Hydrogen Bonds and Biological Activities

Transcription

1 ugo Kubinyi, ydrogen Bonds and Biological Activities ugo Kubinyi Germany omepage ugo Kubinyi, ature of the ydrogen Bond C=... a hydrogen bond is characterized by a shorter X... Y distance than the sum of the atom vdw radii distance Å... angle C=... angle

2 ugo Kubinyi, C in CSD C in PDB distances < vdw 0.3;. Taylor, Acta Cryst. D58, (2002) ugo Kubinyi, Donor and Acceptor Positions around a ydroxy Group (without consideration of steric hindrance) courtesy of Dr. G. Wolber, inte:ligand, Vienna, Austria

3 ugo Kubinyi, Donor contacts around an ester group ugo Kubinyi, and as ydrogen Bond Acceptors a) C, contour map a c b d b) isoxazole, bonds c) ester group, bonds with d) amide group, bonds with

4 ugo Kubinyi, Isostar: Contacts Around thotrexate M. L. Verdonk et al., J. Mol. Biol. 307, (2001) ugo Kubinyi, Typical Interand Intramolecular Interactions Between and in Amides. Taylor, Acta Cryst. D58, (2002)

5 ugo Kubinyi, Typical Interand Intramolecular Interactions Between and in Amides. Taylor, Acta Cryst. D58, (2002) ugo Kubinyi, Lipophilicity of ydrocarbons, Ethers and Secondary Amines nctanol/water log P* values (dchemdatabase, Daylight Chemical Information Systems, Mission Viejo, CA, USA) Compound X = C 2 X = /C 2 EtXEt PheXEt PheXPhe Compound X = C 2 X = /C 2 EtXEt PheXEt PheXPhe

6 ugo Kubinyi, Ligand ecognition Specificity of Estrogen and Progesterone eceptors W 2.82 Glu Estrogen receptor Arg 394 Gln } 3.1 W } Progesterone receptor Arg 766 A. M. Brzozowski et al., ature 389, (1997) S. P. Williams and P. B. Sigler, ature 393, (1998) ugo Kubinyi, Estrogen eceptor binding modes of and raloxifen oestrone (agonist) (antagonist)

7 ugo Kubinyi, DF Ligand rientation of Dihydrofolate eductase Inhibitors + DF 3 C MTX ugo Kubinyi, Ligand rientation of MTX and DF

8 ugo Kubinyi, rientation of DF Inhibitors ugo Kubinyi, The ppa Transporter ecognizes Any Peptide Ala, Glu, Trp recognition of any di to pentapeptide Arg CTerm Term Asp binding pocket filled with water molecules, bond interactions only with C and backbone and C s.

9 ugo Kubinyi, Ligand ecognition in DA eplication thymine F F 2,4difluorotoluene ugo Kubinyi, F Ligand ecognition in DA eplication F S. Moran et al., J. Am. Chem. Soc. 119, (1997) 2,4difluorotoluene as thymine isostere

10 ugo Kubinyi, AT Pair in DA (Watson and Crick, 1953) nonpolar base pair J. C. Morales et al., J. Am. Chem. Soc. 122, (2000) ibose ibose bases: adenine thymine F ibose F ibose 4benzimidazole 2,4difluorotoluene ugo Kubinyi, Insertion of nonpolar bases into DA (M 3Dstructure of a duplex DA12mer) K. M. Guckian et al., J. Am. Chem. Soc. 122, (2000)

11 2 ugo Kubinyi, Purine ucleoside Phosphorylase Inhibitors S S IC 50 = 11 µm IC 50 = 0.16 µm S S IC 50 = µm?? ugo Kubinyi, Purine ucleoside Phosphorylase Inhibitors Asn 243 Asn 243 Thr 242 Thr 242 C 3 C 3 favorable 2 2 hydrogen bond IC 50 = 11 µm IC 50 = 0.16 µm favorable hydrogen Asn 243 Asn 243 bonds Thr 242 Thr 242 C 3 C 3 unfavorable polar/ nonpolar and steric 2 2 interactions IC 50 = µm IC 50 = 0.63 µm

12 ugo Kubinyi, Pharmacophore ecognition of Scytalone Dehydratase Inhibitors C To be (similar) or not to be (similar) that s the question... if William Shakespeare had been a medicinal chemist ugo Kubinyi, ecognition of Scytalone Dehydratase Inhibitors Salicylamide = C(C 3 )C 6 4 pbr = 0.14 nm Asn131 Asn131 Quinazoline is133 = C 2 C 2 C(C 6 5 ) 2 = 0.15 nm Trp26 Tyr30 Tyr50 is110 is85 J. M. Chen et al., Biochemistry 37, (1998)

13 ugo Kubinyi, Favourable eplacement of a Water Molecule Asn131 Quinazoline Quinoline 3Cyanoquinoline = 0.15 nm C Tyr30 Tyr50 = 200 nm Tyr30 Tyr50 = nm ugo Kubinyi, Bioisosteric eplacement of a Water Molecule in the Binding Site of EGF Kinase } } C 2 Thr830 = 0.07 µm Thr830 = 0.19 µm A. Wissner et al., J. d. Chem. 43, (2000)

14 ugo Kubinyi, Change of Substrate Specificity of an Enzyme Gln wild type enzyme native enzyme Q102 mutant pyruvate C Arg 102 k cat /K m oxalacetate k cat /K m pyruvate k cat /K m oxalacetate k cat /K m pyruvate Q102 mutant oxalacetate = = 10,000 C ugo Kubinyi, Trimethoprim esistance of Staphylococcus aureus F98 L05 F92 + trimethoprim, = 0.01 µm F92 Y98 F98Y mutant, = 4.1 µm L05 F98Y double and triple mutants (30, 149, L20V, 59I), = µm G. E. Dale et al., J. Mol. Biol. 266, 2330 (1997)

15 ugo Kubinyi, ydrogen Bonds and Ligand Affinities Gln 195 Asp 38 is 48 2 Asp 176 Tyr 169 Asp 38 + P Cys 35 Thr 51 Gly 36 Gly 192 Tyr 34 In tyrosylta synthase, the exchange of Tyr 34 or Tyr 169 against Phe leads to a loss of one hydrogen bond and, correspondingly, to lower binding affinities. ugo Kubinyi, ydrogen Bonds and Ligand Affinities Affinity Values log 1/ n = 79; r 2 = 0.21 umber of ydrogen Bonds in the Complex

16 ugo Kubinyi, Correlation of ydrogen Bonds and Ligand Affinities: an Energy Values, Ionic and eutral ydrogen Bonds eutral hydrogen bonds 26 kj/mol (increase affinities by a factor 215) Ionic hydrogen bonds up to 20 kj/mol (increase affinities up to a factor 3,000) Many exceptions, e.g. Affinity of 2,3diphosphoglycerate to hemoglobin seven ionic hydrogen bonds, but only millimolar affinity to hemoglobin Affinity of sulfate to a sulfatebinding protein (SBP) seven neutral hydrogen bonds, but nanomolar affinity to the sulfatebinding protein from Salmonella typhimurium ugo Kubinyi, Binding of 2,3Diphosphoglycerate to emoglobin β 2 1 β 2 is 143 β 2 is 2 P P β 1 is 2 β 1 1 β 1 is 143 β 1 Lys 82 K m ca. 1 mm Binding of Sulfate to a Sulfatebinding Protein (SBP) Ala 173 Ser 130 Asp 11 S Trp 192 Gly 132 Ser 45 Gly 131 = 120 nm

17 ugo Kubinyi, Unfavorable eplacement of a Water Molecule in Cyclosporin A W (5ydroxynorvaline)2cyclosporin A, = C 2 C 2, exerts a 89fold lower affinity than cyclosporin A ( = C 3 ) (Mikol et al., J. d. Chem. 38, (1995)) ugo Kubinyi, Unfavorable eplacement of a Water Molecule in uperzine (±)huperzine = 24 nm 2 catechol not active at 68 µm G. Campiani et al., Bioorg. d. Chem. Lett. 8, (1998)

18 ugo Kubinyi, ydrogen Bonds in LigandProtein Interactions + + protein ligand ligandprotein complex ugo Kubinyi, ydrogen Bonds in Ligand Protein Interactions Inhibition Constants in µm X = C Gly Leu Cbz Ala113 P X Zn 2+ C 3 C 3

19 ugo Kubinyi, Vancomycin 2 Cl Vancomycin esistance of Enterococci LysDAlaDAla: sensitive LysDAlaDLac: resistant (factor 1,000) C Cl 2 LysDAlaDAla ugo Kubinyi, () 2 P ydrogen Bonds in LigandProtein Interactions X EP Inhibitors C a, X = IC 50 = 1.6 nm b, X = IC 50 = 10 nm c, X = C 2 IC 50 = nm d, X = S IC 50 = 800 nm

20 ugo Kubinyi, ydrogen Bonds in LigandProtein Interactions Thrombin Inhibitors C 3 X Gly216 Pro Arg 2 C X ProArg X = IC 50 = 9 ng/ml X = IC 50 = 130 ng/ml X = C 2 IC 50 = 70 ng/ml X = 2 IC 50 = 49 nm X = IC 50 = 390 nm ugo Kubinyi, ydrogen Bonds in LigandProtein Interactions 3 C X X X = C IC 50 = 150 nm X = C 2 IC 50 = nm ProArg X = C IC 50 = 0.9 nm X = C 2 IC 50 = nm C 2 Cl 2 X = C IC 50 = 28 ng/ml X = C 2 IC 50 = ng/ml Boc X X X = C = 500 nm X = C 2 = nm C 3 C 3 C 3 ProArg 2

21 ugo Kubinyi, Use of a Water Molecule in Cytidine Deaminase 3,4dihydrozebularine 3 4 zebularine = 30,000 nm = nm ibose ibose Glu104 Zn 2+ Glu104 Zn 2+ 2 Cys129 Cys129 ibose ibose Ala103 Ala103