To date the crystal structures of HIV IN

To date, the crystal structures of HIV-1 IN complexed with ligands and related proteins could help us in studying the interactions between the inhibitors and IN. Until now, 114 co-crystal structures of HIV-1 IN with small molecular ligands 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35 have been deposited in the Protein Data Bank (PDB), as shown in Table 1 (not including apo IN). Most crystal structures include the residues forming the LEDGF binding site, and 12 structures describe allosteric Cephalexin 33, 34, 35. Only one of these structures has an INSTI (5CITEP) bound (PDB code: 1QS4) [20]. However, there are several structures of the prototype foamy virus (PFV) intasome co-crystallized with HIV-1 INSTIs available (PDB codes: 4BE0, 4BE1, 4BE2, 4BDY, 4BDZ and 4IKF). The ligand interaction patterns are known to be highly similar to those of HIV-1 INSTIs and IN and can hence provide valuable information for the design of new agents 36, 37. The cavity where 3′P occurs in HIV-1 IN is primarily formed by Asp64, Cys65, Thr66, His67, Glu92, Asp116 and Asn120 [38], which are part of the β1 sheet (Fig. 1a). Of these residues, Asp64, Thr66, His67 and Asp116 can form hydrophilic interactions with a potential ligand. Furthermore, Asp64 and Asp116 could form a chelation with Mg2+, the existence of which is a necessary condition for the 3′P step [38]. According to previous reports, many compounds have shown 3′P inhibitory activity, such as chicory acids, coumarin and double sulfones, among others [39]. Recently, much attention has been paid to HIV-1 INSTIs for the treatment of AIDS 40, 41. The cavity involved in the ST process includes a loop consisting of residues Phe139–Ile151. They are on random loops and the start of the α4 helix (Fig. 1). The pocket is formed by the hydrophilic residues Gln146, Ser147, Gln148 and the hydrophobic residues Ile141, Pro142, Tyr143, Pro145, Val150 and Ile151. The co-crystal structure HIV-IN–5CITEP (PDB code: 1QS4) was reported in 1999 [20], which is shown in Fig. 2a[40]. The inhibitor 5CITEP has an IC50 value of 2.2μm, and several H-bonds are formed between the ligand and the IN residues. Gln148 forms a H-bond with the nitrogen atom of the indole ring, and another H-bond is located between the enol hydroxyl and Glu152. The four nitrogen atoms in the tetrazole ring are H-bonded to Asn155, Thr66, Lys159 and Lys156, respectively. In addition, it was suggested that the magnesium ion in the binding site contacts the indole ring of 5CITEP via van der Waals forces. Figure 2b [40] shows a docking result of SD1997, which is a molecule reported by Di Santo et al.[42]. Mg2+ forms chelations with the residues Asp64, Asp116 and the enol hydroxyl, carboxyl hydroxyl of the ligand. This indicates that the chelation of Mg2+ might be important for enhancing the interaction between an inhibitor and the IN. LEDGF/p75 is a member of the hepatoma-derived growth factor family identified by co-immunoprecipitation [43], and is the dominant cellular binding partner of HIV-1 [44]. The binding of IN and LEDGF/p75 enhances ST activity of HIV-1 IN in vitro[43]. Therefore, the interaction of HIV-1 IN with LEDGF/p75 could constitute a target for antiretroviral therapy [45]. Gln168, Glu170 and His171 are key residues located at the cavity where LEDGF/p75 binds (marked in green in Fig. 1a). Leu102, Thr125, Ala128, Ala129 and Trp132 from IN B-chain and Thr174 and Met178 from A-chain together form a hydrophobic pocket, which the LEDGF residue Ile365 projects into. Figure 3 shows the interactions between the small molecule ZT0 and key residues of IN at the LEDGF/p75 site (PDB code: 3ZT0). The carboxy hydroxyl oxygen atom of the ligand ZT0 forms a H-bond with Glu170, and the other carboxy oxygen atom forms H-bonds with His171 and Thr174. A nitrogen atom close to the carbonyl forms a H-bond with Gln168. Many structures of LEDGF inhibitors are available 46, 47, such as the 5-carbonyl-1H-imidazole-4-carboxamide class [46] and aryl- or heteroaryl-tert-butoxy-acetic acid [47].