The IND - Investigative New Drug Application

Before you can start Phase 1 clinical trials with an experimental medicine, you must file an IND with the FDA - the United States’ regulatory agency which oversees all exploratory and market approved medications. You need to submit an IND if you are testing a New Molecular Entity, or a known drug for a new indication. 

The purpose of the IND is to:

• Allow a non-market approved drug to be moved across state lines

• Allow the FDA to control experimental medicine

• Allows to agency to overview the safety of the experimental compound to ensure patients and volunteers are not subjected to unreasonable risk

There are three types of INDs, of most relevance to a biotech startup is the investigator IND - for the human testing of a new drug and/or new use. There is also an emergency use IND, for the use of an experimental drug outside of standard clinical trial use. A treatment IND is for experimental drugs that have already shown some efficacy signal in clinical trials for use in emergency or life-threatening situations before final FDA review for NDA/BLA (New Drug Application/Biologics Licensing Application - the final market approval of the drug) takes place. INDs are either commercial or research; a start up’s IND will be considered commercially.

Once the 30-day period passes, the IND is considered ‘open’. It is the investigator’s responsibility to keep it updated (IND amendments). These include: Protocol amendments, informational amendments (e.g., toxic, chemistry, etc), safety reports (adverse events in clinical trials or ongoing laboratory animals), and annual reports.

Within the IND, there are three broad segments:

• Animal Pharmacology and Toxicology Studies

  • Preclinical data which upholds the experimental medicines’ reasonable safety for use in humans

  • Guidance for dosing and rationale 

  • Previous use in humans if applicable

• Manufacturing Information

  • Details on the structure, composition, and final formulation of your drug + relevant data such as stability and manufacturer data

  • Potential risks to patient directly caused by the chemistry of the drug

  • Assessment demonstrating ability to manufacture the drug in large enough batches, and consistently across batches

• Clinical Protocols

  • Protocols for the clinical studies

  • Relevance of clinical protocols to the drug’s proposed safety and efficacy

  • Clinical investigator’s qualifications

  • Institutional review board & informed consent

After submitting, the FDA has 30 days to review the IND and object. If no objection is received, the investigator may commence the study detailed in the IND. Common causes of deficiencies and required clinical holds include:

• unreasonable risk of human subject harm

• unqualified investigators

• Inadequate protocol design

• Starting dosage disagreement

• Inadequate CMC information

• misleading, incomplete or erroneous Investigator’s Brochure

• insufficient information to allow assessment of risk

• gender bias in a study of patients with a life-threatening disease that affects both genders

Summary of preclinical safety, PK/PD considerations

• Dose formulation analysis

• Genomic toxicity

• Mutagenicity

• Chromosomal aberrations

• Range-finding for tox

• Repeated dose tox

• Acute tox

• Metabolism

• hERG test

• Cardiovascular

• Respiratory

• CNS safety

IND Table of Contents

The IND itself takes the following form (this is not complete):

1. Form FDA 1571

2. Table of Contents

3. Introductory Statement 

4. General Investigation Plan

5. Investigator's Brochure

6. Protocol(s) Phase I

   1. Study Protocol(s)

      1. Outline of study

      2. Estimate of # of patients

      3. Safety exclusions

      4. Dosing

      5. Monitoring for AEs

   2. Investigator Data

   3. Facilities Data

   4. Institutional Review Board Data or Completed Forms

7. Chemistry, Manufacturing, and Control Data

   1. Drug substance

   2. Drug product

   3. Placebo

   4. Labeling

   5. Environmental Assessment or Claim for Exclusion

      1. (Most submissions will qualify for exclusion)

8. Pharmacology and Toxicology Data

   1. Pharmacology summary

   2. Pharmacokinetics

   3. Toxicology Summary

   4. Qualifications of those who evaluated the safety data

9. Previous Human Experience

10. Additional Information

GMP & GLP - Good Manufacturing and Good Laboratory Practices

Once you start considering testing or using a compound in humans, generally speaking GLP and GMP regulations apply. 

Good Laboratory Practice is a set of quality management controls for research laboratories. It is a data quality system. 

Good Manufacturing Practice is a system for ensuring consistency in quality for manufacturing. It covers from starting materials to staff training.

Generally speaking, any work conducted under GMP/GLP conditions will be more expensive and complicated. 

Animal Pharmacology and Toxicology Studies

The purpose of preclinical studies is to develop a quantitative understanding of the probable pharmacology of your experimental drug in humans, and evidence that the drug will be safe and not put patients or subjects under undue risk. It is important to conduct preclinical studies across mammalian species to avoid unintentional bias or masking of important drug characteristics, especially as relevant to safety. 

Planning is very important here - many of these studies are interdependent.

Pharmacology studies in the IND package include:

• ADME (adsorption, distribution, metabolism, and excretion)

• Efficacy in an appropriate model

• Mechanism of action 

• Starting dose

• Pharmacodynamic drug interactions

Toxicology studies in the IND package include:

• Acute, subacute, and chronic toxicology tests

• Effects of the drug on reproduction and the developing fetus

• Toxicity relevant to the modality and use case

• Target organ toxicity

• Local tolerance (toxicity related to the mode of administration)

• In vitro studies 

• Toxicokinetic

• Carcinogenic potential

• Genotoxicity studies

Can also include, depending on the characteristics of the drug:

• Phototoxicity

• Immunotoxicity

• Juvenile animal toxicity

• Abuse liability

Extra considerations for a biologic drug include:

• Special consideration to the relevancy of the animal species, age, and physiological state

• Consideration of the stability of your biologic in different animals

• Dosing regimen and the impact of animal species (e.g., on half life)

• Whether all studies need to be conducted in primates due to cross-reactivity

• Transgenic animals expressing the target may be used in studies if there is no relevant animal

• Extra studies to determine e.g. receptor occupancy, affinity

• Immunological properties for antibodies

There are modifications of the standard preclinical package for drugs indicated for severe diseases, to optimize and expedite the drug development process.

—Pharmacology

Primary pharmacology (systemic) and secondary pharmacology (organ), with special focus on cardiovascular, CNS, and respiratory systems. Pharmacology studies especially help elucidate undesirable effects directly due to the pharmacodynamic effects of the drug. The mechanism of action of these adverse pharmacodynamic effects is elucidated here if possible. These studies also help define a dose-response relationship.

PD studies investigate the mode of action of a substance's effect on the desired therapeutic target. Not necessarily GLP. Drug/drug interactions may also be explored here. Generally not GLP.

—Pharmacokinetic Studies

Metabolic, plasma protein binding, and exposure data should be conducted. ADME studies in vitro and in vivo. 

Absorption includes rate of absorption, kinetic parameters, bioavailability in the blood. Relationship between the dose level, systemic exposure, and serum levels.

Distribution studies include tissue distribution of the drug, protein binding, and placental transfer studies if relevant.

Metabolism studies include characterization of metabolites in various biological samples, metabolic pathways, various in vitro studies of metabolism such as cytochrome p450 studies (liver enzyme)

Excretion studies include routes of excretion of the drug from the body and special studies in breast milk if relevant. Generally not GLP.

—Toxicity Studies

Toxicity studies are usually done after PK/PD studies, and are conducted using the same route as human delivery. Importantly, the duration of your clinical trial is limited by the duration of your preclinical toxicity repeated dose studies. Toxicity studies should be conducted at low (no effect), mid (near anticipated human dose), and high (10-100x higher than anticipated human clinical dose).   

Acute Toxicity Studies

Single-dose study of a very high concentration of the drug. Dose-ranging/escalating studies can be used to find the acute toxicity/maximum tolerated dose (MTD) in the model animals. Acute toxicity studies are helpful for better understanding human overdose situations. Generally animals are given the dose and then observed for 2 weeks.

Repeated-dose Toxicity

Repeated dose studies include subacute, chronic, and subchronic dosing. These studies be conducted in two species (one nonrodent). Subacute and subchronic differ by their duration: subacute toxicity is toxicity that occurs due to multiple doses between 24 hours to 28 days; subchronic refers to toxicities up to 90 days. Chronic toxicity is a toxicity that develops due to the long-term exposure to the drug - these studies are not usually included in the phase 1 enabling IND. 

Generally speaking, repeated dose toxicity studies should be conducted in two mammals (one nonrodent) for a length of time equal or exceeding that of human clinical trials up to the maximum recommended time on dose. If your trial will test drugs for longer than 6 months, a rodent study of 6 months and nonrodent study of 9 months is appropriate. 

Dosing

The maximum feasible dose (MFD) for acute, subchronic, and chronic toxicity studies is 1000 mg/kg/day for rodents/nonrodents. For toxicity studies, you should show a 10-fold exposure to that of the clinical dose/exposure and the clinical dose exceeds 1 g/day - in which case, limit the toxicity doses to 10-fold exposure margin, a dose of 2000mg/kg/day, or the MFD - whichever is lower. Depending on the clinical dose, a 50-fold margin of exposure is also seen as acceptable for the animal acute and repeated dose tox. It is helpful/potentially necessary to find the dose-limiting tox in at least one species

Estimating the first dose in humans

Generally, studies start with the no observed adverse event level (NOAEL) and plan a dose escalation to a dose thought to be pharmacologically relevant. 

—Genotoxicity & carcinogenicity studies

Genotoxicity is a toxicity that directly damages the genome. Carcinogenicity refers to the tumorigenic potential of the drug, regardless of the exact molecular mechanism; these studies are not usually necessary unless the specific drug’s biology warrants it. An assay for genotoxicity is sufficient for a single dose trial; for a multiple dose trial, preclinical studies should include an assay capable of detecting chromosomal damage in mammalian studies. Usually upon progression to phase II clinical studies, there are a number of additional studies under this category to complete. 

Carcinogenicity studies are only necessary in certain situations and may be delayed until post-market approval for certain diseases, usually more severe indications. 

—Reproductive Safety Studies

Generally, the biggest concern regarding safety is in women of child-bearing potential (WOCBP). Specifically, the risk of women in your clinical study becoming pregnant. You can approach this by either/both conducting reproduction studies to characterize the risk to fetus or by implementing precautions to prevent pregnancy in the patients receiving your therapy. 

In the United States, you can generally commence early-phase clinical trials without assessing embryo-fetal development, if proper precautions are taken; this is generally not the case in the EU and Japan.  For early phase studies, it is not always necessary to complete developmental toxicity studies - for example, if the CT is short duration, or if theindiction is predominant in women and therefore it is necessary to include WOCBP. Another example where this may not be necessary is when the biology of the drug is known enough to make it unliekly to have a negative effect on embryo - for example, with monoclonal antibody drugs, embryo-fetal exposure is known to be low and a developer can generally complete reproductive studies in phase 3. 

For women that are already pregnant, all female reproduction toxicity and genotoxicity tests should be completed. 

Within these groups, the studies are divided into three segments: segment I, fertility and early embryonic development to implantation, segment II, embryo-fetal development (teratogenicity studies - do the offspring look and act normally?), and segment III, prenatal and postnatal development (can the offspring reproduce). It should be noted that these studies are very time consuming and expensive .

—Chemistry, Manufacturing, and Control (CMC)

Drug substance - the active ingredient e.g., caffeine

Drug product - final formulation e.g., soda 

New molecular entity - active pharmaceutical substance not previously contained in any registered drug product

New dosage form - a drug product that has the same active substance, different formulation type (tablet, capsule, solution, cream, etc)

Excipients - parts of drug product that are not the active product/drug substance 

API - active pharmaceutical ingredient 

QA - Quality Assurance, a structure to ensure the API are of suitable quality and that QS is maintained

QS - Quality Systems 

QC - Quality Control, testing to ensure specifications met

The necessary CMC requirements to facilitate a Phase 1 clinical trial include (this is not a complete list; many of these apply to both the drug substance and the drug product):

• Compound description (physical, chemical, biological characteristics)

• Compound source & class

• Dosage 

• Manufacturer

• Formulation and routes of administration to be used in the clinical trial

• Grade and quality of excipients used in the manufacturing of the product

  • Both intentional and side components of the manufacturing 

• List of starting materials, reagents, solvents, and catalysts used to manufacture your product, and purification steps; sterilization steps if relevant

• Analytical methods to ensure the drug’s identity, strength, quality, and purity

  • Quality: drug substance/product’s suitability for its intended use

  • Purity: related substances, heavy metals, residual solvents

• Stability data & assay

• Container information

• List of all materials in the drug product including inactive

• Placebo composition, manufacturer, control, & other data as done foir the drug substance and product

• Tests showing absence of active product in the placebo

• Batch similarity from the batches used for nonclinical toxicology/pharmacology testing and that used in clinical trials.

  • Identity & structure including optical rotation if relevant)

  • reducing/non-reducing electrophoresis for proteins

  • Purity assay

  • Impurity profile

  • Potency assay for biologics (the product’s specific ability to achive a defined biological effect)

Biologics submissions vary slightly from that of a small molecule drug. They are more complicated, and additionally contain:

• Source material & characterization (e.g., the cell line)

• Cell substrate (the cells used to manufacture the product) source, history, and generation

• Manufacturing process including cell culture, purification, modification, storage, and shipping

• Cell banking system details 

• Cell line stability

• Impurities due to synthesis, manufacturing, degradation of the product

• Viral contaminants if applicable, and their removal 

• Bioactivity assessments 

• Description of the biological activity

• For the product: primary, secondary, tertiary structure, post-translational forms, immunochemical properties

—Clinical Protocols

You will need to provide your Phase I clinical protocol, and details of the investigator responsible for the trial and the subjects. As a note, the clinical protocol is not always a Phase 1 protocol - if, for example, the drug has been previously tested in another country, the IND may be filed with a Phase 2a (smaller studies to assess safety and efficacy) or 2b (higher powered efficacy) study. 

The IND can be held by the FDA not only if they do not approve of the clinical protocol, but also if they do not believe that the primary investigator is adequate! 

The definition of a good trial as considered by the FDA includes: 21 cfr 314.126

• Study design allows the experimental drug to be adequately compared to a control and lead to a quantitative assessment of the drug effect

• Standardized drug product

• Subject recruitment and selection is adequate for the disease being investigated

• Comparability across control and treatment groups, controling for age, sex, disease severity and duration, and other non-study drugs used previously or concurrently. 

• Reliable and well-defined methods to measure the patient response to the drug. 

• Consideration and minimization of bias at all stages of the trial

• Results analysis 

The IND will include a General Investigational Plan, which gives an overview of:

• The drug rationale

• Indication

• How the drug will be evaluated

• The type of clinical trials 

• Number of patients in these clinical trials

• Particular risks to be considered as informed by preclinical data or prior human studies.

Most likely, the IND will include a protocol for a Phase 1 study. The protocol for a Phase 1 study is more flexible. It should describe:

• Outline of study

• Number of patients

• Safety exclusions

• Dosing plan

• Safety criticalities 

—Type of Clinical Trials

Placebo-concurrent control - Test drug compared with inactive formulation that closely resembles drug

Dose-comparison concurrent control - Compare two different doses of the same drug

No treatment concurrent control - When no anticipation of a placebo effect, no comparison/control

Active treatment concurrent control - Compared to a known effective therapeutic - usually used in situations where no treatment/placebo would not be ethical. 

Historical control - Compared to historical data 

Randomized - Patients randomly allocated to one group or another

Open-label - Both the patient and the physician/data analyst know which treatment they are recieving 

Blinded - The patient does not know if they are in the control or treatment group

Double-blinded - Both the patient and the physician/data analyst do not know which group they are in

Note - your placebo and drug product will need to look and be packaged identically to prevent inadvertent unblinding.

—Exploratory Clinical Trials

Super early clinical trials to get insight on the dosing, PK/PD, therapeutic relevance to disease, etc. These shoudl have:

• Early in phase 1 process

• Limited human exposure

• No therapeutic intent

• Not intended to examine clinical tolerability

• Can be healthy or patient populations

This can be approached as a microdose trial (< 100ug) to investigate target receptor binding, tissue distribution in a PET study; this can be followed by <= 5 doses of <= 100ug each. 

Another strategy is a single-dose study that starts at subtherapeutic doses and potentially escalates into the anticipated therapeutic range. This allows PK parameters to be determined  closer to the PD active dose.