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Article: Structural basis for VLDLR recognition by eastern equine encephalitis virus.

Yang, Pan / Li, Wanyu / Fan, Xiaoyi / Pan, Junhua / Mann, Colin J / Varnum, Haley / Clark, Lars E / Clark, Sarah A / Coscia, Adrian / Smith, Katherine Nabel / Brusic, Vesna / Abraham, Jonathan

bioRxiv : the preprint server for biology

2023

Abstract: Alphaviruses are arthropod-borne enveloped RNA viruses that include several important human pathogens with outbreak potential. Among them, eastern equine encephalitis virus (EEEV) is the most virulent, and many survivors develop neurological sequelae, ... ...

Abstract	Alphaviruses are arthropod-borne enveloped RNA viruses that include several important human pathogens with outbreak potential. Among them, eastern equine encephalitis virus (EEEV) is the most virulent, and many survivors develop neurological sequelae, including paralysis and intellectual disability. The spike proteins of alphaviruses comprise trimers of heterodimers of their envelope glycoproteins E2 and E1 that mediate binding to cellular receptors and fusion of virus and host cell membranes during entry. We recently identified very-low density lipoprotein receptor (VLDLR) and apolipoprotein E receptor 2 (ApoER2), two closely related proteins that are expressed in the brain, as cellular receptors for EEEV and a distantly related alphavirus, Semliki forest virus (SFV)
Language	English
Publishing date	2023-11-14
Publishing country	United States
Document type	Preprint
DOI	10.1101/2023.11.14.567065
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Article ; Online: Host receptor-targeted therapeutic approach to counter pathogenic New World mammarenavirus infections.

Hickerson, Brady T / Daniels-Wells, Tracy R / Payes, Cristian / Clark, Lars E / Candelaria, Pierre V / Bailey, Kevin W / Sefing, Eric J / Zink, Samantha / Ziegenbein, James / Abraham, Jonathan / Helguera, Gustavo / Penichet, Manuel L / Gowen, Brian B

Nature communications

2022 Volume 13, Issue 1, Page(s) 558

Abstract: Five New World mammarenaviruses (NWMs) cause life-threatening hemorrhagic fever (HF). Cellular entry by these viruses is mediated by human transferrin receptor 1 (hTfR1). Here, we demonstrate that an antibody (ch128.1/IgG1) which binds the apical domain ... ...

Abstract	Five New World mammarenaviruses (NWMs) cause life-threatening hemorrhagic fever (HF). Cellular entry by these viruses is mediated by human transferrin receptor 1 (hTfR1). Here, we demonstrate that an antibody (ch128.1/IgG1) which binds the apical domain of hTfR1, potently inhibits infection of attenuated and pathogenic NWMs in vitro. Computational docking of the antibody Fab crystal structure onto the known structure of hTfR1 shows an overlapping receptor-binding region shared by the Fab and the viral envelope glycoprotein GP1 subunit that binds hTfR1, and we demonstrate competitive inhibition of NWM GP1 binding by ch128.1/IgG1 as the principal mechanism of action. Importantly, ch128.1/IgG1 protects hTfR1-expressing transgenic mice against lethal NWM challenge. Additionally, the antibody is well-tolerated and only partially reduces ferritin uptake. Our findings provide the basis for the development of a novel, host receptor-targeted antibody therapeutic broadly applicable to the treatment of HF of NWM etiology.
MeSH term(s)	A549 Cells ; Animals ; Antibodies, Monoclonal/immunology ; Antibodies, Monoclonal/metabolism ; Antibodies, Monoclonal/pharmacology ; Antigens, CD/immunology ; Antigens, CD/metabolism ; Arenaviridae/drug effects ; Arenaviridae/metabolism ; Arenaviridae/physiology ; Chlorocebus aethiops ; Hemorrhagic Fever, American/metabolism ; Hemorrhagic Fever, American/prevention & control ; Hemorrhagic Fever, American/virology ; Host-Pathogen Interactions/drug effects ; Humans ; Junin virus/drug effects ; Junin virus/physiology ; Mice, Inbred C57BL ; Mice, Transgenic ; Molecular Docking Simulation ; Protein Binding/drug effects ; Receptors, Transferrin/antagonists & inhibitors ; Receptors, Transferrin/immunology ; Receptors, Transferrin/metabolism ; Vero Cells ; Viral Envelope Proteins/metabolism ; Mice
Chemical Substances	Antibodies, Monoclonal ; Antigens, CD ; CD71 antigen ; Receptors, Transferrin ; Viral Envelope Proteins
Language	English
Publishing date	2022-01-28
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S.
ZDB-ID	2553671-0
ISSN	2041-1723 ; 2041-1723
ISSN (online)	2041-1723
ISSN	2041-1723
DOI	10.1038/s41467-021-27949-3
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Article ; Online: Correction for Ferrero et al., "Antibody-Based Inhibition of Pathogenic New World Hemorrhagic Fever Mammarenaviruses by Steric Occlusion of the Human Transferrin Receptor 1 Apical Domain".

Ferrero, Sol / Flores, Maria D / Short, Connor / Vazquez, Cecilia A / Clark, Lars E / Ziegenbein, James / Zink, Samantha / Fuentes, Daniel / Payes, Cristian / Batto, María V / Collazo, Michael / García, Cybele C / Abraham, Jonathan / Cordo, Sandra M / Rodriguez, Jose A / Helguera, Gustavo

Journal of virology

2022 Volume 96, Issue 4, Page(s) e0216321

Language	English
Publishing date	2022-02-23
Publishing country	United States
Document type	Journal Article ; Published Erratum
ZDB-ID	80174-4
ISSN	1098-5514 ; 0022-538X
ISSN (online)	1098-5514
ISSN	0022-538X
DOI	10.1128/jvi.02163-21
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Article ; Online: SARS-CoV-2 evolution in an immunocompromised host reveals shared neutralization escape mechanisms.

Clark, Sarah A / Clark, Lars E / Pan, Junhua / Coscia, Adrian / McKay, Lindsay G A / Shankar, Sundaresh / Johnson, Rebecca I / Brusic, Vesna / Choudhary, Manish C / Regan, James / Li, Jonathan Z / Griffiths, Anthony / Abraham, Jonathan

Cell

2021 Volume 184, Issue 10, Page(s) 2605–2617.e18

Abstract: Many individuals mount nearly identical antibody responses to SARS-CoV-2. To gain insight into how the viral spike (S) protein receptor-binding domain (RBD) might evolve in response to common antibody responses, we studied mutations occurring during ... ...

Abstract	Many individuals mount nearly identical antibody responses to SARS-CoV-2. To gain insight into how the viral spike (S) protein receptor-binding domain (RBD) might evolve in response to common antibody responses, we studied mutations occurring during virus evolution in a persistently infected immunocompromised individual. We use antibody Fab/RBD structures to predict, and pseudotypes to confirm, that mutations found in late-stage evolved S variants confer resistance to a common class of SARS-CoV-2 neutralizing antibodies we isolated from a healthy COVID-19 convalescent donor. Resistance extends to the polyclonal serum immunoglobulins of four out of four healthy convalescent donors we tested and to monoclonal antibodies in clinical use. We further show that affinity maturation is unimportant for wild-type virus neutralization but is critical to neutralization breadth. Because the mutations we studied foreshadowed emerging variants that are now circulating across the globe, our results have implications to the long-term efficacy of S-directed countermeasures.
MeSH term(s)	Antibodies, Neutralizing ; Antibodies, Viral/immunology ; COVID-19/genetics ; COVID-19/immunology ; Evolution, Molecular ; Female ; HEK293 Cells ; Humans ; Immune Evasion/immunology ; Immunocompromised Host ; Immunoglobulin Fab Fragments/immunology ; Male ; Protein Domains ; SARS-CoV-2/genetics ; SARS-CoV-2/immunology ; Spike Glycoprotein, Coronavirus/genetics ; Spike Glycoprotein, Coronavirus/immunology
Chemical Substances	Antibodies, Neutralizing ; Antibodies, Viral ; Immunoglobulin Fab Fragments ; Spike Glycoprotein, Coronavirus ; spike protein, SARS-CoV-2
Language	English
Publishing date	2021-03-16
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	187009-9
ISSN	1097-4172 ; 0092-8674
ISSN (online)	1097-4172
ISSN	0092-8674
DOI	10.1016/j.cell.2021.03.027
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Article: Molecular basis for a germline-biased neutralizing antibody response to SARS-CoV-2.

Clark, Sarah A / Clark, Lars E / Pan, Junhua / Coscia, Adrian / McKay, Lindsay G A / Shankar, Sundaresh / Johnson, Rebecca I / Griffiths, Anthony / Abraham, Jonathan

bioRxiv : the preprint server for biology

2020

Abstract: The SARS-CoV-2 viral spike (S) protein mediates attachment and entry into host cells and is a major target of vaccine and drug design. Potent SARS-CoV-2 neutralizing antibodies derived from closely related antibody heavy chain genes (IGHV3-53 or 3-66) ... ...

Abstract	The SARS-CoV-2 viral spike (S) protein mediates attachment and entry into host cells and is a major target of vaccine and drug design. Potent SARS-CoV-2 neutralizing antibodies derived from closely related antibody heavy chain genes (IGHV3-53 or 3-66) have been isolated from multiple COVID-19 convalescent individuals. These usually contain minimal somatic mutations and bind the S receptor-binding domain (RBD) to interfere with attachment to the cellular receptor angiotensin-converting enzyme 2 (ACE2). We used antigen-specific single B cell sorting to isolate S-reactive monoclonal antibodies from the blood of a COVID-19 convalescent individual. The seven most potent neutralizing antibodies were somatic variants of the same IGHV3-53-derived antibody and bind the RBD with varying affinity. We report X-ray crystal structures of four Fab variants bound to the RBD and use the structures to explain the basis for changes in RBD affinity. We show that a germline revertant antibody binds tightly to the SARS-CoV-2 RBD and neutralizes virus, and that gains in affinity for the RBD do not necessarily correlate with increased neutralization potency, suggesting that somatic mutation is not required to exert robust antiviral effect. Our studies clarify the molecular basis for a heavily germline-biased human antibody response to SARS-CoV-2.
Keywords	covid19
Language	English
Publishing date	2020-11-13
Publishing country	United States
Document type	Preprint
DOI	10.1101/2020.11.13.381533
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Article ; Online: Antibody-Based Inhibition of Pathogenic New World Hemorrhagic Fever Mammarenaviruses by Steric Occlusion of the Human Transferrin Receptor 1 Apical Domain.

Journal of virology

2021 Volume 95, Issue 17, Page(s) e0186820

Abstract: Pathogenic clade B New World mammarenaviruses (NWM) can cause Argentine, Venezuelan, Brazilian, and Bolivian hemorrhagic fevers. Sequence variability among NWM glycoproteins (GP) poses a challenge to the development of broadly neutralizing therapeutics ... ...

Abstract	Pathogenic clade B New World mammarenaviruses (NWM) can cause Argentine, Venezuelan, Brazilian, and Bolivian hemorrhagic fevers. Sequence variability among NWM glycoproteins (GP) poses a challenge to the development of broadly neutralizing therapeutics against the entire clade of viruses. However, blockade of their shared binding site on the apical domain of human transferrin receptor 1 (hTfR1/CD71) presents an opportunity for the development of effective and broadly neutralizing therapeutics. Here, we demonstrate that the murine monoclonal antibody OKT9, which targets the apical domain of hTfR1, can sterically block cellular entry by viral particles presenting clade B NWM glycoproteins (GP1-GP2). OKT9 blockade is also effective against viral particles pseudotyped with glycoproteins of a recently identified pathogenic Sabia-like virus. With nanomolar affinity for hTfR1, the OKT9 antigen binding fragment (OKT9-Fab) sterically blocks clade B NWM-GP1s and reduces infectivity of an attenuated strain of Junin virus. Binding of OKT9 to the hTfR1 ectodomain in its soluble, dimeric state produces stable assemblies that are observable by negative-stain electron microscopy. A model of the OKT9-sTfR1 complex, informed by the known crystallographic structure of sTfR1 and a newly determined structure of the OKT9 antigen binding fragment (Fab), suggests that OKT9 and the Machupo virus GP1 share a binding site on the hTfR1 apical domain. The structural basis for this interaction presents a framework for the design and development of high-affinity, broadly acting agents targeting clade B NWMs.
MeSH term(s)	A549 Cells ; Amino Acid Sequence ; Antibodies, Monoclonal/administration & dosage ; Antibodies, Monoclonal/immunology ; Antibodies, Neutralizing/administration & dosage ; Antibodies, Neutralizing/immunology ; Antibodies, Viral/administration & dosage ; Antibodies, Viral/immunology ; Arenaviruses, New World/physiology ; Glycoproteins/immunology ; Hemorrhagic Fever, American/immunology ; Hemorrhagic Fever, American/prevention & control ; Hemorrhagic Fever, American/virology ; Humans ; Protein Structure, Tertiary ; Receptors, Transferrin/chemistry ; Receptors, Transferrin/genetics ; Receptors, Transferrin/immunology
Chemical Substances	Antibodies, Monoclonal ; Antibodies, Neutralizing ; Antibodies, Viral ; Glycoproteins ; Receptors, Transferrin
Language	English
Publishing date	2021-08-10
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S.
ZDB-ID	80174-4
ISSN	1098-5514 ; 0022-538X
ISSN (online)	1098-5514
ISSN	0022-538X
DOI	10.1128/JVI.01868-20
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Article ; Online: VLDLR and ApoER2 are receptors for multiple alphaviruses.

Clark, Lars E / Clark, Sarah A / Lin, ChieYu / Liu, Jianying / Coscia, Adrian / Nabel, Katherine G / Yang, Pan / Neel, Dylan V / Lee, Hyo / Brusic, Vesna / Stryapunina, Iryna / Plante, Kenneth S / Ahmed, Asim A / Catteruccia, Flaminia / Young-Pearse, Tracy L / Chiu, Isaac M / Llopis, Paula Montero / Weaver, Scott C / Abraham, Jonathan

Nature

2021 Volume 602, Issue 7897, Page(s) 475–480

Abstract: Alphaviruses, like many other arthropod-borne viruses, infect vertebrate species and insect vectors separated by hundreds of millions of years of evolutionary history. Entry into evolutionarily divergent host cells can be accomplished by recognition of ... ...

Abstract	Alphaviruses, like many other arthropod-borne viruses, infect vertebrate species and insect vectors separated by hundreds of millions of years of evolutionary history. Entry into evolutionarily divergent host cells can be accomplished by recognition of different cellular receptors in different species, or by binding to receptors that are highly conserved across species. Although multiple alphavirus receptors have been described
MeSH term(s)	Animals ; LDL-Receptor Related Proteins ; Ligands ; Mice ; Mosquito Vectors ; Receptors, LDL ; Semliki forest virus/metabolism ; Sindbis Virus/physiology
Chemical Substances	LDL-Receptor Related Proteins ; Ligands ; Receptors, LDL ; VLDL receptor ; low density lipoprotein receptor-related protein 8
Language	English
Publishing date	2021-12-20
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	120714-3
ISSN	1476-4687 ; 0028-0836
ISSN (online)	1476-4687
ISSN	0028-0836
DOI	10.1038/s41586-021-04326-0
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Article ; Online: Vaccine-elicited receptor-binding site antibodies neutralize two New World hemorrhagic fever arenaviruses.

Clark, Lars E / Mahmutovic, Selma / Raymond, Donald D / Dilanyan, Taleen / Koma, Takaaki / Manning, John T / Shankar, Sundaresh / Levis, Silvana C / Briggiler, Ana M / Enria, Delia A / Wucherpfennig, Kai W / Paessler, Slobodan / Abraham, Jonathan

Nature communications

2018 Volume 9, Issue 1, Page(s) 1884

Abstract: While five arenaviruses cause human hemorrhagic fevers in the Western Hemisphere, only Junin virus (JUNV) has a vaccine. The GP1 subunit of their envelope glycoprotein binds transferrin receptor 1 (TfR1) using a surface that substantially varies in ... ...

Abstract	While five arenaviruses cause human hemorrhagic fevers in the Western Hemisphere, only Junin virus (JUNV) has a vaccine. The GP1 subunit of their envelope glycoprotein binds transferrin receptor 1 (TfR1) using a surface that substantially varies in sequence among the viruses. As such, receptor-mimicking antibodies described to date are type-specific and lack the usual breadth associated with this mode of neutralization. Here we isolate, from the blood of a recipient of the live attenuated JUNV vaccine, two antibodies that cross-neutralize Machupo virus with varying efficiency. Structures of GP1-Fab complexes explain the basis for efficient cross-neutralization, which involves avoiding receptor mimicry and targeting a conserved epitope within the receptor-binding site (RBS). The viral RBS, despite its extensive sequence diversity, is therefore a target for cross-reactive antibodies with activity against New World arenaviruses of public health concern.
MeSH term(s)	Amino Acid Sequence ; Antibodies, Neutralizing/chemistry ; Antibodies, Neutralizing/isolation & purification ; Antibodies, Viral/chemistry ; Antibodies, Viral/isolation & purification ; Antigens, CD/chemistry ; Antigens, CD/genetics ; Antigens, CD/immunology ; Antigens, Viral/chemistry ; Antigens, Viral/genetics ; Antigens, Viral/immunology ; Arenaviruses, New World/genetics ; Arenaviruses, New World/immunology ; Binding Sites, Antibody ; Cross Reactions ; Epitopes/chemistry ; Epitopes/genetics ; Epitopes/immunology ; HEK293 Cells ; Hemorrhagic Fever, American/immunology ; Hemorrhagic Fever, American/prevention & control ; Hemorrhagic Fever, American/virology ; Humans ; Immune Sera/chemistry ; Immunoglobulin Fab Fragments/chemistry ; Immunoglobulin Fab Fragments/isolation & purification ; Junin virus/genetics ; Junin virus/immunology ; Models, Molecular ; Protein Binding ; Protein Conformation, alpha-Helical ; Protein Conformation, beta-Strand ; Protein Interaction Domains and Motifs ; Protein Structure, Tertiary ; Protein Subunits/chemistry ; Protein Subunits/genetics ; Protein Subunits/immunology ; Receptors, Transferrin/chemistry ; Receptors, Transferrin/genetics ; Receptors, Transferrin/immunology ; Receptors, Virus/chemistry ; Receptors, Virus/genetics ; Receptors, Virus/immunology ; Sequence Alignment ; Sequence Homology, Amino Acid ; Viral Envelope Proteins/chemistry ; Viral Envelope Proteins/genetics ; Viral Envelope Proteins/immunology ; Viral Vaccines/administration & dosage
Chemical Substances	Antibodies, Neutralizing ; Antibodies, Viral ; Antigens, CD ; Antigens, Viral ; CD71 antigen ; Epitopes ; Immune Sera ; Immunoglobulin Fab Fragments ; Protein Subunits ; Receptors, Transferrin ; Receptors, Virus ; Viral Envelope Proteins ; Viral Vaccines
Language	English
Publishing date	2018-05-14
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	2553671-0
ISSN	2041-1723 ; 2041-1723
ISSN (online)	2041-1723
ISSN	2041-1723
DOI	10.1038/s41467-018-04271-z
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Article ; Online: Structural basis for continued antibody evasion by the SARS-CoV-2 receptor binding domain.

Nabel, Katherine G / Clark, Sarah A / Shankar, Sundaresh / Pan, Junhua / Clark, Lars E / Yang, Pan / Coscia, Adrian / McKay, Lindsay G A / Varnum, Haley H / Brusic, Vesna / Tolan, Nicole V / Zhou, Guohai / Desjardins, Michaël / Turbett, Sarah E / Kanjilal, Sanjat / Sherman, Amy C / Dighe, Anand / LaRocque, Regina C / Ryan, Edward T /

Tylek, Casey / Cohen-Solal, Joel F / Darcy, Anhdao T / Tavella, Davide / Clabbers, Anca / Fan, Yao / Griffiths, Anthony / Correia, Ivan R / Seagal, Jane / Baden, Lindsey R / Charles, Richelle C / Abraham, Jonathan

Science (New York, N.Y.)

2022 Volume 375, Issue 6578, Page(s) eabl6251

Abstract: Many studies have examined the impact of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants on neutralizing antibody activity after they have become dominant strains. Here, we evaluate the consequences of further viral evolution. We ... ...

Abstract	Many studies have examined the impact of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants on neutralizing antibody activity after they have become dominant strains. Here, we evaluate the consequences of further viral evolution. We demonstrate mechanisms through which the SARS-CoV-2 receptor binding domain (RBD) can tolerate large numbers of simultaneous antibody escape mutations and show that pseudotypes containing up to seven mutations, as opposed to the one to three found in previously studied variants of concern, are more resistant to neutralization by therapeutic antibodies and serum from vaccine recipients. We identify an antibody that binds the RBD core to neutralize pseudotypes for all tested variants but show that the RBD can acquire an N-linked glycan to escape neutralization. Our findings portend continued emergence of escape variants as SARS-CoV-2 adapts to humans.
MeSH term(s)	Angiotensin-Converting Enzyme 2/chemistry ; Angiotensin-Converting Enzyme 2/metabolism ; Antibodies, Neutralizing/immunology ; Antibodies, Viral/immunology ; BNT162 Vaccine/immunology ; Betacoronavirus/immunology ; COVID-19/immunology ; COVID-19/virology ; Cross Reactions ; Cryoelectron Microscopy ; Crystallography, X-Ray ; Epitopes ; Evolution, Molecular ; Humans ; Immune Evasion ; Models, Molecular ; Mutation ; Polysaccharides/analysis ; Protein Binding ; Protein Domains ; Receptors, Coronavirus/chemistry ; Receptors, Coronavirus/metabolism ; SARS-CoV-2/genetics ; SARS-CoV-2/immunology ; Spike Glycoprotein, Coronavirus/chemistry ; Spike Glycoprotein, Coronavirus/genetics ; Spike Glycoprotein, Coronavirus/immunology ; Viral Pseudotyping
Chemical Substances	Antibodies, Neutralizing ; Antibodies, Viral ; Epitopes ; Polysaccharides ; Receptors, Coronavirus ; Spike Glycoprotein, Coronavirus ; spike glycoprotein, SARS-CoV ; spike protein, SARS-CoV-2 ; ACE2 protein, human (EC 3.4.17.23) ; Angiotensin-Converting Enzyme 2 (EC 3.4.17.23) ; BNT162 Vaccine (N38TVC63NU)
Language	English
Publishing date	2022-01-21
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural
ZDB-ID	128410-1
ISSN	1095-9203 ; 0036-8075
ISSN (online)	1095-9203
ISSN	0036-8075
DOI	10.1126/science.abl6251
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