4,136
Views
6
CrossRef citations to date
0
Altmetric
Research Article

Mixed and non-competitive enzyme inhibition: underlying mechanisms and mechanistic irrelevance of the formal two-site model

Article: 2245168 | Received 13 Jun 2023, Accepted 01 Aug 2023, Published online: 14 Aug 2023

References

  • Symbolism and terminology in enzyme kinetics. Recommendations 1981. Biochem J. 1983;213(3):561–571.
  • Luo L, Parrish CA, Nevins N, McNulty DE, Chaudhari AM, Carson JD, Sudakin V, Shaw AN, Lehr R, Zhao H, et al. ATP-competitive inhibitors of the mitotic kinesin KSP that function via an allosteric mechanism. Nat Chem Biol. 2007;3(11):722–726.
  • Copeland RA. Evaluation of enzyme inhibitors in drug discovery. Ch. 3, 2nd ed. Hoboken: John Wiley & Sons, Inc.; 2013.
  • Osterman AL, Rodionova I, Li X, Sergienko E, Ma CT, Catanzaro A, Pettigrove ME, Reed RW, Gupta R, Rohde KH, et al. Novel antimycobacterial compounds suppress NAD biogenesis by targeting a unique pocket of NaMN adenylyltransferase. ACS Chem Biol. 2019;14(5):949–958.
  • Copeland RA, Anderson PS. Enzymes and Enzyme Inhibitors” in Textbook of Drug Design and Discovery. 3rd ed., P. Krogsgaard-Larsen, T. Liljefors, U. Madsen, editors. New York: Taylor and Francis; 2002
  • Cornish-Bowden A. Fundamentals of enzyme kinetics. Ch. 7, 3rd ed. London: Portland Press; 2004.
  • Johnson KA. Kinetic analysis for the new enzymology. Ch. 6. Austin (TX): KinTek Corporation; 2019.
  • Arya A, Kumar A. Inconsistencies in some common terms and notations in enzymology: Textbook examples and suggestions. Biochem Mol Biol Educ. 2019;47(2):140–144.
  • Srinivasan B. Words of advice: teaching enzyme kinetics. Febs J. 2021;288(7):2068–2083.
  • Strelow J, Dewe W, Iversen PW, Brooks HB, Radding JA, McGee J, Weidner J, et al. Mechanism of Action Assays for Enzymes. In Markossian S, Grossman A, Brimacombe K, editors. Assay Guidance Manual. Bethesda (MD): Eli Lilly & Company and the National Center for Advancing Translational Sciences; 2012. https://www.ncbi.nlm.nih.gov/books/NBK92001/
  • Sharma R. Enzyme inhibition: mechanisms and scope. In: Sharma RR, editor. Enzyme inhibition and bioapplications. Rijeka (Croatia): InInTech; 2012.
  • Cornish-Bowden A. Fundamentals of enzyme kinetics Ch. 5, 3rd ed. London: Portland Press; 2004.
  • Kumawat A, Raheem S, Ali F, Dar TA, Chakrabarty S, Rizvi MA. Organoselenium Compounds as acetylcholinesterase inhibitors: evidence and mechanism of mixed inhibition. J Phys Chem B. 2021;125(6):1531–1541. vol.
  • Qi D, Li H, Liang C, Peng P, Yang Z, Gao Y, Li Z, Zhang Q, Liu Z. Herb-drug interaction of Xingnaojing injection and Edaravone via pharmacokinetics, mixed inhibition of UGTs, and molecular docking. Phytomedicine. 2023;112:154696.
  • Le Corre L, Padovani D. Mechanism-based and computational modeling of hydrogen sulfide biogenesis inhibition: interfacial inhibition. Sci Rep. 2023;13(1):7287.
  • Converti A, Perego P, Torre P, Silverio da Silva S. Mixed inhibitions by methanol, furfural and acetic acid on xylitol production by Candida guilliermondii. Biotechnol Lett. 2000;22(23):1861–1865.
  • Deri B, Kanteev M, Goldfeder M, Lecina D, Guallar V, Adir N, Fishman A. The unravelling of the complex pattern of tyrosinase inhibition. Sci Rep. 2016;6 (6):34993.
  • Kim SB, Cho HJ, Kim YS, Kim DD, Yoon IS. Modulation of cytochrome P450 activity by 18β-glycyrrhetic acid and its consequence on buspirone pharmacokinetics in rats. Phytother Res. 2015;29(8):1188–1194.
  • Wang Y, Liu X, Schneider B, Zverina EA, Russ K, Wijeyesakere SJ, Fierke CA, Richardson RJ, Philbert MA. Mixed inhibition of adenosine deaminase activity by 1,3-dinitrobenzene: a model for understanding cell-selective neurotoxicity in chemically-induced energy deprivation syndromes in brain. Toxicol Sci. 2012;125(2):509–521.
  • Wang Z, Tan X, Lu G, Liu Y, Naidu R, He W. Soil properties influence kinetics of soil acid phosphatase in response to arsenic toxicity. Ecotoxicol Environ Saf. 2018;147:266–274.
  • Misko TA, Wijerathna SR, Radivoyevitch T, Berdis AJ, Ahmad MF, Harris ME, Dealwis CG. Inhibition of yeast ribonucleotide reductase by Sml1 depends on the allosteric state of the enzyme. FEBS Lett. 2016;590(12):1704–1712.
  • Nakahara H, Okada S, Mochida K. Kinetic studies on pancreatic lipase activity in micellar systems. I. Inhibition by sodium deoxycholate micelles. Chem Pharm Bull (Tokyo)). 1982;30(8):2673–2681.
  • Prescott TA, Panaretou B, Veitch NC, Simmonds MS. A yeast chemical genetics approach identifies the compound 3,4,5-trimethoxybenzyl isothiocyanate as a calcineurin inhibitor. FEBS Lett. 2014;588(3):455–458.
  • Bounias M, Morgan MRJ. An in vitro kinetic study of the mixed inhibition of honeybee hemolymph PNP-α-D-glucosidase by sucrose. Experientia. 1981;37(11):1147–1149.
  • Dhital S, Gidley MJ, Warren FJ. Inhibition of α-amylase activity by cellulose: Kinetic analysis and nutritional implications. Carbohydr Polym. 2015;123:305–312.
  • Liu J, Liu Y, He X, Teng B, McRae JM. Valonea Tannin: Tyrosinase Inhibition Activity, Structural Elucidation and Insights into the Inhibition Mechanism. Molecules. 2021;26(9):2747.
  • Pogacean F, Baldea I, Olenic L, Pruneanu S, Biris AS. Kinetic Determination of Drug Particles Concentration via Enzyme-Catalyzed Decomposition of Hydrogen Peroxide. Part Sci Technol. 2011;29(6):493–502.
  • Zhang C, Schilirò T, Gea M, Bianchi S, Spinello A, Magistrato A, Gilardi G, Di Nardo G. Molecular Basis for Endocrine Disruption by Pesticides Targeting Aromatase and Estrogen Receptor. Int J Environ Res Public Health. 2020;17(16):5664.
  • Alam MT, Olin-Sandoval V, Stincone A, Keller MA, Zelezniak A, Luisi BF, Ralser M. The self-inhibitory nature of metabolic networks and its alleviation through compartmentalization. Nat Commun. 2017;8:16018.
  • Holdgate GA, Meek TD, Grimley RL. Mechanistic enzymology in drug discovery: a fresh perspective. Nat Rev Drug Discov. 2018;17(2):115–132.
  • Robin T, Reuveni S, Urbakh M. Single-molecule theory of enzymatic inhibition. Nat Commun. 2018;9(1):779.
  • Cha SH, Hong J, McGuffie M, Yeom B, VanEpps JS, Kotov NA. Shape-Dependent Biomimetic Inhibition of Enzyme by Nanoparticles and Their Antibacterial Activity. ACS Nano. 2015;9(9):9097–9105.
  • Swinney D. Biochemical mechanisms of drug action: what does it take for success? Nat Rev Drug Discov. 2004;3(9):801–808.
  • Cornish-Bowden A. Why is uncompetitive inhibition so rare? A possible explanation, with implications for the design of drugs and pesticides. FEBS Lett. 1986;203(1):3–6.
  • Blat Y. Non-competitive inhibition by active site binders. Chem Biol Drug Des. 2010;75(6):535–540.
  • Johnson KA, Simpson ZB, Blom T. Global kinetic explorer: a new computer program for dynamic simulation and fitting of kinetic data. Anal Biochem. 2009;387(1):20–29.
  • Johnson KA, Simpson ZB, Blom T. FitSpace explorer: an algorithm to evaluate multidimensional parameter space in fitting kinetic data. Anal Biochem. 2009;387(1):30–41.
  • Chang A, Jeske L, Ulbrich S, Hofmann J, Koblitz J, Schombu I, Neumann-Schaal M, Jahn D, Schomburg D. BRENDA, the ELIXIR core data resource in 2021: new developments and updates. Nucleic Acids Res. 2021;49(D1):D498–D508.
  • Mannervik B, Jakobson I, Warholm M. Error structure as a function of substrate and inhibitor concentration in enzyme kinetic experiments. Biochem J. 1986;235(3):797–804.
  • Johnson KA. A century of enzyme kinetic analysis, 1913 to 2013. FEBS Lett. 2013;587(17):2753–2766.
  • Cornish-Bowden A. Fundamentals of enzyme kinetics. Ch. 6, 3rd ed. London: Portland Press; 2004.
  • Copeland RA. Enzymes: a practical introduction to structure, mechanism, and data analysis. Ch. 9, 2nd ed. New York: John Wiley & Sons, Inc.; 2000.
  • Waley SG. The kinetics of slow-binding and slow, tight-binding inhibition: The effects of substrate depletion. Biochem J. 1993;294 (Pt 1)(Pt 1):195–200. :
  • Turner PM, Lerea KM, Kull FJ. The ribonuclease inhibitors from porcine thyroid and liver are slow, tight-binding inhibitors of bovine pancreatic ribonuclease A. Biochem Biophys Res Commun. 1983;114(3):1154–1160.
  • Morrison JF, Walsh CT. The behavior and significance of slow-binding enzyme inhibitors. Adv Enzymol Relat Areas Mol Biol. 1988;61:201–301.
  • Lamba D, Pesaresi A. Kinetic modeling of time-dependent enzyme inhibition by pre-steady-state analysis of progress curves: the case study of the anti-Alzheimer’s drug galantamine. Int J Mol Sci. 2022;23:5072.
  • Cleland WW. The kinetics of enzyme-catalyzed reactions with two or more substrates or products. I. Nomenclature and rate equations. Biochim Biophys Acta. 1963;67:104–137.
  • Cleland WW. The kinetics of enzyme-catalyzed reactions with two or more substrates or products. II. Inhibition: nomenclature and theory. Biochim Biophys Acta. 1963;67:173–187.
  • Cleland WW. The kinetics of enzyme-catalyzed reactions with two or more substrates or products. III. Prediction of initial velocity and inhibition patterns by inspection. Biochim Biophys Acta. 1963;67:188–196.
  • Rebholz L, Northrop DB. Kinetics of enzymes with iso-mechanisms: dead-end inhibition of fumarase and carbonic anhydrase II. Arch Biochem Biophys. 1994;312(1):227–233.
  • Rebholz KL, Northrop DB. Kinetics of iso mechanisms. Methods Enzymol. 1995;249:211–240.
  • Adediran SA, Morrison MJ, Pratt RF. Detection of an enzyme isomechanism by means of the kinetics of covalent inhibition. Biochim Biophys Acta Proteins Proteom. 2021;1869(9):140681.
  • Rebholz KL, Northrop DB. Kinetics of enzymes with iso-mechanisms: analysis of product inhibition. Biochem J. 1993;296 (Pt 2)(Pt 2):355–360. :
  • Northrop DB. Problems in defining limits: how slow is very slow? Biochem J. 1994;301(Pt 2):623.
  • Krupka RM, Laidler KJ. Molecular mechanisms for hydrolytic enzyme action. I. apparent non-competitive inhibition, with special reference to acetylcholinesterase. Richard M. J Am Chem Soc. 1961;83(6):1445–1447.
  • Colandene JD, Topal MD. The domain organization of NaeI endonuclease: separation of binding and catalysis. Proc Natl Acad Sci U S A. 1998;95(7):3531–3536.
  • Horiuchi KY, Scherle PA, Trzaskos JM, Copeland RA. Competitive inhibition of MAP kinase activation by a peptide representing the alpha C helix of ERK. Biochemistry. 1998;37(25):8879–8885.
  • Jordan SP, Mao SS, Lewis SD, Shafer JA. Reaction pathway for inhibition of blood coagulation factor Xa by tick anticoagulant peptide. Biochemistry. 1992;31(23):5374–5380.
  • Ebert T, Tran N, Schurgers L, Stenvinkel P, Shiels PG. Ageing - oxidative stress, PTMs and disease. Mol Aspects Med. 2022;86:101099.
  • Krishnaswamy S. Exosite-driven substrate specificity and function in coagulation. J Thromb Haemost. 2005;3(1):54–67.
  • Ogawa T, Verhamme IM, Sun MF, Bock PE, Gailani D. Exosite-mediated substrate recognition of factor IX by factor XIa. The factor XIa heavy chain is required for initial recognition of factor IX. J Biol Chem. 2005;280(25):23523–23530.
  • Berman HM, Westbrook J, Feng Z, Gilliland G, Bhat GN, Weissig H, Shindyalov IN, Bourne PE. The Protein Data Bank. Nucleic Acids Res. 2000;28(1):235–242.
  • Bevc S, Konc J, Stojan J, Hodošček M, Penca M, Praprotnik M, Janežič D. ENZO: a web tool for derivation and evaluation of kinetic models of enzyme catalyzed reactions. PLoS One. 2011;6(7):e22265.