Margaret A. Daugherty. Announcements! Fall Michaelis Menton Kinetics and Inhibition. Lecture 14: Enzymes & Kinetics III

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1 Lecture 14: Enzymes & Kinetics III Michaelis Menton Kinetics and Inhibition Margaret A. Daugherty Fall 2004 Announcements! Monday 10/11 lecture: starts at 10:15; Taught by Dr. Stephen Everse o ffice our/review Session Tuesday evening. Review sessions Thurs & Fri from 5:30-7:00 omework due Friday 10/15 by 7 pm in my office. Key will be posted on Saturday. Late homework will be penalized! Exam II on Monday 10/18. Problems? See me!

2 Announcements! Kinetics lecture notes: Inhibition lecture: reading: C 13: pages C 14: pages Due to time constraints: We will not cover enzyme catalyzed bimolecular rxns or catalytic RAs or catalytic Abs (and these will not be on the exam). We will not cover b structure & function. :( utline Inihibition Kinetics Reversible competitive non-competitive Mixed non-competitive Uncompetitive inhibition Irreversible Distinguishable by kinetic inhibition patterns

3 Enzyme Inhibition Inhibitor (I): compound that decreases the rate of a catalyzed reaction Two modes of action: Reversible: I interacts via non-covalent interactions with E Irreversible: I interacts via covalent interactions with E (affinity labels; suicide inhibitors) Reversible Inhibition Inhibitors interact with the enzymes through noncovalent interactions. They can easily associate and dissociate from the enzyme. Competitive Inhibition: I binds to same site as S oncompetitive Inhibition: I binds to different site than S Mixed non-competitive Inhibition: I binds with differing affinities to E and ES complex Uncompetitive Inhibition: I binds only to ES complex

4 Competitive Inhibition I mimics S for binding; I reversibly binds into active site; Binding of I prevents S from binding owever, increasing S can compete off I Results in an apparent increase in K M for S substrate inhibitor Competitive Inhibition Michaelis-Menton Equation [E] t = [E] + [ES] + [EI] V = Vmax [S] K M (1+[I]/K I ) + [S] V = Vmax [S] K M app + [S]

5 V vs. [ S ] Graph for Competitive Inhibition Competitive inhibitors alter K m but do not change V max [ I ] = [ I ] = 1 velocity [ I ] = [ S ] Identification of Competitive Inhibition In the presence of a competitive inhibitor K M increase; V max remains the same; Slope = K M /V max ; Slope increases with [I] Inhibition can be overcome by increasing [S] - hence competitive!

6 Example of Competitive Inhibition Phosphonate analog Ribonuclease catalyses the hydrolysis of the phosphodiester bond between 2 nucleotides; UpcA is a strong competitive inhibitor of ribonuclease; Competitive inhibitors are not cures: IV/AIDS TERAPY Epidemiology *Global summary of the IV and AIDS epidemic in 2003 (July 2004) *umber of people living with IV globally in 2003: 37.8 million ( million) *umber of new infections globally in 2003: 4.8 million ( million) *umber of deaths due to AIDS globally in 2003: 2.9 million ( million) umber of people cured of IV <1 umber of infections prevented by vaccination <1 from UAIDS website, Sept. 2004

7 Young people (15-24 years old) living with IV, by region, end 2003 Sub-Saharan Africa 62 % Total: 10 million Asia 22% Eastern Europe & Central Asia 6% igh-income countries 2% orth Africa & Middle East 1% Latin America & Caribbean 7% Source: UAIDS/UICEF/W, Report on the Global AIDS Epidemic (Fig 30) From UAIDS 2004 global report ppt IV Infection Kills helper T cells; B cells can t efficiently proliferate in response to antigen stimulation.

8 IV Protease Characteristics Aspartyl protease (pepsin family); omodimer, 99AAs/monomer; All β structure; Active site Asp from each monomer Kd = 440 nm; kcat = 6.8 / sec (pepsin 400/sec) Substrates ydrophobic, unbranched AAs at the terminal side of the bond to be cleaved; Small peptides (7 AAs). Wlodawer 2002 IV protease cleaves a poly-protein R substrate specificity Phe Pro R'

9 Competitive Inhibitors - IV protease inhibitors Ritonavir and saquinavir are used to treat IV / AIDS. Inhibits IV protease (a aspartic protease) which cleaves larger viral protein precursors into IV proteins needed for the virus particle. R Phe Pro R' S Ritonavir S 2 Saquinavir Why are AIDS treatments not cures? Problem 1: inhibitors bind reversibly! atural substrates can compete for active site! Problem 2: inhibitor clearance - drugs can be metabolized in the body. Problem 3: IV mutation rate gives rise to drug resistance. 3.4 x 10-5 IV-1 mutations/base/replication event; IV-1 replications/day; Thus, 340,000 mutations/base/day

10 Ritonavir S S K i ~ 15 pm; igh (> 10 5 ) specificity for IV protease over pepsin; 70% bio-availability Good absorption t 1/2 ~ 1.5 hr What drugs have been developed for IV infection? Twenty drugs have been approved for treating individuals with IV infection. They are called antiretroviral drugs because they attack IV, which is a retrovirus. nce inside the cell, IV uses specific enzymes to survive. The first approved classes of antiretroviral drugs that were approved work by interfering with the virus' ability to use these enzymes. They fall into two categories: *Reverse transcriptase (RT) inhibitors. RT inhibitors interfere with an enzyme called reverse transcriptase or RT that IV needs to make copies of itself. There are two main types of RT inhibitors, and they each work differently. * ucleoside/nucleotide drugs provide faulty DA building blocks, halting the DA chain that the virus uses to make copies of itself. * on-nucleoside RT inhibitors bind RT so the virus cannot carry out its copying function. *Protease inhibitors (PI). Protease Inhibitors interfere with the protease enzyme that IV uses to produce infectious viral particles.. *Fusion inhibitors interfere with the virus' ability to fuse with and enter the host cell. Drugs Approved for IV Infection ucleoside/ucleotide RT Inhibitors on-nucleoside RT Inhibitors Protease Inhibitors Fusion Inhibitors abacavir delavirdine ritonavir pentafuside ddc nevirapine saquinavir ddi efavirenz indinavir d4t amprenavir 3TC nelfinavir ZDV lopinavir tenofovir atazanavir entricitabine fosamprenavir calcium

11 on-competitive Inhibition I binds to a site other than the active site Does not compete with S for binding to its site. K M remains unchanged. I can bind to both E and ES I prevents catalysis from occurring. V max is altered I can not be competed off by increasing [S] on-competitive Inhibition Michaelis-Menton Equation Chem 204 k cat app = k cat /(1+[I]/K I ) et result: enzyme becomes less effective in catalyzing chemical reactions V max app = k cat app [E] t V = V max app [S] K M + [S]

12 V vs. [ S ] Graph for on-competitive Inhibition Binding of S to E is unchanged ---> K M unchanged Presence of I affects V max ---> Vmax decreases Identification of oncompetitive Inhibition In the presence of a noncompetitive inhibitor K M is unchanged; V max decreases; The effects of noncompetitive inhibition cannot be overcome by increasing [S].

13 Mixed non-competitive inhibition I can bind to E or ES; Affinity differs for E and ES Key point: Vmax still changes, however Km also different Uncompetitive inhibition I + ES ESI I only combines with the ES complex!

14 Irreversible Inhibition Inhibitors interact with the enzymes through covalent attachment of the inhibitor to the enzyme; The formation of the covalent bond is a slow process. A time-dependent decrease in enzymatic activity is observed; Derivatized enzyme is no longer functional.

15 Time-dependent Decrease in Enzyme Activity v i t c a g n i n i a m e r Decrease in enzyme activity over time [ I ] v i t c a g n i n i a m e r Protection by substrate Constant [ I ] [ S ] % % time time Example of Irreversible Inhibition rganophosphates are used in insecticides and nerve gases Irreversible inhibitors of acetylcholinesterase React with the active site serine LD 50 of sarin in humans is ~ 0.01mg/kg!

16 Inhibitors as Affinity Labels Inhibitor contains a chemically reactive functional group which forms a covalent bond between the enzyme and inhibitor.elps to identify the active site of an enzyme! k 1 E + I E I E I k 2 k -1 where k 2 = k inact or k app Ly s (C 2)4 Ly s (C 2)4 2 R R C C2 B r C C2 R Penicillin - an affinity inhibitor penicillin S C R S C C 2 Ser C 2 Ser glycopeptide transpeptidase penicillin-enzyme complex

17 Suicide Inhibitors as Drugs Used to inactivate the enzyme; Relatively unreactive until bind to active site; Very reactive when combine irreversibly with the enzyme; Rational drug design; Very effective and few side effects. Review 1). Enzymes can be either reversibly or irreversibly inhibited. 2). An inhibitor is a compound that decreases that rate of a catalyzed reaction. 3). Reversible inhibition: (know the effects on the substrate saturation curves; Lineweaver-Burke plot) 4). Irreversible inhibition occurs when the inhibitor binds irreversibly (covalently) to the active site, thus completely preventing the substrate from having access to it.