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Article: Biotherapeutic Antibodies for the Treatment of Head and Neck Cancer: Current Approaches and Future Considerations of Photothermal Therapies.

Al Qaraghuli, Mohammed M

2020 Volume 10, Page(s) 559596

Abstract: Head and neck cancer (HNC) is a heterogeneous disease that includes a variety of tumors originating in the hypopharynx, oropharynx, lip, oral cavity, nasopharynx, or larynx. HNC is the sixth most common malignancy worldwide and affects thousands of ... ...

Abstract	Head and neck cancer (HNC) is a heterogeneous disease that includes a variety of tumors originating in the hypopharynx, oropharynx, lip, oral cavity, nasopharynx, or larynx. HNC is the sixth most common malignancy worldwide and affects thousands of people in terms of incidence and mortality. Various factors can trigger the development of the disease such as smoking, alcohol consumption, and repetitive viral infections. HNC is currently treated by single or multimodality approaches, which are based on surgery, radiotherapy, chemotherapy, and biotherapeutic antibodies. The latter approach will be the focus of this article. There are currently three approved antibodies against HNCs (cetuximab, nivolumab, and pembrolizumab), and 48 antibodies under development. The majority of these antibodies are of humanized (23 antibodies) or human (19 antibodies) origins, and subclass IgG
Language	English
Publishing date	2020-11-26
Publishing country	Switzerland
Document type	Journal Article ; Review
ZDB-ID	2649216-7
ISSN	2234-943X
ISSN	2234-943X
DOI	10.3389/fonc.2020.559596
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: The Role of Antibodies in the Treatment of SARS-CoV-2 Virus Infection, and Evaluating Their Contribution to Antibody-Dependent Enhancement of Infection.

Farouq, Mohammed A H / Acevedo, Reinaldo / Ferro, Valerie A / Mulheran, Paul A / Al Qaraghuli, Mohammed M

International journal of molecular sciences

2022 Volume 23, Issue 11

Abstract: Antibodies play a crucial role in the immune response, in fighting off pathogens as well as helping create strong immunological memory. Antibody-dependent enhancement (ADE) occurs when non-neutralising antibodies recognise and bind to a pathogen, but are ...

Abstract	Antibodies play a crucial role in the immune response, in fighting off pathogens as well as helping create strong immunological memory. Antibody-dependent enhancement (ADE) occurs when non-neutralising antibodies recognise and bind to a pathogen, but are unable to prevent infection, and is widely known and is reported as occurring in infection caused by several viruses. This narrative review explores the ADE phenomenon, its occurrence in viral infections and evaluates its role in infection by SARS-CoV-2 virus, which causes coronavirus disease 2019 (COVID-19). As of yet, there is no clear evidence of ADE in SARS-CoV-2, though this area is still subject to further study.
MeSH term(s)	Antibodies, Neutralizing ; Antibodies, Viral/therapeutic use ; Antibody-Dependent Enhancement ; COVID-19 ; Humans ; SARS-CoV-2
Chemical Substances	Antibodies, Neutralizing ; Antibodies, Viral
Language	English
Publishing date	2022-05-28
Publishing country	Switzerland
Document type	Journal Article ; Review
ZDB-ID	2019364-6
ISSN	1422-0067 ; 1422-0067 ; 1661-6596
ISSN (online)	1422-0067
ISSN	1422-0067 ; 1661-6596
DOI	10.3390/ijms23116078
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Article ; Online: Functionalisation of Inorganic Material Surfaces with Staphylococcus Protein A: A Molecular Dynamics Study.

Farouq, Mohammed A H / Kubiak-Ossowska, Karina / Al Qaraghuli, Mohammed M / Ferro, Valerie A / Mulheran, Paul A

International journal of molecular sciences

2022 Volume 23, Issue 9

Abstract: Staphylococcus protein A (SpA) is found in the cell wall ... ...

Abstract	Staphylococcus protein A (SpA) is found in the cell wall of
MeSH term(s)	Adsorption ; Antibodies ; Molecular Dynamics Simulation ; Silicon Dioxide/chemistry ; Staphylococcal Protein A ; Staphylococcus ; Surface Properties
Chemical Substances	Antibodies ; Staphylococcal Protein A ; Silicon Dioxide (7631-86-9)
Language	English
Publishing date	2022-04-27
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2019364-6
ISSN	1422-0067 ; 1422-0067 ; 1661-6596
ISSN (online)	1422-0067
ISSN	1422-0067 ; 1661-6596
DOI	10.3390/ijms23094832
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Article ; Online: Recent Advances in Photothermal Therapies Against Cancer and the Role of Membrane Transporter Modulators on the Efficacy of This Approach.

Al-Ali, Ahmed A Abdulhussein / Al Ward, Nameer / Obeid, Mohammad A / Uhd Nielsen, Carsten / Mulheran, Paul A / Al Qaraghuli, Mohammed M

Technology in cancer research & treatment

2023 Volume 22, Page(s) 15330338231168016

Abstract: Recently, much research is focused on the use of photothermal therapy (PTT) as an advanced method to treat various types of cancer. The PTT approach primarily utilizes nanoparticles (NPs) made from metals, carbon, or semiconductors that can convert near- ... ...

Abstract	Recently, much research is focused on the use of photothermal therapy (PTT) as an advanced method to treat various types of cancer. The PTT approach primarily utilizes nanoparticles (NPs) made from metals, carbon, or semiconductors that can convert near-infrared laser irradiation, which penetrates tissues, into local heat that induces cancer cell death. An alternative approach is to utilize NPs (such as liposomes) to carry suitable dye molecules to the same end. Numerous studies concerning PTT have shown that local heat released in cancer cells may suppress the expression of membrane transporter proteins such as P-glycoprotein (P-gp) and multidrug resistance-associated protein 1 (MRP1), thus enhancing cytotoxicity and reverse multidrug resistance. In addition, because NPs may be loaded with different substances, researchers have designed multifunctional NPs for PTT by including several agents such as membrane transporter modulators, anticancer drugs, and photothermal agents. This review will focus on the recent advances in PTT utilizing various types of NPs, and their components and characteristics. In addition, the role of membrane transporters in PTT will be highlighted and different methods of transporter modulation will be summarized from several PTT studies in which multifunctional NPs were used to treat cancers
MeSH term(s)	Humans ; Photothermal Therapy ; Cell Line, Tumor ; Phototherapy/methods ; Nanoparticles ; Infrared Rays ; Membrane Transport Proteins ; Neoplasms/therapy
Chemical Substances	Membrane Transport Proteins
Language	English
Publishing date	2023-04-27
Publishing country	United States
Document type	Journal Article ; Review
ZDB-ID	2146365-7
ISSN	1533-0338 ; 1533-0346
ISSN (online)	1533-0338
ISSN	1533-0346
DOI	10.1177/15330338231168016
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Article: Structural Analysis of Anti-Hapten Antibodies to Identify Long-Range Structural Movements Induced by Hapten Binding.

Al Qaraghuli, Mohammed M / Kubiak-Ossowska, Karina / Ferro, Valerie A / Mulheran, Paul A

Frontiers in molecular biosciences

2021 Volume 8, Page(s) 633526

Abstract: Antibodies are well known for their high specificity that has enabled them to be of significant use in both therapeutic and diagnostic applications. Antibodies can recognize different antigens, including proteins, carbohydrates, peptides, nucleic acids, ... ...

Abstract	Antibodies are well known for their high specificity that has enabled them to be of significant use in both therapeutic and diagnostic applications. Antibodies can recognize different antigens, including proteins, carbohydrates, peptides, nucleic acids, lipids, and small molecular weight haptens that are abundantly available as hormones, pharmaceuticals, and pesticides. Here we focus on a structural analysis of hapten-antibody couples and identify potential structural movements originating from the hapten binding by comparison with unbound antibody, utilizing 40 crystal structures from the Protein Data Bank. Our analysis reveals three binding surface trends; S1 where a pocket forms to accommodate the hapten, S2 where a pocket is removed when the hapten binds, and S3 where no pockets changes are found. S1 and S2 are expected for induced-fit binding, whereas S3 indicates that a pre-existing population of optimal binding antibody conformation exists. The structural analysis reveals four classifications of structural reorganization, some of which correlate to S2 but not to the other binding surface changes. These observations demonstrate the complexity of the antibody-antigen interaction, where structural changes can be restricted to the binding sites, or extend through the constant domains to propagate structural changes. This highlights the importance of structural analysis to ensure successful and compatible transformation of small antibody fragments at the early discovery stage into full antibodies during the subsequent development stages, where long-range structural changes are required for an Fc effector response.
Language	English
Publishing date	2021-03-24
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2814330-9
ISSN	2296-889X
ISSN	2296-889X
DOI	10.3389/fmolb.2021.633526
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Article: Biomolecular interactions with nanoparticles: applications for coronavirus disease 2019.

Farouq, Mohammed A H / Al Qaraghuli, Mohammed M / Kubiak-Ossowska, Karina / Ferro, Valerie A / Mulheran, Paul A

Current opinion in colloid & interface science

2021 Volume 54, Page(s) 101461

Abstract: Nanoparticles are small particles sized 1-100 nm, which have a large surface-to-volume ratio, allowing efficient adsorption of drugs, proteins, and other chemical compounds. Consequently, functionalized nanoparticles have potential diagnostic and ... ...

Abstract	Nanoparticles are small particles sized 1-100 nm, which have a large surface-to-volume ratio, allowing efficient adsorption of drugs, proteins, and other chemical compounds. Consequently, functionalized nanoparticles have potential diagnostic and therapeutic applications. A variety of nanoparticles have been studied, including those constructed from inorganic materials, biopolymers, and lipids. In this review, we focus on recent work targeting the severe acute respiratory syndrome coronavirus 2 virus that causes coronavirus disease (COVID-19). Understanding the interactions between coronavirus-specific proteins (such as the spike protein and its host cell receptor angiotensin-converting enzyme 2) with different nanoparticles paves the way to the development of new therapeutics and diagnostics that are urgently needed for the fight against COVID-19, and indeed for related future viral threats that may emerge.
Language	English
Publishing date	2021-04-23
Publishing country	England
Document type	Journal Article ; Review
ZDB-ID	2019683-0
ISSN	1359-0294
ISSN	1359-0294
DOI	10.1016/j.cocis.2021.101461
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Article ; Online: The Role of Antibodies in the Treatment of SARS-CoV-2 Virus Infection, and Evaluating Their Contribution to Antibody-Dependent Enhancement of Infection

Mohammed A. H. Farouq / Reinaldo Acevedo / Valerie A. Ferro / Paul A. Mulheran / Mohammed M. Al Qaraghuli

International Journal of Molecular Sciences, Vol 23, Iss 6078, p

2022 Volume 6078

Abstract	Antibodies play a crucial role in the immune response, in fighting off pathogens as well as helping create strong immunological memory. Antibody-dependent enhancement (ADE) occurs when non-neutralising antibodies recognise and bind to a pathogen, but are unable to prevent infection, and is widely known and is reported as occurring in infection caused by several viruses. This narrative review explores the ADE phenomenon, its occurrence in viral infections and evaluates its role in infection by SARS-CoV-2 virus, which causes coronavirus disease 2019 (COVID-19). As of yet, there is no clear evidence of ADE in SARS-CoV-2, though this area is still subject to further study.
Keywords	coronavirus ; SARS-CoV-2 ; antibody-dependent enhancement ; COVID-19 ; Biology (General) ; QH301-705.5 ; Chemistry ; QD1-999
Language	English
Publishing date	2022-05-01T00:00:00Z
Publisher	MDPI AG
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Antibody-protein binding and conformational changes: identifying allosteric signalling pathways to engineer a better effector response.

Al Qaraghuli, Mohammed M / Kubiak-Ossowska, Karina / Ferro, Valerie A / Mulheran, Paul A

Scientific reports

2020 Volume 10, Issue 1, Page(s) 13696

Abstract: Numerous monoclonal antibodies have been developed successfully for the treatment of various diseases. Nevertheless, the development of biotherapeutic antibodies is complex, expensive, and time-consuming, and to facilitate this process, careful ... ...

Abstract	Numerous monoclonal antibodies have been developed successfully for the treatment of various diseases. Nevertheless, the development of biotherapeutic antibodies is complex, expensive, and time-consuming, and to facilitate this process, careful structural analysis beyond the antibody binding site is required to develop a more efficacious antibody. In this work, we focused on protein antigens, since they induce the largest antibody changes, and provide interesting cases to compare and contrast. The structures of 15 anti-protein antibodies were analysed to compare the antigen-bound/unbound forms. Surprisingly, three different classes of binding-induced changes were identified. In class (B1), the antigen binding fragment distorted significantly, and we found changes in the loop region of the heavy chain's constant domain; this corresponds well with expected allosteric movements. In class (B2), we found changes in the same loop region without the overall distortion. In class (B3), these changes did not present, and only local changes at the complementarity determining regions were found. Consequently, structural analysis of antibodies is crucial for therapeutic development. Careful evaluation of allosteric movements must be undertaken to develop better effector responses, especially during the transformation of these antibodies from small fragments at the discovery stage to full antibodies at the subsequent development stages.
MeSH term(s)	Allosteric Site ; Animals ; Antibodies/chemistry ; Antibodies/metabolism ; Antigens/chemistry ; Antigens/metabolism ; Binding Sites, Antibody ; Crystallography, X-Ray ; Humans ; Mice ; Models, Molecular ; Protein Binding ; Protein Conformation
Chemical Substances	Antibodies ; Antigens
Language	English
Publishing date	2020-08-13
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2615211-3
ISSN	2045-2322 ; 2045-2322
ISSN (online)	2045-2322
ISSN	2045-2322
DOI	10.1038/s41598-020-70680-0
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Article ; Online: Thinking outside the Laboratory: Analyses of Antibody Structure and Dynamics within Different Solvent Environments in Molecular Dynamics (MD) Simulations.

Al Qaraghuli, Mohammed M / Kubiak-Ossowska, Karina / Mulheran, Paul A

Antibodies (Basel, Switzerland)

2018 Volume 7, Issue 3

Abstract: Monoclonal antibodies (mAbs) have revolutionized the biomedical field, directly influencing therapeutics and diagnostics in the biopharmaceutical industry, while continuing advances in computational efficiency have enabled molecular dynamics (MD) ... ...

Abstract	Monoclonal antibodies (mAbs) have revolutionized the biomedical field, directly influencing therapeutics and diagnostics in the biopharmaceutical industry, while continuing advances in computational efficiency have enabled molecular dynamics (MD) simulations to provide atomistic insight into the structure and function of mAbs. Despite the success of MD tools, further optimizations are still required to enhance the computational efficiency of complex mAb simulations. This issue can be tackled by changing the way the solvent system is modelled to reduce the number of atoms to be tracked but must be done without compromising the accuracy of the simulations. In this work, the structure of the IgG
Language	English
Publishing date	2018-06-24
Publishing country	Switzerland
Document type	Journal Article
ISSN	2073-4468
ISSN (online)	2073-4468
DOI	10.3390/antib7030021
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Article ; Online: Functionalisation of Inorganic Material Surfaces with Staphylococcus Protein A

Mohammed A. H. Farouq / Karina Kubiak-Ossowska / Mohammed M. Al Qaraghuli / Valerie A. Ferro / Paul A. Mulheran

International Journal of Molecular Sciences, Vol 23, Iss 4832, p

A Molecular Dynamics Study

2022 Volume 4832

Abstract: Staphylococcus protein A (SpA) is found in the cell wall of Staphylococcus aureus bacteria. Its ability to bind to the constant Fc regions of antibodies means it is useful for antibody extraction, and further integration with inorganic materials can lead ...

Abstract	Staphylococcus protein A (SpA) is found in the cell wall of Staphylococcus aureus bacteria. Its ability to bind to the constant Fc regions of antibodies means it is useful for antibody extraction, and further integration with inorganic materials can lead to the development of diagnostics and therapeutics. We have investigated the adsorption of SpA on inorganic surface models such as experimentally relevant negatively charged silica, as well as positively charged and neutral surfaces, by use of fully atomistic molecular dynamics simulations. We have found that SpA, which is itself negatively charged at pH7, is able to adsorb on all our surface models. However, adsorption on charged surfaces is more specific in terms of protein orientation compared to a neutral Au (111) surface, while the protein structure is generally well maintained in all cases. The results indicate that SpA adsorption is optimal on the siloxide-rich silica surface, which is negative at pH7 since this keeps the Fc binding regions free to interact with other species in solution. Due to the dominant role of electrostatics, the results are transferable to other inorganic materials and pave the way for new diagnostic and therapeutic designs where SpA might be used to conjugate antibodies to nanoparticles.
Keywords	staphylococcus protein A ; therapeutics ; diagnostics ; biomolecular simulation ; Biology (General) ; QH301-705.5 ; Chemistry ; QD1-999
Subject code	612
Language	English
Publishing date	2022-04-01T00:00:00Z
Publisher	MDPI AG
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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