EMBM − A New Enzyme Mechanism-Based Method for Rational Design of Chemical Sites of Covalent Inhibitors

Abstract

We introduce an enzyme mechanism-based method, EMBM, aimed at rational design of chemical sites, CS, of reaction coordinate analog inhibitors. The energy of valence reorganization of CS, caused by the formation of the enzyme-inhibitor covalent complex, is accounted for by new covalent descriptors W1 and W2. We considered CS fragments with a carbonyl reactivity center, like in native protease substrates. The W1 and W2 descriptors are calculated quantum mechanically on small molecular clusters simulating the reaction core of the formed covalent tetrahedral complex -anionic TC(O−) or neutral TC(OH). The modeling on a reaction core allows generation of various CS and corresponding TC(O−) and TC(OH) as universal building blocks of real inhibitors and their covalent complexes with serine or cysteine hydrolases. Moreover, the approach avoids the need for 3D structure of the target enzyme, so EMBM may be used for ligand-based design. We have built a Chemical Site of Inhibitors (CSI) databank with pairs of W1 and W2 descriptors pre-calculated for both CH 3 O(−) and CH 3 S(−) nucleophiles for every collected CS fragment. We demonstrated that contribution of a CS fragment to the binding affinity of an inhibitor depends on both its covalent reorganization during the chemical transformation and its non-covalent interactions in the enzyme active site. Consequently, prediction of inhibitors binding trend can be done only by accounting for all of these factors, using W1 and W2 in combination with non-covalent QSAR descriptors.

Application of EMBM to Structure‐Based Design of Warheads for Protease Inhibitors

“…Sequential exclusion of variables from Model 1 demonstrates that there is a synergistic effect of W1 and the non-covalent variables; good prediction is possible only when they are combined, whereas W1 alone is inadequate for either correlation on the training sets or prediction on the test sets (Figure 6b,c and Table 2 ). This conclusion corresponds well to previous results of ligand-based QSAR, [21,33] and QM/MM modeling [34,35] of FAAH inhibition: the potency of FAAH inhibitors does not correlate with electronic effects of substituents, but it depends on a combination of the covalent bond of CS to the catalytic Ser241 and non-covalent interactions with specific recognition elements in the enzyme active site.…”

“…They were used as precalculated values from our ICS databank. [21] We considered CS fragments with a carbonyl reactivity center, similar to native substrates of proteases. The W1 and W2 descriptors are calculated quantum mechanically on small molecular clusters simulating the reaction core of the formed covalent tetrahedral complex -either anionic TC(OÀ) or neutral TC(OH).…”

“…The results obtained in the current study, applying the covalent descriptors W1 and W2 and EMBM for a structurebased binding trend analysis, are in good agreement with a previous study in which the methodology was examined in a ligand-based approach. [21] Both approaches identified the dominant contribution of the enzyme-inhibitor new covalent bond energy to the trend of binding affinity in thrombin, and provided very poor correlation and prediction based on the non-covalent interactions only. Both approaches also identified the synergistic effect of the covalent and non-covalent interactions for the prediction of inhibitors binding trend to FAAH, though the structure-based approach exhibited better predictability in the contribution of the non-covalent interactions.…”

“…[21] Modeling on a reaction core allows generation of various CS and corresponding TC(OÀ) and TC(OH) as universal building blocks of real inhibitors and their covalent complexes with serine/threonine or cysteine hydrolases.…”

From Catalytic Mechanism to Rational Design of Reversible Covalent Inhibitors of Serine and Cysteine Hydrolases

“…W1 and W2 are calculated quantum mechanically on small molecular clusters that simulate the reaction core of the formed covalent TC, either anionic TC(O À ) or neutral TC(OH) ( Figure 5). [113,114] The electrophilicity of the carbon atom and the PA of the oxygen atom of the carbonyl group have the opposite influence on the binding trend of a series of warheads. The contribution of hydrogen bonds in the oxyanion hole to TC(O À ) stabilization is much smaller than the energy released in the formation of the enzymeÀinhibitor covalent bond.…”