• Suomi
  • English

Half of all drug ingredients affect only three protein families

Up to 50% of all the approved drugs affect only three protein families: nuclear receptors, G protein receptors and ion channels.

Drugs usually affect the cell receptors or enzymes in the body, both of which are proteins. Many drug molecules also bind themselves to enzyme receptors and transport proteins on the cell membrane. The drug may, for example, bind itself to the active site of an enzyme, thereby inhibiting the chemical reaction controlled by the enzyme. Most often the enzymes that catalyse the chemical reaction caused by the drug are metabolised by cytochrome P450 enzymes before they are in active form.

Most of the target proteins of drugs belong to only ten protein families, and up to half to only three families. Proteins belonging to a specific family have a similarly folded three-dimensional structure, function and significant similarity in amino acid sequences, which usually indicates a common ancient history. Proteins of the same family are derived from a single original form which, through evolution, has adapted and specialised due to environmental pressures as well as functional roles that differ from their original role in cellular processes.

 

Nuclear receptors and endocrine diseases

From left to right: the oestrogen receptor, androgen receptor, vitamin D receptor and progesterone receptor. These proteins are similar in structure and their molecular mechanism, althougs they affect entirely different functions in the body. The receptors belong to the same protein family of nuclear receptors. This means, among other things, that the receptors share the same prehistoric origin. The small molecule interacting with each receptor, such as testosterone in the androgen receptor, is visible at the top of the structure as a grey ball-and-stick model. The Protein Data Bank, i.e. the PDB protein database, includes more than 100,000 protein structures divided into protein families. The members of a protein family are usually similar in terms of their three-dimensional structure, which is why they also function in a similar manner.

 

Protein families were discovered when the structure and amino acid sequences of a few proteins began to be known. It was then found that proteins consist of several independent, structurally distinct areas with a special task. These became known as domains.

New protein families have been discovered when studying the underlying mechanisms of various diseases. Nuclear receptors, for example, were discovered while studying breast cancer. It has been known for a long time that tumour growth ceased in one third of women with breast cancer whose ovaries or adrenal glands had been removed. However, the molecular basis of breast cancer was still a mystery. In 1947, medical researcher Elwood Jensen began to investigate this. Jensen discovered the estrogen receptor and found that the estrogen receptor is activated when its natural estrogen, estradiol, binds itself to it. After this, the activated estrogen receptor travels to the nucleus of the cell where it participates in regulating the function of genes.

The estrogen receptor, a protein molecule belonging to the nuclear receptor family, is very important to humans. If changes occur in its function, they have a great significance for cell health. The estrogen receptor plays an important role in the emergence of breast cancer. Normally, estrogens regulate the activity of the estrogen receptor in the cell. The changed shape of the estrogen receptor is active all the time, meaning that the normal regulation mechanisms of the cell based on the level of estrogen do not function correctly. This can lead to cancer, i.e. uncontrolled growth of abnormal cells.

Elwood Jensen proved that breast cancer patients with a low estrogen receptor concentration in their cancer cells did not benefit from the removal of the ovaries. The ovaries produce a large proportion of women’s active oestrogen. The receptor concentration indicates who should have surgery and who should skip it. In the mid-1970s, Jensen and his colleague Craig Jordan discovered that cancer patients whose mutated tumour cells had a large number of oestrogen receptors were also likely to benefit from tamoxifen. It is an antioestrogen, meaning that it overrides the effect of estrogen in cells. The patients with low numbers of receptors, in turn, could immediately be transferred to other treatments. By 1980, the test developed by Jensen, which was used to measure the number of receptors in breast cancer samples, had become a standard test for breast cancer patients.

Estradiol is an estrogen steroid hormone.

 

Estrogen receptor and tamoxifen. Tamoxifen is used to treat breast cancer. In the case of breast cancer, estrogen can enhance unnatural growth and make the disease worse. The drug tamoxifen is used to treat cancer by blocking the action of estrogen. Tamoxifen is a small drug that mimics the shape of estrogen and binds tightly to the estrogen receptor. When it binds, it changes the shape of a signaling loop on the surface the receptor, colored green here. The lower structure has the drug bound. Since the drug is larger than the hormone, it forces the activation loop out into an inactive conformation, blocking the signal to grow. Image: Protein Data Base

 

The discoveries revealed a protein superfamily functioning in the cells, the nuclear receptors, which includes the oestrogen receptor. The nuclear receptor family includes, among others, the estrogen receptors alpha and beta, androgen receptor, progesterone receptor and vitamin D receptor. What nuclear receptors have in common is that they are activated when a cell membrane-penetrating the signal molecule, i.e. a ligand, a nuclear receptor hormone, binds itself to them, after which they travel to the nucleus to influence cellular processes. Hormones that activate the members of the nuclear receptor superfamily include, among others, testosterone, estradiol, progesterone, glucocorticoids, mineralocorticoids and vitamin D as well as molecules created through drug design that mimic the structure of natural ligands. For example, the lip balm of Therese Johaug of Norway’s 2016 national skiing team may have contained clostebol, a ligand of the androgen receptor. Clostebol functions as an anabolic factor, meaning that it promotes muscle cell protein growth.

Small molecules introduced to the human body through drugs or other routes can thus affect nuclear receptors by activating or deactivating them, thereby affecting the functioning of the cell’s genes. The discovery of nuclear receptors has revolutionised biochemical endocrinology research. Endocrinology is a speciality that studies and treats diseases of hormone-producing organs. The diseases can result from the excessive production of hormones or lack thereof; furthermore, both benign and malignant tumours can occur in endocrine tissues. Prior to the discovery of nuclear receptors, the functioning of the hormones in the human body was a complete mystery. Now it can already be slightly modified.

 

G proteins and cell signal transduction

 

In order for an organism to function, signals must be transmitted in the body’s cells and the organs they form. The body as a whole sends and receives signals through electrical currents and certain molecules. Martin Rodbell and Alfred Gilman determined how signal transduction occurs through the cell membrane via cooperation of molecules. In 1970, Martin Rodbell proved that the signal transmission takes place in three stages: signal reception, transmission and amplification. The transmission takes place so that a cell surface protein transmits a command to exchange the guanosine diphosphate (GDP) bound to the protein located on the other side of the cell membrane for guanosine triphosphate (GTP). This phenomenon is data transfer at the molecular level.

In 1980, Alfred Gilman studied leukaemia cells and found that they did not respond to the external signals transmitted by hormones. This was due to a mutation of the receptor protein which caused the signal transduction of hormones to be inhibited. Gilman isolated the protein from normal cells, and, with these proteins, he was able to repair the damaged cell. The molecules involved in the signal transduction are a large family of proteins that bind themselves to guanosine triphosphate. When they are bound to GTP, they are ‘on’, and, when they are bound to GDP, they are ‘off’.  He called them G proteins (also known as guanine nucleotide-binding proteins).

G proteins are perhaps the most important molecules involved in signal transduction. In addition to some forms of cancer, they are associated with diabetes, alcoholism and the underlying molecular mechanisms of many other diseases.

The protein family of the G protein-coupled receptors in the cell membrane conveys signals to the G proteins inside the cell membrane. G proteins, in turn, respond by exchanging GDP for GTP. The consequence of this activation is, for example, an enzyme released for the breakdown work in the cytoplasm inside the cell, opening or closing of an ion channel located in the cell membrane.

This mechanism is how rhodopsin, with which we detect light, or see, with our eyes, works in the eye, for example. One third of all the known drug ingredients affect G protein-coupled receptors. Catecholamines (e.g. adrenaline, noradrenaline and dopamine), peptides, glycoprotein hormones and rhodopsin are examples of ligands that bind themselves to these receptors. Alfred Gilman and Martin Rodbell received the 1994 Nobel Prize in Medicine for the discovery of G proteins. In 2012, the Nobel Prize for Chemistry was awarded to Robert Lefkowitz and Brian Kobilka for explaining the workings of G protein-coupled receptors.

Dopamine

Proteins perform their work cyclically and accurately by exchanging shapes and molecules based on signals. The shapes of the G protein and G protein-coupled receptors are in a continuous, dynamically changing biochemical equilibrium reaction with each other. Changes in the sensitive balance of G proteins may result in illness. For example, the toxin of the cholera bacterium locks G proteins into one shape and affects the nerves that control the absorption of salt and liquid in the intestines.

 

Activity of ion channel receptors in the treatment of addiction

 

Beta-amyloid (Abeta) peptide, 3D rendering. Major component of plaques found in Alzheimer’s disease. Stick representation combined with semi-transparent molecular surface.

Some ion channels are complex, multi-part structures that are huge in terms of molecule size. Huge ion channel-coupled receptors react directly to tiny ligand molecules, such as the ionotropic receptor located in the brain that reacts to the amino acid glutamate. The protein, consisting of four domains, readily changes its shape as the thousands of times smaller glutamate binds itself to the domain for signal transduction and opens the ion channel permeating the cell membrane. Memantine is used for Alzheimer’s disease. It protects brain neurons from destruction by blocking the excessive glutamate transmitter effect.

Receptor-gated ion channels open when a particular chemical compound binds itself to them. The chemical compound may be an extracellular molecule, such as a hormone, a neurotransmitter, a drug ingredient or a toxin, or an intracellular molecule.

By understanding the functioning of ion channel receptors, researchers can develop, for example, treatments for addiction by changing the activity of the receptors.

Ari Turunen

Tommi Nyrönen

 

Article in PDF

 

CSC – IT Center for Science

CSC – The Finnish IT Center For Science is a non-profit, state-owned company administered by the Ministry of Education and Culture. CSC maintains and develops the state-owned, centralised IT infrastructure.
http://www.csc.fi
https://research.csc.fi/cloud-computing

ELIXIR

ELIXIR builds infrastructure in support of the biological sector. It brings together the leading organisations of 21 European countries and the EMBL European Molecular Biology Laboratory to form a common infrastructure for biological information. CSC – IT Center for Science is the Finnish
centre within this infrastructure.
http://www.elixir-finland.org
http://www.elixir-europe.org

 

 

 

IMAGE: G proteins, also known as guanine nucleotide-binding proteins

 

Ion channels are integral cell membrane proteins, i.e. proteins that are part of the cell membrane structure. They can be ligand-gated, receptor-gated and voltage-gated.