1
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Melillo B, Liang S, Park J, Schön A, Courter JR, LaLonde JM, Wendler DJ, Princiotto AM, Seaman MS, Freire E, Sodroski J, Madani N, Hendrickson WA, Smith AB. Small-Molecule CD4-Mimics: Structure-Based Optimization of HIV-1 Entry Inhibition. ACS Med Chem Lett 2016; 7:330-4. [PMID: 26985324 DOI: 10.1021/acsmedchemlett.5b00471] [Citation(s) in RCA: 73] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2015] [Accepted: 01/13/2016] [Indexed: 11/29/2022] Open
Abstract
The optimization, based on computational, thermodynamic, and crystallographic data, of a series of small-molecule ligands of the Phe43 cavity of the envelope glycoprotein gp120 of human immunodeficiency virus (HIV) has been achieved. Importantly, biological evaluation revealed that the small-molecule CD4 mimics (4-7) inhibit HIV-1 entry into target cells with both significantly higher potency and neutralization breadth than previous congeners, while maintaining high selectivity for the target virus. Their binding mode was characterized via thermodynamic and crystallographic studies.
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Affiliation(s)
- Bruno Melillo
- Department
of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | | | - Jongwoo Park
- Department
of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Arne Schön
- Department
of Biology, The Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Joel R. Courter
- Department
of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Judith M. LaLonde
- Department
of Chemistry, Bryn Mawr College, Bryn Mawr, Pennsylvania 19010, United States
| | - Daniel J. Wendler
- Department
of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | | | | | - Ernesto Freire
- Department
of Biology, The Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Joseph Sodroski
- Department
of Immunology and Infectious Diseases, Harvard School of Public Health, Boston, Massachusetts 02115, United States
| | | | | | - Amos B. Smith
- Department
of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
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2
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Malachowski WP, Winters M, DuHadaway JB, Lewis-Ballester A, Badir S, Wai J, Rahman M, Sheikh E, LaLonde JM, Yeh SR, Prendergast GC, Muller AJ. O-alkylhydroxylamines as rationally-designed mechanism-based inhibitors of indoleamine 2,3-dioxygenase-1. Eur J Med Chem 2016; 108:564-576. [PMID: 26717206 PMCID: PMC4724314 DOI: 10.1016/j.ejmech.2015.12.028] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2015] [Revised: 11/12/2015] [Accepted: 12/14/2015] [Indexed: 01/21/2023]
Abstract
Indoleamine 2,3-dioxygenase-1 (IDO1) is a promising therapeutic target for the treatment of cancer, chronic viral infections, and other diseases characterized by pathological immune suppression. Recently important advances have been made in understanding IDO1's catalytic mechanism. Although much remains to be discovered, there is strong evidence that the mechanism proceeds through a heme-iron bound alkylperoxy transition or intermediate state. Accordingly, we explored stable structural mimics of the alkylperoxy species and provide evidence that such structures do mimic the alkylperoxy transition or intermediate state. We discovered that O-benzylhydroxylamine, a commercially available compound, is a potent sub-micromolar inhibitor of IDO1. Structure-activity studies of over forty derivatives of O-benzylhydroxylamine led to further improvement in inhibitor potency, particularly with the addition of halogen atoms to the meta position of the aromatic ring. The most potent derivatives and the lead, O-benzylhydroxylamine, have high ligand efficiency values, which are considered an important criterion for successful drug development. Notably, two of the most potent compounds demonstrated nanomolar-level cell-based potency and limited toxicity. The combination of the simplicity of the structures of these compounds and their excellent cellular activity makes them quite attractive for biological exploration of IDO1 function and antitumor therapeutic applications.
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Affiliation(s)
| | - Maria Winters
- Department of Chemistry, Bryn Mawr College, Bryn Mawr, Pennsylvania 19010, USA
| | - James B. DuHadaway
- Lankenau Institute for Medical Research, Wynnewood, Pennsylvania 19096, USA
| | - Ariel Lewis-Ballester
- Department of Physiology and Biophysics, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, New York 10461, United States
| | - Shorouk Badir
- Department of Chemistry, Bryn Mawr College, Bryn Mawr, Pennsylvania 19010, USA
| | - Jenny Wai
- Department of Chemistry, Bryn Mawr College, Bryn Mawr, Pennsylvania 19010, USA
| | - Maisha Rahman
- Department of Chemistry, Bryn Mawr College, Bryn Mawr, Pennsylvania 19010, USA
| | - Eesha Sheikh
- Department of Chemistry, Bryn Mawr College, Bryn Mawr, Pennsylvania 19010, USA
| | - Judith M. LaLonde
- Department of Chemistry, Bryn Mawr College, Bryn Mawr, Pennsylvania 19010, USA
| | - Syun-Ru Yeh
- Department of Physiology and Biophysics, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, New York 10461, United States
| | - George C. Prendergast
- Lankenau Institute for Medical Research, Wynnewood, Pennsylvania 19096, USA
- Department of Pathology, Anatomy & Cell Biology, Thomas Jefferson University, Philadelphia, Pennsylvania 19104, USA
- Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, Pennsylvania 19104, USA
| | - Alexander J. Muller
- Lankenau Institute for Medical Research, Wynnewood, Pennsylvania 19096, USA
- Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, Pennsylvania 19104, USA
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3
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Courter JR, Madani N, Sodroski J, Schön A, Freire E, Kwong PD, Hendrickson WA, Chaiken IM, LaLonde JM, Smith AB. Structure-based design, synthesis and validation of CD4-mimetic small molecule inhibitors of HIV-1 entry: conversion of a viral entry agonist to an antagonist. Acc Chem Res 2014; 47:1228-37. [PMID: 24502450 PMCID: PMC3993944 DOI: 10.1021/ar4002735] [Citation(s) in RCA: 72] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
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This
Account provides an overview of a multidisciplinary consortium focused
on structure-based strategies to devise small molecule antagonists
of HIV-1 entry into human T-cells, which if successful would hold
considerable promise for the development of prophylactic modalities
to prevent HIV transmission and thereby alter the course of the AIDS
pandemic. Entry of the human immunodeficiency virus (HIV) into
target T-cells entails an interaction between CD4 on the host T-cell
and gp120, a component of the trimeric envelope glycoprotein spike
on the virion surface. The resultant interaction initiates a series
of conformational changes within the envelope spike that permits binding
to a chemokine receptor, formation of the gp41 fusion complex, and
cell entry. A hydrophobic cavity at the CD4–gp120 interface,
defined by X-ray crystallography, provided an initial site for small
molecule antagonist design. This site however has evolved to facilitate
viral entry. As such, the binding of prospective small molecule inhibitors
within this gp120 cavity can inadvertently trigger an allosteric entry
signal. Structural characterization of the CD4–gp120
interface, which provided the foundation for small molecule structure-based
inhibitor design, will be presented first. An integrated approach
combining biochemical, virological, structural, computational, and
synthetic studies, along with a detailed analysis of ligand binding
energetics, revealed that modestly active small molecule inhibitors
of HIV entry can also promote viral entry into cells lacking the CD4
receptor protein; these competitive inhibitors were termed small molecule
CD4 mimetics. Related congeners were subsequently identified with
both improved binding affinity and more potent viral entry inhibition.
Further assessment of the affinity-enhanced small molecule CD4 mimetics
demonstrated
that premature initiation of conformational change within the viral envelope spike, prior to cell encounter, can lead to irreversible
deactivation of viral entry machinery. Related congeners, which bind the same gp120 site, possess different propensities to elicit the
allosteric response that underlies the undesired enhancement of CD4-independent viral entry. Subsequently, key hotspots in the CD4–gp120 interface were categorized using mutagenesis and isothermal titration calorimetry according to the capacity to increase binding affinity without triggering the allosteric signal. This analysis, combined with cocrystal structures of small molecule viral entry agonists with gp120, led to the development of fully functional antagonists of HIV-1 entry. Additional structure-based design exploiting two hotspots followed by synthesis has now yielded low micromolar inhibitors of viral entry.
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Affiliation(s)
- Joel R. Courter
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Navid Madani
- Department of Cancer Immunology and AIDS, Dana-Farber Cancer Institute, Harvard Medical School, 450 Brookline Avenue, Boston, Massachusetts 02115, United States
| | - Joseph Sodroski
- Department of Cancer Immunology and AIDS, Dana-Farber Cancer Institute, Harvard Medical School, 450 Brookline Avenue, Boston, Massachusetts 02115, United States
- Department
of Microbiology and Immunology, Harvard Medical School, Department of Immunology and Infectious Diseases, Harvard School of Public Health, Ragon Institute of MGH, MIT and Harvard, Boston, Massachusetts 02115, United States
| | - Arne Schön
- Department of Biology, The Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Ernesto Freire
- Department of Biology, The Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Peter D. Kwong
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Wayne A. Hendrickson
- Department of Biochemistry and Molecular Biophysics and Department of Physiology and Cellular Biophysics, Columbia University, New York, New York 10032, United States
| | - Irwin M. Chaiken
- Department of Biochemistry and Molecular
Biology, Drexel University College of Medicine, Philadelphia, Pennsylvania 19102, United States
| | - Judith M. LaLonde
- Department of Chemistry, Bryn Mawr College, Bryn Mawr, Pennsylvania 19010, United States
| | - Amos B. Smith
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
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4
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Kwon YD, LaLonde JM, Yang Y, Elban MA, Sugawara A, Courter JR, Jones DM, Smith AB, Debnath AK, Kwong PD. Crystal structures of HIV-1 gp120 envelope glycoprotein in complex with NBD analogues that target the CD4-binding site. PLoS One 2014; 9:e85940. [PMID: 24489681 PMCID: PMC3904841 DOI: 10.1371/journal.pone.0085940] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2013] [Accepted: 12/05/2013] [Indexed: 11/19/2022] Open
Abstract
Efforts to develop therapeutic agents that inhibit HIV-1 entry have led to the identification of several small molecule leads. One of the most promising is the NBD series, which binds within a conserved gp120 cavity and possesses para-halogen substituted aromatic rings, a central oxalamide linker, and a tetramethylpiperidine moiety. In this study, we characterized structurally the interactions of four NBD analogues containing meta-fluoro substitution on the aromatic ring and various heterocyclic ring replacements of the tetramethylpiperidine group. The addition of a meta-fluorine to the aromatic ring improved surface complementarity and did not alter the position of the analogue relative to gp120. By contrast, heterocyclic ring replacements of the tetramethylpiperidine moiety exhibited diverse positioning and interactions with the vestibule of the gp120 cavity. Overall, the biological profile of NBD-congeners was modulated by ligand interactions with the gp120-cavity vestibule. Herein, six co-crystal structures of NBD-analogues with gp120 provide a structural framework for continued small molecule-entry inhibitor optimization.
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Affiliation(s)
- Young Do Kwon
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Judith M. LaLonde
- Department of Chemistry, Bryn Mawr College, Bryn Mawr, Pennsylvania, United States of America
| | - Yongping Yang
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Mark A. Elban
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Akihiro Sugawara
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Joel R. Courter
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - David M. Jones
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Amos B. Smith
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Asim K. Debnath
- Laboratory of Molecular Modeling and Drug Design, Lindsey F. Kimball Research Institute of the New York Blood Center, New York, New York, United States of America
| | - Peter D. Kwong
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, United States of America
- * E-mail:
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5
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Abstract
β-lapachone is a naturally occurring 1,2-naphthoquinone-based compound that has been advanced into clinical trials based on its tumor-selective cytotoxic properties. Previously, we focused on the related 1,4-naphthoquinone pharmacophore as a basic core structure for developing a series of potent indoleamine 2,3-dioxygenase 1 (IDO1) enzyme inhibitors. In this study, we identified IDO1 inhibitory activity as a previously unrecognized attribute of the clinical candidate β-lapachone. Enzyme kinetics-based analysis of β-lapachone indicated an uncompetitive mode of inhibition, while computational modeling predicted binding within the IDO1 active site consistent with other naphthoquinone derivatives. Inhibition of IDO1 has previously been shown to breach the pathogenic tolerization that constrains the immune system from being able to mount an effective anti-tumor response. Thus, the finding that β-lapachone has IDO1 inhibitory activity adds a new dimension to its potential utility as an anti-cancer agent distinct from its cytotoxic properties, and suggests that a synergistic benefit can be achieved from its combined cytotoxic and immunologic effects.
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Affiliation(s)
- Hollie E. Flick
- Lankenau Institute for Medical Research, Wynnewood, Pennsylvania
- Department of Biochemistry, Drexel University College of Medicine, Philadelphia, Pennsylvania
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6
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LaLonde JM, Le-Khac M, Jones DM, Courter JR, Park J, Schön A, Princiotto AM, Wu X, Mascola JR, Freire E, Sodroski J, Madani N, Hendrickson WA, Smith AB. Structure-Based Design and Synthesis of an HIV-1 Entry Inhibitor Exploiting X-Ray and Thermodynamic Characterization. ACS Med Chem Lett 2013; 4:338-343. [PMID: 23667716 DOI: 10.1021/ml300407y] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
The design, synthesis, thermodynamic and crystallographic characterization of a potent, broad spectrum, second-generation HIV-1 entry inhibitor that engages conserved carbonyl hydrogen bonds within gp120 has been achieved. The optimized antagonist exhibits a sub-micromolar binding affinity (110 nM) and inhibits viral entry of clade B and C viruses (IC50 geometric mean titer of 1.7 and 14.0 μM, respectively), without promoting CD4-independent viral entry. thermodynamic signatures indicate a binding preference for the (R,R)-over the (S,S)-enantiomer. The crystal structure of the small molecule-gp120 complex reveals the displacement of crystallographic water and the formation of a hydrogen bond with a backbone carbonyl of the bridging sheet. Thus, structure-based design and synthesis targeting the highly conserved and structurally characterized CD4:gp120 interface is an effective tactic to enhance the neutralization potency of small molecule HIV-1 entry inhibitors.
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Affiliation(s)
- Judith M. LaLonde
- Department of Chemistry, Bryn Mawr College, Bryn Mawr, Pennsylvania 19010, United
States
| | | | - David M. Jones
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania
19104, United States
| | - Joel R. Courter
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania
19104, United States
| | - Jongwoo Park
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania
19104, United States
| | - Arne Schön
- Department
of Biology, The Johns Hopkins University, Baltimore, Maryland 21218,
United States
| | - Amy M. Princiotto
- Department of Cancer
Immunology and
AIDS, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Xueling Wu
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, Bethesda,
Maryland 20892, United States
| | - John R. Mascola
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, Bethesda,
Maryland 20892, United States
| | - Ernesto Freire
- Department
of Biology, The Johns Hopkins University, Baltimore, Maryland 21218,
United States
| | - Joseph Sodroski
- Department of Cancer
Immunology and
AIDS, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts 02115, United States
- Department of Microbiology and
Immunobiology, Harvard Medical School; Department of Immunology and
Infectious Diseases, Harvard School of Public Health; Ragon Institute
of MGH, MIT, and Harvard, Boston, Massachusetts 02115, United States
| | - Navid Madani
- Department of Cancer
Immunology and
AIDS, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Wayne A. Hendrickson
- Department of Physiology and
Cellular Biophysics, Columbia University, New York, New York 10032, United States
| | - Amos B. Smith
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania
19104, United States
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7
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Shrivastava IH, Wendel K, LaLonde JM. Spontaneous rearrangement of the β20/β21 strands in simulations of unliganded HIV-1 glycoprotein, gp120. Biochemistry 2012; 51:7783-93. [PMID: 22963284 DOI: 10.1021/bi300878d] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Binding of the viral spike drives cell entry and infection by HIV-1 to the cellular CD4 and chemokine receptors with associated conformational change of the viral glycoprotein envelope, gp120. Crystal structures of the CD4-gp120-antibody ternary complex reveal a large internal gp120 cavity formed by three domains-the inner domain, outer domain, and bridging sheet domain-and are capped by CD4 residue Phe43. Several structures of gp120 envelope in complex with various antibodies indicated that the bridging sheet adopts varied conformations. Here, we examine bridging sheet dynamics using a crystal structure of gp120 bound to the F105 antibody exhibiting an open bridging sheet conformation and with an added V3 loop. The two strands of the bridging sheet β2/β3 and β20/β21 are dissociated from each other and are directed away from the inner and outer domains. Analysis of molecular dynamics (MD) trajectories indicates that the β2/β3 and β20/β21 strands rapidly rearrange to interact with the V3 loop and the inner and outer domains, respectively. Residue N425 on β20 leads the conformational rearrangement of the β20/β21 strands by interacting with W112 on the inner domain and F382 on the outer domain. An accompanying shift is observed in the inner domain as helix α1 exhibits a loss in helicity and pivots away from helix α5. The two simulations provide a framework for understanding the conformational diversity of the bridging sheet and the propensity of the β20/β21 strand to refold between the inner and outer domains of gp120, in the absence of a bound ligand.
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Affiliation(s)
- Indira H Shrivastava
- Department of Systems and Computational Biology, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania 15213, United States.
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8
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LaLonde JM, Kwon YD, Jones DM, Sun AW, Courter JR, Soeta T, Kobayashi T, Princiotto AM, Wu X, Schön A, Freire E, Kwong PD, Mascola JR, Sodroski J, Madani N, Smith AB. Structure-based design, synthesis, and characterization of dual hotspot small-molecule HIV-1 entry inhibitors. J Med Chem 2012; 55:4382-96. [PMID: 22497421 PMCID: PMC3376652 DOI: 10.1021/jm300265j] [Citation(s) in RCA: 79] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Cellular infection by HIV-1 is initiated with a binding event between the viral envelope glycoprotein gp120 and the cellular receptor protein CD4. The CD4-gp120 interface is dominated by two hotspots: a hydrophobic gp120 cavity capped by Phe43(CD4) and an electrostatic interaction between residues Arg59(CD4) and Asp368(gp120). The CD4 mimetic small-molecule NBD-556 (1) binds within the gp120 cavity; however, 1 and related congeners demonstrate limited viral neutralization breadth. Herein, we report the design, synthesis, characterization, and X-ray structures of gp120 in complex with small molecules that simultaneously engage both binding hotspots. The compounds specifically inhibit viral infection of 42 tier 2 clades B and C viruses and are shown to be antagonists of entry into CD4-negative cells. Dual hotspot design thus provides both a means to enhance neutralization potency of HIV-1 entry inhibitors and a novel structural paradigm for inhibiting the CD4-gp120 protein-protein interaction.
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Affiliation(s)
- Judith M. LaLonde
- Department of Chemistry, Bryn Mawr College, Bryn Mawr, Pennsylvania 19010
| | - Young Do Kwon
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, Bethesda MD 20892
| | - David M. Jones
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA 19104
| | - Alexander W. Sun
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA 19104
| | - Joel R. Courter
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA 19104
| | - Takahiro Soeta
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA 19104
| | - Toyoharu Kobayashi
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA 19104
| | - Amy M. Princiotto
- Department of Cancer Immunology and AIDS, Dana-Farber Cancer Institute, Harvard Medical School, 450 Brookline Ave., Boston, MA 02115
| | - Xueling Wu
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, Bethesda MD 20892
| | - Arne Schön
- Department of Biology, The Johns Hopkins University, Baltimore, MD 21218
| | - Ernesto Freire
- Department of Biology, The Johns Hopkins University, Baltimore, MD 21218
| | - Peter D. Kwong
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, Bethesda MD 20892
| | - John R. Mascola
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, Bethesda MD 20892
| | - Joseph Sodroski
- Department of Cancer Immunology and AIDS, Dana-Farber Cancer Institute, Harvard Medical School, 450 Brookline Ave., Boston, MA 02115
- Department of Microbiology and Immunology, Harvard Medical School; Department of Immunology and Infectious Diseases, Harvard School of Public Health; Ragon Institute of MGH, MIT and Harvard, Boston, MA 02115
| | - Navid Madani
- Department of Cancer Immunology and AIDS, Dana-Farber Cancer Institute, Harvard Medical School, 450 Brookline Ave., Boston, MA 02115
| | - Amos B. Smith
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA 19104
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9
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Emileh A, Tuzer F, Moreira DR, LaLonde JM, Bewley CA, Chaiken IM, Abrams CF. A Molecular Dynamics Simulation of Peptide-Triazole HIV Entry Inhibitor Binding to gp120 Hydrophobic Core. Biophys J 2012. [DOI: 10.1016/j.bpj.2011.11.3383] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
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10
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Acharya P, Dogo-Isonagie C, LaLonde JM, Lam SN, Leslie GJ, Louder MK, Frye LL, Debnath AK, Greenwood JR, Luongo TS, Martin L, Watts KS, Hoxie JA, Mascola JR, Bewley CA, Kwong PD. Structure-based identification and neutralization mechanism of tyrosine sulfate mimetics that inhibit HIV-1 entry. ACS Chem Biol 2011; 6:1069-77. [PMID: 21793507 DOI: 10.1021/cb200068b] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Tyrosine sulfate-mediated interactions play an important role in HIV-1 entry. After engaging the CD4 receptor at the cell surface, the HIV-1 gp120 glycoprotein binds to the CCR5 co-receptor via an interaction that requires two tyrosine sulfates, at positions 10 and 14 in the CCR5-N terminus. Building on previous structure determinations of this interaction, here we report the targeting of these tyrosine sulfate binding sites for drug design through in silico screening of small molecule libraries, identification of lead compounds, and characterization of biological activity. A class of tyrosine sulfate-mimicking small molecules containing a "phenyl sulfonate-linker-aromatic" motif was identified that specifically inhibited binding of gp120 to the CCR5-N terminus as well as to sulfated antibodies that recognize the co-receptor binding region on gp120. The most potent of these compounds bound gp120 with low micromolar affinity and its CD4-induced conformation with K(D)'s as tight as ∼50 nM. Neutralization experiments suggested the targeted site to be conformationally inaccessible prior to CD4 engagement. Primary HIV-1 isolates were weakly neutralized, preincubation with soluble CD4 enhanced neutralization, and engineered isolates with increased dependence on the N terminus of CCR5 or with reduced conformational barriers were neutralized with IC(50) values as low as ∼1 μM. These results reveal the potential of targeting the tyrosine sulfate interactions of HIV-1 and provide insight into how mechanistic barriers, evolved by HIV-1 to evade antibody recognition, also restrict small-molecule-mediated neutralization.
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Affiliation(s)
| | | | - Judith M. LaLonde
- Department of Chemistry, Bryn Mawr College, Bryn Mawr, Pennsylvania 19010, United States
| | | | - George J. Leslie
- Department of Medicine, Hematology-Oncology Division, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | | | - Leah L. Frye
- Schrödinger, LLC, Portland, Oregon 97204, United States
| | - Asim K. Debnath
- Laboratory of Molecular Modeling and Drug Design, Lindsley F. Kimball Research Institute, New York Blood Center, 310 E 67th Street, New York, New York 10021, United States
| | | | | | - Loïc Martin
- CEA, iBiTecS, Service d’Ingénierie Moléculaire des Protéines, Gif sur Yvette F-91191, France
| | | | - James A. Hoxie
- Department of Medicine, Hematology-Oncology Division, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
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11
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Abstract
HIV cell entry and infection are driven by binding events to the CD4 and chemokine receptors with associated conformational change of the viral glycoprotein, gp120. Scyllatoxin miniprotein CD4 mimetics and a small molecule inhibitor of CD4 binding, NBD-556, also effectively induce gp120 conformational change. In this study we examine the fluctuation profile of gp120 in context of CD4, a miniprotein mimetic, and NBD-556 with the aim of understanding the effect of ligand binding on gp120 conformational dynamics. Analysis of molecular dynamics trajectories indicate that NBD-556 binding in the Phe 43 cavity enhances the overall mobility of gp120, especially in the outer domain in comparison to CD4 or miniprotein bound complex. Interactions with the more flexible bridging sheet strengthen upon NBD-556 binding and may contribute to gp120 restructuring. The enhanced mobility of D368, E370, and I371 with NBD-556 bound in the Phe 43 cavity suggests that interactions with α3-helix in the outer domain are not optimal, providing further insights into gp120--small molecule interactions that may impact small molecule designs.
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Affiliation(s)
- Indira Shrivastava
- Department of Computational and Systems Biology, School of Medicine, University of Pittsburgh 3083 Biomedical Science Tower 3, 3501 Fifth Avenue, Pittsburgh PA 15213
| | - Judith M. LaLonde
- Chemistry Department, Bryn Mawr College, 101 N. Merion Avenue, Bryn Mawr, PA 19010
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12
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Shrivastava I, LaLonde JM. Fluctuation dynamics analysis of gp120 envelope protein reveals a topologically based communication network. Proteins 2011; 78:2935-49. [PMID: 20718047 DOI: 10.1002/prot.22816] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Human Immunodeficiency Virus (HIV) infection is initiated by binding of the viral glycoprotein gp120, to the cellular receptor CD4. On CD4 binding, gp120 undergoes conformational change, permitting binding to the chemokine receptor. Crystal structures of gp120 ternary complex reveal the CD4 bound conformation of gp120. We report here the application of the Gaussian network model (GNM) to the crystal structures of gp120 bound to CD4 or CD4 mimic and 17b, to study the collective motions of the gp120 core and determine the communication propensities of the residue network. The GNM fluctuation profiles identify residues in the inner domain and outer domain that may facilitate conformational change or stability, respectively. Communication propensities delineate a residue network that is topologically suited for signal propagation from the Phe43 cavity throughout the gp120 outer domain. These results provide a new context for interpreting gp120 core envelope structure-function relationships.
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Affiliation(s)
- Indira Shrivastava
- Department of Computational Biology, School of Medicine, University of Pittsburgh, 3083 Biomedical Science Tower 3, 3501 Fifth Avenue, Pittsburgh, PA 15213, USA.
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Kumar S, Malachowski WP, DuHadaway JB, LaLonde JM, Carroll PJ, Jaller D, Metz R, Prendergast GC, Muller AJ. Indoleamine 2,3-Dioxygenase Is the Anticancer Target for a Novel Series of Potent Naphthoquinone-Based Inhibitors. J Med Chem 2008. [DOI: 10.1021/jm8013053] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Kumar S, Jaller D, Patel B, LaLonde JM, DuHadaway JB, Malachowski WP, Prendergast GC, Muller AJ. Structure based development of phenylimidazole-derived inhibitors of indoleamine 2,3-dioxygenase. J Med Chem 2008; 51:4968-77. [PMID: 18665584 PMCID: PMC3159384 DOI: 10.1021/jm800512z] [Citation(s) in RCA: 132] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Indoleamine 2,3-dioxygenase (IDO) is emerging as an important new therapeutic target for the treatment of cancer, chronic viral infections, and other diseases characterized by pathological immune suppression. With the goal of developing more potent IDO inhibitors, a systematic study of 4-phenylimidazole (4-PI) derivatives was undertaken. Computational docking experiments guided design and synthesis efforts with analogues of 4-PI. In particular, three interactions of 4-PI analogues with IDO were studied: the active site entrance, the interior of the active site, and the heme iron binding. The three most potent inhibitors (1, 17, and 18) appear to exploit interactions with C129 and S167 in the interior of the active site. All three inhibitors are approximately 10-fold more potent than 4-PI. The study represents the first example of enzyme inhibitor development with the recently reported crystal structure of IDO and offers important lessons in the search for more potent inhibitors.
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Affiliation(s)
- Sanjeev Kumar
- Department of Chemistry, Bryn Mawr College, Bryn Mawr, Pennsylvania 19010, USA
| | - Daniel Jaller
- Lankenau Institute for Medical Research, Wynnewood, Pennsylvania 19096, USA
| | - Bhumika Patel
- Department of Chemistry, Bryn Mawr College, Bryn Mawr, Pennsylvania 19010, USA
| | - Judith M. LaLonde
- Department of Chemistry, Bryn Mawr College, Bryn Mawr, Pennsylvania 19010, USA
| | - James B. DuHadaway
- Lankenau Institute for Medical Research, Wynnewood, Pennsylvania 19096, USA
| | | | - George C. Prendergast
- Lankenau Institute for Medical Research, Wynnewood, Pennsylvania 19096, USA
- Department of Pathology, Anatomy & Cell Biology and Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, Pennsylvania 19104, USA
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Kumar S, Malachowski WP, DuHadaway JB, LaLonde JM, Carroll PJ, Jaller D, Metz R, Prendergast GC, Muller AJ. Indoleamine 2,3-dioxygenase is the anticancer target for a novel series of potent naphthoquinone-based inhibitors. J Med Chem 2008; 51:1706-18. [PMID: 18318466 PMCID: PMC4384695 DOI: 10.1021/jm7014155] [Citation(s) in RCA: 136] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Indoleamine 2,3-dioxygenase (IDO) is emerging as an important new therapeutic target for the treatment of cancer, chronic viral infections, and other diseases characterized by pathological immune suppression. While small molecule inhibitors of IDO exist, there remains a dearth of high-potency compounds offering in vivo efficacy and clinical translational potential. In this study, we address this gap by defining a new class of naphthoquinone-based IDO inhibitors exemplified by the natural product menadione, which is shown in mouse tumor models to have similar antitumor activity to previously characterized IDO inhibitors. Genetic validation that IDO is the critical in vivo target is demonstrated using IDO-null mice. Elaboration of menadione to a pyranonaphthoquinone has yielded low nanomolar potency inhibitors, including new compounds which are the most potent reported to date (K(i) = 61-70 nM). Synthetic accessibility of this class will facilitate preclinical chemical-genetic studies as well as further optimization of pharmacological parameters for clinical translation.
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MESH Headings
- Animals
- Antineoplastic Agents/chemical synthesis
- Antineoplastic Agents/chemistry
- Antineoplastic Agents/pharmacology
- Binding Sites
- Cell Proliferation/drug effects
- Cell Survival/drug effects
- Computer Simulation
- Crystallography, X-Ray
- Disease Models, Animal
- Dose-Response Relationship, Drug
- Drug Screening Assays, Antitumor
- Enzyme Inhibitors/chemical synthesis
- Enzyme Inhibitors/chemistry
- Enzyme Inhibitors/pharmacology
- Indoleamine-Pyrrole 2,3,-Dioxygenase/antagonists & inhibitors
- Indoleamine-Pyrrole 2,3,-Dioxygenase/genetics
- Mice
- Mice, Knockout
- Mice, Nude
- Models, Molecular
- Molecular Structure
- Naphthoquinones/chemical synthesis
- Naphthoquinones/chemistry
- Naphthoquinones/pharmacology
- Pyrones/chemistry
- Pyrones/pharmacology
- Stereoisomerism
- Structure-Activity Relationship
- Vitamin K 3/chemistry
- Vitamin K 3/pharmacology
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Affiliation(s)
- Sanjeev Kumar
- Department of Chemistry, Bryn Mawr College, Bryn Mawr, Pennsylvania 19010
| | | | | | - Judith M. LaLonde
- Department of Chemistry, Bryn Mawr College, Bryn Mawr, Pennsylvania 19010
| | - Patrick J. Carroll
- Department of Chemistry, X-ray Crystallography Facility, University of Pennsylvania, Philadelphia, Pennsylvania 19104
| | - Daniel Jaller
- Lankenau Institute for Medical Research, Wynnewood, Pennsylvania 19096
| | - Richard Metz
- LIMR Development, Inc., Wynnewood, Pennsylvania 19096
| | - George C. Prendergast
- Lankenau Institute for Medical Research, Wynnewood, Pennsylvania 19096
- Department of Pathology, Anatomy & Cell Biology, Jefferson Medical School, Thomas Jefferson University, Philadelphia, Pennsylvania 19104
- Kimmel Cancer Center, Jefferson Medical School, Thomas Jefferson University, Philadelphia, Pennsylvania 19104
| | - Alexander J. Muller
- Lankenau Institute for Medical Research, Wynnewood, Pennsylvania 19096
- Kimmel Cancer Center, Jefferson Medical School, Thomas Jefferson University, Philadelphia, Pennsylvania 19104
- Department of Microbiology and Immunology, Jefferson Medical School, Thomas Jefferson University, Philadelphia, Pennsylvania 19104
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Affiliation(s)
- Shashidhar N. Rao
- GlaxoSmithKline, 1250 South Collegeville Road, Collegeville, Pennsylvania 19426, Accelrys Inc., 9685 Scranton Road, San Diego, California 92121, and Chemistry Department, Bryn Mawr College, 101 North Merion Avenue, Bryn Mawr, Pennsylvania 19010
| | - Martha S. Head
- GlaxoSmithKline, 1250 South Collegeville Road, Collegeville, Pennsylvania 19426, Accelrys Inc., 9685 Scranton Road, San Diego, California 92121, and Chemistry Department, Bryn Mawr College, 101 North Merion Avenue, Bryn Mawr, Pennsylvania 19010
| | - Amit Kulkarni
- GlaxoSmithKline, 1250 South Collegeville Road, Collegeville, Pennsylvania 19426, Accelrys Inc., 9685 Scranton Road, San Diego, California 92121, and Chemistry Department, Bryn Mawr College, 101 North Merion Avenue, Bryn Mawr, Pennsylvania 19010
| | - Judith M. LaLonde
- GlaxoSmithKline, 1250 South Collegeville Road, Collegeville, Pennsylvania 19426, Accelrys Inc., 9685 Scranton Road, San Diego, California 92121, and Chemistry Department, Bryn Mawr College, 101 North Merion Avenue, Bryn Mawr, Pennsylvania 19010
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Abstract
Cathepsin K is a cysteine protease present in human osteoclasts that plays an important role in bone resorption. Cathepsin K is synthesized as an inactive proenzyme and activated under conditions of low pH. Autoproteolytic processing of the N-terminal 99 amino acid propeptide produces the active, mature form of cathepsin K. It is presumed that the activation of procathepsin K in vivo occurs in the bone resorption pit, which has a low-pH environment. We have determined the structure of human procathepsin K at 2.8 A resolution. The structure of the mature enzyme domain within procathepsin K is virtually identical to that of mature cathepsin K. The fold of the propeptide of procathepsin K is similar to that observed in procathepsins B and L despite differences in length and sequence. A portion of the propeptide occupies the active site cleft of cathepsin K. Hydrophobic interactions, salt bridges, and hydrogen-bonding interactions are observed in the structure of the propeptide and between the propeptide and the mature enzyme of procathepsin K. These interactions suggest an explanation for the stability of the proenzyme. The structure of procathepsin K contributes to an understanding of the molecular basis of inhibition by the propeptide portion of the molecule and activation of this important member of the cysteine protease family.
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Affiliation(s)
- J M LaLonde
- Department of Structural Biology, SmithKline Beecham Pharmaceuticals, King of Prussia, Pennsylvania 19406, USA
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LaLonde JM, Zhao B, Smith WW, Janson CA, DesJarlais RL, Tomaszek TA, Carr TJ, Thompson SK, Oh HJ, Yamashita DS, Veber DF, Abdel-Meguid SS. Use of papain as a model for the structure-based design of cathepsin K inhibitors: crystal structures of two papain-inhibitor complexes demonstrate binding to S'-subsites. J Med Chem 1998; 41:4567-76. [PMID: 9804696 DOI: 10.1021/jm980249f] [Citation(s) in RCA: 57] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Papain has been used as a surrogate enzyme in a drug design effort to obtain potent and selective inhibitors of cathepsin K, a new member of the papain superfamily of cysteine proteases that is selectively and highly expressed in osteoclasts and is implicated in bone resorption. Here we report the crystal structures of two papain-inhibitor complexes and the rational design of novel cathepsin K inhibitors. Unlike previously known crystal structures of papain-inhibitor complexes, our papain structures show ligand binding extending deep within the S'-subsites. The two inhibitor complexes, carbobenzyloxyleucinyl-leucinyl-leucinal and carbobenzyloxy-L-leucinyl-L-leucinyl methoxymethyl ketone, were refined to 2.2- and 2.5-A resolution with R-factors of 0.190 and 0. 217, respectively. The S'-subsite interactions with the inhibitors are dominated by an aromatic-aromatic stacking and an oxygen-aromatic ring edge interaction. The knowledge of S'-subsite interactions led to a design strategy for an inhibitor spanning both subsites and yielded a novel, symmetric inhibitor selective for cathepsin K. Simultaneous exploitation of both S- and S'-sites provides a general strategy for the design of cysteine protease inhibitors having high specificity to their target enzymes.
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Affiliation(s)
- J M LaLonde
- Departments of Structural Biology, Protein Biochemistry, Physical and Structural Chemistry, Molecular Recognition, and Medicinal Chemistry, SmithKline Beecham Pharmaceuticals, Prussia, Pennsylvania 19406, USA
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Abstract
The up-and-down beta-barrel is a common folding motif found frequently in proteins that bind and transport hydrophobic ligands. It is formed by an array of beta-strands arranged in an antiparallel manner with each strand hydrogen-bonded to neighboring strands nearly always adjacent in the amino acid sequence. The arrangement is completed by forming hydrogen bonds between the first and last strands. The barrel motif so formed produces interior and exterior components. Proteins belonging to this class of up-and-down beta-barrels are found typically to be lipid-binding proteins in which the interior surface forms a cavity or pit that serves as the ligand binding region. Two evolutionarily distinct but structurally related families of such carriers have been identified by comparing known crystal structures. One group found intracellularly uses a 10-stranded beta-structure and a second family of proteins typically found extracellularly utilizes an 8-stranded motif. The 10-stranded beta-barrels have a large, hydrophilic water-filled interior cavity that serves as the ligand-binding domain. Hydrophobic lipids such as fatty acids and retinoids bind within the cavity, totally sequestered from the external milieu. The 8-stranded beta-barrel proteins have a hydrophobic pit, which serves as the ligand-binding domain for compounds such as bilins and retinoids. The up-and-down beta-barrel motif appears to be one of nature's primary choices for hydrophobic ligand transport proteins.
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Affiliation(s)
- J M LaLonde
- Department of Biochemistry, University of Minnesota, St. Paul 55108
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LaLonde JM, Levenson MA, Roe JJ, Bernlohr DA, Banaszak LJ. Adipocyte lipid-binding protein complexed with arachidonic acid. Titration calorimetry and X-ray crystallographic studies. J Biol Chem 1994; 269:25339-47. [PMID: 7929228 DOI: 10.2210/pdb1adl/pdb] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
The association of the adipocyte lipid-binding protein (ALBP) with arachidonic acid (all cis, 20:4 delta 5,8,11,14) and oleic acid (cis, 18:1 delta 9) has been examined by titration calorimentry. In addition, the crystal structure of ALBP with bound arachidonic acid has also been obtained. Crystallographic analysis of the arachidonic acid.ALBP complex along with the previously reported oleic acid-ALBP structure (Xu, Z., Bernlohr, D. A., and Banaszak, L. J. (1993) J. Biol. Chem. 268, 7874-7884) provides a framework for the molecular examination of protein-lipid association. Isothermal titration calorimetry revealed high affinity association of both unsaturated fatty acids with the protein. The calorimetric data yielded the following thermodynamic parameters for arachidonic acid: Kd = 4.4 microM, n = 0.8, delta G = -7370 cal/mol, delta H = -6770 cal/mol, and T delta S = +600 cal/mol. For oleic acid, the thermodynamic parameters were Kd = 2.4 microM, n = 0.9, delta G = -7770 cal/mol, delta H = -6050 cal/mol, and T delta S = +1720 cal/mol. The identification of thermodynamically dominating enthalpic factors for both fatty acids are consistent with the crystallographic studies demonstrating the interaction of the fatty acid carboxylate with a combination of Arg106, Arg126, and Tyr128. The crystallographic refinement of the protein-arachidonate complex was carried out to 1.6 A with the resultant R factor of 0.19. Within the cavity of the crystalline binding protein, the arachidonate was found in a hairpin conformation. The conformation of the bound ligand is consistent with acceptable torsional angles and the four cis double bonds in arachidonate. These results demonstrate that arachidonate is a ligand for ALBP. They provide thermodynamic and structural data concerning the physical basis for protein-lipid interaction and suggest that intracellular lipid-binding proteins may mediate the biological effects of polyunsaturated fatty acids in vivo.
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Affiliation(s)
- J M LaLonde
- Department of Biochemistry, School of Medicine, University of Minnesota, Minneapolis 55455
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LaLonde JM, Bernlohr DA, Banaszak LJ. X-ray crystallographic structures of adipocyte lipid-binding protein complexed with palmitate and hexadecanesulfonic acid. Properties of cavity binding sites. Biochemistry 1994; 33:4885-95. [PMID: 8161548 DOI: 10.1021/bi00182a017] [Citation(s) in RCA: 56] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Adipocyte lipid-binding protein is a 14.6-kDa polypeptide that is responsible for the intracellular trafficking of fatty acids. Its structure previously has been solved in the apo and holo forms complexed with stearate and oleate. To examine the binding of lipids other than those with a carboxylate headgroup, we have determined the structure of ALBP in complex with a sulfonic acid, hexadecanesulfonic acid, and compared its structure with the natural fatty acid analog, palmitate. Crystallographic refinement led to similar models, both with R-factors of about 20% and a resolution of 1.6 A. results can be compared with earlier studies on C18 fatty acids, both saturated and unsaturated. The previously refined complexes with stearate and oleate in combination with the complexes of palmitate and hexadecanesulfonic acid demonstrate specific positions for water molecules bound in the internal cavity. Many of the water-binding sites are present in both the apo form and the holo forms of the protein. With ligand present, a network of 10 internalized water molecules appear to form a hydrophobic hydration region. In spite of the sp3 geometry of the sulfonic acid derivative, the headgroup occupies the same site as that of the planar carboxylate in natural fatty acids. These results demonstrate that intracellular lipid-binding proteins are capable of binding a wider variety of lipids than previously considered and reveal the importance of interior ordered water molecules in the binding cavity.
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Affiliation(s)
- J M LaLonde
- Department of Biochemistry, School of Medicine, University of Minnesota, Minneapolis 55455
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