MEDICINAL CHEMISTRY HD LECTURE NOTES UTS COURSE CODE COMPLETED 2017 SPRING

Transcription

1 MEDICINAL CHEMISTRY HD LECTURE NOTES UTS COURSE CODE COMPLETED 2017 SPRING

2 Enzymes: Structure and Functin Prtein Structure and Enzymes: Prteins cntain amin acid residues sticking ut frm the plypeptide backbne. These are critical t prtein shape, functin and drug binding Nte that amin acid residues are anything sticking ut frm the back bne Enzymes are prteins that act as catalysts They catalyze bth frward and reverse reactin, are therefre serve t accelerate a reactins prgress twards equilibrium by lwering transitin state energy, withut affecting equilibrium psitin During an enzyme catalysed reactin, the substrate binds t the enzyme, the reactin ccurs and than the prducts are released Enzymes catalyse reactin by: Prviding a reactin surface (active site) Bringing reactants tgether (including cfactrs) Psitining reactants crrectly fr reactin Weakening bnds in the reactants Prviding acid/base catalysis Prviding nuclephilic grups Stabilising the transitin state with intermlecular bnds

3 The Active Site Substrates bind t active site, usually a hydrphbic grve in the enzymes Cntains tw types f amin acid residues: Catalytic carry ut reactin (invlved in mechanism) Binding bind and hld substrate in active site, rients substrate crrectly with catalytic residues Knwledge f pssible bnding interactin types fr an enzyme s substrate allws us t guess what the enzyme active site might lk like, r if a chemical will bind Enzyme Mechanisms Binding Interactins: Old mechanism - lck and key with rigid enzyme and ligand But many enzymes can accmmdate structurally diverse substrates Current thery - induced fit, whereby upn substrate binding, the enzyme active site mlds t the substrate In induced fit, bnding distance is shrted t maximize the strengths f interactins As lng as active site desn t have t distrt t much, catalysis can ccur Therefre enzymes have sme substrate specificity rughly same shape As an induced fit ccurs, the substrate als changes shape Bnds are rtated, stretched and weakened, t facilitate the reactin Substrate binding must have apprpriate strength T weak = n reactin T strng = prducts may be trapped in active site Transitin state is als bund t the enzyme, and these interactins lwer transitin state energy (stabilise), which causes reactin t ccur quicker Enzyme Mechanisms Acid/Base Catalysis: Sme reactin require the remval r additin f a prtn (H+) t the substrate, and enzymes can act as bth a prtn acceptr r dnatr Acidic and basic amin acid residues in enzymes can act as bth

4 Enzyme Mechanisms Nuclephilic Grups: Sme enzymes catalyse reactins by prviding nuclephilic grups (OH and SH frm serine and cysteine, respectively) Eg. When serine is the nuclephile, an OH is added t the substrate Hwever, serine OH is nt a gd nuclephile, s it must be part f a catalytic triad cntaining a nuclephile, acid/base catalyst, and an rientatr fr the acid/base Enzyme Mechanisms Cfactrs: Sme enzymes require cfactrs t catalyse reactins Cfactrs are usually metal ins (eg. Zn r Fe) r small rganic mlecules called cenzymes (eg. NAD + ) Will have a substrate binding pcket and a cfactr binding pcket separate Regulatin f Enzymes: Activities f enzymes are highly regulated, which may invlve enhancement r inhibitin f an enzyme Sme enzymes self-regulate, where the prduct they prduce inhibits the enzyme Regulatin typically ccurs at a secnd binding site n the enzyme called an allsteric binding site Mst enzymes under allsteric cntrl are at the start f a bisynthetic pathway and the enzyme is cntrlled by the final prduct f the pathway Regulatin at a separate allsteric site (instead f active site) is preferable because: The final prduct has a different shape that may nt fit active site The final prduct desn t have t cmplete with the substrate External regulatin f enzymes als ccurs, where external signals (Eg. hrmnes, neurtransmitters) can als regulate the activity f the enzyme A chemical messenger initiates a signal cascade which activates enzymes called prtein kinases, which phsphrylate target enzymes t affect activity (switch n) Summary: Enzymes are catalysts. Hw enzymes wrk- transitin state energy Substrates t enzymes binding- induced fit, rle in catalysis Nuclephilic reactins f enzymes- mechanism, catalytic triad. What cfactrs are. Hw enzyme activity is regulated- allsteric binding sites, external regulatin

5 Review Questins: 1. The first step in drug discvery is usually: a) Phase I clinical trial b) Finding a lead cmpund c) Finding a drug target d) Drug design 2. A drug that cntains a carbxylate grup is able t participate in which f the fllwing binding interactins: a) Hydrgen bnds b) Inic bnds c) In-diple bnds d) All f the abve 3. The fllwing cmpund is enzymatically metablised. A. Suggest what srt f binding interactins might be invlved in hlding the cmpund in the active site. The psitively charged amine grup cause frm inic interactins. The psitive charge can als set up a diple in an armatic ring. The partially psitive H s can frm H bnds. The partially psitive N can act as a HBD fr H bnds. The partially negative O can act as a HBA fr H bnds. Methyl grups act in van der Waals interactins. B. Hw d these binding interactins might make the cmpund mre susceptible t the enzymatic reactin? The interactins twist and stretch the cmpund, which weakens the bnds. This makes it mre susceptible t the reactin. 4. Lactate dehydrgenase has a 1000-fld selectivity fr lactate as a substrate ver malate. Hwever if a mutatin ccurs that alters an active site glutamine fr a arginine, the enzyme shws a fld selectivity fr malate ver lactate. Explain this astnishing transfrmatin. The amide grup is replaced with a psitively charged guanine. Therefre, it can frm an additinal inic bnd with malate and has a preference fr it.

6 Enzymes As Targets Enzyme Inhibitrs: Useful when a deficiency in substrate r an excess f metablite causes disease Substrate deficiency Disease seizures frm lw levels f GABA Drug anticnvulsant inhibits the enzyme that degrades GABA Metablite excess Disease - inflammatin frm excess prstaglandins (cramps) Drugs aspirin inhibits the COX enzymes that make prstaglandins Inhibitrs als make great pisns by inhibiting enzymes vital t rganism health Cyanide inhibits cytchrme Nerve agents inhibit acetylchlinesterase Als useful t treat infectin (bacteria, fungus, virus) be selectively targeting enzymes specific t the freign rganism Penicillin inhibits an enzyme invlved in bacterial cell wall synthesis The reduce txicity enzyme inhibitrs are designed t be selective t targets Hw Enzyme Inhibitrs Wrk: If the prduct binds t tightly t the active site f an enzyme, the enzyme becmes blcked (inhibited) This implies a fine balance f binding interactins Mst enzyme inhibitrs are cmpunds that bind mre strngly t the active site than the enzymes substrate, thus blcking the active site Enzyme inhibitrs are classed based n: 1. Where they bind Active site inhibitrs (mst cmmn) Allsteric site inhibitrs 2. Hw they bind Reversible inhibitrs (bind thrugh intermlecular bnds) Irreversible inhibitrs (bind thrugh cvalent bnds) Reversible Active Site Inhibitrs: Reversible inhibitrs (cmpetitive inhibitrs) bind t active site by intermlecular bnds, s an equilibrium acts between free and bund inhibitrs and substrate Strnger inhibitr binding results in strnger inhibitin Increasing substrate cncentratin reverses inhibitin Cmpetitive inhibitrs are usually similar in structure t the natural substrate, but have additin binding grups that make them bind mre strngly t the active site The statins are a gd example, which inhibit 3-hydrxy-3-methylglutarylcenzyme A reductase (HMGR), an enzyme invlved in chlesterl synthesis HMG-CA. Statins mimic HMGRs natural substrate (S)-HMGCA.

7 Nt all cmpetitive inhibitrs are structurally similar t the natural substrate Sme have different structures and bind t ther binding regin within the active site (eg. might lk similar t the cfactr instead) Cmpetitive inhibitrs can bind t the site nrmally ccupied by the enzymes cfactr, and therefre cmpetes with the cfactr Enzyme inhibitrs may be based ff f transitin states rather than substrates: Effective catalysis needs enzyme t stabilise transitin state by binding it mre tightly than the substrate r prduct Therefre, inhibitrs that mimic the transitin state are very strng inhibitrs Transitin states cannt be islated, s drug design based n intermediates, which are clser t transitin state than substrates/prducts Reactin intermediates are ften unstable, s drug design als addresses stabilisatin f the structure Irreversible Active Site Inhibitrs: Frm cvalent bnds with amin acid residues in active site and permanently blck functin Enzymes cntinually made t replace irreversibly inhibited nes, drug actin nt permanent Irreversible inhibitrs are nt cmpetitive, increasing substrate will nt reverse inhibitin Tw main classes: Irreversible inhibitrs Mechanism-based inhibitrs (suicide substrates) Irreversible inhibitrs: Cntain reactive functinal grups that frm cvalent bnds Likely t be similar in structure t the substrate Risk f txicity because sme irreversible inhibitrs can ptentially react with any prtein (lack target selectivity) Mechanism-based inhibitrs: Als frm cvalent bnds with enzymes They dn t cntain a reactive functin grup, but instead nly becme reactive nce they underg an enzyme catalysed reactin Because they must be activated by the target enzyme, they are usually mre target selective than ther irreversible inhibitrs Allsteric Site Inhibitrs: Bind t an allsteric site used by endgenus cmpunds t regulate enzyme activity Upn binding f the inhibitr t the allsteric sire an induced fit changes the shape f the active site, preventing substrate access Increasing substrate cncentratin des nt reverse inhibitin Binding t the allsteric site can be reversible r irreversible Nt similar in structure t substrate (similar t allsteric regulatr) Reversible: Temprary inhibitin, lw txicity risk Cnstant redsing required t maintain drug cncentratin Irreversible: Less frequent dsing required Multiple pathways t txicity (build up f substrate, reactivity t ther prteins) Iszymes: Different amin acid sequence that catalyse that same reactins Appear at different lcatins and times in the bdy and can be selectivity targeted Fr example, cyclxygenase (COX) has 2 iszymes: COX-1 is always active and make prstaglandins essential t health COX-2 is activated in arthritis t prduce inflammatry prstaglandins Use f nn-selective COX inhibitrs causes txicity, but selectivity can be achieved fr COX-2 due t its active site having a valine residue, where COX-1 has isleucine, meaning the drug will nly fit int COX-2