Old exam 2021 may Flashcards
A. The development of modern pharmaceuticals that are effective in treating disease is a rather long, complex, and costly process that consist 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 (Fig. 1).
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 basic strategies for drug discovery.
- Activity centered discovery and (2p)
- Target centered discovery. (2p)
Explain these two strategies and give an example of one drug that have originated from each of these two 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 from natural products.
- Which of the following drugs has been identified from synthetic chemistry or from natural products?
o Penicillin (antibiotics) (0.5p)
o Taxol (cancer chemotherapy) (0.5p)
o Benzodiazepines (psychoactive drug) (0.5p)
o Omeprazole (peptic ulcer disease)
Pencillin and taxol natural products
Omeprazole and Benzodiazepines synthetic
For all types of drug development, “lead compounds” that have been identified during the discovery phases needs to be optimized further by medicinal chemists. This optimization is necessary since there are often some general problems with the lead compounds that are identified during the initial discovery phases.
- Describe three of these problems and how you can prevent them.
Enhancing Bioavailability from an Oral Dose:
Improving solubility, Medicinal chemists can modify the chemical structure of lead compounds to enhance their solubility in water or biological fluids. This can involve adding or modifying functional groups, altering the lipophilicity, or employing prodrug strategies to improve the compound’s solubility.
Increasing stability, Lead compounds may undergo degradation or metabolism before reaching their target site, reducing their bioavailability. Medicinal chemists can modify the structure to enhance stability, such as protecting vulnerable functional groups or altering the metabolism-prone regions.
Optimizing pharmacokinetics, Pharmacokinetic properties, such as absorption, distribution, metabolism, and excretion (ADME), impact bioavailability. Medicinal chemists can optimize lead compounds to improve these properties, ensuring adequate absorption and minimizing clearance rates to enhance bioavailability.
Minimizing Reactive Metabolites: Structure-activity relationship (SAR) studies: Medicinal chemists examine the relationship between the structure of a compound and its biological activity, including the formation of reactive metabolites. By understanding how specific structural features contribute to the formation of reactive metabolites, chemists can modify the compound to minimize or eliminate these problematic metabolic pathways.
Prodrug strategies: Prodrugs are inactive compounds that are designed to undergo specific metabolic reactions to generate the active drug. Medicinal chemists can develop prodrugs that are less likely to produce reactive metabolites, reducing the potential for toxicity or adverse effects.
Managing Drug-Drug Interactions:
Metabolic pathway considerations: Medicinal chemists take into account the metabolic pathways of both the lead compound and potential co-administered drugs. They aim to design compounds that have a lower likelihood of interfering with or being affected by the metabolic enzymes responsible for drug-drug interactions.
Molecular docking and modeling: Computational techniques, such as molecular docking and modeling, can predict potential drug-drug interactions by examining the binding affinities and potential interactions between the lead compound and other drugs or target proteins. This information guides medicinal chemists in optimizing the lead compound to minimize potential interactions.
Clinical trials can be divided into 4 different phases. Explain the objective and purpose of these four phases.
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.
A. There are numerous different types of toxicities and adverse drug reactions (ADRs), for example nausea, allergic reactions, myelosuppression, and neuropathy.
- Describe chronic and acute toxicity as well as their differences and give examples of two drugs, one with chronic toxicity and one with acute toxicity.
Chronic and acute toxicity refer to different types of adverse effects caused by substances, including drugs. Here’s an explanation of each and examples of drugs associated with chronic and acute toxicity:
Chronic Toxicity:
Chronic toxicity refers to the long-term or cumulative toxic effects that occur after repeated or prolonged exposure to a substance. It typically develops over an extended period, often resulting from the continuous or repeated use of a substance. Chronic toxicity can lead to organ damage, impaired physiological functions, or the development of chronic diseases. Examples of drugs associated with chronic toxicity include:
Methotrexate: Methotrexate is a chemotherapy drug used to treat various cancers and autoimmune diseases. Prolonged or high-dose use of methotrexate can lead to chronic toxicity, particularly affecting the liver. It can cause hepatotoxicity, which may manifest as elevated liver enzymes, liver fibrosis, or cirrhosis over time.
Acute Toxicity:
Acute toxicity refers to the immediate or rapid-onset toxic effects that occur shortly after a single exposure or within a short period. It usually results from a high dose or a significant, acute exposure to a substance. Acute toxicity can cause severe symptoms or even be life-threatening. Examples of drugs associated with acute toxicity include:
Acetaminophen (Paracetamol): Acetaminophen is a commonly used over-the-counter pain reliever and fever reducer. However, taking an excessive dose of acetaminophen within a short period can cause acute liver toxicity. This can lead to severe liver damage, liver failure, and potentially life-threatening complications if not treated promptly.
Opioids (e.g., Morphine, Fentanyl): Opioids are potent analgesic drugs used for pain management. An acute overdose of opioids can cause respiratory depression, leading to a significant decrease in breathing rate or even respiratory arrest. This acute toxicity can be fatal if not promptly addressed through appropriate medical intervention, such as naloxone administration.
Differences between Chronic and Acute Toxicity:
Time Course: Chronic toxicity develops over an extended period, often resulting from repeated or prolonged exposure, while acute toxicity occurs rapidly or immediately after a single exposure.
Duration: Chronic toxicity persists over time and may cause long-term or permanent damage, whereas acute toxicity is typically of short duration and may resolve once the exposure is removed or treated.
Symptoms: Chronic toxicity often involves gradual, subtle symptoms or the development of chronic diseases, whereas acute toxicity typically presents with sudden and severe symptoms or acute health crises.
Many different models for studying toxicity are used during drug discovery and drug development. Briefly, describe the three general models, in silico, in vitro and in vivo, (including why/how/when they are used for studying toxicity) and give one specific example of an assay that is used for each general model.
- in silico, max 250 words (2p)
- in vitro, max 250 words (2p)
- in vivo, max 250 words
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 specificity, both during and after drug discovery/development, is an important task. Especially if drugs are targeting specific receptors such as the ERBB2 receptor and not the ERBB1 receptor.
- Explain the concept of drug specificity.
The concept of drug specificity refers to a drug’s ability to selectively interact with its intended target or targets in the body. It means that a drug has a high degree of selectivity and interacts primarily with specific molecules involved in a particular disease or biological process. This selectivity allows the drug to produce the desired therapeutic effect while minimizing interactions with unrelated molecules, reducing the risk of adverse effects and improving therapeutic outcomes.
Visualize using dose-response curves one drug that is specific for the ERBB2 receptor and not the ERBB1 and visualize using dose-response curves one drug that is not specific for neither ERBB1 nor ERBB2, but rather targets both.
For the specific drug it will look like a normal dose response curve it will increase and then plateau while the non specific it will be more of a straight line.
The development of illicit new psychoactive substances (NPSs) is often lacking essential part of the drug development process (Fig 2) 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 (2p)
- Phenethylamines (2p)
- Synthetic opioids (2p)
Especially focusing on how the neurotransmitters are affected or what the receptor activation leads to.
Cathinones and phenethylamines:
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.
Proteins and peptides have been used as drugs for a rather long time and were previously isolated from natural sources, but today most protein drugs are derived from recombinant DNA-technology.
- Plasmids are very popular genetic vectors for protein expression. Draw a general schematic of a plasmid and explain its 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 many 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.
Efficient vaccine development is a hot topic these days.
- When it comes to the Influenza vaccine. Why is the development dependent on deep knowledge about the two viral proteins Haemaglutinin and Neuramidinase?
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.
