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Roark RS, Habib R, Gorman J, Li H, Connell AJ, Bonsignori M, Guo Y, Hogarty MP, Olia AS, Sowers K, Zhang B, Bibollet-Ruche F, Callaghan S, Carey JW, Cerutti G, Harris DR, He W, Lewis E, Liu T, Mason RD, Park Y, Rando JM, Singh A, Wolff J, Lei QP, Louder MK, Doria-Rose NA, Andrabi R, Saunders KO, Seaman MS, Haynes BF, Kulp DW, Mascola JR, Roederer M, Sheng Z, Hahn BH, Shaw GM, Kwong PD, Shapiro L. HIV-1 neutralizing antibodies in SHIV-infected macaques recapitulate structurally divergent modes of human V2 apex recognition with a single D gene. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.11.598384. [PMID: 38903070 PMCID: PMC11188099 DOI: 10.1101/2024.06.11.598384] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/22/2024]
Abstract
Broadly neutralizing antibodies targeting the V2 apex of the HIV-1 envelope trimer are among the most common specificities elicited in HIV-1-infected humans and simian-human immunodeficiency virus (SHIV)-infected macaques. To gain insight into the prevalent induction of these antibodies, we isolated and characterized 11 V2 apex-directed neutralizing antibody lineages from SHIV-infected rhesus macaques. Remarkably, all SHIV-induced V2 apex lineages were derived from reading frame two of the rhesus DH3-15*01 gene. Cryo-EM structures of envelope trimers in complex with antibodies from nine rhesus lineages revealed modes of recognition that mimicked three canonical human V2 apex-recognition modes. Notably, amino acids encoded by DH3-15*01 played divergent structural roles, inserting into a hole at the trimer apex, H-bonding to an exposed strand, or forming part of a loop scaffold. Overall, we identify a DH3-15*01-signature for rhesus V2 apex broadly neutralizing antibodies and show that highly selected genetic elements can play multiple roles in antigen recognition. Highlights Isolated 11 V2 apex-targeted HIV-neutralizing lineages from 10 SHIV-infected Indian-origin rhesus macaquesCryo-EM structures of Fab-Env complexes for nine rhesus lineages reveal modes of recognition that mimic three modes of human V2 apex antibody recognitionAll SHIV-elicited V2 apex lineages, including two others previously published, derive from the same DH3-15*01 gene utilizing reading frame twoThe DH3-15*01 gene in reading frame two provides a necessary, but not sufficient, signature for V2 apex-directed broadly neutralizing antibodiesStructural roles played by DH3-15*01-encoded amino acids differed substantially in different lineages, even for those with the same recognition modePropose that the anionic, aromatic, and extended character of DH3-15*01 in reading frame two provides a selective advantage for V2 apex recognition compared to B cells derived from other D genes in the naïve rhesus repertoireDemonstrate that highly selected genetic elements can play multiple roles in antigen recognition, providing a structural means to enhance recognition diversity.
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Yue S, Ding G, Zheng Y, Song C, Xu P, Yu B, Li J. Dimethyl sulfate and diisopropyl sulfate as practical and versatile O-sulfation reagents. Nat Commun 2024; 15:1861. [PMID: 38424087 PMCID: PMC10904734 DOI: 10.1038/s41467-024-46214-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Accepted: 02/19/2024] [Indexed: 03/02/2024] Open
Abstract
O-Sulfation is a vital post-translational modification in bioactive molecules, yet there are significant challenges with their synthesis. Dialkyl sulfates, such as dimethyl sulfate and diisopropyl sulfate are commonly used as alkylation agents in alkaline conditions, and result in the formation of sulfate byproducts. We report herein a general and robust approach to O-sulfation by harnessing the tunable reactivity of dimethyl sulfate or diisopropyl sulfate under tetrabutylammonium bisulfate activation. The versatility of this O-sulfation protocol is interrogated with a diverse range of alcohols, phenols and N-OH compounds, including carbohydrates, amino acids and natural products. The enhanced electrophilicity of the sulfur atom in dialkyl sulfates, facilitated by the interaction with bisulfate anion (HSO4-), accounts for this pioneering chemical reactivity. We envision that our method will be useful for application in the comprehension of biological functions and discovery of drugs.
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Affiliation(s)
- Shuaishuai Yue
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082, P. R. China
| | - Guoping Ding
- State Key Laboratory of Chemical Biology, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Lingling Road, Shanghai, 200032, P. R. China
- Key Laboratory of Structure-based Drug Design & Discovery (Ministry of Education), School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, Shenyang, 110016, P. R. China
| | - Ye Zheng
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082, P. R. China
| | - Chunlan Song
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082, P. R. China.
| | - Peng Xu
- State Key Laboratory of Chemical Biology, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Lingling Road, Shanghai, 200032, P. R. China.
| | - Biao Yu
- State Key Laboratory of Chemical Biology, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Lingling Road, Shanghai, 200032, P. R. China
| | - Jiakun Li
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082, P. R. China.
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D’Antona AM, Lee JM, Zhang M, Friedman C, He T, Mosyak L, Bennett E, Lin L, Silverman M, Cometa F, Meade C, Hageman T, Sousa E, Cohen J, Marquette K, Ferguson D, Zhong X. Tyrosine Sulfation at Antibody Light Chain CDR-1 Increases Binding Affinity and Neutralization Potency to Interleukine-4. Int J Mol Sci 2024; 25:1931. [PMID: 38339208 PMCID: PMC10855961 DOI: 10.3390/ijms25031931] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Revised: 01/30/2024] [Accepted: 02/01/2024] [Indexed: 02/12/2024] Open
Abstract
Structure and function of therapeutic antibodies can be modulated by a variety of post-translational modifications (PTM). Tyrosine (Tyr) sulfation is a type of negatively charged PTM that occurs during protein trafficking through the Golgi. In this study, we discovered that an anti-interleukin (IL)-4 human IgG1, produced by transiently transfected HEK293 cells, contained a fraction of unusual negatively charged species. Interestingly, the isolated acidic species exhibited a two-fold higher affinity to IL-4 and a nearly four-fold higher potency compared to the main species. Mass spectrometry (MS) showed the isolated acidic species possessed an +80-Dalton from the expected mass, suggesting an occurrence of Tyr sulfation. Consistent with this hypothesis, we show the ability to control the acidic species during transient expression with the addition of Tyr sulfation inhibitor sodium chlorate or, conversely, enriched the acidic species from 30% to 92% of the total antibody protein when the IL-4 IgG was co-transfected with tyrosylprotein sulfotransferase genes. Further MS and mutagenesis analysis identified a Tyr residue at the light chain complementarity-determining region-1 (CDRL-1), which was sulfated specifically. These results together have demonstrated for the first time that Tyr sulfation at CDRL-1 could modulate antibody binding affinity and potency to a human immune cytokine.
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Affiliation(s)
- Aaron M. D’Antona
- BioMedicine Design, Pfizer Research & Development, 610 Main Street, Cambridge, MA 02139, USA (T.H.); (T.H.); (E.S.)
| | - Julie M. Lee
- Translational Clinical Sciences, Pfizer Discovery & Early Development, 610 Main Street, Cambridge, MA 02139, USA
| | - Melvin Zhang
- Inflammation and Immunology Research Unit, Pfizer Research & Development, 610 Main Street, Cambridge, MA 02139, USA
| | - Clarence Friedman
- BioMedicine Design, Pfizer Research & Development, 610 Main Street, Cambridge, MA 02139, USA (T.H.); (T.H.); (E.S.)
| | - Tao He
- BioMedicine Design, Pfizer Research & Development, 610 Main Street, Cambridge, MA 02139, USA (T.H.); (T.H.); (E.S.)
| | - Lidia Mosyak
- BioMedicine Design, Pfizer Research & Development, 610 Main Street, Cambridge, MA 02139, USA (T.H.); (T.H.); (E.S.)
| | - Eric Bennett
- BioMedicine Design, Pfizer Research & Development, 610 Main Street, Cambridge, MA 02139, USA (T.H.); (T.H.); (E.S.)
| | - Laura Lin
- BioMedicine Design, Pfizer Research & Development, 610 Main Street, Cambridge, MA 02139, USA (T.H.); (T.H.); (E.S.)
| | - Maddison Silverman
- BioMedicine Design, Pfizer Research & Development, 610 Main Street, Cambridge, MA 02139, USA (T.H.); (T.H.); (E.S.)
| | - Funi Cometa
- BioMedicine Design, Pfizer Research & Development, 610 Main Street, Cambridge, MA 02139, USA (T.H.); (T.H.); (E.S.)
| | - Caryl Meade
- BioMedicine Design, Pfizer Research & Development, 610 Main Street, Cambridge, MA 02139, USA (T.H.); (T.H.); (E.S.)
| | - Tyler Hageman
- BioMedicine Design, Pfizer Research & Development, 610 Main Street, Cambridge, MA 02139, USA (T.H.); (T.H.); (E.S.)
| | - Eric Sousa
- BioMedicine Design, Pfizer Research & Development, 610 Main Street, Cambridge, MA 02139, USA (T.H.); (T.H.); (E.S.)
| | - Justin Cohen
- BioMedicine Design, Pfizer Research & Development, 610 Main Street, Cambridge, MA 02139, USA (T.H.); (T.H.); (E.S.)
| | - Kimberly Marquette
- BioMedicine Design, Pfizer Research & Development, 610 Main Street, Cambridge, MA 02139, USA (T.H.); (T.H.); (E.S.)
| | - Darren Ferguson
- BioMedicine Design, Pfizer Research & Development, 610 Main Street, Cambridge, MA 02139, USA (T.H.); (T.H.); (E.S.)
| | - Xiaotian Zhong
- BioMedicine Design, Pfizer Research & Development, 610 Main Street, Cambridge, MA 02139, USA (T.H.); (T.H.); (E.S.)
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Faivre N, Verollet C, Dumas F. The chemokine receptor CCR5: multi-faceted hook for HIV-1. Retrovirology 2024; 21:2. [PMID: 38263120 PMCID: PMC10807162 DOI: 10.1186/s12977-024-00634-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Accepted: 01/13/2024] [Indexed: 01/25/2024] Open
Abstract
Chemokines are cytokines whose primary role is cellular activation and stimulation of leukocyte migration. They perform their various functions by interacting with G protein-coupled cell surface receptors (GPCRs) and are involved in the regulation of many biological processes such as apoptosis, proliferation, angiogenesis, hematopoiesis or organogenesis. They contribute to the maintenance of the homeostasis of lymphocytes and coordinate the function of the immune system. However, chemokines and their receptors are sometimes hijacked by some pathogens to infect the host organism. For a given chemokine receptor, there is a wide structural, organizational and conformational diversity. In this review, we describe the evidence for structural variety reported for the chemokine receptor CCR5, how this variability can be exploited by HIV-1 to infect its target cells and what therapeutic solutions are currently being developed to overcome this problem.
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Affiliation(s)
- Natacha Faivre
- Institut de Pharmacologie et de Biologie Structurale (IPBS), Université de Toulouse, CNRS, Université Toulouse III - Paul Sabatier (UPS), Toulouse, France
- International Research Laboratory (IRP) CNRS "IM-TB/HIV", Toulouse, France
- International Research Laboratory (IRP) CNRS "IM-TB/HIV", Buenos Aires, Argentina
| | - Christel Verollet
- Institut de Pharmacologie et de Biologie Structurale (IPBS), Université de Toulouse, CNRS, Université Toulouse III - Paul Sabatier (UPS), Toulouse, France
- International Research Laboratory (IRP) CNRS "IM-TB/HIV", Toulouse, France
- International Research Laboratory (IRP) CNRS "IM-TB/HIV", Buenos Aires, Argentina
| | - Fabrice Dumas
- Institut de Pharmacologie et de Biologie Structurale (IPBS), Université de Toulouse, CNRS, Université Toulouse III - Paul Sabatier (UPS), Toulouse, France.
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Yu Y, Feng Y, Zhou Z, Li K, Hu X, Liao L, Xing H, Shao Y. Substitution of gp120 C4 region compensates for V3 loss-of-fitness mutations in HIV-1 CRF01_AE co-receptor switching. Emerg Microbes Infect 2023; 12:e2169196. [PMID: 36647730 PMCID: PMC9980400 DOI: 10.1080/22221751.2023.2169196] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
HIV-1 infection is mediated by a viral envelope subsequently binding to CD4 receptor and two main coreceptors, CCR5 (R5) for primary infection and CXCR4 (X4) in chronic infection. Switching from R5 to X4 tropism in HIV-1 infection is associated with increased viral pathogenesis and disease progression. The coreceptor switching is mainly due to variations in the V3 loop, while the mechanism needs to be further elucidated. We systematically studied the determinant for HIV-1 coreceptor switching by substitution of the genes from one R5 and one X4 pseudoviruses. The study results in successfully constructing two panels of chimeric viruses of R5 to X4 forward and X4 to R5 reverse switching. The determinants for tropism switching are the combined substitution of the V3 loop and C4 region of the HIV-1 envelope. The possible mechanism of the tropism switching includes two components, the V3 loop to enable the viral envelope binding to the newly switched coreceptor and the C4 region, to compensate for the loss of fitness caused by deleterious V3 loop mutations to maintain the overall viral viability. The combined C4 and V3 substitution showed at least an eightfold increase in replication activity compared with the pseudovirus with only V3 loop substitution. The site-directed mutations of N425R and S440-I442 with charged amino acids could especially increase viral activity. This study could facilitate HIV-1 phenotype surveillance and select right entry inhibitor, CCR5 or CXCR4 antagonists, for antiviral therapy.
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Affiliation(s)
- Yueyang Yu
- School of Medicine, Nankai University, Tianjin, People’s Republic of China
| | - Yi Feng
- State Key Laboratory for Infectious Disease Prevention and Control, National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, People’s Republic of China
| | - Zehua Zhou
- School of Medicine, Nankai University, Tianjin, People’s Republic of China
| | - Kang Li
- School of Medicine, Nankai University, Tianjin, People’s Republic of China
| | - Xiaoyan Hu
- School of Medicine, Nankai University, Tianjin, People’s Republic of China
| | - Lingjie Liao
- State Key Laboratory for Infectious Disease Prevention and Control, National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, People’s Republic of China
| | - Hui Xing
- State Key Laboratory for Infectious Disease Prevention and Control, National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, People’s Republic of China
| | - Yimig Shao
- School of Medicine, Nankai University, Tianjin, People’s Republic of China,State Key Laboratory for Infectious Disease Prevention and Control, National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, People’s Republic of China,Changping Laboratory, Beijing, People’s Republic of China, Yimig Shao State Key Laboratory for Infectious Disease Prevention and Control, National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, People’s Republic of China
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6
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Glögl M, Friedrich N, Cerutti G, Lemmin T, Kwon YD, Gorman J, Maliqi L, Mittl PRE, Hesselman MC, Schmidt D, Weber J, Foulkes C, Dingens AS, Bylund T, Olia AS, Verardi R, Reinberg T, Baumann NS, Rusert P, Dreier B, Shapiro L, Kwong PD, Plückthun A, Trkola A. Trapping the HIV-1 V3 loop in a helical conformation enables broad neutralization. Nat Struct Mol Biol 2023; 30:1323-1336. [PMID: 37605043 PMCID: PMC10497408 DOI: 10.1038/s41594-023-01062-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Accepted: 07/11/2023] [Indexed: 08/23/2023]
Abstract
The third variable (V3) loop on the human immunodeficiency virus 1 (HIV-1) envelope glycoprotein trimer is indispensable for virus cell entry. Conformational masking of V3 within the trimer allows efficient neutralization via V3 only by rare, broadly neutralizing glycan-dependent antibodies targeting the closed prefusion trimer but not by abundant antibodies that access the V3 crown on open trimers after CD4 attachment. Here, we report on a distinct category of V3-specific inhibitors based on designed ankyrin repeat protein (DARPin) technology that reinstitute the CD4-bound state as a key neutralization target with up to >90% breadth. Broadly neutralizing DARPins (bnDs) bound V3 solely on open envelope and recognized a four-turn amphipathic α-helix in the carboxy-terminal half of V3 (amino acids 314-324), which we termed 'αV3C'. The bnD contact surface on αV3C was as conserved as the CD4 binding site. Molecular dynamics and escape mutation analyses underscored the functional relevance of αV3C, highlighting the potential of αV3C-based inhibitors and, more generally, of postattachment inhibition of HIV-1.
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Affiliation(s)
- Matthias Glögl
- Institute for Medical Virology, University of Zurich (UZH), Zurich, Switzerland
| | - Nikolas Friedrich
- Institute for Medical Virology, University of Zurich (UZH), Zurich, Switzerland
| | - Gabriele Cerutti
- Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY, USA
| | - Thomas Lemmin
- Institute for Medical Virology, University of Zurich (UZH), Zurich, Switzerland
| | - Young D Kwon
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Jason Gorman
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Liridona Maliqi
- Institute for Medical Virology, University of Zurich (UZH), Zurich, Switzerland
| | - Peer R E Mittl
- Department of Biochemistry, University of Zurich (UZH), Zurich, Switzerland
| | - Maria C Hesselman
- Institute for Medical Virology, University of Zurich (UZH), Zurich, Switzerland
| | - Daniel Schmidt
- Institute for Medical Virology, University of Zurich (UZH), Zurich, Switzerland
| | - Jacqueline Weber
- Institute for Medical Virology, University of Zurich (UZH), Zurich, Switzerland
| | - Caio Foulkes
- Institute for Medical Virology, University of Zurich (UZH), Zurich, Switzerland
| | - Adam S Dingens
- Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Tatsiana Bylund
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Adam S Olia
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Raffaello Verardi
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Thomas Reinberg
- Department of Biochemistry, University of Zurich (UZH), Zurich, Switzerland
| | - Nicolas S Baumann
- Institute for Medical Virology, University of Zurich (UZH), Zurich, Switzerland
| | - Peter Rusert
- Institute for Medical Virology, University of Zurich (UZH), Zurich, Switzerland
| | - Birgit Dreier
- Department of Biochemistry, University of Zurich (UZH), Zurich, Switzerland
| | - Lawrence Shapiro
- Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY, USA
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA
| | - Peter D Kwong
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Andreas Plückthun
- Department of Biochemistry, University of Zurich (UZH), Zurich, Switzerland
| | - Alexandra Trkola
- Institute for Medical Virology, University of Zurich (UZH), Zurich, Switzerland.
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Dimitrov JD, Mwangi W, Zhong X. Editorial: Mechanisms and strategies of unconventional antibody diversification for greater immune adaptability. Front Immunol 2023; 14:1267556. [PMID: 37727783 PMCID: PMC10506071 DOI: 10.3389/fimmu.2023.1267556] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Accepted: 08/14/2023] [Indexed: 09/21/2023] Open
Affiliation(s)
- Jordan D. Dimitrov
- Centre de Recherche des Cordeliers, INSERM, CNRS, Sorbonne Université, Université Paris Cité, Paris, France
| | - Waithaka Mwangi
- Department of Diagnostic Medicine/Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, KS, United States
| | - Xiaotian Zhong
- BioMedicine Design, Medicinal Sciences, Pfizer Worldwide Research & Development (R&D), Cambridge, MA, United States
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8
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Campbell ESB, Goens MM, Cao W, Thompson B, Susta L, Banadyga L, Wootton SK. Recent Advancements in AAV-Vectored Immunoprophylaxis in the Nonhuman Primate Model. Biomedicines 2023; 11:2223. [PMID: 37626720 PMCID: PMC10452516 DOI: 10.3390/biomedicines11082223] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2023] [Revised: 08/01/2023] [Accepted: 08/02/2023] [Indexed: 08/27/2023] Open
Abstract
Monoclonal antibodies (mAbs) are important treatment modalities for preventing and treating infectious diseases, especially for those lacking prophylactic vaccines or effective therapies. Recent advances in mAb gene cloning from naturally infected or immunized individuals has led to the development of highly potent human mAbs against a wide range of human and animal pathogens. While effective, the serum half-lives of mAbs are quite variable, with single administrations usually resulting in short-term protection, requiring repeated doses to maintain therapeutic concentrations for extended periods of time. Moreover, due to their limited time in circulation, mAb therapies are rarely given prophylactically; instead, they are generally administered therapeutically after the onset of symptoms, thus preventing mortality, but not morbidity. Adeno-associated virus (AAV) vectors have an established record of high-efficiency in vivo gene transfer in a variety of animal models and humans. When delivered to post-mitotic tissues such as skeletal muscle, brain, and heart, or to organs in which cells turn over slowly, such as the liver and lungs, AAV vector genomes assume the form of episomal concatemers that direct transgene expression, often for the lifetime of the cell. Based on these attributes, many research groups have explored AAV-vectored delivery of highly potent mAb genes as a strategy to enable long-term expression of therapeutic mAbs directly in vivo following intramuscular or intranasal administration. However, clinical trials in humans and studies in nonhuman primates (NHPs) indicate that while AAVs are a powerful and promising platform for vectored immunoprophylaxis (VIP), further optimization is needed to decrease anti-drug antibody (ADA) and anti-capsid antibody responses, ultimately leading to increased serum transgene expression levels and improved therapeutic efficacy. The following review will summarize the current landscape of AAV VIP in NHP models, with an emphasis on vector and transgene design as well as general delivery system optimization. In addition, major obstacles to AAV VIP, along with implications for clinical translation, will be discussed.
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Affiliation(s)
| | - Melanie M. Goens
- Department of Pathobiology, University of Guelph, Guelph, ON N1G 2W1, Canada
| | - Wenguang Cao
- Public Health Agency of Canada, Winnipeg, MB R3E 3R2, Canada
| | | | - Leonardo Susta
- Department of Pathobiology, University of Guelph, Guelph, ON N1G 2W1, Canada
| | - Logan Banadyga
- Public Health Agency of Canada, Winnipeg, MB R3E 3R2, Canada
| | - Sarah K. Wootton
- Department of Pathobiology, University of Guelph, Guelph, ON N1G 2W1, Canada
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9
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Pawnikar S, Akhter S, Miao Y. Structural dynamics of chemokine receptors. VITAMINS AND HORMONES 2023; 123:645-662. [PMID: 37718001 DOI: 10.1016/bs.vh.2023.05.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/19/2023]
Abstract
Membrane proteins such as G protein-coupled receptors (GPCRs) are involved in awide range of physiological and pathological cellular processes. Binding of extracellular signals to GPCRs, including hormones, neurotransmitters, peptides and proteins, can activate intracellular signaling cascades via G protein interaction. Chemokine receptors are key GPCRs implicated in cancers, immune responses, cell migration and inflammation. Specifically, the CCR5 and CXCR4 chemokine receptors serve as important therapeutic targets against Human Immunodeficiency virus (HIV) entry into human cells. Maraviroc and Vicriviroc, two clinically used HIV entry inhibitors, are antagonists of the CCR5 receptor. These drugs block HIV entry, but ultimately resistance develops, due to emergence of viruses that can utilize the CXCR4 co-receptor. Unfortunately, development of chemokine receptor antagonists as selective drugs of HIV infection has been greatly hindered as their target orthosteric site is conserved among different receptor subtypes. Accordingly, it is important to understand the structural dynamics of these receptors to develop more effective therapeutics. In this chapter, we describe the latest advances in studies of these two key chemokine receptors with respect to their structures, dynamics and function.
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Affiliation(s)
- Shristi Pawnikar
- Center for Computational Biology and Department of Molecular Biosciences, University of Kansas, Lawrence, KS, United States
| | - Sana Akhter
- Center for Computational Biology and Department of Molecular Biosciences, University of Kansas, Lawrence, KS, United States
| | - Yinglong Miao
- Center for Computational Biology and Department of Molecular Biosciences, University of Kansas, Lawrence, KS, United States.
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10
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Liu MT, Shen JX, Li XW, Yang L, Li Y, Sang P, Yang LQ. Study on molecular mechanisms of CD4 dependency and independency of HIV-1 gp120. RSC Adv 2023; 13:6274-6286. [PMID: 36825290 PMCID: PMC9942563 DOI: 10.1039/d3ra00433c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Accepted: 02/16/2023] [Indexed: 02/25/2023] Open
Abstract
Different HIV-1 strains have different antibody neutralization phenotypes (or CD4-dependencies). However, the molecular mechanisms underlying these differences remain to be elucidated. In this study, we constructed gp120 structural models from the CD4-dependent, neutralization-resistant JR-FL strain and the CD4-independent, neutralization-sensitive R2 strain and carried out several conventional molecular dynamics (MD) simulations and free energy landscape (FEL) constructions. Comparative analyses of the MD simulations and FELs indicated that R2 gp120 had higher global structural flexibility and greater conformational diversity than JR-FL gp120. This provides the preconditions for R2 gp120 to adopt a more open conformation than JR-FL gp120. Essential dynamics (ED) analysis showed that the collective motions of R2 gp120 tend towards an open state while those of JR-FL gp120 tend to retain a closed state. Based on conformational selection theory, R2 gp120's more readily sampled open state makes it more sensitive to neutralizing antibodies (or more CD4-independent) than JR-FL gp120, which may explain why the HIV-1 R2 and JR-FL strains show CD4-independent and -dependent phenotypes, respectively. Our study provides thermodynamic and kinetic insights into the CD4-dependent and -independent molecular mechanisms of HIV-1 gp120 and helps shed light on HIV-1 immune evasion.
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Affiliation(s)
- Meng-Ting Liu
- College of Agriculture and Biological Science, Dali University Dali 671000 China .,Key Laboratory of Bioinformatics and Computational Biology of the Department of Education of Yunnan Province, Dali University Dali 671000 China
| | - Jian-Xin Shen
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, School of Life Sciences, Yunnan UniversityKunmingChina
| | - Xin-Wei Li
- College of Agriculture and Biological Science, Dali University Dali 671000 China .,Key Laboratory of Bioinformatics and Computational Biology of the Department of Education of Yunnan Province, Dali University Dali 671000 China
| | - Li Yang
- College of Mathematics and Computer Science, Dali UniversityDali 671000China
| | - Yi Li
- College of Mathematics and Computer Science, Dali UniversityDali 671000China
| | - Peng Sang
- College of Agriculture and Biological Science, Dali University Dali 671000 China .,Key Laboratory of Bioinformatics and Computational Biology of the Department of Education of Yunnan Province, Dali University Dali 671000 China.,Yunnan Key Laboratory of Screening and Research on Anti-pathogenic Plant Resources from West Yunnan, Dali University Dali 671000 China
| | - Li-Quan Yang
- College of Agriculture and Biological Science, Dali University Dali 671000 China .,Key Laboratory of Bioinformatics and Computational Biology of the Department of Education of Yunnan Province, Dali University Dali 671000 China.,Yunnan Key Laboratory of Screening and Research on Anti-pathogenic Plant Resources from West Yunnan, Dali University Dali 671000 China
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11
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Shao J, Liu G, Lv G. Mutation in the D1 domain of CD4 receptor modulates the binding affinity to HIV-1 gp120. RSC Adv 2023; 13:2070-2080. [PMID: 36712621 PMCID: PMC9832346 DOI: 10.1039/d2ra06628a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Accepted: 12/23/2022] [Indexed: 01/13/2023] Open
Abstract
The gp120 surface subunit of HIV-1 envelope lycoprotein (Env) is the key component for the viral entry process through interaction with the CD4 binding site (CD4bs) of the primary receptor CD4. The point mutant was introduced into SD1, a CD4 D1 variant, to enhance the interaction with HIV-1 gp120.The three-dimensional structures of gp120 and SD1 were determined using homology modeling based on the results previously determined by X-ray crystallography. The binding models were carried out via protein-protein docking tools. The 5 best docking solutions were retained according to the docking scores and were used for structural assessment. Our results demonstrated the consistency between the 3D models of gp120 and SD1 predicted by molecular docking calculations and the co-crystallized data available. We first discovered that most residues in SD1 that interacted with gp120 were located within the region 6-94 of the first N-terminal D1 domain of CD4. SD1 bound to gp120 stably at which 15 residues formed 20 hydrogen bonds with 16 residues of gp120. Five pairs of electrostatic interactions between positively and negatively charged side chains of amino acids were identified in the SD1-gp120 interface, which showed an increased number of electrostatic interactions with gp120. The mutant in the D1 domain of human CD4 receptor could strengthen binding affinity with HIV-1 gp120 and might improve the interaction pattern of the neighboring residues. The sequence analysis of gp120 suggested that Asp186, Asn189, Arg191, Glu293, Phe318 and Tyr319 were located in the variable regions of gp120, which may be HIV-1 AE strain-specific amino acid residues. Together, the results presented in this study contributed to a better understanding of the changes in the interaction between the gp120 protein and the human host CD4 receptor associated with point mutation in the D1 domain. The stabilized derivative of human CD4 D1 should serve as a promising target for therapeutics development in HIV-1 vaccine and viral entry inhibitor and may warrant further investigation.
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Affiliation(s)
- Jiping Shao
- Department of Pathogen Biology, Hainan Medical UniversityHaikou 571199P. R. China
| | - Gezhi Liu
- University of MarylandMaryland 20850USA
| | - Gang Lv
- Department of Pathogen Biology, Hainan Medical UniversityHaikou 571199P. R. China,Key Laboratory of Translation Medicine Tropical Diseases, Hainan Medical UniversityHaikou 571199P. R. China,Hainan Medical University-The University of Hong Kong Joint Laboratory of Tropical Infectious Diseases, Hainan Medical UniversityHaikou 571199P. R. China
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12
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Zhang C, Lan Y, Li L, He R, Meng Y, Li J, Chen W. HIV-1 tropism in low-level viral load HIV-1 infections during HAART in Guangdong, China. Front Microbiol 2023; 14:1159763. [PMID: 37152735 PMCID: PMC10158941 DOI: 10.3389/fmicb.2023.1159763] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Accepted: 03/13/2023] [Indexed: 05/09/2023] Open
Abstract
Background Since only a few studies have been conducted on the factors associated with different HIV-1 tropisms in low-level viral load HIV-1 infections in China, we investigated the sequences of HIV-1 V3 loop in prevalent HIV-1 subtypes and factors related to HIV-1 tropism and immune recovery in HIV-1 infections after 6 months of highly active antiretroviral therapy (HAART) in Guangdong, China. Methods Plasma samples with HIV-1 RNA of 400-999 copies/mL were collected. We analyzed the amino acid sequence of the V3 loop by in silico prediction algorithms. Mann-Whitney and Chi-square tests were used for statistical comparison. Furthermore, logistic regression and multiple linear regression were used, respectively, for factors associated with 351 HIV-1 tropism and immune recovery of 67 cases with continued CD4+ T cell count during HAART. Results There was a lower percentage of HIV-1 R5-tropic virus in CRF01_AE (66.3%) (p < 0.0001) and CRF55_01B (52.6%) (p < 0.0001) compared with both CRF07_BC (96.1%) and CRF08_BC (97.4%), respectively. Compared with the R5-tropic virus, higher proportions of IIe8/Val8, Arg11/Lys11, and Arg18/His18/Lys18 were observed in the X4-tropic virus of CRF01_AE and CRF07_BC (p < 0.0001). The baseline CD4+ T cell count (p < 0.0001) and baseline CD4+ T/CD8+ T ratio (p = 0.0006) of all R5-tropic infections were higher than those in the X4-tropic infection. The baseline CD4+ T cell count (odds ratio [OR] 0.9963, p = 0.0097), CRF07_BC (OR 0.1283, p = 0.0002), and CRF08_BC (OR 0.1124, p = 0.0381) were associated with less HIV-1 X4-tropism. The baseline CD4+ T cell count was a positive factor (p < 0.0001) in the recovery of CD4+ T cell count during HAART. Conclusion R5-tropism represented the majority in low-level viral load HIV-1 infections receiving HAART for more than 6 months in Guangdong, China. The baseline immune level in the HIV-1 R5-tropic infections was higher than that in the X4-tropic infections. The amino acids of the 8th, 11th, and 18th of the HIV-1 V3 loop were more variable in the X4-tropic HIV-1. CRF01_AE, CRF55_01B, and lower baseline CD4+ T cell count were associated with more HIV-1 X4-tropism. The immune recovery during HAART was positively related to baseline CD4+ T cell count.
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Affiliation(s)
- Chuyu Zhang
- Institute of Infectious Diseases, Guangzhou Eighth People’s Hospital, Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Yun Lan
- Institute of Infectious Diseases, Guangzhou Eighth People’s Hospital, Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Linghua Li
- Infectious Disease Center, Guangzhou Eighth People’s Hospital, Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Ruiying He
- Institute of Infectious Diseases, Guangzhou Eighth People’s Hospital, Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Yu Meng
- Infectious Disease Center, Guangzhou Eighth People’s Hospital, Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Jian Li
- Institute of Infectious Diseases, Guangzhou Eighth People’s Hospital, Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Weilie Chen
- Institute of Infectious Diseases, Guangzhou Eighth People’s Hospital, Guangzhou Medical University, Guangzhou, Guangdong, China
- *Correspondence: Weilie Chen,
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13
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Zhong X, D’Antona AM. A potential antibody repertoire diversification mechanism through tyrosine sulfation for biotherapeutics engineering and production. Front Immunol 2022; 13:1072702. [PMID: 36569848 PMCID: PMC9774471 DOI: 10.3389/fimmu.2022.1072702] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Accepted: 11/23/2022] [Indexed: 12/13/2022] Open
Abstract
The diversity of three hypervariable loops in antibody heavy chain and light chain, termed the complementarity-determining regions (CDRs), defines antibody's binding affinity and specificity owing to the direct contact between the CDRs and antigens. These CDR regions typically contain tyrosine (Tyr) residues that are known to engage in both nonpolar and pi stacking interaction with antigens through their complementary aromatic ring side chains. Nearly two decades ago, sulfotyrosine residue (sTyr), a negatively charged Tyr formed by Golgi-localized membrane-bound tyrosylprotein sulfotransferases during protein trafficking, were also found in the CDR regions and shown to play an important role in modulating antibody-antigen interaction. This breakthrough finding demonstrated that antibody repertoire could be further diversified through post-translational modifications, in addition to the conventional genetic recombination. This review article summarizes the current advances in the understanding of the Tyr-sulfation modification mechanism and its application in potentiating protein-protein interaction for antibody engineering and production. Challenges and opportunities are also discussed.
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14
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Enhancement of CD4 Binding, Host Cell Entry, and Sensitivity to CD4bs Antibody Inhibition Conferred by a Natural but Rare Polymorphism in the HIV-1 Envelope. J Virol 2022; 96:e0185121. [PMID: 35862673 PMCID: PMC9327689 DOI: 10.1128/jvi.01851-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
A rare but natural polymorphism in the HIV-1 envelope (Env) glycoprotein, lysine at position 425 was selected as a mutation conferring resistance to maraviroc (MVC) in vitro. N425K has not been identified in HIV-infected individuals failing an MVC-based treatment. This study reports that the rare K425 polymorphism in an HIV-1 subtype A Env has increased affinity for CD4, resulting in faster host cell entry kinetics and the ability to scavenge for low cell surface expression of CD4 to mediate entry. Whereas the subtype A wild-type isolate-74 Env (N425) is inhibited by soluble (s) CD4, HIV-1 with K425 A74 Env shows enhanced infection and the ability to infect CCR5+ cells when pretreated with sCD4. Upon adding K425 or N425 HIV-1 to CD4+/CCR5+ cells along with RANTES/CCL3, only K425 HIV-1 was able to infect cells when CCR5 recycled/returned to the cell surface at 12 h post-treatment. These findings suggest that upon binding to CD4, K425 Env may maintain a stable State 2 "open" conformation capable of engaging CCR5 for entry. Only K425 was significantly more sensitivity than wild-type N425 A74 to inhibition by the CD4 binding site (bs) compound, BMS-806, the CD4bs antibody, VRC01 and N6, and the single-chain CD4i antibody, SCm9. K425 A74 was also capable of activating B cells expressing the VRC01 surface immunoglobulin. In summary, despite increased replicative fitness, we propose that K425 HIV-1 may be counterselected within infected individuals if K425 HIV-1 is rapidly eliminated by CD4bs-neutralizing antibodies. IMPORTANCE Typically, a natural amino acid polymorphism is found as the wild-type sequence in the HIV-1 population if it provides a selective advantage to the virus. The natural K425 polymorphism in HIV-1 Env results in higher host cell entry efficiency and greater replicative fitness by virtue of its high binding affinity to CD4. The studies presented herein suggest that the rare K425 HIV-1, compared to the common N425 HIV-1, may be more sensitive to inhibition by CD4bs-neutralizing antibodies (i.e., antibodies that bind to the CD4 binding pocket on the HIV-1 envelope glycoprotein). If CD4bs antibodies did emerge in an infected individual, the K425 HIV-1 may be hypersensitive to inhibition, and thus this K425 virus variant may be removed from the HIV-1 swarm despite its higher replication fitness. Studies are now underway to determine whether addition of the K425 polymorphism into the Envelope-based HIV-1 vaccines could enhance protective immunity.
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15
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Stewart V, Ronald PC. Sulfotyrosine residues: interaction specificity determinants for extracellular protein-protein interactions. J Biol Chem 2022; 298:102232. [PMID: 35798140 PMCID: PMC9372746 DOI: 10.1016/j.jbc.2022.102232] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Revised: 06/21/2022] [Accepted: 06/22/2022] [Indexed: 11/28/2022] Open
Abstract
Tyrosine sulfation, a post-translational modification, can determine and often enhance protein–protein interaction specificity. Sulfotyrosyl residues (sTyrs) are formed by the enzyme tyrosyl-protein sulfotransferase during protein maturation in the Golgi apparatus and most often occur singly or as a cluster within a six-residue span. With both negative charge and aromatic character, sTyr facilitates numerous atomic contacts as visualized in binding interface structural models, thus there is no discernible binding site consensus. Found exclusively in secreted proteins, in this review, we discuss the four broad sequence contexts in which sTyr has been observed: first, a solitary sTyr has been shown to be critical for diverse high-affinity interactions, such as between peptide hormones and their receptors, in both plants and animals. Second, sTyr clusters within structurally flexible anionic segments are essential for a variety of cellular processes, including coreceptor binding to the HIV-1 envelope spike protein during virus entry, chemokine interactions with receptors, and leukocyte rolling cell adhesion. Third, a subcategory of sTyr clusters is found in conserved acidic sequences termed hirudin-like motifs that enable proteins to interact with thrombin; consequently, many proven and potential therapeutic proteins derived from blood-consuming invertebrates depend on sTyrs for their activity. Finally, several proteins that interact with collagen or similar proteins contain one or more sTyrs within an acidic residue array. Refined methods to direct sTyr incorporation in peptides synthesized both in vitro and in vivo, together with continued advances in mass spectrometry and affinity detection, promise to accelerate discoveries of sTyr occurrence and function.
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Affiliation(s)
- Valley Stewart
- Department of Microbiology & Molecular Genetics, University of California, Davis, USA.
| | - Pamela C Ronald
- Department of Plant Pathology, University of California, Davis, USA; Genome Center, University of California, Davis, USA.
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16
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Sun J, Zhao G, Bylund T, Lee M, Adibhatla S, Kwong PD, Chuang GY, Rawi R, Bewley CA. C3-Symmetric Aromatic Core of Griffithsin Is Essential for Potent Anti-HIV Activity. ACS Chem Biol 2022; 17:1450-1459. [PMID: 35537058 PMCID: PMC10091857 DOI: 10.1021/acschembio.1c00990] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Lectins, carbohydrate-binding proteins of nonimmune origin, bind to carbohydrates and glycan shields present on the surfaces of cells and viral spike proteins. Lectins thus hold great promise as therapeutic and diagnostic proteins, exemplified by their potent antiviral activities and the desire to engineer synthetic carbohydrate receptors based on lectin recognition principles. Here, we describe a new carbohydrate-binding architectural motif─namely, a C3-symmetric tyrosine-based aromatic core, present in the therapeutic lectin griffithsin (GRFT). By using structure-based amino acid substitutions, X-ray crystallography, molecular dynamics (MD) simulations, and HIV-1 neutralization assays, we show that this core is critical for potent (pM) antiviral activity and nanomolar binding to the glycan shield largely consisting of high mannose glycans. Crystal structures and MD simulations show that CH-π interactions stabilize the aromatic cluster to maintain the three pseudo-symmetric carbohydrate-binding sites, nonaromatic amino acid substitutions (Tyr to Ala) abrogate antiviral activity, and increasing the aromatic CH-π edge-to-centroid interface via a Tyr to Trp substitution yields a GRFT variant with improved potency and increased residence time of Man-9 observed in MD simulations. NMR titrations of a Tyr-to-Ala variant indicate that disruption of the aromatic prevents the intermolecular crosslinking between two equivalents of Man-9 and one carbohydrate-binding face observed in wild-type GRFT and known to be critical for picomolar potency of this lectin. This C3-symmetric aromatic core defines a new recognition motif for the design of carbohydrate receptors and suggests principles for engineering known lectins to have increased affinity and stability.
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Affiliation(s)
- Jiadong Sun
- Laboratory of Bioorganic Chemistry, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Gengxiang Zhao
- Laboratory of Bioorganic Chemistry, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Tatsiana Bylund
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Myungjin Lee
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Srikar Adibhatla
- Laboratory of Bioorganic Chemistry, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Peter D. Kwong
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Gwo-Yu Chuang
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Reda Rawi
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Carole A. Bewley
- Laboratory of Bioorganic Chemistry, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892, United States
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17
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Lewandowski EM, Kroeck KG, Jacobs LM, Fenske TG, Witt RN, Hintz AM, Ramsden ER, Zhang X, Peterson F, Volkman BF, Veldkamp CT, Chen Y. Structural Insights into Molecular Recognition by Human Chemokine CCL19. Biochemistry 2022; 61:311-318. [PMID: 35156805 PMCID: PMC9254573 DOI: 10.1021/acs.biochem.1c00759] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The human chemokines CCL19 and CCL21 bind to the G protein-coupled receptor (GPCR) CCR7 and play an important role in the trafficking of immune cells as well as cancer metastasis. Conserved binding sites for sulfotyrosine residues on the receptor contribute significantly to the chemokine/GPCR interaction and have been shown to provide promising targets for new drug-discovery efforts to disrupt the chemokine/GPCR interaction and, consequently, tumor metastasis. Here, we report the first X-ray crystal structure of a truncated CCL19 (residues 7-70) at 2.50 Å resolution, revealing molecular details crucial for protein-protein interactions. Although the overall structure is similar to the previously determined NMR model, there are important variations, particularly near the N terminus and the so-called 30's and 40's loops. Computational analysis using the FTMap server indicates the potential importance of these areas in ligand binding and the differences in binding hotspots compared to CCL21. NMR titration experiments using a CCR7-derived peptide (residues 5-11, TDDYIGD) further demonstrate potential receptor recognition sites, such as those near the C terminus and 40's loop, which consist of both positively charged and hydrophobic residues that may be important for receptor binding. Taken together, the X-ray, NMR, and computational analysis herein provide insights into the overall structure and molecular features of CCL19 and enables investigation into this chemokine's function and inhibitor development.
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Affiliation(s)
- Eric M. Lewandowski
- Department of Molecular Medicine, University of South Florida Morsani College of Medicine, 12901 Bruce B. Downs Blvd., Tampa, Florida 33612, United States
| | - Kyle G. Kroeck
- Department of Molecular Medicine, University of South Florida Morsani College of Medicine, 12901 Bruce B. Downs Blvd., Tampa, Florida 33612, United States
| | - Lian M.C. Jacobs
- Department of Molecular Medicine, University of South Florida Morsani College of Medicine, 12901 Bruce B. Downs Blvd., Tampa, Florida 33612, United States
| | - Tyler G. Fenske
- Department of Biochemistry and Program in Chemical Biology, Medical College of Wisconsin, Milwaukee, Wisconsin 53226, United States
| | - Robin N. Witt
- Department of Chemistry, University of Wisconsin Whitewater, Whitewater, Wisconsin 53190, United States
| | - Alyssa M. Hintz
- Department of Chemistry, University of Wisconsin Whitewater, Whitewater, Wisconsin 53190, United States
| | - Elizabeth R. Ramsden
- Department of Chemistry, University of Wisconsin Whitewater, Whitewater, Wisconsin 53190, United States
| | - Xiujun Zhang
- Department of Molecular Medicine, University of South Florida Morsani College of Medicine, 12901 Bruce B. Downs Blvd., Tampa, Florida 33612, United States
| | - Francis Peterson
- Department of Biochemistry and Program in Chemical Biology, Medical College of Wisconsin, Milwaukee, Wisconsin 53226, United States
| | - Brian F. Volkman
- Department of Biochemistry and Program in Chemical Biology, Medical College of Wisconsin, Milwaukee, Wisconsin 53226, United States,Corresponding authors: Brian F. Volkman, , Christopher T. Veldkamp, , Yu Chen,
| | - Christopher T. Veldkamp
- Department of Chemistry, University of Wisconsin Whitewater, Whitewater, Wisconsin 53190, United States,Corresponding authors: Brian F. Volkman, , Christopher T. Veldkamp, , Yu Chen,
| | - Yu Chen
- Department of Molecular Medicine, University of South Florida Morsani College of Medicine, 12901 Bruce B. Downs Blvd., Tampa, Florida 33612, United States,Corresponding authors: Brian F. Volkman, , Christopher T. Veldkamp, , Yu Chen,
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18
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Evolution of CCR5 and CCR2 Genes in Bats Showed Multiple Independent Gene Conversion Events. Viruses 2022; 14:v14020169. [PMID: 35215768 PMCID: PMC8877049 DOI: 10.3390/v14020169] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Revised: 01/12/2022] [Accepted: 01/15/2022] [Indexed: 11/16/2022] Open
Abstract
Chemokine receptors are an important determinant for the infectiousness of different pathogens, which are able to target the host cells by binding to the extracellular domains of these proteins. This is the mechanism of infection of HIV-1, among other concerning human diseases. Over the past years, it has been shown that two chemokine receptors, CCR2 and CCR5, have been shaped by events of gene conversion in different mammalian lineages, which has been linked to a possible selective advantage against pathogens. Here, by taking advantage of available bat genomes, we present the first insight of CCR2 and CCR5 evolution within the Chiroptera order. In total, four independent events of recombination between CCR2 and CCR5 were detected: two in a single species, Miniopterus natalensis; one in two species from the Rhinolophoidea superfamily; and one in four species from the Pteropodidae family. The regions affected by the gene conversions were generally extensive and always encompassed extracellular domains. Overall, we demonstrate that CCR2 and CCR5 have been subject to extensive gene conversion in multiple species of bats. Considering that bats are known to be large reservoirs of virus in nature, these results might indicate that chimeric CCR2-CCR5 genes might grant some bat species a selective advantage against viruses that rely in the extracellular portions of either CCR2 or CCR5 as gateways into the cell.
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19
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Moseri A, Akabayov SR, Cohen LS, Naider F, Anglister J. Multiple binding modes of an N-terminal CCR5-peptide in complex with HIV-1 gp120. FEBS J 2021; 289:3132-3147. [PMID: 34921512 DOI: 10.1111/febs.16328] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Revised: 10/09/2021] [Accepted: 12/16/2021] [Indexed: 11/26/2022]
Abstract
The N-terminal segment of CCR5 contains four tyrosine residues, sulphation of two of which is essential for high-affinity binding to gp120. In the present study, the interactions of gp120YU2 with a 27-residue N-terminal CCR5 peptide sulphated at position Y10 and Y14, i.e. Nt-CCR5, were studied using 13 C-edited-HMQC methyl-NOESY [1 H(13 C)-1 H], combined with transferred NOE NMR spectroscopy. A large number of pairwise interactions were observed between the methyl protons of methionine, threonine, valine and isoleucine residues of gp120, and the aromatic tyrosine-protons of Nt-CCR5. M434, V120 and V200 of gp120 were found to interact with all four tyrosine residues, Y3, sY10, sY14 and Y15. Particularly intriguing was the observation that Y3 and Y15 interact with the same gp120 methyl protons. Such interactions cannot be explained by the single cryo-EM structure of gp120/CD4/CCR5 complex published recently (Nature, 565, 318-323, 2019). Rather, they are consistent with the existence of a dynamic equilibrium involving two or more binding modes of Nt-CCR5 to gp120. These different modes of binding can coexist because the surface of gp120 contains two sites that can optimally interact with a sulphated tyrosine residue and two sites that can interact favorably with a non-sulphated tyrosine residue. Modelling of gp120YU2 complexed with the Nt-CCR5 peptide or with the entire CCR5 receptor provides an explanation for the NMR observations and the existence of these different binding modes of the disordered N-terminus of CCR5. The data presented extend our understanding of the two-step model and suggest a more variable binding mode of Nt-CCR5 with gp120.
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Affiliation(s)
- Adi Moseri
- Department of Chemical and Structural Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Sabine R Akabayov
- Department of Chemical and Structural Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Leah S Cohen
- Department of Chemistry and Macromolecular Assembly Institute, College of Staten Island of the City University of New York, Staten Island, NY, USA.,The Graduate Center of the City University of New York, NY, USA
| | - Fred Naider
- Department of Chemistry and Macromolecular Assembly Institute, College of Staten Island of the City University of New York, Staten Island, NY, USA.,The Graduate Center of the City University of New York, NY, USA
| | - Jacob Anglister
- Department of Chemical and Structural Biology, Weizmann Institute of Science, Rehovot, Israel
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20
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Cunningham O, Scott M, Zhou ZS, Finlay WJJ. Polyreactivity and polyspecificity in therapeutic antibody development: risk factors for failure in preclinical and clinical development campaigns. MAbs 2021; 13:1999195. [PMID: 34780320 PMCID: PMC8726659 DOI: 10.1080/19420862.2021.1999195] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Antibody-based drugs, which now represent the dominant biologic therapeutic modality, are used to modulate disparate signaling pathways across diverse disease indications. One fundamental premise that has driven this therapeutic antibody revolution is the belief that each monoclonal antibody exhibits exquisitely specific binding to a single-drug target. Herein, we review emerging evidence in antibody off-target binding and relate current key findings to the risk of failure in therapeutic development. We further summarize the current state of understanding of structural mechanisms underpining the different phenomena that may drive polyreactivity and polyspecificity, and highlight current thinking on how de-risking studies may be best implemented in the screening triage. We conclude with a summary of what we believe to be key observations in the field to date, and a call for the wider antibody research community to work together to build the tools needed to maximize our understanding in this nascent area.
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Affiliation(s)
| | - Martin Scott
- Department of Biopharm Discovery, GlaxoSmithKline Research & Development, Hertfordshire, UK
| | - Zhaohui Sunny Zhou
- Department of Chemistry and Chemical Biology, Barnett Institute for Chemical and Biological Analysis, Northeastern University, Boston, Massachusetts, USA
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21
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Aptamers in Virology-A Consolidated Review of the Most Recent Advancements in Diagnosis and Therapy. Pharmaceutics 2021; 13:pharmaceutics13101646. [PMID: 34683938 PMCID: PMC8540715 DOI: 10.3390/pharmaceutics13101646] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Revised: 09/28/2021] [Accepted: 10/01/2021] [Indexed: 01/05/2023] Open
Abstract
The use of short oligonucleotide or peptide molecules as target-specific aptamers has recently garnered substantial attention in the field of the detection and treatment of viral infections. Based on their high affinity and high specificity to desired targets, their use is on the rise to replace antibodies for the detection of viruses and viral antigens. Furthermore, aptamers inhibit intracellular viral transcription and translation, in addition to restricting viral entry into host cells. This has opened up a plethora of new targets for the research and development of novel vaccines against viruses. Here, we discuss the advances made in aptamer technology for viral diagnosis and therapy in the past decade.
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22
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Mueller S. Rarely Recognized Antibody Diversification in Covid-19 Evolution to Counteract Advanced SARS-CoV-2 Evasion Strategies, and Implications for Prophylactic Treatment. Front Physiol 2021; 12:624675. [PMID: 34413782 PMCID: PMC8369989 DOI: 10.3389/fphys.2021.624675] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2020] [Accepted: 07/06/2021] [Indexed: 11/13/2022] Open
Abstract
The ongoing Covid-19 pandemic underscores the importance of finding effective and safe ways to combat the virus, and to optimally understand the immune response elicited upon natural infection. This likely involves all components of the immune system, both innate and adaptive. The impetus for the rapid development of prophylactic treatment options has led to an intense focus on neutralizing antibodies (Abs), and many novel and specialized platforms have been designed to achieve that goal. B-cell immunity relies on the generation of a diverse repertoire of Abs. Their structural variation is defined in terms of amino acid composition that is encoded in the genome or acquired through somatic mutations. Yet, key examples of frequently neglected antibody diversification mechanisms involving post-translational modifications such as N- or O-linked glycosylation are present in significant portions of the population. During the last few years, these and other beyond gene sequence determined humoral immune response mechanisms have in some specific cases revealed their potent immunomodulatory effects. Nonetheless, such more unusual mechanisms have not received much attention in the context of SARS-CoV-2. Thus, with specific focus on the latter, this paper presents, (1) the rationale for considering beyond sequence determined strategies, (2) evidence for their possible involvement in Covid-19 disease evolution, (3) consequences for vaccine design exemplified by one of the vaccine candidates that is currently undergoing trial, and (4) more general implications. Based on a critical interpretation of published literature, the hypotheses developed in this study point to a crucial role of non-genetic antibody diversification mechanisms in disease evolution to counteract unique immunogenicity determinants of SARS-CoV-2 infection. The involvement of post translational mechanisms may also help explain the widely varied immune response observed, not only among different patient groups, but also in terms of their observed incompatibility with SARS-CoV-2 infection in several human cell types. The article highlights potentials and challenges of these refined humoral immune response mechanisms to most optimally target non-genetic viral evasion strategies.
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Species-Specific Valid Ternary Interactions of HIV-1 Env-gp120, CD4, and CCR5 as Revealed by an Adaptive Single-Amino Acid Substitution at the V3 Loop Tip. J Virol 2021; 95:e0217720. [PMID: 33883222 DOI: 10.1128/jvi.02177-20] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Molecular interactions of the variable envelope gp120 subunit of HIV-1 with two cellular receptors are the first step of viral infection, thereby playing pivotal roles in determining viral infectivity and cell tropism. However, the underlying regulatory mechanisms for interactions under gp120 spontaneous variations largely remain unknown. Here, we show an allosteric mechanism in which a single gp120 mutation remotely controls the ternary interactions between gp120 and its receptors for the switch of viral cell tropism. Virological analyses showed that a G310R substitution at the tip of the gp120 V3 loop selectively abolished the viral replication ability in human cells, despite evoking enhancement of viral replication in macaque cells. Molecular dynamics (MD) simulations predicted that the G310R substitution at a site away from the CD4 interaction site selectively impeded the binding ability of gp120 to human CD4. Consistently, virions with the G310R substitution exhibited a reduced binding ability to human lymphocyte cells. Furthermore, the G310R substitution influenced the gp120-CCR5 interaction in a CCR5-type dependent manner as assessed by MD simulations and an infectivity assay using exogenously expressed CCR5s. Interestingly, an I198M mutation in human CCR5 restored the infectivity of the G310R virus in human cells. Finally, MD simulation predicted amino acid interplays that physically connect the V3 loop and gp120 elements for the CD4 and CCR5 interactions. Collectively, these results suggest that the V3 loop tip is a cis-allosteric regulator that remotely controls intra- and intermolecular interactions of HIV-1 gp120 for balancing ternary interactions with CD4 and CCR5. IMPORTANCE Understanding the molecular bases for viral entry into cells will lead to the elucidation of one of the major viral survival strategies, and thus to the development of new effective antiviral measures. As shown recently, HIV-1 is highly mutable and adaptable in growth-restrictive cells, such as those of macaque origin. HIV-1 initiates its infection by sequential interactions of Env-gp120 with two cell surface receptors, CD4 and CCR5. A recent epoch-making structural study has disclosed that CD4-induced conformation of gp120 is stabilized upon binding of CCR5 to the CD4-gp120 complex, whereas the biological significance of this remains totally unknown. Here, from a series of mutations found in our extensive studies, we identified a single-amino acid adaptive mutation at the V3 loop tip of Env-gp120 critical for its interaction with both CD4 and CCR5 in a host cell species-specific way. This remarkable finding could certainly provoke and accelerate studies to precisely clarify the HIV-1 entry mechanism.
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Cortés A, Coral J, McLachlan C, Corredor JAG, Benítez R. Molecular transduction in receptor-ligand systems by planar electromagnetic fields. BRAZ J BIOL 2021; 82:e232525. [PMID: 34076160 DOI: 10.1590/1519-6984.232525] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2019] [Accepted: 09/26/2020] [Indexed: 11/22/2022] Open
Abstract
The coupling of a ligand with a molecular receptor induces a signal that travels through the receptor, reaching the internal domain and triggering a response cascade. In previous work on T-cell receptors and their coupling with foreign antigens, we observed the presence of planar molecular patterns able to generate electromagnetic fields within the proteins. These planes showed a coherent (synchronized) behavior, replicating immediately in the intracellular domain that which occurred in the extracellular domain as the ligand was coupled. In the present study, we examined this molecular transduction - the capacity of the coupling signal to penetrate deep inside the receptor molecule and induce a response. We verified the presence of synchronized behavior in diverse receptor-ligand systems. To appreciate this diversity, we present four biochemically different systems - TCR-peptide, calcium pump-ADP, haemoglobin-oxygen, and gp120-CD4 viral coupling. The confirmation of synchronized molecular transduction in each of these systems suggests that the proposed mechanism would occur in all biochemical receptor-ligand systems.
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Affiliation(s)
- A Cortés
- Department of Molecular Physics, Synthetic Vaccine and New Drug Research Institute - IVSI, Popayán, Colombia
| | - J Coral
- Department of Molecular Physics, Synthetic Vaccine and New Drug Research Institute - IVSI, Popayán, Colombia
| | - C McLachlan
- Department of Molecular Physics, Synthetic Vaccine and New Drug Research Institute - IVSI, Popayán, Colombia
| | - J A G Corredor
- Chemistry Department, Universidad del Cauca, Popayán, Colombia
| | - R Benítez
- Chemistry Department, Chemical of Natural Products group, Universidad del Cauca, Popayán, Colombia
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Magar R, Yadav P, Barati Farimani A. Potential neutralizing antibodies discovered for novel corona virus using machine learning. Sci Rep 2021; 11:5261. [PMID: 33664393 PMCID: PMC7970853 DOI: 10.1038/s41598-021-84637-4] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Accepted: 02/17/2021] [Indexed: 02/07/2023] Open
Abstract
The fast and untraceable virus mutations take lives of thousands of people before the immune system can produce the inhibitory antibody. The recent outbreak of COVID-19 infected and killed thousands of people in the world. Rapid methods in finding peptides or antibody sequences that can inhibit the viral epitopes of SARS-CoV-2 will save the life of thousands. To predict neutralizing antibodies for SARS-CoV-2 in a high-throughput manner, in this paper, we use different machine learning (ML) model to predict the possible inhibitory synthetic antibodies for SARS-CoV-2. We collected 1933 virus-antibody sequences and their clinical patient neutralization response and trained an ML model to predict the antibody response. Using graph featurization with variety of ML methods, like XGBoost, Random Forest, Multilayered Perceptron, Support Vector Machine and Logistic Regression, we screened thousands of hypothetical antibody sequences and found nine stable antibodies that potentially inhibit SARS-CoV-2. We combined bioinformatics, structural biology, and Molecular Dynamics (MD) simulations to verify the stability of the candidate antibodies that can inhibit SARS-CoV-2.
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Affiliation(s)
- Rishikesh Magar
- Department of Mechanical Engineering, Carnegie Mellon University, Pittsburgh, PA, 15213, USA
| | - Prakarsh Yadav
- Department of Biomedical Engineering, Carnegie Mellon University, Pittsburgh, PA, 15213, USA
| | - Amir Barati Farimani
- Department of Mechanical Engineering, Carnegie Mellon University, Pittsburgh, PA, 15213, USA.
- Department of Biomedical Engineering, Carnegie Mellon University, Pittsburgh, PA, 15213, USA.
- Machine Learning Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA, 15213, USA.
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Magar R, Yadav P, Barati Farimani A. Potential neutralizing antibodies discovered for novel corona virus using machine learning. Sci Rep 2021; 11:5261. [PMID: 33664393 DOI: 10.1101/2020.03.14.992156] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Accepted: 02/17/2021] [Indexed: 05/22/2023] Open
Abstract
The fast and untraceable virus mutations take lives of thousands of people before the immune system can produce the inhibitory antibody. The recent outbreak of COVID-19 infected and killed thousands of people in the world. Rapid methods in finding peptides or antibody sequences that can inhibit the viral epitopes of SARS-CoV-2 will save the life of thousands. To predict neutralizing antibodies for SARS-CoV-2 in a high-throughput manner, in this paper, we use different machine learning (ML) model to predict the possible inhibitory synthetic antibodies for SARS-CoV-2. We collected 1933 virus-antibody sequences and their clinical patient neutralization response and trained an ML model to predict the antibody response. Using graph featurization with variety of ML methods, like XGBoost, Random Forest, Multilayered Perceptron, Support Vector Machine and Logistic Regression, we screened thousands of hypothetical antibody sequences and found nine stable antibodies that potentially inhibit SARS-CoV-2. We combined bioinformatics, structural biology, and Molecular Dynamics (MD) simulations to verify the stability of the candidate antibodies that can inhibit SARS-CoV-2.
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Affiliation(s)
- Rishikesh Magar
- Department of Mechanical Engineering, Carnegie Mellon University, Pittsburgh, PA, 15213, USA
| | - Prakarsh Yadav
- Department of Biomedical Engineering, Carnegie Mellon University, Pittsburgh, PA, 15213, USA
| | - Amir Barati Farimani
- Department of Mechanical Engineering, Carnegie Mellon University, Pittsburgh, PA, 15213, USA.
- Department of Biomedical Engineering, Carnegie Mellon University, Pittsburgh, PA, 15213, USA.
- Machine Learning Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA, 15213, USA.
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Serra PA, Taveira N, Guedes RC. Computational Modulation of the V3 Region of Glycoprotein gp125 of HIV-2. Int J Mol Sci 2021; 22:1948. [PMID: 33669351 PMCID: PMC7920276 DOI: 10.3390/ijms22041948] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Revised: 02/10/2021] [Accepted: 02/13/2021] [Indexed: 12/03/2022] Open
Abstract
HIV-2 infection is frequently neglected in HIV/AIDS campaigns. However, a special emphasis must be given to HIV-2 as an untreated infection that also leads to AIDS and death, and for which the efficacy of most available drugs is limited against HIV-2. HIV envelope glycoproteins mediate binding to the receptor CD4 and co-receptors at the surface of the target cell, enabling fusion with the cell membrane and viral entry. Here, we developed and optimized a computer-assisted drug design approach of an important HIV-2 glycoprotein that allows us to explore and gain further insights at the molecular level into protein structures and interactions crucial for the inhibition of HIV-2 cell entry. The 3D structure of a key HIV-2ROD gp125 region was generated by a homology modeling campaign. To disclose the importance of the main structural features and compare them with experimental results, 3D-models of six mutants were also generated. These mutations revealed the selective impact on the behavior of the protein. Furthermore, molecular dynamics simulations were performed to optimize the models, and the dynamic behavior was tackled to account for structure flexibility and interactions network formation. Structurally, the mutations studied lead to a loss of aromatic features, which is very important for the establishment of π-π interactions and could induce a structural preference by a specific coreceptor. These new insights into the structure-function relationship of HIV-2 gp125 V3 and surrounding regions will help in the design of better models and the design of new small molecules capable to inhibit the attachment and binding of HIV with host cells.
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Affiliation(s)
- Patrícia A. Serra
- Department of Pharmaceutical Sciences and Medicines and Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa, Avenida Professor Gama Pinto, 1649-003 Lisboa, Portugal;
| | - Nuno Taveira
- Department of Pharmaceutical Sciences and Medicines and Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa, Avenida Professor Gama Pinto, 1649-003 Lisboa, Portugal;
- Centro de Investigação Interdisciplinar Egas Moniz (CiiEM), Instituto Universitário Egas Moniz, Monte de Caparica, 2829-511 Caparica, Portugal
| | - Rita C. Guedes
- Department of Pharmaceutical Sciences and Medicines and Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa, Avenida Professor Gama Pinto, 1649-003 Lisboa, Portugal;
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28
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He S, Wu Y. Relationships Between HIV-Mediated Chemokine Coreceptor Signaling, Cofilin Hyperactivation, Viral Tropism Switch and HIV-Mediated CD4 Depletion. Curr HIV Res 2021; 17:388-396. [PMID: 31702526 DOI: 10.2174/1570162x17666191106112018] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2019] [Revised: 10/27/2019] [Accepted: 10/31/2019] [Indexed: 11/22/2022]
Abstract
HIV infection causes CD4 depletion and immune deficiency. The virus infects CD4 T cells through binding to CD4 and one of the chemokine coreceptors, CXCR4 (X4) or CCR5 (R5). It has also been known that HIV tropism switch, from R5 to X4, is associated with rapid CD4 depletion, suggesting a key role of viral factors in driving CD4 depletion. However, the virological driver for HIV-mediated CD4 depletion has not been fully elucidated. We hypothesized that HIV-mediated chemokine coreceptor signaling, particularly chronic signaling through CXCR4, plays a major role in CD4 dysfunction and depletion; we also hypothesized that there is an R5X4 signaling (R5X4sig) viral subspecies, evolving from the natural replication course of R5-utilizing viruses, that is responsible for CD4 T cell depletion in R5 virus infection. To gain traction for our hypothesis, in this review, we discuss a recent finding from Cui and co-authors who described the rapid tropism switch and high pathogenicity of an HIV-1 R5 virus, CRF01_AE. We speculate that CRF01_AE may be the hypothetical R5X4sig viral species that is rapidly evolving towards the X4 phenotype. We also attempt to discuss the intricate relationships between HIV-mediated chemokine coreceptor signaling, viral tropism switch and HIV-mediated CD4 depletion, in hopes of providing a deeper understanding of HIV pathogenesis in blood CD4 T cells.
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Affiliation(s)
- Sijia He
- National Center for Biodefense and Infectious Diseases, School of Systems Biology, George Mason University, Manassas, Virginia, United States
| | - Yuntao Wu
- National Center for Biodefense and Infectious Diseases, School of Systems Biology, George Mason University, Manassas, Virginia, United States
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29
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Retroviral Restriction Factors and Their Viral Targets: Restriction Strategies and Evolutionary Adaptations. Microorganisms 2020; 8:microorganisms8121965. [PMID: 33322320 PMCID: PMC7764263 DOI: 10.3390/microorganisms8121965] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Revised: 11/30/2020] [Accepted: 12/08/2020] [Indexed: 12/17/2022] Open
Abstract
The evolutionary conflict between retroviruses and their vertebrate hosts over millions of years has led to the emergence of cellular innate immune proteins termed restriction factors as well as their viral antagonists. Evidence accumulated in the last two decades has substantially increased our understanding of the elaborate mechanisms utilized by these restriction factors to inhibit retroviral replication, mechanisms that either directly block viral proteins or interfere with the cellular pathways hijacked by the viruses. Analyses of these complex interactions describe patterns of accelerated evolution for these restriction factors as well as the acquisition and evolution of their virus-encoded antagonists. Evidence is also mounting that many restriction factors identified for their inhibition of specific retroviruses have broader antiviral activity against additional retroviruses as well as against other viruses, and that exposure to these multiple virus challenges has shaped their adaptive evolution. In this review, we provide an overview of the restriction factors that interfere with different steps of the retroviral life cycle, describing their mechanisms of action, adaptive evolution, viral targets and the viral antagonists that evolved to counter these factors.
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Tolbert WD, Sherburn R, Gohain N, Ding S, Flinko R, Orlandi C, Ray K, Finzi A, Lewis GK, Pazgier M. Defining rules governing recognition and Fc-mediated effector functions to the HIV-1 co-receptor binding site. BMC Biol 2020; 18:91. [PMID: 32693837 PMCID: PMC7374964 DOI: 10.1186/s12915-020-00819-y] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Accepted: 06/22/2020] [Indexed: 01/14/2023] Open
Abstract
BACKGROUND The binding of HIV-1 Envelope glycoproteins (Env) to host receptor CD4 exposes vulnerable conserved epitopes within the co-receptor binding site (CoRBS) which are required for the engagement of either CCR5 or CXCR4 co-receptor to allow HIV-1 entry. Antibodies against this region have been implicated in the protection against HIV acquisition in non-human primate (NHP) challenge studies and found to act synergistically with antibodies of other specificities to deliver effective Fc-mediated effector function against HIV-1-infected cells. Here, we describe the structure and function of N12-i2, an antibody isolated from an HIV-1-infected individual, and show how the unique structural features of this antibody allow for its effective Env recognition and Fc-mediated effector function. RESULTS N12-i2 binds within the CoRBS utilizing two adjacent sulfo-tyrosines (TYS) for binding, one of which binds to a previously unknown TYS binding pocket formed by gp120 residues of high sequence conservation among HIV-1 strains. Structural alignment with gp120 in complex with the co-receptor CCR5 indicates that the new pocket corresponds to TYS at position 15 of CCR5. In addition, structure-function analysis of N12-i2 and other CoRBS-specific antibodies indicates a link between modes of antibody binding within the CoRBS and Fc-mediated effector activities. The efficiency of antibody-dependent cellular cytotoxicity (ADCC) correlated with both the level of antibody binding and the mode of antibody attachment to the epitope region, specifically with the way the Fc region was oriented relative to the target cell surface. Antibodies with poor Fc access mediated the poorest ADCC whereas those with their Fc region readily accessible for interaction with effector cells mediated the most potent ADCC. CONCLUSION Our data identify a previously unknown binding site for TYS within the assembled CoRBS of the HIV-1 virus. In addition, our combined structural-modeling-functional analyses provide new insights into mechanisms of Fc-effector function of antibodies against HIV-1, in particular, how antibody binding to Env antigen affects the efficiency of ADCC response.
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Affiliation(s)
- William D Tolbert
- Infectious Disease Division, Department of Medicine, Uniformed Services University of the Health Sciences, 4301 Jones Bridge Road, Bethesda, MD, 20814-4712, USA
- Division of Vaccine Research of Institute of Human Virology, University of Maryland School of Medicine, Baltimore, USA
| | - Rebekah Sherburn
- Infectious Disease Division, Department of Medicine, Uniformed Services University of the Health Sciences, 4301 Jones Bridge Road, Bethesda, MD, 20814-4712, USA
- Division of Vaccine Research of Institute of Human Virology, University of Maryland School of Medicine, Baltimore, USA
| | - Neelakshi Gohain
- Division of Vaccine Research of Institute of Human Virology, University of Maryland School of Medicine, Baltimore, USA
| | - Shilei Ding
- Centre de Recherche du CHUM, Université de Montréal, Montreal, Quebec, Canada
- Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montreal, Quebec, Canada
| | - Robin Flinko
- Division of Vaccine Research of Institute of Human Virology, University of Maryland School of Medicine, Baltimore, USA
| | - Chiara Orlandi
- Division of Vaccine Research of Institute of Human Virology, University of Maryland School of Medicine, Baltimore, USA
| | - Krishanu Ray
- Infectious Disease Division, Department of Medicine, Uniformed Services University of the Health Sciences, 4301 Jones Bridge Road, Bethesda, MD, 20814-4712, USA
| | - Andrés Finzi
- Centre de Recherche du CHUM, Université de Montréal, Montreal, Quebec, Canada
- Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montreal, Quebec, Canada
- Department of Microbiology and Immunology, McGill University, Montreal, Quebec, Canada
| | - George K Lewis
- Division of Vaccine Research of Institute of Human Virology, University of Maryland School of Medicine, Baltimore, USA
| | - Marzena Pazgier
- Infectious Disease Division, Department of Medicine, Uniformed Services University of the Health Sciences, 4301 Jones Bridge Road, Bethesda, MD, 20814-4712, USA.
- Division of Vaccine Research of Institute of Human Virology, University of Maryland School of Medicine, Baltimore, USA.
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Hajduczki A, Danielson DT, Elias DS, Bundoc V, Scanlan AW, Berger EA. A Trispecific Anti-HIV Chimeric Antigen Receptor Containing the CCR5 N-Terminal Region. Front Cell Infect Microbiol 2020; 10:242. [PMID: 32523897 PMCID: PMC7261873 DOI: 10.3389/fcimb.2020.00242] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2020] [Accepted: 04/27/2020] [Indexed: 01/24/2023] Open
Abstract
Anti-HIV chimeric antigen receptors (CARs) promote direct killing of infected cells, thus offering a therapeutic approach aimed at durable suppression of infection emerging from viral reservoirs. CD4-based CARs represent a favored option, since they target the essential conserved primary receptor binding site on the HIV envelope glycoprotein (Env). We have previously shown that adding a second Env-binding moiety, such as the carbohydrate recognition domain of human mannose-binding lectin (MBL) that recognizes the highly conserved oligomannose patch on gp120, increases CAR potency in an in vitro HIV suppression assay; moreover it reduces the undesired capacity for the CD4 of the CAR molecule to act as an entry receptor, thereby rendering CAR-expressing CD8+ T cells susceptible to infection. Here, we further improve the bispecific CD4-MBL CAR by adding a third targeting moiety against a distinct conserved Env determinant, i.e. a polypeptide sequence derived from the N-terminus of the HIV coreceptor CCR5. The trispecific CD4-MBL-R5Nt CAR displays enhanced in vitro anti-HIV potency compared to the CD4-MBL CAR, as well as undetectable HIV entry receptor activity. The high anti-HIV potency of the CD4-MBL-R5Nt CAR, coupled with its all-human composition and absence of immunogenic variable regions associated with antibody-based CARs, offer promise for the trispecific construct in therapeutic approaches seeking durable drug-free HIV remission.
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Affiliation(s)
- Agnes Hajduczki
- Laboratory of Viral Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States
| | - David T Danielson
- Laboratory of Viral Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States
| | - David S Elias
- Laboratory of Viral Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States
| | - Virgilio Bundoc
- Laboratory of Viral Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States
| | - Aaron W Scanlan
- Laboratory of Viral Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States
| | - Edward A Berger
- Laboratory of Viral Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States
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32
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Da LT, Lin M. Opening dynamics of HIV-1 gp120 upon receptor binding is dictated by a key hydrophobic core. Phys Chem Chem Phys 2019; 21:26003-26016. [PMID: 31764922 DOI: 10.1039/c9cp04613e] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
HIV-1 entry is mediated firstly by the molecular recognition between the viral glycoprotein gp120 and its receptor CD4 on host T-cells. As a key antigen that can be targeted by neutralizing antibodies, gp120 has been a focus for extensive studies with efforts to understand its structural properties and conformational dynamics upon receptor binding. An atomistic-level revelation of gp120 opening dynamics activated by CD4, however, is still unknown. Here, by constructing a Markov State Model (MSM) based on hundreds of Molecular Dynamics (MD) simulations with an aggregated simulation time of ∼20 microseconds (μs), we identify the key metastable states of gp120 during its opening dynamics upon CD4 binding. The MSM provides a clear dynamic model whereby the identified metastable states coexist and can reach an equilibrium. More importantly, a hydrophobic core flanked by variable loops (V1V2 and V3) and the β20/21 region plays an essential role in triggering the gp120 opening. Any destabilizing effects introduced into the hydrophobic core, therefore, can be expected to promote transition of gp120 to an open state. Moreover, the variable loops demonstrate high flexibilities in fully open gp120. In particular, the V3 region is capable of exploring both closed and open conformations, even with the V1/V2 loops largely adopting an open form. In addition, the bridging sheet formation in gp120 is likely induced by the incoming co-receptor/antibody recognitions, since the V1/V2 structure is highly heterogeneous so that the bridging-sheet formed conformation is not the most populated state. Our studies provide deep insights into the dynamic features of gp120 and its molecular recognitions to the broadly neutralizing antibodies, which guides future attempts to design more effective gp120 immunogens.
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Affiliation(s)
- Lin-Tai Da
- Key Laboratory of System Biomedicine (Ministry of Education), Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China.
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33
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Yang Z, Wang H, Liu AZ, Gristick HB, Bjorkman PJ. Asymmetric opening of HIV-1 Env bound to CD4 and a coreceptor-mimicking antibody. Nat Struct Mol Biol 2019; 26:1167-1175. [PMID: 31792452 PMCID: PMC6899201 DOI: 10.1038/s41594-019-0344-5] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2019] [Accepted: 10/29/2019] [Indexed: 11/09/2022]
Abstract
The human immunodeficiency virus (HIV-1) envelope (Env) glycoprotein, a (gp120-gp41)3 trimer, mediates fusion of viral and host cell membranes after gp120 binding to host receptor CD4. Receptor binding triggers conformational changes allowing coreceptor (CCR5) recognition through CCR5's tyrosine-sulfated amino (N) terminus, release of the gp41 fusion peptide and fusion. We present 3.3 Å and 3.5 Å cryo-EM structures of E51, a tyrosine-sulfated coreceptor-mimicking antibody, complexed with a CD4-bound open HIV-1 native-like Env trimer. Two classes of asymmetric Env interact with E51, revealing tyrosine-sulfated interactions with gp120 mimicking CCR5 interactions, and two conformations of gp120-gp41 protomers (A and B protomers in AAB and ABB trimers) that differ in their degree of CD4-induced trimer opening and induction of changes to the fusion peptide. By integrating the new structural information with previous closed and open envelope trimer structures, we modeled the order of conformational changes on the path to coreceptor binding site exposure and subsequent viral-host cell membrane fusion.
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Affiliation(s)
- Zhi Yang
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena CA, USA
| | - Haoqing Wang
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena CA, USA.,Molecular and Cellular Physiology, Stanford University, Stanford, CA, USA
| | - Albert Z Liu
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena CA, USA.,Biochemistry, Cellular, and Molecular Biology Graduate Program, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Harry B Gristick
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena CA, USA
| | - Pamela J Bjorkman
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena CA, USA.
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Suttisintong K, Kaewchangwat N, Thanayupong E, Nerungsi C, Srikun O, Pungpo P. Recent Progress in the Development of HIV-1 Entry Inhibitors: From Small Molecules to Potent Anti-HIV Agents. Curr Top Med Chem 2019; 19:1599-1620. [DOI: 10.2174/1568026619666190712204050] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2019] [Revised: 06/07/2019] [Accepted: 06/21/2019] [Indexed: 01/21/2023]
Abstract
Viral entry, the first process in the reproduction of viruses, primarily involves attachment of the viral envelope proteins to membranes of the host cell. The crucial components that play an important role in viral entry include viral surface glycoprotein gp120, viral transmembrane glycoprotein gp41, host cell glycoprotein (CD4), and host cell chemokine receptors (CCR5 and CXCR4). Inhibition of the multiple molecular interactions of these components can restrain viruses, such as HIV-1, from fusion with the host cell, blocking them from reproducing. This review article specifically focuses on the recent progress in the development of small-molecule HIV-1 entry inhibitors and incorporates important aspects of their structural modification that lead to the discovery of new molecular scaffolds with more potency.
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Affiliation(s)
- Khomson Suttisintong
- National Nanotechnology Center (NANOTEC), National Science and Technology, Development Agency (NSTDA), 111 Thailand Science Park, Phahonyothin Road, Khlong Nueng, Khlong Luang, Pathum Thani 12120, Thailand
| | - Narongpol Kaewchangwat
- National Nanotechnology Center (NANOTEC), National Science and Technology, Development Agency (NSTDA), 111 Thailand Science Park, Phahonyothin Road, Khlong Nueng, Khlong Luang, Pathum Thani 12120, Thailand
| | - Eknarin Thanayupong
- National Nanotechnology Center (NANOTEC), National Science and Technology, Development Agency (NSTDA), 111 Thailand Science Park, Phahonyothin Road, Khlong Nueng, Khlong Luang, Pathum Thani 12120, Thailand
| | - Chakkrapan Nerungsi
- The Government Pharmaceutical Organization, 75/1 Rama VI Road, Ratchathewi, Bangkok 10400, Thailand
| | - Onsiri Srikun
- The Government Pharmaceutical Organization, 75/1 Rama VI Road, Ratchathewi, Bangkok 10400, Thailand
| | - Pornpan Pungpo
- Department of Chemistry, Faculty of Science, Ubon Ratchathani University, 85 Sathonlamark Road, Warinchamrap, Ubon Ratchathani 34190, Thailand
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Fellinger CH, Gardner MR, Weber JA, Alfant B, Zhou AS, Farzan M. eCD4-Ig Limits HIV-1 Escape More Effectively than CD4-Ig or a Broadly Neutralizing Antibody. J Virol 2019; 93:e00443-19. [PMID: 31068428 PMCID: PMC6600210 DOI: 10.1128/jvi.00443-19] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2019] [Accepted: 04/23/2019] [Indexed: 01/30/2023] Open
Abstract
The engineered antibody-like entry inhibitor eCD4-Ig neutralizes every human immunodeficiency virus type 1 (HIV-1), HIV-2, and simian immunodeficiency virus isolate it has been tested against. The exceptional breadth of eCD4-Ig derives from its ability to closely and simultaneously emulate the HIV-1 receptor CD4 and coreceptors, either CCR5 or CXCR4. Here we investigated whether viral escape from eCD4-Ig is more difficult than that from CD4-Ig or the CD4-binding site antibody NIH45-46. We observed that a viral swarm selected with high concentrations of eCD4-Ig was increasingly resistant to but did not fully escape from eCD4-Ig. In contrast, viruses selected under the same conditions with CD4-Ig or NIH45-46 fully escaped from those inhibitors. eCD4-Ig-resistant viruses acquired unique changes in the V2 apex, V3, V4, and CD4-binding regions of the HIV-1 envelope glycoprotein (Env). Most of the alterations did not directly affect neutralization by eCD4-Ig or neutralizing antibodies. However, alteration of Q428 to an arginine or lysine resulted in markedly greater resistance to eCD4-Ig and CD4-Ig, with correspondingly dramatic losses in infectivity and greater sensitivity to a V3 antibody and to serum from an infected individual. Compensatory mutations in the V3 loop (N301D) and in the V2 apex (K171E) partially restored viral fitness without affecting serum or eCD4-Ig sensitivity. Collectively, these data suggest that multiple mutations will be necessary to fully escape eCD4-Ig without loss of viral fitness.IMPORTANCE HIV-1 broadly neutralizing antibodies (bNAbs) and engineered antibody-like inhibitors have been compared for their breadths, potencies, and in vivo half-lives. However, a key limitation in the use of antibodies to treat an established HIV-1 infection is the rapid emergence of fully resistant viruses. Entry inhibitors of similar breadths and potencies can differ in the ease with which viral escape variants arise. Here we show that HIV-1 escape from the potent and exceptionally broad entry inhibitor eCD4-Ig is more difficult than that from CD4-Ig or the bNAb NIH45-46. Indeed, full escape was not observed under conditions under which escape from CD4-Ig or NIH45-46 was readily detected. Moreover, viruses that were partially resistant to eCD4-Ig were markedly less infective and more sensitive to antibodies in the serum of an infected person. These data suggest that eCD4-Ig will be more difficult to escape and that even partial escape will likely extract a high fitness cost.
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Affiliation(s)
- Christoph H Fellinger
- Department of Immunology and Microbiology, The Scripps Research Institute, Jupiter, Florida, USA
| | - Matthew R Gardner
- Department of Immunology and Microbiology, The Scripps Research Institute, Jupiter, Florida, USA
| | - Jesse A Weber
- Department of Immunology and Microbiology, The Scripps Research Institute, Jupiter, Florida, USA
| | - Barnett Alfant
- Department of Immunology and Microbiology, The Scripps Research Institute, Jupiter, Florida, USA
| | - Amber S Zhou
- Department of Immunology and Microbiology, The Scripps Research Institute, Jupiter, Florida, USA
| | - Michael Farzan
- Department of Immunology and Microbiology, The Scripps Research Institute, Jupiter, Florida, USA
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36
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Chen B. Molecular Mechanism of HIV-1 Entry. Trends Microbiol 2019; 27:878-891. [PMID: 31262533 DOI: 10.1016/j.tim.2019.06.002] [Citation(s) in RCA: 143] [Impact Index Per Article: 28.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2019] [Revised: 05/20/2019] [Accepted: 06/05/2019] [Indexed: 11/19/2022]
Abstract
HIV-1 envelope glycoprotein [Env; trimeric (gp160)3 cleaved to (gp120/gp41)3] attaches the virion to a susceptible cell and induces fusion of viral and cell membranes to initiate infection. It interacts with the primary receptor CD4 and coreceptor (e.g., chemokine receptor CCR5 or CXCR4) to allow viral entry by triggering large structural rearrangements and unleashing the fusogenic potential of gp41 to induce membrane fusion. Recent advances in structural biology of HIV-1 Env and its complexes with the cellular receptors have revealed molecular details of HIV-1 entry and yielded new mechanistic insights. In this review, I summarize our latest understanding of the HIV-1 membrane fusion process and discuss possible pathways for productive viral entry.
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Affiliation(s)
- Bing Chen
- Division of Molecular Medicine, Boston Children's Hospital, and Department of Pediatrics, Harvard Medical School, 3 Blackfan Street, Boston, MA 02115, USA.
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Conformational Engineering of HIV-1 Env Based on Mutational Tolerance in the CD4 and PG16 Bound States. J Virol 2019; 93:JVI.00219-19. [PMID: 30894475 DOI: 10.1128/jvi.00219-19] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2019] [Accepted: 03/16/2019] [Indexed: 12/22/2022] Open
Abstract
HIV-1 infection is initiated by viral Env engaging the host receptor CD4, triggering Env to transition from a "closed" to "open" conformation during the early events of virus-cell membrane fusion. To understand how Env sequence accommodates this conformational change, mutational landscapes decoupled from virus replication were determined for Env from BaL (clade B) and DU422 (clade C) isolates interacting with CD4 or antibody PG16 that preferentially recognizes closed trimers. Sequence features uniquely important to each bound state were identified, including glycosylation and binding sites. Notably, the Env apical domain and trimerization interface are under selective pressure for PG16 binding. Based on this key observation, mutations were found that increase presentation of quaternary epitopes associated with properly conformed trimers when Env is expressed at the plasma membrane. Many mutations reduce electrostatic repulsion at the Env apex and increase PG16 recognition of Env sequences from clades A and B. Other mutations increase hydrophobic packing at the gp120 inner-outer domain interface and were broadly applicable for engineering Env from diverse strains spanning tiers 1, 2, and 3 across clades A, B, C, and BC recombinants. Core mutations predicted to introduce steric strain in the open state show markedly reduced CD4 interactions. Finally, we demonstrate how our methodology can be adapted to interrogate interactions between membrane-associated Env and the matrix domain of Gag. These findings and methods may assist vaccine design.IMPORTANCE HIV-1 Env is dynamic and undergoes large conformational changes that drive fusion of virus and host cell membranes. Three Env proteins in a trimer contact each other at their apical tips to form a closed conformation that presents epitopes recognized by broadly neutralizing antibodies. The apical tips separate, among other changes, to form an open conformation that binds tightly to host receptors. Understanding how Env sequence facilitates these structural changes can inform the biophysical mechanism and aid immunogen design. Using deep mutational scans decoupled from virus replication, we report mutational landscapes for Env from two strains interacting with conformation-dependent binding proteins. Residues in the Env trimer interface and apical domains are preferentially conserved in the closed conformation, and conformational diversity is facilitated by electrostatic repulsion and an underpacked core between domains. Specific mutations are described that enhance presentation of the trimeric closed conformation across diverse HIV-1 strains.
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Zhang C, Huang LS, Zhu R, Meng Q, Zhu S, Xu Y, Zhang H, Fang X, Zhang X, Zhou J, Schooley RT, Yang X, Huang Z, An J. High affinity CXCR4 inhibitors generated by linking low affinity peptides. Eur J Med Chem 2019; 172:174-185. [PMID: 30978562 DOI: 10.1016/j.ejmech.2019.03.056] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2018] [Revised: 03/20/2019] [Accepted: 03/23/2019] [Indexed: 01/04/2023]
Abstract
G-protein coupled receptors (GPCRs) are implicated in many diseases and attractive targets for drug discovery. Peptide fragments derived from protein ligands of GPCRs are commonly used as probes of GPCR function and as leads for drug development. However, these peptide fragments lack the structural integrity of their parent full-length protein ligands and often show low receptor affinity, which limits their research and therapeutic values. It remains a challenge to efficiently generate high affinity peptide inhibitors of GPCRs. We have investigated a combinational approach involving the synthetic covalent linkage of two low affinity peptide fragments to determine if the strategy can yield high affinity GPCR inhibitors. We examined this design approach using the chemokine receptor CXCR4 as a model of GPCR system. Here, we provide a proof of concept demonstration by designing and synthesizing two peptides, AR5 and AR6, that combine a peptide fragment derived from two viral ligands of CXCR4, vMIP-II and HIV-1 envelope glycoprotein gp120. AR5 and AR6 display nanomolar binding affinity, in contrast to the weak micromolar CXCR4 binding of each peptide fragment alone, and inhibit HIV-1 entry via CXCR4. Further studies were carried out for the representative peptide AR6 using western blotting and site-directed mutagenesis in conjunction with molecular dynamic simulation and binding free energy calculation to determine how the peptide interacts with CXCR4 and inhibits its downstream signaling. These results demonstrate that this combinational approach is effective for generating nanomolar active inhibitors of CXCR4 and may be applicable to other GPCRs.
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Affiliation(s)
- Chaozai Zhang
- Department of Medicine, Division of Infectious Diseases, School of Medicine, University of California San Diego, La Jolla, CA, 92037, USA; School of Pharmaceutical Sciences, Jilin University, Changchun, 130021, China
| | - Lina S Huang
- Department of Medicine, Division of Infectious Diseases, School of Medicine, University of California San Diego, La Jolla, CA, 92037, USA; College of Arts and Sciences, Cornell University, Ithaca, NY, 14853, USA
| | - Ruohan Zhu
- School of Life Sciences, Tsinghua University, Beijing, China
| | - Qian Meng
- School of Life Sciences, Tsinghua University, Beijing, China
| | - Siyu Zhu
- Department of Medicine, Division of Infectious Diseases, School of Medicine, University of California San Diego, La Jolla, CA, 92037, USA; School of Life Sciences, Tsinghua University, Beijing, China
| | - Yan Xu
- School of Life Sciences, Tsinghua University, Beijing, China
| | - Huijun Zhang
- Department of Medicine, Division of Infectious Diseases, School of Medicine, University of California San Diego, La Jolla, CA, 92037, USA; School of Life Sciences, Tsinghua University, Beijing, China
| | - Xiong Fang
- School of Life Sciences, Tsinghua University, Beijing, China
| | - Xingquan Zhang
- Department of Medicine, Division of Infectious Diseases, School of Medicine, University of California San Diego, La Jolla, CA, 92037, USA
| | - Jiao Zhou
- Nobel Institute of Biomedicine, Zhuhai, Guangdong, China
| | - Robert T Schooley
- Department of Medicine, Division of Infectious Diseases, School of Medicine, University of California San Diego, La Jolla, CA, 92037, USA
| | - Xiaohong Yang
- School of Pharmaceutical Sciences, Jilin University, Changchun, 130021, China.
| | - Ziwei Huang
- Department of Medicine, Division of Infectious Diseases, School of Medicine, University of California San Diego, La Jolla, CA, 92037, USA.
| | - Jing An
- Department of Medicine, Division of Infectious Diseases, School of Medicine, University of California San Diego, La Jolla, CA, 92037, USA.
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Guryanov I, Real-Fernández F, Sabatino G, Prisco N, Korzhikov-Vlakh V, Biondi B, Papini AM, Korzhikova-Vlakh E, Rovero P, Tennikova T. Modeling interaction between gp120 HIV protein and CCR5 receptor. J Pept Sci 2019; 25:e3142. [PMID: 30680875 DOI: 10.1002/psc.3142] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2018] [Revised: 11/22/2018] [Accepted: 11/23/2018] [Indexed: 02/06/2023]
Abstract
The study of the process of HIV entry into the host cell and the creation of biomimetic nanosystems that are able to selectively bind viral particles and proteins is a high priority research area for the development of novel diagnostic tools and treatment of HIV infection. Recently, we described multilayer nanoparticles (nanotraps) with heparin surface and cationic peptides comprising the N-terminal tail (Nt) and the second extracellular loop (ECL2) of CCR5 receptor, which could bind with high affinity some inflammatory chemokines, in particular, Rantes. Because of the similarity of the binding determinants in CCR5 structure, both for chemokines and gp120 HIV protein, here we expand this approach to the study of the interactions of these biomimetic nanosystems and their components with the peptide representing the V3 loop of the activated form of gp120. According to surface plasmon resonance results, a conformational rearrangement is involved in the process of V3 and CCR5 fragments binding. As in the case of Rantes, ECL2 peptide showed much higher affinity to V3 peptide than Nt (KD = 3.72 × 10-8 and 1.10 × 10-6 M, respectively). Heparin-covered nanoparticles bearing CCR5 peptides effectively bound V3 as well. The presence of both heparin and the peptides in the structure of the nanotraps was shown to be crucial for the interaction with the V3 loop. Thus, short cationic peptides ECL2 and Nt proved to be excellent candidates for the design of CCR5 receptor mimetics.
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Affiliation(s)
- I Guryanov
- Institute of Chemistry, St. Petersburg State University, St. Petersburg, 198504, Russia
| | - F Real-Fernández
- Laboratory of Peptide and Protein Chemistry and Biology, Department of Chemistry "Ugo Schiff", University of Florence, 50019, Sesto Fiorentino, Italy
| | - G Sabatino
- Laboratory of Peptide and Protein Chemistry and Biology, Department of Chemistry "Ugo Schiff", University of Florence, 50019, Sesto Fiorentino, Italy.,CNR Istituto di Biostrutture e Bioimmagini, 95126, Catania, Italy
| | - N Prisco
- Laboratory of Peptide and Protein Chemistry and Biology, Department of NeuroFarBa, University of Florence, 50019, Sesto Fiorentino, Italy
| | - V Korzhikov-Vlakh
- Institute of Chemistry, St. Petersburg State University, St. Petersburg, 198504, Russia
| | - B Biondi
- CNR-ICB, Padova Unit, Department of Chemistry, University of Padova, 35131, Padova, Italy
| | - A M Papini
- Laboratory of Peptide and Protein Chemistry and Biology, Department of Chemistry "Ugo Schiff", University of Florence, 50019, Sesto Fiorentino, Italy.,PeptLab@UCP Platform and Laboratory of Chemical Biology EA4505, University Paris-Seine, 95031, Cergy-Pontoise CEDEX, France
| | - E Korzhikova-Vlakh
- Institute of Chemistry, St. Petersburg State University, St. Petersburg, 198504, Russia
| | - P Rovero
- CNR Istituto di Biostrutture e Bioimmagini, 95126, Catania, Italy.,Laboratory of Peptide and Protein Chemistry and Biology, Department of NeuroFarBa, University of Florence, 50019, Sesto Fiorentino, Italy
| | - T Tennikova
- Institute of Chemistry, St. Petersburg State University, St. Petersburg, 198504, Russia
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Denard B, Han S, Kim J, Ross EM, Ye J. Regulating G protein-coupled receptors by topological inversion. eLife 2019; 8:40234. [PMID: 30835201 PMCID: PMC6400500 DOI: 10.7554/elife.40234] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2018] [Accepted: 02/13/2019] [Indexed: 02/01/2023] Open
Abstract
G protein-coupled receptors (GPCRs) are a family of proteins containing seven transmembrane helices, with the N- and C-terminus of the protein located at the extracellular space and cytosol, respectively. Here, we report that ceramide or related sphingolipids might invert the topology of many GPCRs that contain a GXXXN motif in their first transmembrane helix. The functional significance of this topological regulation is illustrated by the CCR5 chemokine receptor. In the absence of lipopolysaccharide (LPS), CCR5 adopts a topology consistent with that of GPCR, allowing mouse peritoneal macrophages to migrate toward its ligand CCL5. LPS stimulation results in increased production of dihydroceramide, which inverts the topology of CCR5, preventing macrophages from migrating toward CCL5. These results suggest that GPCRs may not always adopt the same topology and can be regulated through topological inversion. Editorial note: This article has been through an editorial process in which the authors decide how to respond to the issues raised during peer review. The Reviewing Editor's assessment is that major issues remain unresolved (see decision letter).
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Affiliation(s)
- Bray Denard
- Department of Molecular Genetics, University of Texas Southwestern Medical Center, Dallas, United States
| | - Sungwon Han
- Department of Molecular Genetics, University of Texas Southwestern Medical Center, Dallas, United States
| | - JungYeon Kim
- Department of Molecular Genetics, University of Texas Southwestern Medical Center, Dallas, United States
| | - Elliott M Ross
- Department of Pharmacology, Green Center for Systems Biology, University of Texas Southwestern Medical Center, Dallas, United States
| | - Jin Ye
- Department of Molecular Genetics, University of Texas Southwestern Medical Center, Dallas, United States
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41
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A Coreceptor-Mimetic Peptide Enhances the Potency of V3-Glycan Antibodies. J Virol 2019; 93:JVI.01653-18. [PMID: 30541842 DOI: 10.1128/jvi.01653-18] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2018] [Accepted: 12/02/2018] [Indexed: 12/23/2022] Open
Abstract
Broadly neutralizing antibodies (bNAbs) target five major epitopes on the HIV-1 envelope glycoprotein (Env). The most potent bNAbs have median half-maximal inhibitory concentration (IC50) values in the nanomolar range, and the broadest bNAbs neutralize up to 98% of HIV-1 strains. The engineered HIV-1 entry inhibitor eCD4-Ig has greater breadth than bNAbs and similar potency. eCD4-Ig is markedly more potent than CD4-Ig due to its C-terminal coreceptor-mimetic peptide. Here we investigated whether the coreceptor-mimetic peptide mim6 improved the potency of bNAbs with different epitopes. We observed that when mim6 was appended to the C terminus of the heavy chains of bNAbs, this sulfopeptide improved the potency of all classes of bNAbs against HIV-1 isolates that are sensitive to neutralization by the sulfopeptide alone. However, mim6 did not significantly enhance neutralization of other isolates when appended to most classes of bNAbs, with one exception. Specifically, mim6 improved the potency of bNAbs of the V3-glycan class, including PGT121, PGT122, PGT128, and 10-1074, by an average of 2-fold for all HIV-1 isolates assayed. Despite this difference, 10-1074 does not induce exposure of the coreceptor-binding site, and addition of mim6 to 10-1074 did not promote shedding of the gp120 subunit of Env. Mixtures of 10-1074 and an Fc domain fused to mim6 neutralized less efficiently than a 10-1074/mim6 fusion, indicating that mim6 enhances the avidity of this fusion. Our data show that mim6 can consistently improve the potency of V3-glycan antibodies and suggest that these antibodies bind in an orientation that facilitates mim6 association with Env.IMPORTANCE HIV-1 requires both the cellular receptor CD4 and a tyrosine-sulfated coreceptor to infect its target cells. CD4-Ig is a fusion of the HIV-1-binding domains of CD4 with an antibody Fc domain. Previous studies have demonstrated that the potency of CD4-Ig is markedly increased by appending a coreceptor-mimetic sulfopeptide to its C terminus. We investigated whether this coreceptor-mimetic peptide improves the potency of broadly neutralizing antibodies (bNAbs) targeting five major epitopes on the HIV-1 envelope glycoprotein (Env). We observed that inclusion of the sulfopeptide dramatically improved the potency of all bNAb classes against isolates with more-open Env structures, typically those that utilize the coreceptor CXCR4. In contrast, the sulfopeptide improved only V3-glycan antibodies when neutralizing primary isolates, on average by 2-fold. These studies improve the potency of one class of bNAbs, show that coreceptor-mimetic sulfopeptides enhance neutralization through distinct mechanisms, and provide insight for the design of novel multispecific entry inhibitors.
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Identification of a Helical Segment within the Intrinsically Disordered Region of the PCSK9 Prodomain. J Mol Biol 2019; 431:885-903. [PMID: 30653992 DOI: 10.1016/j.jmb.2018.11.025] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2018] [Revised: 11/06/2018] [Accepted: 11/26/2018] [Indexed: 01/03/2023]
Abstract
Proprotein convertase subtilisin/kexin 9 (PCSK9) is a key regulator of lipid metabolism by degrading liver LDL receptors. Structural studies have provided molecular details of PCSK9 function. However, the N-terminal acidic stretch of the PCSK9 prodomain (Q31-T60) has eluded structural investigation, since it is in a disordered state. The interest in this region is intensified by the presence of human missense mutations associated with low and high LDL-c levels (E32K, D35Y, and R46L, respectively), as well as two posttranslationally modified sites, sulfated Y38 and phosphorylated S47. Herein we show that a segment within this region undergoes disorder-to-order transition. Experiments with acidic stretch-derived peptides demonstrated that the folding is centered at the segment Y38-L45, which adopts an α-helix as determined by NMR analysis of free peptides and by X-ray crystallography of peptides in complex with antibody 6E2 (Ab6E2). In the Fab6E2-peptide complexes, the structured region features a central 2 1/4-turn α-helix and encompasses up to 2/3 of the length of the acidic stretch, including the missense mutations and posttranslationally modified sites. Experiments with helix-breaking proline substitutions in peptides and in PCSK9 protein indicated that Ab6E2 specifically recognizes the helical conformation of the acidic stretch. Therefore, the observed quantitative binding of Ab6E2 to native PCSK9 from various cell lines suggests that the disorder-to-order transition is a true feature of PCSK9 and not limited to peptides. Because the helix provides a constrained spatial orientation of the missense mutations and the posttranslationally modified residues, it is probable that their biological functions take place in the context of an ordered conformational state.
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Latinovic OS, Reitz M, Heredia A. CCR5 Inhibitors and HIV-1 Infection. JOURNAL OF AIDS AND HIV TREATMENT 2019; 1:1-5. [PMID: 31414081 PMCID: PMC6693856 DOI: 10.33696/aids.1.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Olga S. Latinovic
- Institute of Human Virology, University of Maryland School of Medicine, Baltimore, Maryland, USA
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Marvin Reitz
- Institute of Human Virology, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Alonso Heredia
- Institute of Human Virology, University of Maryland School of Medicine, Baltimore, Maryland, USA
- School of Medicine, University of Maryland School of Medicine, Baltimore, Maryland, USA
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Structural basis of coreceptor recognition by HIV-1 envelope spike. Nature 2018; 565:318-323. [PMID: 30542158 PMCID: PMC6391877 DOI: 10.1038/s41586-018-0804-9] [Citation(s) in RCA: 140] [Impact Index Per Article: 23.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2018] [Accepted: 11/02/2018] [Indexed: 01/26/2023]
Abstract
HIV-1 envelope glycoprotein (Env), which consists of trimeric (gp160)3 cleaved to (gp120 and gp41)3, interacts with the primary receptor CD4 and a coreceptor (such as chemokine receptor CCR5) to fuse viral and target-cell membranes. The gp120-coreceptor interaction has previously been proposed as the most crucial trigger for unleashing the fusogenic potential of gp41. Here we report a cryo-electron microscopy structure of a full-length gp120 in complex with soluble CD4 and unmodified human CCR5, at 3.9 Å resolution. The V3 loop of gp120 inserts into the chemokine-binding pocket formed by seven transmembrane helices of CCR5, and the N terminus of CCR5 contacts the CD4-induced bridging sheet of gp120. CCR5 induces no obvious allosteric changes in gp120 that can propagate to gp41; it does bring the Env trimer close to the target membrane. The N terminus of gp120, which is gripped by gp41 in the pre-fusion or CD4-bound Env, flips back in the CCR5-bound conformation and may irreversibly destabilize gp41 to initiate fusion. The coreceptor probably functions by stabilizing and anchoring the CD4-induced conformation of Env near the cell membrane. These results advance our understanding of HIV-1 entry into host cells and may guide the development of vaccines and therapeutic agents.
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Colin P, Zhou Z, Staropoli I, Garcia-Perez J, Gasser R, Armani-Tourret M, Benureau Y, Gonzalez N, Jin J, Connell BJ, Raymond S, Delobel P, Izopet J, Lortat-Jacob H, Alcami J, Arenzana-Seisdedos F, Brelot A, Lagane B. CCR5 structural plasticity shapes HIV-1 phenotypic properties. PLoS Pathog 2018; 14:e1007432. [PMID: 30521629 PMCID: PMC6283471 DOI: 10.1371/journal.ppat.1007432] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2018] [Accepted: 10/24/2018] [Indexed: 01/20/2023] Open
Abstract
CCR5 plays immune functions and is the coreceptor for R5 HIV-1 strains. It exists in diverse conformations and oligomerization states. We interrogated the significance of the CCR5 structural diversity on HIV-1 infection. We show that envelope glycoproteins (gp120s) from different HIV-1 strains exhibit divergent binding levels to CCR5 on cell lines and primary cells, but not to CD4 or the CD4i monoclonal antibody E51. This owed to differential binding of the gp120s to different CCR5 populations, which exist in varying quantities at the cell surface and are differentially expressed between different cell types. Some, but not all, of these populations are antigenically distinct conformations of the coreceptor. The different binding levels of gp120s also correspond to differences in their capacity to bind CCR5 dimers/oligomers. Mutating the CCR5 dimerization interface changed conformation of the CCR5 homodimers and modulated differentially the binding of distinct gp120s. Env-pseudotyped viruses also use particular CCR5 conformations for entry, which may differ between different viruses and represent a subset of those binding gp120s. In particular, even if gp120s can bind both CCR5 monomers and oligomers, impairment of CCR5 oligomerization improved viral entry, suggesting that HIV-1 prefers monomers for entry. From a functional standpoint, we illustrate that the nature of the CCR5 molecules to which gp120/HIV-1 binds shapes sensitivity to inhibition by CCR5 ligands and cellular tropism. Differences exist in the CCR5 populations between T-cells and macrophages, and this is associated with differential capacity to bind gp120s and to support viral entry. In macrophages, CCR5 structural plasticity is critical for entry of blood-derived R5 isolates, which, in contrast to prototypical M-tropic strains from brain tissues, cannot benefit from enhanced affinity for CD4. Collectively, our results support a role for CCR5 heterogeneity in diversifying the phenotypic properties of HIV-1 isolates and provide new clues for development of CCR5-targeting drugs.
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Affiliation(s)
- Philippe Colin
- Viral Pathogenesis Unit, Department of Virology, Institut Pasteur, Paris, France
- INSERM Unit U1108, Institut Pasteur, Paris, France
- Paris Diderot University, Sorbonne Paris Cité, Cellule Pasteur, Rue du Docteur Roux, Paris, France
| | - Zhicheng Zhou
- Viral Pathogenesis Unit, Department of Virology, Institut Pasteur, Paris, France
- INSERM Unit U1108, Institut Pasteur, Paris, France
| | - Isabelle Staropoli
- Viral Pathogenesis Unit, Department of Virology, Institut Pasteur, Paris, France
- INSERM Unit U1108, Institut Pasteur, Paris, France
| | | | - Romain Gasser
- Centre de Physiopathologie Toulouse-Purpan (CPTP), Université de Toulouse, CNRS, Inserm, UPS, Toulouse, France
| | - Marie Armani-Tourret
- Centre de Physiopathologie Toulouse-Purpan (CPTP), Université de Toulouse, CNRS, Inserm, UPS, Toulouse, France
| | - Yann Benureau
- Viral Pathogenesis Unit, Department of Virology, Institut Pasteur, Paris, France
- INSERM Unit U1108, Institut Pasteur, Paris, France
| | - Nuria Gonzalez
- AIDS Immunopathogenesis Unit, Instituto de Salud Carlos III, Madrid, Spain
| | - Jun Jin
- Viral Pathogenesis Unit, Department of Virology, Institut Pasteur, Paris, France
- INSERM Unit U1108, Institut Pasteur, Paris, France
| | - Bridgette J. Connell
- Grenoble Alpes University, CNRS, CEA, Institut de Biologie Structurale (IBS), Grenoble, France
| | - Stéphanie Raymond
- Centre de Physiopathologie Toulouse-Purpan (CPTP), Université de Toulouse, CNRS, Inserm, UPS, Toulouse, France
- CHU de Toulouse, Laboratoire de Virologie, Toulouse, France
| | - Pierre Delobel
- Centre de Physiopathologie Toulouse-Purpan (CPTP), Université de Toulouse, CNRS, Inserm, UPS, Toulouse, France
- CHU de Toulouse, Service des Maladies Infectieuses et Tropicales, Toulouse, France
| | - Jacques Izopet
- Centre de Physiopathologie Toulouse-Purpan (CPTP), Université de Toulouse, CNRS, Inserm, UPS, Toulouse, France
- CHU de Toulouse, Laboratoire de Virologie, Toulouse, France
| | - Hugues Lortat-Jacob
- Grenoble Alpes University, CNRS, CEA, Institut de Biologie Structurale (IBS), Grenoble, France
| | - Jose Alcami
- AIDS Immunopathogenesis Unit, Instituto de Salud Carlos III, Madrid, Spain
| | - Fernando Arenzana-Seisdedos
- Viral Pathogenesis Unit, Department of Virology, Institut Pasteur, Paris, France
- INSERM Unit U1108, Institut Pasteur, Paris, France
| | - Anne Brelot
- Viral Pathogenesis Unit, Department of Virology, Institut Pasteur, Paris, France
- INSERM Unit U1108, Institut Pasteur, Paris, France
| | - Bernard Lagane
- Viral Pathogenesis Unit, Department of Virology, Institut Pasteur, Paris, France
- INSERM Unit U1108, Institut Pasteur, Paris, France
- Centre de Physiopathologie Toulouse-Purpan (CPTP), Université de Toulouse, CNRS, Inserm, UPS, Toulouse, France
- * E-mail:
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Kamau E, Bonneau R, Kong XP. Computational-guided determination of the functional role of 447-52D long CDRH3. Protein Eng Des Sel 2018; 31:479-487. [PMID: 31038677 PMCID: PMC6890530 DOI: 10.1093/protein/gzz007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2019] [Revised: 03/06/2019] [Accepted: 03/20/2019] [Indexed: 11/13/2022] Open
Abstract
447-52D (447) is a human monoclonal antibody that recognizes a conserved epitope in the crown region of the third variable loop (V3) of HIV-1 gp120, and like many anti-HIV-1 antibodies with broad neutralization capabilities, it has a long heavy-chain complementarity determining region (CDRH3). Here, we use a combination of computational mutagenesis and modeling in tandem with fluorescence polarization assays to interrogate the molecular basis of 447 CDRH3 length and the individual contribution of selected CDRH3 residues to affinity. We observe that 447 CDRH3 length provides a large binding surface area and the best enthalpic contributions derived from hydrophobic packing, main-chain hydrogen bonds, electrostatic and van der Waals interactions. We also found out that CDRH3 residue Try100I is critical to 447 binding affinity.
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Affiliation(s)
- Edwin Kamau
- Department of Biochemistry and Molecular Pharmacology, NYU School of Medicine, New York NY, USA
| | - Richard Bonneau
- Department of Biology, Center for Genomics and Systems Biology and Computer Science Department, Courant Institute of Mathematical Sciences, New York University, New York NY, USA
- Center for Computational Biology, Flatiron Institute, New York NY, USA
| | - Xiang-Peng Kong
- Department of Biochemistry and Molecular Pharmacology, NYU School of Medicine, New York NY, USA
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48
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Yang E, Gardner MR, Zhou AS, Farzan M, Arvin AM, Oliver SL. HIV-1 inhibitory properties of eCD4-Igmim2 determined using an Env-mediated membrane fusion assay. PLoS One 2018; 13:e0206365. [PMID: 30359435 PMCID: PMC6201953 DOI: 10.1371/journal.pone.0206365] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2018] [Accepted: 10/11/2018] [Indexed: 11/19/2022] Open
Abstract
Human Immunodeficiency Virus-1 (HIV-1) entry is dependent on the envelope glycoprotein (Env) that is present on the virion and facilitates fusion between the envelope and the cellular membrane. The protein consists of two subunits, gp120 and gp41, with the former required for binding the CD4 receptor and either the CXCR4 or CCR5 coreceptor, and the latter for mediating fusion. The requirement of fusion for infection has made Env an attractive target for HIV therapy development and led to the FDA approval of enfuvirtide, a fusion inhibitor. Continued development of entry inhibitors is warranted because enfuvirtide resistant HIV-1 strains have emerged. In this study, a novel HIV-1 fusion assay was validated using neutralizing antibodies and then used to investigate the mechanism of action of eCD4-Igmim2, an HIV-1 inhibitor proposed to cooperatively bind the CD4 binding site and the sulfotyrosine-binding pocket of gp120. Greater reduction in fusion levels was observed with eCD4-Igmim2 in the fusion assay than all of the gp120 antibodies evaluated. Lab adapted isolates, HIV-1HXB2 and HIV-1YU2, were sensitive to eCD4-Igmim2 in the fusion assay, while primary isolates, HIV-1BG505 and HIV-1ZM651 were resistant. These results correlated with greater IC50 values for primary isolates compared to the lab adapted isolates observed in a virus neutralization assay. Analysis of gp120 models identified differences in the V1 and V2 domains that are associated with eCD4-Igmim2 sensitivity. This study highlights the use of a fusion assay to identify key areas for improving the potency of eCD4-Igmim2.
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Affiliation(s)
- Edward Yang
- Departments of Pediatrics and Microbiology & Immunology, Stanford University School of Medicine, Stanford, California, United States of America
- * E-mail:
| | - Matthew R. Gardner
- Department of Infectious Diseases, The Scripps Research Institute, Jupiter, Florida, United States of America
| | - Amber S. Zhou
- Department of Infectious Diseases, The Scripps Research Institute, Jupiter, Florida, United States of America
| | - Michael Farzan
- Department of Infectious Diseases, The Scripps Research Institute, Jupiter, Florida, United States of America
| | - Ann M. Arvin
- Departments of Pediatrics and Microbiology & Immunology, Stanford University School of Medicine, Stanford, California, United States of America
| | - Stefan L. Oliver
- Departments of Pediatrics and Microbiology & Immunology, Stanford University School of Medicine, Stanford, California, United States of America
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49
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Srivastava G, Moseri A, Kessler N, Arshava B, Naider F, Anglister J. Defining specific residue‐to‐residue interactions between the gp120 bridging sheet and the N‐terminal segment ofCCR5: applications of transferredNOE NMR. FEBS J 2018; 285:4296-4310. [DOI: 10.1111/febs.14673] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2018] [Revised: 09/20/2018] [Accepted: 10/02/2018] [Indexed: 01/16/2023]
Affiliation(s)
- Gautam Srivastava
- Department of Structural Biology Weizmann Institute of Science Rehovot Israel
| | - Adi Moseri
- Department of Structural Biology Weizmann Institute of Science Rehovot Israel
| | - Naama Kessler
- Department of Structural Biology Weizmann Institute of Science Rehovot Israel
| | - Boris Arshava
- Department of Chemistry and Macromolecular Assembly Institute College of Staten Island of the City University of New York NY USA
- The Graduate Center of the City University of New York NY USA
| | - Fred Naider
- Department of Chemistry and Macromolecular Assembly Institute College of Staten Island of the City University of New York NY USA
- The Graduate Center of the City University of New York NY USA
| | - Jacob Anglister
- Department of Structural Biology Weizmann Institute of Science Rehovot Israel
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50
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Structural Comparison of Human Anti-HIV-1 gp120 V3 Monoclonal Antibodies of the Same Gene Usage Induced by Vaccination and Chronic Infection. J Virol 2018; 92:JVI.00641-18. [PMID: 29997214 DOI: 10.1128/jvi.00641-18] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2018] [Accepted: 06/30/2018] [Indexed: 01/01/2023] Open
Abstract
Elucidating the structural basis of antibody (Ab) gene usage and affinity maturation of vaccine-induced Abs can inform the design of immunogens for inducing desired Ab responses in HIV vaccine development. Analyses of monoclonal Abs (MAbs) encoded by the same immunoglobulin genes at different stages of maturation can help to elucidate the maturation process. We have analyzed four human anti-V3 MAbs with the same VH1-3*01 and VL3-10*01 gene usage. Two MAbs, TA6 and TA7, were developed from a vaccinee in the HIV vaccine phase I trial DP6-001 with a polyvalent DNA prime/protein boost regimen, and two others, 311-11D and 1334, were developed from HIV-infected patients. The somatic hypermutation (SHM) rates in VH of vaccine-induced MAbs are lower than in chronic HIV infection-induced MAbs, while those in VL are comparable. Crystal structures of the antigen-binding fragments (Fabs) in complex with V3 peptides show that these MAbs bind the V3 epitope with a new cradle-binding mode and that the V3 β-hairpin lies along the antigen-binding groove, which consists of residues from both heavy and light chains. Residues conserved from the germ line sequences form specific binding pockets accommodating conserved structural elements of the V3 crown hairpin, predetermining the Ab gene selection, while somatically mutated residues create additional hydrogen bonds, electrostatic interactions, and van der Waals contacts, correlating with an increased binding affinity. Our data provide a unique example of germ line sequences determining the primordial antigen-binding sites and SHMs correlating with affinity maturation of Abs induced by vaccine and natural HIV infection.IMPORTANCE Understanding the structural basis of gene usage and affinity maturation for anti-HIV-1 antibodies may help vaccine design and development. Antibodies targeting the highly immunogenic third variable loop (V3) of HIV-1 gp120 provide a unique opportunity for detailed structural investigations. By comparing the sequences and structures of four anti-V3 MAbs at different stages of affinity maturation but of the same V gene usage, two induced by vaccination and another two by chronic infection, we provide a fine example of how germ line sequence determines the essential elements for epitope recognition and how affinity maturation improves the antibody's recognition of its epitope.
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