Crystal Structure and Structural Mechanism of a Novel Anti-Human Immunodeficiency Virus and d-Amino Acid-Containing Chemokine

ABSTRACT Chemokines and their receptors play important roles in normal physiological functions and the pathogeneses of a wide range of human diseases, including the entry of human immunodeficiency virus type 1 (HIV-1). However, the use of natural chemokines to probe receptor biology or to develop therapeutic drugs is limited by their lack of selectivity and the poor understanding of mechanisms in ligand-receptor recognition. We addressed these issues by combining chemical and structural biology in research into molecular recognition and inhibitor design. Specifically, the concepts of chemical biology were used to develop synthetically and modularly modified (SMM) chemokines that are unnatural and yet have properties improved over those of natural chemokines in terms of receptor selectivity, affinity, and the ability to explore receptor functions. This was followed by using structural biology to determine the structural basis for synthetically perturbed ligand-receptor selectivity. As a proof-of-principle for this combined chemical and structural-biology approach, we report a novel d-amino acid-containing SMM-chemokine designed based on the natural chemokine called viral macrophage inflammatory protein II (vMIP-II). The incorporation of unnatural d-amino acids enhanced the affinity of this molecule for CXCR4 but significantly diminished that for CCR5 or CCR2, thus yielding much more selective recognition of CXCR4 than wild-type vMIP-II. This d-amino acid-containing chemokine also showed more potent and specific inhibitory activity against HIV-1 entry via CXCR4 than natural chemokines. Furthermore, the high-resolution crystal structure of this d-amino acid-containing chemokine and a molecular-modeling study of its complex with CXCR4 provided the structure-based mechanism for the selective interaction between the ligand and chemokine receptors and the potent anti-HIV activity of d-amino acid-containing chemokines.

[1]  Ziwei Huang,et al.  Drug Discovery Research: New Frontiers in the Post-Genomic Era , 2007 .

[2]  Santosh Kumar,et al.  Crystal structure of chemically synthesized vMIP‐II , 2007, Proteins.

[3]  D. Richman,et al.  Basic and Translational Research of Chemokine Ligands and Receptors and Development of Novel Therapeutics , 2006 .

[4]  Won-Tak Choi,et al.  Unique Ligand Binding Sites on CXCR4 Probed by a Chemical Biology Approach: Implications for the Design of Selective Human Immunodeficiency Virus Type 1 Inhibitors , 2005, Journal of Virology.

[5]  J. Sodroski,et al.  Different stereochemical requirements for CXCR4 binding and signaling functions as revealed by an anti-HIV, D-amino acid-containing SMM-chemokine ligand. , 2005, Journal of medicinal chemistry.

[6]  Won-Tak Choi,et al.  Distinct Functional Sites for Human Immunodeficiency Virus Type 1 and Stromal Cell-Derived Factor 1α on CXCR4 Transmembrane Helical Domains , 2005, Journal of Virology.

[7]  John B. O. Mitchell,et al.  D‐amino acid residues in peptides and proteins , 2003, Proteins.

[8]  J. Sodroski,et al.  Exploring the Stereochemistry of CXCR4-Peptide Recognition and Inhibiting HIV-1 Entry with d-Peptides Derived from Chemokines* , 2002, The Journal of Biological Chemistry.

[9]  A. Proudfoot.  Chemokine receptors: multifaceted therapeutic targets , 2002, Nature Reviews Immunology.

[10]  Zhaowen Luo,et al.  Structural and Functional Characterization of Human CXCR4 as a Chemokine Receptor and HIV-1 Co-receptor by Mutagenesis and Molecular Modeling Studies* , 2001, The Journal of Biological Chemistry.

[11]  E. Fernandez,et al.  Comparison of the structure of vMIP-II with eotaxin-1, RANTES, and MCP-3 suggests a unique mechanism for CCR3 activation. , 2000, Biochemistry.

[12]  M. Price,et al.  Effect of D-amino acid substitution in a mucin 2 epitope on mucin-specific monoclonal antibody recognition. , 2000, Archives of biochemistry and biophysics.

[13]  James W. Hall,et al.  Molecular modeling and site‐directed mutagenesis of CCR5 reveal residues critical for chemokine binding and signal transduction , 2000, European journal of immunology.

[14]  Y. Qian,et al.  Nuclear magnetic resonance solution structure of truncated human GRObeta [5-73] and its structural comparison with CXC chemokine family members GROalpha and IL-8. , 1999, Journal of molecular biology.

[15]  A. LiWang,et al.  The solution structure of the anti‐HIV chemokine vMIP‐II , 1999, Protein science : a publication of the Protein Society.

[16]  H Luecke,et al.  Structure of bacteriorhodopsin at 1.55 A resolution. , 1999, Journal of molecular biology.

[17]  Joseph Sodroski,et al.  Tyrosine Sulfation of the Amino Terminus of CCR5 Facilitates HIV-1 Entry , 1999, Cell.

[18]  Kouji Matsushima,et al.  The chemokine receptor CXCR4 is essential for vascularization of the gastrointestinal tract , 1998, Nature.

[19]  Masahiko Kuroda,et al.  Function of the chemokine receptor CXCR4 in haematopoiesis and in cerebellar development , 1998, Nature.

[20]  E. Fernandez,et al.  Crystal structure of chemically synthesized [N33A] stromal cell-derived factor 1α, a potent ligand for the HIV-1 “fusin” coreceptor , 1998 .

[21]  B. Sykes,et al.  Solution structure and basis for functional activity of stromal cell‐derived factor‐1; dissociation of CXCR4 activation from binding and inhibition of HIV‐1 , 1997, The EMBO journal.

[22]  T. Schwartz,et al.  A broad-spectrum chemokine antagonist encoded by Kaposi's sarcoma-associated herpesvirus. , 1997, Science.

[23]  Jean Salamero,et al.  HIV Coreceptor Downregulation as Antiviral Principle: SDF-1α–dependent Internalization of the Chemokine Receptor CXCR4 Contributes to Inhibition of HIV Replication , 1997, The Journal of experimental medicine.

[24]  C. Boshoff,et al.  Molecular Mimicry of Human Cytokine and Cytokine Response Pathway Genes by KSHV , 1996, Science.

[25]  William C. Olson,et al.  CD4-dependent, antibody-sensitive interactions between HIV-1 and its co-receptor CCR-5 , 1996, Nature.

[26]  Joseph Sodroski,et al.  CD4-induced interaction of primary HIV-1 gp120 glycoproteins with the chemokine receptor CCR-5 , 1996, Nature.

[27]  J. Sodroski,et al.  The lymphocyte chemoattractant SDF-1 is a ligand for LESTR/fusin and blocks HIV-1 entry , 1996, Nature.

[28]  Bernhard Moser,et al.  The CXC chemokine SDF-1 is the ligand for LESTR/fusin and prevents infection by T-cell-line-adapted HIV-1 , 1996, Nature.

[29]  D. Littman,et al.  Natural resistance to HIV? , 1996, Nature.

[30]  S. Nishikawa,et al.  Defects of B-cell lymphopoiesis and bone-marrow myelopoiesis in mice lacking the CXC chemokine PBSF/SDF-1 , 1996, Nature.

[31]  J. Sodroski,et al.  Use of cis- and trans-acting viral regulatory sequences to improve expression of human immunodeficiency virus vectors in human lymphocytes. , 1996, Virology.

[32]  C. Broder,et al.  CC CKR5: A RANTES, MIP-1α, MIP-1ॆ Receptor as a Fusion Cofactor for Macrophage-Tropic HIV-1 , 1996, Science.

[33]  Virginia Litwin,et al.  HIV-1 entry into CD4+ cells is mediated by the chemokine receptor CC-CKR-5 , 1996, Nature.

[34]  Stephen C. Peiper,et al.  Identification of a major co-receptor for primary isolates of HIV-1 , 1996, Nature.

[35]  Paul E. Kennedy,et al.  HIV-1 Entry Cofactor: Functional cDNA Cloning of a Seven-Transmembrane, G Protein-Coupled Receptor , 1996, Science.

[36]  J. Navaza,et al.  AMoRe: an automated package for molecular replacement , 1994 .

[37]  F. de Wolf,et al.  Biphasic rate of CD4+ cell count decline during progression to AIDS correlates with HIV‐1 phenotype , 1992, AIDS.

[38]  J. Zou,et al.  Improved methods for building protein models in electron density maps and the location of errors in these models. , 1991, Acta crystallographica. Section A, Foundations of crystallography.

[39]  R. Henderson,et al.  Model for the structure of bacteriorhodopsin based on high-resolution electron cryo-microscopy. , 1990, Journal of molecular biology.

[40]  J. Goudsmit,et al.  ASSOCIATION BETWEEN BIOLOGICAL PROPERTIES OF HUMAN IMMUNODEFICIENCY VIRUS VARIANTS AND RISK FOR AIDS AND AIDS MORTALITY , 1989, The Lancet.

[41]  C. Cheng‐Mayer,et al.  Biologic features of HIV-1 that correlate with virulence in the host. , 1988, Science.

[42]  R. Gallo,et al.  Characterization of the reverse transcriptase from a new retrovirus (HTLV) produced by a human cutaneous T-cell lymphoma cell line. , 1981, Virology.

[43]  D. Richman,et al.  SMM-chemokines: a class of unnatural synthetic molecules as chemical probes of chemokine receptor biology and leads for therapeutic development. , 2006, Chemistry & biology.

[44]  Elias Lolis,et al.  Structure, function, and inhibition of chemokines. , 2002, Annual review of pharmacology and toxicology.

[45]  J. Farber,et al.  Chemokine receptors as HIV-1 coreceptors: roles in viral entry, tropism, and disease. , 1999, Annual review of immunology.

[46]  G. Sheldrick,et al.  SHELXL: high-resolution refinement. , 1997, Methods in enzymology.

[47]  Z. Otwinowski,et al.  Processing of X-ray diffraction data collected in oscillation mode. , 1997, Methods in enzymology.

[48]  B Dewald,et al.  Human chemokines: an update. , 1997, Annual review of immunology.

[49]  P. Murphy.  The molecular biology of leukocyte chemoattractant receptors. , 1994, Annual review of immunology.