Patents by Inventor Sander Sebastiaan Van Berkel

Sander Sebastiaan Van Berkel has filed for patents to protect the following inventions. This listing includes patent applications that are pending as well as patents that have already been granted by the United States Patent and Trademark Office (USPTO).

  • Patent number: 11957763
    Abstract: The invention relates to a novel linker for use in bioconjugates such as antibody-drug-conjugates. The linker according to the invention is represented by formula: wherein: BM is a branching moiety; E is a capping group; SG is a sulfamide group; b, c, d, e, g, i, k, l are independently 0 or 1; f is an integer in the range of 1 to 10; Sp1, Sp2, Sp3, Sp4, Sp5 and Sp6 are a spacer moieties; Z1 and Z2 are connecting groups. The linker according to the invention is useful in the preparation of linker-conjugates and bioconjugates, and can be used for (a) improving conjugation efficiency in the preparation of the bioconjugate, (b) reducing aggregation during the preparation of the bioconjugate and/or of the bioconjugate, (c) increasing stability of the bioconjugate, and/or (d) increasing therapeutic index of the bioconjugate.
    Type: Grant
    Filed: December 28, 2020
    Date of Patent: April 16, 2024
    Assignee: SYNAFFIX B.V.
    Inventors: Sander Sebastiaan Van Berkel, Ryan Heesbeen, Jorge Merijn Mathieu Verkade, Maria Antonia Wijdeven, Floris Louis Van Delft
  • Patent number: 11850286
    Abstract: The present invention relates to a compound comprising an alpha-end and an omega-end, the compound comprising on the alpha-end a reactive group Q1 capable of reacting with a functional group F1 present on a biomolecule and on the omega-end a target molecule, the compound further comprising a group according to formula (1) or a salt thereof: Said compound may also be referred to as a linker-conjugate. The invention also relates to a process for the preparation of a bioconjugate, the process comprising the step of reacting a reactive group Q1 of a linker-conjugate according to the invention with a functional group F1 of a biomolecule. The invention further relates to a bioconjugate obtainable by the process according to the invention.
    Type: Grant
    Filed: October 5, 2020
    Date of Patent: December 26, 2023
    Assignee: SYNAFFIX B.V.
    Inventors: Jorge Merijn Mathieu Verkade, Maria Antonia Wijdeven, Petrus Josephus Jacobus Maria Van De Sande, Sander Sebastiaan Van Berkel, Floris Louis Van Delft
  • Publication number: 20230364262
    Abstract: The present invention provides antibody-payload conjugates having a payload-to-antibody ratio of 1. The antibody-payload conjugate having structure (1): wherein: a, b and c are each independently 0 or 1; L1, L2 and L3 are linkers; D is a payload; BM is a branching moiety; Z are connecting groups obtainable by a cycloaddition reaction. The invention further provides a method for preparing the antibody-payload conjugate according to the invention, an intermediate compound in that preparation method, and medical uses of the antibody-payload conjugate according to the invention.
    Type: Application
    Filed: July 12, 2022
    Publication date: November 16, 2023
    Inventors: Floris Louis VAN DELFT, Jorin HOOGENBOOM, Sorraya POPAL, Arnoldus Jacobus VAN SCHAIK, Laureen DE BEVER, Remon VAN GEEL, Maria Antonia WIJDEVEN, Sander Sebastiaan VAN BERKEL
  • Publication number: 20230355791
    Abstract: The present invention provides antibody-conjugates which are conjugated via the glycan and still bind to a cell comprising an Fc-gamma receptor. The antibody conjugates according to the invention have structure (1): Ab-[(GlcNAc(Fuc)b-(G)e-(Su-(Z-L-(D)r)x)s]y ??(1) Herein, Ab is an antibody; GlcNAc is an N-acetylglucosamine moiety; Fuc is a fucose moiety; b is 0 or 1; G is a monosaccharide; e is an integer in the range of 4-10; Su is a monosaccharide; Z is a connecting group obtained by a cycloaddition or a nucleophilic reaction; L is a linker; D is a payload; s is 1 or 2; r is an integer in the range of 1-4; x is 1 or 2; y is 2 or 4.
    Type: Application
    Filed: June 22, 2023
    Publication date: November 9, 2023
    Inventors: Floris Louis VAN DELFT, Sander Sebastiaan VAN BERKEL, Remon VAN GEEL, Lianne LELIEVELDT
  • Publication number: 20230338562
    Abstract: The present invention concerns a method for the preparation of an alkyne-linker-payload construct of structure Q-L-C(O)—NR3-D (1), comprising reacting (i) an alkyne compound of structure Q-L-C(O)-X (2), wherein Q is an alkyne moiety selected from the group consisting of terminal alkyne and (hetero)cycloalkyne; L is a linker, and X is a leaving group selected from halogen, SR1, O-succinimidyl, O-(hetero)aryl(R2)1-5, wherein R1 is selected from C1-C6 alkyl and (hetero)aryl; and R2 is C1-C6 alkyl, halogen or NO2; with (ii) a molecule of structure D-NHR3 (3), wherein D is a payload, and R3 is selected from hydrogen, optionally substituted C1-C24 alkyl, optionally substituted aryl. The activated ester derivatives (2) are highly stable and provide for smooth and high-yielding attachment to a cytotoxic payload. The invention further concerns a method for preparing bioconjugates and alkyne compound of structure Q-L-C(O)-X (2).
    Type: Application
    Filed: December 22, 2022
    Publication date: October 26, 2023
    Inventors: Jorge Merijn Mathieu VERKADE, Sander Sebastiaan VAN BERKEL, Floris Louis VAN DELFT
  • Publication number: 20230330245
    Abstract: The present invention concerns an antibody-drug conjugate, having structure (1) wherein AB is an antibody; L1 and L2 are linkers; w is 0 or 1; Z is a connecting group obtained by a metal-free click reaction or by thiol ligation; each R17 is individually an amino acid side chain; n is an integer in the range of 1-5; A is a 5- or 6-membered aromatic or heteroaromatic ring; x is an integer in the range of 1-8; R21 is selected from H, R22, C(O)OH and C(O)R22, wherein R22 is C1-C24 (hetero)alkyl groups, C3-C10 (hetero)cycloalkyl groups, C2-C10 (hetero)aryl groups, C3-C10 alkyl(hetero)aryl groups and C3-C10 (hetero)arylalkyl groups, which optionally substituted and optionally interrupted by one or more heteroatoms selected from O, S and NR23 wherein R23 is independently selected from the group consisting of hydrogen and C1-C4 alkyl groups.
    Type: Application
    Filed: March 14, 2023
    Publication date: October 19, 2023
    Inventors: Jorin HOOGENBOOM, Arnoldus Jacobus VAN SCHAIK, Sorraya POPAL, Laureen DE BEVER, Maria Antonia WIJDEVEN, Remon VAN GEEL, Inge Catharina Josephina HURKMANS, Peter VAN DE SANDE, Sander Sebastiaan VAN BERKEL, Floris Louis VAN DELFT
  • Patent number: 11713453
    Abstract: The invention concerns fusion proteins, wherein two endoglycosidases are fused, possibly via a linker. The fusion enzymes according to the invention have structure (1): EndoX-(L)p-EndoY (1), wherein EndoX is an endoglycosidase, EndoY is an endoglycosidase distinct from EndoX, L is a linker and p is 0 or 1. Such fusion enzymes capable of trimming glycoproteins comprising at least two distinct glycoforms in a single step. The invention further concerns the use of the fusion enzyme according to the invention for trimming glycoproteins. In another aspect, the invention relates to the process of production of the fusion enzyme. In a further aspect, the inventions concerns a process for trimming glycoproteins, comprising trimming the glycoprotein with a fusion enzyme according to the invention, to obtain a trimmed glycoprotein.
    Type: Grant
    Filed: December 7, 2020
    Date of Patent: August 1, 2023
    Assignee: SYNAFFIX B.V.
    Inventors: Remon Van Geel, Maria Antonia Wijdeven, Inge Catharina Josephina Hurkmans, Floris Louis Van Delft, Sander Sebastiaan Van Berkel
  • Publication number: 20230226208
    Abstract: A surfactant for a bioconjugation reaction is disclosed, wherein a biomolecule comprising one or more azide moieties is connected to an cyclic alkyne comprising payload. More specifically, the invention concerns a method for the preparation of a bioconjugate of structure B—(Z—L—D)x (1), comprising reacting (i) an alkyne or alkene compound of structure Q—L—D (2), wherein Q is a click probe comprising a cyclic alkyne moiety or a cyclic alkene moiety, L is a linker, and D is a payload; with (ii) a molecule of structure B—(F)x (3), wherein B is a biomolecule that is functionalized with x click probes F; F is a click probe capable of reacting with Q, and x is an integer in the range of 1-10, in presence of a surfactant.
    Type: Application
    Filed: March 1, 2023
    Publication date: July 20, 2023
    Inventors: Maria Antonia WIJDEVEN, Remon VAN GEEL, Laureen DE BEVER, Sander Sebastiaan VAN BERKEL, Floris Louis VAN DELFT
  • Publication number: 20230190951
    Abstract: The present invention concerns a process for preparing a multispecific antibody construct, comprising conjugating a functionalized antibody Ab(F)x containing x reactive moieties F, wherein x is an integer in the range 1 -10, and an immune cell-engaging polypeptide containing one or two reactive moieties Q, wherein the antibody is specific for a tumour cell and the immune cell-engaging polypeptide is specific for an immune cell, wherein the reaction forms a covalent linkage between the functionalized antibody and the immune cell-engaging polypeptide by reaction of Q with F. The invention further concerns the multispecific antibody constructs obtainable by the process according to the invention and medical uses thereof.
    Type: Application
    Filed: July 12, 2022
    Publication date: June 22, 2023
    Inventors: Remon VAN GEEL, Willem Johannes Petrus VUGS, Sander Sebastiaan VAN BERKEL, Floris Louis VAN DELFT
  • Publication number: 20230127659
    Abstract: The present invention concerns novel and improved antibody-conjugates for targeting HER2. The inventors found that when antibody-conjugates were prepared using a specific mode of conjugation, they exhibit an improved therapeutic index.
    Type: Application
    Filed: May 20, 2022
    Publication date: April 27, 2023
    Applicant: SYNAFFIX B.V.
    Inventors: Sander Sebastiaan VAN BERKEL, Jorge Merijn Mathieu VERKADE, Maria Antonia WIJDEVEN, Ryan HEESBEEN, Petrus Josephus Jacobus Maria VAN DE SANDE, Remon VAN GEEL, Brian Maria Gerardus JANSSEN, Inge Catharina Josephina HURKMANS, Floris Louis VAN DELFT
  • Publication number: 20230114866
    Abstract: The present invention provides antibody-payload conjugates having a payload-to-antibody ratio of 1. The antibody-payload conjugate is according to structure (1): wherein: a, b, c and d are each independently 0 or 1; e is an integer in the range of 0-10; L1, L2 and L3 are linkers; D is a payload; BM is a branching moiety; Su is a monosaccharide; G is a monosaccharide moiety; GlcNAc is an N-acetylglucosamine moiety; Fuc is a fucose moiety; Z are connecting groups. The invention further provides a method for preparing the antibody-payload conjugate according to the invention, an intermediate compound in that preparation method, and medical uses of the antibody-payload conjugate according to the invention.
    Type: Application
    Filed: July 12, 2022
    Publication date: April 13, 2023
    Inventors: Floris Louis VAN DELFT, Jorin HOOGENBOOM, Sorraya POPAL, Arnoldus Jacobus VAN SCHAIK, Laureen DE BEVER, Remon VAN GEEL, Maria Antonia WIJDEVEN, Sander Sebastiaan VAN BERKEL
  • Publication number: 20230100074
    Abstract: The present invention relates to a process for the enzymatic modification of a glycoprotein. The process comprises the step of contacting a glycoprotein comprising a glycan comprising a terminal GlcNAc-moiety, in the presence of glycosyltransferase that is, or is derived from, a ?-(1,4)-N-acetylgalactosaminyltransferase, with a non-natural sugar-derivative nucleotide. The non-natural sugar-derivative nucleotide is according to formula (3): wherein A is selected from the group consisting of —N3, —C(O)R3, —(CH2)iC?C—R4, —SH, —SC(O)R8, —SC(O)OR8, —SC(S)OR8, —F, —Cl, —Br —I, —OS(O)2R5, terminal C2-C24 alkenyl groups, C3-C5 cycloalkenyl groups, C4-C8 alkadienyl groups, terminal C3-C24 allenyl groups and amino groups.
    Type: Application
    Filed: April 1, 2022
    Publication date: March 30, 2023
    Applicant: Synaffix B.V.
    Inventors: Sander Sebastiaan VAN BERKEL, Remon VAN GEEL, Maria Antonia WIJDEVEN, Floris Louis VAN DELFT
  • Patent number: 11590239
    Abstract: The present invention concerns novel and improved antibody-conjugates for targeting CD30. The inventors found that when antibody-conjugates were prepared using a specific mode of conjugation, they exhibit an improved therapeutic index.
    Type: Grant
    Filed: February 8, 2017
    Date of Patent: February 28, 2023
    Assignee: SYNAFFIX B.V.
    Inventors: Sander Sebastiaan Van Berkel, Jorge Merijn Mathieu Verkade, Maria Antonia Wijdeven, Ryan Heesbeen, Petrus Josephus Jacobus Maria Van De Sande, Remon Gvan Eel, Brian Maria Gerardus Janssen, Inge Catharina Josephina Hurkmans, Floris Louis Van Delft
  • Publication number: 20220162252
    Abstract: The current invention concerns methods for the synthesis of 6-azido-6-deoxy-2-N-acetyl-monosaccharide-nucleoside diphosphate, in particular 6-azido-6-deoxy-2-N-acetyl-D-galactosamine-nucleoside diphosphate or 6-azido-6-deoxy-2-N-acetyl-D-glucosamine-nucleoside diphosphate. The synthesis method according to the invention is characterized by being highly efficient and high yielding. Also part of the present invention are key intermediates of this process.
    Type: Application
    Filed: January 24, 2022
    Publication date: May 26, 2022
    Inventors: Jorin HOOGENBOOM, Maria Antonia WIJDEVEN, Jorge Merijn Mathieu VERKADE, Floris Louis VAN DELFT, Sander Sebastiaan VAN BERKEL
  • Patent number: 11338043
    Abstract: The present invention concerns novel and improved antibody-conjugates for targeting HER2. The inventors found N that when antibody-conjugates were prepared using a specific mode of conjugation, they exhibit an improved therapeutic index.
    Type: Grant
    Filed: February 8, 2017
    Date of Patent: May 24, 2022
    Assignee: SYNAFFIX B.V.
    Inventors: Sander Sebastiaan Van Berkel, Jorge Merijn Mathieu Verkade, Maria Antonia Wijdeven, Ryan Heesbeen, Petrus Josephus Jacobus Maria Van De Sande, Remon Van Geel, Brian Maria Gerardus Janssen, Inge Catharina Josephina Hurkmans, Floris Louis Van Delft
  • Patent number: 11299759
    Abstract: The present invention relates to a process for the enzymatic modification of a glycoprotein. The process comprises the step of contacting a glycoprotein comprising a glycan comprising a terminal GlcNAc-moiety, in the presence of glycosyltransferase that is, or is derived from, a ?-(1,4)-N-acetylgalactosaminyltransferase, with a non-natural sugar-derivative nucleotide. The non-natural sugar-derivative nucleotide is according to formula (3): wherein A is selected from the group consisting of —N3, —C(O)R3, —(CH2)iC?C—R4, —SH, —SC(O)R8, —SC(O)OR8, —SC(S)OR8, —F, —Cl, —Br —I, —OS(O)2R5, terminal C2-C24 alkenyl groups, C3-C5 cycloalkenyl groups, C4-C8 alkadienyl groups, terminal C3-C24 allenyl groups and amino groups.
    Type: Grant
    Filed: May 4, 2018
    Date of Patent: April 12, 2022
    Assignee: SYNAFFIX B.V.
    Inventors: Sander Sebastiaan Van Berkel, Remon Van Geel, Maria Antonia Wijdeven, Floris Louis Van Delft
  • Publication number: 20220096652
    Abstract: The current invention concerns compounds, such as antibody-conjugates, with an enhanced selectivity of payload release inside a tumour or in the tumour microenvironment versus payload release in circulation or in healthy cells. The enhanced selectivity is achieved by incorporation of a cleavable linker that requires two consecutive mechanisms for release of the payload. The compounds according to the invention have structure (1): or a salt thereof, wherein AB is an antibody or a reactive moiety capable of reacting with a functional group on an antibody, L1 and L2 are linkers, moiety I contains an activating group and an aromatic ring, X is O or N and D is the payload. The invention further concerns application of these compounds in for example a method of targeting a cell and a method for enhancing the bystander effect of an amino-containing payload. The invention also concerns the payloads that may be released from the compounds according to the invention.
    Type: Application
    Filed: December 1, 2021
    Publication date: March 31, 2022
    Applicant: Synaffix B.V.
    Inventors: Jorge Merijn Mathieu VERKADE, Arnoldus Jacobus VAN SCHAIK, Remon VAN GEEL, Maria Antonia WIJDEVEN, Sander Sebastiaan VAN BERKEL, Floris Louis VAN DELFT
  • Publication number: 20210393792
    Abstract: The present invention concerns antibody-conjugate having general structure (2): AB-[(L6)-{Z-(L1)n-(L2)o-(L3)p-(L4)q-D}xx]yy?? (2) wherein AB is an antibody capable of targeting Trop-2-expressing tumours and D is selected from the group consisting of taxanes, anthracyclines, camptothecins, epothilones, mytomycins, combretastatins, vinca alkaloids, maytansinoids, enediynes such as calicheamicins, duocarmycins, tubulysins, amatoxins, bleomycins, dolastatins and auristatins, pyrrolobenzodiazepine dimers, indolinobenzodiazepine dimers, radioisotopes, therapeutic proteins and peptides (or fragments thereof), kinase inhibitors, MEK inhibitors, KSP inhibitors, and analogues or prodrugs thereof. These antibody-conjugates exhibit an improved therapeutic index. The invention further concerns a process for preparing the antibody-conjugate according to the invention, a method for targeting Trop-2-expressing cells, medical uses of the antibody-conjugates according to the invention.
    Type: Application
    Filed: May 4, 2021
    Publication date: December 23, 2021
    Inventors: Maria Antonia WIJDEVEN, Jorge Merijn Mathieu VERKADE, Jorin HOOGENBOOM, Sander Sebastiaan VAN BERKEL, Floris Louis VAN DELFT, Petrus Josephus Jacobus Maria VAN DE SANDE
  • Publication number: 20210353766
    Abstract: The invention relates to a novel linker for use in bioconjugates such as antibody-drug-conjugates. The linker according to the invention is represented by formula: wherein: BM is a branching moiety; E is a capping group; SG is a sulfamide group; b, c, d, e, g, i, k, l are independently 0 or 1; f is an integer in the range of 1 to 10; Sp1, Sp2, Sp3, Sp4, Sp5 and Sp6 are a spacer moieties; Z1 and Z2 are connecting groups. The linker according to the invention is useful in the preparation of linker-conjugates and bioconjugates, and can be used for (a) improving conjugation efficiency in the preparation of the bioconjugate, (b) reducing aggregation during the preparation of the bioconjugate and/or of the bioconjugate, (c) increasing stability of the bioconjugate, and/or (d) increasing therapeutic index of the bioconjugate.
    Type: Application
    Filed: December 28, 2020
    Publication date: November 18, 2021
    Applicant: SYNAFFIX B.V.
    Inventors: Sander Sebastiaan VAN BERKEL, Ryan HEESBEEN, Jorge Merijn Mathieu VERKADE, Maria Antonia WIJDEVEN, Floris Louis VAN DELFT
  • Publication number: 20210332342
    Abstract: The invention concerns fusion proteins, wherein two endoglycosidases are fused, possibly via a linker. The fusion enzymes according to the invention have structure (1): EndoX-(L)p-EndoY (1), wherein EndoX is an endoglycosidase, EndoY is an endoglycosidase distinct from EndoX, L is a linker and p is 0 or 1. Such fusion enzymes capable of trimming glycoproteins comprising at least two distinct glycoforms in a single step. The invention further concerns the use of the fusion enzyme according to the invention for trimming glycoproteins. In another aspect, the invention relates to the process of production of the fusion enzyme. In a further aspect, the inventions concerns a process for trimming glycoproteins, comprising trimming the glycoprotein with a fusion enzyme according to the invention, to obtain a trimmed glycoprotein.
    Type: Application
    Filed: December 7, 2020
    Publication date: October 28, 2021
    Applicant: Synaffix B.V.
    Inventors: Remon Van Geel, Maria Antonia WIJDEVEN, Inge Catharina Josephina HURMANS, Floris Louis Van Delft, Sander Sebastiaan Van Berkel