Biophysics is the use of light, sound or particle emission waves to study a biological sample. A wave

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Medicinal chemistry and biophysics

Lecture 1 Introduction 21/09/2020 Matthew Groves

Medicinal chemistry allows us to develop new medicines for existing and new diseases. The majority of these medicines are small molecules. There is a recent trend towards biologics. These normally are antibodies which are relatively easy to create, because you simply need the diseased target and then raise competent antibodies, so all the work is done in the cell. However, biologics are very expensive to create, store and ship. Whereas the small molecules are chemical entities which are synthesisable in a lab and purifiable quite simply. Still, 80% of the new medicines are small molecules.Medicines are limited in the number and types of atoms. The 3D structure of the medicines are very important for how they interact with e.g. the body, the target.

Biophysics is the use of light, sound or particle emission (waves) to study a biological sample. A wave has a dynamic path with crests and troughs. The distance between two crests or two troughs is called a wavelength. The type of wavelength defines what we can look at. In case of life cell images (microscopy), the information content has to be the same as the wavelength. So you can get away with visible light which is compatible for cellular objects (membranes, organelles). When we want to look in more detail, the wavelength needs to decrease so e.g. X-ray.

For all clinically used drugs that are covered in the lectures, the indication must be learned. This is important for pharmaceutical knowledge (e.g. aspirin – inflammation).

Know the chemical structures of amino acids and the first two rows in the periodic table!!

When looking at aspirin and paracetamol, you see that they are small. This because it is easier for small molecules to cross membranes and thereby reach the target. If they are too big they will not cross the membrane. If they are too small, they will not be able to make sufficient interactions with the protein target to be selective between different protein targets. C, O, H and N are the core elements of most drugs since they are the biologically relevant atoms. The way that these atoms are connected together will give a 3D structure that determines the biological activity of the drug. So although aspirin and paracetamol are used for the same indication, due to their different structure they will interact with fundamentally different targets.

Ethanol is the smallest available drug and it has its biological effect because it interacts with many different proteins.

The less specific your drug is to the target site, the more side effects will occur. To get to the target site, you first have to pass a series of membranes. So orally taken drugs must be soluble enough to get into the gut. However, if they are too soluble, they cannot pass the GI tract membrane anymore.Once the membrane is passed (right balance between solubility and lipophilicity), the drug is in the blood stream. Then the drug has to survive metabolism, degradation and tissue deposition before it reaches the membrane of its actual target site. 1 / 4

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The environment outside the membrane and within the membrane is water driven. Water molecules carry a charge. So drugs are soluble because they can possess charges that can compensate with the water molecule charges. So polar drugs (highly charged) are quite happy outside a membrane. If they are too charged the drugs will simply not get into the membrane. The exterior of the lipid bilayer is composed of polar headgroups. So the polar drugs can bind to the membrane or stay in solution.Inside the membrane, it is highly uncharged. Amphiphilic drugs have a polar and a hydrophobic nature. So they will insert themselves in the membrane, keeping one site to the solvent and one site in the lipid membrane. They may flip across the membrane, but also these drugs are quite happy in this position. Non-polar drugs are unhappy in the watery solution, so they will embed themselves in the membrane and they will stay there. So these types of drugs are not quite good. There are ways through this. There are protein pores that allow selective uptake of molecules across the membrane.These transport proteins are natural proteins which make active transport possible. However, the majority of drugs still passes the membrane via passive transport. Passive diffusion can be estimated by the log P value which is defined by the physical/chemical properties of the drug. log P says something about lipophilicity. So a balance between charged and non-polar sections is necessary so that the drug is happy to get into the membrane but also is happy to leave again.

Log P is a measure of lipophilicity. It is the log of the maximum concentration of a drug in octanol divided by the maximum concentration of a drug in un-ionized, uncharged water. Successful drugs have a log P of about 5 or slightly lower. This indicates that successful drugs have large contributions of hydrophobic/non-charged groups.

Lipinski’s rule of five:

• Molecular mass less than 500 → because otherwise the membrane cannot be passed.
• Log P less than 5
• Less than ten hydrogen bond acceptors (-O-, -N-, etc.)
• Less than five hydrogen bond donors (NH, OH, etc.) → atoms in an unionized state have a

protonated oxygen or nitrogen.

• and 4 together mean that if you would have more acceptors and donors, the charge would go up

leading to increased solubility and a lower log P which is unwanted. However some charges are needed to find selectivity. So a competent drug requires good solubility in both water and membranes in order to have a good absorption. This is driven by the Lipinski’s rule of five.

Lipid membranes contain a polar headgroup and a lipid tail. These are phospholipids. There is a connecting moiety (glycerol) that links the charged group to the long apolar tails which can consist of unsaturated and saturated fatty acids. These tails exclude water from interactions with each other to allow membranes to form.

Paul Ehrlich introduced the idea that the biological effect of almost all compounds was due to its binding to a target. So bodies do not act if they are not bound. So the drug will do nothing unless it binds to the target. This has been refined significantly resulting in the Lock and Key principle. So 2 / 4

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there are molecular entities with a specific shape that allows them to choose the correct target. If the Key (substrate) fits in the Lock (enzyme), biological action will be exerted. Nowadays, we moved to the concept of induced fit. So this is not only that the key fits the lock, but also that the process of fitting the lock to the key actually changes both things. So the process of binding is dynamic. Once the substrate is bound to the active site of the enzyme, there is initial binding resulting in a complex.Then the protein is allowed to go through a process of movement to make the fit even more precise.This will provide better energetics. Then the enzyme will form a chemical reaction on the substrate, providing two products which can then release from the enzyme so that the active site can be occupied again.

Thermodynamics → things exist in different energy states. And nature drives things towards lower energy states. It describes the final equilibrium state. In case of medicinal chemistry and drug design, we hope that the equilibrium state is the bound state where the molecule is bound to the target protein. The parameter for this is K. E.g. when you hold a cup of coffee high in the air, you have to put energy in it or otherwise the cup of coffee will fall.Kinetics → the rate of the process. The parameter for this is k. E.g. the rate at which the coffee cup falls.In this case, the complex AB will only happen when that is the lower energy state. If A and B separate have a lower energy state, the equilibrium will drive the system to this state where the substrate is not bound to the protein.

The more product we have (more C and D), so the more bound state, the higher K is going to be. The lower the K, the more unbound substrate there is. So since we would like to see a lot of bound state, we prefer a high K.

Within this, there are still different kinds of interactions:

• Covalent interactions → drug molecules that bind to the target and then form a

physical/chemical bond between the drug and the target. So in this case there is no dissociation. So there is no equilibrium. If you give this enough time, all of the system will become bound. So there is no K, there only is a kinetic rate k. These kind of drugs are difficult to generate. They often bind to the wrong protein target and then they will not become unbound. This results in significant side effects.

• Non-covalent interactions → this allows a potential target protein to bind a drug molecule. If

it is the wrong one, it can unbind again so that the drug can look for a new binding partner.Here there is an association rate and a dissociation rate. So there is an equilibrium.

Keq is then an association (binding) constant that can be referred to as Kass.For Kdiss (= [A]+[B]/[AB]) you want K to be as small as possible.

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Each new interaction provides a change in the Gibb’s free energy. Gibb’s free energy (G) is the energy required to build the system from nothing. So you have your reactants which have a certain energy. Then there is an activation barrier. Then you reach the products which have a lower energy than the reactants. This means that the equilibrium lies to the right. The rate at which this reaction happens is driven by how much of the activation barrier is there. It can also be that the energy state of the reactants is lower than that of the products. This means that in order to get to the products, you have to put in energy. If you do not put in energy, the reaction will not happen and the equilibrium will lie to the left.ΔG is the change in energy between the reactants and the products. If ΔG is negative, so you have moved to a lower energy state, the reaction will happen naturally.

The change in Gibb’s free energy (ΔG) has two components: enthalpy and entropy. These are the driving forces of a reaction.

Enthalpy (ΔH) is a way of saying heat. Ice soaks up heat from the environment. This means that heat/energy is absorbed, meaning that it takes energy from the environment. So the overall energy that is going into it is positive (ΔH > 0). The reaction is then endothermic. The opposite case is a fire, where heat/energy is released. Then ΔH < 0 resulting in an exothermic reaction. Ice melts naturally and fire burns naturally, so the overall ΔG must be negative.

Entropy (ΔS) is a statistical measure of the ordering of the system. For example, you have a protein and a ligand which are not bound to each other. Both are bound to a water molecule. These water molecules are coordinated so are not able to explore the rest of the universe. They are in a fixed position. However, when the protein binds to the ligand, the two water molecules will come free and be able to explore the universe. This creates a significant increase in the disordering of the universe around it → entropy has increased. This is also the case in hydrophobic interactions between the protein and the ligand. When you have a hydrophobic atom, the water molecule cannot get close to it since the water carries a charge that does not want to get close to the hydrophobic surface. When the protein and the ligand undergo a hydrophobic interaction, water is allowed to explore a much larger region of the universe → entropy has increased.

There is a link between the dissociation/association constant and the Gibb’s free energy. The dissociation constant is related to the exponential of the ΔG divided by the universal gas constant and the absolute temperature.

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