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Powerful Potential of Polyfluoroalkyl-Containing 4-Arylhydrazinylidenepyrazol-3-ones for Pharmaceuticals. MOLECULES (BASEL, SWITZERLAND) 2022; 28:molecules28010059. [PMID: 36615256 PMCID: PMC9821843 DOI: 10.3390/molecules28010059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Revised: 12/08/2022] [Accepted: 12/13/2022] [Indexed: 12/24/2022]
Abstract
4-Arylhydrazinylidene-5-(polyfluoroalkyl)pyrazol-3-ones (4-AHPs) were found to be obtained by the regiospecific cyclization of 2-arylhydrazinylidene-3-(polyfluoroalkyl)-3-oxoesters with hydrazines, by the azo coupling of 4-nonsubstituted pyrazol-5-oles with aryldiazonium chlorides or by the firstly discovered acid-promoted self-condensation of 2-arylhydrazinylidene-3-oxoesters. All the 4-AHPs had an acceptable ADME profile. Varying the substituents in 4-AHPs promoted the switching or combining of their biological activity. The polyfluoroalkyl residue in 4-AHPs led to the appearance of an anticarboxylesterase action in the micromolar range. An NH-fragment and/or methyl group instead of the polyfluoroalkyl one in the 4-AHPs promoted antioxidant properties in the ABTS, FRAP and ORAC tests, as well as anti-cancer activity against HeLa that was at the Doxorubicin level coupled with lower cytotoxicity against normal human fibroblasts. Some Ph-N-substituted 4-AHPs could inhibit the growth of N. gonorrhoeae bacteria at MIC 0.9 μg/mL. The possibility of using 4-AHPs for cell visualization was shown. Most of the 4-AHPs exhibited a pronounced analgesic effect in a hot plate test in vivo at and above the diclofenac and metamizole levels except for the ones with two chlorine atoms in the aryl group. The methylsulfonyl residue was proved to raise the anti-inflammatory effect also. A mechanism of the antinociceptive action of the 4-AHPs through blocking the TRPV1 receptor was proposed and confirmed using in vitro experiment and molecular docking.
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Khudina OG, Elkina NA, Burgart YV, Ezhikova MA, Kodess MI, Esaulkova YL, Zarubaev VV, Shtro AA, Triandafilova GA, Krasnykh OP, Malysheva KO, Gerasimova NA, Evstigneeva NP, Saloutin VI. Synthesis and biological activity of 2-sulfonarylhydrazinylidene 1,3-diketones and their pyrazole derivatives. Russ Chem Bull 2022. [DOI: 10.1007/s11172-022-3696-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/02/2023]
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Senapathi J, Bommakanti A, Vangara S, Kondapi AK. Design, synthesis, and evaluation of HIV-1 entry inhibitors based on broadly neutralizing antibody 447-52D and gp120 V3loop interactions. Bioorg Chem 2021; 116:105313. [PMID: 34517280 DOI: 10.1016/j.bioorg.2021.105313] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2021] [Revised: 08/25/2021] [Accepted: 08/27/2021] [Indexed: 10/20/2022]
Abstract
The third variable loop region (V3 loop) on gp120 plays an important role in cellular entry of HIV-1. Its interaction with the cellular CD4 and coreceptors is an important hallmark in facilitating the bridging by gp41 and subsequent fusion of membranes for transfer of viral genetic material. Further, the virus phenotype determines the cell tropism via respective co- receptor binding. Thus, coreceptor binding motif of envelope is considered to be a potent anti-viral drug target for viral entry inhibition. However, its high variability in sequence is the major hurdle for developing inhibitors targeting the region. In this study, we have used an in silico Virtual Screening and "Fragment-based" method to design small molecules based on the gp120 V3 loop interactions with a potent broadly neutralizing human monoclonal antibody, 447-52D. From the in silico analysis a potent scaffold, 1,3,5-triazine was identified for further development. Derivatives of 1,3,5-triazine with specific functional groups were designed and synthesized keeping the interaction with co-receptor intact. Finally, preliminary evaluation of molecules for HIV-1 inhibition on two different virus strains (clade C, clade B) yielded IC50 < 5.0 μM. The approach used to design molecules based on broadly neutralizing antibody, was useful for development of target specific potent antiviral agents to prevent HIV entry. The study reported promising inhibitors that could be further developed and studied.
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Affiliation(s)
- Jagadeesh Senapathi
- Dept. of Biotechnology and Bioinformatics, School of Life Sciences, University of Hyderabad, India
| | - Akhila Bommakanti
- Dept. of Biotechnology and Bioinformatics, School of Life Sciences, University of Hyderabad, India
| | - Srinivas Vangara
- School of Chemistry, University of Hyderabad, Hyderabad 500046, India
| | - Anand K Kondapi
- Dept. of Biotechnology and Bioinformatics, School of Life Sciences, University of Hyderabad, India.
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Chuang GY, Lai YT, Boyington JC, Cheng C, Geng H, Narpala S, Rawi R, Schmidt SD, Tsybovsky Y, Verardi R, Xu K, Yang Y, Zhang B, Chambers M, Changela A, Corrigan AR, Kong R, Olia AS, Ou L, Sarfo EK, Wang S, Wu W, Doria-Rose NA, McDermott AB, Mascola JR, Kwong PD. Development of a 3Mut-Apex-Stabilized Envelope Trimer That Expands HIV-1 Neutralization Breadth When Used To Boost Fusion Peptide-Directed Vaccine-Elicited Responses. J Virol 2020; 94:e00074-20. [PMID: 32295908 PMCID: PMC7307166 DOI: 10.1128/jvi.00074-20] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Accepted: 03/31/2020] [Indexed: 01/21/2023] Open
Abstract
HIV-1 envelope (Env) trimers, stabilized in a prefusion-closed conformation, can elicit humoral responses capable of neutralizing HIV-1 strains closely matched in sequence to the immunizing strain. One strategy to increase elicited neutralization breadth involves vaccine priming of immune responses against a target site of vulnerability, followed by vaccine boosting of these responses with prefusion-closed Env trimers. This strategy has succeeded at the fusion peptide (FP) site of vulnerability in eliciting cross-clade neutralizing responses in standard vaccine-test animals. However, the breadth and potency of the elicited responses have been less than optimal. Here, we identify three mutations (3mut), Met302, Leu320, and Pro329, that stabilize the apex of the Env trimer in a prefusion-closed conformation and show antigenically, structurally, and immunogenically that combining 3mut with other approaches (e.g., repair and stabilize and glycine-helix breaking) yields well-behaved clade C-Env trimers capable of boosting the breadth of FP-directed responses. Crystal structures of these trimers confirmed prefusion-closed apexes stabilized by hydrophobic patches contributed by Met302 and Leu320, with Pro329 assuming canonically restricted dihedral angles. We substituted the N-terminal eight residues of FP (FP8, residues 512 to 519) of these trimers with the second most prevalent FP8 sequence (FP8v2, AVGLGAVF) and observed a 3mut-stabilized consensus clade C-Env trimer with FP8v2 to boost the breadth elicited in guinea pigs of FP-directed responses induced by immunogens containing the most prevalent FP8 sequence (FP8v1, AVGIGAVF). Overall, 3mut can stabilize the Env trimer apex, and the resultant apex-stabilized Env trimers can be used to expand the neutralization breadth elicited against the FP site of vulnerability.IMPORTANCE A major hurdle to the development of an effective HIV-1 vaccine is the elicitation of serum responses capable of neutralizing circulating strains of HIV, which are extraordinarily diverse in sequence and often highly neutralization resistant. Recently, we showed how sera with 20 to 30% neutralization breadth could, nevertheless, be elicited in standard vaccine test animals by priming with the most prevalent N-terminal 8 residues of the HIV-1 fusion peptide (FP8), followed by boosting with a stabilized BG505-envelope (Env) trimer. Here, we show that subsequent boosting with a 3mut-apex-stabilized consensus C-Env trimer, modified to have the second most prevalent FP8 sequence, elicits higher neutralization breadth than that induced by continued boosting with the stabilized BG505-Env trimer. With increased neutralizing breadth elicited by boosting with a heterologous trimer containing the second most prevalent FP8 sequence, the fusion peptide-directed immune-focusing approach moves a step closer toward realizing an effective HIV-1 vaccine regimen.
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Affiliation(s)
- Gwo-Yu Chuang
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Yen-Ting Lai
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Jeffrey C Boyington
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Cheng Cheng
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Hui Geng
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Sandeep Narpala
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Reda Rawi
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Stephen D Schmidt
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Yaroslav Tsybovsky
- Electron Microscopy Laboratory, Cancer Research Technology Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland, USA
| | - Raffaello Verardi
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Kai Xu
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Yongping Yang
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Baoshan Zhang
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Michael Chambers
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Anita Changela
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Angela R Corrigan
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Rui Kong
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Adam S Olia
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Li Ou
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Edward K Sarfo
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Shuishu Wang
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Winston Wu
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Nicole A Doria-Rose
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Adrian B McDermott
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - John R Mascola
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Peter D Kwong
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
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Chen Z, Cho E, Lee J, Lee S, Lee TH. Inhibitory Effects of N-[2-(4-acetyl-1-piperazinyl) phenyl]-2-(2-chlorophenoxy) acetamide on Osteoclast Differentiation In Vitro via the Downregulation of TRAF6. Int J Mol Sci 2019; 20:ijms20205196. [PMID: 31635168 PMCID: PMC6829416 DOI: 10.3390/ijms20205196] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2019] [Revised: 10/18/2019] [Accepted: 10/18/2019] [Indexed: 12/11/2022] Open
Abstract
Osteoclasts are poly-nuclear cells that resorb mineral components from old or damaged bone tissue. Primary mononuclear cells are activated by receptor activator of nuclear factor kappa-Β ligand (RANKL) and differentiate into large multinucleated cells. Dysregulation of osteoclast differentiation can lead to pathological bone loss and destruction. Many studies have focused on the development of new molecules to regulate RANKL-mediated signaling. In this study, N-[2-(4-acetyl-1-piperazinyl)phenyl]-2-(2-chlorophenoxy) acetamide (PPOA-N-Ac-2-Cl) led to a significant decrease in the formation of multinucleated tartrate-resistant acid phosphatase (TRAP)-positive cells in a dose-dependent manner, without inducing significant cytotoxicity. PPOA-N-Ac-2-Cl affected the expression of osteoclast-specific marker genes, such as TRAF6, c-fos, DC-STAMP, NFATc1, MMP9, CtsK, and TRAP (Acp5), during RANKL-mediated osteoclastogenesis. Moreover, PPOA-N-Ac-2-Cl significantly attenuated the protein levels of CtsK, a critical protease involved in bone resorption. Accordingly, bone resorption activity and F-actin ring formation decreased in the presence of PPOA-N-Ac-2-Cl. In conclusion, this study shows that PPOA-N-Ac-2-Cl acts as an inhibitor of osteoclast differentiation and may serve as a potential candidate agent for the treatment of osteoclast-related bone diseases by virtue of attenuating bone resorption.
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Affiliation(s)
- Zhihao Chen
- Department of Molecular Medicine (BK21plus), Chonnam National University Graduate School, Gwangju 61186, Korea.
| | - Eunjin Cho
- Department of Oral Biochemistry, Dental Science Research Institute, School of Dentistry, Chonnam National University, Gwangju 61186, Korea.
| | - Jinkyung Lee
- Department of Oral Biochemistry, Dental Science Research Institute, School of Dentistry, Chonnam National University, Gwangju 61186, Korea.
| | - Sunwoo Lee
- Department of Chemistry, Chonnam National University, Gwangju 61186, Korea.
| | - Tae-Hoon Lee
- Department of Molecular Medicine (BK21plus), Chonnam National University Graduate School, Gwangju 61186, Korea.
- Department of Oral Biochemistry, Dental Science Research Institute, School of Dentistry, Chonnam National University, Gwangju 61186, Korea.
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Kumar A, Zhang KYJ. Advances in the Development of Shape Similarity Methods and Their Application in Drug Discovery. Front Chem 2018; 6:315. [PMID: 30090808 PMCID: PMC6068280 DOI: 10.3389/fchem.2018.00315] [Citation(s) in RCA: 81] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2018] [Accepted: 07/09/2018] [Indexed: 12/21/2022] Open
Abstract
Molecular similarity is a key concept in drug discovery. It is based on the assumption that structurally similar molecules frequently have similar properties. Assessment of similarity between small molecules has been highly effective in the discovery and development of various drugs. Especially, two-dimensional (2D) similarity approaches have been quite popular due to their simplicity, accuracy and efficiency. Recently, the focus has been shifted toward the development of methods involving the representation and comparison of three-dimensional (3D) conformation of small molecules. Among the 3D similarity methods, evaluation of shape similarity is now gaining attention for its application not only in virtual screening but also in molecular target prediction, drug repurposing and scaffold hopping. A wide range of methods have been developed to describe molecular shape and to determine the shape similarity between small molecules. The most widely used methods include atom distance-based methods, surface-based approaches such as spherical harmonics and 3D Zernike descriptors, atom-centered Gaussian overlay based representations. Several of these methods demonstrated excellent virtual screening performance not only retrospectively but also prospectively. In addition to methods assessing the similarity between small molecules, shape similarity approaches have been developed to compare shapes of protein structures and binding pockets. Additionally, shape comparisons between atomic models and 3D density maps allowed the fitting of atomic models into cryo-electron microscopy maps. This review aims to summarize the methodological advances in shape similarity assessment highlighting advantages, disadvantages and their application in drug discovery.
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Affiliation(s)
| | - Kam Y. J. Zhang
- Laboratory for Structural Bioinformatics, Center for Biosystems Dynamics Research, RIKEN, Yokohama, Japan
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Jones CL, Marsden EA, Nevin AC, Kariuki BM, Bhadbhade MM, Martin AD, Easun TL. Investigating the geometrical preferences of a flexible benzimidazolone-based linker in the synthesis of coordination polymers. ROYAL SOCIETY OPEN SCIENCE 2017; 4:171064. [PMID: 29308246 PMCID: PMC5750013 DOI: 10.1098/rsos.171064] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/04/2017] [Accepted: 10/31/2017] [Indexed: 06/07/2023]
Abstract
A series of new group 2 coordination polymers, MgL ={MgL(H2O)(DMF)0.75}∞, CaL = {CaL(DMF)2}∞, SrL = {SrL(H2O)0.5}∞ and BaL = {BaL(H2O)0.5}∞, were synthesized using a flexible benzimidazolone diacetic acid linker (H2L) in which the two carboxylic acid binding sites are connected to a planar core via {-CH2-} spacers that can freely rotate in solution. In a 'curiosity-led' diversion from group 2 metals, the first row transition metal salts Mn2+, Cu2+ and Zn2+ were also reacted with L to yield crystals of MnL = {MnL(DMF)(H2O)3.33}∞, Cu3L2 = {Cu3L2(DMF)2(CHO2)2}∞ and ZnL = {ZnL(DMF)}∞. Crystal structures were obtained for all seven materials. All structures form as two-dimensional sheets and contain six-coordinate centres, with the exception of ZnL, which displays tetrahedrally coordinated metal centres, and Cu3L2 , which contains square planar coordinated metal centres and Cu paddle-wheels. In each structure, the linker adopts one of two distinct conformations, with the carboxylate groups either cis or trans with respect to the planar core. All materials were also characterized by powder X-ray diffraction and thermogravimetric analysis.
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Affiliation(s)
- Corey L. Jones
- School of Chemistry, Cardiff University, Main Building, Park Place, Cardiff CF10 3AT, UK
| | - Elizabeth A. Marsden
- School of Chemistry, Cardiff University, Main Building, Park Place, Cardiff CF10 3AT, UK
| | - Adam C. Nevin
- School of Chemistry, Cardiff University, Main Building, Park Place, Cardiff CF10 3AT, UK
| | - Benson M. Kariuki
- School of Chemistry, Cardiff University, Main Building, Park Place, Cardiff CF10 3AT, UK
| | - Mohan M. Bhadbhade
- School of Chemistry, Mark Wainwright Analytical Centre, The University of New South Wales, Sydney, NSW 2052, Australia
| | - Adam D. Martin
- School of Chemistry, The Australian Centre for Nanomedicine and the ARC Centre of Excellence in Convergent Bio-Nano Science, The University of New South Wales, Sydney, NSW 2052, Australia
| | - Timothy L. Easun
- School of Chemistry, Cardiff University, Main Building, Park Place, Cardiff CF10 3AT, UK
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Patel MS, Miranda-Nieves D, Chen J, Haller CA, Chaikof EL. Targeting P-selectin glycoprotein ligand-1/P-selectin interactions as a novel therapy for metabolic syndrome. Transl Res 2017; 183:1-13. [PMID: 28034759 PMCID: PMC5393932 DOI: 10.1016/j.trsl.2016.11.007] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/05/2016] [Accepted: 11/13/2016] [Indexed: 12/22/2022]
Abstract
Obesity-induced insulin resistance and metabolic syndrome continue to pose an important public health challenge worldwide as they significantly increase the risk of type 2 diabetes and atherosclerotic cardiovascular disease. Advances in the pathophysiologic understanding of this process has identified that chronic inflammation plays a pivotal role. In this regard, given that both animal models and human studies have demonstrated that the interaction of P-selectin glycoprotein ligand-1 (PSGL-1) with P-selectin is not only critical for normal immune response but also is upregulated in the setting of metabolic syndrome, PSGL-1/P-selectin interactions provide a novel target for preventing and treating resultant disease. Current approaches of interfering with PSGL-1/P-selectin interactions include targeted antibodies, recombinant immunoglobulins that competitively bind P-selectin, and synthetic molecular therapies. Experimental models as well as clinical trials assessing the role of these modalities in a variety of diseases have continued to contribute to the understanding of PSGL-1/P-selectin interactions and have demonstrated the difficulty in creating clinically relevant therapeutics. Most recently, however, computational simulations have further enhanced our understanding of the structural features of PSGL-1 and related glycomimetics, which are responsible for high-affinity selectin interactions. Leveraging these insights for the design of next generation agents has thus led to development of a promising synthetic method for generating PSGL-1 glycosulfopeptide mimetics for the treatment of metabolic syndrome.
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Affiliation(s)
- Madhukar S Patel
- Department of Surgery, Massachusetts General Hospital, Boston, Mass; Department of Surgery, Beth Israel Deaconess Medical Center, Boston, Mass; Harvard Medical School, Boston, Mass
| | - David Miranda-Nieves
- Department of Surgery, Beth Israel Deaconess Medical Center, Boston, Mass; Harvard Medical School, Boston, Mass; Division of Health Sciences and Technology, Massachusetts Institute of Technology, Cambridge, Mass
| | - Jiaxuan Chen
- Department of Surgery, Beth Israel Deaconess Medical Center, Boston, Mass; Harvard Medical School, Boston, Mass
| | - Carolyn A Haller
- Department of Surgery, Beth Israel Deaconess Medical Center, Boston, Mass; Harvard Medical School, Boston, Mass
| | - Elliot L Chaikof
- Department of Surgery, Beth Israel Deaconess Medical Center, Boston, Mass; Harvard Medical School, Boston, Mass.
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Connell BJ, Chang SY, Prakash E, Yousfi R, Mohan V, Posch W, Wilflingseder D, Moog C, Kodama EN, Clayette P, Lortat-Jacob H. A Cinnamon-Derived Procyanidin Compound Displays Anti-HIV-1 Activity by Blocking Heparan Sulfate- and Co-Receptor- Binding Sites on gp120 and Reverses T Cell Exhaustion via Impeding Tim-3 and PD-1 Upregulation. PLoS One 2016; 11:e0165386. [PMID: 27788205 PMCID: PMC5082894 DOI: 10.1371/journal.pone.0165386] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2016] [Accepted: 10/11/2016] [Indexed: 11/18/2022] Open
Abstract
Amongst the many strategies aiming at inhibiting HIV-1 infection, blocking viral entry has been recently recognized as a very promising approach. Using diverse in vitro models and a broad range of HIV-1 primary patient isolates, we report here that IND02, a type A procyanidin polyphenol extracted from cinnamon, that features trimeric and pentameric forms displays an anti-HIV-1 activity against CXCR4 and CCR5 viruses with 1–7 μM ED50 for the trimer. Competition experiments, using a surface plasmon resonance-based binding assay, revealed that IND02 inhibited envelope binding to CD4 and heparan sulphate (HS) as well as to an antibody (mAb 17b) directed against the gp120 co-receptor binding site with an IC50 in the low μM range. IND02 has thus the remarkable property of simultaneously blocking gp120 binding to its major host cell surface counterparts. Additionally, the IND02-trimer impeded up-regulation of the inhibitory receptors Tim-3 and PD-1 on CD4+ and CD8+ cells, thereby demonstrating its beneficial effect by limiting T cell exhaustion. Among naturally derived products significantly inhibiting HIV-1, the IND02-trimer is the first component demonstrating an entry inhibition property through binding to the viral envelope glycoprotein. These data suggest that cinnamon, a widely consumed spice, could represent a novel and promising candidate for a cost-effective, natural entry inhibitor for HIV-1 which can also down-modulate T cell exhaustion markers Tim-3 and PD-1.
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Affiliation(s)
- Bridgette Janine Connell
- Institut de Biologie Structurale, UMR 5075, Univ. Grenoble Alpes, CNRS, CEA, F-38027 Grenoble, France
| | - Sui-Yuan Chang
- School of Medical Technology, College of Medicine, National Taiwan University Hospital, Taipei, Taiwan
| | | | - Rahima Yousfi
- Laboratoire de Neurovirologie, Bertin Pharma, CEA, 92265 Fontenay aux Roses, France
| | | | - Wilfried Posch
- Division of Hygiene and Medical Microbiology, Innsbruck Medical University, Innsbruck, Austria
| | - Doris Wilflingseder
- Division of Hygiene and Medical Microbiology, Innsbruck Medical University, Innsbruck, Austria
| | - Christiane Moog
- INSERM U1110, Fédération de médecine translationnelle de Strasbourg (FMTS), Institut de Virologie, 3 rue Koeberlé, 67000 Strasbourg, France
| | - Eiichi N. Kodama
- Division of Emerging Infectious Diseases, Miyagi Communitiy Health Promotion, Tohoku University School of Medicine, Bldg. 1, Rm. 515, 2–1 Seiryocho, Aoba-ku, Sendai 980–8575, Japan
| | - Pascal Clayette
- Laboratoire de Neurovirologie, Bertin Pharma, CEA, 92265 Fontenay aux Roses, France
| | - Hugues Lortat-Jacob
- Institut de Biologie Structurale, UMR 5075, Univ. Grenoble Alpes, CNRS, CEA, F-38027 Grenoble, France
- * E-mail: (HLJ); (EP)
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Dogo-Isonagie C, Lee SL, Lohith K, Liu H, Mandadapu SR, Lusvarghi S, O'Connor RD, Bewley CA. Design and synthesis of small molecule-sulfotyrosine mimetics that inhibit HIV-1 entry. Bioorg Med Chem 2016; 24:1718-28. [PMID: 26968647 PMCID: PMC7261409 DOI: 10.1016/j.bmc.2016.02.044] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2016] [Revised: 02/22/2016] [Accepted: 02/28/2016] [Indexed: 02/01/2023]
Abstract
In the absence of a cure or vaccine for HIV/AIDS, small molecule inhibitors remain an attractive choice for antiviral therapeutics. Recent structural and functional studies of the HIV-1 surface envelope glycoprotein gp120 have revealed sites of vulnerability that can be targeted by small molecule and peptide inhibitors, thereby inhibiting HIV-1 infection. Here we describe a series of small molecule entry inhibitors that were designed to mimic the sulfated N-terminal peptide of the HIV-1 coreceptor CCR5. From a panel of hydrazonothiazolyl pyrazolinones, we demonstrate that compounds containing naphthyl di- and tri-sulfonic acids inhibit HIV-1 infection in single round infectivity assays with the disulfonic acids being the most potent. Molecular docking supports the observed structure activity relationship, and SPR confirmed binding to gp120. In infectivity assays treatment with a representative naphthyl disulfonate and a disulfated CCR5 N-terminus peptide results in competitive inhibition, with combination indices >2. In total this work shows that gp120 and HIV-1 infection can be inhibited by small molecules that mimic the function of, and are competitive with the natural sulfated CCR5 N-terminus.
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Affiliation(s)
- Cajetan Dogo-Isonagie
- Laboratory of Bioorganic Chemistry, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892-0820, United States
| | - Su-Lin Lee
- Laboratory of Bioorganic Chemistry, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892-0820, United States
| | - Katheryn Lohith
- Laboratory of Bioorganic Chemistry, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892-0820, United States
| | - Hongbing Liu
- Laboratory of Bioorganic Chemistry, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892-0820, United States
| | - Sivakoteswara R Mandadapu
- Laboratory of Bioorganic Chemistry, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892-0820, United States
| | - Sabrina Lusvarghi
- Laboratory of Bioorganic Chemistry, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892-0820, United States
| | - Robert D O'Connor
- Laboratory of Bioorganic Chemistry, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892-0820, United States
| | - Carole A Bewley
- Laboratory of Bioorganic Chemistry, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892-0820, United States.
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11
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Battles MB, Langedijk JP, Furmanova-Hollenstein P, Chaiwatpongsakorn S, Costello HM, Kwanten L, Vranckx L, Vink P, Jaensch S, Jonckers THM, Koul A, Arnoult E, Peeples ME, Roymans D, McLellan JS. Molecular mechanism of respiratory syncytial virus fusion inhibitors. Nat Chem Biol 2016; 12:87-93. [PMID: 26641933 PMCID: PMC4731865 DOI: 10.1038/nchembio.1982] [Citation(s) in RCA: 112] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2015] [Accepted: 10/29/2015] [Indexed: 12/21/2022]
Abstract
Respiratory syncytial virus (RSV) is a leading cause of pneumonia and bronchiolitis in young children and the elderly. Therapeutic small molecules have been developed that bind the RSV F glycoprotein and inhibit membrane fusion, yet their binding sites and molecular mechanisms of action remain largely unknown. Here we show that these inhibitors bind to a three-fold-symmetric pocket within the central cavity of the metastable prefusion conformation of RSV F. Inhibitor binding stabilizes this conformation by tethering two regions that must undergo a structural rearrangement to facilitate membrane fusion. Inhibitor-escape mutations occur in residues that directly contact the inhibitors or are involved in the conformational rearrangements required to accommodate inhibitor binding. Resistant viruses do not propagate as well as wild-type RSV in vitro, indicating a fitness cost for inhibitor escape. Collectively, these findings provide new insight into class I viral fusion proteins and should facilitate development of optimal RSV fusion inhibitors.
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Affiliation(s)
- Michael B Battles
- Department of Biochemistry, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, USA
| | | | | | - Supranee Chaiwatpongsakorn
- Center for Vaccines & Immunity, The Research Institute at Nationwide Children’s Hospital, Columbus, Ohio, USA
| | - Heather M Costello
- Center for Vaccines & Immunity, The Research Institute at Nationwide Children’s Hospital, Columbus, Ohio, USA
| | - Leen Kwanten
- Respiratory Infections Research, Janssen Infectious Diseases & Vaccines BVBA, Beerse, Belgium
| | - Luc Vranckx
- Respiratory Infections Research, Janssen Infectious Diseases & Vaccines BVBA, Beerse, Belgium
| | - Paul Vink
- Discovery Sciences, Janssen Pharmaceutica NV, Beerse, Belgium
| | - Steffen Jaensch
- Discovery Sciences, Janssen Pharmaceutica NV, Beerse, Belgium
| | - Tim H M Jonckers
- Medicinal Chemistry Department, Janssen Infectious Diseases & Vaccines BVBA, Beerse, Belgium
| | - Anil Koul
- Respiratory Infections Research, Janssen Infectious Diseases & Vaccines BVBA, Beerse, Belgium
| | - Eric Arnoult
- Computational Chemistry, Janssen R&DLLC, Spring House, Pennsylvania, USA
| | - Mark E Peeples
- Center for Vaccines & Immunity, The Research Institute at Nationwide Children’s Hospital, Columbus, Ohio, USA
- Department of Pediatrics, The Ohio State University College of Medicine, Columbus, Ohio, USA
| | - Dirk Roymans
- Respiratory Infections Research, Janssen Infectious Diseases & Vaccines BVBA, Beerse, Belgium
| | - Jason S McLellan
- Department of Biochemistry, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, USA
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12
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Zoppe JO, Johansson LS, Seppälä J. Manipulation of cellulose nanocrystal surface sulfate groups toward biomimetic nanostructures in aqueous media. Carbohydr Polym 2015; 126:23-31. [DOI: 10.1016/j.carbpol.2015.03.005] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2015] [Revised: 02/25/2015] [Accepted: 03/04/2015] [Indexed: 12/29/2022]
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13
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Costa GCDS, Nunes MRT, Jesus JG, Novaes T, Cardoso JF, Sousa Júnior EC, Santos EDS, Galvão-Castro B, Zanette DL, Gonçalves MDS, Alcantara LCJ. Amino- and Carboxyl-Terminal CCR5 Mutations in Brazilian HIV-1-Infected Women and Homology Model of p.L55Q CCR5 Mutant. AIDS Res Hum Retroviruses 2015; 31:685-91. [PMID: 25825809 DOI: 10.1089/aid.2014.0140] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Genetic factors from an HIV-1 host can affect the rate of progression to AIDS and HIV infection. To investigate the frequency of mutations in the CCR5 gene, HIV-1 samples from infected women and uninfected individuals were selected for sequencing of the CCR5 gene regions encoding the N- and C-terminal protein domains. Physicochemical CCR5 modeling and potential protein domain analysis were performed in order to evaluate the impact of the mutations found in the properties and structure of CCR5. The p.L55Q mutation in the N-terminal protein domain was observed only in uninfected individuals, with an allelic frequency of 1.8%. Physicochemical analysis revealed that the p.L55Q mutation magnified the flexibility and accessibility profiles and the modeling of CCR5 structures showed resulting in a small deviation to the right, as well as a hydrophobic to hydrophilic property alteration. The p.L55Q mutation also resulted in a slight modification of the electrostatic load of this region. Additionally, three novel silent mutations were found at the C-terminal coding region among HIV-1-infected women. The results suggest that the p.L55Q mutation might alter CCR5 conformation. Further studies should be conducted to verify the role of this mutation in HIV-1 susceptibility.
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Affiliation(s)
- Giselle Calasans de Souza Costa
- Centro de Pesquisa Gonçalo Moniz, Fundação Oswaldo Cruz, Salvador, Bahia, Brazil
- Universidade Federal da Bahia, Salvador, Bahia, Brazil
| | - Marcio Roberto T. Nunes
- Bioinformatic Core, Center for Technological Innovation, Evandro Chagas Institute, Pará, Brazil
| | - Jaqueline Goes Jesus
- Centro de Pesquisa Gonçalo Moniz, Fundação Oswaldo Cruz, Salvador, Bahia, Brazil
| | - Thiago Novaes
- Centro de Pesquisa Gonçalo Moniz, Fundação Oswaldo Cruz, Salvador, Bahia, Brazil
| | - Jedson Ferreira Cardoso
- Bioinformatic Core, Center for Technological Innovation, Evandro Chagas Institute, Pará, Brazil
| | | | | | | | | | - Marilda de Souza Gonçalves
- Centro de Pesquisa Gonçalo Moniz, Fundação Oswaldo Cruz, Salvador, Bahia, Brazil
- Universidade Federal da Bahia, Salvador, Bahia, Brazil
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14
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Krishnamurthy VR, Sardar MYR, Ying Y, Song X, Haller C, Dai E, Wang X, Hanjaya-Putra D, Sun L, Morikis V, Simon SI, Woods RJ, Cummings RD, Chaikof EL. Glycopeptide analogues of PSGL-1 inhibit P-selectin in vitro and in vivo. Nat Commun 2015; 6:6387. [PMID: 25824568 PMCID: PMC4423566 DOI: 10.1038/ncomms7387] [Citation(s) in RCA: 59] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2014] [Accepted: 01/26/2015] [Indexed: 12/21/2022] Open
Abstract
Blockade of P-selectin/PSGL-1 interactions holds significant potential for treatment of disorders of innate immunity, thrombosis, and cancer. Current inhibitors remain limited due to low binding affinity or by the recognized disadvantages inherent to chronic administration of antibody therapeutics. Here we report an efficient approach for generating glycosulfopeptide mimics of N-terminal PSGL-1 through development of a stereoselective route for multi-gram scale synthesis of the C2 O-glycan building block and replacement of hydrolytically labile tyrosine sulfates with isosteric sulfonate analogs. Library screening afforded a compound of exceptional stability, GSnP-6, that binds to human P-selectin with nanomolar affinity (Kd ~ 22 nM). Molecular dynamics simulation defines the origin of this affinity in terms of a number of critical structural contributions. GSnP-6 potently blocks P-selectin/PSGL-1 interactions in vitro and in vivo and represents a promising candidate for the treatment of diseases driven by acute and chronic inflammation.
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Affiliation(s)
- Venkata R Krishnamurthy
- 1] Department of Surgery, Center for Drug Discovery and Translational Research, Beth Israel Deaconess Medical Center, Harvard Medical School, 110 Francis Street, Suite 9F, Boston, Massachusetts 02215, USA [2] Wyss Institute of Biologically Inspired Engineering, Harvard University, 110 Francis Street, Suite 9F, Boston, Massachusetts 02115, USA
| | - Mohammed Y R Sardar
- 1] Department of Surgery, Center for Drug Discovery and Translational Research, Beth Israel Deaconess Medical Center, Harvard Medical School, 110 Francis Street, Suite 9F, Boston, Massachusetts 02215, USA [2] Wyss Institute of Biologically Inspired Engineering, Harvard University, 110 Francis Street, Suite 9F, Boston, Massachusetts 02115, USA
| | - Yu Ying
- Department of Biochemistry, Emory University, Atlanta, Georgia 30322, USA
| | - Xuezheng Song
- Department of Biochemistry, Emory University, Atlanta, Georgia 30322, USA
| | - Carolyn Haller
- 1] Department of Surgery, Center for Drug Discovery and Translational Research, Beth Israel Deaconess Medical Center, Harvard Medical School, 110 Francis Street, Suite 9F, Boston, Massachusetts 02215, USA [2] Wyss Institute of Biologically Inspired Engineering, Harvard University, 110 Francis Street, Suite 9F, Boston, Massachusetts 02115, USA
| | - Erbin Dai
- 1] Department of Surgery, Center for Drug Discovery and Translational Research, Beth Israel Deaconess Medical Center, Harvard Medical School, 110 Francis Street, Suite 9F, Boston, Massachusetts 02215, USA [2] Wyss Institute of Biologically Inspired Engineering, Harvard University, 110 Francis Street, Suite 9F, Boston, Massachusetts 02115, USA
| | - Xiaocong Wang
- Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia 30602, USA
| | - Donny Hanjaya-Putra
- 1] Department of Surgery, Center for Drug Discovery and Translational Research, Beth Israel Deaconess Medical Center, Harvard Medical School, 110 Francis Street, Suite 9F, Boston, Massachusetts 02215, USA [2] Wyss Institute of Biologically Inspired Engineering, Harvard University, 110 Francis Street, Suite 9F, Boston, Massachusetts 02115, USA
| | - Lijun Sun
- Department of Surgery, Center for Drug Discovery and Translational Research, Beth Israel Deaconess Medical Center, Harvard Medical School, 110 Francis Street, Suite 9F, Boston, Massachusetts 02215, USA
| | - Vasilios Morikis
- Department of Biomedical Engineering, University of California Davis, Davis, California 95616, USA
| | - Scott I Simon
- Department of Biomedical Engineering, University of California Davis, Davis, California 95616, USA
| | - Robert J Woods
- 1] Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia 30602, USA [2] School of Chemistry, National University of Ireland, Galway, University Road, Galway, Ireland
| | - Richard D Cummings
- Department of Biochemistry, Emory University, Atlanta, Georgia 30322, USA
| | - Elliot L Chaikof
- 1] Department of Surgery, Center for Drug Discovery and Translational Research, Beth Israel Deaconess Medical Center, Harvard Medical School, 110 Francis Street, Suite 9F, Boston, Massachusetts 02215, USA [2] Wyss Institute of Biologically Inspired Engineering, Harvard University, 110 Francis Street, Suite 9F, Boston, Massachusetts 02115, USA
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15
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Abayev M, Moseri A, Tchaicheeyan O, Kessler N, Arshava B, Naider F, Scherf T, Anglister J. An extended CCR5 ECL2 peptide forms a helix that binds HIV-1 gp120 through non-specific hydrophobic interactions. FEBS J 2015; 282:1906-1921. [PMID: 25703038 DOI: 10.1111/febs.13243] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2014] [Revised: 01/06/2015] [Accepted: 02/17/2015] [Indexed: 11/30/2022]
Abstract
UNLABELLED C-C chemokine receptor 5 (CCR5) serves as a co-receptor for HIV-1. The CCR5 N-terminal segment, the second extracellular loop (ECL2) and the transmembrane helices have been implicated in binding the envelope glycoprotein gp120. Peptides corresponding to the sequence of the putative ECL2 as well as peptides containing extracellular loops 1 and 3 (ECL1 and ECL3) were found to inhibit HIV-1 infection. The aromatic residues in the C-terminal half of an ECL2 peptide were shown to interact with gp120. In the present study, we found that, in aqueous buffer, the segment Q188-Q194 in an elongated ECL2 peptide (R168-K197) forms an amphiphilic helix, which corresponds to the beginning of the fifth transmembrane helix in the crystal structure of CCR5. Two-dimensional saturation transfer difference NMR spectroscopy and dynamic filtering studies revealed involvement of Y187, F189, W190 and F193 of the helical segment in the interaction with gp120. The crystal structure of CCR5 shows that the aromatic side chains of F189, W190 and F193 point away from the binding pocket and interact with the membrane or with an adjacent CCR5 molecule, and therefore could not interact with gp120 in the intact CCR5 receptor. We conclude that these three aromatic residues of ECL2 peptides interact with gp120 through hydrophobic interactions that are not representative of the interactions of the intact CCR5 receptor. The HIV-1 inhibition by ECL2 peptides, as well as by ECL1 and ECL3 peptides and peptides corresponding to ECL2 of CXCR4, which serves as an alternative HIV-1 co-receptor, suggests that there is a hydrophobic surface in the envelope spike that could be a target for HIV-1 entry inhibitors. DATABASE The structures and NMR data of ECL2S (Q186-T195) were deposited under Protein Data Bank ID 2mzx and BioMagResBank ID 25505.
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Affiliation(s)
- Meital Abayev
- Department of Structural Biology, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Adi Moseri
- Department of Structural Biology, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Oren Tchaicheeyan
- Department of Structural Biology, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Naama Kessler
- Department of Structural Biology, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Boris Arshava
- Department of Chemistry and Macromolecular Assembly Institute, College of Staten Island of the City University of New York, Staten Island, New York 10314, USA
| | - Fred Naider
- Department of Chemistry and Macromolecular Assembly Institute, College of Staten Island of the City University of New York, Staten Island, New York 10314, USA
| | - Tali Scherf
- Department of Chemical Research Support, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Jacob Anglister
- Department of Structural Biology, Weizmann Institute of Science, Rehovot 76100, Israel
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16
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Acharya P, Lusvarghi S, Bewley CA, Kwong PD. HIV-1 gp120 as a therapeutic target: navigating a moving labyrinth. Expert Opin Ther Targets 2015; 19:765-83. [PMID: 25724219 DOI: 10.1517/14728222.2015.1010513] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
INTRODUCTION The HIV-1 gp120 envelope (Env) glycoprotein mediates attachment of virus to human target cells that display requisite receptors, CD4 and co-receptor, generally CCR5. Despite high-affinity interactions with host receptors and proof-of-principle by the drug maraviroc that interference with CCR5 provides therapeutic benefit, no licensed drug currently targets gp120. AREAS COVERED An overview of the role of gp120 in HIV-1 entry and of sites of potential gp120 vulnerability to therapeutic inhibition is presented. Viral defenses that protect these sites and turn gp120 into a moving labyrinth are discussed together with strategies for circumventing these defenses to allow therapeutic targeting of gp120 sites of vulnerability. EXPERT OPINION The gp120 envelope glycoprotein interacts with host proteins through multiple interfaces and has conserved structural features at these interaction sites. In spite of this, targeting gp120 for therapeutic purposes is challenging. Env mechanisms that have evolved to evade the humoral immune response also shield it from potential therapeutics. Nevertheless, substantial progress has been made in understanding HIV-1 gp120 structure and its interactions with host receptors, and in developing therapeutic leads that potently neutralize diverse HIV-1 strains. Synergies between advances in understanding, needs for therapeutics against novel viral targets and characteristics of breadth and potency for a number of gp120-targetting lead molecules bodes well for gp120 as a HIV-1 therapeutic target.
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Affiliation(s)
- Priyamvada Acharya
- National Institute of Allergy and Infectious Diseases/National Institutes of Health, Vaccine Research Center, Structural Biology Section , Room 4609B, 40 Convent Drive, Bethesda, MD 20892 , USA
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17
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Kumar A, Zhang KYJ. Hierarchical virtual screening approaches in small molecule drug discovery. Methods 2015; 71:26-37. [PMID: 25072167 PMCID: PMC7129923 DOI: 10.1016/j.ymeth.2014.07.007] [Citation(s) in RCA: 98] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2014] [Revised: 07/16/2014] [Accepted: 07/17/2014] [Indexed: 02/06/2023] Open
Abstract
Virtual screening has played a significant role in the discovery of small molecule inhibitors of therapeutic targets in last two decades. Various ligand and structure-based virtual screening approaches are employed to identify small molecule ligands for proteins of interest. These approaches are often combined in either hierarchical or parallel manner to take advantage of the strength and avoid the limitations associated with individual methods. Hierarchical combination of ligand and structure-based virtual screening approaches has received noteworthy success in numerous drug discovery campaigns. In hierarchical virtual screening, several filters using ligand and structure-based approaches are sequentially applied to reduce a large screening library to a number small enough for experimental testing. In this review, we focus on different hierarchical virtual screening strategies and their application in the discovery of small molecule modulators of important drug targets. Several virtual screening studies are discussed to demonstrate the successful application of hierarchical virtual screening in small molecule drug discovery.
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Affiliation(s)
- Ashutosh Kumar
- Structural Bioinformatics Team, Center for Life Science Technologies, RIKEN, 1-7-22 Suehiro, Tsurumi, Yokohama, Kanagawa 230-0045, Japan
| | - Kam Y J Zhang
- Structural Bioinformatics Team, Center for Life Science Technologies, RIKEN, 1-7-22 Suehiro, Tsurumi, Yokohama, Kanagawa 230-0045, Japan.
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18
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Jones LH, Narayanan A, Hett EC. Understanding and applying tyrosine biochemical diversity. MOLECULAR BIOSYSTEMS 2014; 10:952-69. [PMID: 24623162 DOI: 10.1039/c4mb00018h] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
This review highlights some of the recent advances made in our understanding of the diversity of tyrosine biochemistry and shows how this has inspired novel applications in numerous areas of molecular design and synthesis, including chemical biology and bioconjugation. The pathophysiological implications of tyrosine biochemistry will be presented from a molecular perspective and the opportunities for therapeutic intervention explored.
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Affiliation(s)
- Lyn H Jones
- Pfizer R&D, Chemical Biology Group, BioTherapeutics Chemistry, WorldWide Medicinal Chemistry, 200 Cambridge Park Drive, Cambridge, MA 02140, USA.
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19
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Zoppe JO, Ruottinen V, Ruotsalainen J, Rönkkö S, Johansson LS, Hinkkanen A, Järvinen K, Seppälä J. Synthesis of Cellulose Nanocrystals Carrying Tyrosine Sulfate Mimetic Ligands and Inhibition of Alphavirus Infection. Biomacromolecules 2014; 15:1534-42. [DOI: 10.1021/bm500229d] [Citation(s) in RCA: 69] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Affiliation(s)
- Justin O. Zoppe
- Polymer
Technology, Department of Biotechnology and Chemical Technology, Aalto University School of Chemical Technology, P.O. Box 16100, 00076 Aalto, Finland
| | | | | | | | - Leena-Sisko Johansson
- Department
of Forest Products Technology, Aalto University School of Chemical Technology, P.O. Box
16300, 00076 Aalto, Finland
| | | | | | - Jukka Seppälä
- Polymer
Technology, Department of Biotechnology and Chemical Technology, Aalto University School of Chemical Technology, P.O. Box 16100, 00076 Aalto, Finland
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20
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Rudick JG, Laakso MM, Schloss AC, DeGrado WF. Template-constrained cyclic sulfopeptide HIV-1 entry inhibitors. Org Biomol Chem 2013; 11:7096-100. [PMID: 24065278 PMCID: PMC3889485 DOI: 10.1039/c3ob41395k] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Template-constrained cyclic sulfopeptides that inhibit HIV-1 entry were rationally designed based on a loop from monoclonal antibody (mAb) 412d. A focused set of sulfopeptides was synthesized using Fmoc-Tyr(SO3DCV)-OH (DCV = 2,2-dichlorovinyl). Three cyclic sulfopeptides that inhibit entry of HIV-1 and complement the activity of known CCR5 antagonists were identified.
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Affiliation(s)
- Jonathan G. Rudick
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Meg M. Laakso
- Department Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Ashley C. Schloss
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - William F. DeGrado
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
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21
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Heavy chain-only IgG2b llama antibody effects near-pan HIV-1 neutralization by recognizing a CD4-induced epitope that includes elements of coreceptor- and CD4-binding sites. J Virol 2013; 87:10173-81. [PMID: 23843638 DOI: 10.1128/jvi.01332-13] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The conserved HIV-1 site of coreceptor binding is protected from antibody-directed neutralization by conformational and steric restrictions. While inaccessible to most human antibodies, the coreceptor site has been shown to be accessed by antibody fragments. In this study, we used X-ray crystallography, surface plasmon resonance, and pseudovirus neutralization to characterize the gp120-envelope glycoprotein recognition and HIV-1 neutralization of a heavy chain-only llama antibody, named JM4. We describe full-length IgG2b and IgG3 versions of JM4 that target the coreceptor-binding site and potently neutralize over 95% of circulating HIV-1 isolates. Contrary to established trends that show improved access to the coreceptor-binding region by smaller antibody fragments, the single-domain (VHH) version of JM4 neutralized less well than the full-length IgG2b version of JM4. The crystal structure at 2.1-Å resolution of VHH JM4 bound to HIV-1 YU2 gp120 stabilized in the CD4-bound state by the CD4-mimetic miniprotein, M48U1, revealed a JM4 epitope that combined regions of coreceptor recognition (including the gp120 bridging sheet, V3 loop, and β19 strand) with gp120 structural elements involved in recognition of CD4 such as the CD4-binding loop. The structure of JM4 with gp120 thus defines a novel CD4-induced site of vulnerability involving elements of both coreceptor- and CD4-binding sites. The potently neutralizing JM4 IgG2b antibody that targets this newly defined site of vulnerability adds to the expanding repertoire of broadly neutralizing antibodies that effectively neutralize HIV-1 and thereby potentially provides a new template for vaccine development and target for HIV-1 therapy.
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22
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Acharya P, Luongo TS, Louder MK, McKee K, Yang Y, Kwon YD, Mascola JR, Kessler P, Martin L, Kwong PD. Structural basis for highly effective HIV-1 neutralization by CD4-mimetic miniproteins revealed by 1.5 Å cocrystal structure of gp120 and M48U1. Structure 2013; 21:1018-29. [PMID: 23707685 DOI: 10.1016/j.str.2013.04.015] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2012] [Revised: 04/09/2013] [Accepted: 04/12/2013] [Indexed: 12/13/2022]
Abstract
The interface between the HIV-1 gp120 envelope glycoprotein and the CD4 receptor contains an unusual interfacial cavity, the "Phe43 cavity", which CD4-mimetic miniproteins with nonnatural extensions can potentially utilize to enhance their neutralization of HIV-1. Here, we report cocrystal structures of HIV-1 gp120 with miniproteins M48U1 and M48U7, which insert cyclohexylmethoxy and 5-hydroxypentylmethoxy extensions, respectively, into the Phe43 cavity. Both inserts displayed flexibility and hydrophobic interactions, but the M48U1 insert showed better shape complementarity with the Phe43 cavity than the M48U7 insert. Subtle alteration in the gp120 conformation played a substantial role in optimizing fit. With M48U1, these translated into a YU2-gp120 affinity of 0.015 nM and neutralization of all 180 circulating HIV-1 strains tested, except clade-A/E isolates with noncanonical Phe43 cavities. Ligand chemistry, shape complementarity, surface burial, and gp120 conformation act in concert to modulate binding of ligands to the gp120-Phe43 cavity and, when optimized, can effect near-pan-neutralization of HIV-1.
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Affiliation(s)
- Priyamvada Acharya
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
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23
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Schnur E, Kessler N, Zherdev Y, Noah E, Scherf T, Ding FX, Rabinovich S, Arshava B, Kurbatska V, Leonciks A, Tsimanis A, Rosen O, Naider F, Anglister J. NMR mapping of RANTES surfaces interacting with CCR5 using linked extracellular domains. FEBS J 2013; 280:2068-84. [PMID: 23480650 DOI: 10.1111/febs.12230] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2013] [Revised: 02/21/2013] [Accepted: 03/04/2013] [Indexed: 11/29/2022]
Abstract
Chemokines constitute a large family of small proteins that regulate leukocyte trafficking to the site of inflammation by binding to specific cell-surface receptors belonging to the G-protein-coupled receptor (GPCR) superfamily. The interactions between N-terminal (Nt-) peptides of these GPCRs and chemokines have been studied extensively using NMR spectroscopy. However, because of the lower affinities of peptides representing the three extracellular loops (ECLs) of chemokine receptors to their respective chemokine ligands, information concerning these interactions is scarce. To overcome the low affinity of ECL peptides to chemokines, we linked two or three CC chemokine receptor 5 (CCR5) extracellular domains using either biosynthesis in Escherichia coli or chemical synthesis. Using such chimeras, CCR5 binding to RANTES was followed using (1)H-(15)N-HSQC spectra to monitor titration of the chemokine with peptides corresponding to the extracellular surface of the receptor. Nt-CCR5 and ECL2 were found to be the major contributors to CCR5 binding to RANTES, creating an almost closed ring around this protein by interacting with opposing faces of the chemokine. A RANTES positively charged surface involved in Nt-CCR5 binding resembles the positively charged surface in HIV-1 gp120 formed by the C4 and the base of the third variable loop of gp120 (V3). The opposing surface on RANTES, composed primarily of β2-β3 hairpin residues, binds ECL2 and was found to be analogous to a surface in the crown of the gp120 V3. The chemical and biosynthetic approaches for linking GPCR surface regions discussed herein should be widely applicable to the investigation of interactions of extracellular segments of chemokine receptors with their respective ligands.
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Affiliation(s)
- Einat Schnur
- Department of Structural Biology, Weizmann Institute of Science, Rehovot, Israel
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24
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Abstract
This chapter reviews studies that have used in silico techniques to design or identify potential HIV-1 entry inhibitors targeting cellular receptors CD4, CCR5, and CXCR4 and envelope glycoproteins, gp120 and gp41 of HIV-1. Both structure- and ligand-based design techniques have been used in those studies by applying diverse modeling techniques such as quantitative structure-activity relationship analysis, conformational analysis, molecular dynamics, pharmacophore generation, docking, virtual screening (using docking software and also shape-based ROCS techniques), and fragment-based design.
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Affiliation(s)
- Asim K Debnath
- Lindsley F. Kimball Research Institute, New York Blood Center, New York, NY, USA
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25
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Tuzer F, Madani N, Kamanna K, Zentner I, LaLonde J, Holmes A, Upton E, Rajagopal S, McFadden K, Contarino M, Sodroski J, Chaiken I. HIV-1 Env gp120 structural determinants for peptide triazole dual receptor site antagonism. Proteins 2012; 81:271-90. [PMID: 23011758 DOI: 10.1002/prot.24184] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2012] [Revised: 08/18/2012] [Accepted: 09/03/2012] [Indexed: 11/09/2022]
Abstract
Despite advances in HIV therapy, viral resistance and side-effects with current drug regimens require targeting new components of the virus. Dual antagonist peptide triazoles (PT) are a novel class of HIV-1 inhibitors that specifically target the gp120 component of the viral spike and inhibit its interaction with both of its cell surface protein ligands, namely the initial receptor CD4 and the co-receptor (CCR5/CXCR4), thus preventing viral entry. Following an initial survey of 19 gp120 alanine mutants by ELISA, we screened 11 mutants for their importance in binding to, and inhibition by the PT KR21 using surface plasmon resonance. Key mutants were purified and tested for their effects on the peptide's affinity and its ability to inhibit binding of CD4 and the co-receptor surrogate mAb 17b. Effects of the mutations on KR21 viral neutralization were measured by single-round cell infection assays. Two mutations, D474A and T257A, caused large-scale loss of KR21 binding, as well as losses in both CD4/17b and viral inhibition by KR21. A set of other Ala mutants revealed more moderate losses in direct binding affinity and inhibition sensitivity to KR21. The cluster of sensitive residues defines a PT functional epitope. This site is in a conserved region of gp120 that overlaps the CD4 binding site and is distant from the co-receptor/17b binding site, suggesting an allosteric mode of inhibition for the latter. The arrangement and sequence conservation of the residues in the functional epitope explain the breadth of antiviral activity, and improve the potential for rational inhibitor development.
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Affiliation(s)
- Ferit Tuzer
- Department of Biochemistry and Molecular Biology, Drexel University College of Medicine, Philadelphia, Pennsylvania 19102, USA
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Connell BJ, Baleux F, Coic YM, Clayette P, Bonnaffé D, Lortat-Jacob H. A synthetic heparan sulfate-mimetic peptide conjugated to a mini CD4 displays very high anti- HIV-1 activity independently of coreceptor usage. ACTA ACUST UNITED AC 2012; 19:131-9. [PMID: 22284360 DOI: 10.1016/j.chembiol.2011.12.009] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2011] [Revised: 11/30/2011] [Accepted: 12/12/2011] [Indexed: 12/01/2022]
Abstract
The HIV-1 envelope gp120, which features both the virus receptor (CD4) and coreceptor (CCR5/CXCR4) binding sites, offers multiple sites for therapeutic intervention. However, the latter becomes exposed, thus vulnerable to inhibition, only transiently when the virus has already bound cellular CD4. To pierce this defense mechanism, we engineered a series of heparan sulfate mimicking tridecapeptides and showed that one of them target the gp120 coreceptor binding site with μM affinity. Covalently linked to a CD4-mimetic that binds to gp120 and renders the coreceptor binding domain available to be targeted, the conjugated tridecapeptide now displays nanomolar affinity for its target. Using solubilized coreceptors captured on top of sensorchip we show that it inhibits gp120 binding to both CCR5 and CXCR4 and in peripheral blood mononuclear cells broadly inhibits HIV-1 replication with an IC(50) of 1 nM.
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Affiliation(s)
- Bridgette Janine Connell
- CEA, CNRS, Université Joseph Fourier - Grenoble 1, Institut de Biologie Structurale Jean-Pierre Ebel, UMR 5075, 38000 Grenoble, France
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Dogo-Isonagie C, Lam S, Gustchina E, Acharya P, Yang Y, Shahzad-ul-Hussan S, Clore GM, Kwong PD, Bewley CA. Peptides from second extracellular loop of C-C chemokine receptor type 5 (CCR5) inhibit diverse strains of HIV-1. J Biol Chem 2012; 287:15076-86. [PMID: 22403408 DOI: 10.1074/jbc.m111.332361] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
To initiate HIV entry, the HIV envelope protein gp120 must engage its primary receptor CD4 and a coreceptor CCR5 or CXCR4. In the absence of a high resolution structure of a gp120-coreceptor complex, biochemical studies of CCR5 have revealed the importance of its N terminus and second extracellular loop (ECL2) in binding gp120 and mediating viral entry. Using a panel of synthetic CCR5 ECL2-derived peptides, we show that the C-terminal portion of ECL2 (2C, comprising amino acids Cys-178 to Lys-191) inhibit HIV-1 entry of both CCR5- and CXCR4-using isolates at low micromolar concentrations. In functional viral assays, these peptides inhibited HIV-1 entry in a CD4-independent manner. Neutralization assays designed to measure the effects of CCR5 ECL2 peptides when combined with either with the small molecule CD4 mimetic NBD-556, soluble CD4, or the CCR5 N terminus showed additive inhibition for each, indicating that ECL2 binds gp120 at a site distinct from that of N terminus and acts independently of CD4. Using saturation transfer difference NMR, we determined the region of CCR5 ECL2 used for binding gp120, showed that it can bind to gp120 from both R5 and X4 isolates, and demonstrated that the peptide interacts with a CD4-gp120 complex in a similar manner as to gp120 alone. As the CCR5 N terminus-gp120 interactions are dependent on CD4 activation, our data suggest that gp120 has separate binding sites for the CCR5 N terminus and ECL2, the ECL2 binding site is present prior to CD4 engagement, and it is conserved across CCR5- and CXCR4-using strains. These peptides may serve as a starting point for the design of inhibitors with broad spectrum anti-HIV activity.
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Affiliation(s)
- Cajetan Dogo-Isonagie
- Laboratory of Bioorganic Chemistry, NIAID, National Institutes of Health, Bethesda, Maryland 20892, USA
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