Computer-Aided Drug Design Using the Fragment Molecular Orbital Method: Current Status and Future Applications for SBDD.

Owing to the increasing use of computers, computer-aided drug design (CADD) has become an essential component of drug discovery research. In structure-based drug design (SBDD), including inhibitor design and in silico screening of drug target molecules, concordance with wet experimental data is important to provide insights on unique perspectives derived from calculations. Fragment molecular orbital (FMO) method is a quantum chemical method that facilitates precise energy calculations. Fragmentation method makes it possible to apply the quantum chemical method to biological macromolecules for energy calculation based on the electron behavior. Furthermore, interaction energies calculated on a residue-by-residue basis via fragmentation aid in the analysis of interactions between the target and ligand molecule residues and molecular design. In this review, we outline the recent developments in SBDD and FMO methods and highlight the prospects of developing machine learning approaches for large computational data using the FMO method.

Interaction Analysis by Fragment Molecular Orbital Method for Drug Discovery Research.

The use of computational methods in drug discovery research has increased substantially in recent years. Computational chemistry techniques, such as quantum chemical calculations and molecular dynamics simulations, continue to be widely used. In this review, we focused on drug discovery-related studies that employ fragment molecular orbital methods. Furthermore, we focused on inhibitor discovery, protein-protein interaction analysis, including antigen-antibody interaction analysis, and integration with molecular dynamics simulations.

Immunoactive signatures of circulating tRNA- and rRNA-derived RNAs in chronic obstructive pulmonary disease.

Chronic obstructive pulmonary disease (COPD) is the most prevalent lung disease, and macrophages play a central role in the inflammatory response in COPD. We here report a comprehensive characterization of circulating short non-coding RNAs (sncRNAs) in plasma from patients with COPD. While circulating sncRNAs are increasingly recognized for their regulatory roles and biomarker potential in various diseases, the conventional RNA sequencing (RNA-seq) method cannot fully capture these circulating sncRNAs due to their heterogeneous terminal structures. By pre-treating the plasma RNAs with T4 polynucleotide kinase, which converts all RNAs to those with RNA-seq susceptible ends (5'-phosphate and 3'-hydroxyl), we comprehensively sequenced a wide variety of non-microRNA sncRNAs, such as 5'-tRNA halves containing a 2',3'-cyclic phosphate. We discovered a remarkable accumulation of the 5'-half derived from tRNAValCAC in plasma from COPD patients, whereas the 5'-tRNAGlyGCC half is predominant in healthy donors. Further, the 5'-tRNAValCAC half activates human macrophages via Toll-like receptor 7 and induces cytokine production. Additionally, we identified circulating rRNA-derived fragments that were upregulated in COPD patients and demonstrated their ability to induce cytokine production in macrophages. Our findings provide evidence of circulating, immune-active sncRNAs in patients with COPD, suggesting that they serve as inflammatory mediators in the pathogenesis of COPD.

Contamination by microplastics and sorbed organic pollutants in the surface waters of the Tietê River, São Paulo-SP, Brazil.

Microplastics (MPs) are particles between 1 µm and 5 mm in size, originating mainly from poor solid waste and effluent management, that can reach water bodies from various sources. In freshwater environments, the occurrence, distribution, and characterization of this new class of pollutants are still little explored, especially in Brazil. The aim of this study was to assess the occurrence of MPs, as well as the presence and concentration of polychlorinated biphenyls (PCBs) sorbed to these particles in the surface waters of the Tietê River - SP. Surface water samples were collected in duplicate during the dry and wet seasons. The identification and characterization of the MPs was carried out through visual inspection and the chemical identity of the particles was verified using Fourier transform infrared spectroscopy with attenuated total reflectance (FTIR-ATR). For the analysis of PCBs adsorbed to the MPs, the sample extracts were analyzed by gas chromatography coupled with mass spectrometry (GC-MS). The MPs were found in concentrations ranging from 6.67 to 1530 particles m-3, with a predominance of the polymers polyethylene (PE, with 58.17 %) and polypropylene (PP, with 23.53 %). The main morphological categories identified were fragments (56.63 %), fibers (28.42 %), and transparent films (13.06 %). Higher abundances of PCBs were observed in the lower size range, between 0.106 and 0.35 mm. The total concentrations of PCBs in MPs ranged from 20.53 to 133.12 ng g-1. The results obtained here are relevant for understanding the dynamics and level of contamination of MPs and organic pollutants sorbed to these particles in the Tietê River, as well as helping with mitigation measures for the restoration and preservation of this ecosystem.

Single Nucleotide Polymorphism-based Identification of Bacterial Artificial Chromosome-mediated Homologous Recombination.

Bacterial Artificial chromosome (BAC) recombineering is a powerful genetic manipulation tool for the efficient development of recombinant genetic resources. Long homology arms of more than 150 kb composed of BAC constructs not only substantially enhance genetic recombination events, but also provide a variety of single nucleotide polymorphisms (SNPs) that are useful markers for accurately docking BAC constructs at target sites. Even if the BAC construct is homologous to the sequences of the target region, different variations may be distributed between various SNPs within the region and those within the BAC construct. Once the BAC construct carrying these variations was precisely replaced in the target region, the SNP profiles within the target genomic locus were directly replaced with those in the BAC. This alteration in SNP profiles ensured that the BAC construct accurately targeted the designated site. In this study, we introduced restriction fragment length polymorphism or single-strand conformation polymorphism analyses to validate and evaluate BAC recombination based on changes in SNP patterns. These methods provide a simple and economical solution to validation steps that can be cumbersome with large homologous sequences, facilitating access to the production of therapeutic resources or disease models based on BAC-mediated homologous recombination.

Versatile and efficient mammalian genome editing with Type I-C CRISPR System of Desulfovibrio vulgaris.

CRISPR-Cas tools for mammalian genome editing typically rely on single Cas9 or Cas12a proteins. While type I CRISPR systems in Class I may offer greater specificity and versatility, they are not well-developed for genome editing. Here, we present an alternative type I-C CRISPR system from Desulfovibrio vulgaris (Dvu) for efficient and precise genome editing in mammalian cells and animals. We optimized the Dvu type I-C editing complex to generate precise deletions at multiple loci in various cell lines and pig primary fibroblast cells using a paired PAM-in crRNA strategy. These edited pig cells can serve as donors for generating transgenic cloned piglets. The Dvu type I-C editor also enabled precise large fragment replacements with homology-directed repair. Additionally, we adapted the Dvu-Cascade effector for cytosine and adenine base editing, developing Dvu-CBE and Dvu-ABE systems. These systems efficiently induced C-to-T and A-to-G substitutions in human genes without double-strand breaks. Off-target analysis confirmed the high specificity of the Dvu type I-C editor. Our findings demonstrate the Dvu type I-C editor's potential for diverse mammalian genome editing applications, including deletions, fragment replacement, and base editing, with high efficiency and specificity for biomedicine and agriculture.

Pythium and Globisporangium species associated with cucumber rhizosphere causing damping-off and their effects on cucumber seed decay in Oman.

Pythium sensu lato (s.l.) is a pathogenic oomycete. The present study was conducted to isolate and identify Pythium s.l. species associated with the rhizosphere and roots of greenhouse-growing cucumbers showing damping-off symptoms in 10 Omani governorates (provinces). A total of 166 isolates were recovered from 276 rhizosphere soil and root samples and were identified based on the ribosomal DNA (rDNA) internal transcribed spacer (ITS) region and the cytochrome c oxidase subunit I (COX I) gene region. Pythium aphanidermatum, P. myriotylum, Globisporangium spinosum, Globisporangium sp.1 (isolates Kb003/PySyCu-1 and Kb004/PySyCu-2), and Globisporangium sp.2 (isolate Ib002R) were identified. Among these species, P. aphanidermatum was the most abundant species, represented by 143 isolates (86.1%), followed by G. spinosum with 18 isolates (10.8%), Globisporangium sp.1 and P. myriotylum each with 2 isolates (2.4%), and Globisporangium sp.2 with 1 isolate (0.6%). Pathogenicity tests were also conducted for 38 isolates, including P. aphanidermatum (25), P. myriotylum (2), Globisporangium sp.2 (1), G. spinosum (8), and Globisporangium sp.1 (2). Among the tested isolates, only Globisporangium sp.2 isolate was avirulent, and none of the seeds were rotted at the end of the treatment. However, the other species induced the symptoms of seed decay with the incidence ranged from 86.7 to 100%. Phylogenetic analyses were conducted based on 222 ITS and 53 COX I sequences, and confirmed morphological identification. In addition, the genetic diversity of 93 P. aphanidermatum isolates was assessed via the amplified fragment length polymorphism (AFLP) method. The analysis produced 93 genotypes and 449 polymorphic loci. Pythium aphanidermatum populations were found to have moderate levels of genetic diversity (H = 0.2) and a moderate Shannon information index (I = 0.3793). Analysis of molecular variance (FST = 0.1, P = 0.0) revealed a moderate level of genetic differentiation among P. aphanidermatum isolates between Oman governorates. The sensitivity of 15 P. aphanidermatum isolates was evaluated against hymexazol at different concentrations (10, 100, and 1000 ppm). The results revealed that P. aphanidermatum could grow well at concentrations of up to 100 ppm hymexazol. However, hymexazol at 1000 ppm retarded the growth of P. aphanidermatum. This study showed that P. aphanidermatum is the most prevalent species in greenhouses in Oman and exhibited a moderate level of genetic diversity. Most of the isolates exhibited differences in tolerance to hymexazol but showed no resistance.

Mapping protein conformational landscapes from crystallographic drug fragment screens.

Proteins are dynamic macromolecules. Knowledge of a protein's thermally accessible conformations is critical to determining important transitions and designing therapeutics. Accessible conformations are highly constrained by a protein's structure such that concerted structural changes due to external perturbations likely track intrinsic conformational transitions. These transitions can be thought of as paths through a conformational landscape. Crystallographic drug fragment screens are high-throughput perturbation experiments, in which thousands of crystals of a drug target are soaked with small-molecule drug precursors (fragments) and examined for fragment binding, mapping potential drug binding sites on the target protein. Here, we describe an open-source Python package, COLAV (COnformational LAndscape Visualization), to infer conformational landscapes from such large-scale crystallographic perturbation studies. We apply COLAV to drug fragment screens of two medically important systems: protein tyrosine phosphatase 1B (PTP-1B), which regulates insulin signaling, and the SARS CoV-2 Main Protease (MPro). With enough fragment-bound structures, we find that such drug screens also enable detailed mapping of proteins' conformational landscapes.

Analysis of variation of serum CEA, SCC, CYFRA21-1 in patients with lung cancer and their diagnostic value with EBUS-TBNA.

Background: To explore the variation of serum carcinoembryonic antigen (CEA), cytokeratin 19 fragment (CYFRA21-1), and squamous cell carcinoma (SCC) antigen in patients with lung cancer (LC) and their diagnostic value with endobronchial ultrasound-guided transbronchial needle aspiration (EBUS-TBNA). Methods: This study examined the diagnostic value of serum tumor marker testing and EBUS-TBNA joint detection for LC in 150 patients with suspected LC. Results: Compared to benign patients, the serum levels of CYFRA21-1, SCC, and CEA in LC were higher (P<0.05). In patients with squamous cell carcinoma (LSCC), small cell lung cancer (SCLC), and lung adenocarcinoma, lung adenocarcinoma had higher serum CEA levels (P<0.05). In comparison, LSCC patients had higher serum SCC and CYFRA21-1 levels (P<0.05). As compared to each index detected alone, the AUC of combined detection of each index to diagnose LC and identify pathological types of LC was elevated. Conclusions: The clinical significance of serum CYFRA21-1, SCC, and CEA conjugated with EBUS-TBNA is demonstrated for diagnostic purposes and identification of LC pathological types.

Different Approaches to the Treatment of Anterior Tooth Fractures: Three Clinical Cases and Behavior Report.

Fractures of the anterior teeth are a common form of dental trauma. This article includes three case reports of uncomplicated fractures of upper anterior teeth in which collaborators had different treatment protocols. The choice of the treatment method is based on the direction of the specific clinical case and the clinical findings. Of great importance to the treatment approach are the measures taken by the patient to preserve the fractured fragment, the age of the fracture, and the time available to patients and clinicians. When the fractured fragment is available and is well-preserved, the best approach is to fix it to the crown of the tooth. This protocol is extremely fast and inexpensive, with minimal potential for problems in esthetics and function. In the absence of the fractured fragment, the treatment approaches are different, as described in cases 2 and 3. If the patient or the clinician is unable to make a repeat visit, the restoration is carried out using a freehand technique. Protocols involving fracture repair using composite materials are more labor-intensive. Esthetic complications are often observed, which may be due to wrong determined shade, loss of luster, and change over the years in the color of the restoration, as well as fracture of the restoration. With advances in dentistry, these disadvantages have been minimized.

Characterization of alternate encounter assemblies of SARS-CoV-2 main protease.

The assembly of two monomeric constructs spanning segments 1-199 (MPro1-199) and 10-306 (MPro10-306) of SARS-CoV-2 main protease (MPro) was examined to assess the existence of a transient heterodimer intermediate in the N-terminal autoprocessing pathway of MPro model precursor. Together, they form a heterodimer population accompanied by a 13-fold increase in catalytic activity. Addition of inhibitor GC373 to the proteins increases the activity further by ∼7-fold with a 1:1 complex and higher order assemblies approaching 1:2 and 2:2 molecules of MPro1-199 and MPro10-306 detectable by analytical ultracentrifugation and native mass estimation by light scattering. Assemblies larger than a heterodimer (1:1) are discussed in terms of alternate pathways of domain III association, either through switching the location of helix 201-214 onto a second helical domain of MPro10-306 and vice versa or direct interdomain III contacts like that of the native dimer, based on known structures and AlphaFold 3 prediction, respectively. At a constant concentration of MPro1-199 with molar excess of GC373, the rate of substrate hydrolysis displays first order dependency on the MPro10-306 concentration and vice versa. An equimolar composition of the two proteins with excess GC373 exhibits half-maximal activity at ∼6 µM MPro1-199. Catalytic activity arises primarily from MPro1-199 and is dependent on the interface interactions involving the N-finger residues 1-9 of MPro1-199 and E290 of MPro10-306. Importantly, our results confirm that a single N-finger region with its associated inter-subunit contacts is sufficient to form a heterodimeric MPro intermediate with enhanced catalytic activity.

Characterization of SSR markers from draft genome assembly and genotypic data in Hedychium spicatum (Zingiberaceae).

The plant family Zingiberaceae consists of many medicinally important tropical herbs. Here, we provide a contig level genome assembly for Hedychium spicatum, one of the medicinally utilized species in this family. We used genome assembly to identify candidate Simple Sequence Repeat (SSR) markers in the nuclear, chloroplast and mitochondrial compartments. We identified a total of 60,695 SSRs, which consisted of di-, tri-, tetra-, penta- and complex repeat types, and primers were designed for 14,851 SSR loci from both coding and non-coding parts of the genome. A total of 62 sets of candidate SSR primers were tested, out of which a final set of 20 SSR markers were characterized and they met the criteria of amplification success and retention of the repeat motif and homology. Out of these 20 markers, we genotyped 11 markers by amplifying and sizing 99 accessions of H. spicatum from 13 different geographic locations. The 11 markers were also characterised for four congeneric species, H. ellipticum, H. gomezianum, H. venustum, and H. yunnanense. All 11 SSR markers were found to be polymorphic and showed cross-species amplification. The total number of alleles per locus varied from 5 to 25. SSR markers continue to be a valuable tool for researchers because of their cost-effectiveness and simplicity. The cross-species amplification and variability of the SSR markers generated here further extend the utility of the markers to other Hedychium spp. The markers presented in this dataset can be used for a variety of studies, such as population genetics of invasive Hedychium species, QTL mapping, DNA fingerprinting, parentage analysis and genetic diversity assessments.

All-body concept and quantified limits of cooperativity and related effects in homodromic cyclic water clusters from a molecular-wide and electron density-based approach.

We strongly advocate distinguishing cooperativity from cooperativity-induced effects. From the MOWeD-based approach, the origin of all-body cooperativity is synonymous with physics- and quantum-based processes of electron (e) delocalization throughout water clusters. To this effect, over 10 atom-pairs contribute to the total e-density at a BCP(H,O) between water molecules in a tetramer. Intermolecular all-body e-delocalization, that is, cooperativity, is an energy-minimizing process that fully explains non-additive increase in stability of a water molecule in clusters with an increase in their size. A non-linear change in cooperativity and cooperativity-induced effects, such as (i) structural (e.g., a change in d(O,O)) or topological intra- and intermolecular properties in water clusters (e.g., electron density or potential energy density at bond critical points) is theoretically reproduced by the proposed expression. It predicted the limiting value of delocalized electrons by a H2O molecule in homodromic cyclic clusters to be 1.58e. O-atoms provide the vast majority of electrons that "travel throughout a cluster predominantly on a privileged exchange quantum density highway" (⋅⋅⋅O-H⋅⋅⋅O-H⋅⋅⋅O-H⋅⋅⋅) using Bader's classical bond paths as density bridges linking water molecules. There are, however, additional electron exchange channels that are not seen on molecular graphs as bond paths. A 3D visual representation of the "privileged" and "additional" exchange channels as well as detailed intra- and inter-molecular patterns of e-sharing and (de)localizing is presented. The energy stabilizing contribution made by three O-atoms of neighboring water molecules was found to be large (-597 kcal/mol in cyclic hexamer) and 5 times more significant than that of a classical O-H⋅⋅⋅O intermolecular H-bond.

How to Find a Fragment: Methods for Screening and Validation in Fragment-Based Drug Dscovery.

Fragment-based drug discovery (FBDD) is a crucial strategy for developing new drugs that have been applied to diverse targets, from neglected infectious diseases to cancer. With at least seven drugs already launched to the market, this approach has gained interest in both academics and industry in the last 20 years. FBDD relies on screening small libraries with about 1000-2000 compounds of low molecular weight (about 300 Da) using several biophysical methods. Because of the reduced size of the compounds, the chemical space and diversity can be better explored than large libraries used in high throughput screenings. This review summarises the most common biophysical techniques used in fragment screening and orthogonal validation. We also explore the advantages and drawbacks of the different biophysical techniques and examples of applications and strategies.

[Identification of chemical components of large-leaf yellow tea by ultra performance liquid chromatography-quadrupole time-of-flight mass spectrometry].

Large-leaf yellow tea, a slightly fermented yellow tea that is unique to China, has a stronger hypoglycemic effect than other tea varieties, such as green and black tea. Research on large-leaf yellow tea has focused on its hypoglycemic effect owing to the lack of comprehensive techniques to characterize its chemical components; thus, its development and further promotion are limited. Therefore, the development of a reliable analytical method to fully characterize the chemical components of large-leaf yellow tea is urgently required. In this study, a reliable strategy based on the data-acquisition technology of ultra performance liquid chromatography-quadrupole time-of-flight mass spectrometry (UPLC-Q TOF/MS) was established to rapidly screen and analyze the main chemical components of large-leaf yellow tea by combining the information of neutral loss groups and characteristic fragment ions. The chromatographic separation experiments were performed on a Waters ACQUITY UPLC BEH C18 column (100 mm×2.1 mm, 1.7 µm) with gradient elution using 0.1% formic acid aqueous solution and acetonitrile as the mobile phases. The flow rate was 0.2 mL/min, the sample volume was 2 µL, and the column temperature was 35 ℃. The mass spectral information of the components in a large-leaf yellow tea solution was collected using the full-information tandem MS (MSE) technique in positive and negative ion modes. The specific chemical components of large-leaf yellow tea was identified as follows. First, a self-established database of tea chemical components was constructed based on the literature. The mass spectral cleavage pathways of different types of compounds in large-leaf yellow tea were then sorted using reference substances, and the characteristics of the fragment ions and neutral loss groups were summarized. The precise mass-to-charge ratio of the target chemical components were then obtained based on the mass spectral information. Finally, the structures of the compounds in large-leaf yellow tea were confirmed based on their chromatographic retention times, mass spectral cleavage pathways, characteristic fragment ions, and neutral loss groups. A total of 87 chemical components, including 10 catechins, 32 flavonoids, 16 phenolic acids, 12 tannins, 6 theaflavins, and 11 compounds in other classes, were identified in large-leaf yellow tea. Representative compounds of various classes, including gallocatechin gallate, quercetin, vitexin, gallic acid, chlorogenic acid, 1,3,6-tri-O-galloyl-ß-D-glucose, and theaflavin, were selected, and their characteristic fragment ions and neutral loss groups were investigated in detail to reveal the cleavage pathways of different types of compounds in large-leaf yellow tea. The UPLC-Q TOF/MS method established in this study can comprehensively identify the main chemical components of large-leaf yellow tea in a simple, highly sensitive, stable, and reliable manner. This study provides a scientific basis and data support for the discovery of functional ingredients and quality evaluation of large-leaf yellow tea.

Unravelling tRNA fragments in DENV pathogenesis: Insights from RNA sequencing.

Small non-coding RNAs (sncRNAs) derived from tRNAs are known as tRNA-derived small RNAs (tsRNAs). These tsRNAs are further categorized into tRNA-derived fragments (tRFs) and tRNA halves (tiRNAs), which play significant roles in the various molecular mechanisms underlying certain human diseases. However, the generation of tsRNAs and their potential roles during Dengue virus (DENV) infection is not yet known. Here, we performed small RNA sequencing to identify the generation and alterations in tsRNAs expression profiles of DENV-infected Huh7 cells. Upon DENV infection, tRNA fragmentation was found to be increased. We identified a significant number of differentially expressed tsRNAs during DENV infection. Interestingly, the 3'tRF population showed upregulation, while the i-tRF population exhibited downregulation. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis was performed to analyze the impact of differentially expressed tsRNAs on DENV pathogenesis. Our results suggest that differentially expressed tsRNAs are involved in transcriptional regulation via RNA polymerase II promoter and metabolic pathways. Overall, our study contributes significantly to our understanding of the roles played by tsRNAs in the complex dynamics of DENV infection.

Comparative Analysis of Commercial Immunoassays for the Determination of Total, Intact, and Nonintact Luteinizing Hormone in Urine.

BACKGROUND: In our recent publications, we reported the identification of three different molecular forms of total luteinizing hormone (LH) in urine, the intact LH, the free beta-subunit (LHß), and its core fragment of LHß (LHßcf), the latter two establishing the nonintact portion of LH. Following the discontinuation of the Delfia immunofluorometric assay (IFMA) (Wallac, PerkinElmer Finland, Finland), a leading method for detecting urinary LH for 30 years, this study seeks to assess the efficacy of three alternative commercial immunoassays in identifying various forms of U-LH. METHODS: Diluted urine samples underwent gel filtration to separate them into fractions, each containing different forms of LH. These were then assayed using Delfia IFMA, Architect LH (Abbott, USA), Elecsys LH Cobas (Roche, Switzerland), and Immulite 2000 LH (Siemens, Germany) immunoassays. RESULTS: Both Delfia and Immulite assays detected total U-LH, that is, all three forms of U-LH, including intact LH, LHß, and LHßcf. Cobas detected only intact LH and LHß, whereas Architect detected solely the intact LH. CONCLUSIONS: Immulite assay can be an alternative tool to detect all forms of urinary LH, a feature likely to be instrumental in developing noninvasive, practical, and scalable solutions for evaluating total U-LH changes during minipuberty in neonates, during the onset of central puberty in peripubertal children, puberty-associated disorders in adolescents, and the fertility window in women, with a special focus on postpeak changes.

Application of engineered antibodies (scFvs and nanobodies) targeting pathological protein aggregates in Alzheimer's disease.

INTRODUCTION: The misfolding and aggregation of proteins are associated with various neurodegenerative diseases, such as Alzheimer's disease (AD). The small-molecule engineered antibodies, such as single-chain fragment variable (scFv) antibodies and nanobodies (Nbs), have gained attention in recent years due to their strong conformational specificity, ability to cross the blood-brain barrier (BBB), low immunogenicity, and enhanced proximity to active sites within aggregates. AREAS COVERED: We have reviewed recent advances in therapies involving scFvs and Nbs that efficiently and specifically target pathological protein aggregates. Relevant publications were searched for in MEDLINE, GOOGLE SCHOLAR, Elsevier ScienceDirect and Wiley Online Library. EXPERT OPINION: We reviewed the recent and specific targeting of pathological protein aggregates by scFvs and Nbs. These engineered antibodies can inhibit the aggregation or promote the disassembly of misfolded proteins by recognizing antigenic epitopes or through conformational specificity. Additionally, we discuss strategies for improving the effective application of engineered antibodies in treating AD. These technological strategies will lay the foundation for the clinical application of small-molecule antibody drugs in developing effective treatments for neurological diseases. Through rational application strategies, small-molecule engineered antibodies are expected to have significant potential in targeted therapy for neurological disorders.

Repurposing Anidulafungin for Alzheimer's Disease via Fragment-Based Drug Discovery.

The misfolding and aggregation of beta-amyloid (Aß) peptides have been implicated as key pathogenic events in the early stages of Alzheimer's disease (AD). Inhibiting Aß aggregation represents a potential disease-modifying therapeutic approach to AD treatment. Previous studies have identified various molecules that inhibit Aß aggregation, some of which share common chemical substructures (fragments) that may be key to their inhibitory activity. Employing fragment-based drug discovery (FBDD) methods may facilitate the identification of these fragments, which can subsequently be used to screen new inhibitors and provide leads for further drug development. In this study, we used an in silico FBDD approach to identify 17 fragment clusters that are significantly enriched among Aß aggregation inhibitors. These fragments were then used to screen anti-infective agents, a promising drug class for repurposing against amyloid aggregation. This screening process identified 16 anti-infective drugs, 5 of which were chosen for further investigation. Among the 5 candidates, anidulafungin, an antifungal compound, showed high efficacy in inhibiting Aß aggregation in vitro. Kinetic analysis revealed that anidulafungin selectively blocks the primary nucleation step of Aß aggregation, substantially delaying Aß fibril formation. Cell viability assays demonstrated that anidulafungin can reduce the toxicity of oligomeric Aß on BV2 microglia cells. Molecular docking simulations predicted that anidulafungin interacted with various Aß species, including monomers, oligomers, and fibrils, potentially explaining its activity against Aß aggregation and toxicity. This study suggests that anidulafungin is a potential drug to be repurposed for AD, and FBDD is a promising approach for discovering drugs to combat Aß aggregation.

Hit me with your best shot: Integrated hit discovery for the next generation of drug targets.

Identification of high-quality hit chemical matter is of vital importance to the success of drug discovery campaigns. However, this goal is becoming ever harder to achieve as the targets entering the portfolios of pharmaceutical and biotechnology companies are increasingly trending towards novel and traditionally challenging to drug. This demand has fuelled the development and adoption of numerous new screening approaches, whereby the contemporary hit identification toolbox comprises a growing number of orthogonal and complementary technologies including high-throughput screening, fragment-based ligand design, affinity screening (affinity-selection mass spectrometry, differential scanning fluorimetry, DNA-encoded library screening), as well as increasingly sophisticated computational predictive approaches. Herein we describe how an integrated strategy for hit discovery, whereby multiple hit identification techniques are tactically applied, selected in the context of target suitability and resource priority, represents an optimal and often essential approach to maximise the likelihood of identifying quality starting points from which to develop the next generation of medicines.