메뉴 건너뛰기




Volumn 56, Issue 15, 2013, Pages 6175-6189

Pharmacophore binding motifs for nicotinamide adenine dinucleotide analogues across multiple protein families: A detailed contact-based analysis of the interaction between proteins and NAD(P) cofactors

Author keywords

[No Author keywords available]

Indexed keywords

ADENINE NUCLEOTIDE DERIVATIVE; NICOTINAMIDE DERIVATIVE; PYROPHOSPHATE;

EID: 84881447803     PISSN: 00222623     EISSN: 15204804     Source Type: Journal    
DOI: 10.1021/jm400644z     Document Type: Article
Times cited : (11)

References (44)
  • 1
    • 0023989973 scopus 로고
    • Inhibin: Definition and nomenclature, including related substances
    • Burger, H. G.; Igarashi, M. Inhibin: definition and nomenclature, including related substances Endocrinology 1988, 122, 1701-1702
    • (1988) Endocrinology , vol.122 , pp. 1701-1702
    • Burger, H.G.1    Igarashi, M.2
  • 2
    • 67650649489 scopus 로고    scopus 로고
    • IMP dehydrogenase: Structure, mechanism, and inhibition
    • Hedstrom, L. IMP dehydrogenase: structure, mechanism, and inhibition Chem. Rev. 2009, 109, 2903-2928
    • (2009) Chem. Rev. , vol.109 , pp. 2903-2928
    • Hedstrom, L.1
  • 7
    • 77649133016 scopus 로고    scopus 로고
    • NAD+ depletion is necessary and sufficient for poly(ADP-ribose) polymerase-1-mediated neuronal death
    • Alano, C. C.; Garnier, P.; Ying, W.; Higashi, Y.; Kauppinen, T. M.; Swanson, R. A. NAD+ depletion is necessary and sufficient for poly(ADP-ribose) polymerase-1-mediated neuronal death J. Neurosci. 2010, 30, 2967-2978
    • (2010) J. Neurosci. , vol.30 , pp. 2967-2978
    • Alano, C.C.1    Garnier, P.2    Ying, W.3    Higashi, Y.4    Kauppinen, T.M.5    Swanson, R.A.6
  • 8
    • 0036890399 scopus 로고    scopus 로고
    • The cytochrome P450 superfamily: Biochemistry, evolution and drug metabolism in humans
    • Danielson, P. B. The cytochrome P450 superfamily: biochemistry, evolution and drug metabolism in humans Curr. Drug Metab. 2002, 3, 561-597
    • (2002) Curr. Drug Metab. , vol.3 , pp. 561-597
    • Danielson, P.B.1
  • 10
    • 0345133299 scopus 로고    scopus 로고
    • The isoniazid-NAD adduct is a slow, tight-binding inhibitor of InhA, the Mycobacterium tuberculosis enoyl reductase: Adduct affinity and drug resistance
    • Rawat, R.; Whitty, A.; Tonge, P. J. The isoniazid-NAD adduct is a slow, tight-binding inhibitor of InhA, the Mycobacterium tuberculosis enoyl reductase: adduct affinity and drug resistance Proc. Natl. Acad. Sci. U. S. A. 2003, 100, 13881-13886
    • (2003) Proc. Natl. Acad. Sci. U. S. A. , vol.100 , pp. 13881-13886
    • Rawat, R.1    Whitty, A.2    Tonge, P.J.3
  • 13
    • 0035931561 scopus 로고    scopus 로고
    • A disubstituted NAD+ analogue is a nanomolar inhibitor of trypanosomal glyceraldehyde-3-phosphate dehydrogenase
    • Kennedy, K. J.; Bressi, J. C.; Gelb, M. H. A disubstituted NAD+ analogue is a nanomolar inhibitor of trypanosomal glyceraldehyde-3-phosphate dehydrogenase Bioorg. Med. Chem. Lett. 2001, 11, 95-98
    • (2001) Bioorg. Med. Chem. Lett. , vol.11 , pp. 95-98
    • Kennedy, K.J.1    Bressi, J.C.2    Gelb, M.H.3
  • 14
    • 0035368077 scopus 로고    scopus 로고
    • Conformational changes in Leishmania mexicana glyceraldehyde-3-phosphate dehydrogenase induced by designed inhibitors
    • Suresh, S.; Bressi, J. C.; Kennedy, K. J.; Verlinde, C. L. M. J.; Gelb, M. H.; Hol, W. G. J. Conformational changes in Leishmania mexicana glyceraldehyde-3-phosphate dehydrogenase induced by designed inhibitors J. Mol. Biol. 2001, 309, 423-435
    • (2001) J. Mol. Biol. , vol.309 , pp. 423-435
    • Suresh, S.1    Bressi, J.C.2    Kennedy, K.J.3    Verlinde, C.L.M.J.4    Gelb, M.H.5    Hol, W.G.J.6
  • 15
    • 0033538049 scopus 로고    scopus 로고
    • Chloroquine Binds in the Cofactor Binding Site of Plasmodium falciparum Lactate Dehydrogenase
    • Read, J. A.; Wilkinson, K. W.; Tranter, R.; Sessions, R. B.; Brady, R. L. Chloroquine Binds in the Cofactor Binding Site of Plasmodium falciparum Lactate Dehydrogenase J. Biol. Chem. 1999, 274, 10213-10218
    • (1999) J. Biol. Chem. , vol.274 , pp. 10213-10218
    • Read, J.A.1    Wilkinson, K.W.2    Tranter, R.3    Sessions, R.B.4    Brady, R.L.5
  • 16
    • 0017187837 scopus 로고
    • Exploring structural homology of proteins
    • Rossmann, M. G.; Argos, P. Exploring structural homology of proteins J. Mol. Biol. 1976, 105, 75-95
    • (1976) J. Mol. Biol. , vol.105 , pp. 75-95
    • Rossmann, M.G.1    Argos, P.2
  • 17
    • 0036396532 scopus 로고    scopus 로고
    • GXXXG and GXXXA Motifs Stabilize FAD and NAD(P)-binding Rossmann Folds Through Cα-H···O Hydrogen Bonds and van der Waals Interactions
    • Kleiger, G.; Eisenberg, D. GXXXG and GXXXA Motifs Stabilize FAD and NAD(P)-binding Rossmann Folds Through Cα-H···O Hydrogen Bonds and van der Waals Interactions J. Mol. Biol. 2002, 323, 69-76
    • (2002) J. Mol. Biol. , vol.323 , pp. 69-76
    • Kleiger, G.1    Eisenberg, D.2
  • 18
    • 0032546730 scopus 로고    scopus 로고
    • New insights for dinucleotide backbone binding in conserved C5′-H···O hydrogen bonds
    • Chu, P.; Hwang, M. New insights for dinucleotide backbone binding in conserved C5′-H···O hydrogen bonds J. Mol. Biol. 1998, 279, 695-701
    • (1998) J. Mol. Biol. , vol.279 , pp. 695-701
    • Chu, P.1    Hwang, M.2
  • 19
    • 33845318295 scopus 로고
    • Interaction of pyrophosphate moieties with alpha-helixes in dinucleotide-binding proteins
    • Wierenga, R. K.; De Maeyer, M. C. H.; Hol, W. G. J. Interaction of pyrophosphate moieties with alpha-helixes in dinucleotide-binding proteins Biochemistry 1985, 24 (6) 1346-1357
    • (1985) Biochemistry , vol.24 , Issue.6 , pp. 1346-1357
    • Wierenga, R.K.1    De Maeyer, M.C.H.2    Hol, W.G.J.3
  • 20
    • 84862068214 scopus 로고    scopus 로고
    • Hidden Relationship between Conserved Residues and Locally Conserved Phosphate-Binding Structures in NAD(P)-Binding Proteins
    • Wu, C. Y.; Hwa, Y. H.; Chen, Y. C.; Lim, C. Hidden Relationship between Conserved Residues and Locally Conserved Phosphate-Binding Structures in NAD(P)-Binding Proteins J. Phys. Chem. B 2012, 116, 5644-5652
    • (2012) J. Phys. Chem. B , vol.116 , pp. 5644-5652
    • Wu, C.Y.1    Hwa, Y.H.2    Chen, Y.C.3    Lim, C.4
  • 21
    • 34447642328 scopus 로고    scopus 로고
    • Recent development of IMP dehydrogenase inhibitors for the treatment of cancer
    • Chen, L.; Pankiewicz, K. W. Recent development of IMP dehydrogenase inhibitors for the treatment of cancer Curr. Opin. Drug Discovery Dev. 2007, 10, 403-412
    • (2007) Curr. Opin. Drug Discovery Dev. , vol.10 , pp. 403-412
    • Chen, L.1    Pankiewicz, K.W.2
  • 22
    • 77953800819 scopus 로고    scopus 로고
    • Triazole-linked inhibitors of inosine monophosphate dehydrogenase from human and Mycobacterium tuberculosis
    • Chen, L.; Wilson, D. J.; Xu, Y.; Aldrich, C. C.; Felczak, K.; Sham, Y. Y.; Pankiewicz, K. W. Triazole-linked inhibitors of inosine monophosphate dehydrogenase from human and Mycobacterium tuberculosis J. Med. Chem. 2010, 53, 4768-4778
    • (2010) J. Med. Chem. , vol.53 , pp. 4768-4778
    • Chen, L.1    Wilson, D.J.2    Xu, Y.3    Aldrich, C.C.4    Felczak, K.5    Sham, Y.Y.6    Pankiewicz, K.W.7
  • 24
    • 0028961335 scopus 로고
    • SCOP: A Structural Classification of Proteins Database for the Investigation of Sequences and Structures
    • Murzin, A. G.; Brenner, S. E.; Hubbard, T.; Chothia, C. SCOP: A Structural Classification of Proteins Database for the Investigation of Sequences and Structures J. Mol. Biol. 1995, 247, 536-540
    • (1995) J. Mol. Biol. , vol.247 , pp. 536-540
    • Murzin, A.G.1    Brenner, S.E.2    Hubbard, T.3    Chothia, C.4
  • 26
    • 0000573263 scopus 로고
    • Configurations of Polypeptide Chains with Favored Orientations Around Single Bonds: Two New Pleated Sheets
    • Pauling, L.; Corey, R. B. Configurations of Polypeptide Chains With Favored Orientations Around Single Bonds: Two New Pleated Sheets Proc. Natl. Acad. Sci. U. S. A. 1951, 37, 729-740
    • (1951) Proc. Natl. Acad. Sci. U. S. A. , vol.37 , pp. 729-740
    • Pauling, L.1    Corey, R.B.2
  • 27
    • 0038497542 scopus 로고
    • Molecular structure of Nucleic Acids: A Structure for Deoxyribose Nucleic Acid
    • Watson, D. J.; Crick, F. Molecular structure of Nucleic Acids: A Structure for Deoxyribose Nucleic Acid Nature 1953, 171, 737-738
    • (1953) Nature , vol.171 , pp. 737-738
    • Watson, D.J.1    Crick, F.2
  • 28
    • 20544433165 scopus 로고
    • Van der Waals Volumes and Radii
    • Bondi, A. van der Waals Volumes and Radii J. Phys. Chem. 1964, 68, 441-451
    • (1964) J. Phys. Chem. , vol.68 , pp. 441-451
    • Bondi, A.1
  • 29
    • 33748546968 scopus 로고    scopus 로고
    • Intermolecular Nonbonded Contact Distances in Organic Crystal Structures: Comparison with Distances Expected from van der Waals Radii
    • Rowland, R. S.; Taylor, R. Intermolecular Nonbonded Contact Distances in Organic Crystal Structures: Comparison with Distances Expected from van der Waals Radii J. Phys. Chem. 1996, 100, 7384-7391
    • (1996) J. Phys. Chem. , vol.100 , pp. 7384-7391
    • Rowland, R.S.1    Taylor, R.2
  • 31
    • 84856776282 scopus 로고    scopus 로고
    • Thermodynamic analysis of water molecules at the surface of proteins and applications to binding site prediction and characterization
    • Beuming, T.; Che, Y.; Abel, R.; Kim, B.; Shanmugasundaram, V.; Sherman, W. Thermodynamic analysis of water molecules at the surface of proteins and applications to binding site prediction and characterization Proteins 2012, 80, 871-883
    • (2012) Proteins , vol.80 , pp. 871-883
    • Beuming, T.1    Che, Y.2    Abel, R.3    Kim, B.4    Shanmugasundaram, V.5    Sherman, W.6
  • 32
    • 77950423114 scopus 로고    scopus 로고
    • Identification of NAD interacting residues in proteins
    • Ansari, H. R.; Raghava, G. P. Identification of NAD interacting residues in proteins BMC Bioinform. 2010, 11, 160-167
    • (2010) BMC Bioinform. , vol.11 , pp. 160-167
    • Ansari, H.R.1    Raghava, G.P.2
  • 33
    • 0025008168 scopus 로고
    • Sequence logos: A new way to display consensus sequences
    • Schneider, T. D.; Stephens, R. M. Sequence logos: a new way to display consensus sequences Nucleic Acids Res. 1990, 18, 6097-6100
    • (1990) Nucleic Acids Res. , vol.18 , pp. 6097-6100
    • Schneider, T.D.1    Stephens, R.M.2
  • 34
    • 79951773256 scopus 로고    scopus 로고
    • Structural signatures of enzyme binding pockets from order-independent surface alignment: A study of metalloendopeptidase and NAD binding proteins
    • Dundas, J.; Adamian, L.; Liang, J. Structural signatures of enzyme binding pockets from order-independent surface alignment: a study of metalloendopeptidase and NAD binding proteins J. Mol. Biol. 2011, 406, 713-729
    • (2011) J. Mol. Biol. , vol.406 , pp. 713-729
    • Dundas, J.1    Adamian, L.2    Liang, J.3
  • 35
    • 84855711573 scopus 로고    scopus 로고
    • Cofactor-binding sites in proteins of deviating sequence: Comparative analysis and clustering in torsion angle, cavity, and fold space
    • Stegemann, B.; Klebe, G. Cofactor-binding sites in proteins of deviating sequence: comparative analysis and clustering in torsion angle, cavity, and fold space Proteins 2011, 80, 626-648
    • (2011) Proteins , vol.80 , pp. 626-648
    • Stegemann, B.1    Klebe, G.2
  • 36
    • 31344462177 scopus 로고    scopus 로고
    • Conformational Diversity of Ligands Bound to Proteins
    • Stockwell, G. R.; Thornton, J. M. Conformational Diversity of Ligands Bound to Proteins J. Mol. Biol. 2006, 356, 928-944
    • (2006) J. Mol. Biol. , vol.356 , pp. 928-944
    • Stockwell, G.R.1    Thornton, J.M.2
  • 37
  • 38
    • 79959326215 scopus 로고    scopus 로고
    • Linking distinct conformations of nicotinamide adenine dinucleotide with protein fold/function
    • Kuppuraj, G.; Sargsyan, K.; Hua, Y. H.; Merrill, A. R.; Lim, C. Linking distinct conformations of nicotinamide adenine dinucleotide with protein fold/function J. Phys. Chem. B 2011, 115, 7932-7939
    • (2011) J. Phys. Chem. B , vol.115 , pp. 7932-7939
    • Kuppuraj, G.1    Sargsyan, K.2    Hua, Y.H.3    Merrill, A.R.4    Lim, C.5
  • 39
    • 0034100411 scopus 로고    scopus 로고
    • Conformations of nicotinamide adenine dinucleotide (NAD(+)) in various environments
    • Smith, P. E.; Tanner, J. J. Conformations of nicotinamide adenine dinucleotide (NAD(+)) in various environments J. Mol. Recognit. 2000, 13, 27-34
    • (2000) J. Mol. Recognit. , vol.13 , pp. 27-34
    • Smith, P.E.1    Tanner, J.J.2
  • 40
    • 0015498966 scopus 로고
    • Some effects of environment on the folding of nicotinamide-adenine dinucleotides in aqueous solutions
    • McDonald, G.; Brown, B.; Hollis, D.; Walter, C. Some effects of environment on the folding of nicotinamide-adenine dinucleotides in aqueous solutions Biochemistry 1972, 11, 1920-1930
    • (1972) Biochemistry , vol.11 , pp. 1920-1930
    • McDonald, G.1    Brown, B.2    Hollis, D.3    Walter, C.4
  • 42
    • 0030893657 scopus 로고    scopus 로고
    • NADP-dependent enzymes. I: Conserved stereochemistry of cofactor binding
    • Carugo, O.; Argos, P. NADP-dependent enzymes. I: Conserved stereochemistry of cofactor binding Proteins 1997, 28, 10-28
    • (1997) Proteins , vol.28 , pp. 10-28
    • Carugo, O.1    Argos, P.2
  • 43
    • 34249794278 scopus 로고    scopus 로고
    • Structure of the Q67H mutant of R67 dihydrofolate reductase-NADP+ complex reveals a novel cofactor binding mode
    • Divya, N.; Grifith, E.; Narayana, N. Structure of the Q67H mutant of R67 dihydrofolate reductase-NADP+ complex reveals a novel cofactor binding mode Protein Sci. 2007, 16, 1063-1068
    • (2007) Protein Sci. , vol.16 , pp. 1063-1068
    • Divya, N.1    Grifith, E.2    Narayana, N.3
  • 44
    • 77956040809 scopus 로고    scopus 로고
    • Pocket similarity: Are alpha carbons enough?
    • Feldman, H. J.; Labute, P. Pocket similarity: are alpha carbons enough? J. Chem. Inf. Model. 2010, 50, 1466-1475
    • (2010) J. Chem. Inf. Model. , vol.50 , pp. 1466-1475
    • Feldman, H.J.1    Labute, P.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.