title: Rational design of inhibitors of HIV-1 TAR RNA through the stabilisation of electrostatic "hot spots".
abstract: The targeting of RNA for the design of novel anti-viral compounds has until now proceeded largely without incorporating direct input from structure-based design methodology, partly because of lack of structural data, and complications arising from substrate flexibility. We propose a paradigm to explain the physical mechanism for ligand-induced refolding of trans-activation response element (TAR RNA) from human immunodeficiency virus 1 (HIV-1). Based upon Poisson-Boltzmann analysis of the TAR structure, as bound by a peptide derived from the transcriptional activator protein, Tat, our hypothesis shows that two specific electrostatic interactions are necessary to stabilise the conformation. This result contradicts the belief that a single argininamide residue is responsible for stabilising the TAR fold, as well as the conventional wisdom that electrostatic interactions with RNA are non-specific or dominated by phosphates. We test this hypothesis by using NMR and computational methods to model the interaction of a series of novel inhibitors of the in vitro RNA-binding activities for a peptide derived from Tat. A subset of inhibitors, including the bis-guanidine compound rbt203 and its analogues, induce a conformation in TAR similar to that brought about by the protein. Comparison of the interactions of two of these ligands with the RNA and structure-activity relationships observed within the compound series, confirm the importance of the two specific electrostatic interactions in the stabilisation of the Tat-bound RNA conformation. This work illustrates how the use of medicinal chemistry and structural analysis can provide a rational basis for prediction of ligand-induced conformational change, a necessary step towards the application of structure-based methods in the design of novel RNA or protein-binding drugs.
authors.affiliation: RiboTargets Ltd, Granta Park, Abington, CB1 6GB, Cambridge, UK.
authors.forename: Ben
authors.initials: B
authors.lastname: Davis
authors.forename: Mohammad
authors.initials: M
authors.lastname: Afshar
authors.forename: Gabriele
authors.initials: G
authors.lastname: Varani
authors.forename: Alastair I H
authors.initials: AI
authors.lastname: Murchie
authors.forename: Jonathan
authors.initials: J
authors.lastname: Karn
authors.forename: Georg
authors.initials: G
authors.lastname: Lentzen
authors.forename: Martin
authors.initials: M
authors.lastname: Drysdale
authors.forename: Justin
authors.initials: J
authors.lastname: Bower
authors.forename: Andrew J
authors.initials: AJ
authors.lastname: Potter
authors.forename: Ian D
authors.initials: ID
authors.lastname: Starkey
authors.forename: Terry
authors.initials: T
authors.lastname: Swarbrick
authors.forename: Fareed
authors.initials: F
authors.lastname: Aboul-ela
mesh_terms: D019380:Anti-HIV Agents / Q000737:chemistry / Q000378:metabolism* / Q000494:pharmacology; D001120:Arginine / Q000031:analogs & derivatives* / Q000378:metabolism / Q000494:pharmacology; D001483:Base Sequence; D001665:Binding Sites; D015195:Drug Design; D031541:Fluorescence Resonance Energy Transfer; D015696:Gene Products, tat / Q000378:metabolism; D006146:Guanidines / Q000378:metabolism / Q000494:pharmacology; D016325:HIV Long Terminal Repeat / Q000235:genetics*; D015497:HIV-1 / Q000235:genetics*; D008024:Ligands; D009682:Magnetic Resonance Spectroscopy; D008958:Models, Molecular; D008970:Molecular Weight; D009690:Nucleic Acid Conformation; D012367:RNA, Viral / Q000037:antagonists & inhibitors* / Q000737:chemistry* / Q000378:metabolism; D055672:Static Electricity; D013329:Structure-Activity Relationship; D013379:Substrate Specificity; D020349:Surface Plasmon Resonance; D054322:tat Gene Products, Human Immunodeficiency Virus
chemical_list: D019380:Anti-HIV Agents; D015696:Gene Products, tat; D006146:Guanidines; D008024:Ligands; D012367:RNA, Viral; C482038:rbt203; D054322:tat Gene Products, Human Immunodeficiency Virus; C069339:argininamide; D001120:Arginine