DOI: 10.1002/cmdc.200800213 Discovery of DPP IV Inhibitors by Pharmacophore Modeling and QSAR Analysis followed by in silico Screening Ihab M. Al-masri, Mohammad K. Mohammad, and Mutasem O. Taha* [a] Introduction Dipeptidyl peptidase IV (DPP IV) is a multifunctional protein engaged in many physiological processes. It functions as bind- ing protein, receptor, and proteolytic enzyme. It is a serine peptidase belonging to the S9b protein family. [1] DPP IV exists in two forms: a soluble homodimer and ubiquitous type II in- tegral plasma membrane glycoprotein. [2–6] It has a strong corre- lation with many diseases such as diabetes, obesity, and tumor progression, making it an attractive target in drug discovery ACHTUNGTRENNUNGresearch. [7–12] DPP IV degrades endogenous peptides by cleaving the pe- nultimate (N-terminal) proline or alanine. It cleaves several bio- active peptides, for example, growth hormone releasing hor- mone and substance P. [13, 14] However, its most important sub- strates are incretins: glucagonlike peptide 1 (GLP-1) and glu- cose-dependent insulinotopic polypeptide (GIP). GLP-1 is re- leased from intestinal l-cells in response to meals. [15] It stimulates insulin biosynthesis and secretion, reduces glucagon release, slows gastric emptying, reduces appetite, and stimu- lates regeneration and differentiation of islet b-cells. [16–18] On the other hand, GIP is produced by the duodenal K-cells and is extensively involved in glucose metabolism by enhancing insu- lin secretion. [19] Both peptides have very short half-lives ACHTUNGTRENNUNGbecause of their rapid degradation by DPP IV (approximately two minutes). [20, 21] Therefore, inhibiting DPP IV should promote the hypoACHTUNGTRENNUNGglycemic effects of GLP-1 and GIP. In fact, DPP IV in- hibitors have been shown to reduce postprandial hyperglyce- mia. [22] Controlling postprandial glucose excursions is currently considered an essential objective for managing type II ACHTUNGTRENNUNGdiabetes. [22] Various crystallographic studies on DPP IV have uncovered features involved in its ligand binding and enzymatic catalysis, most notably, the catalytic triad Ser630-Asp708-His740, the oxyanion hole Tyr631-Tyr 547, the hydrophobic S1 pocket Tyr631-Val 656-Trp 659-Tyr662-Tyr 666-Val711, the P2 region Arg 125-Asn 710, and the N-terminal recognition region Glu 205-Glu 206-Tyr 662. [23, 24] Many research groups were, and still are, involved in the dis- covery and optimization of new DPP IV inhibitors as leads for new hypoACHTUNGTRENNUNGglycemic therapeutic agents for the treatment of type II diabetes. [25–29] These efforts culminated in the discovery and optimization of a number of reversible and irreversible DPP IV inhibitors, some of which are under clinical evaluation (for example, NVP-DPP728, Vildagliptin, P93/01). [30–34] In fact one of the potent inhibitors, MK-0431 (Sitagliptin), has been re- cently approved by the FDA for treating type II diabetes. [35] Clinically useful DPP IV inhibitors have several potential advan- tages over classical antiACHTUNGTRENNUNGdiabetic therapies, including: their adaptability for oral administration in a once-per-day dosing regimen, [25] being less prone to causing dangerous hypo- ACHTUNGTRENNUNGglycemia, and being able to promote regeneration and differ- entiation of b-cells. [36–38] [a] I. M. Al-masri, M. K. Mohammad, M. O. Taha Department of Pharmaceutical Sciences, Faculty of Pharmacy University of Jordan, Amman (Jordan) Fax: (+ 962) 653-39-649 E-mail : mutasem@ju.edu.jo Supporting information for this article is available on the WWW under http://dx.doi.org/10.1002/cmdc.200800213. Dipeptidyl peptidase IV (DPP IV) deactivates the natural hypo- ACHTUNGTRENNUNGglycemic incretin hormones. Inhibition of this enzyme should re- store glucose homeostasis in diabetic patients making it an at- tractive target for the development of new antiACHTUNGTRENNUNGdiabetic drugs. With this in mind, the pharmacophoric space of DPP IV was ex- plored using a set of 358 known inhibitors. Thereafter, genetic al- gorithm and multiple linear regression analysis were employed to select an optimal combination of pharmacophoric models and physicochemical descriptors that yield selfconsistent and predic- tive quantitative structure–activity relationships (QSAR) (r 2 287 = 0.74, F-statistic = 44.5, r 2 BS = 0.74, r 2 LOO = 0.69, r 2 PRESS against 71 external testing inhibitors = 0.51). Two orthogonal pharmaco- phores (of cross-correlation r 2 = 0.23) emerged in the QSAR equa- tion suggesting the existence of at least two distinct binding modes accessible to ligands within the DPP IV binding pocket. Docking experiments supported the binding modes suggested by QSAR/pharmacophore analyses. The validity of the QSAR equa- tion and the associated pharmacophore models were established by the identification of new low-micromolar anti-DPP IV leads re- trieved by in silico screening. One of our interesting potent anti- DPP IV hits is the fluoroquinolone gemifloxacin (IC 50 = 1.12 mm). The fact that gemifloxacin was recently reported to potently in- hibit the prodiabetic target glycogen synthase kinase 3b ACHTUNGTRENNUNG(GSK-3b) suggests that gemifloxacin is an excellent lead for the develop- ment of novel dual antiACHTUNGTRENNUNGdiabetic inhibitors against DPP IV and GSK-3b. ChemMedChem 2008, 3, 1763 – 1779  2008 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim 1763