Thermal proteome profiling reveals insight to antiproliferative and pro-apoptotic effects of Lagunamide A in the modulation of DNA damage repair.

Lagunamide A is a biologically active natural product with a yet unidentified molecular mode of action. Cellular studies revealed that lagunamide A is a potent inhibitor of cancer cell proliferation, promotes apoptosis and causes mitochondrial dysfunction. To decipher the cellular mechanism responsible for these effects, we utilized thermal protein profiling (TPP) and identified EYA3 as a stabilized protein in cells upon lagunamide A treatment. EYA3, involved in the DNA damage repair process, was functionally investigated via siRNA based knockdown studies and corresponding effects of lagunamide A on DNA repair were confirmed. Furthermore, we showed that lagunamide A sensitized tumor cells to treatment with the drug doxorubicin highlighting a putative therapeutic strategy.

Chemical Ligation-Mediated Total Synthesis of Corramycin.

The ligation-mediated total synthesis of corramycin, a myxobacterial natural product of the strain Corallococcus coralloides, is presented. The synthetic strategy included using two consecutive chemical ligations for a modular and efficient preparation. Finally, the synthesis employed a Ser/Thr ligation (STL) at a new ligation site combined with classical fragment coupling. This study provides the total synthesis of corramycin and enhances the preparative toolbox of STL in organic synthesis.

Synthesis and Late-Stage Modification of (-)-Doliculide Derivatives Using Matteson's Homologation Approach.

(-)-Doliculide, a marine cyclodepsipeptide derived from the Japanese sea hare, Dolabella auricularia, exhibits potent cytotoxic properties, sparking interest in the field of synthetic chemistry. It is comprised of a peptide segment and a polyketide moiety, rendering it amenable to Matteson's homologation methodology. This technique facilitates the diversification of the distinctive polyketide side chain, thereby permitting the introduction of functional groups in late stages for modifications of the derived compounds and studies on structure-activity relationships.

Homo-BacPROTAC-induced degradation of ClpC1 as a strategy against drug-resistant mycobacteria.

Antimicrobial resistance is a global health threat that requires the development of new treatment concepts. These should not only overcome existing resistance but be designed to slow down the emergence of new resistance mechanisms. Targeted protein degradation, whereby a drug redirects cellular proteolytic machinery towards degrading a specific target, is an emerging concept in drug discovery. We are extending this concept by developing proteolysis targeting chimeras active in bacteria (BacPROTACs) that bind to ClpC1, a component of the mycobacterial protein degradation machinery. The anti-Mycobacterium tuberculosis (Mtb) BacPROTACs are derived from cyclomarins which, when dimerized, generate compounds that recruit and degrade ClpC1. The resulting Homo-BacPROTACs reduce levels of endogenous ClpC1 in Mycobacterium smegmatis and display minimum inhibitory concentrations in the low micro- to nanomolar range in mycobacterial strains, including multiple drug-resistant Mtb isolates. The compounds also kill Mtb residing in macrophages. Thus, Homo-BacPROTACs that degrade ClpC1 represent a different strategy for targeting Mtb and overcoming drug resistance.

Matteson Homologation-Based Total Synthesis of Meliponamycin A.

The first total synthesis of meliponamycin A, an antimicrobial cyclodepsipeptide isolated from Streptomyces, is reported. Two key building blocks, the substituted tetrahydropyranyl side chain and an azido analogue of protected ß-hydroxyleucine, were constructed via iterative Matteson homologations. A fragment coupling of a tetrapeptide, a depsidipeptide building block, macrocyclization, Staudinger reduction, and N-acylation are further steps in the synthesis.

Stereoselective Synthesis of Secondary and Tertiary Boronic Esters via Matteson Homologation.

Matteson homologations of chiral boronic esters with lithium dichlorocarbenoids and various nucleophiles proved to be a useful method for the synthesis of functionalized polyketides in a highly stereoselective fashion. Via repeated homologation steps, only 1,2-anti- and 1,3-syn-configured products were obtained. Homologation with substituted carbenoids followed by reaction with carbon nucleophiles resulted in configurationally inverted products and tertiary boronic esters in a highly stereoselective fashion. This approach significantly expands the potential of the Matteson reaction.

Isomerization-Free Matteson Homologations of Substituted Allylboronic Esters.

Substituted allyl derivatives with an internal double bond can be homologated under standard conditions via a 1,2-shift, whereas allylboronic esters with terminal double bonds can also be homologated via a SN' reaction. This allyl isomerization is catalyzed by ZnCl2 and can be suppressed by omitting ZnCl2 during the formation of α-chloroboronic ester. However, in the second step with Grignard reagents, ZnCl2 was added to suppress side reactions of the product formed.

The Microtubule-Targeting Agent Pretubulysin Impairs the Inflammatory Response in Endothelial Cells by a JNK-Dependent Deregulation of the Histone Acetyltransferase Brd4.

The anti-inflammatory effects of depolymerizing microtubule-targeting agents on leukocytes are known for a long time, but the potential involvement of the vascular endothelium and the underlying mechanistic basis is still largely unclear. Using the recently synthesized depolymerizing microtubule-targeting agent pretubulysin, we investigated the anti-inflammatory potential of pretubulysin and other microtubule-targeting agents with respect to the TNF-induced leukocyte adhesion cascade in endothelial cells, to improve our understanding of the underlying biomolecular background. We found that treatment with pretubulysin reduces inflammation in vivo and in vitro via inhibition of the TNF-induced adhesion of leukocytes to the vascular endothelium by down-regulation of the pro-inflammatory cell adhesion molecules ICAM-1 and VCAM-1 in a JNK-dependent manner. The underlying mechanism includes JNK-induced deregulation and degradation of the histone acetyltransferase Bromodomain-containing protein 4. This study shows that depolymerizing microtubule-targeting agents, in addition to their established effects on leukocytes, also significantly decrease the inflammatory activation of vascular endothelial cells. These effects are not based on altered pro-inflammatory signaling cascades, but require deregulation of the capability of cells to enter constructive transcription for some genes, setting a baseline for further research on the prominent anti-inflammatory effects of depolymerizing microtubule-targeting agents.

Synthesis of HC-Toxin via Matteson Homologation and C-H Functionalization.

A new synthetic route toward host-specific HC-toxin was developed. The HC-toxin belongs to a group of cyclic, tetrapeptide histone deacetylase inhibitors containing the unusual amino acid Aeo. Key steps in the synthesis of this building block include the Matteson homologation to generate the stereogenic centers in the side chain and a C-H functionalization to connect the side chain to a protected alanine.

Total synthesis and biological evaluation of histone deacetylase inhibitor WF-3161.

A novel synthesis of the naturally occurring HDAC inhibitor WF-3161 is described. Key steps include the Matteson homologation to generate the stereogenic centres in the side chain, and Pd-catalysed C-H functionalisation to connect the side chain to the peptide backbone. WF-3161 was found to be highly selective for HDAC1, whereas no activity was observed towards HDAC6. High activity was also found against the cancer cell line HL-60.

Total Synthesis of Thiamyxins A-C and Thiamyxin E, a Potent Class of RNA-Virus-Inhibiting (Cyclo)depsipeptides.

We present the first total synthesis of the thiamyxins A-C and the now fully characterized thiamyxin E, an interesting class of thiazole- and thiazoline-rich depsipeptides with diverse antiviral activity. The synthesis features a parallel closing of two methyl thiazoline units, with low epimerization of the very labile adjacent stereocenter. It also includes the three-step synthesis of an uncommon hydroxy acid and the oxidation-free elimination of a phenylselenide to form a dehydroalanine moiety. The exploitation of the acid-labile stereocenter at the isoleucine moiety and the reopening of the macrolactones gave access to the four thiamyxins with good yields and diastereomeric purities from a single precursor. The modular total synthesis allows further testing of the biological activity and gives opportunities to explore the pharmacophore and antiviral target through derivatization.

Clp-targeting BacPROTACs impair mycobacterial proteostasis and survival.

The ClpC1:ClpP1P2 protease is a core component of the proteostasis system in mycobacteria. To improve the efficacy of antitubercular agents targeting the Clp protease, we characterized the mechanism of the antibiotics cyclomarin A and ecumicin. Quantitative proteomics revealed that the antibiotics cause massive proteome imbalances, including upregulation of two unannotated yet conserved stress response factors, ClpC2 and ClpC3. These proteins likely protect the Clp protease from excessive amounts of misfolded proteins or from cyclomarin A, which we show to mimic damaged proteins. To overcome the Clp security system, we developed a BacPROTAC that induces degradation of ClpC1 together with its ClpC2 caretaker. The dual Clp degrader, built from linked cyclomarin A heads, was highly efficient in killing pathogenic Mycobacterium tuberculosis, with >100-fold increased potency over the parent antibiotic. Together, our data reveal Clp scavenger proteins as important proteostasis safeguards and highlight the potential of BacPROTACs as future antibiotics.

Stereoselective Synthesis of Highly Substituted O-Heterocycles via Matteson Homologation: A Ring-Closing Metathesis Approach.

Matteson homologations of chiral boronic esters with the aid of unsaturated nucleophiles are powerful for gaining access to a range of different O-heterocycles via subsequent ring-closing metatheses. Using this protocol, six- to eight-membered rings become available and almost any position of the ring can be substituted and/or functionalized.

Total synthesis of Myxoprincomide, a secondary metabolite from Myxococcus xanthus.

Myxoprincomide, a secondary metabolite of the myxobacterium Myxococcus xanthus DK 1622, is synthesised for the first time. The central, unusual α-ketoamide is generated at the end of the synthesis to avoid side reactions during the synthesis of this rather reactive subunit. Nevertheless, the synthetic natural product is obtained as an isomeric mixture. Detailed analytical investigations show that the identical isomeric mixture is found in the isolated natural product.

Total Synthesis and Biological Evaluation of Modified Ilamycin Derivatives.

Ilamycins/rufomycins are marine cycloheptapeptides containing unusual amino acids. Produced by Streptomyces sp., these compounds show potent activity against a range of mycobacteria, including multidrug-resistant strains of Mycobacterium tuberculosis. The cyclic peptides target the AAA+ protein ClpC1 that, together with the peptidases ClpP1/ClpP2, forms an essential ATP-driven protease. Derivatives of the ilamycins with a simplified tryptophane unit are synthesized in a straightforward manner. The ilamycin derivative 26 with a cyclic hemiaminal structure is active in the nM-range against several mycobacterial strains and shows no significant cytotoxicity. In contrast, derivative 27, with a glutamic acid at this position, is significantly less active, with MICs in the mid µM-range. Detailed investigations of the mode of action of 26 indicate that 26 deregulates ClpC1 activity and strongly enhances ClpC1-WT ATPase activity. The consequences of 26 on ClpC1 proteolytic activities were substrate-specific, suggesting dual effects of 26 on ClpC1-WT function. The positive effect relates to ClpC1-WT ATPase activation, and the negative to competition with substrates for binding to the ClpC1 NTD.

Stereoselective Synthesis of a Protected Side Chain of Callipeltin A.

Matteson homologations of chiral boronic esters proved to be an excellent tool for the synthesis of highly functionalized amino and hydroxy acid residues. This method provides straightforward stereoselective access to the side chain of callipeltin A, a natural marine product with interesting biological activities. Furthermore, this protocol should allow for variations in the substitution pattern in future SAR studies, simply by choosing suitable nucleophiles during the homologation steps.

Actin stabilization in cell migration.

Actin is a cytoskeletal filament involved in numerous biological tasks, such as providing cells a shape or generating and transmitting forces. Particularly important for these tasks is the ability of actin to grow and shrink. To study the role of actin in living cells this dynamic needs to be targeted. In the past, such alterations were performed by destabilizing actin. In contrast, we used the natural compound miuraenamide A in living retinal pigmented epithelial (RPE-1) cells to stabilize actin filaments and show that it decreases actin filament dynamics and elongates filament length. Cells treated with miuraenamide A increased their adhesive area and express more focal adhesion sites. These alterations result in a lower migration speed as well as a shift of nuclear position. We therefore postulate that miuraenamide A is a promising new tool to stabilize actin polymerization and study cellular behavior such as migration.

BacPROTACs mediate targeted protein degradation in bacteria.

Hijacking the cellular protein degradation system offers unique opportunities for drug discovery, as exemplified by proteolysis-targeting chimeras. Despite their great promise for medical chemistry, so far, it has not been possible to reprogram the bacterial degradation machinery to interfere with microbial infections. Here, we develop small-molecule degraders, so-called BacPROTACs, that bind to the substrate receptor of the ClpC:ClpP protease, priming neo-substrates for degradation. In addition to their targeting function, BacPROTACs activate ClpC, transforming the resting unfoldase into its functional state. The induced higher-order oligomer was visualized by cryo-EM analysis, providing a structural snapshot of activated ClpC unfolding a protein substrate. Finally, drug susceptibility and degradation assays performed in mycobacteria demonstrate in vivo activity of BacPROTACs, allowing selective targeting of endogenous proteins via fusion to an established degron. In addition to guiding antibiotic discovery, the BacPROTAC technology presents a versatile research tool enabling the inducible degradation of bacterial proteins.

Application of Vinyl Nucleophiles in Matteson Homologations.

The Matteson homologation with vinyl nucleophiles was found to be a versatile tool for the synthesis of highly substituted and functionalized allyl boronic esters. High yields and stereoselectivities are obtained with sterically demanding alkyl boronic esters and/or Grignard reagents. With the application of such vinyl Matteson homologations, the polyketide fragment of lagunamide B is synthesized.

Stereoselective Synthesis of a Protected Side Chain of Meliponamycin A.

The Matteson homologation was found to be a versatile tool for the construction of the linear polyketide side chain of meliponamycin and related compounds in only four steps. The ester dienolate version of this reaction allowed the introduction of the unsaturated ester moiety in a highly stereoselective fashion. Boronate oxidation/deoxygenation and Sharpless dihydroxylation are additional key steps in the stereoselective construction of this highly functionalized tetrahydropyran ring system, which is characteristic of this substance class.