Design and investigation of novel iridoid-based peptide conjugates for targeting EGFR and its mutants L858R and T790M/L858R/C797S: an in silico study

In this work, we designed novel peptide conjugates with plant-based iridoid and lichen-derived depside derivatives to target the wild-type EGFR (WT) and its mutants, L858R and T790M/L858R/C797S triple mutant. These mutations are often expressed in multiple cancers, particularly lung cancer. Specifically, the iridoids included 7-deoxyloganetic acid (7-DGA) and loganic acid (LG), while the depside derivative was sekikaic acid (SK). These compounds are known for their innate anticancer properties and were conjugated with two separate peptide sequences KLPGWSG (K) and YSIPKSS (Y). These sequences have been shown to target EGFR in previous phage display library screening, although the mechanism is unknown. Thus, we created the di-conjugates for dual targeting and investigated their interactions of the di-conjugates and that of the neat peptides with the kinase domain of EGFR (WT) and the two mutants using molecular docking, molecular dynamics (MD) simulations, and MM-GBSA analysis. Docking studies revealed that the (7-DGA)2-K showed the highest binding affinity at - 9.3 kcal/mol with the L858R mutant, while (LG)2-Y displayed the highest binding affinity at - 9.0 kcal/mol for the triple mutant receptor. Our results indicated that several of the conjugates interacted with crucial residues of the kinase domain, including ASP855 and THR854 (activation loop), MET793 and PRO794 (hinge region), ARG841 (catalytic loop), and LYS728 and LEU718 of the glycine-rich P-loop. Interestingly, strong hydrophobic interactions were also observed with the C-terminal tail residues, such as PHE997 and ALA1000 as well as with ARG999 for the YSIPKSS peptide and most of the conjugates. The hydroxyl group of the cyclopentane ring and the oxygen of the pyran ring of the (7-DGA)2-peptide conjugates contributed to binding particularly in the hinge region, while the peptide components formed an extended structure that bound well into the C-lobe. The (SK)2-Y di-conjugate and KLPGWSG peptide formed hydrogen bonds with the SER797 residue of the triple mutant. Overall, our results show that the (7-DGA)2-K, di-conjugate, the (7-DGA)2-Y di-conjugate, and the neat YSIPKSS demonstrated strong and stable binding with the L858R mutant and the highly resistant triple mutant EGFR, respectively. The novel designed conjugates demonstrate potential for further optimization for laboratory studies aimed at developing new therapeutics for targeting specific EGFR mutant expressing cells.

PocketSCP: A Method for Spatiotemporal Topological Visualization and Analysis of Protein Pocket Dynamics

The identification and analysis of pockets are crucial for understanding the functional mechanisms and therapeutic potential of proteins. However, it is challenging to track the dynamic characteristics of the pockets. In this paper, we present a method for the visualization and analysis of protein pocket dynamics called PocketSCP. Initially, the representation of lining amino acid atoms is proposed to characterize the spatiotemporal and topological properties of pockets. Subsequently, 3D mapping based on a reference molecular conformation is designed to generate 3D distribution maps of pockets. To facilitate observation and analysis, 3D to 2D plane mapping based on equidistant azimuthal projection is designed, leveraging the near-spherical shape properties of protein molecules. Finally, the efficacy of our method in identifying potential patterns within protein pockets is demonstrated through experimental validation.

Exploring hidden natural resources for bioactive compounds: Focused chemical and biological studies on some Anthemis species

The present study investigated the phytochemical composition and biological activities of extracts from the aerial parts of Anthemis austriaca, A. cretica subsp. albida, A. pauciloba, A. tinctoria and A. wiedemanniana. About 150 compounds belonging to hydroxybenzoic acids, hydroxycinnamic acids, phenylethanoid glycosides, acylquinic acids, acylhexaric acids, flavonoids and sesquiterpene lactones were identified. A. tinctoria also displayed significant antiradical activity, obtained from its MeOH and 70 % MeOH extracts. EtOAc and MeOH extracts of A. pauciloba revealed the highest anti-acetylcholinesterase activity (3.51 and 3.50 mg GALAE/g; p > 0.05). Extracts had a higher affinity towards human carbonic anhydrase isoenzymes I (CAI) than CAII, and the best inhibition effect was exerted by EtOAc extract of A. wiedemanniana a (IC50 7.02 μg/mL). Network pharmacology analysis identified IL6 and TNFα as key targets of these plant-derived molecules, underscoring their multi-target potential. Anthemis extracts' efficacy in blunting LPS-induced IL6 and TNFα gene expression in isolated mouse colon has confirmed these predictions. Molecular docking studies further confirmed that these compounds interact with multiple transcription factors (TFs), suggesting broad pharmacological activity. These results indicated that the five Anthemis species could be a promising source of bioactive molecules.

Chain-length preference of trans-acting enoylreductases involved in the biosynthesis of fungal polyhydroxy polyketides

Fungal polyketides are diverse natural products synthesized by iterative polyketide synthases (i-PKSs) and modified by enzymes such as trans-acting enoylreductases (trans-ERs). In this study, we investigated PhiaB and PhomB, trans-ERs involved in the biosynthesis of polyhydroxy polyketides, phialotides, and phomenoic acids. In vitro assays using substrate analogs revealed distinct chain-length preferences. X-ray structural analysis of PhiaB revealed distinct N-terminal, central, and C-terminal regions. The importance of the central region, which possesses a canonical Rossmann fold for cofactor recognition, was further supported by biosynthetic refactoring using a chimeric enzyme. Docking studies revealed key amino acid residues that may be involved in substrate/cofactor recognition. These findings advance our understanding of trans-ER function, providing opportunities for the synthesis of structurally different polyhydroxy polyketides by genetic engineering of polyhydroxy polyketide biosynthesis.

Lipophilic Extracts of Portulaca oleracea L.: Analysis of Bioactive Fatty Acids Targeting Microbial and Cancer Pathways

Background/Objectives:Portulaca oleracea L. (purslane) is a widely distributed plant known for its medicinal and nutritional properties. This study aims to evaluate the fatty acid composition and bioactivities of crude lipophilic extracts (chloroform/methanol 2:1) from purslane collected in Serbia and Greece, with a focus on its antimicrobial and anticancer potential. Methods: Chemical analysis was conducted to determine the fatty acid composition of the extracts. Antibacterial activity was assessed using standard microdilution assays, while antibiofilm assays evaluated the extracts' ability to inhibit biofilm formation. Cytotoxicity was tested on cancer cell lines (MCF7, HeLa, CaCo2, HepG2) and normal keratinocyte cells (HaCaT). Molecular docking and dynamics simulations were performed to explore the interactions of bioactive fatty acids with microbial and cancer-related proteins. Results: The analysis revealed significant levels of polyunsaturated fatty acids, with linoleic acid as the predominant fatty acid in both samples (31.42% and 34.51%). The Greek extract exhibited stronger antibacterial activity than the Serbian extract, particularly against Aspergillus versicolor, Pseudomonas aeruginosa, and Staphylococcus aureus. Antibiofilm assays showed up to 89.54% destruction at MIC levels, with notable reductions in exopolysaccharide and extracellular DNA production, especially for Greek samples. Cytotoxicity testing indicated moderate effects on cancer cell lines (IC50 = 178.17-397.31 µg/mL) while being non-toxic to keratinocytes. Molecular docking identified strong interactions between key fatty acids and microbial and cancer-related proteins. Conclusions: These results highlight purslane's potential as a source of bioactive compounds, particularly in antimicrobial and anticancer applications. The findings suggest that purslane extracts could be developed for therapeutic purposes targeting microbial infections and cancer.

Unveiling multiple copies of MlaC highlights its multifaceted nature

The maintenance of the lipid asymmetry (Mla) system plays a critical role in facilitating the transport of phospholipids between the inner and outer membranes of the Gram-negative bacteria. In E. coli, the system consists of six proteins: MlaA-OmpF/C complex (outer membrane), MlaC (periplasm), and MlaFEDB complex (inner membrane). Despite extensive research on the core proteins (MlaFED) of the Mla system, the occurrence of Mla components like MlaA, MlaB, and MlaC in diderm remains uncertain. Therefore, this gap presents a significant opportunity for further investigation, particularly regarding MlaC, which serves as the sole mobile component of the Mla system. This has led to the identification of multiple copies of MlaC in 63 distinct genera of Proteobacteria and related phyla. Interestingly, amongst these genera, the genetic arrangements of the mla operon were observed to be varying and, thus, were further categorized into four distinct groups. The variations among the genetic organization of the mla operons suggest their evolution through various processes, such as duplications, losses, rearrangements, and fusions. Further, the results of this study highlight the MlaC's substrate promiscuity, illuminating new avenues for the Mla system.

The Biopotential of Bellardia trixago in Replacing Synthetic Compounds for Health-Promoting Applications: Is It a Promising Candidate?

Bellardia trixago (L.) All. (family Orobanchaceae) is a facultative hemiparasitic plant used traditionally to cure many diseases. The present study was designed to evaluate the phenolic constituents, antioxidant, enzyme inhibitory, and cytotoxic properties of the aerial parts of B. trixago. Ethyl acetate (EtOAc), ethanol (EtOH), and 70% EtOH extracts were prepared by maceration, while the aqueous extract was prepared by infusion. Rutin, 4-hydroxy benzoic acid, ferulic acid, p-coumaric acid, hyperoside, delphinidin 3,5 diglucoside, kaempferol, and isoquercitrin were identified in most extracts with variable concentrations, but generally, the EtOH or 70% EtOH accumulated the highest contents. The 70% EtOH extract displayed the best antiradical (DPPH = 13.55 mg TE/g; ATBS = 53.78 mg TE/g) and ion-reducing (CUPRAC = 50.09 mg TE/g; FRAP = 24.73 mg TE/g) properties. The aqueous extract recorded the highest chelating iron power (12.91 mg EDTAE/g) while EtOAc and EtOH exerted the highest total antioxidant activity (2.29 and 2.49 mmol TE/g, p > 0.05). The best cholinesterase (anti-AChE = 2.91 mg GALAE/g; and anti-BchE = 2.62 mg GALAE/g) and α-glucosidase (1.19 mmol ACAE/g) inhibition activity was recorded from the EtOH extract, while that against the α-amylase was obtained from the EtOAc extract (0.69 mmol ACAE/g). The plant was most cytotoxic toward the HT-29 cell line, where the best effect was exerted by the 70% EtOH (IC50 38.42 μg/mL) extract. Furthermore, network pharmacology analysis revealed critical gene targets and pathways associated with the bioactive compounds. Molecular docking studies revealed favorable binding modes and interaction patterns of major compounds with key colon cancer-related proteins, which were further supported by molecular dynamics simulations. As the first investigation into the phenolic composition and pharmacological effects of B. trixago, this study highlights its potential as a promising source of bioactive compounds with therapeutic relevance for oxidative stress-related conditions.

Exploring the Utility of Prunus mahaleb Extracts as a Source of Natural Bioactive Compounds for Functional Applications

Prunus mahaleb has garnered attention as a potent medicinal agent and functional component. We aimed to detect the chemical composition and biological activities of several parts (fruit, leaves, and twigs) of P. mahaleb. Biological activities were assessed for antioxidant properties, enzyme inhibition, mutagenic/antimutagenic effects, and antibacterial efficacy. Antioxidant capabilities were evaluated using various assays, including DPPH, ABTS, CUPRAC, FRAP, phosphomolybdenum, and metal chelating. The chemical constituents of the extracts were identified and quantified using the HPLC-ESI-MS/MS method. The effects of enzyme inhibition were examined on some enzymes, including AChE, BChE, tyrosinase, amylase, and glucosidase. The Ames test was used to evaluate the mutagenic and antimutagenic properties of the plant extracts. Furthermore, a broth microdilution assay was employed to evaluate the possible antibacterial effects of the extracts against microorganisms. The methanol extract of twigs showed superior antioxidant capabilities (DPPH: 388.39 mg TE/g; ABTS: 701.50 mg TE/g; CUPRAC: 459.05 mg TE/g; FRAP: 264.99 mg TE/g). The methanol extract of twigs demonstrated the highest tyrosinase inhibitory activity (61.91 mg KAE/g). A total of 40 metabolites, mainly flavonoids, were detected through HPLC-ESI-MS/MS analysis, revealing that ferulic acid, naringenin, and herniarin were the predominant compounds. In the Ames test, the tested extracts exhibited no mutagenic potential. The antimutagenicity assay demonstrated that methanol and ethyl acetate extracts from twigs and leaves were particularly efficient against frameshift and base pair substitution mutations induced by recognized mutagens. The metabolic activation system amplified these strong activities to inhibition rates ranging from 85% to 98%. The results from the antibacterial assay indicated antibacterial effectiveness at dosages between 6.25 and 0.195 mg/mL, particularly effective against Sarcina lutea, Bacillus cereus, Candida albicans, and Staphylococcus aureus. Our findings indicate that P. mahaleb can serve as a versatile raw material for the development of health-promoting applications, including medicines, cosmeceuticals, and nutraceuticals.

Biochemical and Structural Characterization of a Highly Glucose-Tolerant β-Glucosidase from the Termite Reticulitermes perilucifugus

The enzymatic hydrolysis of lignocellulose is often hindered by the glucose-mediated inhibition of β-glucosidases, a major bottleneck in industrial cellulose degradation. Identifying novel glucose-tolerant β-glucosidases is essential for enhancing saccharification efficiency. In this study, we cloned and heterologously expressed a novel β-glucosidase, RpBgl8, from the termite Reticulitermes perilucifugus in Escherichia coli. Sequence and structural analyses classified RpBgl8 as a glycoside hydrolase family 1 enzyme. The purified enzyme exhibited optimal activity at 45 °C and pH 7.0, with broad stability across pH 4.0-8.0. Notably, RpBgl8 demonstrated high tolerance to lignocellulose-derived inhibitors and organic solvents, maintaining 100% activity in 15% ethanol. Furthermore, RpBgl8 exhibited outstanding glucose tolerance, retaining 100% activity at 2.5 M glucose and 82% activity at 4.0 M glucose-outperforming most previously reported β-glucosidases. A structural analysis revealed a narrow, hydrophobic substrate pocket, with residue F124 at the glycone-binding site critical for minimizing glucose accumulation. The F124W mutation significantly reduced glucose tolerance, confirming that hydrophobic interactions at the active site mitigate inhibition. These findings establish RpBgl8 as a promising candidate for high-solid biomass processing and simultaneous saccharification and fermentation applications, highlighting termites as underexplored sources of biocatalysts with unique industrial potential.

Biochemical and Structural Insights of the N-Methyltransferase CyaF in Cyanogramide Biosynthesis

N-Methyltransferases involved in indole methylation have seldom been discovered in natural product biosynthesis. This study focuses on the enzyme CyaF, which catalyzes a critical N-methylation step of indole in the β-carboline skeleton during cyanogramide biosynthesis. Seven β-carboline analogues (3-9) were isolated from the recombinant strain Streptomyces coelicolor YF11/cyaABC, including three new compounds (5-7). In vitro assays revealed CyaF's substrate flexibility. The crystal structure of the CyaF/S-adenosyl-L-homocysteine (SAH) complex, combined with the AlphaFold-predicted model and site-directed mutagenesis, elucidated the catalytic mechanism and structural features that enable CyaF to accommodate diverse substrates, highlighting its potential for biocatalytic applications.

Enlightening the multifarious attributes of the Escherichia coli Sap transport system: a computational perspective

Antimicrobial peptides (AMPs) are majorly utilized by the hosts to clear off the invading bacterial pathogens. The AMPs help in the clearance of bacterial pathogens primarily by disrupting their membrane homeostasis. However, most Gram-negative pathogens have developed multiple machineries, enabling them to resist the action of AMPs. One such machinery is the sensitivity to the antimicrobial peptides (Sap) transport system. The Sap system belongs to the ATP-binding cassette (ABC) transporters and consists of five components, viz. SapABCDF. It is reported that it uptakes AMPs inside the cell that are proteolytically degraded by proteases. In contrast, in Escherichia coli, the Sap (EcSap) transport system was suggested as a putrescine exporter. In this study, with the aid of computational biological approaches, the functional prospects of the EcSap transporter were investigated. The results of this study suggest that the protein EcSapA can bind dipeptides having aromatic amino acids. Further, it can bind to oligopeptides, including AMPs. AMPs such as protamine and protegrin-1 show binding to the protein EcSapA. In addition, the molecule heme shows binding affinity toward the protein EcSapA. In summary, EcSapA seems to be involved in the uptake of a wide range of molecules, such as dipeptides, AMPs and heme. The results of this study can be utilized to design inhibitors targeting the protein SapA, as inhibiting this protein may render the bacterial system sensitive to the attacking AMPs, hence allowing the host machinery to clear off the invading pathogen.

Escherichia coli phage ΦPNJ-9 adheres to mucus via a variant Hoc protein

Phages, as antagonists of bacteria, hold significant promise for combating drug-resistant bacterial infections. Their host specificity allows phages to target pathogenic bacteria without disrupting the gut microbiota, offering distinct advantages in the prevention and control of intestinal pathogens. The interaction between the phage and the gut plays a crucial role in the efficacy of phage-mediated bacterial killing. However, the mechanisms underlying these interactions remain poorly understood. In this study, we demonstrate that the clinically isolated T4-like phage, ΦPNJ-9, effectively adheres to the intestinal mucosa in vivo. This adhesion is mediated by the phage's Hoc protein, which interacts with MUC2 in the mucus. The Hoc protein of ΦPNJ-9 represents a variant, consisting of only three domains and lacking Domain 3, in contrast to phage T4. The key interacting sites on ΦPNJ-9 Hoc are amino acids S183, L184, and T185 within Domain 2. Displaying Domain 2 of ΦPNJ-9 Hoc on the surface of M13 phage significantly enhances its adhesion to the intestinal mucosa. Additionally, we identify fucose residues in MUC2 as the critical binding sites for the phage. Through this adhesion, the phage occupies the intestinal niche, thereby protecting the mucosal layer from pathogenic Escherichia coli infections. Our findings highlight the role of Hoc proteins in phage adhesion to intestinal mucus and the variation in binding sites, providing key insights for phage-based strategies aimed at preventing and controlling intestinal pathogens.IMPORTANCEThe rise in antibiotic-resistant pathogenic bacteria has sparked renewed interest in phage therapy as a promising alternative, particularly for targeting intestinal pathogens due to phage's host specificity. However, clinical applications have revealed that many phages are ineffective in eliminating bacteria within the gut, primarily due to the complex interactions between the phage and the gut environment. However, the mechanisms underlying these interactions remain poorly understood. Our previous study demonstrated that a T4-like phage adheres to the intestinal mucosa through the interaction between its Hoc protein and MUC2 in the mucus. Whether this model is widespread among T4-like phages remains unknown. Here, we characterize a variant Hoc protein from a T4-like phage, and identify new binding sites within this protein. Our findings suggest that the interaction between Hoc and MUC2 is likely common, but the critical binding sites vary depending on the specific phage.

Structural insights into ACE2 interactions and immune activation of SARS-CoV-2 and its variants: an in-silico study

The initial interaction between COVID-19 and the human body involves the receptor-binding domain (RBD) of the viral spike protein with the angiotensin-converting enzyme 2 (ACE2) receptor. Likewise, the spike protein can engage with immune-related proteins, such as toll-like receptors (TLRs) and pulmonary surfactant proteins A (SP-A) and D (SP-D), thereby triggering immune responses. In this study, we utilize computational methods to investigate the interactions between the spike protein and TLRs (specifically TLR2 and TLR4), as well as (SP-A) and (SP-D). The study is conducted on four variants of concern (VOC) to differentiate and identify common virus behaviours. An assessment of the structural stability of various variants indicates slight changes attributed to mutations, yet overall structural integrity remains preserved. Our findings reveal the spike protein's ability to bind with TLR4 and TLR2, prompting immune activation. In addition, our in-silico results reveal almost similar docking scores and therefore affinity for both ACE2-spike and TLR4-spike complexes. We demonstrate that even minor changes due to mutations in all variants, surfactant A and D proteins can function as inhibitors against the spike in all variants, hindering the ACE2-RBD interaction.Communicated by Ramaswamy H. Sarma.

Design and Development of Natural-Product-Derived Nanoassemblies and Their Interactions with Alpha Synuclein

Biomimetic nanoassemblies derived from natural products are considered promising nanomaterials due to their self-assembling ability and their favorable interactions with biological molecules leading to their numerous applications as therapeutic agents or as molecular probes. In this work, we have created peptide nanoconjugates of two natural products, β-Boswellic acid (BA) and β-glycyrrhetinic acid (GH). Both BA and GH are known for their medicinal value, including their role as strong antioxidants, anti-inflammatory, neuroprotective and as anti-tumor agents. To enhance the bioavailability of these molecules, they were functionalized with three short peptides (YYIVS, MPDAHL and GSGGL) to create six conjugates with amphiphilic structures capable of facile self-assembly. The peptides were also derived from natural sources and have been known to display antioxidant activity. Depending upon the conjugate, nanofibers, nanovesicles or a mixture of both were formed upon self-assembly. The binding interactions of the nanoconjugates with α-Synuclein, a protein implicated in Parkinson's disease (PD) was examined through in silico studies and FTIR, circular dichroism and imaging studies. Our results indicated that the nanoassemblies interacted with alpha-synuclein fibrils efficaciously. Furthermore, the nanoassemblies were found to demonstrate high viability in the presence of microglial cells, and were found to enhance the uptake and interactions of α-Synuclein with microglial cells. The nanoconjugates designed in this work may be potentially utilized as vectors for peptide-based drug delivery or for other therapeutic applications.

Identification of potent TMPRSS4 inhibitors through structural modeling and molecular dynamics simulations

TMPRSS4, a transmembrane serine protease type II, is associated with various pathological illnesses. It has been found to activate SARS-CoV-2, enhance viral infection of human small-intestinal enterocytes and is overexpressed in different types of cancers. Therefore, this study aims to disover potential TMPRSS4 inhibitors that have better binding affinity than the approved inhibitors: 2-hydroxydiarylamide and tyroserleutide. Since no 3D-structure is known for TMPRSS4, structural models for the TMPRSS4 serine protease domain were developed. The modeled structures were validated and subjected to molecular dynamics simulations. FDA-approved, clinical/preclinical drugs and natural products were docked to the pocket of TMPRSS4. Moreover, through a systematic analysis, MD simulations and MM-GBSA binding free energy calculations revealed that the best candidates Ergotamine, S55746, NPC478048, Lifirafenib, and NPC77101 are highly stable drug candidates in complex with TMPRSS4, displaying low RMSD and RMSF values with strong binding stability. Among these compounds, Ergotamine showed the most favorable binding energy (-33.73 kcal/mol). Overall, our in silico results revealed that these compounds could act as potent TMPRSS4 inhibitors and need to be validated by future experimental studies.

Integration of In Vitro and In Silico Results From Chemical and Biological Assays of Rheum turkestanicum and Calendula officinalis Flower Extracts

In this study, we conducted a thorough analysis of Rheum turkestanicum (RT) and Calendula officinalis flowers (COF) extracts with varying polarities using LC-MS chemical profiling and biological tests (antioxidant, antimicrobial, enzyme inhibition, and cytotoxic effects). The highest level of total phenolic content in the ethanol extract of RT with 75.82 mg GAE/g, followed by the infusions of RT (65.00 mg GAE/g) and COF (40.99 mg GAE/g). A total of 20 bioactive compounds were identified and quantified. The ethanol extract of COF was rich in terms of 5-O-caffeoylquinic acid (2780.56 μg/g), isorhamnetin-O-rutinoside (1653.59 μg/g), and rutin (1356.97 μg/g). However, RF extracts were rich in catechin gallate (21.66-80.01 μg/g) and 5-O-caffeoylquinic acid. Except for metal chelating ability, the ethanol extract of RT exhibited the strongest ability (DPPH: 171.5 mg TE/g; ABTS: 387.35 mg TE/g; CUPRAC: 449.80 mg TE/g; FRAP: 195.60 mg TE/g; and PBD: 1.52 mmol TE/g). In the enzyme inhibition tests, the tested ethanol extracts for both species were more active than the infusion. The highest values for tyrosinase were recorded as 72.47 mg KAE/g (in RT extracts) and 71.74 mg KAE/g (in COF extracts). Furthermore, all extracts underwent assessment for their antibacterial and antifungal properties, targeting both Gram-positive and Gram-negative bacteria, as well as clinical yeast and fungal microorganisms. In silico studies yielded valuable insights into the potential therapeutic applications of the bioactive compounds identified in COF and RT extracts. Stable interactions were observed between key compounds, such as isorhamnetin 3-O-glucoside and 3-O-caffeoylquinic acid, with crucial target proteins (AChE, BChE, and MurE). These compounds formed stable hydrogen bonds with minimal root mean square deviation (RMSD) fluctuations, particularly in the isorhamnetin 3-O-glucoside-Staphylococcus aureus MurE and 3-O-caffeoylquinic acid-MurE of S. aureus complexes. These findings further underscore the potential of these compounds as promising candidates for therapeutic development.

Integrating Network Pharmacology and In vivo Experimental Validation to Reveal the Mechanism of FuZheng YiLiu Formula on Estrogen Receptor Positive Breast Cancer

BACKGROUND AND PURPOSE

FuZheng YiLiu Formula (FZYL) is a commonly used formula for postoperative estrogen receptor-positive (ER+) breast cancer and post-radiotherapy deficiency of both Qi and Yin. FZYL has been used in clinical practice for decades because of its ability to effectively improve the symptoms of deficiency in cancer patients. However, its mechanism needs to be further clarified. In this paper, we will observe the effect of FZYL on mice with ER+ breast cancer and explore the mechanism by which it improves the symptoms of ER+ breast cancer.

MATERIALS AND METHODS

A tumor xenograft mouse model was established to detect tumor growth in vivo in order to evaluate the pharmacological effects of FZYL on ER+ breast cancer. The main targets of FZYL were identified by extracting the FZYL components and the corresponding potential target genes of breast cancer from the established database and constructing a proteinprotein interaction network of shared genes using the string database. GO functional annotation and KEGG pathway enrichment analysis were performed, and molecular docking, molecular dynamics simulations, western blotting analysis, and RT-qPCR were performed to confirm the validity of targets in the relevant pathways.

RESULTS

FZYL was able to significantly reduce the size of tumors in vivo and had a significant therapeutic effect on tumor xenograft mice. GO and KEGG pathway enrichment analyses indicated that the effects of FZYL may be mediated by oxidative stress levels, apoptotic signaling pathways, and cell cycle proliferation. By RT-qPCR and protein blotting assays, FZYL targeted the key targets of TP53, JUN, ESR1, RELA, MYC, and MAPK1 to exert its effects. The key active components of FZYL are quercetin, luteolin, stigmasterol, and glycitein. Molecular docking and molecular dynamics simulation results further demonstrated that the key active components of FZYL are stably bound to the core targets.

CONCLUSION

In this study, the potential active ingredients, potential core targets, key biological pathways, and signaling pathways involved in the treatment of breast cancer with FZYL were identified, providing a theoretical basis for further anti ER+ breast cancer research.

Engineering dual-functional and thermophilic BMHETase for efficient degradation of polyethylene terephthalate

Polyethylene terephthalate (PET) biodegradation is hindered by the intermediates bis (2-hydroxyethyl) terephthalate (BHET) and mono (2-hydroxyethyl) terephthalate (MHET). BMHETase, a thermophilic hydrolase identified from the UniParc database, exhibits degradation activity towards both BHET and MHET. BMHETase showed higher activity on BHET than LCCICCG and FASTPETase at temperatures ranging from 50 to 70℃. To enhance its activity in degrading MHET, BMHETase was engineered to mimic Ideonella sakaiensis MHETase. The resulting 6-point mutant's activities on MHET and BHET were 8 and 2 times those of the WT, with both optimal temperatures increased by 5℃. This enhancement may be attributed to the BMHETase6M's intensified binding ability with MHET and enlarged binding pocket. When combined with LCCICCG, BMHETase6M achieved complete degradation of MHET in PET films to terephthalic acid, indicating broad application potential. These findings suggest that BMHETase6M holds promise as a candidate for enhancing PET biodegradation efficiency and plastic waste management.

Databases of ligand-binding pockets and protein-ligand interactions

Many research groups and institutions have created a variety of databases curating experimental and predicted data related to protein-ligand binding. The landscape of available databases is dynamic, with new databases emerging and established databases becoming defunct. Here, we review the current state of databases that contain binding pockets and protein-ligand binding interactions. We have compiled a list of such databases, fifty-three of which are currently available for use. We discuss variation in how binding pockets are defined and summarize pocket-finding methods. We organize the fifty-three databases into subgroups based on goals and contents, and describe standard use cases. We also illustrate that pockets within the same protein are characterized differently across different databases. Finally, we assess critical issues of sustainability, accessibility and redundancy.

Design and investigation of interactions of novel peptide conjugates of purine and pyrimidine derivatives with EGFR and its mutant T790M/L858R: an in silico and laboratory study

Peptide-based therapeutics have been gaining attention due to their ability to actively target tumor cells. Additionally, several varieties of nucleotide derivatives have been developed to reduce cell proliferation and induce apoptosis of tumor cells. In this work, we have developed novel peptide conjugates with newly designed purine analogs and pyrimidine derivatives and explored the binding interactions with the kinase domain of wild-type EGFR and its mutant EGFR [L858R/ T790M] which are known to be over-expressed in tumor cells. The peptides explored included WNWKV (derived from sea cucumber) and LARFFS, which in previous work was predicted to bind to Domain I of EGFR. Computational studies conducted to explore binding interactions include molecular docking studies, molecular dynamics simulations and MMGBSA to investigate the binding abilities and stability of the complexes. The results indicate that conjugation enhanced binding capabilities, particularly for the WNWKV conjugates. MMGBSA analysis revealed nearly twofold higher binding toward the T790M/L858R double mutant receptor. Several conjugates were shown to have strong and stable binding with both wild-type and mutant EGFR. As a proof of concept, we synthesized pyrimidine conjugates with both peptides and determined the KD values using SPR analysis. The results corroborated with the computational analyses. Additionally, cell viability and apoptosis studies with lung cancer cells expressing the wild-type and double mutant proteins revealed that the WNWKV conjugate showed greater potency than the LARFFS conjugate, while LARFFS peptide alone showed poor binding to the kinase domain. Thus, we have designed peptide conjugates that show potential for further laboratory studies for developing therapeutics for targeting the EGFR receptor and its mutant T790M/L858R.

Screening of promising molecules against potential drug targets in Yersinia pestis by integrative pan and subtractive genomics, docking and simulation approach

This study focuses on Yersinia pestis, the bacterium responsible for plague, which posed a severe threat to public health in history. Despite the availability of antibiotics treatment, the emergence of antibiotic resistance in this pathogen has increased challenges of controlling the infections and plague outbreaks. The development of new drug targets and therapies is urgently needed. This research aims to identify novel protein targets from 28 Y. pestis strains by the integrative pan-genomic and subtractive genomics approach. Additionally, it seeks to screen out potential safe and effective alternative therapies against these targets via high-throughput virtual screening. Targets should lack homology to human, gut microbiota, and known human 'anti-targets', while should exhibit essentiality for pathogen's survival and virulence, druggability, antibiotic resistance, and broad spectrum across multiple pathogenic bacteria. We identified two promising targets: the aminotransferase class I/class II domain-containing protein and 3-oxoacyl-[acyl-carrier-protein] synthase 2. These proteins were modeled using AlphaFold2, validated through several structural analyses, and were subjected to molecular docking and ADMET analysis. Molecular dynamics simulations determined the stability of the ligand-target complexes, providing potential therapeutic options against Y. pestis.

Computational docking of FtsZ: Survey of promising antibiotic compounds

The bacterial cell-division protein FtsZ has been a promising antibiotic target for over a decade now, but there is still a need for more work in this area. So far there are no FtsZ targeting drugs commercially available. We have analyzed a wide variety of prospective drugs and their interactions with multiple FtsZ species using both free and directed docking simulations. Our goal is to present a standardized computational screening method for potential drug compounds targeting FtsZ. Our work is an example of a way to compare many proposed drugs and FtsZ species combinations relatively quickly. A common method for comparison can yield new results that individual studies and varying methods might not show, as we demonstrate here. To our knowledge this is one of the first, if not the first, computational docking study on the new E. coli FtsZ structures obtained in 2020.

Integrating genome-wide CRISPR screens and in silico drug profiling for targeted antidote development

Numerous toxins threaten humans, but specific antidotes are unavailable for most of them. Although CRISPR screening has aided the discovery of the mechanisms of some toxins, developing targeted antidotes remains a significant challenge. Recently, we established a systematic framework to develop antidotes by combining the identification of novel drug targets by using a genome-wide CRISPR screen with a virtual screen of drugs approved by the US Food and Drug Administration. This approach allows for a comprehensive understanding of toxin mechanisms at the whole-genome level and facilitates the identification of promising antidote drugs targeting specific molecules. Here, we present step-by-step instructions for executing genome-scale CRISPR-Cas9 knockout screens of toxins in HAP1 cells. We also provide detailed guidance for conducting an in silico drug screen and an in vivo drug validation. By using this protocol, it takes ~4 weeks to perform the genome-scale screen, 4 weeks for sequencing and data analysis, 4 weeks to validate candidate genes, 1 week for the virtual screen and 2 weeks for in vitro drug validation. This framework has the potential to accelerate the development of antidotes for a wide range of toxins and can rapidly identify promising drug candidates that are already known to be safe and effective. This could lead to the development of new antidotes much more quickly than traditional methods, protecting lives from diverse toxins and advancing human health.

Developing New Peptides and Peptide-Drug Conjugates for Targeting the FGFR2 Receptor-Expressing Tumor Cells and 3D Spheroids

In this work, we utilized a biomimetic approach for targeting KATO (III) tumor cells and 3D tumoroids. Specifically, the binding interactions of the bioactive short peptide sequences ACSAG (A-pep) and LPHVLTPEAGAT (L-pep) with the fibroblast growth factor receptor (FGFR2) kinase domain was investigated for the first time. Both peptides have been shown to be derived from natural resources previously. We then created a new fusion trimer peptide ACSAG-LPHVLTPEAGAT-GASCA (Trimer-pep) and investigated its binding interactions with the FGFR2 kinase domain in order to target the fibroblast growth factor receptor 2 (FGFR2), which is many overexpressed in tumor cells. Molecular docking and molecular dynamics simulation studies revealed critical interactions with the activation loop, hinge and glycine-rich loop regions of the FGFR2 kinase domain. To develop these peptides for drug delivery, DOX (Doxorubicin) conjugates of the peptides were created. Furthermore, the binding of the peptides with the kinase domain was further confirmed through surface plasmon resonance studies. Cell studies with gastric cancer cells (KATO III) revealed that the conjugates and the peptides induced higher cytotoxicity in the tumor cells compared to normal cells. Following confirmation of cytotoxicity against tumor cells, the ability of the conjugates and the peptides to penetrate 3D spheroids was investigated by evaluating their permeation in co-cultured spheroids grown with KATO (III) and colon tumor-associated fibroblasts (CAFs). Results demonstrated that Trimer-pep conjugated with DOX showed the highest permeation, while the ACSAG conjugate also demonstrated reasonable permeation of the drug. These results indicate that these peptides may be further explored and potentially utilized to create drug conjugates for targeting tumor cells expressing FGFR2 for developing therapeutics.

Subpocket-Based Analysis Approach for the Protein Pocket Dynamics

Structural and dynamic characteristics of protein pockets remarkably influence their biological functions and are also important for enzyme engineering and new drug research and development. To date, several softwares have been developed to analyze the dynamic properties of protein pockets. However, due to the complexity and diversity of the pocket information during the kinetic relaxation, further improvement and capacity expansion of current tools are required. Here, we developed a platform software AlphaTraj in which a computational strategy that divides the whole protein pocket into subpockets and examines various properties of the subpockets such as survival time, stability, and correlation was proposed and implemented. We also proposed a scoring function for the subpockets as well as the whole pocket to visualize the quality of the pocket. Furthermore, we implemented automated conformational search functions for ligand docking and ligand optimization. These functions may help us to gain a deep understanding of the dynamic properties of protein pockets and accelerate the protein engineering and the design of inhibitors and small-molecule drugs. The software is freely available at https://github.com/dooo12332/AlphaTraj.git under the GNU GPL license.

Honokiol targeting ankyrin repeat domain of TRPV4 ameliorates endothelial permeability in mice inflammatory bowel disease induced by DSS

ETHNOPHARMACOLOGICAL RELEVANCE

As a classic traditional Chinese medicine, Magnolia officinalis (M. officinalis) is widely used in digestive diseases. It has rich gastrointestinal activity including inflammatory bowel disease (IBD) treatment, but the mechanism is not clear.

AIM OF THE STUDY

In recent years, there has been a growing interest in investigating the regulatory effects of herbal compounds on transient receptor potential (TRP) channel proteins. Transient receptor potential vanilloid 4 (TRPV4), a subtype involved in endothelial permeability regulation, was discussed as the target of M. officinalis in the treatment of IBD in the study. Based on the targeting effect of TRPV4, this study investigated the active ingredients and mechanism of M. officinalis extract in treating IBD.

MATERIALS AND METHODS

To reveal the connection between the active ingredients in M. officinalis and TRPV4, a bioactivity-guided high performance liquid chromatography system coupled with mass spectrometry identification was utilized to screen for TRPV4 antagonists. TRPV4 siRNA knockdown experiment was employed to validate the significance of TRPV4 as a crucial target in regulating endothelial permeability by honokiol (HON). The interaction of the active ingredient representing HON with TRPV4 was confirmed by molecular docking, fluorescence-based thermal shift and live cell calcium imaging experiments. The potential binding sites and inhibitory mechanisms of HON in TRPV4 were analyzed by molecular dynamics simulation and microscale thermophoresis. The therapeutic effect of HON based on TRPV4 was discussed in DSS-IBD mice.

RESULTS

Our finding elucidated that the inhibitory activity of M. officinalis against TRPV4 is primarily attributed to HON analogues. The knockdown of TRPV4 expression significantly impaired the calcium regulation and permeability protection in endothelial cells. The mechanism study revealed that HON specifically targets the Q239 residue located in the ankyrin repeat domain of TRPV4, and competitively inhibits channel opening with adenosine triphosphate (ATP) binding. The immunofluorescence assay demonstrated that the administration of HON enhances the expression and location of VE-Cadherin to protect the endothelial barrier and attenuates immune cell infiltration.

CONCLUSIONS

The finding suggested that HON alleviates IBD by improving endothelial permeability through TRPV4. The discovery provides valuable insights into the potential therapeutic strategy of active natural products for alleviating IBD.

GPER binding site detection and description: A flavonoid-based docking and molecular dynamics simulations study

Flavonoids, a phenolic compounds class widely distributed in the plant kingdom, have attracted much interest for their implications on several health and disease processes. Usually, the consumption of this type of compounds is approximately 1 g/d, primarily obtained from cereals, chocolate, and dry legumes ensuring its beneficial role in maintaining the homeostasis of the human body. In this context, in cancer disease prominent data points to the role of flavonoids as adjuvant treatment aimed at the regression of the disease. GPER, an estrogen receptor on the cell surface, has been postulated as a probable orchestrator of the beneficial effects of several flavonoids through modulation/inhibition of various mechanisms that lead to cancer progression. Therefore, applying pocket and cavity protein detection and docking and molecular dynamics simulations (MD), we generate, from a cluster composed of 39 flavonoids, crucial insights into the potential role as GPER ligands, of Puerarin, Isoquercetin, Kaempferol 3-O-glucoside and Petunidin 3-O-glucoside, aglycones whose sugar moiety delimits a new described sugar-acceptor sub-cavity into the cavity binding site on the receptor, as well as of the probable activation mechanism of the receptor and the pivotal residues involved in it. Altogether, our results shed light on the potential use of the aforementioned flavonoids as GPER ligands and for further evaluations in in vitro and in vivo assays to elucidate their probable anti-cancer activity.

Zhisou powder suppresses airway inflammation in LPS and CS-induced post-infectious cough model mice via TRPA1/TRPV1 channels

ETHNOPHARMACOLOGICAL RELEVANCE

Zhisou Powder (ZSP), a traditional Chinese medicine (TCM) prescription, has been widely used in the clinic for the treatment of post-infectious cough (PIC). However, the exact mechanism is not clear.

AIM OF THE STUDY

The aim of this study was to investigate the ameliorative effect of ZSP on PIC in mice. The possible mechanisms of action were screened based on network pharmacology, and the potential mechanisms were explored through molecular docking and in vivo experimental validation.

MATERIALS AND METHODS

Lipopolysaccharide (LPS) (80μg/50 μL) was used to induce PIC in mice, followed by daily exposure to cigarette smoke (CS) for 30 min for 30 d to establish PIC model. The effects of ZSP on PIC mice were observed by detecting the number of coughs and cough latency, peripheral blood and bronchoalveolar lavage fluid (BALF) inflammatory cell counts, enzyme-linked immunosorbent assay (ELISA), and histological analysis. The core targets and key pathways of ZSP on PIC were analyzed using network pharmacology, and TRPA1 and TRPV1 were validated using RT-qPCR and western blotting assays.

RESULTS

ZSP effectively reduced the number of coughs and prolonged the cough latency in PIC mice. Airway inflammation was alleviated by reducing the expression levels of the inflammatory mediators TNF-α and IL-1β. ZSP modulated the expression of Substance P, Calcitonin gene-related peptide (CGRP), and nerve growth factor (NGF) in BALF. Based on the results of network pharmacology, the mechanism of action of ZSP may exert anti-neurogenic airway-derived inflammation by regulating the expression of TRPA1 and TRPV1 through the natural active ingredients α-spinastero, shionone and didehydrotuberostemonine.

CONCLUSION

ZSP exerts anti-airway inflammatory effects through inhibition of TRPA1/TRPV1 channels regulating neuropeptides to alleviate cough hypersensitivity and has a favorable therapeutic effect on PIC model mice. It provides theoretical evidence for the clinical application of ZSP.

ANN based prediction of ligand binding sites outside deep cavities to facilitate drug designing

The ever-changing environmental conditions and pollution are the prime reasons for the onset of several emerging and re-merging diseases. This demands the faster designing of new drugs to curb the deadly diseases in less waiting time to cure the animals and humans. Drug molecules interact with only protein surface on specific locations termed as ligand binding sites (LBS). Therefore, the knowledge of LBS is required for rational drug designing. Existing geometrical LBS prediction methods rely on search of cavities based on the fact that 83% of the LBS found in deep cavities, however, these methods usually fail where LBS localize outside deep cavities. To overcome this challenge, the present work provides an artificial neural network (ANN) based method to predict LBS outside deep cavities in animal proteins including human to facilitate drug designing. In the present work a feed-forward backpropagation neural network was trained by utilizing 38 structural, atomic, physiochemical, and evolutionary discriminant features of LBS and non-LBS residues localized in the extracted roughest patch on protein surface. The performance of this ANN based prediction method was found 76% better for those proteins where cavity subspace (extracted by MetaPocket 2.0, a consensus method) failed to predict LBS due to their localization outside the deep cavities. The prediction of LBS outside deep cavities will facilitate in drug designing for the proteins where it is not possible due to lack of LBS information as the geometrical LBS prediction methods rely on extraction of deep cavities.

An investigation of binding interactions of tumor-targeted peptide conjugated polyphenols with the kinase domain of ephrin B4 and B2 receptors

Recent studies have shown that Ephrin receptors may be upregulated in several types of cancers including breast, ovarian and endometrial cancers, making them a target for drug design. In this work, we have utilized a target-hopping approach to design new natural product-peptide conjugates and examined their interactions with the kinase-binding domain of EphB4 and EphB2 receptors. The peptide sequences were generated through point mutations of the known EphB4 antagonist peptide TNYLFSPNGPIA. Their anticancer properties and secondary structures were analyzed computationally. Conjugates of most optimum of peptides were then designed by binding the N-terminal of the peptides with the free carboxyl group of the polyphenols sinapate, gallate and coumarate, which are known for their inherent anticancer properties. To investigate if these conjugates have a potential to bind to the kinase domain, we carried out docking studies and MMGBSA free energy calculations of the trajectories based on the molecular dynamics simulations, with both the apo and the ATP bound kinase domains of both receptors. In most cases binding interactions occurred within the catalytic loop region, while in some cases the conjugates were found to spread out across the N-lobe and the DFG motif region. The conjugates were further tested for prediction of pharmacokinetic properties using ADME studies. Our results indicated that the conjugates were lipophilic and MDCK permeable with no CYP interactions. These findings provide an insight into the molecular interactions of these peptides and conjugates with the kinase domain of the EphB4 and EphB2 receptor. As a proof of concept, we synthesized and carried out SPR analysis with two of the conjugates (gallate-TNYLFSPNGPIA and sinapate-TNYLFSPNGPIA). Results indicated that the conjugates showed higher binding with the EphB4 receptor and minimal binding to EphB2 receptor. Sinapate-TNYLFSPNGPIA showed inhibitory activity against EphB4. These studies reveal that some of the conjugates may be developed for further investigation into in vitro and in vivo studies and potential development as therapeutics.

Druggable site near the upper vestibule determines the high affinity and P2X3 homotrimer selectivity of sivopixant/S-600918 and its analogue DDTPA

BACKGROUND AND PURPOSE

The P2X3 receptor, a trimeric ionotropic purinergic receptor, has emerged as a potential therapeutic target for refractory chronic cough (RCC). Nevertheless, gefapixant/AF-219, the only marketed P2X3 receptor antagonist, might lead taste disorders by modulating the human P2X2/3 (hP2X2/3) heterotrimer. Hence, in RCC drug development, compounds exhibiting strong affinity for the hP2X3 homotrimer and a weak affinity for the hP2X2/3 heterotrimer hold promise. An example of such a molecule is sivopixant/S-600918, a clinical Phase II RCC candidate with a reduced incidence of taste disturbance compared to gefapixant. Sivopixant and its analogue, (3-(4-([3-chloro-4-isopropoxyphenyl]amino)-3-(4-methylbenzyl)-2,6-dioxo-3,6-dihydro-1,3,5-triazin-1(2H)-yl)propanoic acid (DDTPA), exhibit both high affinity and high selectivity for hP2X3 homotrimers, compared with hP2X2/3 heterotrimers. The mechanism underlying the druggable site and its high selectivity remains unclear.

EXPERIMENTAL APPROACH

To analyse mechanisms that distinguish this drug candidate from other inhibitors of the P2X3 receptors we used a combination of chimera construction, site covalent occupation, metadynamics, mutagenesis and whole-cell recording.

KEY RESULTS

The high affinity and selectivity of sivopixant/DDTPA for hP2X3 receptors was determined by the tri-symmetric site located close to the upper vestibule. Substitution of only four amino acids inside the upper body domain of hP2X2 with those of hP2X3, enabled the hP2X2/3 heterotrimer to exhibit a similar level of apparent affinity for sivopixant/DDTPA as the hP2X3 homotrimer.

CONCLUSION AND IMPLICATIONS

From the receptor-ligand recognition perspective, we have elucidated the molecular basis of novel RCC clinical candidates' cough-suppressing properties and reduced side effects, offering a promising approach to the discovery of novel drugs that specifically target P2X3 receptors.

A multifunctional flavoprotein monooxygenase HspB for hydroxylation and C-C cleavage of 6-hydroxy-3-succinoyl-pyridine

Flavoprotein monooxygenases catalyze reactions, including hydroxylation and epoxidation, involved in the catabolism, detoxification, and biosynthesis of natural substrates and industrial contaminants. Among them, the 6-hydroxy-3-succinoyl-pyridine (HSP) monooxygenase (HspB) from Pseudomonas putida S16 facilitates the hydroxylation and C-C bond cleavage of the pyridine ring in nicotine. However, the mechanism for biodegradation remains elusive. Here, we refined the crystal structure of HspB and elucidated the detailed mechanism behind the oxidative hydroxylation and C-C cleavage processes. Leveraging structural information about domains for binding the cofactor flavin adenine dinucleotide (FAD) and HSP substrate, we used molecular dynamics simulations and quantum/molecular mechanics calculations to demonstrate that the transfer of an oxygen atom from the reactive FAD peroxide species (C4a-hydroperoxyflavin) to the C3 atom in the HSP substrate constitutes a rate-limiting step, with a calculated reaction barrier of about 20 kcal/mol. Subsequently, the hydrogen atom was rebounded to the FAD cofactor, forming C4a-hydroxyflavin. The residue Cys218 then catalyzed the subsequent hydrolytic process of C-C cleavage. Our findings contribute to a deeper understanding of the versatile functions of flavoproteins in the natural transformation of pyridine and HspB in nicotine degradation.IMPORTANCEPseudomonas putida S16 plays a pivotal role in degrading nicotine, a toxic pyridine derivative that poses significant environmental challenges. This study highlights a key enzyme, HspB (6-hydroxy-3-succinoyl-pyridine monooxygenase), in breaking down nicotine through the pyrrolidine pathway. Utilizing dioxygen and a flavin adenine dinucleotide cofactor, HspB hydroxylates and cleaves the substrate's side chain. Structural analysis of the refined HspB crystal structure, combined with state-of-the-art computations, reveals its distinctive mechanism. The crucial function of Cys218 was never discovered in its homologous enzymes. Our findings not only deepen our understanding of bacterial nicotine degradation but also open avenues for applications in both environmental cleanup and pharmaceutical development.

The SARS-CoV-2 Mpro Dimer-Based Screening System: A Synthetic Biology Tool for Identifying Compounds with Dimerization Inhibitory Potential

The COVID-19 endemic remains a global concern. The search for effective antiviral candidates is still needed to reduce disease risk. However, the availability of high biosafety level laboratory facilities for drug screening is limited in number. To address this issue, a screening system that could be utilized at lower biosafety levels remains essential. This study aimed to develop a novel SARS-CoV-2 main protease (Mpro) dimer-based screening system (DBSS) utilizing synthetic biology in Escherichia coli BL21(DE3). We linked the SARS-CoV-2 Mpro with the DNA-binding domain of AraC regulatory protein, which regulates the reporter gene expression. Protein modeling and molecular docking showed that saquinavir could bind to AraC-Mpro both in its monomer and dimer forms. The constructed DBSS assay indicated the screening system could detect saquinavir inhibitory activity at a concentration range of 4-10 μg/mL compared to the untreated control (P ≤ 0.05). The Vero E6 cell assay validated the DBSS result that saquinavir at 4-10 μg/mL exhibited antiviral activity against SARS-CoV-2. Our DBSS could be used for preliminary screening of numerous drug candidates that possess a dimerization inhibitor activity of SARS-CoV-2 Mpro and also minimize the use of a high biosafety level laboratory.

In silico investigations and molecular insights for designing tRNA-encoded peptides as potential therapeutics for targeting over-expressed receptors in breast cancer

tRNA- Encoded Peptides (tREPs) have recently been discovered as new functional peptides and hold promise as therapeutics for anti-parasitic applications. In this study, in silico investigations were conducted to design tRNA-encoded peptides with the potential to target over-expressed receptors in breast cancer cells. tRNA genes were translated into corresponding peptides (tREPs) using computational tools. The tREPs, which were predicted as anticancer peptides, were then screened for various ADMET properties. Molecular docking studies were conducted for three cancer target receptors, the Estrogen Receptor (ER), Peroxisome Proliferator-Activated Receptor (PPAR) and the Epidermal Growth Factor Receptor (EGFR). Based on the docking results, specific tREPs were screened and molecular dynamics simulations were performed, and the binding energies were further explored using MMPBSA calculations. The peptide Pep1 (DWIAWRHHNDIVSWLTCGPRFKSWS) and Pep2 (GFIAWWSRHLELAQTRFKSWWS) exhibited a good binding affinity against the Estrogen Receptor (ER) and the Peroxisome Proliferator-Activated Receptor Alpha (PPAR) cancer target. The Pep1-ER and Pep1-PPAR complex maintained an average of two hydrogen bonds throughout the simulation and demonstrated a higher negative binding free energy of -72.27 kcal/mol and -65.16 kcal/mol respectively, as calculated by MMPBSA. Therefore, the tREPs designed as anticancer peptides in this study provide novel approaches for potential anticancer therapeutic modalities.

CRAFT: a web-integrated cavity prediction tool based on flow transfer algorithm

Numerous computational methods, including evolutionary-based, energy-based, and geometrical-based methods, are utilized to identify cavities inside proteins. Cavity information aids protein function annotation, drug design, poly-pharmacology, and allosteric site investigation. This article introduces "flow transfer algorithm" for rapid and effective identification of diverse protein cavities through multidimensional cavity scan. Initially, it identifies delimiter and susceptible tetrahedra to establish boundary regions and provide seed tetrahedra. Seed tetrahedron faces are precisely scanned using the maximum circle radius to transfer seed flow to neighboring tetrahedra. Seed flow continues until terminated by boundaries or forbidden faces, where a face is forbidden if the estimated maximum circle radius is less or equal to the user-defined maximum circle radius. After a seed scanning, tetrahedra involved in the flow are clustered to locate the cavity. The CRAFT web interface integrates this algorithm for protein cavity identification with enhanced user control. It supports proteins with cofactors, hydrogens, and ligands and provides comprehensive features such as 3D visualization, cavity physicochemical properties, percentage contribution graphs, and highlighted residues for each cavity. CRAFT can be accessed through its web interface at http://pitools.niper.ac.in/CRAFT , complemented by the command version available at https://github.com/PGlab-NIPER/CRAFT/ .Scientific contribution: Flow transfer algorithm is a novel geometric approach for accurate and reliable prediction of diverse protein cavities. This algorithm employs a distinct concept involving maximum circle radius within the 3D Delaunay triangulation to address diverse van der Waals radii while existing methods overlook atom specific van der Waals radii or rely on complex weighted geometric techniques.

Understanding Pseudophosphatase Function Through Biochemical Interactions

Pseudophosphatases have been solidified as important signaling molecules that regulate signal transduction cascades. However, their mechanisms of action remain enigmatic. Reflecting this mystery, the prototypical pseudophosphatase STYX (phospho-serine-threonine/tyrosine-binding protein) was named with allusion to the river of the dead in Greek mythology to emphasize that these molecules are "dead" phosphatases. Although proteins with STYX domains do not catalyze dephosphorylation, this does not preclude their having other functions, including as integral elements of signaling networks. Thus, understanding their roles may mark them as potential novel drug targets. This chapter outlines common strategies used to characterize the functions of pseudophosphatases, using as an example MK-STYX [MAPK (mitogen-activated protein kinase) phospho-serine-threonine/tyrosine-binding], which has been linked to tumorigenesis, hepatocellular carcinoma, glioblastoma, apoptosis, and neuronal differentiation. We start with the importance of "restoring" (when possible) phosphatase activity in a pseudophosphatase, so the active mutant may be used as a comparison control throughout immunoprecipitation and mass spectrometry analyses. To this end, we provide protocols for site-directed mutagenesis, mammalian cell transfection, co-immunoprecipitation, phosphatase activity assays, and immunoblotting that we have used to investigate MK-STYX and the active mutant MK-STYXactive. We also highlight the importance of utilizing RNA interference (RNAi) "knockdown" technology to determine a cellular phenotype in various cell lines. Therefore, we outline our protocols for introducing short hairpin RNA (shRNA) expression plasmids into mammalian cells and quantifying knockdown of gene expression with real-time quantitative PCR (qPCR). We also provide a bioinformatic approach to investigating MK-STYX and MK-STYX(active mutant). These bioinformatic approaches can stand alone experimentally but also complement and enhance "wet" bench approaches such as binding assays and/or activity assays. A combination of cellular, molecular, biochemical, proteomic, and bioinformatic techniques has been a powerful tool in identifying novel functions of MK-STYX. Likewise, the information provided here should be a helpful guide to elucidating the functions of other pseudophosphatases.

Structure of methyltransferase RedM that forms the dimethylpyrrolinium of the bisindole reductasporine

Bisindoles are biologically active natural products that arise from the oxidative dimerization of two molecules of l-tryptophan. In bacterial bisindole pathways, a core set of transformations is followed by the action of diverse tailoring enzymes that catalyze reactions that lead to diverse bisindole products. Among bisindoles, reductasporine is distinct due to its dimethylpyrrolinium structure. Its previously reported biosynthetic gene cluster encodes two unique tailoring enzymes, the imine reductase RedE and the dimethyltransferase RedM, which were shown to produce reductasporine from a common bisindole intermediate in recombinant E. coli. To gain more insight into the unique tailoring enzymes in reductasporine assembly, we reconstituted the biosynthetic pathway to reductasporine in vitro and then solved the 1.7 Å resolution structure of RedM. Our work reveals RedM adopts a variety of conformational changes with distinct open and closed conformations, and site-directed mutagenesis alongside sequence analysis identifies important active site residues. Finally, our work sets the stage for understanding how RedM evolved to react with a pyrrolinium scaffold and may enable the development of new dimethyltransferase catalysts.

Toxicological evaluation of TBBPA by common carp (Cyprinus carpio) about the in vivo/vitro disturbance of the AHR pathway

Tetrabromobisphenol A (TBBPA) is a widely used plastic additive with high bioaccumulation potential and toxicity on both humans and wildlife. Currently, research on its ecotoxicity and the underlying mechanism is limited. Using common carp (Cyprinus carpio), we evaluated the toxicity of TBBPA, especially focusing on its alteration of a key metabolism-related pathway aryl hydrocarbon receptor (AHR), using in vivo/vitro assays and in silico simulation. The 96 h LC50 of TBBPA of common carp was 4.2 mg/L and belonged to the acute toxic level II. The bioaccumulation potential of TBBPA follows the role of liver > gill > brain and varies between 3- and 14-day exposure. On the AHR pathway respect, as expected, the metabolism-related cyp1a1 and cyp1b1 were upregulated in the liver and brain. Ahr2, the receptor, was also upregulated in the brain under TBBPA exposure. The alteration of gene expression was tissue-specific while the difference between 3- or 14-day exposure was minor. AHR inhibition assay indicated the 2, 3, 7, 8-tetrachlorodibenzo-p-dioxin (TCDD)-induced AHR transactivation can be inhibited by TBBPA suggesting it is not a potent agonist but a competitive antagonist. In silico analysis indicated TBBPA can be successfully docked into the binding cavity with similar poses but still have AHR-form-specific interactions. Molecular dynamics simulation proved TBBPA can be more flexible than the coplanar ligand TCDD, especially in ccaAHR1b with greater root-mean-square deviation (RMSD), of which TCDD-induced transactivation seemed not to be blocked by TBBPA. This research increased the understanding of TBBPA toxicity and alteration of the AHR pathway, and pointed out the need to perform additional toxicology evaluation of emerging contaminants, especially on non-model species.

Molecular characterization of glutor-GLUT interaction and prediction of glutor's drug-likeness: implications for its utility as an antineoplastic agent

Recent experimental evidence from our and other laboratories has strongly indicated that glutor, a piperazine-2-one derivative, which is a pan-GLUT inhibitor, displays a promising antineoplastic action by hampering glucose uptake owing to its ability to inhibit GLUT1 and GLUT3, which are overexpressed in neoplastic cells. However, the molecular mechanism(s) of the inhibiting action of glutor has remained elusive. Thus, for optimal utilization of the antineoplastic potential of glutor, it is essential to decipher the precise mechanism(s) of its interaction with GLUTs. Therefore, the present investigation was carried out to understand the molecular mechanism(s) of the binding of glutor to GLUT1 and GLUT3 in silico. This study suggests that glutor can effectively bind to GLUTs at the reported binding site. Moreover, the docking of glutor to GLUT was stabilised by several contacts between these two partners as shown by the 200 ns long molecular dynamic simulation carried out using Gromacs, indicating the formation of a stable complex. Moreover, glutor was found to possess all characteristics conducive to its drug-likeness. Hence, these observations suggest that glutor has the potential to be used in antineoplastic therapeutic applications.Communicated by Ramaswamy H. Sarma.

Naringenin improves muscle endurance via activation of the Sp1-ERRγ transcriptional axis

Skeletal muscle function declines in the aging process or disease; however, until now, skeletal muscle has remained one of the organs most undertreated with medication. In this study, naringenin (NAR) was found to build muscle endurance in wild-type mice of different ages by increasing oxidative myofiber numbers and aerobic metabolism, and it ameliorates muscle dysfunction in mdx mice. The transcription factor Sp1 was identified as a direct target of NAR and was shown to mediate the function of NAR on muscle. Moreover, the binding site of NAR on Sp1 was further validated as GLN-110. NAR enhances the binding of Sp1 to the CCCTGCCCTC sequence of the Esrrg promoter by promoting Sp1 phosphorylation, thus upregulating Esrrg expression. The identification of the Sp1-ERRγ transcriptional axis is of great significance in basic muscle research, and this function of NAR has potential implications for the improvement of muscle function and the prevention of muscle atrophy.

c-di-GMP inhibits the DNA binding activity of H-NS in Salmonella

Cyclic di-GMP (c-di-GMP) is a second messenger that transduces extracellular stimuli into cellular responses and regulates various biological processes in bacteria. H-NS is a global regulatory protein that represses expression of many genes, but how H-NS activity is modulated by environmental signals remains largely unclear. Here, we show that high intracellular c-di-GMP levels, induced by environmental cues, relieve H-NS-mediated transcriptional silencing in Salmonella enterica serovar Typhimurium. We find that c-di-GMP binds to the H-NS protein to inhibit its binding to DNA, thus derepressing genes silenced by H-NS. However, c-di-GMP is unable to displace H-NS from DNA. In addition, a K107A mutation in H-NS abolishes response to c-di-GMP but leaves its DNA binding activity unaffected in vivo. Our results thus suggest a mechanism by which H-NS acts as an environment-sensing regulator in Gram-negative bacteria.

Analysis of Zinc and Stromal Immunity in Disuse Osteoporosis: Mendelian Randomization and Transcriptomic Analysis

OBJECTIVE

Disuse osteoporosis is known to be primarily caused by a lack of exercise. However, the causal relationships between zinc and immunity and disuse osteoporosis remain unknown. This study investigated these relationships and their potential mechanisms.

METHODS

This study was an integrative study combining genome-wide association studies and transcriptomics. Two-sample Mendelian randomization analysis (MR) was used to analyze the causal relationships between exposures (zinc, immunity, physical activity) and the outcome (osteoporosis) with the aid of single-nucleotide polymorphisms (SNPs) as instrumental variables (IVs). Four models, MR-Egger, inverse variance weighted, weighted median and MR-Pleiotrophy RESidual Sum and Outlier (MRPRESSO), were used to calculate odds ratio values. Sensitivity and heterogeneity analyses were also performed using MRPRESSO and MR-Egger methods. The mRNA transcriptomic analysis was subsequently conducted. Zinc metabolism scores were acquired through single-sample Gene Set Enrichment Analysis algorithms. Stromal scores were obtained using the R Package "estimate" algorithms. Important Kyoto Encyclopedia of Genes and Genomes and Gene Ontology pathways were also derived through gene set variation analysis. Cytoscape software helped construct the transcription factor (TF)-mRNA-microRNA (miRNA) network. Virtual screening and molecular docking were performed. Polymerase chain reaction validation was also carried out in vivo.

RESULTS

Causal relationships were demonstrated between zinc and exercise (95% confidence interval [CI] = 1.30-2.95, p = 0.001), exercise and immunity (95% CI = 0.36-0.80, p = 0.002), exercise and osteoporosis (95% CI = 0.97-0.99, p = 0.0007), and immunity disorder and osteoporosis (95% CI = 1.30-2.03, p = 0.00002). One hundred and seventy-nine mRNAs in important modules were screened. Combining the differential expressional genes (DEGs) and the Boruta selection, six DEGs were screened (AHNAK, CSF2, ADAMTS12, SRA1, RUNX2, and SLC39A14). TF HOXC10 and miRNA hsa-miR-204 were predicted. Then, the TF-mRNA-miRNA network was successfully constructed. RUNX2 and SLC39A14 were identified as hub mRNAs in the TF-mRNA-miRNA network. Eventually, the novel small drug C6O4NH5 was designed according to the pharmacophore structure of SLC39A14. The docking energy for the novel drug was -5.83 kcal/mol. SLC39A14 and RUNX2 were downregulated (of statistical significance p-value < 0.05) in our animal experiment.

CONCLUSION

This study revealed that zinc had a protective causal relationship with disuse osteoporosis by promoting exercise and immunity. SLC39A14 and RUNX2 mRNA participated in this zinc-related mechanism.

High-throughput virtual screening and molecular dynamics simulation reveals NPC170742 a novel chalconoid compound as a potential inhibitor of D-glycero-D-manno-heptose-1,7-bisphosphate 7-phosphatase in Helicobacter pylori

Helicobacter pylori is a gram negative spiral shaped bacteria that causes peptic ulcer and gastric cancer. It Is the sixth most prevalent cancer in the world and the third leading cause of cancer death. The increase in reported cases of H. pylori resistance to the drugs and antibiotics shows the need for the development of new and efficient drugs against the pathogen. In the present study, D-glycero-D-manno-heptose-1,7-bisphosphate 7-phosphatase (GmhB), an enzyme involved in the biosynthesis of lipopolysaccharides that encourages bacterial adherence, self-aggregation and identifying the host cells was modelled and the active sites were predicted through POCASA which is an automated ligand binding site prediction server. Natural product activity and species source (NPASS) is a database of 96,481 natural compounds that were subjected to virtual screening workflow that includes Qikprop, Lipinski rule, filtering out reactive functional groups followed by high throughput virtual screening and the top 10 compounds were selected for further induced fit docking along with the substrate D-glycero-β-D-manno-heptose 1,7-bisphosphate. The compound NPC170742 (Alpha, Beta, 3,4,5,2',4',6'-Octahydroxy dihydrochalcone) showed higher affinity than the substrate, and both the substrate D-glycero-β-D-manno-heptose 1,7-bisphosphate and the compound NPC170742 were subjected to molecular dynamics simulation. The results exposed the compound NPC170742 could be a potential lead compound against the enzyme D-glycero-D-manno-heptose-1,7-bisphosphate 7-phosphatase of H. pylori.Communicated by Ramaswamy H. Sarma.

Construction and Catalytic Study of Affinity Peptide Orientation and Light Crosslinking Immobilized Sucrose Isomerase

A novel affinity peptide orientation and light-controlled covalent immobilized method was developed. Sucrose isomerase (SI) was selected as the model enzyme. Molecular simulation was first performed to select the targeted immobilization region. Subsequently, a short peptide (H2N-VNIGGX-COOH, VG) with high affinity to this region was rationally designed. Thereafter, 4-benzoyl-l-phenylalanine with the photosensitive group of benzophenone was introduced. Then, the affinity between the ligand and the SI was validated using molecular dynamics simulation. Thereafter, the SI was directionally immobilized onto the surface of the epoxy resin (EP) guided by VG via photo-crosslinking, and thus the oriented photo-crosslinking enzymes were obtained. The enzymatic activity, thermostability, and reusability of the affinity directional photo-crosslinked immobilized sucrose isomerase (hv-EP-VG-SI) were systematically studied. The oriented immobilization enzymes were significantly improved in recycling and heat resistance. Moreover, hv-EP-VG-SI retained more than 90% of the original activity and 50% of the activity after 11 cycles.

Magnolol alleviates pulmonary fibrosis inchronic obstructive pulmonary disease by targeting transient receptor potential vanilloid 4-ankyrin repeat domain

Transient receptor potential vanilloid 4 (TRPV4) plays a role in regulating pulmonary fibrosis (PF). While several TRPV4 antagonists including magnolol (MAG), have been discovered, the mechanism of action is not fully understood. This study aimed to investigate the effect of MAG on alleviating fibrosis in chronic obstructive pulmonary disease (COPD) based on TRPV4, and to further analyze its mechanism of action on TRPV4. COPD was induced using cigarette smoke and LPS. The therapeutic effect of MAG on COPD-induced fibrosis was evaluated. TRPV4 was identified as the main target protein of MAG using target protein capture with MAG probe and drug affinity response target stability assay. The binding sites of MAG at TRPV4 were analyzed using molecular docking and small molecule interaction with TRPV4-ankyrin repeat domain (ARD). The effects of MAG on TRPV4 membrane distribution and channel activity were analyzed by co-immunoprecipitation, fluorescence co-localization, and living cell assay of calcium levels. By targeting TRPV4-ARD, MAG disrupted the binding between phosphatidylinositol 3 kinase γ and TRPV4, leading to hampered membrane distribution on fibroblasts. Additionally, MAG competitively impaired ATP binding to TRPV4-ARD, inhibiting TRPV4 channel opening activity. MAG effectively blocked the fibrotic process caused by mechanical or inflammatory signals, thus alleviating PF in COPD. Targeting TRPV4-ARD presents a novel treatment strategy for PF in COPD.

SiteFerret: Beyond Simple Pocket Identification in Proteins

We present a novel method for the automatic detection of pockets on protein molecular surfaces. The algorithm is based on an ad hoc hierarchical clustering of virtual probe spheres obtained from the geometrical primitives used by the NanoShaper software to build the solvent-excluded molecular surface. The final ranking of putative pockets is based on the Isolation Forest method, an unsupervised learning approach originally developed for anomaly detection. A detailed importance analysis of pocket features provides insight into which geometrical (clustering) and chemical (amino acidic composition) properties characterize a good binding site. The method also provides a segmentation of pockets into smaller subpockets. We prove that subpockets are a convenient representation to pinpoint the binding site with great precision. SiteFerret is outstanding in its versatility, accurately predicting a wide range of binding sites, from those binding small molecules to those binding peptides, including difficult shallow sites.

Insights into human eNOS, nNOS and iNOS structures and medicinal indications from statistical analyses of their interactions with bound compounds

83 Structures of human nNOS, 55 structures of human eNOS, 13 structures of iNOS, and about 126 reported NOS-bound compounds are summarized and analyzed. Structural and statistical analysis show that, at least one copy of each analyzed compound binds to the active site (the substrate arginine binding site) of human NOS. And binding features of the three isoforms show differences, but the binding preference of compounds is not in the way helpful for inhibitor design targeting nNOS and iNOS, or for activator design targeting eNOS. This research shows that there is a strong structural and functional similarity between oxygenase domains of human NOS isoforms, especially the architecture, residue composition, size, shape, and distribution profile of hydrophobicity, polarity and charge of the active site. The selectivity and efficacy of inhibitors over the rest of isoforms rely a lot on chance and randomness. Further increase of selectivity via rational improvement is uncertain, unpredictable and unreliable, therefore, to achieve high selectivity through targeting this site is complicated and requires combinative investigation. After analysis on the current two targeting sites in NOS, the highly conserved arginine binding pocket and H4B binding pocket, new potential drug-targeting sites are proposed based on structure and sequence profiling. This comprehensive analysis on the structure and interaction profiles of human NOS and bound compounds provides fresh insights for drug discovery and pharmacological research, and the new discovery here is practically applied to guide protein-structure based drug discovery.

Tandem intermolecular [4 + 2] cycloadditions are catalysed by glycosylated enzymes for natural product biosynthesis

Tandem Diels-Alder reactions are frequently used in the construction of polycyclic ring systems in complex organic compounds. Unlike the many Diels-Alderases (DAases) that catalyse a single cycloaddition, enzymes for multiple Diels-Alder reactions are rare. Here we demonstrate that two calcium-ion-dependent glycosylated enzymes, EupfF and PycR1, independently catalyse sequential, intermolecular Diels-Alder reactions in the biosynthesis of bistropolone-sesquiterpenes. We elucidate the origins of catalysis and stereoselectivity within these DAases through analysis of enzyme co-crystal structures, together with computational and mutational studies. These enzymes are secreted as glycoproteins with diverse N-glycans. The N-glycan at N211 in PycR1 significantly increases the affinity to the calcium ion, which in turn regulates the active cavity, making it specifically interact with substrates to accelerate the tandem [4 + 2] cycloaddition. The synergistic effect of the calcium ion and N-glycan on the catalytic centre of enzymes involved in secondary metabolism, especially for complex tandem reactions, can extend our understanding of protein evolution and improve the artificial design of biocatalysts.

Analyzing the Geometry and Dynamics of Viral Structures: A Review of Computational Approaches Based on Alpha Shape Theory, Normal Mode Analysis, and Poisson-Boltzmann Theories

The current SARS-CoV-2 pandemic highlights our fragility when we are exposed to emergent viruses either directly or through zoonotic diseases. Fortunately, our knowledge of the biology of those viruses is improving. In particular, we have more and more structural information on virions, i.e., the infective form of a virus that includes its genomic material and surrounding protective capsid, and on their gene products. It is important to have methods that enable the analyses of structural information on such large macromolecular systems. We review some of those methods in this paper. We focus on understanding the geometry of virions and viral structural proteins, their dynamics, and their energetics, with the ambition that this understanding can help design antiviral agents. We discuss those methods in light of the specificities of those structures, mainly that they are huge. We focus on three of our own methods based on the alpha shape theory for computing geometry, normal mode analyses to study dynamics, and modified Poisson-Boltzmann theories to study the organization of ions and co-solvent and solvent molecules around biomacromolecules. The corresponding software has computing times that are compatible with the use of regular desktop computers. We show examples of their applications on some outer shells and structural proteins of the West Nile Virus.