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Introduction to Medicinal and Organic Chemistry, Lecture notes of Pharmaceutical Chemistry

Medicinal and organic chemistry is a significant subject concerned with the design, synthesis, and investigation of molecules having possible uses in medicine. The material on this site introduces medicinal and organic chemistry, emphasising the relevance of each of these subjects, important principles, and practical applications in a variety of sectors and situations. This topic is critical in both the development of novel medications and the study of chemical mechanisms in organisms that exist.

Typology: Lecture notes

2022/2023

Available from 07/26/2023

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PHARMACY REVIEWER NOTES (BBYN)
Module 1 : Introduction to PMOC
Medicinal Chemistry
- Branch of chemistry involved in identification,
design, synthesis, and development of biologically
active compounds ( chemical compounds that
targets our biological compounds producing effects :
Alter Physiological action in the body )
- An interdisciplinary science : Organic Chemistry,
Biochemistry, Computational Chemistry,
Pharmacology, Pharmacognosy, Molecular biology,
Physical Chemistry
- 14, 315 drugs
Drugs:
- Are low MW chemical substances that interact with
macromolecular targets ( CHAINS - Proteins, Nucleic
Acids ) in the body to produce effect.
- DRUG affects the BODY ( Pharmacodynamics ),
BODY affects the DRUGS ( Pharmacokinetics )
1. Pharmacodynamics
a. What the drug does to the body
i. GOAL: Design a drug that will interact
as powerfully and selectively as
possible for the target
b. ENDOGENOUS COMPOUNDS ( Natural)
i. body’s own natural chemicals (
Hormones AUtacoids, NT)
c. EXOGENOUS COMPOUNDS
i. foreign substances (XENOBIOTICS)
DRUGS
d. Drug -> Target -> Response/Effect (
Therapeutic, Subtherapeutic - less powerful,
and toxic - less selective)
2. Pharmacokinetics ( destiny of the drug)
a. What the body does to the drug
b. Design the drug so that it is capable of
reaching that target
c. ADME ( Absorption, Distribution, Metabolism,
Excretion)
Liberation ( Drug release) API - Dissolution
- When the conventional dosage forms are
administered orally or topically , the active drug in the
dosage form is immediately released and absorbed
into the systemic circulation .
- Diffusion is the most common mechanism
controlling drug release.
Drug Absorption
- Absorbed : LUNA
- Lipophilic
- Unionized
- Non- polar
- Excreted : HIPE
- Hydrophilic
- Ionized
- Polar
- Drugs
- Weak Electrolyte
- Weak Acids
- Weak Basics
Oral Administration - GIT
- The most common and popular route
- Stomach = Absorption environment ( Acidic)
*pH 1.5-2 fed state; pH 2-6 fasting state
- Small Intestine ( Basic) * main site of
absorption
- High surface Area ( Villi or Microvilli)
- High perfusion -> high blood supply
Predicting the Degree of Ionization at a given pH
Acidic drug + Acidic medium = UNIONIZED
(ABS)
Basic drug + Basic medium = UNIONIZED
(ABS)
Acidic drug + Basic medium = IONIZED (EX)
Basic drug + Acidic medium = IONIZED (EX)
At what medium are acidic drugs readily
absorbed?
More absorbed > UNIONIZED = A + A
At what medium are acidic drugs readily
excreted?
More excreted > IONIZED = A + B
Parenteral Administration
- Direct to Systemic Circulation
- Rapidly distributed
- IV, IM, SC, Intraspinal, Intracerebral
BLOOD BRAIN BARRIER -> Lipophilic
- Protects the brain from exposure to
chemicals and metabolites, due to the
presence of tightly joined epithelial cells
lining the cerebral capillaries
Drug Distribution
- Drug movement from the systemic circulation going
to different organs and tissues
- Blood Flow
- Perfusion : High P = High A
- Delivery of drug to the tissue is controlled by
the specific blood flow to a given tissue
- Delivery to target site
Drug Metabolism
BIOTRANSFORMATION
Chemical Conversion -> Inactive form ( HIPE
-> e), Chemical -> Enzymes, Enzymes -> HIgh
Concentration = Liver Main
- All substances in the circulatory system,
including drugs, metabolites, and nutrients,
will pass through the liver .
- Most molecules absorbed from the GIT enter
the portal vein and are initially transported to
the liver.
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Module 1 : Introduction to PMOC

Medicinal Chemistry

  • Branch of chemistry involved in identification, design, synthesis, and development of biologically active compounds ( chemical compounds that targets our biological compounds producing effects : Alter Physiological action in the body)
  • An interdisciplinary science : Organic Chemistry, Biochemistry, Computational Chemistry, Pharmacology, Pharmacognosy, Molecular biology, Physical Chemistry
  • 14, 315 drugs Drugs:
  • Are low MW chemical substances that interact with macromolecular targets ( CHAINS - Proteins, Nucleic Acids ) in the body to produce effect.
  • DRUG affects the BODY ( Pharmacodynamics ), BODY affects the DRUGS ( Pharmacokinetics )
  1. Pharmacodynamics a. What the drug does to the body i. GOAL: Design a drug that will interact as powerfully and selectively as possible for the target b. ENDOGENOUS COMPOUNDS ( Natural) i. body’s own natural chemicals ( Hormones AUtacoids, NT) c. EXOGENOUS COMPOUNDS i. foreign substances (XENOBIOTICS) DRUGS d. Drug -> Target -> Response/Effect ( Therapeutic, Subtherapeutic - less powerful, and toxic - less selective)
  2. Pharmacokinetics ( destiny of the drug) a. What the body does to the drug b. Design the drug so that it is capable of reaching that target c. ADME ( Absorption, Distribution, Metabolism, Excretion)

Liberation ( Drug release) API - Dissolution

  • When the conventional dosage forms are administered orally or topically, the active drug in the dosage form is immediately released and absorbed into the systemic circulation.
  • Diffusion is the most common mechanism controlling drug release. Drug Absorption
  • Absorbed : LUNA
  • Lipophilic
  • Unionized
  • Non- polar
  • Excreted : HIPE
  • Hydrophilic
  • Ionized
  • Polar
  • Drugs
  • Weak Electrolyte
  • Weak Acids
  • Weak Basics

● Oral Administration - GIT

  • The most common and popular route
  • Stomach = Absorption environment ( Acidic) *pH 1.5-2 fed state; pH 2-6 fasting state
  • Small Intestine ( Basic) *main site of absorption - High surface Area ( Villi or Microvilli) - High perfusion -> high blood supply ➔ Predicting the Degree of Ionization at a given pH ◆ Acidic drug + Acidic medium = UNIONIZED (ABS) ◆ Basic drug + Basic medium = UNIONIZED (ABS) ◆ Acidic drug + Basic medium =IONIZED (EX) ◆ Basic drug + Acidic medium = IONIZED (EX) ◆ At what medium are acidic drugs readily absorbed? ● More absorbed > UNIONIZED = A + A ◆ At what medium are acidic drugs readily excreted? ● More excreted > IONIZED = A + B ● Parenteral Administration
  • Direct to Systemic Circulation
  • Rapidly distributed
  • IV, IM, SC, Intraspinal, Intracerebral ● BLOOD BRAIN BARRIER -> Lipophilic
  • Protects the brain from exposure to chemicals and metabolites, due to the presence of tightly joined epithelial cells lining the cerebral capillaries Drug Distribution
  • Drug movement from the systemic circulation going to different organs and tissues
  • Blood Flow
  • Perfusion : High P = High A
  • Delivery of drug to the tissue is controlled by the specific blood flow to a given tissue
  • Delivery to target site Drug Metabolism ● BIOTRANSFORMATION ○ Chemical Conversion -> Inactive form ( HIPE -> e), Chemical -> Enzymes, Enzymes -> HIgh Concentration = Liver Main
  • All substances in the circulatory system, including drugs, metabolites, and nutrients, will pass through the liver.
  • Most molecules absorbed from the GIT enter the portal vein and are initially transported to the liver.
  • GIT : ABS- Liver - SC effect = Pre- Maturely Metabolism ● BIOACTIVATION - Prodrugs A. Azathioprine (immunosuppressant)
  1. 6-mercaptopurine B. Acyclovir (antiviral)
  2. Acyclovir triphosphate ● First-Pass Effect
  • Pre systemic metabolism
  • Low Bioavailability = ST
  • HIgh Dose / Change ROA
  • a significant proportion of a drug is metabolized by hepatic enzymes during the initial trip through the liver
  • Drug removal by the liver after absorption
  • Example: LIDOCAINE (IV) – antiarrhythmic (60% is metabolized when given orally)
  • ABSORPTION -(first pass effect)- METABOLISM- DISTRIBUTION- EXCRETION ● Alteration of Enzymatic Action I. ENZYME INDUCTION ( Stimulate) High IA A. increased metabolism, low Cp II. ENZYME INHIBITION Low IA A. decreased metabolism, high Cp ● ENTEROHEPATIC CIRCULATION
  • drug re enters the intestinal tract from the liver through bile duct
  • BILIARY RECYCLING = Bile acid -> reabsorption

DRUG EXCRETION

  • Excretion into the urine is a major route of elimination for metabolites and unchanged drugs. RENAL CLEARANCE I. Glomerular Filtration A. An unbound drug is passively filtered by the glomerulus. II. Tubular Secretion A. The drug is actively secreted ( Urine) III. Tubular Reabsorption A. The drug is passively reabsorbed back into the blood.

MODULE 2 : DRUG TARGETS

Key Concepts

  • The vast majority of drugs used in medicine are targeted to proteins, such as receptors, enzymes, and transport proteins
  • Therefore, it is important to understand protein structure in order to understand drug action on proteins. Protein Structures or Conformations
  • AA -> Folding
  1. Primary Structure ( Amino Acid) a) Polypeptide Chain NF = Nascent
  2. Secondary structure ( Alpha Helix) a) # of bonds
  3. Tertiary structure a) Functional Groups b) Polypeptide ( Single Subunit) i) Myoglobin
  4. Quaternary Structure a) MTI b) SU Translation and Post Translational Modifications
  • Proline -> Hydroxylation -> Hydroxyproline
  • Cofactor : Vitamin C, Chem r-alpha-n
  • Prothrombin -> Carboxylation -> Prothrombin
  • Clotting factor - Warfarin ( Prevents Clotting )
  • Clotting Stroke Ml Importance
  • There then comes the problem of identifying what role the protein has in the cell and whether it would serve as a useful drug target.
  • If it does show promise as a target, the final problem is to discover or design a drug that will interact with it.

Types of Proteins Targeted by Drugs ( Mitosis Cell ) ➔ Structural Proteins ◆ Cell Movement ◆ Axondin Movement of NT ◆ Inflammatory Cells = Neutrophils ◆ Colchicine = Anti Gout ( High Urate - High Neutrophils) ◆ Ex: tubulins - Polymerize - Microtubules ◆ Case ● Cancer Patient = High Daughter cancer cells -> HIgh Mitosis -> Vincristine and Vinblastine, Paclitaxel : Blocks T and MT ( Anti Cancer) ➔ Transport Proteins ◆ Cell membrane proteins that undergo conformational Changes when substance binds into them ● Conformational : Changes in shape to allow movements of the compounds. ◆ High HCL = hyperacidity ◆ K+ - H Pump ( Proton Inhibitor) ● Found in the Stomach ● Proton Pump Inhibitors - Prazole