Sulfonated Nonsaccharide Heparin Mimetics Are Potent and Noncompetitive Inhibitors of Human Neutrophil Elastase.

Human neutrophil elastase (HNE) is a serine protease that plays vital roles in inflammation, innate immune response, and tissue remodeling processes. HNE has been actively pursued as a drug target, particularly for the treatment of cardiopulmonary diseases. Although thousands of molecules have been reported to inhibit HNE, yet very few are being evaluated in early clinical trials, with sivelestat as the only approved HNE inhibitor. We report here a novel chemotype of sulfonated nonsaccharide heparin mimetics as potent and noncompetitive inhibitors of HNE. Using a chromogenic substrate hydrolysis assay, 14 sulfonated nonsaccharide heparin mimetics were tested for their inhibitory activity against HNE. Only 12 molecules inhibited HNE with IC50 values of 0.22-88.3 μM. The inhibition of HNE by these molecules was salt-dependent. Interestingly, a specific hexa-sulfonated molecule inhibited HNE with an IC50 value of 0.22 μM via noncompetitive mechanism, as demonstrated by Michaelis-Menten kinetics. The hexa-sulfonated derivative demonstrated at least 455-, 221-, 1590-, 21-, and 381-fold selectivity indices over other heparin-binding coagulation proteins including factors IIa, Xa, IXa, XIa, and FXIIIa, respectively. At the highest concentrations tested, the molecule also did not significantly inhibit other serine proteases of plasmin, trypsin, and chymotrypsin. Further supporting its selectivity, the molecule did not show heparin-like effects on clotting times of human plasma. The molecule also did not affect the proliferation of three cell lines at a concentration as high as 10 μM. Interestingly, the hexa-sulfonated molecule also inhibited cathepsin G with an IC50 value of 0.57 μM alluding to a dual anti-inflammatory action. A computational approach was exploited to identify putative binding site(s) for this novel class of HNE inhibitors. Overall, the reported hexa-sulfonated nonsaccharide heparin mimetic serves as a new platform to develop potent, selective, and noncompetitive inhibitors of HNE for therapeutic purposes.

Introduction

Human neutrophil elastase (HNE) is a serine protease belonging to the chymotrypsin family. It consists of a single polypeptide chain of 218 amino acids that folds into a globular glycoprotein of ∼30 kDa.[1] HNE has the classical catalytic triad of Ser195, Asp102, and His57, which facilitates its ability to degrade a host of extracellular matrix and plasma proteins. Particularly, HNE is reported to degrade collagen,[2] laminin,[3,4] fibronectin,[3] and proteoglycans.[5,6] Other HNE physiological substrates include coagulation factors, plasminogen, immunoglobulins, complement factors, and viral proteins among others.[1,5−7] HNE can also digest other proteases inside neutrophil granules as well as some protease inhibitors resulting in their activation or inactivation.[8,9]

Physiologically, the proteolytic activity of HNE is strictly controlled by several endogenous inhibitors, i.e., antiproteases such as α1-antitrypsin,[10] monocyte/HNE inhibitor,[11] elafin,[12] and secretory leukocyte protease inhibitor.[13] Yet, conditions that compromise the activity of the antiproteases, mostly genetics, can occur leading to excessive HNE activity and thus resulting in serious health problems. In fact, uncontrolled HNE activity may lead to severe cardiopulmonary diseases including chronic obstructive pulmonary disease,[14,15] cystic fibrosis,[16] bronchiectasis,[17] acute lung injury,[18] acute respiratory distress syndrome,[19] pulmonary arterial hypertension,[20] and idiopathic pulmonary fibrosis.[21] Furthermore, several studies have provided significant evidence establishing the contribution of HNE to psoriasis and inflammatory skin disease,[22−24] rheumatoid arthritis,[25] the development and the progression of cancer,[26−30] type-1 diabetes,[31] neuropathic pain,[32,33] and chronic kidney disease.[34] Moreover, Crohn’s disease, inflammatory bowel disease,[35] severe pneumonia,[36] atherosclerosis,[37] and neurological diseases[38,39] are all found to also be related to excessive HNE activity. Most recently, targeting neutrophils by HNE inhibitors has been proposed to treat acute respiratory distress syndrome in COVID-19.[40] Therefore, drugs inhibiting HNE appear to present a promising therapeutic strategy to prevent and/or treat a wide variety of cardiopulmonary and inflammatory diseases.

Despite promises, only one small-molecule HNE inhibitor is clinically available, and few others are in early clinical trials (Figure ). Sivelestat is an active site inhibitor of HNE that is parenterally used in Japan and South Korea for the treatment of acute lung injury and acute respiratory distress syndrome associated with systemic inflammatory response syndrome.[41] Importantly, the limited number of small-molecule HNE inhibitors in clinical use or under development can be partially attributed to the difficulty in designing selective active site inhibitors that can specifically modulate the activity of a multifunctional enzyme such as HNE. In addition, HNE also shares a conserved active site with several other serine proteases, which further complicates the drug design efforts. Therefore, an alternative approach to design more clinically relevant, selective HNE modulators has been proposed via targeting potential allosteric sites on HNE.[42−48]

Figure 1

Chemical structures of the only approved HNE inhibitor as well as those in advanced clinical trials, along with their IC50 values. The presented molecules are active site, competitive inhibitors.

HNE exhibits strong basic properties owing to its 19 Arg residues, which leads to an isoelectric point of ∼11.[1] The Arg residues have been proposed to form multiple potential allosteric, anion-binding sites that can be targeted by anionic molecules for HNE modulation. Previously, negatively charged molecules such as DNAs,[42] heparins,[43−46] and sulfated nonsaccharide glycosaminoglycan mimetics[47,48] have been studied in the context of allosteric modulation of HNE. While DNAs and heparins are heterogeneous polymers that limit their potential development as drugs, the sulfated nonsaccharide glycosaminoglycan mimetics appear to be under development for cystic fibrosis.[48] Susceptibility to hydrolysis by DNAse, sulfatase, and/or heparanase can also be problematic.

In this report, we present sulfonated nonsaccharide heparin mimetics as a new class of HNE inhibitors. The selection of molecules reported in this paper was based on having a bioisosteric negatively charged moiety that mimics the sulfate group of heparin and the previously reported nonsaccharide glycosaminoglycan heparin mimetics. This bioisosteric replacement offers three important advantages: (1) greater chemical stability as sulfonate cannot be removed by sulfatases or by high temperatures in nucleophilic solvents; (2) better chemical environment to form a prodrug that enhances the molecule’s bioavailability; and (3) synthetic feasibility given the commercial availability of sulfonated precursors and the less likelihood of producing partially sulfonated end products, which typically complicate the synthesis of sulfated molecules. The reported derivatives are allosteric, nonpolymeric, homogeneous, and highly water-soluble agents. The reported inhibitors do not possess functional groups that are susceptible to enzymatic hydrolysis by DNAse (phosphodiester hydrolysis), sulfatase (sulfate ester hydrolysis), or heparanase (heparin/heparan hydrolysis). In addition, the derivatives are less likely to penetrate the blood–brain barrier or placenta owing to their anionic nature, and this further improves their safety profile. Importantly, the chemical synthesis of these derivatives is well established[49−51] and is amenable to scale-up. Not only that but also strategies to design sulfonate prodrugs have been reported so as to enhance their oral bioavailability.[52,53] In particular, this work puts forward inhibitor 3 (IC50 = 220 nM) as a promising allosteric, potent, selective, and nontoxic HNE inhibitor for future development as a potential treatment for HNE-related cardiopulmonary and inflammatory diseases.

Results and Discussion

Direct Inhibition of HNE by Sulfonated Nonsaccharide Heparin Mimetics

A small library of 14 sulfonated nonsaccharide heparin mimetics (Figure ) was screened for the inhibition of HNE using the corresponding chromogenic substrate hydrolysis assay under near-physiological conditions in 4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid (HEPES) buffer at pH 7.4 and 37 °C and in the presence of 100 mM NaCl, as described earlier.[48] The molecules are structurally diverse. They belong to four chemical subclasses of diphenyl-urea derivatives (1–8), pyridoxal-phosphate derivatives (9–11), diazo-biaryl derivatives (12 and 13), and dinaphthyl-urea derivative (14). The derivatives have a different number of sulfonate groups: two (inhibitors 9–11 and 14), four (inhibitors 5, 7, 12, and 13), six (inhibitors 1–4), and eight (8). In addition to the sulfonate group, few inhibitors also have phosphonate/phosphate groups (inhibitors 6 and 9–11). All diphenyl-urea derivatives (1–8) were structurally symmetrical with either linear (unbranched) shape (1–6) or globular (branched) shape (7 and 8). The extended diphenyl-urea derivatives had long linkers (inhibitors 1–3 and 6) or short linkers (inhibitors 4 and 5).

Figure 2

Chemical structures of a small library of sulfonated nonsaccharide heparin mimetics. (A) Sulfonated diphenyl-urea derivatives (1–8); (B) sulfonated pyridoxal-phosphate derivatives (9–11); (C) sulfonated diazo-biaryl derivatives (12 and 13); and (D) sulfonated dinaphthyl-urea derivative (14). Chemical synthesis of inhibitors 1–8 was reported previously along with their characterization data.[49−51]9–14 are commercially available.

In the chromogenic substrate hydrolysis assay, the initial rate of substrate hydrolysis, as measured by absorbance at 405 nm, is indicative of the catalytic activity of HNE. The fractional decrease in the initial rate of hydrolysis in the presence of an inhibitor is analyzed using the dose–response (eq ) to calculate the potency (IC50, HS) and the efficacy (Y0, YM) parameters (see Section ). Figure shows the semilog inhibition curves observed for representative inhibitors. Only 12 sulfonated molecules inhibited HNE in a concentration-dependent fashion. Molecules 9 and 10 did not inhibit HNE at the highest concentration tested of 100 μM. The range of inhibitory potency was found to be broad (0.22–88.3 μM), while the efficacy for most inhibitors was moderate to high (>62%) (Table ).

Figure 3

Representative profiles of direct inhibition of HNE by sulfonated nonsaccharide heparin mimetics. The inhibition of HNE was measured spectrophotometrically by a chromogenic substrate (S-1384) hydrolysis assay at pH 7.4 and 37 °C. Solid lines represent sigmoidal fits to the data to obtain the values of IC50, HS, YM, and Y0 using eq , as described in Section .

Table 1

Inhibition of HNE by Sulfonated Nonsaccharide Heparin Mimeticsa

sulfonated inhibitor	IC50 (μM)	HS	ΔY (%)
1	13.4 ± 1.1b	1.8 ± 0.3	86.3 ± 2.9
2	13.7 ± 1.6	2.3 ± 0.6	84.6 ± 4.6
3	0.22 ± 0.00	2.6 ± 0.1	105.4 ± 1.0
4	33.4 ± 9.9	1.2 ± 0.5	62.7 ± 6.9
5	88.3 ± 25.1	1.2 ± 0.4	103.8 ± 13.6
6	16.6 ± 2.6	1.4 ± 0.3	95.4 ± 5.9
7	2.1 ± 0.1	2.3 ± 0.3	103.8 ± 2.7
8	4.1 ± 1.1	0.9 ± 0.3	80.2 ± 8.6
9	>100c	NAd	NA
10	>100	NA	NA
11	21.9 ± 1.9	1.7 ± 0.2	104.8 ± 4.4
12	0.54 ± 0.04	2.0 ± 0.2	97.0 ± 3.2
13	2.1 ± 0.3	1.9 ± 0.4	107.8 ± 5.3
14	24.4 ± 2.5	2.1 ± 0.4	103.8 ± 4.7

The values of IC50, HS, and ΔY were obtained following the nonlinear regression analysis of direct inhibition of human HNE in appropriate HEPES buffer of pH 7.4 at 37 °C. Inhibition was monitored by the spectrophotometric measurement of residual enzyme activity.

Errors represent ±1 SE.

Estimated values were based on the highest concentration of the inhibitor used in the experiment.

Not available.

Important structure–activity relationship aspects can be inferred from this study. First, while the sulfonate groups appear to be intrinsically essential for HNE inhibition, the number of sulfonate groups appears to be marginally critical. Although the most potent inhibitor was the hexa-sulfonated derivative 3 (IC50 = 0.22 μM), yet significant inhibition was also brought about by tetra-sulfonated derivatives 7, 12, and 13 (IC50 values are 2.1, 0.54, and 2.1 μM, respectively) and even by disulfonated derivative 14 (IC50 = 24.4 μM). Second, sulfonated diphenyl-urea derivatives with extended linkers were more potent than similar molecules with shorter linkers (inhibitors 1 and 2 were ∼2.5-fold more potent than inhibitor 4). Nevertheless, the potency of those with short linkers was enhanced through structural rigidification as in replacing the diphenyl-urea linker of inhibitors 4 and 5 with the biaryl linker of inhibitors 12 and 13. Such a modification resulted in at least a 6-fold increase in HNE inhibition potency. Third, the phosphonate group can substitute the sulfonate group while maintaining a moderate inhibition potency, as in inhibitor 6 (IC50 = 16.6 μM). Furthermore, inhibitors with globular structures appear to have better inhibition potency than the corresponding linear structures with the same number of sulfonate groups. For example, the globular tetra-sulfonated inhibitor 7 was 44-fold more potent than the linear tetra-sulfonated inhibitor 5. Finally, by comparing the inhibition potency of molecules 1 and 2 with that of inhibitor 3, it is evident that the most optimal position for the trisulfonated naphthalene-4-formamido(benzamido) substituent is the para-position relative to the urea moiety, i.e., R2-position. In fact, although all three inhibitors are hexa-sulfonated derivatives, inhibitor 3 is about 61-fold more potent than inhibitors 1 and 2. Overall, the most potent inhibitor identified in this exercise was the sulfonated molecule 3, which completely inhibited HNE with an IC50 value of 0.22 μM. In fact, molecule 3 inhibitory potential was also studied using factor IX (FIX) as a physiological substrate for HNE. Reducing sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) experiments suggested that inhibitor 3 did affect the hydrolysis of FIX by HNE (see the Supporting Information for details). This indicates that the activity of inhibitor 3 is physiologically relevant.

Effect of Salt Concentration on HNE Inhibition by Sulfonated Nonsaccharide Heparin Mimetics

To investigate the nature of HNE inhibition by these derivatives, we measured the IC50 values of two inhibitors 1 and 2 under variable salt concentrations. The rationale for choosing these two derivatives in this exercise was that they are structurally closely related. The two inhibitors possess the same number of sulfonate groups (six sulfonates as in inhibitor 3) and the same number of aromatic rings (eight rings as in inhibitor 3). In contrast to inhibitor 3, inhibitors 1 and 2 have the same substitution pattern (the sulfonated moiety is substituted at the meta-position of the central domain in Figure A, while it is at the para-position of the central domain in inhibitor 3), with only a minor structural difference (CH3 vs F). Thus, the potential inhibition potency variation, under different salt concentrations, can largely be attributed to the sulfonate groups. In addition, inhibitors 1 and 2 have moderate inhibition potencies, which would make it easier to detect distinct changes in potency. In this direction, the two derivatives exhibited moderate inhibition potencies (13.4 and 13.7 μM, respectively) toward HNE in the presence of 100 mM concentration of NaCl solution. Figure shows that decreasing the salt concentration from 100 to 0 mM gradually increased the potency of HNE inhibition by derivative 1 by ∼48-fold (13.4 μM vs 0.28 μM; Table ). Likewise, decreasing the salt concentration from 100 to 0 mM gradually increased the potency of HNE inhibition by derivative 2 by ∼51-fold (13.7 μM vs 0.27 μM; Table ). In the two cases, the efficacy of the inhibition was unaffected. Overall, the sulfonated derivatives appear to reversibly inhibit HNE primarily via electrostatic/hydrogen bond interactions, largely directed by the sulfonate groups. Conceptually, given that decreasing the salt concentration from 100 to 0 mM results in an ∼50-fold increase in the potency of linear sulfonated inhibitors having six sulfonate groups with no change in the efficacy of the inhibition; a projection can be made that the IC50 of inhibitor 3, under no salt condition, can be about 4.4 nM (220 nM/50) with ∼100% efficacy.

Figure 4

Salt-dependent direct inhibition of HNE by inhibitors 1 and 2, using the corresponding chromogenic substrate (S-1384) hydrolysis assay. Salt concentrations used are 0 μM (solid circles), 50 μM (open circles), and 100 μM (solid diamonds). Solid lines represent sigmoidal fits to the data to obtain the inhibition values using eq , as described in Section .

Table 2

Salt-Dependent Inhibition of HNE by Sulfonated Inhibitors 1 and 2a

sulfonated inhibitor	NaCl (mM)	IC50 (μM)	HS	ΔY (%)
1	0	0.28 ± 0.02b	1.4 ± 0.1	98.4 ± 2.9
	50	4.8 ± 0.4	1.3 ± 0.1	107.8 ± 2.9
	100	13.4 ± 1.1	1.8 ± 0.3	86.3 ± 2.9
2	0	0.27 ± 0.04	1.4 ± 0.2	101.1 ± 5.4
	50	3.5 ± 0.2	1.5 ± 0.1	120.2 ± 2.1
	100	13.7 ± 1.6	2.3 ± 0.6	84.6 ± 4.6

The values of IC50, HS, and ΔY were obtained following the nonlinear regression analysis of direct inhibition of human HNE in appropriate HEPES buffer of pH 7.4 at 37 °C. Inhibition was monitored by the spectrophotometric measurement of residual enzyme activity.

Errors represent ±1 SE.

Inhibition Mechanism: Michaelis–Menten Kinetics of Chromogenic Hydrolysis by HNE in the Presence of Inhibitor 3

To understand the mechanistic basis of HNE inhibition by sulfonated derivatives, the Michaelis–Menten kinetics of S-1384 hydrolysis by HNE was performed in the presence of inhibitor 3 at pH 7.4 and 37 °C. Figure shows the initial rate profiles in the presence of inhibitor 3 (0–600 nM). Each profile displays a characteristic rectangular hyperbolic trend, which could be fitted using eq to give the apparent KM and VMAX (Table ). The KM for S-1384 did not significantly change (0.25 ± 0.044–0.23 ± 0.035 mM) in the presence or absence of inhibitor 3. However, the VMAX decreased from 37.8 ± 2.16 mAU/min in the absence of inhibitor 3 to 6.13 ± 0.30 mAU/min at 600 nM of inhibitor 3. Thus, the inhibitor appears to bring about structural changes in the active site of HNE, which do not affect the formation of the Michaelis complex but lead to a significant disruption in the HNE catalytic activity. This indicates that inhibitor 3 is an allosteric inhibitor of HNE.

Figure 5

Michaelis–Menten kinetics of S-1384 hydrolysis by HNE in the presence of inhibitor 3. The initial rate of hydrolysis at various substrate concentrations was measured in pH 7.4 buffer as described in Section using HNE. The concentrations of inhibitor 3 chosen in the study were 0 nM (solid squares), 100 nM (open circles), 200 nM (solid diamonds), 300 nM (open triangles), 400 nM (solid circles), and 600 nM (open squares). Solid lines represent nonlinear regressional fits to the data by the Michaelis–Menten equation (eq ).

Table 3

Michaelis–Menten Kinetics of Chromogenic Substrate Hydrolysis by HNE in the Presence of Inhibitor 3a

[3] (nM)	KM (μM)	VMAX (mAU/min)
0	250 ± 43.5b	37.8 ± 2.16
100	249 ± 38.6	30.6 ± 1.56
200	262 ± 33.4	29.9 ± 1.28
300	216 ± 55.1	21.5 ± 1.72
400	250 ± 31.7	18.3 ± 0.77
600	225 ± 34.5	6.13 ± 0.30

KM and VMAX values of the chromogenic substrate hydrolysis by HNE were measured as described in Section . mAU indicates milliabsorbance units.

Error represents ±1 SE.

Selectivity Studies: Inhibition of Heparin-Binding, Coagulation Proteins by Molecules 3 and 12

To determine the selectivity of this class of HNE inhibitors over heparin-binding, coagulation serine proteases, we have chosen the two most potent inhibitors 3 (0.22 μM) and 12 (0.54 μM) identified in this study. The activity of inhibitors 3 and 12 toward factors IIa (also known as thrombin), Xa, IXa, and XIa was studied using the corresponding chromogenic substrate hydrolysis assays under physiological conditions, as described earlier.[54−57] In these assays, the inhibition potential was determined by spectrophotometric measurement of the residual protease activity in the presence of varying concentrations of inhibitors 3 and 12 (Figure ). Furthermore, the molecules’ activity against human FXIIIa was also studied using the bisubstrate, fluorescence-based trans-glutamination assay, as described earlier.[54,55] Based on the highest concentration tested of inhibitor 3 against the above enzymes, the calculated IC50 values were measured to be >100 μM for thrombin, ∼49 μM for FXa, >350 μM for FIXa, ∼5 μM for FXIa, and ∼84 μM for FXIIIa (Table ), suggesting selectivity indices of >455-, 223-, >1590-, 23-, and 382-fold, respectively. In contrast, the calculated IC50 values of inhibitor 12 were measured to be ∼8 μM for thrombin, ∼13 μM for FXa, ∼1 μM for FXIa, and ∼6 μM for FXIIIa (Table ), suggesting a lack of substantial selectivity. Overall, the above results indicate that inhibitor 3 is a selective inhibitor of HNE over heparin-binding, coagulation proteins, as determined by the corresponding in vitro assays. In fact, the observed selectivity of inhibitor 3 highlights the significance of the flexibility of diphenyl-urea linker over the rigid biaryl linker in inhibitor 12.

Figure 6

Direct inhibition of heparin-binding, coagulation proteins by inhibitors 3 and 12. The inhibition of HNE (solid circles), FXIa (open circles), FXIIIa (solid diamonds), FXa (open diamonds), and thrombin (solid triangles) by 3 and 12 was studied as described in Section . Solid lines represent sigmoidal dose–response fits (eq ) to the data to obtain the values of IC50, ΔY, and HS.

Table 4

Inhibition of Heparin-Binding, Coagulation Serine Proteases by Molecules 3 and 12a

inhibitor	inhibition parameters	neutrophil elastase	thrombin	factor Xa	factor IXa	factor XIa	factor XIIIa
3	IC50 (μM)	0.22 ± 0.00b	>100	48.6 ± 14.8	>350	4.6 ± 0.4	83.9 ± 27.6
	HS	2.6 ± 0.1	ND	1.8 ± 1.0	NDc	2.3 ± 0.4	1.5 ± 0.8
	ΔY (%)	105.4 ± 1.0	ND	83.3 ± 15.0	ND	101.8 ± 4.0	90.7 ± 15.2
12	IC50 (μM)	0.54 ± 0.04	8.2 ± 1.3	12.7 ± 0.7	ND	1.2 ± 0.1	5.7 ± 1.8
	HS	2.0 ± 0.2	2.6 ± 1.0	1.9 ± 0.2	ND	1.9 ± 0.3	1.5 ± 0.6
	ΔY (%)	97.0 ± 3.2	62.1 ± 4.9	80.0 ± 2.0	ND	104.0 ± 3.0	84.5 ± 8.8

The values of IC50, HS, and ΔY were obtained following the nonlinear regression analysis of direct inhibition of human enzymes in appropriate buffer of pH 7.4 at 25–37 °C.

Errors represent ±1 SE.

Not determined.

Selectivity Studies: Inhibition of Inflammatory, Digestive, and Fibrinolysis Serine Proteases by Molecule 3

To further determine the selectivity of inhibitor 3, we measured its inhibitory potential toward other serine proteases important for inflammation (cathepsin G and proteinase 3), digestion (trypsin and chymotrypsin), and fibrinolysis (plasmin) using the corresponding chromogenic substrate hydrolysis assays, as described earlier.[48,54−57] In these assays, the inhibition potential was determined by spectrophotometric measurement of the residual protease activity in the presence of varying concentrations of inhibitor 3. Interestingly, the molecule potently inhibited cathepsin G with an IC50 value of ∼0.57 ± 0.05 μM and marginally inhibited proteinase 3 with an IC50 value of 34.2 ± 12.7 μM (Figure and Table ). Nevertheless, the molecule demonstrated at least 818-fold selectivity over trypsin, chymotrypsin, and plasmin (Table ). Overall, the above results reveal that inhibitor 3 potently and selectively targets inflammatory serine proteases of HNE and cathepsin G and, to a lesser extent, proteinase 3, as determined by the corresponding in vitro assays.

Figure 7

Direct inhibition of inflammatory serine proteases by inhibitor 3. The inhibition of HNE (solid circles), CG (cathepsin G; open diamonds), and P3 (proteinase 3; solid triangles) by 3 was studied as described in Section . Solid lines represent sigmoidal dose–response fits (eq ) to the data to obtain the values of IC50, ΔY, and HS.

Table 5

Inhibition of Inflammatory, Digestive, and Fibrinolysis Serine Proteases by Inhibitor 3a

inhibitor	inhibition parameters	neutrophil elastase	cathepsin G	proteinase 3	plasmin	trypsin	chymotrypsin
3	IC50 (μM)	0.22 ± 0.00b	0.57 ± 0.05	34.2 ± 12.7	>180	>180	>180
	HS	2.6 ± 0.1	1.8 ± 0.3	0.8 ± 0.2	NDc	ND	ND
	ΔY (%)	105.4 ± 1.0	89.7 ± 2.9	49.2 ± 8.0	ND	ND	ND

The values of IC50, HS, and ΔY were obtained following the nonlinear regression analysis of direct inhibition of human enzymes in appropriate buffer of pH 7.4 at 25–37 °C.

Errors represent ±1 SE.

Not determined.

Effects of Inhibitor 3 on Human Plasma Coagulation and Cell Proliferation

To further evaluate the selectivity as well as the antiproliferative properties of inhibitor 3, we studied its effects on the clotting times of normal human plasma as well as its effects on the proliferation of three cell lines. On the one hand, the inhibitor’s effects on activated partial thromboplastin time (APTT) and prothrombin time (PT) were measured, as described earlier under in vitro conditions,[54−57] using variable concentrations (0–550 μM) (Figure A). Results indicated that the inhibitor’s concentrations estimated to double APTT or PT are >430 or >470 μM (∼2000-fold of the IC50), respectively, suggesting the lack of a significant effect on heparin-binding coagulation proteins such as thrombin, FXa, FIXa, FXIa, and antithrombin. On the other hand, the antiproliferative properties of the inhibitor were evaluated in three cell lines of breast (MCF-7), intestine (CaCo-2), and kidney (HEK-293) (Figure B), as described earlier.[58,59] Similar to testing in human plasma, results indicated that 10 μM of the inhibitor (45-fold of the IC50) does not significantly affect the proliferation of the above cell lines. Together, inhibitor 3 appears to exhibit significant selectivity indices over other heparin-binding proteins in human plasma and it is not associated with cellular toxicity at the highest concentration tested of 10 μM. Overall, inhibitor 3 can be considered for further development as a potent, selective, and nontoxic inhibitor of HNE.

Figure 8

(A) Effects of inhibitor 3 on human plasma clotting times as determined in APTT and PT assays. (B) Effects of inhibitor 3 on the cell viability of three cell lines: breast (MCF-7), kidney (HEK-293), and intestine (CaCo-2).

Molecular Modeling Studies

To identify a plausible binding mode for inhibitor 3 on HNE, we performed molecular docking studies, as described in the experimental part, by considering two clamp-like regions of Arg clusters at the ends of the interdomain crevice: a top clamp region (Arg129, Arg147, Arg177, Arg178, and Arg217) and a bottom clamp region (Arg36, Arg65, Arg75, Arg76, and Arg80) (Figure A).[60] The inhibitor was found to reasonably fit into the two proposed regions (Figure B,C). In fact, inhibitor 3 has shown multiple salt bridge, H-bond, and π–cation interactions with basic and nonbasic amino acid residues in the two sites, as depicted in Figure D,E. In particular, four sulfonate groups of inhibitor 3 appear to interact with Arg129, Arg147, Arg178, and Gly219 in the top clamp region. Asn99 and Arg177 also appear to be important in this region. Likewise, the four sulfonate groups also appear to interact with Arg21, Val82, Thr113, and Ser153 in the bottom clamp region. Gly38, Arg80, and Gly150 also appear to be important in this region. Although we report no mutagenesis studies or X-ray crystallography results, binding in the bottom clamp region is more likely. In this region, the inhibitor appears to recognize Gly38, Arg80, Gly150, and Ser153 residues, which were previously implicated in interactions with other glycosaminoglycan mimetics as well as DNA.[48] Conceptually, considering the results of the above molecular modeling studies, we should theoretically be able to design a tetra-sulfonated HNE inhibitor and maintain high potency and efficacy. This should further facilitate aspects related to pharmaceutical formulation.

Figure 9

(A) Cartoon representation of HNE showing the Arg residues of two potential anion-binding sites: top clamp and bottom clamp as well as the catalytic triad residues of the active site. (B) Cartoon representation of inhibitor 3 being docked into the top clamp residues (−7.321 kcal/mol). (C) Cartoon representation of inhibitor 3 being docked into the bottom clamp residues (−7.11 kcal/mol). The inhibitor is represented as spheres in which carbon atoms are depicted in green spheres, sulfur atoms are depicted in yellow spheres, nitrogen atoms are depicted in blue spheres, and oxygen atoms are depicted in red spheres. (D, E) Two-dimensional representations of inhibitor 3′s interactions with the two putative Arg-rich binding sites.

Conclusions

In this work, we identified a potent, selective, allosteric, sulfonated, and nonsaccharide heparin mimetic inhibitor of HNE. Inhibitor 3 can be potentially developed as a treatment for HNE-related cardiopulmonary and inflammatory diseases. Inhibitor 3 offers several advantages: (1) it is a homogeneous molecule that does not possess functional groups that are susceptible to enzymatic hydrolysis by DNAse, sulfatase, or heparanase; (2) it can be developed as a prodrug using reported strategies so as to enhance its oral bioavailability; (3) it is less likely to penetrate the blood–brain barrier or placenta owing to its anionic nature, and this further improves its safety profile; (4) it does not significantly affect coagulation proteases, and thus, no bleeding complication is expected; (5) it does not affect the viability of various cell lines suggesting a high margin of safety; and (6) inhibitor 3 also inhibits cathepsin G and, to a lesser extent, proteinase 3, suggesting a potential additional benefit in treating inflammatory conditions. In fact, cathepsin G is known to be significantly upregulated in the pathogenesis of lung inflammatory conditions.[61] It is one of the neutrophil serine proteases, the excessive activity of which leads to chronic inflammatory lung diseases.[47] Thus, the dual inhibition phenomenon demonstrated by inhibitor 3 is expected to be useful in inflammatory conditions such as cystic fibrosis.[47,48]

Given the presented findings, inhibitor 3 will be tested in appropriate in vivo models of cardiopulmonary diseases or inflammation diseases, and results will be reported in due time. As mentioned in Section , the diseases that may benefit from HNE inhibitors include cystic fibrosis, acute lung injury, acute respiratory distress syndrome, idiopathic pulmonary fibrosis, severe pneumonia, chronic kidney diseases, Crohn’s diseases, and psoriasis, among others.

Materials and Methods

Chemicals, Reagents, Enzymes, and Substrates

Inhibitors 1–8 were synthesized following the modified version of previously reported protocols.[49−51] The modifications were in the steps involving generating and isolating the corresponding pure sodium salts. Particularly, the pure sodium salts were generated using SP Sephadex-Na cation-exchange chromatography followed by Sephadex G10 size exclusion chromatography. Final products were retrieved after the overnight drying process using a Labconco Benchtop Freeze Dryer (Fort Scott, KS). The inhibitors were characterized by nuclear magnetic resonance (NMR), and the corresponding chemical shifts were found to be identical to reported values.[49−51] Inhibitors 9–11 were purchased from Santa Cruz Biotechnology (Dallas, TX). Inhibitors 12–14 were purchased from Sigma-Aldrich (St. Louis, MO). The purity of all molecules was >95%.

For the enzyme kinetics studies, HNE was obtained from Elastin Products Company (Owensville, MO). Human plasma proteins including thrombin (or FIIa), FXa, FIXa, FXIa, FXIIIa, and plasmin were obtained from Haematologic Technologies (Essex Junction, VT). Bovine α-chymotrypsin and bovine trypsin were obtained from Sigma-Aldrich (St. Louis, MO). Cathepsin G and proteinase 3 were obtained from Fisher Scientific (Pittsburgh, PA). The chromogenic substrates N-succinyl-Ala-Ala-Val-p-nitroanilide (S-1384) for HNE, N-succinyl-Ala-Ala-Pro-Phe-p-nitroanilide (S7388) for cathepsin G, N-methoxysuccinyl-Ala-Ala-Pro-Val-p-nitroanilide (M4765) for proteinase 3, and N-succinyl Ala-Ala-Pro-Phe-p-nitroanilide were from Sigma-Aldrich. Other chromogenic substrates including spectrozyme TH, spectrozyme FXa, spectrozyme FIXa, and spectrozyme PL were obtained from Biomedica Diagnostics (Windsor, NS, Canada). FXIa chromogenic substrate (S-2366) and trypsin chromogenic substrate (S-2222) were obtained from Diapharma (West Chester, OH). N,N-Dimethylcasein, dansylcadaverine, and dithiothreitol (DTT) were also from Sigma-Aldrich. Stock solutions of HNE were prepared by reconstituting 1 mg with 100 μL of 1:1 glycerol/200 mM sodium acetate buffer, pH 5, which was then diluted using HEPES buffer, pH 7.4, containing 125 mM HEPES, 0.125% Triton-X 100, and 100 mM NaCl. Stock solutions of thrombin, FXIa, cathepsin G, proteinase 3, plasmin, trypsin, and chymotrypsin were all prepared in 50 mM Tris–HCl buffer, pH 7.4, containing 150 mM NaCl, 0.1% PEG8000, and 0.02% Tween80. Stock solution of FIXa was prepared in 20 mM Tris–HCl buffer, pH 7.4, containing 100 mM NaCl, 2.5 mM CaCl2, 0.1% PEG8000, 0.02% Tween80, and 33% v/v ethylene glycol. Stock solution of FXa was prepared in 20 mM Tris–HCl buffer, pH 7.4, containing 100 mM NaCl, 2.5 mM CaCl2, 0.1% PEG8000, and 0.02% Tween80. Stock solution of FXIIIa was prepared in 50 mM Tris–HCl, 1 mM CaCl2, 100 mM NaCl, 0.1% PEG8000, 0.02% Tween80, and 2 mg/mL N,N-dimethylcasein.

For the clotting assays, pooled normal human plasma for coagulation assays was purchased from George King Bio-Medica (Overland Park, KS). The activated partial thromboplastin time reagent containing ellagic acid, thromboplastin-D (PT reagent), and 25 mM solution of CaCl2 was purchased from Thermo Fisher Scientific (Waltham, MA). All experiments in this paper were repeated at least two times.

Direct Inhibition of HNE by Sulfonated Nonsaccharide Heparin Mimetics

A library of 14 heparin-like, sulfonated molecules was screened for the inhibition of HNE using a chromogenic substrate (S-1384) hydrolysis assay in a 96-well plate format, as described earlier.[48] Briefly, each well of the 96-well microplate contained 92 μL of pH 7.4 HEPES buffer (0, 50, or 100 mM NaCl), to which 1 μL of potential HNE inhibitor (or solvent reference) and 4 μL of HNE (80 nM in the well) were sequentially added. After 5 min of incubation, 3 μL of S-1384 (750 μM in the well) was rapidly added and the residual HNE activity was measured from the initial rate of increase in absorbance at 405 nm (at 37 °C). Stocks of potential HNE inhibitors were serially diluted to generate 6–12 different concentrations. The relative residual HNE activity at each concentration of the inhibitor was calculated from the ratio of the HNE activity in the presence and absence of the inhibitor. Logistic equation (eq ) was used to fit the inhibitor concentration vs the residual HNE activity curve (dose–response curve), so as to obtain the potency (IC50) and efficacy (ΔY) of inhibitionIn this equation, Y is the ratio of the residual HNE activity in the presence of the inhibitor to that in its absence (fractional residual activity), YM and Y0 are the maximum and minimum possible values of the fractional residual HNE activity, respectively, IC50 is the concentration of the inhibitor that results in 50% inhibition of enzyme activity, and HS is the Hill slope. Nonlinear curve fitting resulted in YM, Y0, IC50, and HS values. The positive control used in the HNE chromogenic assay was UFH. Its IC50 value, under similar testing condition, is 0.04 ± 0.01 μM.[62]

Michaelis–Menten Kinetics of Chromogenic Hydrolysis by HNE in the Presence of Inhibitor 3

The initial rate of S-1384 hydrolysis by HNE was obtained from the linear increase in the absorbance at 405 nm, as reported previously.[48] The initial rate was measured as a function of various concentrations of the substrate (0.0–1.25 mM) in the presence of a fixed concentration of HNE inhibitor 3 in HEPES buffer, pH 7.4, containing 100 mM NaCl, 0.1% PEG8000, and 0.02% Tween80 at 37 °C. The inhibitor’s concentrations used were 0, 100, 200, 300, 400, and 600 nM. The data was fitted using the standard Michaelis–Menten equation (eq ) to determine the KM and VMAX

Inhibition of Related Heparin-Binding Proteins by Inhibitors 3 and 12

The inhibition potential of inhibitors 3 and 12 against human thrombin, FXa, FIXa, and FXIa was evaluated using chromogenic substrate hydrolysis assays as well as against human FXIIIa using a bisubstrate fluorescence-based trans-glutamination assay, as reported in the literature under physiological conditions.[55−57] The inhibitory potentials of molecule 3 were also evaluated against inflammatory proteases (cathepsin G and proteinase 3), fibrinolytic protease (plasmin), and digestive proteases (trypsin and chymotrypsin) using the corresponding chromogenic substrate hydrolysis assays, as reported earlier.[48,55−57] These assays were performed using substrates and conditions appropriate for the enzyme under investigation. At least six serially diluted concentrations of inhibitors 3 or 12 were exploited, and the fractional residual enzyme activity was measured at each concentration. The inhibition profile was determined over a range of inhibitor concentrations to determine the IC50, HS, and ΔY. The concentrations of enzymes and substrates in microplate cells were identical to those reported in our previous studies.[48,55−57]

In the chromogenic hydrolysis assay, each well of the 96-well microplate generally contained 85 (FXIa, plasmin, and FIXa) or 185 μL (thrombin, FXa, cathepsin G, proteinase 3, trypsin, and chymotrypsin) of Tris–HCl pH 7.4 buffer to which 5 μL of HNE inhibitor (or solvent reference) and 5 μL of enzyme were sequentially added. After 5–10 min of incubation, 5 μL of the chromogenic substrate was rapidly added and the residual enzyme activity was measured from the initial rate of increase in absorbance at 405 nm. The buffer of FIXa also contained 33% ethylene glycol. In the FXIIIa assay, 1 μL of inhibitor 3 or inhibitor 12 was diluted with 87 μL of Tris–HCl pH 7.4 buffer and 5 μL of DTT (20 mM) at 37 °C followed by the addition of 2 μL of FXIIIa (0.3 μM) and incubation for 10 min. The activity of FXIIIa was evaluated by the addition of 5 μL of dansylcadaverine (2 mM) and measuring the initial rate of increase in fluorescence emission (λex = 360 nm and λem = 490 nm). In the above assays, the dose dependence of the fractional residual enzyme activity at each concentration of inhibitor 3 or inhibitor 12 was analyzed using eq to obtain the apparent concentration of the HNE inhibitor required to reduce enzyme activity to 50% of its initial value.

Human Plasma Coagulation Studies

Clotting time was measured in a standard one-stage recalcification assay with a BBL Fibrosystem fibrometer (Becton–Dickinson, Sparles, MD), as reported previously.[54,55] In the PT assay, thromboplastin-D was reconstituted according to the manufacturer’s directions and warmed to 37 °C. A 10 μL amount of inhibitor 3, to give the desired concentration, was brought up to 100 μL with citrated human plasma, incubated for 30 s at 37 °C followed by the addition of 200 μL of prewarmed thromboplastin-D, and the time to clot was recorded. In the APTT assay, 10 μL of the same inhibitor was mixed with 90 μL of citrated human plasma and 100 μL of prewarmed APTT reagent (0.2% ellagic acid). After incubation for 4 min at 37 °C, clotting was initiated by adding 100 μL of prewarmed 0.025 M CaCl2, and the time to clot was noted. The data were fit to a quadratic trend line, which was used to determine the concentration of the inhibitor necessary to double the clotting time. Clotting time in the absence of inhibitor 3 was determined in a similar fashion using 10 μL of deionized water and was found to be 15.9 s for PT and 31.9 s for APTT.

Effect of Inhibitor 3 on Cellular Proliferation: Toxicity Studies

MCF-7 human breast carcinoma cells,[63] HEK-293 human embryonic kidney cells,[64] and CaCo-2 heterogeneous human epithelial colorectal adenocarcinoma cells[65] were maintained as previously described.[58,59] The test was done by the cellular and molecular biology core of the Xavier University of Louisiana’s Research Centers in Minority Institutions Program using a modified procedure in which Alamar Blue (resazurin) fluorescent dye was used.[58,59] Briefly, MCF-7, HEK-293, and CaCo-2 cells were seeded in a 96-well plate at an optimized concentration to allow them to be in the log growth phase. Each cell line was individually optimized. The number of cells was determined by adding Alamar Blue dye, incubating for 2 h at 37 °C, and then reading the plate in a fluorescent reader with λex of 560 nm and λem of 590 nm on the Synergy H1 multiplate reader (BioTek, Winooski, VT). The lids were always kept on the plates during this experiment as the cells need to be kept sterile for the remainder of the experiment. The number of cells was determined in the absence and the presence of inhibitor 3 (10 μM), which was incubated with the cells for 3 days. Distilled water control was included in each assay to ensure that the effect observed was due to the molecule and was not because of apoptotic/necrotic effects of the vehicle. The experiments were repeated four times to determine the corresponding standard deviations.

Potential Binding Sites for Inhibitor 3: Molecular Modeling Studies

All molecular docking studies were carried out using Glide of Schrodinger Suite 2017-1.[66] The structure file for HNE was retrieved from the Protein Data Bank (PDB ID: 1HNE).[67] The protein structure was prepared by removing the crystallographic water molecules and the associated ligand and by adding hydrogen atoms consistent with the physiologic pH of 7 using Maestro 11.1 of the Schrodinger Suite. The protein molecule was then energy-minimized with a root-mean-square deviation (RMSD) cutoff value of 0.3 Å for all heavy atoms. The initial structure for inhibitor 3 was built and energy-minimized using the Schrodinger Suite. The HNE protein was shown to have two clamp-like regions of Arg clusters at the ends of the interdomain crevice (elastase fold): a top clamp region (Arg177, Arg178, and Arg217) and a bottom clamp region (Arg36, Arg65, Arg75, and Arg76).[60] Two ligand binding sites were considered in this study. The top clamp region and the bottom clamp region were separately specified as the two binding sites for inhibitor 3. The receptor grids for the target protein were generated using the OPLS3 force field.[68] The grid center for each binding site was set to be the centroid of the top clamp and the bottom clamp Arg clusters, with a cubic grid box of 10 Å on each side. No constraints were applied for the receptor grid generations. The docking calculations were done using the default parameters under the stand precision mode. All of the poses were subjected to postdocking minimization. The best-docked structure based on the docking score was selected for further analysis of potential HNE inhibitor 3 interactions.