SUMMARY STATEMENT

PROGRAM CONTACT: ( Privileged Communication ) Release Date: 10/20/2016

Revised Date:

Application Number: 1 R43 AI132075-01

Principal Investigators (Listed Alphabetically):

BAILEY-KELLOGG, CHRIS

BROOKS, BENJAMIN DELBERT (Contact) 

COHEN, GARY H

EISENBERG, ROSELYN J

Applicant Organization: WASATCH MICROFLUIDICS

Review Group: ZRG1 IMST-K (14)

Center for Scientific Review Special Emphasis Panel

Small Business: Computational, Modeling, and Biodata Management

Meeting Date: 10/13/2016 RFA/PA: PA16-302

Council: JAN 2017 PCC: M34

Requested Start: 07/01/2017 Dual PCC: P146SS

Dual IC(s): GM

Project Title: High-throughput, multiplexed characterization and modeling of antibody:antigen 

binding, with application to HSV

SRG Action: Impact Score:

Next Steps: Visithttp://grants.nih.gov/grants/next_steps.htm

Human Subjects: 10-No human subjects involved

Animal Subjects: 10-No live vertebrate animals involved for competing appl.

Project

Year

Direct Costs

Requested

Estimated

Total Cost 

1 

TOTAL

ADMINISTRATIVE BUDGET NOTE: The budget shown is the requested budget and has not been adjusted 

to reflect any recommendations made by reviewers. If an award is planned, the costs will be calculated by 

Institute grants management staff based on the recommendations outlined below in the COMMITTEE 

BUDGET RECOMMENDATIONS section.

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Contact Information. Email NIAID's Office of Knowledge and Educational Resources at deaweb@niaid.nih.gov.
 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

1 R43 AI132075-01 2 ZRG1 IMST-K (14) 

BROOKS, B 

1R43AI132075-01 BROOKS, BENJAMIN 

COMMITTEE BUDGET RECOMMENDATIONS 

SCIENTIFIC REVIEW OFFICER'S NOTES 

RESUME AND SUMMARY OF DISCUSSION: Investigators at Wasatch Microfluidics, Dartmouth 

College, and the University of Pennsylvania seek to develop an integrated solution combining surface 

plasmon resonance (SPR) with computational modeling to identify specific residues involved in 

antigen:antibody binding. Reviewers noted that if successful, the availability of tools that provide 

structural insight into the residues involved in epitope binding potentially would have a significant 

impact on the development of novel therapeutic antibodies. The assigned reviewers initially expressed 

a high level of enthusiasm for this application. Strengths that were identified included the significance 

of the topic to be addressed, the strong premise that was supported by preliminary data, the 

exceptional investigative team, and the clear Aims that were presented with alternative strategies. 

Minor concerns were noted that included the lack of details around the metrics to be used to assess the 

accuracy of clustering antibodies and the lack of a more detailed description of the measures for 

assessing the performance of epitope identification. At the conclusion of the discussion however, 

enthusiasm for the significance of the topic to be addressed, the superior investigative team, and the 

clearly presented approach was not dampened by the minor concerns raised around details in the 

approach. As a consequence, the panel’s final evaluation of the application’s potential overall impact 

was noted to be exceptional. 

DESCRIPTION (provided by applicant): All therapeutic antibodies and most vaccines critically 

depend on the ability of antibodies to specifically recognize particular antigens; consequently, detailed 

characterization of antibody:antigen binding can provide invaluable information to understand and guide 

development. Unfortunately, due to the time and expense required, atomic resolution structure 

determination is typically used sparingly, late in a development process or for a small number of 

different antibodies or antigen variants. We seek to enable earlier and larger-scale, but still detailed, 

characterization and modeling of antibody:antigen binding, applicable to panels of antibodies that could 

result from screening polyclonal samples or engineered libraries, along with panels of antigens that 

could result from attempts to understand and account for diversity across populations. While not at 

atomic resolution, our approach will still allow residue-level localization of specific epitopes for specific 

antibodies, as well as group-level identification of functionally similar antibodies and their associated 

binding regions on the antigen. The approach will be enabled by a unique integration of a powerful 

experimental platform, the high-throughput multiplexed Wasatch Surface Plasmon Resonance (SPR), 

with powerful computational methods to design and analyze binding experiments. Studies of 

glycoprotein D (gD) of herpes simplex virus (HSV) will provide a solid foundation for developing, testing, 

and applying the technology to better understand critical differences across antibodies and antigenic 

variation. Ultimately, the approaches developed here will allow researchers to leverage extensive 

epitope characterization data generated with Wasatch's SPR instrument in order to broadly and deeply 

characterize the basis for antibody:antigen recognition in wide-ranging vaccine and therapeutic 

antibody discovery and development programs. 

PUBLIC HEALTH RELEVANCE: Detailed characterization of antibody:antigen binding is fundamental 

to understanding and potentially improving mechanisms of action of biotherapeutics and vaccines. 

Here, in order to support such characterization for large panels of related antibodies and antigen 

variants, computational design and analysis methods will be integrated with a high-throughput 

multiplexed experimental platform, enabling the overall grouping of antibodies by binding preferences 

as well as the detailed localization of particular antibody epitopes. By enabling a rich analysis at much 
 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

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BROOKS, B 

higher throughput than traditional structural studies, this approach promises to better drive discovery 

and development of vaccines and therapeutic antibodies. 

CRITIQUE 1: 

Significance: 2 

Investigator(s): 1 

Innovation: 2 

Approach: 1 

Environment: 2 

Overall Impact: Antibodies are a major class of therapeutic agents, and a critical determinant of the 

functional effect of binding of an antibody to its target antigen is mediated by the specific residues 

involved in the binding epitope. Currently, antibodies are typically developed with little structural insight 

into the residues involved in the binding epitope. The investigators propose to address this limitation of 

current technologies by developing a faster and more efficient approach to identify specific residues 

involved in antigen:antibody binding through an integrated solution combining multiplex surface 

plasmon resonance (SPR) with computational modeling. The investigators will implement and 

leveraged two elegantly complementary approaches: antibody vs. antibody binning to identify clusters 

of similar antibodies, and antibody vs. antigen binding to identify candidate residues at the binding 

epitope. 

The proposal builds upon current independent approaches for SPR and modeling, and will validate the 

platform using the herpes simplex virus (HSV) glycoprotein D (gD) antigen bound with a collection of 

diverse antibodies with a variety of epitopes. This outstanding proposal has a strong scientific premise 

with convincing preliminary evidence supporting the approach, excellent scientific rigor with a clear and 

logical set of well-defined aims, an extraordinary team of scientists working together to deliver this 

innovative proposal, and the potential to significantly illuminate the structural details of antibody:antigen 

interactions. 

1. Significance: 

Strengths 

 Improved structural insight into antibody:antigen binding epitopes will have significant benefits in 

the selection and optimization of antibodies for therapeutic assessment. 

 The proposal has a strong scientific premise with preliminary data demonstrating that multiplex 

SPF can successfully cluster antibodies with similar antigen binding patterns, as well as initial 

evidence demonstrating that the approach can localize binding epitopes. 

 The increased speed by which this proposal will provide structural insight regarding binding 

epitopes will enable this determination to be made much earlier in the drug discovery process, 

and will enable a more diverse set of candidate mAbs to be investigated. 

Weaknesses 

 None that are apparent to this reviewer 

2. Investigator(s): 

Strengths 
 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

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BROOKS, B 

 The investigators are leaders in the development and application of multiplex SPR to 

antibody:antigen structure determination, the basic biology of HSV and in particular 

characterization of glycoprotein D, and computational modeling of antibody:antigen interfaces. 

 The investigators represent a unique collection of expertise and are well-positioned to 

successfully implement this multidisciplinary proposal. 

 This proposal will require an extraordinary level of collaboration and cooperation across the 

three labs and institutions. The investigators have established productive interactions such as 

the Wasatch employee who is embedded at U Penn in the laboratory of Gary Cohen and 

Roselyn Eisenberg. 

Weaknesses 

 None that are apparent to this reviewer 

3. Innovation: 

Strengths 

 Combining the multiplexed experimental technique (SPR) with computational modeling of 

antibody:antigen epitopes is novel. 

 By including biologists who have significant gold-standard insight into the structure and function 

of HSV gD and antibodies, the antibody binning and computational model predictions can be 

assessed and the predictions refined and optimized. 

Weaknesses 

 None that are apparent to this reviewer 

4. Approach: 

Strengths 

 This fit-for-purpose approach does not attempt to generate atomic-resolution structural insight: 

rather it focuses on the critical need for residue-level information at significantly higher 

throughput than is currently available. 

 The two aims of the proposal are clearly articulated and build on each other: first the 

investigators will define clusters of antibodies with similar antigen binding patterns, and then 

seek to map the epitopes onto specific hot-spot residues. 

 The two techniques proposed by the investigators (antibody vs. antibody binning, and antibody 

vs. antigen binding) are designed to leverage the advantage of the multiplex SPR approach, 

specifically the ability to measure relative binding affinities between pairs of antibodies for a 

common antigen, and the binding affinity for a single antibody towards two related antigens. 

 The investigators clearly articulate potential risks and pitfalls associated with each aim, and 

provide alternatives to deliver on these aims in the event of challenges. 

 While not required for this phase I proposal, the investigators presented a phase II plan that 

builds upon the intended results from phase I and extends and amplifies in new directions: 

development of an integrated software package for the analytic pipeline, validation of the 

predicted epitope residues via X-ray structure determination by Felix Rey (letter of support 

included in proposal), and extension to larger-scale antibody libraries. 

Weaknesses 

 None that are apparent to this reviewer 
 

 

 

 

 

 

 

 

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BROOKS, B 

5. Environment: 

Strengths 

 The proposal represents a joint cross-disciplinary and cross-institution effort composed of 

recognized leaders in SPR and 3D printing (Wasatch), biophysical analysis and characterization 

(U Penn), and computational modeling (Dartmouth). 

 The combined resources of Wasatch (microfluidics and SPR imagers), the University of 

Pennsylvania (cell and tissue culture, FACS, SPR and biophysics), and Dartmouth College 

(computation) have the necessary capability to deliver this proposal. 

Weaknesses 

 None that are apparent to this reviewer 

Protections for Human Subjects: Not Applicable (No Human Subjects) 

Vertebrate Animals: Not Applicable (No Vertebrate Animals) 

Biohazards: Not Applicable (No Biohazards) 

Authentication of Key Biological and/or Chemical Resources: Unacceptable 

 The investigators will use a collection of HSV reagents including gD variants. This reviewer was 

unable to find a discussion of the authentication of these reagents. 

Budget and Period of Support: Recommend as Requested 

 This reviewer did not see any section where the investigators explicitly discussed the reasons 

that their proposal exceeds the hard cap of $ The investigators did delineate the activities 

that will be performed and appropriately justify their cost: the investigators should also discuss 

why this Phase I proposal requires such a significant investment. 

CRITIQUE 2: 

Significance: 2 

Investigator(s): 2 

Innovation: 3 

Approach: 3 

Environment: 2 

Overall Impact: The project aims to develop a powerful experimental platform – the high-throughput 

multiplexed Wasatch Surface Plasmon Resonance (SPR) coupled with computational methods to 

model antibody-antigen binding and apply it to study glycoprotein D (gD) of herpes simplex virus (HSV). 

The application is put forward by a team of experts that have complementary expertise in computational 
 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

1 R43 AI132075-01 6 ZRG1 IMST-K (14) 

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and experimental study of antibody-antigen interactions. If successful, the project will develop a 

technique that can generate rich information about antibody-antigen binding at large scale, which is not 

possible with existing methods and is useful for the design of biotherapeutics and vaccine. The idea of 

integrating a multiplexed antibody-antigen binding technique with computational analysis is innovative. 

The preliminary data on both computational and experimental work is solid. The approaches for 

identifying antibody clusters and localizing epitopes are generally well reasoned. However, some 

aspects of the approach such as metrics for clustering antibodies and measures for assessing the 

performance of epitope identification lack details. Overall, the project will likely have a relatively high 

impact on the field. 

1. Significance: 

Strengths 

 If successful, the project may produce a technique that can generate detailed information about 

antibody-antigen binding at a large scale, which is not possible with existing techniques such as 

X-ray crystallography, NMR and alanine scanning. 

 The proposed technique, if it works, will be useful for designing of biotherapeutics. 

 The application of the technique to herpes simplex viruses can help understand the impacts of 

antigenic variability on antibody recognition. 

 Since Wasatch SPR platform was reported to improve some drug discovery process, the 

scientific premise of the project appears to be strong. 

Weaknesses 

 None identified 

2. Investigator(s): 

Strengths 

 The PI has expertise in developing immunoassays, surface functionalization, surface property 

measurements, business experience, and software management, which is relevant to this 

project. 

 The co-PI Dr. Bailey-Kellogg has expertise in protein-protein interaction, immunoinfomatics and 

bioinformatics that is relevant to modeling protein recognition and interaction in this project. 

 The co-PIs Drs. Cohen and Eisenberg are experts of studying the infection process of herpes 

simplex virus (HSV), who can lead the application of the proposed technology to HSV infection. 

Weaknesses 

 None identified 

3. Innovation: 

Strengths 

 Integration of computational docking with experimental characterization of antibody:antigen 

binding is new. 

 Designing mutations based on prior knowledge and modeling to evaluate putative binding 

modes is interesting. 

 The analysis of antibody competition assays across multiple antigens is different from traditional 

antibody competition with respect to a single antigen. 
 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

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Weaknesses 

 It is unclear that how new the proposed method of analyzing the relationship between sequence 

difference and binding difference is since existing methods in this area is not surveyed in detail. 

4. Approach: 

Strengths 

 The preliminary work of Aim 1 clearly demonstrates that communities of antibodies that have 

similar binding patterns can be identified, and the structural difference between the communities 

may be recognized. 

 The experimental plan for Aim 1 is feasible. The approach for clustering antibodies in Aim 1 is 

well designed. 

 The preliminary work of Aim 2 on experimentally mapping epitopes and computationally 

designing disruptive mutations is solid. 

 The plan of Aim 2 for localizing antibody epitopes is well designed. 

 The potential for Phase II development is well defined. 

 The integration of experimental work and computational analysis strengthens the scientific rigor 

of the approach. 

Weaknesses 

 The custom metrics for clustering antibodies are not described in detail. 

 The statistical metrics for assessing of the accuracy of recognizing epitopes is not clearly 

defined. No baseline method is used to compare with the proposed method. This weakens the 

scientific rigor. 

5. Environment: 

Strengths 

 The research team has sufficient experimental equipment and lab/office space to carry out the 

project. 

 The research team has necessary computing equipment for the project. 

Weaknesses 

 None. 

Protections for Human Subjects: Not Applicable (No Human Subjects) 

Vertebrate Animals: Not Applicable (No Vertebrate Animals) 

Biohazards: Not Applicable (No Biohazards) 

Authentication of Key Biological and/or Chemical Resources: Unacceptable 

 Some experimental assays are proposed. But there is no plan for authentication of key 

biological and chemical resources. 
 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

1 R43 AI132075-01 8 ZRG1 IMST-K (14) 

BROOKS, B 

Budget and Period of Support: Recommend as Requested 

CRITIQUE 3: 

Significance: 1 

Investigator(s): 2 

Innovation: 3 

Approach: 4 

Environment: 2 

Overall Impact: Antibodies are central to modern biomedicine. Understanding how antibodies interact 

with their antigens is critical for Lead Identification (LI) and Lead Optimization (affinity, function, epitope, 

freedom to operate). Traditional computational and experimental techniques are quite expense, and not 

amenable to high throughput techniques, so not typically run early in a project. Here the proposal is to 

integrate two complementary high-throughput approaches: the experimental measurement of binding 

via multiplexed Wasatch Microfluidics Surface Plasmon Resonance (SPR) and the computational 

modeling and design of interactions. Glycoprotein D (gD) from herpes simplex virus (HSV) us an ideal 

system for development, testing, and application of the new approaches. This is a good scientific 

question and project. This approach can certainly speed up and reduce costs for LI and LO for 

biologics. 

1. Significance: 

Strengths 

 The computational approach combined with high throughput (and high dimensional data) 

investigating antibody epitope and affinities 

 This could reduce screening times significantly 

Weaknesses 

 None to note 

2. Investigator(s): 

Strengths 

 The PIs have a strong history of working well together, and completing grants 

 Excellent cross disciplinary teams, with the right experience 

 Good test / benchmarking with HSV 

Weaknesses 

 None to note 

3. Innovation: 

Strengths 
 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

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BROOKS, B 

 Novel territory in analyzing data across large panels of antibodies and antigens for general 

binding patterns and localizing binding regions 

 Integration of computational and experimental methods to rationally design antigenic variants 

(beyond simple alanine scans and natural variants) so as to improve resulting experimental 

information 

Weaknesses 

 None to note 

4. Approach: 

Strengths 

 Model system (HSV) with high throughput data generation with computational approach 

Weaknesses 

 A better description of the computational approach is needed 

5. Environment: 

Strengths 

 Wasatch Microfluidics has strong experience in the space with needed computing power 

 Bailey-Kellogg group is one of the right computational labs in the world 

 Eisenberg very strong in model system 

Weaknesses 

 None to note 

Protections for Human Subjects: Not Applicable (No Human Subjects) 

Vertebrate Animals: Not Applicable (No Vertebrate Animals) 

Authentication of Key Biological and/or Chemical Resources: Not Applicable (No Relevant 

Resources) 

Budget and Period of Support: Recommend as Requested 

THE FOLLOWING SECTIONS WERE PREPARED BY THE SCIENTIFIC REVIEW OFFICER TO 

SUMMARIZE THE OUTCOME OF DISCUSSIONS OF THE REVIEW COMMITTEE, OR REVIEWERS’ 

WRITTEN CRITIQUES, ON THE FOLLOWING ISSUES: 

SCIENTIFIC REVIEW OFFICER'S NOTES: During the review of this application, reviewers and/or NIH 

staff noted that one or more biosketches did not comply with the recent change to the required format 

(NOT-OD-15-032). Please review the new policy and check that all of the biosketches associated with 

your applications comply with the new format. NIH has the authority to withdraw noncompliant 

applications from review or consideration for funding. 
 

 

 

 

 

 

 

 

 

 

 

 

 

 

1 R43 AI132075-01 10 ZRG1 IMST-K (14) 

BROOKS, B 

COMMITTEE BUDGET RECOMMENDATIONS: 

It was noted during the discussion that while the amount requested is reasonable, the budget is over 

the mandatory cap and that this was not justified as required. 

Footnotes for 1 R43 AI132075-01; PI Name: Brooks, Benjamin Delbert 

NIH has modified its policy regarding the receipt of resubmissions (amended applications). 

See Guide Notice NOT-OD-14-074 at http://grants.nih.gov/grants/guide/notice-files/NOT-OD14-074.html. The impact/priority score is calculated after discussion of an application by 

averaging the overall scores (1-9) given by all voting reviewers on the committee and 

multiplying by 10. The criterion scores are submitted prior to the meeting by the individual 

reviewers assigned to an application, and are not discussed specifically at the review meeting 

or calculated into the overall impact score. Some applications also receive a percentile 

ranking. For details on the review process, see 

http://grants.nih.gov/grants/peer_review_process.htm#scoring.