Biologically-validated HIV integrase inhibitors with nucleobase scaffolds: Structure, synthesis, chemical biology, molecular modeling, and antiviral activity

Article abstract of DOI:10.1080/15257770701490563

Integrase, an enzyme of the pol gene of HIV, is a significant viral target for the discovery of anti-HIV agents. In this presentation, we report on the continuation of our work on the discovery of diketo acids, constructed on nucleobase scaffolds, that ar

Full text of DOI:10.1080/15257770701490563

Nucleosides, Nucleotides, and Nucleic Acids, 26:665–668, 2007
Copyright ꢀ Taylor & Francis Group, LLC
C
ISSN: 1525-7770 print / 1532-2335 online
DOI: 10.1080/15257770701490563
BIOLOGICALLY-VALIDATED HIV INTEGRASE INHIBITORS WITH
NUCLEOBASE SCAFFOLDS: STRUCTURE, SYNTHESIS, CHEMICAL
BIOLOGY, MOLECULAR MODELING, AND ANTIVIRAL ACTIVITY
Vasu Nair, Vinod Uchil, Guochen Chi, Iwona Dams, Arthur Cox,
and Byung Seo
Center for Drug Discovery and the Department of Pharmaceutical
2
and Biomedical Sciences, University of Georgia, Athens, Georgia, USA
Integrase, an enzyme of the pol gene of HIV, is a significant viral target for the discovery of
2
anti-HIV agents. In this presentation, we report on the continuation of our work on the discovery of
diketo acids, constructed on nucleobase scaffolds, that are inhibitors of HIV integrase. An example
of our synthetic approach to inhibitors with purine nucleobase scaffolds is given. Comparison is
made between integrase inhibition data arising from compounds with pyrimidine versus purine
nucleobase scaffold. Antiviral results are cited.
Keywords Integrase; nucleobase scaffold; inhibitors; anti-HIV
INTRODUCTION
HIV-1 integrase is a 32 kDa protein encoded at the 3ꢁ-end of the HIV pol
gene and is responsible for the integration of HIV DNA into host chromoso-
mal DNA.[1−3] Prior to the initiation of integration, there is assembly of viral
DNA, previously produced by reverse transcription, on HIV integrase. Fol-
lowing this assembly, endonucleatic cleavage of two nucleotides from each
3ꢁ-end of double-stranded viral DNA (3ꢁ-processing) produces tailored vi-
ral DNA recessed by two nucleotides. In the next step, which occurs in the
nucleus and is identified as strand transfer, there is staggered nicking of
chromosomal DNA and joining of each 3ꢁ-end of the recessed viral DNA to
the 5ꢁ-ends of the host DNA. The strand transfer step, occurring in the nu-
cleus, is partitioned from 3ꢁ-processing and is carried out after transport of
the processed, preintegration complex from the cytoplasm into the nucleus.
While a number of structurally diverse compounds have been reported to
be inhibitors of HIV integrase, only some compounds of one group, the
This project was supported by the National Institutes of Health (NIAID). Its contents are solely the
responsibility of the authors and do not necessarily represent the official views of the NIH.
Address correspondence to Vasu Nair Department of Pharmaceutical and Biomedical Sciences,
University of Georgia, Athens, GA 30602-2352, USA. E-mail: vnair@rx.uga.edu
665

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V. Nair et al.
FIGURE 1 Structures of representative diketo acids.
β-diketo acids and their related systems,[4−10] represent the most convinc-
ing, biologically-validated inhibitors of this viral enzyme. In this report, we
disclose the synthesis and inhibition data of β-diketo acids with purine nu-
cleobase scaffolds (Figure 1) that show selectivity of inhibition of the strand
transfer step of HIV-1 integrase. Comparison is made between integrase in-
hibition data arising from compounds with purine versus pyrimidine nucle-
obase scaffold (Figure 1). Relevant in vitro antiviral results are cited.
RESULTS AND DISCUSSION
A representative example of the synthesis of a diketo acid with a purine
scaffold is illustrated in Scheme 1. Hypoxanthine (8), the starting material,
was benzylated with NaH/benzyl bromide and then converted to 10 utiliz-
ing a free-radical bromination with N-bromosuccinimide (NBS). Palladium-
catalyzed cross-coupling with ethoxyvinyl tributylstannane gave 11. An ad-
dition/ elimination reaction of 11 with methyl chlorooxalate and pyridine
furnished 12, which was deprotected with ferric chloride hexahydrate to
give ketoester 13. Final deprotection of the latter in methanol with sodium
hydroxide followed by acid work-up resulted in the target molecule 6. Inte-
grase inhibition studies were conducted with recombinant wild-type HIV-1
integrase and a 21-mer oligonucleotide substrate.[7,9,10] The data are sum-
marized in Table 1. Compounds 6 and 7, with the β-keto acid functionality
at the 8- and 2-positions, respectively, were strong inhibitors of the strand

HIV Integrase Inhibitors with Nucleobase Scaffolds
667
SCHEME 1 Synthetic methodology for the preparation of a purine diketo acid.
transfer step of HIV-1 integrase. However, both compounds showed much
lower inhibition of the 3ꢁ-processing step of HIV integrase action. In sharp
contrast, β-diketo acids with pyrimidine nucleobase scaffolds (1–3) are po-
tent inhibitors of both the 3ꢁ-processing and strand transfer steps. The
reason for this difference is not entirely clear. However, our molecular
modeling data reveal that the regiochemical arrangement and preferred
conformation of the β-diketo acids with pyrimidine nucleobase scaffolds
allow for more effective overlap of these diketo acids with both the 3ꢁ-
processing and strand transfer pockets within the catalytic site.
These compounds were evaluated for anti-HIV activity in a PBMC cell-
based, microtiter anti-HIV assay against the clinical isolate, HIV-1TEKI (NSI
phenotype), and HIV-1NL4-3 (SI phenotype).[7] Compounds 1-3 exhibited
potent to highly potent in vitro anti-HIV activity. However, the purine-based
compounds, 6 and 7, while showing strong inhibition of the strand trans-
fer step of HIV integrase, exhibited low anti-HIV activity. Investigations of
TABLE 1 Data summarizing the inhibition of wild type HIV-1
integrase by inhibitors 1–7
Inhibitors
3ꢁ-processing (µM)
Strand transfer (µM)
1
2
3
4
5
6
7
3.7
4.1
3.9
10.0
100
31.5
30.0
0.2
<0.6
<0.7
0.5
10.0
4.1
2.7

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V. Nair et al.
other integrase inhibitors related to the anti-HIV active compounds are in
progress.
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