Protein Footprinting and X-ray Crystallography Reveal the Interaction of PD-L1 and a Macrocyclic Peptide

Niu, Ben; Appleby, T.C.; Wang, Ruth; Morar, Mariya; Voight, Johannes; Villaseñor, Armando G.; Clancy, Sheila; Wise, Sarah; Belzile, Jean-Philippe; Papalia, Giuseppe A.; Wong, Melanie; Brendza, Katherine M.; Lad, Latesh; Gross, Michael L.

doi:10.1021/acs.biochem.9b00822

Cited by 30 publications

(29 citation statements)

References 77 publications

(140 reference statements)

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“…Both general labeling strategies and amino acid specific methods have proven useful in the study of proteins. Combination of footprinting strategies or other MS‐based structural techniques such as ion mobility, top‐down proteomics, and X‐ray crystallography (Niu et al, 2020) have demonstrated the complementary nature of protein footprinting. Michael Gross has been at the forefront of innovation in the field.…”

Section: Resultsmentioning

confidence: 99%

The Making of a Footprint in Protein Footprinting: A Review in Honor of Michael L. Gross

McKenzie‐Coe

Shortt

Jones

2020

Mass Spectrometry Reviews

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Within the past decade protein footprinting in conjunction with mass spectrometry has become a powerful and versatile means to unravel the higher order structure of proteins. Footprintingbased approaches has demonstrated the capacity to inform on interaction sites and dynamic regions that participate in conformational changes. These findings when set in a biological perspective inform on protein folding/unfolding, protein-protein interactions, and protein-ligand interactions. In this review, we will look at the contribution of Dr. Michael L. Gross to protein footprinting approaches such as hydrogen deuterium exchange mass spectrometry and hydroxyl radical protein footprinting. This review details the development of novel footprinting methods as well as their applications to study higher order protein structure.

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Section: Resultsmentioning

confidence: 99%

The Making of a Footprint in Protein Footprinting: A Review in Honor of Michael L. Gross

McKenzie‐Coe

Shortt

Jones

2020

Mass Spectrometry Reviews

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“…To analyze the data, raw data files were subjected to Byos (Protein Metrics) for database searching against the amino acid sequences of the corresponding proteins and reversed decoys of all possible peptides (Bern et al, 2012;Niu et al, 2020). The modification of acetylation (+42.010565) was added as variable modifications targeting protein N-termini, Lys, Ser, Thr, and Tyr residues for searching of Sulfo-NHS-Acetate modified samples (Brier et al, 2010).…”

Section: Discussionmentioning

confidence: 99%

Systematic workflow for studying domain contributions of bispecific antibodies to selectivity in multimodal chromatography

Parasnavis

Niu

Aspelund

et al. 2021

Biotech & Bioengineering

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In this article, a systematic workflow was formulated and implemented to understand selectivity differences and preferred binding patches for bispecific monoclonal antibodies (mAbs) and their parental mAbs on three multimodal cation exchange resin systems. This workflow incorporates chromatographic screening of the parent mAbs and their fragments at various pH followed by surface property mapping and protein footprinting using covalent labeling followed by liquid chromatography-mass spectrometry analysis. The chromatography screens on multimodal resins with the intact mAbs indicated enhanced selectivity as compared to single-mode interaction systems. While the bispecific antibody (bsAb) eluted between the two parental mAbs on most of the resins, the retention of the bispecific transitioned from co-eluting with one parental mAb to the other parental mAb on Capto MMC. To investigate the contribution of different domains, mAb fragments were evaluated and the results indicated that the interactions were likely dominated by the Fab domain at higher pH. Protein surface property maps were then employed to hypothesize the potential preferred binding patches in the solvent-exposed regions of the parental Fabs. Finally, protein footprinting was carried out with the parental mAbs and the bsAb in the bound and unbound states at pH 7.5 to identify the preferred binding patches. Results with the intact mAb analysis supported the hypothesis that interactions with the resins were primarily driven by the residues in the Fab fragments and not the Fc. Furthermore, peptide mapping data indicated that the light chain may be playing a more important role in the higher binding of Parent A as compared with Parent B in these resin systems. Finally, results with the bsAb indicated that both halves of the molecule contributed to binding with the resins, albeit with subtle differences as compared to the parental mAbs. The workflow presented in this paper lays the foundation to systematically study the chromatographic selectivity of large multidomain molecules which can provide insights into improved biomanufacturability and expedited downstream bioprocess development.

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“…Several groups have reported the crystal structures of PD-1 7 and PD-L1 8 . These data have determined that the interacting domains of these proteins lack cavities to host low-molecular-weight compounds.…”

Section: Introductionmentioning

confidence: 99%

“…These data have determined that the interacting domains of these proteins lack cavities to host low-molecular-weight compounds. Consequently, the many attempts to develop pharmochemical inhibitors of PD-1 and PD-L1 have not been successful enough 8,9 . In contrast, monoclonal antibodies effectively block the immunosuppressive actions that are triggered by PD-1 and PD-L1.…”

Section: Introductionmentioning

confidence: 99%

Anti-PD-1 And Anti-PD-L1 Antibodies as Immunotherapy Against Cancer: A Structural Perspective

Córdova-Bahena¹,

Velasco-Velázquez²

2021

RIC

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Programmed cell death protein 1 (PD-1) and its ligand, programmed death-ligand-1 (PD-L1), play key roles in the suppression of the cytotoxic activity of T cells. PD-L1 is overexpressed on various types of cancer cells, leading to immune evasion. In the past decade, therapeutic antibodies that target the PD-1/PD-L1 axis have been developed to inhibit the immune suppression triggered by these two proteins. At present, five antibodies (two anti-PD-1 and three anti-PD-L1) have received approval by regulatory agencies in the US and Europe. In this work, we aimed to review their clinical applications and adverse effects. Furthermore, using their reported crystal structures, we discuss the similarities and differences between the PD-1/PD-L1 interface and the epitopes that are recognized by the antibodies. Detailed analyses of the contact residues involved in the ligand-receptor and target-antibody interactions have shown partial overlap. Altogether, the data presented here demonstrate that: (1) in contrast to other therapeutic antibodies, anti-PD-1/PD-L1 has a wide range of clinical applications; (2) these targeted therapies are not exempt from adverse effects; and (3) the characterization of the structural domains that are recognized by the antibodies can guide the development of new PD-1-and PD-L1-blocking agents. (REV INVEST CLIN. [AHEAD OF PRINT])

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Protein Footprinting and X-ray Crystallography Reveal the Interaction of PD-L1 and a Macrocyclic Peptide

Cited by 30 publications

References 77 publications

The Making of a Footprint in Protein Footprinting: A Review in Honor of Michael L. Gross

The Making of a Footprint in Protein Footprinting: A Review in Honor of Michael L. Gross

Systematic workflow for studying domain contributions of bispecific antibodies to selectivity in multimodal chromatography

Anti-PD-1 And Anti-PD-L1 Antibodies as Immunotherapy Against Cancer: A Structural Perspective

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