Design, construction and screening of encoded combinatorial libraries, for the identification of small molecule ligands against disease targets. Philochem is a leader in the field of DNA-encoded chemical libraries

Encoded Combinatorial Libraries

The discovery of small organic ligands to protein targets has been traditionally performed by screening very large sets of organic molecules (termed “chemical libraries”), one by one, using high-throughput screening procedures. The assembly of such libraries is very expensive and time consuming. While the value of high-throughput library screening has been demonstrated in various pharmaceutical applications, it is not uncommon that binding molecules of sufficient affinity and specificity (called “hits”) cannot be discovered using conventional screening campaigns.

In light of these considerations, considerable efforts have been devoted to the establishment of encoded libraries which enable the construction and screening of compound sets of unprecedented size in a cost-efficient fashion. Encoded libraries enable a physical connection between a phenotype (i.e., a ligand) and the corresponding genetic information.

Philochem has been practicing antibody-phage display technology for the last 25 years. All antibody-ligands, that Philochem has moved to clinical trials, stem from research activities which have been conducted using its proprietary libraries.

In 2004, our group pioneered the construction of DNA-encoded combinatorial libraries of organic molecules. The technology allows the rapid selection of specific binders (“Phenotype”), physically connected to unique DNA tags (“Genotype”) that work as amplifiable identification barcodes. Since then, Philochem has synthesized several DNA-encoded chemical libraries, featuring different designs, that have yielded high affinity and selective binders to a variety of target proteins of pharmaceutical interest.

To date, Philochem uses encoded libraries for both in house discover programs and in the frame of collaborations with pharmaceutical industrial or academic partners.

References

Selective tumor targeting enabled by picomolar fibroblast activation protein inhibitors isolated from a DNA-encoded affinity maturation library

Puglioli et al. (2022) Chem, doi: 10.1016/j.chempr.2022.10.006

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Isolation of a Natural Killer Group 2D Small-Molecule Ligand from DNA-Encoded Chemical Libraries

Dakhel et al. (2022) ChemMedChem, 17, e202200350

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Specific Inhibitor of Placental Alkaline Phosphatase Isolated from a DNA-Encoded Chemical Library Targets Tumor of the Female Reproductive Tract

Bassi et al. (2021) J Med Chem, 64, 15799-15809

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Affinity Selections of DNA-Encoded Chemical Libraries on Carbonic Anhydrase IX-Expressing Tumor Cells Reveal a Dependence on Ligand Valence

Oehler et al. (2021) Chemistry, 27, 8985-8993

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Stereo- and regiodefined DNA-encoded chemical libraries enable efficient tumour-targeting applications

Favalli et al. (2021) Nat Chem, 13, 540-548

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Identification and Validation of New Interleukin-2 Ligands Using DNA-Encoded Libraries

Gironda-Martinez et al. (2021) J Med Chem 64, 17496-17510

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A Single‐Stranded DNA‐Encoded Chemical Library Based on a Stereoisomeric Scaffold Enables Ligand Discovery by Modular Assembly of Building Blocks

Bassi et al. (2020) Advanced Science, 7(22): 2001970

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On-DNA hit validation methodologies for ligands identified from DNA-encoded chemical libraries

Prati et al. (2020) Biochem Biopsy’s Res Commun, 533, 235-240

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Reflections on DNA-encoded chemical libraries

Lerner and Neri (2020) Biochem Biopsy’s Res Commun, 527, 757-759

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Quantitative Assessment of Affinity Selection Performance by Using DNA-Encoded Chemical Libraries

Sannino et al. (2019) Chembiochem, 20, 955-962

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Versatile protein recognition by the encoded display of multiple chemical elements on a constant macrocyclic scaffold

Li et al. (2018) Nat Chem, 10, 441-8

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Affinity Enhancement of Protein Ligands by Reversible Covalent Modification of Neighboring Lysine Residues

Dal Corso et al. (2018) Agew Chem Int Ed Engl, 57, 17178-82

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DNA-Encoded Chemical Libraries: A Selection System Based on Endowing Organic Compounds with Amplifiable Information

Neri and Lerner (2018) Annu Rev Biochem, 8, 479-502

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Impact of a Central Scaffold on the Binding Affinity of Fragment Pairs Isolated from DNA-Encoded Self-Assembling Chemical Libraries

Bigatti et al. (2017) ChemMedChem 12,1748

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Optimized Reaction Conditions for Amide Bond Formation in DNA-Encoded Combinatorial Libraries

Li et al. (2016) ACS Comb Sci, 18, 438-43

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Identification of Structure–Activity Relationships from Screening a Structurally Compact DNA-Encoded Chemical Library

Franzini et al. (2015) Anger Chem Int Ed Engl, 23, 3927-31

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Dual-pharmacophore DNA-encoded chemical libraries

Scheuermann et al. (2015) Curr Open Chem Viol, 26, 99-103

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DNA-Encoded Chemical Libraries: A Tool for Drug Discovery and for Chemical Biology

Scheuermann et al. (2010) Chembiochem 11, 931-7

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High-throughput sequencing allows the identification of binding molecules isolated from DNA-encoded chemical libraries

Mannocci et al. (2008) Proc Natl Acad Sci USA, 105, 17670-5

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Encoded self-assembling chemical libraries

Melkko et al. (2004), Nature Biotechnol, 22-568-74

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2. Discovery and validation of pharmaceutical targets

The development of targeted therapeutics crucially relies on the identification of target antigens, which are specifically expressed at the site of disease, and which are readily accessible for agents coming from the bloodstream.

In collaboration with with ETH Zürich, Philochem has pioneered chemical proteomics methods for the characterization of accessible markers of pathology, which can be drugged by antibodies and small molecule ligands.

In a simple setup, cell lines can be submitted to surface biotinylation followed by capture on streptavidin resin and mass spectrometric analysis of tryptic peptides.

In a more complex setup, in vivo biotinylation procedures of rodent models of pathology enable the chemical proteomic characterization of vascular proteins in health and in disease. The technology has been extended to the ex vivo perfusion of surgically-resected human organs with cancer.

More broadly, we use MS-based chemical proteomics approaches to study the mechanism of action of our drugs. This includes the mass spectrometric quantification of drug delivery and release, as well as MHC-I peptidome analysis

References

Mass Spectrometry-Based Method for the Determination of the Biodistribution of Tumor-Targeting Small Molecule–Metal Conjugates
Gilardoni et al. (2022) Anal Chem, 93, 10715

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Antibody-based Delivery of TNF to the Tumor Neovasculature Potentiates the Therapeutic Activity of a Peptide Anticancer Vaccine
Probst et al. (2019) Clin Cancer Res, 25, 698-709

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Sarcoma Eradication by Doxorubicin and Targeted TNF Relies upon CD8+ T-cell Recognition of a Retroviral Antigen

Probst et al. (2017) Cancer Res, 77, 3644-54

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Purification of soluble HLA class I complexes from human serum or plasma deliver high quality immuno-peptidomes required for biomarker discovery

Ritz et al. (2017) Proteomics, 17, 10.1002/pmic.201600364

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Mass spectrometric analysis of the HLA class I peptidome of melanoma cell lines as a promising tool for the identification of putative tumor-associated HLA epitopes

Gloger et al. (2016) Cancer Immunol Immunother, 65, 1377-93

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High-sensitivity HLA class I peptidome analysis enables a precise definition of peptide motifs and the identification of peptides from cell lines and patients’ sera

Ritz et al. (2016) Proteomics, 16, 1570-80

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High-resolution analysis of the murine MHC class II immunopeptidome

Sofron et al. (2016) Eur J Immunol, 46, 319-28

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From target discovery to clinical trials with armed antibody products

Elia et al. (2014) J Proteomics, 107, 50-5

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Interfering with pH regulation in tumours as a therapeutic strategy

Neri and Supuran (2011) Nat Rev Drug Discov, 10, 767-77

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Proteomic identification of vanin-1 as a marker of kidney damage in a rat model of type 1 diabetic nephropathy

Fugmann et al. (2011) Kidney Int, 80, 272-81

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The accessible cerebral vascular proteome in a mouse model of cerebral β-amyloidosis

Roesli et al. (2011) J Proteomics, 74, 539-46

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In vivo biotinylation of the vasculature in B-cell lymphoma identifies BST-2 as a target for antibody-based therapy

Schliemann et al. (2010) Blood, 115, 736-44

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A Proteomic Approach for the Identification of Vascular Markers of Liver Metastasis

Borgia et al. (2010) Cancer Res, 70, 309-18

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DeepQuanTR: MALDI-MS-based label-free quantification of proteins in complex biological samples

Fugmann et al. (2010) Proteomics, 10, 2631-43

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Quantitative Recovery of Biotinylated Proteins from Streptavidin-Based Affinity Chromatography Resins

Rösli et al. (2008) Methods Mol Biol, 418, 89-100

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Identification of new accessible tumor antigens in human colon cancer by ex vivo protein biotinylation and comparative mass spectrometry analysis

Conrotto et al. (2008) Int J Cancer, 123, 2856-64

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A Chemical Proteomics Approach for the Identification of Accessible Antigens Expressed in Human Kidney Cancer

Castronovo et al. (2006) Mol Cell Proteomics, 5, 2083-91

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Tumor-Targeting Properties of Novel Antibodies Specific to the Large Isoform of Tenascin-C

Brack et al. (2006) Clin Cancer Res, 12, 3200-8

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Identification and relative quantification of membrane proteins by surface biotinylation and two-dimensional peptide mapping

Scheurer et al. (2005) Proteomics, 5,2718-28

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In vivo protein biotinylation for identification of organ-specific antigens accessible from the vasculature

Rybak et al. (2005) Nat Methods, 2, 291-98

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Tumour vascular targeting

Neri and Bicknell (2005) Nat Rev Cancer, 5,436-46

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Small Molecule Therapeutics

Low molecular weight compounds represent attractive alternatives to antibodies for tumor targeting applications. The advantages of small molecule therapeutics include a fast extravasation, a deep and homogeneous penetration into solid tumors, as well as faster development timelines.

Thanks to technological advances in the field of DNA-encoded chemical libraries, we are able to generate small molecule ligands with antibody-like properties featuring ultra-high affinity to their target antigen and long residence time at the tumor site.

Philochem uses small ligands with exceptional targeting performance for the selective delivery of (i) radionuclides, (ii) cytotoxic agents, (ii) immunomodulators, or (iv) adaptors for universal Chimeric Antigen Receptor T cell therapy.

Please visit our pipeline section for more information about individual programs.