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IMPLEMENTATION GUIDE

Complete NDA Submission Generation Guide

Step-by-step workflow for generating FDA New Drug Application (NDA) submissions with AI automation

📖 18 min read•Last updated: November 2025

Table of Contents

NDA Overview & TypesPre-Submission PlanningModule 1: AdministrativeModule 2: CTD SummariesModule 3: Quality (CMC)Module 4: NonclinicalModule 5: ClinicalAI-Powered Generation WorkflowValidation & Compliance ChecksSubmission Timeline

NDA Overview & Types

What is an NDA?

A New Drug Application (NDA) is the formal request to the FDA for approval to market a new pharmaceutical drug in the United States. It contains comprehensive data from preclinical, clinical, and manufacturing studies demonstrating the drug's safety and efficacy.

Types of NDAs

1

505(b)(1) NDA

Full NDA with complete clinical data package. Required for new molecular entities (NMEs) or new indications requiring new clinical studies.

Typical for: Novel drugs, first-in-class therapies
2

505(b)(2) NDA

Hybrid application that can rely partially on FDA's findings for an approved drug (the "reference listed drug"). Reduces clinical data requirements.

Typical for: New formulations, new indications, combination products

When to File an NDA vs. BLA

CriteriaNDA (New Drug Application)BLA (Biologics License Application)
Product TypeChemical drugs (small molecules)Biological products (proteins, vaccines, gene therapies)
SynthesisChemically synthesizedDerived from living organisms
ExamplesAspirin, statins, antibioticsMonoclonal antibodies, insulin, CAR-T therapies
Regulatory CenterCDER (Center for Drug Evaluation)CBER (Center for Biologics Evaluation)

Pre-Submission Planning

📋 Pre-NDA Meeting with FDA

Schedule a Pre-NDA meeting 3-6 months before planned submission to discuss:

  • •Content and format of the NDA
  • •Design of Phase 3 studies (if not yet complete)
  • •Data requirements for specific populations (pediatric, geriatric)
  • •Risk Evaluation and Mitigation Strategy (REMS) if needed

Document Collection Checklist

Module 1

FDA Forms (1571, 356h, 3674)Cover LetterComprehensive IndexPrescribing Information (label)Patent Certifications

Module 2

CTD SummariesClinical OverviewNonclinical OverviewQuality Overall Summary (QOS)

Module 3

Drug Substance (API) dataDrug Product (formulation) dataStability StudiesManufacturing ProcessAnalytical Methods

Module 4

Pharmacology StudiesToxicology StudiesPK/ADME StudiesCarcinogenicity StudiesReproductive Toxicology

Module 5

Clinical Study ReportsIndividual Patient DataSafety DataEfficacy ResultsStatistical Analysis

AI-Powered Generation Workflow

DossiAIr automates the end-to-end NDA generation process with a 4-step intelligent workflow:

1

Upload Source Documents

⏱️ 30 minutes

Drag-and-drop your stability studies, clinical reports, manufacturing SOPs, and other source documents.

  • Batch upload support for 100+ documents
  • Auto-classification into eCTD sections (3.2.P.8, 5.3.5.1, etc.)
  • Multi-modal AI extracts tables, figures, and text
  • Quality scoring for completeness
2

AI Generates Draft Sections

⏱️ 2-4 hours

Our 3,400+ FDA-specific regulatory prompts draft compliant content for all 5 modules.

  • Module 2 summaries generated from Module 3-5 data
  • Integrated cross-references across modules
  • Regulatory terminology automatically applied
  • ICH M4 structure enforced
3

Expert Review & Refinement

⏱️ 1-2 days

Regulatory affairs team reviews AI-generated content with real-time compliance feedback.

  • Rich text editor with regulatory spell-check
  • Compliance score displayed per section
  • Side-by-side comparison with source documents
  • Track changes and version history
4

Export Validated eCTD

⏱️ 1 hour

Download submission-ready eCTD package with XML backbone and all hyperlinks validated.

  • eCTD 4.0 compliant XML backbone
  • Automated hyperlink validation
  • FDA ESG-ready structure
  • MD5 checksums for all files
⚡

Total Time: 2-3 Days

Traditional manual NDA preparation takes 3-6 months. DossiAIr reduces this to 2-3 days—a 75% time reduction.

Validation & Compliance Checks

Before submission, DossiAIr runs 200+ automated validation rules across 3 categories:

📐

Structural Validation

  • ✓ eCTD 4.0 folder structure
  • ✓ Required sections present
  • ✓ File naming conventions
  • ✓ XML backbone syntax
  • ✓ Sequence numbering
🔗

Cross-Reference Validation

  • ✓ All hyperlinks functional
  • ✓ Relative paths correct
  • ✓ Referenced sections exist
  • ✓ No orphaned links
  • ✓ Anchor targets valid
⚖️

Regulatory Compliance

  • ✓ ICH M4 format adherence
  • ✓ FDA-specific requirements
  • ✓ Required fields populated
  • ✓ Terminology consistency
  • ✓ Date format compliance

🚨 Common Deficiency Prevention

DossiAIr proactively flags issues that account for 60% of FDA deficiency letters:

•Missing or incomplete Module 2 summaries
•Broken cross-references between modules
•Non-compliant XML structure
•Incorrect file naming conventions

Submission Timeline

Typical timeline from NDA generation to FDA approval (using DossiAIr):

1

NDA Generation

2-3 days

Using DossiAIr AI automation

2

Internal QC Review

1-2 weeks

Regulatory team final review and approval

3

FDA Filing

1 day

Submit via FDA Electronic Submissions Gateway (ESG)

4

FDA Filing Review

60 days

FDA determines if NDA is complete and can be filed

5

FDA Substantive Review

6-10 months

Standard or Priority Review by FDA review team

6

FDA Action (Approval/CRL)

—

FDA issues approval or Complete Response Letter

🚀 Priority Review

For drugs treating serious conditions with significant advantage over existing treatments:

6 months
vs. 10 months standard

⚡ Breakthrough Therapy

For drugs with substantial improvement over available therapy:

~4 months
Rolling review + intensive FDA guidance

Ready to Generate Your NDA 90% Faster?

See how DossiAIr can transform your regulatory submission workflow