Ver registro no DEDALUS
Exportar registro bibliográfico



Effects of the protonation state in the interaction of an HIV-1 reverse transcriptase (RT) amino acid, Lys101, and a non nucleoside RT inhibitor, GW420867X (2014)

  • Authors:
  • USP affiliated authors: GALEMBECK, SERGIO EMANUEL - FFCLRP
  • USP Schools: FFCLRP
  • DOI: 10.1007/s00894-014-2332-3
  • Language: Inglês
  • Imprenta:
  • Source:
  • Acesso online ao documento

    Online accessDOI or search this record in
    Informações sobre o DOI: 10.1007/s00894-014-2332-3 (Fonte: oaDOI API)
    • Este periódico é de assinatura
    • Este artigo é de acesso aberto
    • URL de acesso aberto
    • Cor do Acesso Aberto: bronze
    Versões disponíveis em Acesso Aberto do: 10.1007/s00894-014-2332-3 (Fonte: Unpaywall API)

    Título do periódico: Journal of Molecular Modeling

    ISSN: 1610-2940,0948-5023

      Não possui versão em Acesso aberto
    Informações sobre o Citescore
  • Título: Journal of Molecular Modeling

    ISSN: 1610-2940

    Citescore - 2017: 1.17

    SJR - 2017: 0.36

    SNIP - 2017: 0.461

  • Exemplares físicos disponíveis nas Bibliotecas da USP
    BibliotecaCód. de barrasNúm. de chamada
    FCLRP2654854pcd 2654854 Estantes Deslizantes
    How to cite
    A citação é gerada automaticamente e pode não estar totalmente de acordo com as normas

    • ABNT

      GALEMBECK, Sergio Emanuel; BICKELHAUPT, F. Matthias; GUERRA, Célia Fonseca; GALEMBECK, Eduardo. Effects of the protonation state in the interaction of an HIV-1 reverse transcriptase (RT) amino acid, Lys101, and a non nucleoside RT inhibitor, GW420867X. Journal of Molecular Modeling, Heidelberg, v. 20, n. 7, p. 2332-1-2332-11, 2014. Disponível em: < > DOI: 10.1007/s00894-014-2332-3.
    • APA

      Galembeck, S. E., Bickelhaupt, F. M., Guerra, C. F., & Galembeck, E. (2014). Effects of the protonation state in the interaction of an HIV-1 reverse transcriptase (RT) amino acid, Lys101, and a non nucleoside RT inhibitor, GW420867X. Journal of Molecular Modeling, 20( 7), 2332-1-2332-11. doi:10.1007/s00894-014-2332-3
    • NLM

      Galembeck SE, Bickelhaupt FM, Guerra CF, Galembeck E. Effects of the protonation state in the interaction of an HIV-1 reverse transcriptase (RT) amino acid, Lys101, and a non nucleoside RT inhibitor, GW420867X [Internet]. Journal of Molecular Modeling. 2014 ; 20( 7): 2332-1-2332-11.Available from:
    • Vancouver

      Galembeck SE, Bickelhaupt FM, Guerra CF, Galembeck E. Effects of the protonation state in the interaction of an HIV-1 reverse transcriptase (RT) amino acid, Lys101, and a non nucleoside RT inhibitor, GW420867X [Internet]. Journal of Molecular Modeling. 2014 ; 20( 7): 2332-1-2332-11.Available from:

    Referências citadas na obra
    Sharp PM, Hahn B (2011) Origins of HIV and the AIDS pandemic. Cold Spring Harb Perspect Med 1:1–22
    Piot P, Quinn TC (2013) Response to the AIDS pandemic—a global health model. N Engl J Med 368:2210–2218
    De Clercq EA (2011) A 40-year journey in search of selective antiviral chemotherapy. Annu Rev Pharmacol Toxicol 51:1–27
    Panos G, Samonis G, Alexiou VG, Kavarnou GA, Charatsis G, Falagas ME (2008) Mortality and morbidity of HIV infected patients receiving HAART: a cohort study. Curr HIV Res 6:257–260
    de Bethune M-P (2010) Non-nucleoside reverse transcriptase inhibitors (NNRTIs), their discovery, development, and use in the treatment of HIV-1 infection: a review of the last 20 years (1989–2009). Antivir Res 85:75–90
    Joly V, Descamps D, Yeni P (2002) NNRTI plus PI combinations in the perspective of nucleoside-sparing or nucleoside-failing antiretroviral regimens. AIDS Rev 4:128–139
    Singh K, Marchand B, Rai DK, Sharma B, Michailidis E, Ryan EM, Matzek KB, Leslie MD, Hagedorn AN, Li Z, Norden PR, Hachiya A, Parniak MA, Xu H-T, Wainberg MA, Sarafianos SG (2012) Biochemical mechanism of HIV-1 resistance to rilpivirine. J Biol Chem 287:38110–38123
    FDA. Safety. Intelence (Etravirine). . Accessed 26 January 2014
    FDA. Approval of edurant (rilpivirine) a new NNRTI) for the treatment of HIV in treatment naive patients . Accessed 26 January 2014
    Delviks-Frankenberry KA, Nikolenko GN, Pathak VK (2010) The “connection” between HIV drug resistance and RNase H. Viruses 1476:1503
    Li JZ, Paredes R, Ribaudo HJ, Svarovskaia ES, Metzner KJ, Kozal MJ, Hullsiek KH, Balduin M, Jakobsen MR, Geretti AM, Thiebaut R, Ostergaard L, Masquelier B, Johnson JA, Miller MD, Kuritzkes DR (2012) Low-frequency HIV-1 drug resistance mutations and risk of NNRTI-based antiretroviral treatment failure: a systematic review and pooled analysis. JAMA 305:1327–1335
    Li D, Zhan P, De Clercq E, Liu X (2012) Strategies for the design of HIV-1 non-nucleoside reverse transcriptase inhibitors: lessons from the development of seven representative paradigms. J Med Chem 55:3595–3613
    Das K, Martinez SE, Bauman JD, Arnold E (2012) HIV-1 reverse transcriptase complex with DNA and nevirapine reveals non-nucleoside inhibition mechanism. Nat Struct Mol Biol 19:253–259
    Wright DW, Kashif Sadiq S, De Fabritiis G, Coveney PV (2012) Thumbs down for HIV: domain level rearrangements do occur in the NNRTI-bound HIV-1 reverse transcriptase. J Am Chem Soc 134:12885–12888
    Kuroda DG, Bauman JD, Challa JR, Patel D, Troxler T, Das K, Arnold E, Hochstrasser RM (2013) Snapshot of the equilibrium dynamics of a drug bound to human immunodeficiency virus 1 reverse transcriptase. Nat Chem 5:174–181
    Singh K, Marchand B, Rai DK, Sharma B, Michailidis E, Ryan EM, Matzek KB, Leslie MD, Hagedorn AN, Li Z, Norden PR, Hachiya A, Parniak MA, Xu H-T, Wainberg MA, Sarafianos SG (2012) Biochemical mechanism of HIV-1 resistance to rilpivirine. J Biol Chem 287:38110–38223
    Kroeger SMB, Rader LH, Franklin AM, Taylor EV, Smith KD, Smith RH Jr, Tirado-Rives J, Jorgensen WL (2008) Energetic effects for observed and unobserved HIV-1 reverse transcriptase mutations of residues L100, V106, and Y181 in the presence of nevirapine and efavirenz. Bioorg Med Chem Lett 18:969–972
    Udier-Blagovic M, Tirado-Rives J, Jorgensen WL (2004) Structural and energetic analyses of the effects of the K103N mutation of HIV-1 reverse transcriptase on efavirenz analogues. J Med Chem 47:2389–2392
    Kar P, Knecht V (2012) Energetics of mutation-induced changes in potency of lersivirine against HIV-1 reverse transcriptase. J Phys Chem B 116:6269–6278
    Saparpakorn P, Wolschann P, Karpfen A, Pungpo P, Hannongbua S (2011) Systematic investigation on the binding of GW420867X as HIV-1 reverse transcriptase inhibitor. Monatsh Chem 142:961–971, and references cited therein
    He X, Mei Y, Xiang Y, Zhang DW, Zhang JZH (2005) Quantum computational analysis for drug resistance of HIV-1 reverse transcriptase to nevirapine through point mutations. Proteins 61:423–432
    Raju RK, Burton NA, Hillier IH (2010) Modelling the binding of HIV-reverse transcriptase and nevirapine: an assessment of quantum mechanical and force field approaches and predictions of the effect of mutations on binding. Phys Chem Chem Phys 12:7117–7125
    Freitas RF, Galembeck SE (2006) Effect of C–H⋯S and C–H⋯Cl interactions on the conformational preference of inhibitors of TIBO family. Chem Phys Lett 423:131–137
    Freitas RF, Galembeck SE (2006) Computational study of the interaction between TIBO inhibitors and Y181 (C181), K101, and Y188 amino acids. J Phys Chem B 110:21287–21298
    Ribone SR, Leen V, Madrid M, Dehaen W, Daelemans D, Pannecouque C, Briñón MC (2012) Synthesis, biological evaluation and molecular modeling of 4,6-diarylpyrimidines and diarylbenzenes as novel non-nucleosides HIV-1 reverse transcriptase inhibitors. Eur J Med Chem 58:485–492
    Ren J, Nichols CE, Stamp A, Chamberlain PP, Weaver KL, Short SA, Chan JH, Kleim J-PK, Stammers DK (2007) Relationship of potency and resilience to drug resistant mutations for GW420867X revealed by crystal structures of inhibitor complexes for wild-type, Leu100Ile, Lys101Glu, and Tyr188Cys mutant HIV-1 reverse transcriptases. J Med Chem 50:2301–2309
    Accelrys Software Inc. (2010) Discovery studio modeling environment, Release 3.0, San Diego: Accelrys Software Inc
    Schaftenaar G, Noordik JH (2000) Molden: a pre- and post-processing program for molecular and electronic structures. J Comput Aided Mol Des 14:123–134
    Becke AD (1997) Density-functional thermochemistry. V. Systematic optimization of exchange-correlation functionals. J Chem Phys 107:8554–8560
    Grimme S (2006) Semiempirical GGA-type density functional constructed with a long-range dispersion correction. J Comput Chem 27:1787–1799
    Weigend F, Ahlrichs R (2005) Phys Chem Chem Phys 7:3297–3305
    Zhao Y, Truhlar DG (2008) The M06 suite of density functionals for main group thermochemistry, thermochemical kinetics, noncovalent interactions, excited states, and transition elements: two new functionals and systematic testing of four M06-class functionals and 12 other functionals. Theor Chem Accounts 120:215–241
    Dunning TH Jr (1989) Gaussian basis sets for use in correlated molecular calculations. I. The atoms boron through neon and hydrogen. J Chem Phys 90:1007–1023
    Distasio RA Jr, Head-Gordon M (2007) Optimized spin-component scaled second-order Møller-Plesset perturbation theory for intermolecular interaction energies. Mol Phys 105:1073–1083
    Boys SF, Bernardi F (1970) The calculations of small molecular interactions by the diferences of separate total energies. Some procedures with reduced errors. Mol Phys 19:553–566
    Gaussian 09, Revision A.02, Frisch MJ, Trucks GW, Schlegel HB, Scuseria GE, Robb MA, Cheeseman JR, Scalmani G, Barone V, Mennucci B, Petersson GA, Nakatsuji H, Caricato M, Li X, Hratchian HP, Izmaylov AF, Bloino J, Zheng G, Sonnenberg JL, Hada M, Ehara M, Toyota K, Fukuda R, Hasegawa J, Ishida M, Nakajima T, Honda Y, Kitao O, Nakai H, Vreven T, Montgomery JA Jr, Peralta JE, Ogliaro F, Bearpark M, Heyd JJ, Brothers E, Kudin KN, Staroverov VN, Kobayashi R, Normand J, Raghavachari K, Rendell A, Burant JC, Iyengar SS, Tomasi J, Cossi M, Rega N, Millam JM, Klene M, Knox JE, Cross JB, Bakken V, Adamo C, Jaramillo J, Gomperts R, Stratmann RE, Yazyev O, Austin AJ, Cammi R, Pomelli C, Ochterski J. W, Martin R. L, Morokuma K, Zakrzewski VG, Voth GA, Salvador P, Dannenberg JJ, Dapprich S, Daniels AD, Farkas O, Foresman J. B, Ortiz JV, Cioslowski J, Fox DJ (2009) Gaussian, Inc., Wallingford CT
    Ahlrichs R, Bär M, Häser M, Horn H, Kölmel C (1989) Electronic structure calculations on workstation computers: the program system Turbomole. Chem Phys Lett 162:165–169
    Glendening ED, Badenhoop JK, Reed AE, Carpenter JE, Bohmann JA, Morales CM, Weinhold F (2001) NBO 5.0. Theoretical Chemistry Institute, University of Wisconsin, Madison
    Keith TA (2011) AIMAll (Version 11.06.19) TK Gristmill Software, Overland Park, KS ( )
    Johnson ER, Keinan S, Mori-Sanchez P, Contreras-Garcia J, Cohen AJ, Yang W (2010) Revealing noncovalent interactions. J Am Chem Soc 132:6498–6506
    Jmol: an open-source Java viewer for chemical structures in 3D.
    Humphrey W, Dalke A, Schulten K (1996) VMD: visual molecular dynamics. J Mol Graph 14:33–38
    Youngs TGA (2010) Aten–an application for the creation, editing, and visualization of coordinates for glasses, liquids, crystals, and molecules. J Comput Chem 31:639–648
    Schuchardt KL, Didier BT, Elsethagen T, Sun L, Gurumoorthi V, Chase J, Li J, Windus TL (2007) Basis set exchange: a community database for computational sciences. J Chem Inf Model 47:1045–1052
    te Velde G, Bickelhaupt FM, Baerends EJ, Fonseca Guerra C, van Gisbergen SJA, Snijders JG, Ziegler T (2001) Chemistry with ADF. J Comput Chem 22:931–967, See also
    Grimme S, Anthony J, Ehrlich S, Krieg H (2010) A consistent and accurate ab initio parametrization of density functional dispersion correction (DFT-D) for the 94 elements H-Pu. J Chem Phys 132:154104
    van der Wijst T, Fonseca Guerra C, Swart M, Bickelhaupt FM, Lippert B (2009) A ditopic ion-pair receptor based on stacked nucleobase quartets. Angew Chem Int Ed 48:3285–3287
    Fonseca Guerra C, van der Wijst T, Swart M, Poater J, Bickelhaupt FM (2010) Adenine versus guanine quartets in aqueous solution: dispersion-corrected DFT study on the differences in p-stacking and hydrogen-bonding behavior. Theor Chem Accounts 125:245–252
    Bickelhaupt FM, Baerends EJ (2000) Kohn-Sham density functional theory: predicting and understanding chemistry. In: Lipkowitz KB, Boyd DB (eds) Reviews in computational chemistry vol 15. Wiley-VCH, New York, pp 1–86
    Gilli P, Pretto L, Bertolasi V, Gilli G (2009) Predicting hydrogen-bond strengths from acid–base molecular properties. The pK a slide rule: toward the solution of a long-lasting problem. Acc Chem Res 42:33–44
    Urashima S, Asami H, Ohba M, Saigusa H (2010) Microhydration of the guanine-guanine and guanine-cytosine base pairs. J Phys Chem A 114:11231–11237
    Ebrahimi A, Habibi Khorassani SM, Delarami H (2009) Estimation of individual binding energies in some dimers involving multiple hydrogen bonds using topological properties of electron charge density. Chem Phys 365:18–23
    Poater J, Sodupe M, Bertran J, Sola M (2005) Hydrogen bonding and aromaticity in the guanine–cytosine base pair interacting with metal cations (M = Cu+, Ca2+ and Cu2+). Mol Phys 103:163–173
    Grimme S, Goerigk L, Fink RF (2012) Spin-component-scaled electron correlation methods. WIREs Comput Mol Sci 2:886–906
    Hobza P (2012) Calculations on noncovalent interactions and databases of benchmark interaction energies. Acc Chem Res 45:663–672
    Hohenstein EG, Sherrill CD (2012) Wavefunction methods for noncovalent interactions. WIREs Comput Mol Sci 2:304–326
    Riley KE, Pitonak M, Jurecka P, Hobza P (2010) Stabilization and structure calculations for noncovalent interactions in extended molecular systems based on wave function and density functional theories. Chem Rev 110:5023–5063
    Kozuch S, Martin JML (2013) Halogen bonds: benchmarks and theoretical analysis. J Chem Theory Comput 9:1918–1931
    Cerny J, Pitonak M, Riley KE, Hobza P (2011) Complete basis set extrapolation and hybrid schemes for geometry gradients of noncovalent complexes. J Chem Theory Comput 7:3924–3934
    Fonseca Guerra C, Bickelhaupt FM, Snijders JG, Baerends EJ (2000) Hydrogen bonding in DNA base pairs: reconciliation of theory and experiment. J Am Chem Soc 122:4117–4128
    Fonseca Guerra C, van der Wijst T, Bickelhaupt FM (2006) Supramolecular switches based on the guanine–cytosine (GC) Watson–Crick pair: effect of neutral and ionic substituents. Chem Eur J 12:3032–3042
    Fonseca Guerra C, Szekeres Z, Bickelhaupt FM (2011) Remote communication in a DNA-based nanoswitch. Chem Eur J 17:8816–8818
    Fonseca Guerra C, Zijlstra H, Paragi G, Bickelhaupt FM Telomere structure and stability: covalency in hydrogen bonds, not resonance assistance, causes cooperativity in guanine quartets. Chem Eur J 17:12612–12622
    Parreira RLT, Galembeck SE (2003) Characterization of hydrogen bonds in the interactions between the hydroperoxyl radical and organic acids. J Am Chem Soc 125:15614–15622
    Rauk A (1994) Orbital interaction theory of organic chemistry. Wiley, New York
    Popelier PLA (2000) Atoms in molecules: an introduction. Prentice Hall, New Jersey
    Bader RFW (1990) Atoms in molecules, a quantum theory. Oxford, Oxford
    Bader RFW (2009) Bond paths are not chemical bonds. J Phys Chem A 113:10391–10396
    Matta CF, Hernandez-Trujillo J, Tang T-H, Bader RFW (2003) Hydrogen–hydrogen bonding: a stabilizing interaction in molecules and crystals. Chem Eur J 9:1940–1951
    Pendás AM, Francisco E, Blanco MA, Gatti C (2007) Bond paths as privileged Exchange chanels. Chem Eur J 13:9362–9371
    Poater J, Visser R, Solà M, Bickelhaupt FM (2007) Polycyclic benzenoids: why kinked is more stable than straight. J Org Chem 72:1134–1142
    Grimme S, Muck-Lichtenfeld C, Erker G, Kehr G, Wang H, Beckers H, Willner H (2009) When do interacting atoms form a chemical bond? spectroscopic measurements and theoretical analyses of dideuteriophenanthrene. Angew Chem Int Ed 48:2592–2595
    Cerpa E, Krapp A, Flores-Moreno R, Donald KJ, Merino G (2009) Influence of endohedral confinement on the electronic interaction between He atoms: a He2@C20H20 Case Study. Chem Eur J 15:1985–1990
    Cerpa E, Krapp A, Vela A, Merino G (2008) The implications of symmetry of the external potential on bond paths. Chem Eur J 14:10232–10234
    Poater J, Sola M, Bickelhaupt FM (2006) Hydrogen–hydrogen bonding in planar biphenyl, predicted by atoms-In-molecules theory, does not exist. Chem Eur J 12:2889–2895
    Strenalyuk T, Haaland A (2008) Chemical bonding in the inclusion complex of He in adamantane (He@adam): the origin of the barrier to dissociation. Chem Eur J 14:10223–10226
    Dem’yanov P, Polestshuk P (2012) A bond path and an attractive Ehrenfest force do not necessarily indicate bonding interactions: case study on M2X2 (M = Li, Na, K; X = H, OH, F, Cl). Chem Eur J 18:4982–4993
    Grabowski SJ (2011) What is the covalency of hydrogen bonding? Chem Rev 111:2597–2625
    Rozas I, Alkorta I, Elguero J (2000) Behavior of ylides containing N, O, and C atoms as hydrogen bond acceptors. J Am Chem Soc 122:11154–11161
    Ziołkowski M, Grabowski SJ, Leszczynski J (2006) Cooperativity in hydrogen-bonded interactions: ab initio and “atoms in molecules” analyses. J Phys Chem A 110:6514–6521
    Popelier PLA (1998) Characterization of a dihydrogen bond on the basis of the electron density. J Phys Chem A 102:1873–1878