Tailored Ahp‐cyclodepsipeptides as Potent Non‐covalent Serine Protease Inhibitors

Abstract

The S1 serine protease family is one of the largest and most biologically important protease families.D espite their biomedical significance,g eneric approaches to generate potent, class-specific, bioactive non-covalent inhibitors for these enzymes are still limited. In this work, we demonstrate that Ahp-cyclodepsipeptides represent as uitable scaffold for generating target-tailored inhibitors of serine proteases.F or efficient synthetic access,wedeveloped apractical mixed solidand solution-phase synthesis that we validated through performing the first chemical synthesis of the two natural products Tasipeptin Aand B. The suitability of the Ahp-cyclodepsipeptide scaffold for tailored inhibitor synthesis is showcased by the generation of the most potent human HTRA protease inhibitors to date.W ea nticipate that our approach maya lso be applied to other serine proteases,thus opening new avenues for asystematic discovery of serine protease inhibitors.Serine proteases of the S1 family (trypsin/chymotrypsinlike) are one of the largest and biomedically relevant protease families.[1] In contrast to the design of covalent inhibitors or activity-based probes for this enzyme class, [2] generic approaches for designing potent, enzyme-class-specific,c ellactive,and non-covalent small-molecule inhibitors are highly limited and have been achieved only for distinct serine proteases.[3] Consequently,a lternative approaches for the systematic generation of such chemical probes are urgently required.Ahp-cyclodepsipeptides (also termed cyanopeptolins or peptolides) are aclass of over 100 peptidic natural products of non-ribosomal origin that display potent inhibitory properties against serine proteases.[4] All Ahp-cyclodepsipeptides are containing an Ahp (3-amino-6-hydroxy-2-piperidone) unit and an N-methyl aromatic amino acid at conserved positions in their 19-membered ring structure,while other residues are much less conserved (Figure 1a). Crystal structures of Ahpcyclodepsipeptides in complex with serine proteases indicate that inhibition is based on as ubstrate-like binding mode in which distinct amino acid residues occupy the S-and S'-pockets,h owever,p roteolytic cleavage does not occur (Figure 1b,S chechter and Berger nomenclature is used).[5] Accordingly,t hey act in as imilar manner to proteinaceous canonical serine protease inhibitors,w ith the conserved residues stabilizing the inhibitory fold, while the other less conserved residues define serine protease selectivity through optimal accommodation to the specific Sa nd S'-sites.T his suggests that Ahp-cyclodepsipeptides may represent as uit- Figure 1. Structural features and determinants of Ahp-cyclodepsipeptides for serine protease inhibition. a) Chemicals tructures of the natural product Ahp-cyclodepsipeptides TasA (1)a nd TasB (2). The red color indicates strictly conserved residues found in all so far known Ahp-cyclodepsipeptides; residues only rarely modified in Ahp-cyclodepsipeptides are depicted in green, and fully variable residues in blue. Note that th...

Structural Diversity and Anticancer Activity of Marine‐Derived Elastase Inhibitors: Key Features and Mechanisms Mediating the Antimetastatic Effects in Invasive Breast Cancer

“…As the IC 50 value for a covalent inhibitor would vary depending on pre‐incubation time with the enzyme, we also obtained the progress curve of HNE treated with sivelestat without the pre‐incubation step (Figure S1). With regard to the mode of inhibition of the Ahp‐containing depsipeptides, prior studies and X‐ray co‐crystallization data of another Ahp‐containing elastase inhibitor, lyngbyastatin 7, did not show covalent bond formation between the Abu moiety and HNE . In all subsequent biological and molecular studies, we focused on 3 , which was isolated in higher yield compared to 1 and 2 , to allow rigorous biological evaluation.…”

“…We previously investigated the cellular effects of Ahp‐containing cyanobacterial cyclodepsipeptides on bronchial epithelial cells for treating inflammatory conditions in respiratory diseases and subsequently reported a total synthesis strategy to enable further biological studies and catalyze the development of these compounds . Others have also developed and reported synthetic approaches of tailored Ahp‐cyclodepsipeptide, further supporting that this scaffold is a promising starting structure for the generation of customized serine protease inhibitors . However, there are no rigorous studies describing the cellular effects of these compounds in cancer.…”

Synthesis of New Cyclomarin Derivatives and Their Biological Evaluation towards Mycobacterium Tuberculosis and Plasmodium Falciparum

“…Inspired by Kaiser et al. we started the fragment synthesis with protected glutamic acid 15 , which was first activated as mixed anhydride and then reduced by NaBH 4 (Scheme ) . Masking the resulting alcohol as TBS ether yielded 16 , subsequent saponification and N‐methylation generated N ‐methyl‐δ‐hydroxy norvaline 18 almost quantitatively on a gram scale.…”

Solid-state conformations of linear depsipeptide amides with an alternating sequence of α,α-disubstituted α-amino acid and α-hydroxy acid

“…In particular, cyclic depsipeptides are still of broad chemical, biological and medicinal interest, which is reflected in a large number of recent review articles [e.g. structure and isolation (Wang et al, 2018;Ding et al, 2016;Tarsis et al, 2015;Pelay-Gimeno et al, 2013), synthesis (Kö cher et al, 2017;Qi et al, 2016;Boecker et al, 2016;Weiss et al, 2013;Xu et al, 2013) and biological activity (Wang et al, 2018;Weiss et al, 2017;Kitagaki et al, 2015;Sivanathan & Scherkenbeck, 2014;Smelcerovic et al, 2014)]. Their general structures can be assigned to different classes, containing, besides -amino acids, a simple hydroxy acid, like in solonamide A (Kitir et al 2014), or a complex hydroxy acid, as in calcaripeptide A (Silber et al, 2013), being characterized by a head-to-side-chain lactonization, as in kahalalide A (Bourel-Bonnet et al, 2005), or with an alternating sequence of -amino and -hydroxy acids.…”