Next Issue
Volume 7, December
Previous Issue
Volume 7, June
 
 

Antibodies, Volume 7, Issue 3 (September 2018) – 15 articles

  • Issues are regarded as officially published after their release is announced to the table of contents alert mailing list.
  • You may sign up for e-mail alerts to receive table of contents of newly released issues.
  • PDF is the official format for papers published in both, html and pdf forms. To view the papers in pdf format, click on the "PDF Full-text" link, and use the free Adobe Reader to open them.
Order results
Result details
Section
Select all
Export citation of selected articles as:
16 pages, 2237 KiB  
Article
Relative Contribution of Framework and CDR Regions in Antibody Variable Domains to Multimerisation of Fv- and scFv-Containing Bispecific Antibodies
by Pallavi Bhatta and David P. Humphreys
Antibodies 2018, 7(3), 35; https://doi.org/10.3390/antib7030035 - 31 Aug 2018
Cited by 9 | Viewed by 10330
Abstract
Bispecific antibodies represent an emerging class of antibody drugs that are commonly generated by fusion of Fv or scFv antigen binding domains to IgG or Fab scaffolds. Fv- or scFv-mediated multimerisation of bispecific antibodies via promiscuous vH-vL pairing can result in sub-optimal monomer [...] Read more.
Bispecific antibodies represent an emerging class of antibody drugs that are commonly generated by fusion of Fv or scFv antigen binding domains to IgG or Fab scaffolds. Fv- or scFv-mediated multimerisation of bispecific antibodies via promiscuous vH-vL pairing can result in sub-optimal monomer levels during expression, and hence, undesirable therapeutic protein yields. We investigate the contribution of disulphide stabilised Fv and scFv to Fab-Fv and Fab-scFv multimerisation. We show that monomer levels of isolated Fv/scFv cannot always be used to predict monomer levels of Fab-linked Fv/scFv, and that Fab-scFv monomer levels are greater than the equivalent Fab-Fv. Through grafting bispecifics with framework/CDR-‘swapped’ Fv and scFv, we show that monomer levels of disulphide stabilised Fab-Fv and Fab-scFv can be improved by Fv framework ‘swapping’. The Fab-Fv and Fab-scFv can be considered representative of the significant number of bispecific antibody formats containing appended Fv/scFv, as we also used Fv framework ‘swapping’ to increase the monomer level of an IgG-scFv bispecific antibody. This research may, therefore, be useful for maximising the monomeric yield of numerous pharmaceutically-relevant bispecific formats in pre-clinical development. Full article
(This article belongs to the Special Issue Bispecific Antibodies-Opportunities and Challenges)
Show Figures

Figure 1

1 pages, 149 KiB  
Correction
Correction: Verkade, J.M.M.; et al. A Polar Sulfamide Spacer Significantly Enhances the Manufacturability, Stability, and Therapeutic Index of Antibody–Drug Conjugates. Antibodies 2018, 7, 12
by Jorge M. M. Verkade, Marloes A. Wijdeven, Remon Van Geel, Brian M. G. Janssen, Sander S. Van Berkel, Floris L. Van Delft and Antibodies Editorial Office
Antibodies 2018, 7(3), 34; https://doi.org/10.3390/antib7030034 - 30 Aug 2018
Cited by 2 | Viewed by 4447
Abstract
The conflict of interest section of the published paper [1] has been updated as follows[...] Full article
1 pages, 171 KiB  
Addendum
Addendum: Hoffmann, C.; et al. Autoantibodies in Neuropsychiatric Disorders. Antibodies 2016, 5, 9
by Carolin Hoffmann, Shenghua Zong, Marina Mané-Damas, Peter Molenaar, Mario Losen, Pilar Martinez-Martinez and Antibodies Editorial Office
Antibodies 2018, 7(3), 33; https://doi.org/10.3390/antib7030033 - 27 Aug 2018
Cited by 1 | Viewed by 4332
Abstract
The conflict of interest section was missing in the published paper [1]. It has been updated as follows: [...] Full article
1 pages, 129 KiB  
Correction
Correction: Mehrling, T.; et al. Challenges in Optimising the Successful Construction of Antibody Drug Conjugates in Cancer Therapy. Antibodies 2018, 7, 11
by Thomas Mehrling, Daniel Soltis and The Antibodies Editorial Office
Antibodies 2018, 7(3), 32; https://doi.org/10.3390/antib7030032 - 27 Aug 2018
Cited by 3 | Viewed by 4187
Abstract
The Conflict of Interest section of the published paper [1] has been updated as follows: [...] Full article
1 pages, 131 KiB  
Correction
Correction: Moeker, N.; et al. Antibody Selection for Cancer Target Validation of FSH-Receptor in Immunohistochemical Settings. Antibodies 2017, 6, 15
by Nina Möker, Solveig Peters, Robert Rauchenberger, Nicolae Ghinea, Christian Kunz and Antibodies Editorial Office
Antibodies 2018, 7(3), 31; https://doi.org/10.3390/antib7030031 - 24 Aug 2018
Viewed by 4441
Abstract
The authors wish to make the following correction to the Conflict of Interests section in their published paper[...] Full article
13 pages, 2683 KiB  
Article
Applicability of Traditional In Vitro Toxicity Tests for Assessing Adverse Effects of Monoclonal Antibodies: A Case Study of Rituximab and Trastuzumab
by Arathi Kizhedath, Simon Wilkinson and Jarka Glassey
Antibodies 2018, 7(3), 30; https://doi.org/10.3390/antib7030030 - 17 Aug 2018
Viewed by 9083
Abstract
Monoclonal antibody (mAb) therapeutics have a promising outlook within the pharmaceutical industry having made positive strides in both research and development as well as commercialisation, however this development has been hampered by manufacturing failures and attrition. This study explores the applicability of traditional [...] Read more.
Monoclonal antibody (mAb) therapeutics have a promising outlook within the pharmaceutical industry having made positive strides in both research and development as well as commercialisation, however this development has been hampered by manufacturing failures and attrition. This study explores the applicability of traditional in vitro toxicity tests for detecting any off-target adverse effect elicited by mAbs on specific organ systems using hepatocarcinoma cell line (HepG2) and human dermal fibroblasts neonatal (HDFn), respectively. The mechanism of antibody dependent cytotoxicity (ADCC), complement dependent cytotoxicity (CDC) via complement activation, and complement dependent cellular cytotoxicity (CDCC) were assessed. Major results: no apparent ADCC, CDCC, or CDC mediated decrease in cell viability was measured for HepG2 cells. For HDFn cells, though ADCC or CDCC mediated decreases in cell viability wasn’t detected, a CDC mediated decrease in cell viability was observed. Several considerations have been elucidated for development of in vitro assays better suited to detect off target toxicity of mAbs. Full article
Show Figures

Figure 1

13 pages, 4772 KiB  
Article
Tuning Relative Polypeptide Expression to Optimize Assembly, Yield and Downstream Processing of Bispecific Antibodies
by Giovanni Magistrelli, Guillemette Pontini, Yves Poitevin, Pauline Malinge, Jérémie Bourguignon, Florence Gauye, Elise Fleury, Nicolas Plèche, Lydia Galissaires and Nicolas Fischer
Antibodies 2018, 7(3), 29; https://doi.org/10.3390/antib7030029 - 10 Aug 2018
Cited by 7 | Viewed by 6295
Abstract
Bispecific antibodies (bsAbs) are often composed of several polypeptide chains that have to be expressed adequately to enable optimal assembly and yield of the bsAb. κλ bodies are a bispecific format with a native IgG structure, composed of two different light chains that [...] Read more.
Bispecific antibodies (bsAbs) are often composed of several polypeptide chains that have to be expressed adequately to enable optimal assembly and yield of the bsAb. κλ bodies are a bispecific format with a native IgG structure, composed of two different light chains that pair with a common heavy chain. Introduction of non-optimal codons into the sequence of a particular polypeptide is an effective strategy for down modulating its expression. Here we applied this strategy but restricted the modification of the codon content to the constant domain of one light chain. This approach facilitates parallel optimization of several bsAbs by using the same modified constant domains. Partial sequence de-optimization reduced expression of the targeted polypeptide. Stable cell pools could be isolated displaying increased bispecific antibody titers as well as changes in the abundance of undesired by-products that require elimination during downstream processing. Thus, modulating the relative expression of polypeptides can have a significant impact on bsAb titer and product related impurities; which are important factors for large scale manufacturing for clinical supply. Full article
(This article belongs to the Special Issue Bispecific Antibodies-Opportunities and Challenges)
Show Figures

Figure 1

10 pages, 1101 KiB  
Review
Engineering IgG-Like Bispecific Antibodies—An Overview
by Simon Krah, Harald Kolmar, Stefan Becker and Stefan Zielonka
Antibodies 2018, 7(3), 28; https://doi.org/10.3390/antib7030028 - 1 Aug 2018
Cited by 41 | Viewed by 17864
Abstract
Monoclonal antibody therapeutics have proven to be successful treatment options for patients in various indications. Particularly in oncology, therapeutic concepts involving antibodies often rely on the so-called effector functions, such as antibody dependent cellular cytotoxicity (ADCC) and complement dependent cytotoxicity (CDC), which are [...] Read more.
Monoclonal antibody therapeutics have proven to be successful treatment options for patients in various indications. Particularly in oncology, therapeutic concepts involving antibodies often rely on the so-called effector functions, such as antibody dependent cellular cytotoxicity (ADCC) and complement dependent cytotoxicity (CDC), which are programed in the antibody Fc region. However, Fc-mediated effector mechanisms often seem to be insufficient in properly activating the immune system to act against tumor cells. Furthermore, long term treatments can lead to resistance against the applied drug, which is monospecific by nature. There is promise in using specific antibodies to overcome such issues due to their capability of recruiting and activating T-cells directly at the tumor site, for instance. During the last decade, two of these entities, which are referred to as Blinatumomab and Catumaxomab, have been approved to treat patients with acute lymphoblastic leukemia and malignant ascites. In addition, Emicizumab, which is a bispecific antibody targeting clotting factors IXa and X, was recently granted market approval by the FDA in 2017 for the treatment of hemophilia A. However, the generation of these next generation therapeutics is challenging and requires tremendous engineering efforts as two distinct paratopes need to be combined from two different heavy and light chains. This mini review summarizes technologies, which enable the generation of antibodies with dual specificities. Full article
(This article belongs to the Special Issue Bispecific Antibodies-Opportunities and Challenges)
Show Figures

Figure 1

28 pages, 4399 KiB  
Article
Design Principles for Bispecific IgGs, Opportunities and Pitfalls of Artificial Disulfide Bonds
by Lilach Vaks, Dana Litvak-Greenfeld, Stav Dror, LeeRon Shefet-Carasso, Galia Matatov, Limor Nahary, Shiran Shapira, Rahely Hakim, Iris Alroy and Itai Benhar
Antibodies 2018, 7(3), 27; https://doi.org/10.3390/antib7030027 - 28 Jul 2018
Cited by 11 | Viewed by 13533
Abstract
Bispecific antibodies (bsAbs) are antibodies with two binding sites directed at different antigens, enabling therapeutic strategies not achievable with conventional monoclonal antibodies (mAbs). Since bispecific antibodies are regarded as promising therapeutic agents, many different bispecific design modalities have been evaluated, but as many [...] Read more.
Bispecific antibodies (bsAbs) are antibodies with two binding sites directed at different antigens, enabling therapeutic strategies not achievable with conventional monoclonal antibodies (mAbs). Since bispecific antibodies are regarded as promising therapeutic agents, many different bispecific design modalities have been evaluated, but as many of them are small recombinant fragments, their utility could be limited. For some therapeutic applications, full-size IgGs may be the optimal format. Two challenges should be met to make bispecific IgGs; one is that each heavy chain will only pair with the heavy chain of the second specificity and that homodimerization be prevented. The second is that each heavy chain will only pair with the light chain of its own specificity and not with the light chain of the second specificity. The first solution to the first criterion (knobs into holes, KIH) was presented in 1996 by Paul Carter’s group from Genentech. Additional solutions were presented later on. However, until recently, out of >120 published bsAb formats, only a handful of solutions for the second criterion that make it possible to produce a bispecific IgG by a single expressing cell were suggested. We present a solution for the second challenge—correct pairing of heavy and light chains of bispecific IgGs; an engineered (artificial) disulfide bond between the antibodies’ variable domains that asymmetrically replaces the natural disulfide bond between CH1 and CL. We name antibodies produced according to this design “BIClonals”. Bispecific IgGs where the artificial disulfide bond is placed in the CH1-CL interface are also presented. Briefly, we found that an artificial disulfide bond between VH position 44 to VL position 100 provides for effective and correct H–L chain pairing while also preventing the formation of wrong H–L chain pairs. When the artificial disulfide bond links the CH1 with the CL domain, effective H–L chain pairing also occurs, but in some cases, wrong H–L pairing is not totally prevented. We conclude that H–L chain pairing seems to be driven by VH–VL interfacial interactions that differ between different antibodies, hence, there is no single optimal solution for effective and precise assembly of bispecific IgGs, making it necessary to carefully evaluate the optimal solution for each new antibody. Full article
(This article belongs to the Special Issue Bispecific Antibodies-Opportunities and Challenges)
Show Figures

Figure 1

14 pages, 7767 KiB  
Article
BPSL1626: Reverse and Structural Vaccinology Reveal a Novel Candidate for Vaccine Design against Burkholderia pseudomallei
by Riccardo Capelli, Claudio Peri, Riccardo Villa, Arnone Nithichanon, Oscar Conchillo-Solé, Daniel Yero, Paola Gagni, Marcella Chiari, Ganjana Lertmemongkolchai, Marina Cretich, Xavier Daura, Martino Bolognesi, Giorgio Colombo and Louise J. Gourlay
Antibodies 2018, 7(3), 26; https://doi.org/10.3390/antib7030026 - 19 Jul 2018
Cited by 14 | Viewed by 7795
Abstract
Due to significant advances in computational biology, protein prediction, together with antigen and epitope design, have rapidly moved from conventional methods, based on experimental approaches, to in silico-based bioinformatics methods. In this context, we report a reverse vaccinology study that identified a panel [...] Read more.
Due to significant advances in computational biology, protein prediction, together with antigen and epitope design, have rapidly moved from conventional methods, based on experimental approaches, to in silico-based bioinformatics methods. In this context, we report a reverse vaccinology study that identified a panel of 104 candidate antigens from the Gram-negative bacterial pathogen Burkholderia pseudomallei, which is responsible for the disease melioidosis. B. pseudomallei can cause fatal sepsis in endemic populations in the tropical regions of the world and treatment with antibiotics is mostly ineffective. With the aim of identifying potential vaccine candidates, we report the experimental validation of predicted antigen and type I fimbrial subunit, BPSL1626, which we show is able to recognize and bind human antibodies from the sera of Burkholderia infected patients and to stimulate T-lymphocytes in vitro. The prerequisite for a melioidosis vaccine, in fact, is that both antibody- and cell-mediated immune responses must be triggered. In order to reveal potential antigenic regions of the protein that may aid immunogen re-design, we also report the crystal structure of BPSL1626 at 1.9 Å resolution on which structure-based epitope predictions were based. Overall, our data suggest that BPSL1626 and three epitope regions here-identified can represent viable candidates as potential antigenic molecules. Full article
(This article belongs to the Collection Computational Antibody and Antigen Design)
Show Figures

Graphical abstract

16 pages, 1592 KiB  
Article
Molecular Recognition between Aβ-Specific Single-Domain Antibody and Aβ Misfolded Aggregates
by Mingzhen Zhang, Jie Zheng, Ruth Nussinov and Buyong Ma
Antibodies 2018, 7(3), 25; https://doi.org/10.3390/antib7030025 - 13 Jul 2018
Cited by 35 | Viewed by 7286
Abstract
Aβ is the toxic amyloid polypeptide responsible for Alzheimer’s disease (AD). Prevention and elimination of the Aβ misfolded aggregates are the promising therapeutic strategies for the AD treatments. Gammabody, the Aβ-Specific Single-domain (VH) antibody, recognizes Aβ aggregates with high affinity and specificity and [...] Read more.
Aβ is the toxic amyloid polypeptide responsible for Alzheimer’s disease (AD). Prevention and elimination of the Aβ misfolded aggregates are the promising therapeutic strategies for the AD treatments. Gammabody, the Aβ-Specific Single-domain (VH) antibody, recognizes Aβ aggregates with high affinity and specificity and reduces their toxicities. Employing the molecular dynamics simulations, we studied diverse gammabody-Aβ recognition complexes to get insights into their structural and dynamic properties and gammabody-Aβ recognitions. Among many heterogeneous binding modes, we focused on two gammabody-Aβ recognition scenarios: recognition through Aβ β-sheet backbone and on sidechain surface. We found that the gammabody primarily uses the complementarity-determining region 3 (CDR3) loop with the grafted Aβ sequence to interact with the Aβ fibril, while CDR1/CDR2 loops have very little contact. The gammabody-Aβ complexes with backbone binding mode are more stable, explaining the gammabody’s specificity towards the C-terminal Aβ sequence. Full article
(This article belongs to the Collection Computational Antibody and Antigen Design)
Show Figures

Figure 1

12 pages, 1096 KiB  
Review
Engaging with Raman Spectroscopy to Investigate Antibody Aggregation
by Ilokugbe Ettah and Lorna Ashton
Antibodies 2018, 7(3), 24; https://doi.org/10.3390/antib7030024 - 7 Jul 2018
Cited by 32 | Viewed by 11109
Abstract
In the last decade, a number of studies have successfully demonstrated Raman spectroscopy as an emerging analytical technique for monitoring antibody aggregation, especially in the context of drug development and formulation. Raman spectroscopy is a robust method for investigating protein conformational changes, even [...] Read more.
In the last decade, a number of studies have successfully demonstrated Raman spectroscopy as an emerging analytical technique for monitoring antibody aggregation, especially in the context of drug development and formulation. Raman spectroscopy is a robust method for investigating protein conformational changes, even in highly concentrated antibody solutions. It is non-destructive, reproducible and can probe samples in an aqueous environment. In this review, we focus on the application and challenges associated with using Raman spectroscopy as a tool to study antibody aggregates. Full article
(This article belongs to the Special Issue Aggregation of Antibodies)
Show Figures

Graphical abstract

24 pages, 3598 KiB  
Article
OptMAVEn-2.0: De novo Design of Variable Antibody Regions against Targeted Antigen Epitopes
by Ratul Chowdhury, Matthew F. Allan and Costas D. Maranas
Antibodies 2018, 7(3), 23; https://doi.org/10.3390/antib7030023 - 30 Jun 2018
Cited by 34 | Viewed by 13530
Abstract
Monoclonal antibodies are becoming increasingly important therapeutic agents for the treatment of cancers, infectious diseases, and autoimmune disorders. However, laboratory-based methods of developing therapeutic monoclonal antibodies (e.g., immunized mice, hybridomas, and phage display) are time-consuming and are often unable to target a specific [...] Read more.
Monoclonal antibodies are becoming increasingly important therapeutic agents for the treatment of cancers, infectious diseases, and autoimmune disorders. However, laboratory-based methods of developing therapeutic monoclonal antibodies (e.g., immunized mice, hybridomas, and phage display) are time-consuming and are often unable to target a specific antigen epitope or reach (sub)nanomolar levels of affinity. To this end, we developed Optimal Method for Antibody Variable region Engineering (OptMAVEn) for de novo design of humanized monoclonal antibody variable regions targeting a specific antigen epitope. In this work, we introduce OptMAVEn-2.0, which improves upon OptMAVEn by (1) reducing computational resource requirements without compromising design quality; (2) clustering the designs to better identify high-affinity antibodies; and (3) eliminating intra-antibody steric clashes using an updated set of clashing parts from the Modular Antibody Parts (MAPs) database. Benchmarking on a set of 10 antigens revealed that OptMAVEn-2.0 uses an average of 74% less CPU time and 84% less disk storage relative to OptMAVEn. Testing on 54 additional antigens revealed that computational resource requirements of OptMAVEn-2.0 scale only sub-linearly with respect to antigen size. OptMAVEn-2.0 was used to design and rank variable antibody fragments targeting five epitopes of Zika envelope protein and three of hen egg white lysozyme. Among the top five ranked designs for each epitope, recovery of native residue identities is typically 45–65%. MD simulations of two designs targeting Zika suggest that at least one would bind with high affinity. OptMAVEn-2.0 can be downloaded from our GitHub repository and webpage as (links in Summary and Discussion section). Full article
(This article belongs to the Collection Computational Antibody and Antigen Design)
Show Figures

Figure 1

15 pages, 2471 KiB  
Review
In Silico Methods in Antibody Design
by Jun Zhao, Ruth Nussinov, Wen-Jin Wu and Buyong Ma
Antibodies 2018, 7(3), 22; https://doi.org/10.3390/antib7030022 - 29 Jun 2018
Cited by 29 | Viewed by 16546
Abstract
Antibody therapies with high efficiency and low toxicity are becoming one of the major approaches in antibody therapeutics. Based on high-throughput sequencing and increasing experimental structures of antibodies/antibody-antigen complexes, computational approaches can predict antibody/antigen structures, engineering the function of antibodies and design antibody-antigen [...] Read more.
Antibody therapies with high efficiency and low toxicity are becoming one of the major approaches in antibody therapeutics. Based on high-throughput sequencing and increasing experimental structures of antibodies/antibody-antigen complexes, computational approaches can predict antibody/antigen structures, engineering the function of antibodies and design antibody-antigen complexes with improved properties. This review summarizes recent progress in the field of in silico design of antibodies, including antibody structure modeling, antibody-antigen complex prediction, antibody stability evaluation, and allosteric effects in antibodies and functions. We listed the cases in which these methods have helped experimental studies to improve the affinities and physicochemical properties of antibodies. We emphasized how the molecular dynamics unveiled the allosteric effects during antibody-antigen recognition and antibody-effector recognition. Full article
(This article belongs to the Collection Computational Antibody and Antigen Design)
Show Figures

Figure 1

14 pages, 4515 KiB  
Article
Thinking outside the Laboratory: Analyses of Antibody Structure and Dynamics within Different Solvent Environments in Molecular Dynamics (MD) Simulations
by Mohammed M. Al Qaraghuli, Karina Kubiak-Ossowska and Paul A. Mulheran
Antibodies 2018, 7(3), 21; https://doi.org/10.3390/antib7030021 - 24 Jun 2018
Cited by 20 | Viewed by 9102
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 [...] Read more.
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 IgG2a antibody was analyzed in three solvent systems: explicit water and ions, implicit water and ions, and implicit water and explicit ions. Root-mean-square distance (RMSD), root-mean-square fluctuations (RMSF), and interchain angles were used to quantify structural changes. The explicit system provides the most atomistic detail but is ~6 times slower in its exploration of configurational space and required ~4 times more computational time on our supercomputer than the implicit simulations. Overall, the behavior of the implicit and explicit simulations is quantifiably similar, with the inclusion of explicit ions in the implicit simulation stabilizing the antibody to reproduce well the statistical fluctuations of the fully explicit system. Therefore, this approach holds promise to maximize the use of computational resources to explore antibody behavior. Full article
(This article belongs to the Collection Computational Antibody and Antigen Design)
Show Figures

Figure 1

Previous Issue
Next Issue
Back to TopTop