Dossier assembly and review · Training guide

IND Application

Assemble a complete initial IND under 21 CFR 312.23, with each item tracked to its eCTD location, the clinical hold risks checked and the earliest start date set.

Writes: IND 1571 IND (a)(3)
Product type: Small molecule and biologics
Guidance it follows: 21 CFR 312.20–312.23, 312.40–312.42, 312.53; FDA Content and Format of Investigational New Drug Applications (INDs) for Phase 1 Studies (1995); FDA Investigator's Brochure and IND content guidance; FDA Estimating the Maximum Safe Starting Dose (2005); ICH M3(R2); FDA Providing Regulatory Submissions in Electronic Format (eCTD); 21 CFR 25.31(e)
Time to learn: About 20 minutes with the example

Open the tool at https://app.cmcfy.com/app/ind-application.html. This guide is also online at https://cmcfy.com/guides/ind-application.html

1. What this module does

You give the sponsor, drug, indication and IND type, the first trial with its dosing duration and doses, the safety safeguards and the status of each IND item.

The tool lists the items 21 CFR 312.23 requires (an Investigator's Brochure is not needed for a sponsor-investigator IND), flags the clinical hold risks FDA reviews (toxicology shorter than the dosing, a starting dose above the MRSD, no stopping rules) and writes the cover letter, introductory statement and general investigational plan.

What you get

Two Word or PDF files: cover letter with introductory statement and general investigational plan; IND content checklist with the Form FDA 1571 commitments.

2. Before you start

Have these ready. You can still start with the example data and replace it piece by piece.

The pre-IND meeting minutes.
The first protocol, its dosing duration and doses.
The MRSD from the Nonclinical Overview.

Your data stays on your computer. The bar under the title counts every network request the page makes; it stays at 0 because your data never leaves your computer. Download offline copy saves a single file that opens from your own computer with all network access blocked, for air-gapped PCs.

3. Step by step with the example

Open the tool at app.cmcfy.com/app/ind-application.html. The example is loaded when the page opens, so every panel already has realistic data. Follow the steps to see how it works, then replace the example with your own data.

Describe the sponsor and product
Choose commercial or research IND and give the indication, review division and planned submission date.
Describe the first trial
Give the longest dosing, the longest toxicology study, the starting dose, MRSD and highest dose, and tick the safeguards.
Read the result
The headline gives the readiness: "11 of 14 IND parts ready · 3 still open".
IND content under 21 CFR 312.23.
Resolve alerts and download
Toxicology shorter than the dosing, a starting dose above the MRSD, no stopping rules and a missing required item are critical. Then preview and download.

4. Field reference

Every input in the tool, panel by panel. Tables accept rows pasted straight from Excel, comma-separated text, or a loaded file; check the columns after loading a file. Fields marked “when it applies” appear only for the choices that need them.

1 · Sponsor and product

Field	What to enter
Drug	Type it in.
Sponsor	Type it in.
IND type	Choose one: Commercial (eCTD required); Research (sponsor-investigator).
Indication	Type it in.
FDA review division	Type it in.
Pre-IND meeting held (date and key agreements)	Type it in.
DMFs or other INDs referenced	Tick the box if it applies.
Planned submission date	Type it in.

2 · Clinical plan and safety

Field	What to enter
First trial	Choose one: Phase 1 (first in human); Phase 1 (not first in human); Phase 2; Phase 3.
First protocol	Type it in.
Longest planned dosing in the trial (weeks)	Type a number.
Longest GLP repeat-dose toxicity study, rodent and non-rodent (weeks)	Type a number.
Starting dose (mg)	Type a number.
Maximum recommended starting dose from the NOAEL (mg)	Type a number.
Highest planned dose (mg)	Type a number.
Sentinel dosing and staggered cohorts	Tick the box if it applies.
Stopping rules and dose escalation criteria in the protocol	Tick the box if it applies.
General investigational plan for the coming year	Type or paste text.
Rationale for the drug and the research	Type or paste text.
Previous human experience	Type it in.

3 · IND content

Status: complete, in progress, not started or not applicable. Add the document or the module where it sits.

Field	What to enter
Items	Write the status as complete, in progress, not started or not applicable. A table. Columns: Item \| Status \| Document or location. Paste rows from Excel, type comma-separated rows, or press Load file (Excel, CSV, Word, PDF or a scan).

5. Checks and alerts

Calculations and pass/fail outcomes always come from fixed rules, never from AI. The tool checks:

Every 21 CFR 312.23 item and the forms that go with it.
Toxicology duration, starting dose and first-in-human safeguards.
Earliest start 30 days after receipt.

How to resolve alerts

Critical alerts block the download and must be fixed in the data. A failing result can instead be linked to an investigation: type the investigation reference and outcome and press Record.
Major alerts block the download until you fix them or type a justification and press Accept justification.
Minor alerts do not block anything. They are listed in the documents so the reviewer sees them.
Some alerts have an Apply fix button that makes the change for you. Reopen undoes a justification.

Narratives

This module writes: Introductory statement; General investigational plan. Each narrative is written by fixed rules from your data. You can edit it in the box. Rewrite with AI (where your plan includes AI) rewrites it in regulatory style; every number in the text is checked against your data, and a number that does not match is flagged under the box and blocks the download until you correct it. Reset to rule-based text brings back the original.

6. Preview, gap review and download

Press Preview next to a section, or Preview and download all. The document opens in a preview window, exactly as the Word file will read.
The left side lists the review, run on your device: gaps in the data (missing values, open alerts), gaps in the report (missing content the guidance expects, placeholders such as [site] or TBD left in the text) and, if you load the approved protocol under Compare with the protocol, differences from the protocol (requirements, criteria, batches or time points it plans that the report does not show).
Click a finding to jump to the place in the preview. Fix it in the tool, then preview again.
Optional AI review: a second read for contradictions, claims without data and vague wording. The report text is sent to Claude only when you press it, and only where your plan includes AI. Check every AI finding; AI can be wrong.
Press Download Word (.docx) or Download PDF. With several documents open, All as Word (.zip) and All as PDF (.zip) download the set. The download buttons stay disabled while a blocking alert is open; the preview still works.

Documents this module produces

Section	Document
IND (a)(3)	Cover letter, introductory statement and investigational plan
IND 1571	IND content checklist

Use Save project to keep your work as a file on your computer, and Open project to continue later. Start blank clears every field; Load example brings the example back. Nothing is stored on CMCfy servers.

7. US and EU submissions

US only: FDA IND under 21 CFR Part 312. For an EU clinical trial application use the IMPD in IND & IMPD Quality.

8. Working with other modules

Write the CMC part in IND & IMPD Quality and the pharmacology and toxicology part in Nonclinical Overview & Summaries.

9. Common pitfalls

A 4-week toxicology package for a 12-week trial.
Marking the IB not applicable for a commercial IND.

10. Practice exercises

Each exercise starts from the example (press Load example to reset). We run these on every update of this guide, so the result you see should match.

Plan a longer trial
Change the longest planned dosing from 2 to 12 weeks.
Expected resultThe headline shows a clinical hold risk: toxicology is shorter than the dosing.