Identification of novel non-peptide CXCR4 antagonists by ligand-based design approach Satoshi Ueda a , Manabu Kato a , Shinsuke Inuki a , Hiroaki Ohno a , Barry Evans b , Zi-xuan Wang b , Stephen C. Peiper b , Kazuki Izumi c , Eiichi Kodama c , Masao Matsuoka c , Hideko Nagasawa d , Shinya Oishi a, * , Nobutaka Fujii a, * a Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan b Department of Pathology, Medical College of Georgia, GA 30912, USA c Institute for Virus Research, Kyoto University, Sakyo-ku, Kyoto 606-8507, Japan d Gifu Pharmaceutical University, Mitahora-higashi, Gifu 502-8585, Japan article info Article history: Received 6 April 2008 Revised 21 May 2008 Accepted 22 May 2008 Available online 29 May 2008 Keywords: Chemokine CXCR4 SDF-1 Anti-HIV Indole abstract The design and synthesis of novel non-peptide CXCR4 antagonists is described. The peptide backbone of highly potent cyclic peptide-based CXCR4 antagonists was entirely replaced by an indole framework, which was expected to reproduce the disposition of the key pharmacophores consistent with those of potential bioactive conformations of the original peptides. A structure–activity relationship study on a series of modified indoles identified novel small-molecule antagonists having three pharmacophore func- tional groups through the appropriate linkers. Ó 2008 Elsevier Ltd. All rights reserved. Chemokines are a family of small proteins with chemotactic and proactivatory effects on leukocytes. Chemokines mediate their bio- logical effects by binding to the specific G-protein coupled receptor subtypes that are differentially and widely expressed in blood cells. Among these chemokine receptors, CXCR4 has a broad tissue dis- tribution and the activation by its endogenous ligand CXCL12 (SDF-1, stromal cell-derived factor 1) leads to chemotaxis, immu- nomodulation, and other regulatory functions including progenitor cell migration during embryologic development of the cardiovas- cular, hematopoietic, and central nervous systems. In addition to its physiological roles, CXCR4 also plays important roles in patho- logical conditions. These include tumor growth and metastasis 1 and rheumatoid arthritis (RA). 2 CXCR4 has also been reported to act as a major co-receptor involved in the entry of T-cell-line-tropic human immunodeficiency virus type 1 (HIV-1) strains into target cells. 3 Thus, CXCR4 is considered as an important therapeutic tar- get for multiple diseases. Inhibitory compounds of CXCL12 or HIV-1 binding to CXCR4 could be novel classes of anti-cancer, anti-RA, and anti-HIV-1 drugs. Previously, we found highly potent peptide-based CXCR4 antagonists such as 1, 2, and 3 (Fig. 1). 4,5 Peptide 1 and its derivatives effectively blocked X4-HIV-1 entry to the cell by specifically binding to CXCR4, 6 and also showed an anti-metastatic effect against breast cancer 7 and anti-RA activity 8 in mouse models. Although peptides are excellent lead molecules for develop- ment of pharmaceutical agents, special drug delivery systems are usually required for their clinical use because of the poor bioavailability and instability against enzymes. Whereas several peptide-based CXCR4 antagonists have been reported, only small numbers of small-molecule CXCR4 antagonists have been 0960-894X/$ - see front matter Ó 2008 Elsevier Ltd. All rights reserved. doi:10.1016/j.bmcl.2008.05.092 * Corresponding authors. Tel: +81 75 753 4551; fax: +81 75 753 4570 (N. Fujii). E-mail addresses: soishi@pharm.kyoto-u.ac.jp (S. Oishi), nfujii@pharm.kyoto-u. ac.jp (N. Fujii). H-Arg 1 -Arg 2 -Nal 3 -Cys 4 -Tyr 5 -Arg 6 -Lys 7 HO-Arg 14 -Cys 13 -Cit 12 -Arg 11 -Tyr 10 D-Lys 8 Pro 9 S S 2 cyclo(-D-Tyr 1 -L-Arg 2 -L-Arg 3 -L-Nal 4 -L-Gly 5 -) 3 cyclo(-D-Tyr 1 -D-Arg 2 -L-Arg 3 -L-Nal 4 -L-Gly 5 -) 1 Figure 1. Structures of 1 and its downsized peptides 2 and 3. Bold residues are the indispensable residues for the potent CXCR4-antagonistic activity. Nal, L-3-(2- naphthyl)alanine; Cit, L-citrulline. Bioorganic & Medicinal Chemistry Letters 18 (2008) 4124–4129 Contents lists available at ScienceDirect Bioorganic & Medicinal Chemistry Letters journal homepage: www.elsevier.com/locate/bmcl