Medicinal Chem Exam 3

Action of Estrogen Receptor

Estradiol binds to the receptor binding site which causes dimerization and exposure of AF-2 reigons. The Coactivator Nuclear transcription factor then binds and allows transcription to occur

Binding interactions for estradiol

Phenol and alcohol of estradiol are important binding groups

Binding site is spacious and hydrophobic

Phenol group of estradiol is positioned in narrow slot

Orientates rest of molecule

Acts as agonist

Raloxifene

Raloxifene is an antagonist (anticancer agent)

Phenol groups mimic phenol and alcohol of estradiol

Interaction with Asp-351 is important for antagonist activity

Side chain prevents receptor helix H12 folding over as lid

AF-2 binding region not revealed

Co-activator cannot bind

Tamoxifen

Antagonist for estrogen receptor

Anticancer agent

Letrazole

Aromatase Inhibitor

Treatment for estrogen positive breast cancer

Important for estradiol synthesis

Intercalating Agents Mechanism of action

They have planar aromatic or heteroaromatic ring systems that allow for them to slip between the layers of nucleic acid pairs and disrupt the helix shape.

Preference for minor or major groove

Prevents replication and transcription

Can inhibit topos

Proflavine

Intercalating Agents

Planar tricyclic system

Amino substituents are protonated and charged

Topical antibacterial during WWII

Targets bacterial DNA

Too toxic for systemic use

Proflavine interactions

Has van der Walls interactions between base pair and drug.

Ionic interactions between NH3 and O- of backbone

Electrostatic possible from stacking

Dactinomycin

Intercalating Agents

Extra binding to sugar phosphate backbone by cyclic peptides

Intercalates by minor grooves

Prevents DNA unwinding

Blocks transcription by blocking DNA-dependent RNA pol

Doxorubicin (Adriamycin)

Intercalating Agents

Extra binding to sugar phosphate backbone by NH3

Intercalates via major groove

Blocks action of topo II by stabilizing DNA-Enzyme complex

Topo poison

Bleomycin

Intercalating Agent & chain cutter

Anticancer Agent- Skin cancer

Intercalated by means of bithiazole ring system

Ferrous ion Fe2+ then chelated by nitrogens of primary amines, amide & pyrimidine ring

Reaction with O2 results in Fe2+ ion and ROS

Results in radical formation (from abstracting H from DNA) and chain cutting

Prevents DNA ligase from repairing damage

Etoposide

Topo poison- non intercalating

Stabalizes complex between DNA & Topo enzymes

Anticancer agent

Causes Chain cutting

Teniposide

Topo poison- non intercalating

Stabalizes complex between DNA & Topo enzymes

Anticancer agent

Causes Chain cutting

Camptothecin

Topo poison- non intercalating

Stabalizes complex between DNA and topo I

Single-Strand breaks accumulate in the chain

Irreversible double-strand breaks occur during transcription

Semi-synthetic analogs used as anticancer agents

Quinolones & Fluoroquinilones

Nalidixic acid & Ciprofloxacin

Topo poison- non intercalating

Synthetic agents used as antibacterials

Stabalizes complex between bacterial DNA & Topo

Binding site for agents revealed once DNA strands are nicked

Quinolones and fluoroquinilones

Four drug molecules are stacked in the bound complex

Bound to DNA and enzyme by hydrogen binding & ionic interactions - no stacking

Alkylating Agents

Contains highly electrophilic groups

Forms covalent bonds to nucleophilic groups in DNA

Prevents replication and transcription

Anticancer agents but could have toxic side effects

Can cause interstrand and intrastrand crosslinking if two electrophilic groups are present

Can result in miscoding

Nucleophilic groups on nucleic acid bases

Miscoding

Alkylated nucleic acid guanine prefers enol tautomer while regular G prefers keto tautomer. These differences cause incorrect binding instead of G-C it is G-T

Chlormethine (nitrogen mustard)

Alkylating Agent

Used in 1942

Causes intra & interstrand linking

Prevents replication

Mono-alkylation of guanine possible

Analogues with better properties have been prepared

Nitrosoureas

Lomustine & Carmustine

Alkylating Agent

Decomposes in body to form an alkylating (Cl-CH2-CH2+) agent and carbamoylating agent (O=C=N-R)

Alkylating agent unlikely, R-N+=- N more likely

Nitrosoureas Alkylating Agent

Causes interstrand crosslinking between G-G or G-C

Nitrosoureas carbamoylating agent

Reacts with lysine residues on proteins, may inactivate DNA repair enzymes

Busulfan

Alkylating Agent

Synthetic agent used as an anticancer agent

Causes interstrand crosslinking

Dacarbazine

Alkylating Agent

Prodrug activated by demethylation in liver

Decomposes to form methyldiazonium ion (N=-N+-CH3)

Alkylated guanine groups

Mitomycin C

Alkylating Agents

Prodrug activated in the body to form an alkylating agent

One of the most toxic anticancer drugs in clinical use

Cisplantin

Metallating Agent

Neutral inactive molecule acting as prodrug

Platinum covalently inked to chloro subsitiuents

Ammonia acts as ligands

Activated in cells with low chloride ion conc.

Chloro subs replaced with neutral water ligands

Produced positively charged species

Binds to DNA in G rich reigons

Intrastrand links

Localized unwinding of DNA helix

Inhibits transcription

Calicheamicin y1

Chain cutter

Antitumor agent

Generates DNA diradical that reacts with oxygen and results in chain cutting

Azidothymidine (AZT)

(Zidovudine;Retrovir)

Chain terminator

Prodrug used to treat HIV

Phosphorylated to triphosphate in body

Has two mechs of action: inhibit a viral enzyme (reverse transcriptase) & is added to growing DNA chain and acts as a terminator

Aciclovir (Zovirax) & Famciclovir

(Famvir)

Chain terminators

Prodrug used as antiviral

Same mech as AZT

Used on herpes simplex & shingles

Chain termination mechanism

Instead of base binding to growing strand and have OH substituent, the drug binds with an H substituent which keeps more bases from being able to be added.

Control of Gene Transcription

Design of synthetic molecules than can recognize and bind to specific base pairs

Hairpin polyamides containing heterocylic rings can bind to minor grooves

Binding involves amide groups and heterocycles

Particular patterns of heterocyclic rings allow recognition of particular base pairs

Capable of inhibiting transcription

Designed to bind to regulatory element of a gene

Drugs acting on rRNA

Antisense Therapy Advantages

Same effect as an enzyme inhibitor or receptor antagonist

Highly specific where the oligonucleotide is 17 nucleotides or more

Smaller dose levels required compared to inhibitors or antagonists

Potentially less side effects

Antisense Therapy disadvantages

‘Exposed’ sections of mRNA must be targeted

Instability and polarity of oligonucleotides (pharmacokinetics)

Short lifetime of oligonucleotides and poor absorption across cell membranes

Micro-RNA (miRNA)

Short segments of double stranded RNA

Recognized by enzyme complex RISC to produce single stranded RNA - small interfering or small inhibitory RNA (siRNA)

Binds to complementary region of mRNA

mRNA is cleaved by enzyme complex

miRNA advantages

siRNAs have potential to be used in gene therapy

Greater efficiency in silencing mRNA than conventional antisense therapy

One siRNA could lead to cleavage of several mRNA molecules

miRNA disadvantages

siRNAs need to be metabolically stable

Need to reach target cells

Need to enter target cells

Agents Blocking Transport Proteins

Agents binding to transport proteins prevents the re uptake of neurostransmitters

Results in increased levels of affected neurostransmitters

Result is similar to using an agonist

Cocaine

Reuptake inhibitor for dopamin in CNS

Causes euphoric effects

Reuptake inhibitor of noradrenaline in peripheral system

suppresses hunger

Fluoxetine (Prozac)

Selective serotonin reuptake inhibitor (SSRI)

Antidepressant

Desipramine

Tricyclic antidepressant

Non-selective reuptake inhibitor for noradrenaline

Principle treatment for depression from 60s-80s

Reboxetine

Selective noradrenaline reuptake inhibitor (SNRI)

antidepressent uses since 2003

Not marketed in US

Venlafaxine

Dual noradrenaline & serotinin reuptake inhibitor

Antidepressant

Bupropion (Wellbutrin)

Reuptake inhibitor for noradrenaline & dopamine

Antidepressant & aid smoking cessation

Sibutramine (Meridia)

Reuptake inhibitor of serotonin, noradrenaline & dopamine

Anit-obesity agent

Methylphenidate (Ritalin)

Reuptake inhibitor for noradrenaline & dopamine

Used for ADHD

Agents binding to a viral structural protein

gp 41 helices fold over on each other to form twice as many helices that are half as long, this draws virus and host cell together leading to fusion.

Enfuvirtide is a polypeptide with 36 AA used for HIV since 2003. It acts as a fusion inhibitor by binding gp41 and preventing folding, so the cells aren’t pulled together and fusion is blocked.

Colchicine

Inhibitor of tubulin polymerization

used in gout

Vinblastine

Inhibitor of tubulin polymerization

anticancer agent

Tubulin polymerization

Microtubules are long hollow cylinders made up of polymerizaed a & b tubulin dimers. These polymerize end to end in protofilamnets, which are the building blocks for microtubule structures

Paclitaxel (Taxol)

inhibitor of tubulin deplolymerization

Important anticancer agent isolated from yew tree

accelerates tubulin polymerization and stabilizes microtubules

Cell division cycle halted

Binds to tubulin via side chain, acetyl, benzoyl & oxetane

Vancomycin

Agent acting on Biosynthetic Building blocks

antibacterial agent

caps the building block used in synthesis of bacterial cell wall

contains a peptide chain which forms H-bond to the target

acts as a receptor for building blocks

Binds to D-Ala-D-Ala peptide chain and caps it, disguises building block from enzyme

Cell Wall Synthesis

Building blocks are partially constructed in the cytoplasm from sugar (NAM) and peptide chain. This is then transported across the cell membrane and completed (NAM + glycines)

Linked to growing cell wall by enzyme (transglyconsidation)

Puromycin

Protein synthesis chain terminator

antibiotic

acts as a chain terminator during translation

mimics aminoacyl-tRNA molecules used during translation

Binds to ribosome instead of the tRNA and interacts with the bound tRNA that has the attached protein chain, which is transferred to the drug.

Drug departs from the ribosome carrying away stunted protein

Protein-Protein binding inhibitors

These interactions are important to biochem mechanisms and sometimes involve relatively few AA on each protein.

Small molecules that mimic these groups on one of the proteins can be designed and should be capable of binding to the other protein and prevent the interaction.

Ex) drugs interacting with tubulin

Tirofibrin

Protein-Protein binding inhibitor

Mimic a tripeptide sequence (Arg-Gly-Asp) found in fibrinogen

Binds to an integrin that normally binds fibrinogen and blocks their interactions

Anticoagulant

p53

restricts cell growth or produce cell death in damaged cells or cells under stress (cancer).

It is normally supressed by interactions with MDM2

Some cancer have excess MDM2

3 residues on p53 are like fingers that fit into the 3 binding pockets of MDM2 protein

Nutlin-2

protein-protein binding inhibitor

anticancer agent

mimics the 3 amino acids (Leu, Trp, Phe) found in p53 mimicked by Bromophenyl groups and ethoxy in nutlin

p53 as a Cancer Drug Target

p53 is a tumor suppressor gene and encodes a transcription factor

Master regulator of cellular response to DNA damage, inappropriate oncogene activation, hypoxia, inadequate nucleotide supply and defects in DNA methylation

Mutated in half of human cancers

function is frequently inactivated in remaining cancers

MDM2 as a Cancer Drug Target

Binds to p53 transactivation domain and inhibits p53 mediated transcription.

Contains signal sequence similar to nuclear export signal of various viral proteins and after binding it induces p53 nuclear export. p53 can no longer carry out its nuclear functions

Uniquitin ligase. able to target p53 for degradation by proteasome

Overexpression blocks p53 cell cycle arrest and apoptosis

Amplified or over expressed in many cancers

Terphenyl-based structure

Binds to protein BCl-x1- plays an important role in suppressing apoptosis

Compound may be useful in promoting apoptosis in tumor cells

Similar compounds synthesized in Hamiltons lab at yale for MDM2

Terphenyl-based structures

Have a scaffold design that mimics backbone of an alpha helix

Substituents mimic AA residues at 1,4,7 residues of helix

Antagonist for calmodulin

Varying substituents varies target proteins

Targeting transcription factor-coactivator interactions

Interactions between the ESX transcription factor and the co-activator protein Sur-2 involved 8 AA a-helix of ESX

Trp forms a particular important interaction

Adamanolol

Lead compound for targeting transcription factor-coactivator interactions

Searched for lead compounds contain indole ring to mimic Trp

Adamantane though ti mimic Ile and Leu residues

Isopropyl group for enforcing shape

Wrenchnolol

Drug optimized for trageting transcription factor-coactivator interactions

More active and water soluble

Two hydrophobic jaws and polar handle

Amphiphilic molecule mimicking alpha helix

non-polar components cluster on one face

Jaws mimic Trp, Leu & Ile

Amphotericin B

Antifungal that acts on cell membrane lipids

builds tunnels through membrane and drains cell

forms polar tunnel that is an escape route for ions

Gramicidin

Interacts with cell membrane lipids

Peptide antibiotic thought to form a helix in membrane

Two helices align end to end to form escape tunnel

Hydrophobic exterior interacts with lipids, interior allows ion passage

Magainins

Polypeptide antibiotics containing 23 AA.

Form helices in cell membrane

Interact with polar head groups of cell membrane lipids

Create wormholes that disrupt permeability

Killer nanotubes

Synthetic cyclic peptides that self assemble in bacterial cell membranes to form nanotubes alternating L- & D- AA.

Amide groups perpendicular to plane of cyclic peptides

Allows H bonding between each layer of cyclic peptide

Residues sticking out in the same plane do not interfere

Lysine aids selectivity for bacterial cells which have a negatively charged surface – the lysine side chain is positively charged

Valinomycin

Agent interacting with cell membrane lipid

Alternating ester and amide links

Hydrophobic residues on exterior

Polar carbonyl groups inside

Killer Nanotubes Mech of Action

Acts as an ion carrier

Hydrophobic groups on exterior interact with membrane lipids

Carbonyl groups interact with potassium ion

Allows uncontrolled escape of potassium ions from cell

Carbohydrates

Carbs play a role in cell recognition, regulation and growth

Targets of treatment of bacterial and viral infections, cancer and autoimmune disease

Act as antigens

Carb tags

Ceramide unit is in the cell membrane and a carb tag sticks out of the membrane.

Ceramide made up of fatty acid and sphingosine

Antibodies

Proteins produced by immune system

Recognizes and binds to foreign antigens

Y-shaped molecules consisting of 2 heavy and two light chains

variable region at tips of the arms

Bind to foreign antigens on foreign cells and mark it for destruction.

Cell destroyed by immune system

Antibodies have been designed as anticancer agents

Pharmacokinetics

Factors affecting whether a drug will reach its target

Active drugs in vitro may be inactive in vivo

most potent drug at its target may be useless clinically

drug design should consider binding interactions and pharmacokinetics

Consider ADME factors: Absorption, Distribution, Metabolism & Excretion

Drug Absorption

Orally taken drugs must cross the gut wall to reach blood supply, so they have to pass through cell lining. Pass through two fatty acid cell membranes which requires the balance of hydrophilic/phobic character.

Polar drugs can be administered through injection or can be used to target gut infections

Lipinski’s Rule of Five

Orally active drugs generally show a balance of hydrophilic / hydrophobic properties and obey at least three of the following rules:

MW< 500

No more than 5 HBD groups (H attached to O/N)

No more than 10 HBA groups (O/N groups)

log P< +5- partition coefficent

guidelines many exceptions

Lipinski’s Rule of Five Exceptions

Small polar molecules (MW <200) that cross the gut wall through small pores between cells

Polar molecules carried across the membrane by transport proteins - amino acids, nucleic acid bases and some drugs (e.g. lisinopril)

Pinocytosis

A process allowing passage of large polar drugs into a cell without actually crossing the cell membrane

Drug Metabolism

Foreign chemicals are modified by enzyme-catalyzed reactions, mostly in the liver - detoxification

Rxns can also occur in blood, gut wall and other organs

Drug metabolites are products formed from metabolism, usually less active or inactive (exception- prodrugs)

Modification of a structure may interfere or prevent binding interactions with a target (pharmacodynamics)

Orally absorbed compounds generally pass through the liver before distribution to the rest of the body

First Pass effect

A percentage of orally absorbed drug is metabolized in the liver prior to distribution round the body

Non orally absorbed drugs

Compounds absorbed by other routes avoid the first pass effect and circulate round the body before reaching the liver

A percentage of non-orally absorbed compounds never reaches the liver due to distribution into fat, cells and tissue)

Phase I & II reactions

Metabolic reactions are defined as phase I or phase II

Most phase I reactions add a polar ‘handle’ to the molecule

Phase II reactions are often carried out on functional groups which have been added by Phase I reactions

Increasing the polarity of a compound increases the rate of drug excretion (see drug excretion)

Cytochrome P450 enzymes catalyze phase

Cytochrome P450 enzymes

Located in liver

At least 12 families in human biochemistry

Individuals differ in types of Cyt. P450 enzymes present

Patient variability in drug metabolism complicates dose levels and leads to different susceptibilities to drugs

Drugs which affect the activity of Cyt. P450 enzymes may affect the activity of other drugs (drug-drug interactions)

Phase I Reactions Part 1

Oxidations (catalysed by cytochrome P450 enzymes)

Phase I Reactions Part 2

Discovery of Anti-cancer Drugs

First select a suitable biochemical target involved in tumor progression and metastasis

Discover small molecule that can interact with target

Optimize interaction of lead compound for increase binding affinity, selectivity and optimum ADME

Discover compound that can be tested in human clinical trails

Drug Design and Development

Identify target disease

Identify drug target

Establish testing procedures

Find lead

Structure Activity Relationship (SAR)

Identify Pharmacophore

Optimize target interactions

Optimized pharmacokinetic properties

Toxicology and Safety

Chemical development & production

Patenting and regulations

Clinical trials

Target Disease Pharm Industry Priority

Can the profits from marketing a new drug outweigh the cost of developing and testing that drug?

Target Disease Addressed Questions

Is the disease widespread? (e.g. cancer, cardiovascular disease, ulcers, malaria)

Does the disease affect the first world? (e.g. cardiovascular disease, ulcers)

Are there drugs already on the market? If so, what are there advantages and disadvantages? (e.g. side effects)

Can one identify a market advantage for a new therapy?

Drug Targets

LIPIDS: Cell Membrane Lipids

PROTEINS: Receptors, Enzymes, Carrier Proteins. Structural Proteins (tubulin)

NUCLEIC ACIDS: DNA, RNA

CARBOHYDRATES: Cell surface carbohydrates, Antigens and recognition molecules

Drug Target Selectivity Between Species

Antibacterial and antiviral agents

Identify targets which are unique to the invading pathogen

Identify targets which are shared but which are significantly different in structure

Drug Target Selectivity within the body

Selectivity between different enzymes, receptors etc.

Selectivity between receptor types and subtypes

Selectivity between isozymes

Organ selectivity

Testing Drugs

Tests are required in order to find lead compounds and for drug optimization

Tests can be in vivo or in vitro

A combination of tests is often used in research programs

In vivo Tests

Tests on live animals or humans.

Measures an observed physiological effect, a drug’s ability to interact with target and its ability to reach target.

Can identify side affects

Rationalization of results can be difficult

Transgenic animals

genetically modified animals

Drug Potency

concentration of drug required to produce

50% of the maximum possible effect

Therapeutic ratio/index

compares the dose level of a drug required to produce a desired effect in 50% of the test sample (ED50) versus the dose level that is lethal to 50% of the sample (LD50)

In vitro tests

Carried out on target molecules, cells, tissues, organs, micro-organisms

Suitable for routine testing

Used in high throughput screening (HTS)

Measures interaction of drug with target but not ability to reach target

Results are easier to rationalize

Can’t identify effective prodrugs