A systems biology approach to dissection of the effects of small bicyclic peptidomimetics on a panel of saccharomyces cerevisiae mutants

A Highlight on the Inhibition of Fungal Carbonic Anhydrases as Drug Targets for the Antifungal Armamentarium

Carbon dioxide (CO2), a vital molecule of the carbon cycle, is a critical component in living organisms' metabolism, performing functions that lead to the building of compounds fundamental for the life cycle. In all living organisms, the CO2/bicarbonate (HCO3-) balancing is governed by a superfamily of enzymes, known as carbonic anhydrases (CAs, EC 4.2.1.1). CAs catalyze the pivotal physiological reaction, consisting of the reversible hydration of the CO2 to HCO3- and protons. Opportunistic and pathogenic fungi can sense the environmental CO2 levels, which influence their virulence or environmental subsistence traits. The fungal CO2-sensing is directly stimulated by HCO3- produced in a CA-dependent manner, which directly activates adenylyl cyclase (AC) involved in the fungal spore formation. The interference with CA activity may impair fungal growth and virulence, making this approach interesting for designing antifungal drugs with a novel mechanism of action: the inhibition of CAs linked to the CO2/HCO3-/pH chemosensing and signaling. This review reports that sulfonamides and their bioisosteres as well as inorganic anions can inhibit in vitro the β- and α-CAs from the fungi, suggesting how CAs may be considered as a novel "pathogen protein" target of many opportunistic, pathogenic fungi.

Bicyclic acetals: biological relevance, scaffold analysis, and applications in diversity-oriented synthesis

The chemoinformatics analysis of fused, spiro, and bridged bicyclic acetals is instrumental for the DOS of natural product-inspired molecular collections.

Deciphering the mechanism of action of 089, a compound impairing the fungal cell cycle

Fungal infections represent an increasingly relevant clinical problem, primarily because of the increased survival of severely immune-compromised patients. Despite the availability of active and selective drugs and of well-established prophylaxis, classical antifungals are often ineffective as resistance is frequently observed. The quest for anti-fungal drugs with novel mechanisms of action is thus important. Here we show that a new compound, 089, acts by arresting fungal cells in the G2 phase of the cell cycle through targeting of SWE1, a mechanism of action unexploited by current anti-fungal drugs. The cell cycle impairment also induces a modification of fungal cell morphology which makes fungal cells recognizable by immune cells. This new class of molecules holds promise to be a valuable source of novel antifungals, allowing the clearance of pathogenic fungi by both direct killing of the fungus and enhancing the recognition of the pathogen by the host immune system.

Relations between Effects and Structure of Small Bicyclic Molecules on the Complex Model System Saccharomyces cerevisiae

The development of compounds able to modify biological functions largely took advantage of parallel synthesis to generate a broad chemical variance of compounds to be tested for the desired effect(s). The budding yeast Saccharomyces cerevisiae is a model for pharmacological studies since a long time as it represents a relatively simple system to explore the relations among chemical variance and bioactivity. To identify relations between the chemical features of the molecules and their activity, we delved into the effects of a library of small compounds on the viability of a set of S. cerevisiae strains. Thanks to the high degree of chemical diversity of the tested compounds and to the measured effect on the yeast growth rate, we were able to scale-down the chemical library and to gain information on the most effective structures at the substituent level. Our results represent a valuable source for the selection, rational design, and optimization of bioactive compounds.

Diversity-oriented synthesis as a tool for chemical genetics

Chemical genetics is an approach for identifying small molecules with the ability to induce a biological phenotype or to interact with a particular gene product, and it is an emerging tool for lead generation in drug discovery. Accordingly, there is a need for efficient and versatile synthetic processes capable of generating complex and diverse molecular libraries, and Diversity-Oriented Synthesis (DOS) of small molecules is the concept of choice to give access to new chemotypes with high chemical diversity. In this review, the combination of chemical genetics and diversity-oriented synthesis to identify new chemotypes as hit compounds in chemical biology and drug discovery is reported, giving an overview of basic concepts and selected case studies.

Carbonic anhydrase inhibitors. Benzenesulfonamides incorporating cyanoacrylamide moieties strongly inhibit Saccharomyces cerevisiae β-carbonic anhydrase

A series of benzenesulfonamides incorporating cyanoacrylamide moieties (tyrphostine analogs) were assayed as inhibitors of the β-carbonic anhydrase (CA, EC 4.2.1.1) from Saccharomyces cerevisiae, ScCA. Some of these compounds were low nanomolar or subnanomolar ScCA inhibitors and showed selectivity ratios in the range of 4.91-69.86 for inhibiting the yeast enzyme over the offtarget human (h) isoforms hCA I and of 6.46-13.52 for inhibiting ScCA over hCA II. The model organism S. cerevisiae and this particular enzyme may be useful for detecting antifungals with a novel mechanism of action compared to the classical azole drugs to which significant drug resistance emerged. Indeed, some of these sulfonamides inhibited the growth of the yeast with CC50-s in the range of 0.73-6.54 μM.

Genome-wide investigation of cellular targets and mode of action of the antifungal bacterial metabolite 2,4-diacetylphloroglucinol in Saccharomyces cerevisiae

Saccharomyces cerevisiae is a proven model to investigate the effects of small molecules and drugs on fungal and eukaryotic cells. In this study, the mode of action of an antifungal metabolite, 2,4-diacetylphloroglucinol (DAPG), was determined. Applying a combination of genetic and physiological approaches, it was established that this bacterial metabolite acts as a proton ionophore and dissipates the proton gradient across the mitochondrial membrane. The uncoupling of respiration and ATP synthesis ultimately leads to growth inhibition and is the primary toxic effect of DAPG. A genome-wide screen identified 154 DAPG-tolerant mutants and showed that there are many alterations in cellular metabolism that can confer at least some degree of tolerance to this uncoupler. One mutant, ydc1, was studied in some more detail as it displayed increased tolerance to both DAPG and the uncoupler carbonylcyanide m-chlorophenylhydrazone (CCCP) and appears to be unconnected to other tolerant mutant strains. Deleting YDC1 alters sphingolipid homoeostasis in the cell, and we suggest here that this may be linked to reduced drug sensitivity. Sphingolipids and their derivatives are important eukaryotic signal molecules, and the observation that altering homoeostasis may affect yeast response to metabolic uncoupling agents raises some intriguing questions for future studies.

Yeast systems biology: the challenge of eukaryotic complexity

In this chapter, we present an up-to-date view of the optimal characteristics of the yeast Saccharomyces cerevisiae as a model eukaryote for systems biology studies, with main molecular mechanisms, biological networks, and sub-cellular organization essentially conserved in all eukaryotes, derived from a complex common ancestor. The existence of advanced tools for molecular studies together with high-throughput experimental and computational methods, most of them being implemented and validated in yeast, with new ones being developed, is opening the way to the characterization of the core modular architecture and complex networks essential to all eukaryotes. Selected examples of the latest discoveries in eukaryote complexity and systems biology studies using yeast as a reference model and their applications in biotechnology and medicine are presented.