Exam 3: Drug discovery: finding a lead

What is the term used for drugs that are similar in structure to a known drug and which are used for the same purpose?

'me-too' drugs

Some scaffolds are already common in medicinal chemistry

(benzodiazepine, hydantonin, tetrahydroisoquinoline, benzensulphonamide and biaryls) and are associated with a diverse range of activities. Such scaffolds are termed privileged scaffolds.

scaffolds can be flexible

(e.g peptide backbone) or rigid (a cyclic system) They may contain heteroatoms that are capable of forming useful bonding interactions with the binding site, or they may not.

Big Data

1.5 billion gigabytes of information was produced in 1999 and 3 billion gigabytes in 2003 big data represents collections of information too large to manually curate

If you change OH group on morphine to a double bond to oxygen it turns into

6-oxymorphine and activity is unaffected

recursive deconvolution: example

9 possible tripeptides in active mixture all end in valine add valine to the three retained and dipeptide mixtures two vials have inactive mictures. active component narrowed down to one of three possible tripeptides synthesize each tripeptide and test

The lead compound

A compound demonstrating a property likely to be therapeutically useful The level of activity and target selectivity are not crucial used as the starting point for drug design and development found by design ( molecular modelling or NMR) or by screening compounds ( natural or synthetic) Need to identify a suitable test in order to find a lead compound Active principle : a compound that is isolated from natural extract and which is principally responsible for the extract's pharmacological activity. Often used as a lead compound.

Structure (I) has a highly flexible side chain.

A flexible molecule is more likely to adopt conformations that will bind to different targets, resulting in side effects. Option b) is correct. A flexible molecule can adopt several conformations, and this increases the chances of it interacting with a variety of targets, resulting in side effects. Option a) is wrong since a flexible molecule is less likely to be in its active conformation, resulting in decreased activity. Option c) is correct in so far as a flexible molecule may be able to bind in different binding modes to the one target, but this is more likely to result in decreased activity. Option d) is wrong since a flexible molecule is less likely to show target selectivity.

localising drugs to a target area: Example

Adrenaline and procain ( local anaesthetic) Adrenaline constricts blood vessels at the injection area procaine is localized at the injection area

What sort of factors might affect the stability of a compound in a pharmaceutical preparation?

All of the above Feedback: A large variety of factors have to be considered that might affect the stability of a compound in a pharmaceutical preparation.

Protein Data Bank (PDB)

An international database that archives the data describing the three-dimensional structure of nearly all macromolecules for which structures have been published.

Surface Plasmon resonance

BIAcore Assay: The angle of incidence of the polarized light reflecting off the gold surface depends on the refractive index of the buffer solution. This will change if a drug binds to the protein.

Microcalorimetry/Thermodenaturation Assays

Based on the fact that drug releases energy when binding: Isothermal titration calorimetry (ITC) Differential scanning calorimetry (DSC) Differntial fluorimetry (DSF) Differential static light scattering (DSLS)

Genetic Algorithms

Based on the idea of the survival of the fittest - create a population - score the population - create a new population from the surviving members Crossover: switch genes between two members of the population Mutation: randomly change the value of one gene

Drug targets: target selectivity

Between species within body

protecting agents and synthetic strategy: synthetic strategy in peptide synthesis

Boc/benzyle protection stratgey: - N-terminus of amino acids protected by t-butyloxycarbonyl group - protecting group removed by TFA

Which of the intermolecular bonding interactions below are possible for a primary amine?

Both hydrogen bonding and ionic bonding The hydrogens of an un-ionised primary amine can act as hydrogen bond donors while the nitrogen can act as a hydrogen bond acceptor. If the amine is protonated and ionised, it can form ionic interactions. In the ionised situation, the hydrogens can still act as hydrogen bond donors, but the nitrogen can no longer act as a hydrogen bond acceptor.

SMILES

C aliphatic carbon c aromatic carbon - single bond = double bond : aromatic bond ( ) branching hydrogens are normally explicit

sentry drug example

Carbidopa notes: carbidope protects L-dopa it inhibits the decarboxylase enxyme in the peripheral blood supply it is polar and does not cross the blood brain barrier it has no effect on the decarboxylation of L-dopa in the cns smaller doses of L-dopa can be administered-less side effects other examples: Clavulanic acid and candoxatril

Chemical genetics drug discovery

Chemistry-->phenotypic screen--->target ID--->target hypothesis--->target validation--->with LMW leads

What term is used to describe the patenting of the active enantiomer of a racemic drug which is already on the market?

Chiral switches Feedback: Option b) is the correct answer. The other terms are not used in medicinal chemistry.

Scintillation proximity assay

Competitive method to detect whether a ligand binds to a target Target is immobilized on bead coated with scintillant Known ligand labeled with 125I (or 3H, 14C, 33P) is added 125I in proximity to scintillant causes it to emit light compounds to be assayed is added to the solution if the compound bindsm the labeled ligand will be displaced, reducing the light emission

DNA encoded libraries

DNA is used as a tag to identify the small molecule produced by combinatorial synthesis Binders can be amplified by polymerase chain reaction (PSR) and identified through their DNA code.

In Parkinson's disease, there is a lack of the neurotransmitter dopamine in the brain. Adding dopamine itself is not very effective for a variety of reasons. Which of the following statements is not a valid explanation?

Dopamine is chemically unstable. Feedback: Option b) is wrong. Dopamine is chemically stable. The other statements are valid explanations as to why dopamine would make a poor drug for the treatment of Parkinson's disease. It cannot access the brain easily. It shows poor selectivity between different types of receptors and it is rapidly metabolised.

Terms in a typical molecular mechanics force field

E= E bond + Eangle + Edihedral + Bonded terms Eelectrostatic + E vanderwaals non bonded terms sometimes an explicit H-bonding or dipole term is also incluceded note the similarity between the non bonded terms and the interactions we have discussed as important to drug binding

Which of the following terms is used to describe the dose of a drug required to produce a measurable effect in 50% of the animals tested?

ED50 Feedback: The ED50 is the dose of drug required to produce an effect in 50% of the animals tested. The ED99 is the dose of drug required to produce an effect in 99% of the animals tested. The LD1 and LD50 values represent the dose of drug which kills 1% and 50 % respectively of the animals tested.

identification of structures from combinatorial synthesis : Bar coding

Efficient method of tagging use coding or encryption method employing a triplet code three tags (A-C) can be used to represent up to seven reagents for the first stage of a synthesis three different tags (D-F) are chosen up to seven reagents in the second stage of the synthesis Tags D-F are chosen to have a longer retention time on a gas chromatograph compared to tags A-C

Natural substrates for enzymes

Enkephalins ----> enkephalinade inhibitors Peptides ----> protease inhibitors

What are we missing?

Entropy solvation electronic effects ( resonance, polarizability)

Esters are frequently used as prodrugs. Which of the following statements is false?

Esters are more susceptible to hydrolysis if the alcohol moiety has an electron donating group. Feedback: Option b) is wrong. Esters are more susceptible to hydrolysis if the alcohol moiety has an electron-withdrawing group. This stabilises the alkoxide leaving group and makes it a better leaving group.

Prodrugs to increase chemical stability

Example: Hetacillin for amplicillin Notes: Ampicillin is chemically unstable in solution due to the alpha NH2 group attacking the B lactam ring nitrogen atom in heteracillin is locked up within a heterocyclic ring

prodrugs used to target drugs

Example: Hexamine notes: stable and inactive at pH>5 stable at blood pH used for urinary infections where pH>5 Degrades at pH<5 to form formaldehyde ( antibacterial agent)

prodrugs activated by external influences-sleeping agents

Example: photodynamic therapy-Foscan notes: inactive and accumulates in cells Activated by light-method oftargeting tumour cells Foscan is excited and reacts with oxygen to produce toxic singlet oxygen cell destruction is caused by singlet oxygen

N-Phenethylmorphine was synthesised from morphine and found to have enhanced activity.

Extension Extension involves the addition of extra binding groups to interact with extra binding regions. This is what has been carried out here by adding an extra aromatic ring.

reducing drug toxicity: varying substituents

Fluconazole (Diflucan)- antifungal agent UK-47265 has chloro groups, changed to fluorine groups less toxic substituents varied, less toxic

ADMET prediction : solubility

Fsp3 >= .4 aromatic rings <= 3

Which of the following statements is not true of herbal medicines?

Herbal medicines have no side effects compared to conventional medicines. Feedback: There is no reason why herbal medicines should be free of side effects. They contain active components which will vary in their selectivity for their targets. Some will produce more side effects than others.

testing for activity

High throughput screening and screening 'on bead' off bead

Which of the intermolecular bonding interactions below are possible for a ketone?

Hydrogen bonding only The carbonyl oxygen of a ketone can act as a hydrogen bond acceptor.

Which of the intermolecular bonding interactions below are possible for a secondary amide?

Hydrogen bonding only The carbonyl oxygen of a secondary amide group can act as a hydrogen bond acceptor while the NH proton can act as a hydrogen bond donor. The nitrogen cannot act as a hydrogen bond acceptor since its lone pair of electrons interacts with the carbonyl group.

Possible binding interactions for OH

If you add CH3I you get an ether If you as CH3COCl you get an ester If you ass CH3SO2Cl and LiAIH4 you get an alkane

It is common practice to vary the length and size of alkyl groups when making analogues of a lead compound. Which of the following statements is not true?

Increasing the chain length or size of an alkyl group increases activity and selectivity by stabilising the analogue. There is no obvious reason why an increase in the length or size of an alkyl group should stabilise a molecule, or why increased stability should lead to higher activity and selectivity.

LLE: ligand lipophilic efficiency

Is the binding all due simply to hydrophobic effects ( and so non-specific)

Which of the following statements is true regarding an ether?

It can only participate in hydrogen bonding as a hydrogen bond acceptor. An ether consists of oxygen linked to two alkyl or aromatic groups. The oxygen can act as a hydrogen bond acceptor. There is no hydrogen attached to oxygen and so the group cannot act as a hydrogen bond donor.

Which of the following statements is true regarding a secondary amide?

It can participate in hydrogen bonding both as a hydrogen bond donor and a hydrogen bond acceptor. The secondary amide (RNHCOR) has a carbonyl oxygen that can act as a hydrogen bond acceptor. There is also a hydrogen attached to nitrogen which could act as a hydrogen bond donor. The nitrogen itself does not act as a hydrogen bond acceptor since its lone pair interacts with the carbonyl group.

Which of the following statements is true regarding an alkene?

It cannot participate in hydrogen bonding at all. The alkene functional group is a C=C double bond. There are no heteroatoms present and no hydrogens attached to heteroatoms. Therefore, the group cannot participate in hydrogen bonding. This group can form van der Waals interactions with a hydrophobic region of a binding site.

L791456 is an anti-arthritic drug with a shorter lifetime in the body than L787257. The only difference in the structures is a methyl substituent on one of the pyridine rings. Why does the presence of a methyl group decrease the lifetime of the drug?

It is metabolised by oxidative enzymes to an alcohol or carboxylic acid. The resulting polar metabolites are rapidly excreted. Feedback: The methyl group is an exposed group which is susceptible to oxidative metabolism by cytochrome P450 enzymes. The resulting metabolites are more polar than the original drug and are quickly excreted. The other options are not impossible, but do not occur in this case.

Which of the following terms is used to describe the dose of a drug required to kill 50% of a group of animals?

LD50 Feedback: The ED50 is the dose of drug required to produce an effect in 50% of the animals tested. The ED99 is the dose of drug required to produce an effect in 99% of the animals tested. The LD1 and LD50 values represent the dose of drug which kills 1% and 50 % respectively of the animals tested.

Therapeutic ratio

LD50/ED50 Bigger number better

Prodrugs to mask toxicity and side effects Example: LDZ for diazepam

LDZ---> a.) aminopeptidase b.) cyclisation-> diazepam avoids drowsy side effects of diazepam

LELP

LELP= Clop/LE LE=((RTlnKd)/(HA)) LLE=pIC50- clogP

Requirements for Drug discovery

Lead molecules Identifying lead molecules

how do we figure out the energy of the most stable conformation of our molecule or drug receptor complex?

Local minimization

ADMET prediction: Oral bioavailability

MW<= 500 clogP<= 5 H bond donors <= 5 N + O <= 10 rotatable bonds <= 10 PSA <= 140

photolithography is a technique involving a solid support surface containing functional groups protected by photolabile groups

Masks are used to receal defined areas of the plate to light, thus removing the protecting groups and allowing a reactant to be linked to the solid support. A record of the masks and reagents used determines what reactions have been carried out at different regions of the plate

DSF: a fluorescent dye is used which will bind to the hydrophobic portions of the protein when it is denatured by temperature A more stable complex will denature at a higher temperature

Microcalorimetry/Thermodenaturation Assays DSF

peptoids

N-substituted glycine units were used to produce structures known as____________. where the side chain is attached to the nitrogen rather than the alpha carbon.

Boc/benzyle protection stratgey:

N-terminus of amino acids protected by t-butyloxycarbonyl group - protecting group removed by TFA Functional groups of residues protected by benzyl protecting group stable TFA used to deprotect Boc group Removed by HF HF used to remove peptide chain from solid support

molecular properties

Naive Bayesian Classifiers

Chemistry driven

Natural products Endogenous ligands Compound libraries

prodrugs to mask toxicity and side effects: antiviral drugs example: penciclovir

Notes: first phosphorylation requires viral thymidine kinase only activated in virally infected cells non toxic to uninfected cells

Which of the following techniques is the most suitable for detecting a metabolite labelled with 13C?

Nuclear magnetic resonance spectroscopy Feedback: Nuclear magnetic resonance can be used to detect metabolites labelled with stable isotopes such as 13C. Scintillation counting is used to detect metabolites labelled with radioactive isotopes such as 14C or 3H. Mass spectrometry can be used to detect metabolites labelled with isotopes such as deuterium.

What term is applied to a drug which is effective against a relatively rare medical problem?

Orphan drug Feedback: The correct term is an orphan drug. A new chemical entity is any novel pharmaceutical agent. A lead compound is a compound that has a useful biological activity and is the starting point for the design of a new drug. A parent drug is an established drug that acts as the reference point for related drugs.

ADMET prediction: membrane permeability

PSA <= 120 MW <= 500 LogD .5-5

ADMET prediction: BBB penetration

PSA <= 70

Some peptides and proteins have been used as drugs. Which of the following statements is untrue?

Peptide drugs are susceptible to metabolic enzymes but not to digestive enzymes. Feedback: Peptides and proteins are susceptible to hydrolysis by digestive enzymes as well as by metabolic enzymes, and so option d) is the false statement. The other statements are true. Proteins and polypeptides are large molecules and can induce an immune response. They are poorly absorbed when taken orally due to their polar nature. The peptide bonds are also prone to hydrolysis by digestive and metabolic enzymes.

SAR shows that the important binding groups in morphine are the phenol, aromatic ring and amine. A diagram can be drawn which shows these functional groups and their relative orientations. What is the term for this?

Pharmacophore A pharmacophore indicates the important binding groups and their relative positions. Pharmacodynamics is the study of how a drug interacts with its target binding site. Pharmacokinetics is the study of how a drug is absorbed, distributed, metabolised and excreted in the body. A chromophore is a conjugated unsaturated system responsible for the colour in coloured compounds.

Which of the following statements is true with respect to phosphate prodrugs?

Phosphate esters are more polar in nature than the parent drug. Feedback: Phosphate esters are more polar and more water soluble than the parent drug. As a result, they are less likely to cross cell membranes. They are susceptible to metabolism. Otherwise they would not be prodrugs!

Target Disease

Priority for the pharmaceutical industry: can the profits from marketing a new drug outweigh the cost of developing and testing that drug? Questions to be addressed: Is the disease widespread? Does the disease affect the first world? Are there drugs already on the market? If so, what are their advantages and disadvantages can one identify a market advantage for a new therapy?

Which of the following strategies will increase the polarity and water solubility of a drug?

Replacing an aromatic ring with a nitrogen containing heterocyclic ring Feedback: The extra nitrogen atom increases polarity and water solubility. The other options all increase the hydrophobic character of the drug and will decrease water solubility.

MDL SDF (structure data file)

SDF was designed for storing molecular information in a chemical database

Which of the following techniques would be used to detect a metabolite labelled with 14C?

Scintillation counting (detection of radioactivity) Feedback: Nuclear magnetic resonance can be used to detect metabolites labelled with stable isotopes such as 13C. Scintillation counting is used to detect metabolites labelled with radioactive isotopes such as 14C or 3H. Mass spectrometry can be used to detect metabolites labelled with isotopes such as deuterium.

Which of the following techniques would be used to detect a metabolite labelled with 3H?

Scintillation counting (detection of radioactivity) Feedback: Nuclear magnetic resonance can be used to detect metabolites labelled with stable isotopes such as 13C. Scintillation counting is used to detect metabolites labelled with radioactive isotopes such as 14C or 3H. Mass spectrometry can be used to detect metabolites labelled with isotopes such as deuterium.

Which of the following techniques would be used to detect a metabolite labelled with 2H?

Scintillation counting (detection of radioactivity) Mass spectrometry Feedback: Nuclear magnetic resonance can be used to detect metabolites labelled with stable isotopes such as 13C. Scintillation counting is used to detect metabolites labelled with radioactive isotopes such as 14C or 3H. Mass spectrometry can be used to detect metabolites labelled with isotopes such as deuterium.

Designing compound libraries for lead optimization

Should take into account the biological and physical properties of the compound, its binding interactions with the target and the potential problems of particular substituents For example: if the target is a zinc-containing protease (angiotensin-converting enzyme), a library of compounds containing a carboxylic acid or thiol group would be relevant

Scintillation proximity assay

Step 1: capture molecule ( target) is coated onto the wells step 2: radioligand and samples are added and incubated step 3: unbound radioligand is not detected. Radioligand bound to target is detected

Structures (I) and (II) are prodrugs of the antibiotic chloramphenicol.

Structure II is more water soluble than chloramphenicol. Feedback: Structure I has a hydrophobic ester which lowers water solubility. As a result, it reduces the bitter taste of the drug when it is taken by mouth. Structure II has a polar ester due to the carboxylic acid, and so it has good water solubility. It can be used to achieve high concentrations of the drug for injection.

Which of the following areas of study is not part of preclinical trials?

Structure-activity relationships Feedback: Studies on structure-activity relationships are carried out on various analogues of a lead compound to see what effects alteration in structure have on activity. This is in the early stages of drug design and development.

After the product is formed from the adding the carboxylic acid to the wang resin, peptide synthesis forms

TFA cleavage removes carboxylic acid and returns to original state

Lidocaine is a longer lasting local anaesthetic than procaine. Which of the following statements is false?

The NH2 group in procaine makes procaine less stable than lidocaine. Feedback: Option d) is wrong. The amino group plays no role in the stability of the molecule. It is present as an extra binding group for the target binding site. The other options are accurate. Procaine has an ester group which is susceptible to hydrolysis. Lidocaine has an amide group which is more resistant to hydrolysis, and which is also protected by the two methyl groups on the aromatic ring, which act as steric shields.

Tioconazole is a non-polar antifungal agent which is used topically, whereas fluconazole is a polar drug which is used systemically. Which of the following statements is correct?

The alcohol group in fluconazole increases polarity. Feedback: Fluconazole is more polar and more water soluble than tioconazole due to the extra nitrogen atoms and the alcohol group. Option d) is the only correct statement. Option a) is wrong since the nitrogen atoms make the drug more polar and not less polar. Option b) is wrong since increased polarity increases water solubility. Option c) is wrong since the fluorine substituents have little effect on water solubility.

Carbachol is more stable than acetylcholine to hydrolysis. Which of the following statements is not true?

The blue coloured methyl group of acetylcholine is susceptible to oxidation by cytochrome p450 enzymes. Feedback: Acetylcholine is metabolised by esterases which hydrolyse the ester group. It is not metabolised by cytochrome p450 enzymes. Replacing the acyl methyl group of acetylcholine with an amino group alters the ester functional group to a urethane functional group. Urethanes are more resistant to hydrolysis, since the nitrogen's lone pair interacts with the neighbouring carbonyl group and makes it less reactive to nucleophiles such as water.

Fluphenazine decanoate is an ester prodrug for the antipsychotic drug fluphenazine, and is administered by intramuscular injection. Which of the following statements is true?

The ester is hydrophobic which means that it is taken up in fat tissue. As a result, it can only enter the blood supply at a slow rate. Feedback: Option b) is correct. Option a) is wrong since an alcohol group is revealed on fluphenazine following hydrolysis. Option c) is false since the ester is hydrophobic and is taken up in fat tissue as stated in option b). Option d) is wrong. The statement implies that the ester spontaneously hydrolyses at slightly alkaline pH, whereas it is the action of esterase enzymes in the blood that results in rapid hydrolysis.

What is the most likely problem that you can foresee in labelling a drug as shown? The functional group is an alcohol.

The isotope could be easily lost since it is exchangeable with water. Feedback: The isotope is tritium and it is attached to oxygen as part of an alcohol functional group. The hydrogen atom of an alcohol group exchanges rapidly with water, and tritium will also exchange rapidly. Option b) is also a possibility if metabolic oxidation converts the alcohol to a ketone or a carboxylic acid. In both situations, the label would be lost. However, it is likely that the label would have been lost by exchange with water before such an oxidation takes place.

What problem might you foresee in labelling a drug as shown?

The isotope could be lost as a result of a metabolic oxidation. Feedback: N-Methyl groups are known to be prone to oxidative metabolism and can be lost from the molecule. The mechanisms given in options a), c) and d) are not possible with a 14C labelled N-methyl group.

What problem might you foresee in labelling a drug as shown?

The isotope could be lost as a result of hydrolysis. Feedback: The labelled carbon is on the alkoxy moiety of an ester. Esters are susceptible to enzyme-catalysed hydrolysis which would result in the loss of the isotope from the drug.

What problem might you foresee in labelling a drug as shown?

The isotope could be lost since it is acidic. Feedback: The labelled tritium atoms are attached to a carbon which is next to a carbonyl group. The electron withdrawing effect of the carbonyl group makes these atoms acidic and they can be easily lost from the molecule.

Hooke's Law

The law stating that the stress of a solid is directly proportional to the strain applied to it. zero energy corresponds to the most stable (equilibrium) state Ebond= SigmabondsKb (d-d0)^2

Which of the following major aims in drug design is not related to the pharmacodynamics of a drug?

The maximisation of oral bioavailability The aims described in options a), b), and c) can all be achieved by improving the affinity and selectivity of the drug for its target. Oral bioavailability has nothing to do with the target, and is a pharmacokinetic issue.

Why does chlorpropamide have a longer antibiotic activity than tolbutamide?

The methyl group of tolbutamide is susceptible to drug metabolism whereas the chloro substituent of chlorpropamide is not. Feedback: The major metabolic reaction carried out on tolbutamide is oxidation of the methyl group to a carboxylic acid. The chloro substituent in chlorpropamide is resistant to this metabolism.

Candoxatril is an ester prodrug for candoxatrilat which inhibits protease enzymes. Which of the following statements is incorrect?

The parent drug can be administered orally, whereas the ester prodrug cannot. Feedback: The statement made in option b) is false. The parent drug is too polar to be given orally and has to be administered by injection. The prodrug is less polar and can be given orally. The other statements are all accurate.

Which of the following statements is false with respect to nmr screening to detect drug-target interactions?

The procedure relies on small molecules (drugs) having shorter relaxation times than large molecules (targets). The procedure relies on small molecules (drugs) having longer relaxation times than large molecules (targets). When a small drug binds to a macromolecular target, it essentially becomes part of that target and the signals for that compound will have shorter relaxation times. If there is a time delay in measuring the nmr spectrum, the signals for molecules that bind to the protein will disappear from the spectrum.

What is meant by the therapeutic ratio or index?

The ratio of LD50 to ED50 Feedback: The therapeutic ratio is the ratio of LD50 to ED50.

Losartin was developed from structure (I) as an antihypertensive agent by replacing a carboxylic acid group with a tetrazole ring. Which of the following statements is incorrect?

The tetrazole ring is more polar than a carboxylic acid. Feedback: The tetrazole ring is ten times less polar than a carboxylic acid. The other statements are accurate.

Which of the following is not true of analogues produced by a rigidification strategy?

They are easier to synthesise. In general, more rigid molecules tend to be more complex and more difficult to synthesise. The other statements are true since rigid molecules retaining the active conformation are more likely to fit their target binding site and less likely to form the active conformations recognised by the binding sites of other targets.

LCAO approximation

Treat molecular orbitals as linear combinations of hydrogen like atomic orbitals ( only hydrogen can actually be solved) - Valence bond theory: represent molecule through localized interactions of electrons shared by atoms - Molecular orbital theory: represent molecule ass electrons delocalized into molecular orbitals

SAR: morphine , add CH3 group

Turns into codeine and activity drops

Agglomerative Hierarchical Clustering

Type of cluster-based segmentation technique which clusters group in a hierarchy by combining groups from bottom to top - group the two most similar compounds - find the nect most similar group or compound and merge them - continue until there is only one group -results are displayed as a dendrogram -after clustering, one must still determine what cutoff to use to form the groups

requirements for drug discovery

Validated target Assay Lead molecules

prodrugs to prolong activity Example

Valium for nordazepam valium---N-demethylation---> Nordazepam

Which of the intermolecular bonding interactions below are possible for an alkene?

Van der Waals interactions only The alkene group has no heteroatoms and can form neither hydrogen bonds nor ionic bonds. Van der Waals interactions are possible.

Example of Linker

Wang resin Has OH functional group

What is meant by a lead compound in medicinal chemistry? a) A drug containing the element lead. b) A leading drug in a particular area of medicine. c) A compound that acts as the starting point for drug design and development. d) A drug which is normally the first to be prescribed for a particular ailment.

What is meant by a lead compound in medicinal chemistry? a compound that acts as the starting point for drug design and development

Time Independent Schrodinger Equation

Where V and T are the potential and kinetic enery operators, E is the total energy and w is the wave function.

FLIPR

a CA2+ sensitive fluorescent dye is used and the level of fluorescence indicates the concentration of intracellular Ca2+

Rink resin in

a bead linker with an NH2 group on the end.

NMR

a compound is radiated with short pulse of energy which excites the nuclei of specific atoms such as hydrogen, carbon, or nitrogen. once the pulse of radiation has stopped, the excited nuclei slowly relax back to the ground state giving off energy as they do so.

virtual library

a computer representation of compounds that either have been made or it is believed can be made - compound from in house databases -compounds from vendor databases - high throughput screening libraries ---consists of sets of compounds built around a specific core ----reagents are selected for lead likeness and diversity

True negative

a correct negative prediction ex: dont have measels, says you dont

true positive

a correct positive prediction

The essential requirements for solid phase synthesis are:

a cross linked insoluble polymeric support which is inert to the synthetic conditions (e.g. resin) an anchor or linker covalently linked to the resin-the anchor or linker covalently linked to the resin-the anchor has a reactive functional group that can be used to attach a substrate a bond linking the substrate to the linker, which will be stable to the reaction conditions used in the synthesis a means of cleaving the product or the intermediates from the linker protecting groups for functional groups not involved in the synthetic route

Sentry drugs

a drug that is added to protect another drug

The potential energy is determined by Coulomb's law

a law stating that like charges repel and opposite charges attract, with a force proportional to the product of the charges and inversely proportional to the square of the distance between them.

If you add carboxylic acid to the Rink resin (which has NH2) it adds

a modification that goes under further modifications and cleavage with TFA causes a primary amide

Solid phase techniques: Anchor or linker

a molecular moiety which is covalently attached to the solid support and which contains reactive functional group Allows attachment of the first reactant The link must be stable to the reaction conditions in the synthesis but easily cleaved to release the final compound Different linkers are available depending on the functional group on the product

planning a combinatorial synthesis: or possibly the Rule of Three for lead-lead compounds

a molecular weight less than 300 a calculated log P value less than 3 no more than 3 hydrogen bond donating groups no more than 3 H bond accepting groups

planning a combinatorial synthesis:target molecule should obey lipinksi's rule of five for oral activity

a molecular weight less than 500 a calculated log P values less than 5 no more than 5 H bond donating groups no more than 10 H bond accepting groups

The solid support consists of

a polymeric surface and a linker molecule which allows a starting material to be covalently linked to the support

In parallel synthesis

a reaction or series of reactions is carried out in a series of wells to produce a range of analogues. each reaction well contains a single product

solid phase techniques requirements

a resin bead or functionalised surface to act as a solid support an anchor linker a bond linking the compound to the linker. The bond must be stable to the reaction conditions used in synthesis A means of cleaving the product from the linker at the end protecting groups for functional groups not involved in the synthesis

scoring function: Empirical

a sum of free energy terms for interactions believed to be important delta G= sum of Ci deltaGi where delta Gi correspond to terms like hydrogen bonds, salt bridges, vdW interactions, possible entropy or solvation terms

eigenvalues

acceptable values of E that satisfy the Schrodinger equation

eigenvectors

acceptable values of the wave function that satisfy the Schrodinger equation

vary alkyl substituents example viagra: methylene shuffle

added extra bulk, methylene shuffle causes extension on methyl group on bottom of molecule, shortens by one methyl group on top part

Adding polar groups

adding polar groups increases polarity and decreases hydrophobic character useful for targeting drugs vs. gut infections useful for reducing CNS side effects

FlexX Docking

additional fragments are added after the base fragment has been positioned

endogenous ligands for receptors

adrenaline----> propranolol (antagonist) histamine-----> cimetidine ( antagonist)

natural ligands for receptors

adrenaline---> salbutamol (agonist) 5-hydroxytryptamine---> sumatriptan (agonist)

microwave technology can prove

advantageous over conventional heating

Clustering example

agglomerative hierarchical clustering

planning a combinatorial synthesis : computer modelling

aims: to maximize the number of possible pharmacophores from the miniumum number of compounds. to maximize the diversity of structures produced

Which of the following is not an endogenous lead compound?

alkaloid Feedback: Alkaloids are plant natural products containing nitrogen. The other options are endogenous compounds in the body.

Notes on linking a biosynthetic building block

alkylating group is attached to a nucleic acid base cancer cells grow faster than normal cells and have a greater demand for nucleic acid bases drug is concentrated in cancer cells- trojan horse tactic

biological diversity

all compounds modulate at least one known target modulated targets span multiple families and biologic functions

Testing

all models need to be tested, the best way is to divide the data into a training set for building the model and a test set for evaluating the model

Nuclear Magnetic Resonance (NMR) Spectroscopy

analytic tool which has been used for many years to determine the molecular structure of compounds. It has been used to detect whether a compound binds to a protein target

between species

anitbacterial, antifungal and antiviral agents identify targets which are unique to the invading pathogen identify targets which are shared but which are significantly different in structure

example of varying pKa

antithrombotic: too basic PRO3112: Decreased basicity nitrogen locked into heterocyclic ring

The chance of identifying an orally active lead compound can be imporved by

applying lipinskis rule of five when planning compound libraries. More rigid rigid guidelines may be used if the lead compound is likely to undergo substantial optimization

semi- Empirical quantum mechanics

approximate the integrals of quantum mechanics using empirical data. MOPAC and AMPAC are the best known implementations.

conformational space

are all the geometries accessible to a molecule as the result of changing the torsion angles look at example: rotating the bond in either irection initially raises the energy-until you rotate the bond enough and find another local minimum

orbital approximation

assume electrons behave independently of each other ( they don't- thus requiring Moeller-Plesset, coupled cluster or density functional theory to correct for electron correlation

Mix and split example: using three amino acids

attache to beads in three different wells combine all three into one well you split back into three different wells after mixing you add a second reaction to each three wells you then mix all three wells into one well you then split this one well back into 3 seperate wells. You add another reaction (same amino acid like before) to the three seperate wells Then you distribute the mix into another set of 3 wells for each original well. There should be 9 total number of peptides in each new well for each amino acid group. 27 tripeptides total in 3 vials. You then test each mixture of activity and you synthesize each tripeptide and test

most combinatorial syntheses are carried out using

automated or semi automated synthesizers

Automated parallel synthesis

automated synthesizers are availbale with 96 or 384 or larger reaction vessels or wells reactions and work ups are carried out automatically same synthetic route with different reagents for each vessel different product obtained per vessel

biology-oriented synthesis

based on the principle that conservation in protein structure can be linked to a small number of biologically relevant compound classes starts with analysis of natural products consistent with the idea of privileged substructures

High throughput screening

because solid phase synthesis can produce a large quantitiy of structures in a very short period of time, biological testing has to be carried out quickly and automatically. The process is known as high throughput screening (HTS) and was developed before combinatorial and parallel synthetic methods were devised.

Dynamic combinatorial chemistry involves the formation of a mixture of compounds in the presence of a target under equilibrium conditions

binding of a product with the target amplifies that product in the equilibrium mixture.

Which of the following needs to be established before the search for a lead compound takes place?

bioassay The lead compound has to have some sort of desirable biological activity, and so a bioassay to detect that activity is required. Structure-activity relationships and the identification of a pharmacophore are stages in the drug design process that come after the discovery of the lead compound. Patents are taken out at a later stage once potentially useful compounds have been designed and developed.

quantum mechanics calculations require a lot of computer time, but are required for accurate determination of properties such as:

bond energies charges molecular orbitals dipole moments UV spectral transitions

Naive Bayesian classifiers

calculate the probabilty that X will happen given a, b, c , d.... The Naive part: the probabilities of a, b, c, d.. are independent of each other Bayes' theorem: p(xI a, b, c)= p(x)p(a, b, c I X)/ p(a, b, c)= p(X)p(aIx)p(aIX)p(bIX)p(cIX)/p(a,b,c) the problem then becomes getting the probabilities

molecular mechanics can be used

can be used when bonds are not broken and the electronic state of the molecule is not critical. Much faster than QM methods and so can be used on large structures ( proteins) without extensive computational facilities.

In vivo tests

carried out on live animals or humans measure an observed physiological effect measure a drugs ability to interact with its target and its ability to reach that target can identify possible side effects rationalism may be difficult due to the number of factors involved transgenic animals : modified animals drug potency: concentration of drug required to produce 50% of the maximum possible effect Therapeutic ratio/index:

Ligand-based drug design strategy

carry out drug design based on the activities and physiochemical properties of compounds known to bind to the target

Structure based drug design Strategy:

carry out drug design based on the interactions between the lead compound and the target binding site

Identifying targets at the protein level

change in protein expression as a result of drug treatment or disease protein-protein interactions ( interaction domains, catalytic domains) Annotation of uncharacterized proteins similar to proteins with known metabolic effect Identifying proteins: 1. gel electrophoresis: can seperate on size and isoelectric point 2. Mass spectroscopy 3. yeast assays

The synthetic worls

chemical synthesis ( traditional) combinatorial synthesis

target oriented synthesis

classical ' textbook synthesis aimed at producing specific compounds typically starts with retrosynthetic analysis

ADMET prediction: toxicity

clogP <= 3 PSA >=75 LLE >= 5

but we also need diversity: select a metric or metrics that are related to the activity of the compound: group compounds by similarity based on the metrics

clustering exclusion cell based methods select representatives from each group metrics can be anything from physical properties to tanimoto coefficients

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)

Natural products are often used as lead compounds in the design and synthesis of novel drugs. Which of the following general characteristics of a natural product is most likely to be a disadvantage in synthesising analogues?

complexity of structure Feedback: Natural products are often complex in structure which makes their synthesis difficult. As a result, the synthesis of analogues can also be difficult.

the compounds synthesized in a combinatorial synthesis are stored as

compounds libraries

Chemical diversity

compounds with distinct structural characteristics compounds with distinct physiochemical properties

The virtual worls

computer aided drug design

De novo design

concept of generating lead compounds entirely through computer simulations

Barlos resin

contains a trityl linker and was designed to avoid this problem of wang resin (prone to racemization). The final product can be cleaved under very mild conditions (HOAc/TFE/CH2Cl2 or TFA/CH2Cl2) due to the high stability of the trityl cations that are formed. Molecules can also be linked to the resin by means of an alcohol group.

a scaffold is the

core structure of a molecule rounf which variations are possible through the use of different substituents

Design of lead compounds using NMR spectroscopy

could determine whether a small molecule with/could bind to a protein optimize epitope (small molecule binds to protein but not big enough to provide response) look at slides design of a lead compound as an immunosuppressant---epitope A and B connect through alkane chain

Validated target

critically involved in disease process inhibited or activated by drug molecules

introducing susceptible metabolic groups: Anti-asthmatic agents

cromakalim: produces cardiovascular side effects if it reaches the blood supply add metabolic instability such that the compound is rapidly metabolized in blood UK143220- ester is quickly hydrolysed by esterases to an inactive acid UK 157147- phenol is quickly conjugated and eliminated

drugs must be sufficiently 'fatty' to

cross cell membranes

testing can also be done by

cross validation

targeting gut infections

design the antibacterial agent to be highly polar or ionised agent will be too polar to cross the gut wall agent will be concentrated at the site of infection Example- highly ionised sulfonamides

Which of the following is not an endogenous compound?

desipramine Feedback: Endogenous compounds are any compounds occurring naturally in the body. Desipramine is a synthetic drug and is not an endogenous compound. Page reference: 204-206

prediction

determining a value for a new observation from a model built from previous observations example: calculating the solubility of a drug candidate prediction methods can be: - De novo: based on 'first principles' as in physics based force fields - Empirical: based on parametrizing an equation, as in QSAR

Classification

determining the group to which a new example belongs: example: is the new drug candidate soluble or insoluble Classification can be: -supervised: you know the classes ahead of time - unsupervised: you try to discern what the classes should be

Stereochemical diversity

diversity in location of interacting groups through varying chiral centers

functional group diversity

diversity of molecular interactions by varying type and location of functional groups on the scaffold

reducing drug toxicity: varying substituent position

dopamine antagonists inhibits P450 enzymes no inhibition of P450 enzymes - NC group switched

linking a biosynthetic building block rationale

drug 'smuggled' into cell by carrier proteins for natural building block ( e.g. amino acids or nucleic acid bases) increases selectivity of drugs to target cells and reduces toxicity to other cells example: anticancer drugs ( non selective alkylating agent toxic, uracil mustard)

prodrugs to prolong activity: add hydrophobic groups

drug concentrated in fat tissue slow removal of hydrophobic group slow release into blood supply Example: cycloguanil pamoate ( antimalarial)

Drug Alliances- Synergism

drugs which have beneficial effect on the activity or pharmokinetic properties of another drug

Assay

easily measured effect amendable to automation

parallel synthesis allows the synthesis of a large number of easily identifiable analogues which can be quickly and

easily tested, speeding up the optimization process

Born-Oppenheimer

electrons move so much faster than nuclei that there motions can be decoupled- solve only for position of electrons E= Eelectronic + Evi brational rotational translational

one caveat-

elementary particles are very small, and must be treated with wave mechanics

results from computer modelling

eliminates structures which do not contribute significant numbers of new pharmacophores reduces the number of target structures by 80-90% whilst retaining 90% of possible pharmacophores increases efficiency in finding lead compounds

What is the term used for small molecules that bind to different regions of a binding site?

epitopes Feedback: The correct answer is epitopes. Epimers are diastereomers differing in their configuration at one asymmetric centre. Isomers are different structures having the same molecular formula. Isotopes are elements which have the same number of protons and electrons, but a different number of neutrons.

The following diagram illustrates the detection system known as surface plasmon resonance. What is represented by D?

evanescent wave look at diagram D is the evanescent wave which interacts with free oscillating electrons called plasmons in the metal film, when the angle of incidence (α) is correct. Symbol A represents a receptor which is covalently linked to the dextran matrix, and which will bind ligands present in the buffer flow. B is monochromatic plane-polarised light. C is the flow of buffer solution.

prodrugs to mask toxicity and side effects

example: cyclophosphoramide for phosphoramide mustard ( anticancer agent)

combinatorial synthesis: mix and split method

example: synthesis of all possible dipeptides using 5 amino acids. Standard methods would involve 24 separate syntheses mix and split procedure involves five separate syntheses

example of adding polar groups

examples: Tioconazole ( antifungal agent with poor solubility-skin infections only) Fluconazole ( systemic antifungal agent improved blood solubility)

prodrugs to improve membrane permability

examples: candoxatril for candoxatrilat ( protease inhibitor) Notes: varying the ester varies the rate of hydrolysis electron withdrawing groups increase rate of hydrolysis (e.g. 5-indanyl) leaving group (5-indanol) is non toxic

matched molecular pairs

find pairs of compounds which differ by only one atom or group calculate the difference in some key property resulting from the change when optimizing lead molecules, to change a property by finding the paired group that is statistically likely to change the property in the desired direction example: a pair transform to modify solubility

Global energy minimization

finds the lowest possible state some methods are: molecular dynamics, monte carlo and genetic algorithms

Advantage of fragment-based drug design

fragment evolution fragment linking fragment self assembly fragment optimization

skeletal diversity

generate different scaffolds a common goal these days- the question then becomes how much enumeration around a given scaffold? initially thousands, then hundreds, now possibly dozens of compounds per scaffold are made this feeds into the strategy of fragment-based design

Requirements for drug discovery: validated target Identifying targets at the gene level:

genes differentially expressed between individuals who are or are not in need of treatment for a disease or condition genes differentially expressed when an individual is exposed to a drug that alleviates or exacerbates symptoms of interest genes co-expressed with other genes presumed to be involved in the metabolic pathway of interest Methods rely on feedback loop that adjusts expression in response to the action of a drug

Biology driven

genomics protemics chemical genetics

Benzodiazepines, hydantoins, pyridines, beta lactams, dipeptides are

good scaffolds spider like low molecular weight variety of synthetic routes available

wang resin

has a linker which is suitable for the attachment and release of carboxylic acids. it can be used in peptide synthesis by linking N-protected amino acid to the resin by means of an ester link. This ester link remains stable to coupling and deprotection steps in the peptide synthesis, and can then be cleaved using trifluoroacetic acid (TFA) to release the final peptide from the bead.

continuous data

has an infinite range of values, such as a person's height

discrete data

has specific values, such as a person's sex

What is the term used for the automated in vitro testing of large numbers of compounds using genetically modified cells?

high throughput screening As well as being automated and capable of handling large numbers of compounds, high throughput screening (HTS) can be carried out on small scale, allowing results to be obtained quickly and efficiently.

introducing chemically susceptable groups

hoffmann elimination

prodrugs to prolong activity: add hydrophobic groups

hydrophobic esters of fluphenazine ( antipsychotic) given by intramuscular injection concentrated in fatty tissue slowly released into the blood supply rapidly hydrolysed in the blood supply

method for computer modelling

identify all possible target structures rank in order of rigidity by identifying number of rotatable bonds identify the most rigid structure identfiy the possible conformations of the most rigid structure identify the pharmacophore triangles for each conformation repeat for the next most rigid structure compare the pharmacophores for both structures retain the second structure if it contains more than 10% new pharmocaphores add together both sets of pharmacophores and compare with the next most rigid structure repeat cycle

Enzyme inhibition tests

identify competitive or non competitive inhibition strength of inhibition measured as IC50 IC50: concentration of inhibitor required to reduce enzyme activity by 50%

Chemical genetics

identify compounds that elicit a desired biological response on a whole biological systems: 1. single cell organisms 2.Pathological cells 3. Whole organisms (fly,worm, zebrafish,mouse...) Remove compounds that produce non specific response identify the mechanism of action 1. screen against proteins with known mechanism of action 2. determine importance of protein in pathway Prioritize compounds for further analysis 1. past assays 2. similarity to known drugs in a target class 3. physiochemical properties Validate the target 1. does the target mediate biological response in cell based assay 2. binding strength

Structure Activity Relationships

identify which functional groups are important for binding and/or activity Method: Alter, remove or mask a functional group test the analogue for activity conclusions depend on the method of testing in vitro: tests binding interactions with target In vivo: tests for target binding interactions and/ or pharmokinetics If in vitro activity drops, it implies group is important for binding if in vivo activity unaffected, it implies group is not important

Overfit data

if the model contains so many variables, that it can't predict new observations

Underfit data

if the model does not contain enough variables to explain the results

uses of prodrugs

improving membrane permeability prolonging activity masking toxicity and side effects varying water solubility drug targeting improving chemical stability 'sleeping agents'

simplification

in a stationary state the total energy is independent of time, we can seperate the time and spatial components of the wave function and deal only with the location of the nuclei and electrons.

computer software is available to assist

in planning of compound libraries

prodrugs

inactive compounds which are converted to active compounds in the body

virtual libraries:focused library

incorporate knowledge of the therapeutic target

Targeting peripheral regions over CNS

increase polarity of the drug drug is less likely to cross the blood brain barrier

Machine learning: Neural networks

input layer hidden layer output layer neural networks must be trained- sets weights for the connections between the nodes

Microfluidics

involves the manipulation of tiny volumes of liquids in confined space.

a binary fingerprint

is a set of boxes representing the presence or absence of a particular fragment usings 1s and 0's. Typically a fingerprint will be 100's to 1000's of bits.

A priviliged scaffold

is one which is commonly present in known drugs

one disadvantage of polystyrene beads

is the fact that they are hydrophobic and the growing peptide chain is hydrophilic. As a result the growing peptide chain is not solvated and often folds in on itself to form internal hydrogen bonds. This, in turn, hinders access of further amino acids to the exposed end of the growing chain.

LE: ligand efficiancy

is the ligand an efficient binder, or simply large?

Which of the following drugs was not isolated from a natural source?

isoniazid Isoniazid was synthesised in the laboratory. The other three compounds were derived from natural sources. Quinine was isolated from the bark of the cinchona tree. Morphine was isolated from the seed pods of poppies. Artemisinin was isolated from a Chinese plant.

Computer-designed libraries

it has been stated that a relatively small number of moieties account for the large majority of side chains in known drugs. This may imply that it is possible to define drug like molecules and use computer software programs to design more focused compound libraries. Descriptors used in this approach include Log P, molecular weight, number of hydrogen bond donors, number of rotatable bonds, aromatic density, the degree of branching in the structure, and the presence or abscence of specific functional groups. One can also choose to filter out compounds that do not obey the rules mentioned in sec. 16.3.2

Lead molecules

lead like optimization typically increases molecular weight and logP selective Good ADMET properties

Lead molecules

lead-like selective Good ADMET properties

prodrugs to increase water solubility: phosphate ester of clindamycin

less painful on injection

procaine

local anaesthetic susceptible to esterases short duration

scoring function: Potential of mean force

look at a radial distribution around each atom and determine the probabilities of seeing specific interactions W(r)=-RTln(g(r)) where g(r) is the probability of seeing the interaction within a radius r.

sample size and variability:

look at examples

2D searching: substructure searching

look for a specific piece of a larger molecule that is felt to be important to binding to the target

2D Searching: similarity searching

look for compounds based on similar values of a 2D metric

molecular mechanics

looks at the motion of nuclei. Useful for sampling conformational states and calculating IR spectra

machine learning: support vector machines

looks for hyperplane that optimally seperates a set of points if the points are not lineraly seperable-transform the data with a kernel function support vectors are the points that lie closest to the place- maximize their seperation ( the margin) choose the line ( plane) that gives an optimal seperation example: seperating drug like from non drug like compounds

prodrugs to increase water solubility: Example: lysine ester of oestrone

lysine ester of oestrone is better absorbed orally than oestrone increased water solubility prevents formation of fat globules in gut better interaction with the gut wall hydrolysis in blood releases oestrone and a non toxic amino acid

Biological diversity

made possible by the growth of biologically annotated databases biologically diverse compounds libraries at Novartis: compounds modulate at least one known target, modulated targets span multiple families and biological functions Diversity can be assessed by maximizing the number of targets represented biological activity assumes reasonable ADME properties, which will improve hit rate

Monte Carlo

make random changes of torsion angles the energy might go up or down- what conformations do we keep? Metropolis criterion: if the energy is lower, keep the new conformation if the energy is higher: generate a random number if e^-(v'-v)/kT> random number, keep the new conformation stimulated annealing can also be used here

Which source has been particularly fruitful in finding novel antitumour agents such as bryostatins and dolostatins?

marine sources Marine life such as coral, fish and cyanobacteria have proved useful sources of novel lead compounds having antitumour properties.

prodrugs to mask toxicity and side effects

mask groups responsible for toxicity/side effects used when groups are important for activity example: aspirin for salicyclic acid Salicyclic acid: analgesic, causes stomach ulcers, due to phenol group aspirin: phenol masked by ester hydrolysed by esterases in bloodstream

masking or removing polar groups

masking or removing polar groups decreases polarity and increases hydrophobic character

disadvantage of varying pKa

may affect binding interactions

disadvantage of varying alkyl substituents

may interefere with target binding for steric reasons

disadvantage of adding polar groups

may introduce unwanted side effects

stopping rules

medical trials are expensive..many pharmaceutical companies develop "stopping rules", which allow investigators to end a study early. how significant an effect is compared with a placebo can be measured using the P value what if we stopped at a high P value.. we wouldn't actually see the true P value stopping early

First successful example of solid phase synthesis was the

merrifield peptide synthesis

metabolic blockers rationale

metabolism of drugs usually occurs at specfic sites introduce groups at a susceptible site to block the reaction increases metabolic stability and drug lifetime

Identification of structures from combinatorial synthesis: recursive deconvolution

method of identifying the active component in a mixture quicker than separately synthesizing all possible components need to retain samples before each mix and split stage. Example: consider all 27 tripeptides synthesized by the mix and split strategy from glycine, alanine and valine.

identification of structures from combinatorial synthesis: Tagging

method of identifying the structure present on a bead tagging molecule is constructed on the same bead as the target molecule each amino acids or nucleotides is used to indicate a specific reagent or reactant used at each step An amino acid or nucleotide is added after each step in the reaction sequence peptide tag is identified using automated peptide sequencing oligonucleotide sequence is identified using DNA sequencing require a linker with two functional groups (e.g. SCAL)

Inceasing absorption example

metoclopramide notes: administered with analgesics in the treatment of migraine increases gastric motility and causes faster absorption of analgesics leads to faster pain relief

Notes on analogues

modification may disrupt binding by electronic/ steric effects easiest analogues to make are those made from lead compound possible modifications may depend on other groups present some analogues may have to be made by a full synthesis- replacing an aromatic ring with a cyclohexane ring allows identification of important groups involved in binding allows identification of the pharmacophore

molecular properties: fragment approaches

molecular property treated as the sum of fragment or atomic properties logP (theory) Log P (observed) example: meta chlorobenzamide = logP(benzene) + piCl + pi CONH 2.13+ .71 -1.49= 1.35 log p observed = 1.51

drugs must be sufficiently polar to interact with

molecular targets

levodopa

more polar amino acid carried across cell membranes by carrier proteins for amino acids Decarboxylated in cell to dopamine

swelling is important because

most reactions involved in solid phase synthesis take place in the interior of the bead rather than on the surface

Synthesis of scaffolds

most scaffolds are used using the synthetic route employed for the solid-phase synthesis, and this also determines the number and variety of substituents that can be attached to the scaffold.

Identifying lead molecules

natural products endogenous ligands compound libraries: existing collections, high throughput synthesis

spider like scaffolds

need to be used because of the structural diversity. they consist of a general body ( called the centroid or scaffold) from which various 'arms' (substituents) radiate These arms contain different functional groups which are used to probe a binding site for binding regions once the spider molecule has entered. The chances of success are greater if the 'arms' are evenly spread around the scaffold, as this allows a more thorough exploration of the three dimensional space ( conformational space) around the molecule.

In vitro test

not carried out in humans: molecules ( isolated enzymes or receptors) cells ( cloned cells) Tissues ( muscle tissue) organs micro organisms ( for antibacterial agents)

Testing with receptors

not easy to isolate membrane bound receptors carried out on whole cells, tissue cultures, or isolated organs Affinity: strength which compounds bind to a receptor Efficacy: measure of maximum biochemical effect resulting from binding of a compound to a receptor Potency: concentration of an agonist required to produce 50% of the maximum possible effect

Tanimoto coefficient

number of bits set in both fingerprints/number of bits set in either fingerprint look at example coefficients range from 0 to 1

Accuracy

number of correct predictions divided by the size of the dataset, i.e. how often were we right

specificity

number of true negatives divided by the number of true negatives plus the false positives

sensitivity

number of true positives divided by the number of true positives plus the false negatives ( same as recall)

Recall

number of true positives divided by the number of true positives plus the false negatives, i.e. the fraction of correct positive predictions

precision

number of true positives divided by the number of true positives plus the number of false positives, i.e., how well is a true possitve predicted

methods on how to vary alkyl substituents

often feasible to remove alkyl groups from heteroatoms and replace with different alkyl groups usually difficult to remove alkyl groups from the carbon skeleton-full synthesis often required

What are we missing: entropy

often handled by a simple formalism of counting rotatable bonds really requires molecular dynamics or Monte Carlo calculations to determine the population of conformational states, from which entropy can be calculated

Flexible Docking

often involves splitting the target molecule into pieces dock the base piece add additional pieces by sample the local conformational space either lead compound and lead compound and protein may be considered flexible

Small data

often locally in scope, a single experiment or single researcher usually better vetted, i.e. more trustworthy often smaller in scope, i.e. covers a narrower range of values

prodrugs to increase water solubility

often used for IV drugs allows higher concentration and smaller dose volume may decrease pain at site of injection Example: succinate ester of chloramphenicol succinate ester----Esterase--->chloramphenicol

Primary and secondary alcohols (ROH) can be linked to a dihydropyran-functionalized resin. Lunking the alcohol is done in the presence of pyridinium 4-toluenesulphonate (PPts) in dichloromethane.

once the reaction has been completed, cleavage can be carried out use TFA

starting materials with a carboxylic acid (RCO2H) can be linked to the Rink Resin via an amide link.

once the reactions sequence is complete, treatment with TFA releases the product with a primary amide group, rather than the original carboxylic acid

lambda=2a

one wave ( looksl ike hill)

molecular dynamics

one way to overcome local energy barriers is to add energy to the system ( raise the temp). Usually this is done using classical physics and requires solving for atomic positions as a function of time. simulated annealing: alternatively heat and cool the molecule in order to sample conformation space. look at graph

lidocaine

ortho methyl groups act as steric shields hinder hydrolysis by esterases amide more stable than ester ( electronic effect)

Lead compounds from the natureal world: micro organisms

penicillin cephalosporins tetracyclines streptomycin chloramphenicol

Phage display

peptides are incorporated into the coat of a phage virus. The phages are the introduced to the immobilized protein. Phages that do not bind are washed off. Those that do bind are released to infect bacteria that produce more of the phages with the binding peptides

combinatorial synthesis has been used for the synthesis of

peptides, peptoids, and heterocylcic structures. Most organic reactions are feasible.

an aqueous phase can be seperated from an organic phase using

phase seperation columns or by freezing the aqueous phase onto a solid surface

If you add carboxylic acid to wang resin, product is formed and

piperidine causes deprotection

The natural world

plantlife ( flowers, trees, bushes) micro organisms ( bacteria, fungi) animal life ( frogs, snakes, scorpions) biochemicals ( neurotransmitters, hormones) marine chemistry ( corals, bacteria, fish etc.)

Machine learning: Receiver Characteristic (ROC) curves:

plot sensitivity versus 1- specificity used to visually evaluate the quality of a classification method the straight line sensitivity=1-specificity is what one would expect from random selection ex: comparing the ability of three docking programs to identify active compounds In medicine it is used to assess tests and treatments

disadvantage of masking or removing polar groups

polar group may be involved in target binding unnecessary polar groups are likely to have been removed already ( simplification strategy) see also prodrugs

false negative

predicted negative, but actually positive ex: says you don't have measels but you do

false positvie

predicted positive, but actually negative ex: says you have measels but you don't

The goal of machine learning falls into two broad classes

prediction and classification

diversity-oriented synthesis

preparation of diverse, complex compounds from simple starting materials diverse, complex libraries have been shown to produce higher hit rates starts with forward synthetic analysis

prodrugs to improve membrane permeability: Trojan horse strategy

prodrug designed to mimic biosynthetic building block transported across cell membranes by carrier proteins example: Levodopa for dopamine

Some drugs containing an ester group are inactive in vitro, but are active once the drug has been absorbed in vivo. What term is used for such drugs?

prodrugs Feedback: These drugs are described as prodrugs. They do not bind to a target binding site in vivo since an important binding group has been masked by the ester. The ester group is hydrolysed in vivo to reveal the binding group. There are no such things as postdrugs or predrugs. Metabolites are the structures which are formed after metabolic reactions.

protecting agents and synthetic strategy: protecting groups

protect reactive functional groups that are not meant to react. must be added easily in high yield under mild conditions must be stable under the reactions conditions used in the synthesis must be removed easily in high yield under mild conditions different protecting groups should be removed under different conditions

drugs must be sufficiently fatty to avoid

rapid excretion

solid phase techniques

reactants are bound to polymeric surface and modified whilst still attached. final product is released at the end of the synthesis

1,4-benzodiazepines have been synthesized by linking a selection of amino acids to resin beads through the carboxylic acid group.

reaction with a variety of imines gave the adducts which then cyclized to give final products. The advantage of this synthesis lies in the fact that the functional group released from the resin takes part in the final cyclization and does not remain as an extra, and possibly redundant, group. The final product has four variable substituents spread evenly around the bicyclic ring system. This allows exploration of conformational space around the whole molecule when searching for binding interactions with a drug target

catch and release strategies involve

reagents which are linked to a solid support. Reactants are taken out of solution when they react with the reagent, and are then released when a subsequent reaction takes place

prodrugs to prolong activity: mark polar groups

reduces rate of excretion example: Azathioprine for 6-mercaptopurine 6-Mercatopurine: suppresses immune response, shor tlifetime, eliminated too quickly Azathioprine: slow conversion to 6-mercaptopurine, longer lifetime

remove/replace susceptible metabolic groups rationale

remove susceptible group or replace it with a metabolically stable group e.g. modification of tolbutamide ( antibiotic) replaced methyl group with chlorine group

Bio-isosteres rationale

replace susceptible group with a different group without affecting activity bio-isostere shows improved pharmacokinetic properties bio-isosteres are not necassarily isosteres examples: amides and urethanes for esters (see earlier) Du122290 ( dopamine antagonist)

Rigid docking

requires generating a conformational ensemble of each compound to dock typically additional minimization is carried out on the best conformers

screening can be carried out on compounds attached to

resin beads, or on compounds which have been released into solution

privileged scaffols

scaffolds which are common in medicinal chemistry and are associated with diverse range of activities benzodiazepines, hydantoins, benzensulphonamides etc.

a high throughput approach to drug discovery

screening library--> targeted/ focused library---> optimize--> drug candidate

There are several sources and methods of discovering new compounds. Which of the following is most likely to lead to the discovery of a complex structure quite unlike any other previously discovered?

screening plant extracts There are no preconceived ideas when screening plant extracts for active lead compounds. Some natural products are quite bizarre in structure! Combinatorial chemistry involves the synthesis of a large number of compounds using a standard synthetic route, and so the types of structures that will be synthesised are predictable and belong to a similar family of compounds. Database mining involves the computerised search of known compounds for particular pharmacophores. Me-too drugs are analogues of an established drug.

within the body

selectivity between different enzymes, receptors etc. selectivity between receptor types and subtypes selectivity between isozymes organ and tissue selectivity

SMILES

simplified molecular-input line-entry system

The ideal scaffold should be

small in order to allow wide variation of substiutents. It should also have its subtituents widely dispersed round its structure ( spider like) rather than restricted to one part of the structure ( tadpole like) if the conformation space around it is to be fully explored Finally, The synthesis should allow each of the substitutents to be varied independently of each other.

Small-Molecule Microarrays

small molecules are bound to the microarray. The protein is introduced and then a fluorscent tag ( such as a fluorescently labeled antibody) is introduced. Array locations where the protein has bound will fluoresce

parallel synthesis can be carried out on

solid phase or in solution

drugs must be sufficiently polar to be

soluble in aqueous conditions

Advantages of solid phase techniques

specific reactants can be bound to specific beafs beads can be mixed and reacted in the same reaction vessel products formed are distinctive for each bead and physically distinct excess reagents can be used to drive reactions to completion excess reagents and by products are easily removed reaction intermediates are attached to the bead and do not need to be isolated and purified individual beads can be seperated to isolate individual products polymeric support can be regenerated and re-used after cleaving the product automation possible

notes on atracurium

stable at acid pH, unstable at blood pH (slightly alkaline) self destructs by hoffmann elimination and has short lifetime allows anaesthetist to control dose levels accurately quick recovery times after surgery

circular fingerprints

start with each atom and work your way out in concentric rings

local minimization

start with initial geometry pick a bond or angle and change it keep the result that lowers the energy look at graph: energetically unstable st ructure is top molecule, energy minimum bottom molecule arrows: variation in bond lengths and angles

Notes for computer modelling

start with rigid structures since these contain less possible conformations and a smaller number of possible pharmacophores pharmacophores are more likely to be fairly represented in rigid structures than in flexible

stereoelectronic effects rationale

steric and electronic effects used in combination increases chemical and metabolic stability Example: procaine and lidocaine

virtual libraries: diverse library

structures are chosen to be as different as possible

spider like scaffolds allow

substitutent variation around the whole molecule, making it possible to explore all the conformational space around the scaffold. This increases the posssibility of finding a lead compound which will bind to a target binding site

2D searching

substructure searching similarity searching

Lead compounds from the synthetic world

sulfanilamide ( antibiotic) combinatorial synthesis - peptide synthesis ( resin bead--->amino acid--->amino acids----> peptide) look at slides

BIAcore is a detection system patented by Pharmacia Biosensor to detect a ligand binding to a target. What is the name of the phenomenon used in this detection procedure?

surface plasmon resonance Feedback: Nuclear magnetic resonance and electron spin resonance are both forms of spectroscopy. BIAcore makes use of surface plasmon resonance, which involves the interaction of a reflected wave of plane polarised light with free oscillating electrons called plasmons in a metal film. Scintillation proximate assay involves the immobilisation of a target molecule on beads coated with a scintillant. A ligand labelled with 125I binds to the target and the radioisotope interacts with the scintillant to emit light. Page reference: 195-196

taggind involves the construction of a tagging molecule on the same solid support as the target molecule

tagging molecules are normally peptides or oligonucleotides. After each stage of the target synthesis, the peptide or oligonucleotide is extended and the amino acid or nucleotife used defines the reactant or reagent used in that stage.

bar coding

tags are linked to bead by a photocleavable bond irradiation removes all the tags at the same time mixture is passed through a gas chromatograph tags are identified by their retention time absence or prescence of tags identifies reagents used at different stages of the synthesis identifies the product ( assuming reaction goes as predicted)

Traditional target based drug discovery

target ID--->target hypothesis--> target validation---> new DA program--->HTS->chemistry

Combinatorial synthesis

the automated synthesis of a large number of compounds in a short time period using a defined reaction route and a large variety or reactants normally carried out on small scale using solid phase synthesis and automated synthetic machines mictures of compounds formed in each reaction vessel useful for finding lead compounds

Parallel synthesis

the automated synthesis of a large number of compounds in a short time period using defined reaction route and alarge variety or reactants single product formed in each reaction vessel useful for SAR and drug optimization

Important groups for activity for morphine are

the benzene ring with OH and the NMe group

high throuhgput screening automatically analyses

the biological activity of large numbers of samples against a defined targets. The analysis requires only small quantities of each sample

'drug like' molecules

the chance of oral activity are increased if the structure obeys lipinskis rule of five or veber's parameters. Howeverr, allowance has to be made for the fact that any lead compounds identified are almost certainly going to require substantial optimization, in which case more stringent guidelines should be applied. Other restrictions should be considered. For example, groups such as esters should be avoided because they are easily metabolized. Scaffolds or substituents likely to result in toxic compounds should also be avoided; for example alkylating groups or aromatic nitro groups.

Standing waves: a wave must satisfy boundary conditions- the amplitude must be zero at the boundaries

the correspondance to atoms are orbitals

De novo drug design

the design of novel agents based on a knowledge of the target binding site

The mix and split method allows

the efficient synthesis of large numbers of compounds with a minimum number of operations

problem with wang resin

the first amino acid linked to the resin is prone to racemization.

Different linkers are used depending on

the functional group which will be present on the starting material the functional group which is desired on the final product once it is released

solid supported reagents are easily removed at the end of a reaction

the potential toxicity of the reagent or its by product is reduced when attached to a solid support

Affinity selection mass spectometry

the protein of interest is combined with a mixture of small molecules. Those that do not bind are washed away. Those that remain are freed from the complex and identified by mass spectometry

solid phase extraction is often used in parallel synthesis for work up. It involves

the use of columns to remove impurities and excess reagents

substituent variation

the variety of substituents chosen in a combinatorial synthesis depends on their availability and the diversity required. This would include such considerations as structure, size, shape, lipophilicity, dipole moment, electrostatic charge, and functional groups present. It is usually best to identify which of these factors should be diversified before commencing the synthesis.

The difference between docking and scoring: Consensus scoring

there are many scoring functions a structure is more likely to be a true hit if several scoring functions agree consensus - count number of times the hits is in the top 50% of compounds for a given score - prefer hits with the highest consensus score Caveat: best to validate the scoring functions on the target of interest and only use ones that work for that target

Possible effect of analogues on binding (e.g ether)

there is no interaction in binding site for

for parameterized models

there may also need to be a validation set for determining the optimum values of the parameters

heterocycles are less susceptible to metabolism, and have better pharmacokinetic properties.

they are more rigid, and diversity is possible by varying the substituents around the heterocyclic 'core'.

pharmacophores

they can be used also-typically pharmacophore triplets are binned and matched to bit locations triangle picture

Local energy minimization methods will stop if there is no way for the energy to go down--

this may not be the lowest possible energy!

de novo design

thymidylate inhibitors lead compound-->optimisation---> anticancer agent

planning a combinatorial synthesis

to generate a large number of compounds to generate a diverse range of compounds to increase the chances of finding a lead compound that will bind to a binding site synthesis is based on producing a molecular core or scaffold with functionality attached.

pharmokinetics-Drug design

to improve pharmacokinetic properties of lead compound to optimize chemical and metabolic stability to optimize hydrophilic/ hydrophobic balance to optimize solubility to optimize drug half life to optimize distribution characteristics

combinatorial synthesis aims

to use a standard synthetic route to produce a large variety of different analogues each reaction vessel contains a mixture of products products are physically distinct-attached to different beads the identities of the structures in each vessel are not known with certainty useful for finding a lead compound allows rapid synthesis of large numbers of compounds each mixture is tested for activity as the mixture inactive mixtures are stored in combinatorial libraries active mixtures are studied further to identify the active component

parallel synthesis: Aims

to use a standard synthetic route to produce a range of analogues, with a different analogue in each reaction vessel, tube or well The identity of each structure is known useful for producing a range of analogues for SAR or drug optimization

Chemistry is generally concerned with nuclei and electrons and how they interact. This requires solving the equations of motion. at the most basic level:

total energy= potential energy + kinetic energy

Reducing drug toxicity rationale

toxicity is often due to specific functional groups 1.) remove or replace functional groups known to be toxic: - aromatic nitro groups - aromatic amines -bromoarenes -hydrazines -polyhalogenated groups -hydroxylamines vary substituents vary position of substituents

F=K(d-d0)^2

treating bond like spring

scoring function: molecular mechanics based

use a subset of the molecular mechanics force fields we discussed earlier

what are we missing: solvation

use explicit water molecules use implicit correction for water - GB/SA uses a generalized born model for determining solvent screening and electrostatic desolvation effects and a term based on the solvent accessible surface to approximate hydrophobic effects.

machine learning: Decision trees, random forest

use molecular descriptors to classify molecules best values of each descriptor is chosen to provide the optimal split at each level example: decision tree for activity-100 compounds ( 60 active, 40 inactive)

Docking isnt the only way to find lead compounds: molecular similarity

use molecular descriptors to compare compounds: physiochemical properties molecular fingerprints pharmacophore matching shape

shifting susceptible metabolic groups rationale

used if the metabolically susceptible group is important for binding shift its position to make it unrecognisable to metabolic enzyme must still be recognizable to target e.g. salbutamol

introducing chemically susceptible groups rationale

used to decrease drug lifetime avoids reliance on metabolic enzymes and individual variations example: atracurium-i.v. neuromuscular blocking agent

introducing susceptible metabolic groups rationale

used to decrease metabolic stability and drug lifetime used for drugs which 'linger' too long in the body and cause side effects add groups known to be susceptible to phase 1 and phase 2 metabolic reactions examples: anti-arthritic agents L787257 ( resistant to metabolism, excessively long half life) and L791456 ( metabolically susceptible)

Steric shields rationale

used to increase chemical and metabolic stability introduce bulky group as shield protects a susceptible functional group (e.g. ester) from hydrolysis Hinders attack by nucleophiles or enzymes example: antirheumatic agent D1927 (blocks hydrolysis of terminal amide)

prodrugs to improve membrane permeability: Esters

used to mask polar and ionisable carboxylic acids hydrolyzed in blood by esterases used when a carboxylic acid is required for target binding leaving group ( alcohol) should ideally be non toxic Examples: Enalapril for enalaprilate ( antihypertensive) R=Et Enalapril R=H Enalaprilit

prodrugs to improve membrane permeability: N-Methylation of amines

used to reduce polarity of amines demethylated in liver Examples: Hexobarbitone

Prodrugs to lower water solubility

used to reduce solubility of foul tasting orally active drugs less soluble on tongue less revolting taste example: palitate ester of chloramphenicol (antibiotic)

electronic shielding of NH2 rationale

used to stabilise labile functional groups (.e.g. esters) replace labile ester with more stable urethane or amide nitrogen feeds electrons into carbonyl group and makes it less reactive increases chemical and metabolic stability

save space by representing molecules as chemical graphs

usedful for building chemical databases programs are available to produce 3D coordinates

linking drugs to monoclonal antibodies

useful for targeting drugs to cancer cells identify an antigen which is overexpressed on a cancer cell clone a monoclonal antibody for the antigen attach a drug or poison ( e.g. ricin) to the monoclonal antibody antibody carries the drug to the cancer cell drug is released at the cancer cell

dopamine

useful in treating parkinson's disease too polar to cross cell membranes and BBB

what are we missing? electronic effects

usually only considered in terms of changes in the atomic partial charges

scaffolds: Tadpole scaffols

variation restricted to a specific region around the molecule less chance of favourable interactions with a binding site

method of varying pKa

vary alkyl substituents on amine nitrogens vary aryl substituents to influence aromatic amines or aromatic carboxylic acids

Vary Pka rationale

varying pKa alters percentage of drug which is ionised alter pKa to obtain required ratio of ionised to unionised drug

solubility and membrane permeability: Vary alkyl substituents: rationale

varying size of alkyl groups varies the hydrophilic/hydrophobic balance of the structure larger alkyl groups increase hydrophobicity

how do we screen them for affinity?

virtual docking - rigid docking -flexible docking

lambda=a

wave with high and low point

Pharmacophore searching:

what do they have in common in 2D? what do they have in common in 3D? Alignment example: tagament and Zantac: both do the same thing in the body ( bind to the same receptor)

The difference between docking and scoring

when docking (especially a large number of compounds) the method that scores the result must be fast : often emperical simple methods are generally sufficient to place the molecule in the protein in a reasonable conformation Simple methods are genereally not able to provide a good relative ranking of the resulting poses - entropy is not considered - solvation is not considered - very simple charge models are used