Validation of Database Compounds
In order to validate the pharmacophoric pattern of above mentioned four database compounds, their conformations were generated and mapped onto the pharmacophore derived from structure-based strategy. Out of different conformations of four compounds, 19 (various conformations) hits were obtained and three hits (each from BTB01434, BTB14348, and BTB13591) exhibited a perfect five-feature mapping and rest all showed a four-feature interaction. Analysis of the best five feature hit exhibited by highest estimated compound BTB01434, revealed that two HBA and two HY features were mapped exactly on the same groups as that of mapping obtained onto the pharmacophore obtained from HypoGen study. An additional feature i.e. hydrogen bond donor (HBD) which was additionally retrieved through receptor-based approach was mapped onto the H group of suphonamide moiety. This similar pattern of accurate mapping (common mapping fashion) was seen, when rest of three database compounds were mapped onto the structure-based pharmacophore, hence proving the precision of our predicted database compounds. Therefore, on the basis of above validation of these database compounds through mapping onto structurebased pharmacophore, we conclude that these database compounds would ensure good Ki values if experimentally synthesized and pharmacologically evaluated for HIV-1 enzyme inhibitory activity.
Abstract
The mechanisms of successful epigenetic reprogramming in cancer are not well characterized as they involve coordinated removal of repressive marks and deposition of activating marks by a large number of histone and DNA modification enzymes. Here, we have used a cross-species functional genomic approach to identify conserved genetic interactions to improve therapeutic effect of the histone deacetylase inhibitor (HDACi) valproic acid, which increases survival in more than 20% of patients with advanced acute myeloid leukemia (AML). Using a bidirectional synthetic lethality screen revealing genes that increased or decreased VPA sensitivity in C. elegans, we identified novel conserved sensitizers and synthetic lethal interactors of VPA. One sensitizer identified as a conserved determinant of therapeutic success of HDACi was UTX (KDM6A), which demonstrates a functional relationship between protein acetylation and lysine-specific methylation. The synthetic lethal screen identified resistance programs that compensated for the HDACi-induced global hyper-acetylation, and confirmed MAPKAPK2, HSP90AA1, HSP90AB1 and ACTB as conserved hubs in a resistance program for HDACi that are drugable in human AML cell lines. Hence, these resistance hubs represent promising novel targets for refinement of combinatorial epigenetic anti-cancer therapy.
Citation: Forthun RB, SenGupta T, Skjeldam HK, Lindvall JM, McCormack E, et al. (2012) Cross-Species Functional Genomic Analysis Identifies Resistance Genes of the Histone Deacetylase Inhibitor Valproic Acid. PLoS ONE 7(11): e48992. doi:10.1371/journal.pone.0048992 ?�dicale (INSERM), France Editor: Ivan Cruz Moura, Institut national de la sante et de la recherche me Received April 24, 2012; Accepted October 3, 2012; Published November 14, 2012 Copyright: ?2012 Forthun et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Funding: This work was supported by grants from The National Program for Research in Functional Genomics at The Research Council of Norway (H.N., H.K.S., B.T.G., and R.B.F.), Helse Vest grants (E.M.C.), and a grant from the Norwegian Cancer Society. H.N. and T.S. were supported by the University of Oslo and the Norwegian Cancer Society. R.B.F. was a recipient of EU COST action CANGENIN BM0703 and C. elegans NordForsk Travel grants. B.T.G. participates in COST action EuGESMA BM0801. H.N. and B.T.G. participate in COST action BM0703 and Nordforsk Network on Genomic Integrity. J.M.L. was the recipient of an Exchange Grant (no. 3054) from the European Science Foundation Research Networking Programme Frontiers of Functional Genomics (FFG). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. Competing Interests: The authors have declared that no competing interests exist.
Introduction
Epigenetic changes in cancer involve cooperation of multiple processes including covalent modification of histones, where histone acetylation and methylation are among the modifications shown to contribute to epigenetic reprogramming in cancer [1,2,3]. Histone deacetylase inhibitors (HDACi) have antitumor potential [4] and represent important therapeutic supplements in acute myeloid leukemia (AML) [5,6] where the need for effective low toxic therapy in an elderly patient population is critical [7]. Although current HDACi are criticized for being too unspecific, they have properties recommending them as therapeutic drugs, such as low general toxicity and promising effects at low doses. Moreover, many HDACis show synergy with standard chemotherapy [8]. The histone deacetylase class I and II inhibitor valproic acid (VPA) is an example of a well-tolerated anticonvulsant with a safety profile that allows long-term use in children [9]. VPA affects cell growth, differentiation and apoptosis [10,11] and is well tolerated in combination with chemotherapeutics and targeted therapy [12,13,14,15,16]. Myelodysplastic syndromes(MDS) and advanced AML are both diseases where genetic and epigenetic changes interact to promote initiation and progression of the cancer phenotype [17]. In approximately 30% of these patients, VPA induces pronounced cytostatic effects, disease stabilization and promising hematological responses [13]. Hence, identification of resistance mechanisms and effective co-therapeutics are important in order to improve VPA-efficacy in the nonresponsive patients. Epigenetic changes in cancer are global and a large number of enzymes are known to covalently modify histones and DNA with varying effects on different genes [1]. Given this complexity, there is lack of clarity of mechanisms and interrelation between different types of histone marks and the enzymes that deposit them. Appropriate functional genomic strategies are well suited to analyze the global biological end-points of such wide-ranging responses [17].