Prostate cancer (PCa) remains a major global health burden. Although androgen deprivation and receptor-targeted therapies initially benefit patients, resistance often leads to metastatic castration-resistant prostate cancer, with limited treatment options. Aldehyde dehydrogenase 7A1 (ALDH7A1) is an emerging oncogenic driver of PCa, but selective inhibitors are lacking. Here, we report irreversible ALDH7A1 inhibitors targeting the catalytic Cys330, identified from a library of 3-bromo-4,5-dihydroisoxazole derivatives. These compounds show minimal inhibition of ALDH4A1 and GAPDH, supporting selectivity for ALDH7A1. Compounds 3b and 4b reduced DU145 cell viability (low μM IC50), impaired migration, and altered the cell cycle. No significant effects were observed in LNCaP cells (low ALDH7A1 expression) or Hs27 fibroblasts. Treatment of DU145 cells resulted in the inhibition of intracellular ALDH activity and accumulation of malondialdehyde, consistent with increased oxidative stress. These findings validate ALDH7A1 as a druggable target and introduce a new chemical space for selective covalent ALDH inhibitors in oncology.

Infections caused by Staphylococcus aureus depend on its ability to access essential nutrients, including acquiring iron from human hemoglobin (Hb) through the iron-regulated surface determinant (Isd) system. The compound 4-[(2-{[5-(1H-indol-3-yl)-1,3,4-oxadiazol-2-yl]sulfanyl}acetyl)amino]benzoic acid (C35) was recently identified as a promising antimicrobial agent for its ability to bind Hb and hamper its interaction with the staphylococcal hemophore IsdB in vitro. Here, we show that C35 inhibits S. aureus growth by targeting the hemophore-driven iron-acquisition system, highlighting its potential as an inhibitor and validating hemophores as antibacterial targets. Furthermore, for drug design purposes, we solved the X-ray structure of Hb:C35 complex. In contrast to the predicted binding pose, C35 binds tetrameric Hb in a cleft between the α subunits, stabilizing a relaxed conformation (R2) and increasing Hb oxygen affinity. This serendipitous result hints to C35 as a promising scaffold for developing compounds with diverse, or even dual, therapeutic aims, with antimicrobial and Hb-modulating activity.

Siderophore production, along with heme scavenging by hemophores, is one of the main mechanisms exploited by bacteria to achieve an adequate iron supply. Staphylococcus aureus produces two main siderophores, staphyloferrin A (SA) and staphyloferrin B (SB), with the latter produced only by the most invasive, coagulase-positive S. aureus strains. Along the seven steps of the SB biosynthetic pathway, N-(2-amino-2-carboxyethyl)-l-glutamate synthase (SbnA) catalyzes the crucial formation of the intermediate N-(2-amino-2-carboxyethyl)-l-glutamate from O-phospho-L-serine and glutamate. Our functional characterization of the enzyme highlighted that citrate inhibits SbnA with an inhibitory constant (Ki) in the order of magnitude of the physiological concentration of the metabolite. We searched for inhibitors of SbnA within citrate analogues and identified 2-phenylmaleic acid (2-PhMA) as the best hit, with a Ki of 16 ± 2 μm and a mechanism of inhibition that is competitive with O-phospho-L-serine for active site binding. The methyl ester of 2-PhMA at a 2 mm concentration was effective in inhibiting siderophore biosynthesis in S. aureus. These results pave the way for the discovery of promising inhibitors of iron acquisition that might find application as innovative antimicrobials.

Siderophore production, along with heme scavenging by hemophores, is one of the main mechanisms exploited by bacteria to achieve an adequate iron supply. Staphylococcus aureus produces two main siderophores, staphyloferrin A (SA) and staphyloferrin B (SB), with the latter produced only by the most invasive, coagulase-positive S. aureus strains. Along the seven steps of the SB biosynthetic pathway, N -(2-amino-2-carboxyethyl)- l -glutamate synthase (SbnA) catalyzes the crucial formation of the intermediate N -(2-amino-2-carboxyethyl)- l -glutamate from O-phospho-L-serine and glutamate. Our functional characterization of the enzyme highlighted that citrate inhibits SbnA with an inhibitory constant ( K i ) in the order of magnitude of the physiological concentration of the metabolite. We searched for inhibitors of SbnA within citrate analogues and identified 2-phenylmaleic acid (2-PhMA) as the best hit, with a K i of 16 ± 2 μ m and a mechanism of inhibition that is competitive with O-phospho-L-serine for active site binding. The methyl ester of 2-PhMA at a 2 m m concentration was effective in inhibiting siderophore biosynthesis in S. aureus . These results pave the way for the discovery of promising inhibitors of iron acquisition that might find application as innovative antimicrobials.

Human hemoglobin (Hb) is the preferred iron source of Staphylococcus aureus. This pathogenic bacterium exploits a sophisticated protein machinery called Iron-regulated surface determinant (Isd) system to bind Hb, extract and internalize heme and finally degrade it to complete iron acquisition. IsdB, the surface exposed Hb receptor, is a proven virulence factor of S. aureus and the inhibition of its interaction with Hb can be pursued as a strategy to develop new classes of antimicrobials. To identify small molecules able to disrupt IsdB:Hb protein-protein interactions (PPIs), we carried out a structure-based virtual screening campaign and developed an ad-hoc immunoassay to screen the retrieved set of commercially available compounds. Saturation-transfer difference (STD) NMR was applied to verify specific interactions of a sub-set of molecules, chosen based on their efficacy in reducing the amount of Hb bound to IsdB. Among molecules for which direct binding was verified, the best hit was submitted to ITC analysis to measure the binding affinity to Hb, which was found to be in the sub-micromolar range. The results demonstrate the viability of the proposed in silico/in vitro experimental pipeline to discover and test IsdB:Hb PPI inhibitors. The identified lead compound will be the starting point for future SAR and molecule optimization campaigns.

Infections caused by Staphylococcus aureus depend on its ability to acquire nutrients. One essential nutrient is iron, which is obtained from the heme of the human host hemoglobin (Hb) through a protein machinery called Iron-regulated surface determinant (Isd) system. IsdB is the protein in charge of heme extraction from Hb, which is the first step of the chain of events leading to iron transfer to the bacterium cell interior. In order to elucidate the molecular events leading from the formation of the initial IsdB:Hb complex to heme extraction, we use time-resolved X-ray solution scattering (TR-XSS) in combination with rapid mixing triggering. We succeed in defining the stoichiometry of IsdB:Hb binding and in describing the kinetics of the subsequent structural changes. The presented approach is potentially applicable to unveil the complex kinetic pathways generated by protein-protein interaction in different biological systems.

Infections caused by Staphylococcus aureus are closely linked to its ability to secure essential nutrients, including iron, which is extracted from the heme of human hemoglobin (Hb) through the iron-regulated surface determinant (Isd) system. The compound 4-[[2-[[5- (1H-indol-3-yl)-1,3,4-oxadiazol-2-yl]sulfanyl]acetyl]amino]benzoate (C35) was recently identified as a new potential antimicrobial agent for its ability to bind Hb and hamper its interaction with the staphylococcal hemophore IsdB in vitro . Here, we show that C35 inhibits S. aureus growth by specifically targeting the hemophore-driven iron acquisition system. Our findings confirm both the potential of C35 as a first-in-class protein-protein interaction inhibitor with antimicrobial activity, and the effectiveness of targeting hemophores as a strategy to inhibit S. aureus growth. To gain information for drug discovery purposes, the X-ray structure of Hb in the presence of the compound was solved. Unexpectedly, we discovered that, rather than the predicted binding pose, the molecule binds to tetrameric Hb in a cleft between the alpha subunits, stabilizing an R2 relaxed Hb conformation. This triggered further investigation of the effect of C35 on Hb functional properties, which showed a pronounced left-shift activity on oxygen binding curve (i.e., it strongly increases the Hb oxygen affinity). These results highlight C35 as a promising dual-acting compound with both antimicrobial activity and the ability to modulate Hb function through non-covalent stabilization of a high-affinity state. Author Summary Staphylococcus aureus is a dangerous bacterium that can cause severe infections in humans. To grow and survive it needs iron, which it steals from our red blood cells by taking it from hemoglobin, the protein that carries oxygen in the blood. In this study, we focused on a small molecule, called C35, that blocks the interaction between hemoglobin and a key bacterial protein involved in heme acquisition. We found that C35 strongly inhibits the growth of S. aureus when hemoglobin is the only available source of iron, showing a potential new method to starve the pathogen and consequently fight the infection. Surprisingly, we also found that C35 increases the affinity of hemoglobin for oxygen. This dual action makes C35 a unique molecule for future therapeutic development, with potential applications both as a new antimicrobial agent and in the treatment of diseases related to hemoglobin function. ### Competing Interest Statement The authors have declared no competing interest. Ministry of Education, Universities and Research, https://ror.org/0166hxq48, 2020AE3LTA Ministry of Education, Universities and Research Ministry of Education, Universities and Research, PNRR MUR Â-M4C2–Investimento 1.4–Avviso “Centri Nazionali”–D.D. n. 3138 del 16 dicembre 2021 University of Turin, SPYF\_RILO\_01_23, LAZL\_RILO\_01_23

The overexpression of two arginase (ARG) isoforms, ARG1 and ARG2, contributes to the onset of numerous disorders, including cardiovascular and immune-mediated diseases, as well as tumors. To elucidate the specific roles of ARG1 and ARG2 without interfering with their physiological functions, it is crucial to develop effective ARG inhibitors that target only one isoform, while maintaining low toxicity and an adequate pharmacokinetic profile. In this context, we present a comprehensive overview of the different generations of ARG inhibitors. Given the general lack of selectivity in most existing inhibitors, we analyzed the structural features and plasticity of the ARG1 and ARG2 binding sites to explore the potential for designing inhibitors with novel binding patterns. We also review ongoing preclinical and clinical studies on selected inhibitors, highlighting both progress and challenges in developing potent, selective ARG inhibitors. Furthermore, we discuss medicinal chemistry strategies that may accelerate the discovery of selective ARG inhibitors.

Protein-protein interactions mediate most molecular processes in the cell, offering a significant opportunity to expand the set of known druggable targets. Unfortunately, targeting these interactions can be challenging due to their typically flat and featureless interaction surfaces, which often change as the complex forms. Such surface changes may reveal hidden (cryptic) druggable pockets. Here, we analyse a set of well-characterised protein-protein interactions harbouring cryptic pockets and investigate the predictive power of current computational methods. Based on our observations, we develop a new computational strategy, SWISH-X (SWISH Expanded), which combines the established cryptic pocket identification capabilities of SWISH with the rapid temperature range exploration of OPES MultiThermal. SWISH-X is able to reliably identify cryptic pockets at protein-protein interfaces while retaining its predictive power for revealing cryptic pockets in isolated proteins, such as TEM-1 β -lactamase.

BACKGROUND:Several factors contribute to ischemia/reperfusion injury (IRI), including activation of the NLRP3 inflammasome and its byproducts, such as interleukin-1β (IL-1β) and caspase-1. However, NLRP3 may paradoxically exhibit cardioprotective properties. This study aimed to assess the protective effects of the novel NLRP3 inhibitor, INF195, both in vitro and ex vivo. METHODS:To investigate the relationship between NLRP3 and myocardial IRI, we synthetized a series of novel NLRP3 inhibitors, and investigated their putative binding mode via docking studies. Through in vitro studies we identified INF195 as optimal for NLRP3 inhibition. We measured infarct-size in isolated mouse hearts subjected to 30-min global ischemia/one-hour reperfusion in the presence of three different doses of INF195 (5, 10, or 20-μM). We analyzed caspase-1 and IL-1β concentration in cardiac tissue homogenates by ELISA. Statistical significance was determined using one-way ANOVA followed by Tukey's test. RESULTS AND CONCLUSION:INF195 reduces NLRP3-induced pyroptosis in human macrophages. Heart pre-treatment with 5 and 10-μM INF195 significantly reduces both infarct size and IL-1β levels. Data suggest that intracardiac NLRP3 activation contributes to IRI and that low doses of INF195 exert cardioprotective effects by reducing infarct size. However, at 20-μM, INF195 efficacy declines, leading to a lack of cardioprotection. Research is required to determine if high doses of INF195 have off-target effects or dual roles, potentially eliminating both harmful and cardioprotective functions of NLRP3. Our findings highlight the potential of a new chemical scaffold, amenable to further optimization, to provide NLRP3 inhibition and cardioprotection in the ischemia/reperfusion setting.

Human hemoglobin (Hb) is the preferred iron source of Staphylococcus aureus. This pathogenic bacterium exploits a sophisticated protein machinery called Iron-regulated surface determinant (Isd) system to bind Hb, extract and internalize heme, and finally degrade it to complete iron acquisition. IsdB, the surface exposed Hb receptor, is a proven virulence factor of S. aureus and the inhibition of its interaction with Hb can be pursued as a strategy to develop new classes of antimicrobials. To identify small molecules able to disrupt IsdB:Hb protein–protein interactions (PPIs), we carried out a structure-based virtual screening campaign and developed an ad hoc immunoassay to screen the retrieved set of commercially available compounds. Saturation-transfer difference (STD) NMR was applied to verify specific interactions of a sub-set of molecules, chosen based on their efficacy in reducing the amount of Hb bound to IsdB. Among molecules for which direct binding was verified, the best hit was submitted to ITC analysis to measure the binding affinity to Hb, which was found to be in the low micromolar range. The results demonstrate the viability of the proposed in silico/in vitro experimental pipeline to discover and test IsdB:Hb PPI inhibitors. The identified lead compound will be the starting point for future SAR and molecule optimization campaigns.

The protein NLRP3 and its complexes are associated with an array of inflammatory pathologies, among which neurodegenerative, autoimmune, and metabolic diseases. Targeting the NLRP3 inflammasome represents a promising strategy for easing the symptoms of pathologic neuroinflammation. When the inflammasome is activated, NLRP3 undergoes a conformational change triggering the production of pro-inflammatory cytokines IL-1β and IL-18, as well as cell death by pyroptosis. NLRP3 nucleotide-binding and oligomerization (NACHT) domain plays a crucial role in this function by binding and hydrolysing ATP and is primarily responsible, together with conformational transitions involving the PYD domain, for the complex-assembly process. Allosteric ligands proved able to induce NLRP3 inhibition. Herein, we examine the origins of allosteric inhibition of NLRP3. Through the use of molecular dynamics (MD) simulations and advanced analysis methods, we provide molecular-level insights into how allosteric binding affects protein structure and dynamics, remodelling of the conformational ensembles populated by the protein, with key reverberations on how NLRP3 is preorganized for assembly and ultimately function. The data are used to develop a Machine Learning model to define the protein as Active or Inactive, only based on the analysis of its internal dynamics. We propose this model as a novel tool to select allosteric ligands.

Iron is an essential nutrient for almost all organisms. In the human body, it is primarily bound to the heme cofactor of hemoglobin (Hb), myoglobin and other heme-binding proteins. During infection, Staphylococcus aureus exploits Hb heme pool as its favored iron source, capturing and internalizing it by cell wall hemophores. The first step is performed by IsdB, which intercepts free Hb and extracts heme. IsdB, a proven virulence factor, is an attractive putative target for antimicrobials development but its mechanism of action needs to be further detailed. To this aim, we used cryo-EM single-particle analysis to study IsdB:Hb complex formation and heme extraction. The key complexes before and after heme extraction were solved at 2.9 angstrom and 5.8 angstrom resolution using carboxyHb, resistant to heme removal, and oxidized Hb, the physiologic IsdB substrate. IsdB first binds to Hb beta -chains, enhancing Hb dimerization to favor a second IsdB molecule binding to alpha -chains before extraction. These results greatly improve our current knowledge

The worldwide emergence and dissemination of Gram-negative bacteria expressing metallo-β-lactamases (MBLs) menace the efficacy of all β-lactam antibiotics, including carbapenems, a last-line treatment usually restricted to severe pneumonia and urinary tract infections. Nonetheless, no MBL inhibitor is yet available in therapy. We previously identified a series of 1,2,4-triazole-3-thione derivatives acting as micromolar inhibitors of MBLs in vitro, but devoid of synergistic activity in microbiological assays. Here, via a multidisciplinary approach, including molecular modelling, synthesis, enzymology, microbiology, and X-ray crystallography, we optimized this series of compounds and identified low micromolar inhibitors active against clinically relevant MBLs (NDM-1- and VIM-type). The best inhibitors increased, to a certain extent, the susceptibility of NDM-1- and VIM-4-producing clinical isolates to meropenem. X-ray structures of three selected inhibitors in complex with NDM-1 elucidated molecular recognition at the base of potency improvement, confirmed in silico predicted orientation, and will guide further development steps.

Inspired by the recent advancements in understanding the binding mode of sulfonylurea-based NLRP3 inhibitors to the NLRP3 sensor protein, we developed new NLRP3 inhibitors by replacing the central sulfonylurea moiety with different heterocycles. Computational studies evidenced that some of the designed compounds were able to maintain important interaction within the NACHT domain of the target protein similarly to the most active sulfonylurea-based NLRP3 inhibitors. Among the studied compounds, the 1,3,4-oxadiazol-2-one derivative 5 (INF200) showed the most promising results being able to prevent NLRP3-dependent pyroptosis triggered by LPS/ATP and LPS/MSU by 66.3 ± 6.6% and 61.6 ± 11.5% and to reduce IL-1β release (35.5 ± 8.8% μM) at 10 μM in human macrophages. The selected compound INF200 (20 mg/kg/day) was then tested in an in vivo rat model of high-fat diet (HFD)-induced metaflammation to evaluate its beneficial cardiometabolic effects. INF200 significantly counteracted HFD-dependent "anthropometric" changes, improved glucose and lipid profiles, and attenuated systemic inflammation and biomarkers of cardiac dysfunction (particularly BNP). Hemodynamic evaluation on Langendorff model indicate that INF200 limited myocardial damage-dependent ischemia/reperfusion injury (IRI) by improving post-ischemic systolic recovery and attenuating cardiac contracture, infarct size, and LDH release, thus reversing the exacerbation of obesity-associated damage. Mechanistically, in post-ischemic hearts, IFN200 reduced IRI-dependent NLRP3 activation, inflammation, and oxidative stress. These results highlight the potential of the novel NLRP3 inhibitor, INF200, and its ability to reverse the unfavorable cardio-metabolic dysfunction associated with obesity.

The COVID-19 pandemic continues to pose a substantial threat to human lives and is likely to do so for years to come. Despite the availability of vaccines, searching for efficient small-molecule drugs that are widely available, including in low- and middle-income countries, is an ongoing challenge. In this work, we report the results of a community effort, the “Billion molecules against Covid-19 challenge”, to identify small-molecule inhibitors against SARS-CoV-2 or relevant human receptors. Participating teams used a wide variety of computational methods to screen a minimum of 1 billion virtual molecules against 6 protein targets. Overall, 31 teams participated, and they suggested a total of 639,024 potentially active molecules, which were subsequently ranked to find ‘consensus compounds’. The organizing team coordinated with various contract research organizations (CROs) and collaborating institutions to synthesize and test 878 compounds for activity against proteases (Nsp5, Nsp3, TMPRSS2), nucleocapsid N, RdRP (Nsp12 domain), and (alpha) spike protein S. Overall, 27 potential inhibitors were experimentally confirmed by binding-, cleavage-, and/or viral suppression assays and are presented here. All results are freely available and can be taken further downstream without IP restrictions. Overall, we show the effectiveness of computational techniques, community efforts, and communication across research fields (i.e., protein expression and crystallography, in silico modeling, synthesis and biological assays) to accelerate the early phases of drug discovery.

The COVID‐19 pandemic continues to pose a substantial threat to human lives and is likely to do so for years to come. Despite the availability of vaccines, searching for efficient small‐molecule drugs that are widely available, including in low‐ and middle‐income countries, is an ongoing challenge. In this work, we report the results of an open science community effort, the “Billion molecules against COVID‐19 challenge”, to identify small‐molecule inhibitors against SARS‐CoV‐2 or relevant human receptors. Participating teams used a wide variety of computational methods to screen a minimum of 1 billion virtual molecules against 6 protein targets. Overall, 31 teams participated, and they suggested a total of 639,024 molecules, which were subsequently ranked to find ‘consensus compounds’. The organizing team coordinated with various contract research organizations (CROs) and collaborating institutions to synthesize and test 878 compounds for biological activity against proteases (Nsp5, Nsp3, TMPRSS2), nucleocapsid N, RdRP (only the Nsp12 domain), and (alpha) spike protein S. Overall, 27 compounds with weak inhibition/binding were experimentally identified by binding‐, cleavage‐, and/or viral suppression assays and are presented here. Open science approaches such as the one presented here contribute to the knowledge base of future drug discovery efforts in finding better SARS‐CoV‐2 treatments.