Amidrazone analogues of D-ribofuranose as transition-state inhibitors of nucleoside hydrolase

M. Boutellier, B. A. Horenstein, A. Semenyaka, V. L. Schramm, Vern L. Schramm

Research output: Contribution to journalArticle

40 Citations (Scopus)

Abstract

The transition state of inosine during hydrolysis by nucleoside hydrolase has been characterized by kinetic isotope effects, bond-energy/bond-order vibrational analysis, and molecular electrostatic potential surface calculations [Horenstein, B. A., Parkin, D. W., Estupinan, B., and Schramm, V. L. (1991) Biochemistry 30, 10788-10795; Horenstein, B. A., and Schramm, V. L. (1993) Biochemistry 32, 7089-7097]. The heterocyclic base is protonated and the anomeric carbon of the ribofuranosyl ring is flattened to form a transition-state with extensive oxocarbenium ion character. With their delocalized charge and flattened structures, amidrazone analogues of D- ribofuranose provide both geometric and electronic mimics of the ribosyl group at the transition-state of nucleoside hydrolase. A family of riboamidrazones was synthesized with H, phenyl, and p-nitrophenyl N- substituents. The analogues were competitive inhibitors with respect to inosine and gave K(i) values of 10-5, 2 x 10-7, and 1 x 10-8 M, respectively. (p-Nitrophenyl)riboamidrazone exhibited slow-onset, tight- binding inhibition, with an overall dissociation constant of 2 x 10-9 M. The binding is reversible with an off-rate of 3 x 10-3 s-1. Tight binding can be attributed to the close spatial match between the molecular geometry of (p-nitrophenyl)riboamidrazone and the transition-state stabilized by nucleoside hydrolase. The favorable binding interactions of the (p- nitrophenyl)riboamidrazone include oxocarbenium ion mimicry, isosteric ribosyl hydroxyls, and hydrophobic and H-bonding interactions at the nitrophenyl group. Analysis of the conformational space available to the (p- nitrophenyl)riboamidrazone indicates that the geometry that approximates the enzyme-stabilized transition state is 7-14 kcal/mol unfavorable relative to the global conformational minimum for free inhibitor. The apparent overall K(d) of 2 nM represents only a fraction of the intrinsic energy available for transition-state interactions with nucleoside hydrolase. When corrected for the energy of distortion required to achieve the transition-state conformation, (p-nitrophenyl)riboamidrazone binds with an affinity near that expected for an ideal transition-state analogue.

Original languageEnglish (US)
Pages (from-to)3994-4000
Number of pages7
JournalBiochemistry
Volume33
Issue number13
StatePublished - 1994

Fingerprint

N-Glycosyl Hydrolases
Inosine
Biochemistry
Ions
Geometry
Static Electricity
Isotopes
Hydroxyl Radical
Conformations
Electrostatics
Hydrolysis
Carbon
Kinetics
Enzymes

ASJC Scopus subject areas

  • Biochemistry

Cite this

Boutellier, M., Horenstein, B. A., Semenyaka, A., Schramm, V. L., & Schramm, V. L. (1994). Amidrazone analogues of D-ribofuranose as transition-state inhibitors of nucleoside hydrolase. Biochemistry, 33(13), 3994-4000.

Amidrazone analogues of D-ribofuranose as transition-state inhibitors of nucleoside hydrolase. / Boutellier, M.; Horenstein, B. A.; Semenyaka, A.; Schramm, V. L.; Schramm, Vern L.

In: Biochemistry, Vol. 33, No. 13, 1994, p. 3994-4000.

Research output: Contribution to journalArticle

Boutellier, M, Horenstein, BA, Semenyaka, A, Schramm, VL & Schramm, VL 1994, 'Amidrazone analogues of D-ribofuranose as transition-state inhibitors of nucleoside hydrolase', Biochemistry, vol. 33, no. 13, pp. 3994-4000.
Boutellier M, Horenstein BA, Semenyaka A, Schramm VL, Schramm VL. Amidrazone analogues of D-ribofuranose as transition-state inhibitors of nucleoside hydrolase. Biochemistry. 1994;33(13):3994-4000.
Boutellier, M. ; Horenstein, B. A. ; Semenyaka, A. ; Schramm, V. L. ; Schramm, Vern L. / Amidrazone analogues of D-ribofuranose as transition-state inhibitors of nucleoside hydrolase. In: Biochemistry. 1994 ; Vol. 33, No. 13. pp. 3994-4000.
@article{80d076793a4a414e867b2d81f85d1349,
title = "Amidrazone analogues of D-ribofuranose as transition-state inhibitors of nucleoside hydrolase",
abstract = "The transition state of inosine during hydrolysis by nucleoside hydrolase has been characterized by kinetic isotope effects, bond-energy/bond-order vibrational analysis, and molecular electrostatic potential surface calculations [Horenstein, B. A., Parkin, D. W., Estupinan, B., and Schramm, V. L. (1991) Biochemistry 30, 10788-10795; Horenstein, B. A., and Schramm, V. L. (1993) Biochemistry 32, 7089-7097]. The heterocyclic base is protonated and the anomeric carbon of the ribofuranosyl ring is flattened to form a transition-state with extensive oxocarbenium ion character. With their delocalized charge and flattened structures, amidrazone analogues of D- ribofuranose provide both geometric and electronic mimics of the ribosyl group at the transition-state of nucleoside hydrolase. A family of riboamidrazones was synthesized with H, phenyl, and p-nitrophenyl N- substituents. The analogues were competitive inhibitors with respect to inosine and gave K(i) values of 10-5, 2 x 10-7, and 1 x 10-8 M, respectively. (p-Nitrophenyl)riboamidrazone exhibited slow-onset, tight- binding inhibition, with an overall dissociation constant of 2 x 10-9 M. The binding is reversible with an off-rate of 3 x 10-3 s-1. Tight binding can be attributed to the close spatial match between the molecular geometry of (p-nitrophenyl)riboamidrazone and the transition-state stabilized by nucleoside hydrolase. The favorable binding interactions of the (p- nitrophenyl)riboamidrazone include oxocarbenium ion mimicry, isosteric ribosyl hydroxyls, and hydrophobic and H-bonding interactions at the nitrophenyl group. Analysis of the conformational space available to the (p- nitrophenyl)riboamidrazone indicates that the geometry that approximates the enzyme-stabilized transition state is 7-14 kcal/mol unfavorable relative to the global conformational minimum for free inhibitor. The apparent overall K(d) of 2 nM represents only a fraction of the intrinsic energy available for transition-state interactions with nucleoside hydrolase. When corrected for the energy of distortion required to achieve the transition-state conformation, (p-nitrophenyl)riboamidrazone binds with an affinity near that expected for an ideal transition-state analogue.",
author = "M. Boutellier and Horenstein, {B. A.} and A. Semenyaka and Schramm, {V. L.} and Schramm, {Vern L.}",
year = "1994",
language = "English (US)",
volume = "33",
pages = "3994--4000",
journal = "Biochemistry",
issn = "0006-2960",
publisher = "American Chemical Society",
number = "13",

}

TY - JOUR

T1 - Amidrazone analogues of D-ribofuranose as transition-state inhibitors of nucleoside hydrolase

AU - Boutellier, M.

AU - Horenstein, B. A.

AU - Semenyaka, A.

AU - Schramm, V. L.

AU - Schramm, Vern L.

PY - 1994

Y1 - 1994

N2 - The transition state of inosine during hydrolysis by nucleoside hydrolase has been characterized by kinetic isotope effects, bond-energy/bond-order vibrational analysis, and molecular electrostatic potential surface calculations [Horenstein, B. A., Parkin, D. W., Estupinan, B., and Schramm, V. L. (1991) Biochemistry 30, 10788-10795; Horenstein, B. A., and Schramm, V. L. (1993) Biochemistry 32, 7089-7097]. The heterocyclic base is protonated and the anomeric carbon of the ribofuranosyl ring is flattened to form a transition-state with extensive oxocarbenium ion character. With their delocalized charge and flattened structures, amidrazone analogues of D- ribofuranose provide both geometric and electronic mimics of the ribosyl group at the transition-state of nucleoside hydrolase. A family of riboamidrazones was synthesized with H, phenyl, and p-nitrophenyl N- substituents. The analogues were competitive inhibitors with respect to inosine and gave K(i) values of 10-5, 2 x 10-7, and 1 x 10-8 M, respectively. (p-Nitrophenyl)riboamidrazone exhibited slow-onset, tight- binding inhibition, with an overall dissociation constant of 2 x 10-9 M. The binding is reversible with an off-rate of 3 x 10-3 s-1. Tight binding can be attributed to the close spatial match between the molecular geometry of (p-nitrophenyl)riboamidrazone and the transition-state stabilized by nucleoside hydrolase. The favorable binding interactions of the (p- nitrophenyl)riboamidrazone include oxocarbenium ion mimicry, isosteric ribosyl hydroxyls, and hydrophobic and H-bonding interactions at the nitrophenyl group. Analysis of the conformational space available to the (p- nitrophenyl)riboamidrazone indicates that the geometry that approximates the enzyme-stabilized transition state is 7-14 kcal/mol unfavorable relative to the global conformational minimum for free inhibitor. The apparent overall K(d) of 2 nM represents only a fraction of the intrinsic energy available for transition-state interactions with nucleoside hydrolase. When corrected for the energy of distortion required to achieve the transition-state conformation, (p-nitrophenyl)riboamidrazone binds with an affinity near that expected for an ideal transition-state analogue.

AB - The transition state of inosine during hydrolysis by nucleoside hydrolase has been characterized by kinetic isotope effects, bond-energy/bond-order vibrational analysis, and molecular electrostatic potential surface calculations [Horenstein, B. A., Parkin, D. W., Estupinan, B., and Schramm, V. L. (1991) Biochemistry 30, 10788-10795; Horenstein, B. A., and Schramm, V. L. (1993) Biochemistry 32, 7089-7097]. The heterocyclic base is protonated and the anomeric carbon of the ribofuranosyl ring is flattened to form a transition-state with extensive oxocarbenium ion character. With their delocalized charge and flattened structures, amidrazone analogues of D- ribofuranose provide both geometric and electronic mimics of the ribosyl group at the transition-state of nucleoside hydrolase. A family of riboamidrazones was synthesized with H, phenyl, and p-nitrophenyl N- substituents. The analogues were competitive inhibitors with respect to inosine and gave K(i) values of 10-5, 2 x 10-7, and 1 x 10-8 M, respectively. (p-Nitrophenyl)riboamidrazone exhibited slow-onset, tight- binding inhibition, with an overall dissociation constant of 2 x 10-9 M. The binding is reversible with an off-rate of 3 x 10-3 s-1. Tight binding can be attributed to the close spatial match between the molecular geometry of (p-nitrophenyl)riboamidrazone and the transition-state stabilized by nucleoside hydrolase. The favorable binding interactions of the (p- nitrophenyl)riboamidrazone include oxocarbenium ion mimicry, isosteric ribosyl hydroxyls, and hydrophobic and H-bonding interactions at the nitrophenyl group. Analysis of the conformational space available to the (p- nitrophenyl)riboamidrazone indicates that the geometry that approximates the enzyme-stabilized transition state is 7-14 kcal/mol unfavorable relative to the global conformational minimum for free inhibitor. The apparent overall K(d) of 2 nM represents only a fraction of the intrinsic energy available for transition-state interactions with nucleoside hydrolase. When corrected for the energy of distortion required to achieve the transition-state conformation, (p-nitrophenyl)riboamidrazone binds with an affinity near that expected for an ideal transition-state analogue.

UR - http://www.scopus.com/inward/record.url?scp=0028329721&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=0028329721&partnerID=8YFLogxK

M3 - Article

VL - 33

SP - 3994

EP - 4000

JO - Biochemistry

JF - Biochemistry

SN - 0006-2960

IS - 13

ER -