Mechanism Of Enzyme Inhibition Research Articles

Reversible Mechanisms of Enzyme Inhibition and Resulting Clinical Significance.

Inhibition of a drug-metabolizing enzyme by the reversible interaction of a drug with the enzyme, thus decreasing the metabolism of another drug, is a major cause of clinically significant drug-drug interactions. This chapter defines the four reversible mechanisms of inhibition exhibited by drugs: competitive, noncompetitive, uncompetitive, and mixed competitive/noncompetitive. An in vitro procedure to determine the potential of a drug to be a reversible inhibitor is also provided. Finally, a number of examples of clinically significant drug-drug interactions resulting from reversible inhibition are described.

Metallo-β-Lactamases: Influence of the Active Site Structure on the Mechanisms of Antibiotic Resistance and Inhibition

The review focuses on bacterial metallo-β-lactamases (MβLs) responsible for the inactivation of β-lactams and associated antibiotic resistance. The diversity of the active site structure in the members of different MβL subclasses explains different mechanisms of antibiotic hydrolysis and should be taken into account when searching for potential MβL inhibitors. The review describes the features of the antibiotic inactivation mechanisms by various MβLs studied by X-ray crystallography, NMR, kinetic measurements, and molecular modeling. The mechanisms of enzyme inhibition for each MβL subclass are discussed.

The Potency of Senggani (Melastoma malabathricum L) Leaves in Repair of Pancreatic Beta Cells for Diabetes Mellitus Patients: A Narrative Review

Diabetes mellitus is often caused by damage to pancreatic beta cells which play a role in secreting insulin in the body. Damage to pancreatic beta cells causes the body to lack insulin. Dipeptidyl peptidase-4 (DPP-4) is a peptidase enzyme complex located on the surface of the cell membrane. Inhibition of the DPP4 enzyme will increase blood GLP-1 levels and induce regeneration of pancreatic beta cells. Senggani leaf (Melastoma malabathricum) boiled water is believed by the people of the Ciamis area to be used as a diabetes medicine. There have been many studies and reviews related to Senggani (Melastoma malabathricum) and its potential. This review focuses on the discussion of Senggani as an antidiabetic by analyzing the reduction in glucose levels and the repair ability of pancreatic beta cells. The results of the literature study that show that senggani leaves have the ability to reduce blood glucose levels and repair activity of pancreatic beta cells through the DPP-4 enzyme inhibition mechanism supported by molecular docking simulation data. There are 12 active compounds that have a binding site similarity above 50% with the comparison compound vildagliptin. Rutin is the best active compound which has a 100% similarity of the binding site. Based on in vivo research and toxicity analysis on the admetsar database, senggani leaf extract and active compounds of senggani leaves have low toxicity, making it safe to be used as antidiabetic herbal preparations.

The Se…S/N interactions as a possible mechanism of δ-aminolevulinic acid dehydratase enzyme inhibition by organoselenium compounds: A computational study

Organoselenium compounds present many pharmacological properties and are promising drugs. However, toxicological effects associated with inhibition of thiol-containing enzymes, such as the δ-aminolevulinic acid dehydratase (δ-AlaD), have been described. The molecular mechanism(s) by which they inhibit thiol-containing enzymes at the atomic level, is still not well known. The use of computational methods to understand the physical–chemical properties and biological activity of chemicals is essential to the rational design of new drugs. In this work, we propose an in silico study to understand the δ-AlaD inhibition mechanism by diphenyl diselenide (DPDS) and its putative metabolite, phenylseleninic acid (PSA), using δ-AlaD enzymes from Homo sapiens (Hsδ-AlaD), Drosophila melanogaster (Dmδ-AlaD) and Cucumis sativus (Csδ-AlaD). Protein modeling homology, molecular docking, and DFT calculations are combined in this study. According to the molecular docking, DPDS and PSA might bind in the Hsδ-AlaD and Dmδ-AlaD active sites interacting with the cysteine residues by Se…S interactions. On the other hand, the DPDS does not access the active site of the Csδ-AlaD (a non-thiol protein), while the PSA interacts with the amino acids residues from the active site, such as the Lys291. These interactions might lead to the formation of a covalent bond, and consequently, to the enzyme inhibition. In fact, DFT calculations (mPW1PW91/def2TZVP) demonstrated that the selenylamide bond formation is energetically favored. The in silico data showed here are in accordance with previous experimental studies, and help us to understand the reactivity and biological activity of organoselenium compounds.

Inhibition effects of isoproterenol, chlorpromazine, carbamazepine, tamoxifen drugs on glutathione S-transferase, cholinesterases enzymes and molecular docking studies

Nowadays, inhibition of acetylcholinesterase (AChE), butyrylcholinesterase (BChE) and glutathione S-transferases (GSTs) have been a very crucial issue for pharmacological treatments of several disasters. Herein, we investigated inhibition effects of Tamoxifen (TAM), Isoprenaline (ISO), Chlorpromazines (CPZ) and Carbamazepine (CBZ) on GST, AChE, BChE and then molecular structures and active sides of the tested drugs by molecular docking process. The enzyme activity results showed that nearly the whole tested drugs inhibited GST, BChE, AChE efficiently. Chlorpromazine was found to be the best inhibitor for the GST enzyme and the Ki value of this drug was found to be 42.83 ± 8.52 nM. Besides, Isoproterenol drug with the Ki value of 51.80 ± 9.44 nM was found to be the most effective inhibitor on the AChE enzyme. Molecular docking studies showed that the receptor-binding sites of GST, AChE, and BChE were found to 1.069, 1.090, and 1.15 of Sitecore and 0.992, 1.113, and 1.217 of Dscore, respectively. The method was validated by doing validation studies and these validations revealed that re-docked ligands located a very closed position with co-crystallized ligand into the active site for all receptors. Calculation studies for determining the possible enzyme inhibition mechanism with the used drugs revealed that amino and aromatic ring in the structure of the drugs used are effective in inhibition reactions.Communicated by Ramaswamy H. Sarma

Design, Synthesis, Biological Evaluation and Inhibition Mechanism of 3-/4-Alkoxy Phenylethylidenethiosemicarbazides as New, Potent and Safe Tyrosinase Inhibitors.

Tyrosinase plays important roles in many different disease related processes, and the development of its inhibitors is particularly important in biotechnology. In this study, thirty-nine 3-/4-alkoxyphenylethylidenethiosemicarbazides were synthesized as novel tyrosinase inhibitors based on structure-based molecular design. Our experimental results demonstrated that thirty-one of them possess remarkable tyrosinase inhibitory activities with IC50 value below 1 µM, and 5a, 6e, 6g and 6t did not display any toxicity to 293T cell line at the concentration of 1000 µmol/L. According to the inhibitory activities, several compounds were selected for detail investigation on the structure-activity relationships (SARs), mechanisms of enzyme inhibition, inhibitory kinetics and cytotoxicity. In particular, the interaction between the selected inhibitors and the active center of tyrosinase was considered and discussed in detail based on their structural characteristics. Taken together, the results presented here demonstrated that the newly designed compounds are promising candidates for the treatment of tyrosinase-related disorders and further development of them may have significant contribution in biomedical science.

Nauclea latifolia Sm. Leaf Extracts Extenuates Free Radicals, Inflammation, and Diabetes-Linked Enzymes.

This study was carried out to assess the in vitro antioxidant, anti-inflammatory and antidiabetic effects of Nauclea latifolia (Sm.) leaf extracts. Ethanolic (NLE) and aqueous (NLA) extract of N. latifolia leaves were prepared and assessed for their anti-inflammatory activity, antioxidant potential, α-amylase and α-glucosidase inhibitory activities, and the mechanism of enzyme inhibition in vitro using standard established methods. From the results, phytochemicals such as flavonoids, phenolics, glycosides, and tannins were detected in both extracts of N. latifolia with NLE having a significantly (p < 0.05) higher phytochemical content. NLE displayed significantly (p < 0.05) better total antioxidant capacity, reducing power, 2,2-diphenyl-2-picrylhydrazyl, and hydrogen peroxide radical scavenging activities. For anti-inflammatory activities, 70.54 ± 2.45% albumin denaturation inhibition was observed for NLE while 68.05 ± 1.03% was recorded for NLA. Likewise, 16.07 ± 1.60 and 14.08 ± 1.76% were obtained against hypotonic solution and heat-induced erythrocyte haemolysis, respectively, for NLE while 20.59 ± 4.60 and 24.07 ± 1.60% were respective NLA values. NLE (IC50: 4.20 ± 0.18 and 1.19 ± 0.11 mg/mL) and NLA (IC50: 11.21 ± 0.35 and 2.64 ± 0.48 mg/mL) α-glucosidase and α-amylase inhibitory activities were dose-dependent with uncompetitive and competitive inhibition elicited, respectively, by the extracts. A significant positive association (p < 0.01 and 0.05) was identified between antioxidant activity and carbohydrate-metabolising enzyme inhibitory activity. The obtained result suggests N. latifolia leaf could serve as an alternative candidate for managing diabetes mellitus due to its antioxidant and anti-inflammatory association with diabetes-linked enzymes.

Anti-elastase and anti-hyaluronidase activity of phosvitin isolated from hen egg yolk

ABSTRACT1. Phosvitin, a major phosphoprotein found in egg yolk, has strong antioxidant activity. Activation of elastase, collagenase, and hyaluronidase by reactive oxygen species are related to the degradation of ECM and skin aging. The objective of this study was to determine the anti-elastase and anti-hyaluronidase activity of phosvitin.2. Elastase from porcine pancreas and hyaluronidase from bovine testes were used to study the inhibitory activity of phosvitin. To elucidate the mechanism of enzyme inhibition, a Lineweaver-Burk plot was constructed.3. Phosvitin inhibited elastase and hyaluronidase activity in a dose-dependent manner. The IC50 value of phosvitin was 31.6 μg/ml and 1,270 μg/ml against elastase and hyaluronidase, respectively. The analysis of elastase and hyaluronidase kinetics indicated that the apparent Michaelis constant (appKm) was increased by phosvitin but the Vmax value was not affected.4. In conclusion, phosvitin exhibited competitive inhibitory activity against elastase and hyaluronidase. Thus, phosvitin could be used as a natural anti-aging agent in the cosmetics industry.

Antiureolytic Activity of Substituted 2,5-Diaminobenzoquinones.

A series of 2,5-bis(alkyl/arylamino)-1,4-benzoquinones (1-12) were investigated in vitro for their potential to inhibit the activity of jack bean urease. Compounds 1-6, 8, 9, 11 and 12 effectively inhibited the jack bean urease activity by 90.8 % when tested at 5 μm, whereas 7 and 10 had relatively little effect. The IC50 for most compounds was in the nanomolar range (31.4 nm and 36.0 nm for 2 and 8, respectively). The mechanism of enzyme inhibition shown by 2 and 8 is typical of mixed-type inhibitors, whose affinity for the active site is over 6- and 2-fold higher (Ki =30.0 and 22.8 nm, for 2 and 8, respectively) than that of an allosteric site. Molecular docking studies revealed that both 2 and 8 establish hydrogen bonds with the amino acids residues Asp494, Met588, His593 and Ala636 in the active site of jack bean urease. These results indicate that such aminoquinones are useful leads for the development of more efficient urease inhibitors of wider utility.

Combining Charge Density Analysis with Machine Learning Tools To Investigate the Cruzain Inhibition Mechanism.

Trypanosoma cruzi, a flagellate protozoan parasite, is responsible for Chagas disease. The parasite major cysteine protease, cruzain (Cz), plays a vital role at every stage of its life cycle and the active-site region of the enzyme, similar to those of other members of the papain superfamily, is well characterized. Taking advantage of structural information available in public databases about Cz bound to known covalent inhibitors, along with their corresponding activity annotations, in this work, we performed a deep analysis of the molecular interactions at the Cz binding cleft, in order to investigate the enzyme inhibition mechanism. Our toolbox for performing this study consisted of the charge density topological analysis of the complexes to extract the molecular interactions and machine learning classification models to relate the interactions with biological activity. More precisely, such a combination was useful for the classification of molecular interactions as “active-like” or “inactive-like” according to whether they are prevalent in the most active or less active complexes, respectively. Further analysis of interactions with the help of unsupervised learning tools also allowed the understanding of how these interactions come into play together to trigger the enzyme into a particular conformational state. Most active inhibitors induce some conformational changes within the enzyme that lead to an overall better fit of the inhibitor into the binding cleft. Curiously, some of these conformational changes can be considered as a hallmark of the substrate recognition event, which means that most active inhibitors are likely recognized by the enzyme as if they were its own substrate so that the catalytic machinery is arranged as if it is about to break the substrate scissile bond. Overall, these results contribute to a better understanding of the enzyme inhibition mechanism. Moreover, the information about main interactions extracted through this work is already being used in our lab to guide docking solutions in ongoing prospective virtual screening campaigns to search for novel noncovalent cruzain inhibitors.

Synthesis of new indazole based dual inhibitors of α-glucosidase and α-amylase enzymes, their in vitro, in silico and kinetics studies.

The current study describes the discovery of novel inhibitors of α-glucosidase and α-amylase enzymes. For that purpose, new hybrid analogs of N-hydrazinecarbothioamide substituted indazoles 4-18 were synthesized and fully characterized by EI-MS, FAB-MS, HRFAB-MS, 1H-, and 13C NMR spectroscopic techniques. Stereochemistry of the imine double bond was established by NOESY measurements. All derivatives 4-18 with their intermediates 1-3, were evaluated for in vitro α-glucosidase and α-amylase enzyme inhibition. It is worth mentioning that all synthetic compounds showed good inhibition potential in the range of 1.54 ± 0.02-4.89 ± 0.02 µM for α-glucosidase and for α-amylase 1.42 ± 0.04-4.5 ± 0.18 µM in comparison with the standard acarbose (IC50 value of 1.36 ± 0.01 µM). In silico studies were carried out to rationalize the mode of binding interaction of ligands with the active site of enzymes. Moreover, enzyme inhibitory kinetic characterization was also performed to understand the mechanism of enzyme inhibition.

Amphiphilic silicone-bridged bis-triazoles as effective, selective metal ligands and biologically active agents in lipophilic environment

Pairs of different substituted 3-mercapto-1,2,4-triazole units are coupled, through thioether bridges, to organic-inorganic substrates consisting in short hydrophobic silicone segment. A library of six compounds are isolated as crystalline solids and structurally characterized by X-ray single crystal diffraction, elemental, spectral and thermal analysis. The flexibility of the silicone spacer makes the small molecular compounds exhibit glass transition in the negative domain. The metal binding capacity is evaluated by quantum mechanics calculations, the results being in line with experimental data obtained by UV–vis spectroscopy titration. The results indicate that the prepared compounds can act as ligands for metal ions with high selectivity for Cu2+, an element of interest in biological processes, forming 1:1 stable mononuclear complexes with an association constant up to 8.87 × 103 M−1. The presence of the highly hydrophobic silicone spacer makes the behavior of bis-triazoles obtained more sensitive to the nature of the environment. The preliminary bioassay indicates lipophilic medium more suitable for biocide action of silicone-bridged bis-triazoles, which in some cases far exceeds that of reference. The mechanism of enzyme inhibition is demonstrated by molecular docking, and the results indicate that, in all docked complexes, the ligands are directly coordinated to the heme ferric iron.

Redox-Dependent Loss of Flavin by Mitochondrial Complex I in Brain Ischemia/Reperfusion Injury.

Aims: Brain ischemia/reperfusion (I/R) is associated with impairment of mitochondrial function. However, the mechanisms of mitochondrial failure are not fully understood. This work was undertaken to determine the mechanisms and time course of mitochondrial energy dysfunction after reperfusion following neonatal brain hypoxia-ischemia (HI) in mice. Results: HI/reperfusion decreased the activity of mitochondrial complex I, which was recovered after 30 min of reperfusion and then declined again after 1 h. Decreased complex I activity occurred in parallel with a loss in the content of noncovalently bound membrane flavin mononucleotide (FMN). FMN dissociation from the enzyme is caused by succinate-supported reverse electron transfer. Administration of FMN precursor riboflavin before HI/reperfusion was associated with decreased infarct volume, attenuation of neurological deficit, and preserved complex I activity compared with vehicle-treated mice. In vitro, the rate of FMN release during oxidation of succinate was not affected by the oxygen level and amount of endogenously produced reactive oxygen species. Innovation: Our data suggest that dissociation of FMN from mitochondrial complex I may represent a novel mechanism of enzyme inhibition defining respiratory chain failure in I/R. Strategies preventing FMN release during HI and reperfusion may limit the extent of energy failure and cerebral HI injury. The proposed mechanism of acute I/R-induced complex I impairment is distinct from the generally accepted mechanism of oxidative stress-mediated I/R injury. Conclusion: Our study is the first to highlight a critical role of mitochondrial complex I-FMN dissociation in the development of HI-reperfusion injury of the neonatal brain. Antioxid. Redox Signal. 31, 608-622.

Gnidia glauca- and Plumbago zeylanica-Mediated Synthesis of Novel Copper Nanoparticles as Promising Antidiabetic Agents.

Rapid, eco-friendly, and cost-effective one-pot synthesis of copper nanoparticles is reported here using medicinal plants like Gnidia glauca and Plumbago zeylanica. Aqueous extracts of flower, leaf, and stem of G. glauca and leaves of P. zeylanica were prepared which could effectively reduce Cu2+ ions to CuNPs within 5 h at 100°C which were further characterized using UV-visible spectroscopy, field emission scanning electron microscopy, high-resolution transmission electron microscopy, energy dispersive spectroscopy, dynamic light scattering, X-ray diffraction, and Fourier-transform infrared spectroscopy. Further, the CuNPs were checked for antidiabetic activity using porcine pancreatic α-amylase and α-glucosidase inhibition followed by evaluation of mechanism using circular dichroism spectroscopy. CuNPs were found to be predominantly spherical in nature with a diameter ranging from 1 to 5 nm. The phenolics and flavonoids in the extracts might play a critical role in the synthesis and stabilization process. Significant change in the peak at ∼1095 cm−1 corresponding to C-O-C bond in ether was observed. CuNPs could inhibit porcine pancreatic α-amylase up to 30% to 50%, while they exhibited a more significant inhibition of α-glucosidase from 70% to 88%. The mechanism of enzyme inhibition was attributed due to the conformational change owing to drastic alteration of secondary structure by CuNPs. This is the first study of its kind that provides a strong scientific rationale that phytogenic CuNPs synthesized using G. glauca and P. zeylanica can be considered to develop candidate antidiabetic nanomedicine.

Pharmacokinetics and Pharmacodynamics of β-Lactamase Inhibitors.

Novel β-lactamase inhibitors have extended the reach of new and existing β-lactams against multidrug-resistant bacteria expressing β-lactamases. The efficacy of these combination therapeutics relies on a complex two-component pharmacodynamic (PD) system where the β-lactamase inhibitor inactivates the bacterial β-lactamase enzyme and frees the companion β-lactam to act against its penicillin-binding protein target. Despite considerable investigation into the pharmacokinetics (PK) and pharmacodynamics of β-lactams, the pharmacology of their companion β-lactamase inhibitors has only recently been rigorously explored. This review describes the diversity of β-lactamase enzymes, mechanisms of enzyme inhibition, and factors impacting the efficacy of clinically available β-lactamase inhibitors. Relevant PK differences among available inhibitors and the PK/PD properties of these agents are described independently of their companion β-lactams. In the modern era of antibiotic resistance, a comprehensive understanding of the pharmacology, PK, and PD of β-lactamase inhibitors is paramount to maximizing the therapeutic efficacy of existing β-lactam/β-lactamase inhibitor combinations and protecting novel agents in the drug development pipeline.

Three-Dimensional Visualization of Kinase Inhibitors as Therapeutically Relevant Examples To Reinforce Types of Enzyme Inhibitors

An activity is described that incorporates three-dimensional visualization of therapeutic agents to reinforce lecture concepts of enzyme structure and inhibition and further relate these concepts to applications for drug action. Investigational and FDA-approved kinase inhibitors developed as anticancer agents were utilized as therapeutically relevant examples of enzyme inhibitors to illustrate enzyme–inhibitor interactions and correlate mechanisms of enzyme inhibition to drug action. Student cohorts were required to answer a series of questions while visualizing the three-dimensional enzyme active site and inhibitor-bound enzyme complexes. Student impressions of the activity based on a survey were positive. Student learning for concepts covered as part of the activity was evaluated using performance on examination questions.

Assessing CYP2C19 Ontogeny in Neonates and Infants Using Physiologically Based Pharmacokinetic Models: Impact of Enzyme Maturation Versus Inhibition.

The objective of this study was to develop pediatric physiologically based pharmacokinetic (PBPK) models for pantoprazole and esomeprazole. Pediatric PBPK models were developed by Simcyp version 15 by incorporating cytochrome P450 (CYP)2C19 maturation and auto‐inhibition. The predicted‐to‐observed pantoprazole clearance (CL) ratio ranged from 0.96–1.35 in children 1–17 years of age and 0.43–0.70 in term infants. The predicted‐to‐observed esomeprazole CL ratio ranged from 1.08–1.50 for children 6–17 years of age, and 0.15–0.33 for infants. The prediction was markedly improved by assuming no auto‐inhibition of esomeprazole in infants in the PBPK model. Our results suggested that the CYP2C19 auto‐inhibition model was appropriate for esomeprazole in adults and older children but could not be directly extended to infants. A better understanding of the complex interplay of enzyme maturation, inhibition, and compensatory mechanisms for CYP2C19 is necessary for PBPK modeling in infants.

The exploration of novel Alzheimer’s therapeutic agents from the pool of FDA approved medicines using drug repositioning, enzyme inhibition and kinetic mechanism approaches

Novel drug development is onerous, time consuming and overpriced process with particularly low success and relatively high enfeebling rates. To overcome this burden, drug repositioning approach is being used to predict the possible therapeutic effects of FDA approved drugs in different diseases. Herein, we designed a computational and enzyme inhibitory mechanistic approach to fetch the promising drugs from the pool of FDA approved drugs against AD. The binding interaction patterns and conformations of screened drugs within active region of AChE were confirmed through molecular docking profiles. The possible associations of selected drugs with AD genes were predicted by pharmacogenomics analysis and confirmed through data mining. The stability behaviour of docked complexes (Drugs-AChE) were checked by MD simulations. The possible therapeutic potential of repositioned drugs against AChE were checked by in vitro analysis. Taken together, Cinitapride displayed a comparable results with standard and can be used as possible therapeutic agent in the treatment of AD.

Rosmarinic Acid Derivatives' Inhibition of Glycogen Synthase Kinase-3β Is the Pharmacological Basis of Kangen-Karyu in Alzheimer's Disease.

Inhibition of glycogen synthase kinase 3β (GSK-3β) is considered to be the central therapeutic approach against Alzheimer’s disease (AD). In the present study, boiled water extracts of the Kangen-karyu (KK) herbal mixture and its constituents were screened for GSK-3β inhibitory activity. KK is used in traditional Kampo and Chinese medicines for improving cognitive function. The GSK-3β inhibition potential was evaluated by using the Kinase-Glo luminescent kinase assay platform. Furthermore, enzyme kinetics and in silico modeling were performed by using AutoDockTools to demonstrate the mechanism of enzyme inhibition. KK extract significantly inhibited GSK-3β in a concentration-dependent manner (IC50: 17.05 ± 1.14 μg/mL) when compared with the reference drug luteolin (IC50: 2.18 ± 0.13 μM). Among the six components of KK, extracts of Cyperi Rhizoma and Salviae Miltiorrhizae Radix significantly inhibited GSK-3β with IC50 values of 20.68 ± 2.50 and 7.77 ± 1.38 μg/mL, respectively. Among the constituents of the roots of S. miltiorrhiza water extract, rosmarinic acid, magnesium lithospermate B, salvianolic acid A, salvianolic acid B, and salvianolic acid C inhibited GSK-3β with IC50 values ranging from 6.97 to 135.5 μM. Salvianolic acid B was found to be an ATP-competitive inhibitor of GSK-3β and showed the lowest IC50 value (6.97 ± 0.96 µM). In silico modeling suggested a mechanism of action by which the hydrophobic, π–cation, and hydrophilic interactions of salvianolic acid B at ATP and substrate sites are critical for the observed GSK-3β inhibition. Therefore, one of the mechanisms of action of KK against AD may be the inhibition of GSK-3β and one of the active components of KK is the root of S. miltiorrhiza and its constituents: rosmarinic acid, magnesium lithospermate B, and salvianolic acids A, B, and C. Our results demonstrate the pharmacological basis for the use of KK against AD.

Mechanism of Selective Enzyme Inhibition through Uncompetitive Regulation of an Allosteric Agonist.

Classical uncompetitive inhibitors are potent pharmacological modulators of enzyme function. Since they selectively target enzyme-substrate complexes (E:S), their inhibitory potency is amplified by increasing substrate concentrations. Recently, an unconventional uncompetitive inhibitor, called CE3F4R, was discovered for the exchange protein activated by cAMP isoform 1 (EPAC1). Unlike conventional uncompetitive inhibitors, CE3F4R is uncompetitive with respect to an allosteric effector, cAMP, as opposed to the substrate (i.e., CE3F4R targets the E:cAMP rather than the E:S complex). However, the mechanism of CE3F4R as an uncompetitive inhibitor is currently unknown. Here, we elucidate the mechanism of CE3F4R's action using NMR spectroscopy. Due to limited solubility and line broadening, which pose major challenges for traditional structural determination approaches, we resorted to a combination of protein- and ligand-based NMR experiments to comparatively analyze EPAC mutations, inhibitor analogs, and cyclic nucleotide derivatives that trap EPAC at different stages of activation. We discovered that CE3F4R binds within the EPAC cAMP-binding domain (CBD) at a subdomain interface distinct from the cAMP binding site, acting as a wedge that stabilizes a cAMP-bound mixed-intermediate. The mixed-intermediate includes attributes of both the apo/inactive and cAMP-bound/active states. In particular, the intermediate targeted by CE3F4R traps a CBD's hinge helix in its inactive conformation, locking EPAC into a closed domain topology that restricts substrate access to the catalytic domain. The proposed mechanism of action also explains the isoform selectivity of CE3F4R in terms of a single EPAC1 versus EPAC2 amino acid difference that destabilizes the active conformation of the hinge helix.