PyMOL Software Research Articles

Molecular Docking to Predict a Novel Bioactive Compound as an Inhibitor of Beta Catenin in Oral Squamous Cell Carcinoma

Background: Efforts aimed at enhancing patient survival have focused on early detection and diagnosis, followed by prompt treatment of potentially malignant disorders, aiming to halt their advancement into oral cancer. Recent research has shed light on the pivotal role of the Wnt/B-catenin signaling pathway in the pathogenesis of potentially malignant oral conditions. This pathway undergoes a progressive activation process across various degrees of epithelial dysplasia, including mild, moderate, and severe dysplasia. Beta-catenin (B-catenin) triggers the activation of genes associated with crucial cellular processes, which include cell growth, viability, differentiation, and migration. Aims: In the present study, we aimed to design a novel drug with 3 bioactive compounds through insilico analysis, assess its efficacy against B-catenin, and develop a new pharmacophore with an emphasis on B-catenin inhibition. Materials and Methods: Based on prior literature, three molecules possessing potent beta-cateninblocking properties were selected, namely rosmarinic acid, zosterin, and stigmasterol. To evaluate their binding affinities, molecular docking studies were conducted using the Lamarckian Genetic Algorithm implemented in AutoDock Tools 1.5.7. Initially, AutoGrid was employed to construct a grid box for docking purposes. The estimated binding poses of each compound were subjected to clustering analysis. The interactions between the compounds and beta-catenin were visualized and explored using PyMOL software. Results: Stigmasterol displayed the most substantial binding energy with a value of -3.86 kcal/mol, followed by rosmarinic acid and zosterin. Conclusion: Bioactive components can be used for beta-catenin pathway blocking. Future research should be carried out to assess these substances in more clinically relevant cancer models.

Serological and molecular characterization of novel ABO variants including an interesting B(A) subgroup.

ABO grouping is the most important pretransfusion testing that is directly related to the safety of blood transfusion. A weak ABO subgroup is one of the important causes of an ABO grouping discrepancy. Here, we investigated the characterization of four novel ABO variants including a novel B(A) subgroup. RBCs were phenotyped by standard serology methods. The full coding regions of the ABO gene and the erythroid cell-specific regulatory elements in intron one were sequenced. The effect of the possible splice site variant was predicted by Alamut software. The 3D structural modeling of three relative B(A) enzymes (p.Met214Thr, p.Met214Val, and p.Met214Leu) were performed by PyMOL software. Four novel ABO alleles were identified with weak ABO expression in this study, in which two would lead to premature terminations, and two resulted in amino acid changes. In silico analysis revealed that the splice site variant c.155G>T had the potential to alter splice transcripts. 3D structural view shown that the variant amino acid position 214 was spatially adjacent to the donor recognition pocket residues (266Met and 268Ala) and just next to the 211DVD213 motif. The size of the side chain of Thr and Val is the smallest, Leu is medium, and Met is the largest, and the size changes in the critical position 214 may affect the donor recognition pocket. Four ABO subgroup alleles were newly linked to different kinds of ABO variants and the possible mechanism through which they produce weak ABO subgroups was analyzed in silico.

Network Pharmacology and in vitro Experimental Verification on Intervention of Oridonin on Non-Small Cell Lung Cancer.

To explore the key target molecules and potential mechanisms of oridonin against non-small cell lung cancer (NSCLC). The target molecules of oridonin were retrieved from SEA, STITCH, SuperPred and TargetPred databases; target genes associated with the treatment of NSCLC were retrieved from GeneCards, DisGeNET and TTD databases. Then, the overlapping target molecules between the drug and the disease were identified. The protein-protein interaction (PPI) was constructed using the STRING database according to overlapping targets, and Cytoscape was used to screen for key targets. Molecular docking verification were performed using AutoDockTools and PyMOL software. Using the DAVID database, Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis were conducted. The impact of oridonin on the proliferation and apoptosis of NSCLC cells was assessed using cell counting kit-8, cell proliferation EdU image kit, and Annexin V-FITC/PI apoptosis kit respectively. Moreover, real-time quantitative PCR and Western blot were used to verify the potential mechanisms. Fifty-six target molecules and 12 key target molecules of oridonin involved in NSCLC treatment were identified, including tumor protein 53 (TP53), Caspase-3, signal transducer and activator of transcription 3 (STAT3), mitogen-activated protein kinase kinase 8 (MAPK8), and mammalian target of rapamycin (mTOR). Molecular docking showed that oridonin and its key target molecules bind spontaneously. GO and KEGG enrichment analyses revealed cancer, apoptosis, phosphoinositide-3 kinase/protein kinase B (PI3K/Akt), and other signaling pathways. In vitro experiments showed that oridonin inhibited the proliferation, induced apoptosis, downregulated the expression of Bcl-2 and Akt, and upregulated the expression of Caspase-3. Oridonin can act on multiple targets and pathways to exert its inhibitory effects on NSCLC, and its mechanism may be related to upregulating the expression of Caspase-3 and downregulating the expressions of Akt and Bcl-2.

Exploring the Mechanism of Action of the "Scutellaria Barbata D.Don-Prunella Vulgaris L." Herb Pair in the Treatment of Lung Cancer Using Network Pharmacology and Molecular Docking Techniques

Objective: To explore the mechanism of action of the herbal pair "Scutellaria barbata D.Don-Prunella vulgaris L." in the treatment of lung cancer through network pharmacology and molecular docking techniques. Methods: Active ingredients and their targets of Scutellaria barbata D.Don and Prunella vulgaris L. were collected and screened from the Traditional Chinese Medicine Systems Pharmacology Database and Analysis Platform (TCMSP). Disease-related targets were obtained and screened from the Genecards and OMIM databases. The intersection Venn diagram of the targets of "Scutellaria barbata D.Don-Prunella vulgaris L." and lung cancer disease targets was obtained using R 4.4.1 software and packages such as "ggvenn". A drug-active ingredient-target-disease association network was constructed in Cytoscape 3.10.0, and core active ingredients were screened using the Analyze Network function. A PPI network for drug-disease common targets was constructed using the String database website, and the TSV format of protein interaction relationship files was imported into Cytoscape 3.10.0 software,install and run CytoHubba to calculate and obtain the core targets in the network. GO function and KEGG pathway enrichment analyses were performed on drug-disease common targets using R 4.4.1 software. Finally, molecular docking validation was performed on core ingredients and core targets using AutoDock, and the three best binding molecular docking patterns were displayed using PyMol software. Results: A total of 33 active drug components and 108 drug-disease common targets were obtained. Among them, there are 5 core active components: quercetin, luteolin, wogonin, kaempferol, and baicalein; core targets include TP53, AKT1, JUN, HSP90AA1, etc. GO analysis yielded 2, 010 related entries. KEGG analysis identified 147 signaling pathways. Molecular docking showed that the core active components have strong affinity with the core targets. Conclusion: The drug pair of Scutellaria barbata D.Don and Prunella vulgaris L. may exert anti-tumor effects by acting on targets such as TP53, AKT1, JUN, HSP90AA1, and through signaling pathways like PI3K-AKT, inhibiting tumor cell proliferation, promoting tumor cell apoptosis, suppressing its proliferation, differentiation, and metastasis, thereby achieving therapeutic effects on lung cancer.

Genetic investigations on singleton school aged children reveal novel variants and new candidate genes for hearing loss

Hearing loss affects around 5% of the global population. Two preliminary studies have described genetic variants in sporadic individuals with hearing loss from Pakistan. Here we extend these studies to determine the spectrum of variants in a cohort of individuals with no previous history of hearing loss. Individuals with hearing loss born to consanguineous couples were identified from special schools. Audiograms were assessed. DNA from participants negative for GJB2 pathogenic variants was subjected to exome sequencing. Data were filtered to include variants with frequencies < 0.01 in the public databases. The effects of the missense variants on respective amino acids were analyzed by using PyMol software. Among the 44 participants, hearing loss was moderate for two individuals; 14 exhibited moderately-severe hearing loss while 25 had a severe degree of hearing loss. Hearing loss was reported to have been progressive in four participants and was currently profound in three participants. Variants were unambiguously identified in 17 genes, of which the majority affected SLC26A4. CDH23, MYO15A and OTOF were other significant contributors. Deleterious variants detected in two genes suggest new associations for hearing loss. Molecular characterization of hearing loss in our cohort revealed high genetic heterogeneity with a 75% diagnostic rate.

Mechanism of Anchang Decoction in Treatment of Anti-Inflammatory Effect Based on Network Pharmacology, Molecular Docking and Experimental Verification

Context A prescription medication called Anchang Decoction (ACD) has anti-inflammatory properties. Objective To evaluate the mechanism of ACD against inflammation. Materials and methods The “pharmacodynamic constituents - potential targets” and “protein interaction networks” were mapped using Cytoscape software and the STRING database, respectively. The degree of binding between important pharmacodynamic components of ACD and possible targets was then examined using molecular docking analysis using Autodock Vina and PyMOL software, and GO and KEGG pathway enrichment analysis using the David database and the Weishengxin online tool. These findings were eventually confirmed in vitro. Results After the intersection of the two, 539 inflammatory targets and 217 related targets, 34 main active components, and 42 potential anti-inflammatory targets were obtained. These include AKT1, MAPK14, SRC, EGFR, GSK3B, MMP9, MMP2, PTGS2, SYK, ESR1, and MMP2 and GO enrichment results. These three key targets are chosen as downstream validation targets for experimental verification. Furthermore, the colonic tissue and mucosa of ACD group were undamaged in comparison to the model group, and there was no sign of inflammatory cell infiltration. According to CCK-8 data, treatment with 20% ACD drug-containing serum resulted in a significant increase in RAW264.7 cell viability (P &lt; 0.05) when compared to the normal serum group; Serum of ACD-containing medication may considerably lower the NO content of macrophage inflammation and prevent the production of inflammatory markers like TNF-α and IL-6 (P &lt; 0.05); The expression levels of AKT1, MAPK14, and SRC proteins were considerably reduced by ACD in RAW264.7 macrophage inflammation, according to Western Blot data (P &lt; 0.05). Discussion and conclusions ACD exerts anti-inflammatory effects through multi-component interaction with the target, and the mechanism may involve the inhibition of the release of inflammatory cytokines by AKT, MAPK and non-receptor tyrosine kinase signaling pathways. Here, the molecular mechanism of ACD against inflammation was partially clarified and experimentally validated, offering theoretical evidence for more effective clinical application.

Genetic and mechanistic evaluation of an individual with para-Bombay phenotype associated with a compound heterozygote comprising two novel FUT1 variants.

As is well documented, the para-Bombay phenotype is typically characterized by the reduction or absence of ABH antigens on red blood cells but the presence of corresponding antigens in saliva. Herein, the underlying molecular mechanism of an individual with para-Bombay AB phenotype combined with two novel variants of the FUT1 gene was investigated. ABH antigens and antibodies were detected in the serum of the proband using conventional serological methods. The coding region nucleotides of the ABO, FUT1, and FUT2 genes were directly sequenced by polymerase chain reaction. Moreover, the FUT1 haploid type in the proband was analyzed by TA clone sequencing. The 3D structure of wild-type and mutant fucosyltransferases were simulated and analyzed using Phyre2 and Pymol software. Lastly, the effect of missense substitution on the function of fucosyltransferase was predicted by the Polymorphism Phenotyping algorithm (PolyPhen-2) and MutationTaster. ABH antigens were noted to be absent on the surface of red blood cells of the proband. The ABO genotype was ABO*A1.02/ABO*B.01, while the FUT2 genotype was FUT2*01/FUT2*c.357T. Interestingly, two novel missense variants (c.289G>A, p.Ala97Thr and c.575G>C, p.Arg192Pro) and one synonymous SNP (c.840G>A) were identified in the FUT1 gene. Furthermore, c.289G>A was detected in one haploid type, whereas c.575G>C and c.840G>A were discovered in another haploid type. Meanwhile, in silico analysis revealed that amino acid substitution caused by missense variants altered the partial spatial structure of the α-helices where residues 97 and 298 were located using 3D homology modeling software. Finally, both missense variants were defined as probably damaging based on PolyPhen-2 prediction. Two novel FUT1 variants were identified in a Chinese individual with para-Bombay AB phenotype, which can expand our understanding of the molecular mechanism underlying the para-Bombay phenotype and contribute to improving the safety of blood transfusion.

Analysis of Phylogenetics and Structural Relationships of the Cytochrome b Gene Protein in Mahseer Fish (Tor sp.)

Abstract The Cytochrome b gene from mitochondrial DNA encodes a protein that can be used as a genetic marker to identify species. This study aims to determine the bioinformatic characteristics of the gene encoding Cyt b isolated from various Mahseer species, Tor tambroides, Tor douronensis, Tor khudree, and Tor putitora. Mahseer Cyt b sequences can be used for detailed computational investigation of the properties of 3D protein models and phylogenetics. The data analysis technique uses nucleotides with a sequence length of 330 bp obtained from NCBI. The MEGA X program was used for phylogenetic analysis. 3D protein structure predictions were obtained through the Swiss model and protein homology program using PYMOL software. The results of phylogenetics show close kinship relationships with the closest genetic distance of 0.000, while the farthest distance is 0.068. The nucleotide composition contains Thymine (30.23%), Cytosine (25.81%), Arginine (28.05%), and Guanine (15.92%). 3D modeling of the Cyt b protein Mahseer referring to the species Neolissochilus hexagonolepis (McClelland, 1839). The 3D protein structure prediction was assessed via a Ramachandran plot of 99.07%. This study can be used as a reference to support sustainable conservation efforts by observing the populations and habitat conditions.

Peptidomic profiling of endogenous peptides in the spleens of mouse models of Graves' disease

BackgroundGraves' disease (GD) is a common autoimmune thyroid disorder. The pathogenesis of GD involves an autoimmune response to the A subunit of the human thyrotropin receptor (hTSHR), although the specific mechanisms are not fully elucidated. MethodsThis study established a GD model by immunizing BALB/c mice with a recombinant adenovirus expressing the hTSHR A subunit. Spleen tissues were collected and analyzed using liquid chromatography-tandem mass spectrometry (LC-MS/MS) to identify differentially expressed peptides (DEPs). Gene Ontology (GO) analysis and KEGG pathway analysis were further utilized to annotate the functions of these DEPs. Additionally, peptide bioactivity prediction and molecular docking studies were conducted using Alphafold and Pymol software, respectively, to assess the binding affinity of specific peptides to the hTSHR A subunit. ResultsThe GD mouse model was successfully established, and 1,428 DEPs were identified in the spleen, with 368 upregulated and 1,060 downregulated. Functional analysis indicated that these DEPs are mainly involved in cellular endocytosis, regulation of gene expression, and nucleocytoplasmic transport. Notably, molecular docking studies revealed that the abnormally highly expressed peptide HG2A-24aa demonstrated potential bioactivity and strong binding affinity with hTSHR-289aa. ConclusionThe specific bioactive peptides may play key roles in the pathogenesis of GD, particularly HG2A-24aa, which may have a significant role in the MHC II antigen presentation pathway mediated by the hTSHR A subunit.

Identification of Novel PBP2B Protein Inhibitors against Streptococcus pneumoniae in Marine Natural Products using an In-Silico Approach

Background: The aim of this research is to identify marine natural compounds derived from green, red, and brown algae that might possibly inhibit the Penicillin-Binding Proteins (PBPs) protein, which is responsible for the development of antibiotic resistance in Streptococcus pneumoniae (mutated resistant 5204-PBP2B strain). We obtained this by using virtual screening and molecular docking. In AutoDock Vina and the Schrodinger suite software, we screened a library of marine natural chemicals and discovered four intriguing candidates that had strong binding affinities to the active region of the PBPs protein. Based on our findings, four naturally occurring marine chemicals show great promise as new inhibitors of S. pneumoniae 5204-PBP2B protein. These discoveries reveal important new information on the potential application of marine natural products as a source of new drugs to combat antibiotic resistance in Streptococcus pneumoniae and other bacterial infections. Methods: The 3318 compounds in the Comprehensive Marine Natural Products Database (CMNPD) derived from green algae (293 compounds), brown algae (1212 compounds) and red algae (1813 compounds) were taken into consideration for this study. Through virtual screening and molecular docking investigations, we found the optimum compounds for the Penicillin-Binding Proteins (PBPs) protein in Streptococcus pneumoniae. Utilizing AutoDock Vina and Schrodinger Suite software, the 5204-PBP2B protein selected for this investigation was examined. The structure and binding interaction have been displayed using PyMOL software. Results: Through virtual screening and molecular docking investigations for the 5204-PBP2B protein in Streptococcus pneumoniae, we were able to identify four marine natural products that are present in brown algae from the Comprehensive Marine Natural Products Database. Conclusion: The study has indicated that the main cause of bacterial resistance to antibiotics is 5204-PBP2B in S. pneumoniae. This study's methodology has been shown to be effective in identifying four strong inhibitors of the CMNPD. In this work, potent molecules from CMNPD compounds were screened using the 3D structure of mutated resistant 5204 strain, named 5204- PBP2B (PDB ID: 2WAE) of S. pneumoniae. Out of 3318 compounds that showed strong interactions with PBP2B, docking studies revealed that four of the compounds were inhibitory for the protein and could be used to treat PBP2B. These four marine products were selected as a result of our earlier research on Klebsiella pneumonia’s New Delhi metallo-β-lactamase-1 (NDM-1) protein. This study thus reveals the importance of marine natural products for improving the drug development process, as well as the ability of four marine products generated from brown algae to inhibit both the NDM-1 protein of Klebsiella pneumoniae and the 5204-PBP2B protein in Streptococcus pneumoniae. It is also possible to expand this approach by investigating how different receptor inhibitors interact in a lab setting. Potential inhibitors can be discovered by evaluating the biological activity of the drugs and applying virtual screening and molecular docking techniques.

The immunotherapy mechanism of Hedyotis Diffusae Herba in treating liver cancer: a study based on network pharmacology, bioinformatics, and experimental validation.

Liver cancer is a malignant tumor that develops on or inside the liver. Hedyotis diffusa Willd (HDW) plays a significant role in anti-tumor activities; however, its mechanism against liver cancer remains unclear. This study aims to evaluate the immunotherapeutic mechanism of HDW in treating liver cancer through network pharmacology, bioinformatics analysis, and experimental validation. Network pharmacology was utilized to identify the active components and potential targets of HDW from the TCMSP database. A potential target protein-protein interaction (PPI) network was constructed using the STRING database, followed by function and pathway enrichment analysis of the targets using GO and KEGG methods. In addition, the key targets for HDW against liver cancer were identified using five different algorithms in Cytoscape. The TCGA and HPA databases were used to assess the mRNA and protein expression of core target genes in normal liver and liver cancer tissues and their relationship with overall survival in liver cancer, as well as their role in immune infiltration. Molecular docking between the core components of HDW and the core targets was performed using PyMOL software. The effects of HDW on the proliferation and apoptosis of liver cancer cells were examined using MTT and flow cytometry. The regulatory effects of the core component quercetin on core targets were validated using RT-qPCR and Western blot. A total of 163 potential targets were identified by searching for intersections among 7 types of active components and all potential and liver cancer targets. PPI network analysis revealed the core targets IL6 and TNF. GO enrichment analysis involved 2089 biological processes, 76 cellular components, and 196 molecular functions. KEGG enrichment analysis suggested that the anti-cancer effects of HDW might be mediated by the AGE-RAGE signaling pathway, IL-17 signaling pathway, TNF signaling pathway, PI3K-Akt signaling pathway, and NF-κB signaling pathway. Database validation of key targets showed that mRNA and protein expression results for the IL6 gene were contradictory, while those for the TNF gene were consistent, both being underexpressed in liver cancer. Importantly, the expression of IL6 and TNF was related to the infiltration of 24 types of immune cells, with the highest correlation with macrophages. Molecular docking showed that IL6 and TNF had high binding stability with quercetin, with binding energies of - 7.4 and - 6.0kJ∙mol-1, respectively. Experimental validation showed that quercetin inhibited liver cancer cell proliferation and promoted apoptosis in a dose-dependent manner, with protein results indicating that quercetin downregulated the mRNA and protein expression of IL6 and TNF, and upregulated key proteins in the AGE-RAGE signaling pathway, AGEs, and RAGE. This study comprehensively elucidates the activity, potential targets, and molecular mechanisms of HDW against liver cancer, providing a promising strategy for the scientific basis and treatment mechanism of traditional Chinese medicine in treating liver cancer.

Exploring the therapeutic efficacy and pharmacological mechanism of Guizhi Fuling Pill on ischemic stroke: a meta-analysis and network pharmacology analysis.

The role of Guizhi Fuling Pill (GZFL) in the treatment of ischemic stroke (IS) is still controversial, and its pharmacological mechanism remains unclear. To evaluate the efficacy and potential pharmacological mechanisms of GZFL on IS, a comprehensive method integrating meta-analysis, network pharmacology, and molecular docking was employed. Eight electronic databases were searched from inception to November 2023. Review Manager 5.4.1 software was used for meta-analysis. Active compounds and targets of GZFL were retrieved from the Traditional Chinese Medicine Systems Pharmacology Database, Bioinformatics Analysis Tool for Molecular mechANism of Traditional Chinese Medicine, and Encyclopaedia of Traditional Chinese Medicine. Relevant targets of IS were obtained from the DisGeNet, Genecards, and DrugBank databases. GO biological function analysis and KEGG enrichment analysis were performed in the Metascape database. AutoDock Tools and PyMOL software were employed for Molecular docking. The intervention group significantly increased the total effective rate and decreased the NIHSS score. Administration of GZFL also improved the whole blood viscosity (low and high shear rates) and levels of fibrinogen, TNF-α, and IL-6. The key active compounds included quercetin, kaempferol, catechin, and beta-sitosterol, and the core target proteins included SRC, MAPK1, TP53, JUN, RELA, AKT1, and TNF. GO analysis mainly involved inflammation response, cellular response to lipids, and regulation of ion transport. The core pathways were lipid and atherosclerosis, cAMP, calcium, IL-17, and MAPK signaling pathways. Key active compounds showed good affinity with the core targets. The underlying mechanisms of GZFL in IS treatment are primarily related to its anti-inflammatory, anti-atherosclerosis, and neuroprotective effects.

Study On the Mechanism of Action of Qili Qiangxin Capsule in the Treatment of Heart Failure Based on Network Pharmacology and Molecular Docking Method

Objective: To investigate the pharmacodynamic substances and mechanism of action of Qili Qiangxin Capsule in the treatment of heart failure based on network pharmacology and molecular docking technology. Methods: The active ingredients and drug targets of Qili Qiangxin Capsule were obtained from databases such as TCMSP, GeneCards, OMIM, PharmGkb, TTD, and DrugBank databases were searched for heart failure disease targets. The drug targets and disease targets were corrected by the UniProt database, then the Venn diagram was drawn, and the intersecting genes were screened. Cytoscape 3.8.0 software was used to draw the active ingredient-disease target network for topological analysis. PPI network was constructed in the STRING database platform to predict the core targets. Bioconductor package was used to perform KEGG pathway analysis. autoDock Vina software was used to molecularly dock the core targets with the main active ingredients, and Pymol software visualised the results. Results: Screening of 209 active ingredients of Qili Qiangxin Capsule, including quercetin, luteolin, cryptotanshinone, etc. 11,432 heart failure disease targets, 249 genes intersecting with drugs, including the core targets containing TP53, STAT3, JUN, MAPK1, etc. These genes are mainly involved in the AGE-RAGE, fluid shear stress, and atherosclerosis, PI3K-Akt signaling pathways. Conclusion: This study initially revealed the multi-component, multi-target, multi-pathway mechanism of action of Qili Qiangxin Capsule in the treatment of heart failure, which provides a theoretical basis for further research.

MFRP variations cause nanophthalmos in five Chinese families with distinct phenotypic diversity.

Nanophthalmos is a congenital ocular structural anomaly that can cause significant visual loss in children. The early diagnosis and then taking appropriate clinical and surgical treatment remains a challenge for many ophthalmologists because of genetic and phenotypic heterogeneity. The objective of this study is to identify the genetic cause of nanophthalmos in the affected families and analyze the clinical phenotype of nanophthalmos with MFRP gene variation (Microphthalmia, isolated; OMIM#611040 and Nanophthalmos 2; OMIM#609549, respectively). Comprehensive ophthalmic examinations were performed on participants to confirm the phenotype. The genotype was identified using whole exome sequencing, and further verified the results among other family members by Sanger sequencing. The normal protein structure was constructed using Alphafold. Mutant proteins were visualized using pymol software. Pathogenicity of identified variant was determined by in silico analysis and the guidelines of American College of Medical Genetics and Genomics (ACMG). The relationship between genetic variants and clinical features was analyzed. Five nanophthalmos families were autosomal recessive, of which four families carried homozygous variants and one family had compound heterozygous variants in the MFRP gene. Both family one and family three carried the homozygous missense variant c.1486G>A (p.Glu496Lys) in the MFRP gene (Clinvar:SCV005060845), which is a novel variant and evaluated as likely pathogenic according to the ACMG guidelines and in silico analysis. The proband of family one presented papilloedema in both eyes, irregular borders, thickened retinas at the posterior pole, tortuous and dilated retinal vessels, and indistinguishable arteries and veins, while the proband of family three presented uveal effusion syndrome-like changes in the right eye. In families one and 3, despite carrying the same gene variant, the probands had completely different clinical phenotypes. The homozygous nonsense variant c.271C>T (p.Gln91Ter) (Clinvar:SCV005060846) of the MFRP gene was detected in family 2, presenting shallow anterior chamber in both eyes, pigmentation of peripheral retina 360° from the equator to the serrated rim showing a clear demarcation from the normal retina in the form of strips. Family four proband carried the homozygous missense variant c.1411G>A (p.Val471Met) in the MFRP gene (Clinvar:SCV005060847), family five proband carried compound heterozygous missense variants c.1486G>A (p.Glu496Lys) and c.602G>T (p.Arg201Leu) in the MFRP gene (Clinvar:SCV005060848), which is a novel variant and evaluated as likely pathogenic according to the ACMG guidelines and in silico analysis, and they all presented clinically with binocular angle-closure glaucoma, family four also had retinal vein occlusion in the right eye during the follow-up. In this study, pathogenic variants of the MFRP gene were detected in five nanophthalmos families, including two novel variants. It also revealed a distinct phenotypic diversity among five probands harboring variants in the MFRP gene. Our findings extend the phenotype associated with MFRP variants and is helpful for ophthalmologists in early diagnosis and making effective treatment and rehabilitation strategies.

Network pharmacology and molecular dynamics study of the effect of the Astragalus-Coptis drug pair on diabetic kidney disease.

Diabetic kidney disease (DKD) is the primary cause of end-stage renal disease. The Astragalus-Coptis drug pair is frequently employed in the management of DKD. However, the precise molecular mechanism underlying its therapeutic effect remains elusive. To investigate the synergistic effects of multiple active ingredients in the Astragalus-Coptis drug pair on DKD through multiple targets and pathways. The ingredients of the Astragalus-Coptis drug pair were collected and screened using the TCMSP database and the SwissADME platform. The targets were predicted using the SwissTargetPrediction database, while the DKD differential gene expression analysis was obtained from the Gene Expression Omnibus database. DKD targets were acquired from the GeneCards, Online Mendelian Inheritance in Man database, and DisGeNET databases, with common targets identified through the Venny platform. The protein-protein interaction network and the "disease-active ingredient-target" network of the common targets were constructed utilizing the STRING database and Cytoscape software, followed by the analysis of the interaction relationships and further screening of key targets and core active ingredients. Gene Ontology (GO) function and Kyoto Ency-clopedia of Genes and Genomes (KEGG) pathway enrichments were performed using the DAVID database. The tissue and organ distributions of key targets were evaluated. PyMOL and AutoDock software validate the molecular docking between the core ingredients and key targets. Finally, molecular dynamics (MD) simulations were conducted to simulate the optimal complex formed by interactions between core ingredients and key target proteins. A total of 27 active ingredients and 512 potential targets of the Astragalus-Coptis drug pair were identified. There were 273 common targets between DKD and the Astragalus-Coptis drug pair. Through protein-protein interaction network topology analysis, we identified 9 core active ingredients and 10 key targets. GO and KEGG pathway enrichment analyses revealed that Astragalus-Coptis drug pair treatment for DKD involves various biological processes, including protein phosphorylation, negative regulation of apoptosis, inflammatory response, and endoplasmic reticulum unfolded protein response. These pathways are mainly associated with the advanced glycation end products (AGE)-receptor for AGE products signaling pathway in diabetic complications, as well as the Lipid and atherosclerosis. Molecular docking and MD simulations demonstrated high affinity and stability between the core active ingredients and key targets. Notably, the quercetin-AKT serine/threonine kinase 1 (AKT1) and quercetin-tumor necrosis factor (TNF) protein complexes exhibited exceptional stability. This study demonstrated that DKD treatment with the Astragalus-Coptis drug pair involves multiple ingredients, targets, and signaling pathways. We propose a novel approach for investigating the molecular mechanism underlying the therapeutic effects of the Astragalus-Coptis drug pair on DKD. Furthermore, we suggest that quercetin is the most potent active ingredient and specifically targets AKT1 and TNF, providing a theoretical foundation for further exploration of pharmacologically active ingredients and elucidating their molecular mechanisms in DKD treatment.

Fatty Acid Esters and Acyclic Monoterpenoid from Justicia insularis Leaf Fractions Attenuated Malaria Pathogenesis Through Docking with Plasmodium falciparum Serine Hydroxymethyl Transferase and Plasmodium falciparum Erythrocyte Membrane Protein 1 Proteins

Background Justicia insularis (Acanthaceae) T. Anderson is ethnopharmacologically used in Nigeria for the treatment of diseases including malaria. Therefore, this study was designed to investigate in vivo antiplasmodial effect of J. insularis leaf in Plasmodium berghei-infected mice, characterize its constituents, and carryout in silico studies of its compounds. Methods Standard protocols were followed in the processing of the plant leaves, extraction, fractionation, isolation, and characterization, evaluation of in vivo antiplasmodial assay, retrieval of Plasmodium falciparum serine hydroxymethyl transferase (PfSHMT) and Plasmodium falciparum erythrocyte membrane protein 1 (PfEMP-1) proteins, absorption, distribution, metabolism, excretion, and toxicity (ADMET), and docking studies. Gas chromatography-mass spectrometry (GC-MS) was employed to isolate and characterize the compounds; SWISSADME and ADMET lab 2 enhanced the evaluation of pharmacokinetic properties, PyRx for docking analysis; Biovia discovery studio for 2D visualization, and PyMol software for 3D visualization of the ligand-protein interactions. Results The dichloromethane (61.59%) and ethyl acetate (73.15%) fractions had the best therapeutic indices and compared favorably with chloroquine (81.58%) in the curative antiplasmodial assay. The GC-MS analysis revealed 20 already reported antiplasmodial compounds with hexanoic acid 1,1-dimethylethyl ester, octadecanoic acid docosyl ester, and trans-β-ocimene as the lead compounds based on their binding affinities, permeation of the blood-brain-barrier, non-inhibition of metabolizing enzymes, ease of excretion, non-carcinogenicity, as well as non-violation of Lipinski's criteria. Conclusion Octadecanoic acid docosyl ester and hexanoic acid 1,1-dimethylethyl ester bonded the tetrahydrofolate-binding sites of PfSHMT, caused inhibition of DNA synthesis, and apoptosis, whereas trans-β-ocimene inhibited PfEMP-1, reversed the attachment of parasitized red blood cells to micro-vascular endothelium as their mechanism of action for parasitemia clearance. Moreover, these lead compounds reported for the first time in the dichloromethane and EtoAc fractions of this plant are responsible for the remarkable antiplasmodial activity observed in this study.

Synthesis, characterisation, DFT and biological evaluation of 4-(1-ethylbenzimidazol-2-yl)-2-(arylamino)thiazoles

The compounds 4-(1-ethylbenzimidazol-2-yl)-2-(arylamino)thiazoles were expected to have many biological activities and were synthesized from 1,2-diaminobenzene and lactic acid. The synthesized compounds are characterised by FT-IR, 1H NMR and mass spectroscopy. Thiazole moiety present in the compounds was found to possess anticancer, anti-HIV activities. Theoretical information on the optimized geometry, vibrational frequencies and atomic charges in the ground state were determined by means of density functional theory (DFT) using standard B3LYP/6-31G basis set with Gaussian ’09 software. Mulliken population analysis was performed on the atomic charges and the HOMO-LUMO energies were calculated. From the HOMO-LUMO energy gap, we know that the charge transfer occurs within the molecule. Docking studies are also done by using PyRx and are visualized by PyMoL software. By 2, 2-diphenyl-1-picrylhydrazyl (DPPH) free radical scavenging method, anti-oxidant activity of the synthesized compounds was evaluated. In vitro cytotoxic activity of the compounds against A549 cell lines was evaluated by MTT assay.

Molecular mechanism of Saikosaponin-d in the treatment of gastric cancer based on network pharmacology and in vitro experimental verification.

The study aimed to utilize network pharmacology combined withcell experiments to research the mechanism of action of Saikosaponin-d in the treatment of gastric cancer. Drug target genes were obtained from the PubChem database and the Swiss Target Prediction database. Additionally, target genes for gastric cancer were obtained from the GEO database and the Gene Cards database. The core targets were then identified and further analyzed through gene ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG), and GESA enrichment. The clinical relevance of the core targets was assessed using the GEPIA and HPA databases. Molecular docking of drug monomers and core target proteins was performed using Auto Duck Tools and Pymol software. Finally, in vitro cellular experiments including cell viability, apoptosis, cell scratch, transwell invasion, transwell migration, qRT-PCR, and Western blot were conducted to verify these findings of network pharmacology. The network pharmacology analysis predicted that the drug monomers interacted with 54 disease targets. Based on clinical relevance analysis, six core targets were selected: VEGFA, IL2, CASP3, BCL2L1, MMP2, and MMP1. Molecular docking results showed binding activity between the Saikosaponin-d monomer and these core targets. Saikosaponin-d could inhibit gastric cancer cell proliferation, induce apoptosis, and inhibit cell migration and invasion.

Mechanism of Cnidii Fructus in the Treatment of Infertility Based on Network Pharmacology and Molecular Docking Analysis Technology.

Infertility is a condition characterized by a low fertility rate, which significantly affects the physical and mental health of women of reproductive age. Typically, the treatment duration is prolonged, and the therapeutic outcomes are often unsatisfactory. Professor Cheng-yao He, a renowned expert in traditional Chinese medicine, commonly uses the herb Cnidii Fructus (SCZ) for the treatment of infertility. However, the exact mechanism remains unclear, and there is limited research available on this topic. The active ingredients of SCZ were obtained from the traditional chinese medicine system pharmacology (TCMSP) database and screened for pharmacokinetics (PK), involving absorption, distribution, metabolism, and excretion (ADME). Target prediction was performed by SwissTargetPrediction database, and infertility-related disease targets were searched in GeneCards, TTD, DrugBank, and OMIM database. The protein-protein interaction (PPI) network was constructed using the STRING database (Version 11.5) and analyzed by Cytoscape software (Version 3.9.1). Additionally, the target genes were subjected to biological enrichment analysis in the Metascape database, including gene ontology (GO) and kyoto encyclopedia of genes and genomes (KEGG) enrichment analysis, and the "Disease-Ingredient-pathway-target" network was constructed using Cytoscape software. With the assistance of AutoDockVina, Ligplot, and PyMOL software, a validation of Molecular docking results and a visualization of the results were performed. This study identified 11 retained active ingredients of SCZ, 447 drug targets, 233 of which were related to infertility, and 5393 disease targets. GO enrichment analysis mainly involved 221 biological processes such as cellular response to chemical stress and gland development. KEGG enrichment analysis mainly involved 68 pathways such as thyroid hormone signaling pathway, estrogen signaling pathway, FOXO signaling pathway, and PI3K/Akt signaling pathway. Molecular docking showed that the core active ingredients of SCZ, including Ammidin, Diosmetin, Xanthoxylin N, and Prangenidin, had strong binding abilities with core targets such as MDM2, MTOR, CCND1, EGFR, and AKT1. This study preliminarily demonstrated that SCZ may act on the PI3K/Akt signaling pathway, exerting its therapeutic effects on infertility by improving energy metabolism disorders and endometrial receptivity, inducing primordial follicle activation, regulating oocyte proliferation, differentiation, and apoptosis, and promoting the release of dominant follicles.

In silico prospective analysis of the medicinal plants activity on the CagA oncoprotein from Helicobacter pylori.

Colonization with Helicobacter pylori (H. pylori) has a strong correlation with gastric cancer, and the virulence factor CagA is implicated in carcinogenesis. Studies have been conducted using medicinal plants with the aim of eliminating the pathogen; however, the possibility of blocking H. pylori-induced cell differentiation to prevent the onset and/or progression of tumors has not been addressed. This type of study is expensive and time-consuming, requiring in vitro and/or in vivo tests, which can be solved using bioinformatics. Therefore, prospective computational analyses were conducted to assess the feasibility of interaction between phenolic compounds from medicinal plants and the CagA oncoprotein. To perform a computational prospecting of the interactions between phenolic compounds from medicinal plants and the CagA oncoprotein of H. pylori. In this in silico study, the structures of the phenolic compounds (ligands) kaempferol, myricetin, quercetin, ponciretin (flavonoids), and chlorogenic acid (phenolic acid) were selected from the PubChem database. These phenolic compounds were chosen based on previous studies that suggested medicinal plants as non-drug treatments to eliminate H. pylori infection. The three-dimensional structure model of the CagA oncoprotein of H. pylori (receptor) was obtained through molecular modeling using computational tools from the I-Tasser platform, employing the threading methodology. The primary sequence of CagA was sourced from GenBank (BAK52797.1). A screening was conducted to identify binding sites in the structure of the CagA oncoprotein that could potentially interact with the ligands, utilizing the GRaSP online platform. Both the ligands and receptor were prepared for molecular docking using AutoDock Tools 4 (ADT) software, and the simulations were carried out using a combination of ADT and AutoDock Vina v.1.2.0 software. Two sets of simulations were performed: One involving the central region of CagA with phenolic compounds, and another involving the carboxy-terminus region of CagA with phenolic compounds. The receptor-ligand complexes were then analyzed using PyMol and BIOVIA Discovery Studio software. The structure model obtained for the CagA oncoprotein exhibited high quality (C-score = 0.09) and was validated using parameters from the MolProbity platform. The GRaSP online platform identified 24 residues (phenylalanine and leucine) as potential binding sites on the CagA oncoprotein. Molecular docking simulations were conducted with the three-dimensional model of the CagA oncoprotein. No complexes were observed in the simulations between the carboxy-terminus region of CagA and the phenolic compounds; however, all phenolic compounds interacted with the central region of the oncoprotein. Phenolic compounds and CagA exhibited significant affinity energy (-7.9 to -9.1 kcal/mol): CagA/kaempferol formed 28 chemical bonds, CagA/myricetin formed 18 chemical bonds, CagA/quercetin formed 16 chemical bonds, CagA/ponciretin formed 13 chemical bonds, and CagA/chlorogenic acid formed 17 chemical bonds. Although none of the phenolic compounds directly bound to the amino acid residues of the K-Xn-R-X-R membrane binding motif, all of them bound to residues, mostly positively or negatively charged, located near this region. In silico, the tested phenolic compounds formed stable complexes with CagA. Therefore, they could be tested in vitro and/or in vivo to validate the findings, and to assess interference in CagA/cellular target interactions and in the oncogenic differentiation of gastric cells.