Organic Pharmacy

Md. Tarekur Rahman

Lecturer, Department of Pharmacy
World University of Bangladesh
Introduction
• Pharmacy is the science and practice of discovering, producing, preparing, dispensing,
reviewing and monitoring of medications to ensure the safe, effective, and affordable use
of medicines. Pharmacists are vital to ensuring that consumers receive safe and quality
treatment; healthcare and education about their care journeys.
• Chemistry is the science that deals with the properties, composition, and structure of
substances, their transformations, and the released or absorbed energy during these
processes. It is divided into organic and inorganic domains. Organic chemistry deals with
organic compounds and the other one deals with inorganic compounds.
• Pharmaceutical organic chemistry (organic pharmacy) is the branch of organic chemistry
that studies structure and reactions of organic compounds, which have pharmaceutical
effects. As organic pharmacy deals with all the chemical reactions related to life, its study
is important for pharmacy education.
Organic compounds
• Organic compounds contain carbon as an essential element. So, organic chemistry is
defined as the study of carbon compounds.
• In 1828, the German chemist Wohler accidentally discovered urea, (a well-known
organic compound derived from urine), by boiling the aqueous solution of
ammonium cyanate, a typical inorganic compound.
• This was the first organic compound synthesized artificially from inorganic material.
Functional groups of organic compounds
1. Acyclic Compounds: Organic compounds that do not contain any ring structure.
i. Straight Chain: Carbon atoms are connected in a single, unbranched line. Example: n-
butane (C₄H₁₀)
ii. Branched Chain: At least one carbon is connected to more than two others, forming
branches. Example: isobutane (C₄H₁₀)
2. Cyclic Compounds: Compounds in which carbon atoms form one or more closed ring
structures.
i. Aromatic Compounds: Contain one or more benzene-like rings with delocalized π-
electrons.
• Benzenoid: Contain a benzene ring. Example: Benzene (C₆H₆), Toluene (C₇H₈)
• Non-benzenoid: Aromatic compounds without a benzene ring. Example: Tropolone,
Azulene
• Heterocyclic Aromatic: Aromatic rings that include atoms other than carbon (e.g., N, O,
S). Example: Pyridine (C₅H₅N), Furan (C₄H₄O)
ii. Alicyclic Compounds: Non-aromatic cyclic compounds with properties similar to aliphatic
compounds.
• Homocyclic: Ring made only of carbon atoms. Example: Cyclohexane (C₆H₁₂)
• Heterocyclic: Ring includes one or more heteroatoms (N, O, S). Example: Tetrahydrofuran
(C₄H₈O), Piperidine (C₅H₁₁N)
Examples of some organic drugs
Scopes of Organic Pharmacy
Organic Pharmacy integrates the principles of organic chemistry with pharmaceutical
sciences. It plays a critical role in understanding, developing, analyzing, and producing
pharmaceutical compounds. Below are the major scopes:
1. Drug Discovery and Development
• Organic chemistry provides the foundation for identifying lead compounds with potential
therapeutic activity.
• Modifying molecular structures to improve potency, reduce toxicity, and enhance
specificity.
• Use of Structure-Activity Relationship and Quantitative Structure-Activity Relationship
techniques to predict how structural changes affect biological activity.
• Designing prodrugs—inactive compounds that metabolize into active drugs in the body.
2. Synthesis of Active Pharmaceutical Ingredients (APIs)
• Designing and executing synthetic pathways to produce drug molecules from simpler
substances.
• Use of various organic reactions like alkylation, acylation, oxidation, reduction, and
cyclization.
• Developing stereoselective synthesis to produce optically active drugs (important
because many drugs are chiral).
• Enhancing yield, purity, and scalability for industrial production.
3. Medicinal Chemistry
• Medicinal chemistry is an advanced branch of organic pharmacy concerned with the
design and chemical modification of biologically active molecules.
• Optimization of pharmacokinetics (absorption, distribution, metabolism, excretion -
ADME).
• Studying structure-toxicity relationships (STR) to minimize side effects.
• Designing drugs that can target specific receptors, enzymes, or DNA sequences.
4. Pharmacokinetics and Drug Metabolism
• Understanding the metabolic pathways of drugs using organic chemistry principles.
• Studying Phase I (functionalization) and Phase II (conjugation) reactions in the liver, such as:
i. Oxidation (by cytochrome P450 enzymes)
ii. Reduction
iii. Hydrolysis
iv. Conjugation (with glucuronic acid, sulfate, glutathione)
• Helps in predicting bioavailability, half-life, and excretion routes of drugs.
5. Natural Product Chemistry (Phytochemistry)
• Extraction, isolation, purification, and structural elucidation of phytochemicals and secondary
metabolites (alkaloids, flavonoids, terpenoids, etc.).
• Studying the chemical structure of plant-based compounds and modifying them to
enhance their pharmacological profile.
• Developing semi-synthetic drugs from natural products (e.g., oxycodone, morphine,
quinine).
6. Analytical Chemistry
• Identifying and quantifying organic pharmaceutical compounds.
• Characterization using spectroscopic techniques:
i. NMR (Nuclear Magnetic Resonance) for structure determination.
ii. IR (Infrared Spectroscopy) for functional group identification.
iii. UV-Vis Spectroscopy for conjugated systems.
iv. Mass Spectrometry (MS) for molecular weight and structure analysis.
• Ensuring purity, stability, and quality control of drugs.
7. Pharmaceutical Biotechnology and Drug Delivery
• Synthesis of drug-carrier conjugates, such as PEGylated drugs, antibody-drug conjugates
(ADCs).
• Design of biodegradable polymers, hydrogels, micelles, and nanoparticles for targeted
and controlled drug delivery.
• Surface modification of materials using organic functional groups for enhanced
biocompatibility.
8. Formulation Development and Excipients
• Organic compounds are used as solvents, stabilizers, preservatives, emulsifiers, and other
excipients.
• Understanding organic excipient-drug compatibility and interactions.
• Designing stable formulations by preventing oxidation, hydrolysis, or degradation.
9. Industrial Applications
• Scaling up laboratory synthesis to pilot and commercial scale.
• Designing green and sustainable processes for drug manufacturing using organic
chemistry.
• Managing regulatory compliance by ensuring synthesis meets GMP (Good Manufacturing
Practice) standards.
10. Academic Research and Innovation
• Engaging in research to develop new synthetic routes, novel drug molecules, and
reaction mechanisms.
• Teaching and mentoring in organic chemistry for pharmacy and pharmaceutical sciences
students.
• Publishing in scientific journals and presenting at international conferences.
Physical properties of Organic
substances
Organic substances exhibit a wide range of physical properties depending on their
structure, functional groups, and intermolecular forces. These properties influence
solubility, stability, melting/boiling points, and biological activity.
1. Melting Point (MP)
• The temperature at which a solid turns into a liquid.
• Purity indicator: Pure organic compounds have sharp melting points; impurities
cause depression and broadening.
• Intermolecular forces (e.g., hydrogen bonding, van der Waals) significantly affect
melting point.
• Example: Benzoic acid melts at 122 °C due to hydrogen bonding.
2. Boiling Point (BP)
• The temperature at which a liquid changes to vapor.
• Higher BP with:
i. Increased molecular weight
ii. Hydrogen bonding
iii. Dipole-dipole interactions
• Important for distillation and solvent selection.
• Example: Ethanol (78 °C) boils higher than ether (35 °C) due to H-bonding.
3. Solubility
• Ability to dissolve in a solvent, mainly water or organic solvents.
• Depends on polarity, hydrogen bonding, and molecular size.
• "Like dissolves like": Polar solutes dissolve in polar solvents (e.g., water), and non-polar in
non-polar (e.g., hexane).
• Example: Phenol is soluble in water due to its –OH group.
4. Density
• Mass per unit volume (g/mL or g/cm³).
• Organic compounds are usually less dense than water (density < 1 g/mL), but
halogenated ones (e.g., chloroform) are denser.
• Example: Chloroform has a density of 1.49 g/cm³.
5. Viscosity
• Resistance to flow.
• Increases with molecular size and intermolecular forces.
• Important in liquid formulations (syrup, suspension etc.)
• Example: Glycerol is more viscous than water.
6. Refractive Index
• Measure of how light bends as it passes through a compound.
• Used to identify or assess purity of organic liquids.
• Example: Refractive index of toluene = 1.496.
7. Optical Activity
• Ability of chiral compounds to rotate plane-polarized light.
• Measured using polarimetry.
• Dextrorotatory (+) and levorotatory (–) forms exist.
• Example: Lactic acid has a chiral center and shows optical activity.
8. Polarity
• Arises from differences in electronegativity and bond dipoles.
• Polar compounds interact with water and other polar solvents.
• Affects solubility, biological transport, and binding to targets.
• Example: Alcohols are polar; alkanes are non-polar.
9. Color and Odor
• Many organic compounds are colorless and volatile, giving distinct odors.
• Conjugated double bonds or aromatic rings may show color (chromophores).
• Odor may indicate functional groups (e.g., esters have fruity smells).
• Example: Vanillin has a pleasant odor due to its aromatic aldehyde group.
10. Crystalline or Amorphous Nature
• Crystalline: Well-defined shape and melting point.
• Amorphous: Irregular structure, softer, and lower melting range.
• Impacts drug solubility and bioavailability.
• Example: Crystalline paracetamol is more stable than amorphous.
Sources of Organic Compounds
 Organic compounds originate from various natural and synthetic sources. Their origin
determines their structure, function, and application in pharmaceuticals, food, agriculture,
and industry.
1. Natural Sources:
These are organic compounds obtained directly from living organisms or natural materials.
a. Plants (Phytochemicals)
• Produce alkaloids, flavonoids, tannins, glycosides, terpenoids.
• Widely used in herbal medicine and drug discovery.
Example:
i. Morphine (from Papaver somniferum)
ii. Quinine (from Cinchona bark)
b. Animals
• Provide steroids, hormones, enzymes, fatty acids, and proteins.
• Some compounds are biologically active and used in drug synthesis.
Example:
i. Cholesterol (precursor for steroid hormones)
ii. Heparin (anticoagulant from animal tissues)
c. Microorganisms
• Bacteria, fungi produce antibiotics, toxins, vitamins.
• Many secondary metabolites are used in pharmaceuticals.
Example:
i. Penicillin (from Penicillium fungus)
ii. Streptomycin (from Streptomyces griseus)
d. Marine Sources
• Marine organisms like sponges, corals, and algae produce unique bioactive compounds.
• A growing field for discovering anticancer, antiviral, and anti-inflammatory agents.
Example:
i. Bryostatin (from marine bryozoans)
ii. Ecteinascidin (anticancer agent from sea squirts)
2. Synthetic Sources
These are man-made compounds, prepared in labs using organic reactions. Synthetic
methods allow large-scale production and structural modification.
a. Petrochemicals (Petroleum and Natural Gas)
• Primary industrial source of organic chemicals like alkanes, alkenes, aromatics.
• Used to manufacture plastics, solvents, dyes, and drugs.
Example:
i. Benzene → Aniline → Paracetamol
ii. Ethylene → Ethanol → Ethyl acetate
b. Coal and Coal Tar
• Provides aromatic hydrocarbons and phenols.
• Historically important for producing dyes, explosives, and analgesics.
Example:
i. Phenol → Aspirin
ii. Naphthalene → Synthetic dyes
c. Laboratory Synthesis
• Organic compounds are systematically designed and synthesized using organic reactions.
• Allows development of new drugs, polymers, and materials.
• Key in structure-activity relationship (SAR) studies and medicinal chemistry.
Example:
i. Sulfonamides, barbiturates, benzodiazepines—all synthetically derived drugs.
3. Biotechnological Sources
• Involves genetic engineering, enzyme-based synthesis, and fermentation.
• Offers greener and more efficient production of complex molecules.
Example:
i. Recombinant insulin from genetically modified E. coli
ii. Vitamin B12 produced by fermentation
4. Renewable Sources
• Derived from biomass, agricultural waste, and biofuels.
• Supports sustainable synthesis of organic molecules.
Example:
i. Ethanol from fermentation of sugars
ii. Lactic acid from starch fermentation
Inorganic vs organic compounds
Carbocation
Carbanion ions
Electrophiles
Nucleophiles
Free radicals
Electronegativity in bonds
Polarity of molecules
Intermolecular force
Sources
• https://www.britannica.com/science/chemistry
• https://psiberg.com/organic-vs-inorganic-compounds/
• https://byjus.com/chemistry/aromatic-compounds/
• https://en.wikipedia.org/wiki/Heterocyclic_compound
• https://en.wikipedia.org/wiki/Carbonium_ion
• https://en.wikipedia.org/wiki/Carbanion
• https://en.wikipedia.org/wiki/Radical_(chemistry)
• https://openoregon.pressbooks.pub/introductoryorganic/chapter/intermolecu
lar_forces/