Novel acridinedione derivatives: Design, synthesis, SIRT1 enzyme and tumor cell growth inhibition studies Mallika Alvala a , Shubhmita Bhatnagar a , Alvala Ravi b , Variam Ullas Jeankumar a , Thimmappa H Manjashetty a , Perumal Yogeeswari a , Dharmarajan Sriram a,⇑ a Drug Discovery Research Laboratory, Department of Pharmacy, Birla Institute of Technology and Science, Pilani-Hyderabad Campus, Hyderabad 500 078, India b G. Pulla Reddy College of Pharmacy, Mehdipatnam, Hyderabad 500 028, India article info Article history: Received 9 January 2012 Revised 27 February 2012 Accepted 7 March 2012 Available online 13 March 2012 Keywords: Antiproliferative activity Acridinedione derivatives hSIRT1 MDA-MB231 abstract A new scaffold N-(9-(ortho/meta/para-(benzyloxy)phenyl)-3,3,6,6-tetramethyl-1,8-dioxo-1,2,3,4,5,6,7,8- octahydroacridin-10(9H)-yl) isonicotinamide (H1-3) was discovered as a hSIRT1 inhibitor through virtual screening of in-house database. Based on these hits, a library of compounds were designed, synthesized and tested for in vitro hSIRT1 activity. The most potent compound 4d in the series showed a significant inhibition of SIRT1 activity. Further antitumor studies of compound 4d, showed a dose dependent increase in acetylation of p53K382 and decrease in SIRT1 with an IC 50 of 0.25 lM in MDA-MB231 breast cancer cell lines. Individual 3D-QSAR analysis using Schrödinger showed distribution of hydrophobic and non polar positive co-efficient at ortho position essential for bioactivity based on 4d. Ó 2012 Elsevier Ltd. All rights reserved. SIRT1 also known as NAD-dependent deacetylase sirtuin-1, the closest mammalian homolog of yeast Sir2, belongs to the family of the class III histone deacetylase. The complicated interaction loops established between human sirtuins and various critical cellular pathways suggest them to be possible drug targets. 1–5 Several lines of evidence have indicated that SIRT1 deacetylates not only the ly- sine residues of histones, preferentially H3 and H4 6 but also non histone proteins. It has been found to be up-regulated in many tu- mor types and are able to deacetylate various substrates including p53, 7–9 BCL6, 10 HIV Tat, 11 PGC-1a, 12,13 AceCS1, 14 Ku70, Smad7, and NF-kB 15 and Rb 16 which are associated with various disease condi- tions such as cancer and HIV. 17 Therefore, SIRT1 inhibitors are of interest as potential therapeutic agents. 4 Several inhibitors of SIRT1 have been reported, 18 including nicotinamide, 18 EX-527 ana- logues, 19 splitomicin analogues 20–22 sirtinol analogues, 23 cambi- nol, 10 2-anilinobenzamides, 24 aristoforin 25 and various other compounds reported 26–29 (Fig. 1). The first synthetic inhibitor that was discovered is sirtinol. 30 In the present study we describe the synthesis and structural characterization of a series of acridinedi- one derivatives as well as their hSIRT1 inhibitory activity sup- ported with in silico , biochemical and in vitro cell-proliferation assay. Since the crystal structure of human SIRT1 is not available, the three dimensional model of catalytic domain of the hSIRT1 (Q96EB6; 244–498 AA) was developed by comparative modeling using PRIME homology modeling program (Schrödinger L.L.C., USA) as described previously 31 and the fitness of the model was checked by PROCHECK program. 32 This model has 83.7% residues in most favored regions and ProSA-Web Z score of À6.38 similar to the template structure scores. Binding site pocket was identified by using SITEMAP (Schrödinger L.L.C., USA). With an aim of identi- fying novel hSIRT1 inhibitors, virtual screening of in-house data- base of 2500 molecules was carried out by using GLIDE (Schrödinger L.L.C., USA), GOLD and AUTODOCK 4.0 software’s against catalytic core of hSIRT1. Based on docking score, binding energy and fitness values compounds H1, H2, and H3 were selected for (Fig. 2) in vitro enzymatic assay at 50 lM concentration along with reference compound suramin. Binding energy, docking score, fitness and percentage inhibition values are presented in Table 1. Further to explore the structure–activity relationship of hit compounds (Fig. 2) as SIRT1 inhibitors, different derivatives were designed by computational and medicinal chemistry approaches. Docking studies for the designed compounds were performed by using three different softwares (Schrödinger, GOLD, and Autodock 4.0). Docking score, fitness values and binding affinity values of all the designed molecules along with reference compound suramin are shown in Table 2. The designed compounds having better scores than the initial hit compounds (H1-3), were derivatized by using a one pot synthetic protocol previously reported by our group. 33 The target molecules (4a–r) were synthesized via a microwave assisted one-pot three component reaction (Scheme 1) of either ortho, meta or para substituted benzyloxy benzaldehydes (1a–c), 0960-894X/$ - see front matter Ó 2012 Elsevier Ltd. All rights reserved. http://dx.doi.org/10.1016/j.bmcl.2012.03.030 ⇑ Corresponding author. Tel.: +91 40 66303506; fax: +91 40 66303998. E-mail address: drdsriram@yahoo.com (D. Sriram). Bioorganic & Medicinal Chemistry Letters 22 (2012) 3256–3260 Contents lists available at SciVerse ScienceDirect Bioorganic & Medicinal Chemistry Letters journal homepage: www.elsevier.com/locate/bmcl