background

Discovery Platforms Integrating Ultrahigh-throughput Experimental Screening with Machine Learning and Computational Biophysics

CCM Bio’s proprietary discovery platforms are licensed from the affiliated R&D institute Chakrabarti Advanced Technology, LLC

Small Molecule Discovery Platform

  • DNA-Encoded Library Technology
  • DEL platform-based optimization of SIRT3 modulators

header

DNA-Encoded Libraries : New Chemical Entities

  • Ultrahigh-throughput drug discovery using DNA-encoded library (DEL) techniques. Mixture of various molecules identified by the code of life : DNA
  • Orders of magnitude larger and faster than traditional high-throughput small molecules screening: DEL HTS : 50 experiments to test 1 million compounds for 50 specific targets, compare to 50 millions experiments with classical methods
dna image

chemists and biologists team dedicated to generate DNA libraries with ‘split and pool’ and/or perform selection with protein targets

dedicated laboratory to perform chemistry and biology experiments as well as massively parallel NGS sequencing and data analyses

Integration with computational biophysics and machine learning methods to accelerate optimization of small molecule designs compared to DEL alone

Applications

  • Identification of new small molecules binding to a target biomacromolecule and exert a desired pharmaceutical effect (inhibition, activation, or protein degradation)

  • Enabled CCM Bio Rx Programs:

Case Study: Application to the discovery of new activators/inhibitors of Sirtuin3, a key regulator of mitochondrial metabolism.

We produced and screened a DNA encoded library consisting of the coupling of amino acids with carboxylic acids.

crdmo-platform crdmo-platform
7 compounds were synthesized off-DNA (6 compounds that showed the best enrichments and one compound serving as a negative control) in order to measure their binding (KD) and their modulation effect on SIRT3 activity

Patents:
  • Methods for the design of mechanism-based sirtuin activating compounds.US Patent 11,118,211 B2 (2021)
  • Methods for the design of mechanism-based sirtuin activating compounds. US Patent 11,459,597 (2022)
  • Methods for the design of nonallosteric sirtuin activating compounds. US patent application 2022/0002778 A1 (2021)
  • Sirtuin modulating compounds and applications thereof. US patent application 18/090,953 (2022)
Research article(s):
 

Drug Delivery Platform

  • Drug Delivery Technology
  • Polyaminoacid and Lipid Nanoparticles for Passive Drug Delivery
  • Polyaminoacid and Lipid Nanoparticles for Active Drug Delivery

header

New Excipients

  • New polymers (PolyAminoacids - PAA) research and development
  • Excipients with excellent biodegradability, easy functionalization, easy conjugation, bioavailability properties.
  • Polymers characterization, process development and scale-up
  • Unique know-how and integration from raw materials to PolyAminoAcids production
dna image

New Drug Delivery Systems

  • Drug delivery systems with versatile architecture and functionality
  • Superior biodegradability and biocompatibility
  • High cargo loadings and improved bioavailability of your APIs
  • Modulation of interactions with biological barriers allowing to explore multiple administration routes

Enabled CCM Bio Programs

encapsulation image

Polyaminoacids for PASSIVE drug delivery

encapsulation image
polypeptides image


Patents:
  • Amphiphilic polyamino acid block copolymers and nanoparticles thereof for drug delivery applications. EP patent application 22305766.2 – 1102, Filed 2022
Research article(s):

Polyaminoacids for ACTIVE drug delivery

encapsulation image

polypeptides image
ACTIVE DELIVERY:
Engineered peptide or antibody (identified by Phage Display) conjugated to PAA micelle

Biological interaction between ligands on the surface of nanoparticles and the cell target Several types of ligands could be used for facilitating active targeting of NPs : bind to specific receptors on the surface of the target cells and increase cellular uptake of drug-containing NPs and increase therapeutic efficacy.

Additional capabilities:
Delivery of gene therapy APIs (nucleic acids -- DNA/RNA drugs) by cationic polymers through conjugation or encapsulation

Patents:
  • New EGFRvIII-binding peptides, conjugates and uses thereof. European patent application B77140EP; International patent application PCT/EP2022/087500, Filed 2022
Research article(s):

Biologics Discovery Platform

  • Machine Learning-enabled Phage Display Technology
  • CASE STUDY (active Drug Delivery Application): EGFR vIII peptide binder

header

Phage Display: New Biologics

  • Ultrahigh-throughput drug discovery using Phage Display: a combinatorial biology technique
  • Identify hit peptides and antibodies as therapeutic agents, vaccines, diagnostic reagents, as well as gene and drug delivery systems
  • Ability to generate very high diverse exogenous peptides or proteins displayed on the surface of the phage using standard molecular biology
dna image

A biologists team dedicated to generate and screen P.D. libraries

A dedicated laboratory to perform chemistry and biology experiments as well as massively parallel NGS sequencing and data analyses

Integration with computational biophysics and machine learning methods to accelerate optimization of small molecule designs compared to DEL alone

Applications

  • Identification of new molecules binding to a target biomacromolecule and exert a desired pharmaceutical effect

  • Enabled CCM Bio Rx Programs:

CASE STUDY (active drug delivery application) : EGFR vIII peptide binder

Background:


One of the few known cancer-specific cell surface markers is the epidermal growth factor (EGFR) tyrosine kinase receptor mutation variant III (EGFRvIII). Tumor-targeting ligands such as peptides and antibodies may effectively aid certain cytotoxic agents (either biological or synthetic) to deliver to the tumor cells, thereby improving therapeutic efficacy while limiting the exposure of normal tissues to the cytotoxic agents
dna image

Project goal: identification of novel peptide ligands targeted EGFRvIII, which could be used as a targeting ligand assisting specific delivery of cytotoxic drug specifically into the tumor vasculature, tumor microenvironment or into the cancer cells




Patents:
  • New EGFRvIII-binding peptides, conjugates and uses thereof. European patent application B77140EP; International patent application PCT/EP2022/087500, Filed 2022
Research article(s):

Enzyme Engineering Platform

  • Ultrahigh-throughput Droplet Microfluidics
  • Droplet Microfluidics: Further Details

header

Protein/Enzyme Engineering: New Enzymes

  • Enzyme engineering using ultrahigh-throughput droplet microfluidics
  • Upstream processing: Proteins/biologics production by fermentation; Nucleic acids production by biocatalysis
  • Downstream processing: Purification, scale-up and characterization
  • Antibodies, bioconjugates manufacturing
dna image

A biologists team dedicated to produce, purify and characterize proteins

A dedicated laboratory to perform molecular biology and enzyme engineering, production and characterization

Integration with computational biophysics and machine learning methods to accelerate optimization of enzyme designs beyond directed evolution alone

Applications

Droplet Microfluidics: Further Details

dna image



dna image

Patents:
  • System and methods for determination of temperature cycling protocols for polymerase chain reactions. US Patent 10,861,586 B2 (2020)
  • System and methods for determination of temperature cycling protocols for polymerase chain reactions. EP Patent 3,000,366 B1 (2020)
  • System and methods for determination of temperature cycling protocols for polymerase chain reactions: optimally controlled PCR. US patent application 2019/0182944 A1, Filed 2019
  • System for determination of temperature cycling protocols for polymerase chain reactions: polymerase extension. US patent application 2019/0279739 A1, Filed 2019
  • System for determination of temperature cycling protocols for polymerase chain reactions: oligonucleotide annealing. US patent application 2019/0270189245, Filed 2019
  • System for determination of temperature cycling protocols for polymerase chain reactions: DNA melting. US patent application 2019/0295686 A1, Filed 2019
  • Polymerases for mixed aqueous-organic media and uses thereof,  International patent application PCT/US2022/011076. Filed 2022
  • Compositions and methods for enhancing PCR and other polynucleotide amplification reactions. US Patent 6,949,368 (2005)
  • Compositions and methods for enhancing polynucleotide amplification reactions. US Patent 7,276,357 (2007)
  • Chemical PCR: Compositions and methods for enhancing polynucleotide amplification reactions. US Patent 7,772,383 (2010)
Research article(s):