Rational design of inhibitors of HIV-1 TAR RNA through the stabilisation of electrostatic "hot spots".
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.
Davis
Ben
B
RiboTargets Ltd, Granta Park, Abington, CB1 6GB, Cambridge, UK.
Afshar
Mohammad
M
Varani
Gabriele
G
Murchie
Alastair I H
AI
Karn
Jonathan
J
Lentzen
Georg
G
Drysdale
Martin
M
Bower
Justin
J
Potter
Andrew J
AJ
Starkey
Ian D
ID
Swarbrick
Terry
T
Aboul-ela
Fareed
F
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
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