Identification of enzyme inhibitory mechanisms from steady-state kinetics

Inhibition mechanism: Phytic acid, NADH as a peroxidase inhibitor

Peroxidase, a key enzyme causing enzymatic browning, and affected the potential values of fruit and vegetables. Phytic acid and NADH inhibited peroxidase in a competitive manner due to their reducing properties, and it's IC₅₀ (1.18 ± 0.32) × 10^-8, (8.02 ± 0.45) × 10^-6 mol L^-1, respectively. The interaction between phytic acid, NADH and peroxidase contributed to intrinsic fluorescence quenching and conformation alternation with a accuracy determination by multispectroscopic techniques (fluorescence spectra, FT-IR and CD spectra), respectively. Molecular docking simulation revealed that phytic acid, NADH interacted with His170, Ala34, Arg38, Ser73, Arg31, Lys174, Gln176, Asn175, Arg75; Gln176, Asn175, Phe221, Lys174, Gly173, Ser167, Phe172, Gly169, His170 in peroxidase, respectively and blocked substrates into catalytic reactions.

The inhibition mechanism of luteolin on peroxidase based on multispectroscopic techniques

Luteolin, a plant-derived flavonoid, was found to exert effective inhibitory effect to peroxidase activity in a non-competitive manner with an IC50 of (6.62 ± 0.45) × 10-5 mol L-1. The interaction between luteolin and peroxidase induced the formation of a static complex with a binding constant (Ksv) of 7.31 × 103 L mol-1 s-1 driven by hydrogen bond and hydrophobic interaction. Further, the molecular interaction between luteolin and peroxidase resulted in intrinsic fluorescence quenching, structural and conformational alternations which were determined by multispectroscopic techniques combined with computational molecular docking. Molecular docking results revealed that luteolin bound to peroxidase and interacted with relevant amino acid residues in the hydrophobic pocket. These results will provide information for screening additional peroxidase inhibitors and provide evidence of luteolin's potential application in preservation and processing of fruit and vegetables and clinical disease remedy.

Microplate fluorescence protease assays test the inhibition of select North American snake venoms' activities with an anti-proteinase library

Snake envenomation is a relatively neglected significant world health problem, designated an orphan disease by the WHO. While often effective, antivenins are insufficient. Could another approach greatly aid inhibition of the venom toxins? New fluorescent substrates for measuring protease activity in microplate assays suitable for high throughput screening were tested and found reproducible with snake venom. Representative North American venoms showed relatively strong proteinase and collagenase, but weaker elastase activities. Caseinolytic activity is inhibited by the nonspecific proteinase inhibitor 1,10-phenanthroline and by EDTA, as is collagenase activity, consistent with the action of metalloproteinases. Both general protease and collagenase assays CV average 3%, and Km measured were above normal working conditions. Using a library of anti -proteinase compounds with multiple venoms revealed high inhibitor activity by three agents with known multiple metalloproteinase inhibitor activity (Actinonin, GM6001, and NNGH), which incidentally supports the concept that much of the degradative activity of certain venoms is due to metalloproteinases with collagenase activity. These results together support the use of microplate proteinase assays, particularly this collagenase assay, in future drug repurposing studies leading to the development of new treatments for those envenomations that have a major proteolytic component in their pathophysiology.

Representação do efeito de inibição enzimática reversível para o modelo cinético de Michaelis-Menten no estado transiente

ResumoOs processos enzimáticos que seguem o modelo cinético de Michaelis-Menten foram estudados a partir de diferentes propostas para descrever a etapa de inibição reversível. As propostas de inibição foram comparadas a partir de um processo genérico, onde as constantes cinéticas receberam valores unitários e o valor numérico da concentração de substrato foi dez (10) vezes superior ao valor numérico da concentração de enzima. Para cada proposta de modelo de inibição foram obtidas soluções numéricas a partir de sistema não linear de equações diferenciais ordinárias, gerando gráficos que apresentaram, separadamente, a variação das concentrações da enzima, dos complexos enzimáticos, do substrato e do produto da reação. Foi obtido um modelo, dentre as propostas avaliadas, com desempenho indicando comportamento similar ao verificado no modelo clássico de Michaelis-Menten, onde o complexo de reação é rapidamente formado e, ao longo do processo, decai até tender a zero. Em contrapartida, diferentemente do modelo clássico, na nova proposta de modelo o efeito de inibição começa em zero e, ao longo do processo, tende ao valor nominal da concentração inicial da enzima. Tais respostas mostraram-se válidas para valores distintos de concentração de enzima e de tempo de processo, mostrando robustez e indicando uma tendência do somatório do substrato e do produto atingir o valor nominal da concentração inicial do substrato ao longo do tempo de processamento.

Fusidic acid targets elongation factor G in several stages of translocation on the bacterial ribosome

The antibiotic fusidic acid (FA) targets elongation factor G (EF-G) and inhibits ribosomal peptide elongation and ribosome recycling, but deeper mechanistic aspects of FA action have remained unknown. Using quench flow and stopped flow experiments in a biochemical system for protein synthesis and taking advantage of separate time scales for inhibited (10 s) and uninhibited (100 ms) elongation cycles, a detailed kinetic model of FA action was obtained. FA targets EF-G at an early stage in the translocation process (I), which proceeds unhindered by the presence of the drug to a later stage (II), where the ribosome stalls. Stalling may also occur at a third stage of translocation (III), just before release of EF-G from the post-translocation ribosome. We show that FA is a strong elongation inhibitor (K50% ≈ 1 μm), discuss the identity of the FA targeted states, and place existing cryo-EM and crystal structures in their functional context.