Toxicology & Lead Generation Flashcards
What are the 4 ways to discover a new drug?
- Follow-on compounds
- computational modelling and sequencing
- serendipitous discovery
- evergreening
What are follow-on compounds?
- new indication discovered
- need to get lucky for this to happen
What is computational modelling and sequencing?
- increasing number of solved protein x-ray crystal structures
What is serendepitous discovery?
- same mechanism as previously reported drug
- “fast followers” or “me too” drugs
- provide professionals and patients with options, keep prices low and comes with a degree of reassurance
What is evergreening?
- extreme form of a “me too” drug
- requires an in depth knowledge of medicinal discovery
- extending the duration of a patent with minimal chemical intervation
What is target validation?
- first step
- exploring relationship between pharmacological modulation of a target and a pathological condition
- what are you trying to achieve?
What is hit identification?
- second step
- finding a chemically accessible (able to be synthesised easily) compound displaying an initial activity towards a target
What characteristics does a compound have for hit identification?
- small organic molecule
- moderate affinity
- low MW (150 < 400)
- c Log P < 4.5
- 1-4 rings
- < 8 H bond acceptors
- < 5 H bond donors
What is rational design?
- based on physiological binders (substrates, co-factors) gives us idea of shape as it binds to target of interest already
- utilises structural info to improve ligand interactions in binding site
- smaller less complex molecules with a smaller number of functional groups and tend to rule of 3
What is the rule of 3?
- MW < 300
- cLogP <= 3
- HBDs <= 3
- HBAs <= 3
What is high throughput screening?
- if you don’t know much about your target rational design isnt useful
- screen as many compounds and hope
- high number of sp2 centres = general flat nature
What are the two types of high-throughput screening?
- unselected screens
- hit rates ~ 1%
- screen millions of compounds to get a decent number of hit families to follow up
- limited by budget, time, rescources and intrinsic throughput
- limited to a number of compounds at a single concentration
- generates noise (false positives or negatives)
- selected screens
- enough info about target to inform screening
- combination of rational design and unselected screening
- greatly increases speed, reduces costs and makes identification easier
How can you recognise natural compounds?
- high number of stereocentres and complex structure
- lots of fused-ring systems
- macrocycles
- presence of a number of basic Nitrogen atoms (alkaloids)
- chemical produced by organism
- trying to control synthesis is difficult
What are PAINs?
pan-assay interference compounds (PAINs)
- positive hit compounds which turned out to be due non-specific binding
- defined structures, containing several chemical classes
- time and research money wasted
- known PAINs bearing known troublesome chemical groups which have non-specific binding/false positives (eg quinones) are filtered out before screening
Why shouldnt you excludes PAINs completely?
structures can be important in final molecules
What is the rule of 3 derived from?
Lipinski’s rule of 5
What is fragment screening?
method of reducing ligand complexity to increase rhe chance of a match with target site
samples chemical space at finer resolution
What are prerequisites before starting a hit-2-lead campaign?
- chemically acceptable
- can you do this chemistry on scale?
- starting hit responds to chemical modulation, quantifiable SAR
- freedom to operate
- preliminary ADME profile looks favourable
What can be a limiting factor in absorption?
low water solubility/high lipophilicity
How can you prevent a molecule from passing BBB?
modulate pKa by changing functional groups
decrease pKa
What are the 4 strategies for optimisation?
- homologation
- disjunction
- conformational constraining
- biostere substitution
What is homologation?
- a homologous series is a group of compounds that differ by a constant unit
- idenity SARs (affinity, selectivity, solubility, half-life)
What is disjunction?
- identify minimal structure associated with activity at sought target and remove rest
- good for natural products
What is conformational constraining?
- ‘freeze’ drug in particular conformation to best suit target
- ideal conformation - bioactive conformation - can be determine by trial and error/rational
What is biostere substitution?
substituents that have chemical or physical similarities and related molecular shapes
- structural: geometry, size, shape, polarizabilitiy, hydrogen bonding
- receptor interaction: all parameteres (except lipid/water solubility)
- pharmacokinetics: lipophilicity, pKa, hydrogen bonding
- metabolism: metabolic reactivity
most common change: COOH to imedazole
What causes drug toxicity?
- tagret driven
- idiosyncratic toxicity
- drug interactions
- generation of reactive metabolites
- carcinogenicity
- other causes
What are enthalpic (increasing energy) interactions?
- loss of ligand-water bonding
- loss of protein-water bonding
What are enthalpic (decreasing energy) interactions?
- formation of bonding interactions
- energetic changes in protein or ligand
What are entropic (increasing energy) interactions?
- loss of conformational flexibility in protein
- loss of conformational flexibility in ligand
What are entropic (decreasing energy) interactions?
- desolvation of ligands
- return of bound water to bulk state
Describe hydrophilic ligands.
- bind predominantly through bonding interactions
- enthalpic
- enthalpic - increasing energy (endothermic)
- loss of ligand-water bonding interactions
- enthalpic - decreasing energy (exothermic)
- formation of bonding interactions with protein (target)
Describe lipophilic ligands.
- bind predominantly through entropic effects
- interaction is less specific
- enthalpic - endothermic
- loss of protein-water bonding interactions
- energetic changes in protein/ligand
- enthalpic - exothermic
- energetic changes in protein or ligand
- entropic - endothermic
- loss of conformational flexibility in protein
- loss of conformation flexibility in ligand
- entropic - exothermic
- desolvation of ligands
- return of bound water to bulk state
What is considered secondary pharmacology?
biological target or effect which is not linked to its efficacy
What are the mechanisms of phase I metabolism?
- oxidation
- aliphatic or aromatic hydroxylation
- N/S oxidation
- N/O/S delkylation
- reduction
- nitro group into hydroxylamine or amine
- carbonyl into alcohol
- hydrolysis
- ester, amide or phosphate into coressponding acid and alcohol/amine
- hydrazides into acid and substituted hydrazine
What is the main class of protein involved in phase I metabolism and what does it carry out?
cytochrome P450s
carry out oxidation in liver cells
also found in liver cells
What is the rate of oxidation determined by?
stereo-electronics of the oxidation and the concentrations
how available are electrons to form and break bonds?
Why are more lipophilic drugs likely to be more rapidly cleared?
more driven by entropic factors
dissociation constant’s consistent effects are the solvent based (entropic) factors
What is F% formula and what does it mean for a more lipophilic molecule?
F% = Fabs x Fprehepatic x Fhepatic
more lipophilic:
- less hepatic clearance as its been metabolised already
- less Fabs due to low solubility
What is the most common cause of drug-drug interaction?
- taking a drug that is an inhibitor of CYP enzymes - binds to metal centre
- unhindered aromatic nitrogen atoms are likely to be CYP inhibitors as N lone pair is good at co-ordinating to iron
- exposure increases of other drug due to decreased metabolism
What are the two approaches to avoid reactive metabolites?
- exclude chemical functionalities undergoing metabolic activation
- screen for reactive metabolite formation (RM Assays)
What are the mechanisms of phase II metabolism?
- glucuronidation
- seen in carboxylic acid, alcohols, phenols and amines
- mr of 194
- can lead to idiosyncratic toxicity
- sulphation
- alcohols, phenols, amines
- mr 70/80
- glutathione (GSH) conjugation
- halogenated compounds, epoxides, arene oxides, quinone-imines, DNA
- mr 312
What is type b toxicity?
- idiosyncratic toxicity
- levels of glucuronide may be high or they develop an extreme immune response to low levels of alkylated proteins, leading to serious liver injury
What is the role of GSH conjugation in paracetamol?
- paracetamol forms NAPQI after phase I
- phenol alcohol group oxidised to ketone
- this is an active metabolite
- phase II is GSH conjugation
- if GSH levels depleted, NAPQI levels accumulate, leading to non-specific alkylation of proteins in liver
- proteins seen as foreign to immune system
- inflammatory response and cell damage
What is the purpose for mutagenicity models and give an example?
eg Ames Assay
opportunity to highlight drugs that may show particularly high mutagenicity
amines are likely to give a fale positive result
Why can mutagenicity often be attributed to the presence of a masked aromatic amine?
amines may exist as part of an amide bond thats hydrolysed as part of phase I metabolism
