메뉴 건너뛰기




Volumn 25, Issue 1, 2011, Pages 31-49

Computer-assisted combinatorial design of bicyclic thymidine analogs as inhibitors of Mycobacterium tuberculosis thymidine monophosphate kinase

Author keywords

ADME properties; Combinatorial library design; Gibbs free energy of binding; In silico screening; Mycobacterium tuberculosis; QSAR model; TMPK inhibitors

Indexed keywords

BINDING ENERGY; BINDING SITES; CARBOXYLATION; COMPUTATIONAL CHEMISTRY; DIGITAL LIBRARIES; ENZYMES; FREE ENERGY; MOLECULAR GRAPHICS; STRUCTURAL DESIGN;

EID: 78651245106     PISSN: 0920654X     EISSN: 15734951     Source Type: Journal    
DOI: 10.1007/s10822-010-9399-4     Document Type: Article
Times cited : (20)

References (64)
  • 1
    • 67349147683 scopus 로고    scopus 로고
    • WHO report 2009.411, World Health Organization, Geneva 1/9/2010
    • Global Tuberculosis Control-Epidemiology, Strategy, Financing (2009) WHO report 2009.411, World Health Organization, Geneva. Retrieved from http://www.who.int/tb/publications/global-report/2009/en/index.html. 1/9/2010
    • (2009) Global Tuberculosis Control-Epidemiology, Strategy, Financing
  • 2
    • 33847704942 scopus 로고    scopus 로고
    • Challenges in tuberculosis drug research and development: Commentary
    • DOI 10.1038/nm0307-290, PII NM0307290
    • AM Ginsberg M Spigelman 2007 Challenges in tuberculosis drug research and development Nat Med 13 290 294 1:CAS:528:DC%2BD2sXisVKkur4%3D 10.1038/nm0307-290 (Pubitemid 46376672)
    • (2007) Nature Medicine , vol.13 , Issue.3 , pp. 290-294
    • Ginsberg, A.M.1    Spigelman, M.2
  • 3
    • 40949133609 scopus 로고    scopus 로고
    • WHO press release, World Health Organization, Geneva 1/9/2010
    • WHO Global Task Force: Outlines Measures to Combat XDR-TB Worldwide (2006) WHO press release, World Health Organization, Geneva. Retrieved from http://www.who.int/mediacentre/news/notes/2006/np29/en/index.html. 1/9/2010
    • (2006) WHO Global Task Force: Outlines Measures to Combat XDR-TB Worldwide
  • 4
    • 65649136872 scopus 로고    scopus 로고
    • Tuberculosis pharmacotherapy: Strategies to optimize patient care
    • 1:CAS:528:DC%2BD1MXhsVaitbk%3D 10.1517/14656560802694564
    • CD Mitnick B McGee CA Peloquin 2009 Tuberculosis pharmacotherapy: strategies to optimize patient care Expert Opin Pharmacother 10 381 401 1:CAS:528:DC%2BD1MXhsVaitbk%3D 10.1517/14656560802694564
    • (2009) Expert Opin Pharmacother , vol.10 , pp. 381-401
    • Mitnick, C.D.1    McGee, B.2    Peloquin, C.A.3
  • 6
    • 33646513715 scopus 로고    scopus 로고
    • Structure-activity relationship for nucleoside analogs as inhibitors or substrates of adenosine kinase from Mycobacterium tuberculosis. I. Modifications to the adenine moiety
    • 1:CAS:528:DC%2BD28XkvVOlur8%3D 10.1016/j.bcp.2006.03.006
    • MC Long WB Parker 2006 Structure-activity relationship for nucleoside analogs as inhibitors or substrates of adenosine kinase from Mycobacterium tuberculosis. I. Modifications to the adenine moiety Biochem Pharmacol 71 1671 1682 1:CAS:528:DC%2BD28XkvVOlur8%3D 10.1016/j.bcp.2006.03.006
    • (2006) Biochem Pharmacol , vol.71 , pp. 1671-1682
    • Long, M.C.1    Parker, W.B.2
  • 7
    • 34248636300 scopus 로고    scopus 로고
    • Current strategies for identifying and validating targets for new treatment-shortening drugs for TB
    • DOI 10.2174/156652407780598575
    • KJ Williams K Duncan 2007 Current strategies for identifying and validating targets for new treatment-shortening drugs for TB Curr Mol Med 7 297 307 1:CAS:528:DC%2BD2sXlvFKqtL8%3D 10.2174/156652407780598575 (Pubitemid 46767787)
    • (2007) Current Molecular Medicine , vol.7 , Issue.3 , pp. 297-307
    • Williams, K.J.1    Duncan, K.2
  • 8
    • 0035000378 scopus 로고    scopus 로고
    • Thymidylate kinase of Mycobacterium tuberculosis: A chimera sharing properties common to eukaryotic and bacterial enzymes
    • DOI 10.1110/ps.45701
    • H Munier-Lehmann A Chafotte S Pochet G Labesse 2001 Thymidylate kinase of Mycobacterium tuberculosis: a chimera sharing properties common to eukaryotic and bacterial enzymes Protein Sci 10 1195 1205 1:CAS:528:DC%2BD3MXksFCjs78%3D 10.1110/ps.45701 (Pubitemid 32476480)
    • (2001) Protein Science , vol.10 , Issue.6 , pp. 1195-1205
    • Munier-Lehmann, H.1    Chaffotte, A.2    Pochet, S.3    Labesse, G.4
  • 9
    • 77956943185 scopus 로고
    • P.D. Boyer (eds). Academic Press New York
    • Anderson E (1973) In: Boyer PD (ed) The enzymes, vol 8. Academic Press, New York, pp 49-96
    • (1973) The Enzymes , vol.8 , pp. 49-96
    • Anderson, E.1
  • 10
    • 0038329967 scopus 로고
    • Yeast gene CDC8 encodes thymidylate kinase and is complemented by herpes thymidine kinase gene TK
    • 1:CAS:528:DyaL2MXht1ym 10.1073/pnas.81.18.5821
    • RA Sclafani WL Fangman 1984 Yeast gene CDC8 encodes thymidylate kinase and is complemented by herpes thymidine kinase gene TK Proc Natl Acad Sci USA 81 5821 5825 1:CAS:528:DyaL2MXht1ym 10.1073/pnas.81.18.5821
    • (1984) Proc Natl Acad Sci USA , vol.81 , pp. 5821-5825
    • Sclafani, R.A.1    Fangman, W.L.2
  • 11
    • 0035800652 scopus 로고    scopus 로고
    • X-ray structure of TMP kinase from Mycobacterium tuberculosis complexed with TMP at 1.95 A resolution
    • DOI 10.1006/jmbi.2001.4843
    • I Li de la Sierra H Munier-Lehmann AM Gilles O Bârzu M Delarue 2001 X-ray structure of TMP kinase from Mycobacterium tuberculosis complexed with TMP at 1.95 A resolution J Mol Biol 311 87 100 10.1006/jmbi.2001.4843 (Pubitemid 32735316)
    • (2001) Journal of Molecular Biology , vol.311 , Issue.1 , pp. 87-100
    • Li De La Sierra, I.1    Munier-Lehmann, H.2    Gilles, A.M.3    Barzu, O.4    Delarue, M.5
  • 13
    • 0037037402 scopus 로고    scopus 로고
    • Synthesis and evaluation of thymidine-5′-O-monophosphate analogues as inhibitors of Mycobacterium tuberculosis thymidylate kinase
    • DOI 10.1016/S0960-894X(02)00551-6, PII S0960894X02005516
    • V Vanheusden H Munier-Lehmann S Pochet P Herdewijna S Van Calenbergh 2002 Synthesis and evaluation of thymidine-5′-O-monophosphate analogues as inhibitors of Mycobacterium tuberculosis thymidylate kinase Bioorg Med Chem Lett 12 2695 2698 1:CAS:528:DC%2BD38XmslGisbY%3D 10.1016/S0960-894X(02)00551-6 (Pubitemid 35247620)
    • (2002) Bioorganic and Medicinal Chemistry Letters , vol.12 , Issue.19 , pp. 2695-2698
    • Vanheusden, V.1    Munier-Lehmann, H.2    Pochet, S.3    Herdewijn, P.4    Van Calenbergh, S.5
  • 14
    • 9744241646 scopus 로고    scopus 로고
    • Discovery of bicyclic thymidine analogues as selective and high-affinity inhibitors of Mycobacterium tuberculosis thymidine monophosphate kinase
    • DOI 10.1021/jm040847w
    • V Vanheusden H Munier-Lehmann M Froeyen R Busson J Rozenski P Herdewijn S Van Calenbergh 2004 Discovery of bicyclic thymidine analogues as selective and high-affinity inhibitors of Mycobacterium tuberculosis thymidine monophosphate kinase J Med Chem 47 6187 6194 1:CAS:528:DC%2BD2cXpt1Sktbo%3D 10.1021/jm040847w (Pubitemid 39587243)
    • (2004) Journal of Medicinal Chemistry , vol.47 , Issue.25 , pp. 6187-6194
    • Vanheusden, V.1    Munier-Lehmann, H.2    Froeyen, M.3    Busson, R.4    Rozenski, J.5    Herdewijn, P.6    Van Calenbergh, S.7
  • 15
    • 0038136960 scopus 로고    scopus 로고
    • Enzymatic and structural analysis of inhibitors designed against Mycobacterium tuberculosis thymidylate kinase: New insights into the phosphoryl transfer mechanism
    • DOI 10.1074/jbc.M209630200
    • A Haouz V Vanheusden H Munier-Lehmann M Froeyen P Herdewijn S Van Calenbergh M Delarue 2003 Enzymatic and structural analysis of inhibitors designed against Mycobacterium tuberculosis thymidylate kinase. New insights into the phosphoryl transfer mechanism J Biol Chem 278 4963 4971 1:CAS:528:DC%2BD3sXhtVKltr8%3D 10.1074/jbc.M209630200 (Pubitemid 36801005)
    • (2003) Journal of Biological Chemistry , vol.278 , Issue.7 , pp. 4963-4971
    • Haouz, A.1    Vanheusden, V.2    Munier-Lehmann, H.3    Froeyen, M.4    Herdewijn, P.5    Van Calenbergh, S.6    Delarue, M.7
  • 16
    • 0037016645 scopus 로고    scopus 로고
    • Nucleoside analogues as inhibitors of thymidylate kinases: Possible therapeutic applications
    • DOI 10.1002/1439-7633(20020104)3 :1<108::AID-CBIC108>3.0.CO;2-B
    • S Pochet L Dugué D Douguet G Labesse H Munier-Lehmann 2002 Nucleoside analogues as inhibitors of thymidylate kinases: possible therapeutic applications ChemBioChem 3 108 110 1:CAS:528:DC%2BD38XkvFWjtw%3D%3D 10.1002/1439-7633(20020104)3:1<108::AID-CBIC108>3.0.CO;2-B (Pubitemid 34464803)
    • (2002) ChemBioChem , vol.3 , Issue.1 , pp. 108-110
    • Pochet, S.1    Dugue, L.2    Douguet, D.3    Labesse, G.4    Munier-Lehmann, H.5
  • 17
    • 0041519319 scopus 로고    scopus 로고
    • Thymidine and thymidine-5′-O-monophosphate analogues as inhibitors of Mycobacterium tuberculosis thymidylate kinase
    • DOI 10.1016/S0960-894X(03)00643-7
    • V Vanheusden P Van Rompaey H Munier-Lehmann S Pochet P Herdewijn S Van Calenbergh 2003 Thymidine and thymidine-5′-O-monophosphate analogues as inhibitors of Mycobacterium tuberculosis thymidylate kinase Bioorg Med Chem Lett 13 3045 3048 1:CAS:528:DC%2BD3sXms1Gmtrw%3D 10.1016/S0960-894X(03)00643-7 (Pubitemid 36993633)
    • (2003) Bioorganic and Medicinal Chemistry Letters , vol.13 , Issue.18 , pp. 3045-3048
    • Vanheusden, V.1    Van Rompaey, P.2    Munier-Lehmann, H.3    Pochet, S.4    Herdewijn, P.5    Van Calenbergh, S.6
  • 19
    • 0042970469 scopus 로고    scopus 로고
    • Comparative study of purine and pyrimidine nucleoside analogues acting on the thymidylate kinases of Mycobacterium tuberculosis and of humans
    • DOI 10.1002/cbic.200300608
    • S Pochet L Dugué G Labesse M Delepierre H Munier-Lehmann 2003 Comparative study of purine and pyrimidine nucleoside analogues acting on the thymidylate kinases of Mycobacterium tuberculosis and of humans ChemBioChem 4 742 747 1:CAS:528:DC%2BD3sXmtlyksro%3D 10.1002/cbic.200300608 (Pubitemid 37010599)
    • (2003) ChemBioChem , vol.4 , Issue.8 , pp. 742-747
    • Pochet, S.1    Dugue, L.2    Labesse, G.3    Delepierre, M.4    Munier-Lehmann, H.5
  • 21
    • 35848946837 scopus 로고    scopus 로고
    • Rational design of 5′-thiourea-substituted α-thymidine analogues as thymidine monophosphate kinase inhibitors capable of inhibiting mycobacterial growth
    • DOI 10.1021/jm0706158
    • I Van Daele H Munier-Lehmann M Froeyen J Balzarini S Van Calenbergh 2007 Rational design of 5′-thiourea-substituted alpha-thymidine analogues as thymidine monophosphate kinase inhibitors capable of inhibiting mycobacterial growth J Med Chem 50 5281 5292 10.1021/jm0706158 (Pubitemid 350057840)
    • (2007) Journal of Medicinal Chemistry , vol.50 , Issue.22 , pp. 5281-5292
    • Van Daele, I.1    Munier-Lehmann, H.2    Froeyen, M.3    Balzarini, J.4    Van Calenbergh, S.5
  • 22
    • 44449114750 scopus 로고    scopus 로고
    • Substituted benzyl-pyrimidines targeting thymidine monophosphate kinase of Mycobacterium tuberculosis: Synthesis and in vitro anti-mycobacterial activity
    • DOI 10.1016/j.bmc.2008.04.045, PII S0968089608003738
    • C Gasse D Douguet V Huteau G Marchal H Munier-Lehmann S Pochet 2008 Substituted benzyl-pyrimidines targeting thymidine monophosphate kinase of Mycobacterium tuberculosis: synthesis and in vitro anti-mycobacterial activity Bioorg Med Chem 16 6075 6085 1:CAS:528:DC%2BD1cXmvFegtLo%3D 10.1016/j.bmc.2008. 04.045 (Pubitemid 351766718)
    • (2008) Bioorganic and Medicinal Chemistry , vol.16 , Issue.11 , pp. 6075-6085
    • Gasse, C.1    Douguet, D.2    Huteau, V.3    Marchal, G.4    Munier-Lehmann, H.5    Pochet, S.6
  • 24
    • 23644443977 scopus 로고    scopus 로고
    • Combinatorial design of nonsymmetrical cyclic urea inhibitors of aspartic protease of HIV-1
    • DOI 10.1016/j.bmc.2005.06.026, PII S0968089605005420
    • V Frecer E Burello S Miertus 2005 Combinatorial design of nonsymmetrical cyclic urea inhibitors of aspartic protease of HIV-1 Bioorg Med Chem 13 5492 5501 1:CAS:528:DC%2BD2MXnslyjsrs%3D 10.1016/j.bmc.2005.06.026 (Pubitemid 41132625)
    • (2005) Bioorganic and Medicinal Chemistry , vol.13 , Issue.18 , pp. 5492-5501
    • Frecer, V.1    Burello, E.2    Miertus, S.3
  • 25
    • 67349188389 scopus 로고    scopus 로고
    • Design and in silico screening of combinatorial library of antimalarial analogs of triclosan inhibiting Plasmodium falciparum enoyl-acyl carrier protein reductase
    • 1:CAS:528:DC%2BD1MXltl2lur4%3D 10.1016/j.ejmech.2008.12.028
    • V Frecer E Megnassan S Miertus 2009 Design and in silico screening of combinatorial library of antimalarial analogs of triclosan inhibiting Plasmodium falciparum enoyl-acyl carrier protein reductase Eur J Med Chem 44 3009 3019 1:CAS:528:DC%2BD1MXltl2lur4%3D 10.1016/j.ejmech.2008.12.028
    • (2009) Eur J Med Chem , vol.44 , pp. 3009-3019
    • Frecer, V.1    Megnassan, E.2    Miertus, S.3
  • 26
    • 62349104787 scopus 로고    scopus 로고
    • Design of oseltamivir analogs inhibiting neuraminidase of avian influenza virus H5N1
    • 1:CAS:528:DC%2BD1MXjsV2mtLg%3D 10.1016/j.antiviral.2009.01.008
    • T Rungrotmongkol V Frecer W De-Eknamkul S Hannongbua S Miertus 2009 Design of oseltamivir analogs inhibiting neuraminidase of avian influenza virus H5N1 Antivir Res 82 51 58 1:CAS:528:DC%2BD1MXjsV2mtLg%3D 10.1016/j.antiviral. 2009.01.008
    • (2009) Antivir Res , vol.82 , pp. 51-58
    • Rungrotmongkol, T.1    Frecer, V.2    De-Eknamkul, W.3    Hannongbua, S.4    Miertus, S.5
  • 27
    • 77949855256 scopus 로고    scopus 로고
    • Combinatorial design of avian influenza neuraminidase inhibitors containing pyrrolidine core with a reduced susceptibility to viral drug resistance
    • 1:CAS:528:DC%2BC3cXkvFGqsrk%3D 10.2174/138620710790980504
    • T Rungrotmongkol T Udommaneethanakit V Frecer S Miertus 2010 Combinatorial design of avian influenza neuraminidase inhibitors containing pyrrolidine core with a reduced susceptibility to viral drug resistance Comb Chem High Throughput Screen 13 268 277 1:CAS:528:DC%2BC3cXkvFGqsrk%3D 10.2174/138620710790980504
    • (2010) Comb Chem High Throughput Screen , vol.13 , pp. 268-277
    • Rungrotmongkol, T.1    Udommaneethanakit, T.2    Frecer, V.3    Miertus, S.4
  • 28
    • 77954942481 scopus 로고    scopus 로고
    • Design, structure-based focusing and in silico screening of combinatorial library of peptidomimetic inhibitors of Dengue virus NS2B-NS3 protease
    • 1:CAS:528:DC%2BC3cXltV2jtLg%3D 10.1007/s10822-010-9326-8
    • V Frecer S Miertus 2010 Design, structure-based focusing and in silico screening of combinatorial library of peptidomimetic inhibitors of Dengue virus NS2B-NS3 protease J Comput Aided Mol Des 24 195 212 1:CAS:528: DC%2BC3cXltV2jtLg%3D 10.1007/s10822-010-9326-8
    • (2010) J Comput Aided Mol des , vol.24 , pp. 195-212
    • Frecer, V.1    Miertus, S.2
  • 30
    • 2542482709 scopus 로고    scopus 로고
    • Novel bicyclic sugar modified nucleosides: Synthesis, conformational analysis and antiviral evaluation
    • DOI 10.1016/j.bmc.2004.03.072, PII S0968089604002755
    • N Kifli E De Clercq J Balzarini C Simons 2004 Novel bicyclic sugar modified nucleosides: synthesis, conformational analysis and antiviral evaluation Bioorg Med Chem 12 3247 4252 1:CAS:528:DC%2BD2cXkt1Snu7c%3D 10.1016/j.bmc.2004.03.072 (Pubitemid 38680714)
    • (2004) Bioorganic and Medicinal Chemistry , vol.12 , Issue.12 , pp. 3247-3257
    • Kifli, N.1    Htar, T.T.2    De Clercq, E.3    Balzarini, J.4    Simons, C.5
  • 31
    • 85135598060 scopus 로고    scopus 로고
    • version 4.6 (2002) Accelrys, San Diego, CA
    • 2 Life Sciences software, version 4.6 (2002) Accelrys, San Diego, CA
    • 2 Life Sciences Software
  • 32
    • 0029935202 scopus 로고    scopus 로고
    • The automatic search for ligand binding sites in proteins of known three-dimensional structure using only geometric criteria
    • DOI 10.1006/jmbi.1996.0077
    • KP Peters J Fauck C Frommel 1996 The automatic search for ligand binding sites in proteins of known three-dimensional structure using only geometric criteria J Mol Biol 256 201 213 1:CAS:528:DyaK28XhtVCks7k%3D 10.1006/jmbi.1996.0077 (Pubitemid 26104219)
    • (1996) Journal of Molecular Biology , vol.256 , Issue.1 , pp. 201-213
    • Peters, K.P.1    Fauck, J.2    Frommel, C.3
  • 33
    • 0015680655 scopus 로고
    • Clustering using a similarity measure based on shared near neighbors
    • 10.1109/T-C.1973.223640
    • RA Jarvis EA Patrick 1973 Clustering using a similarity measure based on shared near neighbors IEEE Trans Comput C22 1025 1034 10.1109/T-C.1973.223640
    • (1973) IEEE Trans Comput , vol.22 , pp. 1025-1034
    • Jarvis, R.A.1    Patrick, E.A.2
  • 34
    • 67349104587 scopus 로고    scopus 로고
    • Targeted scoring functions for virtual screening
    • 10.1016/j.drudis.2009.03.013
    • MH Seifert 2009 Targeted scoring functions for virtual screening Drug Discov Today 14 562 569 10.1016/j.drudis.2009.03.013
    • (2009) Drug Discov Today , vol.14 , pp. 562-569
    • Seifert, M.H.1
  • 35
    • 0028454828 scopus 로고
    • The development of a simple empirical scoring function to estimate the binding constant for a protein-ligand complex of known three-dimensional structure
    • 10.1007/BF00126743
    • HJ Böhm 1994 The development of a simple empirical scoring function to estimate the binding constant for a protein-ligand complex of known three-dimensional structure J Comput Aided Mol Des 8 243 256 10.1007/BF00126743
    • (1994) J Comput Aided Mol des , vol.8 , pp. 243-256
    • Böhm, H.J.1
  • 36
    • 0028522983 scopus 로고
    • On the use of LUDI to search the Fine Chemicals Directory for ligands of proteins of known three-dimensional structure
    • 10.1007/BF00123669
    • HJ Böhm 1994 On the use of LUDI to search the Fine Chemicals Directory for ligands of proteins of known three-dimensional structure J Comput Aided Mol Des 8 623 632 10.1007/BF00123669
    • (1994) J Comput Aided Mol des , vol.8 , pp. 623-632
    • Böhm, H.J.1
  • 37
    • 0033545622 scopus 로고    scopus 로고
    • A general and fast scoring function for protein-ligand interactions: A simplified potential approach
    • DOI 10.1021/jm980536j
    • I Muegge YC Martin 1999 A general and fast scoring function for protein-ligand interactions: a simplified potential approach J Med Chem 42 791 804 1:CAS:528:DyaK1MXht1aksrk%3D 10.1021/jm980536j (Pubitemid 29136170)
    • (1999) Journal of Medicinal Chemistry , vol.42 , Issue.5 , pp. 791-804
    • Muegge, I.1    Martin, Y.C.2
  • 38
    • 0033566211 scopus 로고    scopus 로고
    • Evaluation of PMF scoring in docking weak ligands to the FK506 binding protein
    • DOI 10.1021/jm990073x
    • I Muegge YC Martin PJ Hajduk SW Fesik 1999 Evaluation of PMF scoring in docking weak ligands to the FK506 binding protein J Med Chem 42 2498 2503 1:CAS:528:DyaK1MXktVWhtb8%3D 10.1021/jm990073x (Pubitemid 29344291)
    • (1999) Journal of Medicinal Chemistry , vol.42 , Issue.14 , pp. 2498-2503
    • Muegge, I.1    Martin, Y.C.2    Hajduk, P.J.3    Fesik, S.W.4
  • 39
    • 0001745748 scopus 로고    scopus 로고
    • Effect of Ligand Volume Correction on PMF Scoring
    • DOI 10.1002/1096-987X(200103)22 :4<418::AID-JCC1012>3.0.CO;2-3
    • I Muegge 2001 Effect of Ligand Volume Correction on PMF Scoring J Comput Chem 22 418 425 1:CAS:528:DC%2BD3MXhs1Oht7w%3D 10.1002/1096-987X(200103)22: 4<418::AID-JCC1012>3.0.CO;2-3 (Pubitemid 33640780)
    • (2001) Journal of Computational Chemistry , vol.22 , Issue.4 , pp. 418-425
    • Muegge, I.1
  • 40
    • 0029294584 scopus 로고
    • Molecular recognition of the inhibitor AG-1343 by HIV-1 protease: Conformationally flexible docking by evolutionary programming
    • 1:CAS:528:DyaK2MXmvVClsbg%3D 10.1016/1074-5521(95)90050-0
    • DK Gehlhaar GM Verkhivker PA Rejto CJ Sherman DB Fogel LJ Fogel ST Freer 1995 Molecular recognition of the inhibitor AG-1343 by HIV-1 protease: conformationally flexible docking by evolutionary programming Chem Biol 2 317 324 1:CAS:528:DyaK2MXmvVClsbg%3D 10.1016/1074-5521(95)90050-0
    • (1995) Chem Biol , vol.2 , pp. 317-324
    • Gehlhaar, D.K.1    Verkhivker, G.M.2    Rejto, P.A.3    Sherman, C.J.4    Fogel, D.B.5    Fogel, L.J.6    Freer, S.T.7
  • 43
    • 11144255694 scopus 로고    scopus 로고
    • Evaluation of library ranking efficacy in virtual screening
    • DOI 10.1002/jcc.20141
    • M Kontoyianni GS Sokol LM McClellan 2005 Evaluation of library ranking efficacy in virtual screening J Comput Chem 26 11 22 1:CAS:528: DC%2BD2cXhtFaiur3M 10.1002/jcc.20141 (Pubitemid 40021619)
    • (2005) Journal of Computational Chemistry , vol.26 , Issue.1 , pp. 11-22
    • Kontoyianni, M.1    Sokol, G.S.2    Mcclellan, L.M.3
  • 44
    • 2942720960 scopus 로고    scopus 로고
    • Impact of scoring functions on enrichment in docking-based virtual screening: An application study on renin inhibitors
    • 1:CAS:528:DC%2BD2cXivVagur8%3D
    • EM Krovat T Langer 2004 Impact of scoring functions on enrichment in docking-based virtual screening: an application study on renin inhibitors J Chem Inf Comput Sci 44 1123 1129 1:CAS:528:DC%2BD2cXivVagur8%3D
    • (2004) J Chem Inf Comput Sci , vol.44 , pp. 1123-1129
    • Krovat, E.M.1    Langer, T.2
  • 45
    • 0037763817 scopus 로고    scopus 로고
    • Comparative evaluation of 11 scoring functions for molecular docking
    • DOI 10.1021/jm0203783
    • R Wang Y Lu S Wang 2003 Comparative evaluation of 11 scoring functions for molecular docking J Med Chem 47 2287 2303 10.1021/jm0203783 (Pubitemid 36637914)
    • (2003) Journal of Medicinal Chemistry , vol.46 , Issue.12 , pp. 2287-2303
    • Wang, R.1    Lu, Y.2    Wang, S.3
  • 47
    • 84962338894 scopus 로고    scopus 로고
    • Design of peptidomimetic inhibitors of aspartic protease of HIV-1 including-PheΨPro-core and favorable ADME properties
    • 1:CAS:528:DC%2BD1cXht1KnsLrM 10.1016/j.jmgm.2008.06.006
    • V Frecer F Berti F Benedetti S Miertus 2008 Design of peptidomimetic inhibitors of aspartic protease of HIV-1 including-PheΨPro-core and favorable ADME properties J Mol Graphics Model 27 376 387 1:CAS:528: DC%2BD1cXht1KnsLrM 10.1016/j.jmgm.2008.06.006
    • (2008) J Mol Graphics Model , vol.27 , pp. 376-387
    • Frecer, V.1    Berti, F.2    Benedetti, F.3    Miertus, S.4
  • 48
    • 84986527718 scopus 로고
    • Derivation of class II force fields. I. Methodology and quantum force field for the alkyl functional group and alkane molecules
    • 1:CAS:528:DyaK2cXhvFSlt7s%3D 10.1002/jcc.540150207
    • JR Maple MJ Hwang TP Stockfish U Dinur M Waldman CS Ewing AT Hagler 1994 Derivation of class II force fields. I. Methodology and quantum force field for the alkyl functional group and alkane molecules J Comput Chem 15 162 182 1:CAS:528:DyaK2cXhvFSlt7s%3D 10.1002/jcc.540150207
    • (1994) J Comput Chem , vol.15 , pp. 162-182
    • Maple, J.R.1    Hwang, M.J.2    Stockfish, T.P.3    Dinur, U.4    Waldman, M.5    Ewing, C.S.6    Hagler, A.T.7
  • 50
    • 0034728673 scopus 로고    scopus 로고
    • Prediction of properties from simulations: Free energies of solvation in hexadecane, octanol, and water
    • DOI 10.1021/ja993663t
    • EM Duffy WL Jorgensen 2000 Prediction of properties from simulations: free energies of solvation in hexadecane, octanol, and water J Am Chem Soc 122 2878 2888 1:CAS:528:DC%2BD3cXhsFyhtro%3D 10.1021/ja993663t (Pubitemid 30191048)
    • (2000) Journal of the American Chemical Society , vol.122 , Issue.12 , pp. 2878-2888
    • Duffy, E.M.1    Jorgensen, W.L.2
  • 51
    • 0034608316 scopus 로고    scopus 로고
    • Prediction of drug solubility from Monte Carlo simulations
    • DOI 10.1016/S0960-894X(00)00172-4, PII S0960894X00001724
    • WL Jorgensen EM Duffy 2000 Prediction of drug solubility from Monte Carlo simulations Bioorg Med Chem Lett 10 1155 1158 1:CAS:528:DC%2BD3cXktF2qtro%3D 10.1016/S0960-894X(00)00172-4 (Pubitemid 30345080)
    • (2000) Bioorganic and Medicinal Chemistry Letters , vol.10 , Issue.11 , pp. 1155-1158
    • Jorgensen, W.L.1    Duffy, E.M.2
  • 52
    • 0037204544 scopus 로고    scopus 로고
    • Prediction of drug solubility from structure
    • DOI 10.1016/S0169-409X(02)00008-X, PII S0169409X0200008X
    • WL Jorgensen EM Duffy 2002 Prediction of drug solubility from structure Adv Drug Deliv Rev 54 355 366 1:CAS:528:DC%2BD38Xitlartbc%3D 10.1016/S0169-409X(02)00008-X (Pubitemid 34260958)
    • (2002) Advanced Drug Delivery Reviews , vol.54 , Issue.3 , pp. 355-366
    • Jorgensen, W.L.1    Duffy, E.M.2
  • 53
    • 33748481964 scopus 로고
    • Charge equilibration for molecular dynamics simulations
    • 10.1021/j100161a070
    • AK Rappé WA Goddard III 1991 Charge equilibration for molecular dynamics simulations J Phys Chem 95 3358 3363 10.1021/j100161a070
    • (1991) J Phys Chem , vol.95 , pp. 3358-3363
    • Rappé, A.K.1    Goddard Iii, W.A.2
  • 54
    • 84860062463 scopus 로고    scopus 로고
    • version 3.0, Symyx Technologies, Santa Clara, CA
    • Available Chemicals Directory, version 3.0, Symyx Technologies, Santa Clara, CA
    • Available Chemicals Directory
  • 55
    • 0028291887 scopus 로고
    • Improved spectrophotometric assay of nucleoside monophosphate kinase activity using the pyruvate kinase/lactate dehydrogenase coupling system
    • DOI 10.1006/abio.1994.1326
    • C Blondin L Serina L Wiesmüller AM Gilles O Bârzu 1994 Improved spectrophotometric assay of nucleoside monophosphate kinase activity using the pyruvate kinase/lactate dehydrogenase coupling system Anal Biochem 220 219 222 1:CAS:528:DyaK2cXlslenu7w%3D 10.1006/abio.1994.1326 (Pubitemid 24227246)
    • (1994) Analytical Biochemistry , vol.220 , Issue.1 , pp. 219-221
    • Blondin, C.1    Serina, L.2    Wiesmuller, L.3    Gilles, A.-M.4    Barzu, O.5
  • 58
    • 0034212858 scopus 로고    scopus 로고
    • Use of MM-PBSA in estimating the free energies of proteins: Application to native, intermediates, nand unfolded villin headpiece
    • 1:CAS:528:DC%2BD3cXjslChs7g%3D 10.1002/(SICI)1097-0134 (20000601)39:4<309::AID-PROT40>3.0.CO;2-S
    • MR Lee Y Duan PA Kollman 2000 Use of MM-PBSA in estimating the free energies of proteins: application to native, intermediates, nand unfolded villin headpiece Proteins Struct Funct Genet 39 309 316 1:CAS:528:DC%2BD3cXjslChs7g%3D 10.1002/(SICI)1097-0134(20000601)39:4<309::AID-PROT40>3.0.CO;2-S
    • (2000) Proteins Struct Funct Genet , vol.39 , pp. 309-316
    • Lee, M.R.1    Duan, Y.2    Kollman, P.A.3
  • 59
    • 0034811498 scopus 로고    scopus 로고
    • Use of MM-PBSA in reproducing the binding free energies to HIV-1 RT of TIBO derivatives and predicting the binding mode to HIV-1 RT of efavirenz by docking and MM-PBSA
    • DOI 10.1021/ja003834q
    • J Wang P Morin W Wang PA Kollman 2001 Use of MM-PBSA in reproducing the binding free energies to HIV-1 RT of TIBO derivatives and predicting the binding mode to HIV-1 RT of efavirenz by docking and MM-PBSA J Am Chem Soc 123 5221 5230 1:CAS:528:DC%2BD3MXjtlyqtrc%3D 10.1021/ja003834q (Pubitemid 32910665)
    • (2001) Journal of the American Chemical Society , vol.123 , Issue.22 , pp. 5221-5230
    • Wang, J.1    Morin, P.2    Wang, W.3    Kollman, P.A.4
  • 60
    • 0026110673 scopus 로고
    • The inclusion of electrostatic hydration energies in molecular mechanics calculations
    • 1:CAS:528:DyaK3MXlt1Shtr0%3D 10.1007/BF00173467
    • MK Gilson B Honig 1991 The inclusion of electrostatic hydration energies in molecular mechanics calculations J Comput Aided Mol Des 5 5 20 1:CAS:528:DyaK3MXlt1Shtr0%3D 10.1007/BF00173467
    • (1991) J Comput Aided Mol des , vol.5 , pp. 5-20
    • Gilson, M.K.1    Honig, B.2
  • 61
    • 0037080244 scopus 로고    scopus 로고
    • Rapid grid-based construction of the molecular surface and the use of induced surface charge to calculate reaction field energies: Applications to the molecular systems and geometric objects
    • DOI 10.1002/jcc.1161
    • W Rocchia S Sridharan A Nicholls E Alexov A Chiabrer B Honig 2002 Rapid grid-based construction of the molecular surface and the use of induced surface charge to calculate reaction field energies: applications to the molecular systems and geometric objects J Comput Chem 23 128 137 1:CAS:528: DC%2BD38Xht1KqsQ%3D%3D 10.1002/jcc.1161 (Pubitemid 34063137)
    • (2002) Journal of Computational Chemistry , vol.23 , Issue.1 , pp. 128-137
    • Rocchia, W.1    Sridharan, S.2    Nicholls, A.3    Alexov, E.4    Chiabrera, A.5    Honig, B.6
  • 62
    • 0035940247 scopus 로고    scopus 로고
    • Dissecting the vibrational entropy change on protein/ligand binding: Burial of a water molecule in bovine pancreatic trypsin inhibitor
    • DOI 10.1021/jp0120920
    • S Fischer JC Smith C Verma 2001 Dissecting the vibrational entropy change on protein/ligand binding: burial of a water molecule in bovine pancreatic trypsin inhibitor J Phys Chem B 105 8050 8055 1:CAS:528:DC%2BD3MXlsFels7c%3D 10.1021/jp0120920 (Pubitemid 35338875)
    • (2001) Journal of Physical Chemistry B , vol.105 , Issue.33 , pp. 8050-8055
    • Fischer, S.1    Smith, J.C.2    Verma, C.S.3
  • 63
    • 0036722785 scopus 로고    scopus 로고
    • Can the calculation of ligand binding free energies be improved with continuum solvent electrostatics and an ideal-gas entropy correction?
    • DOI 10.1002/jcc.10112
    • SM Schwarzl TB Tschopp JC Smith S Fischer 2002 Can the calculation of ligand binding free energies be improved with continuum solvent electrostatics and an ideal-gas entropy correction? J Comput Chem 23 1143 1149 1:CAS:528:DC%2BD38XlvV2hurk%3D 10.1002/jcc.10112 (Pubitemid 34854445)
    • (2002) Journal of Computational Chemistry , vol.23 , Issue.12 , pp. 1143-1149
    • Schwarzl, S.M.1    Tschopp, T.B.2    Smith, J.C.3    Fischer, S.4
  • 64
    • 0035289779 scopus 로고    scopus 로고
    • Experimental and computational approaches to estimate solubility and permeability in drug discovery and development settings
    • DOI 10.1016/S0169-409X(00)00129-0, PII S0169409X00001290
    • CA Lipinski F Lombardo BW Dominy PJ Feeney 2001 Experimental and computational approaches to estimate solubility and permeability in drug discovery and development settings Adv Drug Delivery Rev 46 3 26 1:CAS:528:DC%2BD3MXitVOhs7o%3D 10.1016/S0169-409X(00)00129-0 (Pubitemid 33653411)
    • (2000) Advanced Drug Delivery Reviews , vol.46 , Issue.1-3 , pp. 3-26
    • Lipinski, C.A.1    Lombardo, F.2    Dominy, B.W.3    Feeney, P.J.4


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.