5TUQ

Crystal Structure of a 6-Cyclohexylmethyl-3-hydroxypyrimidine-2,4-dione Inhibitor in Complex with HIV Reverse Transcriptase

Summary for 5TUQ

• Entry DOI: 10.2210/pdb5tuq/pdb
• Descriptor: HIV-1 REVERSE TRANSCRIPTASE, 1-[(benzyloxy)methyl]-6-(cyclohexylmethyl)-3-hydroxy-5-(propan-2-yl)pyrimidine-2,4(1H,3H)-dione, MAGNESIUM ION, ... (5 entities in total)
• Functional Keywords: hiv-1, reverse transcriptase, inhibitor, transferase-transferase inhibitor complex, transferase/transferase inhibitor
• Biological source: Human immunodeficiency virus type 1 group M subtype B (isolate BH10) (HIV-1); More
• Total number of polymer chains: 2
• Total formula weight: 114612.77

Authors

Kirby, K.A.,Sarafianos, S.G. (deposition date: 2016-11-07, release date: 2017-06-28, Last modification date: 2023-10-04)

Primary citation

Tang, J.,Kirby, K.A.,Huber, A.D.,Casey, M.C.,Ji, J.,Wilson, D.J.,Sarafianos, S.G.,Wang, Z.
6-Cyclohexylmethyl-3-hydroxypyrimidine-2,4-dione as an inhibitor scaffold of HIV reverase transcriptase: Impacts of the 3-OH on inhibiting RNase H and polymerase.
Eur J Med Chem, 128:168-179, 2017

PubMed Abstract: 3-Hydroxypyrimidine-2,4-dione (HPD) represents a versatile chemical core in the design of inhibitors of human immunodeficiency virus (HIV) reverse transcriptase (RT)-associated RNase H and integrase strand transfer (INST). We report herein the design, synthesis and biological evaluation of an HPD subtype (4) featuring a cyclohexylmethyl group at the C-6 position. Antiviral testing showed that most analogues of 4 inhibited HIV-1 in the low nanomolar to submicromolar range, without cytotoxicity at concentrations up to 100 μM. Biochemically, these analogues dually inhibited both the polymerase (pol) and the RNase H functions of RT, but not INST. Co-crystal structure of 4a with RT revealed a nonnucleoside RT inhibitor (NNRTI) binding mode. Interestingly, chemotype 11, the synthetic precursor of 4 lacking the 3-OH group, did not inhibit RNase H while potently inhibiting pol. By virtue of the potent antiviral activity and biochemical RNase H inhibition, HPD subtype 4 could provide a viable platform for eventually achieving potent and selective RNase H inhibition through further medicinal chemistry.

PubMed: 28182989
DOI: 10.1016/j.ejmech.2017.01.041

Experimental method

X-RAY DIFFRACTION (2.705 Å)