enzyme inhibition, drugs interfering with enzymes

how can enzymes be inhibited?

• by specific small molecuels and ions through a major control mechanism

• drugs and txic agents

• irreversible inhibiton: covalent binding to the enzyme

• reversible inhibition: noncovalent interactions - dissociation

what is suicide inhibition?

• an irreversible form of enzyme inhibition
• the inhibitor binds to the active site of the enzyme and forms an irreversible complex through a covalent bond during the normal catalysis reaction
• e.g. aspirin, penicillin, fluorouracil

what is competitive inhibition?

• the inhibitor competes with the substrate for binding to the enzyme
• e.g. statins: competitive inhibitors of HMG-CoA reductase
  it can bind to the:
• active site: inhibitor competes with the substrate for the active site
• anywhere else: allosteric competitive inhibitor binds to an allosteric site, changes the conformation of the active site, and the substrate can no longer bind there; they compete for the enzyme

what is uncompetitive inhibition?

• the inhibitor binds only to the enzyme-substrate complex
• can prevent catalysis rather than substrate binding
• e.g. camptothecin: topoisomerase inhibitor

what are the types of reversible inhibition?

competitive, uncompetitive, noncompetitive

what is noncompetitive inhibition?

• inhibitor binds either the enzyme or enzyme-substrate complex
• can prevent catalysis rather than substrate binding
• e.g. doxycycline: collagenase inhibitor
• types: pure, mixed

what are pure noncompetitive inhibitors?

• bind equally well to the enzyme with or without substrate bound
• only the turnover number is decreased

what are mixed noncompetitive inhibitors?

• bind preferentially to either the free enzyme or the enzyme-substrate complex
• both substrate binding and turnover number are altered

what are the general principles of enzyme kinetics?

• V = rate of an enzyme reaction
• V_max = max rate of a reaction
• Km = substrate concentration at which the reaction velocity is half of the max

what are the enzyme kinetics in competitive inhibition?

• increase the apparent value of Km
• V_max remains unchanges
• can be overcome by a sufficiently high [S]

what are the enzyme kinetics in noncompetitive inhibition?

• inhibitor lowers the concentration of functional enzyme
• V_max is decreased
• Km is unchanged
• cannot be overcome by increasing substrate concentration

what are the enzyme kinetics in uncompetitive inhibition?

• inhibitor binds to ES to form ESI, depleting ES
• V_max and Km is decreased
• decrease in free enzyme corresponds to an enzyme with greater affinity for its substrate

what is the comparison of competitive vs noncompetitive inhibitors as potential drugs?

• drugs that act by noncompetitive and competitive mechanisms can be equally potent and selective
• competitive: only bind free enzymes and prevent the substrate from binding to the enzyme → higher concentrations of the inhibitor is requried when substrate concentrations are high
• noncompetitive: bind equally well to free enzyme and the enzyme-substrate complex → unaffected by high substrate concentrations

what are the total targets and drugs of human protein?

• targets: 667
• drugs: 1194

what are the total targets and drugs of pathogen protein?

• targets: 189
• drugs: 220

what are antibiotics?

• e.g. penicillin
• compounds produced by bacteria and fungi which are capable of killing, or inhibiting, competing microbial species

what is penicillin?

• one of the most widely used antibiotics in the world
• naturally produced by penicillium mold
• against many bacterial infections caused by staphylococci and streptococci
• treatment of diphtheria, gonorrhea, pneumonia, syphilis, and others
• estimated to have saved > 200 million lives

what is the MOA of penicillin?

• irreversibly inactivates bacterial transpeptidase
• interferes with the synthesis of cell walls of reproducing bacteria
• irreversibly inhibits transpeptidase: enzyme that catalyzes the last step in bacteria cell-wall biosynthesis
• suicide inhibitor
• defective walls cause bacterial cells to burst
• human cells are not affected: no cell walls

what is aspirin?

• extracts from the bark and leaves of the willow tree
• used for pain relief
• active compound: salicylic acid
• by neutralizing salicylic acid, which often irritated the stomach, with a base and acetyl chloride, acettylsalicylic acid (aspirin) is formed

what is the MOA of aspirin?

• irreversible inhibitor
• inhibits the cyclooxygenase (COX) enzymatic activity of prostaglandin H2 synthase (PGH2)
• prostaglandins promote the inflammatory response (swelling, pain, fever)
• cyclooxygenase inhibitors blunt this response
• the acetyl group in aspirin is transferred to the side chain of a Ser residue in the hydrophobic channel, blocking the active site
• both aspirin and salicylic acid bind in the same pocket on the enzyme, but the acetyl group of aspirin dramatically increases its effectiveness as a drug

what are ACE inhibitors?

• angiotensin converting enzyme inhibitors
• drugs that block the production of angiotensin II (competitive)
• help relax veins and arteries to lower BP: treat and manage hypertension
• prevent death from heart failure and lessen the frequency of hospitalizations
• reduce heart attacks in patients with diabetes
• protect kidney function in patients with diabetes or mild kidney disease

what is angiotensin II?

• hormone that circulates in the blood
• main role to constrict blood vessels
• can cause high BP
• present in abnormally high quantities in many cardiovascular diseases

what are angiotensin converting enzymes (ACE)?

• zinc metalloproteases
• hydrolyze peptides
• convert the inactive angiotensin I to the active angiotensin II by removing a dipeptide

what is thrombin?

• converts fibrinogen to fibrin to create a blood clot
• fine line between hemorrhage and thrombosis → the clotting process must be precisely regulated
• serine protease, final enzyme of blood coagulation cascade

what is the blood clotting cascade?

• enzymatic cascade: series of zymogen activations → rapid response
• the activated form of one clotting factor catalyzes the activation of the next precursor
• at each step, the signal is amplified
• a very small amount of inital factors suffice to trigger the cascade → rapid response to trauma

what are anticoagulant drugs?

• medicines that reduce blood clot formation
• prevent stroke, myocardial infarction, and pulmonary embolism in patients with increased clotting risk

what are direct thrombin inhibitors (DTI)?

• anticoagulant drugs
• univalent: bind only to the active site (e.g. argatroban, melagatran)
• bivalent: bind to both active and regulatory sites (e.g. hirudin, bivalirudin)

what is warfarin?

• anticoagulant drug
• vitamin K antagonist: inhibits enzymes required to regenerate the active form of vitamin K
• vitamin K is essential for the synthesis of prothrombin and several other clotting factors

what is HIV protease inhibitor?

• cleaves multidomain viral proteins into their active forms
• aspartyl protease
• e.g. indinavir, retrovir, etc.
• inhibits HIV protease: blocks the process completely, preventing the virus from being infectious
• in combination with inhibitors of other key enzymes, have dramatically reduced deaths from AIDS

what is indinavir?

• designed to resemble a peptide substrate of the enzyme
• the OH group central alcohol interacts with the 2 aspartate residues of the active site of HIV proteases, but generally absent in cellular aspartyl proteases
• specificity for HIV protease

what is paxlovid?

• SARS-Co-2 protease inhibitor
• antiviral drug combination (nirmatrelvir and ritonavir) that treats COVID-19
• nirmatrelvir: 3C-like (3CL) protease inhibitor
• ritonavir: strong cytochrome P450 (CYP) 3A4 inhibitor and pharmacokinetic boosting agent
• bioavailable orally
• prevents transmission and reduces hospitalization rate and mortality

what is 3CL?

protease that SARS-CoV-2, the virus that causes COVID-19, uses to make more copies of itself

what are protein kinases?

• transfer a 𝛾-phosphate group from ATP to serine, threonine, or tyrosine residues of a protein
• phosphorylate >30% of the cellular proteins
• classified by the amino acid substrate preference: serine-threonine; tyrosine; dual (phosphorylates serine, threonine, or tyrosine residues)

what are phosphatases?

transfer the phosphate from a phosphoprotein to a water molecule

what is gleevec (imatinib)?

• inhibits bcr-abl kinase by blocking the ATP-binding site
• highly specific
• used to treat CML by targeting tumor cells specifically, minimizing side effects
• 83.8% rate of 10-year overall survival
• effective inhibitor of several tyrosine kinases

what is chronic myelogenous leukemia (CML)?

• most cases involve the chromosomal translocation in which the tyrosine kinase encoding gene c-abl on chromosome 9 is randomly inserted into the bcr gene on chromosome 22
• leads to overexpression of the bcr-abl fusion gene