Halogen bonding for the design of inhibitors by targeting the S1 pocket of serine proteases

Abstract

Halogen bonding (or X bonding) has attracted increasing interest due to its significant role in molecular recognition in biological systems. Trypsin-like serine proteases have many physiological and pathophysiological functions. There is therefore extensive interest in generating specific inhibitors for pharmacological intervention in their enzymatic activity. We study here if it is possible to use halogenated compounds as the P1 group to bind to the S1 specificity pocket of trypsin-like serine proteases to avoid the low bioavailability of the amidine or guanidine P1 group that is typically used in many inhibitors. We used 4-chlorobenzylamine (ClBA), 4-bromobenzylamine (BrBA) and 4-iodobenzylamine (IBA) as probes to test their binding modes to a trypsin-like serine protease, urokinasetype plasminogen activator (uPA), which has been recognized as a marker for breast cancer and an important target for inhibitor development. The results showed that these compounds inhibited uPA with stronger efficacies compared with their non-halogenated analogues. We also determined the highresolution crystal structures of uPA in complex with BrBA and IBA, respectively. The structures revealed that BrBA bound to the S1 pocket of uPA via halogen bonds, but IBA did not make halogen bonds with uPA, demonstrating that the iodine may not be the best choice as a target moiety for serine proteases.These results advocate halogen bonding, especially bromine bonding, as an efficient strategy for the future design of novel inhibitors against trypsin-like serine proteases to provide strong potency and promote bioavailability.

Green by Design: Convergent Synthesis, Computational Analyses, and Activity Evaluation of New FXa Inhibitors Bearing Peptide Triazole Linking Units

“…In addition, the presence of Br in compound 8p in the p position of the phenyl ring establishes a halogen-π interaction with the Tyr228 residue (3.74 Å) located on one side of the S1 pocket (Figure 4d). The halogen-π interaction has been described for some FXa inhibitors already, such as the anticoagulant rivaroxaban, featuring Cl and Br atoms in their structure [18,43]. The specific alignment of rivaroxaban in the active site allows for the chlorine on the thiophene moiety to interact with the Tyr228 residue in the S1 pocket, mainly through noncovalent halogen-π interactions.…”

“…However, the developed class of compounds was later replaced due to their low bioavailability and inadequate pharmacokinetics [17]. The current strategy uses several types of specific interactions for the design of neutral groups with high affinities to the S1, e.g., halogen bonding, which has been described as essential in FXa inhibitors displaying a halo-aryl group [18][19][20]. For example, the structure of the FXa-rivaroxaban complex revealed a halogen-π interaction between the chlorine of the thiophene group, and the Tyr228 residue located in the lower part of the S1 pocket (Figure 1b, highlighted in blue).…”

Urokinase plasminogen activator as an anti-metastasis target: inhibitor design principles, recent amiloride derivatives, and issues with human/mouse species selectivity

“…4-Bromobenzylamine 26 is a weak inhibitor of uPA (Ki 1.28 mM), however, its uPA X-ray co-crystal (PDB 5YC6; 1.18 Å) revealed that this simple compound buries deeply into the S1 pocket and forms a non-covalent halogen bond between the electron-withdrawing bromine atom and the electron-rich Asp189. The bromine atom also made two interactions with the backbone carbonyl and side chain hydroxyl of Ser190, and van der Waals interactions were seen between its phenyl group and Ser190, Cys191, Gln192, Trp215, Gly216 and Arg217 (Jiang et al 2018).…”

1′-Acetoxychavicol Acetate from Alpinia galanga Represses Proliferation and Invasion, and Induces Apoptosis via HER2-signaling in Endocrine-Resistant Breast Cancer Cells

“…The crystal structures of HER2 Kinase Domain Complexed with TAK-285 (PDB ID: 3RCD [39]), AKT1 (PDB ID: 4GV1 [40]), ERK2 (PDB ID: 5NHJ [41]), estrogen receptor (PDB ID: 3ERT [42]), uPA (PDB ID: 5YC7 [43]), CDK6 (PDB ID: 1XO2 [44]), and FGF2 (PDB ID: 1FQ9 [45]) were obtained from Protein Data Bank. The 3-dimensional structure of all the studied ligands were built and fully optimized by the HF/6-31(d) level of theory using Gaussian09 program [46].…”