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  1. Article: De novo discovery of peptide-based affinity ligands for the fab fragment of human immunoglobulin G

    Xiao, Xingqing / Kilgore, Ryan / Sarma, Sudeep / Chu, Wenning / Menegatti, Stefano / Hall, Carol K.

    Journal of chromatography. 2022 Apr. 26, v. 1669

    2022  

    Abstract: Antibody fragments and their engineered variants show true potential as next-generation therapeutics as they combine excellent targeting with superior biodistribution and blood clearance. Unlike full antibodies, however, antibody fragments do not yet ... ...

    Abstract Antibody fragments and their engineered variants show true potential as next-generation therapeutics as they combine excellent targeting with superior biodistribution and blood clearance. Unlike full antibodies, however, antibody fragments do not yet have a standard platform purification process for large-scale production. Short peptide ligands are viable alternatives to protein ligands in affinity chromatography. In this work, an integrated computational and experimental scheme is described to de novo design 9-mer peptides that bind to Fab fragments. The first cohort of designed sequences was tested experimentally using human polyclonal Fab, and the top performing sequence was selected as a prototype for a subsequent round of ligand refinement in silico. The resulting peptides were conjugated to chromatographic resins and evaluated via equilibrium and dynamic binding studies using human Fab-κ and Fab-λ. The equilibrium studies returned values of binding capacities up to 32 mg of Fab per mL of resin with mild affinity (KD ∼ 10⁻⁵ M) that are conducive to high product capture and recovery. Dynamic studies returned values of product yield up to ∼90%. Preliminary purification studies provided purities of 83–93% and yields of 11–89%. These results lay the groundwork for future development of these ligands towards biomanufacturing translation.
    Keywords affinity chromatography ; antibodies ; blood ; computer simulation ; humans ; immunoglobulin G ; ligands ; peptides ; prototypes ; purification methods ; therapeutics
    Language English
    Dates of publication 2022-0426
    Publishing place Elsevier B.V.
    Document type Article
    ZDB-ID 218139-3
    ISSN 0021-9673 ; 0378-4355 ; 0376-737X
    ISSN 0021-9673 ; 0378-4355 ; 0376-737X
    DOI 10.1016/j.chroma.2022.462941
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  2. Article: Development of Peptide Ligands for the Purification of α-1 Antitrypsin from Cell Culture Fluids

    Chu, Wenning / Prodromou, Raphael / Moore, Brandyn / Elhanafi, Driss / Kilgore, Ryan / Shastry, Shriarjun / Menegatti, Stefano

    Journal of chromatography. 2022 July 20,

    2022  

    Abstract: α-1 antitrypsin (AAT) deficiency, a major risk factor for chronic obstructive pulmonary disease, is one of the most prevalent and fatal hereditary diseases. The rising demand of AAT poses a defined need for new processes of AAT manufacturing from ... ...

    Abstract α-1 antitrypsin (AAT) deficiency, a major risk factor for chronic obstructive pulmonary disease, is one of the most prevalent and fatal hereditary diseases. The rising demand of AAT poses a defined need for new processes of AAT manufacturing from recombinant sources. Commercial affinity adsorbents for AAT purification present the intrinsic limitations of protein ligands – chiefly, the high cost and the lability towards the proteases in the feedstocks and the cleaning-in-place utilized in biomanufacturing – which limit their application despite their high capacity and selectivity. This work presents the development of small peptide affinity ligands for the purification of AAT from Chinese hamster ovary (CHO) cell culture harvests. An ensemble of ligand candidates identified via library screening were conjugated on Toyopearl resin and evaluated via experimental and in silico AAT-binding studies. Initial ranking based on equilibrium binding capacity indicated WHAKKSKFG- (12.9 mg of AAT per mL of resin), WHAKKSHFG- (16.3 mg/mL), and KWKHSHKWG- (15.8 mg/mL) Toyopearl resins as top performing adsorbents. Notably, the fitting of adsorption data to Langmuir isotherms concurred with molecular docking and dynamics in returning values of dissociation constant (KD) between 1 – 10 μM. These peptide-based adsorbents were thus selected for AAT purification from CHO fluids, affording values of AAT binding capacity up to 13 grams per liter of resin, and product yield and purity up to 77% and 97%. WHAKKSHFG-Toyopearl resin maintained its purification activity upon 20 consecutive uses, demonstrating its potential for AAT manufacturing from recombinant sources.
    Keywords Cricetulus griseus ; adsorbents ; adsorption ; cell culture ; chromatography ; cleaning in place ; computer simulation ; dissociation ; feedstocks ; ligands ; peptides ; proteinases ; respiratory tract diseases ; risk factors
    Language English
    Dates of publication 2022-0720
    Publishing place Elsevier B.V.
    Document type Article
    Note Pre-press version
    ZDB-ID 218139-3
    ISSN 0021-9673 ; 0378-4355 ; 0376-737X
    ISSN 0021-9673 ; 0378-4355 ; 0376-737X
    DOI 10.1016/j.chroma.2022.463363
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  3. Article ; Online: De novo discovery of peptide-based affinity ligands for the fab fragment of human immunoglobulin G.

    Xiao, Xingqing / Kilgore, Ryan / Sarma, Sudeep / Chu, Wenning / Menegatti, Stefano / Hall, Carol K

    Journal of chromatography. A

    2022  Volume 1669, Page(s) 462941

    Abstract: Antibody fragments and their engineered variants show true potential as next-generation therapeutics as they combine excellent targeting with superior biodistribution and blood clearance. Unlike full antibodies, however, antibody fragments do not yet ... ...

    Abstract Antibody fragments and their engineered variants show true potential as next-generation therapeutics as they combine excellent targeting with superior biodistribution and blood clearance. Unlike full antibodies, however, antibody fragments do not yet have a standard platform purification process for large-scale production. Short peptide ligands are viable alternatives to protein ligands in affinity chromatography. In this work, an integrated computational and experimental scheme is described to de novo design 9-mer peptides that bind to Fab fragments. The first cohort of designed sequences was tested experimentally using human polyclonal Fab, and the top performing sequence was selected as a prototype for a subsequent round of ligand refinement in silico. The resulting peptides were conjugated to chromatographic resins and evaluated via equilibrium and dynamic binding studies using human Fab-κ and Fab-λ. The equilibrium studies returned values of binding capacities up to 32 mg of Fab per mL of resin with mild affinity (K
    MeSH term(s) Humans ; Immunoglobulin Fab Fragments/chemistry ; Immunoglobulin G ; Ligands ; Peptides ; Tissue Distribution
    Chemical Substances Immunoglobulin Fab Fragments ; Immunoglobulin G ; Ligands ; Peptides
    Language English
    Publishing date 2022-03-06
    Publishing country Netherlands
    Document type Journal Article
    ZDB-ID 1171488-8
    ISSN 1873-3778 ; 0021-9673
    ISSN (online) 1873-3778
    ISSN 0021-9673
    DOI 10.1016/j.chroma.2022.462941
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  4. Article ; Online: Development of peptide ligands for the purification of α-1 antitrypsin from cell culture fluids.

    Chu, Wenning / Prodromou, Raphael / Moore, Brandyn / Elhanafi, Driss / Kilgore, Ryan / Shastry, Shriarjun / Menegatti, Stefano

    Journal of chromatography. A

    2022  Volume 1679, Page(s) 463363

    Abstract: α-1 antitrypsin (AAT) deficiency, a major risk factor for chronic obstructive pulmonary disease, is one of the most prevalent and fatal hereditary diseases. The rising demand of AAT poses a defined need for new processes of AAT manufacturing from ... ...

    Abstract α-1 antitrypsin (AAT) deficiency, a major risk factor for chronic obstructive pulmonary disease, is one of the most prevalent and fatal hereditary diseases. The rising demand of AAT poses a defined need for new processes of AAT manufacturing from recombinant sources. Commercial affinity adsorbents for AAT purification present the intrinsic limitations of protein ligands - chiefly, the high cost and the lability towards the proteases in the feedstocks and the cleaning-in-place utilized in biomanufacturing - which limit their application despite their high capacity and selectivity. This work presents the development of small peptide affinity ligands for the purification of AAT from Chinese hamster ovary (CHO) cell culture harvests. An ensemble of ligand candidates identified via library screening were conjugated on Toyopearl resin and evaluated via experimental and in silico AAT-binding studies. Initial ranking based on equilibrium binding capacity indicated WHAKKSKFG- (12.9 mg of AAT per mL of resin), WHAKKSHFG- (16.3 mg/mL), and KWKHSHKWG- (15.8 mg/mL) Toyopearl resins as top performing adsorbents. Notably, the fitting of adsorption data to Langmuir isotherms concurred with molecular docking and dynamics in returning values of dissociation constant (K
    MeSH term(s) Animals ; CHO Cells ; Cell Culture Techniques ; Chromatography, Affinity ; Cricetinae ; Cricetulus ; Ligands ; Molecular Docking Simulation ; Peptides ; alpha 1-Antitrypsin
    Chemical Substances Ligands ; Peptides ; alpha 1-Antitrypsin
    Language English
    Publishing date 2022-07-22
    Publishing country Netherlands
    Document type Journal Article
    ZDB-ID 1171488-8
    ISSN 1873-3778 ; 0021-9673
    ISSN (online) 1873-3778
    ISSN 0021-9673
    DOI 10.1016/j.chroma.2022.463363
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  5. Article: Molecular engineering of cyclic azobenzene-peptide hybrid ligands for the purification of human blood Factor VIII via photo-affinity chromatography.

    Prodromou, Raphael / Moore, Brandyn / Chu, Wenning / Deal, Halston / Miguel, Adriana San / Brown, Ashley C / Daniele, Michael A / Pozdin, Vladimir / Menegatti, Stefano

    Advanced functional materials

    2023  Volume 33, Issue 14

    Abstract: The use of benign stimuli to control the binding and release of labile biologics for their isolation from complex feedstocks is a key goal of modern biopharmaceutical technology. This study introduces cyclic azobenzene-peptide (CAP) hybrid ligands for ... ...

    Abstract The use of benign stimuli to control the binding and release of labile biologics for their isolation from complex feedstocks is a key goal of modern biopharmaceutical technology. This study introduces cyclic azobenzene-peptide (CAP) hybrid ligands for the rapid and discrete photo-responsive capture and release of blood coagulation Factor VIII (FVIII). A predictive method - based on amino acid sequence and molecular architecture of CAPs - was developed to correlate the conformation of
    Language English
    Publishing date 2023-01-25
    Publishing country Germany
    Document type Journal Article
    ZDB-ID 2039420-2
    ISSN 1616-3028 ; 1616-301X
    ISSN (online) 1616-3028
    ISSN 1616-301X
    DOI 10.1002/adfm.202213881
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  6. Article ; Online: The downstream bioprocess toolbox for therapeutic viral vectors

    Kilgore, Ryan / Minzoni, Arianna / Shastry, Shriarjun / Smith, Will / Barbieri, Eduardo / Wu, Yuxuan / LeBarre, Jacob P. / Chu, Wenning / O'Brien, Juliana / Menegatti, Stefano

    Journal of Chromatography A. 2023 Oct., v. 1709 p.464337-

    2023  

    Abstract: Viral vectors are poised to acquire a prominent position in modern medicine and biotechnology owing to their role as delivery agents for gene therapies, oncolytic agents, vaccine platforms, and a gateway to engineer cell therapies as well as plants and ... ...

    Abstract Viral vectors are poised to acquire a prominent position in modern medicine and biotechnology owing to their role as delivery agents for gene therapies, oncolytic agents, vaccine platforms, and a gateway to engineer cell therapies as well as plants and animals for sustainable agriculture. The success of viral vectors will critically depend on the availability of flexible and affordable biomanufacturing strategies that can meet the growing demand by clinics and biotech companies worldwide. In this context, a key role will be played by downstream process technology: while initially adapted from protein purification media, the purification toolbox for viral vectors is currently undergoing a rapid expansion to fit the unique biomolecular characteristics of these products. Innovation efforts are articulated on two fronts, namely (i) the discovery of affinity ligands that target adeno-associated virus, lentivirus, adenovirus, etc.; (ii) the development of adsorbents with innovative morphologies, such as membranes and 3D printed monoliths, that fit the size of viral vectors. Complementing these efforts are the design of novel process layouts that capitalize on novel ligands and adsorbents to ensure high yield and purity of the product while safeguarding its therapeutic efficacy and safety; and a growing panel of analytical methods that monitor the complex array of critical quality attributes of viral vectors and correlate them to the purification strategies. To help explore this complex and evolving environment, this study presents a comprehensive overview of the downstream bioprocess toolbox for viral vectors established in the last decade, and discusses present efforts and future directions contributing to the success of this promising class of biological medicines.
    Keywords Adenoviridae ; Dependoparvovirus ; Lentivirus ; adsorbents ; bioprocessing ; biotechnology ; chromatography ; genes ; ligands ; medicine ; sustainable agriculture ; therapeutics ; three-dimensional printing ; vaccines ; Viral vectors ; Gene therapy ; Affinity ligands ; AAV
    Language English
    Dates of publication 2023-10
    Publishing place Elsevier B.V.
    Document type Article ; Online
    ZDB-ID 218139-3
    ISSN 0021-9673 ; 0378-4355 ; 0376-737X
    ISSN 0021-9673 ; 0378-4355 ; 0376-737X
    DOI 10.1016/j.chroma.2023.464337
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  7. Article ; Online: Mixed-mode size-exclusion silica resin for polishing human antibodies in flow-through mode.

    LeBarre, Jacob P / Chu, Wenning / Altern, Scott H / Kocot, Andrew J / Bhandari, Dipendra / Barbieri, Eduardo / Sly, Jae / Crapanzano, Michael / Cramer, Steven M / Phillips, Michael / Roush, David / Carbonell, Ruben / Boi, Cristiana / Menegatti, Stefano

    Journal of chromatography. A

    2024  Volume 1720, Page(s) 464772

    Abstract: The polishing step in the downstream processing of therapeutic antibodies removes residual impurities from Protein A eluates. Among the various classes of impurities, antibody fragments are especially challenging to remove due to the broad biomolecular ... ...

    Abstract The polishing step in the downstream processing of therapeutic antibodies removes residual impurities from Protein A eluates. Among the various classes of impurities, antibody fragments are especially challenging to remove due to the broad biomolecular diversity generated by a multitude of fragmentation patterns. The current approach to fragment removal relies on ion exchange or mixed-mode adsorbents operated in bind-and-gradient-elution mode. However, fragments that bear strong similarity to the intact product or whose biophysical features deviate from the ensemble average can elude these adsorbents, and the lack of a chromatographic technology enabling robust antibody polishing is recognized as a major gap in downstream bioprocessing. Responding to this challenge, this study introduces size-exclusion mixed-mode (SEMM) silica resins as a novel chromatographic adsorbent for the capture of antibody fragments irrespective of their biomolecular features. The pore diameter of the silica beads features a narrow distribution and is selected to exclude monomeric antibodies, while allowing their fragments to access the pores where they are captured by the mixed-mode ligands. The static and dynamic binding capacity of the adsorbent ranged respectively between 30-45 and 25-33 gs of antibody fragments per liter of resin. Selected SEMM-silica resins also demonstrated the ability to capture antibody aggregates, which adsorb on the outer layer of the beads. Optimization of the SEMM-silica design and operation conditions - namely, pore size (10 nm) and ligand composition (quaternary amine and alkyl chain) as well as the linear velocity (100 cm/h), ionic strength (5.7 mS/cm), and pH (7) of the mobile phase - afforded a significant reduction of both fragments and aggregates, resulting into a final antibody yield up to 80% and monomeric purity above 97%.
    MeSH term(s) Humans ; Antibodies, Monoclonal/chemistry ; Chromatography, Ion Exchange/methods ; Immunoglobulin G/metabolism ; Immunoglobulin Fragments ; Ligands
    Chemical Substances Antibodies, Monoclonal ; Immunoglobulin G ; Immunoglobulin Fragments ; Ligands
    Language English
    Publishing date 2024-02-27
    Publishing country Netherlands
    Document type Journal Article
    ZDB-ID 1171488-8
    ISSN 1873-3778 ; 0021-9673
    ISSN (online) 1873-3778
    ISSN 0021-9673
    DOI 10.1016/j.chroma.2024.464772
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  8. Article ; Online: Development of peptide affinity ligands for the purification of polyclonal and monoclonal Fabs from recombinant fluids.

    Kilgore, Ryan / Chu, Wenning / Bhandari, Dipendra / Fischler, David / Carbonell, Ruben G / Crapanzano, Michael / Menegatti, Stefano

    Journal of chromatography. A

    2022  Volume 1687, Page(s) 463701

    Abstract: Engineered multi-specific monoclonal antibodies (msAbs) and antibody fragments offer valuable therapeutic options against metabolic disorders, aggressive cancers, and viral infections. The advancement in molecular design and recombinant expression of ... ...

    Abstract Engineered multi-specific monoclonal antibodies (msAbs) and antibody fragments offer valuable therapeutic options against metabolic disorders, aggressive cancers, and viral infections. The advancement in molecular design and recombinant expression of these next-generation drugs, however, is not equaled by the progress in downstream bioprocess technology. The purification of msAbs and fragments requires affinity adsorbents with orthogonal biorecognition of different portions of the antibody structure, namely its Fc (fragment crystallizable) and Fab (fragment antigen-binding) regions or the C
    Language English
    Publishing date 2022-12-05
    Publishing country Netherlands
    Document type Journal Article
    ZDB-ID 1171488-8
    ISSN 1873-3778 ; 0021-9673
    ISSN (online) 1873-3778
    ISSN 0021-9673
    DOI 10.1016/j.chroma.2022.463701
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  9. Article ; Online: The downstream bioprocess toolbox for therapeutic viral vectors.

    Kilgore, Ryan / Minzoni, Arianna / Shastry, Shriarjun / Smith, Will / Barbieri, Eduardo / Wu, Yuxuan / LeBarre, Jacob P / Chu, Wenning / O'Brien, Juliana / Menegatti, Stefano

    Journal of chromatography. A

    2023  Volume 1709, Page(s) 464337

    Abstract: Viral vectors are poised to acquire a prominent position in modern medicine and biotechnology owing to their role as delivery agents for gene therapies, oncolytic agents, vaccine platforms, and a gateway to engineer cell therapies as well as plants and ... ...

    Abstract Viral vectors are poised to acquire a prominent position in modern medicine and biotechnology owing to their role as delivery agents for gene therapies, oncolytic agents, vaccine platforms, and a gateway to engineer cell therapies as well as plants and animals for sustainable agriculture. The success of viral vectors will critically depend on the availability of flexible and affordable biomanufacturing strategies that can meet the growing demand by clinics and biotech companies worldwide. In this context, a key role will be played by downstream process technology: while initially adapted from protein purification media, the purification toolbox for viral vectors is currently undergoing a rapid expansion to fit the unique biomolecular characteristics of these products. Innovation efforts are articulated on two fronts, namely (i) the discovery of affinity ligands that target adeno-associated virus, lentivirus, adenovirus, etc.; (ii) the development of adsorbents with innovative morphologies, such as membranes and 3D printed monoliths, that fit the size of viral vectors. Complementing these efforts are the design of novel process layouts that capitalize on novel ligands and adsorbents to ensure high yield and purity of the product while safeguarding its therapeutic efficacy and safety; and a growing panel of analytical methods that monitor the complex array of critical quality attributes of viral vectors and correlate them to the purification strategies. To help explore this complex and evolving environment, this study presents a comprehensive overview of the downstream bioprocess toolbox for viral vectors established in the last decade, and discusses present efforts and future directions contributing to the success of this promising class of biological medicines.
    Language English
    Publishing date 2023-09-09
    Publishing country Netherlands
    Document type Journal Article
    ZDB-ID 1171488-8
    ISSN 1873-3778 ; 0021-9673
    ISSN (online) 1873-3778
    ISSN 0021-9673
    DOI 10.1016/j.chroma.2023.464337
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  10. Article ; Online: Peptide ligands for the affinity purification of adeno-associated viruses from HEK 293 cell lysates.

    Chu, Wenning / Shastry, Shriarjun / Barbieri, Eduardo / Prodromou, Raphael / Greback-Clarke, Paul / Smith, Will / Moore, Brandyn / Kilgore, Ryan / Cummings, Christopher / Pancorbo, Jennifer / Gilleskie, Gary / Daniele, Michael A / Menegatti, Stefano

    Biotechnology and bioengineering

    2023  Volume 120, Issue 8, Page(s) 2283–2300

    Abstract: Adeno-associated viruses (AAVs) are the vector of choice for delivering gene therapies that can cure inherited and acquired diseases. Clinical research on various AAV serotypes significantly increased in recent years alongside regulatory approvals of AAV- ...

    Abstract Adeno-associated viruses (AAVs) are the vector of choice for delivering gene therapies that can cure inherited and acquired diseases. Clinical research on various AAV serotypes significantly increased in recent years alongside regulatory approvals of AAV-based therapies. The current AAV purification platform hinges on the capture step, for which several affinity resins are commercially available. These adsorbents rely on protein ligands-typically camelid antibodies-that provide high binding capacity and selectivity, but suffer from low biochemical stability and high cost, and impose harsh elution conditions (pH < 3) that can harm the transduction activity of recovered AAVs. Addressing these challenges, this study introduces peptide ligands that selectively capture AAVs and release them under mild conditions (pH = 6.0). The peptide sequences were identified by screening a focused library and modeled in silico against AAV serotypes 2 and 9 (AAV2 and AAV9) to select candidate ligands that target homologous sites at the interface of the VP1-VP2 and VP2-VP3 virion proteins with mild binding strength (K
    MeSH term(s) Humans ; Dependovirus/genetics ; HEK293 Cells ; Ligands ; Peptides/genetics ; Peptides/metabolism ; Amino Acid Sequence ; Genetic Vectors
    Chemical Substances Ligands ; Peptides
    Language English
    Publishing date 2023-07-12
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, P.H.S. ; Research Support, U.S. Gov't, Non-P.H.S.
    ZDB-ID 280318-5
    ISSN 1097-0290 ; 0006-3592
    ISSN (online) 1097-0290
    ISSN 0006-3592
    DOI 10.1002/bit.28495
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