Lead Molecular Design
Lead Molecular Design develops cheminformatics software — the ONIRO platform, MassMetaSite, MassChemSite, and MetaSite — for drug discovery, used by pharmaceutical companies, academic groups, and biotech firms for metabolite identification, structure elucidation, and Site of Metabolism prediction.
- Company typePrivate
- Founded2002
- HeadquartersSant Cugat Del Vallès, Spain
- Headcount1–10
- GTM typeB2B
- OfferingSoftware
What Lead Molecular Design does
Lead Molecular Design, S.L. is a Spain-based cheminformatics software developer founded in 2002 and headquartered in Sant Cugat del Vallès near Barcelona. The company builds specialized algorithms and software applications for drug discovery and lead optimization, with core technology focused on mass spectrometry data interpretation, metabolite identification, and structure elucidation. Its product stack combines proprietary computational methods for MS/MS fragmentation analysis, NMR spectral prediction, and metabolic pathway prediction, supporting both small molecules and macromolecules up to 15,000 Da including peptides and oligonucleotides. The portfolio centers on the ONIRO platform — an integrated environment combining WebMetabase, WebChembase, Compound Library, and WebQuant modules — alongside standalone products MassMetaSite (automated metabolite identification from LC-HRMS data), MassChemSite (structure elucidation from chemical reaction samples), MetaSite (Site of Metabolism prediction for cytochrome P450), and Charming NMR (NMR-based structure confirmation).
The company's customer base spans major pharmaceutical firms (Merck & Co., Hoffmann-La Roche, Bristol-Myers Squibb, Biogen), chemical companies, academic research groups (University of Almería, Pompeu Fabra University), and biotechnology organizations developing peptide and oligonucleotide therapeutics. Lead Molecular Design monetizes through three streams: (1) software licensing — distributed exclusively via a long-standing partnership with Molecular Discovery, Ltd. established in 2002, (2) contract research services for pharmaceutical clients abroad, and (3) paid training programs priced at $250 per day or $500 for three days. Go-to-market relies on enterprise direct engagement, conference presentations (ACS, EuroFAST, ASMS, European Peptide Symposium), webinars ("Practical Applications for Drug Discovery 2020"), and peer-reviewed publications rather than traditional demand generation, supported by a small in-house team of one to ten employees including multiple PhD-level scientists.
The business is bootstrapped and founder-controlled — no external funding rounds are disclosed in any source, and global software distribution is fully delegated to Molecular Discovery, Ltd., which handles licensing, support, and end-customer relationships. This singular channel dependency, combined with limited headcount and an absence of disclosed revenue figures, defines the operating structure: high scientific depth and accumulated intellectual property (reflected in 20+ years of peer-reviewed publications) constrained by a narrow distribution model and no external scale capital.
Lead Molecular Design firmographics
Firmographics- Name
- Lead Molecular Design
- Legal name
- Lead Molecular Design, S.L.
- Website
- https://leadmolecular.com
- Company type
- Private
- Founded year
- 2002
- Operating status
- Operating
- Headcount range
- 1–10 employees
- Short description
- Lead Molecular Design develops cheminformatics software — the ONIRO platform, MassMetaSite, MassChemSite, and MetaSite — for drug discovery, used by pharmaceutical companies, academic groups, and biotech firms for metabolite identification, structure elucidation, and Site of Metabolism prediction.
- Ownership category
- akta.pro rank
Lead Molecular Design industry classification
Industry- Product category
- Drug Discovery Software
- NAICS
- Scientific Research and Development Services (5417), Research and Development in Biotechnology (except Nanobiotechnology) (541714)
- SIC
- Services-Commercial Physical & Biological Research (8731)
- akta.pro primary industry
- Cheminformatics & Molecular Modeling / CADD (HLAGAJAE)
- akta.pro secondary industries
- AI/ML Platforms for Drug Discovery & Experiment Optimization (HLAGAJAO), Drug Discovery (Target ID/Validation & Hit Discovery) (HLAIALAA)
Keywords
Where Lead Molecular Design is headquartered
LocationHeadquarters
- HQ city
- Sant Cugat Del Vallès
- HQ country
- Spain
- HQ region
- Europe
Offices2 records
Markets served
Lead Molecular Design business model
Business model- GTM type
- B2B
- Offering type
- Software
- Cost components
- Personnel, Technology or R&D, Marketing or Sales, Operations
Revenue model
- Software Licensing: The company develops software (MetaSite, MassMetaSite, WebMetabase, MassChemSite) that is distributed under agreement by Molecular Discovery, Ltd. Revenue is generated through software licensing fees.
- Contract Research Services: Lead Molecular Design conducts contract research organizations in drug design and lead optimization for pharmaceutical companies abroad, providing specialized analytical and computational services.
- Training Services: On-line, on-site, and personalized training sessions on software products. Training pricing at $250 per day or $500 for 3 days.
Pricing tiers
| Model | Billing | Price |
|---|---|---|
| Other | One-time | Single-day training session |
| Other | One-time | Three-day comprehensive training |
| Unit Pricing | Pay-as-you-go | Computer rental |
Go-to-market motion2 records
Distribution channels1 record
Marketing channels5 records
Lead Molecular Design product offering
Product offeringCore offering
Lead Molecular Design develops specialized cheminformatics software for drug discovery and lead optimization, focused on mass spectrometry data analysis, metabolite identification, Site of Metabolism prediction, and NMR-based structure elucidation. The product portfolio centers on the ONIRO integrated platform and standalone tools (MetaSite, MassMetaSite, MassChemSite, WebMetabase) used by pharmaceutical, chemical, biotechnology, and academic research organizations. The company also provides contract research services in drug design and lead optimization, plus training on its software products.
Product overview
Lead Molecular Design develops a suite of specialized cheminformatics software for drug discovery and lead optimization. The product portfolio centers on the ONIRO platform, an integrated environment combining WebMetabase (database and analysis), WebChembase (chemical database), Compound Library, and WebQuant (quantification) modules. Supporting products include MassMetaSite for metabolite identification from LC-HRMS data, MassChemSite for chemical reaction analysis and structure elucidation, MetaSite for Site of Metabolism prediction, MS File Converter for data format conversion, and Charming NMR prediction for NMR-based structure confirmation. The software supports both small molecules and macromolecules including peptides and oligonucleotides, distributed in partnership with Molecular Discovery, Ltd.
Differentiator
Problem solved
Functional benefit
Brands
- ONIRO: Platform with enhanced modules including WebMetabase, WebChembase, Compound Library and WebQuant for metabolite identification and data analysis.
- WebMetaBase
- WebChembase
- Compound Library
- WEBQUANT
- MassChemSite
- MassMetaSite
- MS File Converter
- MetaSite
- Charming NMR prediction
Products and services
- ONIRO Platform Integrated platform combining WebMetabase, WebChembase, Compound Library and WebQuant modules for comprehensive metabolite identification, quantification, and data management with enhanced automation and machine learning capabilities. Targeted at pharmaceutical and chemical companies, research centers, and academic groups performing drug design and lead optimization.
- MassMetaSite Software for automated metabolite identification from LC-HRMS data with specialized modes for GSH adducts, peptides, isotope labeling, and batch processing. Supports both small molecules and macromolecules up to 15,000 Da including oligonucleotides and macro-cyclic peptides. Used by pharmaceutical and biotech companies for DMPK and metabolite profiling.
- MassChemSite Software for structure elucidation from LC-HRMS analytical data for chemical reaction samples, featuring reaction tracking workflow, unknown structure elucidation algorithms, and NMR data integration for compound identification. Targeted at chemical companies, agrochemical researchers, and academic groups needing pesticide residue identification.
- WebMetaBase Database system for storing, managing, and analyzing mass spectrometry and metabolism data with tools for protocol definition, approval workflows, kinetic analysis, and multi-experiment analysis including docking, MetaDesign, and fragment analysis. Targeted at pharmaceutical, chemical, and academic researchers performing multi-experiment MS/NMR studies.
- MetaSite Software for prediction of Site of Metabolism (SoM) using computational methods. Targeted at pharmaceutical medicinal chemists and DMPK scientists identifying metabolic soft spots during lead optimization.
- MS File Converter Utility for converting mass spectrometry file formats to enable data processing across different instrument platforms. Targeted at analytical chemistry labs using multiple instrument vendors.
- Charming NMR Prediction NMR prediction module for structure elucidation supporting compound identification when LC-HRMS analysis cannot provide unique solutions. Targeted at analytical chemistry and natural products researchers.
- WebChembase Chemical database module within the ONIRO platform for managing and analyzing chemical compound data. Targeted at chemists and analytical labs handling large chemical libraries.
- WEBQUANT Quantification workflow module for in-vitro and in-vivo data analysis within the ONIRO platform. Targeted at DMPK and bioanalytical scientists requiring customized quantification workflows.
- Compound Library Compound library management module integrated within the ONIRO platform. Targeted at medicinal chemists managing compound collections for high-throughput screening and SAR analysis.
- Software Training Services On-line, on-site, and personalized training sessions on the company's software products (MetaSite, MassMetaSite, WebMetabase, MassChemSite), with European trainings held in Italy and Spain and West Coast US training in California. Priced at $250 per day or $500 for three days.
- Contract Research Services Contract research organization services in drug design and lead optimization for pharmaceutical companies abroad, providing specialized analytical and computational chemistry services leveraging the company's proprietary software.
Quantifiable outcome
- Automated pesticide identification in food samples processing up to 10 different pesticides in less than five minutes of data processing
- +3 more outcomes
Companies that use Lead Molecular Design
Customer profileNamed customers6 records
Segments4 records
Ideal customer profiles4 records
Lead Molecular Design technology and API
TechnologyTechnology focussed Yes
API detail
- Has API
- No
- API docs
- API detail
Core technology
AI maturity
App detail
Integration2 records
AI capability6 records
Feature9 records
Lead Molecular Design partnerships and signals
Strategic signalPartnerships
One partnership is on record.
- Molecular Discovery, Ltd.coreLong-term strategic partnership established in 2002 for research and development of software solutions. Molecular Discovery distributes Lead Molecular Design's software products (MetaSite, MassMetaSite, WebMetabase, MassChemSite) under a distribution agreement. Lead Molecular Design develops the technology while Molecular Discovery handles global distribution, licensing, and customer support.
Scale indicators2 records
Recent moves6 records
Expansion highlights5 records
Lead Molecular Design competitors and assessment
Company assessmentDirect peers
- ACD/Labs (Advanced Chemistry Development): Specialist in analytical chemistry software with MS fragmentation, structure elucidation, and NMR prediction tools. Direct overlap with MassChemSite and Charming NMR Prediction capabilities for pharmaceutical and chemical customers.
- OpenEye Scientific (Cadence Molecular Sciences): Developer of cheminformatics toolkits (RDKit-era equivalents, molecular modeling platforms) for pharma R&D. Comparable in serving computational chemists and DMPK groups with structure-based software tools.
- Chemical Computing Group (CCG, MOE): Developer of Molecular Operating Environment (MOE), a widely used cheminformatics platform in pharma R&D. Comparable in offering interactive computational chemistry tools for medicinal chemists and DMPK groups.
- Molecular Networks / Revvity Signals: Cheminformatics vendor (3D structure handling, retrosynthesis, metabolism prediction) serving pharma and chemical R&D. Comparable in offering computational chemistry tools targeted at medicinal chemists and analytical scientists.
- Molecular Discovery, Ltd. Lead Molecular Design's exclusive distribution partner, also a cheminformatics vendor (MetaSite, Mass Frontier) focused on drug metabolism, MS interpretation and reaction prediction. Highly comparable product scope and shared scientific lineage, while also serving as LMD's go-to-market channel.
- Simulations Plus (now Certara LMC): Developer of Meteor, ADMET Predictor, and GastroPlus — directly competing in metabolite prediction, ADME modeling, and cheminformatics software for pharma. Same buyer (DMPK scientists), same workflow (LC-MS metabolite ID, SoM prediction), different ownership structure.
Emerging players
- Collaborative Drug Discovery (CDD): Cloud-based drug discovery data platform (CDD Vault) with cheminformatics and ADMET modules. Comparable in targeting pharma R&D data management and computational workflow needs.
Broad incumbents
- Schrödinger: Established computational chemistry platform spanning molecular modeling, docking, and ADMET prediction. Broader than LMD but competes for the same pharma computational chemistry budget.
- Certara: Large DMPK and PBPK software platform (Phoenix WinNonlin, Simcyp, now incorporating Simulations Plus). Competes with LMD's SoM/metabolite ID tools as part of a broader regulatory and modeling suite.
- Biovia (Dassault Systèmes): Large, diversified scientific software portfolio (Discovery Studio, Pipeline Pilot, BIOVIA Workbook) including metabolism and analytical chemistry tools. Broad incumbent competing for the same enterprise software spend.
Market position
Strengths5 records
Weaknesses5 records
Competitive moat5 records
Key risks6 records
Key highlights6 records
Customer concentration
Lead Molecular Design social profiles
Digital presenceLead Molecular Design financial estimates
Financial estimateRevenue estimate
Valuation estimate
Lead Molecular Design leadership team
Management profileNumber of profiles
Profiles7 records
Lead Molecular Design funding detail
Funding detailFunding overview
Funding rounds
Investors
Funding detail is available on the Subscription and Enterprise plan.Contact sales →
Lead Molecular Design M&A and investment
M&A and investmentM&A
Investments
M&A and investment is available on the Subscription and Enterprise plan.Contact sales →
Frequently asked questions about Lead Molecular Design
What does Lead Molecular Design do?
Lead Molecular Design develops specialized cheminformatics software for drug discovery and lead optimization, focused on mass spectrometry data analysis, metabolite identification, Site of Metabolism prediction, and NMR-based structure elucidation. The product portfolio centers on the ONIRO integrated platform and standalone tools (MetaSite, MassMetaSite, MassChemSite, WebMetabase) used by pharmaceutical, chemical, biotechnology, and academic research organizations. The company also provides contract research services in drug design and lead optimization, plus training on its software products.
Is Lead Molecular Design a public or private company?
Lead Molecular Design is a private company. It is classified as founder individual operated bootstrapped and is currently operating.
When was Lead Molecular Design founded?
Lead Molecular Design was founded in 2002. It employs 1 to 10 people.
Where is Lead Molecular Design based?
Lead Molecular Design is headquartered in Sant Cugat Del Vallès, Spain, in the Europe region.
How does Lead Molecular Design make money?
Three revenue lines are on record. Software Licensing is the primary driver. The others are contract Research Services and training Services.
Who are Lead Molecular Design's main competitors?
Direct peers on record are ACD/Labs (Advanced Chemistry Development), OpenEye Scientific (Cadence Molecular Sciences), Chemical Computing Group (CCG, MOE), Molecular Networks / Revvity Signals, Molecular Discovery, Ltd. and Simulations Plus (now Certara LMC). Collaborative Drug Discovery (CDD) is listed as an emerging player. Broad incumbents are Schrödinger, Certara and Biovia (Dassault Systèmes).
Does Lead Molecular Design have an API?
No public API is recorded for Lead Molecular Design.
What industry is Lead Molecular Design in?
Lead Molecular Design's product category is Drug Discovery Software. Its primary akta.pro industry code is HLAGAJAE, Cheminformatics & Molecular Modeling / CADD, with a secondary code of HLAGAJAO, AI/ML Platforms for Drug Discovery & Experiment Optimization. Its NAICS code is 5417 and its SIC code is 8731.