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Article ; Online: Exploring cryo-electron microscopy with molecular dynamics.

Vant, John W / Sarkar, Daipayan / Nguyen, Jonathan / Baker, Alexander T / Vermaas, Josh V / Singharoy, Abhishek

2022 Volume 50, Issue 1, Page(s) 569–581

Abstract: Single particle analysis cryo-electron microscopy (EM) and molecular dynamics (MD) have been complimentary methods since cryo-EM was first applied to the field of structural biology. The relationship started by biasing structural models to fit low- ... ...

Abstract	Single particle analysis cryo-electron microscopy (EM) and molecular dynamics (MD) have been complimentary methods since cryo-EM was first applied to the field of structural biology. The relationship started by biasing structural models to fit low-resolution cryo-EM maps of large macromolecular complexes not amenable to crystallization. The connection between cryo-EM and MD evolved as cryo-EM maps improved in resolution, allowing advanced sampling algorithms to simultaneously refine backbone and sidechains. Moving beyond a single static snapshot, modern inferencing approaches integrate cryo-EM and MD to generate structural ensembles from cryo-EM map data or directly from the particle images themselves. We summarize the recent history of MD innovations in the area of cryo-EM modeling. The merits for the myriad of MD based cryo-EM modeling methods are discussed, as well as, the discoveries that were made possible by the integration of molecular modeling with cryo-EM. Lastly, current challenges and potential opportunities are reviewed.
MeSH term(s)	Algorithms ; Cryoelectron Microscopy/methods ; Macromolecular Substances ; Molecular Dynamics Simulation ; Single Molecule Imaging
Chemical Substances	Macromolecular Substances
Language	English
Publishing date	2022-02-25
Publishing country	England
Document type	Journal Article ; Research Support, U.S. Gov't, Non-P.H.S. ; Review
ZDB-ID	184237-7
ISSN	1470-8752 ; 0300-5127
ISSN (online)	1470-8752
ISSN	0300-5127
DOI	10.1042/BST20210485
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Article ; Online: Corrigendum to To clot or not to clot? Ad is the question-Insights on mechanisms related to vaccine-induced thrombotic thrombocytopenia [J Thromb Haemost. 2021 Nov;19(11):2845-2856. doi: 10.1111/jth.15485].

Othman, Maha / Baker, Alexander T / Gupalo, Elena / Elsebaie, Abdelrahman / Bliss, Carly M / Rondina, Matthew T / Lillicrap, David / Parker, Alan L

Journal of thrombosis and haemostasis : JTH

2023 Volume 21, Issue 4, Page(s) 1066

Language	English
Publishing date	2023-02-01
Publishing country	England
Document type	Published Erratum
ZDB-ID	2112661-6
ISSN	1538-7836 ; 1538-7933
ISSN (online)	1538-7836
ISSN	1538-7933
DOI	10.1016/j.jtha.2023.01.022
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Zs.A 5805: Show issues			Location: Je nach Verfügbarkeit (siehe Angabe bei Bestand) bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular Jg. 1995 - 2021: Lesesall (2.OG) ab Jg. 2022: Lesesaal (EG)
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Article ; Online: Broad sialic acid usage amongst species D human adenovirus.

Mundy, Rosie M / Baker, Alexander T / Bates, Emily A / Cunliffe, Tabitha G / Teijeira-Crespo, Alicia / Moses, Elise / Rizkallah, Pierre J / Parker, Alan L

Npj viruses

2023 Volume 1, Issue 1, Page(s) 1

Abstract: Human adenoviruses (HAdV) are widespread pathogens causing usually mild infections. The Species D (HAdV-D) cause gastrointestinal tract infections and epidemic keratoconjunctivitis (EKC). Despite being significant pathogens, knowledge around HAdV-D ... ...

Abstract	Human adenoviruses (HAdV) are widespread pathogens causing usually mild infections. The Species D (HAdV-D) cause gastrointestinal tract infections and epidemic keratoconjunctivitis (EKC). Despite being significant pathogens, knowledge around HAdV-D mechanism of cell infection is lacking. Sialic acid (SA) usage has been proposed as a cell infection mechanism for EKC causing HAdV-D. Here we highlight an important role for SA engagement by many HAdV-D. We provide apo state crystal structures of 7 previously undetermined HAdV-D fiber-knob proteins, and structures of HAdV-D25, D29, D30 and D53 fiber-knob proteins in complex with SA. Biologically, we demonstrate that removal of cell surface SA reduced infectivity of HAdV-C5 vectors pseudotyped with HAdV-D fiber-knob proteins, whilst engagement of the classical HAdV receptor CAR was variable. Our data indicates variable usage of SA and CAR across HAdV-D. Better defining these interactions will enable improved development of antivirals and engineering of the viruses into refined therapeutic vectors.
Language	English
Publishing date	2023-09-26
Publishing country	England
Document type	Journal Article
ISSN	2948-1767
ISSN (online)	2948-1767
DOI	10.1038/s44298-023-00001-5
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Article: Multi-modal efficacy of a chimeric vesiculovirus expressing the Morreton glycoprotein in sarcoma.

Watters, Chelsae R / Barro, Oumar / Elliott, Natalie M / Zhou, Yumei / Gabere, Musa / Raupach, Elizabeth / Baker, Alexander T / Barrett, Michael T / Buetow, Kenneth H / Jacobs, Bertram / Seetharam, Mahesh / Borad, Mitesh J / Nagalo, Bolni Marius

Molecular therapy oncolytics

2023 Volume 29, Page(s) 4–14

Abstract: Vesiculoviruses are attractive oncolytic virus platforms due to their rapid replication, appreciable transgene capacity, broad tropism, limited preexisting immunity, and tumor selectivity through type I interferon response defects in malignant cells. We ... ...

Abstract	Vesiculoviruses are attractive oncolytic virus platforms due to their rapid replication, appreciable transgene capacity, broad tropism, limited preexisting immunity, and tumor selectivity through type I interferon response defects in malignant cells. We developed a synthetic chimeric virus (VMG) expressing the glycoprotein (G) from Morreton virus (MorV) and utilizing the remaining structural genes from vesicular stomatitis virus (VSV). VMG exhibited
Language	English
Publishing date	2023-03-01
Publishing country	United States
Document type	Journal Article
ISSN	2372-7705
ISSN	2372-7705
DOI	10.1016/j.omto.2023.02.009
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Article ; Online: Oncolytic virotherapy: Challenges and solutions.

Goradel, Nasser Hashemi / Baker, Alexander T / Arashkia, Arash / Ebrahimi, Nasim / Ghorghanlu, Sajjad / Negahdari, Babak

Current problems in cancer

2020 Volume 45, Issue 1, Page(s) 100639

Abstract: Viruses as cancer therapies have attracted attention since the 19th century. Scientists observation that viruses can preferentially lyse cancer cells rather than healthy cells, created the field of oncolytic virology. Like other therapeutic strategies, ... ...

Abstract	Viruses as cancer therapies have attracted attention since the 19th century. Scientists observation that viruses can preferentially lyse cancer cells rather than healthy cells, created the field of oncolytic virology. Like other therapeutic strategies, oncolytic virotherapy has challenges, such as penetration into tumor bulk, anti-viral immune responses, off-target infection, adverse conditions in the tumor microenvironment, and the lack of specific predictive and therapeutic biomarkers. Whilst much progress has been made, as highlighted by the first Food and Drug Administration approval of an oncolytic virus talimogene laherparepvec (T-VEC) in 2015, addressing these issues remains a significant hurdle. Here we discuss different types of oncolytic viruses, their application in clinical trials, and finally challenges faced by the field of oncolytic virotherapy and strategies to overcome them.
MeSH term(s)	Humans ; Immunotherapy/methods ; Neoplasms/therapy ; Oncolytic Virotherapy/methods ; Oncolytic Viruses
Language	English
Publishing date	2020-08-15
Publishing country	United States
Document type	Journal Article ; Review
ZDB-ID	441816-5
ISSN	1535-6345 ; 0147-0272
ISSN (online)	1535-6345
ISSN	0147-0272
DOI	10.1016/j.currproblcancer.2020.100639
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Article: Designer Oncolytic Adenovirus: Coming of Age.

Baker, Alexander T / Aguirre-Hernández, Carmen / Halldén, Gunnel / Parker, Alan L

Cancers

2018 Volume 10, Issue 6

Abstract: The licensing of talimogene laherparepvec (T-Vec) represented a landmark moment for oncolytic virotherapy, since it provided unequivocal evidence for the long-touted potential of genetically modified replicating viruses as anti-cancer agents. Whilst T- ... ...

Abstract	The licensing of talimogene laherparepvec (T-Vec) represented a landmark moment for oncolytic virotherapy, since it provided unequivocal evidence for the long-touted potential of genetically modified replicating viruses as anti-cancer agents. Whilst T-Vec is promising as a locally delivered virotherapy, especially in combination with immune-checkpoint inhibitors, the quest continues for a virus capable of specific tumour cell killing via systemic administration. One candidate is oncolytic adenovirus (Ad); it’s double stranded DNA genome is easily manipulated and a wide range of strategies and technologies have been employed to empower the vector with improved pharmacokinetics and tumour targeting ability. As well characterised clinical and experimental agents, we have detailed knowledge of adenoviruses’ mechanisms of pathogenicity, supported by detailed virological studies and in vivo interactions. In this review we highlight the strides made in the engineering of bespoke adenoviral vectors to specifically infect, replicate within, and destroy tumour cells. We discuss how mutations in genes regulating adenoviral replication after cell entry can be used to restrict replication to the tumour, and summarise how detailed knowledge of viral capsid interactions enable rational modification to eliminate native tropisms, and simultaneously promote active uptake by cancerous tissues. We argue that these designer-viruses, exploiting the viruses natural mechanisms and regulated at every level of replication, represent the ideal platforms for local overexpression of therapeutic transgenes such as immunomodulatory agents. Where T-Vec has paved the way, Ad-based vectors now follow. The era of designer oncolytic virotherapies looks decidedly as though it will soon become a reality.
Language	English
Publishing date	2018-06-14
Publishing country	Switzerland
Document type	Journal Article ; Review
ZDB-ID	2527080-1
ISSN	2072-6694
ISSN	2072-6694
DOI	10.3390/cancers10060201
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Article ; Online: To clot or not to clot? Ad is the question-Insights on mechanisms related to vaccine-induced thrombotic thrombocytopenia.

Othman, Maha / Baker, Alexander T / Gupalo, Elena / Elsebaie, Abdelrahman / Bliss, Carly M / Rondina, Matthew T / Lillicrap, David / Parker, Alan L

Journal of thrombosis and haemostasis : JTH

2021 Volume 19, Issue 11, Page(s) 2845–2856

Abstract: Vaccine-induced immune thrombotic thrombocytopenia (VITT) has caused global concern. VITT is characterized by thrombosis and thrombocytopenia following COVID-19 vaccinations with the AstraZeneca ChAdOx1 nCov-19 and the Janssen Ad26.COV2.S vaccines. ... ...

Abstract	Vaccine-induced immune thrombotic thrombocytopenia (VITT) has caused global concern. VITT is characterized by thrombosis and thrombocytopenia following COVID-19 vaccinations with the AstraZeneca ChAdOx1 nCov-19 and the Janssen Ad26.COV2.S vaccines. Patients present with thrombosis, severe thrombocytopenia developing 5-24 days following first dose of vaccine, with elevated D-dimer, and PF4 antibodies, signifying platelet activation. As of June 1, 2021, more than 1.93 billion COVID-19 vaccine doses had been administered worldwide. Currently, 467 VITT cases (0.000024%) have been reported across the UK, Europe, Canada, and Australia. Guidance on diagnosis and management of VITT has been reported but the pathogenic mechanism is yet to be fully elucidated. Here, we propose and discuss potential mechanisms in relation to adenovirus induction of VITT. We provide insights and clues into areas warranting investigation into the mechanistic basis of VITT, highlighting the unanswered questions. Further research is required to help solidify a pathogenic model for this condition.
MeSH term(s)	Ad26COVS1 ; COVID-19 ; COVID-19 Vaccines ; ChAdOx1 nCoV-19 ; Humans ; SARS-CoV-2 ; Thrombocytopenia ; Thrombosis ; Vaccines/adverse effects
Chemical Substances	Ad26COVS1 (JT2NS6183B) ; COVID-19 Vaccines ; Vaccines ; ChAdOx1 nCoV-19 (B5S3K2V0G8)
Language	English
Publishing date	2021-08-23
Publishing country	England
Document type	Journal Article
ZDB-ID	2112661-6
ISSN	1538-7836 ; 1538-7933
ISSN (online)	1538-7836
ISSN	1538-7933
DOI	10.1111/jth.15485
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Zs.A 5805: Show issues			Location: Je nach Verfügbarkeit (siehe Angabe bei Bestand) bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular Jg. 1995 - 2021: Lesesall (2.OG) ab Jg. 2022: Lesesaal (EG)
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Article ; Online: Human adenovirus type 26 uses sialic acid-bearing glycans as a primary cell entry receptor.

Baker, Alexander T / Mundy, Rosie M / Davies, James A / Rizkallah, Pierre J / Parker, Alan L

Science advances

2019 Volume 5, Issue 9, Page(s) eaax3567

Abstract: Adenoviruses are clinically important agents. They cause respiratory distress, gastroenteritis, and epidemic keratoconjunctivitis. As non-enveloped, double-stranded DNA viruses, they are easily manipulated, making them popular vectors for therapeutic ... ...

Abstract	Adenoviruses are clinically important agents. They cause respiratory distress, gastroenteritis, and epidemic keratoconjunctivitis. As non-enveloped, double-stranded DNA viruses, they are easily manipulated, making them popular vectors for therapeutic applications, including vaccines. Species D adenovirus type 26 (HAdV-D26) is both a cause of EKC and other diseases and a promising vaccine vector. HAdV-D26-derived vaccines are under investigation as protective platforms against HIV, Zika, and respiratory syncytial virus infections and are in phase 3 clinical trials for Ebola. We recently demonstrated that HAdV-D26 does not use CD46 or Desmoglein-2 as entry receptors, while the putative interaction with coxsackie and adenovirus receptor is low affinity and unlikely to represent the primary cell receptor. Here, we establish sialic acid as a primary entry receptor used by HAdV-D26. We demonstrate that removal of cell surface sialic acid inhibits HAdV-D26 infection, and provide a high-resolution crystal structure of HAdV-D26 fiber-knob in complex with sialic acid.
MeSH term(s)	Adenovirus Vaccines/metabolism ; Adenoviruses, Human/chemistry ; Adenoviruses, Human/metabolism ; Crystallography, X-Ray ; HEK293 Cells ; Humans ; Keratoconjunctivitis/epidemiology ; Keratoconjunctivitis/metabolism ; Keratoconjunctivitis/pathology ; N-Acetylneuraminic Acid/chemistry ; N-Acetylneuraminic Acid/metabolism ; Receptors, Virus/chemistry ; Receptors, Virus/metabolism ; Viral Proteins/chemistry ; Viral Proteins/metabolism
Chemical Substances	Adenovirus Vaccines ; Receptors, Virus ; Viral Proteins ; adenovirus receptor ; N-Acetylneuraminic Acid (GZP2782OP0)
Language	English
Publishing date	2019-09-04
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2810933-8
ISSN	2375-2548 ; 2375-2548
ISSN (online)	2375-2548
ISSN	2375-2548
DOI	10.1126/sciadv.aax3567
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Article: In Vitro and In Vivo Evaluation of Human Adenovirus Type 49 as a Vector for Therapeutic Applications

Bates, Emily A. / Counsell, John R. / Alizert, Sophie / Baker, Alexander T. / Suff, Natalie / Boyle, Ashley / Bradshaw, Angela C. / Waddington, Simon N. / Nicklin, Stuart A. / Baker, Andrew H. / Parker, Alan L.

Viruses. 2021 July 28, v. 13, no. 8

2021

Abstract: The human adenovirus phylogenetic tree is split across seven species (A–G). Species D adenoviruses offer potential advantages for gene therapy applications, with low rates of pre-existing immunity detected across screened populations. However, many ... ...

Abstract	The human adenovirus phylogenetic tree is split across seven species (A–G). Species D adenoviruses offer potential advantages for gene therapy applications, with low rates of pre-existing immunity detected across screened populations. However, many aspects of the basic virology of species D—such as their cellular tropism, receptor usage, and in vivo biodistribution profile—remain unknown. Here, we have characterized human adenovirus type 49 (HAdV-D49)—a relatively understudied species D member. We report that HAdV-D49 does not appear to use a single pathway to gain cell entry, but appears able to interact with various surface molecules for entry. As such, HAdV-D49 can transduce a broad range of cell types in vitro, with variable engagement of blood coagulation FX. Interestingly, when comparing in vivo biodistribution to adenovirus type 5, HAdV-D49 vectors show reduced liver targeting, whilst maintaining transduction of lung and spleen. Overall, this presents HAdV-D49 as a robust viral vector platform for ex vivo manipulation of human cells, and for in vivo applications where the therapeutic goal is to target the lung or gain access to immune cells in the spleen, whilst avoiding liver interactions, such as intravascular vaccine applications.
Keywords	Mastadenovirus ; blood coagulation ; gene therapy ; humans ; immunity ; liver ; lungs ; phylogeny ; spleen ; vaccines ; virology
Language	English
Dates of publication	2021-0728
Publishing place	Multidisciplinary Digital Publishing Institute
Document type	Article
ZDB-ID	2516098-9
ISSN	1999-4915
ISSN	1999-4915
DOI	10.3390/v13081483
Database	NAL-Catalogue (AGRICOLA)

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Article: Development of a low-seroprevalence, αvβ6 integrin-selective virotherapy based on human adenovirus type 10.

Bates, Emily A / Davies, James A / Váňová, Jana / Nestić, Davor / Meniel, Valerie S / Koushyar, Sarah / Cunliffe, Tabitha G / Mundy, Rosie M / Moses, Elise / Uusi-Kerttula, Hanni K / Baker, Alexander T / Cole, David K / Majhen, Dragomira / Rizkallah, Pierre J / Phesse, Toby / Chester, John D / Parker, Alan L

Molecular therapy oncolytics

2022 Volume 25, Page(s) 43–56

Abstract: Oncolytic virotherapies (OV) hold immense clinical potential. OV based on human adenoviruses (HAdV) derived from HAdV with naturally low rates of pre-existing immunity will be beneficial for future clinical translation. We generated a low-seroprevalence ... ...

Abstract	Oncolytic virotherapies (OV) hold immense clinical potential. OV based on human adenoviruses (HAdV) derived from HAdV with naturally low rates of pre-existing immunity will be beneficial for future clinical translation. We generated a low-seroprevalence HAdV-D10 serotype vector incorporating an αvβ6 integrin-selective peptide, A20, to target αvβ6-positive tumor cell types. HAdV-D10 has limited natural tropism. Structural and biological studies of HAdV-D10 knob protein highlighted low-affinity engagement with native adenoviral receptors CAR and sialic acid. HAdV-D10 fails to engage blood coagulation factor X, potentially eliminating "off-target" hepatic sequestration
Language	English
Publishing date	2022-03-16
Publishing country	United States
Document type	Journal Article
ISSN	2372-7705
ISSN	2372-7705
DOI	10.1016/j.omto.2022.03.007
Database	MEDical Literature Analysis and Retrieval System OnLINE

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