ORIGINAL RESEARCH Molecular modeling studies and synthesis of novel quinoxaline derivatives with potential anti-cancer activity as inhibitors of methionine synthase Hosam Elshihawy • Mohamed Hammad Received: 2 April 2012 / Accepted: 24 October 2012 / Published online: 23 November 2012 Ó Springer Science+Business Media New York 2012 Abstract Methionine synthase (MetS) catalyses the transfer of a methyl group from the methyltetrahydrofolate (MTHF) to homocysteine to produce methionine and tetra- hydrofolate. MetS is over-expressed in the cytosol of certain breast and prostate tumor cells. In this article, we designed, synthesized, and evaluated the biological activity of a series of substituted quinoxaline derivatives that mimic the MTHF in the structure. The main aim was to develop inhibitors that zcould inhibit the enzyme reaction by blocking the binding of MTHF. These inhibitors were docked into the MTHF binding domain in such the same way as MTHF in its binding domain. Compound 4-({(6-nitro-quinoxalin- 2-yl)methylamino}methyl)benzoic acid showed the lowest free energy of the binding (-152.62 kJ/mol) and showed the lowest IC 50 values of 45 ± 9 and 53 ± 9 lM against two types of cancer cell lines PC-3 and MCF-7, respectively. Keywords Cobalamin  MCF-7 cells  Methionine  Methionine synthase  PC-3  Quinoxaline derivatives and tumor Introduction Cobalamin-dependant methionine synthase (MetS) is one of the transmethylase enzymes that utilizes cobalamin derivative methylcobalamin [methylcobalamin (CH 3 -cobalamin I)] as a cofactor (Halpern et al., 1974). MetS catalyses the transfer of the methyl group from 5-methyltetrahydrofolate to homocys- teine via the cobalamin cofactor (CH 3 -cobalamin), which cir- culates between ?1 and ?3 oxidation states (Fig. 1). Crystal structure of cobalamin-dependent MetS revealed that it consists of four functional binding domains. They are homocysteine binding domain, 5-methyltetrahydrofolate binding domain, the third domain binds cobalamin cofactor, and the fourth domain is an allosteric cofactor S-adenosy-L-methionine (S-AdoMet) (Hoffman, 1982). The reaction products methionine and tetra- hydrofolate (THF) are closely correlated to important bio- chemical reactions of the methylation of DNA, lipids, proteins, and polyamine (Kenyon et al., 2002; Pavillard et al., 2006). Some recent studies have showed promising anti-tumor and apoptosis activities in colon with S-adenosylmethionine (SAMe) and its metabolite methylthioadenosine (MTA) (Tony et al., 2011). Some investigations using quinoxaline derivatives such as 3-aryl-2-quinoxaline-carbonitrile 1,4-di-N-oxide deriv- atives showed hypoxic and cytotoxic activities against some of human cell lines (Yunzhen et al., 2012). The present study showed a new approach for deter- mining specific inhibitors of MetS. Quinoxaline derivatives that resemble substructure of 5-MTHF (Fig. 2) have been docked into the MTHF binding domain. The free energy of binding of these ligand-receptor complexes have been obtained and compared to the results obtained from cell free assay and in vitro tumor cell cytotoxicity assay. Materials and methods Molecular modeling procedure Molecular modeling was carried out on Schrodinger com- putational software workstation using Maestro 7.5 graphic H. Elshihawy (&) Organic Chemistry Division, School of Pharmacy, Suez Canal University, Ismailia 41522, Egypt e-mail: h.elshihawy@uea.ac.uk; hosam_sh_27@hotmail.com M. Hammad Centre for Engineering in Medicine and Surgical Services, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA 123 Med Chem Res (2013) 22:3405–3415 DOI 10.1007/s00044-012-0307-4 MEDICINAL CHEMISTR Y RESEARCH