Challenges In Discovery Research Articles

Revealing culturable fungal microbiome communities from the Arabian Peninsula desert representing a unique source of biochemicals for drug discovery and biotechnology

Background Microbes living at extremes evolve unique survival strategies to adapt to challenging environmental conditions. Among these strategies is their distinctive metabolic potential and ability to produce specialized metabolites enabling them to compete for limited resources and defend against predators. These metabolites have significant potential in pharmaceutical and industrial applications, particularly in the development of drugs and biochemicals. Objectives This study aimed to investigate the culturable fungal communities associated with four desert plants and their surrounding soils in the Arabian Peninsula desert to identify their bioactive properties. Methods A total of 12 distinct fungal species were isolated from the plants and soils. Each plant hosted a unique set of fungi, demonstrating the diversity of desert-adapted fungal communities. Biological activities of the fungal extracts were evaluated through various assays, including antimicrobial, antifungal, anticancer, and antioxidant properties. Results Panicum turgidum harbors the most diverse fungal community, dominated by genera such as Mucor, Aspergillus, Colletotrichum, Alternaria, and Chaetomium. Aspergillus species comprise 33% of the total isolates, followed by Fusarium at 16%. All extracts exhibit diverse activities, with Aspergillus species demonstrating the highest antioxidant activities and total phenolic and flavonoid content. Fungi from P. turgidum, particularly Mucor sp., Aspergillus sp., and Curvularia sp., display potent activity against Staphylococcus aureus, while Mucor sp., Chaetomium sp., and Curvularia sp. exhibit moderate inhibition against Pseudomonas aeruginosa. Conclusion This study highlights the importance of exploring extremophilic microorganisms, such as those found in desert ecosystems, as they offer a wealth of compounds that could address current challenges in drug discovery and biotechnology.

Study anti-viral drugs for their efficiency against multiple SARS CoV-2 drug targets within molecular docking, molecular quantum similarity, and chemical reactivity indices frameworks

The study focused on drug discovery for COVID-19, emphasizing the challenges posed by the pandemic and the importance of understanding the virus’s biology. The research utilized molecular docking and quantum similarity analyses to explore potential ligands for SARS-CoV-2 RNA-dependent RNA polymerase. Docking Results Docking outcomes for various ligands, including Oseltamivir, Prochloraz, Valacyclovir, Baricitinib, Molnupiravir, Penciclovir, Famciclovir, Lamivudine, and Nitazoxanide, were presented. Interactions between ligands and specific residues in the RNA-dependent RNA polymerase were analyzed. Reactivity Descriptors Global parameters, such as electronic chemical potential, chemical hardness, global softness, and global electrophilicity, were computed for the ligands. For the local reactivity descriptors, the Fukui Functions were used. Fukui functions, representing electrophilic and nucleophilic sites, were calculated for selected ligands (Valacyclovir and Penciclovir). Nucleophilic character assignments for specific molecular regions were discussed, providing insights into potential charge-donating interactions. Results and Discussion Challenges in COVID-19 drug discovery, such as virus mutability, rapid evolution, and resource limitations, were summarized. Progress in vaccine development and the need for ongoing research to address variants and breakthrough cases were emphasized. Overlap Operator Analysis Higher MQSM between Lamivudine and Molnupiravir (0.5742) indicates structural and electronic similarity. Lowest MQSM between Oseltamivir and Prochloraz (0.2233) implies structural dissimilarity. Coulomb Operator Analysis Higher MQSM between Lamivudine and Molnupiravir (0.9178) suggests both structural and electronic similarity. Lowest MQSM between Baricitinib and Famciclovir (0.6001) indicates greater structural diversity. Measurements above 0.5 in Table 3 suggest electronic similarity, emphasizing the electronic aspects in molecular analysis. In this sense, it study employed a multi-faceted approach combining molecular docking, quantum similarity analyses, and chemical reactivity assessments to explore potential drug candidates for COVID-19. The findings provide valuable insights into ligand interactions, reactivity patterns, and the challenges associated with drug discovery in the context of the global pandemic.

Predation by Coleps sp. (Ciliophora, Prostomatea) on polyps of Hydra (Cnidaria, Hydrozoa)

The present study reveals a novel predator-prey interaction in freshwater ecosystems: that of a free-living protozoan, Coleps sp., and polyps of the genus Hydra. Despite the common perception that larger body size confers competitive advantages, this finding shows that a large number of small-sized phagotrophic organisms, Coleps sp., attack Hydra polyps in groups, first attack their tentacles, and then gradually consuming the entire polyps. This finding was observed in Hydra vulgaris and Hydra sinensis specimens collected in freshwater bodies in São Paulo, Brazil. This discovery challenges traditional notions of size-based competitiveness and demonstrates that Coleps sp. can overcome the defensive barrier of hydra's cnidocytes. The study highlights the adaptability of Coleps sp. in its ability to prey not only on other protozoans, but also on multicellular organisms such as hydras. This suggests an even more complex predation dynamic that could have significant implications for the structure of freshwater zooplankton communities. This work provides a basis for future research into the ecological importance of “minor” predators such as Coleps sp. in regulating aquatic communities and underscores the need for more detailed studies to better understand the interactions between Hydra and Coleps sp., and how these relationships affect zooplankton populations and the overall dynamics of aquatic ecosystems.

Ultra-high-throughput screening of antimicrobial combination therapies using a two-stage transparent machine learning model.

Here, we present M2D2, a two-stage machine learning (ML) pipeline that identifies promising antimicrobial drug combinations, which are crucial for combating drug resistance. M2D2 addresses key challenges in drug combination discovery by predicting drug synergies using computationally generated drug-protein interaction data, thereby circumventing the need for expensive omics data. The model improves the accuracy of drug target identification using high-throughput experimental and computational methods via feedback between ML stages. M2D2's transparent framework provides mechanistic insights into drug interactions and was benchmarked against chemogenomics, transcriptomics, and metabolomics datasets. We experimentally validated M2D2 using high-throughput screening of 946 combinations of Food and Drug Administration (FDA)- approved drugs and antibiotics against Escherichia coli . We discovered synergy between a cerebrovascular drug and a widely used penicillin antibiotic and validated predicted mechanisms of action using genome-wide CRISPR inhibition screens. M2D2 offers a transparent ML tool for rapidly designing combination therapies and guides repurposing efforts while providing mechanistic insights.

Discovery of Elytrurini in Wallacea with a description of Exophthalmida elytrodon sp. nov. from Morotai Island (Coleoptera: Curculionidae: Entiminae).

This study presents the first record of the weevil tribe Elytrurini in Wallacea with the discovery and description of a new species, Exophthalmida elytrodon Yunakov, Bollino, Pancini and Anderson sp. nov., from Morotai Island. Exophthalmida elytrodon sp. nov. is distinguished by its unique morphological traits, including long preapical spines on the elytral declivity in females, which sets it apart from other species in the genus. Remarkably, similar spines are characteristic of other Entiminae of the Australasian region, i.e. Elytrurus Boisduval, 1835 and particularly Ottistira Pascoe, 1872. Distribution maps of Exophthalmida Faust, 1892 and Elytrurni are given. This discovery challenges previous biogeographic assumptions about the distribution of Elytrurini, which were thought to be confined to regions eastward of New Guinea.

The molecular structure, electronic properties, and decomposition mechanism of FOX-7 under external electric field were calculated based on density functional theory.

Based on the density functional theory (DFT), we analyzed the changes of the FOX-7 molecule under external electric field (EEF) from multiple perspectives, including molecular structure, electronic structure, decomposition mechanism, frontier molecular orbitals (FMOs), and density of states (DOS). The results revealed that as the intensity of the positive EEF increased, the detonation performance of the FOX-7 molecule was significantly enhanced, while its thermal stability was also improved. This discovery challenges the traditional concept that explosives are inherently dangerous under external electric fields and provides new insights for research in related fields. To further explore the impact of EEF on the thermal stability of FOX-7, we conducted a thorough analysis of the mechanism by which EEF affects the decomposition process. Our findings indicate that applying a positive EEF significantly increases the energy required to overcome intramolecular hydrogen transfer and C-NO2 bond rupture, while having a relatively minor effect on the nitro isomerization process. This observation further demonstrates that the appropriate application of a positive EEF can enhance the detonation performance of FOX-7 without compromising its thermal stability. Further research revealed that as the intensity of the positive EEF increased, the electronegativity of the nitro group gradually enhanced, leading to an increase in the electronegativity of the oxygen atoms within it. This made the oxygen atoms more prone to participating in chemical reactions. This phenomenon also explains why the energy barrier required for nitro isomerization in FOX-7 gradually decreases as the intensity of the positive EEF increases. Based on the density functional theory (DFT), the structural optimizations were performed both under applied EEF and without EEF at the B3LYP/6-311G (d, p) level. All optimized results were converged and exhibited no imaginary frequencies. Based on the optimized structures, single-point energy calculations were further conducted at the B3LYP/def2-TZVPP level. Subsequently, analyses of molecular structure, electronic structure, decomposition mechanism, frontier molecular orbitals, and density of states were carried out.

Clinical characteristics of patients with granulomatous lobular mastitis associated with Corynebacterium parakroppenstedtii infection and drug sensitivity analysis of the isolated strains

BackgroundIt is presently considered that Corynebacterium especially Corynebacterium kroppenstedtii (CK) infection, is one of the important causes of granulomatous lobular mastitis (GLM). However, the pathogen of mastitis in the past two years has been identified as a newly discovered Corynebacterium. But it is unclear whether the pathogen associated with the occurrence of GLM is also this bacterium.MethodsGLM female patients with positive bacterial culture in pus specimens from February 2023 to February 2024 who were identified as CK infection by mass spectrometer were selected as the research objects in this study, and the clinical isolates were identified by 16S rDNA sequencing technology to identify the specific pathogen of GLM-related bacterial infection. Subsequently, the clinical characteristics of the patients were compared with those of GLM patients without bacterial infection during the same period, to explore the effect of this particular type of Corynebacterium infection on disease development in GLM patients. Finally, we tested the minimum inhibitory concentration (MIC) values of antibiotics when inhibiting these separation strains in vitro through the E-Test experiment, to evaluate their medicine sensitivity.ResultsA total of 31 GLM patients initially diagnosed with Corynebacterium kroppenstedtii (CK) infection via MALDI-TOF MS were enrolled in the study. However, subsequent 16S rDNA sequencing revealed that 28 isolates (90.32%) were actually identified as the newly recognized Corynebacterium parakroppenstedtii (CPK). This discovery challenges the conventional belief that CK is the primary pathogen of GLM, suggesting instead that CPK is the predominant pathogen associated with GLM bacterial infections. Comparative analysis of the clinical characteristics between the two groups revealed a significantly higher recurrence rate among CPK-infected GLM patients compared to those without CPK infection, along with elevated prolactin levels (P < 0.05). The sensitivity test results indicated high sensitivity of the isolates to vancomycin, linezolid, and rifampicin.ConclusionIn conclusion, this study highlights that Corynebacterium kroppenstedtii strains isolated from GLM specimens were Corynebacterium parakroppenstedtii, serving as the primary pathogen closely linked to GLM’s occurrence. CPK infection significantly increases the risk of recurrence in GLM patients, with elevated prolactin levels potentially playing a pivotal role in this process. In clinical antimicrobial treatment, antimicrobials other than penicillin and ciprofloxacin may be empirically administered when sensitivity test results are inconclusive.

Unlocking theoretical strength and ductility in sapphire nanopillars: Insights into size-dependent deformation mechanisms

Developing engineering structures that blend exceptional strength with superior ductility poses a formidable task, given that these attributes typically oppose each other. This is notably evident in brittle materials such as sapphire, where balancing strength and ductility becomes particularly challenging. In our investigation, we illustrate that single-crystal sapphire nanopillars can concurrently achieve both theoretical strength and notable ductility. Through meticulous experimental scrutiny, we have determined that these sapphire pillars exhibit compressive strength levels of up to 22 GPa, in line with the theoretical strength cap of E/10, where E denotes the elastic modulus. This discovery challenges the longstanding belief that ceramics cannot attain their E/10 ideal strength. Furthermore, our research unveils exceptional deformability in these structures, with observed strains reaching up to 20 %. Analyses using Transmission Electron Microscopy (TEM) have unveiled the deformation mechanisms, characterized by dislocation generation and substantial lattice distortions. Additionally, we delve into mechanical modeling to delineate the critical dimensions required to achieve maximum strength and facilitate a transition from brittle to ductile behavior. These revelations demonstrate the feasibility of combining significant strength with remarkable ductility in sapphire at the nanoscale, thereby paving the way for novel applications of brittle materials in precision engineering and nanotechnology.

EvoPath: Evolutionary meta-path discovery with large language models for complex heterogeneous information networks

Heterogeneous Information Networks (HINs) encapsulate diverse entity and relation types, with meta-paths providing essential meta-level semantics for knowledge reasoning, although their utility is constrained by discovery challenges. While Large Language Models (LLMs) offer new prospects for meta-path discovery due to their extensive knowledge encoding and efficiency, their adaptation faces challenges such as corpora bias, lexical discrepancies, and hallucination. This paper pioneers the mitigation of these challenges by presenting EvoPath, an innovative framework that leverages LLMs to efficiently identify high-quality meta-paths. EvoPath is carefully designed, with each component aimed at addressing issues that could lead to potential knowledge conflicts. With a minimal subset of HIN facts, EvoPath iteratively generates and evolves meta-paths by dynamically replaying meta-paths in the buffer with prioritization based on their scores. Comprehensive experiments on three large, complex HINs with hundreds of relations demonstrate that our framework, EvoPath, enables LLMs to generate high-quality meta-paths through effective prompting, confirming its superior performance in HIN reasoning tasks. Further ablation studies validate the effectiveness of each module within the framework.

Rumicidins are a family of mammalian host-defense peptides plugging the 70S ribosome exit tunnel

The antimicrobial resistance crisis along with challenges of antimicrobial discovery revealed the vital necessity to develop new antibiotics. Many of the animal proline-rich antimicrobial peptides (PrAMPs) inhibit the process of bacterial translation. Genome projects allowed to identify immune-related genes encoding animal host defense peptides. Here, using genome mining approach, we discovered a family of proline-rich cathelicidins, named rumicidins. The genes encoding these peptides are widespread among ruminant mammals. Biochemical studies indicated that rumicidins effectively inhibited the elongation stage of bacterial translation. The cryo-EM structure of the Escherichia coli 70S ribosome in complex with one of the representatives of the family revealed that the binding site of rumicidins span the ribosomal A-site cleft and the nascent peptide exit tunnel interacting with its constriction point by the conservative Trp23-Phe24 dyad. Bacterial resistance to rumicidins is mediated by knockout of the SbmA transporter or modification of the MacAB-TolC efflux pump. A wide spectrum of antibacterial activity, a high efficacy in the animal infection model, and lack of adverse effects towards human cells in vitro make rumicidins promising molecular scaffolds for development of ribosome-targeting antibiotics.

Effect of pH on the surface charges of permanently/variably charged soils and clay minerals.

Traditionally, the surface charge number (SCN) of permanently charged soils/clay minerals is believed to be unaffected by environmental pH. However, recent studies have revealed the occurrence of polarization-induced covalent bonding between H+ and the surface O atoms of permanently charged clay minerals. This discovery challenges the traditional notions of "permanently charged soil" and "permanently charged clay mineral". The purpose of this study is to confirm that there are no true "permanently charged clay" or "permanently charged soil". In this study, the SCNs of two permanently charged clay minerals, two variably charged clay minerals, five permanently charged soils (temperate soils), and four variably charged soils (tropical or subtropical soils) were measured at different pH values using the universal determination method of SCN. The results showed that: (1) The SCNs of the permanently/variably charged soils and clay minerals decreased significantly with decreasing pH; (2) the SCN of montmorillonite decreased less with decreasing pH than the SCNs of variably charged minerals, whereas the SCN of illite decreased to nearly the same extent, indicating strong polarization-induced covalent bonding between H+ and the surface O atoms of illite; (3) the SCNs of permanently charged soils decreased to a similar extent as those of variably charged soils with decreasing pH. This study demonstrated that the concepts, "permanently charged clay mineral" or "permanently charged soil", are questionable because of the polarization-induced covalent bonding between H+ and the surface O atoms of clay minerals.

Impact and characterization of serial structural variations across humans and great apes

Modern sequencing technology enables the systematic detection of complex structural variation (SV) across genomes. However, extensive DNA rearrangements arising through a series of mutations, a phenomenon we refer to as serial SV (sSV), remain underexplored, posing a challenge for SV discovery. Here, we present NAHRwhals (https://github.com/WHops/NAHRwhals), a method to infer repeat-mediated series of SVs in long-read genomic assemblies. Applying NAHRwhals to haplotype-resolved human genomes from 28 individuals reveals 37 sSV loci of various length and complexity. These sSVs explain otherwise cryptic variation in medically relevant regions such as the TPSAB1 gene, 8p23.1, 22q11 and Sotos syndrome regions. Comparisons with great ape assemblies indicate that most human sSVs formed recently, after the human-ape split, and involved non-repeat-mediated processes in addition to non-allelic homologous recombination. NAHRwhals reliably discovers and characterizes sSVs at scale and independent of species, uncovering their genomic abundance and suggesting broader implications for disease.

A hidden clock that times cytoplasmic divisions

Our recent study reveals that in fruit fly embryos, the cell's cytoplasm can divide on its own, without waiting for the nucleus or relying on the usual cell division signals. This discovery challenges what we thought we knew about how cells divide and opens up new questions about how these processes are controlled.

Still waters and deep: Habitat characteristics, density and distribution of a lake-dwelling population of the freshwater pearl mussel Margaritifera margaritifera

The freshwater pearl mussel, Margaritifera margaritifera is widely considered to be confined to fast-flowing, near-pristine rivers, and is highly endangered throughout its Holartic range. Here we describe a large population of some 150–200,000 individuals of the freshwater pearl mussel living in an oligotrophic Irish lake.Employing underwater photographic techniques and snorkel diving, mussels were found in two separate locations in the lake. In the first location, 200 m from the shore, mussels were found at a maximum density of 43 m−2, in a largely random distribution in the sandy bed substrate of the lake, up to 9.5 m deep. In the second shoreline location, mussels were observed in dense aggregations up to 118 individuals m−2, in sandy pockets in between boulders and bedrock, in waters 1–2 m deep. In both locations, mussels were found associated with macrophytes – the charophyte Nitella sp. in the deeper location and the quillwort Isoetes lacustris in the shallower shoreline location. Juvenile mussels (>1.5 cm length) were observed lying exposed on the sediment surface in the shallow littoral location, indicating that recruitment occurs in this population, although no estimates of juvenile density were obtained.The discovery of a large population of lentic Margaritifera margaritifera has significant implications for the species’ conservation and indicates that there may be substantial lentic populations of the species elsewhere. The environmental envelope of the species is clearly much wider than thought and our discovery challenges assumptions about the fundamental feeding and reproductive biology of this endangered species.

Exploring the Depths of the Autocorrelation Function: Its Departure from Normality

In this article, we study the autocorrelation function (ACF), which is a crucial element in time series analysis. We compare the distribution of the ACF, both from a theoretical and empirical point of view. We focus on white noise processes (WN), i.e., uncorrelated, centered, and identically distributed variables, whose ACFs are supposed to be asymptotically independent and converge towards the same normal distribution. But, the study of the sum of the sample ACF contradicts this property. Thus, our findings reveal a deviation of the sample ACF from normality beyond a specific lag. Note that this phenomenon is observed for white noise of varying lengths, and evenforn the residuals of an ARMA(p,q) model. This discovery challenges traditional assumptions of normality in time series modeling. Indeed, when modeling a time series, the crucial step is to validate the estimated model by checking that the associated residuals form white noise. In this study, we show that the widely used portmanteau tests are not completely accurate. Box–Pierce appears to be too conservative, whereas Ljung–Box is too liberal. We suggest an alternative method based on the ACF for establishing the reliability of the portmanteau test and the validity of the estimated model. We illustrate our methodology using money stock data in the USA.

Demystifying large language models in second language development research

Evaluating students' textual response is a common and critical task in language research and education practice. However, manual assessment can be tedious and may lack consistency, posing challenges for both scientific discovery and frontline teaching. Leveraging state-of-the-art large language models (LLMs), we aim to define and operationalize LLM-Surprisal, a numeric representation of the interplay between lexical diversity and syntactic complexity, and to empirically and theoretically demonstrate its relevance for automatic writing assessment and Chinese L2 (second language) learners’ English writing development. We developed an LLM-based natural language processing pipeline that can automatically compute text Surprisal scores. By comparing Surprisal metrics with the widely used classic indices in L2 studies, we extended the usage of computational metrics in Chinese learners’ L2 English writing. Our analyses suggested that LLM-Surprisals can distinguish L2 from L1 (first language) writing, index L2 development stages, and predict scores provided by human professionals. This indicated that the Surprisal dimension may manifest itself as critical aspects in L2 development. The relative advantages and disadvantages of these approaches were discussed in depth. We concluded that LLMs are promising tools that can enhance L2 research. Our showcase paves the way for more nuanced approaches to computationally assessing and understanding L2 development. Our pipelines and findings will inspire language teachers, learners, and researchers to operationalize LLMs in an innovative and accessible manner.

Discovery of a novel spotted fever group Rickettsia, "Candidatus Rickettsia kedanie," in unfed larval chigger mites, Leptotrombidium scutellare.

Spotted fever group (SFG) rickettsia, the causative agent of SFG rickettsiosis, is predominantly carried by ticks, whereas Orientia tsutusgamushi, the causative agent of scrub typhus, is primarily transmitted by chigger mites in Japan. In this study, we attempted to isolate intracellular eubacteria from Leptotrombidium scutellare, a major vector of O. tsutsugamushi; moreover, we isolated an SFG rickettsia using a mosquito-derived cell line. Draft genome sequences of this unique isolate, by applying criteria for species delimitation, classified this isolate as a novel strain, proposed as "Rickettsia kedanie." Further genetic analysis identified conserved virulence factors, and the isolate successfully propagated in mammalian cells, suggesting its ability to cause diseases in humans. The presence of SFG rickettsia in unfed larvae implies potential dual-pathogen carriage and reflects a symbiotic relationship similar to that between the mites and O. tsutsugamushi, indicating possibility of its transovarial transmission from female adults. Furthermore, conserved genomic similarity of the novel isolate to known SFG rickettsia suggests potential multiple hosts, including chiggers and ticks. In the natural environment, ticks, chigger mites, and wild animals may carry new isolates, complicating the infection cycle and increasing the transmission risks to humans. This discovery challenges the conventional association of SFG rickettsia with ticks, emphasizing its implications for research and disease control. However, this study was confined to a particular species of chigger mites and geographic area, underscoring the necessity for additional studies to comprehend the ecological dynamics, host interactions, and health implications linked to this newly identified SFG rickettsia.

Targeting SARS-CoV-2 Spike and Main protease with phytochemicals from Herbs and spices: Molecular Docking and dynamics simulation studies.

Abstract COVID-19, a pandemic disease has affected 480 million people and caused 6 million deaths around the world. Despite the progress made in COVID-19 drug discovery, SARS-CoV-2, the causative agent of this disease continuously mutates and rapidly evolves into new variants. This increases the challenges in drug discovery for COVID-19. As natural products serve as sources of drugs forever, this study applies computational techniques in predicting the natural compounds in herbs and spices of household origin as SARS-CoV-2 spike and protease inhibitors and also verifies the top hits against spike and protease mutants associated with SARS-CoV-2 variants of concern. This study reveals Hesperidin, Diosgenin, Fenugreekine, Epigallocatechin gallate and Quercetin as SARS-CoV-2 spike and protease inhibitors, which acts better than the drug Remdesivir. The efficiency of the top hits was also been verified against the mutants, which reveals Diosgenin and Fenugreekine as the most efficient natural compounds against SARS-CoV-2 spike mutants (N501Y, E484K, K417N and K417T), which are associated with SARS-CoV-2 variants of concern. Additionally, Hesperidin is proven to have better binding efficiency against Mpro mutants (Y54C, A191V, T190I and N142S). Overall, this study concludes that Hesperidin, Diosgenin and Fenugreekine could combat both SARS-CoV-2 and its variants effectively.

An Overview on Nocardiopsis Species Originating From North African Biotopes as a Promising Source of Bioactive Compounds and In Silico Genome Mining Analysis of Three Sequenced Genomes.

Actinobacteria are renowned for their prolific production of diverse bioactive secondary metabolites. In recent years, there has been an increasing focus on exploring "rare" genera within this phylum for biodiscovery purposes, notably the Nocardiopsis genus, which will be the subject of the present study. Recognizing the absence of articles describing the research process of finding bioactive molecules from the genus Nocardiopsis in North African environments. We, therefore, present a historical overview of the discoveries of bioactive molecules of the genus Nocardiopsis originating from the region, highlighting their biological activities and associated reported molecules, providing a snapshot of the current state of the field, and offering insights into future opportunities and challenges for drug discovery. Additionally, we present a genome mining analysis of three genomes deposited in public databases that have been reported to be bioactive. A total of 36 biosynthetic gene clusters(BGCs) were identified, including those known to encode bioactive molecules. Notably, a substantial portion of the BGCsshowed little to no similarity to those previously described, suggesting the possibility that the analyzed strains could be potential producers of new compounds. Further research on these genomes is essential to fully uncovering their biotechnological potential. Moving forward, we discuss the experimental designs adopted in the reported studies, as well as new avenues to guide the exploration of the Nocardiopsis genus in North Africa.

Ligandability at the Membrane Interface of GPx4 Revealed through a Reverse Micelle Fragment Screening Platform.

While they account for a large portion of drug targets, membrane proteins present a unique challenge for drug discovery. Peripheral membrane proteins (PMPs), a class of water-soluble proteins that bind to membranes, are also difficult targets, particularly those that function only when bound to membranes. The protein-membrane interface in PMPs is often where functional interactions and catalysis occur, making it a logical target for inhibition. However, protein-membrane interfaces are underexplored spaces in inhibitor design, and there is a need for enhanced methods for small-molecule ligand discovery. In an effort to better initiate drug discovery efforts for PMPs, this study presents a screening methodology using membrane-mimicking reverse micelles (mmRM) and NMR-based fragment screening to assess ligandability at the protein-membrane interface. The proof-of-principle target, glutathione peroxidase 4 (GPx4), is a lipid hydroperoxidase that is essential for the oxidative protection of membranes and thereby the prevention of ferroptosis. GPx4 inhibition is promising for therapy-resistant cancer therapy, but current inhibitors are generally covalent ligands with limited clinical utility. Presented here is the discovery of noncovalent small-molecule ligands for membrane-bound GPx4 revealed through the mmRM fragment screening methodology. The fragments were tested against GPx4 under bulk aqueous conditions and displayed little to no binding to the protein without embedment into the membrane. The 9 hits had varying affinities and partitioning coefficients and revealed properties of fragments that bind within the protein-membrane interface. Additionally, a secondary screen confirmed the potential to progress the fragments by enhancing the affinity from >200 to ∼15 μM with the addition of certain hydrophobic groups. This study presents an advancement of screening capabilities for membrane-associated proteins, reveals ligandability within the GPx4 protein-membrane interface, and may serve as a starting point for developing noncovalent inhibitors of GPx4.