Modeling of the Interaction between New Ethidium Derivatives and TAR RNA of HIV-1

During the HIV-1 replication process, interactions between the first sequence of RNA synthesized named TAR RNA and a viral protein named Tat permit a fast and efficient transcription of viral DNA in RNA. Based on the NMR structure of TAR RNA found on the PDB, new derivatives of ethidium were designed by molecular modeling to inhibit this interaction. The studied molecules are composed of three domains: an arginine, a linker, and an ethidium. Three linkers of different lengths were considered in the first step, with the TAR RNA-arginine interaction and the intercalation of the ethidium simulated by docking methods. In a second step, the structure of the TAR RNA was completed to obtain a whole ethidium interaction site and docking of the whole studied molecules was investigated. Molecules were synthesized and tested on infected cells. The predicted models and activity are in good agreement with the reported experimental results.

[1]  J. Puglisi,et al.  Conformation of the TAR RNA-arginine complex by NMR spectroscopy. , 1992, Science.

[2]  E. Loret,et al.  Conformational Heterogeneity in Two Regions of TAT Results in Structural Variations of This Protein as a Function of HIV-1 Isolates* , 1996, The Journal of Biological Chemistry.

[3]  P. Bayer,et al.  Structural studies of HIV-1 Tat protein. , 1995, Journal of molecular biology.

[4]  A. Rabson,et al.  Regulation of human immunodeficiency virus infection: implications for pathogenesis. , 1994, Advances in virus research.

[5]  J. Karn,et al.  New insights into the mechanism of HIV-1 trans-activation. , 1992, Trends in genetics : TIG.

[6]  B. Peterlin,et al.  Control of RNA initiation and elongation at the HIV-1 promoter. , 1994, Annual review of biochemistry.

[7]  J. Karn,et al.  Structure of HIV-1 TAR RNA in the absence of ligands reveals a novel conformation of the trinucleotide bulge. , 1996, Nucleic acids research.

[8]  D. Draper,et al.  Single base bulges in small RNA hairpins enhance ethidium binding and promote an allosteric transition. , 1987, Nucleic acids research.

[9]  D. Draper,et al.  Effects of single-base bulges on intercalator binding to small RNA and DNA hairpins and a ribosomal RNA fragment. , 1989, Biochemistry.

[10]  A. Kingsman,et al.  The regulation of human immunodeficiency virus type-1 gene expression. , 1996, European journal of biochemistry.

[11]  M. Singh,et al.  HIV‐1 tat protein stimulates transcription by binding to a U‐rich bulge in the stem of the TAR RNA structure. , 1990, The EMBO journal.

[12]  M. Mathews,et al.  HIV-1 Tat protein increases transcriptional initiation and stabilizes elongation , 1989, Cell.

[13]  A. Frankel,et al.  Electrostatic interactions modulate the RNA-binding and transactivation specificities of the human immunodeficiency virus and simian immunodeficiency virus Tat proteins. , 1993, Proceedings of the National Academy of Sciences of the United States of America.

[14]  J. Puglisi,et al.  Role of RNA structure in arginine recognition of TAR RNA. , 1993, Proceedings of the National Academy of Sciences of the United States of America.

[15]  J. Karn,et al.  Human immunodeficiency virus type 1 transactivator protein, tat, stimulates transcriptional read-through of distal terminator sequences in vitro. , 1993, Proceedings of the National Academy of Sciences of the United States of America.

[16]  J. Karn,et al.  The structure of the human immunodeficiency virus type-1 TAR RNA reveals principles of RNA recognition by Tat protein. , 1995, Journal of molecular biology.

[17]  P. Alzari,et al.  cDNA Cloning and Sequencing Reveal the Major Horse Allergen Equ c1 to Be a Glycoprotein Member of the Lipocalin Superfamily* , 1996, The Journal of Biological Chemistry.

[18]  P. S. Ho,et al.  Circular dichroism and molecular modeling yield a structure for the complex of human immunodeficiency virus type 1 trans-activation response RNA and the binding region of Tat, the trans-acting transcriptional activator. , 1992, Proceedings of the National Academy of Sciences of the United States of America.

[19]  J. Puglisi,et al.  Solution Structure of a Bovine Immunodeficiency Virus Tat-TAR Peptide-RNA Complex , 1995, Science.

[20]  J. Gordon,et al.  Inflammatory Bowel Disease and Adenomas in Mice Expressing a Dominant Negative N-Cadherin , 1995, Science.

[21]  W. Wilson,et al.  A molecular mechanics investigation of RNA complexes. I. Ethidium intercalation in an HIV-1 TAR RNA sequence with an unpaired adenosine. , 1992, Journal of biomolecular structure & dynamics.

[22]  K. Jeang,et al.  In vitro and in vivo binding of human immunodeficiency virus type 1 Tat protein and Sp1 transcription factor , 1993, Journal of virology.