br Experimental br Acknowledgments We thank Mintek and Rhode

Experimental
Acknowledgments We thank Mintek and Rhodes University for generous financial support and permission to publish these findings. T.O.O. gratefully acknowledges Obafemi Awolowo University, Ile-Ife, Nigeria for study leave.
Introduction There are ∼35.3 million people living with HIV today. In 2012 2.3 million new infections were reported, which corresponds to about 6300 new HIV infections each day. AIDS caused a death toll of 1.6 million people in 2012 alone. These numbers underline the urgency for new improved schemes to prevent and treat HIV infection [1]. AIDS has cost millions of lives since it was first reported in 1981 and it remains a serious disease for humans. Recent advances in anti-HIV drugs and regimens as well as improved access to treatments have led to a reduction of AIDS-related deaths from 2.3 million in 2005 to 1.7 million in 2011 [1]; however much still has to be done because the infection has not yet been eradicated [2]. HIV-1 is the pathogen causing AIDS, and contains three essential enzymes: reverse transcriptase (RT), protease (PR) and integrase (IN) [3]. Because these three enzymes are essential for viral replication they have attracted attention, and some inhibitors targeting them have been discovered successfully. Most of the FDA-approved drugs used to treat AIDS target RT or PR [4]. Recently introduced drugs also inhibit the fusion of virus with CD4 ODQ (e.g. fusion inhibitors such as enfuvirtide) [5] or inhibit the interaction of the virus with the CC chemokine receptor type 5 (CCR5; inhibited by maraviroc) [6]. Current management of HIV is based on highly active antiretroviral therapy (HAART) [7], which includes the application of multiple antivirals. However, the effectiveness of HAART is slowly declining [7], which raises the need for the development of novel antivirals. Although negative information on HIV PR inhibitors has sometimes been reported [8], IN is still an interesting target for anti-HIV drug design because it has no counterpart in the mammalian body.
HIV-1 IN IN is highly conserved among retroviruses. HIV-1 IN is a 32kDa protein encoded at the 3′ end of the HIV Pol gene [9], and can be divided into three canonical domains: a zinc-binding N-terminal domain, a catalytic core domain and a DNA-binding C-terminal domain [10]. The N-terminal domain consists of residues 1–51, and contains a conserved HHCC motif that binds zinc [11]. In 1997, Cai et al.[12] reported the structure of a dimer of the N-terminal domain solved by NMR. The core domain, spanning residues 52–212, contains the endonuclease and polynucleotidyl transferase site with its three highly conserved acidic residues: Asp64, Asp116 and Glu152. These three residues are referred to as the DDE motif and can bind one or two divalent metal ions, such as Mn2+ or Mg2+[10]. The C-terminal domain, composed of residues 220–288, contributes to DNA binding and oligomerization for the integration process [13]. It links to the catalytic core by residues 196–200, which form an extension of the final helix of the core domain [14], and its structure in the form of a dimer was reported in 1995 (again solved by NMR) [15].
The active site of HIV-1 IN HIV-1 IN is responsible for the integration of DNA, which is reversely transcribed by the viral RNA into the host chromosomal DNA [16]. The enzyme catalyzes the 3′ processing (3′P) [17] step and the strand transfer (ST) reaction [18]. During the first step, IN cleaves two nucleotides from the two 3′ ends of the double-stranded viral DNA. Secondly, the DNA is transferred into the nucleus where the viral DNA is integrated into the host cell DNA with a series of phosphodiester transesterification reactions. Finally, the host cellular DNA repair enzymes complete the integration process [19]. HIV-1 IN thus contains two active sites involved in 3′P and ST reactions. Moreover, the HIV-1 replication depends not only on distinct steps but also lens epithelium-derived growth factor/p75 (LEDGF/p75).