1
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Zheng Y, Feng J, Ling M, Yu Y, Tao Y, Wang X. A comprehensive review on targeting cluster of differentiation: An attractive strategy for inhibiting viruses through host proteins. Int J Biol Macromol 2024; 269:132200. [PMID: 38723834 DOI: 10.1016/j.ijbiomac.2024.132200] [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: 03/04/2024] [Revised: 04/20/2024] [Accepted: 05/06/2024] [Indexed: 05/13/2024]
Abstract
Viral infections continue to pose a significant global public health threat. Targeting host proteins, such as cluster of differentiation (CD) macromolecules, may offer a promising alternative approach to developing antiviral treatments. CDs are cell-surface biological macromolecules mainly expressed on leukocytes that viruses can use to enter cells, thereby evading immune detection and promoting their replication. The manipulation of CDs by viruses may represent an effective and clever means of survival through the prolonged co-evolution of hosts and viruses. Targeting of CDs is anticipated to hinder the invasion of related viruses, modulate the body's immune system, and diminish the incidence of subsequent inflammation. They have become crucial for biomedical diagnosis, and some have been used as valuable tools for resisting viral infections. However, a summary of the structures and functions of CDs involved in viral infection is currently lacking. The development of drugs targeting these biological macromolecules is restricted both in terms of their availability and the number of compounds currently identified. This review provides a comprehensive analysis of the critical role of CD proteins in virus invasion and a list of relevant targeted antiviral agents, which will serve as a valuable reference for future research in this field.
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Affiliation(s)
- Youle Zheng
- National Reference Laboratory of Veterinary Drug Residues (HZAU), MAO Key Laboratory for Detection of Veterinary Drug Residues, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Jin Feng
- National Reference Laboratory of Veterinary Drug Residues (HZAU), MAO Key Laboratory for Detection of Veterinary Drug Residues, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Min Ling
- National Reference Laboratory of Veterinary Drug Residues (HZAU), MAO Key Laboratory for Detection of Veterinary Drug Residues, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Yixin Yu
- National Reference Laboratory of Veterinary Drug Residues (HZAU), MAO Key Laboratory for Detection of Veterinary Drug Residues, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Yanfei Tao
- National Reference Laboratory of Veterinary Drug Residues (HZAU), MAO Key Laboratory for Detection of Veterinary Drug Residues, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Xu Wang
- National Reference Laboratory of Veterinary Drug Residues (HZAU), MAO Key Laboratory for Detection of Veterinary Drug Residues, Huazhong Agricultural University, Wuhan, Hubei 430070, China; MOA Laboratory for Risk Assessment of Quality and Safety of Livestock and Poultry Products, Huazhong Agricultural University, Wuhan, Hubei 430070, China.
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2
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Khare S, Villalba MI, Canul-Tec JC, Cajiao AB, Kumar A, Backovic M, Rey FA, Pardon E, Steyaert J, Perez C, Reyes N. Receptor-recognition and antiviral mechanisms of retrovirus-derived human proteins. Nat Struct Mol Biol 2024:10.1038/s41594-024-01295-6. [PMID: 38671230 DOI: 10.1038/s41594-024-01295-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Accepted: 03/26/2024] [Indexed: 04/28/2024]
Abstract
Human syncytin-1 and suppressyn are cellular proteins of retroviral origin involved in cell-cell fusion events to establish the maternal-fetal interface in the placenta. In cell culture, they restrict infections from members of the largest interference group of vertebrate retroviruses, and are regarded as host immunity factors expressed during development. At the core of the syncytin-1 and suppressyn functions are poorly understood mechanisms to recognize a common cellular receptor, the membrane transporter ASCT2. Here, we present cryo-electron microscopy structures of human ASCT2 in complexes with the receptor-binding domains of syncytin-1 and suppressyn. Despite their evolutionary divergence, the two placental proteins occupy similar positions in ASCT2, and are stabilized by the formation of a hybrid β-sheet or 'clamp' with the receptor. Structural predictions of the receptor-binding domains of extant retroviruses indicate overlapping binding interfaces and clamping sites with ASCT2, revealing a competition mechanism between the placental proteins and the retroviruses. Our work uncovers a common ASCT2 recognition mechanism by a large group of endogenous and disease-causing retroviruses, and provides high-resolution views on how placental human proteins exert morphological and immunological functions.
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Affiliation(s)
- Shashank Khare
- Fundamental Microbiology and Pathogenicity Unit, CNRS, Université de Bordeaux, IECB, Bordeaux, France
| | - Miryam I Villalba
- Fundamental Microbiology and Pathogenicity Unit, CNRS, Université de Bordeaux, IECB, Bordeaux, France
| | - Juan C Canul-Tec
- Fundamental Microbiology and Pathogenicity Unit, CNRS, Université de Bordeaux, IECB, Bordeaux, France
| | | | - Anand Kumar
- Fundamental Microbiology and Pathogenicity Unit, CNRS, Université de Bordeaux, IECB, Bordeaux, France
| | - Marija Backovic
- Institut Pasteur, Université Paris Cité, CNRS UMR3569, Unité de Virologie Structurale, Paris, France
| | - Felix A Rey
- Institut Pasteur, Université Paris Cité, CNRS UMR3569, Unité de Virologie Structurale, Paris, France
| | - Els Pardon
- Structural Biology Brussels, Vrije Universiteit Brussel, VUB, Brussels, Belgium
- VIB-VUB Center for Structural Biology, VIB, Brussels, Belgium
| | - Jan Steyaert
- Structural Biology Brussels, Vrije Universiteit Brussel, VUB, Brussels, Belgium
- VIB-VUB Center for Structural Biology, VIB, Brussels, Belgium
| | - Camilo Perez
- Biozentrum, University of Basel, Basel, Switzerland.
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, USA.
| | - Nicolas Reyes
- Fundamental Microbiology and Pathogenicity Unit, CNRS, Université de Bordeaux, IECB, Bordeaux, France.
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3
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Silva MJA, Marinho RL, Rodrigues YC, Brasil TP, Dos Santos PAS, Silva CS, Sardinha DM, Lima KVB, Lima LNGC. Molecular Role of HIV-1 Human Receptors (CCL5-CCR5 Axis) in neuroAIDS: A Systematic Review. Microorganisms 2024; 12:782. [PMID: 38674726 PMCID: PMC11051963 DOI: 10.3390/microorganisms12040782] [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: 02/20/2024] [Revised: 03/01/2024] [Accepted: 03/14/2024] [Indexed: 04/28/2024] Open
Abstract
Chronic HIV-1 infection can cause neurological illness, also known as HIV-associated neurocognitive disorders (HAND). The elevated level of pro-inflammatory cytokines and chemokines, such as C-C Chemokine Ligand 5 (CCL5/RANTES), is one of the ways of causing HIV-1-mediated neuroinflammation. C-C Chemokine Receptor 5 (CCR5) is the main coreceptor for viral entry into host cells and for mediating induction of CCL5/RANTES. CCR5 and CCL5 are part of a correlated axis of immune pathways used for effective protection against the HIV-1 virus. The purpose of this paper was to review the literary knowledge about the immunopathological relationship between this immune complex and neuroAIDS. A systematic review of the literature was conducted based on the selection and search of articles, available in English, Spanish, or Portuguese in the time frame of 1990-2022, of primary and secondary types in the PUBMED, Science Direct, SciELO, and LILACS databases through descriptors (MeSH) together with "AND": "CCR5"; "CCL5"; "neurological manifestations"; or "HIV". The methodological quality of the articles was assessed using the JBI Checklists and the PRISMA 2020 writing guidelines were followed. A total of 36 articles were included in the final composition of the review. The main cells of the CNS affected by neuroAIDS are: neurons; microglia; astrocytes; and oligodendrocytes. Molecular devices and their associations with cellular injuries have been described from the entry of the virus into the host's CNS cell to the generation of mental disorders. Furthermore, divergent results were found about the levels of CCL5/RANTES secretion and the generation of immunopathogenesis, while all condensed research for CCR5 indicated that elevation of this receptor causes more neurodegenerative manifestations. Therefore, new therapeutic and interventional strategies can be conditioned on the immunological direction proposed in this review for the disease.
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Affiliation(s)
- Marcos Jessé Abrahão Silva
- Postgraduate Program in Parasite Biology in the Amazon (PPGBPA), Evandro Chagas Institute (IEC), Ananindeua 67030-000, PA, Brazil;
| | - Rebecca Lobato Marinho
- Institute of Biological and Health Sciences (ICB), University of Pará State (UEPA), Belém 66087-670, PA, Brazil; (R.L.M.); (P.A.S.D.S.); (C.S.S.); (D.M.S.)
| | - Yan Corrêa Rodrigues
- Institute of Biological and Health Sciences (ICB), University of Pará State (UEPA), Belém 66087-670, PA, Brazil; (R.L.M.); (P.A.S.D.S.); (C.S.S.); (D.M.S.)
| | - Thiago Pinto Brasil
- Faculty of Medicine, Federal University of Ceará (UFC), Fortaleza 60441-750, CE, Brazil;
| | - Pabllo Antonny Silva Dos Santos
- Institute of Biological and Health Sciences (ICB), University of Pará State (UEPA), Belém 66087-670, PA, Brazil; (R.L.M.); (P.A.S.D.S.); (C.S.S.); (D.M.S.)
| | - Caroliny Soares Silva
- Institute of Biological and Health Sciences (ICB), University of Pará State (UEPA), Belém 66087-670, PA, Brazil; (R.L.M.); (P.A.S.D.S.); (C.S.S.); (D.M.S.)
| | - Daniele Melo Sardinha
- Institute of Biological and Health Sciences (ICB), University of Pará State (UEPA), Belém 66087-670, PA, Brazil; (R.L.M.); (P.A.S.D.S.); (C.S.S.); (D.M.S.)
| | - Karla Valéria Batista Lima
- Bacteriology and Mycology Section (SABMI), Evandro Chagas Institute (IEC), Ananindeua 67030-000, PA, Brazil; (K.V.B.L.); (L.N.G.C.L.)
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4
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Khorn PA, Luginina AP, Pospelov VA, Dashevsky DE, Khnykin AN, Moiseeva OV, Safronova NA, Belousov AS, Mishin AV, Borshchevsky VI. Rational Design of Drugs Targeting G-Protein-Coupled Receptors: A Structural Biology Perspective. BIOCHEMISTRY. BIOKHIMIIA 2024; 89:747-764. [PMID: 38831510 DOI: 10.1134/s0006297924040138] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Revised: 02/22/2024] [Accepted: 02/29/2024] [Indexed: 06/05/2024]
Abstract
G protein-coupled receptors (GPCRs) play a key role in the transduction of extracellular signals to cells and regulation of many biological processes, which makes these membrane proteins one of the most important targets for pharmacological agents. A significant increase in the number of resolved atomic structures of GPCRs has opened the possibility of developing pharmaceuticals targeting these receptors via structure-based drug design (SBDD). SBDD employs information on the structure of receptor-ligand complexes to search for selective ligands without the need for an extensive high-throughput experimental ligand screening and can significantly expand the chemical space for ligand search. In this review, we describe the process of deciphering GPCR structures using X-ray diffraction analysis and cryoelectron microscopy as an important stage in the rational design of drugs targeting this receptor class. Our main goal was to present modern developments and key features of experimental methods used in SBDD of GPCR-targeting agents to a wide range of specialists.
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Affiliation(s)
- Polina A Khorn
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, 141701, Russia
| | - Aleksandra P Luginina
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, 141701, Russia
| | - Vladimir A Pospelov
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, 141701, Russia
| | - Dmitrii E Dashevsky
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, 141701, Russia
| | - Andrey N Khnykin
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, 141701, Russia
| | - Olga V Moiseeva
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, 141701, Russia
- Scryabin Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences, Pushchino, Moscow Region, 142290, Russia
| | - Nadezhda A Safronova
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, 141701, Russia
| | - Anatolii S Belousov
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, 141701, Russia
| | - Alexey V Mishin
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, 141701, Russia.
| | - Valentin I Borshchevsky
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, 141701, Russia.
- Joint Institute for Nuclear Research, Frank Laboratory of Neutron Physics, Dubna, Moscow Region, 141980, Russia
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5
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Bennett AL, Edwards R, Kosheleva I, Saunders C, Bililign Y, Williams A, Bubphamala P, Manosouri K, Anasti K, Saunders KO, Alam SM, Haynes BF, Acharya P, Henderson R. Microsecond dynamics control the HIV-1 Envelope conformation. SCIENCE ADVANCES 2024; 10:eadj0396. [PMID: 38306419 PMCID: PMC10836732 DOI: 10.1126/sciadv.adj0396] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Accepted: 01/03/2024] [Indexed: 02/04/2024]
Abstract
The HIV-1 Envelope (Env) glycoprotein facilitates host cell fusion through a complex series of receptor-induced structural changes. Although remarkable progress has been made in understanding the structures of various Env conformations, microsecond timescale dynamics have not been studied experimentally. Here, we used time-resolved, temperature-jump small-angle x-ray scattering to monitor structural rearrangements in an HIV-1 Env SOSIP ectodomain construct with microsecond precision. In two distinct Env variants, we detected a transition that correlated with known Env structure rearrangements with a time constant in the hundreds of microseconds range. A previously unknown structural transition was also observed, which occurred with a time constant below 10 μs, and involved an order-to-disorder transition in the trimer apex. Using this information, we engineered an Env SOSIP construct that locks the trimer in the prefusion closed state by connecting adjacent protomers via disulfides. Our findings show that the microsecond timescale structural dynamics play an essential role in controlling the Env conformation with impacts on vaccine design.
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Affiliation(s)
- Ashley L. Bennett
- Duke Human Vaccine Institute, Duke University Medical Center, Durham, NC 27710, USA
| | - Robert Edwards
- Duke Human Vaccine Institute, Duke University Medical Center, Durham, NC 27710, USA
| | - Irina Kosheleva
- BioCARS, Center for Advanced Radiation Sources, The University of Chicago, 9700 South Cass Ave, Bld 434B, Lemont, IL 60439, USA
| | - Carrie Saunders
- Duke Human Vaccine Institute, Duke University Medical Center, Durham, NC 27710, USA
| | - Yishak Bililign
- Duke Human Vaccine Institute, Duke University Medical Center, Durham, NC 27710, USA
| | - Ashliegh Williams
- Duke Human Vaccine Institute, Duke University Medical Center, Durham, NC 27710, USA
| | - Pimthada Bubphamala
- Duke Human Vaccine Institute, Duke University Medical Center, Durham, NC 27710, USA
| | - Katayoun Manosouri
- Duke Human Vaccine Institute, Duke University Medical Center, Durham, NC 27710, USA
| | - Kara Anasti
- Duke Human Vaccine Institute, Duke University Medical Center, Durham, NC 27710, USA
| | - Kevin O. Saunders
- Duke Human Vaccine Institute, Duke University Medical Center, Durham, NC 27710, USA
- Department of Surgery, Duke University Medical Center, Durham, NC 27710, USA
- Department of Integrative Immunobiology, Duke University Medical Center, Durham, NC 27710, USA
| | - S. Munir Alam
- Duke Human Vaccine Institute, Duke University Medical Center, Durham, NC 27710, USA
- Department of Medicine, Duke University Medical Center, Durham, NC 27710, USA
- Department of Pathology, Duke University School of Medicine, Durham, NC 27710, USA
| | - Barton F. Haynes
- Duke Human Vaccine Institute, Duke University Medical Center, Durham, NC 27710, USA
- Department of Medicine, Duke University Medical Center, Durham, NC 27710, USA
- Department of Integrative Immunobiology, Duke University Medical Center, Durham, NC 27710, USA
| | - Priyamvada Acharya
- Duke Human Vaccine Institute, Duke University Medical Center, Durham, NC 27710, USA
- BioCARS, Center for Advanced Radiation Sources, The University of Chicago, 9700 South Cass Ave, Bld 434B, Lemont, IL 60439, USA
- Department of Biochemistry, Duke University, Durham, NC 27710, USA
| | - Rory Henderson
- Duke Human Vaccine Institute, Duke University Medical Center, Durham, NC 27710, USA
- Department of Medicine, Duke University Medical Center, Durham, NC 27710, USA
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6
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Raju S, Adams LJ, Diamond MS. The many ways in which alphaviruses bind to cells. Trends Immunol 2024; 45:85-93. [PMID: 38135598 PMCID: PMC10997154 DOI: 10.1016/j.it.2023.11.006] [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: 10/22/2023] [Revised: 11/25/2023] [Accepted: 11/26/2023] [Indexed: 12/24/2023]
Abstract
Only a subset of viruses can productively infect many different host species. Some arthropod-transmitted viruses, such as alphaviruses, can infect invertebrate and vertebrate species including insects, reptiles, birds, and mammals. This broad tropism may be explained by their ability to engage receptors that are conserved across vertebrate and invertebrate classes. Through several genome-wide loss-of-function screens, new alphavirus receptors have been identified, some of which bind to multiple related viruses in different antigenic complexes. Structural analysis has revealed that distinct sites on the alphavirus glycoprotein can mediate receptor binding, which opposes the idea that a single receptor-binding site mediates viral entry. Here, we discuss how different paradigms of receptor engagement on cells might explain the promiscuity of alphaviruses for multiple hosts.
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Affiliation(s)
- Saravanan Raju
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Lucas J Adams
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Michael S Diamond
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA; Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA; Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO 63110, USA; Andrew M. and Jane M. Bursky Center for Human Immunology and Immunotherapy Programs, Washington University School of Medicine, St. Louis, MO 63110, USA; Center for Vaccines and Immunity to Microbial Pathogens, Washington University School of Medicine, Saint Louis, MO 63110, USA.
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7
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Kessler N, Akabayov SR, Cohen LS, Scherf T, Naider F, Anglister J. The chemokines CCL5 and CXCL12 exhibit high-affinity binding to N-terminal peptides of the non-cognate receptors CXCR4 and CCR5, respectively. FEBS J 2024; 291:458-476. [PMID: 37997026 DOI: 10.1111/febs.17013] [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: 08/02/2023] [Revised: 10/16/2023] [Accepted: 11/21/2023] [Indexed: 11/25/2023]
Abstract
CC and CXC chemokines are distinct chemokine subfamilies. CC chemokines usually do not bind CXC-chemokine receptors and vice versa. CCR5 and CXCR4 receptors are activated by CCL5 and CXCL12 chemokines, respectively, and are also used as HIV-1 coreceptors. CCL5 contains one conserved binding site for a sulfated tyrosine residue, whereas CXCL12 is unique in having two additional sites for sulfated/nonsulfated tyrosine residues. In this study, N-terminal (Nt) CXCR4 peptides were found to bind CCL5 with somewhat higher affinities in comparison to those of short Nt-CCR5(8-20) peptides with the same number of sulfated tyrosine residues. Similarly, a long Nt-CCR5(1-27)(s Y3,s Y10,s Y14) peptide cross reacts with CXCL12 and with lower KD in comparison to its binding to CCL5. Intermolecular nuclear overhauser effect (NOE) measurements were used to decipher the mechanism of the chemokine/Nt-receptor peptide binding. The Nt-CXCR4 peptides interact with the conserved CCL5 tyrosine sulfate-binding site by an allovalency mechanism like that observed for CCL5 binding of Nt-CCR5 peptides. Nt-CCR5 peptides bind CXCL12 in multiple modes analogous to their binding to HIV-1 gp120 and interact with all three tyrosine/sulfated tyrosine-binding pockets of CXCL12. We suggest that the chemokine-receptors Nt-segments bind promiscuously to cognate and non-cognate chemokines and in a mechanism that is dependent on the number of binding pockets for tyrosine residues found on the chemokine. In conclusion, common features shared among the chemokine-receptors' Nt-segments such as multiple tyrosine residues that are potentially sulfated, and a large number of negatively charged residues are the reason of the cross binding observed in this study.
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Affiliation(s)
- Naama Kessler
- Department of Structural Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Sabine R Akabayov
- Department of 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 Ph.D. Programs in Biochemistry and Chemistry, The Graduate Center of the City University of New York, NY, USA
| | - Tali Scherf
- Department of Chemical Research Support, Weizmann Institute of Science, Rehovot, Israel
| | - Fred Naider
- Department of Structural Biology, Weizmann Institute of Science, Rehovot, Israel
- Department of Chemistry and Macromolecular Assembly Institute, College of Staten Island of the City University of New York, Staten Island, NY, USA
- The Ph.D. Programs in Biochemistry and Chemistry, 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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Wang X, Lu D, Peng D, Liu D, Liu Y, Liu Y, Xu W, Zhang Y, Xu C, Ren R, Li M, Gao J, Pang G. Studying allosteric regulation of chemokines and antagonists using a nanoscale hCCR3 receptor sensor. Int J Biol Macromol 2023; 253:126892. [PMID: 37709231 DOI: 10.1016/j.ijbiomac.2023.126892] [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: 07/08/2023] [Revised: 09/01/2023] [Accepted: 09/11/2023] [Indexed: 09/16/2023]
Abstract
CC chemokine receptor-3 (hCCR3), a G protein-coupled receptor (GPCR) expressed predominantly on eosinophils, is an important drug target. However, it was unclear how chemokine ligands, activators and antagonists recognize hCCR3, and quantitative measurements of hCCR3 inhibition or activation were rare. This study constructed a nanogold receptor sensor using hCCR3 as the molecular recognition element and horseradish peroxidase as the signal amplifier. We quantified the kinetic antagonism between chemokines and hCCR3 before and after adding hCCR3 antagonists. A molecular docking study was carried out to investigate how hCCR3 and its ligands work. The study results indicate chemokines interact with hCCR3 at low concentrations, and reversible hCCR3 inhibitors solely inhibit hCCR3, not CCLs. Moreover, a quantitative evaluation of hCCR3 chemokine activators and their antagonists was carried out using a directed weighted network. This offers a novel approach to quantitatively evaluate chemokine-receptor activation and antagonism together. This research could potentially offer new insights into the mechanisms of action of chemokines and drug screening.
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Affiliation(s)
- Xinqian Wang
- College of Biotechnology & food Science, Tianjin University of Commerce, Tianjin, China
| | - Dingqiang Lu
- College of Biotechnology & food Science, Tianjin University of Commerce, Tianjin, China.
| | - Dandan Peng
- College of Biotechnology & food Science, Tianjin University of Commerce, Tianjin, China
| | - Danyang Liu
- College of Biotechnology & food Science, Tianjin University of Commerce, Tianjin, China
| | - Yujiao Liu
- College of Biotechnology & food Science, Tianjin University of Commerce, Tianjin, China
| | - Yixuan Liu
- College of Biotechnology & food Science, Tianjin University of Commerce, Tianjin, China
| | - Wei Xu
- College of Biotechnology & food Science, Tianjin University of Commerce, Tianjin, China
| | - Yifei Zhang
- College of Biotechnology & food Science, Tianjin University of Commerce, Tianjin, China
| | - Chenyu Xu
- College of Biotechnology & food Science, Tianjin University of Commerce, Tianjin, China
| | - Ruijuan Ren
- Tianjin institute for food safety inspection technology, Tianjin, China.
| | - Ming Li
- College of Biotechnology & food Science, Tianjin University of Commerce, Tianjin, China
| | - Jinghan Gao
- College of Biotechnology & food Science, Tianjin University of Commerce, Tianjin, China
| | - Guangchang Pang
- College of Biotechnology & food Science, Tianjin University of Commerce, Tianjin, China.
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9
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Garg A, Lim JK. A Pocket Guide to CCR5-Neurotropic Flavivirus Edition. Viruses 2023; 16:28. [PMID: 38257729 PMCID: PMC10820758 DOI: 10.3390/v16010028] [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: 11/17/2023] [Revised: 12/19/2023] [Accepted: 12/21/2023] [Indexed: 01/24/2024] Open
Abstract
CCR5 is among the most studied chemokine receptors due to its profound significance in human health and disease. The notion that CCR5 is a functionally redundant receptor was challenged through the demonstration of its unique protective role in the context of West Nile virus in both mice and humans. In the nearly two decades since this initial discovery, numerous studies have investigated the role of CCR5 in the context of other medically important neurotropic flaviviruses, most of which appear to support a broad neuroprotective role for this receptor, although how CCR5 exerts its protective effect has been remarkably varied. In this review, we summarize the mechanisms by which CCR5 controls neurotropic flaviviruses, as well as results from human studies evaluating a genetic link to CCR5, and propose unexplored areas of research that are needed to unveil even more exciting roles for this important receptor.
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Affiliation(s)
| | - Jean K. Lim
- Department of Microbiology, The Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, Box 1124, New York, NY 10029, USA;
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10
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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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11
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Harms M, Fabech Hansson R, Gilg A, Almeida-Hernández Y, Löffler J, Rodríguez-Alfonso A, Habib MMW, Albers D, Ahmed NS, Abadi AH, Winter G, Rasche V, Beer AJ, Weidinger G, Preising N, Ständker L, Wiese S, Sanchez-Garcia E, Zelikin AN, Münch J. Development of N-Terminally Modified Variants of the CXCR4-Antagonistic Peptide EPI-X4 for Enhanced Plasma Stability. J Med Chem 2023; 66:15189-15204. [PMID: 37940118 PMCID: PMC10682998 DOI: 10.1021/acs.jmedchem.3c01128] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Indexed: 11/10/2023]
Abstract
EPI-X4, a natural peptide CXCR4 antagonist, shows potential for treating inflammation and cancer, but its short plasma stability limits its clinical application. We aimed to improve the plasma stability of EPI-X4 analogues without compromising CXCR4 antagonism. Our findings revealed that only the peptide N-terminus is prone to degradation. Consequently, incorporating d-amino acids or acetyl groups in this region enhanced peptide stability in plasma. Notably, EPI-X4 leads 5, 27, and 28 not only retained their CXCR4 binding and antagonism but also remained stable in plasma for over 8 h. Molecular dynamic simulations showed that these modified analogues bind similarly to CXCR4 as the original peptide. To further increase their systemic half-lives, we conjugated these stabilized analogues with large polymers and albumin binders. These advances highlight the potential of the optimized EPI-X4 analogues as promising CXCR4-targeted therapeutics and set the stage for more detailed preclinical assessments.
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Affiliation(s)
- Mirja Harms
- Institute
of Molecular Virology, Ulm University Medical
Center, Ulm 89081, Germany
| | - Rikke Fabech Hansson
- Department
of Chemistry and iNANO Interdisciplinary Nanoscience Centre, Aarhus University, Aarhus 8000, Denmark
| | - Andrea Gilg
- Institute
of Molecular Virology, Ulm University Medical
Center, Ulm 89081, Germany
| | - Yasser Almeida-Hernández
- Department
of Biochemical and Chemical Engineering, Computational Bioengineering, Emil-Figge Str. 66, Dortmund 44227, Germany
| | - Jessica Löffler
- Department
of Nuclear Medicine, Ulm University Medical
Center, Ulm 89081, Germany
| | - Armando Rodríguez-Alfonso
- Core
Facility Functional Peptidomics, Ulm University
Medical Center, Ulm 89081, Germany
- Core Unit
Mass Spectrometry and Proteomics, Ulm University
Medical Center, Ulm 89081, Germany
| | - Monica M. W. Habib
- Department
of Pharmaceutical Chemistry, Faculty of Pharmacy and Biotechnology, German University in Cairo, Cairo 11835, Egypt
- Pharmaceutical
Chemistry Department, School of Life and Medical Sciences, University of Hertfordshire Hosted by Global Academic
Foundation, Cairo 11865, Egypt
| | - Dan Albers
- Institute
of Molecular Virology, Ulm University Medical
Center, Ulm 89081, Germany
| | - Nermin S. Ahmed
- Department
of Pharmaceutical Chemistry, Faculty of Pharmacy and Biotechnology, German University in Cairo, Cairo 11835, Egypt
| | - Ashraf H. Abadi
- Department
of Pharmaceutical Chemistry, Faculty of Pharmacy and Biotechnology, German University in Cairo, Cairo 11835, Egypt
| | - Gordon Winter
- Department
of Nuclear Medicine, Ulm University Medical
Center, Ulm 89081, Germany
| | - Volker Rasche
- Experimental
Cardiovascular Imaging (ExCaVI), Ulm University
Medical Center, Ulm 89081, Germany
| | - Ambros J. Beer
- Department
of Nuclear Medicine, Ulm University Medical
Center, Ulm 89081, Germany
| | - Gilbert Weidinger
- Institute
of Biochemistry and Molecular Biology, Ulm
University, Ulm 89081, Germany
| | - Nico Preising
- Core
Facility Functional Peptidomics, Ulm University
Medical Center, Ulm 89081, Germany
| | - Ludger Ständker
- Core
Facility Functional Peptidomics, Ulm University
Medical Center, Ulm 89081, Germany
| | - Sebastian Wiese
- Core Unit
Mass Spectrometry and Proteomics, Ulm University
Medical Center, Ulm 89081, Germany
| | - Elsa Sanchez-Garcia
- Department
of Biochemical and Chemical Engineering, Computational Bioengineering, Emil-Figge Str. 66, Dortmund 44227, Germany
| | - Alexander N. Zelikin
- Department
of Chemistry and iNANO Interdisciplinary Nanoscience Centre, Aarhus University, Aarhus 8000, Denmark
| | - Jan Münch
- Institute
of Molecular Virology, Ulm University Medical
Center, Ulm 89081, Germany
- Core
Facility Functional Peptidomics, Ulm University
Medical Center, Ulm 89081, Germany
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12
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Zhao J, An K, Mao Z, Qu Y, Wang D, Li J, Min Z, Xue Z. CCL5 promotes LFA-1 expression in Th17 cells and induces LCK and ZAP70 activation in a mouse model of Parkinson's disease. Front Aging Neurosci 2023; 15:1250685. [PMID: 38020765 PMCID: PMC10655117 DOI: 10.3389/fnagi.2023.1250685] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Accepted: 10/20/2023] [Indexed: 12/01/2023] Open
Abstract
Background Parkinson's disease (PD), which is associated to autoimmune disorders, is characterized by the pathological deposition of alpha-synuclein (α-Syn) and loss of dopaminergic (DA) neurons. Th17 cells are thought to be responsible for the direct loss of DA neurons. C-C chemokine ligand 5 (CCL5) specifically induces Th17 cell infiltration into the SN. However, the specific effect of CCL5 on Th17 cells in PD and the relationship between CCL5 and lymphocyte function-associated antigen-1 (LFA-1) expression in Th17 cells are unknown. Methods We evaluated the effects of CCL5 on LFA-1 expression in Th17 cells in mice treated with 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine (MPTP) and examined Th17 cell differentiation upon CCL5 stimulation in vitro. Furthermore, we assessed the effects of CCL5 on tyrosine kinase zeta-chain-associated protein kinase 70 (ZAP70) and lymphocyte-specific protein tyrosine kinase (LCK) activity in CCL5-stimulated Th17 cells in vivo and in vitro. Results CCL5 increased the proportion of peripheral Th17 cells in MPTP-treated mice, LFA-1 expression on Th17 cells, and Th17 cell levels in the SN of MPTP-treated mice. CCL5 promoted Th17 cell differentiation and LFA-1 expression in naive T cells in vitro. Moreover, CCL5 increased Th17 cell differentiation and LFA-1 expression by stimulating LCK and ZAP70 activation in naive CD4+ T cells. Inhibiting LCK and ZAP70 activation reduced the proportion of peripheral Th17 cells and LFA-1 surface expression in MPTP-treated mice, and Th17 cell levels in the SN also significantly decreased. Conclusion CCL5, which increased Th17 cell differentiation and LFA-1 protein expression by activating LCK and ZAP70, could increase the Th17 cell number in the SN, induce DA neuron death and aggravate PD.
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Affiliation(s)
| | | | | | | | | | | | - Zhe Min
- Department of Neurology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Zheng Xue
- Department of Neurology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
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13
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Li W, Qin Z, Nand E, Grunst MW, Grover JR, Bess JW, Lifson JD, Zwick MB, Tagare HD, Uchil PD, Mothes W. HIV-1 Env trimers asymmetrically engage CD4 receptors in membranes. Nature 2023; 623:1026-1033. [PMID: 37993716 PMCID: PMC10686830 DOI: 10.1038/s41586-023-06762-6] [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: 12/24/2022] [Accepted: 10/19/2023] [Indexed: 11/24/2023]
Abstract
Human immunodeficiency virus 1 (HIV-1) infection is initiated by binding of the viral envelope glycoprotein (Env) to the cell-surface receptor CD41-4. Although high-resolution structures of Env in a complex with the soluble domains of CD4 have been determined, the binding process is less understood in native membranes5-13. Here we used cryo-electron tomography to monitor Env-CD4 interactions at the membrane-membrane interfaces formed between HIV-1 and CD4-presenting virus-like particles. Env-CD4 complexes organized into clusters and rings, bringing the opposing membranes closer together. Env-CD4 clustering was dependent on capsid maturation. Subtomogram averaging and classification revealed that Env bound to one, two and finally three CD4 molecules, after which Env adopted an open state. Our data indicate that asymmetric HIV-1 Env trimers bound to one and two CD4 molecules are detectable intermediates during virus binding to host cell membranes, which probably has consequences for antibody-mediated immune responses and vaccine immunogen design.
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Affiliation(s)
- Wenwei Li
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, CT, USA.
| | - Zhuan Qin
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, CT, USA
| | - Elizabeth Nand
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, CT, USA
| | - Michael W Grunst
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, CT, USA
| | - Jonathan R Grover
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, CT, USA
| | - Julian W Bess
- AIDS and Cancer Virus Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Jeffrey D Lifson
- AIDS and Cancer Virus Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Michael B Zwick
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Hemant D Tagare
- Department of Radiology and Biomedical Imaging, Yale University, New Haven, CT, USA
| | - Pradeep D Uchil
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, CT, USA
| | - Walther Mothes
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, CT, USA.
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14
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Di Marino D, Conflitti P, Motta S, Limongelli V. Structural basis of dimerization of chemokine receptors CCR5 and CXCR4. Nat Commun 2023; 14:6439. [PMID: 37833254 PMCID: PMC10575954 DOI: 10.1038/s41467-023-42082-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2021] [Accepted: 09/28/2023] [Indexed: 10/15/2023] Open
Abstract
G protein-coupled receptors (GPCRs) are prominent drug targets responsible for extracellular-to-intracellular signal transduction. GPCRs can form functional dimers that have been poorly characterized so far. Here, we show the dimerization mechanism of the chemokine receptors CCR5 and CXCR4 by means of an advanced free-energy technique named coarse-grained metadynamics. Our results reproduce binding events between the GPCRs occurring in the minute timescale, revealing a symmetric and an asymmetric dimeric structure for each of the three investigated systems, CCR5/CCR5, CXCR4/CXCR4, and CCR5/CXCR4. The transmembrane helices TM4-TM5 and TM6-TM7 are the preferred binding interfaces for CCR5 and CXCR4, respectively. The identified dimeric states differ in the access to the binding sites of the ligand and G protein, indicating that dimerization may represent a fine allosteric mechanism to regulate receptor activity. Our study offers structural basis for the design of ligands able to modulate the formation of CCR5 and CXCR4 dimers and in turn their activity, with therapeutic potential against HIV, cancer, and immune-inflammatory diseases.
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Affiliation(s)
- Daniele Di Marino
- Department of Life and Environmental Sciences - New York-Marche Structural Biology Centre (NY-MaSBiC), Polytechnic University of Marche, Via Brecce Bianche, 60131, Ancona, Italy
- Neuronal Death and Neuroprotection Unit, Department of Neuroscience, Mario Negri Institute for Pharmacological Research-IRCCS, Via Mario Negri 2, 20156, Milan, Italy
- National Biodiversity Future Center (NBFC), Palermo, Italy
| | - Paolo Conflitti
- Università della Svizzera italiana (USI), Faculty of Biomedical Sciences, Euler Institute, Via G. Buffi 13, CH-6900, Lugano, Switzerland
| | - Stefano Motta
- Department of Earth and Environmental Sciences, University of Milano-Bicocca, Piazza della Scienza 1, 20126, Milan, Italy
| | - Vittorio Limongelli
- Università della Svizzera italiana (USI), Faculty of Biomedical Sciences, Euler Institute, Via G. Buffi 13, CH-6900, Lugano, Switzerland.
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15
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Dragan P, Joshi K, Atzei A, Latek D. Keras/TensorFlow in Drug Design for Immunity Disorders. Int J Mol Sci 2023; 24:15009. [PMID: 37834457 PMCID: PMC10573944 DOI: 10.3390/ijms241915009] [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: 09/08/2023] [Revised: 09/21/2023] [Accepted: 09/29/2023] [Indexed: 10/15/2023] Open
Abstract
Homeostasis of the host immune system is regulated by white blood cells with a variety of cell surface receptors for cytokines. Chemotactic cytokines (chemokines) activate their receptors to evoke the chemotaxis of immune cells in homeostatic migrations or inflammatory conditions towards inflamed tissue or pathogens. Dysregulation of the immune system leading to disorders such as allergies, autoimmune diseases, or cancer requires efficient, fast-acting drugs to minimize the long-term effects of chronic inflammation. Here, we performed structure-based virtual screening (SBVS) assisted by the Keras/TensorFlow neural network (NN) to find novel compound scaffolds acting on three chemokine receptors: CCR2, CCR3, and one CXC receptor, CXCR3. Keras/TensorFlow NN was used here not as a typically used binary classifier but as an efficient multi-class classifier that can discard not only inactive compounds but also low- or medium-activity compounds. Several compounds proposed by SBVS and NN were tested in 100 ns all-atom molecular dynamics simulations to confirm their binding affinity. To improve the basic binding affinity of the compounds, new chemical modifications were proposed. The modified compounds were compared with known antagonists of these three chemokine receptors. Known CXCR3 compounds were among the top predicted compounds; thus, the benefits of using Keras/TensorFlow in drug discovery have been shown in addition to structure-based approaches. Furthermore, we showed that Keras/TensorFlow NN can accurately predict the receptor subtype selectivity of compounds, for which SBVS often fails. We cross-tested chemokine receptor datasets retrieved from ChEMBL and curated datasets for cannabinoid receptors. The NN model trained on the cannabinoid receptor datasets retrieved from ChEMBL was the most accurate in the receptor subtype selectivity prediction. Among NN models trained on the chemokine receptor datasets, the CXCR3 model showed the highest accuracy in differentiating the receptor subtype for a given compound dataset.
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Affiliation(s)
- Paulina Dragan
- Faculty of Chemistry, University of Warsaw, Pasteura 1, 02-903 Warsaw, Poland; (P.D.); (A.A.)
| | - Kavita Joshi
- Faculty of Chemistry, University of Warsaw, Pasteura 1, 02-903 Warsaw, Poland; (P.D.); (A.A.)
| | - Alessandro Atzei
- Faculty of Chemistry, University of Warsaw, Pasteura 1, 02-903 Warsaw, Poland; (P.D.); (A.A.)
- Department of Life and Environmental Science, Food Toxicology Unit, University of Cagliari, University Campus of Monserrato, SS 554, 09042 Cagliari, Italy
| | - Dorota Latek
- Faculty of Chemistry, University of Warsaw, Pasteura 1, 02-903 Warsaw, Poland; (P.D.); (A.A.)
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16
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Conserved HIV-1 V3 loop helix offers potential for broad neutralization. Nat Struct Mol Biol 2023; 30:1256-1257. [PMID: 37644218 DOI: 10.1038/s41594-023-01063-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/31/2023]
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17
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Sarker MS. Prevalence of R5 and X4-Tropic strains in HIV-1 Infected bangladeshi population. Indian J Med Microbiol 2023; 45:100377. [DOI: https:/doi.org/10.1016/j.ijmmb.2023.100377] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2023]
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18
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Sarker MS. Prevalence of R5 and X4-Tropic strains in HIV-1 Infected bangladeshi population. Indian J Med Microbiol 2023; 45:100377. [PMID: 37573044 DOI: 10.1016/j.ijmmb.2023.100377] [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: 10/20/2022] [Revised: 04/03/2023] [Accepted: 04/16/2023] [Indexed: 08/14/2023]
Abstract
PURPOSE HIV uses CD4 as main receptor to infect a cell. Also, it uses coreceptor (CCR5 or CXCR4) as a surrogate marker. In Bangladesh, nearly 50% of the identified strains are subtype C. In this study, we have examined viral genotypic co-receptor tropism in Bangladesh People Living with HIV (PLHIV). METHODS We identified a co-receptor on V3 sequences of the HIV env gene. The online Geno2pheno tools was used. The threshold limit of a 10% false-positive rate was used. Samples from HIV-infected individuals aged 5-50 years were taken from which we obtained a good quality of 55 sequences. The viral tropism frequency in different circulating Bangladeshi HIV subtypes was analyzed using SPSS. RESULTS Above two third of the samples, (61.8%; 34 of 55) were HIV-1 subtype C. We identified 83.6% (46 of 55) of the samples were R5tropic, 16.4% (9 of 55) as X4 tropic, HIV-1 strains. The R5 tropic strains among key population infected with different HIV-1 subtype in the Bangladeshi population is common. CONCLUSIONS This finding can help with suitable drug selection in reverse-transcriptase (RT) or protease (PR) drug-resistance strains.
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Affiliation(s)
- Md Safiullah Sarker
- Virology Laboratory, International Centre for Diarrhoeal Diseases Research, Bangladesh (ICDDR,B), Mohakhali, Dhaka-1212, Bangladesh.
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19
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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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20
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Brunetti NS, Davanzo GG, de Moraes D, Ferrari AJR, Souza GF, Muraro SP, Knittel TL, Boldrini VO, Monteiro LB, Virgílio-da-Silva JV, Profeta GS, Wassano NS, Nunes Santos L, Carregari VC, Dias AHS, Veras FP, Tavares LA, Forato J, Castro IMS, Silva-Costa LC, Palma AC, Mansour E, Ulaf RG, Bernardes AF, Nunes TA, Ribeiro LC, Agrela MV, Moretti ML, Buscaratti LI, Crunfli F, Ludwig RG, Gerhardt JA, Munhoz-Alves N, Marques AM, Sesti-Costa R, Amorim MR, Toledo-Teixeira DA, Parise PL, Martini MC, Bispos-Dos-Santos K, Simeoni CL, Granja F, Silvestrini VC, de Oliveira EB, Faca VM, Carvalho M, Castelucci BG, Pereira AB, Coimbra LD, Dias MMG, Rodrigues PB, Gomes ABSP, Pereira FB, Santos LMB, Bloyet LM, Stumpf S, Pontelli MC, Whelan S, Sposito AC, Carvalho RF, Vieira AS, Vinolo MAR, Damasio A, Velloso L, Figueira ACM, da Silva LLP, Cunha TM, Nakaya HI, Marques-Souza H, Marques RE, Martins-de-Souza D, Skaf MS, Proenca-Modena JL, Moraes-Vieira PMM, Mori MA, Farias AS. SARS-CoV-2 uses CD4 to infect T helper lymphocytes. eLife 2023; 12:e84790. [PMID: 37523305 PMCID: PMC10390044 DOI: 10.7554/elife.84790] [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: 11/30/2022] [Accepted: 07/13/2023] [Indexed: 08/02/2023] Open
Abstract
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the agent of a major global outbreak of respiratory tract disease known as Coronavirus Disease 2019 (COVID-19). SARS-CoV-2 infects mainly lungs and may cause several immune-related complications, such as lymphocytopenia and cytokine storm, which are associated with the severity of the disease and predict mortality. The mechanism by which SARS-CoV-2 infection may result in immune system dysfunction is still not fully understood. Here, we show that SARS-CoV-2 infects human CD4+ T helper cells, but not CD8+ T cells, and is present in blood and bronchoalveolar lavage T helper cells of severe COVID-19 patients. We demonstrated that SARS-CoV-2 spike glycoprotein (S) directly binds to the CD4 molecule, which in turn mediates the entry of SARS- CoV-2 in T helper cells. This leads to impaired CD4 T cell function and may cause cell death. SARS-CoV-2-infected T helper cells express higher levels of IL-10, which is associated with viral persistence and disease severity. Thus, CD4-mediated SARS-CoV-2 infection of T helper cells may contribute to a poor immune response in COVID-19 patients.
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Grants
- #2295/20 Fundo de Apoio ao Ensino, à Pesquisa e Extensão, Universidade Estadual de Campinas
- #2021/08354-2 Fundação de Amparo à Pesquisa do Estado de São Paulo
- #2015/15626-8 Fundação de Amparo à Pesquisa do Estado de São Paulo
- #2019/14465-1 Fundação de Amparo à Pesquisa do Estado de São Paulo
- #465489/2014-1 Instituto Nacional de Ciência e Tecnologia em Neuroimunomodulação
- #01.20.0003.00 Financiadora de Estudos e Projetos
- #306248/2017-4 Conselho Nacional de Desenvolvimento Científico e Tecnológico
- #2019/17007-4 Fundação de Amparo à Pesquisa do Estado de São Paulo
- #2019/04726-2 Fundação de Amparo à Pesquisa do Estado de São Paulo
- #2319/20 Fundo de Apoio ao Ensino, à Pesquisa e Extensão, Universidade Estadual de Campinas
- #2274/20 Fundo de Apoio ao Ensino, à Pesquisa e Extensão, Universidade Estadual de Campinas
- #2266/20 Fundo de Apoio ao Ensino, à Pesquisa e Extensão, Universidade Estadual de Campinas
- #2458/20 Fundo de Apoio ao Ensino, à Pesquisa e Extensão, Universidade Estadual de Campinas
- #2019/16116-4 Fundação de Amparo à Pesquisa do Estado de São Paulo
- #2019/06372-3 Fundação de Amparo à Pesquisa do Estado de São Paulo
- #2020/04583-4 Fundação de Amparo à Pesquisa do Estado de São Paulo
- #2013/08293-7 Fundação de Amparo à Pesquisa do Estado de São Paulo
- #2020/04579-7 Fundação de Amparo à Pesquisa do Estado de São Paulo
- #2018/14933-2 Fundação de Amparo à Pesquisa do Estado de São Paulo
- #2020/04746-0 Fundação de Amparo à Pesquisa do Estado de São Paulo
- #2019/00098-7 Fundação de Amparo à Pesquisa do Estado de São Paulo
- #2020/04919-2 Fundação de Amparo à Pesquisa do Estado de São Paulo
- #2017/01184-9 Fundação de Amparo à Pesquisa do Estado de São Paulo
- #2020/04558-0 Fundação de Amparo à Pesquisa do Estado de São Paulo
- #2016/00194-8 Fundação de Amparo à Pesquisa do Estado de São Paulo
- #2016/18031- 8 Fundação de Amparo à Pesquisa do Estado de São Paulo
- #2019/22398-2 Fundação de Amparo à Pesquisa do Estado de São Paulo
- #2019/13552-8 Fundação de Amparo à Pesquisa do Estado de São Paulo
- #2019/05155-9 Fundação de Amparo à Pesquisa do Estado de São Paulo
- #2019/06459-1 Fundação de Amparo à Pesquisa do Estado de São Paulo
- #2017/23920-9 Fundação de Amparo à Pesquisa do Estado de São Paulo
- #2016/24163-4 Fundação de Amparo à Pesquisa do Estado de São Paulo
- #2016/23328-0 Fundação de Amparo à Pesquisa do Estado de São Paulo
- #310287/2018-9 Conselho Nacional de Desenvolvimento Científico e Tecnológico
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Affiliation(s)
- Natalia S Brunetti
- Autoimmune Research Laboratory, Department of Genetics, Microbiology and Immunology, Institute of Biology, University of Campinas (UNICAMP), Campinas, Brazil
| | - Gustavo G Davanzo
- Laboratory of Immunometabolism, Department of Genetics, Microbiology and Immunology, Institute of Biology, University of Campinas (UNICAMP), Campinas, Brazil
| | - Diogo de Moraes
- Laboratory of Aging Biology, Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas (UNICAMP), Campinas, Brazil
- Department of Structural and Functional Biology, Institute of Biosciences, Sao Paulo State University (UNESP), Botucatu, Brazil
| | - Allan J R Ferrari
- Institute of Chemistry and Center for Computing in Engineering and Sciences, University of Campinas, Campinas (UNICAMP), Campinas, Brazil
| | - Gabriela F Souza
- Laboratory of Emerging Viruses, Department of Genetics, Microbiology and Immunology, Institute of Biology, University of Campinas (UNICAMP), Campinas, Brazil
| | - Stéfanie Primon Muraro
- Laboratory of Emerging Viruses, Department of Genetics, Microbiology and Immunology, Institute of Biology, University of Campinas (UNICAMP), Campinas, Brazil
| | - Thiago L Knittel
- Laboratory of Aging Biology, Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas (UNICAMP), Campinas, Brazil
| | - Vinicius O Boldrini
- Autoimmune Research Laboratory, Department of Genetics, Microbiology and Immunology, Institute of Biology, University of Campinas (UNICAMP), Campinas, Brazil
| | - Lauar B Monteiro
- Laboratory of Immunometabolism, Department of Genetics, Microbiology and Immunology, Institute of Biology, University of Campinas (UNICAMP), Campinas, Brazil
| | - João Victor Virgílio-da-Silva
- Laboratory of Immunometabolism, Department of Genetics, Microbiology and Immunology, Institute of Biology, University of Campinas (UNICAMP), Campinas, Brazil
| | - Gerson S Profeta
- Laboratory of Aging Biology, Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas (UNICAMP), Campinas, Brazil
| | - Natália S Wassano
- Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas (UNICAMP), Campinas, Brazil
| | - Luana Nunes Santos
- Brazilian Laboratory on Silencing Technologies (BLaST), Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas (UNICAMP), Campinas, Brazil
| | - Victor C Carregari
- Laboratory of Neuroproteomics, Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas (UNICAMP), Campinas, Brazil
| | - Artur H S Dias
- Institute of Chemistry and Center for Computing in Engineering and Sciences, University of Campinas, Campinas (UNICAMP), Campinas, Brazil
| | - Flavio P Veras
- Center of Research in Inflammatory Diseases, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, São Paulo, Brazil
- Department of BioMolecular Sciences, School of Pharmaceutical Sciences, University of São Paulo, Ribeirão Preto, São Paulo, Brazil
- Department of Pharmacology, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto,, São Paulo, Brazil
| | - Lucas A Tavares
- Department of Cell and Molecular Biology, Center for Virology Research, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, Brazil
| | - Julia Forato
- Laboratory of Emerging Viruses, Department of Genetics, Microbiology and Immunology, Institute of Biology, University of Campinas (UNICAMP), Campinas, Brazil
| | - Icaro M S Castro
- Department of Clinical and Toxicological Analyses, School of Pharmaceutical Sciences, University of São Paulo, São Paulo, Brazil
| | - Lícia C Silva-Costa
- Laboratory of Neuroproteomics, Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas (UNICAMP), Campinas, Brazil
| | - André C Palma
- Department of Internal Medicine, School of Medical Sciences, University of Campinas (UNICAMP), Campinas, Brazil
| | - Eli Mansour
- Department of Internal Medicine, School of Medical Sciences, University of Campinas (UNICAMP), Campinas, Brazil
| | - Raisa G Ulaf
- Department of Internal Medicine, School of Medical Sciences, University of Campinas (UNICAMP), Campinas, Brazil
| | - Ana F Bernardes
- Department of Internal Medicine, School of Medical Sciences, University of Campinas (UNICAMP), Campinas, Brazil
| | - Thyago A Nunes
- Department of Internal Medicine, School of Medical Sciences, University of Campinas (UNICAMP), Campinas, Brazil
| | - Luciana C Ribeiro
- Department of Internal Medicine, School of Medical Sciences, University of Campinas (UNICAMP), Campinas, Brazil
| | - Marcus V Agrela
- Department of Internal Medicine, School of Medical Sciences, University of Campinas (UNICAMP), Campinas, Brazil
| | - Maria Luiza Moretti
- Department of Internal Medicine, School of Medical Sciences, University of Campinas (UNICAMP), Campinas, Brazil
| | - Lucas I Buscaratti
- Brazilian Laboratory on Silencing Technologies (BLaST), Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas (UNICAMP), Campinas, Brazil
| | - Fernanda Crunfli
- Laboratory of Neuroproteomics, Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas (UNICAMP), Campinas, Brazil
| | - Raissa G Ludwig
- Laboratory of Aging Biology, Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas (UNICAMP), Campinas, Brazil
| | - Jaqueline A Gerhardt
- Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas (UNICAMP), Campinas, Brazil
| | - Natália Munhoz-Alves
- Autoimmune Research Laboratory, Department of Genetics, Microbiology and Immunology, Institute of Biology, University of Campinas (UNICAMP), Campinas, Brazil
| | - Ana Maria Marques
- Autoimmune Research Laboratory, Department of Genetics, Microbiology and Immunology, Institute of Biology, University of Campinas (UNICAMP), Campinas, Brazil
| | - Renata Sesti-Costa
- Autoimmune Research Laboratory, Department of Genetics, Microbiology and Immunology, Institute of Biology, University of Campinas (UNICAMP), Campinas, Brazil
- Hematology and Hemotherapy Center, University of Campinas (UNICAMP), Campinas, Brazil
| | - Mariene R Amorim
- Laboratory of Emerging Viruses, Department of Genetics, Microbiology and Immunology, Institute of Biology, University of Campinas (UNICAMP), Campinas, Brazil
| | - Daniel A Toledo-Teixeira
- Laboratory of Emerging Viruses, Department of Genetics, Microbiology and Immunology, Institute of Biology, University of Campinas (UNICAMP), Campinas, Brazil
| | - Pierina Lorencini Parise
- Laboratory of Emerging Viruses, Department of Genetics, Microbiology and Immunology, Institute of Biology, University of Campinas (UNICAMP), Campinas, Brazil
| | - Matheus Cavalheiro Martini
- Laboratory of Emerging Viruses, Department of Genetics, Microbiology and Immunology, Institute of Biology, University of Campinas (UNICAMP), Campinas, Brazil
| | - Karina Bispos-Dos-Santos
- Laboratory of Emerging Viruses, Department of Genetics, Microbiology and Immunology, Institute of Biology, University of Campinas (UNICAMP), Campinas, Brazil
| | - Camila L Simeoni
- Laboratory of Emerging Viruses, Department of Genetics, Microbiology and Immunology, Institute of Biology, University of Campinas (UNICAMP), Campinas, Brazil
| | - Fabiana Granja
- Laboratory of Emerging Viruses, Department of Genetics, Microbiology and Immunology, Institute of Biology, University of Campinas (UNICAMP), Campinas, Brazil
| | - Virgínia C Silvestrini
- Department of Biochemistry and Immunology, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, Brazil
| | - Eduardo B de Oliveira
- Department of Biochemistry and Immunology, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, Brazil
| | - Vitor M Faca
- Department of Biochemistry and Immunology, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, Brazil
| | - Murilo Carvalho
- National Biosciences Laboratory (LNBio), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, Brazil
- Brazilian Synchrotron Light Laboratory (LNLS), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, Brazil
| | - Bianca G Castelucci
- National Biosciences Laboratory (LNBio), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, Brazil
- Brazilian Synchrotron Light Laboratory (LNLS), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, Brazil
| | - Alexandre B Pereira
- National Biosciences Laboratory (LNBio), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, Brazil
| | - Laís D Coimbra
- National Biosciences Laboratory (LNBio), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, Brazil
| | - Marieli M G Dias
- National Biosciences Laboratory (LNBio), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, Brazil
| | - Patricia B Rodrigues
- Laboratory of Immunoinflammation, Department of Genetics, Microbiology and Immunology, Institute of Biology, University of Campinas (UNICAMP), Campinas, Brazil;, Campinas, Brazil
| | - Arilson Bernardo S P Gomes
- Laboratory of Immunoinflammation, Department of Genetics, Microbiology and Immunology, Institute of Biology, University of Campinas (UNICAMP), Campinas, Brazil;, Campinas, Brazil
| | - Fabricio B Pereira
- Hematology and Hemotherapy Center, University of Campinas (UNICAMP), Campinas, Brazil
| | - Leonilda M B Santos
- Neuroimmunology Unit, Department of Genetics, Microbiology and Immunology, University of Campinas (UNICAMP), Campinas, Brazil
- National Institute of Science and Technology on Neuroimmunomodulation (INCT-NIM) - Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Rio de Janeiro, Brazil
| | - Louis-Marie Bloyet
- Washington University in St Louis, Department of Molecular Microbiology, St. Louis, United States
| | - Spencer Stumpf
- Washington University in St Louis, Department of Molecular Microbiology, St. Louis, United States
| | - Marjorie C Pontelli
- Washington University in St Louis, Department of Molecular Microbiology, St. Louis, United States
| | - Sean Whelan
- Washington University in St Louis, Department of Molecular Microbiology, St. Louis, United States
| | - Andrei C Sposito
- Laboratory of Vascular Biology and Arteriosclerosis, School of Medical Sciences, University of Campinas (UNICAMP), Campinas, Brazil
| | - Robson F Carvalho
- Department of Structural and Functional Biology, Institute of Biosciences, Sao Paulo State University (UNESP), Botucatu, Brazil
| | - André S Vieira
- Laboratory of Electrophysiology, Neurobiology and Behavior, University of Campinas (UNICAMP), Campinas, Brazil
| | - Marco A R Vinolo
- Laboratory of Immunoinflammation, Department of Genetics, Microbiology and Immunology, Institute of Biology, University of Campinas (UNICAMP), Campinas, Brazil;, Campinas, Brazil
- Experimental Medicine Research Cluster (EMRC), University of Campinas (UNICAMP), Campinas, Brazil
- Obesity and Comorbidities Research Center (OCRC), University of Campinas (UNICAMP), Campinas, Brazil
| | - André Damasio
- Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas (UNICAMP), Campinas, Brazil
- Experimental Medicine Research Cluster (EMRC), University of Campinas (UNICAMP), Campinas, Brazil
| | - Licio Velloso
- Department of Internal Medicine, School of Medical Sciences, University of Campinas (UNICAMP), Campinas, Brazil
- Obesity and Comorbidities Research Center (OCRC), University of Campinas (UNICAMP), Campinas, Brazil
| | - Ana Carolina M Figueira
- National Biosciences Laboratory (LNBio), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, Brazil
| | - Luis L P da Silva
- Center of Research in Inflammatory Diseases, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, São Paulo, Brazil
| | - Thiago Mattar Cunha
- Center of Research in Inflammatory Diseases, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, São Paulo, Brazil
- Department of Pharmacology, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto,, São Paulo, Brazil
| | - Helder I Nakaya
- Department of Clinical and Toxicological Analyses, School of Pharmaceutical Sciences, University of São Paulo, São Paulo, Brazil
| | - Henrique Marques-Souza
- Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas (UNICAMP), Campinas, Brazil
- Brazilian Laboratory on Silencing Technologies (BLaST), Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas (UNICAMP), Campinas, Brazil
| | - Rafael E Marques
- National Biosciences Laboratory (LNBio), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, Brazil
| | - Daniel Martins-de-Souza
- Laboratory of Neuroproteomics, Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas (UNICAMP), Campinas, Brazil
- Experimental Medicine Research Cluster (EMRC), University of Campinas (UNICAMP), Campinas, Brazil
- D'Or Institute for Research and Education (IDOR), São Paulo, Brazil
- National Institute of Science and Technology in Biomarkers for Neuropsychiatry (INCTINBION), São Paulo, Brazil
| | - Munir S Skaf
- Institute of Chemistry and Center for Computing in Engineering and Sciences, University of Campinas, Campinas (UNICAMP), Campinas, Brazil
| | - Jose Luiz Proenca-Modena
- Laboratory of Emerging Viruses, Department of Genetics, Microbiology and Immunology, Institute of Biology, University of Campinas (UNICAMP), Campinas, Brazil
- Experimental Medicine Research Cluster (EMRC), University of Campinas (UNICAMP), Campinas, Brazil
| | - Pedro M M Moraes-Vieira
- Laboratory of Immunometabolism, Department of Genetics, Microbiology and Immunology, Institute of Biology, University of Campinas (UNICAMP), Campinas, Brazil
- Experimental Medicine Research Cluster (EMRC), University of Campinas (UNICAMP), Campinas, Brazil
- Obesity and Comorbidities Research Center (OCRC), University of Campinas (UNICAMP), Campinas, Brazil
| | - Marcelo A Mori
- Laboratory of Aging Biology, Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas (UNICAMP), Campinas, Brazil
- Experimental Medicine Research Cluster (EMRC), University of Campinas (UNICAMP), Campinas, Brazil
- Obesity and Comorbidities Research Center (OCRC), University of Campinas (UNICAMP), Campinas, Brazil
| | - Alessandro S Farias
- Autoimmune Research Laboratory, Department of Genetics, Microbiology and Immunology, Institute of Biology, University of Campinas (UNICAMP), Campinas, Brazil
- Washington University in St Louis, Department of Molecular Microbiology, St. Louis, United States
- Experimental Medicine Research Cluster (EMRC), University of Campinas (UNICAMP), Campinas, Brazil
- Obesity and Comorbidities Research Center (OCRC), University of Campinas (UNICAMP), Campinas, Brazil
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21
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Bauer A, Lindemuth E, Marino FE, Krause R, Joy J, Docken SS, Mallick S, McCormick K, Holt C, Georgiev I, Felber B, Keele BF, Veazey R, Davenport MP, Li H, Shaw GM, Bar KJ. Adaptation of a transmitted/founder simian-human immunodeficiency virus for enhanced replication in rhesus macaques. PLoS Pathog 2023; 19:e1011059. [PMID: 37399208 PMCID: PMC10348547 DOI: 10.1371/journal.ppat.1011059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2022] [Revised: 07/14/2023] [Accepted: 06/21/2023] [Indexed: 07/05/2023] Open
Abstract
Transmitted/founder (TF) simian-human immunodeficiency viruses (SHIVs) express HIV-1 envelopes modified at position 375 to efficiently infect rhesus macaques while preserving authentic HIV-1 Env biology. SHIV.C.CH505 is an extensively characterized virus encoding the TF HIV-1 Env CH505 mutated at position 375 shown to recapitulate key features of HIV-1 immunobiology, including CCR5-tropism, a tier 2 neutralization profile, reproducible early viral kinetics, and authentic immune responses. SHIV.C.CH505 is used frequently in nonhuman primate studies of HIV, but viral loads after months of infection are variable and typically lower than those in people living with HIV. We hypothesized that additional mutations besides Δ375 might further enhance virus fitness without compromising essential components of CH505 Env biology. From sequence analysis of SHIV.C.CH505-infected macaques across multiple experiments, we identified a signature of envelope mutations associated with higher viremia. We then used short-term in vivo mutational selection and competition to identify a minimally adapted SHIV.C.CH505 with just five amino acid changes that substantially improve virus replication fitness in macaques. Next, we validated the performance of the adapted SHIV in vitro and in vivo and identified the mechanistic contributions of selected mutations. In vitro, the adapted SHIV shows improved virus entry, enhanced replication on primary rhesus cells, and preserved neutralization profiles. In vivo, the minimally adapted virus rapidly outcompetes the parental SHIV with an estimated growth advantage of 0.14 days-1 and persists through suppressive antiretroviral therapy to rebound at treatment interruption. Here, we report the successful generation of a well-characterized, minimally adapted virus, termed SHIV.C.CH505.v2, with enhanced replication fitness and preserved native Env properties that can serve as a new reagent for NHP studies of HIV-1 transmission, pathogenesis, and cure.
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Affiliation(s)
- Anya Bauer
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Emily Lindemuth
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Francesco Elia Marino
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Ryan Krause
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Jaimy Joy
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | | | - Suvadip Mallick
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Kevin McCormick
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Clinton Holt
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University, Nashville, Tennessee, United States of America
| | - Ivelin Georgiev
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University, Nashville, Tennessee, United States of America
| | - Barbara Felber
- Human Retrovirus Pathogenesis Section, Vaccine Branch, Center for Cancer Research, National Cancer Institute, Maryland, United States of America
| | - Brandon F. Keele
- AIDS and Cancer Virus Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland, United States of America
| | - Ronald Veazey
- Department of Pathology and Laboratory Medicine, Tulane School of Medicine, New Orleans, Louisiana, United States of America
| | | | - Hui Li
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
- Departments of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - George M. Shaw
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
- Departments of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Katharine J. Bar
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
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22
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Cervantes M, Hess T, Morbioli GG, Sengar A, Kasson PM. The ACE2 receptor accelerates but is not biochemically required for SARS-CoV-2 membrane fusion. Chem Sci 2023; 14:6997-7004. [PMID: 37389252 PMCID: PMC10306070 DOI: 10.1039/d2sc06967a] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Accepted: 06/05/2023] [Indexed: 07/01/2023] Open
Abstract
The SARS-CoV-2 coronavirus infects human cells via the ACE2 receptor. Structural evidence suggests that ACE2 may not just serve as an attachment factor but also conformationally activate the SARS-CoV-2 spike protein for membrane fusion. Here, we test that hypothesis directly, using DNA-lipid tethering as a synthetic attachment factor in place of ACE2. We find that SARS-CoV-2 pseudovirus and virus-like particles are capable of membrane fusion without ACE2 if activated with an appropriate protease. Thus, ACE2 is not biochemically required for SARS-CoV-2 membrane fusion. However, addition of soluble ACE2 speeds up the fusion reaction. On a per-spike level, ACE2 appears to promote activation for fusion and then subsequent inactivation if an appropriate protease is not present. Kinetic analysis suggests at least two rate-limiting steps for SARS-CoV-2 membrane fusion, one of which is ACE2 dependent and one of which is not. Since ACE2 serves as a high-affinity attachment factor on human cells, the possibility to replace it with other factors implies a flatter fitness landscape for host adaptation by SARS-CoV-2 and future related coronaviruses.
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Affiliation(s)
- Marcos Cervantes
- Departments of Molecular Physiology and Biomedical Engineering, University of Virginia Charlottesville VA 22908 USA
| | - Tobin Hess
- Departments of Molecular Physiology and Biomedical Engineering, University of Virginia Charlottesville VA 22908 USA
| | - Giorgio G Morbioli
- Departments of Molecular Physiology and Biomedical Engineering, University of Virginia Charlottesville VA 22908 USA
| | - Anjali Sengar
- Departments of Molecular Physiology and Biomedical Engineering, University of Virginia Charlottesville VA 22908 USA
| | - Peter M Kasson
- Departments of Molecular Physiology and Biomedical Engineering, University of Virginia Charlottesville VA 22908 USA
- Science for Life Laboratory and Department of Molecular and Cellular Biology, Uppsala University Uppsala SE 75123 USA
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23
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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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24
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Bennett AL, Edwards RJ, Kosheleva I, Saunders C, Bililign Y, Williams A, Manosouri K, Saunders KO, Haynes BF, Acharya P, Henderson R. Microsecond dynamics control the HIV-1 envelope conformation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.17.541130. [PMID: 37292605 PMCID: PMC10245784 DOI: 10.1101/2023.05.17.541130] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
The HIV-1 Envelope (Env) glycoprotein facilitates host cell fusion through a complex series of receptor-induced structural changes. Although significant progress has been made in understanding the structures of various Env conformations and transition intermediates that occur within the millisecond timescale, faster transitions in the microsecond timescale have not yet been observed. In this study, we employed time-resolved, temperature-jump small angle X-ray scattering to monitor structural rearrangements in an HIV-1 Env ectodomain construct with microsecond precision. We detected a transition correlated with Env opening that occurs in the hundreds of microseconds range and another more rapid transition that preceded this opening. Model fitting indicated that the early rapid transition involved an order-to-disorder transition in the trimer apex loop contacts, suggesting that conventional conformation-locking design strategies that target the allosteric machinery may be ineffective in preventing this movement. Utilizing this information, we engineered an envelope that locks the apex loop contacts to the adjacent protomer. This modification resulted in significant angle-of-approach shifts in the interaction of a neutralizing antibody. Our findings imply that blocking the intermediate state could be crucial for inducing antibodies with the appropriate bound state orientation through vaccination.
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Affiliation(s)
- Ashley L Bennett
- Duke Human Vaccine Institute, Duke University Medical Center, Durham, NC 27710, USA
| | - R J Edwards
- Duke Human Vaccine Institute, Duke University Medical Center, Durham, NC 27710, USA
| | - Irina Kosheleva
- BioCARS, Center for Advanced Radiation Sources, The University of Chicago, 9700 South Cass Ave, Bld 434B, Lemont, IL 60439, USA
| | - Carrie Saunders
- Duke Human Vaccine Institute, Duke University Medical Center, Durham, NC 27710, USA
| | - Yishak Bililign
- Duke Human Vaccine Institute, Duke University Medical Center, Durham, NC 27710, USA
| | - Ashliegh Williams
- Duke Human Vaccine Institute, Duke University Medical Center, Durham, NC 27710, USA
| | - Katayoun Manosouri
- Duke Human Vaccine Institute, Duke University Medical Center, Durham, NC 27710, USA
| | - Kevin O Saunders
- Duke Human Vaccine Institute, Duke University Medical Center, Durham, NC 27710, USA
- Department of Surgery, Duke University Medical Center, Durham, NC 27710, USA
| | - Barton F Haynes
- Duke Human Vaccine Institute, Duke University Medical Center, Durham, NC 27710, USA
- Department of Immunology, Duke University Medical Center, Durham, NC 27710, USA
- Department of Biochemistry, Duke University, Durham, NC 27710, USA
| | - Priyamvada Acharya
- Duke Human Vaccine Institute, Duke University Medical Center, Durham, NC 27710, USA
- Department of Surgery, Duke University Medical Center, Durham, NC 27710, USA
- Department of Biochemistry, Duke University, Durham, NC 27710, USA
| | - Rory Henderson
- Duke Human Vaccine Institute, Duke University Medical Center, Durham, NC 27710, USA
- Department of Medicine, Duke University Medical Center, Durham, NC 27710, USA
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25
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Zhu R, Sang X, Zhou J, Meng Q, Huang LSM, Xu Y, An J, Huang Z. CXCR4 Recognition by L- and D-Peptides Containing the Full-Length V3 Loop of HIV-1 gp120. Viruses 2023; 15:1084. [PMID: 37243169 PMCID: PMC10221217 DOI: 10.3390/v15051084] [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: 04/06/2023] [Revised: 04/25/2023] [Accepted: 04/26/2023] [Indexed: 05/28/2023] Open
Abstract
Human immunodeficiency virus-1 (HIV-1) recognizes one of its principal coreceptors, CXC chemokine receptor 4 (CXCR4), on the host cell via the third variable loop (V3 loop) of HIV-1 envelope glycoprotein gp120 during the viral entry process. Here, the mechanism of the molecular recognition of HIV-1 gp120 V3 loop by coreceptor CXCR4 was probed by synthetic peptides containing the full-length V3 loop. The two ends of the V3 loop were covalently linked by a disulfide bond to form a cyclic peptide with better conformational integrity. In addition, to probe the effect of the changed side-chain conformations of the peptide on CXCR4 recognition, an all-D-amino acid analog of the L-V3 loop peptide was generated. Both of these cyclic L- and D-V3 loop peptides displayed comparable binding recognition to the CXCR4 receptor, but not to another chemokine receptor, CCR5, suggesting their selective interactions with CXCR4. Molecular modeling studies revealed the important roles played by many negative-charged Asp and Glu residues on CXCR4 that probably engaged in favorable electrostatic interactions with the positive-charged Arg residues present in these peptides. These results support the notion that the HIV-1 gp120 V3 loop-CXCR4 interface is flexible for ligands of different chiralities, which might be relevant in terms of the ability of the virus to retain coreceptor recognition despite the mutations at the V3 loop.
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Affiliation(s)
- Ruohan Zhu
- School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Xiaohong Sang
- Ciechanover Institute of Precision and Regenerative Medicine, School of Medicine, Chinese University of Hong Kong, Shenzhen 518172, China
| | - Jiao Zhou
- Ciechanover Institute of Precision and Regenerative Medicine, School of Medicine, Chinese University of Hong Kong, Shenzhen 518172, China
| | - Qian Meng
- School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Lina S. M. Huang
- Division of Infectious Diseases and Global Public Heath, Department of Medicine, School of Medicine, University of California at San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Yan Xu
- Ciechanover Institute of Precision and Regenerative Medicine, School of Medicine, Chinese University of Hong Kong, Shenzhen 518172, China
| | - Jing An
- Division of Infectious Diseases and Global Public Heath, Department of Medicine, School of Medicine, University of California at San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Ziwei Huang
- School of Life Sciences, Tsinghua University, Beijing 100084, China
- Ciechanover Institute of Precision and Regenerative Medicine, School of Medicine, Chinese University of Hong Kong, Shenzhen 518172, China
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26
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Heaton SM, Gorry PR, Borg NA. DExD/H-box helicases in HIV-1 replication and their inhibition. Trends Microbiol 2023; 31:393-404. [PMID: 36463019 DOI: 10.1016/j.tim.2022.11.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Revised: 11/07/2022] [Accepted: 11/07/2022] [Indexed: 12/05/2022]
Abstract
Antiretroviral therapy (ART) reduces human immunodeficiency virus type 1 (HIV-1) infection, but selection of treatment-refractory variants remains a major challenge. HIV-1 encodes 16 canonical proteins, a small number of which are the singular targets of nearly all antiretrovirals developed to date. Cellular factors are increasingly being explored, which may present more therapeutic targets, more effectively target certain aspects of the viral replication cycle, and/or limit viral escape. Unlike most other positive-sense RNA viruses that encode at least one helicase, retroviruses are limited to the host repertoire. Accordingly, HIV-1 subverts DEAD-box helicase 3X (DDX3X) and numerous other cellular helicases of the Asp-Glu-x-Asp/His (DExD/H)-box family to service multiple aspects of its replication cycle. Here we review DDX3X and other DExD/H-box helicases in HIV-1 replication and their inhibition.
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Affiliation(s)
- Steven M Heaton
- Infection and Immunity Program, Monash Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria 3800, Australia; Current affiliation: RIKEN Cluster for Pioneering Research and RIKEN Center for Integrative Medical Sciences, 1-chōme-7-22 Suehirochō, Tsurumi-ku, Yokohama 230-0045, Kanagawa, Japan.
| | - Paul R Gorry
- School of Health and Biomedical Sciences, RMIT University, Bundoora, Victoria 3083, Australia
| | - Natalie A Borg
- School of Health and Biomedical Sciences, RMIT University, Bundoora, Victoria 3083, Australia
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27
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Autoantibodies against chemokines post-SARS-CoV-2 infection correlate with disease course. Nat Immunol 2023; 24:604-611. [PMID: 36879067 PMCID: PMC10063443 DOI: 10.1038/s41590-023-01445-w] [Citation(s) in RCA: 32] [Impact Index Per Article: 32.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Accepted: 01/27/2023] [Indexed: 03/08/2023]
Abstract
Infection with severe acute respiratory syndrome coronavirus 2 associates with diverse symptoms, which can persist for months. While antiviral antibodies are protective, those targeting interferons and other immune factors are associated with adverse coronavirus disease 2019 (COVID-19) outcomes. Here we discovered that antibodies against specific chemokines were omnipresent post-COVID-19, were associated with favorable disease outcome and negatively correlated with the development of long COVID at 1 yr post-infection. Chemokine antibodies were also present in HIV-1 infection and autoimmune disorders, but they targeted different chemokines compared with COVID-19. Monoclonal antibodies derived from COVID-19 convalescents that bound to the chemokine N-loop impaired cell migration. Given the role of chemokines in orchestrating immune cell trafficking, naturally arising chemokine antibodies may modulate the inflammatory response and thus bear therapeutic potential.
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28
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Bell BN, Bruun TUJ, Friedland N, Kim PS. HIV-1 prehairpin intermediate inhibitors show efficacy independent of neutralization tier. Proc Natl Acad Sci U S A 2023; 120:e2215792120. [PMID: 36795752 PMCID: PMC9974412 DOI: 10.1073/pnas.2215792120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Accepted: 01/23/2023] [Indexed: 02/17/2023] Open
Abstract
HIV-1 strains are categorized into one of three neutralization tiers based on the relative ease by which they are neutralized by plasma from HIV-1-infected donors not on antiretroviral therapy; tier-1 strains are particularly sensitive to neutralization while tier-2 and tier-3 strains are increasingly difficult to neutralize. Most broadly neutralizing antibodies (bnAbs) previously described target the native prefusion conformation of HIV-1 Envelope (Env), but the relevance of the tiered categories for inhibitors targeting another Env conformation, the prehairpin intermediate, is not well understood. Here, we show that two inhibitors targeting distinct highly conserved regions of the prehairpin intermediate have strikingly consistent neutralization potencies (within ~100-fold for a given inhibitor) against strains in all three neutralization tiers of HIV-1; in contrast, best-in-class bnAbs targeting diverse Env epitopes vary by more than 10,000-fold in potency against these strains. Our results indicate that antisera-based HIV-1 neutralization tiers are not relevant for inhibitors targeting the prehairpin intermediate and highlight the potential for therapies and vaccine efforts targeting this conformation.
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Affiliation(s)
- Benjamin N. Bell
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA94305
- Sarafan ChEM-H, Stanford University, Stanford, CA94305
| | - Theodora U. J. Bruun
- Sarafan ChEM-H, Stanford University, Stanford, CA94305
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA94305
| | - Natalia Friedland
- Sarafan ChEM-H, Stanford University, Stanford, CA94305
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA94305
| | - Peter S. Kim
- Sarafan ChEM-H, Stanford University, Stanford, CA94305
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA94305
- Chan Zuckerberg Biohub, San Francisco, CA94158
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29
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Dragan P, Merski M, Wiśniewski S, Sanmukh SG, Latek D. Chemokine Receptors-Structure-Based Virtual Screening Assisted by Machine Learning. Pharmaceutics 2023; 15:pharmaceutics15020516. [PMID: 36839838 PMCID: PMC9965785 DOI: 10.3390/pharmaceutics15020516] [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: 12/01/2022] [Revised: 01/30/2023] [Accepted: 01/31/2023] [Indexed: 02/08/2023] Open
Abstract
Chemokines modulate the immune response by regulating the migration of immune cells. They are also known to participate in such processes as cell-cell adhesion, allograft rejection, and angiogenesis. Chemokines interact with two different subfamilies of G protein-coupled receptors: conventional chemokine receptors and atypical chemokine receptors. Here, we focused on the former one which has been linked to many inflammatory diseases, including: multiple sclerosis, asthma, nephritis, and rheumatoid arthritis. Available crystal and cryo-EM structures and homology models of six chemokine receptors (CCR1 to CCR6) were described and tested in terms of their usefulness in structure-based drug design. As a result of structure-based virtual screening for CCR2 and CCR3, several new active compounds were proposed. Known inhibitors of CCR1 to CCR6, acquired from ChEMBL, were used as training sets for two machine learning algorithms in ligand-based drug design. Performance of LightGBM was compared with a sequential Keras/TensorFlow model of neural network for these diverse datasets. A combination of structure-based virtual screening with machine learning allowed to propose several active ligands for CCR2 and CCR3 with two distinct compounds predicted as CCR3 actives by all three tested methods: Glide, Keras/TensorFlow NN, and LightGBM. In addition, the performance of these three methods in the prediction of the CCR2/CCR3 receptor subtype selectivity was assessed.
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30
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Marichannegowda MH, Zemil M, Wieczorek L, Sanders-Buell E, Bose M, O'Sullivan AM, King D, Francisco L, Diaz-Mendez F, Setua S, Chomont N, Phanuphak N, Ananworanich J, Hsu D, Vasan S, Michael NL, Eller LA, Tovanabutra S, Tagaya Y, Robb ML, Polonis VR, Song H. Tracking coreceptor switch of the transmitted/founder HIV-1 identifies co-evolution of HIV-1 antigenicity, coreceptor usage and CD4 subset targeting. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.21.525033. [PMID: 36712089 PMCID: PMC9882280 DOI: 10.1101/2023.01.21.525033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
The CCR5 (R5) to CXCR4 (X4) coreceptor switch in natural HIV-1 infection is associated with faster progression to AIDS, but the underlying mechanisms remain unclear. The difficulty in capturing the earliest moment of coreceptor switch in vivo limits our understanding of this phenomenon. Here, by tracking the evolution of the transmitted/founder (T/F) HIV-1 in a prospective cohort of individuals at risk for HIV-1 infection identified very early in acute infection, we investigated this process with high resolution. The earliest X4 variants evolved from the R5 tropic T/F strains. Strong X4 usage can be conferred by a single mutation. The mutations responsible for coreceptor switch can confer escape to neutralization and drive X4 variants to replicate mainly in the central memory and naïve CD4+ T cells. We propose a novel concept to explain the co-evolution of virus antigenicity and entry tropism termed "escape by shifting". This concept posits that for viruses with receptor or coreceptor flexibility, entry tropism alteration represents a mechanism of immune evasion in vivo .
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31
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Santana DS, Silva MJA, de Marin ABR, Costa VLDS, Sousa GSM, de Sousa JG, Silva DC, da Cruz EC, Lima LNGC. The Influence Between C-C Chemokine Receptor 5 Genetic Polymorphisms and the Type-1 Human Immunodeficiency Virus: A 20-Year Review. AIDS Res Hum Retroviruses 2023; 39:13-32. [PMID: 36226448 PMCID: PMC9889015 DOI: 10.1089/aid.2022.0111] [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: 02/04/2023] Open
Abstract
Acquired immune deficiency syndrome (AIDS) is an infectious disease caused by the types 1 and 2 human immunodeficiency virus (HIV-1 and HIV-2). Clinical outcomes in patients are highly varied and delineated by complex interactions between virus, host, and environment, such as with help of co-receptors, for example, the C-C chemokine receptor 5 (CCR5). This work aimed to describe the scientific evidence relating the influence of CCR5 polymorphisms in association studies for HIV-1 disease susceptibility, severity, and transmissibility. This is a systematic review of the literature on single nucleotide polymorphisms (SNPs) and the deletion [Insertion and Deletion (Indel)] Δ32 of CCR5. The search for articles was based on the ScienceDirect, PubMed, and Coordination for the Improvement of Higher Education Personnel (CAPES) databases for the period between 2001 and 2021. The final sample consisted of 32 articles. †SNP rs1799987 is one of the genetic polymorphisms most associated with the criteria of susceptibility and severity of HIV-1, having distinct consequences in genotypic, allelic, and clinical analysis in the variability of investigated populations. As for the transmission character of the disease, the G mutant allele of rs1799987 corresponds to the highest positive association. ‡Furthermore, the results on Indel Δ32 corroborate the absence and rarity of this variant in some populations. Finally, mitigating the severity of cases, SNPs rs1799988 and rs1800023 obtained significant attribution in individuals in the studied populations. It is shown that the reported polymorphisms express significant influences for the evaluation of diagnostic, therapeutic, and prophylactic measures for HIV-1 having fundamental particularities in the molecular, genetic, and transcriptional aspects of CCR5.
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Affiliation(s)
- Davi Silva Santana
- Institute of Health Sciences (ICS), Federal University of Pará (UFPA), Belém, Brazil
| | - Marcos Jessé Abrahão Silva
- Bacteriology and Mycology Section, Evandro Chagas Institute (IEC), Ananindeua, Brazil.,Address correspondence to: Marcos Jessé Abrahão Silva, Bacteriology and Mycology Section, Evandro Chagas Institute (IEC), Ananindeua, Brazil
| | | | | | | | | | - Dihago Cardoso Silva
- Institute of Health Sciences (ICS), Federal University of Pará (UFPA), Belém, Brazil
| | - Eliete Costa da Cruz
- Institute of Health Sciences (ICS), Federal University of Pará (UFPA), Belém, Brazil
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32
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Johnson MM, Jones CE, Clark DN. The Effect of Treatment-Associated Mutations on HIV Replication and Transmission Cycles. Viruses 2022; 15:107. [PMID: 36680147 PMCID: PMC9861436 DOI: 10.3390/v15010107] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Revised: 12/21/2022] [Accepted: 12/28/2022] [Indexed: 12/31/2022] Open
Abstract
HIV/AIDS mortality has been decreasing over the last decade. While promising, this decrease correlated directly with increased use of antiretroviral drugs. As a natural consequence of its high mutation rate, treatments provide selection pressure that promotes the natural selection of escape mutants. Individuals may acquire drug-naive strains, or those that have already mutated due to treatment. Even within a host, mutation affects HIV tropism, where initial infection begins with R5-tropic virus, but the clinical transition to AIDS correlates with mutations that lead to an X4-tropic switch. Furthermore, the high mutation rate of HIV has spelled failure for all attempts at an effective vaccine. Pre-exposure drugs are currently the most effective drug-based preventatives, but their effectiveness is also threatened by viral mutation. From attachment and entry to assembly and release, the steps in the replication cycle are also discussed to describe the drug mechanisms and mutations that arise due to those drugs. Revealing the patterns of HIV-1 mutations, their effects, and the coordinated attempt to understand and control them will lead to effective use of current preventative measures and treatment options, as well as the development of new ones.
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Affiliation(s)
- Madison M. Johnson
- Department of Microbiology, Weber State University, Ogden, UT 84408, USA
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33
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Appiah-Kubi P, Iwuchukwu EA, Soliman MES. Structure-based identification of novel scaffolds as potential HIV-1 entry inhibitors involving CCR5. J Biomol Struct Dyn 2022; 40:13115-13126. [PMID: 34569417 DOI: 10.1080/07391102.2021.1982006] [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: 12/27/2022]
Abstract
C-C chemokine receptor 5 (CCR5), which is part of the chemokine receptor family, is a member of the G protein-coupled receptor superfamily. The interactions of CCR5 with HIV-1 during viral entry position it as an effective therapeutic target for designing potent antiviral therapies. The small-molecule Maraviroc was approved by the FDA as a CCR5 drug in 2007, while clinical trials failure has characterised many of the other CCR5 inhibitors. Thus, the continual identification of potential CCR5 inhibitors is, therefore, warranted. In this study, a structure-based discovery approach has been utilised to screen and retrieved novel potential CCR5 inhibitors from the Asinex antiviral compound (∼ 8,722) database. Explicit lipid-bilayer molecular dynamics simulation, in silico physicochemical and pharmacokinetic analyses, were further performed for the top compounds. A total of 23 structurally diverse compounds with binding scores higher than Maraviroc were selected. Subsequent molecular dynamics (MD) simulations analysis of the top four compounds LAS 51495192, BDB 26405401, BDB 26419079, and LAS 34154543, maintained stability at the CCR5 binding site. Furthermore, these compounds made pertinent interactions with CCR5 residues critical for the HIV-1 gp120-V3 loop binding such as Trp86, Tyr89, Phe109, Tyr108, Glu283 and Tyr251. Additionally, the predicted in silico physicochemical and pharmacokinetic descriptors of the selected compounds were within the acceptable range for drug-likeness. The results suggest positive indications that the identified molecules may represent promising CCR5 entry inhibitors. Further structural optimisations and biochemical testing of the proposed compounds may assist in the discovery of effective HIV-1 therapy.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Patrick Appiah-Kubi
- Molecular Bio-computation and Drug Design Laboratory, School of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Emmanuel Amarachi Iwuchukwu
- Molecular Bio-computation and Drug Design Laboratory, School of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Mahmoud E S Soliman
- Molecular Bio-computation and Drug Design Laboratory, School of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
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34
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Muri J, Cecchinato V, Cavalli A, Shanbhag AA, Matkovic M, Biggiogero M, Maida PA, Moritz J, Toscano C, Ghovehoud E, Furlan R, Barbic F, Voza A, Nadai GD, Cervia C, Zurbuchen Y, Taeschler P, Murray LA, Danelon-Sargenti G, Moro S, Gong T, Piffaretti P, Bianchini F, Crivelli V, Podešvová L, Pedotti M, Jarrossay D, Sgrignani J, Thelen S, Uhr M, Bernasconi E, Rauch A, Manzo A, Ciurea A, Rocchi MBL, Varani L, Moser B, Bottazzi B, Thelen M, Fallon BA, Boyman O, Mantovani A, Garzoni C, Franzetti-Pellanda A, Uguccioni M, Robbiani DF. Anti-chemokine antibodies after SARS-CoV-2 infection correlate with favorable disease course. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2022:2022.05.23.493121. [PMID: 35664993 PMCID: PMC9164443 DOI: 10.1101/2022.05.23.493121] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Infection by SARS-CoV-2 leads to diverse symptoms, which can persist for months. While antiviral antibodies are protective, those targeting interferons and other immune factors are associated with adverse COVID-19 outcomes. Instead, we discovered that antibodies against specific chemokines are omnipresent after COVID-19, associated with favorable disease, and predictive of lack of long COVID symptoms at one year post infection. Anti-chemokine antibodies are present also in HIV-1 infection and autoimmune disorders, but they target different chemokines than those in COVID-19. Monoclonal antibodies derived from COVID- 19 convalescents that bind to the chemokine N-loop impair cell migration. Given the role of chemokines in orchestrating immune cell trafficking, naturally arising anti-chemokine antibodies associated with favorable COVID-19 may be beneficial by modulating the inflammatory response and thus bear therapeutic potential. One-Sentence Summary Naturally arising anti-chemokine antibodies associate with favorable COVID-19 and predict lack of long COVID.
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Affiliation(s)
- Jonathan Muri
- Institute for Research in Biomedicine, Università della Svizzera italiana; Bellinzona, Switzerland
| | - Valentina Cecchinato
- Institute for Research in Biomedicine, Università della Svizzera italiana; Bellinzona, Switzerland
| | - Andrea Cavalli
- Institute for Research in Biomedicine, Università della Svizzera italiana; Bellinzona, Switzerland.,Swiss Institute of Bioinformatics; Lausanne, Switzerland
| | - Akanksha A Shanbhag
- Institute for Research in Biomedicine, Università della Svizzera italiana; Bellinzona, Switzerland
| | - Milos Matkovic
- Institute for Research in Biomedicine, Università della Svizzera italiana; Bellinzona, Switzerland
| | - Maira Biggiogero
- Clinical Research Unit, Clinica Luganese Moncucco; Lugano, Switzerland
| | - Pier Andrea Maida
- Clinical Research Unit, Clinica Luganese Moncucco; Lugano, Switzerland
| | - Jacques Moritz
- Institute for Research in Biomedicine, Università della Svizzera italiana; Bellinzona, Switzerland
| | - Chiara Toscano
- Institute for Research in Biomedicine, Università della Svizzera italiana; Bellinzona, Switzerland
| | - Elaheh Ghovehoud
- Institute for Research in Biomedicine, Università della Svizzera italiana; Bellinzona, Switzerland
| | - Raffaello Furlan
- Department of Biomedical Sciences, Humanitas University, Via Rita Levi Montalcini 4, 20090 Pieve Emanuele, Milan, Italy.,Internal Medicine, IRCCS Humanitas Research Hospital, Via Manzoni 56, 20089 Rozzano, Milan, Italy
| | - Franca Barbic
- Department of Biomedical Sciences, Humanitas University, Via Rita Levi Montalcini 4, 20090 Pieve Emanuele, Milan, Italy.,Internal Medicine, IRCCS Humanitas Research Hospital, Via Manzoni 56, 20089 Rozzano, Milan, Italy
| | - Antonio Voza
- Department of Biomedical Sciences, Humanitas University, Via Rita Levi Montalcini 4, 20090 Pieve Emanuele, Milan, Italy.,Department of Emergency, IRCCS Humanitas Research Hospital, 20089 Rozzano, Milan, Italy
| | - Guendalina De Nadai
- Emergency Medicine Residency School, Department of Biomedical Sciences, Humanitas University, Via Rita Levi Montalcini 4 - 20090 Pieve Emanuele, Milan, Italy
| | - Carlo Cervia
- Department of Immunology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Yves Zurbuchen
- Department of Immunology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Patrick Taeschler
- Department of Immunology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Lilly A Murray
- Lyme & Tick-Borne Diseases Research Center at Columbia University Irving Medical Center, New York, NY, USA
| | | | - Simone Moro
- Institute for Research in Biomedicine, Università della Svizzera italiana; Bellinzona, Switzerland
| | - Tao Gong
- Institute for Research in Biomedicine, Università della Svizzera italiana; Bellinzona, Switzerland
| | - Pietro Piffaretti
- Institute for Research in Biomedicine, Università della Svizzera italiana; Bellinzona, Switzerland
| | - Filippo Bianchini
- Institute for Research in Biomedicine, Università della Svizzera italiana; Bellinzona, Switzerland
| | - Virginia Crivelli
- Institute for Research in Biomedicine, Università della Svizzera italiana; Bellinzona, Switzerland
| | - Lucie Podešvová
- Institute for Research in Biomedicine, Università della Svizzera italiana; Bellinzona, Switzerland
| | - Mattia Pedotti
- Institute for Research in Biomedicine, Università della Svizzera italiana; Bellinzona, Switzerland
| | - David Jarrossay
- Institute for Research in Biomedicine, Università della Svizzera italiana; Bellinzona, Switzerland
| | - Jacopo Sgrignani
- Institute for Research in Biomedicine, Università della Svizzera italiana; Bellinzona, Switzerland
| | - Sylvia Thelen
- Institute for Research in Biomedicine, Università della Svizzera italiana; Bellinzona, Switzerland
| | | | - Enos Bernasconi
- Regional Hospital Lugano, Ente Ospedaliero Cantonale; Lugano, Switzerland.,Università della Svizzera italiana; Lugano, Switzerland
| | - Andri Rauch
- Department of Infectious Diseases, Inselspital, Bern University Hospital, University of Bern; Bern, Switzerland
| | - Antonio Manzo
- Rheumatology and Translational Immunology Research Laboratories (LaRIT), Division of Rheumatology, IRCCS Policlinico San Matteo Foundation, University of Pavia; Pavia, Italy
| | - Adrian Ciurea
- Department of Rheumatology, Zurich University Hospital, University of Zurich; Zurich, Switzerland
| | - Marco B L Rocchi
- Department of Biomolecular Sciences, Biostatistics Unit, University of Urbino; Urbino, Italy
| | - Luca Varani
- Institute for Research in Biomedicine, Università della Svizzera italiana; Bellinzona, Switzerland
| | - Bernhard Moser
- Division of Infection & Immunity, Henry Wellcome Building, Cardiff University School of Medicine; Cardiff, United Kingdom
| | - Barbara Bottazzi
- IRCCS Humanitas Research Hospital, Via Manzoni 56, 20089 Rozzano, Milan, Italy
| | - Marcus Thelen
- Institute for Research in Biomedicine, Università della Svizzera italiana; Bellinzona, Switzerland
| | - Brian A Fallon
- Lyme & Tick-Borne Diseases Research Center at Columbia University Irving Medical Center, New York, NY, USA.,Lyme Research Program at the New York State Psychiatric Institute, New York, NY, USA
| | - Onur Boyman
- Department of Immunology, University Hospital Zurich, University of Zurich, Zurich, Switzerland.,Faculty of Medicine and Faculty of Science, University of Zurich, Zurich, Switzerland
| | - Alberto Mantovani
- Department of Biomedical Sciences, Humanitas University, Via Rita Levi Montalcini 4, 20090 Pieve Emanuele, Milan, Italy.,IRCCS Humanitas Research Hospital, Via Manzoni 56, 20089 Rozzano, Milan, Italy.,The William Harvey Research Institute, Queen Mary University of London, Charterhouse Square, London, UK
| | - Christian Garzoni
- Internal Medicine and Infectious Diseases, Clinica Luganese Moncucco; Lugano, Switzerland
| | | | - Mariagrazia Uguccioni
- Institute for Research in Biomedicine, Università della Svizzera italiana; Bellinzona, Switzerland.,Department of Biomedical Sciences, Humanitas University, Via Rita Levi Montalcini 4, 20090 Pieve Emanuele, Milan, Italy
| | - Davide F Robbiani
- Institute for Research in Biomedicine, Università della Svizzera italiana; Bellinzona, Switzerland
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35
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Prévost J, Anand SP, Rajashekar JK, Zhu L, Richard J, Goyette G, Medjahed H, Gendron-Lepage G, Chen HC, Chen Y, Horwitz JA, Grunst MW, Zolla-Pazner S, Haynes BF, Burton DR, Flavell RA, Kirchhoff F, Hahn BH, Smith AB, Pazgier M, Nussenzweig MC, Kumar P, Finzi A. HIV-1 Vpu restricts Fc-mediated effector functions in vivo. Cell Rep 2022; 41:111624. [PMID: 36351384 PMCID: PMC9703018 DOI: 10.1016/j.celrep.2022.111624] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Revised: 09/02/2022] [Accepted: 10/17/2022] [Indexed: 11/09/2022] Open
Abstract
Non-neutralizing antibodies (nnAbs) can eliminate HIV-1-infected cells via antibody-dependent cellular cytotoxicity (ADCC) and were identified as a correlate of protection in the RV144 vaccine trial. Fc-mediated effector functions of nnAbs were recently shown to alter the course of HIV-1 infection in vivo using a vpu-defective virus. Since Vpu is known to downregulate cell-surface CD4, which triggers conformational changes in the viral envelope glycoprotein (Env), we ask whether the lack of Vpu expression was linked to the observed nnAbs activity. We find that restoring Vpu expression greatly reduces nnAb recognition of infected cells, rendering them resistant to ADCC. Moreover, administration of nnAbs in humanized mice reduces viral loads only in animals infected with a vpu-defective but not with a wild-type virus. CD4-mimetics administration, known to "open" Env and expose nnAb epitopes, renders wild-type viruses sensitive to nnAbs Fc-effector functions. This work highlights the importance of Vpu-mediated evasion of humoral responses.
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Affiliation(s)
- Jérémie Prévost
- Centre de Recherche du CHUM, Montreal, QC H2X 0A9, Canada; Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montreal, QC H2X 0A9, Canada.
| | - Sai Priya Anand
- Centre de Recherche du CHUM, Montreal, QC H2X 0A9, Canada; Department of Microbiology and Immunology, McGill University, Montreal, QC H3A 2B4, Canada
| | - Jyothi Krishnaswamy Rajashekar
- Department of Internal Medicine, Section of Infectious Diseases, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Li Zhu
- Department of Internal Medicine, Section of Infectious Diseases, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Jonathan Richard
- Centre de Recherche du CHUM, Montreal, QC H2X 0A9, Canada; Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montreal, QC H2X 0A9, Canada
| | | | | | | | - Hung-Ching Chen
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA 19104-6323, USA
| | - Yaozong Chen
- Infectious Diseases Division, Department of Medicine, Uniformed Services University of the Health Sciences, Bethesda, MD 20814-4712, USA
| | - Joshua A Horwitz
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA
| | - Michael W Grunst
- Department of Internal Medicine, Section of Infectious Diseases, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Susan Zolla-Pazner
- Department of Medicine, Division of Infectious Diseases, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Barton F Haynes
- Duke Human Vaccine Institute, Departments of Medicine and Immunology, Duke University School of Medicine, Durham, NC 27710, USA; Consortium for HIV/AIDS Vaccine Development (CHAVD), Duke University, Durham, NC 27710, USA
| | - Dennis R Burton
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA; Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA 92037, USA; Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology, Harvard University, Cambridge, MA 02139, USA
| | - Richard A Flavell
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT 06519, USA
| | - Frank Kirchhoff
- Institute of Molecular Virology, Ulm University Medical Center, 89081 Ulm, Germany
| | - Beatrice H Hahn
- Departments of Medicine and Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104-6076, USA
| | - Amos B Smith
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA 19104-6323, USA
| | - Marzena Pazgier
- Infectious Diseases Division, Department of Medicine, Uniformed Services University of the Health Sciences, Bethesda, MD 20814-4712, USA
| | - Michel C Nussenzweig
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA
| | - Priti Kumar
- Department of Internal Medicine, Section of Infectious Diseases, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Andrés Finzi
- Centre de Recherche du CHUM, Montreal, QC H2X 0A9, Canada; Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montreal, QC H2X 0A9, Canada; Department of Microbiology and Immunology, McGill University, Montreal, QC H3A 2B4, Canada.
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36
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Secchi M, Vangelista L. Rational Engineering of a Sub-Picomolar HIV-1 Blocker. Viruses 2022; 14:v14112415. [PMID: 36366513 PMCID: PMC9695723 DOI: 10.3390/v14112415] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Revised: 10/19/2022] [Accepted: 10/25/2022] [Indexed: 11/06/2022] Open
Abstract
With the aim of rationally devising a refined and potent HIV-1 blocker, the cDNA of CCL5 5p12 5m, an extremely potent CCR5 antagonist, was fused to that of C37, a gp41-targeted fusion inhibitor. The resulting CCL5 5p12 5m-C37 fusion protein was expressed in E. coli and proved to be capable of inhibiting R5 HIV-1 strains with low to sub-picomolar IC50, maintaining its antagonism toward CCR5. In addition, CCL5 5p12 5m-C37 inhibits R5/X4 and X4 HIV-1 strains in the picomolar concentration range. The combination of CCL5 5p12 5m-C37 with tenofovir (TDF) exhibited a synergic effect, promoting this antiviral cocktail. Interestingly, a CCR5-targeted combination of maraviroc (MVC) with CCL5 5p12 5m-C37 led to a synergic effect that could be explained by an extensive engagement of different CCR5 conformational populations. Within the mechanism of HIV-1 entry, the CCL5 5p12 5m-C37 chimera may fit as a powerful blocker in several instances. In its possible consideration for systemic therapy or pre-exposure prophylaxis, this protein design represents an interesting lead in the combat of HIV-1 infection.
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Affiliation(s)
- Massimiliano Secchi
- Protein Engineering and Therapeutics Group, Department of Immunology, Transplantation and Infectious Diseases, IRCCS Ospedale San Raffaele, 20132 Milan, Italy
- DNA Enzymology and Molecular Virology Unit, Institute of Molecular Genetics, National Research Council, 27100 Pavia, Italy
| | - Luca Vangelista
- Protein Engineering and Therapeutics Group, Department of Immunology, Transplantation and Infectious Diseases, IRCCS Ospedale San Raffaele, 20132 Milan, Italy
- Department of Biomedical Sciences, School of Medicine, Nazarbayev University, Nur-Sultan 010000, Kazakhstan
- Correspondence:
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37
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Yang S, Hiotis G, Wang Y, Chen J, Wang JH, Kim M, Reinherz EL, Walz T. Dynamic HIV-1 spike motion creates vulnerability for its membrane-bound tripod to antibody attack. Nat Commun 2022; 13:6393. [PMID: 36302771 PMCID: PMC9610346 DOI: 10.1038/s41467-022-34008-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Accepted: 10/06/2022] [Indexed: 12/25/2022] Open
Abstract
Vaccines targeting HIV-1's gp160 spike protein are stymied by high viral mutation rates and structural chicanery. gp160's membrane-proximal external region (MPER) is the target of naturally arising broadly neutralizing antibodies (bnAbs), yet MPER-based vaccines fail to generate bnAbs. Here, nanodisc-embedded spike protein was investigated by cryo-electron microscopy and molecular-dynamics simulations, revealing spontaneous ectodomain tilting that creates vulnerability for HIV-1. While each MPER protomer radiates centrally towards the three-fold axis contributing to a membrane-associated tripod structure that is occluded in the upright spike, tilting provides access to the opposing MPER. Structures of spike proteins with bound 4E10 bnAb Fabs reveal that the antibody binds exposed MPER, thereby altering MPER dynamics, modifying average ectodomain tilt, and imposing strain on the viral membrane and the spike's transmembrane segments, resulting in the abrogation of membrane fusion and informing future vaccine development.
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Affiliation(s)
- Shuang Yang
- grid.134907.80000 0001 2166 1519Laboratory of Molecular Electron Microscopy, The Rockefeller University, New York, NY USA
| | - Giorgos Hiotis
- grid.134907.80000 0001 2166 1519Laboratory of Molecular Electron Microscopy, The Rockefeller University, New York, NY USA ,grid.134907.80000 0001 2166 1519Tri-Institutional PhD Program in Chemical Biology, The Rockefeller University, New York, NY USA
| | - Yi Wang
- grid.65499.370000 0001 2106 9910Laboratory of Immunobiology, Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA USA ,grid.38142.3c000000041936754XDepartment of Medicine, Harvard Medical School, Boston, MA USA
| | - Junjian Chen
- grid.65499.370000 0001 2106 9910Laboratory of Immunobiology, Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA USA ,grid.38142.3c000000041936754XDepartment of Medicine, Harvard Medical School, Boston, MA USA
| | - Jia-huai Wang
- grid.65499.370000 0001 2106 9910Laboratory of Immunobiology, Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA USA ,grid.38142.3c000000041936754XDepartment of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA USA ,grid.65499.370000 0001 2106 9910Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA USA ,grid.38142.3c000000041936754XDepartment of Pediatrics, Harvard Medical School, Boston, MA USA
| | - Mikyung Kim
- grid.65499.370000 0001 2106 9910Laboratory of Immunobiology, Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA USA ,grid.38142.3c000000041936754XDepartment of Dermatology, Harvard Medical School, Boston, MA USA
| | - Ellis L. Reinherz
- grid.65499.370000 0001 2106 9910Laboratory of Immunobiology, Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA USA ,grid.38142.3c000000041936754XDepartment of Medicine, Harvard Medical School, Boston, MA USA
| | - Thomas Walz
- grid.134907.80000 0001 2166 1519Laboratory of Molecular Electron Microscopy, The Rockefeller University, New York, NY USA
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38
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Negi G, Sharma A, Dey M, Dhanawat G, Parveen N. Membrane attachment and fusion of HIV-1, influenza A, and SARS-CoV-2: resolving the mechanisms with biophysical methods. Biophys Rev 2022; 14:1109-1140. [PMID: 36249860 PMCID: PMC9552142 DOI: 10.1007/s12551-022-00999-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Accepted: 09/16/2022] [Indexed: 10/31/2022] Open
Abstract
Attachment to and fusion with cell membranes are two major steps in the replication cycle of many human viruses. We focus on these steps for three enveloped viruses, i.e., HIV-1, IAVs, and SARS-CoV-2. Viral spike proteins drive the membrane attachment and fusion of these viruses. Dynamic interactions between the spike proteins and membrane receptors trigger their specific attachment to the plasma membrane of host cells. A single virion on cell membranes can engage in binding with multiple receptors of the same or different types. Such dynamic and multivalent binding of these viruses result in an optimal attachment strength which in turn leads to their cellular entry and membrane fusion. The latter process is driven by conformational changes of the spike proteins which are also class I fusion proteins, providing the energetics of membrane tethering, bending, and fusion. These viruses exploit cellular and membrane factors in regulating the conformation changes and membrane processes. Herein, we describe the major structural and functional features of spike proteins of the enveloped viruses including highlights on their structural dynamics. The review delves into some of the case studies in the literature discussing the findings on multivalent binding, membrane hemifusion, and fusion of these viruses. The focus is on applications of biophysical tools with an emphasis on single-particle methods for evaluating mechanisms of these processes at the molecular and cellular levels.
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Affiliation(s)
- Geetanjali Negi
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur, India
| | - Anurag Sharma
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur, India
| | - Manorama Dey
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur, India
| | - Garvita Dhanawat
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur, India
| | - Nagma Parveen
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur, India
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39
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Momboisse F, Nardi G, Colin P, Hery M, Cordeiro N, Blachier S, Schwartz O, Arenzana-Seisdedos F, Sauvonnet N, Olivio-Marin JC, Lagane B, Lagache T, Brelot A. Tracking receptor motions at the plasma membrane reveals distinct effects of ligands on CCR5 dynamics depending on its dimerization status. eLife 2022; 11:76281. [PMID: 35866628 PMCID: PMC9307273 DOI: 10.7554/elife.76281] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Accepted: 06/17/2022] [Indexed: 12/30/2022] Open
Abstract
G-protein-coupled receptors (GPCR) are present at the cell surface in different conformational and oligomeric states. However, how these states impact GPCRs biological function and therapeutic targeting remains incompletely known. Here, we investigated this issue in living cells for the CC chemokine receptor 5 (CCR5), a major receptor in inflammation and the principal entry co-receptor for Human Immunodeficiency Viruses type 1 (HIV-1). We used TIRF microscopy and a statistical method to track and classify the motion of different receptor subpopulations. We showed a diversity of ligand-free forms of CCR5 at the cell surface constituted of various oligomeric states and exhibiting transient Brownian and restricted motions. These forms were stabilized differently by distinct ligands. In particular, agonist stimulation restricted the mobility of CCR5 and led to its clustering, a feature depending on β-arrestin, while inverse agonist stimulation exhibited the opposite effect. These results suggest a link between receptor activation and immobilization. Applied to HIV-1 envelope glycoproteins gp120, our quantitative analysis revealed agonist-like properties of gp120s. Distinct gp120s influenced CCR5 dynamics differently, suggesting that they stabilize different CCR5 conformations. Then, using a dimerization-compromized mutant, we showed that dimerization (i) impacts CCR5 precoupling to G proteins, (ii) is a pre-requisite for the immobilization and clustering of receptors upon activation, and (iii) regulates receptor endocytosis, thereby impacting the fate of activated receptors. This study demonstrates that tracking the dynamic behavior of a GPCR is an efficient way to link GPCR conformations to their functions, therefore improving the development of drugs targeting specific receptor conformations.
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Affiliation(s)
- Fanny Momboisse
- Institut Pasteur, Université Paris Cité, CNRS UMR3569, Virus and Immunity Unit, Paris, France
| | - Giacomo Nardi
- Institut Pasteur, Université Paris Cité, CNRS UMR3691, BioImage Analysis Unit, Paris, France
| | - Philippe Colin
- Infinity, Université de Toulouse, CNRS, INSERM, Toulouse, France
| | - Melanie Hery
- Institut Pasteur, Université Paris Cité, CNRS UMR3569, Virus and Immunity Unit, Paris, France
| | - Nelia Cordeiro
- Institut Pasteur, Université Paris Cité, CNRS UMR3569, Virus and Immunity Unit, Paris, France
| | - Simon Blachier
- Institut Pasteur, Université Paris Cité, Dynamics of Host-Pathogen Interactions Unit, Paris, France
| | - Olivier Schwartz
- Institut Pasteur, Université Paris Cité, CNRS UMR3569, Virus and Immunity Unit, Paris, France
| | | | - Nathalie Sauvonnet
- Institut Pasteur, Université Paris Cité, Group Intracellular Trafficking and Tissue Homeostasis, Paris, France
| | | | - Bernard Lagane
- Infinity, Université de Toulouse, CNRS, INSERM, Toulouse, France
| | - Thibault Lagache
- Institut Pasteur, Université Paris Cité, CNRS UMR3691, BioImage Analysis Unit, Paris, France
| | - Anne Brelot
- Institut Pasteur, Université Paris Cité, CNRS UMR3569, Virus and Immunity Unit, Paris, France
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40
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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: 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: 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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41
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Anitha AK, Narayanan P, Ajayakumar N, Sivakumar KC, Kumar KS. Novel small synthetic HIV-1 V3 crown variants: CCR5 targeting ligands. J Biochem 2022; 172:149-164. [PMID: 35708645 PMCID: PMC9445593 DOI: 10.1093/jb/mvac052] [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: 01/03/2022] [Accepted: 06/02/2022] [Indexed: 11/23/2022] Open
Abstract
The CC chemokine receptor 5 (CCR5) antagonism represents a promising pharmacological strategy for therapeutic intervention as it plays a significant role in reducing the severity and progression of a wide range of pathological conditions. Here we designed and generated peptide ligands targeting the chemokine receptor, CCR5, that were derived from the critical interaction sites of the V3 crown domain of envelope protein glycoprotein gp120 (TRKSIHIGPGRAFYTTGEI) of HIV-1 using computational biology approach and the peptide sequence corresponding to this region was taken as the template peptide, designated as TMP-1. The peptide variants were synthesized by employing Fmoc chemistry using polymer support and were labelled with rhodamine B to study their interaction with the CCR5 receptor expressed on various cells. TMP-1 and TMP-2 were selected as the high-affinity ligands from in vitro receptor-binding assays. Specific receptor-binding experiments in activated peripheral blood mononuclear cells and HOS.CCR5 cells indicated that TMP-1 and TMP-2 had significant CCR5 specificity. Further, the functional analysis of TMP peptides using chemotactic migration assay showed that both peptides did not mediate the migration of responsive cells. Thus, template
TMP-1 and TMP-2 represent promising CCR5 targeting peptide candidates.
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Affiliation(s)
- Anju Krishnan Anitha
- Chemical Biology Laboratory, Pathogen biology research program, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram 695014, India.,University of Kerala, Thiruvananthapuram, Kerala, 695014, India
| | - Pratibha Narayanan
- Chemical Biology Laboratory, Pathogen biology research program, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram 695014, India.,University of Kerala, Thiruvananthapuram, Kerala, 695014, India
| | - Neethu Ajayakumar
- Chemical Biology Laboratory, Pathogen biology research program, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram 695014, India.,University of Kerala, Thiruvananthapuram, Kerala, 695014, India
| | - Krishnankutty Chandrika Sivakumar
- Chemical Biology Laboratory, Pathogen biology research program, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram 695014, India
| | - Kesavakurup Santhosh Kumar
- Chemical Biology Laboratory, Pathogen biology research program, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram 695014, India
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42
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De Santis F, Lopez AB, Virtuoso S, Poerio N, Saccomandi P, Olimpieri T, Duca L, Henrici De Angelis L, Aquilano K, D'Andrea MM, Aquaro S, Borsetti A, Ceccherini-Silberstein F, Fraziano M. Phosphatidylcholine Liposomes Down-Modulate CD4 Expression Reducing HIV Entry in Human Type-1 Macrophages. Front Immunol 2022; 13:830788. [PMID: 35663973 PMCID: PMC9160374 DOI: 10.3389/fimmu.2022.830788] [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: 12/07/2021] [Accepted: 04/21/2022] [Indexed: 11/13/2022] Open
Abstract
A strategy adopted to combat human immunodeficiency virus type-1 (HIV-1) infection is based on interfering with virus entry into target cells. In this study, we found that phosphatidylcholine (PC) liposomes reduced the expression of the CD4 receptor in human primary type-1 macrophages but not in CD4+ T cells. The down-regulation was specific to CD4, as any effect was not observed in CCR5 membrane expression. Moreover, the reduction of membrane CD4 expression required the Ca2+-independent protein kinase C (PKC), which in turn mediated serine phosphorylation in the intracytoplasmic tail of the CD4 receptor. Serine phosphorylation of CD4 was also associated with its internalization and degradation in acidic compartments. Finally, the observed CD4 downregulation induced by PC liposomes in human primary macrophages reduced the entry of both single-cycle replication and replication competent R5 tropic HIV-1. Altogether, these results show that PC liposomes reduce HIV entry in human macrophages and may impact HIV pathogenesis by lowering the viral reservoir.
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Affiliation(s)
- Federica De Santis
- Dipartimento di Biologia, Università degli Studi di Roma "Tor Vergata", Roma, Italy
| | - Ana Borrajo Lopez
- Dipartimento di Medicina Sperimentale, Università degli Studi di Roma "Tor Vergata", Roma, Italy
| | - Sara Virtuoso
- Centro Nazionale per la ricerca su HIV/AIDS, Istituto Superiore di Sanità, Roma, Italy
| | - Noemi Poerio
- Dipartimento di Biologia, Università degli Studi di Roma "Tor Vergata", Roma, Italy
| | - Patrizia Saccomandi
- Dipartimento di Medicina Sperimentale, Università degli Studi di Roma "Tor Vergata", Roma, Italy
| | - Tommaso Olimpieri
- Dipartimento di Biologia, Università degli Studi di Roma "Tor Vergata", Roma, Italy
| | - Leonardo Duca
- Dipartimento di Medicina Sperimentale, Università degli Studi di Roma "Tor Vergata", Roma, Italy
| | - Lucia Henrici De Angelis
- Dipartimento di Biologia, Università degli Studi di Roma "Tor Vergata", Roma, Italy.,Dipartimento di Biotecnologie Mediche, Università di Siena, Siena, Italy
| | - Katia Aquilano
- Dipartimento di Biologia, Università degli Studi di Roma "Tor Vergata", Roma, Italy
| | - Marco Maria D'Andrea
- Dipartimento di Biologia, Università degli Studi di Roma "Tor Vergata", Roma, Italy
| | - Stefano Aquaro
- Dipartimento di Farmacia e Scienze della Salute e della Nutrizione, Università della Calabria, Rende, Italy
| | - Alessandra Borsetti
- Centro Nazionale per la ricerca su HIV/AIDS, Istituto Superiore di Sanità, Roma, Italy
| | | | - Maurizio Fraziano
- Dipartimento di Biologia, Università degli Studi di Roma "Tor Vergata", Roma, Italy
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43
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Kuklina EM. T Lymphocytes as Targets for SARS-CoV-2. BIOCHEMISTRY. BIOKHIMIIA 2022; 87:566-576. [PMID: 35790412 PMCID: PMC9201263 DOI: 10.1134/s0006297922060086] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Revised: 05/17/2022] [Accepted: 05/17/2022] [Indexed: 01/11/2023]
Abstract
Despite numerous data on the absence or weak expression of the main functional receptor of SARS-CoV-2 angiotensin-converting enzyme 2 (ACE2) by T cells, it was recently demonstrated that the new coronavirus can efficiently infect T lymphocytes. Here, we analyze the data on the alternative (ACE2-independent) pathways of cell infection, identified T cell subpopulations that serve as the most plausible targets of SARS-CoV-2, discuss the mechanisms of virus-cell interaction, including both infectious and non-infectious pathways of T lymphocyte regulation, and estimate the role of the virus-dependent damage of T lymphocytes in COVID-19 pathogenesis. Particular attention is paid to regulatory T cells as potential targets of SARS-CoV-2, as well as to the possible involvement of exosomes in the sensitivity of peripheral T cells to the virus.
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Affiliation(s)
- Elena M Kuklina
- Perm Federal Research Center, Institute of Ecology and Genetics of Microorganisms, Ural Branch of the Russian Academy of Sciences, Perm, 614081, Russia.
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Structural insights into the lysophospholipid brain uptake mechanism and its inhibition by syncytin-2. Nat Struct Mol Biol 2022; 29:604-612. [PMID: 35710838 DOI: 10.1038/s41594-022-00786-8] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Accepted: 05/01/2022] [Indexed: 12/29/2022]
Abstract
Brain development and function require uptake of essential omega-3 fatty acids in the form of lysophosphatidylcholine via major-facilitator superfamily transporter MFSD2A, a potential pharmaceutical target to modulate blood-brain barrier (BBB) permeability. MFSD2A is also the receptor of endogenous retroviral envelope syncytin-2 (SYNC2) in human placenta, where it mediates cell-cell fusion and formation of the maternal-fetal interface. Here, we report a cryo-electron microscopy structure of the human MFSD2A-SYNC2 complex that reveals a large hydrophobic cavity in the transporter C-terminal domain to occlude long aliphatic chains. The transporter architecture suggests an alternating-access transport mechanism for lipid substrates in mammalian MFS transporters. SYNC2 establishes an extensive binding interface with MFSD2A, and a SYNC2-soluble fragment acts as a long-sought-after inhibitor of MFSD2A transport. Our work uncovers molecular mechanisms important to brain and placenta development and function, and SYNC2-mediated inhibition of MFSD2A transport suggests strategies to aid delivery of therapeutic macromolecules across the BBB.
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Schapiro HM, Khasnis MD, Ahn K, Karagiaridi A, Hayden S, Cilento ME, Root MJ. Regulation of epitope exposure in the gp41 membrane-proximal external region through interactions at the apex of HIV-1 Env. PLoS Pathog 2022; 18:e1010531. [PMID: 35584191 PMCID: PMC9154124 DOI: 10.1371/journal.ppat.1010531] [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: 10/21/2021] [Revised: 05/31/2022] [Accepted: 04/18/2022] [Indexed: 11/19/2022] Open
Abstract
Glycoprotein Env of human immunodeficiency virus type 1 (HIV-1) mediates viral entry through membrane fusion. Composed of gp120 and gp41 subunits arranged as a trimer-of-heterodimers, Env adopts a metastable, highly dynamic conformation on the virion surface. This structural plasticity limits the temporospatial exposure of many highly conserved, neutralizing epitopes, contributing to the difficulty in developing effective HIV-1 vaccines. Here, we employed antibody neutralization of HIV-1 infectivity to investigate how inter- and intra-gp120 interactions mediated by variable loops V1/V2 and V3 at the Env apex regulate accessibility of the gp41 membrane-proximal external region (MPER) at the Env base. Swapping the V3 loop from EnvSF162 into the EnvHXB2 background shifted MPER exposure from the prefusogenic state to a functional intermediate conformation that was distinct from the prehairpin-intermediate state sensitive to gp41-targeted fusion inhibitors. The V3-loop swap had a profound impact on global protein dynamics, biasing the equilibrium to a closed conformation resistant to most anti-gp120 antibodies, stabilizing the protein to both cold- and soluble CD4-induced Env inactivation, and increasing the CD4 requirements for viral entry. Further dissection of the EnvHXB2 V3 loop revealed that residue 306 uniquely modulated epitope exposure and trimer stability. The R306S substitution substantially decreased sensitivity to antibodies targeting the gp41 MPER and, surprisingly, the gp120 V3-loop crown (residues 312–315), but had only modest effects on exposure of intervening gp120 epitopes. Furthermore, the point mutation reduced soluble CD4-induced inactivation, but had no impact on cold inactivation. The residue appeared to exert its effects by electrostatically modifying the strength of intra-subunit interactions between the V1/V2 and V3 loops. The distinct patterns of neutralization and stability pointed to a novel prefusogenic Env conformation along the receptor activation pathway and suggested that apical Env-regulation of gp41 MPER exposure can be decoupled from much of the dynamics of gp120 subunits. Surface glycoprotein Env is the main target for neutralizing antibodies elicited by HIV-1 vaccines. Env spontaneously fluctuates among different structures, limiting exposure of many attractive antibody-binding epitopes and, thereby, confounding vaccine development. To characterize these fluctuations, we examined how exposure of the MPER epitope found at the base of Env is regulated by interactions of the V3 loop located in the apex. Starting with an extremely flexible Env with a readily-exposed MPER, we identified two alterations that substantially restricted antibody access to the epitope. The first, a wholesale swap of V3 loops between HIV-1 strains, energetically stabilized Env in a closed structure that restricted access to antibodies throughout the protein. The second, a point mutation that altered V3-loop charge, specifically destabilized the MPER-exposed conformation but had minimal impact on antibody access to Env regions in between the apex and base. The results indicate that MPER exposure is not explicitly tied to the dynamics of Env regions between the apex and base and suggest a new structural fluctuation during Env activation.
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Affiliation(s)
- Hannah M. Schapiro
- Department of Biochemistry and Molecular Biology, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, Pennsylvania, United States of America
| | - Mukta D. Khasnis
- Department of Biochemistry and Molecular Biology, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, Pennsylvania, United States of America
| | - Koree Ahn
- Department of Biochemistry and Molecular Biology, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, Pennsylvania, United States of America
| | - Alexandra Karagiaridi
- Department of Biochemistry and Molecular Biology, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, Pennsylvania, United States of America
| | - Stephanie Hayden
- Department of Biochemistry and Molecular Biology, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, Pennsylvania, United States of America
| | - Maria E. Cilento
- Department of Biochemistry and Molecular Biology, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, Pennsylvania, United States of America
| | - Michael J. Root
- Department of Microbial Infection and Immunity, The Ohio State University College of Medicine, Columbus, Ohio, United States of America
- * E-mail:
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Jasinska AJ, Pandrea I, Apetrei C. CCR5 as a Coreceptor for Human Immunodeficiency Virus and Simian Immunodeficiency Viruses: A Prototypic Love-Hate Affair. Front Immunol 2022; 13:835994. [PMID: 35154162 PMCID: PMC8829453 DOI: 10.3389/fimmu.2022.835994] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Accepted: 01/10/2022] [Indexed: 12/14/2022] Open
Abstract
CCR5, a chemokine receptor central for orchestrating lymphocyte/cell migration to the sites of inflammation and to the immunosurveillance, is involved in the pathogenesis of a wide spectrum of health conditions, including inflammatory diseases, viral infections, cancers and autoimmune diseases. CCR5 is also the primary coreceptor for the human immunodeficiency viruses (HIVs), supporting its entry into CD4+ T lymphocytes upon transmission and in the early stages of infection in humans. A natural loss-of-function mutation CCR5-Δ32, preventing the mutated protein expression on the cell surface, renders homozygous carriers of the null allele resistant to HIV-1 infection. This phenomenon was leveraged in the development of therapies and cure strategies for AIDS. Meanwhile, over 40 African nonhuman primate species are long-term hosts of simian immunodeficiency virus (SIV), an ancestral family of viruses that give rise to the pandemic CCR5 (R5)-tropic HIV-1. Many natural hosts typically do not progress to immunodeficiency upon the SIV infection. They have developed various strategies to minimize the SIV-related pathogenesis and disease progression, including an array of mechanisms employing modulation of the CCR5 receptor activity: (i) deletion mutations abrogating the CCR5 surface expression and conferring resistance to infection in null homozygotes; (ii) downregulation of CCR5 expression on CD4+ T cells, particularly memory cells and cells at the mucosal sites, preventing SIV from infecting and killing cells important for the maintenance of immune homeostasis, (iii) delayed onset of CCR5 expression on the CD4+ T cells during ontogenetic development that protects the offspring from vertical transmission of the virus. These host adaptations, aimed at lowering the availability of target CCR5+ CD4+ T cells through CCR5 downregulation, were countered by SIV, which evolved to alter the entry coreceptor usage toward infecting different CD4+ T-cell subpopulations that support viral replication yet without disruption of host immune homeostasis. These natural strategies against SIV/HIV-1 infection, involving control of CCR5 function, inspired therapeutic approaches against HIV-1 disease, employing CCR5 coreceptor blocking as well as gene editing and silencing of CCR5. Given the pleiotropic role of CCR5 in health beyond immune disease, the precision as well as costs and benefits of such interventions needs to be carefully considered.
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Affiliation(s)
- Anna J Jasinska
- Division of Infectious Diseases, Department of Medicine, School of Medicine, University of Pittsburgh, Pittsburgh, PA, United States.,Department of Molecular Genetics, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland.,Eye on Primates, Los Angeles, CA, United States
| | - Ivona Pandrea
- Department of Pathology, School of Medicine, University of Pittsburgh, Pittsburgh, PA, United States.,Department of Infectious Diseases and Immunology, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA, United States
| | - Cristian Apetrei
- Division of Infectious Diseases, Department of Medicine, School of Medicine, University of Pittsburgh, Pittsburgh, PA, United States.,Department of Infectious Diseases and Immunology, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA, United States
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Popović-Djordjević J, Quispe C, Giordo R, Kostić A, Katanić Stanković JS, Tsouh Fokou PV, Carbone K, Martorell M, Kumar M, Pintus G, Sharifi-Rad J, Docea AO, Calina D. Natural products and synthetic analogues against HIV: A perspective to develop new potential anti-HIV drugs. Eur J Med Chem 2022; 233:114217. [DOI: 10.1016/j.ejmech.2022.114217] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Revised: 02/13/2022] [Accepted: 02/20/2022] [Indexed: 12/22/2022]
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Plant immunity: Rice XA21-mediated resistance to bacterial infection. Proc Natl Acad Sci U S A 2022; 119:2121568119. [PMID: 35131901 PMCID: PMC8872720 DOI: 10.1073/pnas.2121568119] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/28/2021] [Indexed: 12/27/2022] Open
Abstract
The mechanisms plants employ to resist infection were unknown until just a few decades ago. We now understand that plants utilize diverse classes of immune receptors to recognize and respond to pathogenic microbes and pests. This paper describes the development of the plant immunity field, from early studies on the genetics of disease resistance to our increasing knowledge of how plant receptors interact with their microbial ligands, with an emphasis on the rice immune receptor XA21 and its bacterial ligand. In this article, we describe the development of the plant immunity field, starting with efforts to understand the genetic basis for disease resistance, which ∼30 y ago led to the discovery of diverse classes of immune receptors that recognize and respond to infectious microbes. We focus on knowledge gained from studies of the rice XA21 immune receptor that recognizes RaxX (required for activation of XA21 mediated immunity X), a sulfated microbial peptide secreted by the gram-negative bacterium Xanthomonas oryzae pv. oryzae. XA21 is representative of a large class of plant and animal immune receptors that recognize and respond to conserved microbial molecules. We highlight the complexity of this large class of receptors in plants, discuss a possible role for RaxX in Xanthomonas biology, and draw attention to the important role of sulfotyrosine in mediating receptor–ligand interactions.
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Zayas JP, Mamede JI. HIV Infection and Spread between Th17 Cells. Viruses 2022; 14:v14020404. [PMID: 35215997 PMCID: PMC8874668 DOI: 10.3390/v14020404] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Revised: 02/03/2022] [Accepted: 02/07/2022] [Indexed: 02/07/2023] Open
Abstract
HIV mainly targets CD4+ T cells, from which Th17 cells represent a major cell type, permissive, and are capable of supporting intracellular replication at mucosal sites. Th17 cells possess well-described dual roles, while being central to maintaining gut integrity, these may induce inflammation and contribute to autoimmune disorders; however, Th17 cells’ antiviral function in HIV infection is not completely understood. Th17 cells are star players to HIV-1 pathogenesis and a potential target to prevent or decrease HIV transmission. HIV-1 can be spread among permissive cells via direct cell-to-cell and/or cell-free infection. The debate on which mode of transmission is more efficient is still ongoing without a concrete conclusion yet. Most assessments of virus transmission analyzing either cell-to-cell or cell-free modes use in vitro systems; however, the actual interactions and conditions in vivo are not fully understood. The fact that infected breast milk, semen, and vaginal secretions contain a mix of both cell-free viral particles and infected cells presents an argument for the probability of HIV taking advantage of both modes of transmission to spread. Here, we review important insights and recent findings about the role of Th17 cells during HIV pathogenesis in mucosal surfaces, and the mechanisms of HIV-1 infection spread among T cells in tissues.
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Mohamed H, Gurrola T, Berman R, Collins M, Sariyer IK, Nonnemacher MR, Wigdahl B. Targeting CCR5 as a Component of an HIV-1 Therapeutic Strategy. Front Immunol 2022; 12:816515. [PMID: 35126374 PMCID: PMC8811197 DOI: 10.3389/fimmu.2021.816515] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Accepted: 12/13/2021] [Indexed: 12/26/2022] Open
Abstract
Globally, human immunodeficiency virus type 1 (HIV-1) infection is a major health burden for which successful therapeutic options are still being investigated. Challenges facing current drugs that are part of the established life-long antiretroviral therapy (ART) include toxicity, development of drug resistant HIV-1 strains, the cost of treatment, and the inability to eradicate the provirus from infected cells. For these reasons, novel anti-HIV-1 therapeutics that can prevent or eliminate disease progression including the onset of the acquired immunodeficiency syndrome (AIDS) are needed. While development of HIV-1 vaccination has also been challenging, recent advancements demonstrate that infection of HIV-1-susceptible cells can be prevented in individuals living with HIV-1, by targeting C-C chemokine receptor type 5 (CCR5). CCR5 serves many functions in the human immune response and is a co-receptor utilized by HIV-1 for entry into immune cells. Therapeutics targeting CCR5 generally involve gene editing techniques including CRISPR, CCR5 blockade using antibodies or antagonists, or combinations of both. Here we review the efficacy of these approaches and discuss the potential of their use in the clinic as novel ART-independent therapies for HIV-1 infection.
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Affiliation(s)
- Hager Mohamed
- Department of Microbiology and Immunology, Center for Molecular Virology and Translational Neuroscience, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, PA, United States
| | - Theodore Gurrola
- Department of Microbiology and Immunology, Center for Molecular Virology and Translational Neuroscience, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, PA, United States
| | - Rachel Berman
- Department of Microbiology and Immunology, Center for Molecular Virology and Translational Neuroscience, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, PA, United States
| | - Mackenzie Collins
- Department of Microbiology and Immunology, Center for Molecular Virology and Translational Neuroscience, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, PA, United States
| | - Ilker K. Sariyer
- Department of Microbiology, Immunology, and Inflammation, Center for Neurovirology and Gene Editing, School of Medicine, Temple University, Philadelphia, PA, United States
| | - Michael R. Nonnemacher
- Department of Microbiology and Immunology, Center for Molecular Virology and Translational Neuroscience, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, PA, United States
| | - Brian Wigdahl
- Department of Microbiology and Immunology, Center for Molecular Virology and Translational Neuroscience, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, PA, United States
- *Correspondence: Brian Wigdahl,
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