Activation by substoichiometric inhibition

Abstract

Startling reports described the paradoxical triggering of the human mitogen-activated protein kinase pathway when a small-molecule inhibitor specifically inactivates the BRAF V600E protein kinase but not wt-BRAF. We performed a conceptual analysis of the general phenomenon “activation by inhibition” using bacterial and human HtrA proteases as models. Our data suggest a clear explanation that is based on the classic biochemical principles of allostery and cooperativity. Although substoichiometric occupancy of inhibitor binding sites results in partial inhibition, this effect is overrun by a concomitant activation of unliganded binding sites. Therefore, when an inhibitor of a cooperative enzyme does not reach saturating levels, a common scenario during drug administration, it may cause the contrary of the desired effect. The implications for drug development are discussed.

Atomistic Simulations of the Mechanisms of the Poorly Catalytic Mitochondrial Chaperone Trap1: Insights into the Effects of Structural Asymmetry on Reactivity

“…Furthermore, given the recent detection of Trap1's supramolecular organization into homotetramers 22 adding further complexity to its ATPase control and panorama of recruitable substratesallosteric ligands could also be used to control interfaces responsible for oligomerization. 21 A Reliable Model? To build our model, we have relied on distinct in silico approaches.…”

“…Acting in a fashion similar to that of cochaperones, allosteric modulators specific to Trap1 introduce subtle alterations to its conformational equilibria and catalytic ability ,, and possibly, as in the unrelated chaperone DegP, could even trigger its oligomerization in a concentration-dependent fashion. When they kinetically facilitate attainment of its closed asymmetric state, they can even act as “accelerators”, , with potential benefits in treating pathologies linked to its underexpression.…”

HtrA family proteases of bacterial pathogens: pros and cons for their therapeutic use

“…Therefore, it is necessary to improve the selectivity of inhibitors and evaluate their effect on human HtrA1e4, in view of the central role of human HtrA1e4 in apoptosis and diseases [72]. In contrast, the advantage of the second method is that the allosteric pathway is less conservative but there is a risk of activation by inhibition [19]dthat is, reverse activation caused by the substoichiometric inhibitor, because the allosteric effect caused by the binding should increase the affinity of the unoccupied site for the ligand, which ultimately leads to increased enzyme activity. Therefore, when developing a drug that inhibits HtrA protease, it is necessary to consider the distribution of the inhibitor in different tissues and the reverse activation of protease in a low-concentration drug environment.…”

“…At the same time, attention should also be paid to the possible adverse effects of HtrA inhibitors. For example, the high genetic conservation of the protease domain may cause cross-reactions and adverse effects [18], substoichiometric inhibitors in a low-concentration pharmaceutical environment may cause the reverse activation [19] and the disappearance of biofilm inhibition may lead to an increase in chronic infections [16].…”

Computational Design of Novel Allosteric Inhibitors for Plasmodium falciparum DegP

“…DegP is known to have two binding sites per protomer, the catalytic site and the peptide-binding site of the PDZ domain, linked by an allosteric circuit. The activation domains (consisting of the regulatory loops as described earlier) are shared among the adjacent protomers mediating the coordinated activation of the catalytic sites [ 20 ]. The binding of ligands at the allosteric site channels a signal, opening the entry/exit gates, transferring a conformational change to the catalytic site to cause an activity modulation of the protein and increased substrate degradation ( Figure 2 ).…”