Novel Approaches in Preclinical Research, Pharmacogenomics, Drug Design and Drug Delivery

- Satish WaghChairman
Basic Chemicals, Cosmetics & Dyes
Export Promotion Council (Chemexcil)

Drug discovery is the process by which new chemical entities are discovered. Historically, drugs were discovered by studying and identifying the active component from traditional remedies. Some have been discovered by serendipity. Later in the classical pharmacology methodology chemical libraries of synthetic small molecules, natural products or extracts were screened in vitro or in vivo to identify substances that have a desirable therapeutic effect. Since the recent past pharmacogenomics has gained lot of significance wherein human genome sequencing is the basis and collated with the pharmacology .

In the modern drug design process High throughput screening is carried out on large compounds libraries against isolated biological targets which are hypothesized to be disease modifying. Hits are then tested in cells and then in animals for efficacy. In the drug development cycle, preclinical development, also named preclinical studies and nonclinical studies, is a stage of research that begins before clinical trials (testing in humans) can begin, and during which important feasibility, iterative testing and drug safety data are collected. The main goals of pre-clinical studies are to determine the safe dose for first-in-man study and assess a product's safety profile. On average, only one in every 5,000 compounds that enters drug discovery to the stage of preclinical development becomes an approved drug. Drug delivery studies have come a long way and have reached very advanced levels of research in drug administration such as thin film, magnetic, self microemulsifying , acoustic , neural .

The Drug Discovery Cycle

Modern drug discovery involves the identification of screening hits, and optimization of those hits to increase the affinity, selectivity, efficacy/potency, metabolic stability, and oral bioavailability. The identified compound then undergoes the process of drug development prior to clinical trials. Some steps may involve computer-aided drug design.

Modern drug discovery is a capitalintensive process. However despite advances in technology and understanding of biological systems, drug discovery is still a cumbersome process with low chances of new therapeutic discovery. A singIe new molecular entity (NME) cost was approximately USD 2.0 Billion. Drug discovery is done by pharmaceutical companies, with research assistance from universities. The drug requires very expensive Phase I, II and III clinical trials, and most of them fail. Small companies have a critical role, often then selling the rights to larger companies that have the resources to run the clinical trials.

Discovering drugs that may be a commercial success, or a public health success, involves a complex interaction between investors, industry, academia, patent laws, regulatory exclusivity, marketing and the need to balance secrecy with communication. A drug discovery process ends up in a patent on the potential drug.

The Drug Discovery Techniques

The modern era in pharmacology began with the idea that the effect of a drug in the human body is mediated by specific interactions of the drug molecule with

Figure 1: Drug Discovery Cycle

biological macromolecules, (proteins or nucleic acids in most cases) led scientists to the conclusion that individual chemicals are required for the biological activity of the drug. Thus pure chemicals, instead of crude extracts, became the standard drugs. Morphine, the active agent in opium, and digoxin, a heart stimulant originating from Digitalis lanata are Examples of drug compounds isolated from crude preparations. Organic chemistry also led to the synthesis of many of the natural products isolated from biological sources.

In Classical pharmacology, forward pharmacology or phenotypic drug discovery. historically substances, whether crude extracts or purified chemicals were screened for biological activity without knowledge of the biological target. Only after an active substance was identified was an effort made to identify the target. Small molecules were synthesized to specifically target a known physiological/pathological pathway, rather than adopt the mass screening of banks of stored compounds. This led to great success, such as the work of Gertrude Elion and George H. Hitchings on purine metabolism, the work of James Black on beta blockers and cimetidine, and the discovery of statins by Akira Endo .

Another champion of the approach of developing chemical analogues of known active substances was Sir David Jack at Allen and Hanbury's, later Glaxo, who pioneered the first inhaled selective beta2-adrenergic agonist for asthma, the first inhaled steroid for asthma, ranitidine as a successor to cimetidine, and supported the development of the triptans. Gertrude Elion, working mostly with a group of fewer than 50 people on purine analogues, contributed to the discovery of the first anti-viral; the first immunosuppressant (azathioprine) that allowed human organ transplantation; the first drug to induce remission of childhood leukaemia; pivotal anti-cancer treatments; an anti-malarial; an anti-bacterial; and a treatment for gout.

Cloning of human proteins made possible the screening of large libraries of compounds against specific targets thought to be linked to specific diseases. This approach is known as reverse pharmacology and is the most frequently used approach today. Thus a paradigm shift has occurred in the drug design methodology.

The drug target is usually the naturally existing cellular or molecular structure involved in the pathology of interest that the drug-in-development is meant to act on. There are two types of drug targets, established and new. "Established targets" are those for which there is a good scientific understanding, supported by a lengthy publication history, of both how the target functions in normal physiology and how it is involved in human pathology. target is fully understood. Rather, "established" relates directly to the amount of background information available on a target, in particular functional information. The process of gathering such functional information is called target validation in pharmaceutical industry parlance.

Established targets also include those that the pharmaceutical industry has had experience mounting drug discovery campaigns against in the past; such a history provides information on the chemical feasibility of developing a small molecular therapeutic against the target and can provide licensing opportunities and freedom-to-operate indicators with respect to small-molecule therapeutic candidates.

"New targets" are all those targets that are not "established targets" but which have been or are the subject of drug discovery campaigns. These typically include newly discovered proteins, or proteins whose function has now become clear as a result of basic scientific research.

The majority of targets currently selected for drug discovery efforts are proteins. Two classes predominate: G-proteincoupled receptors (or GPCRs) and protein kinases.

In this decade to date an estimated 435 human genome products were identified as therapeutic drug targets of FDAapproved drugs.

1) High Throughput Screening

The process of finding a new drug against a chosen target for a particular disease usually involves high-throughput screening (HTS), wherein large libraries of chemicals are tested for their ability to modify the target. For example, if the target is a novel GPCR, compounds will be screened for their ability to inhibit or stimulate that receptor (see antagonist and agonist): if the target is a protein kinase, the chemicals will be tested for their ability to inhibit that kinase.

Another important function of HTS is selectivity ie to show how selective the compounds are for the chosen target. To this end, other screening runs will be made to see whether the "hits" against the chosen target will interfere with other related targets - this is the process of cross-screening. Cross-screening is important, because the more unrelated targets a compound hits, the more likely that off-target toxicity will occur with that compound once it reaches the clinic.

It is more often observed that several compounds are found to have some degree of activity, and if these compounds share common chemical features, one or more pharmacophores can then be developed. At this point, medicinal chemists will attempt to use structureactivity relationships (SAR) to improve certain features of the lead compound:

• increase activity against the chosen target
• reduce activity against unrelated targets
• improve the drug likeness or ADME properties of the molecule.

This process will require several iterative screening runs, during which, it is hoped, the properties of the new molecular entities will improve, and allow the favored compounds to go forward to in vitro and in vivo testing for activity in the disease model of choice.

While HTS is a commonly used method for novel drug discovery, it is not the only method. It is often possible to start from a molecule which already has some of the desired properties. Such a molecule might be extracted from a natural product or even be a drug on the market which could be improved upon (so-called "me too" drugs). Other methods, such as virtual high throughput screening, where screening is done using computer-generated models and attempting to "dock" virtual libraries to a target, are also often used.

2) Drug Design

Another important method for drug discovery is drug design, whereby the biological and physical properties of the target are studied, and a prediction is made of the sorts of chemicals that might (e.g.) fit into an active site. One example is fragment-based lead discovery. Novel pharmacophores can emerge very rapidly from these exercises. In general, computer-aided drug design is often but not always used to try to improve the potency and properties of new drug leads.

Once a lead compound series has been established with sufficient target potency and selectivity and favorable drug-like properties, one or two compounds will then be proposed for drug development. The best of these is generally called the lead compound, while the other will be designated as the "backup".

3) Combinatorial Chemistry

Combinatorial chemistry was a key technology enabling the efficient generation of large screening libraries for the needs of high-throughput screening. However, now, after two decades of combinatorial chemistry, it has been pointed out that despite the increased efficiency in chemical synthesis, no increase in lead or drug candidates has been reached. This has led to analysis of chemical characteristics of combinatorial chemistry products, compared to existing drugs or natural products.

The chemo-informatics concept chemical diversity, depicted as distribution of compounds in the chemical space based on their physicochemical characteristics, is often used to describe the difference between the combinatorial chemistry libraries and natural products. The synthetic, combinatorial library compounds seem to cover only a limited and quite uniform chemical space, whereas existing drugs and particularly natural products, exhibit much greater chemical diversity, distributing more evenly to the chemical space.

The most prominent differences between natural products and compounds in combinatorial chemistry libraries are the number of chiral centers (much higher in natural compounds), structure rigidity (higher in natural compounds) and number of aromatic moieties (higher in combinatorial chemistry libraries). Other chemical differences between these two groups include the nature of heteroatoms (O and N enriched in natural products, and S and halogen atoms more often present in synthetic compounds), as well as level of non-aromatic unsaturation (higher in natural products). As both structure rigidity and chirality are both well-established factors in medicinal chemistry known to enhance compounds specificity and efficacy as a drug, it has been suggested that natural products compare favorable to today's combinatorial chemistry libraries as potential lead molecules.

4) Structural Elucidation

The elucidation of the chemical structure is critical to avoid the re-discovery of a chemical agent that is already known for its structure and chemical activity. Mass spectrometry is a method in which individual compounds are identified based on their mass/charge ratio, after ionization.

Chemical compounds exist in nature as mixtures, so the combination of liquid chromatography and mass spectrometry (LCMS) is often used to separate the individual chemicals. Databases of mass spectras for known compounds are available, and can be used to assign a structure to an unknown mass spectrum. Nuclear magnetic resonance spectroscopy is the primary technique for determining chemical structures of natural products. NMR yields information about individual hydrogen and carbon atoms in the structure, allowing detailed reconstruction of the molecule's architecture.


Pharmacogenomics is the study of how genes affect a person's response to drugs. This relatively new field combines pharmacology (the science of drugs) and genomics (the study of genes and their functions) to develop effective, safe medications and doses that will be tailored to a person's genetic makeup.

Many drugs that are currently available are "one size fits all," but they don't work the same way for everyone. It can be difficult to predict who will benefit from a medication, who will not respond at all, and who will experience negative side effects (called adverse drug reactions). Adverse drug reactions are a significant cause of hospitalizations and deaths in the United States.

With the knowledge gained from the Human Genome Project, researchers are learning how inherited differences in genes affect the body's response to medications. These genetic differences will be used to predict whether a medication will be effective for a particular person and to help prevent adverse drug reactions.

Preclinical Research

Each class of product may undergo different types of preclinical research. For instance, drugs may undergo;

• pharmacodynamics (what the drug does to the body) (PD),
• Pharmacokinetics (what the body does to the drug) (PK),

• Absorption, distribution, metabolism, and excretion, (ADME),
• Toxicology testing.
This data allows researchers to estimate a safe starting dose of the drug for clinical trials in humans.

Most preclinical studies must adhere to GLPs in ICH Guidelines to be acceptable for submission to regulatory agencies such as the Food & Drug Administration in the United States.

Typically, both in vitro and in vivo tests will be performed. Studies of a drug's toxicity include which organs are targeted by that drug, as well as if there are any long-term carcinogenic effects or toxic effects on mammalian reproduction.

Animal Testing

The information collected from these studies is vital so that safe human testing can begin. Typically, in drug development studies animal testing involves two species. The most commonly used models are murine and canine, although primate and porcine are also used.

Choice of Species

The choice of species is based on which will give the best correlation to human trials. Differences in the gut, enzyme activity, circulatory system, or other considerations make certain models more appropriate based on the dosage form, site of activity, or noxious metabolites. Depending on a drug's functional groups, it may be metabolized in similar or different ways between species, which will affect both efficacy and toxicology.

Importantly, the regulatory guidelines of FDA, EMA, and other similar international and regional authorities usually require safety testing in at least two mammalian species, including one non-rodent species, prior to human tria ls authorization.


Based on preclinical trials, No Observable Adverse Effect Levels (NOAEL) on drugs are established, which are used to determine initial phase 1 clinical trial dosage levels on a mass API per mass patient basis. Generally a 1/100 uncertainty factor or "safety margin" is included to account for interspecies (1/10) and inter-individual (1/10) differences.

Drug Delivery

This refers to approaches, formulations, technologies, and systems for transporting a pharmaceutical compound in the body to safely achieve its desired therapeutic effect safely as needed . Drug delivery is often approached via a drug's chemical formulation, but it may also involve medical devices or drug-device combination products. The concept of drug delivery is in synchronization with dosage form and route of administration.

Drug delivery technologies modify drug release profile, absorption, distribution and elimination for the benefit of improving product efficacy and safety, as well as patient convenience and compliance. Drug release is from: diffusion, degradation, swelling, and affinity-based mechanisms.

Most common routes of administration include the preferred non-invasive peroral (through the mouth), topical (skin), transmucosal, (nasal, buccal / sublingual, vaginal , ocular and rectal)and inhalation routes. Many medications such as peptide and protein, antibody, vaccine and gene based drugs, in general may not be delivered using these routes because they might be susceptible to enzymatic degradation or can not be absorbed into the systemic circulation efficiently due to molecular size and charge issues to be therapeutically effective. Many protein and peptide drugs have to be delivered by injection or a nano needle array precisely for this reason

Current efforts in the area of drug delivery include the development of targeted delivery in which the drug is only active in the target area of the body (for example, in cancerous tissues), sustained release formulations in which the drug is released over a period of time in a controlled manner from a formulation, and methods to increase survival of peroral agents which must pass through the stomach's acidic environment. In order to achieve efficient targeted delivery, the designed system must avoid the host's defense mechanisms and circulate to its intended site of action. Types of sustained release formulations include liposomes, drug loaded biodegradable microspheres and drug polymer conjugates. Survival of agents as they pass through the stomach typically is an issue for agents which cannot be encased in a solid tablet.