3/17/2011. Enzyme Inhibition (Mechanism)

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1 LECTURE 4: Reaction Mechanism and nhibitors Kinetic data cannot unambiguously establish a reaction mechanism. Although a phenomenological description can be obtained the nature of the reaction intermediates remain indeterminate and other independent measurements are needed. Modes of Antimicrobial Action Cartoon Guide Equation and Description Enzyme nhibition (Mechanism) Competitive Non-competitive Uncompetitive ubstrate nhibitor E Compete for active site E + E E + P + E [] binds to free [E] only, and competes with []; increasing [] overcomes nhibition by []. E Different site E + E E + P + + E+ E [] binds to free [E] or [E] complex; ncreasing [] can not overcome [] inhibition. E E + E E + P + E [] binds to [E] complex only, increasing [] favors the inhibition by []. Juang RH (2004) BCbasics LECTURE LAYOUT NTRODUCTON REACTON MECHANM A. equential Reactions B. Random Bisubstrate Reactions C. Ping-Pong Pong Reactions NHBTOR. rreversible 2. Reversible Competitive inhibition, Uncompetitive inhibition. Noncompetitive inhibition Thus far, we have considered only the simple case of enzymes that act upon a single substrate,. This situation is not common. Usually, enzymes catalyze reactions in which two (or even more) substrates take part. Consider the case of an enzyme catalyzing a reaction involving two substrates, A and B, and yielding the products P and Q:

2 Reaction Mechanisms A: equential Reactions All substrates must combine with enzyme before reaction can occur Bisubstrate reactions C. Ping-Pong Reactions B. Random Bisubstrate Reactions Group transfer reactions One or more products released before all substrates added QUZ (0 min). How is enzyme specificity achieved? 2. Calculate Vmax & KM from the following data, and does the reaction obey Michaelis-Menten Menten kinetics? [DNA] mol total nucleotides/l Free nucleotides in solution, V (pmol/l) 0 min 0 min.0 x x x x x ANWER. The enzyme specificity is achieved through the characteristic of active site 2. Vmax = KM = 2.2E-08 R 2 = , so the reaction obeys Michaelis-Menten Menten kinetics 2

3 NHBTOR An important number of compounds have the ability to combine with certain enzymes in either a reversible or irreversible manner, and thereby block catalysis by that enzyme uch compounds are called NHBTOR and include drugs, antibiotics, poisons, anti metabolites, as well as products of enzymic reactions Two general classes of inhibitors are recognized ; rreversible Reversible nhibitors of Michaelis-Menten Enzymes. RREVERBLE NHBTOR An irreversible inhibitor forms a covalent bond with a specific function, usually an amino acid residue, which may, in some manner, be associated with the catalytic activity of the enzyme There are many examples of enzyme inhibitors which covalently bind not at the active site, but physically block the active site The inhibitor cannot be released by dilution or dialysis; kinetically, the concentration and hence the velocity of active enzyme is lowered in proportion to the concentration of the inhibitor and thus the effect is that of noncompetitive inhibition: rreversible nhibition E + E E + P + K E K Examples of irreversible inhibitors include; diisopropyl fluorophosphate which reacts irreversibly with serine proteases, chymotrypsin, and iodoacetate which reacts with essential sulfhydryl group of an enzyme such as triose phosphate dehydrogenase: E-H+CH2COOH E-CH2COOH+H Reaction of the irreversible inhibitor diisopropylfluorophosphate (DFP) with a serine protease Diisopropyl fluorophosphate 3

4 A unique type of irreversible inhibition has been recently described as k cat inhibition in that a latent inhibitor is activated to an active inhibitor by binding to the active site of the enzyme. The newly generated inhibitor now reacts chemically with the enzyme leading to its irreversible inhibition These inhibitors have great potential as drugs in highly specific probes for active sites since they are not converted from the latent to the active form except by their specific target enzymes An excellent example is the inhibition of D-3-hydroxyl decanoyl ACP clehydrase (of E. coli) by the latent inhibitor 3-decynoyl-N-acetyl cystamine according to the following sequences of events: 2. REVERBLE NHBTON As the term implies, this type of inhibition involves equilibrium between the enzyme and the inhibitor, the equilibrium constant (Ki) being a measure of the affinity of the inhibitor for the enzyme. Three distinct types of reversible inhibition are known; Competitive inhibition, Uncompetitive inhibition Noncompetitive inhibition 4

5 A. Competitive nhibition Compounds that may or may not be structurally related to the natural substrate combine reversibly with the enzyme at or near the active site The inhibitor and the substrate therefore compete for the same site according to the reaction: V [] V max [] K M [] K Product C-OO - C-H C-H C-OO - Competitive nhibition ubstrate Competitive nhibitor uccinate Glutarate Malonate Oxalate C-OO - C-OO - C-OO - C-OO - H-C-H H-C-H H-C-H C-OO - H-C-H H-C-H C-OO - C-OO - H-C-H C-OO - uccinate Dehydrogenase Adapted from Kleinsmith & Kish (995) Principles of Cell and Molecular Biology (2e) p.49 C o m p etitiv e in h ib ito r /V + - E and E complexes are formed, but E complexes are never produced. One can conclude that high concentrations of substrate will overcome the inhibition by causing the reaction sequence to swing to the right. The velocity of reaction can be calculated by the following equation -/KM / -/[K M (+/K)] Among other enzymes that may undergo competitive inhibition (Table ) is succinic dehydrogenase, which readily oxidizes succinic acid to fumaric acid. f increasing concentrations of malonic acid, which closely resembles succinic acid in structure, are added, however, succinic dehydrogenase activity falls markedly. This inhibition can now be reversed by increasing in turn the concentration of the substrate succinic acid. 5

6 HV protease vs Aspartyl protease HV Protease inhibitor is used in treating AD HV protease (homodimer) subunit Asp subunit 2 Asp ymmetric dimer B. Uncompetitive nhibition Compounds that combine only with the E complex, not with the free enzyme, are called uncompetitive inhibitors. The inhibition is not overcome by high substrate concentrations. domain domain 2 Asp Asp Aspartyl protease (monomer) Asymmetric monomer Juang RH (2004) BCbasics HV protease in a complex with the protease inhibitor ritonavir The structure of the protease is shown by the red, blue and yellow ribbons. The inhibitor is shown as the smaller ball-and-stick structure near the centre. Created from PDB Peptide-based protease inhibitor ritonavir K M value is consistently smaller than the K M value of the uninhibited reaction which implies that is more effectively bound to the enzyme in the presence of the inhibitor. The equation used to calculate the velocity of the noncompetitive inhibition is as follows V Vmax [ ] [] K M [ ] K Human immunodeficiency virus canning electron micrograph of HV- (in green) budding from cultured lymphocyte. Multiple round bumps on cell surface represent sites of assembly and budding of virions Uncom petitive inhibitor /V + - (+[]/K )/Vm ax -/V m ax -/K / M -(+[]/K )/K M C. Noncompetitive nhibition Compounds that reversibly bind with either the enzyme or the enzyme substrate complex are designated as noncompetitive inhibitors Noncompetitive inhibition therefore differs from competitive inhibition in that the inhibitor can combine with E, and can combine with E to form in both instances E. This type of inhibition is not completely reversed by high substrate concentration since the closed sequence will occur regardless of the substrate concentration ince the inhibitor binding site is not identical to nor does it modify the active site directly, the K M is not altered. 6

7 /V Noncompetitive + - V Vmax [] [] M K K [] (+[]/K)/Vmax -/Vmax / FEEDBACK NHBTON The switch: Allosteric inhibition Allosteric means other site Active site E Allosteric site 2008 Paul Billiet ODW One site fits the substrate like other enzymes The other site fits an inhibitor molecule witching off These enzymes have two receptor sites ubstrate cannot fit into the active site nhibitor molecule nhibitor fits into allosteric site HOW TO OLVE THE EQUATON 2008 Paul Billiet ODW 7

8 3/7/20. Competitive inhibitor V 2. Uncompetitive Vmax [] V [ ] K M [ ] K Vmax [] [ ] [] K M K [ ] K K M V V max [] V max [ ] K M K V Vmax [ ] V max y =/V; x = /[s] a = /Vmax /Vmax b = KM(+[]/K)/ )/Vmax Vmax y =/V; x = /[s] a = (+[]/K)/Vmax b = K M/Vmax 3. Noncompetitive nhibition Vmax [ ] V K M [] [ ] K [ ] [ ] K M K K V V max [ ] V max y =/V; x = /[s] a = (+[]/K)/Vmax b = KM(+[]/K)/Vmax OAL [] Diketahui suatu reaksi enzimatis tanpa dan dengan inhibitor dengan [] = 2,2.04M. Hitunglah KM dan Vmax tanpa dan dengan serta K V(-) V(+) * * * * *

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