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Mock M, Jacobitz AW, Langmead CJ, Sudom A, Yoo D, Humphreys SC, Alday M, Alekseychyk L, Angell N, Bi V, Catterall H, Chen CC, Chou HT, Conner KP, Cook KD, Correia AR, Dykstra A, Ghimire-Rijal S, Graham K, Grandsard P, Huh J, Hui JO, Jain M, Jann V, Jia L, Johnstone S, Khanal N, Kolvenbach C, Narhi L, Padaki R, Pelegri-O'Day EM, Qi W, Razinkov V, Rice AJ, Smith R, Spahr C, Stevens J, Sun Y, Thomas VA, van Driesche S, Vernon R, Wagner V, Walker KW, Wei Y, Winters D, Yang M, Campuzano IDG. Development of in silico models to predict viscosity and mouse clearance using a comprehensive analytical data set collected on 83 scaffold-consistent monoclonal antibodies. MAbs 2023; 15:2256745. [PMID: 37698932 PMCID: PMC10498806 DOI: 10.1080/19420862.2023.2256745] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Revised: 08/16/2023] [Accepted: 09/05/2023] [Indexed: 09/14/2023] Open
Abstract
Biologic drug discovery pipelines are designed to deliver protein therapeutics that have exquisite functional potency and selectivity while also manifesting biophysical characteristics suitable for manufacturing, storage, and convenient administration to patients. The ability to use computational methods to predict biophysical properties from protein sequence, potentially in combination with high throughput assays, could decrease timelines and increase the success rates for therapeutic developability engineering by eliminating lengthy and expensive cycles of recombinant protein production and testing. To support development of high-quality predictive models for antibody developability, we designed a sequence-diverse panel of 83 effector functionless IgG1 antibodies displaying a range of biophysical properties, produced and formulated each protein under standard platform conditions, and collected a comprehensive package of analytical data, including in vitro assays and in vivo mouse pharmacokinetics. We used this robust training data set to build machine learning classifier models that can predict complex protein behavior from these data and features derived from predicted and/or experimental structures. Our models predict with 87% accuracy whether viscosity at 150 mg/mL is above or below a threshold of 15 centipoise (cP) and with 75% accuracy whether the area under the plasma drug concentration-time curve (AUC0-672 h) in normal mouse is above or below a threshold of 3.9 × 106 h x ng/mL.
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Affiliation(s)
- Marissa Mock
- Biologic Therapeutic Discovery, Amgen Research, Thousand Oaks, CA, USA
| | - Alex W Jacobitz
- Process Development, Amgen Operations, Thousand Oaks, CA, USA
| | | | - Athena Sudom
- Structural Biology, Amgen Research, South San Francisco, CA, USA
| | - Daniel Yoo
- Biologic Therapeutic Discovery, Amgen Research, Thousand Oaks, CA, USA
| | - Sara C Humphreys
- Pharmacokinetics & Drug Metabolism, Amgen Research, South San Francisco, CA, USA
| | - Mai Alday
- Biologic Therapeutic Discovery, Amgen Research, Thousand Oaks, CA, USA
| | | | - Nicolas Angell
- Process Development, Amgen Operations, Thousand Oaks, CA, USA
| | - Vivian Bi
- Biologic Therapeutic Discovery, Amgen Research, Thousand Oaks, CA, USA
| | - Hannah Catterall
- Biologic Therapeutic Discovery, Amgen Research, Thousand Oaks, CA, USA
| | - Chen-Chun Chen
- Biologic Therapeutic Discovery, Amgen Research, Thousand Oaks, CA, USA
| | - Hui-Ting Chou
- Structural Biology, Amgen Research, South San Francisco, CA, USA
| | - Kip P Conner
- Pharmacokinetics & Drug Metabolism, Amgen Research, South San Francisco, CA, USA
| | - Kevin D Cook
- Pharmacokinetics & Drug Metabolism, Amgen Research, South San Francisco, CA, USA
| | - Ana R Correia
- Biologic Therapeutic Discovery, Amgen Research, Thousand Oaks, CA, USA
| | - Andrew Dykstra
- Process Development, Amgen Operations, Thousand Oaks, CA, USA
| | | | - Kevin Graham
- Biologic Therapeutic Discovery, Amgen Research, Thousand Oaks, CA, USA
| | - Peter Grandsard
- Biologic Therapeutic Discovery, Amgen Research, Thousand Oaks, CA, USA
| | - Joon Huh
- Process Development, Amgen Operations, Thousand Oaks, CA, USA
| | - John O Hui
- Biologic Therapeutic Discovery, Amgen Research, Thousand Oaks, CA, USA
| | - Mani Jain
- Biologic Therapeutic Discovery, Amgen Research, Thousand Oaks, CA, USA
| | - Victoria Jann
- Biologic Therapeutic Discovery, Amgen Research, Thousand Oaks, CA, USA
| | - Lei Jia
- Biologic Therapeutic Discovery, Amgen Research, Thousand Oaks, CA, USA
| | - Sheree Johnstone
- Structural Biology, Amgen Research, South San Francisco, CA, USA
| | - Neelam Khanal
- Process Development, Amgen Operations, Thousand Oaks, CA, USA
| | - Carl Kolvenbach
- Biologic Therapeutic Discovery, Amgen Research, Thousand Oaks, CA, USA
| | - Linda Narhi
- Process Development, Amgen Operations, Thousand Oaks, CA, USA
| | - Rupa Padaki
- Process Development, Amgen Operations, Thousand Oaks, CA, USA
| | | | - Wei Qi
- Process Development, Amgen Operations, Thousand Oaks, CA, USA
| | | | - Austin J Rice
- Biologic Therapeutic Discovery, Amgen Research, Thousand Oaks, CA, USA
| | - Richard Smith
- Pharmacokinetics & Drug Metabolism, Amgen Research, South San Francisco, CA, USA
| | - Christopher Spahr
- Biologic Therapeutic Discovery, Amgen Research, Thousand Oaks, CA, USA
| | | | - Yax Sun
- Biologic Therapeutic Discovery, Amgen Research, Thousand Oaks, CA, USA
| | - Veena A Thomas
- Pharmacokinetics & Drug Metabolism, Amgen Research, South San Francisco, CA, USA
| | | | - Robert Vernon
- Biologic Therapeutic Discovery, Amgen Research, Thousand Oaks, CA, USA
| | - Victoria Wagner
- Biologic Therapeutic Discovery, Amgen Research, Thousand Oaks, CA, USA
| | - Kenneth W Walker
- Biologic Therapeutic Discovery, Amgen Research, Thousand Oaks, CA, USA
| | - Yangjie Wei
- Process Development, Amgen Operations, Thousand Oaks, CA, USA
| | - Dwight Winters
- Biologic Therapeutic Discovery, Amgen Research, Thousand Oaks, CA, USA
| | - Melissa Yang
- Biologic Therapeutic Discovery, Amgen Research, Thousand Oaks, CA, USA
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Liu S, Humphreys SC, Cook KD, Conner KP, Correia AR, Jacobitz AW, Yang M, Primack R, Soto M, Padaki R, Lubomirski M, Smith R, Mock M, Thomas VA. Utility of physiologically based pharmacokinetic modeling to predict inter-antibody variability in monoclonal antibody pharmacokinetics in mice. MAbs 2023; 15:2263926. [PMID: 37824334 PMCID: PMC10572049 DOI: 10.1080/19420862.2023.2263926] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Accepted: 09/24/2023] [Indexed: 10/14/2023] Open
Abstract
In this investigation, we tested the hypothesis that a physiologically based pharmacokinetic (PBPK) model incorporating measured in vitro metrics of off-target binding can largely explain the inter-antibody variability in monoclonal antibody (mAb) pharmacokinetics (PK). A diverse panel of 83 mAbs was evaluated for PK in wild-type mice and subjected to 10 in vitro assays to measure major physiochemical attributes. After excluding for target-mediated elimination and immunogenicity, 56 of the remaining mAbs with an eight-fold variability in the area under the curve (A U C 0 - 672 h : 1.74 × 106 -1.38 × 107 ng∙h/mL) and 10-fold difference in clearance (2.55-26.4 mL/day/kg) formed the training set for this investigation. Using a PBPK framework, mAb-dependent coefficients F1 and F2 modulating pinocytosis rate and convective transport, respectively, were estimated for each mAb with mostly good precision (coefficient of variation (CV%) <30%). F1 was estimated to be the mean and standard deviation of 0.961 ± 0.593, and F2 was estimated to be 2.13 ± 2.62. Using principal component analysis to correlate the regressed values of F1/F2 versus the multidimensional dataset composed of our panel of in vitro assays, we found that heparin chromatography retention time emerged as the predictive covariate to the mAb-specific F1, whereas F2 variability cannot be well explained by these assays. A sigmoidal relationship between F1 and the identified covariate was incorporated within the PBPK framework. A sensitivity analysis suggested plasma concentrations to be most sensitive to F1 when F1 > 1. The predictive utility of the developed PBPK model was evaluated against a separate panel of 14 mAbs biased toward high clearance, among which area under the curve of PK data of 12 mAbs was predicted within 2.5-fold error, and the positive and negative predictive values for clearance prediction were 85% and 100%, respectively. MAb heparin chromatography assay output allowed a priori identification of mAb candidates with unfavorable PK.
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Affiliation(s)
- Shufang Liu
- Department of Pharmacokinetics and Drug Metabolism, Amgen Inc, South San Francisco, CA, USA
| | - Sara C. Humphreys
- Department of Pharmacokinetics and Drug Metabolism, Amgen Inc, South San Francisco, CA, USA
| | - Kevin D. Cook
- Department of Pharmacokinetics and Drug Metabolism, Amgen Inc, South San Francisco, CA, USA
| | - Kip P. Conner
- Department of Pharmacokinetics and Drug Metabolism, Amgen Inc, South San Francisco, CA, USA
| | | | | | - Melissa Yang
- Therapeutic Discovery, Amgen, Thousand Oaks, CA, USA
| | - Ronya Primack
- Department of Pharmacokinetics and Drug Metabolism, Amgen Inc, Thousand Oaks, CA, USA
| | - Marcus Soto
- Department of Pharmacokinetics and Drug Metabolism, Amgen Inc, Thousand Oaks, CA, USA
| | - Rupa Padaki
- Process Development, Amgen Inc, Thousand Oaks, CA, USA
| | | | - Richard Smith
- Department of Pharmacokinetics and Drug Metabolism, Amgen Inc, South San Francisco, CA, USA
| | - Marissa Mock
- Therapeutic Discovery, Amgen, Thousand Oaks, CA, USA
| | - Veena A. Thomas
- Department of Pharmacokinetics and Drug Metabolism, Amgen Inc, South San Francisco, CA, USA
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Bley CJ, Nie S, Mobbs GW, Petrovic S, Gres AT, Liu X, Mukherjee S, Harvey S, Huber FM, Lin DH, Brown B, Tang AW, Rundlet EJ, Correia AR, Chen S, Regmi SG, Stevens TA, Jette CA, Dasso M, Patke A, Palazzo AF, Kossiakoff AA, Hoelz A. Architecture of the cytoplasmic face of the nuclear pore. Science 2022; 376:eabm9129. [PMID: 35679405 DOI: 10.1126/science.abm9129] [Citation(s) in RCA: 52] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
INTRODUCTION The subcellular compartmentalization of eukaryotic cells requires selective transport of folded proteins and protein-nucleic acid complexes. Embedded in nuclear envelope pores, which are generated by the circumscribed fusion of the inner and outer nuclear membranes, nuclear pore complexes (NPCs) are the sole bidirectional gateways for nucleocytoplasmic transport. The ~110-MDa human NPC is an ~1000-protein assembly that comprises multiple copies of ~34 different proteins, collectively termed nucleoporins. The symmetric core of the NPC is composed of an inner ring encircling the central transport channel and outer rings formed by Y‑shaped coat nucleoporin complexes (CNCs) anchored atop both sides of the nuclear envelope. The outer rings are decorated with compartment‑specific asymmetric nuclear basket and cytoplasmic filament nucleoporins, which establish transport directionality and provide docking sites for transport factors and the small guanosine triphosphatase Ran. The cytoplasmic filament nucleoporins also play an essential role in the irreversible remodeling of messenger ribonucleoprotein particles (mRNPs) as they exit the central transport channel. Unsurprisingly, the NPC's cytoplasmic face represents a hotspot for disease‑associated mutations and is commonly targeted by viral virulence factors. RATIONALE Previous studies established a near-atomic composite structure of the human NPC's symmetric core by combining (i) biochemical reconstitution to elucidate the interaction network between symmetric nucleoporins, (ii) crystal and single-particle cryo-electron microscopy structure determination of nucleoporins and nucleoporin complexes to reveal their three-dimensional shape and the molecular details of their interactions, (iii) quantitative docking in cryo-electron tomography (cryo-ET) maps of the intact human NPC to uncover nucleoporin stoichiometry and positioning, and (iv) cell‑based assays to validate the physiological relevance of the biochemical and structural findings. In this work, we extended our approach to the cytoplasmic filament nucleoporins to reveal the near-atomic architecture of the cytoplasmic face of the human NPC. RESULTS Using biochemical reconstitution, we elucidated the protein-protein and protein-RNA interaction networks of the human and Chaetomium thermophilum cytoplasmic filament nucleoporins, establishing an evolutionarily conserved heterohexameric cytoplasmic filament nucleoporin complex (CFNC) held together by a central heterotrimeric coiled‑coil hub that tethers two separate mRNP‑remodeling complexes. Further biochemical analysis and determination of a series of crystal structures revealed that the metazoan‑specific cytoplasmic filament nucleoporin NUP358 is composed of 16 distinct domains, including an N‑terminal S‑shaped α‑helical solenoid followed by a coiled‑coil oligomerization element, numerous Ran‑interacting domains, an E3 ligase domain, and a C‑terminal prolyl‑isomerase domain. Physiologically validated quantitative docking into cryo-ET maps of the intact human NPC revealed that pentameric NUP358 bundles, conjoined by the oligomerization element, are anchored through their N‑terminal domains to the central stalk regions of the CNC, projecting flexibly attached domains as far as ~600 Å into the cytoplasm. Using cell‑based assays, we demonstrated that NUP358 is dispensable for the architectural integrity of the assembled interphase NPC and RNA export but is required for efficient translation. After NUP358 assignment, the remaining 4-shaped cryo‑ET density matched the dimensions of the CFNC coiled‑coil hub, in close proximity to an outer-ring NUP93. Whereas the N-terminal NUP93 assembly sensor motif anchors the properly assembled related coiled‑coil channel nucleoporin heterotrimer to the inner ring, biochemical reconstitution confirmed that the NUP93 assembly sensor is reused in anchoring the CFNC to the cytoplasmic face of the human NPC. By contrast, two C. thermophilum CFNCs are anchored by a divergent mechanism that involves assembly sensors located in unstructured portions of two CNC nucleoporins. Whereas unassigned cryo‑ET density occupies the NUP358 and CFNC binding sites on the nuclear face, docking of the nuclear basket component ELYS established that the equivalent position on the cytoplasmic face is unoccupied, suggesting that mechanisms other than steric competition promote asymmetric distribution of nucleoporins. CONCLUSION We have substantially advanced the biochemical and structural characterization of the asymmetric nucleoporins' architecture and attachment at the cytoplasmic and nuclear faces of the NPC. Our near‑atomic composite structure of the human NPC's cytoplasmic face provides a biochemical and structural framework for elucidating the molecular basis of mRNP remodeling, viral virulence factor interference with NPC function, and the underlying mechanisms of nucleoporin diseases at the cytoplasmic face of the NPC. [Figure: see text].
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Affiliation(s)
- Christopher J Bley
- Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 East California Boulevard, Pasadena, CA 91125, USA
| | - Si Nie
- Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 East California Boulevard, Pasadena, CA 91125, USA
| | - George W Mobbs
- Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 East California Boulevard, Pasadena, CA 91125, USA
| | - Stefan Petrovic
- Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 East California Boulevard, Pasadena, CA 91125, USA
| | - Anna T Gres
- Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 East California Boulevard, Pasadena, CA 91125, USA
| | - Xiaoyu Liu
- Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 East California Boulevard, Pasadena, CA 91125, USA
| | - Somnath Mukherjee
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL 60637, USA
| | - Sho Harvey
- Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 East California Boulevard, Pasadena, CA 91125, USA
| | - Ferdinand M Huber
- Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 East California Boulevard, Pasadena, CA 91125, USA
| | - Daniel H Lin
- Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 East California Boulevard, Pasadena, CA 91125, USA
| | - Bonnie Brown
- Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 East California Boulevard, Pasadena, CA 91125, USA
| | - Aaron W Tang
- Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 East California Boulevard, Pasadena, CA 91125, USA
| | - Emily J Rundlet
- Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 East California Boulevard, Pasadena, CA 91125, USA
| | - Ana R Correia
- Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 East California Boulevard, Pasadena, CA 91125, USA
| | - Shane Chen
- Division of Molecular and Cellular Biology, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
| | - Saroj G Regmi
- Division of Molecular and Cellular Biology, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
| | - Taylor A Stevens
- Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 East California Boulevard, Pasadena, CA 91125, USA
| | - Claudia A Jette
- Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 East California Boulevard, Pasadena, CA 91125, USA
| | - Mary Dasso
- Division of Molecular and Cellular Biology, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
| | - Alina Patke
- Division of Biology and Biological Engineering, California Institute of Technology, 1200 East California Boulevard, Pasadena, CA 91125, USA
| | - Alexander F Palazzo
- Department of Biochemistry, University of Toronto, Toronto, ON M5G 1M1, Canada
| | - Anthony A Kossiakoff
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL 60637, USA
| | - André Hoelz
- Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 East California Boulevard, Pasadena, CA 91125, USA
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Riley TP, Chou HT, Hu R, Bzymek KP, Correia AR, Partin AC, Li D, Gong D, Wang Z, Yu X, Manzanillo P, Garces F. Enhancing the Prefusion Conformational Stability of SARS-CoV-2 Spike Protein Through Structure-Guided Design. Front Immunol 2021; 12:660198. [PMID: 33968063 PMCID: PMC8100506 DOI: 10.3389/fimmu.2021.660198] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Accepted: 03/30/2021] [Indexed: 01/08/2023] Open
Abstract
The worldwide pandemic caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is unprecedented and the impact on public health and the global economy continues to be devastating. Although early therapies such as prophylactic antibodies and vaccines show great promise, there are concerns about the long-term efficacy and universal applicability of these therapies as the virus continues to mutate. Thus, protein-based immunogens that can quickly respond to viral changes remain of continued interest. The Spike protein, the main immunogen of this virus, displays a highly dynamic trimeric structure that presents a challenge for therapeutic development. Here, guided by the structure of the Spike trimer, we rationally design new Spike constructs that show a uniquely high stability profile while simultaneously remaining locked into the immunogen-desirable prefusion state. Furthermore, our approach emphasizes the relationship between the highly conserved S2 region and structurally dynamic Receptor Binding Domains (RBD) to enable vaccine development as well as the generation of antibodies able to resist viral mutation.
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Affiliation(s)
- Timothy P. Riley
- Department of Therapeutics Discovery, Amgen Research, Amgen Inc., Thousand Oaks, CA, United States
| | - Hui-Ting Chou
- Department of Therapeutics Discovery, Amgen Research, Amgen Inc., South San Francisco, CA, United States
| | - Ruozhen Hu
- Department of Inflammation and Oncology, Amgen Research, Amgen Inc., South San Francisco, CA, United States
| | - Krzysztof P. Bzymek
- Department of Therapeutics Discovery, Amgen Research, Amgen Inc., Thousand Oaks, CA, United States
| | - Ana R. Correia
- Department of Therapeutics Discovery, Amgen Research, Amgen Inc., Thousand Oaks, CA, United States
| | - Alexander C. Partin
- Department of Therapeutics Discovery, Amgen Research, Amgen Inc., Thousand Oaks, CA, United States
| | - Danqing Li
- Department of Therapeutics Discovery, Amgen Research, Amgen Inc., Thousand Oaks, CA, United States
| | - Danyang Gong
- Department of Therapeutics Discovery, Amgen Research, Amgen Inc., Thousand Oaks, CA, United States
| | - Zhulun Wang
- Department of Therapeutics Discovery, Amgen Research, Amgen Inc., South San Francisco, CA, United States
| | - Xinchao Yu
- Department of Therapeutics Discovery, Amgen Research, Amgen Inc., Thousand Oaks, CA, United States
| | - Paolo Manzanillo
- Department of Inflammation and Oncology, Amgen Research, Amgen Inc., South San Francisco, CA, United States
| | - Fernando Garces
- Department of Therapeutics Discovery, Amgen Research, Amgen Inc., Thousand Oaks, CA, United States
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Gong D, Riley TP, Bzymek KP, Correia AR, Li D, Spahr C, Robinson JH, Case RB, Wang Z, Garces F. Rational selection of building blocks for the assembly of bispecific antibodies. MAbs 2021; 13:1870058. [PMID: 33397191 PMCID: PMC7808324 DOI: 10.1080/19420862.2020.1870058] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Bispecific antibodies, engineered to recognize two targets simultaneously, demonstrate exceptional clinical potential for the therapeutic intervention of complex diseases. However, these molecules are often composed of multiple polypeptide chains of differing sequences. To meet industrial scale productivity, enforcing the correct quaternary assembly of these chains is critical. Here, we describe Chain Selectivity Assessment (CSA), a high-throughput method to rationally select parental monoclonal antibodies (mAbs) to make bispecific antibodies requiring correct heavy/light chain pairing. By deploying CSA, we have successfully identified mAbs that exhibit a native preference toward cognate chain pairing that enables the production of hetero-IgGs without additional engineering. Furthermore, CSA also identified rare light chains (LCs) that permit positive binding of the non-cognate arm in the common LC hetero-IgGs, also without engineering. This rational selection of parental mAbs with favorable developability characteristics is critical to the successful development of bispecific molecules with optimal manufacturability properties.
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Affiliation(s)
- Danyang Gong
- Department of Therapeutics Discovery, Amgen Research, Amgen Inc ., Thousand Oaks, CA USA
| | - Timothy P Riley
- Department of Therapeutics Discovery, Amgen Research, Amgen Inc ., Thousand Oaks, CA USA
| | - Krzysztof P Bzymek
- Department of Therapeutics Discovery, Amgen Research, Amgen Inc ., Thousand Oaks, CA USA
| | - Ana R Correia
- Department of Therapeutics Discovery, Amgen Research, Amgen Inc ., Thousand Oaks, CA USA
| | - Danqing Li
- Department of Therapeutics Discovery, Amgen Research, Amgen Inc ., Thousand Oaks, CA USA
| | - Christopher Spahr
- Department of Therapeutics Discovery, Amgen Research, Amgen Inc ., Thousand Oaks, CA USA
| | - John H Robinson
- Department of Therapeutics Discovery, Amgen Research, Amgen Inc ., Thousand Oaks, CA USA
| | - Ryan B Case
- Department of Therapeutics Discovery, Amgen Research, Amgen Inc ., San Francisco, CA USA
| | - Zhulun Wang
- Department of Therapeutics Discovery, Amgen Research, Amgen Inc ., San Francisco, CA USA
| | - Fernando Garces
- Department of Therapeutics Discovery, Amgen Research, Amgen Inc ., Thousand Oaks, CA USA
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Lin DH, Correia AR, Cai SW, Huber FM, Jette CA, Hoelz A. Structural and functional analysis of mRNA export regulation by the nuclear pore complex. Nat Commun 2018; 9:2319. [PMID: 29899397 PMCID: PMC5998080 DOI: 10.1038/s41467-018-04459-3] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2017] [Accepted: 04/27/2018] [Indexed: 11/25/2022] Open
Abstract
The nuclear pore complex (NPC) controls the passage of macromolecules between the nucleus and cytoplasm, but how the NPC directly participates in macromolecular transport remains poorly understood. In the final step of mRNA export, the DEAD-box helicase DDX19 is activated by the nucleoporins Gle1, Nup214, and Nup42 to remove Nxf1•Nxt1 from mRNAs. Here, we report crystal structures of Gle1•Nup42 from three organisms that reveal an evolutionarily conserved binding mode. Biochemical reconstitution of the DDX19 ATPase cycle establishes that human DDX19 activation does not require IP6, unlike its fungal homologs, and that Gle1 stability affects DDX19 activation. Mutations linked to motor neuron diseases cause decreased Gle1 thermostability, implicating nucleoporin misfolding as a disease determinant. Crystal structures of human Gle1•Nup42•DDX19 reveal the structural rearrangements in DDX19 from an auto-inhibited to an RNA-binding competent state. Together, our results provide the foundation for further mechanistic analyses of mRNA export in humans. The export of mRNA to the cytosol depends on the nuclear pore complex (NPC) and the activation of the helicase DDX19, but their interplay in humans remains poorly understood. Here, the authors present a structural and functional analysis of DDX19 activation, revealing how the human NPC regulates mRNA export.
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Affiliation(s)
- Daniel H Lin
- Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 East California Boulevard, Pasadena, CA, 91125, USA
| | - Ana R Correia
- Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 East California Boulevard, Pasadena, CA, 91125, USA
| | - Sarah W Cai
- Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 East California Boulevard, Pasadena, CA, 91125, USA
| | - Ferdinand M Huber
- Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 East California Boulevard, Pasadena, CA, 91125, USA
| | - Claudia A Jette
- Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 East California Boulevard, Pasadena, CA, 91125, USA
| | - André Hoelz
- Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 East California Boulevard, Pasadena, CA, 91125, USA.
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7
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Skubák P, Araç D, Bowler MW, Correia AR, Hoelz A, Larsen S, Leonard GA, McCarthy AA, McSweeney S, Mueller-Dieckmann C, Otten H, Salzman G, Pannu NS. A new MR-SAD algorithm for the automatic building of protein models from low-resolution X-ray data and a poor starting model. IUCrJ 2018; 5:166-171. [PMID: 29765606 PMCID: PMC5947721 DOI: 10.1107/s2052252517017961] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2017] [Accepted: 12/15/2017] [Indexed: 05/07/2023]
Abstract
Determining macromolecular structures from X-ray data with resolution worse than 3 Å remains a challenge. Even if a related starting model is available, its incompleteness or its bias together with a low observation-to-parameter ratio can render the process unsuccessful or very time-consuming. Yet, many biologically important macromolecules, especially large macromolecular assemblies, membrane proteins and receptors, tend to provide crystals that diffract to low resolution. A new algorithm to tackle this problem is presented that uses a multivariate function to simultaneously exploit information from both an initial partial model and low-resolution single-wavelength anomalous diffraction data. The new approach has been used for six challenging structure determinations, including the crystal structures of membrane proteins and macromolecular complexes that have evaded experts using other methods, and large structures from a 3.0 Å resolution F1-ATPase data set and a 4.5 Å resolution SecYEG-SecA complex data set. All of the models were automatically built by the method to Rfree values of between 28.9 and 39.9% and were free from the initial model bias.
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Affiliation(s)
- Pavol Skubák
- Department of Biophysical Structural Chemistry, Leiden University, Einsteinweg 55, 2333 CC Leiden, The Netherlands
| | - Demet Araç
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL 60637, USA
| | - Matthew W. Bowler
- European Molecular Biology Laboratory, Grenoble Outstation, 71 Avenue des Martyrs, 38000 Grenoble, France
| | - Ana R. Correia
- Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 East California Boulevard, Pasadena, CA 91125, USA
| | - Andre Hoelz
- Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 East California Boulevard, Pasadena, CA 91125, USA
| | - Sine Larsen
- Department of Chemistry, University of Copenhagen, Universitetsparken 5, DK-2100 Copenhagen, Denmark
| | - Gordon A. Leonard
- European Synchrotron Radiation Facility, 71 Avenue des Martyrs, CS 40220, 38043 Grenoble, France
| | - Andrew A. McCarthy
- European Molecular Biology Laboratory, Grenoble Outstation, 71 Avenue des Martyrs, 38000 Grenoble, France
| | - Sean McSweeney
- European Synchrotron Radiation Facility, 71 Avenue des Martyrs, CS 40220, 38043 Grenoble, France
- Department of Photon Sciences, Brookhaven National Laboratory, Upton, NY 11973-5000, USA
| | | | - Harm Otten
- Department of Chemistry, University of Copenhagen, Universitetsparken 5, DK-2100 Copenhagen, Denmark
| | - Gabriel Salzman
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL 60637, USA
| | - Navraj S. Pannu
- Department of Biophysical Structural Chemistry, Leiden University, Einsteinweg 55, 2333 CC Leiden, The Netherlands
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8
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Abstract
The nuclear pore complex (NPC) constitutes the sole gateway for bidirectional nucleocytoplasmic transport. Despite half a century of structural characterization, the architecture of the NPC remains unknown. Here we present the crystal structure of a reconstituted ~400-kilodalton coat nucleoporin complex (CNC) from Saccharomyces cerevisiae at a 7.4 angstrom resolution. The crystal structure revealed a curved Y-shaped architecture and the molecular details of the coat nucleoporin interactions forming the central "triskelion" of the Y. A structural comparison of the yeast CNC with an electron microscopy reconstruction of its human counterpart suggested the evolutionary conservation of the elucidated architecture. Moreover, 32 copies of the CNC crystal structure docked readily into a cryoelectron tomographic reconstruction of the fully assembled human NPC, thereby accounting for ~16 megadalton of its mass.
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Affiliation(s)
- Tobias Stuwe
- Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 East California Boulevard, Pasadena, CA 91125, USA. These authors contributed equally to this work
| | - Ana R Correia
- Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 East California Boulevard, Pasadena, CA 91125, USA. These authors contributed equally to this work
| | - Daniel H Lin
- Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 East California Boulevard, Pasadena, CA 91125, USA
| | - Marcin Paduch
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL 60637, USA
| | - Vincent T Lu
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL 60637, USA
| | - Anthony A Kossiakoff
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL 60637, USA
| | - André Hoelz
- Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 East California Boulevard, Pasadena, CA 91125, USA.
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9
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Correia AR, Naik S, Fisher MT, Gomes CM. Probing the kinetic stabilities of Friedreich's ataxia clinical variants using a solid phase GroEL chaperonin capture platform. Biomolecules 2014; 4:956-79. [PMID: 25333765 PMCID: PMC4279165 DOI: 10.3390/biom4040956] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2014] [Revised: 08/29/2014] [Accepted: 09/19/2014] [Indexed: 11/17/2022] Open
Abstract
Numerous human diseases are caused by protein folding defects where the protein may become more susceptible to degradation or aggregation. Aberrant protein folding can affect the kinetic stability of the proteins even if these proteins appear to be soluble in vivo. Experimental discrimination between functional properly folded and misfolded nonfunctional conformers is not always straightforward at near physiological conditions. The differences in the kinetic behavior of two initially folded frataxin clinical variants were examined using a high affinity chaperonin kinetic trap approach at 25 °C. The kinetically stable wild type frataxin (FXN) shows no visible partitioning onto the chaperonin. In contrast, the clinical variants FXN-p.Asp122Tyr and FXN-p.Ile154Phe kinetically populate partial folded forms that tightly bind the GroEL chaperonin platform. The initially soluble FXN-p.Ile154Phe variant partitions onto GroEL more rapidly and is more kinetically liable. These differences in kinetic stability were confirmed using differential scanning fluorimetry. The kinetic and aggregation stability differences of these variants may lead to the distinct functional impairments described in Friedreich's ataxia, the neurodegenerative disease associated to frataxin functional deficiency. This chaperonin platform approach may be useful for identifying small molecule stabilizers since stabilizing ligands to frataxin variants should lead to a concomitant decrease in chaperonin binding.
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Affiliation(s)
- Ana R Correia
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, EAN, Oeiras 2784-505, Portugal.
| | - Subhashchandra Naik
- Department of Biochemistry and Molecular Biology, Hemenway Life Sciences Innovation Center (HLSIC), University of Kansas Medical Center, 3901 Rainbow Blvd., Kansas City, KS 66160, USA.
| | - Mark T Fisher
- Department of Biochemistry and Molecular Biology, Hemenway Life Sciences Innovation Center (HLSIC), University of Kansas Medical Center, 3901 Rainbow Blvd., Kansas City, KS 66160, USA.
| | - Cláudio M Gomes
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, EAN, Oeiras 2784-505, Portugal.
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10
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Figueiral MH, Fonseca P, Campos JCR, Correia AR, Fernandes MS, Branco FJM. Removable partial denture education in Portugal following the Bologna Process. Eur J Prosthodont Restor Dent 2013; 21:127-134. [PMID: 24261105] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
The aim of this study was to investigate the current guidelines used for the undergraduate course subject Removable Partial Denture in Portuguese Dental Schools following the Bologna Process. All Dental Schools were sent a questionnaire, divided into the following areas: (I) organization and syllabus; (II) teaching methods; (III) materials and techniques; Answers about organization and syllabus of course subjects showed the most variability; teaching methods were identical regarding principal textbook and live demonstrations of laboratory/clinical procedures; the same techniques and materials are used in all the schools' dental clinics. The majority of Dental Schools present similar guidelines for removable partial dentures.
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Affiliation(s)
- M H Figueiral
- Department of Removable Prosthodontics, Faculty of Dental Medicine of the University of Porto, Porto, Portugal
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11
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Correia AR, Wang T, Craig EA, Gomes CM. Iron-binding activity in yeast frataxin entails a trade off with stability in the alpha1/beta1 acidic ridge region. Biochem J 2010; 426:197-203. [PMID: 20001966 PMCID: PMC2819628 DOI: 10.1042/bj20091612] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Frataxin is a highly conserved mitochondrial protein whose deficiency in humans results in Friedreich's ataxia (FRDA), an autosomal recessive disorder characterized by progressive ataxia and cardiomyopathy. Although its cellular function is still not fully clear, the fact that frataxin plays a crucial role in Fe-S assembly on the scaffold protein Isu is well accepted. In the present paper, we report the characterization of eight frataxin variants having alterations on two putative functional regions: the alpha1/beta1 acidic ridge and the conserved beta-sheet surface. We report that frataxin iron-binding capacity is quite robust: even when five of the most conserved residues from the putative iron-binding region are altered, at least two iron atoms per monomer can be bound, although with decreased affinity. Furthermore, we conclude that the acidic ridge is designed to favour function over stability. The negative charges have a functional role, but at the same time significantly impair frataxin's stability. Removing five of those charges results in a thermal stabilization of approximately 24 degrees C and reduces the inherent conformational plasticity. Alterations on the conserved beta-sheet residues have only a modest impact on the protein stability, highlighting the functional importance of residues 122-124.
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Affiliation(s)
- Ana R. Correia
- Instituto Tecnologia Química e Biológica, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Tao Wang
- Department of Biochemistry, University of Wisconsin, Madison, WI 53706, USA
| | - Elizabeth A. Craig
- Department of Biochemistry, University of Wisconsin, Madison, WI 53706, USA
| | - Cláudio M. Gomes
- Instituto Tecnologia Química e Biológica, Universidade Nova de Lisboa, Oeiras, Portugal
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12
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Correia AR, Ow SY, Wright PC, Gomes CM. The conserved Trp155 in human frataxin as a hotspot for oxidative stress related chemical modifications. Biochem Biophys Res Commun 2009; 390:1007-11. [PMID: 19853582 DOI: 10.1016/j.bbrc.2009.10.095] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2009] [Accepted: 10/19/2009] [Indexed: 11/26/2022]
Abstract
Frataxin is a mitochondrial protein that is defective in Friedreich's ataxia resulting in iron accumulation and an environment prone to Fenton reactions. We report that frataxin is susceptible to carbonylation and nitration modifications in residues from the beta-sheet surface (Tyr143, Tyr174, Tyr205 and Trp155). Frataxin functions are not significantly affected: frataxin-mediated protection against ROS is still observed, as well as iron-binding (5 Fe(3+)mol(-1), K(d) from 13-36 microM) necessary for the metallochaperone activity. However, the protein is up to 1.0 kcal mol(-1) destabilized, with conformational opening. Interestingly, the strictly conserved Trp155, which is mutated in patients, may be a functional hotspot in frataxin.
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Affiliation(s)
- Ana R Correia
- Instituto Tecnologia Química e Biológica, Universidade Nova de Lisboa, 2780-756 Oeiras, Portugal
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13
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Abstract
Friedreich's ataxia results from a deficiency in the mitochondrial protein frataxin, which carries single point mutations in some patients. In the present study, we analysed the consequences of different disease-related mutations in vitro on the stability and dynamics of human frataxin. Two of the mutations, G130V and D122Y, were investigated for the first time. Analysis by CD spectroscopy demonstrated a substantial decrease in the thermodynamic stability of the variants during chemical and thermal unfolding (wild-type > W155R > I154F > D122Y > G130V), which was reversible in all cases. Protein dynamics was studied in detail and revealed that the mutants have distinct propensities towards aggregation. It was observed that the mutants have increased correlation times and different relative ratios between soluble and insoluble/aggregated protein. NMR showed that the clinical mutants retained a compact and relatively rigid globular core despite their decreased stabilities. Limited proteolysis assays coupled with LC-MS allowed the identification of particularly flexible regions in the mutants; interestingly, these regions included those involved in iron-binding. In agreement, the iron metallochaperone activity of the Friedreich's ataxia mutants was affected: some mutants precipitate upon iron binding (I154F and W155R) and others have a lower binding stoichiometry (G130V and D122Y). Our results suggest that, in heterozygous patients, the development of Friedreich's ataxia may result from a combination of reduced efficiency of protein folding and accelerated degradation in vivo, leading to lower than normal concentrations of frataxin. This hypothesis also suggests that, although quite different from other neurodegenerative diseases involving toxic aggregation, Friedreich's ataxia could also be linked to a process of protein misfolding due to specific destabilization of frataxin.
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Affiliation(s)
- Ana R Correia
- Instituto Tecnologia Química e Biológica, Universidade Nova de Lisboa, Oeiras, Portugal
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14
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Kirzner CF, Correia AR, Azevedo OM, Maranhão MV, Gonçalves JR, Kirzner MS, Xavier AP, Figueiroa JN. Low-dose aprotinin in heart valve reoperations. J Heart Valve Dis 2001; 10:222-7. [PMID: 11297210] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 02/19/2023]
Abstract
BACKGROUND AND AIM OF THE STUDY Aprotinin is effective in promoting hemostasis, notably in cardiac surgery with cardiopulmonary bypass. Its efficacy has been shown in coronary bypass graft operations. However, few reports exist of aprotinin use in valve operations, and in those studies only the full dose was used. Thus, our aim was to evaluate the effects of low-dose aprotinin in patients undergoing heart valve reoperation. METHODS Eighteen patients having reoperative valve surgery received 10(6) KIU aprotinin after induction of anesthesia, and a further 10(6) KIU in the pump prime. A group of 18 similar patients who were operated on but did not receive aprotinin were used as controls. RESULTS A significant reduction in postoperative blood loss (approximately 470 ml) occurred in patients receiving aprotinin. These patients also presented less postoperative bleeding than untreated patients in 70.4% of cases. No adverse effects of the drug were noted, except for one case of allergic reaction. CONCLUSION The systematic use of low-dose aprotinin should be considered in valve reoperation, except in cases of re-exposure to the drug, or allergic reaction.
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Affiliation(s)
- C F Kirzner
- University of Pernambuco School of Medical Sciences, Recife, Brazil
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