topic guide 9.3: drug discovery and design · of structurally related molecules to enable rapid...

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Unit 9: Medicinal Chemistry

Modern chemical techniques have revolutionised the process of drug design. A knowledge of the structure of receptor sites and computer modelling techniques to predict the binding of drug molecules to these sites means that research is now able to identify likely candidates for new drugs before the drug has even been synthesised by chemists. Once compounds are identified, new combinatorial techniques allow chemists to synthesise large numbers of structurally related molecules to enable rapid identification of the most promising candidate for further development.

In this unit you will look at how these new techniques of computer modelling and combinatorial chemistry are being applied in modern drug design and development.

On successful completion of this topic you will: • understand the stages of drug discovery and design (LO3).

To achieve a Pass in this unit you need to show that you can: • discuss the issues for consideration when designing a new drug (3.1) • explain the concepts of structure-activity relationships with respect to

drug design (3.2) • explain the role of combinatorial chemistry in drug synthesis and

development (3.3).

Drug discovery and design9.3

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9.3: Drug discovery and design

1 Designing a new drug

Dr Richard Lewis is the global head of Computer-aided Drug Design at Novartis International, a multinational pharmaceutical company based in Basel, Switzerland. He talks about the drug discovery process and gives some examples of how the various disciplines involved in the process interact with each other. You can read more about the chemical and biochemical aspects of the research in sections 2 and 3 of this topic guide.

‘The essential principle is that we aim to invent safe drugs for unmet medical needs. With modern chemical and computing techniques we can make and investigate a myriad of new compounds. There are so many avenues we could go down, but ultimately we have to take pragmatic decisions to ensure that we can deliver a successful product in a reasonable time frame.

We need to begin by identifying a disease that is amenable to drug intervention. We will need to know its biology – what is the pathway by which the disease operates? Are there reactions or processes within that pathway which could be somehow disrupted? Can this disruption be enabled by the relatively small molecules, which we will be aiming to design and develop?

Even at this stage we may need to be looking further ahead before we know whether we have a viable project. Assuming that these theoretical studies look promising, we would need to have some confidence that we will be able to evaluate the project at different stages – how will we screen the molecules we develop to help identify the most promising target molecules? Will the effects of the drugs be measurable in clinical trials? Is it likely to be technically and financially feasible to develop this into a marketable drug?

A good example of recent research, which illustrates the principles of drug design, takes Alzheimer’s disease as a target. Clearly the potential market for a drug that has demonstrable efficacy in reducing symptoms or slowing the disease progression would be enormous. The target reaction is one in which an enzyme called BACE-1 cleaves a protein known as the amyloid precursor protein. Cleavage of this protein is known to be an important step along the route that eventually leads to the build-up of the plaques, which are observed in the brains of Alzheimer’s patients.

Once we have identified a target reaction in this way we need to identify molecules – known as lead compounds – which can act as ligands by bonding strongly to the binding site of the enzyme and thereby inhibit it. The starting point for this might be the natural substrate for the enzyme, but even screening analogues of this will be a potentially lengthy and costly process; the conventional method for finding a ‘hit’ in this way might have been to perform high-throughput screening. In this process, maybe as many as a million different compounds are synthesised and their ability to act as a ligand tested by a suitable assay procedure.

In the research projects that I manage, we use computer modelling to carry out structure-based pharmacophore screening. The detailed three-dimensional structure of the binding site is established, using X-ray crystallography allied to NMR spectroscopy. Then computer modelling can be used to deduce the likely structure of the pharmacophore – the part of the ligand molecule that enables it to be recognised at the binding site. Quantitative structure-activity relationship models can be used to predict the most effective ligands based on our knowledge of the pharmacophore and, as a result, we can prioritise the experimental investigation of just the most likely ligands.

It is tempting to imagine that identifying an effective ligand for an enzyme such as BACE-1 might be a real breakthrough in Alzheimer’s research. In reality, however, it is just one very small step along the way towards a treatment that may have some promise in the future. For the lead compounds that we identify to become a drug, other research teams must find ways of adjusting its structure to ensure that it is very specific in its inhibition of BACE-1 and that it has suitable hydrophobic and polar properties to allow it to be absorbed, distributed, metabolised and excreted at a suitable rate. If they achieve this then it is just possible that the drug may show some useful efficacy in human beings.

Drug discovery involves genuine partnership across a wide range of disciplines. It is a wonderfully varied and challenging field to work in, and one in which we know that the data we obtain today may one day lead to a better and longer life for maybe millions of patients.’

Dr Richard Lewis, Global Head of Computer-aided Drug Design at Novartis International

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Target identification� Choosing the disease� Choosing a drug target

Identifying a lead compound� Identifying a screening method� Finding a lead compound� Isolating, purifying and identifying its structure

Optimising the lead compound� Ensuring specificity� Optimising rate of absorption, metabolism, etc.� Maximising efficacy

ActivityThe three key stages of drug discovery and design (see Figure 9.3.1) can be described as:1 target identification2 identifying lead compounds by screening3 lead optimisation.

Look at Dr Lewis’s description of the research into BACE-1 inhibitors. Explain what happened in each of these stages.

2 Structure-activity relationshipsStructure-activity relationship and drug designDrug design is based on the basic premise that molecules with similar structures will display similar activities – this principle is known as the structure-activity relationship. If a molecule, for example, a naturally occurring metabolite, could be shown to have some biological activity, then molecules with similar structures might show the same (or enhanced) activity.

The traditional model of drug design involved screening these molecules by performing in vitro assays on a range of possible drug candidates and hence identifying one or more lead compounds that show promising levels of activity. Lead compounds are then chemically modified to increase their effectiveness in a process known as lead optimisation.

This process can be made more targeted by making use of structure-activity relationships: if the three-dimensional position of functional groups in a binding site is known, then deductions can be made about where a ligand may bind. This is done using powerful computer software, and the use of these computational techniques to screen molecules is often referred to as in silico screening.

PharmacophoreA key aspect of drug design is the identification of the pharmacophore. This can be done by examining the structural features of molecules that show activity in the assays, but modern computing techniques allow the pharmacophore structure to be deduced directly from the structure of the binding site.

Such modelling requires a very detailed knowledge of the three-dimensional structure of the binding site. This is obtained by combining a range of techniques such as X-ray crystallography and NMR spectroscopy.

Figure 9.3.1: The three key stages of drug discovery and design.

LinkYou will learn more about the processes that Dr Lewis describes in the presentation ‘Drug Design’.

Key termsAnalogues: Molecules with structural similarities to the lead compound.

Screening: A procedure used to predict the biological activity of a drug or other biochemical substance.

Lead compound: A molecule with proven biological activity that is the starting point for a development process to become an effective drug.

Pharmacophore: The part of the structure of a drug molecule responsible for its pharmacological action. In the context of drug design it can also mean the part of the molecule which binds to a binding site.

LinkThere are some examples of three-dimensional representations of binding sites and ligands in the presentation ‘Drug Design’.

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Varying the substituents

Once the structure of the pharmacophore is established, a range of molecules with different substituents (for example, by adding a range of groups to free hydroxyl or amine groups in the pharmacophore).

NS

OO

O O

NH

NH

OHN

O

O O

NH

NH

OH

O O

NH

NH

OH

O O

NH

NH

OH

O

NH

OH

O OO

HN

O

NH O

HN

O OHO OH

H2N

NH2

O

Quantitative structure-activity relationships (QSAR)Attempting to quantify structure-activity relationships allows drug designers to more rapidly identify likely drug molecules. While it is true that such methods have a significant level of uncertainty attached to them, the use of quantitative data allied to the chemists’ knowledge of the behaviour of functional groups is providing an increasingly valuable tool.

Surprisingly, QSAR modelling techniques date from well before the era of computer-aided drug design. Early methods involved characterising the groups present in a potential drug molecule by parameters such as their lipophilicity. This is measured by calculating the partition coefficient, P

i, which is calculated

by knowing the concentration of the compound in octan-1-ol and water at equilibrium with one another:

Pi =

concentration of compound in octan-1-olconcentration of compound in water

A high partition coefficient indicates high lipophilicity and low hydrophilicity.

The overall contribution of these parameters to the likely activity of the molecule could then be estimated by mathematical manipulation.

Take it furtherA highly detailed survey of the way in which QSAR has developed, taken from Medicinal Chemistry and Drug Discovery, (Burger, 2003) can be found at http://media.johnwiley.com.au/product_data/excerpt/03/04712709/0471270903.pdf.

This includes information about the different models of combining parameters and tables of data for some of the main parameters that characterise the drug-receptor binding, for example, hydrophobicity P

i, molar refractivity (related to the polarisability) and various steric factors.

QSAR data is frequently included in research papers and you will be able to see how the data is used to produce an overall measure of biological activity.

Figure 9.3.2: A wide variety of possible ligands can be created by

adding substituents to an identified pharmacophore (circled).

LinkYou will find out more about how computer-aided drug design allows chemists to design drugs that bind effectively to the target receptor site in the presentation ‘Drug Design’.

Key termsLipophilicity: The tendency of a molecule to dissolve in non-polar solvents such as lipids.

Partition coefficient: The ratio of the concentrations of a solute in two different solvents once equilibrium has been reached.

Hydrophilicity: The tendency of a molecule to dissolve in water.

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ChecklistAt the end of this section, you should be familiar with the following ideas: knowledge of the structure of the binding site allows the structure of a pharmacophore to be

deduced structure-activity relationships can be used to predict the effect of making changes to the

pharmacophore quantitative structure-activity relationships are used to help design drug structures using

numerical data.

3 Combinatorial chemistryAs seen earlier, drug discovery and development requires that a large number of molecules with structural similarities can be synthesised quickly and cheaply to enable their activity to be assayed (screened).

This is enabled by combinatorial methods. The techniques of combinatorial chemistry were first devised to enable polypeptide synthesis but have now been extended for use in the synthesis of a wide range of products.

A very simple example of a combinatorial method would be the synthesis of a range of amides (see Figure 9.3.3). In each reaction, the reaction conditions and reaction vessels will be the same.

Amine

R1 —NH2

R2 —NH2

R3 —NH2

Acyl chloride

R4 —COCl

R5 —COCl

R6 —COCl

Amide

Products

Combinatorial libraries

R1 R4—NH—CO—

R1 R5—NH—CO—

R1 R6—NH—CO—

R2 R4—NH—CO—

R2 R5—NH—CO—

R2 R6—NH—CO—

R3 R4—NH—CO—

R3 R5—NH—CO—

R3 R6—NH—CO—

+

Combinatorial librariesPrinciples of synthesis

In drug synthesis, the combinatorial reaction involves a starting material that is thought likely to have some biological activity. A range of molecules with a similar structure is prepared to form the first combinatorial library. There will be a core portion of the molecule common to all the members of this library, known as the scaffold structure.

Figure 9.3.3: A simple example of combinatorial chemistry. Nine

different possible products can be formed by combining these

two combinatorial libraries.

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The second combinatorial library used in the synthesis will then consist of a range of related reagents.

The 20 starting materials and 50 reagents would then create a potential for 1000 ‘first round’ products. The synthesis can then continue with a second step to modify the scaffold structure still further; if 50 further reagents are used then there will be 50,000 ‘second round’ products to screen (see Figure 9.3.4).

Starting materials20 molecules

Reagents50 molecules

First round products1000

Reagents50 molecules

Second round products50,000 molecules

Take it furtherA full guide to the current principles of combinatorial chemistry can be found at http://www.combichemistry.com/

There are some interesting examples of combinatorial libraries readily available on the internet. A good example is at http://www.nature.com/nbt/journal/v26/n5/fig_tab/nbt1402_F1.html.

Techniques used in combinatorial chemistry

Combinatorial chemistry was first used in the 1980s as a technique for producing large numbers of oligopeptides and oligonucleotides. Modern combinatorial chemistry is now a critical step in the process of high-throughput screening, which is necessary for the identification of lead compounds and lead optimisation processes.

Solid support method

This was the first combinatorial technique to be used. In this method the starting material is attached to beads of resin and divided into a number of portions. Each of these is then exposed to a different reagent. The product, still attached to the resin, can easily be separated from unreacted reagents and co-products and the process can be continued for as many steps as necessary to produce the required number of products.

In some cases the screening of the product can take place while still attached to the resin.

Solution synthesis

If it is difficult to attach the starting material to a suitable resin, or if it is desired to monitor the progress of the reaction while the product is being formed, then the reactions can be carried out in solution, as in conventional synthesis. This does, however, create problems in separating and purifying a large number of different product molecules.

Figure 9.3.4: The number of possible products which can be produced by

combinatorial techniques multiplies rapidly in multi-step syntheses.

ActivityUse research to find details of combinatorial libraries used in the search for a specific lead compound. Use the structures of the molecules in each library to identify the scaffold structure.

Key termOligo-: A prefix used to denote a small number (<50) of monomer molecules bonded together to form larger molecules.

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Parallel synthesis

Both of these techniques are used in what is called parallel synthesis. A large number of product molecules are synthesised at the same time and all of them are screened concurrently. This is in contrast to more traditional methods of synthesis where a single compound is made and screened, and the results of that screening are then used to inform the decision about which molecule to synthesise next.

Portfolio activity (2.3, 3.1, 3.2, 3.3)Write a description of the processes of drug discovery and design. You should illustrate your description wherever possible with some examples of how these processes have been applied to specific examples of drugs. Suitable examples could come from some of the drugs discussed in Topic guide 9.4 – for example, the penicillins, ACE inhibitors such as captopril and anticancer drugs such as methotrexate. In your description you should cover the following:

• how drug targets are chosen and lead compounds identified • how structure activity relationships are applied to the design of the drug • how combinatorial chemistry is used in the in vitro or in silico screening of possible drug

candidates • how drugs are evaluated for biological activity and safety.

ChecklistAt the end of this section, you should be familiar with the following ideas: large numbers of similar molecules need to be synthesised during the process of drug design combinatorial libraries are used to enable these molecules to be assembled.

AcknowledgementsThe publisher would like to thank the following for their kind permission to reproduce their photographs:

Shutterstock.com: isak55

All other images © Pearson Education

We are grateful to the following for permission to reproduce copyright material:

Dr Richard Lewis, Novartis International AG Investor Relations for a case study. Reproduced with kind permission.

In some instances we have been unable to trace the owners of copyright material, and we would appreciate any information that would enable us to do so.

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