Case Studies and Drug Discovery

What are major classes of therapeutic agents?

Small molecules, peptides/proteins, monoclonal antibodies, nucleic-acid therapies, vaccines, cell therapies, and radiopharmaceuticals.

Small-molecule drugs

Usually taken orally; also given by injection or inhalation

Peptide and protein drugs

Includes hormones and other biologic ligands; usually injected

What discovery approach is also called traditional or phenotypic drug discovery?

Starting with an observed biological effect, often from human, animal, or cell-based screening, before the molecular target is known.

What is rational drug design?

Designing compounds using knowledge of a molecular target, ligand, or target structure.

What are the Five critical phases in the U.S. drug development process in order?

Early Drug Discovery, Preclincial studies, Clinical Development, FDA review and Post-market monitoring

What does IND stand for and when is it submitted?

Investigational New Drug; it is submitted to the FDA before clinical trials.

When may clinical trials begin after an IND is submitted?

After FDA allowance, or after 30 days if FDA does not place the study on clinical hold.

What is an NDA?

New Drug Application; submitted after clinical trials for FDA review of evidence supporting marketing approval.

What is a BLA used for?

A Biologics License Application is used for biological products.

What does CDER regulate?

Small-molecule drugs and some therapeutic biologics.

What does CBER regulate?

Biologics such as vaccines, gene therapies, cell therapies, and blood products.

What does CDRH regulate?

Medical devices and radiation-emitting products.

What does CVM regulate?

Drugs, food, and devices for animals.

What does CFSAN regulate

Food safety, dietary supplements, cosmetics,
infant formula

What does CTP regulate?

Tobacco regulation

What does ORA regulate?

Field operations: inspections, enforcement,
import/export surveillance

What are the main steps of drug discovery and development?

Target/assay selection, hit-to-lead, lead optimization, IND-enabling studies, and clinical trials.

What kinds of disease causes can guide target selection?

An infectious agent, host imbalance, or somatic mutations.

What is a desirable target strategy for bacterial or viral disease?

Identify a target that is absent from human cells.

How can host imbalance be treated through target selection?

Replace an underactive protein (e.g., insulin), inhibit an overactive protein (e.g., an oncogenic kinase), or modulate dysregulated physiological activity (e.g., a GPCR in smooth muscle).

How should targets be selected for cancer?

Choose a tumor-specific target.

What should be true of a potential drug target?

It should have solid biological validation showing it is involved in the disease.

About how many proteins are targeted by existing drugs?

Only about 200 proteins.

What makes a target “druggable”?

It has a stereochemically unique cavity, or binding pocket, that can fit a selective drug with high binding affinity.

What type of molecules are most established drug targets?

Proteins.

What feature makes a protein target especially attractive for drug development?

A well-defined catalytic cleft that normally binds a natural small-molecule ligand

What are examples of druggable targets?

Steroid hormone receptors, GPCRs, ligand-gated ion channels, and kinases with ATP-binding pockets.

What is a pharmacophore?

A model of the essential steric and electronic features a molecule needs to bind a specific biological target and produce or block a biological response.

What does a pharmacophore model explain?

How structurally different ligands can bind the same receptor site and cause similar biological effects.

What are common pharmacophoric features?

Hydrophobic regions, aromatic rings, hydrogen-bond donors or acceptors, cations, and anions.

How is a pharmacophore model usually created?

Using an SAR table that compares compounds, their physical properties, and their biological activities.

Besides binding its target, what must a molecule do to become an oral drug?

It must be potent and selective, dissolve in the GI tract, cross the intestinal barrier into the bloodstream, and remain in the body long enough to work.

What does Lipinski's Rule of Five estimate?

Whether a small molecule may have acceptable oral absorption.

What are Lipinski's Rule-of-Five guidelines?

Molecular weight <500, cLogP <5, no more than 5 H-bond donors, and no more than 10 H-bond acceptors.

Is Lipinski's Rule of Five absolute?

No. It is a heuristic with many exceptions.

What is cLogP?

The log of a compound's partition coefficient between n-octanol and water.

What are the four broad pathways to drug discovery?

Starting from Biology/natural substances, existing molecules, rational design, and screening approaches.

What is natural-substrate optimization?

Starting with an endogenous ligand, metabolite, or substrate and modifying it to improve potency, selectivity, or PK.

What are natural-product derivatives?

Drug candidates inspired by molecules from plants, microbes, or marine organisms.

What did Fleming infer from the clear halo around Penicillium mold?

The mold released a substance that inhibited bacterial growth; that substance was penicillin.

Why are penicillin analogs developed?

To overcome resistance and increase or change the range of bacteria targeted.

What is a “me-too” or patent-busting strategy?

Modifying another company's compound to create a new chemical entity with an improved profile or patentability.

What is drug repurposing?

Evaluating an existing drug for a new indication.

What is a bioisostere?

An atom, functional group, or fragment that can replace another while retaining similar chemical, physical, or biological properties.

Why use bioisosteric replacement?

To reduce toxicity or improve bioavailability, potency, selectivity, metabolic stability, or PK.

What are classical bioisosteres?

Replacements based on atoms with the same valence-electron structure and similar biological properties.

What are nonclassical bioisosteres?

Less straightforward replacements that depend on the ligand's specific binding needs.

What is ligand-based drug design?

Using knowledge of active ligands to design new analogs with better properties.

What is structure-based drug design (SBDD)?

Using a protein structure to design small molecules that fit an active or allosteric site.

What is high-throughput screening (HTS)?

Physically testing large chemical libraries in biological assays to identify hits.

What is virtual screening?

Using computational tools to predict potential binders from virtual libraries.

What is a hit compound?

An initial molecule with measurable activity against a biological target in a biochemical or cell-based assay.

What is the difference between target-based and phenotypic screening?

Target-based screening measures a defined target; phenotypic screening measures cellular or organism-level changes without requiring a known target.

What is the goal of hit identification during screening?

To find hit compounds.

What is a hit compound?

An initial molecule that shows measurable activity against a biological target in a biochemical or cell-based assay.

What is the goal of hit-to-lead (H2L)?

Validate hits, generate derivatives, and identify promising lead series.

What is the goal of lead optimization (LO)?

Refine a lead into a preclinical candidate by optimizing PK and PD in animals.

What does PD evaluate during lead optimization?

The drug's biochemical and physiological effects on an organism, including on-target activity.

What three areas are co-optimized during lead optimization?

Potency/efficacy, PK/ADME profile, and PD/on-target activity.

Approximately how long and how costly is drug discovery and development?

About 10-15 years and roughly $0.5-$2 billion.

What is the difference between first-in-class and follower drugs

A first-in-class drug uses a new mechanism/target approach; a follower drug enters an established therapeutic mechanism or class.

What is FdUMP?

A metabolite formed from several fluoropyrimidine drugs.

What type of inhibitor is FdUMP?

A suicide inhibitor of thymidylate synthase.

What is the result of FdUMP inhibition of thymidylate synthase?

It blocks the conversion of dUMP to dTMP, disrupting DNA synthesis.

What cancers is 5-fluorouracil (5-FU) used to treat?

Breast cancer and colorectal cancer.

How does thymidine phosphorylase activate 5-FU?

It converts 5-FU to 5-fluorodeoxyuridine (FdUrd), which is then converted to FdUMP.

What is the role of thymidine kinase (TK) in 5-FU activation?

It activates FdUrd by adding a phosphate to the 5′ position of its ribose, forming FdUMP.

What is thymidine phosphorylase’s role in pyrimidine salvage?

It converts thymine and deoxyribose-1-phosphate into thymidine, releasing inorganic phosphate (Pi).

What is the role of dihydropyrimidine dehydrogenase (DPYD) in pyrimidine breakdown?

It converts uracil to dihydrouracil.

How does DPYD affect 5-FU therapy?

DPYD inactivates 5-FU by converting it to 5-dihydrofluorouracil. Decreased DPYD activity causes 5-FU accumulation and can lead to severe toxicity.

Why is dosing 5-FU challenging?

5-FU has a narrow therapeutic index and significant patient-to-patient variability in pharmacokinetics.

What does heterozygous mean?

Having two different copies (alleles) of a gene—for example, one normal allele and one recessive variant.

What does homozygous mean?

Having two copies of the same allele—for example, two recessive variants

How common are heterozygous DPYD mutations?

They occur naturally in about 3–5% of patients.

How common are homozygous inactivating DPYD mutations?

They occur naturally in about 0.2% of patients.

What does the DPYD 1 allele represent?

The normal-function reference allele.

What does a DPYD 1/1 genotype mean?

The patient has two normal-function DPYD alleles.

What do DPYD 2 and higher alleles represent?

Variant alleles that may be nonfunctional, functional, or have an unknown effect on DPYD function.

Why is DPYD genetic screening done before fluoropyrimidine treatment?

To identify patients with inactivating mutations who are at high risk for severe toxicity before dosing.

What are examples of thiopurine therapeutics?

6-thioguanine, 6-mercaptopurine, and azathioprine.

What is 6-mercaptopurine used for?

It is an antineoplastic drug.

What is azathioprine used for?

It is an immunosuppressant.

How does thiopurine methyltransferase (TPMT) inactivate 6-MP and 6-thioguanine?

TPMT adds a methyl group to the sulfur atom of 6-MP and 6-thioguanine.

Why is TPMT the major thiopurine-inactivation pathway in hematopoietic cells?

Hematopoietic cells lack xanthine oxidase activity, so TPMT-mediated methylation is the main inactivation route.

What happens with an inactivating NUDT15 mutation?

d6-TG-TP is not adequately broken down, so it accumulates, is incorporated into DNA, and can cause thiopurine-related hematotoxicity.

What does NUDT15 normally do?

NUDT15 breaks down d6-TG-TP into d6-TG-MP.

In which populations are NUDT15 polymorphisms more common?

Asian and Latino populations.

How does xanthine oxidase inactivate 6-mercaptopurine?

It converts 6-mercaptopurine to 6-thiouric acid.

What is the general consequence of an inactivating mutation in a drug-metabolizing enzyme?

Reduced drug inactivation can cause active drug or active metabolites to accumulate, increasing toxicity risk.

What is pharmacogenomics?

The study of how a person’s genetic inheritance affects their response to drugs.

What is pharmacogenetics?

The study of variations in one targeted gene or a group of functionally related genes that can affect drug response.

What is the relationship between pharmacogenomics and pharmacogenetics?

Pharmacogenomics is broader and includes pharmacogenetics.

What is the goal of pharmacogenetics?

To use genetic differences to select safer, more effective drugs and doses for individual patients.

How can polymorphisms in drug-metabolizing enzymes affect drug outcomes?

They can change how quickly a drug is metabolized, which can affect drug levels, effectiveness, and toxicity.

How can variations in drug transporters or receptors affect drug response?

They can alter how a drug is transported or how well it binds to its target, changing the response to the drug

Besides genotype, what factors can influence individual drug response?

Gender, ethnic background, and environmental influences.

What is pharmacokinetics?

What the body does to the drug.

What is pharmacodynamics?

What the drug does to the body.

How can pharmacogenetics improve patient care?

It can identify patients who may have an increased risk of side effects or toxicity from certain drugs