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PubMed2005

Identifying novel modulators of G protein-coupled receptors via interaction at allosteric sites.

Allosteric intervention at G protein-coupled receptors is considered an alternative approach to developing new drugs for both classical and novel biological targets. Allosteric compounds, which by definition bind at sites spatially separated from those of the endogenous ligands, may offer benefits over orthosteric ligands in terms of providing therapeutic benefits with reduced side effects due to increased selectivity and the temporal nature of their duration of action. The aim of this review is to assess, with reference to recent data and concepts, the potential benefits and pitfalls in the discovery and development of small-molecule allosteric compounds as novel therapeutics.

Allosteric Regulation↗

PubMed2007

Crystal structure of human phosphoribosylpyrophosphate synthetase 1 reveals a novel allosteric site.

PRPP (phosphoribosylpyrophosphate) is an important metabolite essential for nucleotide synthesis and PRS (PRPP synthetase) catalyses synthesis of PRPP from R5P (ribose 5-phosphate) and ATP. The enzymatic activity of PRS is regulated by phosphate ions, divalent metal cations and ADP. In the present study we report the crystal structures of recombinant human PRS1 in complexes with SO4(2-) ions alone and with ATP, Cd2+ and SO4(2-) ions respectively. The AMP moiety of ATP binds at the ATP-binding site, and a Cd2+ ion binds at the active site and in a position to interact with the beta- and gamma-phosphates of ATP. A SO4(2-) ion, an analogue of the activator phosphate, was found to bind at both the R5P-binding site and the allosteric site defined previously. In addi-tion, an extra SO4(2-) binds at a site at the dimer interface between the ATP-binding site and the allosteric site. Binding of this SO4(2-) stabilizes the conformation of the flexible loop at the active site, leading to the formation of the active, open conformation which is essential for binding of ATP and initiation of the catalytic reaction. This is the first time that structural stabilization at the active site caused by binding of an activator has been observed. Structural and biochemical data show that mutations of some residues at this site influence the binding of SO4(2-) and affect the enzymatic activity. The results in the present paper suggest that this new SO4(2-)-binding site is a second allosteric site to regulate the enzymatic activity which might also exist in other eukaryotic PRSs (except plant PRSs of class II), but not in bacterial PRSs.

Allosteric Site↗

PubMed2004

Discovery of an allosteric site in the caspases.

Allosteric regulation of proteins by conformational change is a primary means of biological control. Traditionally it has been difficult to identify and characterize novel allosteric sites and ligands that freeze these conformational states. We present a site-directed approach using Tethering for trapping inhibitory small molecules at sites away from the active site by reversible disulfide bond formation. We screened a library of 10,000 thiol-containing compounds against accessible cysteines of two members of the caspase family of proteases, caspase-3 and -7. We discovered a previously unreported and conserved allosteric site in a deep cavity at the dimer interface 14 A from the active site. This site contains a natural cysteine that, when disulfide-bonded with either of two specific compounds, inactivates these proteases. The allosteric site is functionally coupled to the active site, such that binding of the compounds at the allosteric site prevents peptide binding at the active site. The x-ray crystal structures of caspase-7 bound by either compound demonstrates that they inhibit caspase-7 by trapping a zymogen-like conformation. This approach may be useful to identify new allosteric sites from natural or engineered cysteines, to study allosteric transitions in proteins, and to nucleate drug discovery efforts.

Allosteric Regulation↗

PubMed2005

Radiolabeled ligand binding to the catalytic or allosteric sites of PDE5 and PDE11.

Cyclic nucleotide phosphodiesterases (PDEs) have been investigated for years as targets for therapeutic intervention in a number of pathophysiological processes. Phosphodiesterase-5 (PDE5), which is highly specific for guanosine 3'-5'-cyclic-monophosphate (cGMP) at both its catalytic site and its allosteric sites, has generated particular interest because it is potently and specifically inhibited by three drugs: sildenafil (Viagra, Pfizer), tadalafil (Cialis, Lilly-ICOS), and vardenafil (Levitra, Bayer GSK). Previously, we have used [(3)H]cGMP to directly study the interaction of cGMP with the allosteric sites of PDE5, but because cGMP binds with relatively low affinity to the catalytic site, it has been difficult to devise a binding assay for this particular binding reaction. This approach using measurement of radiolabeled ligand binding continues to allow us to more precisely define functional features of the enzyme. We now use a similar approach to study the characteristics of high-affinity [(3)H]inhibitor binding to the PDE5 catalytic domain. For these studies, we have prepared [(3)H]sildenafil and [(3)H]tadalafil, two structurally different competitive inhibitors of PDE5. The results demonstrate that radiolabeled ligands can be used as probes for both catalytic site and allosteric site functions of PDE5. We describe herein the methods that we have established for studying the binding of radiolabeled ligands to both types of sites on PDE5. These techniques have also been successfully applied to the study of binding of radiolabeled PDE5 inhibitors to PDE11, suggesting that these methods are applicable to the study of other PDEs, and perhaps other enzyme families.

3',5'-Cyclic-GMP Phosphodiesterases↗

PubMed1983

The interaction of fructose 2,6-bisphosphate with an allosteric site of rat liver fructose 1,6-bisphosphatase.

Rat liver fructose 1,6-bisphosphatase can be protected against partial inactivation by N-ethylmaleimide by low concentrations of fructose 2,6-bisphosphate or high concentrations of fructose 1,6-bisphosphate. The partially inactivated enzyme has a much reduced sensitivity to high substrate inhibition and has lost the sigmoid component of the inhibition by fructose 2,6-bisphosphate; this compound is a simple linear competitive inhibitor of the modified enzyme. The results suggest that fructose 2,6-bisphosphate can bind to the enzyme at two distinct sites, the catalytic site and an allosteric site. High levels of fructose 1,6-bisphosphate probably inhibit by binding to the allosteric site.

Allosteric Regulation↗

PubMed1999

Identification of allosteric sites in rabbit phosphofructo-1-kinase.

Earlier studies indicated an evolutionary relationship between bacterial and mammalian phosphofructo-1-kinases (PFKs) that suggests duplication, tandem fusion, and divergence of catalytic and effector binding sites of a prokaryotic ancestor to yield in eukaryotes a total of six organic ligand binding sites. The identities of residues involved in the four binding sites for allosteric ligands in mammalian PFK have been inferred from this assumed relationship. In the current study of the C isozyme of rabbit PFK, two arginine residues that can be aligned with important residues in the catalytic and allosteric binding sites of bacterial PFK and that are conserved in all eukaryotic PFKs were mutated. Arg-48 was suggested previously to be part of either the ATP inhibitory or the adenine nucleotide activating site. However, the mutant enzyme showed only slightly less sensitivity to ATP inhibition and was fully activatable by adenine nucleotides. On the other hand, sensitivity to citrate and 3-phosphoglycerate inhibition was lost, indicating an important role for Arg-48 in the binding of these allosteric effectors. Mutation of Arg-481, homologous to an active site residue in bacterial PFK, prevented binding and allosteric activation by fructose 2,6-bisphosphate. A new relationship between the allosteric sites of mammalian PFK and bacterial PFK is proposed.

Adenosine Diphosphate↗

PubMed1995

Probing of the location of the allosteric site on m1 muscarinic receptors by site-directed mutagenesis.

In an attempt to locate the allosteric site on muscarinic receptors to which gallamine binds, 21 residues in the putative external loops and loop/transmembrane helix interfaces have been mutated to alanine. These residues are conserved in mammalian m1-m5 receptors. All mutant receptors can be expressed in COS-7 cells at high levels and appear to be functional, in that acetylcholine binding is sensitive to GTP. The gallamine binding site does not appear to involve the first, second, and most of the third extracellular loops. Tryptophan-400 and -101 inhibit gallamine binding when mutated to alanine or to phenylalanine and may form part of the allosteric site. Several mutations also affect antagonist binding. Surprisingly, tryptophan-91, a residue conserved in monoamine and peptide receptors, is important for antagonist binding. This residue, present in the middle of the first extracellular loop, may have a structural role in many G protein-coupled receptors. Antagonist binding is also affected by mutations of tryptophan-101 and tyrosine-404 to alanine or phenylalanine. In a helical wheel model, trytophan-101 and tyrosine-404, in conjunction with serine-78, aspartate-105, and tyrosine-408, form a cluster of residues that have been reported to affect antagonist binding when mutated, and they may therefore be part of the antagonist binding site. It is suggested that the allosteric site may be located close to and just extracellular to the antagonist binding site. The binding of methoctramine, an antagonist with allosteric properties, is not substantially affected by mutations at tryptophan-91, -101, and -400 and tyrosine-404, and thus these amino acids are not important for its binding. The binding of himbacine, another antagonist with allosteric properties, is affected by these mutations but in a manner different from that of gallamine or competitive antagonists. It has not been possible to determine whether methoctramine and himbacine bind exclusively to the allosteric site or to both the competitive site and the allosteric site.

Acetylcholine↗

PubMed2004

Searching for new allosteric sites in enzymes.

The discovery of new allosteric sites generates opportunities for the identification of novel pharmaceuticals and increases our understanding of basic biological processes. Increasingly, allosteric sites are being discovered in various families of proteins by several methods, paving the way for the development of entirely new classes of drugs with a wide range of chemotypes. New allosteric sites in enzymes have been discovered both incidentally and by directed means, and the mechanisms by which allosteric activation and inhibition occur at these sites have been investigated. By exploring recent structurally well-characterized examples, trends begin to emerge for both the modes of binding and mechanisms of inhibition.

Allosteric Site↗

PubMed1982

Direct photoaffinity labeling of an allosteric site of subunit protein M1 of mouse ribonucleotide reductase by dATP. Evidence for two independent binding interactions within the allosteric specificity site.

The M1 subunit of ribonucleotide reductase contains two kinds of allosteric sites, the activity site and the specificity site, which regulate the overall catalytic activity and the substrate specificity of the enzyme, respectively. The effector nucleotides, dGTP and dTTP, bind only to the specificity site; dATP and ATP bind to both sites. Partially purified protein M1 was photolabeled specifically after UV irradiation in the presence of [32P]dATP. The labeling occurred exclusively at the allosteric specificity site as evidenced by 1) total inhibition of the labeling by dGTP and dTTP, 2) normal photoincorporation of [32P]dATP by mutant protein M1 molecules that lack a functional activity site, and 3) coidentity of one-dimensional peptide maps of protein M1 labeled with either [32P]dATP or [32P]dTTP. A mutant protein M1 that is resistant to normal regulation by dGTP and dTTP (indicating an alteration in the allosteric specificity site) showed normal photoincorporation of [32P]dATP (but not [32P]dTTP). This labeling was not inhibited by dGTP or dTTP. Our data suggest that this mutation has altered the binding of dGTP and dTTP but not dATP (or ATP) at the specificity site. Thus, by the combination of genetic and photolabeling techniques, two independent nucleotide binding interactions occurring within this one complex regulatory domain can be distinguished.

Affinity Labels↗

PubMed1999

Lead inhibits the rat N-methyl-d-aspartate receptor channel by binding to a site distinct from the zinc allosteric site.

Due to the importance of the NMDA receptor in cognitive function and in models of synaptic plasticity, the effect of Pb(+2) on this receptor has been one focus of attempts to define the bases of Pb-induced cognitive impairments seen in young children. The following study was performed to identify the effects on access to the NMDA receptor channel of acute exposure to free Pb(+2) in vitro. Cerebrocortical membranes were prepared from adult male Sprague-Dawley rats, and binding was measured in 50 mM Tris-acetate with (3)H-MK-801 in the presence of saturating concentrations of glutamate and glycine. The potency of Pb(+2) to inhibit access to the receptor channel (IC(50) = 0.55 microM) was greater than that of Zn(+2) (IC(50) = 1.30 microM). Dissociation of MK-801 from its binding site exhibited two-component kinetics, and both rate constants were significantly slowed in the presence of Pb(+2) or Zn(+2). To directly address the question of whether Pb(+2) inhibited the receptor channel by binding to the Zn(+2) modulatory site, changes in inhibitory potency for the receptor channel were measured when both metals were present. The results demonstrate that multiple levels of Pb(+2) produce a concentration-dependent downward shift of the Zn(+2) inhibition curve, indicating a noncompetitive inhibition of MK-801 binding by Pb(+2) with respect to that of Zn(+2). Moreover, Zn(+2) IC(50) values significantly decreased as a function of increasing Pb(+2) concentrations. Analogous results were obtained when Pb(+2) inhibition curves were determined in the presence of multiple levels of Zn(+2). These findings indicate that the inhibitory properties of free Pb(+2) and Zn(+2) on the NMDA receptor channel are similar in nature but are exerted via independent allosteric binding sites.

Allosteric Regulation↗

PubMed2006

Mutational disruption of a conserved disulfide bond in muscarinic acetylcholine receptors attenuates positive homotropic cooperativity between multiple allosteric sites and has subtype-dependent effects on the affinities of muscarinic allosteric ligands.

The 2nd outer loop (o2) of muscarinic acetylcholine receptors (mAChRs) contains a highly conserved cysteine residue that is believed to participate in a disulfide bond and is flanked on either side by epitopes that are critical to the binding of many muscarinic allosteric modulators. We determined the allosteric binding parameters of the modulators gallamine, W84, and tetrahydroaminoacridine (THA) at M2 and M3 mAChRs in which these cysteine residues had been mutated to alanines. THA is known to bind to mAChRs with a strong positive homotropic cooperativity (a Hill slope of approximately 2) that implies that it must interact with multiple allosteric sites. The disulfide cysteine mutations in M2 receptors reduced the allosteric potencies of the tested modulators as if the critical adjacent residue (Tyr177) itself had been mutated. However, in M3 receptors, the disulfide cysteine mutations had no effect on the potencies of gallamine or W84 and even increased the potency of THA. It was most interesting that the strong, positive, homotropic interactions of THA at both M2 and M3 receptors were markedly reduced by the cysteine mutations. In addition, gallamine also displayed positive homotropic cooperativity in its interactions with M3 receptors (but not M2 receptors), and this cooperativity was not evident in the cysteine mutants. Thus, it seems that these cysteine residues play a role in linking cooperating allosteric sites, although it is not currently possible to say whether these multiple sites lie within one receptor or on two linked receptors of a dimer or higher order oligomer.

Allosteric Site↗

PubMed2004

Estradiol 3-glucuronide is transported by the multidrug resistance-associated protein 2 but does not activate the allosteric site bound by estradiol 17-glucuronide.

beta-estradiol 17-(beta-D-glucuronide) (E217G) is a well known cholestatic agent and substrate of multidrug resistance-associated protein 2 (Mrp2), whereas beta-estradiol 3-(beta-D-glucuronide) (E23G) is a noncholestatic regioisomer of E217G with unknown transport properties. The purpose of this study was to compare and contrast the Mrp2-mediated transport of E217G and E23G. The full coding region of rat Mrp2 was cloned into the baculovirus genome, the recombinant baculovirus used to infect Sf9 cells, and ATP-dependent transport of 3H-E23G and 3H-E217G in Sf9 cell membranes was characterized. Mrp2 transported E23G into an osmotically sensitive space, requiring ATP, with S50=55.7 microM, Vmax=326 pmol.mg(-1).min(-1), and a Hill coefficient of 0.88. ATP-dependent Mrp2-mediated E217G transport was markedly stimulated at high E217G concentrations, consistent with positive cooperativity (Hill coefficient 1.5). E217G (5-125 microM) increased S50 but not Vmax for E23G transport, consistent with competitive inhibition. E23G (0.4-400 microM) completely, potently (IC50=14.2 microM), and competitively inhibited E217G transport, but E217G (0.01-250 microM) inhibited only 53% of E23G transport (IC50=33.4 microM). Estriol 16alpha-(beta-D-glucuronide) potently and completely inhibited transport of E23G (IC50=2.23 microM), as did beta-estradiol 3-sulfate 17-(beta-D-glucuronide) (5-50 microM). In summary, E217G binds not only to an Mrp2 transport site, but also to an allosteric site that activates Mrp2 with positive cooperativity, thus activating its own transport and potentially that of other Mrp2 substrates, such as E23G. The noncholestatic E23G is an Mrp2 substrate and competes with E217G for transport, but does not activate the allosteric site.

Allosteric Site↗

PubMed1985

Activation of fructose-1,6-bisphosphatases by monovalent cations and its relationship with a fructose-2,6-bisphosphate allosteric site.

The effects of potassium ions on pig kidney fructose-1,6-bisphosphatase activity have been studied. At low (non-inhibitory) concentrations of fructose-1,6-bisphosphate K+ shows an inhibitory effect and the apparent Km for fructose-1,6-bisphosphate increases as the concentration of monovalent cation increases. The inhibition by high substrate concentrations is decreased by addition of the potassium ions. Modification of a highly reactive cysteine residue with cyanate or N-ethylmaleimide results in the loss of activation of the enzyme by K+. Significant protection to the loss of potassium activation and substrate inhibition is afforded by the presence of low concentrations of fructose-2,6-bisphosphate or inhibitory levels of fructose-1,6-bisphosphate. Non-inhibitory concentrations of the substrate give partial protection against the loss of monovalent cation activation. The inhibitor AMP markedly increases the reactivity of the cysteine residue. The carbamoylated enzyme is not inhibited by excess of Mg2+ as compared to native enzyme. The results suggest that K+ decreases the affinity of the enzyme for fructose-1,6-bisphosphate at both the catalytic site and an allosteric site for fructose-2,6-bisphosphate. Furthermore, they lead to the proposal that monovalent cations activation could be due to the removal of both Mg2+ and substrate inhibitions.

Animals↗

PubMed1987

Affinity labeling of the catalytic and AMP allosteric sites of 3-hydroxy-3-methylglutaryl-coenzyme A reductase kinase by 5'-p-fluorosulfonylbenzoyladenosine.

The nucleotide analogue 5'-p-fluorosulfonylbenzoyladenosine (FSBA) reacts irreversibly with rat liver cytosolic 3-hydroxy-3-methylglutaryl-CoA (HMG-CoA) reductase kinase, causing a rapid loss of the AMP activation capacity and a slower inactivation of the catalytic activity. The rate constant for loss of AMP activation is about 10 times higher (kappa 1 = 0.112 min-1) than the rate constant of inactivation (kappa 2 = 0.0106 min-1). There is a good correspondence between the time-dependent inactivation of reductase kinase and the time-dependent incorporation of 5'-p-sulfonylbenzoyl[14C]adenosine ([14C]SBA). An average of 1.65 mol of reagent/mol of enzyme subunit is bound when reductase kinase is completely inactivated. The time-dependent incorporation is consistent with the postulate that covalent reaction of 1 mol of SBA/mol of subunit causes complete loss of AMP activation, whereas reaction of another mole of SBA/mol of subunit would lead to total inactivation. Protection against inactivation by the reagent is provided by the addition of Mg2+, AMP, Mg-ATP, or Mg-AMP to the incubation mixtures. In contrast, addition of ATP, 2'-AMP, or 3'-AMP has no effect on the rate constants. Mg-ATP protects preferentially the catalytic site against inactivation, whereas Mg-AMP at low concentration protects preferentially the allosteric site. Mg-ADP affords less protection than Mg-AMP to the allosteric site when both nucleotides are present at a concentration of 50 microM with 7.5 mM Mg2+. Experiments done with [14C]FSBA in the presence of some protectants have shown that a close correlation exists between the pattern of protection observed and the binding of [14C]SBA. The postulate is that there exists a catalytic site and an allosteric site in the reductase kinase subunit and that Mg-AMP is the main allosteric activator of the enzyme.

AMP-Activated Protein Kinases↗

PubMed2003

Stopped-flow kinetic investigations of the activation of soybean lipoxygenase-1 and the influence of inhibitors on the allosteric site.

Herein, we report on the role of the allosteric site in the activation mechanism of soybean lipoxygenase-1 utilizing stopped-flow inhibition kinetic studies. The K(D) for the activation was determined to be 25.9 +/- 2.3 microM and the rate constant for the oxidation of the iron cofactor, k(2), to be 182 +/- 4 s(-1). Two inhibitors were employed in this study, (Z)-9-octadecenyl sulfate (OS) and (Z)-9-palmitoleyl sulfate (PS), of which OS is an allosteric inhibitor of the turnover process, while PS is a linear mixed inhibitor with a K(i) of 13.7 +/- 1.3 microM for the catalytic site and a K(i)' of 140 +/- 9 microM for the allosteric site. It was found that OS does not inhibit the activation of soybean lipoxygenase-1, while PS acts as a competitive inhibitor versus the product, 13-hydroperoxy-9,11-(Z,E)-octadecadienoic acid, with a K(i) of 17.5 +/- 3.8 microM. These results suggest that OS binds to an allosteric site that is separate from the catalytic iron site. We further observed that the allosteric site binding selectivity is sensitive to inhibitor length as seen by its preference for OS over that of PS, which is two carbons longer than PS.

Allosteric Site↗

PubMed1984

Effects of verapamil on the binding properties of rat heart muscarinic receptors: evidence for an allosteric site.

The calcium channel antagonist verapamil is known to inhibit competitively antagonist binding to rat heart muscarinic receptors. The present data suggest that this drug recognized two binding sites on the muscarinic receptors: 1) an allosteric site modulating the tracer dissociation rates and 2) the muscarinic drug binding site. The affinity of verapamil for the allosteric site and the efficacy of its effect on muscarinic ligand dissociation rates depended on the ligand studied.

Allosteric Site↗

PubMed1977

Synthesis of AMP analogs and their use for studies on the allosteric site of rabbit muscle glycogen phosphorylase b.

In order to obtain a better understanding of the allosteric site of rabbit muscle phosphorylase b, nine AMP analogs having a bulky hydrophobic benzene ring were synthesized and tested for activity as activators or inhibitors. N6-Benzyl-AMP derivatives activated phosphorylase b to the same extent as AMP but bound to the enzyme more tightly than AMP. N6-p-nitrobenzyl-AMP had the highest affinity (Ka = 7.7 X 10(-7) M) for the AMP site. In an attempt to irreversibly modify the allosteric site of phosphorylase b, N6-p-bromoacetaminobenzyl-AMP was synthesized. Phosphorylase b was maximally activated upon incorporation of 1.0 mol of N6-p-bromoacetaminobenzyl-AMP per enzyme subunit, and its activity was approximately 90% of that of native phosphorylase b measured in the presence of AMP. The modified enzyme showed characteristics (e.g., kinetic parameters, stability, solubility, inhibition by glucose-6-phosphate, and state of aggregation) quite similar to those observed for the native enzyme in the presence of AMP. These results indicate that the AMP site of phosphorylase was specifically labeled by N6-p-bromoacetaminobenzyl-AMP. The nature of the allosteric site of phosphorylase b is discussed based on the results obtained.

Adenosine Monophosphate↗

PubMed2004

Fishing for allosteric sites on GABA(A) receptors.

GABA(A) receptors have structural and functional homology with a super-family of cys-loop ligand-gated ion channel receptors including the nicotinic acetylcholine receptors. Amino acid residues involved in ligand-binding pockets are homologous among super-family members, leading to the multiple-loop model of binding sites situated at subunit interfaces, validated by structural studies on the nicotinic acetylcholine receptor and water-soluble snail acetylcholine binding protein. This article will briefly review the literature on the agonist binding sites on the receptor super-family, and then describe the current situation for attempts to identify sites for allosteric modulators on the GABA(A) receptors. A combination of mutagenesis and photoaffinity labeling with anesthetic ligands has given some leads in this endeavor. Current work by others and ourselves focuses on three putative sites for modulators: (1) within the ion channel domain TM2, near the extracellular end; (2) the agonist binding sites and homologous pockets at other subunit interfaces of the pentameric receptor; and (3) on the linker region stretching from the agonist site loop C to the top of the TM1 region. It is likely that concrete structural information will be forthcoming soon.

Allosteric Site↗