title: Effect of mimetic CDK9 inhibitors on HIV-1-activated transcription.
abstract: Potent anti-retroviral therapy has transformed HIV-1 infection into a chronic manageable disease; however, drug resistance remains a common problem that limits the effectiveness and clinical benefits of this type of treatment. The discovery of viral reservoirs in the body, in which HIV-1 may persist, has helped to explain why therapeutic eradication of HIV-1 has proved so difficult. In the current study, we utilized a combination of structure-based analysis of cyclin/CDK complexes with our previously published Tat peptide derivatives. We modeled the Tat peptide inhibitors with CDKs and found a particular pocket that showed the most stable binding site (Cavity 1) using in silico analysis. Furthermore, we were able to find peptide mimetics that bound to similar regions using in silico searches of a chemical library, followed by cell-based biological assays. Using these methods, we obtained the first-generation mimetic drugs and tested these compounds on HIV-1 long terminal repeat-activated transcription. Using biological assays followed by similar in silico analysis to find second-generation drugs resembling the original mimetic, we found the new targets of Cavity 1 and Cavity 2 regions on CDK9. We examined the second-generation mimetic against various viral isolates and observed a generalized suppression of most HIV-1 isolates. Finally, the drug inhibited viral replication in humanized mouse models of Rag2(-/-)γc(-/-) with no toxicity to the animals at tested concentrations. Our results suggest that it may be possible to model peptide inhibitors into available crystal structures and further find drug mimetics using in silico analysis.
authors.affiliation: National Center for Biodefense and Infectious Diseases, George Mason University, Manassas, VA 20110, USA.
authors.forename: Rachel
authors.initials: R
authors.lastname: Van Duyne
authors.forename: Irene
authors.initials: I
authors.lastname: Guendel
authors.forename: Elizabeth
authors.initials: E
authors.lastname: Jaworski
authors.forename: Gavin
authors.initials: G
authors.lastname: Sampey
authors.forename: Zachary
authors.initials: Z
authors.lastname: Klase
authors.forename: Hao
authors.initials: H
authors.lastname: Chen
authors.forename: Chen
authors.initials: C
authors.lastname: Zeng
authors.forename: Dmytro
authors.initials: D
authors.lastname: Kovalskyy
authors.forename: Mahmoud H
authors.initials: MH
authors.lastname: El Kouni
authors.forename: Benjamin
authors.initials: B
authors.lastname: Lepene
authors.forename: Alexis
authors.initials: A
authors.lastname: Patanarut
authors.forename: Sergei
authors.initials: S
authors.lastname: Nekhai
authors.forename: David H
authors.initials: DH
authors.lastname: Price
authors.forename: Fatah
authors.initials: F
authors.lastname: Kashanchi
mesh_terms: D000818:Animals; D001665:Binding Sites; D015153:Blotting, Western; D002460:Cell Line; D002478:Cells, Cultured; D042863:Cyclin-Dependent Kinase 9 / Q000037:antagonists & inhibitors* / Q000737:chemistry / Q000378:metabolism; D004195:Disease Models, Animal; D005260:Female; D015658:HIV Infections / Q000517:prevention & control / Q000821:virology; D015497:HIV-1 / Q000187:drug effects* / Q000502:physiology; D006367:HeLa Cells; D054884:Host-Pathogen Interactions / Q000187:drug effects; D006801:Humans; D007963:Leukocytes, Mononuclear / Q000187:drug effects / Q000378:metabolism / Q000821:virology; D008297:Male; D051379:Mice; D018345:Mice, Knockout; D008958:Models, Molecular; D015394:Molecular Structure; D011485:Protein Binding; D047428:Protein Kinase Inhibitors / Q000737:chemistry / Q000378:metabolism / Q000494:pharmacology*; D017434:Protein Structure, Tertiary; D015533:Transcriptional Activation / Q000187:drug effects*; D014779:Virus Replication / Q000187:drug effects; D054322:tat Gene Products, Human Immunodeficiency Virus / Q000737:chemistry
chemical_list: D047428:Protein Kinase Inhibitors; D054322:tat Gene Products, Human Immunodeficiency Virus; D042863:Cyclin-Dependent Kinase 9