphoma kinase to crizotinib decoded by multiple replica Gaussian accelerated molecular dynamics, J. Comput. Aid. Mol. Des. 34 (2020), pp. 1289–1305. doi:https://doi.org/10.1007/s10822-020-00355-5.
- R.M. Levy, A.R. Srinivasan, W.K. Olson, and J.A. McCammon, Quasi-harmonic method for studying very low frequency modes in proteins, Biopolymers 23 (1984), pp. 1099–1112. doi:https://doi.org/10.1002/bip.360230610.
- M. Laberge and T. Yonetani, Molecular dynamics simulations of hemoglobin A in different states and bound to DPG: Effector-linked perturbation of tertiary conformations and HbA concerted dynamics, Biophys. J. 94 (2008), pp. 2737–2751. doi:https://doi.org/10.1529/biophysj.107.114942.
- J. Chen, S. Zhang, W. Wang, L. Pang, Q. Zhang, and X. Liu, Mutation-induced impacts on the switch transformations of the GDP- and GTP-bound K-Ras: Insights from multiple replica gaussian accelerated molecular dynamics and free energy analysis, J. Chem. Inf. Model. 61 (2021), pp. 1954–1969. doi:https://doi.org/10.1021/acs.jcim.0c01470.
- L.F. Wang, Y. Wang, Z.Y. Yang, J. Zhao, H.B. Sun, and S.L. Wu, Revealing binding selectivity of inhibitors toward bromodomain-containing proteins 2 and 4 using multiple short molecular dynamics simulations and free energy analyses, SAR QSAR Environ. Res. 31 (2020), pp. 373–398. doi:https://doi.org/10.1080/1062936X.2020.1748107.
- T. Ichiye and M. Karplus, Collective motions in proteins: A covariance analysis of atomic fluctuations in molecular dynamics and normal mode simulations, Proteins 11 (1991), pp. 205–217. doi:https://doi.org/10.1002/prot.340110305.
- J. Chen, J. Wang, B. Yin, L. Pang, W. Wang, and W. Zhu, Molecular Mechanism of binding selectivity of inhibitors toward BACE1 and BACE2 revealed by multiple short molecular dynamics simulations and free-energy predictions, ACS Chem. Neurosci. 10 (2019), pp. 4303–4318. doi:https://doi.org/10.1021/acschemneuro.9b00348.
- J. Chen, W. Wang, L. Pang, and W. Zhu, Unveiling conformational dynamics changes of H-Ras induced by mutations based on accelerated molecular dynamics, Phys. Chem. Chem. Phys. 22 (2020), pp. 21238–21250. doi:https://doi.org/10.1039/D0CP03766D.
- F. Yan, X. Liu, S. Zhang, J. Su, Q. Zhang, and J. Chen, Electrostatic interaction-mediated conformational changes of adipocyte fatty acid binding protein probed by molecular dynamics simulation, J. Biomol. Struct. Dyn. 37 (2019), pp. 3583–3595. doi:https://doi.org/10.1080/07391102.2018.1520648.
- J. Chen, S. Zhang, W. Wang, H. Sun, Q. Zhang, and X. Liu, Binding of inhibitors to BACE1 affected by pH-dependent protonation: An exploration from multiple replica Gaussian accelerated molecular dynamics and MM-GBSA calculations, ACS Chem. Neurosci. 12 (2021), pp. 2591–2607. doi:https://doi.org/10.1021/acschemneuro.0c00813.
- I. Massova and P.A. Kollman, Computational alanine scanning to probe protein−protein interactions: A novel approach to evaluate binding free energies, J. Am. Chem. Soc. 121 (1999), pp. 8133–8143. doi:https://doi.org/10.1021/ja990935j.
- J. Zhao, B. Yin, H. Sun, L. Pang, and J. Chen, Identifying hot spots of inhibitor-CDK2 bindings by computational alanine scanning, Chem. Phys. Lett. 747 (2020), pp. 137329. doi:https://doi.org/10.1016/j.cplett.2020.137329.
- G.S.K.K. Reddy, A. Ali, M.N.L. Nalam, S.G. Anjum, H. Cao, R.S. Nathans, C.A. Schiffer, and T.M. Rana, Design and synthesis of HIV-1 protease inhibitors incorporating oxazolidinones as P2/P2‘ ligands in pseudosymmetric dipeptide isosteres, J. Med. Chem. 50 (2007), pp. 4316–4328. doi:https://doi.org/10.1021/jm070284z.
- D.C. Bas, D.M. Rogers, and J.H. Jensen, Very fast prediction and rationalization of pKa values for protein–ligand complexes, Proteins 73 (2008), pp. 765–783. doi:https://doi.org/10.1002/prot.22102.
- H. Li, A.D. Robertson, and J.H. Jensen, Very fast empirical prediction and rationalization of protein pKa values, Proteins 61 (2005), pp. 704–721. doi:https://doi.org/10.1002/prot.20660.
- R. Salomon-Ferrer, D.A. Case, and R.C. Walker, An overview of the Amber biomolecular simulation package, WIREs Comput. Mol. Sci. 3 (2013), pp. 198–210. doi:https://doi.org/10.1002/wcms.1121.
- D.A. Case, T.E. Cheatham III, T. Darden, H. Gohlke, R. Luo, K.M. Merz Jr, A. Onufriev, C. Simmerling, B. Wang, and R.J. Woods, The Amber biomolecular simulation programs, J. Comput. Chem. 26 (2005), pp. 1668–1688. doi:https://doi.org/10.1002/jcc.20290.
- A. Jakalian, D.B. Jack, and C.I. Bayly, Fast, efficient generation of high-quality atomic charges. AM1-BCC model: II. Parameterization and validation, J. Comput. Chem. 23 (2002), pp. 1623–1641. doi:https://doi.org/10.1002/jcc.10128.
- A. Jakalian, B.L. Bush, D.B. Jack, and C.I. Bayly, Fast, efficient generation of high-quality atomic charges. AM1-BCC model: I. Method, J. Comput. Chem. 21 (2000), pp. 132–146. doi:https://doi.org/10.1002/(SICI)1096-987X(20000130)21:2<132::AID-JCC5>3.0.CO;2-P.
- J.A. Maier, C. Martinez, K. Kasavajhala, L. Wickstrom, K.E. Hauser, and C. Simmerling, ff14SB: Improving the accuracy of protein side chain and backbone parameters from ff99SB, J. Chem. Theory Comput. 11 (2015), pp. 3696–3713. doi:https://doi.org/10.1021/acs.jctc.5b00255.
- D. Vassetti, M. Pagliai, and P. Procacci, Assessment of GAFF2 and OPLS-AA general force fields in combination with the water models TIP3P, SPCE, and OPC3 for the solvation free energy of druglike organic molecules, J. Chem. Theory Comput. 15 (2019), pp. 1983–1995. doi:https://doi.org/10.1021/acs.jctc.8b01039.
- J. Wang, R.M. Wolf, J.W. Caldwell, P.A. Kollman, and D.A. Case, Development and testing of a general amber force field, J. Comput. Chem. 25 (2004), pp. 1157–1174. doi:https://doi.org/10.1002/jcc.20035.
- W.L. Jorgensen, J. Chandrasekhar, J.D. Madura, R.W. Impey, and M.L. Klein, Comparison of simple potential functions for simulating liquid water, J. Chem. Phys. 79 (1983), pp. 926–935. doi:https://doi.org/10.1063/1.445869.
- R. Salomon-Ferrer, A.W. Götz, D. Poole, S. Le Grand, and R.C. Walker, Routine microsecond molecular dynamics simulations with AMBER on GPUs. 2. Explicit solvent particle mesh Ewald, J. Chem. Theory Comput. 9 (2013), pp. 3878–3888.
- A.W. Götz, M.J. Williamson, D. Xu, D. Poole, S. Le Grand, and R.C. Walker, Routine microsecond molecular dynamics simulations with AMBER on GPUs. 1. Generalized born, J. Chem. Theory Comput. 8 (2012), pp. 1542–1555. doi:https://doi.org/10.1021/ct200909j.
- J.-P. Ryckaert, G. Ciccotti, and H.J.C. Berendsen, Numerical integration of the Cartesian equations of motion of a system with constraints: Molecular dynamics of n-alkanes, J. Comput. Phys. 23 (1977), pp. 327–341. doi:https://doi.org/10.1016/0021-9991(77)90098-5.
- J.A. Izaguirre, D.P. Catarello, J.M. Wozniak, and R.D. Skeel, Langevin stabilization of molecular dynamics, J. Chem. Phys. 114 (2001), pp. 2090–2098. doi:https://doi.org/10.1063/1.1332996.
- U. Essmann, L. Perera, M.L. Berkowitz, T. Darden, H. Lee, and L.G. Pedersen, A smooth particle mesh Ewald method, J. Chem. Phys. 103 (1995), pp. 8577–8593. doi:https://doi.org/10.1063/1.470117.
- D.R. Roe and T.E. Cheatham, PTRAJ and CPPTRAJ: Software for processing and analysis of molecular dynamics trajectory data, J. Chem. Theory Comput. 9 (2013), pp. 3084–3095. doi:https://doi.org/10.1021/ct400341p.
- W. Humphrey, A. Dalke, and K. Schulten, VMD: Visual molecular dynamics, J. Mol. Graph. 14 (1996), pp. 33–38. doi:https://doi.org/10.1016/0263-7855(96)00018-5.
- M.R. Shirts, J.W. Pitera, W.C. Swope, and V.S. Pande, Extremely precise free energy calculations of amino acid side chain analogs: Comparison of common molecular mechanics force fields for proteins, J. Chem. Phys. 119 (2003), pp. 5740–5761. doi:https://doi.org/10.1063/1.1587119.
- H. Sun, Y. Li, M. Shen, S. Tian, L. Xu, P. Pan, Y. Guan, and T. Hou, Assessing the performance of MM/PBSA and MM/GBSA methods. 5. Improved docking performance using high solute dielectric constant MM/GBSA and MM/PBSA rescoring, Phys. Chem. Chem. Phys. 16 (2014), pp. 22035–22045. doi:https://doi.org/10.1039/C4CP03179B.
- H. Sun, Y. Li, S. Tian, L. Xu, and T. Hou, Assessing the performance of MM/PBSA and MM/GBSA methods. 4. Accuracies of MM/PBSA and MM/GBSA methodologies evaluated by various simulation protocols using PDBbind data set, Phys. Chem. Chem. Phys. 16 (2014), pp. 16719–16729. doi:https://doi.org/10.1039/C4CP01388C.
- B.R. Miller, T.D. McGee, J.M. Swails, N. Homeyer, H. Gohlke, and A.E. Roitberg, MMPBSA.py: An efficient program for end-state free energy calculations, J. Chem. Theory Comput. 8 (2012), pp. 3314–3321.
- A. Onufriev, D. Bashford, and D.A. Case, Exploring protein native states and large-scale conformational changes with a modified generalized born model, Proteins 55 (2004), pp. 383–394. doi:https://doi.org/10.1002/prot.20033.
- H. Gohlke, C. Kiel, and D.A. Case, Insights into protein–protein binding by binding free energy calculation and free energy decomposition for the Ras–Raf and Ras–RalGDS complexes, J. Mol. Biol. 330 (2003), pp. 891–913. doi:https://doi.org/10.1016/S0022-2836(03)00610-7.
- W. Kabsch and C. Sander, Dictionary of protein secondary structure: Pattern recognition of hydrogen-bonded and geometrical features, Biopolymers 22 (1983), pp. 2577–2637.
- T.T. Tran, Z. Liu, and G.E. Fanucci, Conformational landscape of non-B variants of HIV-1 protease: A pulsed EPR study, Biochem. Biophys. Res. Commun. 532 (2020), pp. 219–224. doi:https://doi.org/10.1016/j.bbrc.2020.08.030.