Entropy-driven binding of picomolar transition state analogue inhibitors to Human 5′-methylthioadenosine phosphorylase

Rong Guan, Meng Chiao Ho, Michael D. Brenowitz, Peter C. Tyler, Gary B. Evans, Steven C. Almo, Vern L. Schramm

Research output: Contribution to journalArticle

17 Citations (Scopus)

Abstract

Human 5′-methylthioadenosine phosphorylase (MTAP) links the polyamine biosynthetic and S-adenosyl-l-methionine salvage pathways and is a target for anticancer drugs. p-Cl-PhT-DADMe-ImmA is a 10 pM, slow-onset tight-binding transition state analogue inhibitor of the enzyme. Titration of homotrimeric MTAP with this inhibitor established equivalent binding and independent catalytic function of the three catalytic sites. Thermodynamic analysis of MTAP with tight-binding inhibitors revealed entropic-driven interactions with small enthalpic penalties. A large negative heat capacity change of -600 cal/(mol K) upon inhibitor binding to MTAP is consistent with altered hydrophobic interactions and release of water. Crystal structures of apo MTAP and MTAP in complex with p-Cl-PhT-DADMe-ImmA were determined at 1.9 and 2.0 Å resolution, respectively. Inhibitor binding caused condensation of the enzyme active site, reorganization at the trimer interfaces, the release of water from the active sites and subunit interfaces, and compaction of the trimeric structure. These structural changes cause the entropy-favored binding of transition state analogues. Homotrimeric human MTAP is contrasted to the structurally related homotrimeric human purine nucleoside phosphorylase. p-Cl-PhT-DADMe-ImmA binding to MTAP involves a favorable entropy term of -17.6 kcal/mol with unfavorable enthalpy of 2.6 kcal/mol. In contrast, binding of an 8.5 pM transition state analogue to human PNP has been shown to exhibit the opposite behavior, with an unfavorable entropy term of 3.5 kcal/mol and a favorable enthalpy of -18.6 kcal/mol. Transition state analogue interactions reflect protein architecture near the transition state, and the profound thermodynamic differences for MTAP and PNP suggest dramatic differences in contributions to catalysis from protein architecture.

Original languageEnglish (US)
Pages (from-to)10408-10417
Number of pages10
JournalBiochemistry
Volume50
Issue number47
DOIs
StatePublished - Nov 29 2011

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Entropy
Catalytic Domain
Thermodynamics
Enthalpy
Purine-Nucleoside Phosphorylase
5'-methylthioadenosine phosphorylase
Salvaging
Water
Polyamines
Enzyme Inhibitors
Catalysis
Titration
Hydrophobic and Hydrophilic Interactions
Methionine
Specific heat
Condensation
Proteins
Compaction
Hot Temperature
Crystal structure

ASJC Scopus subject areas

  • Biochemistry

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Entropy-driven binding of picomolar transition state analogue inhibitors to Human 5′-methylthioadenosine phosphorylase. / Guan, Rong; Ho, Meng Chiao; Brenowitz, Michael D.; Tyler, Peter C.; Evans, Gary B.; Almo, Steven C.; Schramm, Vern L.

In: Biochemistry, Vol. 50, No. 47, 29.11.2011, p. 10408-10417.

Research output: Contribution to journalArticle

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title = "Entropy-driven binding of picomolar transition state analogue inhibitors to Human 5′-methylthioadenosine phosphorylase",
abstract = "Human 5′-methylthioadenosine phosphorylase (MTAP) links the polyamine biosynthetic and S-adenosyl-l-methionine salvage pathways and is a target for anticancer drugs. p-Cl-PhT-DADMe-ImmA is a 10 pM, slow-onset tight-binding transition state analogue inhibitor of the enzyme. Titration of homotrimeric MTAP with this inhibitor established equivalent binding and independent catalytic function of the three catalytic sites. Thermodynamic analysis of MTAP with tight-binding inhibitors revealed entropic-driven interactions with small enthalpic penalties. A large negative heat capacity change of -600 cal/(mol K) upon inhibitor binding to MTAP is consistent with altered hydrophobic interactions and release of water. Crystal structures of apo MTAP and MTAP in complex with p-Cl-PhT-DADMe-ImmA were determined at 1.9 and 2.0 {\AA} resolution, respectively. Inhibitor binding caused condensation of the enzyme active site, reorganization at the trimer interfaces, the release of water from the active sites and subunit interfaces, and compaction of the trimeric structure. These structural changes cause the entropy-favored binding of transition state analogues. Homotrimeric human MTAP is contrasted to the structurally related homotrimeric human purine nucleoside phosphorylase. p-Cl-PhT-DADMe-ImmA binding to MTAP involves a favorable entropy term of -17.6 kcal/mol with unfavorable enthalpy of 2.6 kcal/mol. In contrast, binding of an 8.5 pM transition state analogue to human PNP has been shown to exhibit the opposite behavior, with an unfavorable entropy term of 3.5 kcal/mol and a favorable enthalpy of -18.6 kcal/mol. Transition state analogue interactions reflect protein architecture near the transition state, and the profound thermodynamic differences for MTAP and PNP suggest dramatic differences in contributions to catalysis from protein architecture.",
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