An Introduction to Medicinal Chemistry - Chapter 6 - Nucleic Acids (DNA & RNA) PDF

An Introduction to Medicinal Chemistry Chapter 6 DRUG TARGETS NUCLEIC ACIDS DNA & RNA Salih Al-Jabour,Dr.rar.nat Pharmacy Department AlQuds University Jerusalem, Palesinte 1. DEOXYRIBONUCLEIC ACID (DNA)...

An Introduction to Medicinal Chemistry Chapter 6 DRUG TARGETS NUCLEIC ACIDS DNA & RNA Salih Al-Jabour,Dr.rar.nat Pharmacy Department AlQuds University Jerusalem, Palesinte 1. DEOXYRIBONUCLEIC ACID (DNA) 1.1 Primary Structure 5' 5’ end end 5 ' 1 3 ' ' 3 3’ ' end 3' End Sugar phosphate 1. DEOXYRIBONUCLEIC ACID (DNA) 1.1 Primary Structure Building blocks - Nucleotides Deoxyadenosine Deoxyguanosine Deoxythymidine Deoxycytidine phosphate phosphate phosphate phosphate 1. DEOXYRIBONUCLEIC ACID (DNA) 1.1 Primary Structure Nucleotide = Phosphate + sugar + nucleic acid base NH2 Nucleic acid N base N Deoxyadenosine N N phosphate H2O3PO O Phosphate H H H Sugar H HO H 1. DEOXYRIBONUCLEIC ACID (DNA) 1.1 Primary Structure Nucleosides = Sugar + nucleic acid base Deoxyadenosine Deoxyguanosine Deoxythymidine Deoxycytidine 1. DEOXYRIBONUCLEIC ACID (DNA) 1.1 Primary Structure Sugar Deoxyribose Nucleic acid bases Adenine Guanine Cytosine Thymine Purines Pyrimidines 1. DEOXYRIBONUCLEIC ACID (DNA) 1.1 Primary Structure Adenine (A) Cytosine (C) Guanine (G) Note: Thymine (T) Sugar phosphate backbone is constant Bases attached in apparently random order 1. DEOXYRIBONUCLEIC ACID (DNA) 1.2 Secondary Structure - Double Helix o 10A Notes: G C AT Sugar phosphate backbone is ionised and faces TA T A Majo G C G C outward (favourable interactions with water) groove r TA T A Nucleic acid bases point inward and pair up A-T or G-C T A Mino AT Purine pairs with pyrimidine - constant diameter to groove r A T o T A C G G C 34A helix TA Base bairs are stacked (vdw interactions between pairs) T A GC G C Chains are complementary GC T A A T C G TA T A DNA DOUBLE HELIX 1. DEOXYRIBONUCLEIC ACID (DNA) 1.2 Secondary Structure - Double Helix o 10A G C A T TA T A G C Majo G C groov r e TA T A T A Minor A T groov A T o e T A 34A C G G C TA T A G C G C GC T A A T C G TA T A Base Pairing DNA DOUBLE HELIX G-C base pairing involves 3 H-bonds A-T base pairing involves 2 H-bonds 1. DEOXYRIBONUCLEIC ACID (DNA) 1.2 Secondary Structure - Double Helix Replication New DNA chains Template Template DNA DNA Double Helix Replication Daughter helices 1. DEOXYRIBONUCLEIC ACID (DNA) 1.2 Secondary Structure - Double Helix Replication Trinucleotide Template X Template Template 5 chain 5 5 chain chain ' A ' ' A A A X- C C C X T T A T A 3 C G C G C G ' 3 3 G C ' G C ' G C 3 5 3 5 3 5 ' ' Growing ' ' ' ' Growing Growing chain chain chain Approach of trinucleotide Base pairing Enzyme-catalysed 'splicing' 1. DEOXYRIBONUCLEIC ACID (DNA) 1.2 Secondary Structure - Double Helix Replication 1. DEOXYRIBONUCLEIC ACID (DNA) 1.2 Secondary Structure - Double Helix Replication 1. DEOXYRIBONUCLEIC ACID (DNA) 1.3 Tertiary Structure Notes: Double helix coils into a 3D shape - supercoiling Double helix has to unravel during replication Unravelling leads to strain Relieved by enzyme-catalysed cutting and repair of DNA chain Quinolone and fluoroquinolone antibacterial agents inhibit this enzyme 1. DEOXYRIBONUCLEIC ACID (DNA) 1.4 Action of topoisomerase II Relieves the strain in the DNA helix by temporarily cleaving the DNA chain and crossing an intact strand through the broken strand Tyrosine residues in the enzyme are involved in the chain breaking process The residues form covalent bonds to DNA The enzyme pulls the chains apart to create a gap 1. DEOXYRIBONUCLEIC ACID (DNA) 1.4 Action of topoisomerase II Relieves the strain in the DNA helix by temporarily cleaving the DNA chain and crossing an intact strand through the broken strand Tyrosine residues in the enzyme are involved in the chain breaking process The residues form covalent bonds to DNA The enzyme pulls the chains apart to create a gap The intact strand of DNA is passed through the gap 1. DEOXYRIBONUCLEIC ACID (DNA) 1.4 Action of topoisomerase II Relieves the strain in the DNA helix by temporarily cleaving the DNA chain and crossing an intact strand through the broken strand Tyrosine residues in the enzyme are involved in the chain breaking process The residues form covalent bonds to DNA The enzyme pulls the chains apart to create a gap The intact strand of DNA is passed through the gap The break is resealed  1. DEOXYRIBONUCLEIC ACID (DNA) 1.4 Action of topoisomerase II Relieves the strain in the DNA helix by temporarily cleaving the DNA chain and crossing an intact strand through the broken strand Tyrosine residues in the enzyme are involved in the chain breaking process The residues form covalent bonds to DNA The enzyme pulls the chains apart to create a gap The intact strand of DNA is passed through the gap The break is resealed 1. DEOXYRIBONUCLEIC ACID (DNA) 1.4 Action of topoisomerase II Mechanism of chain cutting 2. RIBONUCLEIC ACID (RNA) 2.1 Primary structure Similar to DNA with the following exceptions Ribose is used instead of deoxyribose Uracil is used rather than thymine Ribose Uracil 2. RIBONUCLEIC ACID (RNA) 2.2 secondary structure Notes Single stranded Some regions of helical secondary structure exist due to base pairing within the same strand (see t-RNA) Adenine pairs to uracil; guanine pairs to cytosine  2. RIBONUCLEIC ACID (RNA) 2.3 Tertiary structure Three types of RNA are involved in protein synthesis; Messenger RNA (mRNA) Relays the code for a protein from DNA to the protein production site Transfer RNA (tRNA) The adapter unit linking the triplet code on mRNA to specific amino acids Ribosomal RNA (rRNA) Present in ribosomes (the production site for protein synthesis). Important both structurally and catalytically 2. RIBONUCLEIC ACID (RNA) 2.3 Tertiary structure 5’ Base Pairing end Yeast alanine-tRNA mI Methylinosine I Inosine UH2 Dihydrouridine T Ribothymidine Ps Pseudouridine mG Methylguanosine m2G Dimethylguanosine Anticodon binding region for m-RNA ANTICODON Anticodon - contains 3 bases that are specific for the attached amino acid - base pairs to the complementary triplet code on m-RNA (the codon) 2. RIBONUCLEIC ACID (RNA) 2.4 Transcription : The copying of a segment of DNA which codes for a specific protein G U A U C U mRNA G U C C G G C T C T G C U A A A U A U T T T A T A C A C U A T G T C G G A G U A T C C C A G T C G U C C A G mRNA C C G C C G T G T C G T A T U A A A A U A T A T DNA double helix DNA unravelled Transcription to reveal gene 2. RIBONUCLEIC ACID (RNA) 2.5 Translation - protein synthesis Growing protein chain His Ribosome 60S P-site A-site GCU GCA CGA CAU GUC mRNA 40S 2. RIBONUCLEIC ACID (RNA) 2.5 Translation - protein synthesis OH Protein chain transferred Protein chain transferred His OH His GCU Ribosome 60S Ribosome 60S P-site A-site GCA P-site A-site CGA CAU GUC mRNA GCU GCA 40S CGA CAU GUC mRNA 40S 2. RIBONUCLEIC ACID (RNA) 2.5 Translation - protein synthesis Protein chain Protein chain transferred transferred His Val His tRNA Ribosome Ribosome 60S 60S P-site A-site P-site A-site GCA CAG GCA CGA CAU GUC CGA CAU GUC mRNA mRNA 40S 40S Translocation 2. RIBONUCLEIC ACID (RNA) 2.5 Translation - protein synthesis Transfer of growing peptide chain to next amino acid 2. RIBONUCLEIC ACID (RNA) 2.5 Translation - protein synthesisHis Growing protein chain OH His GCA His Ribosome Peptide 60S transfer P-site A-site GCU GCU GUA GCU GUA CGA CAU GUC CGA CAU GUC CGACAUGUC mRNA mRNA mRNA 40S 1. DEOXYRIBONUCLEIC ACID (DNA) 1.1 Primary Structure OH Val tRNA His OH His GCU His CAG Translocation A-site GUA GCU GUA P-site GUA CGA CAU GUC CGACAUGUC mRNA mRNA CGA CAU GUC mRNA 1. DEOXYRIBONUCLEIC ACID (DNA) 1.1 Primary Structure mRNA Ribosome DNA mRNA Translation Transcription Nucleus An Introduction to Medicinal Chemistry Chapter 5 DRUG TARGETS SIGNAL TRANSDUCTION Salih Al-Jabour,Dr.rar.nat Pharmacy Department AlQuds University Jerusalem, Palesinte 1. Signal Transduction involving Gs-Proteins GS-Protein -membrane-bound protein of 3 subunits (α, β, γ) -αs subunit has binding site for GDP -GDP bound non-covalently β γ α GDP 1. Signal Transduction involving Gs-Proteins 1.1 Interaction of receptor with Gs-protein Ligand Cell membrane Ligand G-protein binding binds Recepto r γ ß Induced γ ß Induced γ ß fit fit for α α α G-protein G Protein GDP GTP G-protein alters shape Binding site for G-protein opens GDP binding site distorted GDP binding weakened GDP departs 1. Signal Transduction involving Gs-Proteins 1.1 Interaction of receptor with Gs-protein γ ß γ ß GTP binds Fragmentation α α and release γ ß α Induced fit Binding site recognises GTP G-Protein alters shape Complex destablised Notes: Process repeated for as long as ligand bound to receptor Signal amplification - several G-proteins activated by one ligand αs Subunit carries message to next stage 1. Signal Transduction involving Gs-Proteins 1.2 Interaction of αs with adenylate cyclase Notes: Several 100 ATP molecules converted before αs-GTP deactivated Represents another signal amplification Cyclic AMP becomes next messenger (secondary messenger) Cyclic AMP enters cell cytoplasm with message 1. Signal Transduction involving Gs-Proteins 1.3 Interaction of cyclic AMP with protein kinase A (PKA) Notes: Protein kinase A is a serine-threonine kinase Activated by cyclic AMP Catalyses phosphorylation of serine and threonine residues on protein substrates Phosphate unit provided by ATP 1. Signal Transduction involving Gs-Proteins 1.3 Interaction of cyclic AMP with protein kinase A (PKA) Adenyla te cyclase AT cyclic P AMP Activation Protein Kinase A P Enzyme Enzym (inactive e ) (active) Enzyme-catalysed reaction 1. Signal Transduction involving Gs-Proteins 1.3 Interaction of cyclic AMP with protein kinase A (PKA) Protein kinase A - 4 protein subunits - 2 regulatory subunits (R) and 2 catalytic subunits (C) cAMP C Catalytic subunit C R R R R cAMP C binding sites C Catalytic subunit Note: Cyclic AMP binds to PKA Induced fit destabilises complex Catalytic units released and activated 1. Signal Transduction involving Gs-Proteins 1.3 Interaction of cyclic AMP with protein kinase A (PKA) C P Protein Protein + ATP + ADP Notes: Phosphorylation of other proteins and enzymes Signal continued by phosphorylated proteins Further signal amplification 1. Signal Transduction involving Gs-Proteins 1.4 Glycogen Metabolism – triggered by adrenaline in liver cells Adrenaline β-Adrenoreceptor adenylate cyclase 1. Signal Transduction involving Gs-Proteins 1.4 Glycogen Metabolism – triggered by adrenaline in liver cells Notes: Coordinated effect: activation of glycogen metabolism inhibition of glycogen synthesis Adrenaline has different effects on different cells e.g. activates fat metabolism in fat cells 1. Signal Transduction involving Gs-Proteins 1.5 Drugs interacting with cyclic AMP signal transduction Theophylline and caffeine - inhibit phosphodiesterases - phosphodiesterases responsible for metabolising cyclic AMP - cyclic AMP activity prolonged 1. Signal Transduction involving Gi-Proteins Notes: Bind to different receptors from those used by Gs proteins Mechanism of activation is identical αI subunit binds to adenylate cyclase and inhibits it Adenylate cyclase is under dual control (brake/accelerator) Background activity due to constant levels of αs and αi Overall effect depends on dominant alpha subunit Dominant alpha subunit depends on receptors activated 3. Phosphorylation Reactions Prevalent in activation and deactivation of enzymes Phosphorylation radically alters intramolecular binding Results in altered conformations NH3 NH3 NH3 O O P O O O O H O P O O O O O Active site Active site open closed 4. Signal Transduction involving Gq Proteins 4.1 Interaction with phospholipase C (PLC) Notes: Gq proteins - interact with different receptors from those recognised by GS and GI Split by the same mechanism to give an αq subunit The αq subunit activates or deactivates PLC (membrane bound enzyme) Reaction catalysed for as long as αq bound - signal amplification Brake and accelerator effect 4. Signal Transduction involving Gq Proteins 4.1 Interaction with phospholipase C (PLC) Active site Active site (closed) (open) DG α α α PIP2 PLC PLC PLC IP3 Active site αq departs (closed) DG α PIP2 α PLC PLC Phosphate IP3 Enzyme Binding deactivated weakened 4. Signal Transduction involving Gq Proteins 4.1 Interaction with phospholipase C (PLC) Reaction catalysed Inositol triphosphate Diacylglycerol (polar and moves (remains in membrane) into cell cytoplasm) Phosphatidylinositol diphosphate (integral part of cell membrane) R= long chain hydrocarbons P = PO32- 4. Signal Transduction involving Gq Proteins 4.2 Action of diacylglycerol Notes: Activates protein kinase C (PKC) PKC moves from cytoplasm to membrane PKC phosphorylates Ser & Thr residues of protein substrates PKC activates enzymes to catalyse intracellular reactions Linked to inflammation, tumour propagation, smooth muscle activity etc Cell membrane Binding DG DG site for DG DG PKC PKC Enzyme Enzyme PKC Active site (inactive) (active) closed Enzyme-catalysed reaction Cytoplasm Cytoplasm Cytoplasm DG binds to DG PKC moves to Induced fit opens binding site membrane active site 4. Signal Transduction involving Gq Proteins 4.4 Action of inositol triphosphate Notes: IP3 is hydrophilic and enters the cell cytoplasm Mobilises Ca2+ release in cells by opening Ca2+ ion channels Ca2+ activates protein kinases Protein kinases activate intracellular enzymes Cell chemistry is altered leading to a biological effect 4. Signal Transduction involving Gq Proteins 4.4 Action of inositol triphosphate Cell membrane IP3 Cytoplasm Calmodulin Calcium Ca++ Calmodulin Ca++ stores Activation Activation Protein Protein kinase P kinase P Enzyme Enzyme Enzyme Enzyme (inactive) (active) (inactive) (active) Enzyme-catalysed Enzyme-catalysed reaction 4. Signal Transduction involving Gq Proteins 4.5 Resynthesis of PIP2 Several steps IP3 + DG PIP2 Inhibition Li+ salts Lithium salts used vs manic depression 5. Signal Transduction - Tyr Kinase Linked Receptors 5.1 Reaction catalysed by Tyrosine Kinase O Tyrosine O H H N C kinase N C Protein Protein Mg+ Protein Protein + ATP ADP OH O P Tyrosine Phosphorylated residue tyrosine residue 5. Signal Transduction - Tyr Kinase Linked Receptors 5.2 Activation and phosphorylation of receptor Ligand Ligand P P P P P P P P P P Signalling protein 5. Signal Transduction - Tyr Kinase Linked Receptors 5.2 Activation and phosphorylation of receptor Notes: Active site on one half of dimer catalyses phosphorylation of tyrosine residues on other half Dimerisation of receptor is crucial Phosphorylated regions act as binding sites for further proteins and enzymes Results in activation of signalling proteins and enzymes Message carried into cell 5. Signal Transduction - Tyr Kinase Linked Receptors 5.3 Signalling pathways 1-TM Receptors Tyrosine kinase inherent or associated Guanylate cyclase Signalling proteins cGMP PLCγ IP3 GAP Grb2 Others kinase IP3 DG PIP3 Ca++ PKC  5. Signal Transduction - Tyr Kinase Linked Receptors 5.4 Example of a signalling pathway Growth factor 1) Binding of growth factor Dimerisation Phosphorylation 2) Conformational change HO HO HO HO PO PO OH OH OH OH OP OP HO OH HO OH HO OH OH OH PO PO PO OP Binding Grb2 SoS Ras and Grb2 SoS Ras GDP Binding of Grb2 and GTP/GDP Grb2 SoS SoS exchange GTP PO PO OP OP PO PO OP OP PO PO PO OP PO PO PO OP 5. Signal Transduction - Tyr Kinase Linked Receptors 5.4 Example of a signalling pathway Ras Grb2 SoS Gene transcription PO OP PO OP PO PO PO OP Raf (inactive) Raf (active) Mek (inactive) Mek (active) Map kinase (inactive) Map kinase (active) Transcription Transcription