UNIT-VIII: DRUG DESIGN
Drug discovery process
In medicine, biotechnology, and pharmacology, drug discovery is the process by which drugs are discovered and/or designed. In the past most drugs have been discovered either by identifying the active ingredient from traditional remedies using natural resources or by serendipitous discovery.
A new approach has been to understand how disease and infection are controlled at the molecular and physiological level and to target specific entities based on this knowledge.
The combinatorial process of drug discovery involves the identification of candidates, synthesis, characterization, screening, and assays for therapeutic efficacy. Once a compound has shown its value in these tests, it will begin the process of drug development prior to clinical trials.
It would seem modern combinatorial approach to drug discovery may soon prove to be so effective at producing active ingredients that there is virtually no need to seek new drug leads from plants or other natural resources in disappearing tropical forests. But is this really the case.
•Researcher first select or discover a biological target such as a particular enzyme, receptor or ion channel that the scientific team believes may be linked to a pathological process.
2. Target Validation
It involves demonstration of relevance of the target protein in a disease process.
3. Drug selection
•Tens of thousands of potential drug substances (obtained from massive compound libraries) are tested against the target proteins in a robotic process called High Throughput Screening (HTS).
4. High throughput Screening
•High Throughput Screening yields Hit compounds that are further studied in detail for their physical, chemical and biological properties.
•Hit compounds with suitable physical, chemical and biological properties are called Lead Candidates.
5. Lead Optimization
Lead Candidates are then chemically modified and pharmacologically characterized to obtain compounds with suitable pharmacodynamicand pharmacokinetic properties to become a drug.
The compounds with best profile is then chosen for further investigation in the form of preclinical and clinical testing.
Target identification and validation
lead optimization and validation
Drug discovery process
In medicine, biotechnology, and pharmacology, drug discovery is the process by which drugs are discovered and/or designed. In the past most drugs have been discovered either by identifying the active ingredient from traditional remedies using natural resources or by serendipitous discovery.
A new approach has been to understand how disease and infection are controlled at the molecular and physiological level and to target specific entities based on this knowledge.
The combinatorial process of drug discovery involves the identification of candidates, synthesis, characterization, screening, and assays for therapeutic efficacy. Once a compound has shown its value in these tests, it will begin the process of drug development prior to clinical trials.
It would seem modern combinatorial approach to drug discovery may soon prove to be so effective at producing active ingredients that there is virtually no need to seek new drug leads from plants or other natural resources in disappearing tropical forests. But is this really the case.
Process of generating a new idea that is targeted towards chemically modifying a disease process via a drug.
The idea is usually generated from a comprehensive understanding of a disease process and a continuing involvement with research in specific therapeutic areas of interest.
The drug discovery process involves the following steps :
•Target Selection
•Target Validation
•Lead Selection
•Lead Optimization
•Pre-Clinical and Clinical Testing
•New Drug
1. Target Selection
•It involves choosing a disease to treat and then developing a model for that disease.
2. Target Validation
It involves demonstration of relevance of the target protein in a disease process.
3. Drug selection
•Drug Selection or Lead Selection is a process that involves finding a drug or group of drugs which has the ability to interact with target protein and modulate its activity.
•Tens of thousands of potential drug substances (obtained from massive compound libraries) are tested against the target proteins in a robotic process called High Throughput Screening (HTS).
4. High throughput Screening
•High Throughput Screening yields Hit compounds that are further studied in detail for their physical, chemical and biological properties.
•Hit compounds with suitable physical, chemical and biological properties are called Lead Candidates.
5. Lead Optimization
Lead Candidates are then chemically modified and pharmacologically characterized to obtain compounds with suitable pharmacodynamicand pharmacokinetic properties to become a drug.
The compounds with best profile is then chosen for further investigation in the form of preclinical and clinical testing.
Role of bioinformatics in drug design
Bioinformatics heralds beginning of new era in the most complex and challenging world of life sciences research that has witnessed dramatic increase in the data volume with the novel application of computational skills and statistical methods for analysis and for modelling. Bioinformatics is the answer for better and faster progress in research.
Bioinformatics with the use of advanced computational technologies allows us to gather, store, analyze, integrate and represent genetic information effectively. It Bioinformatics is associated typically with massive databases of gene and protein structure and function. It also does comparative analysis using remote computer access.
Exponential growth of biological data requires huge amount of storage space and high speed interpretation. This is possible only by computers. Studies on genomes have brought in a surge of information and that is growing every day. The data also needs to be interpreted as in DNA chips and microarrays. Speed computational cataloguing and retrieval of this information has become pertinent in all fields be it medical literature, understanding metabolic pathways, interpreting protein 3D structure, study of phylogeny, pharmacogenetics, drug designing, comparative genomics or agriculture.
Management of these complex datasets is becoming a bottleneck to scientific advances. By giving a global perspective, Bioinformatics can play a pivotal role for biologists.
Scope of bioinformatics
- Improvement in drug designing to suit individual needs, through personalised genomic medicine using clinical informatics.
- Microbial genome research for Bio fuel and environmental clean up
- More accurate risk assessment by gene mapping
- To be able to analyse data in forensics
- Yield better crops
- To improve economy by all the above
Target identification and validation
In medicine, biotechnology,
and pharmacology, drug discovery is generally thought of as the discovery, creation,
or design of a compound or a complex that possesses the potential to become a
useful therapeutic. It is really an expensive, time-consuming, and difficult process
that involves the identification of candidates and synthesis, characterization,
screening, and assays of their therapeutic efficacy. The word ‘target’ has been
widely used in both medical and pharmaceutical research. However, the
definition of “target” itself is vague and is debated within the pharmaceutical
industry. The number of drug targets is also controversial, due in large degree
to disputes over the definition of what a target is. The exact connotation of
the term “drug target” needs to be elucidated. Target validation is the first
step in completely new drug discovery. Validation of new drug targets is the
process of physiologically, pathologically, and pharmacologically evaluating a biomolecule
and might be performed at the molecular, cellular, or whole animal level.
What
are drug targets?
Target
identification and validation are the first key stages in the drug discovery
pipeline (9). But what is a drug target? Generally speaking, a drug
target is the specific binding site of a drug in vivo through which the
drug exerts its action. A specific drug target might have the following
characteristics:
1) The drug target
is a biomolecule(s), normally a protein that could exist in isolated or complex
modality.
2)The biomolecules
have special sites that match other molecules (commonly small molecules with
special structures). These molecules could be endogenous or extraneous substances
such as chemical molecules (drugs).
3) The biomolecular
structure might change when the biomolecule binds to small molecules and the
changes in structure normally are reversible.
4) Following the
change in the biomolecule’s structure various physiological responses occur and
induce regulation of the cell, organ, tissue, or body status.
5)The physiological
responses triggered by the changes in biomolecule structure play a major role
in complex regulation and have a therapeutic effect on pathological conditions.
6) The expression,
activity, and structure of the biomolecule might change over the duration of the
pathological process.
7) Small molecules
binding to the biomolecules are drugs.
As is apparent from
the above discussion, a drugtarget is a key molecule involved in a particular metabolic
or signal transduction pathway that is specific to a disease condition or a
specific disease. However, the term ‘drug target’ itself has several
limitations and is debated within the pharmaceutical industry. In this respect,
several points should be kept in mind. First, a drug target is a relative concept.
For starters, a drug target is, just like other biomolecules, also a biomolecule
involved in a transduction pathway. The difference between the two is only in
their location and role in the transduction pathway. Another aspect is that a
drug target is disease-dependent, that is, every target is involved in a
special spectrum of diseases. Second, most human diseases are rather
complicated and involve many risk factors, so there are clearly many different
drug targets with respect to a specific disease. Targeting a specific target could
not conceivably cure a kind of disease. However, the involvement of many targets
in a disease does not mean that each target shares equally in the pathogenesis
of the disease and thus drugs targeting these targets would not be equally
effective in the therapy of the disease.
Third, drug targets
can change, which means that with the development of insights into biomolecules
and their role in the pathogenesis of a certain disease, drug targets might be
not as important as or may be much more important than currently believed. In
fact, the establishment of drug targets is based on understanding of the
pathogenesis of the disease. Fourth, there are many drugs targeting the same target
and one drug may have more than one target. The relationship between a drug and
its target is not one-to-one but one-to-many or many-to-one.
Fifth, when a new
drug target is discovered and validated, researchers usually hope to obtain
more specific drugs targeting the target. However, a key understanding to keep
in mind is that the body is a subtle organism and a more specific drug might disrupt
the homeostasis of the body. Compared to aspirin, rofecoxib is a specific COX-2
inhibitor. However, studies had shown that rofecoxib increases cardiovascular
risks, resulting in rofecoxib’s withdrawal from the drug market. Sixth, a drug
target usually refers to a single biomolecule. This connotation should be
revised.
Recent research has
noted that a complex, like HDL, for example, or even a kind of cell, like an
endothelial cell, could be a potential drug target. However, drug target validation
based on this concept is very difficult since reliable, accurate, and robust
indexes to evaluate the effect of drugs targeting these targets are rare. According
to whether there are drugs available, a drug target can be classified into two
classes: established drug targets and potential drug targets. The former are those
for which there is a good scientific understanding, supported by a lengthy
publication history regarding both how the target functions in normal
physiology and how it is involved in human pathology. Furthermore, there are
many drugs targeting this target. The latter are those biomolecules whose
functions are not fully understood and which lack drugs targeting them. Potential
targets suggest directions for completely new drug research.
How
many drug targets are there?
With the development
of modern science and technology, humans became more informed about themselves
than at any time in history. Thousands of drugs had been discovered and
created. However, the mechanisms of their action and the targets of their action
were poorly understood. Furthermore, the number of drug targets in the body is
less consistent than the definition of a drug target. How many drug targets are
there in the body? Drews and Reiser were the first to systematically pose and
answer this question, identifying 483 drug targets. Later, Hopkins and Groom revised
this figure downward to only 120 underlying molecular targets. Subsequently,
Golden proposed that all then-approved drugs acted through 273 proteins. By contrast,
Wishart et al. reported 14,000 targets for all approved and experimental
drugs, although they revised this number to 6,000 targets on the Drug Bank
database
website. Imming et
al. catalogued 218 molecular targets for approved drug substances, whereas Zheng et al. cited 268 ‘successful’
targets in the current version of the Therapeutic Targets Database. John et
al. proposed a consensus number of 324 drug targets for
all classes of
approved therapeutic drugs. With thepublication of draft maps of the human
genome and an interim agreement that the human genome consists of approximately
21,000 genes, there has been considerable anticipation that many novel
disease-specific molecular
targets will be
rapidly identified and that these will form the basis of many new drug
discovery programe. According to the current definition, one could rationally predict
that there are 5,000 to 10,000 established and potential drug targets in humans.
Target
validation
New target
validation is the basis of completely new drug exploration and the initial step
of drug discovery. New drug target validation might be of great help not only
to new drug research and development but also provide more insight into the
pathogenesis of targetrelated diseases. Basically, the target validation
process might include six steps:
1. Discovering a
biomolecule of interest.
2. Evaluating its
potential as a target.
3. Designing a
bioassay to measure biological activity.
4. Constructing a
high-throughput screen.
5. Performing
screening to find hits.
6. Evaluating the
hits.
The drug discovery
process starts with the identification, or growing evidence of, biological
targets that are
believed to be connected to a particular condition or pathology. Information
supporting the role of these targets in disease modulation can come from a
variety of sources. Traditionally, the targets have been researched and largely
discovered in academic laboratories, and to a lesser extent in the laboratories
of pharmaceutical and biotechnology companies. Basic research into understanding
the fundamental, essential processes for signaling within and between cells and
their perturbation in conditions has been the basic approach for establishing
potential targets suitable for drug intervention.
After the identification
of a biological target of interest, the next challenge begins with the
conversion of the target into a bioassay that can give a readout of biological
activity. The range of potential targets is large, from enzymes and receptors
to cellular systems that represent an entire biochemical pathway or a disease
process. Consequently, the range of assay design techniques and types of assay
available have to be correspondingly comprehensive. Once an assay that measures
the biological activity of the target, by some direct or indirect means, has
been developed, then compounds can be tested in the bioassay to see if they inhibit,
enhance, or do nothing to this activity.
After a bioassay to
measure biological activity is designed, the next key step is the establishment
of a high-throughput screening (HTS) method. The basic requirements for HTS assay
are that it be sensitive, stable, highly reproducible, and robust and suitable for
screening thousands or even millions of samples. With sufficient luck, several ‘hit’
compounds will be
discovered by
primary screening.The ‘hit’ compounds must be rescreened to exclude false
positive results. Then, the next step is ‘hit’ identification, which may
include its chemical characteristics, i.e. mainly its stability, its
toxicity in vivo and in vitro, and its pharmacological
evaluation, and particularly its effects in cells and animal models.
Three levels: the
molecular level, the cellular level, and the whole animal model level. Small chemicals
obtained from HTS provide useful tools for the validation of new drug targets.
Most HTS models are at the molecular level, that is, cell-free systems. For
example, screening of a specific enzyme inhibitor usually involves mixing the
enzyme and samples
together to detect
a decrease in the substrate or to determine an increase in the product in this
enzyme catalytic process. The results obtained from this level are not
absolutely reliable since there are many predictable and unpredictable factors.
However, true results from this level convey the point that hits truly act with
the target. There is a significant difference between a cell and cell-free
system. Validation at the cell level provides confirmation of cell-free
results. At this level, the pathological significance of the target might be
rendered more apparent using small chemicals.
The effect of the small
chemicals on a cell system will provide a tentative outline of these chemicals.
Animal models are used to validate the target at the whole level. At this
level, the primary concern is the effect of the ‘hit’. If the hit obtained from
HTS displays a therapeutic
effect in animal models,
then it may be promising. However, more often than not a ‘hit’ displays no
effect in an animal model and the result should be interpreted with caution.
Common shortfalls and/or pitfalls that need to be considered include:
1. Using the wrong
animal model.
2. Using the wrong
route or dosing regimen.
3. Using the wrong
vehicle or formulation of test material.
4. Using the wrong
dose level. In studies where several dose levels are studied, the worst outcome
is to have an effect at the lowest dose level tested (i.e., the safe
dosage in animals remains unknown). The next worst outcome is to have no effect
at the highest dose tested (generally meaning that the signs of toxicity remain
unknown, invalidating the study in the eyes of many regulatory agencies).
5. Making leaps of
faith. An example is to set dosage levels based on others’ data and to then
dose all test animals. Ultimately, all animals at all dose levels die, the
study ends, and the problem remains.
6. Using the wrong concentration
of test materials in screening. Many effects are very concentration dependent.
lead optimization and validation
Drug
Discovery Screening
Once a biochemical or cell-based assay has been
developed successfully, the lead identification, or screening, process begins.
Primary screens identify hits. Subsequently, confirmation screens and counter
screens identify leads out of the pool of hits. This is commonly referred to as
the "hit-to-lead" process. The success of drug discovery screening
depends on the availability of compounds, as well as their quality and
diversity. Efforts to synthesize, collect, and characterize compounds are an
essential and costly part of drug discovery.
Primary
Screens
The goals of primary screens are to minimize the
number of false positives and maximize the number of confirmed hits. Typically,
primary screens are run in multiplets (i.e., two, three, or more) of single
compound concentrations. Readouts are expressed as percent activity in
comparison to positive and negative controls. Hits are retested independently
of the first assay. If a compound exhibits the same activity within a
statistically significant range, it is termed a confirmed hit. The next step is
dose-response screening, typically referred to as a secondary screen.
Secondary
Screens
In a secondary screen, a range of compound
concentrations is tested in an assay to assess the concentration or dose
dependence of the assay's readout. Typically, this dose-response is expressed
as an IC50 in enzyme-, protein-, antibody-, or cell-based assays, or as an EC50
in in vivo experiments. The shape of a dose-response curve often provides
information about the mechanism of action.
Confirmed hits are then profiled or run through a
series of counterscreens. These assays usually include drug targets of the same
protein or receptor family; for example, panels of GPCRs or kinases. These
screens profile the action of a confirmed hit on a defined spectrum of
biological target classes. Counterscreens can also be used to confirm mechanism
of action.
Mechanism
of Action
One of the goals throughout the discovery of novel
drugs is to establish and confirm the mechanism of action. In an ideal scenario,
the mechanism of action remains consistent from the level of molecular
interaction of a drug molecule at the target site through the physiological
response in a disease model.
Molecular Devices provides a range of bioanalytical
systems to support primary and secondary screening, compound profiling, and
mechanism of action studies.
Lead optimization is a complex, non-linear process.
During this stage of drug discovery, the chemical structure of a confirmed hit
is refined to improve its drug characteristics with the goal of producing a
preclinical drug candidate.
Typically, confirmed hits are evaluated in secondary
assays, and a set of related compounds, called analogs, are synthesized and
screened. The testing of analog series results in quantitative information that
correlates changes in chemical structure to biological and pharmacological data
to establish structure-activity relationships (SARs).
Today, lead optimization often involves a series of
standard assays to evaluate toxicity, including P450 inhibition, cytotoxicity
assays, and hERG testing. Toxicity in these relatively simple in vitro assays
flags hits or leads that could have potential safety concerns.
Another characteristic that lead optimization often
evaluates is formulation. Formulation and delivery are closely linked. For
example, a drug intended to be delivered via intramuscular injection might call
for a different formulation than would one intended for oral delivery.
Formulation problems and solutions feed back into the iterative lead
optimization cycle.
Lead identification/optimization is the one of the
most important steps in drug development. The chemical structure of the lead
compound is used as a starting point for chemical modifications in order to
improve potency, selectivity, or pharmacokinetic parameters. Once a molecule is
identified, the next step is to check its ADMET (Adsorption, Distribution,
Metabolism, Excretion and Toxicity) properties. If the molecule has no toxicity
and no mutagenicity either, it has potential for use as lead molecule. Further
optimization gives better quality of lead molecules. These may subsequently be
developed as drug(s).