title: Structural and binding analysis of pyrimidinol carboxylic acid and N-hydroxy quinazolinedione HIV-1 RNase H inhibitors.
abstract: HIV-1 RNase H breaks down the intermediate RNA-DNA hybrids during reverse transcription, requiring two divalent metal ions for activity. Pyrimidinol carboxylic acid and N-hydroxy quinazolinedione inhibitors were designed to coordinate the two metal ions in the active site of RNase H. High-resolution (1.4 Å to 2.1 Å) crystal structures were determined with the isolated RNase H domain and reverse transcriptase (RT), which permit accurate assessment of the metal and water environment at the active site. The geometry of the metal coordination suggests that the inhibitors mimic a substrate state prior to phosphodiester catalysis. Surface plasmon resonance studies confirm metal-dependent binding to RNase H and demonstrate that the inhibitors do not bind at the polymerase active site of RT. Additional evaluation of the RNase H site reveals an open protein surface with few additional interactions to optimize active-site inhibitors.
authors.affiliation: Gilead Sciences, Inc., 333 Lakeside Dr., Foster City, CA 94404, USA. eric.lansdon@gilead.com
authors.forename: Eric B
authors.initials: EB
authors.lastname: Lansdon
authors.forename: Qi
authors.initials: Q
authors.lastname: Liu
authors.forename: Stephanie A
authors.initials: SA
authors.lastname: Leavitt
authors.forename: Mini
authors.initials: M
authors.lastname: Balakrishnan
authors.forename: Jason K
authors.initials: JK
authors.lastname: Perry
authors.forename: Candra
authors.initials: C
authors.lastname: Lancaster-Moyer
authors.forename: Nilima
authors.initials: N
authors.lastname: Kutty
authors.forename: Xiaohong
authors.initials: X
authors.lastname: Liu
authors.forename: Neil H
authors.initials: NH
authors.lastname: Squires
authors.forename: William J
authors.initials: WJ
authors.lastname: Watkins
authors.forename: Thorsten A
authors.initials: TA
authors.lastname: Kirschberg
mesh_terms: D000595:Amino Acid Sequence; D019380:Anti-HIV Agents / Q000494:pharmacology*; D003460:Crystallization; D054303:HIV Reverse Transcriptase / Q000037:antagonists & inhibitors / Q000737:chemistry; D015497:HIV-1 / Q000187:drug effects* / Q000201:enzymology; D008968:Molecular Conformation; D008969:Molecular Sequence Data; D011743:Pyrimidines / Q000737:chemistry / Q000494:pharmacology*; D052999:Quinazolinones / Q000737:chemistry / Q000494:pharmacology*; D016914:Ribonuclease H / Q000037:antagonists & inhibitors* / Q000737:chemistry; D013329:Structure-Activity Relationship
chemical_list: D019380:Anti-HIV Agents; D011743:Pyrimidines; D052999:Quinazolinones; C514824:reverse transcriptase, Human immunodeficiency virus 1; D054303:HIV Reverse Transcriptase; D016914:Ribonuclease H