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Summary Molecular therapy 2025/2026 all lectures

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Complete summary of all the lectures of study year 2025/2026. Extensive summary of the web lectures and the slides.

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MOLECULAR THERAPY
LE DRUG TARGETING AND DELIVERY PART I

Classical drugs are small organic molecules that are lipophilic enough to cross membrane (so they are compatible with
oral delivery) and they distribute more or less freely through the body. They act by inhibiting enzymes and receptors. One
example is paracetamol.

Limitations of classical drugs

- There is always a requirement for certain lipophilicity and because of this chemical diversity is limited. (there are
certain classes of molecules that we cannot make into orally bioavailable drugs, such as mRNA since this will be
digested in the intestine).
- Risk of side effects due to insufficient specificity (so it interacts with other targets) and due to inhibition of important
metabolic routes in organs that are not the target
- Classical drugs are poor inhibitors of protein-protein interactions so they need deep pockets for binding. Protein-
protein interactions are rather shallow but large areas and this makes it difficult for small molecules to disrupt
these interactions because they are designed to bind to pockets in proteins where you have an active site for an
enzyme and a small molecule binds to this pocket of an enzyme to block.
- Oligonucleotides offer a straight-forward way to inhibit/change protein expression in a highly specific manner by
downregulating or upregulating expression. Oligonucleotides are big and charged so they are hydrophilic so they
poorly enter cells.

Drug targeting enhances the concentration of a drug at its site-of-action. This can be done to avoid side effects, use
expensive drugs more effectively, so you need a less total dose and keep a higher concentration for a longer period of time
by protecting the drug from degradation and excretion. For a molecule that could not be a drug, such as siRNA’s, drug
delivery is optimized. Targeting is to the site of action and delivery is into the cell, over a barrier that gets addressed.

Drug targeting has the challenge to remain undetected from the immune system and to find and hit your target. The immune
system clears away unknown particles and we want to avoid that the immune system recognizes it (when it is not a vaccine).

Nanomedicine: the application of molecular assemblies (1-100 nm) in diagnostics and therapy.

The carrier contains the nanomedicine (the drug is encapsulated in order to bring it to the site of action) The main
components of nanomedicine are:

- Surface modifications prevent rapid clearance
- Targeting ligands (antibody)
- Matrix, encapsulates and releases the drug and this could be a liposome or a polymer. Something that
encapsulates very well can sometimes not let go of the drug so it is important to have a balance. The ratio
drug/matrix should be as high as possible

Ester bonds will dissolve over time in the body

To deliver drugs you need to consider some main things

- Minimal design to implement main functionalities (such as targeting, uptake, and release)
- No toxicity
- Elimination of the targeting vehicle (secretion / break-down)
- Compatibility with drug to be targeted (for example if you have a hydrophobic drug then the matrix cannot be very
hydrophilic because then the drug will not embed in the matrix)
- Production costs
- Stability (you want drugs that have a long shelf-life)

The intestines are also considered as the outside, systemic circulation is the blood stream. The outside from the systemic
circulation is separated by the epithelial cell layer, from the blood stream into the surrounding tissue it is separated by an
endothelial cell layer. There are similarities between the epithelial and endothelial cell layers. There are different drug

,delivery routes peroral (mouth), pulmonal (lungs), mucosal (nose), and ophthalmic (eyes) to get drugs in the stomach and
intestine (fits in the outside category). To get drugs through the skin and into the underlying tissue and the muscle you use
injections (called percutane). Intravenous directly goes into the bloodstream and intrathecal goes directly into the brain by
passing the blood-bran-barrier. The BBB is an endothelial cell layer for the blood vessels in the brain and this is difficult to
pass because metabolite import and export into the brain is very tightly regulated, this endothelial is difficult to cross but
you can cross it by injecting directly into the spinal fluid by injection into the spine.




The more barriers can be crossed the more comfortable the route of application (pill vs injection)

The way endothelial are formed are tissue dependent. Endothelial cells that form contact in a continuous layer around the
blood vessel, however this type of endothelial you have in skeletal muscle and in the BBB. A fenestrated endothelial (in
endocrine glands, intestines, pancreas, glomeruli) contains holes in the cells through which small particles can pass. In the
immune related organs (bone marrow, lymph nodes, liver and spleen), sinusoid endothelial is present where you don’t have
proper cell-cell contact where larger particles can pass through, to remove bacteria that are coated with antibodies or
defective blood cells. So larger particles that you want removed.




From a certain size, molecules are not secreted by the kidney anymore.

This image below is focused on the tightly organized endothelial but for epithelial the same would hold since in the intestines
this is also tightly organized. Transcellular is when drugs go through the cells, and paracellular is when drugs go in between
the cells. It is important when you want to bring a nanomedicine across, for a non-destructive transport, there is no
permeation enhancement (getting from one place to another place) without activation of intracellular processes. When you
have your cell barrier it has particles on top but you want to get the particles across. What you need to do is activate cellular
processes and use those for transport.

,Transcellular transport involves endocytosis and to get across the transport part is called transcytosis, because you need
to form endocytic vesicles to travel across. A classical molecules that engaged such a transcytosis pathway in the
intestines is vitamin B12. Classical approach is conjugation of drug to metabolic cargo and conjugation to vitamin B12 to
mediate uptake from the small intestine. Vitamin B12 is the largest and it is a polyaromatic molecule. The intrinsic factor is
a protein in the intestine and it binds to the vitamin B12 when it is in the intestine and it binds to a receptor on the intestinal
epithelial cells. It forms an endosome and this travels through the epithelial cells and it releases the content on the blood
site.




In between the cells there are proteins that make the tight and gap junctions. Paracellular permeation enhancers act by
inducing single transduction inside the cell that make the protein-protein interactions in the tight junctions less sticky which
means that they let go of each other. The gap that we then create is however smaller than what we can transport by
transcytosis. The paracellular transport is restricted to small molecules. If you have a hydrophilic small molecule that is too
hydrophilic to be orally bioavailable because it would not easily cross the epithelial barrier in the intestine, then you could
coformulate that with an intestinal permeation enhancer, which would then create a gap between the cells which would
result in better uptake of the molecule. Permeation enhancer are short fatty acids and they act by activating calcium
signaling inside the cells and the calcium signaling leads to detachment of the cell-cell contact

, The blood brain barrier are endothelial cells lining the capillaries in the
central nervous system. Part of the glia is also part of the blood brain
barrier (BBB). This is a several cell layer that controls the transport from
the blood stream into the brain. It is important to get drugs into the brain
in the case of brain tumors, and neurodegenerative disorders.

Transport across the blood brain barrier exploits ligands that cross by
transcytosis. To get across the brain barrier you can use water soluble
agents that can get across, lipid soluble may go across but they have an
disadvantage because the brain epithelial layers are rich in transporters
and the multidrug resistance proteins and if these hydrophobic
molecules (that are not supposed to enter the BBB under healthy
circumstances), enter the membrane they are directly kicked out again.
So eventhough they can cross the lipid bilayer, you need to figure out
how to get pass these multidrug resistance proteins. One way is to target receptors that are present on the epithelial cells
and if you have a nanoparticle and something that targets this receptor, it will bind and released on the other side (so
transcytosis).




The types of drug delivery vehicles
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