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Small Molecules in Drug Discovery

Overcome your drug discovery challenges with Thermo Fisher Scientific's comprehensive portfolio for small molecule drug discovery. Our range of bioactive molecules can help you select the right assay, then our highly diverse screening libraries provide a higher chance of Hit identification. After which our expansive collection of building blocks and reagents enable you to optimize your hits through Structure Activity Relationship (SAR). Working with a single partner simplifies your discovery process, enhancing efficiency and reproducibility.

Bioactives

Small molecules are crucial throughout the drug development lifecycle, from target identification and mechanistic studies to lead optimization, preclinical validation, and translational research. Their versatility makes them indispensable in both hypothesis-driven research and phenotypic discovery.

At Thermo Scientific, our compound collections—including bioactive molecules, antibiotics, and signal transduction molecules—are used across various development phases in both exploratory studies and targeted assays designed to probe specific pathways or disease mechanisms.

Modern drug discovery favors strategic compound selection using smaller, curated libraries with known bioactivity or target relevance. This quality-over-quantity approach reduces costs, minimizes false positives, and improves translational outcomes.

These molecules are essential in developing therapeutics for:

  • Oncology: where pathway-specific inhibitors block tumor proliferation
  • Cardiovascular Disease: where ion channel modulators and vasodilators are under investigation
  • Anti-infectives: where novel antibiotics address rising resistance
  • Neurological Disorders: where small molecules elucidate neurochemical pathways and modulate neuronal function

Whether you're mapping signaling cascades, validating drug targets, or refining lead compounds, our small molecule tools provide high-impact data and accelerate decision-making throughout discovery and development.

Our Solutions

Diverse

The Thermo Scientific™ Small Molecule Collection includes a highly curated and functionally diverse portfolio of bioactive compounds, antibiotics, and signal transduction molecules. These molecules are used not only in high-throughput screening, but also in mechanistic studies, target validation, and pathway analysis. Their application spans key therapeutic areas e.g. oncology, cardiovascular disease, anti-infectives, and neurological disorders and others. ​

Mechanism-Driven

Unlike traditional hit-like collections, these compounds are selected for their known or predicted biological activity and ability to modulate specific cellular targets or signaling pathways. Their structures are optimized to reflect real-world drug properties, enabling both exploratory research and translational development.​

Reliable

These are high-quality, experimentally validated molecules designed for consistent performance across in vitro, cell-based, and early in vivo models. Whether probing cellular signaling in cancer or investigating antimicrobial resistance, researchers trust these libraries for reproducibility and actionable biological insights.

Benefit

  • Better Data, Faster: A focused yet functionally rich compound library improves the quality of data generated while reducing unnecessary complexity and cost.​
  • Smarter Discovery: Small molecules with validated bioactivity and drug-like properties increase the likelihood of success in early- and mid-stage discovery workflows.​
  • Move Forward Quickly: Enables faster progress from target engagement to lead optimization, while supporting diverse applications across therapeutic research fields.​
  • Supports Your Research Area: Whether you're studying cancer, heart disease, infections, or the brain, these molecules are ready to support your work from basic biology to preclinical development.

Resources and Related Information

Bioactive Small Molecules

A vast array of small, non-peptide, organic compounds that are biologically active. Products include receptor antagonists, molecular probes, metabolites, GPCR ligands, neurotransmitters, ion channel modulators, and signaling activators and inhibitors.

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High-Throughput-Screening

Thermo Scientific™ Screening Collection: The choice of screening library can make or break a small-molecule drug discovery program in its early phases. Our screening libraries are designed to increase the probability of positive results while optimizing cost, time, and effort spent per project

Our Solutions

Diverse

The Maybridge Screening Collection is a highly diverse set of over 53,000 hit-like and lead-like molecules widely acknowledged as a critical tool in screening campaigns.

Hit-Like

The compounds comply with the classic characteristics of drug-like molecules, as defined by Lipinski’s so-called “Rule of 5”. These rules are essentially a pragmatic reduction of the common features of drugs represented by the WDI.

Reliable

High-quality libraries of compounds with the right chemical properties for successful hit-finding.

Benefit

  • A smaller but highly diverse screening collection will provide a greater hit probability than larger, but less diverse libraries​
  • Screening compounds that have the right chemical properties is more likely to achieve successful results faster and at a lower cost​
  • This approach can accelerate your discovery campaigns by giving you an excellent starting point for Hit to Lead Optimization

Resources and Related Information

Increasing Success Rates in Your Drug Discovery Research

High-throughput screening and fragment libraries.

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Fragment Screening

Fragment screening has become a method of choice in the quest for rapid identification of new lead molecules in drug discovery due to the higher hit probability and fewer fragments needing to be screened. 

Our Solutions

Our Maybridge Fragment Libraries contain structurally diverse compounds providing an excellent chance of finding “hits”​.

Guaranteed solubility in PBS buffer means the library can be used with any screening technique.

The library has been pre-screened for Surface Plasmon Resonance (SPR) to ensure it is compatible with the instruments used​.

Compounds with a history of providing false hits are removed so you can be sure yours are genuine​.

Feature Benefits

  • Rule of Three (Ro3) compliance delivers superior ADME attributes​
  • Exceptional diversity – Tanimoto similarity index of 0.66 based on standard Daylight fingerprinting​
  • PAINS Free – The library has been filtered to remove pan assay interference compounds (PAINS) avoiding false hits​
  • Experimentally measured solubility – guaranteed solubility of fragments in PBS buffer (1mM) ensures robust screening data and minimizes candidate attrition​
  • Optimised for SPR – in collaboration with Cytiva Healthcare a “Clean Screen” was run on a Biacore instrument to remove promiscuous binders

Resources and Related Information

Increasing Success Rates in Your Drug Discovery Research

High-throughput screening and fragment libraries.

27156_Brand_C2_P4_Doc1

Contact Us

Please complete the form below if you wish to request a quote and/or receive more information about small molecules in drug discovery products.

Required Field *

  • Academic (College/University)
  • Agriculture
  • Biotechnology
  • Biotools (Life Science Provider)
  • Chemical Manufacturing
  • CMO
  • CRO
  • Education (K-12)
  • Electronics
  • Environmental
  • Food/Beverage Manufacturing
  • Government
  • Healthcare
  • Industrial Manufacturing
  • Medical Equipment Manufacturing
  • Medical Research
  • Mining/Oil and Gas Extraction
  • Pharmaceutical
  • Other

Briefly describe your needs so we can best direct your inquiry to the right person.

Your confidentiality is important to us and all personal information that you provide will be used by us in accordance with our Privacy Policy and you will have the ability to opt out of receiving future marketing information from us at any time.

Monomers (Building Blocks) for Hit to Lead Optimization

The availability of diverse and pharmacophorically relevant synthetic building blocks remains a critical success factor in the drug design process. Where key building blocks are not commercially available, in-house synthesis consumes vital time and can add considerable cost to the project.​

Our focus is to provide medicinal chemists with the ideal building blocks for use in early-phase drug discovery in:​

  • Structure activity relationship (SAR) development ​
  • Generating screening libraries for further hit identification/elaboration​

Our extensive range of medicinally relevant building blocks are specifically designed for lead optimization through structure activity relationship (SAR) development. ​

Our Solutions

Adds to the pharmacophoric profile of your target molecules​.

Facilitates the full breadth of chemical synthesis techniques​.

Enables systematic exploration of structural diversity space​.

Provides easier interpretation of SAR.

Feature Benefits

  • We have > 25,000 building blocks containing over 300 different heterocyclic ring systems​
  • And support all synthetically useful functional groups ​
  • We list all possible ring regioisomers ​
  • And the compounds have minimal additional substitution

Resources and Related Information

Chemical Probes

Our range of chemical probes are selective small-molecule modulators of a protein’s function, designed to allow researchers to ask mechanistic and phenotypic questions about their molecular target in cell-based or animal research studies.​

Chemical probes represent an important component in both academic and pharmaceutical drug discovery research and development. These compounds help reduce the technical and biological risks of pursuing a pathway or target before incurring the time and expense of drug development and clinical trials. Chemical probes are essential in the validation of new molecular targets for a therapeutic indication.​

Our Solutions

Our chemical probes enable researchers to validate the Mode of Action (MoA) of their drug candidates​.

This minimizes the risk of unexpected side effects in clinical trials​.

Offers a greater probability of achieving a successful conclusion to your drug discovery program.

Feature Benefits

  • Biological properties include a known MoA, high in vitro potency, high selectivity, and demonstrated on-target effects in cells.
  • Physicochemical properties include stability, solubility, membrane permeability, and a characterized, reproducible structure
  • Excluded compounds with pan-assay interference (PAINS) properties, such as covalent reactivity, redox activity, and colloidal aggregation

Resources and Related Information

Chemical Probes

Potent and selective modulators of protein functions accelerating drug discovery.

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Bioactive Small Molecules

A vast array of small, non-peptide, organic compounds that are biologically active. Products include receptor antagonists, molecular probes, metabolites, GPCR ligands, neurotransmitters, ion channel modulators, and signaling activators and inhibitors.

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