NKED old exam Flashcards
B. Today, there are mainly two basic strategies for drug discovery;
a) Activity centered discovery and
b) Target centered discovery.
Explain these two strategies and give example of drugs that have originated from 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.
Drug companies often have access to large libraries of molecules (millions of small
molecules).
- What systems are used to evaluate these compounds as potential drugs?
High throughput screening
Historically, conventional small molecule drugs has been discovered from synthetic
chemistry or from natural products.
- Which of the following drugs has been identified from synthetic chemistry or from
natural products?
Penicillin (antibiotics)
Taxol (cancer chemotherapy)
Benzodiazepines (psychoactive drug)
Omeprazole (peptic ulcer disease)
Natural compounds
Penicillin (antibiotics)
Taxol (cancer chemotherapy)
Synthetic
Benzodiazepines (psychoactive drug)
Omeprazole (peptic ulcer disease)
After identifying a potential drug candidate, the mechanism of action of the drug needs to be
confirmed.
- How can the mechanism of action and the potential target be validated?
In vitro assays: In vitro assays involve testing the drug candidate’s activity against isolated target proteins or cell cultures. By exposing the drug candidate to specific protein targets or cells, researchers can observe its effects and determine if it interacts with the intended target. These assays can help identify the mechanism of action and provide preliminary evidence for target validation.
Animal models and in vivo studies: Animal models are used to evaluate the efficacy of the drug candidate in a whole organism and assess its impact on disease-related processes. By administering the drug candidate to animal models with the targeted disease or condition, researchers can observe its effects on physiological parameters, biomarkers, or disease progression. These studies can provide further evidence for the mechanism of action and target validation.
“Lead compounds” that have been identified during the discovery phases needs to be
optimized further, so called lead optimization, because there are problems with these lead
compounds. Describe three of these problems?
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. The purpose of the last phase, Phase 4,
is to monitor the safety and long term side effects after regulatory review and approval of
the drug. What is the objective of the Phase 1, Phase 2 and Phase 3 of the clinical trials?
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. Drugs are often characterized by their “therapeutic window”. Explain the meaning of
therapeutic window. Preferably with a schematic illustration.
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.
There are some general principles for the interaction of drugs with target molecules.
Explain the meaning of the following terms; (3p)
- Affinity
- Agonism and antagonism
- Reversibility
Affinity: Affinity is the strength of the interaction between a drug and its target molecule.
Agonism and antagonism: Agonism refers to a drug’s ability to activate its target, while antagonism refers to a drug’s ability to block or inhibit its target.
Reversibility: Reversibility refers to whether a drug’s binding to its target is temporary or long-lasting.
Drugs can interact with different target molecules. Describe three of the most important
target molecules that are recognized by drugs and give one example of a drug interacting with
the respective target.
G protein-coupled receptors (GPCRs): GPCRs are a large family of cell surface receptors involved in transmitting signals from extracellular molecules to the inside of cells. They play a crucial role in various physiological processes and are targeted by a significant number of drugs. An example of a drug interacting with a GPCR is Propranolol, which binds to beta-adrenergic receptors and is used to treat high blood pressure and cardiac conditions.
Enzymes: Enzymes are proteins that catalyze biochemical reactions in the body. Many drugs target specific enzymes to modulate or inhibit their activity. One example is Statins, a class of drugs that inhibit the enzyme HMG-CoA reductase, which plays a role in cholesterol synthesis. Statins are commonly prescribed to lower cholesterol levels and reduce the risk of cardiovascular diseases.
Ion channels: Ion channels are pore-forming proteins that regulate the flow of ions across cell membranes, influencing various physiological processes such as nerve signaling and muscle contraction. Drugs that target ion channels can modulate ion flow and affect cellular activity. An example is Lidocaine, which acts as a local anesthetic by blocking voltage-gated sodium channels, thereby preventing the generation and conduction of nerve impulses.
Biopharmacuticals is drugs with biological origin and includes, nucleic acids, proteins and
peptides, vaccines, as well as cell based therapies.
A. Oligonucleotides for gene expression interference and gene therapy, are approaches
considered viable and promising for a wide range diseases. However, gene therapy and the
use of oligonucleotides also have major challenges. Explain two problems that are associated
with gene therapy?
Delivery Challenges: One significant challenge in gene therapy is efficiently delivering oligonucleotides to target cells or tissues. Oligonucleotides, including small interfering RNA (siRNA) or antisense oligonucleotides (ASOs), are large molecules that need to overcome various barriers to reach their intended site of action. These barriers include cellular membranes, extracellular matrices, and clearance mechanisms in the body. Additionally, specific tissues or organs may be difficult to target due to their location or physiological properties. Developing effective delivery systems that can protect the oligonucleotides, facilitate their cellular uptake, and ensure their release at the desired site remains a significant hurdle in gene therapy.
Off-Target Effects: Another challenge associated with gene therapy using oligonucleotides is the potential for off-target effects. Oligonucleotides are designed to target specific genes or gene sequences to interfere with their expression. However, unintended interactions or binding to other genes or non-targeted regions of the genome can occur. This can lead to off-target effects, such as the suppression or alteration of unintended genes, potentially causing unwanted side effects or toxicity. Achieving high specificity and minimizing off-target effects is crucial to ensure the safety and efficacy of oligonucleotide-based gene therapy approaches.
Why is efficient vaccine development against influenza dependent on deep knowledge
about the two viral proteins Haemaglutinin and Neuramidinase? (2p)
- How can you modify your strategy for increased response efficacy during repeated
vaccinations?
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.
Neurodegenerative diseases, such as Alzheimer´s and Parkinson´s diseases, as well as the
infectious prion diseases are also rather complex group of disorders that are believed to be
caused by misfolded and aggregated proteins in the brain. Today there are only symptomatic
treatments available for these diseases.
Donepezil Levodopa
- Donepezil and Levodopa are two symptomatic drugs used for Alzheimer´s or
Parkinson´s disease,respectively. What are the respective mechanism of action for
these symptomatic drugs?
Levodopa is a precursor of dopamine and can cross the blood-brain barrier to reach the brain, where it is converted into dopamine by the enzyme aromatic L-amino acid decarboxylase (AADC).
Levodopa is often administered in combination with Carbidopa, a peripheral decarboxylase inhibitor. Carbidopa does not cross the blood-brain barrier, but it inhibits the peripheral metabolism of Levodopa by inhibiting AADC outside the brain.
The primary reason for combining Levodopa with Carbidopa is to enhance the effectiveness of Levodopa therapy while reducing its side effects. By inhibiting the peripheral conversion of Levodopa into dopamine, Carbidopa allows more Levodopa to reach the brain, where it can be converted into dopamine. This results in increased dopamine levels in the brain.
Furthermore, the addition of Carbidopa helps reduce the peripheral side effects of Levodopa. When Levodopa is metabolized peripherally, it can lead to various side effects such as nausea, vomiting, and low blood pressure. By inhibiting the peripheral conversion of Levodopa, Carbidopa helps to minimize these side effects, allowing for a higher dose of Levodopa to be administered without intolerable adverse effects.
The primary mechanism of donepezil involves inhibiting the enzyme acetylcholinesterase, which is responsible for breaking down acetylcholine in the synaptic cleft. By inhibiting acetylcholinesterase, donepezil allows acetylcholine to accumulate and persist in the synaptic cleft, enhancing cholinergic neurotransmission.
The ultimate goal in combating neurodegenerative diseases is to find disease
modifying therapies and a variety of strategies targeting the major pathological
hallmarks, the protein aggregates, have been proposed. Describe two of these
strategies.
Main strategies:
• Lower the precursor protein to avoid protein aggregation (small molecule inhibitors, enhanced clearance antibodies)
• Clear out formed protein aggregates (monoclonal antibodies*)
• Inhibit aggregate formation (small molecules, protein binders)
• Stabilize fibrils to prevent seeded propagation
Lowering the Precursor Protein to Avoid Protein Aggregation:
Small molecule inhibitors: Small molecule inhibitors are compounds designed to interfere with specific processes involved in protein aggregation. These inhibitors can target various steps in the protein aggregation pathway, such as inhibiting protein misfolding, preventing the formation of toxic oligomers, or promoting the clearance of misfolded proteins. By reducing the levels of misfolded proteins, small molecule inhibitors aim to prevent the formation of protein aggregates and their associated toxicity.
Enhanced clearance antibodies: Enhanced clearance antibodies are a type of therapeutic antibodies designed to bind and facilitate the removal of misfolded proteins. These antibodies can recognize specific misfolded proteins or protein aggregates and enhance the clearance mechanisms of the immune system, such as phagocytosis by immune cells or the activity of proteases that degrade the misfolded proteins. By enhancing the clearance of misfolded proteins, these antibodies aim to reduce the burden of protein aggregates and mitigate their detrimental effects.
Clearing out Formed Protein Aggregates:
Monoclonal antibodies: Monoclonal antibodies are highly specific antibodies engineered to target and bind to specific proteins or protein aggregates. In the context of neurodegenerative diseases, monoclonal antibodies can be designed to specifically recognize and bind to the protein aggregates associated with a particular disease, such as amyloid-beta plaques in Alzheimer’s disease or alpha-synuclein aggregates in Parkinson’s disease. By binding to the protein aggregates, monoclonal antibodies can facilitate their clearance through various mechanisms, such as stimulating immune responses or promoting their degradation by proteases. The goal is to reduce the burden of protein aggregates and potentially slow down disease progression.
