Molecular dynamics and DFT study on the structure and dynamics of N-terminal domain HIV-1 capsid inhibitors

References

• Hemelaar J, Gouws E, Ghys PD, et al. Global and regional distribution of HIV-1 genetic subtypes and recombinants in 2004. AIDS. 2006;20:W13–W23. doi: 10.1097/01.aids.0000247564.73009.bc
   PubMed Web of Science ®Google Scholar
• Arts EJ, Hazuda DJ. HIV-1 antiretroviral drug therapy. Cold Spring Harbor Perspect Med. 2012;2:a007161. doi: 10.1101/cshperspect.a007161
   PubMed Web of Science ®Google Scholar
• Lamorte L, Titolo S, Lemke CT, et al. Discovery of novel small-molecule HIV-1 replication inhibitors that stabilize capsid complexes. Antimicrob Agents Chemother. 2013;57:4622–4631. doi: 10.1128/AAC.00985-13
   PubMed Web of Science ®Google Scholar
• Sundquist WI, Kräusslich H-G. HIV-1 assembly, budding, and maturation. Cold Spring Harbor Perspect Med. 2012;2:a006924. doi: 10.1101/cshperspect.a006924
   PubMed Web of Science ®Google Scholar
• Bell NM, Lever AM. HIV Gag polyprotein: processing and early viral particle assembly. Trends Microbiol. 2013;21:136–144. doi: 10.1016/j.tim.2012.11.006
   PubMed Web of Science ®Google Scholar
• Bharat TA, Davey NE, Ulbrich P, et al. Structure of the immature retroviral capsid at 8 [thinsp] A resolution by cryo-electron microscopy. Nature. 2012;487:385–389. doi: 10.1038/nature11169
   PubMed Web of Science ®Google Scholar
• Ganser-Pornillos BK, Cheng A, Yeager M. Structure of full-length HIV-1 CA: a model for the mature capsid lattice. Cell. 2007;131:70–79. doi: 10.1016/j.cell.2007.08.018
   PubMed Web of Science ®Google Scholar
• Pornillos O, Ganser-Pornillos BK, Kelly BN, et al. X-ray structures of the hexameric building block of the HIV capsid. Cell. 2009;137:1282–1292. doi: 10.1016/j.cell.2009.04.063
   PubMed Web of Science ®Google Scholar
• Pornillos O, Ganser-Pornillos BK, Yeager M. Atomic-level modelling of the HIV capsid. Nature. 2011;469:424–427. doi: 10.1038/nature09640
   PubMed Web of Science ®Google Scholar
• Bocanegra R, Rodríguez-Huete A, Fuertes MÁ, et al. Molecular recognition in the human immunodeficiency virus capsid and antiviral design. Virus Res. 2012;169:388–410. doi: 10.1016/j.virusres.2012.06.016
   PubMed Web of Science ®Google Scholar
• Yu J, Butelman ER, Woods JH, et al. Dynorphin A (1–8) analog, E-2078, is stable in human and rhesus monkey blood. J Pharmacol Exp Ther. 1997;280:1147–1151.
   PubMed Web of Science ®Google Scholar
• Biron E, Chatterjee J, Ovadia O, et al. Improving oral bioavailability of peptides by multiple N-methylation: somatostatin analogues. Angew Chem Int Ed. 2008;47:2595–2599. doi: 10.1002/anie.200705797
   PubMed Web of Science ®Google Scholar
• Barreiro EJ, Kümmerle AE, Fraga CA. The methylation effect in medicinal chemistry. Chem Rev. 2011;111:5215–5246. doi: 10.1021/cr200060g
   PubMed Web of Science ®Google Scholar
• Srinivasan J, Cheatham TE, Cieplak P, et al. Continuum solvent studies of the stability of DNA, RNA, and phosphoramidate−DNA helices. J Am Chem Soc. 1998;120:9401–9409. doi: 10.1021/ja981844+
   Web of Science ®Google Scholar
• Gohlke H, Case DA. Converging free energy estimates: MMPB(GB)SA studies on the protein−protein complex Ras−Raf. J Comput Chem. 2003;25:238–250. doi: 10.1002/jcc.10379
   Web of Science ®Google Scholar
• Genheden S, Ryde U. Will molecular dynamics simulations of proteins ever reach equilibrium? Phys Chem Chem Phys. 2012;14:8662–8677. doi: 10.1039/c2cp23961b
   PubMed Web of Science ®Google Scholar
• Kopitz H, Cashman DA, Pfeiffer-Marek S, et al. Influence of the solvent representation on vibrational entropy calculations: Generalized Born versus distance-dependent dielectric model. J Comput Chem. 2012;33:1004–1013. doi: 10.1002/jcc.22933
   PubMed Web of Science ®Google Scholar
• Xu B, Shen H, Zhu X, et al. Fast and accurate computation schemes for evaluating vibrational entropy of proteins. J Comput Chem. 2011;32:3188–3193. doi: 10.1002/jcc.21900
   PubMed Web of Science ®Google Scholar
• Dennington R, Keith T, Millam J. Gauss View, version 5. Wallingford (CT): Semichem Inc, Shawnee Mission, KS; 2009.
   Google Scholar
• Frisch M, Trucks G, Schlegel HB, et al. Gaussian 09, revision D. 01. Wallingford (CT): Gaussian, Inc.; 2009.
   Google Scholar
• DeLano WL. Pymol: An open-source molecular graphics tool. CCP4. Newsletter On Protein Crystallography. 2002;40:82–92.
   Google Scholar
• Case D, Berryman J, Betz R, et al. (2015).
   Google Scholar
• Gordon JC, Myers JB, Folta T, et al. H++: a server for estimating p K as and adding missing hydrogens to macromolecules. Nucleic Acids Res. 2005;33:W368–WW71. doi: 10.1093/nar/gki464
   PubMed Web of Science ®Google Scholar
• Anandakrishnan R, Aguilar B, Onufriev AV. H++ 3.0: automating p K prediction and the preparation of biomolecular structures for atomistic molecular modeling and simulations. Nucleic Acids Res. 2012;40:W537–WW41. doi: 10.1093/nar/gks375
   PubMed Web of Science ®Google Scholar
• Case D, Babin V, Berryman J, et al. AMBER 14. 2014. San Francisco: University of California; 2014.
   Google Scholar
• Li H, Robertson AD, Jensen JH. Very fast empirical prediction and rationalization of protein pKa values. Proteins: Struct, Funct, Bioinf. 2005;61:704–721. doi: 10.1002/prot.20660
   PubMed Web of Science ®Google Scholar
• Case D, Darden T, Cheatham III T, et al. AMBER, version 10. San Francisco (CA): University of California; 2008.
   Google Scholar
• Wang J, Wolf RM, Caldwell JW, et al. Development and testing of a general amber force field. J Comput Chem. 2004;25:1157–1174. doi: 10.1002/jcc.20035
   PubMed Web of Science ®Google Scholar
• Hornak V, Abel R, Okur A, et al. Comparison of multiple amber force fields and development of improved protein backbone parameters. Proteins: Struct, Funct, Bioinf. 2006;65:712–725. doi: 10.1002/prot.21123
   PubMed Web of Science ®Google Scholar
• Ryckaert J-P, Ciccotti G, Berendsen HJ. Numerical integration of the cartesian equations of motion of a system with constraints: molecular dynamics of n-alkanes. J Comput Phys. 1977;23:327–341. doi: 10.1016/0021-9991(77)90098-5
   Web of Science ®Google Scholar
• Harvey M, De Fabritiis G. An implementation of the smooth particle mesh Ewald method on GPU hardware. J Chem Theory Comput. 2009;5:2371–2377. doi: 10.1021/ct900275y
   PubMed Web of Science ®Google Scholar
• Roe DR, Cheatham III TE. PTRAJ and CPPTRAJ: software for processing and analysis of molecular dynamics trajectory data. J Chem Theory Comput. 2013;9:3084–3095. doi: 10.1021/ct400341p
   PubMed Web of Science ®Google Scholar
• Onufriev A, Bashford D, Case DA. Modification of the generalized born model suitable for macromolecules. The Journal of Physical Chemistry B. 2000;104:3712–3720. doi: 10.1021/jp994072s
   Web of Science ®Google Scholar
• Gohlke H, Kiel C, Case DA. 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. 2003;330:891–913. doi: 10.1016/S0022-2836(03)00610-7
   PubMed Web of Science ®Google Scholar
• Reed AE, Curtiss LA, Weinhold F. Intermolecular interactions from a natural bond orbital, donor-acceptor viewpoint. Chem Rev. 1988;88:899–926. doi: 10.1021/cr00088a005
   Web of Science ®Google Scholar
• Duan X, Zhang M, Zhang X, et al. Molecular modeling and docking study on dopamine D2-like and serotonin 5-HT2A receptors. J Mol Graph Model. 2015;57:143–155. doi: 10.1016/j.jmgm.2015.01.014
   PubMed Web of Science ®Google Scholar
• Martinez L. Automatic identification of mobile and rigid substructures in molecular dynamics simulations and fractional structural fluctuation analysis. PloS one. 2015;10:e0119264. doi: 10.1371/journal.pone.0119264
   PubMed Web of Science ®Google Scholar
• Kumalo HM, Soliman ME. Per-residue energy footprints-based pharmacophore modeling as an enhanced in silico approach in drug discovery: a case study on the identification of novel β-Secretase1 (BACE1) inhibitors as Anti-Alzheimer Agents. Cell Mol Bioeng. 2016;9:175–189. doi: 10.1007/s12195-015-0421-8
   Web of Science ®Google Scholar
• Honarparvar B, Govender T, Maguire GE, et al. Integrated approach to structure-based enzymatic drug design: molecular modeling, spectroscopy, and experimental bioactivity. Chem Rev. 2013;114:493–537. doi: 10.1021/cr300314q
   PubMed Web of Science ®Google Scholar
• Minkara MS, Ucisik MN, Weaver MN, et al. Molecular dynamics study of Helicobacter pylori Urease. J Chem Theory Comput. 2014;10:1852–1862. doi: 10.1021/ct5000023
   PubMed Web of Science ®Google Scholar
• Arodola OA, Soliman ME. Molecular dynamics simulations of ligand-Induced Flap Conformational Changes in Cathepsin-D-A comparative study. J Cell Biochem. 2016;117:2643–2657. Epub 2016/04/03. doi: 10.1002/jcb.25564
   PubMed Web of Science ®Google Scholar
• Fakhar Z, Govender T, Maguire GE, et al. Differential flap dynamics in l, d-transpeptidase2 from mycobacterium tuberculosis revealed by molecular dynamics. Mol Biosyst. 2017;13:1223–1234. doi: 10.1039/C7MB00110J
   PubMedGoogle Scholar
• Blair WS, Pickford C, Irving SL, et al. HIV capsid is a tractable target for small molecule therapeutic intervention. PLoS Pathog. 2010;6:e1001220. doi: 10.1371/journal.ppat.1001220
   PubMed Web of Science ®Google Scholar
• Lobanov MY, Bogatyreva NS, Galzitskaya OV. Radius of gyration as an indicator of protein structure compactness. Mol Biol (NY). 2008;42:623–628. doi: 10.1134/S0026893308040195
   Web of Science ®Google Scholar
• Maia AM, da Silva JH, Mencalha AL, et al. Computational modeling of the bHLH domain of the transcription factor TWIST1 and R118C, S144R and K145E mutants. BMC Bioinf. 2012;13:184. Epub 2012/07/31. doi: 10.1186/1471-2105-13-184
   PubMed Web of Science ®Google Scholar
• McGillewie L, Soliman ME. The binding landscape of plasmepsin V and the implications for flap dynamics. Mol Biosyst. 2016;12:1457–1467. doi: 10.1039/C6MB00077K
   PubMedGoogle Scholar
• Singh A, Soliman ME. Understanding the cross-resistance of oseltamivir to H1N1 and H5N1 influenza a neuraminidase mutations using multidimensional computational analyses. Drug Des Devel Ther. 2015;9:4137.
   PubMed Web of Science ®Google Scholar
• Kumalo H, Soliman ME. A comparative molecular dynamics study on BACE1 and BACE2 flap flexibility. J Recept Signal Transduction. 2016;36:505–514. doi: 10.3109/10799893.2015.1130058
   PubMed Web of Science ®Google Scholar
• Caravella JA, Carbeck JD, Duffy DC, et al. Long-Range electrostatic contributions to protein− ligand binding estimated using protein charge ladders, affinity capillary electrophoresis, and continuum electrostatic theory. J Am Chem Soc. 1999;121:4340–4347. doi: 10.1021/ja984195a
   Web of Science ®Google Scholar
• Cottrell D, Tupper P. Energy drift in molecular dynamics simulations. BIT Numer Math. 2007;47:507–523. doi: 10.1007/s10543-007-0134-z
   Web of Science ®Google Scholar
• Genheden S, Ryde U. The MM/PBSA and MM/GBSA methods to estimate ligand-binding affinities. Expert Opin Drug Discov. 2015;10:449–461. doi: 10.1517/17460441.2015.1032936
   PubMed Web of Science ®Google Scholar
• Hou T, Wang J, Li Y, et al. Assessing the performance of the MM/PBSA and MM/GBSA methods. 1. The accuracy of binding free energy calculations based on molecular dynamics simulations. J Chem Inf Model. 2010;51:69–82. doi: 10.1021/ci100275a
   PubMed Web of Science ®Google Scholar
• Sham YY, Muegge I, Warshel A. The effect of protein relaxation on charge-charge interactions and dielectric constants of proteins. Biophys J. 1998;74:1744–1753. doi: 10.1016/S0006-3495(98)77885-3
   PubMed Web of Science ®Google Scholar
• Martins-Costa M, Anglada JM, Ruiz-López MF. Hyperconjugation in adjacent OO bonds: remarkable odd/even effects. Chem Phys Lett. 2009;481:180–182. doi: 10.1016/j.cplett.2009.09.090
   Web of Science ®Google Scholar
• Greenway KT, Bischoff AG, Pinto BM. Probing hyperconjugation experimentally with the conformational deuterium isotope effect. J Org Chem. 2012;77:9221–9226. doi: 10.1021/jo3017988
   PubMed Web of Science ®Google Scholar
• Rauf SMA, Arvidsson PI, Albericio F, et al. The effect of N-methylation of amino acids (Ac-X-OMe) on solubility and conformation: a DFT study. Org Biomol Chem. 2015;13:9993–10006. doi: 10.1039/C5OB01565K
   PubMed Web of Science ®Google Scholar
• Adeowo FY, Honarparvar B, Skelton AA. The interaction of NOTA as a bifunctional chelator with competitive alkali metal ions: a DFT study. RSC Adv. 2016;6:79485–79496. doi: 10.1039/C6RA20203A
   Web of Science ®Google Scholar
• Kwon O, Sevin F, McKee ML. Density functional calculations of methyllithium, t-butyllithium, and phenyllithium oligomers: effect of hyperconjugation on conformation. J Phys Chem A. 2001;105:913–922. doi: 10.1021/jp003345c
   Web of Science ®Google Scholar
• Arnaud R. Ab initio study of some CH3OCXYCH2 radicals: The influence of anomeric effects on their structure and their stability. J Comput Chem. 1994;15:1341–1356. doi: 10.1002/jcc.540151204
   Web of Science ®Google Scholar