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Activities and Technologies

Activities and Technologies

Discovery and characterization of small organic molecules, cyclic peptides, and fully human antibodies specific to targets of interest.

Discovery and validation of pharmaceutical targets for ligand-based pharmacodelivery. Philochem uses state-of-the-art chemical proteomics technologies for the identification of accessible targets and for the characterization of the mechanism of action.

Development of small molecule therapeutics, with the potential to achieve an unprecedented level of activity and selectivity. Philochem is performing pioneering work for the ligand-based delivery of drugs, radionuclides and immunomodulators.

DNA-encoded chemical libraries (DELs)

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 discovery programs and in the frame of collaborations with pharmaceutical industrial or academic partners.

More information on Philochem´s DEL platform is available HERE

For collaboration opportunities, partnerships, or fee-for-service agreements on DNA-encoded chemical libraries, please contact Frederik.Peissert@philochem.ch

References

A DNA-encoded chemical library based on chiral 4-amino-proline enables stereospecific isozyme-selective protein recognition
Oehler et al., Nat. Chem., 2023; 15(10):1431-1443

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Selective tumor targeting enabled by picomolar fibroblast activation protein inhibitors isolated from a DNA-encoded affinity maturation library
Puglioli et al., Chem. 2023, 9, 411-429

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Deep Learning Approach for the Discovery of Tumor-Targeting Small Organic Ligands from DNA-Encoded Chemical Libraries
Torng et al., ACS Omega 2023, 8, 25090-25100

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Impact of library input on the hit discovery rate in DNA-encoded chemical library selections
Puglioli et al., Chem. Sci., 2023; DOI:10.1039/D3SC03688J

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Isolation of a Natural Killer Group 2D Small-Molecule Ligand from DNA-Encoded Chemical Libraries
Dakhel et al., ChemMedChem, 2022, 17(21):e202200350
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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

Encoded Library Technologies

Cyclic peptide phage libraries

Cyclic peptides represent a promising avenue for the development of targeted therapeutics due to their ability to bind to target proteins with high affinity and selectivity, combined with their low inherent toxicity, their relatively high stability, and their ease of production. Cyclic peptides specific to a target of interest can be isolated from large combinatorial libraries such as phage libraries. Philochem has generated innovative cyclic peptide phage libraries comprising over 100 billion library members.
To date, Philochem uses cyclic peptide phage libraries for both in house discovery programs and in the frame of collaborations with pharmaceutical industrial or academic partners.

References

Heinis and Winter (2009) Nat Chem Biol., 5, 502

Encoded Library Technologies

Antibody phage libraries

The discovery of specific binders to protein targets is a crucial step in the discovery of new products at Philochem. Over the last 15 years, we have published the construction and validation of numerous antibody phage libraries comprising more than 100 billion members. These proprietary libraries enable the isolation of specific human monoclonal antibodies against virtually any antigen of interest.

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

References

Generation of a novel fully human non-superagonistic anti-CD28 antibody with efficient and safe T-cell co-stimulation properties
Elsayed et al., Mabs 2023 Jan-Dec;15(1):2220839

Generation and in vivo characterization of a novel high-affinity human antibody targeting carcinoembryonic antigen
Plüss et al., Mabs 2023 Jan-Dec;15(1):2217964

Generation and in vivo validation of an IL-12 fusion protein based on a novel anti-human FAP monoclonal antibody
Nadal et al., J Immunother Cancer. 2022 Sep;10(9):e005282

Selection of a PD-1 blocking antibody from a novel fully human phage display library
Peissert et al., Protein Sci. 2022 Dec;31(12):e4486

Novel human monoclonal antibodies specific to the alternatively spliced domain D of Tenascin C efficiently target tumors in vivo
Nadal et al., MAbs. 2020 Jan-Dec;12(1):1836713

A novel synthetic naïve human antibody library allows the isolation of antibodies against a new epitope of oncofetal fibronectin
Villa et al., MAbs. 2011 May-Jun;3(3):264-72

A high-affinity human monoclonal antibody specific to the alternatively spliced EDA domain of fibronectin efficiently targets tumor neo-vasculature in vivo
Villa et al., Int J Cancer. 2008 Jun 1;122(11):2405-13

A Highly Functional Synthetic Phage Display Library Containing over 40 Billion Human Antibody Clones
Weber et al. (2014) PLoS One, 9, e100000

Selection and characterization of human antibody fragments specific for psoriasin – A cancer associated protein
Cyranka-Czaja et al. (2012) Biochem Biophys Res Commun, 419, 250-5

Design and construction of a naïve mouse antibody phage display library
Sommavilla et al. (2010) J Immunol Methods, 353, 41-3

The Extra-domain A of Fibronectin Is a Vascular Marker of Solid Tumors and Metastases
Rybak et al. (2007) Cancer Res, 67, 10948-57

Tumor-Targeting Properties of Novel Antibodies Specific to the Large Isoform of Tenascin-C
Brack et al. (2006) Clin Cancer Res, 12, 3200-8

Human monoclonal antibodies to domain C of tenascin-C selectively target solid tumors in vivo
Silacci et al. (2006) Protein Eng Des Sel, 19, 471-8

Design, construction, and characterization of a large synthetic human antibody phage display library
Silacci et al. (2005) Proteomics, 5, 2340-50

Isolation of anti-angiogenesis antibodies from a large combinatorial repertoire by colony filter screening
Giovannoni et al. (2001) Nucleic Acids Res, 29, E27

Design and use of phage display libraries for the selection of antibodies and enzymes
Viti et al. (2000) Methods Enzymol, 326, 480-505

A High-Affinity Human Antibody That Targets Tumoral Blood Vessels
Tarli et al. (1999) Blood, 94, 192-8

Human Antibodies With Subnanomolar Affinity Against a Marker of Angiogenesis Eluted from a Two-Dimensional Gel
Pini et al. (1998) J Biol Chem, 273, 21769-76

Targeting by affinity–matured recombinant antibody fragments of an angiogenesis associated fibronectin isoform
Neri et al. (1997) Nat Biotechnol, 15, 1271-5

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

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.

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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Fibroblast Activation Protein Triggers Release of Drug Payload from Non-internalizing Small Molecule Drug Conjugates in Solid Tumors

Zana et al. (2022), Clin Cancer Res CCR-22-1788

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Cross-reactivity to glutamate carboxypeptidase III causes undesired salivary gland and kidney uptake of PSMA-targeted small-molecule radionuclide therapeutics

Lucaroni et al. (2022) Eur J Nucl Med Mol Imaging, doi: 10.1007/s00259-022-05982-8

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A novel dimeric FAP-targeting small molecule-radio conjugate with high and prolonged tumour uptake

Galbiati et al. (2022) J Nucl Med, numed.122.264036

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Translational imaging of the fibroblast activation protein (FAP) using the new ligand [68Ga]Ga-OncoFAP-DOTAGA

Backhaus et al. (2021) Eur J Nucl Med Mol Imaging, 10.21203/rs.3.rs-969176/v1

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An ultra-high-affinity small organic ligand of fibroblast activation protein for tumor-targeting applications

Millul et al. (2021) PNAS, 118, 16, e2101852118

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Immunotherapy with Immunocytokines and PD-1 Blockade Enhances the Anticancer Activity of Small Molecule-Drug Conjugates Targeting Carbonic Anhydrase IX

Millul et al. (2021) Mol Cancer Ther, 20, 512-22

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A Microdosing Study with 99mTc-PHC-102 for the SPECT/CT Imaging of Primary and Metastatic Lesions in Renal Cell Carcinoma Patients

Kulterer et al. (2021) J Nucl Med, 62, 360-5

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Impact of Ligand Size and Conjugation Chemistry on the Performance of Universal Chimeric Antigen Receptor T-Cells for Tumor Killing

Pellegrino et al. (2020) Bioconjug Chem, 31, 1775-83

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Enhanced Therapeutic Activity of Non-Internalizing Small-Molecule-Drug Conjugates Targeting Carbonic Anhydrase IX in Combination with Targeted Interleukin-2

Cazzamalli et al. (2018) Clin Cancer Res, 24, 3656-67

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Chemically Defined Antibody– and Small Molecule–Drug Conjugates for in Vivo Tumor Targeting Applications: A Comparative Analysis

Cazzamalli et al. (2018) JACS, 140, 1617-21

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Linker stability influences the anti-tumor activity of acetazolamide-drug conjugates for the therapy of renal cell carcinoma

Cazzamalli et al. (2017) J Control Release, 246, 39-45

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Acetazolamide Serves as Selective Delivery Vehicle for Dipeptide-Linked Drugs to Renal Cell Carcinoma

Cazzamalli et al. (2016) Mol Cancer Ther, 15, 2926-35

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A 99mTc-Labeled Ligand of Carbonic Anhydrase IX Selectively Targets Renal Cell Carcinoma In Vivo

Krall et al. (2016) J Nucl Med, 57, 943-9

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Dual-display of small molecules enables the discovery of ligand pairs and facilitates affinity maturation

Wichert et al. (2015) Nat Chem, 7, 241-9

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Antibody–Drug Conjugates and Small Molecule–Drug Conjugates: Opportunities and Challenges for the Development of Selective Anticancer Cytotoxic Agents

Casi & Neri (2015) J Med Chem, 58, 8751-61

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[64Cu]XYIMSR-06: A dual-motif CAIX ligand for PET imaging of clear cell renal cell carcinoma

Minn et al. (2016) Oncotarget, 7, 56471-79

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Imaging of carbonic anhydrase IX with an 111In-labeled dual-motif inhibitor

Yang et al. (2015) Oncotarget, 6, 33733-42

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A bivalent small molecule-drug conjugate directed against carbonic anhydrase IX can elicit complete tumour regression in mice

Krall et al. (2014) Chem Sci, 5, 3640-4

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A Small-Molecule Drug Conjugate for the Treatment of Carbonic Anhydrase IX Expressing Tumors

Krall et al. (2014) Angew Chem Int Ed, 53, 4231-5

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Small Targeted Cytotoxics: Current State and Promises from DNA-Encoded Chemical Libraries

Krall et al. (2013) Angew Chem Int Ed Engl, 52, 1384-1402

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DOTA conjugate with an albumin-binding entity enables the first folic acid-targeted 177Lu-radionuclide tumor therapy in mice

Müller et al. (2013) J Nucl Med, 54, 124-31

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Human monoclonal antibodies targeting carbonic anhydrase IX for the molecular imaging of hypoxic regions in solid tumours

Ahlskog et al. (2009) Bioorg Med Chem Lett, 19, 4581-6

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A Portable Albumin Binder from a DNA-Encoded Chemical Library

Dumelin et al. (2008) Angew Chem Int Ed Engl, 47, 3196-3201

Antibody-based Therapeutics

The Philogen Group has pioneered fully human antibody-cytokine fusion proteins (also called “immunocytokines”). Cytokines are naturally produced proteins of the human body, which can either potently boost or suppress the activity of the immune system. A number of recombinant cytokines have been approved for therapeutic use, but their systemic administration at therapeutically active doses is often hindered by strong side effects. To overcome this limitation, we have engineered innovative antibody-cytokine fusion proteins to selectively localize at the site of disease and to obtain an improved therapeutic index.

The cytokine payload is chosen depending on the nature of the disease. For example, pro-inflammatory cytokines such as TNF, IL2 or IL12 can be used in oncology, while anti-inflammatory cytokines such as IL10 can be used to treat inflammatory conditions.

Our Group has generated, produced, tested, and published more than 50 cytokine payloads fused to proprietary targeting antibodies. The most promising candidates have been brought to clinical trials, one of which has recently successfully completed a Phase III trial.

For more information about the individual programs, please visit the pipeline section of the Philogen group.