Introduction to Medicinal Chemistry
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Questions and Answers

What characteristic do bioisosteres share?

  • They possess similar physical properties. (correct)
  • They have identical molecular weights.
  • They are always hydrophilic.
  • They affect unrelated biochemical systems.
  • Which method is typically used when the target of a drug is unknown?

  • Qualitative Structure Activity Relationship (QSAR)
  • Quantitative Structure Activity Relationship (QSAR) (correct)
  • Empirical Drug Design
  • Targeted Molecular Simulation
  • What does the Lineweaver-Burk plot represent?

  • The kinetics of enzyme inhibition. (correct)
  • A method for calculating molecular shapes.
  • The relationship between bioisosteres and agonists.
  • A plot of biological activity versus pharmacological properties.
  • What defines the interaction between an ion and a solvent molecule?

    <p>Ion-dipole bonding (C)</p> Signup and view all the answers

    Who was responsible for an early example linking biological activity to LogP?

    <p>Corwin Hansch (D)</p> Signup and view all the answers

    What is the primary purpose of Clog P in medicinal chemistry?

    <p>It measures the octanol/water coefficient. (B), It assesses the lipophilicity or hydrophilicity of a drug. (D)</p> Signup and view all the answers

    Which of the following correctly describes the term 'pharmacophore'?

    <p>The part of a drug responsible for its biological activity (D)</p> Signup and view all the answers

    Which statement about Lineweaver-Burk plots is true?

    <p>They provide less accurate data than other methods. (B)</p> Signup and view all the answers

    Which of the following is NOT one of Lipinski's Rules for orally active drug substances?

    <p>LogP greater than 5 (B)</p> Signup and view all the answers

    What is the main characteristic of bioisosteres?

    <p>They are biologically equivalent in a certain system (B)</p> Signup and view all the answers

    What do Van Der Waals forces primarily describe?

    <p>Attraction between nearby covalent bonds. (D)</p> Signup and view all the answers

    What is a notable feature of the angiotensinogen pathway?

    <p>It involves complex molecular interactions. (D)</p> Signup and view all the answers

    What type of interaction does π-cation bonding involve?

    <p>A cation with a π-cloud of an aromatic system (B)</p> Signup and view all the answers

    Which of these values is critical for blood-brain barrier penetration?

    <p>PSA less than 60Ų (C)</p> Signup and view all the answers

    Which property is essential for bioisosteric compounds?

    <p>Near equal molecular shapes. (D)</p> Signup and view all the answers

    Which functional group is recognized as a sulfonamide?

    <p>Compound with a sulfur atom bonded to two oxygen atoms and a nitrogen (C)</p> Signup and view all the answers

    How can you distinguish between conformational and configurational isomers?

    <p>Conformational isomers can be interconverted easily without breaking bonds. (B)</p> Signup and view all the answers

    Which drug is an example of a di-zwitterion in terms of its structure?

    <p>Lisinopril (D)</p> Signup and view all the answers

    What best explains the concept of Vmax in pharmacokinetics?

    <p>It represents the maximum rate of substrate conversion by an enzyme (D)</p> Signup and view all the answers

    What is the effect of a higher LogP value on aqueous solubility?

    <p>Decreases water solubility. (B)</p> Signup and view all the answers

    What is one characteristic of a lipophilic compound?

    <p>It has a property of being water-hating. (A)</p> Signup and view all the answers

    Which of the following is true about competitive reversible inhibitors?

    <p>Their effects can be reversed by increasing substrate concentration (C)</p> Signup and view all the answers

    What aspect do regio-isomers share?

    <p>Different connectivity of atoms in the molecule (A)</p> Signup and view all the answers

    Which bond interaction is typically referred to as salt bridge in biological systems?

    <p>Ionic bonding (C)</p> Signup and view all the answers

    What is the primary characteristic of competitive inhibitors?

    <p>They compete for the substrate binding site. (B)</p> Signup and view all the answers

    Which example represents a transition state analog?

    <p>HIV protease inhibitors (C)</p> Signup and view all the answers

    What is a common feature of irreversible inhibitors?

    <p>They can lead to allergic reactions. (D)</p> Signup and view all the answers

    What defines slow, tight-binding inhibitors?

    <p>They have a high affinity and may covalently attach to the enzyme. (C)</p> Signup and view all the answers

    What mechanism do mechanism-based enzyme inactivators utilize?

    <p>They utilize the active site to covalently attach to enzyme residues. (B)</p> Signup and view all the answers

    What is the primary action of statins as enzyme inhibitors?

    <p>They are classified as slow, tight-binding inhibitors. (B)</p> Signup and view all the answers

    What do affinity labeling agents do?

    <p>They covalently attach to active site residues. (C)</p> Signup and view all the answers

    What type of inhibitor are sulfa drugs classified as?

    <p>Competitive inhibitors (B)</p> Signup and view all the answers

    Flashcards

    Ion-dipole Bonding

    Interaction between an ion and a polar molecule, usually a solvent like water.

    Π-Cation Interaction

    Interaction between a positively charged ion and the electron cloud of an aromatic ring.

    Pharmacophore

    A group of atoms within a molecule that is responsible for its biological activity.

    Bioisostere

    A molecule that can replace another molecule in a biological system without significantly altering the biological effect.

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    Sulfonamide Functional Group

    A functional group that is commonly found in drugs and typically contributes to their acidic properties.

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    Vmax

    A drug's maximum rate of reaction when fully saturated with substrate.

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    Km

    The substrate concentration at which the reaction rate is half of Vmax.

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    Inhibitor

    A molecule that binds to an enzyme and prevents it from reacting with its substrate.

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    IC50

    A measurement of a drug's potency, where a lower IC50 value indicates greater potency. It represents the concentration required to inhibit a biological process by 50%.

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    Nucleophiles

    Molecules that attack electron deficient sites (e.g., carbocations, carbonyl groups), readily donate electrons.

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    Electrophiles

    Molecules that readily accept electrons, often have a positive charge or a partially positive site.

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    LogP

    A measure of a molecule's lipophilicity, indicating its preference for oil-like environments compared to water. It's a crucial factor in drug absorption and distribution in the body.

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    Van Der Waals forces

    A type of interaction between molecules where electron clouds of nearby bonds influence each other, resulting in weak attractive forces. Often considered a type of hydrophobic interaction.

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    Competitive Inhibition

    A type of enzyme inhibition where the inhibitor binds reversibly to the active site, competing with the substrate.

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    Transition State Analogs

    Inhibitors that mimic the transition state of the enzyme-substrate reaction, forming strong, stable interactions.

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    Dipole-Dipole Bonding (Hydrogen Bonding)

    A type of interaction between molecules with permanent dipoles, involving a hydrogen atom bonded to a highly electronegative atom (like oxygen or nitrogen). In biological systems, it's crucial for protein folding and drug-receptor interactions.

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    Slow, Tight-Binding Inhibitors

    Inhibitors that bind slowly but tightly, often forming covalent bonds with the enzyme.

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    Ionic Bonding (Salt Bridge)

    A type of strong interaction between oppositely charged ions. It plays a vital role in stabilizing protein structures and drug interactions with biological targets.

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    Lipinski's Rules

    A set of guidelines that predict a drug's potential for oral bioavailability. These rules focus on molecular properties like size, hydrogen bonding capability, and lipophilicity.

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    Affinity Labeling Agents

    A type of irreversible inhibition where a molecule covalently binds to the active site of the enzyme.

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    Mechanism-Based Enzyme Inactivators

    Inhibition where a molecule utilizes the enzyme's mechanism to covalently attach to the enzyme.

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    Blood-Brain Barrier

    A barrier composed of specialized cells that regulate the passage of substances from the bloodstream into the brain. It is essential for protecting the brain from harmful compounds.

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    Irreversible Inhibitor: Michael Acceptor

    A specific type of irreversible inhibition where the inhibitor binds to the enzyme through a Michael addition reaction.

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    Disease State Analysis

    The process of analyzing a disease state to identify potential targets and develop targeted therapies.

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    Quantitative Structure Activity Relationship (QSAR)

    A computational method that links physico-chemical properties to biological activity.

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    Angiotensinogen Pathway

    A pathway in the body that regulates blood pressure, involving an enzyme called angiotensin-converting enzyme (ACE).

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    Angiotensin-Converting Enzyme (ACE)

    An enzyme that plays a key role in regulating blood pressure by converting angiotensin I to angiotensin II, a potent vasoconstrictor.

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    ACE Inhibitor

    A drug that inhibits the action of angiotensin-converting enzyme (ACE), leading to lower blood pressure.

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    Lineweaver-Burk Plot

    A graph used to analyze enzyme kinetics, plotting the inverse of reaction velocity against the inverse of substrate concentration.

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    Study Notes

    Introduction to Medicinal Chemistry

    • Course instructor: Mark J. Olsen
    • Associate Professor of Pharmaceutical Science
    • Phone: (623)572-3568
    • Email: [email protected]
    • Office: Glendale Hall, Room 236-18

    Learning Objectives Hour I

    • Determine most and least potent drug from IC50 data
    • Understand LogP and its relationship to aqueous solubility
    • Judge LogP values based on chemical structure recognition
    • Recognize molecular functional groups via Van Der Waals forces
    • Review conformation vs. configuration, distinguish conformational and configurational isomers
    • Understand the significance of stereochemistry

    Why Medicinal Chemistry?

    Natural Products versus Synthetic Agents

    Drug vs Poison

    Drugs Versus Poisons

    • Images of poppy, scorpion, and skin wound illustrate varying effects of substances

    Origins of Pharmacotherapy

    Modern Drug Discovery

    • Disease State Analysis
    • Specific gene target demonstration
    • Expression and Crystal Structure
    • High Throughput Screening
    • Lead Compound Identification
    • Medicinal Chemistry optimization
    • Proof of Principle Demonstration
    • Pre-clinical Evaluation and Development
    • Clinical Trials
    • FDA Approval

    Physico-Chemical Properties in Medicinal Chemistry

    • Hydrophilic: "Water-loving"
    • Hydrophobic: "Water-hating"
    • Lipophilic: "Lipid-loving"
    • Lipophobic: "Lipid-hating" (rarely used)
    • Log P (octanol/water coefficient): crucial for determining hydrophilicity/lipophilicity
    • Clog P and Mlog P: calculated and experimentally measured Log P

    Lipinski's Rules

    • Not more than 5 hydrogen bond donors
    • Not more than 10 hydrogen bond acceptors
    • Molecular Weight (MW) less than 500 amu
    • LogP less than 5
    • Blood-Brain Barrier Penetration: PSA less than 60Å2, LogP greater than 0

    Molecular Interactions

    • Van Der Waals forces: Weak forces between nearby covalent bonds. Similar to hydrophobic interactions
    • Dipole-dipole bonding: Usually called hydrogen bonding in biological systems.
    • Ionic bonding ("salt bridge"): Between ions with opposing charges
    • Ion-dipole bonding: Between an ion and a dipole (e.g., water).
    • π-cation interaction: Between a cation and a π-cloud of an aromatic molecule, important in drug-protein interactions

    Label Each Bonding Example!

    • Chemical structures illustrating various bonding examples

    Sample Structure Activity Relationship (Part II): Functional Groups, pKa, and Ionization States

    • Chemical structures of various functional groups (halogen, ketone, carboxylic acid, aryl amine, alkyl amine), pKa values, and ionization states in stomach and colon.

    Stereochemistry and Configuration

    • Chemical structures of stereoisomers (R)-(-)-Epinephrine, (S)-(+)-Epinephrine, and N-Methyldopamine are presented.

    Enantiomers versus Diastereomers

    • Chemical structures of enantiomers (e.g., (-)-Ephedrine, (+)-Ephedrine) and Diastereomers (e.g., (-)-Pseudoephedrine, (+)-Pseudoephedrine) are shown to demonstrate their distinguishing properties).

    Regio-Isomers

    • Chemical structures of Regio-Isomers are presented

    Learning Objectives Hour II

    • Review key heterocycles common in drugs
    • Define pharmacophore and Structure Activity Relationship (SAR)
    • Discuss bioisosteres and provide examples
    • Pay close attention to the role of Fluorine
    • Recognize Sulfonamide functional groups
    • Understand drug-poison relationships and metal chelation
    • Defines Vmax and KM
    • Evaluate competitive, reversible inhibitors, irreversible inhibitors, and affinity labels

    Aromaticity and Common Pharmaceutical Heterocycles

    • Chemical structures of various aromatic and heterocyclic molecules (benzene, pyrazine, pyridine, quinoline, indole, indoliIne, benzimidazole, benzofuran, thiophene, furan, pyrrole, imidazole, oxazole, isoxazole, pyran, piperidine, piperazine, morpholine)

    Drug Development and Pharmacophore Identification

    • Chemical structures illustrating drug development and pharmacophore identification (4,5-Epoxymorphinans, Morphinans, Benzodioxanes, Ethanolamines, Diphenhydramine, Benzomorphans, Phenothiazines (Promethazine), Ethylenediamines, 4-Phenylpiperidines, Methadones, Chlorpromazine (antipsychotic), Tripelennamine)

    Sample Structure Activity Relationship (Part I): The role of functional groups

    • Chemical structures illustrating various functional groups and their impact on biological activity (halogen, ketone, carboxylic acid, aryl amine, alkyl amine)
    • Relationship between functional groups and cellular penetration.
    • Correlation between functional groups and pharmacophore, activity spectrum, and potency.

    Bioisosteres

    • Organic structures that are biologically equivalent in a given system.
    • Compunds or groups that possess nearly equal molecular shapes and sizes; similar distribution of electrons; similar physical properties (hydrophobicity)
    • Produce biological properties similar to agonists or antagonists.

    Common “Classical” Bioisosteres

    • Tabulation of monovalent and divalent bioisosteres (e.g., F, H; OH, NH; SH, OH; Cl, Br, CF3), trivalent groups (e.g., -P=, -As=), tetrasubstituted atoms (-P=, -As-), and ring equivalences.)

    "Non-Classical" Bioisosteres

    • Tabulation of chemical structures of compounds with bioisosteric replacements.

    Sulfonamides

    • Chemical structures of Sulfonamide and examples of Sulfonamides.

    Quantitative Structure Activity Relationship (QSAR)

    • Computational method likening physico-chemical properties to biological activities.
    • Famous early example using Corwin Hansch who linked barbiturate biological activity to LogP.
    • Methodology typically uses biological activity (Y-axis) and physico-chemical property (X-axis) plots.

    Structural Biology in Computational Medicinal Chemistry: Captopril and Lisinopril

    • Describes the relevance of structural biology to computational medicinal chemistry in terms of Captopril and Lisinopril.

    Angiotensinogen Pathway

    • Diagram and detailed descriptions of the biochemical pathways, enzymes, and protein sequences involved in the angiotensinogen cascade.

    ACE Crystal Structure

    • Visual representations (images) of the ACE (Angiotensin-Converting Enzyme) crystal structure, including locations of Zinc, Asp, and His residues relevant to substrate binding.

    Development of Captopril

    • Chemical structures are presented for Succinyl-L-proline, D-2-methylsuccinyl-L-proline, 3-Mercaptopropanoyl-L-proline, and Captopril.

    Captopril Complexed to Active Site Zinc

    • Visual representation (image) of Captopril bound to the ACE active site.

    Lisinopril: Di-Zwitterion

    • Chemical structure showing the Zwitterion form of Lisinopril.

    Lisinopril Complexed to Active Site Zinc

    • Visual representation (image) of Lisinopril bound to the ACE active site

    Enzyme Kinetic Equations

    • Michaelis-Menten equation and its graph
    • Mathematical expressions and graphic depictions of enzymatic kinetics, including the Michaelis-Menten equation and its plot.

    Lineweaver-Burk Equation and Plot

    • Lineweaver-Burk equation and its graphical representation.

    Kinetics of Enzyme Inhibition

    • Explanation of competitive, non-competitive types of enzyme inhibitors.
    • Detailed analysis of how the Lineweaver-Burk plot can be used to understand the different modes of enzyme inhibition (competitive, noncompetitive) and related mathematical expressions are presented.

    Nucleophiles and Electrophiles

    • Definitions and illustrative chemical structures of nucleophiles and electrophiles.

    Major Classes of Enzyme Inhibition: Reversible Inhibition

    • Different types of reversible enzyme inhibitors (competitive, alternative substrate, transition state analogs, slow, tight-binding) including definitions, examples (sulfa drugs, HIV protease inhibitors, statins), and a discussion of their application in biochemical pathways, with special emphasis on how they compare to each other.

    Major Classes of Enzyme Inhibition: Irreversible Inhibition

    • Discussion of affinity labeling agents (aspirin, β-lactam antibiotics and their potential for allergic reactions).
    • Explanation of mechanism-based enzyme inactivators (e.g., 5-Fluorouracil) with emphasis on their covalent binding characteristic to active site residues.

    Irreversible Inhibitor: Michael Acceptor

    • Diagrammatic representation of mechanism for irreversible inhibitors and their interaction with enzyme active sites.

    Statins: Example of Slow, Tight Binding Inhibitors

    • Chemical structures and steps in the biochemical pathway for statin drug mechanism and how they inhibit HMG CoA reductase.

    Statin Metabolic Activation and Mechanism of Action

    • Detail of how Statin compounds (e.g., mevastatin, lovastatin) are chemically and biochemically transformed to a more active form.

    Statin family of antihypercholesterolemia agents are classic examples of enzyme inhibitors

    • Chemical structures illustrating the various statin family members, including Lovastatin, Simvastatin, Pravastatin, Fluvastatin, Atorvastatin, and Rosuvastatin.

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    Description

    This quiz covers key concepts in medicinal chemistry, including drug potency, LogP values, and molecular functional groups. Participants will deepen their understanding of stereochemistry, the differences between drugs and poisons, and the modern drug discovery process. Engage with essential learning objectives to enhance your knowledge in pharmaceutical science.

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