메뉴 건너뛰기




Volumn 80, Issue 4, 2012, Pages 1110-1122

Validating the vitality strategy for fighting drug resistance

Author keywords

Binding affinity; Coarse grained model; Empirical valence bond; Mutation screening; Transition state

Indexed keywords

ANTI HUMAN IMMUNODEFICIENCY VIRUS AGENT;

EID: 84857782430     PISSN: 08873585     EISSN: 10970134     Source Type: Journal    
DOI: 10.1002/prot.24012     Document Type: Article
Times cited : (10)

References (59)
  • 3
    • 0036882390 scopus 로고    scopus 로고
    • Structure and mechanism of the pepsin-like family of aspartic peptidases
    • Dunn BM. Structure and mechanism of the pepsin-like family of aspartic peptidases. Chem Rev 2002; 102: 4431-4458.
    • (2002) Chem Rev , vol.102 , pp. 4431-4458
    • Dunn, B.M.1
  • 4
    • 0023477907 scopus 로고
    • Human immunodeficiency virus protease expressed in Escherichia coli exhibits autoprocessing and specific maturation of the gag precursor
    • Debouck C, Gorniak JG, Strickler JE, Meek TD, Metcalf BW, Rosenberg M. Human immunodeficiency virus protease expressed in Escherichia coli exhibits autoprocessing and specific maturation of the gag precursor. Proc Natl Acad Sci USA 1987; 84: 8903-8906.
    • (1987) Proc Natl Acad Sci USA , vol.84 , pp. 8903-8906
    • Debouck, C.1    Gorniak, J.G.2    Strickler, J.E.3    Meek, T.D.4    Metcalf, B.W.5    Rosenberg, M.6
  • 7
    • 0024334170 scopus 로고
    • Role of human immunodeficiency virus type 1-specific protease in core protein maturation and viral infectivity
    • Peng C, Ho BK, Chang TW, Chang NT. Role of human immunodeficiency virus type 1-specific protease in core protein maturation and viral infectivity. J Virol 1989; 63: 2550-2556.
    • (1989) J Virol , vol.63 , pp. 2550-2556
    • Peng, C.1    Ho, B.K.2    Chang, T.W.3    Chang, N.T.4
  • 8
    • 61449189645 scopus 로고    scopus 로고
    • Anti-HIV drugs: 25 compounds approved within 25 years after the discovery of HIV
    • De Clercq E. Anti-HIV drugs: 25 compounds approved within 25 years after the discovery of HIV. Int J Antimicrob Agents 2009; 33: 307-320.
    • (2009) Int J Antimicrob Agents , vol.33 , pp. 307-320
    • De Clercq, E.1
  • 9
    • 0028952146 scopus 로고
    • HIV population dynamics in vivo: implications for genetic variation, pathogenesis, and therapy
    • Coffin JM. HIV population dynamics in vivo: implications for genetic variation, pathogenesis, and therapy. Science 1995; 267: 483-489.
    • (1995) Science , vol.267 , pp. 483-489
    • Coffin, J.M.1
  • 10
    • 0035910029 scopus 로고    scopus 로고
    • Computational study of protein specificity: the molecular basis of HIV-1 protease drug resistance
    • Wang W, Kollman PA. Computational study of protein specificity: the molecular basis of HIV-1 protease drug resistance. Proc Natl Acad Sci USA 2001; 98: 14937-14942.
    • (2001) Proc Natl Acad Sci USA , vol.98 , pp. 14937-14942
    • Wang, W.1    Kollman, P.A.2
  • 11
    • 76549102880 scopus 로고    scopus 로고
    • Detecting and understanding combinatorial mutation patterns responsible for HIV drug resistance
    • Zhang J, Hou T, Wang W, Liu JS. Detecting and understanding combinatorial mutation patterns responsible for HIV drug resistance. Proc Natl Acad Sci USA 2010; 107: 1321-1326.
    • (2010) Proc Natl Acad Sci USA , vol.107 , pp. 1321-1326
    • Zhang, J.1    Hou, T.2    Wang, W.3    Liu, J.S.4
  • 12
    • 42449147045 scopus 로고    scopus 로고
    • Evaluating the potency of HIV-1 protease drugs to combat resistance
    • Hou T, McLaughlin WA, Wang W. Evaluating the potency of HIV-1 protease drugs to combat resistance. Proteins 2008; 71: 1163-1174.
    • (2008) Proteins , vol.71 , pp. 1163-1174
    • Hou, T.1    McLaughlin, W.A.2    Wang, W.3
  • 13
    • 0029151345 scopus 로고
    • Kinetic characterization and cross-resistance patterns of HIV-1 protease mutants selected under drug pressure
    • Gulnik SV, Suvorov LI, Liu B, Yu B, Anderson B, Mitsuya H, Erickson JW. Kinetic characterization and cross-resistance patterns of HIV-1 protease mutants selected under drug pressure. Biochem 1995; 34: 9282.
    • (1995) Biochem , vol.34 , pp. 9282
    • Gulnik, S.V.1    Suvorov, L.I.2    Liu, B.3    Yu, B.4    Anderson, B.5    Mitsuya, H.6    Erickson, J.W.7
  • 14
    • 38349001243 scopus 로고    scopus 로고
    • Predicting drug-resistant mutations of HIV protease
    • Ishikita H, Warshel A. Predicting drug-resistant mutations of HIV protease. Angew Chem Int Ed Engl 2008; 47: 697-700.
    • (2008) Angew Chem Int Ed Engl , vol.47 , pp. 697-700
    • Ishikita, H.1    Warshel, A.2
  • 15
    • 8744303696 scopus 로고    scopus 로고
    • Computational prediction of structure, substrate binding mode, mechanism, and rate for a malaria protease with a novel type of active site
    • Bjelic S, Aqvist J. Computational prediction of structure, substrate binding mode, mechanism, and rate for a malaria protease with a novel type of active site. Biochemistry 2004; 43: 14521-14528.
    • (2004) Biochemistry , vol.43 , pp. 14521-14528
    • Bjelic, S.1    Aqvist, J.2
  • 16
    • 0036286854 scopus 로고    scopus 로고
    • The role and perspective of ab initio molecular dynamics in the study of biological systems
    • Carloni P, Rothlisberger U, Parrinello M. The role and perspective of ab initio molecular dynamics in the study of biological systems. Acc Chem Res 2002: 35: 455-464.
    • (2002) Acc Chem Res , vol.35 , pp. 455-464
    • Carloni, P.1    Rothlisberger, U.2    Parrinello, M.3
  • 17
    • 0036882390 scopus 로고    scopus 로고
    • Structure and mechanism of the pepsin-like family of aspartic peptidases
    • Dunn BM. Structure and mechanism of the pepsin-like family of aspartic peptidases. Chem Rev 2002; 102: 4431-4458.
    • (2002) Chem Rev , vol.102 , pp. 4431-4458
    • Dunn, B.M.1
  • 18
    • 0028717766 scopus 로고
    • Use of steady state kinetic methods to elucidate the kinetic and chemical mechanisms of retroviral proteases
    • Meek TD, Rodriguez EJ, Angeles TS. Use of steady state kinetic methods to elucidate the kinetic and chemical mechanisms of retroviral proteases. Methods Enzymol 1994; 241: 127-156.
    • (1994) Methods Enzymol , vol.241 , pp. 127-156
    • Meek, T.D.1    Rodriguez, E.J.2    Angeles, T.S.3
  • 19
    • 0034778987 scopus 로고    scopus 로고
    • Follow the protons: a low-barrier hydrogen bond unifies the mechanisms of the aspartic proteases
    • Northrop DB. Follow the protons: a low-barrier hydrogen bond unifies the mechanisms of the aspartic proteases. Acc Chem Res 2001: 34: 790-797.
    • (2001) Acc Chem Res , vol.34 , pp. 790-797
    • Northrop, D.B.1
  • 20
    • 0027525478 scopus 로고
    • Use of nitrogen-15 kinetic isotope effects to elucidate details of the chemical mechanism of human immunodeficiency virus 1 protease
    • Rodriguez EJ, Angeles TS, Meek TD. Use of nitrogen-15 kinetic isotope effects to elucidate details of the chemical mechanism of human immunodeficiency virus 1 protease. Biochemistry 1993; 32: 12380-12385.
    • (1993) Biochemistry , vol.32 , pp. 12380-12385
    • Rodriguez, E.J.1    Angeles, T.S.2    Meek, T.D.3
  • 21
    • 0023434194 scopus 로고
    • Binding of a reduced peptide inhibitor to the aspartic proteinase from Rhizopus chinensis: implications for a mechanism of action
    • Suguna K, Padlan EA, Smith CW, Carlson WD, Davies DR. Binding of a reduced peptide inhibitor to the aspartic proteinase from Rhizopus chinensis: implications for a mechanism of action. Proc Natl Acad Sci USA 1987; 84: 7009-7013.
    • (1987) Proc Natl Acad Sci USA , vol.84 , pp. 7009-7013
    • Suguna, K.1    Padlan, E.A.2    Smith, C.W.3    Carlson, W.D.4    Davies, D.R.5
  • 22
    • 33746869326 scopus 로고    scopus 로고
    • Catalysis and linear free energy relationships in aspartic proteases
    • Bjelic S, Aqvist J. Catalysis and linear free energy relationships in aspartic proteases. Biochemistry 2006; 45: 7709-7723.
    • (2006) Biochemistry , vol.45 , pp. 7709-7723
    • Bjelic, S.1    Aqvist, J.2
  • 23
    • 0000728542 scopus 로고
    • Microscopic and semimicroscopic calculations of electrostatic energies in proteins by the POLARIS and ENZYMIX programs
    • Lee FS, Chu ZT, Warshel A. Microscopic and semimicroscopic calculations of electrostatic energies in proteins by the POLARIS and ENZYMIX programs. J Comp Chem 1993; 14: 161-185.
    • (1993) J Comp Chem , vol.14 , pp. 161-185
    • Lee, F.S.1    Chu, Z.T.2    Warshel, A.3
  • 24
    • 0342321950 scopus 로고    scopus 로고
    • Examining methods for calculations of binding free energies: LRA, LIE, PDLD-LRA, and PDLD/S-LRA calculations of ligands binding to an HIV protease
    • Sham YY, Chu ZT, Tao H, Warshel A. Examining methods for calculations of binding free energies: LRA, LIE, PDLD-LRA, and PDLD/S-LRA calculations of ligands binding to an HIV protease. Proteins Struct Funct Genet 2000; 39: 393-407.
    • (2000) Proteins Struct Funct Genet , vol.39 , pp. 393-407
    • Sham, Y.Y.1    Chu, Z.T.2    Tao, H.3    Warshel, A.4
  • 25
    • 77951210462 scopus 로고    scopus 로고
    • Absolute binding free energy calculations: on the accuracy of computational scoring of protein-ligand interactions
    • Singh N, Warshel A. Absolute binding free energy calculations: on the accuracy of computational scoring of protein-ligand interactions. Proteins 2010; 78: 1705-1723.
    • (2010) Proteins , vol.78 , pp. 1705-1723
    • Singh, N.1    Warshel, A.2
  • 27
    • 0000671518 scopus 로고    scopus 로고
    • a's of ionizable residues in proteins: semi-microscopic and microscopic approaches
    • a's of ionizable residues in proteins: semi-microscopic and microscopic approaches. J Phys Chem B 1997; 101: 4458-4472.
    • (1997) J Phys Chem B , vol.101 , pp. 4458-4472
    • Sham, Y.Y.1    Chu, Z.T.2    Warshel, A.3
  • 28
    • 0026596911 scopus 로고
    • Calculations of antibody antigen interactions-microscopic and semimicroscopic evaluation of the free-energies of binding of phosphorylcholine analogs to Mcpc603
    • Lee FS, Chu ZT, Bolger MB, Warshel A. Calculations of antibody antigen interactions-microscopic and semimicroscopic evaluation of the free-energies of binding of phosphorylcholine analogs to Mcpc603. Protein Eng 1992; 5: 215-228.
    • (1992) Protein Eng , vol.5 , pp. 215-228
    • Lee, F.S.1    Chu, Z.T.2    Bolger, M.B.3    Warshel, A.4
  • 29
    • 0032031405 scopus 로고    scopus 로고
    • Electrostatic contributions to protein-protein binding affinities: application to rap/raf interaction
    • Muegge I, Schweins T, Warshel A. Electrostatic contributions to protein-protein binding affinities: application to rap/raf interaction. Proteins Struct Funct Genet 1998; 30: 407-423.
    • (1998) Proteins Struct Funct Genet , vol.30 , pp. 407-423
    • Muegge, I.1    Schweins, T.2    Warshel, A.3
  • 30
    • 0031404601 scopus 로고    scopus 로고
    • A fast estimate of electrostatic group contributions to the free energy of protein-inhibitor binding
    • Muegge I, Tao H, Warshel A. A fast estimate of electrostatic group contributions to the free energy of protein-inhibitor binding. Prot Eng 1997; 10: 1363-1372.
    • (1997) Prot Eng , vol.10 , pp. 1363-1372
    • Muegge, I.1    Tao, H.2    Warshel, A.3
  • 31
    • 0032560959 scopus 로고    scopus 로고
    • Continuum solvent studies of the stability of DNA, RNA, and phosphoramidate-DNA helices
    • Srinivasan J, Cheatham TE, Cieplak P, Kollman PA, Case DA. Continuum solvent studies of the stability of DNA, RNA, and phosphoramidate-DNA helices. J Am Chem Soc 1998; 120: 9401-9409.
    • (1998) J Am Chem Soc , vol.120 , pp. 9401-9409
    • Srinivasan, J.1    Cheatham, T.E.2    Cieplak, P.3    Kollman, P.A.4    Case, D.A.5
  • 32
    • 28144441347 scopus 로고    scopus 로고
    • Evaluating the molecular mechanics Poisson-Boltzmann surface area free energy method using a congeneric series of ligands to p38 MAP kinase
    • Pearlman DA. Evaluating the molecular mechanics Poisson-Boltzmann surface area free energy method using a congeneric series of ligands to p38 MAP kinase. J Med Chem 2005; 48: 7796-7807.
    • (2005) J Med Chem , vol.48 , pp. 7796-7807
    • Pearlman, D.A.1
  • 33
    • 20444377245 scopus 로고    scopus 로고
    • Validation and use of the MM-PBSA approach for drug discovery
    • Kuhn B, Gerber P, Schulz-gasch T, Stahl M. Validation and use of the MM-PBSA approach for drug discovery. J Med Chem 2005; 48: 4040-4048.
    • (2005) J Med Chem , vol.48 , pp. 4040-4048
    • Kuhn, B.1    Gerber, P.2    Schulz-gasch, T.3    Stahl, M.4
  • 34
    • 36549094414 scopus 로고
    • A surface constrained all-atom solvent model for effective simulations of polar solutions
    • King G, Warshel A. A surface constrained all-atom solvent model for effective simulations of polar solutions. J Chem Phys 1989; 91: 3647-3661.
    • (1989) J Chem Phys , vol.91 , pp. 3647-3661
    • King, G.1    Warshel, A.2
  • 35
    • 0000115003 scopus 로고
    • A local reaction field method for fast evaluation of long-range electrostatic interactions in molecular simulations
    • Lee FS, Warshel A. A local reaction field method for fast evaluation of long-range electrostatic interactions in molecular simulations. J Chem Phys 1992; 97: 3100-3107.
    • (1992) J Chem Phys , vol.97 , pp. 3100-3107
    • Lee, F.S.1    Warshel, A.2
  • 39
    • 0027943157 scopus 로고
    • Crystal structure at 1.9-A resolution of human immunodeficiency virus (HIV) II protease complexed with L-735,524, an orally bioavailable inhibitor of the HIV proteases
    • Chen Z, Li Y, Chen E, Hall DL, Darke PL, Culberson C, Shafer JA, Kuo LC. Crystal structure at 1.9-A resolution of human immunodeficiency virus (HIV) II protease complexed with L-735, 524, an orally bioavailable inhibitor of the HIV proteases. J Biol Chem 1994; 269: 26344-26348.
    • (1994) J Biol Chem , vol.269 , pp. 26344-26348
    • Chen, Z.1    Li, Y.2    Chen, E.3    Hall, D.L.4    Darke, P.L.5    Culberson, C.6    Shafer, J.A.7    Kuo, L.C.8
  • 41
    • 46649092697 scopus 로고    scopus 로고
    • Effect of flap mutations on structure of HIV-1 protease and inhibition by saquinavir and darunavir
    • Liu F, Kovalevsky AY, Tie Y, Ghosh AK, Harrison RW, Weber IT. Effect of flap mutations on structure of HIV-1 protease and inhibition by saquinavir and darunavir. J Mol Biol 2008; 381: 102-115.
    • (2008) J Mol Biol , vol.381 , pp. 102-115
    • Liu, F.1    Kovalevsky, A.Y.2    Tie, Y.3    Ghosh, A.K.4    Harrison, R.W.5    Weber, I.T.6
  • 42
    • 0031022510 scopus 로고    scopus 로고
    • Cyclic urea amides: HIV-1 protease inhibitors with low nanomolar potency against both wild type and protease inhibitor resistant mutants of HIV
    • Jadhav PK, Ala P, Woerner FJ, Chang CH, Garber SS, Anton ED, Bacheler LT. Cyclic urea amides: HIV-1 protease inhibitors with low nanomolar potency against both wild type and protease inhibitor resistant mutants of HIV. J Med Chem 1997; 40: 181-191.
    • (1997) J Med Chem , vol.40 , pp. 181-191
    • Jadhav, P.K.1    Ala, P.2    Woerner, F.J.3    Chang, C.H.4    Garber, S.S.5    Anton, E.D.6    Bacheler, L.T.7
  • 46
    • 4243810035 scopus 로고
    • Simulation of enzyme reactions using valence bond force fields and other hybrid quantum/classical approaches
    • Aqvist J, Warshel A. Simulation of enzyme reactions using valence bond force fields and other hybrid quantum/classical approaches. Chem Rev 1993; 93: 2523-2544.
    • (1993) Chem Rev , vol.93 , pp. 2523-2544
    • Aqvist, J.1    Warshel, A.2
  • 47
    • 78049316762 scopus 로고    scopus 로고
    • Exploring challenges in rational enzyme design by simulating the catalysis in artificial kemp eliminase
    • Frushicheva MP, Cao J, Chu ZT, Warshel A. Exploring challenges in rational enzyme design by simulating the catalysis in artificial kemp eliminase. Proc Natl Acad Sci USA 2010; 107: 16869-16874.
    • (2010) Proc Natl Acad Sci USA , vol.107 , pp. 16869-16874
    • Frushicheva, M.P.1    Cao, J.2    Chu, Z.T.3    Warshel, A.4
  • 48
    • 79955625862 scopus 로고    scopus 로고
    • Challenges and advances in validating enzyme design proposals: the case of kemp eliminase catalysis
    • Frushicheva MP, Cao J, Warshel A. Challenges and advances in validating enzyme design proposals: the case of kemp eliminase catalysis. Biochemistry 2011; 50: 3849-3858.
    • (2011) Biochemistry , vol.50 , pp. 3849-3858
    • Frushicheva, M.P.1    Cao, J.2    Warshel, A.3
  • 49
    • 65249154106 scopus 로고    scopus 로고
    • Toward accurate screening in computer-aided enzyme design
    • Roca M, Vardi-Kilshtain A, Warshel A. Toward accurate screening in computer-aided enzyme design. Biochemistry 2009; 48: 3046-3056.
    • (2009) Biochemistry , vol.48 , pp. 3046-3056
    • Roca, M.1    Vardi-Kilshtain, A.2    Warshel, A.3
  • 50
    • 38549143261 scopus 로고    scopus 로고
    • Computational design and experimental study of tighter binding peptides to an inactivated mutant of HIV-1 protease
    • Altman MD, Nalivaika EA, Prabu-Jeyabalan M, Schiffer CA, Tidor B. Computational design and experimental study of tighter binding peptides to an inactivated mutant of HIV-1 protease. Proteins 2008; 70: 678-694.
    • (2008) Proteins , vol.70 , pp. 678-694
    • Altman, M.D.1    Nalivaika, E.A.2    Prabu-Jeyabalan, M.3    Schiffer, C.A.4    Tidor, B.5
  • 51
    • 0032537482 scopus 로고    scopus 로고
    • Resistance to HIV protease inhibitors: a comparison of enzyme inhibition and antiviral potency
    • Klabe RM, Bacheler LT, Ala PJ, Erickson-Viitanen S, Meek JL. Resistance to HIV protease inhibitors: a comparison of enzyme inhibition and antiviral potency. Biochemistry 1998; 37: 8735-8742.
    • (1998) Biochemistry , vol.37 , pp. 8735-8742
    • Klabe, R.M.1    Bacheler, L.T.2    Ala, P.J.3    Erickson-Viitanen, S.4    Meek, J.L.5
  • 52
    • 0028903042 scopus 로고
    • Beta secondary and solvent deuterium kinetic isotope effects and the mechanisms of base-catalyzed and acid-catalyzed hydrolysis of penicillanic acid
    • Deraniyagala SA, Adediran SA, Pratt RF. Beta secondary and solvent deuterium kinetic isotope effects and the mechanisms of base-catalyzed and acid-catalyzed hydrolysis of penicillanic acid. J Org Chem 1995; 60: 1619-1625.
    • (1995) J Org Chem , vol.60 , pp. 1619-1625
    • Deraniyagala, S.A.1    Adediran, S.A.2    Pratt, R.F.3
  • 53
    • 0015520416 scopus 로고
    • Kinetics and mechanism of decarboxylation of N-arylcarbamates. Evidence for kinetically important zwitterionic carbamic acid species of short lifetime
    • Johnson SL, Morrison DL. Kinetics and mechanism of decarboxylation of N-arylcarbamates. Evidence for kinetically important zwitterionic carbamic acid species of short lifetime. J Am Chem Soc 1972; 94: 1323-1334.
    • (1972) J Am Chem Soc , vol.94 , pp. 1323-1334
    • Johnson, S.L.1    Morrison, D.L.2
  • 54
    • 0037442916 scopus 로고    scopus 로고
    • Proton inventory study of the base-catalyzed hydrolysis of formamide. Consideration of the nucleophilic and general base mechanisms
    • Slebocka-Tilk H, Neverov AA, Brown RS. Proton inventory study of the base-catalyzed hydrolysis of formamide. Consideration of the nucleophilic and general base mechanisms. J Am Chem Soc 2003; 125: 1851-1858.
    • (2003) J Am Chem Soc , vol.125 , pp. 1851-1858
    • Slebocka-Tilk, H.1    Neverov, A.A.2    Brown, R.S.3
  • 57
    • 0030584674 scopus 로고    scopus 로고
    • Electrostatic control of GTP and GDP binding in the oncoprotein p21 ras
    • Muegge I, Schweins T, Langen R, Warshel A. Electrostatic control of GTP and GDP binding in the oncoprotein p21 ras. Structure 1996; 4: 475-489.
    • (1996) Structure , vol.4 , pp. 475-489
    • Muegge, I.1    Schweins, T.2    Langen, R.3    Warshel, A.4
  • 58
    • 33745052090 scopus 로고    scopus 로고
    • Simulating the effect of DNA polymerase mutations on transition-state energetics and fidelity: evaluating amino acid group contribution and allosteric coupling for ionized residues in human pol b
    • Xiang Y, Oelschlaeger P, Florian J, Goodman MF, Warshel A. Simulating the effect of DNA polymerase mutations on transition-state energetics and fidelity: evaluating amino acid group contribution and allosteric coupling for ionized residues in human pol b. Biochemistry 2006; 45: 7036-7048.
    • (2006) Biochemistry , vol.45 , pp. 7036-7048
    • Xiang, Y.1    Oelschlaeger, P.2    Florian, J.3    Goodman, M.F.4    Warshel, A.5
  • 59
    • 77951241004 scopus 로고    scopus 로고
    • Multiscale simulations of protein landscapes: using coarse-grained models as reference potentials to full explicit models
    • Messer BM, Roca M, Chu ZT, Vicatos S, Kilshtain AV, Warshel A. Multiscale simulations of protein landscapes: using coarse-grained models as reference potentials to full explicit models. Proteins 78: 1212-1227.
    • Proteins , vol.78 , pp. 1212-1227
    • Messer, B.M.1    Roca, M.2    Chu, Z.T.3    Vicatos, S.4    Kilshtain, A.V.5    Warshel, A.6


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.