Choose a target and find hit/lead compounds I

Question 1

Choosing a target compound

Answer 1

• Requirement for a new drug
• Economic factor
• Understand the macromolecules involved in drug target
• Targeting specific species e.g antiviral
• Target specific to body or tissues

Question 2

Target validation

Answer 2

• Confirm association with disease proton interaction and signalling pathways

Question 3

In-vitro

Answer 3

• Specific to tissue cells and enzymes
• Use bacteria and yeast to produce enzymes IC50 wich are competitive or non competitive
• Receptor agonist or antagonist can be tested on isolectic tissue has target receptor on surface
• pK properties - metabolism of drug

Question 4

In-vivo

Answer 4

• Introduce clinical condition in animals
• Trangenic animal has some human tissue in animal
• Slow and expensive with animal symptoms
• Could be caused due to physiology
• Invalid results sometimes
• Variable according to species

Question 5

High-throughput screening

Answer 5

• Automated test of a large number of compounds to a large number of targets to HIT identification
• False positive HITS can occour

Question 6

Screening NMR

Answer 6

• Detects whether the proton binds to the proton target the screen mixture tests 1000 molecules a day
• Detection of eeak binding so there is no false positive

Question 7

Process of screening NMR

Answer 7

• NMR of the drug is taken
• Protien is added and spectrum is re-run
• If drug didn’t bind then NMR spectrum will be detected
• Drug binding then no NMR spectrum will be detected

Question 8

Isothermal calorimetry

Answer 8

• Determine the thermodynamic between drug and its protein target
• Can see its binding affinity and enthalpy change

Question 9

Finding HIT compound

Screening natural compounds

Answer 9

• Active on compound with low cytotoxicity
• Active principle metabolites are extracted fractionate and isolate
• Plant source - Morphine, Cocaine, Taxol
• Microorganism - Bacteria fungi
• Marine sources - coral, sponges and fishes
• Animal sources - Anti venom and toxin

Question 10

Finding HIT compound

Screening synthetic compound libraries

Answer 10

• Compound or synthetic ingreedient that has been previously synthesised

Question 11

Finding HIT compound

Existing drugs

Answer 11

• Use estabilished drugs from competitors as HIT compound to design compound to modify the structure
• Avoid patient restrictions, retains activity and has better theraputic effect

Question 12

Selective optimisation of side effects activities

Answer 12

• Enhance the desired effect and eliminate major biological activity of existing drugs

Question 13

Repurposing

Answer 13

• Screen existing compounds that are either in use in clinical or have reached late clinical stage againt a new target

Question 14

Starting from natural ligand or modulator

Natural ligand

Answer 14

• Used as a HIT agonist (adrenaline) for the design of an antagonist (histamine)

Question 15

Starting from natural ligand or modulator

Natural substrates for enzymes

Answer 15

• Used as HIT design inhibitors HIV protease enabled development of HIV protease inhibitor

Question 16

Starting from natural ligand or modulator

Ezyme products as HIT compounds

Answer 16

• Use HIT to design inhibitors such as carboxypeptidase

Question 17

Starting from natural ligand or modulator

Natural modulators as HIT compounds

Answer 17

• Receptor enzymes are under allosteric control
• Natural chemicalexert control on mudulators serving as HIT compounds

Question 18

Finding HIT compound

Serendipity

Answer 18

• Found by chance
• Unexpected and benificial spin-offs - lipophilic can cross blood brsin barrier add hydrophobic amide - practonol fewer side effect
• Reaserch from different field

Question 19

Finding HIT compund

Computer aided design

Answer 19

• Stuudy the 3D stucture on the computer
• X-ray crystallography
• Target analysis - rationally design a target to bind
• Easier if co-crystallised ligand where binding site is known

Question 20

HIV protease inhibitor

Answer 20

• Active as a homodimer for viral replication forms the active version of viral non-structure protiens

Question 21

What is target analysis?

Answer 21

• Residue from active binding site analysed to identify key interactions to design new ligand inhibtors

Question 22

Intermolecular bonding forces
Strong to weak

Answer 22

-Ionic
- Hydrophobic
- Hydrogen - donor or acceptor
- Pi bonding
- Weak hydrogen bond
- Vderwaals and induced dipole

Question 23

HIV potent inhibitors

Answer 23

• HAART drugs such as saquinavir and nelfinavir
• Nelfinavir non-peptidic inhibitor occupies active site smaller and compact improved fit to hydrophobic region

Question 24

Pharmacophores modelling

Answer 24

• Extract information on essential functional groups and 3D spatial arrangement required for activity on a given target
• Shows binding groups for essential activity design new mordels or improve existting

Question 25

Virtual screening

Answer 25

• Computer simulations which predicts if the compund is good or not for binding
• Faster, easier, cheaper and safter - forms virtual HITs

Question 26

Structural based virtual screening

Answer 26

• Molecular docking virtual compound explore its possible conformations
• Identify best predicable binding
• Ranks generated pose scoring predict free energy change when binding
• interaction + association + conformation + Rotation + vibration + solvation = Free energy bind

Question 27

Ligand based virtual screening

Answer 27

• Shape similarites with know active molecules - Shape functional group matching with query molecule
• Higher HIT rates

Question 28

Mixed virtual screening

Answer 28

• Matching pharmacophoric query fitting to given model

Question 29

Exclusion volumes

Answer 29

• Added to mixed screening to show actual volume occupied avoid selecting molecules that can clash to the target

Question 30

Fragment base HIT discovery

Answer 30

• Small molecule fragments are screened against a given target binding weakly
• Once multiple fragments are identified the crystal structure is resolved linking fragments together optimised high affinity molecule

Question 31

Linking fragments

Answer 31

• Bigger molecules with good affinity futher optimisation occours

Question 32

What fragments should be used in screening

Answer 32

• Relative molecular mass <300 and >150
• H-bond donating groups 3 or less
• H-bond accepting groups 3 or less
• Log(P) 3 or less
• Number of rotatable bonds 3 or less

Question 33

What fragments should be used in screening

Answer 33

• Relative molecular mass <300 and >150
• H-bond donating groups 3 or less
• H-bond accepting groups 3 or less
• Log(P) 3 or less
• Number of rotatable bonds 3 or less

Question 34

SAR by NMR epitope mapping

Answer 34

• Screen small fragment then combing them to a potent HIT using NMR
• Shifts seen on protien amide signals motier if and where binding takes place
• Repeat to find small ligand binding sub-region then optimised