From mechanism to medicne
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1 From mechanism to medicne a look at proteins and drug design Chem 342 δ δ δ+ M 2009 δ+ δ+ δ M
2 Drug Design - an Iterative DSU Structural Analysis of Receptor Structural Analysis of Ligand-Receptor Complex Drug Lead Computational Analysis Ligand Design Biological Evaluation of Ligand Ligand Synthesis 2
3 Bringing a Drug to the DSU Drug Lead Toxicity Studies Phase I Trials 10,000 compounds 1-2 year 1,000 compounds 3-4 years 10 compounds 2-3 years Phase II Trials Phase III Trials Marketable Drug 1-5 compounds 2-3 years 1-2 compounds 2-3 years 1 compound av 15 years $900M to $1.5B 3
4 Amino DSU ighly polar zwitterions 2 3 R R 4
5 Amino DSU There are 20 common amino acids - 15 eutral glycine alanine valine leucine isoleucine proline S MeS 2 serine threonine cysteine methionine asparagine glutamine phenylalanine tyrosine tryptophan 5
6 Amino DSU Acidic and Basic 2 2 apartic acid glutamic acid lysine histidine arginine 6
7 Peptides - DSU Polymers of Amino Acids alanine valine ala-val dipeptide -terminus C-terminus valine alanine val-ala dipeptide 7
8 Peptide DSU Amide is the main bond - but can have disulfide bonds S S S S 8
9 Disulfide in DSU Vasopressin - antidiuretic hormone from pituitary Cys S S Cys Asp Tyr Phe Glu 9
10 Peptide - Protein DSU Primary Structure - amino acid sequence Secondary Structure - orientation of segments alpha-helix, beta sheets, loops Tertiary Structure - overall shape of the molecule Quaternary Structure - overal structure of protein aggregates 10
11 Alpha - DSU A helical secondary structure from keratin 11
12 Beta DSU Beta sheet secondary structure from Silk fibroin 12
13 DSU Globular protein with 574 amino acid residues 13
14 Types of DSU 14
15 DSU Proteins which act as catalysts for chemical reactions. 15
16 Citrate DSU A dimeric protein that catalyzes an Aldol Reaction 2 C + S CoA C 2 Citrate Synthase 2 C C 2 citrate + S CoA 16
17 Citrate Synthase DSU is is Asp Asp S CoA S CoA is is is 2 C C 2 S CoA is 2 C C 2 17
18 Matrix DSU Family of Zn-dependent enzymes 26 known MMP s Responsible for maintaining extracellular matrix MMP s out of balance in many diseases CACER, Arthritis, Multiple Sclerosis, Stroke Damage, and many more... 18
19 Catalytic Site of DSU S3 S2 S1 Zn 2+ S1' S2' S3' Cleavage site Pro Gln Gly Ile Ala Gly P3 P2 P1 P1' P2' P3' Catalytic Site of MMP-1 with natural collagen substrate 19
20 MMP DSU 20
21 hydroxamic acid DSU Zn binding group R 1 : P1' group - critical for activity and selectivity. Small groups selective for MMP- 1, larger groups will increase selectivity of other MMP's over MMP-1 and MMP-7. R α R 1 R 2 R 3 R 3 : P3' group - functionality widely tolerated. Aromatic groups increase MMP-3 selectivity. R α : P1 group - not necessary for activity, but substitution can lead to increased activity of some MMP's. R 2 : P2' group - wide range of substitution tolerated with aromatic groups preferred. More bulky groups increase oral bioavailability by decreasing amide bond scission. 21
22 ydroxamate Bound to DSU MMP-3 (Stromelysin 1) Me 22
23 Sulfonamide Bound to DSU MMP-3 (Stromelysin 1) S 23
24 2006 obel Prize in Chemistry "for his studies of the molecular basis of eukaryotic transcription" Prof. Roger Kornberg Dept. of Structural Biology Stanford University School of Medicine
25 DA DSU Watson and Crick discovered DA was made up of two strands running in opposite directions The strands are held together by hydrogen bonding from the bases Specific bases bind to each other like lock and key The strands are Complementary 25
26 eterocycles in DA and DSU Adenine Guanine Cytosine 3 C Thymine Uracil 26
27 DSU The DA/RA bases are attached to phosphosugars 27
28 ucleic Acid DSU The nucleotides are connected together by the phosphates on the sugars 28
29 DA Double DSU Two grooves are formed Sugar phosphate runs along the outside The major groove is slightly bigger and deeper than the minor groove 29
30 The DSU DA is a code for the synthesis of proteins. Every 3 base pair sequence is directly correlated with a specific amino acid. 30
31 DSU DA unwinds and codes an RA strand RA Polymerase 31
32 DSU RA encodes the amino acid sequence for protein synthesis 32
33 DA Wraps Around istone DSU 33
34 ucleosomes Coil DSU 34
35 Wrapped Up DSU 35
36 istone DSU Tumor Cell DAC Inhibitor yperacetylated istones Transcription Activation of Preprogrammed Genes Cell Growth Inhibited, Apoptosis, and/or Differentiation 36
37 Effectiveness in Clinical DSU DAC Inhibitors show marked effect in the treatment of cutaneous T-cell lymphoma Phase II clinical trials of FK228 37
38 DAC DSU DAC Like omolog 35.2% sequence homology with human DAC1 Active site homology much higher F i n n i n, e t. a l. a t u r e , 4 0 1,
39 DAC Inhibitor DSU ZBG linker surface binding group Typical DAC Inhibitors 39
40 DAC DSU Carboxylates Cyclic Peptides phenylbutyrate mm Benzamides a Ph Ph CAP50 ydroxamate S S depsipeptide nm MS-275 µm 2 Me 2 TSA Electrophilic Ketones CF 3 SAA nm 40
41 TSA and SAA - ydroxamic DSU Trichostatin A TSA IC nm Suberoylanilide ydroxamic Acid SAA IC nm 41
42 ydroxamic Acid DSU Zn D D 42
43 SAA and DAC DSU 43
44 DSU Proteins are the stuff of life. DA encodes amino acid sequence of proteins. Ezymes are proteins that catalyze chemical reactions. Disease can often be targeted by identifying specific enzymes that is important for the disease state. Synthetic chemistry can provide solutions for drug development. 44
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