Introduction To Medicinal Chemistry Solution Manual

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An overview of Medicinal Chemistry

Medicinal chemistry is an interdisciplinary field of study combining aspects of organic chemistry, physical chemistry, pharmacology, microbiology, biochemistry, as well as computational chemistry. Medicinal chemistry is concerned with the discovery, design, synthesis, and interactions of a pharmaceutical agent (drug) with the body.

Medicinal chemistry is mainly concerned with small organic molecules both natural and synthetic. Compounds in clinical use are primarily small organic compounds. Organometallic compounds, biopharmaceuticals, and inorganic compounds are also used in medicine as therapeutics.

Fig 1. Structures of Certain Drugs

The phases of drug action are divided into:

  • The Pharmaceutical Phase
  • The Pharmacokinetic Phase
  • The Pharmacodynamic Phase

Drug Targets

The main drug targets in the body are macromolecules (large molecules) with molecular weights far greater than small drug molecules.

  • Nucleic Acids
    • Deoxyribonucleic acid (DNA)
    • Ribonucleic acid (RNA)

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  • Proteins (main)
    • Transport proteins
    • Enzymes
    • Structural Proteins
    • Receptors

Drugs bind to their targets in regions known as binding sites. Most drugs interact with their targets through intermolecular bonds. However, some drugs form covalent bonds with their targets (eg. alkylating agents). Covalent bonds are typically strong, requiring around 80 – 440 kJ mol-1 to break these bonds.

Drug-target intermolecular interactions:

  • Ionic Bonds (Charge-Charge Interactions)
    • The electrostatic attraction between ions of opposite charges
    • At physiological pH, cationic environments are provided by protonated basic side chains of amino acids in proteins such as arginine.
    • Anionic environments are typically provided by acid side chains of amino acids such as aspartic acid.
    • Drug molecules may contain acidic and/or basic groups
    • The strength of an ionic bond is inversely proportional to the distance between the charges.
    • The dielectric contant (ε) of the surrounding medium also plays a role.
    • Ionic interactions are typically stronger in hydrophobic environments such as in hydrophobic pockets where ε small
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  • Ion-dipole interactions
      • Molecular groups such as carbonyls (C=O) have a permanent dipole moment which is due to the different electronegativities of the atoms in the group.
      • Ion-dipole interactions are electrostatic interactions between an ion and a neutral group with a dipole.
      • The dipole is represented by the cross-ended arrow. The cross end represents the positive end whereas the arrowhead represents the negative end of the dipole.
  • Dipole-dipole interactions
      • Dipole-dipole interactions are the electrostatic interactions between permanent dipoles
  • Ion-induced dipole interactions
      • Ion-induced dipole interactions occur when:
        • The electric field of an ion induces a dipole in a non-polar molecule.
  • Hydrogen Bonding
    • Hydrogen bonding interactions are attractive interactions involving two groups:
      • One containing an electron-deficient hydrogen covalently bonded to an electronegative atom and one containing an electron-rich heteroatom.
    • Intramolecular hydrogen bonding is possible and is thought to enhance a compound’s membrane permeability. (Med. Chem. Commun., 2011, 2, 669-674)
    • Hydrogen bond donors (HBDs): The functional group that contains the electron-deficient hydrogen covalently bonded to an electronegative atom.
    • Hydrogen bond acceptors (HBAs): The functional group that contains the electron-rich heteroatom and is the recipient of the hydrogen bond.
    • Hydrogen bonds are ubiquitous in the body and vary greatly in strength. This introduction to medicinal chemistry is focussed on the both the strength and distance of these bonds and how they influence these reactions:
    • Drug-target hydrogen bond strengths are typically within the range of 16 to 60 kJ mol-1.
    • Drug-target hydrogen bond distances are typically within the range of 1.5-2.2 Å.
    • Often enhanced by ionic interactions
    • Common HBDs: HR3N+, HR2N, HRN, ROH
    • HBAs:
  • π-π Interactions
    • These are attractive non-covalent interactions that arise between aromatic rings
    • Typically occurs in cooperation with dispersion forces
    • Both π-π interactions and hydrogen bonding feature heavily in nucleic acids
    • Most common: T-shaped
    • Other known modes: Sandwich and Parallel-displaced
  • Dispersion Forces
    • Sometimes referred to as London forces or Van der Waals forces
    • Consists of very weak interactions (about 2-4 kJ mol-1) that occur between the hydrophobic regions of molecules.
    • The interactions are individually weak. However when combined together, these forces can have a significant role in binding.
    • The hydrophobic effect typically plays a role as well when non-polar chemical groups interact.
      • Macromolecular drug targets in the body are surrounded by polar water molecules
      • Water is unable to solvate the non-polar regions of drugs and macromolecules
      • Water surrounds these non-polar regions and forms a highly ordered network of intermolecular hydrogen bonds (negative entropy ΔS).
      • The hydrophobic effect is the observed tendency of non-polar groups to associate in polar environments
      • The interaction of a hydrophobic regions of a drug and its target causes a disruption of the highly ordered network of water molecules (positive entropy ΔS)
      • Positive ΔS contributes to a more negative free energy gained in binding (ΔG)
      • Under normal physiological conditions, hydrophobic interactions between drug and target are mainly entropically driven.

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  • Repulsive Forces
    • Repulsive forces are short-range forces that arise when the molecular orbitals of molecules come too close to each other.

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Drug-target interactions example:


Fig 2: Interactions of the cardiac stimulant and bronchodilator isoprenaline with the β-adrenoceptor binding site. Ionic interactions, hydrogen bonding, hydrophobic interactions, and π- π interactions are shown. Isoprenaline’s affinity for the β-adrenoceptors is thought to be due to the presence of a hydrophobic pocket in β-adrenoceptors which can accommodate the bulky isopropyl group.

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  • The drug design aspect of medicinal chemistry plays an important role in optimising drug-target interactions
  • Drug design is also concerned with:
    • Improving a drug’s pharmacokinetic profile
    • Improving specificity