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• PG05: Analyses of all PDB HIV1-Env trimer (prefusion, closed) structures fulfilling certain parameters of resolution were performed to classify them on the basis of (a) antibody class which was informed by parental B cells as well as structural recognition, and (b) Env residues defining recognized HIV epitopes. Structural features of the 206 HIV epitope and bNAb paratopes were correlated with functional properties of the breadth and potency of neutralization against a 208-strain panel. bNAbs with >25% breadth of neutralization belonged to 20 classes of antibody with a large number of protruding loops and somatic hypermutation (SHM). HIV epitopes recognized placed the bNAbs into 6 categories (viz. V1V2, Glycan-V3, CD4-binding site, Silent face center, Fusion peptide and Subunit Interface). The epitopes contained high numbers of independent sequence segments and glycosylated surface area. PG05-Env formed a distinct group within the Silent Face category, Class VRC-PG05, which recognized even the highly glycosylated center of Env. Crystal structure data on PG05 complexed to HIV-1 Clade AE Strain CNE55 gp120 core that targets the center of the Silent Face on the outer domain of gp120 was found in PDB ID: 6BF4. Chuang2019 (antibody binding site, antibody interactions, neutralization, binding affinity, antibody sequence, structure, antibody lineage, broad neutralizer)
• VRC-PG05: The authors identify a family of antibodies, derived from a single donor, that have high neutralization breadth and recognize the center of the "silent face" (SF) on gp120. Through cryo-EM crystal structure, it was found that SF12 bound to the Env SF with a different orientation than VRC-PG05, the other donor-derived SF-binding Ab. In addition, antibodies SF5 and SF12 bind a different epitope that is present on gp120 monomers, and to both cleaved and uncleaved Env trimers; in particular, SF12 interacts with gp120 glycans N448, N262, and N295. Besides being isolated from a different donor than VRC-PG05, SF12 arose from highly divergent VH and VK genes, suggesting that evolutionary pathways to silent face recognition are diverse. Schoofs2019 (antibody binding site, antibody lineage, broad neutralizer)
• PG05: This paper presents the derivation of VRC-PG05, with details as previously noted in a patent application (Mascola2012). VRC-PG04 and VRC-PG05 were derived from the same patient sample, but are not clonally related and have different binding types. PG05 neutralized 27% of a 208-virus multiclade panel. The crystal structure and NMR of PG05 revealed that it recognizes the silent face of gp120, a region that is shielded by glycans and has had no previously reported antibody recognition. Zhou2018 (antibody binding site, antibody generation, neutralization, structure)
• VRC-PG05: This study demonstrated that bNAb signatures can be utilized to engineer HIV-1 Env vaccine immunogens eliciting Ab responses with greater neutralization breadth. Data from four large virus panels were used to comprehensively map viral signatures associated with bNAb sensitivity, hypervariable region characteristics, and clade effects. The bNAb signatures defined for the V2 epitope region were then employed to inform immunogen design in a proof-of-concept exploration of signature-based epitope targeted (SET) vaccines. V2 bNAb signature-guided mutations were introduced into Env 459C to create a trivalent vaccine which resulted in increased breadth of NAb responses compared with Env 459C alone. PG05 was used for analyzing clade sensitivity. It had poor neutralization breadth and gave no strong signatures so does not impact the overall CD4bs signature analysis Bricault2019 (antibody binding site, vaccine antigen design, computational epitope prediction, broad neutralizer)
• PG-05: This patent describes the derivation and usage of PG04 and PG05. The donor is coded as 27-374, a participant in IAVI Protocol G. Both VRC-PG-04 and VRC-PG-05 were isolated from B cells of this donor by selection for binding to Env peptide RSC3 (resurfaced stabilized core 3). VRC-PG04, but not VRC-PG05, is cross competed by CD4bs antibodies. The two Abs are able to cross-compete themselves, but not each other, indicating that they have different binding sites. Neutralization of a panel of pseudoviruses by PG05 was much weaker than for PG04. Mascola2012 (antibody binding site, antibody generation, neutralization, antibody sequence)

References

Showing 5 of 5 references.

Isolation Paper
Zhou2018 Tongqing Zhou, Anqi Zheng, Ulrich Baxa, Gwo-Yu Chuang, Ivelin S. Georgiev, Rui Kong, Sijy O'Dell, Syed Shahzad-Ul-Hussan, Chen-Hsiang Shen, Yaroslav Tsybovsky, Robert T. Bailer, Syna K. Gift, Mark K. Louder, Krisha McKee, Reda Rawi, Catherine H. Stevenson, Guillaume B. E. Stewart-Jones, Justin D. Taft, Eric Waltari, Yongping Yang, Baoshan Zhang, Sachin S. Shivatare, Vidya S. Shivatare, Chang-Chun D. Lee, Chung-Yi Wu, James C. Mullikin, Carole A. Bewley, Dennis R. Burton, Victoria R. Polonis, Lawrence Shapiro, Chi-Huey Wong, John R. Mascola, Peter D. Kwong, and Xueling Wu. A Neutralizing Antibody Recognizing Primarily N-Linked Glycan Targets the Silent Face of the HIV Envelope. Immunity, 48(3):500-513e6 doi, Mar 2018. PubMed ID: 29548671 Show all entries for this paper.

Bricault2019 Christine A. Bricault, Karina Yusim, Michael S. Seaman, Hyejin Yoon, James Theiler, Elena E. Giorgi, Kshitij Wagh, Maxwell Theiler, Peter Hraber, Jennifer P. Macke, Edward F. Kreider, Gerald H. Learn, Beatrice H. Hahn, Johannes F. Scheid, James M. Kovacs, Jennifer L. Shields, Christy L. Lavine, Fadi Ghantous, Michael Rist, Madeleine G. Bayne, George H. Neubauer, Katherine McMahan, Hanqin Peng, Coraline Chéneau, Jennifer J. Jones, Jie Zeng, Christina Ochsenbauer, Joseph P. Nkolola, Kathryn E. Stephenson, Bing Chen, S. Gnanakaran, Mattia Bonsignori, LaTonya D. Williams, Barton F. Haynes, Nicole Doria-Rose, John R. Mascola, David C. Montefiori, Dan H. Barouch, and Bette Korber. HIV-1 Neutralizing Antibody Signatures and Application to Epitope-Targeted Vaccine Design. Cell Host Microbe, 25(1):59-72.e8, 9 Jan 2019. PubMed ID: 30629920. Show all entries for this paper.

Chuang2019 Gwo-Yu Chuang, Jing Zhou, Priyamvada Acharya, Reda Rawi, Chen-Hsiang Shen, Zizhang Sheng, Baoshan Zhang, Tongqing Zhou, Robert T. Bailer, Venkata P. Dandey, Nicole A. Doria-Rose, Mark K. Louder, Krisha McKee, John R. Mascola, Lawrence Shapiro, and Peter D. Kwong. Structural Survey of Broadly Neutralizing Antibodies Targeting the HIV-1 Env Trimer Delineates Epitope Categories and Characteristics of Recognition. Structure, 27(1):196-206.e6, 2 Jan 2019. PubMed ID: 30471922. Show all entries for this paper.

Mascola2012 J. Mascola, D. R. Burton, W. Koff, P. Kwong, G. Nabel, S. K. Phogat, P. R. G. Poignard, M. D. De Jean De St. Marcel Simek-Lemos, X. Wu, and Z. Y. Yang. HIV-1 Broadly Neutralizing Antibodies. US patent 9,382,311, 5 Jul 2016. URL: https://patentscope.wipo.int/search/en/detail.jsf?docId=US91507326. Show all entries for this paper.

Schoofs2019 Till Schoofs, Christopher O . Barnes, Nina Suh-Toma, Jovana Golijanin, Philipp Schommers, Henning Gruell, Anthony P. West, Jr., Franziska Bach, Yu Erica Lee, Lilian Nogueira, Ivelin S. Georgiev, Robert T. Bailer, Julie Czartoski, John R. Mascola, Michael S. Seaman, M. Juliana McElrath, Nicole A. Doria-Rose, Florian Klein, Michel C. Nussenzweig, and Pamela J. Bjorkman. Broad and Potent Neutralizing Antibodies Recognize the Silent Face of the HIV Envelope. Immunity, 50(6):1513-1529.e9, 18 Jun 2019. PubMed ID: 31126879. Show all entries for this paper.