CHAPTER 1:
The Drug Development Continuum, Preclinical to Market Access
Regulatory Affairs Professionals Society 7
Step 1: Discovery
Discovery research is the first step in the development continuum.
Historically, discovery involved identifying active ingredients in
traditional medicines or simply by chance. An example is the dis-
covery of penicillin by Alexander Fleming in 1928. Fleming was
investigating staphylococcus bacteria, and a speck of dust contami-
nated one of his petri dishes. Around the resulting patch of mold,
a clear, bacteria-free zone formed, which Fleming later identified
as containing the world-changing antibiotic penicillin.
Later, large libraries of small molecules or herbal products were
screened against established drug targets to identify those binding
with high affinity, indicating a potential therapeutic effect.
With the completion of the sequencing of the human ge-
nome, reverse pharmacology has become the preferred way of
identifying new compounds. Here, the first step is the develop-
ment of a hypothesis that the modulation of the activity of a spe-
cific target in the human body has a disease-modifying effect.
Then, based on this hypothesis, the selected target is characterized
in depth, and compounds are tailor-made in the lab to fit the tar-
get. Finally, screening processes test large libraries of compounds
for their affinity, potential efficacy, and safety.18
Traditionally, the discovery has included the following five
steps:
1. Target Identification and Validation
The first step in the discovery phase is identifying a therapeutic
target that plays a significant role in the disease process. A good
target involves a crucial biological pathway, distinct from any pre-
viously known target, extensive functional and structural charac-
terization, and druggability. Druggability is characterized by
having a well-accessible binding site and being capable of binding
standard therapeutic molecules (e.g., small molecules, biologics).
Therapeutic drug targets can be identified via publicly available li-
braries, such as the Sanger Whole Genome CRISPR Library or
the HEAL Targets and Compounds Library. Most known drug
targets are proteins however, many other biomolecules have been
validated as targets. An example is ribonucleic acid (RNA), a key
target for antisense oligonucleotides.
The therapeutic target is then further validated. Target vali-
dation involves establishing a clear link between the target and the
disease, which confirms the functional role of the chosen target in
the disease phenotype and confirms that its modification has a
therapeutic effect. An example of an established disease target is
the Human Epidermal Growth Factor Receptor 2 (HER2), an
epidermal tyrosine kinase that plays a pivotal role in the etiology of
certain types of breast, ovarian, and gastric cancers. This receptor
is targeted by a broad range of marketed monoclonal antibodies
and small molecules (e.g., Herceptin, Tykerb). By interaction with
the HER2 receptor, these compounds prevent the activation of
signaling pathways that further enhance the proliferation of malig-
nant growth.
A typical technique to validate targets is by elucidation of
their function. One such approach is the use of mRNA modula-
tion to suppress gene expression of the chosen target. A drug
sponsor can confirm whether the target merits further develop-
ment by observing the phenotypic effect that results from a de-
crease in the expressed target.18
2. Assay Development and Screening
Following target validation, compound screening assays are devel-
oped. These screening assays are tests that evaluate the effects of the
new drug candidate at the cellular, molecular, and biochemical lev-
els. One example is the enzyme-linked immunosorbent assay
(ELISA), which in its simplest form applies a matching antibody to
the targeted antigen so that it can bind to it. The antibody is linked
to an enzyme, and in a following step, the enzyme’s substrate is
added. If the antibody shows a high affinity to the antigen and bind-
ing occurs, a subsequent reaction produces a detectable signal (usu-
ally a color change), which can also be assessed quantitatively.
Assay development can be a very long and time-consuming
process – from several weeks to 6 months – because standard as-
says often need to be adapted to the smaller volumes used in high
throughput screening (HTS), where processes are conducted in
microtiter plates of high density.18
3. High Throughput Screening
HTS uses robotics, data processing/control software, and sophisti-
cated detection mechanisms to rapidly conduct thousands of phar-
macological, chemical, and genetic tests, such as ELISA, flow
cytometry, fluorescence polarization, and clustered regularly inter-
spaced palindromic repeats (CRISPR)-based tests for gene-based
therapies. HTS assesses large libraries of compounds for their af-
finity to the chosen target.
HTS data are then analyzed to determine and refine further
structure-activity relationships. In addition, these screens also pro-
vide preliminary information about which compounds are nonse-
lective, cytotoxic, and potentially genotoxic and should be
eliminated from further screening.18
4. Hit to Lead
In the hit to lead process, compounds that gave a hit (i.e., were
found to have a high affinity against the investigated target) are
evaluated and structurally pre-optimized into lead compounds.18
5. Lead Optimization
In the lead optimization process, the lead compounds discovered
in the hit to lead process are resynthesized and further modified to
improve affinity and reduce side effects. Potential properties such
as potency (strength), efficacy, selectivity, or bioavailability are im-
proved during the lead optimization process. In addition, lead op-
timization includes experimental testing using animal efficacy
models and in silico tools to predict the absorption, distribution,
The Drug Development Continuum, Preclinical to Market Access
Regulatory Affairs Professionals Society 7
Step 1: Discovery
Discovery research is the first step in the development continuum.
Historically, discovery involved identifying active ingredients in
traditional medicines or simply by chance. An example is the dis-
covery of penicillin by Alexander Fleming in 1928. Fleming was
investigating staphylococcus bacteria, and a speck of dust contami-
nated one of his petri dishes. Around the resulting patch of mold,
a clear, bacteria-free zone formed, which Fleming later identified
as containing the world-changing antibiotic penicillin.
Later, large libraries of small molecules or herbal products were
screened against established drug targets to identify those binding
with high affinity, indicating a potential therapeutic effect.
With the completion of the sequencing of the human ge-
nome, reverse pharmacology has become the preferred way of
identifying new compounds. Here, the first step is the develop-
ment of a hypothesis that the modulation of the activity of a spe-
cific target in the human body has a disease-modifying effect.
Then, based on this hypothesis, the selected target is characterized
in depth, and compounds are tailor-made in the lab to fit the tar-
get. Finally, screening processes test large libraries of compounds
for their affinity, potential efficacy, and safety.18
Traditionally, the discovery has included the following five
steps:
1. Target Identification and Validation
The first step in the discovery phase is identifying a therapeutic
target that plays a significant role in the disease process. A good
target involves a crucial biological pathway, distinct from any pre-
viously known target, extensive functional and structural charac-
terization, and druggability. Druggability is characterized by
having a well-accessible binding site and being capable of binding
standard therapeutic molecules (e.g., small molecules, biologics).
Therapeutic drug targets can be identified via publicly available li-
braries, such as the Sanger Whole Genome CRISPR Library or
the HEAL Targets and Compounds Library. Most known drug
targets are proteins however, many other biomolecules have been
validated as targets. An example is ribonucleic acid (RNA), a key
target for antisense oligonucleotides.
The therapeutic target is then further validated. Target vali-
dation involves establishing a clear link between the target and the
disease, which confirms the functional role of the chosen target in
the disease phenotype and confirms that its modification has a
therapeutic effect. An example of an established disease target is
the Human Epidermal Growth Factor Receptor 2 (HER2), an
epidermal tyrosine kinase that plays a pivotal role in the etiology of
certain types of breast, ovarian, and gastric cancers. This receptor
is targeted by a broad range of marketed monoclonal antibodies
and small molecules (e.g., Herceptin, Tykerb). By interaction with
the HER2 receptor, these compounds prevent the activation of
signaling pathways that further enhance the proliferation of malig-
nant growth.
A typical technique to validate targets is by elucidation of
their function. One such approach is the use of mRNA modula-
tion to suppress gene expression of the chosen target. A drug
sponsor can confirm whether the target merits further develop-
ment by observing the phenotypic effect that results from a de-
crease in the expressed target.18
2. Assay Development and Screening
Following target validation, compound screening assays are devel-
oped. These screening assays are tests that evaluate the effects of the
new drug candidate at the cellular, molecular, and biochemical lev-
els. One example is the enzyme-linked immunosorbent assay
(ELISA), which in its simplest form applies a matching antibody to
the targeted antigen so that it can bind to it. The antibody is linked
to an enzyme, and in a following step, the enzyme’s substrate is
added. If the antibody shows a high affinity to the antigen and bind-
ing occurs, a subsequent reaction produces a detectable signal (usu-
ally a color change), which can also be assessed quantitatively.
Assay development can be a very long and time-consuming
process – from several weeks to 6 months – because standard as-
says often need to be adapted to the smaller volumes used in high
throughput screening (HTS), where processes are conducted in
microtiter plates of high density.18
3. High Throughput Screening
HTS uses robotics, data processing/control software, and sophisti-
cated detection mechanisms to rapidly conduct thousands of phar-
macological, chemical, and genetic tests, such as ELISA, flow
cytometry, fluorescence polarization, and clustered regularly inter-
spaced palindromic repeats (CRISPR)-based tests for gene-based
therapies. HTS assesses large libraries of compounds for their af-
finity to the chosen target.
HTS data are then analyzed to determine and refine further
structure-activity relationships. In addition, these screens also pro-
vide preliminary information about which compounds are nonse-
lective, cytotoxic, and potentially genotoxic and should be
eliminated from further screening.18
4. Hit to Lead
In the hit to lead process, compounds that gave a hit (i.e., were
found to have a high affinity against the investigated target) are
evaluated and structurally pre-optimized into lead compounds.18
5. Lead Optimization
In the lead optimization process, the lead compounds discovered
in the hit to lead process are resynthesized and further modified to
improve affinity and reduce side effects. Potential properties such
as potency (strength), efficacy, selectivity, or bioavailability are im-
proved during the lead optimization process. In addition, lead op-
timization includes experimental testing using animal efficacy
models and in silico tools to predict the absorption, distribution,