Approaches to the Rational Design of Enzyme Inhibitors

Abstract

Selective inhibitors of enzyme‐catalyzed reactions are widely used in both biochemical and medical science. The inhibitor may be used to block either a single enzyme or a metabolic pathway. The utility of an enzyme inhibitor as a mechanistic probe or a therapeutic agent will depend, in part, on the potency of the inhibitor and its specificity toward its target enzyme. These properties will, in turn, depend on the number and type of interactions the inhibitor makes with the enzyme and the overall mode of inhibition. Here we provide a concise overview of the forces involved in inhibitor binding, and a brief summary of the treatment of enzyme kinetic data. Enzyme inhibitors have been divided into two groups, reversible and irreversible, based on whether the inhibitor binds covalently to its target enzyme. Within these groups inhibitors have been classified on the basis of kinetics, structure, and mechanism. Examples are provided in all cases and, where possible, these are of inhibitors possessing therapeutic interest. The criteria for inclusion in each class of inhibitor are described, as well as the kinetic implications, with particular reference to the specificity of the inhibition. Treatment of the examples includes discussion of the design aspects and, if appropriate, a historical perspective that demonstrates the development of a rational approach to inhibitor design.

Structure-Based Drug Design of Bisubstrate Inhibitors of Phenylethanolamine N-Methyltransferase Possessing Low Nanomolar Affinity at Both Substrate Binding Domains1

“…The bisubstrate inhibitors all displayed competitive inhibition versus AdoMet and noncompetitive inhibition versus PEA (Table ). This pattern is consistent with a steady-state ordered mechanism, in which AdoMet binds first . In light of that observation, the data in Table for the bisubstrate inhibitors were calculated using a competitive binding model versus 3 ( K is AdoMet ) and a mixed (noncompetitive) model versus 5 ( K is PEA and K ii PEA ) .…”

“…This pattern is consistent with a steady-state ordered mechanism, in which AdoMet binds first. 85 In light of that observation, the data in Table 1 for the bisubstrate inhibitors were calculated using a competitive binding model versus 3 (K is AdoMet ) and a mixed (noncompetitive) model versus 5 (K is PEA and K ii PEA ). 86 It should be noted that the inhibition patterns were determined by measuring the initial rates at varying concentrations of one reactant and a fixed concentration of the second reactant.…”

Synthesis and Structure−Activity Relationship for a Novel Class of Potent and Selective Carbamoyl-Triazole Based Inhibitors of Hormone Sensitive Lipase

“…Proposed Mechanism of Inhibition. On the basis of the chemical structure, it is expected that all the HSL inhibitors 4b , 4g , 5 , 6, and 7 are pseudosubstrates or pseudoirreversible inhibitors . It is believed that the inhibitors are capable of acylating the active site serine in a time-dependent manner as described for carbamates such as physostigmine and postulated for oxadiazol-2-ones (both AChE inhibitors).…”

Planejamento racional de novos agentes quimioterápicos: Identificação e estudos cinéticos de novos inibidores da gliceraldeído-3-fosfato desidrogenase glicossomal de Trypanosoma cruzi

“…Além disso, em programas de planejamento de fármacos as sinergias entre as diversas técnicas avançadas empregadas no planejamento molecular, como por exemplo, técnicas cristalográficas de raios-x, ensaio virtual, RMN, SAR, QSAR, entre outras75 , contribuem para que o processo possa ser bem-sucedido.3 CINÉTICA ENZIMÁTICAA determinação das constantes cinéticas K M e V max constitui uma etapa essencial para a compreensão da cinética enzimática e para o estudo de reações catalisadas enzimaticamente. O procedimento consiste em medir a velocidade inicial da reação a várias concentrações de substrato 76. Este procedimento inicia com as etapas básicas de formação e quebra do complexo enzima-substrato E•S, Figura 12.…”

“…Em conjunto, ambos os aspectos permitem uma menor necessidade de inibidor, tanto pelo fato de se diminuir sua possibilidade interação com outros sítios através da utilização de uma menor concentração (maior potência), como pela probabilidade menor de originar efeitos indesejados devido à sua ação em outros locais (seletividade), característica própria da estrutura química do inibidor ou dos metabólitos que pode gerar. 76A afinidade e a especificidade envolvida na interação entre o inibidor e os resíduos proteicos da enzima dependem de forças do tipo hidrofóbicas, dispersivas, eletrostáticas, ligação de hidrogênio e interações π-cátion, as quais são de fundamental importância para a formação e estabilização do complexo enzima-inibidor 76. É a soma destas interações que determina o grau de afinidade do complexo formado.…”