Design, Synthesis and Biological Evaluation of N⁴-Sulfonamido-Succinamic, Phthalamic, Acrylic and Benzoyl Acetic Acid Derivatives as Potential DPP IV Inhibitors

General Methods

The proposed structures for compounds 6-21 were confirmed via IR spectroscopy, mass spectroscopy, ¹H- and ¹³C-NMR spectra.

Melting points were measured using Gallenkampf melting point apparatus and are uncorrected. ¹H NMR and ¹³C NMR spectra were collected on a Varian Oxford NMR³⁰⁰ and BRUKER NMR⁵⁰⁰ spectrometers. The samples were dissolved in deuterated DMSO. Mass spectrometry was performed using LC Mass Bruker Apex-IV mass spectrometer utilizing an electrospray interface.

Infrared spectra were recorded using Shimadzu IR Affinity-1 spectrophotometer. The samples were dissolved in CHCl₃ and analysed for IR as thin solid films using NaCl plates. Analytical thin layer chromatography (TLC) was carried out using pre-coated aluminum plates and visualized by UV light (at 254 and/ or 360 nm). Column chromatography was carried out using high- purity grade silica (pore size 60A°, 70-230 mesh, 63-200 µm, Fluka).

Chemicals and solvents were purchased from corresponding companies (Sigma-Aldrich, Riedel-de Haen, Fluka, BDH Laboratory Supplies and Promega Corporation) and were used in the experimentation without further purification.

DPP IV Inhibition Assay

DPP IV inhibitory bioactivities were assayed using commercially available kit (Cayman's DPP IV Inhibitor

Screening Assay Kit, USA) which provides a fluorescence-based method for screening DPP IV inhibitors. The assay uses the fluorogenic substrate, Gly-Pro-Amino-methylcoumarin (AMC), to measure DPP IV activity. Cleavage of the peptide bond by DPP IV releases the free AMC group, resulting in fluorescence that is measured at an excitation wavelength of 350-360 nm and an emission wavelength of 450-465 nm. Inhibition of DPP will prevent AMC release and therefore decrease fluorescence intensity.

The tested compounds were initially dissolved in DMSO to yield 10 mM stock solutions and subsequently diluted to the required concentrations using distilled deionized water and then were added to the assay well in a final volume of 10 μl (and a final concentration of 10 μM). The final concentration of DMSO was adjusted to 0.1 %. The assay procedure can be described briefly as follows: 30 μl of assay buffer, 10 μl of diluted DPP, and 10 μl of the inhibitor were added to the inhibitor wells. The reaction was initiated by adding 50 μl of diluted Substrate Solution. The plate was covered and incubated for 30 minutes at 37 °C. After incubation, fluorescence intensity (Excitation λ:350 nm; Emission λ:465 nm) was read in a FLX800TBI Microplate Fluorimeter (BioTek Instruments, Winooski, USA). The assay is carried out using a black 96-well plate with led.

The percentage of residual activity of DPP IV was determined for each compound by comparing the activity of DPP IV in the presence and absence of the tested compound. DPP IV activity was not affected at the used DMSO concentration. Negative controls lacking DPP IV were used as background. A standard DPP IV inhibitor, Gemifloxacin, was used as a positive control. All measurements were conducted in duplicates.

Docking and Scoring

The binding site of DPP IV was generated from the co-crystallized ligand GVB1771 within the targeted protein (PDB code: 2JID, resolution 2.8 A°). The ligands were docked using LigandFit (Accelrys DS Studio 2.1) and default parameters [29,30]. The resulting docked poses were scored employing PLP1 [31], PLP2 [32], ligscore1 [29], ligscore 2 [29], PMF [33,34] and JAIN [35-37].

Chemistry

In the current work, the desired N⁴-sulfonamido-succinamic, phthalamic, acrylic and benzoyl acetic acid derivatives 6-21 were prepared from the reaction of one of the benzenesulfonamide derivatives 1-5 with the required anhydride i-iv (succinic, maleic, phthalic and homophthalic, respectively) in dimethylformamide at 150 °C with overnight reflux, as illustrated in Scheme 1. Sulfonamides 6-16 were synthesized earlier by other research groups [38-41]. While compounds 17-21 are novel sulfonamide derivatives. The highest yield was obtained upon reacting 4-amino-N-pyrimidin-2-yl-benzenesulfonamide 4 with maleic anhydride ii to give 12 in 83.8% yield.

Scheme 1 shows the synthesized N⁴-sulfonamido-succinamic, phthalamic, acrylic and benzoyl acetic acid derivatives (6-21).

The synthesized compounds were designed to enclose the desired pharmacophoric features responsible for binding to DPP IV receptor site [17]. The chemical features considered were hydrogen bond acceptors, positive ionizable groups, negative ionizable groups and hydrophobic features (Fig. 2 and Fig. 3).

Biological Evaluation

The results of DPP IV inhibition assay, presented in Table 1, demonstrate that compound 17 exhibit appreciable activity against DPP IV. Although our newly synthesized compounds are of lower potency than some published DPP IV inhibitors, these derivatives are characterized by their novel scaffold that can serve as a promising lead for further optimization. Table 1 shows the fit values of the synthesized compounds against Hypo32/8 and Hypo4/10, together with their QSAR-estimated IC₅₀ values and their in vitro bioactivities.

By comparing the synthesized N⁴-sulfonamido-succinamic acid derivatives 6-10 (Scheme 1, Table 1), it was found that compound 10 has the highest activity with 23% inhibition at 10 μM concentration. This can be attributed to the presence of the amidino moiety in compound 10 that is mapped as a positive ionizable feature by Hypo4/10.

Similar results were found when evaluating the synthesized N⁴-sulfonamido-acrylic acid derivatives 11-15 (Scheme 1, Table 1), where compound 11 enclosing the amidino group showed the optimum inhibition. Compound 12 also showed similar inhibition effect as the amidino derivatives which could be attributed to sharing equivalent interactions within the DPP IV binding pocket since similar pharmacophoric features lead to similar activities.

In contrast, regarding the synthesized N⁴-sulfonamido- benzoyl acetic acid derivatives 17-21 (Scheme 1, Table 1), compound 17 had the highest activity with 25% inhibition (IC₅₀= 33.5 μM). This can be caused by the existence of the pyrimidine ring in 17 that is mapped as both hydrophobic and hydrogen bond acceptor feature by Hypo32/8.

Fig. (2) shows how Hypo4/10 maps the synthesized compounds 10, 11, 16 and 21. The positive ionizable feature of Hypo4/10 fits the diaminomethylene group of these compounds, while one of the hydrogen bond acceptor features maps the carboxylic acid group. Furthermore, the other two hydrogen bond acceptors of Hypo4/10 fit the sulfone moiety in the structures.

On the other hand, Fig. (3) shows how Hypo32/8 fits the synthesized compounds 17 and 18. The negative ionizable feature of Hypo32/8 maps the carboxylic acid group of 17 and 18, while the two hydrophobic features fit the lateral aromatic ring and the heterocycle i.e. pyrimidine ring of 17 and thiazole ring of 18. Additionally, the two hydrogen bond acceptors of Hypo32/8 map the sulfone group and the nitrogen atom of the heterocycle.

As a general trend, the activity of the synthesized sulfonamido-derivatives was shown to be affected by the chemical properties of substituents on both N₁ and N₄. The presence of basic N₁ substituent, which is in accordance with the positive ionizable feature of Hypo4/10, together with a rigid acidic N₄ group, may contribute to the increase in DPP IV inhibitory bioactivity. Furthermore, the presence of an electron withdrawing group capable of accepting hydrogen bond may also enhance the inhibitory bioactivity.

Additionally, the hydrophobic aromatic ring present at N₄ may also enhance the inhibitory activity as can be seen in molecules 16-21. Moreover, the presence of carboxylic acid group and a hydrophobic aromatic ring agrees well with the pharmacophoric features of Hypo32/8.

The pharmacophore features obtained by structure-based pharmacophore modeling can be compared with the structure of DPP IV binding site to identify probable residues important for inhibition. The docking parameters output is summarized in Table 2 (under Supplementary Material). Furthermore, illustrating figures that show the interaction of selected synthetic compounds 10, 11, 16, 17, 18 and 21 with the amino acids in the DPP IV binding pocket are shown in figures 2d, 2g, 2j, 2m, 3d and 3g. The figures show the interaction between the functional groups that correspond to the pharmacophoric features. A marked similarity was observed between the features proposed by the pharmacophore models and the ligand binding features in the docked structures. For example, negative ionizable feature in Hypo32/8 corresponds to the interaction with the guanidino group of Arg560, hydrophobic features correspond to stacking with aromatic rings of Tyr547 and Tyr662 while hydrogen bond acceptors correspond to OH group of Tyr547 and guanidino of Arg125 as shown in (Fig. 3).

Whereas Hypo4/10 contains three hydrogen bond acceptors that correspond to the interactions with NH₂ group of Lys554, bridging Water HOH2044, OH group of Tyr662, guanidino group of Arg125, while positive ionizable feature corresponds to carboxylate group of Glu205 as shown in (Fig. 2).

It is important to realize the fact that not all amino acids in the binding pocket are essential for activity, only certain interactions with selected amino acids could be effective as inhibitor, this point was clarified using dbCICA technique [42].

To conclude, the presence of positive and negative ionizable groups combined with electron with drawing moieties that act as hydrogen bond acceptors, together with hydrophobic aromatic ring are found to be necessary features for in vitro DPP IV bioactivity.

Indeed, the synthesized N⁴-sulfonamido-succinamic, phthalamic, acrylic and benzoyl acetic acid compounds 6-21 were shown to have common pharmacophoric features with our DPP IV inhibitor lead, Gemifloxacin. Further research work and study to re-arrange and enhance better matching of these groups with the pharmacophoric features of Hypo4/10 and Hypo32/8 are required in order to improve the DPP IV inhibitory bioactivity.