DISCOVERY OF LEAD COMPOUNDS

A Lead Compound is a chemical compound that demonstrates sufficient

biological or pharmacological activity against a specific target to warrant further
development. Leads are the starting points for drug development and undergo
extensive modification to improve their drug-like properties.
Characteristics of a Good Lead:
• Potency: Exhibits significant activity at low concentrations.
• Selectivity: Specifically interacts with the intended target with minimal
off-target effects.
• Drug-Likeness: Adheres to properties that make it suitable for
development into a drug (e.g., Lipinski's Rule of Five).
• Synthetic Accessibility: Can be synthesized efficiently for further
modification and production.
• Safety Profile: Displays low toxicity in initial assessments
The identification of lead compounds can happen through several different
approaches, each with its strengths and weaknesses.
1. Random Screening
This is one of the earliest methods used in drug discovery, particularly before the
advent of modern techniques like structure-based drug design. In random
screening, large libraries of compounds are tested against biological targets to
identify hits that demonstrate some degree of desirable activity. This approach
doesn’t rely on prior knowledge about the target or the compounds being tested,
making it a "shot in the dark" process.
Key Points:
• Definition: The process of randomly testing large numbers of compounds
against specific biological targets (such as enzymes, receptors, or disease
models) to identify hits that exhibit the desired biological activity.
• Process:
 • Chemical Library Creation: Compounds can be sourced from
natural products (e.g., plants, microbes) or synthetic chemicals.
• High-throughput Screening (HTS): This involves automating the
testing of tens of thousands to millions of compounds, using robotic
systems to rapidly assess biological activity.
• Hit Identification: Compounds that show a measurable response in
the assay are identified as "hits."
• Follow-up Testing: Once hits are identified, they undergo further
testing and optimization to improve their activity, selectivity, and
drug-like properties.
• Advantages:
• Broad Exploration of Chemical Space: Random screening can
identify compounds with novel mechanisms of action or new classes
of drugs.
• Serendipity: It has the potential to find unexpected biological
activity, as in the case of penicillin and other naturally occurring
drugs.
• Natural Products: This method has historically led to the discovery
of important drugs derived from natural sources, such as antibiotics
and anticancer agents.
• Limitations:
• Inefficiency: The approach is time-consuming, expensive, and often
leads to a high rate of false positives.
• Low Success Rate: The vast majority of compounds tested will not
be hits, leading to wasted resources.
• Need for High-Throughput Technology: HTS requires
sophisticated instrumentation and infrastructure.
RANDOM SCREENING EXAMPLES
Example 1: Penicillin

• Discovery: Penicillin is an example of random screening because it was

discovered by chance. Alexander Fleming noticed that a mold
(Penicillium) accidentally contaminating a petri dish killed bacteria around
it. This unplanned observation led to the discovery of penicillin’s
antibacterial properties, which were later developed into a widely used
antibiotic.
• Example 2: Streptomycin
• Discovery: . Streptomycin is an example of random screening because it
was discovered through a systematic search for antibiotics. In 1943,
Selman Waksman and his team screened soil bacteria and found that
Streptomyces griseus produced streptomycin, which was effective against
tuberculosis and other bacterial infections. This discovery came from
testing various microorganisms for antibiotic properties without a specific
target in mind.
Example 3: Cyclosporine

Discovery: Cyclosporin is an example of random screening because it was

discovered during a search for antifungal agents. In 1971, scientists isolated it
from a fungus, Tolypocladium inflatum, and while it was initially tested for
antifungal activity, it was later found to have powerful immunosuppressive
properties. This unexpected discovery led to its use in preventing organ transplant
rejection.
2. Non-Random Screening (Focused Screening)
Non-random screening takes a more systematic and informed approach compared
to random screening. Compounds are chosen for testing based on existing
knowledge about the target or the disease, as well as structure-activity
relationships (SAR) of known bioactive molecules. This method increases the
likelihood of success by focusing on compounds with a higher probability of
being active.
• Definition: A targeted approach in which compounds are selected for
screening based on their structural similarity to known active compounds,
or because they are hypothesized to interact with a biological target of
interest.
• Process:
• Knowledge-Based Selection: Compounds are selected based on
their chemical similarity to known drugs, inhibitors, or bioactive
molecules.
• Target-Specific Libraries: Instead of screening an entire chemical
library, focused libraries are developed with compounds that share
key structural motifs with known active compounds.
• Structure-Activity Relationships (SAR): Understanding the
relationship between the chemical structure of compounds and their
biological activity helps prioritize candidates for testing.
• Assay Development: Focused biological assays are designed to test
compounds against specific biological pathways or targets.
• Advantages:
o Increased Probability of Success: By focusing on compounds
similar to those that are already known to work, this method
improves the efficiency of the drug discovery process.
o Cost and Time Efficiency: Fewer compounds need to be screened
compared to random screening, which saves time and reduces costs.
o Application of Existing Knowledge: This approach leverages prior
research, making it more guided and logical.
• Limitations:
 o Limited Chemical Space: The method might miss novel chemical
entities or mechanisms of action outside of known compound
classes.
o Bias Towards Known Compounds: There is a risk of focusing too
narrowly on known drugs or chemical scaffolds, limiting innovation.
NON-RANDOM SCREENING (FOCUSED SCREENING) EXAMPLES

Example 1: Statins (Cholesterol-Lowering Drugs)

• Discovery: Statins, such as lovastatin, were developed by screening

compounds that mimicked a natural fungal metabolite known to inhibit
HMG-CoA reductase, an enzyme involved in cholesterol synthesis. By
focusing on similar compounds, statins were identified as potent
cholesterol-lowering agents.
Example 2: Beta-Lactam Antibiotics

• Discovery: After the success of penicillin, researchers used non-random

screening to search for similar beta-lactam structures from other natural
sources. This led to the discovery of cephalosporins, another class of
antibiotics with similar but improved properties.
Example 3: HIV Protease Inhibitors

• Discovery: Compounds were screened based on their similarity to peptides

that inhibit the HIV protease enzyme. Researchers knew the enzyme's
structure and tested compounds resembling the enzyme's natural
substrates, eventually leading to the development of drugs like ritonavir
and saquinavir.
3. Drug Metabolism Studies

Drug metabolism studies are an important part of drug discovery, where the
metabolic fate of compounds is studied to identify active metabolites, improve
pharmacokinetic properties, or avoid adverse effects. These studies often focus
on how the body processes drugs, identifying breakdown products that may either
enhance or reduce the drug’s efficacy.

Key Points:

• Definition: The study of how a drug is absorbed, distributed, metabolized,

and excreted (ADME) in the body. These studies can help identify active
metabolites that may serve as lead compounds or guide the modification of
existing drugs to improve their properties.
• Process:
o Identification of Metabolites: Once a drug is administered,
researchers study how it is broken down by enzymes in the liver and
other organs. Sometimes, metabolites (the products of this
breakdown) have biological activity that can be optimized.
o Optimization of Drug Candidates: Drugs are often modified to
improve their stability, bioavailability, and half-life, or to reduce
toxicity.
o Prodrug Design: Some compounds are designed as prodrugs, which
become active only after being metabolized in the body. The
metabolite is the actual active agent.
• Advantages:
o Improved Drug Properties: By understanding metabolism, drug
candidates can be modified to improve their therapeutic effects,
reduce side effects, and increase safety.
o Identification of Active Metabolites: These studies can lead to the
discovery of new drugs by focusing on metabolites with better
pharmacological properties than the parent compound.
o Prodrugs: Many drugs are designed to be inactive until
metabolized, optimizing their delivery and reducing side effects.
• Limitations:
 o Limited to Known Compounds: This approach does not usually
lead to novel drug entities unless the metabolite itself is new.
o Complex Metabolism: Drug metabolism varies between
individuals, and animal models may not always accurately predict
human metabolism.
DRUG METABOLISM STUDIES EXAMPLES

Example 1: Morphine from Codeine

• Discovery: Codeine is a less potent opioid, but through metabolism, it is

converted into morphine in the liver. By understanding this metabolic
pathway, morphine was optimized and used as a more effective pain
reliever. Codeine remains in use as a prodrug for morphine.
Example 2: Fexofenadine (Allegra) from Terfenadine

• Discovery: Terfenadine, an older antihistamine, was found to cause

dangerous heart arrhythmias in some patients. Its active metabolite,
fexofenadine, was later isolated and developed as a safer alternative with
the same anti-allergic effects but without the cardiovascular side effects.
Example 3: Active Metabolites of Tamoxifen

• Discovery: Tamoxifen, used to treat breast cancer, is metabolized into

active metabolites like endoxifen, which have even greater potency in
inhibiting estrogen receptors. This understanding led to improved
formulations and the design of new anti-estrogen drugs.
Example 4: Enalapril from Enalaprilat
• Discovery: Enalapril is a prodrug that is converted into its active form,
enalaprilat, in the body. Enalapril became an effective treatment for high
blood pressure.
4. Rational Approach to Lead Discovery
The rational approach is a highly modern and scientific method for drug
discovery. It involves designing and optimizing lead compounds based on a deep
understanding of the biological target’s structure and function. This method
leverages advances in fields like structural biology, computational chemistry, and
molecular modeling to design drugs that specifically interact with target sites.

Key Points:

• Definition: A scientific, knowledge-driven approach to lead discovery, in

which the structure of the biological target (e.g., protein, enzyme) is used
to design compounds that can modulate the target's function.
• Process:
o Target Identification: Researchers first identify a biological target,
such as an enzyme, receptor, or protein involved in a disease.
o Structure Elucidation: Advanced techniques like X-ray
crystallography, nuclear magnetic resonance (NMR), or cryo-
electron microscopy are used to determine the 3D structure of the
target.
o Computational Design: Using computer-aided drug design
(CADD), scientists simulate the binding of small molecules to the
target. Molecular docking and molecular dynamics help predict how
well a compound fits into the target's active site.
Optimization of Lead Compounds: Once potential leads are identified,
medicinal chemists optimize their structure to
• ADVANTAGES:
o Target-Specific: This approach results in highly specific
compounds that are more likely to interact with the target
effectively, reducing off-target effects and side effects.
 o Efficient and Predictive: By starting with a known target structure,
drug discovery becomes more focused and predictive, saving time
and resources.
o Novel Drug Discovery: This approach allows for the discovery of
entirely new chemical entities with unique mechanisms of action.
• LIMITATIONS:
o Requires Detailed Target Knowledge: The target’s structure and
mechanism must be well-understood, which is not always possible.
o Technologically Intensive: The rational approach requires
expensive technology, computational tools, and expertise.
o Not Applicable to All Targets: Some biological targets are not
easily amenable to structure-based approaches, limiting the
method’s applicability.
improve potency, selectivity, and pharmacokinetic properties
RATIONAL APPROACH TO LEAD DISCOVERY EXAMPLES
Example 1: Gleevec (Imatinib)
• Discovery: Gleevec was rationally designed to specifically inhibit the
BCR-ABL fusion protein in chronic myeloid leukemia (CML). By
knowing the structure of this abnormal protein, scientists created a
molecule that fit precisely into its active site, leading to targeted cancer
therapy.
Example 2: ACE Inhibitors (Captopril)
• Discovery: Angiotensin-converting enzyme (ACE) was identified as a key
player in blood pressure regulation. Using the enzyme's structure,
researchers designed captopril, the first ACE inhibitor, which effectively
lowers blood pressure by blocking the enzyme’s activity.
Example 3: Relenza (Zanamivir)
• Discovery: The structure of the neuraminidase enzyme in the influenza
virus was studied, and researchers used this information to design
 zanamivir (Relenza), a drug that blocks the enzyme and prevents the virus
from spreading in the body.

LEAD MODIFICATION
Lead Modification involves the systematic alteration of the chemical structure
of a lead compound to enhance its properties and transform it into a viable drug
candidate. This step is crucial for several reasons:
• Enhancing Efficacy: Increasing the compound's ability to achieve the
desired therapeutic effect.
• Improving Selectivity: Reducing interactions with unintended targets to
minimize side effects.
• Optimizing Pharmacokinetics (ADME): Ensuring the drug is well-
absorbed, distributed to the target tissues, metabolized appropriately, and
excreted without causing harm.
• Reducing Toxicity: Minimizing adverse effects to improve the safety
profile.
• Increasing Stability: Enhancing chemical and metabolic stability to
ensure the drug remains effective throughout its shelf-life and within the
body.
• Facilitating Drug Formulation: Making the compound suitable for
various delivery methods (e.g., oral, intravenous).
Effective lead modification accelerates the transition from a promising compound
to a drug candidate ready for preclinical and clinical testing.
LEAD MODIFICATION
The three key strategies for lead modification are:
1. Pharmacophore Identification
2. Modification of Structure or Functional Group
3. Structure-Activity Relationship (SAR)
Steps in Pharmacophore Identification
• Step 1: Analyze the active lead compound: Study how the lead interacts
with the target to determine which parts of the molecule are essential for
activity.
• Step 2: Develop a pharmacophore model: A simplified model is created
showing the key features responsible for binding to the target.
• Step 3: Test variations: Create analogs by modifying parts of the lead
compound that do not affect activity and test their biological effects.
• Step 4: Optimize structure: Once the pharmacophore is identified,
modifications are made to improve drug properties like potency and
selectivity.
Applications of Pharmacophore Identification
• Lead Optimization: Use the pharmacophore model to modify lead
compounds:
• Substitution: Replace functional groups to enhance binding affinity.
• Addition: Add new functional groups that complement the
pharmacophore.
• Conformation Changes: Adjust the conformation of the molecule
to better fit the target.
• Virtual Screening: Employ the pharmacophore model in virtual screening
to identify new compounds that may possess similar or improved activity.
Why Pharmacophore Identification is Important:

Identifying the pharmacophore allows drug designers to focus on the key

features required for biological activity, while optimizing the rest of the
molecule to enhance potency, selectivity, and reduce side effects