APIGENEX s.r.o. is a Prague-based Contract Research Organization delivering integrated chemistry and pharmacology solutions across the drug development pathway, built on over 30 years of experience.

We combine organic synthesis, peptide and peptidomimetic chemistry, analytical expertise, experimental pharmacology, and GMP manufacturing into a fully connected workflow — enabling efficient progression from initial idea to validated lead compound and clinical batch, reducing risk and accelerating timelines.

With 6,000+ small molecule projects and 10,000+ peptide projects, APIGENEX has extensive experience in complex chemistry, including side-chain and linker design, impurity synthesis, and advanced functionalization, delivering decorated peptides, conjugates, peptidomimetics, and hybrid structures.

Core Capabilities:

• Organic Synthesis
• Custom synthesis and FTE-based research, including lead design, building blocks, and impurities
• Peptide, PNA & Peptidomimetic Chemistry
• Sequences to modified peptides, conjugates, libraries and complex architectures
• Analytical & HPLC Purification Services
• NMR, LC-MS/MS, UPLC, impurity profiling, and robotic prep HPLC (mg to kg scale)
• GMP Manufacturing & Clinical Supply
• Process development, scale-up, and GMP production of preclinical and clinical batches
• Theranostics & Radiomedicine
• Ultra-pure chelators (DOTA, NOTA, HBED), targeting ligands, and conjugates
• Experimental Pharmacology (GLP)
• In vitro and in vivo models in diabetes, metabolic diseases, and oncology (4T1, CT26, Panc02, melanoma)
• APIGENEX operates advanced infrastructure, including robotic synthesizers and preparative HPLC systems, enabling reliable scale-up from mg to kilogram quantities.

Deep MedChem develops CHEESE, an AI-powered virtual screening platform that finds the best drug candidates across vast chemical spaces in seconds. Built on a proprietary molecular embedding architecture, CHEESE aligns compound space to client needs: clustering similar molecules together so that searching billions of compounds becomes as fast as a nearest-neighbour lookup rather than an exhaustive computational screen.

The platform supports 40+ billion enumerated molecules and tens of trillions of combinatorial molecules across 14+ commercial chemical spaces from leading vendors including eMolecules, Enamine, Mcule, ChemSpace, Molport, and others. CHEESE offers multiple similarity search methods (2D, 3D shape, 3D electrostatics, substructure, and pharmacophore) with built-in ADMET property predictions and direct molecule ordering through integrated vendor partnerships.

In independent customer evaluations, CHEESE Navigator delivered 109× less docking than exhaustive screening while maintaining equivalent results. In a documented case study with BridGene Biosciences, CHEESE achieved a 147× improved hit rate at sub-10nM potency, completing in 25 hours what previously required 200 days. The platform consistently achieves state-of-the-art results across public benchmarks including LIT-PCBA, DUD-E, and Side-Chain Virtual Screening.

CHEESE is available as a cloud platform, a dedicated instance, or an on-premise deployment, making it suitable for both agile biotech teams and large pharmaceutical organizations with strict data security requirements. Deep MedChem works with leading pharma companies worldwide and offers flexible engagement models: from self-service platform access to co-development partnerships combining CHEESE’s computational capabilities with partners’ drug discovery expertise.

Deep MedChem is headquartered in Prague, Czechia.