Protein reactivity of natural product-derived γ-butyrolactones

Diastereodivergent α-Homoallylation of Cyclic Enones

α,β-Unsaturated carbonyls are essential structural motifs for nucleophiles of disease-related proteins. Methods for stereoselective functionalizations at the α-position include the Morita-Baylis-Hillman, Negishi, Sonogashira, Stille, and Rauhut-Currier reactions. Described here is a method for the diastereodivergent α-homoallylation of cyclic enones via a sequence of conjugate addition, aldol condensation, and diastereoselective [3,3]-sigmatropic rearrangement. Mechanistic investigations revealed that the [3,3]-sigmatropic rearrangement proceeds with transfer of chirality. These inspire a photocatalyzed olefin isomerization of the aldol condensation product leading to a highly diastereoselective [3,3]-sigmatropic rearrangement to furnish the α-homoallylation of cyclic enones. Importantly, this photocatalyzed olefin isomerization/diastereoselective [3,3]-sigmatropic rearrangement reaction sequence permits a full stereocontrol of the exo-β-position featuring an allyl group as a synthetic functional handle.

Chemoproteomic Approaches for Unraveling Prokaryotic Biology

Bacteria are ubiquitous lifeforms with important roles in the environment, biotechnology, and human health. Many of the functions that bacteria perform are mediated by proteins and enzymes, which catalyze metabolic transformations of small molecules and modifications of proteins. To better understand these biological processes, chemical proteomic approaches, including activity-based protein profiling, have been developed to interrogate protein function and enzymatic activity in physiologically relevant contexts. Here, chemoproteomic strategies and technological advances for studying bacterial physiology, pathogenesis, and metabolism are discussed. The development of chemoproteomic approaches for characterizing protein function and enzymatic activity within bacteria remains an active area of research, and continued innovations are expected to provide breakthroughs in understanding bacterial biology.

Interaction of obtusilactone B and related butanolide lactones with the barrier-to-autointegration factor 1 (BAF1). A computational study

The barrier-to-autointegration factor 1 (BAF1) protein is a DNA-binding protein implicated in nuclear envelop repair and reformation after mitosis. This nuclear protein is frequently overexpressed in cancer cells and plays a role in the occurrence and development of different tumors. It is a potential therapeutic target for gastric cancer, breast cancer and other malignancies. For this reason, BAF1 inhibitors are searched. The butanolide lactone obtusilactone B (Ob-B) has been found to inhibit VRK1-dependent phosphorylation of BAF1, upon direct binding to the nuclear protein. Taking advantage of the known crystallographic structure of BAF1, we have elaborated molecular models of Ob-B bound to BAF1 to delimit the binding site and binding configuration. The long endoolefinic alkyl side chain of Ob-B extends into a small groove on the protein surface, and the adjacent exomethylene-γ-lactone moiety occupies a pocket comprising to the Ser-4 phosphorylation site of BAF1. Twenty butanolide lactones structurally close to ObB were screened for BAF1 binding. Several natural products with BAF1-binding capacity potentially superior to Ob-B were identified, including mahubanolide, kotomolide B, epilitsenolide D2, and a few other known anticancer plant natural products. Our study provides new ideas to guide the discovery and design of BAF1 inhibitors.

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Obtusilactone B (Ob-B) is an anticancer inhibitor of VRK1-mediated BAF1 phosphorylation.

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Molecular models of Ob-B bound to BAF1 have been constructed and the binding site determined.

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Screening of 20 butanolide lactones led to the identification of new potential BAF1 binders.

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Mahubanolide, kotomolide B and epilitsenolide D2 emerge as potential BAF1 inhibitors.

Electrophilic reactivities of cyclic enones and α,β-unsaturated lactones

The reactivities of cyclic enones and α,β-unsaturated lactones were characterized by following the kinetics of their reactions with colored carbon-centered reference nucleophiles in DMSO at 20 °C. The experimentally determined second-order rate constants k₂ were analyzed with the Mayr–Patz equation, lg k = s_N(N + E), to furnish the electrophilicity descriptors E for the Michael acceptors. Cyclic enones and lactones show different reactivity trends than their acyclic analogs. While cyclization reduces the reactivity of enones slightly, α,β-unsaturated lactones are significantly more reactive Michael acceptors than analogously substituted open-chain esters. The observed reactivity trends were rationalized through quantum-chemically calculated Gibbs energy profiles (at the SMD(DMSO)/M06-2X/6-31+G(d,p) level of theory) and distortion interaction analysis for the reactions of the cyclic Michael acceptors with a sulfonium ylide. The electrophilicities of simplified electrophilic fragments reflect the general reactivity pattern of structurally more complex terpene-derived cyclic enones and sesquiterpene lactones, such as parthenolide.

Different reactivity trends for cyclic and acyclic Michael acceptors were found within the framework of Mayr's experimental reactivity scales and analyzed through quantum-chemical studies.

Protein modification by thiolactone homocysteine chemistry: a multifunctionalized human serum albumin theranostic

As the most abundant protein with a variety of physiological functions, albumin has been used extensively for the delivery of therapeutic molecules. Thiolactone chemistry provides a powerful tool to prepare spin-labeled albumin-based multimodal imaging probes and therapeutic agents. We report the synthesis of a tamoxifen homocysteine thiolactone derivative and its use in thiol-'click' chemistry to prepare multi-functionalized serum albumin. The released sulfhydryl group of the homocysteine functional handle was labeled with a nitroxide reagent to prepare a spin-labeled albumin-tamoxifen conjugate confirmed by MALDI-TOF-MS, EPR spectroscopy, UV-vis and fluorescent emission spectra. This is the basis for a novel multimodal tamoxifen-albumin theranostic with a significant (dose-dependent) inhibitory effect on the proliferation of malignant cells. The response of human glioblastoma multiforme T98G cells and breast cancer MCF-7 cells to tamoxifen and its albumin conjugates was different in tumor cells with different expression level of ERα in our experiments. These results provide further impetus to develop a serum protein for delivery of tamoxifen to cancer cells.

Multiplexed Thiol Reactivity Profiling for Target Discovery of Electrophilic Natural Products

Electrophilic groups, such as Michael acceptors, expoxides, are common motifs in natural products (NPs). Electrophilic NPs can act through covalent modification of cysteinyl thiols on functional proteins, and exhibit potent cytotoxicity and anti-inflammatory/cancer activities. Here we describe a new chemoproteomic strategy, termed multiplexed thiol reactivity profiling (MTRP), and its use in target discovery of electrophilic NPs. We demonstrate the utility of MTRP by identifying cellular targets of gambogic acid, an electrophilic NP that is currently under evaluation in clinical trials as anticancer agent. Moreover, MTRP enables simultaneous comparison of seven structurally diversified α,β-unsaturated γ-lactones, which provides insights into the relative proteomic reactivity and target preference of diverse structural scaffolds coupled to a common electrophilic motif and reveals various potential druggable targets with liganded cysteines. We anticipate that this new method for thiol reactivity profiling in a multiplexed manner will find broad application in redox biology and drug discovery.

Covalent Modifiers: A Chemical Perspective on the Reactivity of α,β-Unsaturated Carbonyls with Thiols via Hetero-Michael Addition Reactions

Although Michael acceptors display a potent and broad spectrum of bioactivity, they have largely been ignored in drug discovery because of their presumed indiscriminate reactivity. As such, a dearth of information exists relevant to the thiol reactivity of natural products and their analogues possessing this moiety. In the midst of recently approved acrylamide-containing drugs, it is clear that a good understanding of the hetero-Michael addition reaction and the relative reactivities of biological thiols with Michael acceptors under physiological conditions is needed for the design and use of these compounds as biological tools and potential therapeutics. This Perspective provides information that will contribute to this understanding, such as kinetics of thiol addition reactions, bioactivities, as well as steric and electronic factors that influence the electrophilicity and reversibility of Michael acceptors. This Perspective is focused on α,β-unsaturated carbonyls given their preponderance in bioactive natural products.

Activity-Based Protein Profiling in Bacteria

Understanding the molecular mechanisms of bacterial pathogenesis and virulence is of great importance from both an academic and clinical perspective, especially in view of an alarming increase in bacterial resistance to existing antibiotics and antibacterial agents. Use of small molecules to dissect the basis of these dynamic processes is a very attractive approach due to their ability for rapid spatiotemporal control of specific biochemical functions. Activity-based protein profiling (ABPP), employing small molecule probes to interrogate enzyme activities in complex proteomes, has emerged as a powerful tool to study bacterial pathogenesis. In this chapter, we present a set of ABPP methods to identify and analyze enzymes essential for growth, metabolism and virulence of different pathogens including S. aureus and L. monocytogenes using natural product-inspired activity-based probes.

Target identification for small bioactive molecules: finding the needle in the haystack

Identification and confirmation of bioactive small-molecule targets is a crucial, often decisive step both in academic and pharmaceutical research. Through the development and availability of several new experimental techniques, target identification is, in principle, feasible, and the number of successful examples steadily grows. However, a generic methodology that can successfully be applied in the majority of the cases has not yet been established. Herein we summarize current methods for target identification of small molecules, primarily for a chemistry audience but also the biological community, for example, the chemist or biologist attempting to identify the target of a given bioactive compound. We describe the most frequently employed experimental approaches for target identification and provide several representative examples illustrating the state-of-the-art. Among the techniques currently available, protein affinity isolation using suitable small-molecule probes (pulldown) and subsequent mass spectrometric analysis of the isolated proteins appears to be most powerful and most frequently applied. To provide guidance for rapid entry into the field and based on our own experience we propose a typical workflow for target identification, which centers on the application of chemical proteomics as the key step to generate hypotheses for potential target proteins.

Target analysis of α-alkylidene-γ-butyrolactones in uropathogenic E. coli

α-Alkylidene-γ-butyrolactones are quite common in nature and exhibit a broad spectrum of biological activities. We therefore synthesized a small library of xanthatine inspired α-alkylidene-γ-butyrolactones to screen non-pathogenic and uropathogenic E. coli strains by activity based protein profiling (ABPP). The identified targets are involved in cellular redox processes and give first insight into the preferred binding sites of this privileged motif. Furthermore the gene of one protein, c2450, which was only identified in uropathogenic E. coli belongs to a genomic island which encodes a hybrid polyketide/non-ribosomal peptide synthetase (PKS/NRPS). This system is responsible for the synthesis of colibactin, a natural product which causes DNA double strand breaks in eukaryotic cells leading to the activation of the DNA damage checkpoint pathway and subsequent cell cycle arrest. While the role of several proteins that are involved in the colibactin synthesis has been elucidated, the function of c2450 remains elusive. Investigation of the binding site showed that c2450 is modified at a cysteine residue which may be important for the catalytic activity.

An allenic Pauson-Khand approach to 6,12-guaianolides

Cyclocarbonylation of α-methylene butyrolactone-containing allene-ynes affords 6,12-guaianolide ring systems. Incorporation of the α-methylene butyrolactone early in a synthetic sequence is rare for reactivity reasons; however, this moiety proves to be beneficial to the allenic Pauson-Khand reaction. The three double bonds and the ketone in the resulting 5-7-5 ring system bear significant differences in their reactivity and are ideally positioned for synthetic application to 6,12-guaianolides and analogs.

Unraveling the protein targets of vancomycin in living S. aureus and E. faecalis cells

Vancomycin is a potent glycopeptide antibiotic that has evolved to specifically bind to the D-Ala-D-Ala dipeptide termini of nascent peptidoglycans. Although this mode of action is well established, several studies indicate that vancomycin and analogues exploit noncanonical target sites. In order to address all vancomycin targets in clinically relevant Staphylococcus aureus and Enterococcus faecalis strains we developed a series of small-molecule photoaffinity probes based on vancomycin. Proteomic profiling revealed the specific labeling of two previously unknown vancomycin targets that are likely to contribute to its antibiotic activity. The specific inhibition of the major staphylococcal autolysin Atl confirms previous observations that vancomycin alters S. aureus cell morphology by interaction with the autolytic machinery. Moreover, in E. faecalis the vancomycin photoprobe specifically binds to an ABC transporter protein, which likely impedes the uptake of essential nutrients such as sugars and peptides. The labeling of these two prominent membrane targets in living cells reveals a thus far unexplored mode of vancomycin binding and inhibition that could allow a rational design of variants with improved activity.

Activity-based protein profiling for natural product target discovery

Natural products represent an important treasure box of biologically active molecules, from which many drug candidates have been sourced. The identification of the target proteins addressed by these natural products is a foremost goal for which new techniques are required. Activity-based protein profiling (ABPP), exploiting protein-reactive functional groups present in many natural products, offers unseen opportunities in this respect. This review article describes the current status of this field. Many examples are given for the annotation of biological target proteins of natural products containing epoxides, lactones, lactams, Michael acceptors, and other electrophilic groups. In addition, the development of probe molecules identified from biomimetic natural product libraries is discussed.