25. May 2026
Comparative Kinetic Analysis of Transglutaminase Inhibitors Under Standardized Conditions
Christian Büchold, Christiane Pelzer, Michael Sommer, Robert Jähnig, Martin Hils, Ralf Pasternack
Zedira, Rösslerstraße 83, Darmstadt, Germany
Key Messages
Standard conditions in a nutshell
Introduction
Tissue transglutaminase 2 (TG2) is a validated therapeutic target for celiac disease (CeD), with ZED1227 (aka TAK-227) as the most advanced clinical candidate. This direct-acting oral TG2 inhibitor has been tested in hundreds of healthy volunteers and CeD patients, including the ongoing dose-finding trial NCT07298343 (CEC-13), which evaluates efficacy under simulated inadvertent gluten exposure [1-3].
Beyond the development of proprietary clinical entities like ZED1227, Zedira provides a wide variety of tool compounds to catalyze research in the field of human transglutaminases. Notably, this is only part of a larger chemical space explored in academia and industry. A wide range of compounds, including inhibition data, has been published. However, the individual assay conditions vary considerably, making any direct comparison between inhibitors virtually impossible.
Here, we present a comparative analysis of commonly used tool compounds. Inhibition data were generated under uniform, standardized conditions using the classic transamidation assay, conducted at 37°C: dansylcadaverine (15.9 µM) is enzymatically incorporated into the highly competitive glutamine-donor substrate N,N-dimethyl casein (3.8 µM) [4]. Measuring in the presence of 10 nM of each respective recombinant transglutaminase, provides in depth kinetic data that enables a meaningful analysis and comparison of the efficacy of inhibitors. The assay procedure is described in detail by Büchold et al. [3].
First, we compare potency, selectivity, and kinetics of TG2 inhibitors across different classes and warheads, to elucidate the relative contributions of intrinsic reactivity and binding affinity.
The inhibitors are classified based on their respective mechanism-of-action inactivating the exceptionally nucleophilic cysteine in the catalytic center of transglutaminases via: Michael addition (Michael acceptor class, Figure 1) [3, 5], alkylation (diazooxonorleucine “DON” compounds, Figure 2) [6, 7], and acetonylation (thioimidazolium carbonyl derivatives, Figure 3) [8].
Figure 1. Mechanism of inhibition involving nucleophilic attack by the active site cysteine on an α,β-unsaturated methyl ester (Michael acceptor inhibitor).
Figure 2. Irreversible alkylation resulting from nucleophilic attack of the active-site cysteine on the diazooxonorleucine “DON” carbonyl group under nitrogen release.
Figure 3. Nucleophilic attack of the active site cysteine residue on the thioimidazolium carbonyl group under thione release and irreversible cysteine acetonylation.
Kinetic Evaluation
All presented tool compounds are irreversible-acting inhibitors and should ideally be characterized by the second-order rate constant k2nd, considering both the dissociation constant Ki (target affinity, kon / koff ratio) and kinact (inactivation rate constant). Importantly, k2nd is defined as the ratio of kinact to Ki [9]. However, to enable straightforward, easy interpretable comparisons of efficacy across isoenzymes (selectivity), potency was primarily assessed using IC50 values (Table 1). For potent inhibitors, k2nd values were additionally determined against their primary target enzyme(s) TG2 and/or FXIIIa (Tables 2 and 3).
Table 1. Potency and selectivity based on standardized IC₅₀ values across electrophilic warheads and compound designs.
*Inhibition data for the potential drug candidate ZED3197 targeting FXIIIa were originally published in 2019 [10], prior to the current standardized assay conditions. For improved comparability, these data have now been re-evaluated (Table 1). The selectivity remains consistent with the results obtained in 2019.
Given the selectivity profile as indicated we would like to underline and revisit some important features. When targeting TG2, the well-established Z006 (aka “Z DON”) compound is first choice. Z006 shows excellent potency not only for TG2, but also for the TG3 and TG6 isoenzymes. In comparison, “Boc-DON” (B003) is a medium potent pan-transglutaminase inhibitor lacking activity for only FXIIIa.
In sharp contrast, peptidic ZED1301 readily blocks coagulation FXIIIa with an unprecedented selectivity profile. The improved peptidemimetic analogue ZED3197 [10] surpasses this performance, achieving a single-digit nanomolar IC₅₀ value. It has not escaped our awareness that both T101 and D004 show remarkable potency to inhibit FXIIIa, TG6, and TG1 at the same level. Z013 is the peptidic lead compound from the Michael acceptor class for CeD clinical development targeting TG2. Biotinylated B015 can be employed as an advanced, highly effective tag for labeling, while peptidemimetic ZED1227 - the most advanced clinical candidate - combines an exceptional potency with excellent selectivity which explains the safety profile in clinical trials.
Figure 4. The dissociation constant Ki defines the non-covalent binding [EI] of the inhibitor [I] to the target enzyme [E]. kinact describes rate at which a covalent inhibitor inactivates the enzyme, forming the irreversible [E-I] complex.
The second‑order rate constants k2nd for the presented covalent inhibitors were experimentally determined using activity assays under Kitz and Wilson conditions [11-13]. Enzyme activity was monitored fluorometrically in reaction mixtures containing substrate and increasing concentrations of the respective inhibitor. Relative fluorescence units (RFU) were plotted against time (Figure 5). For each inhibitor concentration, pseudo-first-order rate constants (kobs) for enzyme inactivation were determined by nonlinear fitting to a monoexponential model (eq 1).
The competition between substrate N,N-dimethyl casein and inhibitor was corrected by application of the factor α (eq 2), using the Michaelis constants (KM) for TG2 (2.78 µM) and FXIIIa (17.5 µM) from literature [14]. Subsequently, kobs values were plotted against α‑corrected inhibitor concentration (Figure 6), yielding hyperbolic saturation kinetics, characteristic of a two‑step covalent inhibition mechanism. Non‑linear regression of these saturation plots enabled independent determination of Ki and kinact according to equation (eq 3).
Figure 5. Time dependent TG2 activity (RFU); measured in serial dilutions of Z006 from 2.5 µM to 2.4 nM - compared to the control without inhibitor (red) - for the determination of pseudo-first-order rate constants (kobs).
Figure 6. Hyperbolic saturation kinetics, consistent with a two-step covalent inhibition mechanism for independent determination of Ki and kinact, as illustrated for Z006.
Table 2. Detailed kinetic evaluation of TG2-targeting compounds across different electrophilic warheads.*
Data reveal that inhibition rates across all electrophilic warheads are remarkably similar (0.03 to 0.05 min-1]. This is surprising, as theoretical considerations predict substantial differences in their intrinsic reactivities. Actually, α,β-unsaturated methyl esters (Michael acceptors) are the least reactive of the present warheads, reflecting their deliberately tuned electrophilicity. In contrast, DON type warheads display higher intrinsic, less tunable reactivity. Thioimidazolium carbonyl warheads exhibit the highest intrinsic electrophilicity. The highly polarized, positively charged carbonyl mimic is prone to rapid and irreversible reaction with thiols or other nucleophilic moieties [3, 15-17].
Accordingly, potency seems to be predominantly driven by non-covalent binding affinity (Ki) guiding the warhead into the catalytic center. The range of Ki values covers 34 nM to 6,410 nM. Finally, combining these isolated contributions accounts for the broad range for the potency observed (6,000 to 1,223,000 M-1 min-1), as indicated by k2nd (second-order rate constant). On the top of the list are back-to-back ZED1227 and Z006 (aka “Z-DON”) while the simplest compound D003 (developed by Merck Sharp and Dohme) represents the lower end of TG2 inhibitors evaluated. The factor XIIIa inhibitor ZED3197 also shows good affinity for TG2, overall the potency is quite similar to ZED754.
Table 3. Detailed kinetic evaluation of FXIIIa-targeting compounds across Michael acceptor and thioimidazolium carbonyl warheads.*
* Following a critical review, data will be reanalyzed within an optimized evaluation window in which the irreversible reaction has not yet reached completion, to obtain more practically relevant rate constants. This approach is intended to clarify the expected differences and enable discrimination between the various warhead classes. A revised blog article will be provided in the coming weeks.
Just a few commercial compounds targeting coagulation factor XIII (FXIII, F13) are available as indicated in Table 3. Again, data reveal that the rate of inhibition (kinact) across both electrophilic warheads is quite similar (0.015 to 0.021 min-1], roughly half of the inactivation values obtained for TG2. This supports the concept that transglutaminases do not discriminate the intrinsic reactivity or complementary interaction with the catalytic center – for the inhibitor classes in this particular study. Again, the potency of the compounds could be primarily assigned to the affinity as indicated by Ki in a range covering 10 nM to 140 nM. The apparent affinities are substantially higher than those measured for TG2, most likely reflecting the sixfold higher Michaelis constant of the casein substrate for FXIII relative to TG2.
In our drug discovery efforts targeting FXIIIa, we identified that potency requires detailed structure-activity-optimization and rather large molecules [13]. In sharp contrast, the small molecules developed by Merck Sharp & Dohme, despite lacking a peptidic backbone to drive target engagement, exhibit remarkably high apparent affinity. The combined contributions yield a potency spectrum of 215,000 to 1,500,000 M-1 min-1) as indicated by k2nd. As expected, ZED3197 ranks highest, while D004 unexpectedly claims second place. We may revisit those compounds in future drug discovery programs, despite their metabolic instability.
Correlation of k2nd values versus IC50
In accordance with former studies [18], we confirm a linear correlation between k2nd assessment and the more descriptive IC50 values (Figure 7). Under standardized assay conditions, potency can be reliably compared using IC50 values [19], which appears particularly appropriate for lead optimization of closely related compounds. Surprisingly, data suggest that this correlation, at least to some extent, may also extend across different electrophilic warheads and drug design concepts. We found that potency is primarily driven by affinity rather than by the intrinsic reactivity of the respective warhead. However, this relationship differs substantially for other inhibitor classes, e.g. acrylamide and chloroacetamide containing warheads [12], and further research is required to fully understand the complex interactions between transglutaminases and small molecule modulators.
Figure 7. Correlation between k2nd and IC50 values for targets TG2 (A) and FXIIIa (B).
Appendix: Overview of the selected tool compounds representing three distinct mechanisms of action, arising from their respective warhead classes.
References
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Zedira, Rösslerstraße 83, Darmstadt, Germany
Key Messages
- Comparative analysis of inhibitors requires standardized, controlled conditions
- Potency can be reliably compared using IC50 values
- For in depth analysis of suicide inhibitors, the second-order rate constant k2nd considers the contributions of intrinsic reactivity (kinact) and binding affinity (Ki)*
Standard conditions in a nutshell
- Transamidation assay at 37°C (MTP reader recommended)
- 10 nM of each respective recombinant transglutaminase
- Dansylcadaverine (15.9 µM) / N,N-dimethyl casein (3.8 µM)
Introduction
Tissue transglutaminase 2 (TG2) is a validated therapeutic target for celiac disease (CeD), with ZED1227 (aka TAK-227) as the most advanced clinical candidate. This direct-acting oral TG2 inhibitor has been tested in hundreds of healthy volunteers and CeD patients, including the ongoing dose-finding trial NCT07298343 (CEC-13), which evaluates efficacy under simulated inadvertent gluten exposure [1-3].
Beyond the development of proprietary clinical entities like ZED1227, Zedira provides a wide variety of tool compounds to catalyze research in the field of human transglutaminases. Notably, this is only part of a larger chemical space explored in academia and industry. A wide range of compounds, including inhibition data, has been published. However, the individual assay conditions vary considerably, making any direct comparison between inhibitors virtually impossible.
Here, we present a comparative analysis of commonly used tool compounds. Inhibition data were generated under uniform, standardized conditions using the classic transamidation assay, conducted at 37°C: dansylcadaverine (15.9 µM) is enzymatically incorporated into the highly competitive glutamine-donor substrate N,N-dimethyl casein (3.8 µM) [4]. Measuring in the presence of 10 nM of each respective recombinant transglutaminase, provides in depth kinetic data that enables a meaningful analysis and comparison of the efficacy of inhibitors. The assay procedure is described in detail by Büchold et al. [3].
First, we compare potency, selectivity, and kinetics of TG2 inhibitors across different classes and warheads, to elucidate the relative contributions of intrinsic reactivity and binding affinity.
The inhibitors are classified based on their respective mechanism-of-action inactivating the exceptionally nucleophilic cysteine in the catalytic center of transglutaminases via: Michael addition (Michael acceptor class, Figure 1) [3, 5], alkylation (diazooxonorleucine “DON” compounds, Figure 2) [6, 7], and acetonylation (thioimidazolium carbonyl derivatives, Figure 3) [8].
Figure 1. Mechanism of inhibition involving nucleophilic attack by the active site cysteine on an α,β-unsaturated methyl ester (Michael acceptor inhibitor).
Figure 2. Irreversible alkylation resulting from nucleophilic attack of the active-site cysteine on the diazooxonorleucine “DON” carbonyl group under nitrogen release.
Figure 3. Nucleophilic attack of the active site cysteine residue on the thioimidazolium carbonyl group under thione release and irreversible cysteine acetonylation.
Kinetic Evaluation
All presented tool compounds are irreversible-acting inhibitors and should ideally be characterized by the second-order rate constant k2nd, considering both the dissociation constant Ki (target affinity, kon / koff ratio) and kinact (inactivation rate constant). Importantly, k2nd is defined as the ratio of kinact to Ki [9]. However, to enable straightforward, easy interpretable comparisons of efficacy across isoenzymes (selectivity), potency was primarily assessed using IC50 values (Table 1). For potent inhibitors, k2nd values were additionally determined against their primary target enzyme(s) TG2 and/or FXIIIa (Tables 2 and 3).
Table 1. Potency and selectivity based on standardized IC₅₀ values across electrophilic warheads and compound designs.
*Inhibition data for the potential drug candidate ZED3197 targeting FXIIIa were originally published in 2019 [10], prior to the current standardized assay conditions. For improved comparability, these data have now been re-evaluated (Table 1). The selectivity remains consistent with the results obtained in 2019.
Given the selectivity profile as indicated we would like to underline and revisit some important features. When targeting TG2, the well-established Z006 (aka “Z DON”) compound is first choice. Z006 shows excellent potency not only for TG2, but also for the TG3 and TG6 isoenzymes. In comparison, “Boc-DON” (B003) is a medium potent pan-transglutaminase inhibitor lacking activity for only FXIIIa.
In sharp contrast, peptidic ZED1301 readily blocks coagulation FXIIIa with an unprecedented selectivity profile. The improved peptidemimetic analogue ZED3197 [10] surpasses this performance, achieving a single-digit nanomolar IC₅₀ value. It has not escaped our awareness that both T101 and D004 show remarkable potency to inhibit FXIIIa, TG6, and TG1 at the same level. Z013 is the peptidic lead compound from the Michael acceptor class for CeD clinical development targeting TG2. Biotinylated B015 can be employed as an advanced, highly effective tag for labeling, while peptidemimetic ZED1227 - the most advanced clinical candidate - combines an exceptional potency with excellent selectivity which explains the safety profile in clinical trials.
Figure 4. The dissociation constant Ki defines the non-covalent binding [EI] of the inhibitor [I] to the target enzyme [E]. kinact describes rate at which a covalent inhibitor inactivates the enzyme, forming the irreversible [E-I] complex.
The second‑order rate constants k2nd for the presented covalent inhibitors were experimentally determined using activity assays under Kitz and Wilson conditions [11-13]. Enzyme activity was monitored fluorometrically in reaction mixtures containing substrate and increasing concentrations of the respective inhibitor. Relative fluorescence units (RFU) were plotted against time (Figure 5). For each inhibitor concentration, pseudo-first-order rate constants (kobs) for enzyme inactivation were determined by nonlinear fitting to a monoexponential model (eq 1).
The competition between substrate N,N-dimethyl casein and inhibitor was corrected by application of the factor α (eq 2), using the Michaelis constants (KM) for TG2 (2.78 µM) and FXIIIa (17.5 µM) from literature [14]. Subsequently, kobs values were plotted against α‑corrected inhibitor concentration (Figure 6), yielding hyperbolic saturation kinetics, characteristic of a two‑step covalent inhibition mechanism. Non‑linear regression of these saturation plots enabled independent determination of Ki and kinact according to equation (eq 3).
Figure 5. Time dependent TG2 activity (RFU); measured in serial dilutions of Z006 from 2.5 µM to 2.4 nM - compared to the control without inhibitor (red) - for the determination of pseudo-first-order rate constants (kobs).
Figure 6. Hyperbolic saturation kinetics, consistent with a two-step covalent inhibition mechanism for independent determination of Ki and kinact, as illustrated for Z006.
Table 2. Detailed kinetic evaluation of TG2-targeting compounds across different electrophilic warheads.*
Data reveal that inhibition rates across all electrophilic warheads are remarkably similar (0.03 to 0.05 min-1]. This is surprising, as theoretical considerations predict substantial differences in their intrinsic reactivities. Actually, α,β-unsaturated methyl esters (Michael acceptors) are the least reactive of the present warheads, reflecting their deliberately tuned electrophilicity. In contrast, DON type warheads display higher intrinsic, less tunable reactivity. Thioimidazolium carbonyl warheads exhibit the highest intrinsic electrophilicity. The highly polarized, positively charged carbonyl mimic is prone to rapid and irreversible reaction with thiols or other nucleophilic moieties [3, 15-17].
Accordingly, potency seems to be predominantly driven by non-covalent binding affinity (Ki) guiding the warhead into the catalytic center. The range of Ki values covers 34 nM to 6,410 nM. Finally, combining these isolated contributions accounts for the broad range for the potency observed (6,000 to 1,223,000 M-1 min-1), as indicated by k2nd (second-order rate constant). On the top of the list are back-to-back ZED1227 and Z006 (aka “Z-DON”) while the simplest compound D003 (developed by Merck Sharp and Dohme) represents the lower end of TG2 inhibitors evaluated. The factor XIIIa inhibitor ZED3197 also shows good affinity for TG2, overall the potency is quite similar to ZED754.
Table 3. Detailed kinetic evaluation of FXIIIa-targeting compounds across Michael acceptor and thioimidazolium carbonyl warheads.*
* Following a critical review, data will be reanalyzed within an optimized evaluation window in which the irreversible reaction has not yet reached completion, to obtain more practically relevant rate constants. This approach is intended to clarify the expected differences and enable discrimination between the various warhead classes. A revised blog article will be provided in the coming weeks.
Just a few commercial compounds targeting coagulation factor XIII (FXIII, F13) are available as indicated in Table 3. Again, data reveal that the rate of inhibition (kinact) across both electrophilic warheads is quite similar (0.015 to 0.021 min-1], roughly half of the inactivation values obtained for TG2. This supports the concept that transglutaminases do not discriminate the intrinsic reactivity or complementary interaction with the catalytic center – for the inhibitor classes in this particular study. Again, the potency of the compounds could be primarily assigned to the affinity as indicated by Ki in a range covering 10 nM to 140 nM. The apparent affinities are substantially higher than those measured for TG2, most likely reflecting the sixfold higher Michaelis constant of the casein substrate for FXIII relative to TG2.
In our drug discovery efforts targeting FXIIIa, we identified that potency requires detailed structure-activity-optimization and rather large molecules [13]. In sharp contrast, the small molecules developed by Merck Sharp & Dohme, despite lacking a peptidic backbone to drive target engagement, exhibit remarkably high apparent affinity. The combined contributions yield a potency spectrum of 215,000 to 1,500,000 M-1 min-1) as indicated by k2nd. As expected, ZED3197 ranks highest, while D004 unexpectedly claims second place. We may revisit those compounds in future drug discovery programs, despite their metabolic instability.
Correlation of k2nd values versus IC50
In accordance with former studies [18], we confirm a linear correlation between k2nd assessment and the more descriptive IC50 values (Figure 7). Under standardized assay conditions, potency can be reliably compared using IC50 values [19], which appears particularly appropriate for lead optimization of closely related compounds. Surprisingly, data suggest that this correlation, at least to some extent, may also extend across different electrophilic warheads and drug design concepts. We found that potency is primarily driven by affinity rather than by the intrinsic reactivity of the respective warhead. However, this relationship differs substantially for other inhibitor classes, e.g. acrylamide and chloroacetamide containing warheads [12], and further research is required to fully understand the complex interactions between transglutaminases and small molecule modulators.
Figure 7. Correlation between k2nd and IC50 values for targets TG2 (A) and FXIIIa (B).
Appendix: Overview of the selected tool compounds representing three distinct mechanisms of action, arising from their respective warhead classes.
References
| [1] | Schuppan, D., et al. A Randomized Trial of a Transglutaminase 2 Inhibitor for Celiac Disease, N. Engl. J. Med. 2021, 385, 35. |
| [2] | Dotsenko, V., et al. Transcriptomic analysis of intestine following administration of a transglutaminase 2 inhibitor to prevent gluten-induced intestinal damage in celiac disease, Nat. Immunol. 2024, 1. |
| [3] | Büchold, C., et al. Features of ZED1227: The first‑in‑class tissue transglutaminase inhibitor undergoing clinical evaluation for the treatment of celiac disease, Cells 2022, 11, 1667. |
| [4] | Lorand, L., et al. Transamidating enzymes: II. A continuous fluorescent method suited for automating measurements of factor XIII in plasma, Anal. Biochem. 1971, 44, 221. |
| [5] | Lindemann, I., et al. Transglutaminase 2 in complex with a novel inhibitor, Protein Data Bank (PDB) entry: 3S3P, 2012. |
| [6] | Dion, H. W., et al. 6‑Diazo‑5‑oxo‑L‑norleucine, A New Tumor‑inhibitory Substance. II. Isolation and Characterization, J. Am. Chem. Soc. 1956, 78, 3075. |
| [7] | Hausch, F., et al. Design, Synthesis, and Evaluation of Gluten Peptide Analogs as Selective Inhibitors of Human Tissue Transglutaminase, Chem. Biol. 2003, 10, 225. |
| [8] | Freund, K. F., et al. Transglutaminase inhibition by 2‑[(2‑oxopropyl)thio]imidazolium derivatives: mechanism of factor XIIIa inactivation, Biochem. 1994, 33, 10109. |
| [9] | Bauer, R. A. Covalent inhibitors in drug discovery: from accidental discoveries to avoided liabilities and designed therapies, Drug Discov. Today 2015, 20, 1061. |
| [10] | Pasternack, R., et al. Novel inhibitor ZED3197 as potential drug candidate in anticoagulation targeting coagulation FXIIIa (F13a), J. Thromb. Haemost. 2019, e14646. |
| [11] | Kitz, R.; Wilson, I. B. Esters of methanesulfonic acid as irreversible inhibitors of acetylcholinesterase, J. Biol. Chem. 1962, 237, 3245. |
| [12] | Gates, E. W. J., et al. Peptidic Inhibitors and a Fluorescent Probe for the Selective Inhibition and Labelling of Factor XIIIa Transglutaminase, Molecules 2023, 28. |
| [13] | Mader, L. K., et al. A practical guide for the assay‑dependent characterisation of irreversible inhibitors, RSC Med. Chem. 2025, 16, 63. |
| [14] | Hauser, S., et al. Application of a Fluorescence Anisotropy‑Based Assay to Quantify Transglutaminase 2 Activity in Cell Lysates, Int. J. Mol. Sci. 2022, 23. |
| [15] | Pasternack, R., et al. Novel inhibitor ZED3197 as potential drug candidate in anticoagulation targeting coagulation FXIIIa (F13a), J. Thromb. Haemost. 2020, 18, 191. |
| [16] | McAulay, K., et al. Reactivity of Covalent Fragments and Their Role in Fragment Based Drug Discovery, Pharmaceuticals 2022, 15. |
| [17] | Hillebrand, L., et al. Emerging and Re‑emerging Warheads for Targeted Covalent Inhibitors: An Update, J. Med. Chem. 2024, 67, 7668. |
| [18] | Schaertl, S., et al. A profiling platform for the characterization of transglutaminase 2 (TG2) inhibitors, J. Biomol. Screen. 2010, 15, 478. |
| [19] | Wodtke, R., et al. Solution‑phase synthesis of the fluorogenic TGase 2 acyl donor Z‑Glu(HMC)‑Gly‑OH and its use for inhibitor and amine substrate characterisation, Anal. Biochem. 2020, 595, 113612. |
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