Old exam Eagle Flashcards
1 A) The development of modern pharmaceuticals that are effective in treating disease is rather long and complex and a costly process that consists of different phases.
Describe the overview of the main phases and processes of drug discovery and drug development that are necessary to go from a therapeutic concept to a final product.
After deciding the therapeutic concept, e.g. what you want to treat you start by identifying the target. The target may be a protein, enzyme, receptor, or other molecule that is involved in a biological pathway or process that contributes to the disease. It can be selected through biological knowledge, screening of compound libraries etc.
After identifying a potential target, the next step is to validate its relevance to the disease. This can be done through in vitro assays, animal studies or patient samples.
For lead finding this involves screening large libraries of compounds to identify those that show activity against the target. Lead finding may involve a variety of approaches, such as high-throughput screening for example. High-throughput screening is screening large libraries of compounds to test sometimes thousands of compounds at the same time. The goal of HTS is to identify a small number of lead compounds that shows activity against target of interest to then be optimized.
Lead optimization includes improving their efficacy, safety, and pharmacokinetic properties. This involves modifying the structure of the lead compounds through iterative rounds of synthesis and testing to identify compounds with improved activity, selectivity, and pharmacological properties. This will then lead to a candidate drug.
Preclinical development includes testing the drug candidate in laboratory and animal studies to examine the efficacy, safety, toxicity and pharmacokinetics of the drug.
Clinical development includes testing it on humans in a series of clinical trials. Phase 1 on a small group of healthy individuals to determine the drugs safety and side effects, phase 2 on a large number of patients with the disease to determine the efficacy and further evaluate safety. Phase 3 is a even larger trial that is meant to determine efficacy, safety and optimal dosage.
Regulatory approval is submitting the data from the previous stages for approval.
Today there are mainly two strategies for drug discovery activity centered discovery and target centered discovery. Explain these two strategies and explain one drug that has originated from each of these strategies.
Activity based discovery means identifying a small molecule that has an effect either on cultured cells or in animal models and then optimize the properties of the molecule and solve the mechanism of action. Salicylic acid from the bark of vitpil was discovered by activity based discovery.
Target based discovery you first begin to understand the disease mechanism, identify a “druggable” target for example an enzyme, a receptor, ion channel or nuclear receptor, and show that the target is coupled to disease mechanism in for example animal models. Then one identifies a lead series and optimizes the properties of these lead molecules. Imatinib is an anticancer drug that was discovered by target based discovery.
Historically, conventional small molecule drugs have been discovered from synthetic chemistry or natural products.
Which of the following drugs has been identified from synthetic chemistry or from natural products?
Penicillin
Insulin
Benzodizepines
Omeprazole
Penicillin was identified from natural products, specifically the Penicillium fungus.
Insulin was also initially extracted from the pancreas of animals, but now it is produced through recombination DNA technology, which is a form of synthetic chemistry.
Benzodiazepines and Omeprazole were both discovered through synthetic chemistry.
For all types of drug development, “lead compounds” that have been identified durin the discovery phases needs to be optimized further by medicinal chemists. This optimization is ecessary since there are often some general problems with the lead compounds that are identified during the intitial discovery phases. Describe three of these problems and how you can prvent them.
The physicochemical and DMPK attributes that will allow a compound to meet this target profile would be: good solubility and permeability, high oral bioavailability, low clearance and reasonable half-life (if PD half-life is not much longer than PK half life), and absence of ‘drug–drug interaction’ potential. Likewise to be orally active, a compound should have good oral bioavailability and be able to reach the target organ at high enough concentration to engage the target.
• Absorption and bioavailability
As the preferred route of administration for most indications is oral, it is important to characterize oral bioavailability (F). F is defined as the percentage of dosed drug that reaches the systemic circulation compared to the IV route. It can be considered to be dependent on three serial steps: the fraction of dosed drug absorbed (fa), the fraction escaping intestinal metabolism (fg) and the fraction extracted by the liver as it passes from the portal vein to the systemic circulation (fh).
Enhance absorption, reduce intestinal metabolism, reduce hepatic metabolism and use prodrugs. Looking at chemical structure of the drug to minimize its susceptibility to enzymatic degradation, improve drug absorption and adding excipients that are inactive ingredients added to a medication or drug formulation to aid in the manufacturing process, improve stability and enhance drug delivery or adding solid dispersions which is layers covering the drug that melts so the drug is absorbed in the right place.
• Avoiding PK-based drug–drug interactions
PK based drug-drug interactions are when a patient is taking multiple drugs that interact with each other. selecting a candidate drug with low risk of this can be done by analyzing the drug in CYP inhibition assays to identify potential drugs that does not interact with these enzymes.
• Achieving/avoiding CNS exposure
The CNS is protected by the blood brian barrier. Tp keep in mind is that drugs with low molecular weight, high water solubility, different transporters and prodrugs can cross the BBB.
• Clearance
Metabolic clearance refers to the rate at which a drug is metabolized and eliminated from the body, primarily by the liver and kidneys. Looking at prodrugs, drug-drug interactions, route of administration, chemical structures and enzyme inhibition is ways to affect this.
• Role of metabolite identification:
-Active metabolites
Active metabolites are metabolites that are formed as a result of drug metabolism and retain some of the pharmacological activity of the parent drug. Active metabolites can be desirable if they contribute to the overall therapeutic effect of the drug or if they are responsible for the drug’s prolonged duration of action.
-Minimizing risk for reactive metabolites.
Is achieved through looking at molecular structure, metabolic inhibition of different enzymes that metabolize the drug and prodrugs.
Clinical trials can be divided into 4 different phases. Explain the objective and purouse of these 4 phases, in more detailed compared to question 1.
Clinical trials are research studies that are conducted to evaluate the safety and effectiveness of medical interventions, such as drugs, vaccines, or medical devices, in humans. Clinical trials are typically divided into four different phases, each with its own objective and purpose.
Phase 1:
The primary objective of Phase 1 clinical trials is to evaluate the safety and tolerability of the medical intervention in a small group of healthy volunteers. This phase also aims to determine the appropriate dosage and identify any potential side effects of the intervention. Phase 1 trials typically involve 20 to 100 participants and can last several months.
Phase 2:
The primary objective of Phase 2 clinical trials is to evaluate the effectiveness and safety of the medical intervention in a larger group of patients with the condition or disease targeted by the intervention. This phase also aims to determine the optimal dosage and identify any potential side effects of the intervention. Phase 2 trials typically involve several hundred participants and can last up to two years.
Phase 3:
The primary objective of Phase 3 clinical trials is to confirm the effectiveness and safety of the medical intervention in a much larger group of patients with the targeted condition or disease. This phase also aims to identify any rare or long-term side effects of the intervention. Phase 3 trials typically involve several thousand participants and can last several years.
Phase 4:
The primary objective of Phase 4 clinical trials is to monitor the long-term safety and effectiveness of the medical intervention after it has been approved and made available to the general population. This phase also aims to identify any rare or long-term side effects of the intervention that may have been missed during the earlier phases. Phase 4 trials involve a large number of participants and can last for many years.
There are different types of toxicities and adverse reactions, for example nausea, allergic reactions, myelosupression, and neuropathy. Generally the toxicities ca be described as local, systemic and acute and/or chronic. How would you characterize following drugs and their toxic side effects? Local or systemic and acute or chronic?
Loratidine-induced sedation
Ibroproufen-induced gastrointestinal bleeding
ciclosporin-induced nephrotoxcity
carboplatin-induced myelosupression
Loratidine-induced sedation:
This is a systemic and acute toxicity. Loratidine is a non-sedating antihistamine, but sedation can occur in some individuals. This side effect is systemic because it affects the entire body and acute because it occurs shortly after taking the medication.
Ibuprofen-induced gastrointestinal bleeding:
This is a local and acute toxicity. Ibuprofen can cause damage to the gastrointestinal tract lining, which can result in bleeding. This side effect is local because it occurs in the gastrointestinal tract, and acute because it occurs shortly after taking the medication.
Ciclosporin-induced nephrotoxicity:
This is a systemic and chronic toxicity. Ciclosporin can cause damage to the kidneys, resulting in reduced kidney function. This side effect is systemic because it affects the entire body and chronic because it occurs over a prolonged period of time.
Carboplatin-induced myelosuppression:
This is a systemic and acute toxicity. Carboplatin can cause damage to the bone marrow, resulting in a reduction in the number of blood cells produced. This side effect is systemic because it affects the entire body and acute because it occurs shortly after treatment with carboplatin.
Many different models for studying toxicity are used during drug discovery and drug development. Briefly describe three general methods, in silico, in vitro and in vivo. Include why, how and when they are used for studying toxicity and give at least one specific example of an assay that’s used for each general model.
In Silico:
In silico methods use computational modeling and simulations to predict the potential toxicity of compounds before they are synthesized or tested in animals. These methods are cost-effective, fast, and provide an efficient way to screen a large number of compounds in a relatively short amount of time. In silico models can also provide insights into the mechanism of toxicity and help in the rational design of safer drugs.
In Vitro:
In vitro methods involve testing the toxicity of a compound in a controlled environment outside of a living organism. These methods use cell cultures or isolated tissues to determine the potential toxicity of a compound. In vitro assays provide a reliable and cost-effective way to screen compounds for toxicity, and they can also provide mechanistic insights into the toxic effects of compounds.
In Vivo:
In vivo methods involve testing the toxicity of a compound in living organisms such as mice, rats, or non-human primates. In vivo methods provide the most relevant information on the potential toxicity of a compound as they take into account the complexity of biological systems and the potential interactions between the compound and various organs and tissues.
Investigating and understanding drug toxcitity, both during and after drug discovery/developmeant the theraputic index is a very relevant measurmeant.
Explain the TI and how it relates to the effective and toxic dose.
Visualize the TI for two drugs, one with a large TI and one with a small TI.
TI stands for therapeutic index.
The effective dose is the dose of the drug that produces the desired therapeutic effect, while the toxic dose is the dose that produces adverse effects. The larger the TI, the safer the drug, as the effective dose is further away from the toxic dose.
The development of illicit new psychoactive substances NPSs is often lacking essential part of the drug development process and its different phases.
Describe what is often lacking during the emergence of NPS drugs when it comes to Phase I studies.
Illicit new psychoactive substances (NPSs) are often developed outside of the regulatory framework that governs the development of traditional pharmaceuticals. As a result, many of these substances do not undergo the rigorous testing and evaluation that is typically required for drugs that are intended for medical use.
In particular, NPSs may lack proper Phase I studies, which are typically the first stage of clinical drug development. Phase I studies involve the initial testing of a drug in human volunteers, and they are designed to evaluate the safety, pharmacokinetics, and pharmacodynamics of the drug. This phase typically involves a small number of healthy volunteers who are closely monitored for adverse effects.
One of the main issues with the emergence of NPS drugs is that they are often introduced into the market without any prior testing in humans. This means that there is often little to no information about the safety and efficacy of these substances, and the risks associated with their use may be unknown. Additionally, NPS drugs may be formulated in ways that make them more dangerous or prone to abuse, such as by using highly potent ingredients or by combining multiple drugs together.
There are multiple classes of NPS drugs, either they are divided into groups based on their pharmacological structure or their mechanism of action. Please describe the mechanism of action of:
Cathinones
Synthetic cannabionoids
synthetic opioids
Especially focusing on how the neurotransmitters are affected or which neuroreceptor that is activated.
Cathinones:
Cathinones are a class of synthetic stimulant drugs that are structurally similar to cathinone, a natural stimulant found in the khat plant. The mechanism of action of cathinones involves the release of neurotransmitters such as dopamine, serotonin, and norepinephrine from presynaptic nerve terminals. Cathinones act as reuptake inhibitors of these neurotransmitters, leading to an increase in their concentration in the synaptic cleft and enhancing their stimulatory effects.
In particular, cathinones have a high affinity for the dopamine transporter (DAT) and the serotonin transporter (SERT), blocking the reuptake of these neurotransmitters and increasing their extracellular concentration. This results in a feeling of euphoria and increased energy levels. Cathinones also have some activity at the norepinephrine transporter (NET), contributing to their stimulant effects.
Synthetic Cannabinoids:
Synthetic cannabinoids are a class of drugs that act on the same receptors as delta-9-tetrahydrocannabinol (THC), the active ingredient in cannabis. These drugs are structurally diverse, and their mechanism of action varies depending on the specific compound. However, in general, synthetic cannabinoids act as full agonists at the cannabinoid type 1 receptor (CB1) and the cannabinoid type 2 receptor (CB2).
Activation of CB1 receptors in the brain leads to a range of psychoactive effects, including altered perception, impaired memory, and euphoria. CB2 receptors are mainly found in immune cells and may play a role in inflammation and pain regulation.
Synthetic Opioids:
Synthetic opioids are a class of drugs that act on opioid receptors in the brain, spinal cord, and other organs. These drugs mimic the effects of endogenous opioids such as endorphins, enkephalins, and dynorphins. Synthetic opioids can be classified into three main categories: full agonists, partial agonists, and antagonists.
Full agonists, such as fentanyl and morphine, activate opioid receptors fully and produce strong analgesic and euphoric effects. Partial agonists, such as buprenorphine, activate opioid receptors but have a lower efficacy than full agonists and produce less euphoria and respiratory depression. Antagonists, such as naloxone, block opioid receptors and can reverse the effects of opioid overdose.
Activation of opioid receptors leads to a range of effects, including pain relief, sedation, and euphoria. Opioid receptors are mainly found in the central nervous system, where they modulate the transmission of pain signals and affect mood and behavior. The mu-opioid receptor is the primary target of opioids, and activation of this receptor leads to the majority of opioid effects.
Plasmids are a popular genetic vectors for protein expression. Draw a general schematic of a plasmid and explain it’s key elements.
Promoter: This is a DNA sequence that is recognized by RNA polymerase and initiates transcription of the gene of interest. The promoter can be specific to certain types of cells or tissues, or it can be a strong, constitutive promoter that is active in many cell types.
Start codon: This is the DNA sequence that signals the start of translation of the gene of interest. The most common start codon is ATG.
Gene of interest: This is the DNA sequence that encodes the protein of interest that is to be expressed in the host cell.
Stop codon: This is the DNA sequence that signals the end of translation of the gene of interest. There are three possible stop codons: TAA, TAG, and TGA.
Terminator: This is a DNA sequence that signals the end of transcription of the gene of interest. It is usually located downstream of the stop codon.
Selection marker: This is a DNA sequence that confers resistance to a particular antibiotic or other drug. This allows for selection and isolation of cells that have taken up the plasmid and are expressing the gene of interest.
Origin of replication: This is a DNA sequence that allows the plasmid to replicate independently of the host cell’s chromosomal DNA. This ensures that the plasmid is maintained in the host cell and that the gene of interest is continuously expressed.
Explain what a selection marker could be and why it is crucial for recombinant DNA technology using plasmids.
A selection marker is a gene that confers a selectable phenotype, allowing researchers to distinguish cells that have taken up a recombinant plasmid from those that have not. In recombinant DNA technology, selection markers are used to ensure that cells that have taken up the desired recombinant plasmid are selected for and propagated, while cells that have not taken up the plasmid are eliminated.
Selection markers can confer a variety of selectable phenotypes, such as antibiotic resistance or resistance to toxic chemicals. For example, a plasmid may contain a gene that confers resistance to the antibiotic ampicillin. When the plasmid is introduced into bacteria, only those bacteria that have taken up the plasmid will be able to grow on a culture medium containing ampicillin, while bacteria that have not taken up the plasmid will be unable to grow. This allows researchers to selectively propagate cells that contain the desired recombinant plasmid and eliminate those that do not.
In recombinant DNA technology, plasmids are often used as vectors to introduce foreign DNA into cells. By including a selection marker in the plasmid, researchers can ensure that only cells that have successfully taken up the plasmid are selected for and propagated, increasing the efficiency of the cloning process. Selection markers are therefore crucial for recombinant DNA technology, as they allow researchers to identify and propagate cells that contain the desired recombinant plasmid, while eliminating those that do not.
Explain why plasmids include two selection markers.
Plasmids used in genetic engineering often include two selection markers, one for selection and one for counter-selection. This is done to increase the efficiency and accuracy of the selection process and to reduce the occurrence of false positives.
The selection marker is the gene that confers a selectable phenotype, allowing cells that have taken up the plasmid to be identified and selected for. For example, a selection marker might be a gene that confers antibiotic resistance or resistance to a toxic chemical.
The counter-selection marker is a gene that allows cells that have lost the plasmid to be identified and eliminated. For example, the counter-selection marker may be a gene that confers sensitivity to an antibiotic or toxin that the cells would normally be resistant to due to the presence of the plasmid. This means that cells that have lost the plasmid will not survive when grown on a medium containing the counter-selection agent.
By including both a selection marker and a counter-selection marker, researchers can increase the accuracy of the selection process. Cells that have taken up the plasmid and have the desired phenotype (e.g., antibiotic resistance) will grow on the selection medium, while cells that have lost the plasmid and have the undesired phenotype (e.g., antibiotic sensitivity) will be eliminated on the counter-selection medium. This reduces the occurrence of false positives, which can result from cells that have taken up the plasmid but do not have the desired phenotype, and increases the accuracy and efficiency of the genetic engineering process.
When it comes to the influenza vaccine why is the development dependent on deep knowledge about the two viral proteins hemagglutinin and neuraminidase?
The influenza vaccine targets the two surface proteins on the influenza virus, hemagglutinin (HA) and neuraminidase (NA), which are important for the virus to enter and exit host cells.
Hemagglutinin is responsible for the attachment of the virus to host cells, while neuraminidase is responsible for the release of newly formed viral particles from infected cells. Because these two proteins are essential for the influenza virus life cycle, they are the primary targets for the development of vaccines and antiviral drugs.
The development of an effective influenza vaccine is dependent on a deep understanding of these two viral proteins. Hemagglutinin is a glycoprotein that is highly variable, with different subtypes of influenza virus having different versions of hemagglutinin. The specificity of the immune response to influenza virus is largely determined by the antigenic properties of hemagglutinin. Therefore, to develop an effective vaccine against influenza, researchers must have a detailed understanding of the structure and function of hemagglutinin and the ways in which it interacts with the immune system.
Similarly, neuraminidase is also a glycoprotein that is important for the release of viral particles from infected cells. Because neuraminidase is also variable between different influenza virus subtypes, it is also an important target for the development of antiviral drugs. The effectiveness of these drugs is dependent on a deep understanding of the structure and function of neuraminidase and the ways in which it interacts with the influenza virus.
In summary, a deep knowledge of the two viral proteins hemagglutinin and neuraminidase is essential for the development of effective vaccines and antiviral drugs against influenza.
During the corona pandemic we have not onle seen the fastest production of new vaccines but also witnessed the first implementation of RNA based vaccines for human use. Briefly explain the mechanism of action of a RNA-base or DNA-based vaccine.
In RNA-based vaccines, a piece of messenger RNA (mRNA) is introduced into the cells. The mRNA provides instructions for the cells to produce a viral protein, which then triggers an immune response. Once the protein is produced, the immune system recognizes it as foreign and generates an immune response to attack it. This response creates memory cells, which remember how to recognize and attack the pathogen if it is encountered in the future.
In DNA-based vaccines, a small piece of DNA containing the genetic instructions for a viral protein is introduced into the cells. The DNA enters the nucleus of the cell and provides the instructions for the cell to produce the viral protein. The immune system recognizes the protein as foreign and generates an immune response against it.
