Receptor Binding Sites Research Articles

PD07-11 VITAMIN D HAS A STRONGER IMPACT ON PROSTATE TUMOR GENE EXPRESSION IN BLACK MEN

You have accessJournal of UrologyCME1 May 2022PD07-11 VITAMIN D HAS A STRONGER IMPACT ON PROSTATE TUMOR GENE EXPRESSION IN BLACK MEN Neil Mistry, Cordero McCall, Moray Campbell, and Adam Murphy Neil MistryNeil Mistry More articles by this author , Cordero McCallCordero McCall More articles by this author , Moray CampbellMoray Campbell More articles by this author , and Adam MurphyAdam Murphy More articles by this author View All Author Informationhttps://doi.org/10.1097/JU.0000000000002526.11AboutPDF ToolsAdd to favoritesDownload CitationsTrack CitationsPermissionsReprints ShareFacebookLinked InTwitterEmail Abstract INTRODUCTION AND OBJECTIVE: Black men have a higher risk of prostate cancer (PCa) mortality and also have a higher prevalence of vitamin D deficiency. The VITAL clinical trial showed that patients randomized to 2000 IU of vitamin D3 had a significant reduction in advanced cancers compared to placebo (1.7% vs. 2.1%; HR, 0.83; P = .04). Black men also trended towards lower PCa mortality in that trial. Thus, we sought to investigate prostate cancer responsiveness to vitamin D by evaluating differentially expressed genes (DEG) in Black vs. non-Black men’s prostate tumors in high and low vitamin D states. METHODS: We enrolled 169 men in a cross-sectional study evaluating serum vitamin D status and adverse pathology at radical prostatectomy. We selected 78 men. RNA sequencing was done using punch biopsies of >70% epithelium in the dominant tumor nodule and contralateral benign tissue to assess DEG between Black and non-Black tumors. ChIP-seq for vitamin D receptor (VDR) binding sites was used on RC43T (Black PCa cell line) and LNCaP to identify vitamin D responsive genes. Samples were stratified by vitamin D status (above vs. below race-specific median) and race (Black vs non-Black). RESULTS: There were 57 Black and 21 non-Black men. There were 39 lower risk tumors (Gleason score ≤ 3+4) and 39 higher risk tumors (GS ≥ 3+4 with tertiary 5). In a high vitamin D state, we found 2,101 DEGs in Black tumors vs normal tissue (Figure 1a) compared to only 15 DEGs in non-Black tumors vs normal tissue (Figure 1b). A direct comparison of Black vs non-Black tumors in a high vitamin D state demonstrated 434 DEGs (Figure 1c). When comparing tumors with above vs below-median vitamin D in all patients, we found 2,992 DEGs. Of these, 1,746 DEGs contained VDR binding sites and were found in RC43T while only 10 DEGs with VDR binding sites were found in LNCaP (Figure 1d). CONCLUSIONS: Vitamin D directly impacts gene expression in prostate cancer. Tumors in Black men express more genes that have VDR binding sites than tumors in non-Black men. Due to this unique relationship, Vitamin D may have a role in chemoprevention for clinically localized prostate cancer in Black men. Source of Funding: None © 2022 by American Urological Association Education and Research, Inc.FiguresReferencesRelatedDetails Volume 207Issue Supplement 5May 2022Page: e103 Advertisement Copyright & Permissions© 2022 by American Urological Association Education and Research, Inc.MetricsAuthor Information Neil Mistry More articles by this author Cordero McCall More articles by this author Moray Campbell More articles by this author Adam Murphy More articles by this author Expand All Advertisement PDF DownloadLoading ...

Cell Surface Glycan Engineering to Examine Receptor Specificities of Influenza and Other Viruses

The transmission of viruses from animal reservoirs to humans poses great threats to public health. Preparedness for future zoonotic outbreaks requires a fundamental understanding how viruses of animal origin have adapted to replication in humans. In particular, it necessitates insight how viruses have evolved to binding to a cell surface component, or receptor, of the new host. We have developed glycan arrays and glycan cell surface engineering strategies to examine receptor specificities of viruses. The approaches were employed to examine receptor specificities of evolutionary distinct A/H3N2 influenza viruses. Recent A/H3N2 influenza viruses exhibit altered receptor specificities, and as a result they have lost the ability to agglutinate erythrocytes critical for antigenic characterization and give low yields and acquire adaptive mutations when cultured in eggs and cells, contributing to recent vaccine challenges. Glycan array technology showed that these viruses have compensated for decreased binding of the prototypic human receptor by recognizing α2,6‐sialosides on extended LacNAc moieties. Erythrocyte glycomics showed an absence of extended glycans, providing a rationale for lack of agglutination by recent A/H3N2 viruses. A glycan remodeling approach installed functional receptors on erythrocytes, allowing antigenic characterization of recent A/H3N2 viruses and confirming the cocirculation of antigenically different viruses in humans. Computational studies of HAs in complex with sialosides having extended LacNAc moieties reveal that mutations distal to the RBD reoriented the Y159 side chain, resulting in an extended receptor binding site. The approach was extended to examining the receptor specificity of Lass Virus.

Design and Synthesis of Bovine Leukemia Virus-Associated Peptide-Based Qβ Conjugate Eliciting Long-Lasting Neutralizing Antibodies in Mice.

Bovine leukemia virus (BLV) is a C-type retrovirus of cattle that causes huge economic losses with high infection rates in the majority of countries worldwide. To develop an anti-BLV vaccine, we constructed a peptide conjugate using the envelope glycoprotein gp51-peptide epitope, a putative receptor-binding site. This highly antigenic peptide was covalently linked to a mutant bacteriophage carrier (mQβ) using two different linker strategies, isothiocyanate (NCS) and dinitrophenyl adipate. Both constructs elicited higher anti-BLV peptide IgG titers than the corresponding conjugate with keyhole limpet hemocyanin protein carrier (gold standard) in mice with the NCS linker strategy requiring less sample processing. The mQβ-gp51-peptide construct is the first BLV peptide-based vaccine candidate to generate durable immunity (>539 days), which recognized both native gp51 protein and BLV particles and significantly decreased fusion of a susceptible cell line exposed to infectious BLV. These results support the high translational and animal health potential of the vaccine construct.

Orphan Nuclear Receptor NR4A2 Is Constitutively Expressed in Cartilage and Upregulated in Inflamed Synovium From hTNF-Alpha Transgenic Mice.

Orphan nuclear receptor 4A2 (NR4A2/Nurr1) is a constitutively active transcription factor with potential roles in the onset and progression of inflammatory arthropathies. NR4A2 is overexpressed in synovium and cartilage from individuals with rheumatoid arthritis (RA), psoriatic arthritis, and osteoarthritis. This study documents the expression and tissue localization of NR4A2 and upstream regulator nuclear factor kappa B (NF-κB) in the human tumor necrosis factor-alpha (hTNF-α) transgenic mouse model of RA. Since TNF-α is a potent inducer of NR4A2 in vitro, we hypothesized that NR4A2 would also be upregulated and active during disease progression in this model. Expression levels of NR4A2, related receptors NR4A1 (Nur77) and 3 (NOR1), and NF-κB1 transcripts were quantified by RT-qPCR in hTNF-α and wild-type joints at three stages of disease. The protein distribution of NR4A2 and NF-κB subunit RelA (p65) was analyzed by quantitative immunohistochemistry. Global gene expression of 88 RA-related genes was also screened and compared between groups. Consistent with previous reports on the hTNF-α model, transgenic mice exhibited significant weight loss and severely swollen paws by 19 weeks of age compared to age-matched wild-type controls. NR4A1-3 and NF-κB1 were constitutively expressed at disease onset and in healthy joints. NF-κB1 transcript levels increased 2-fold in hTNF-α paws with established disease (12 weeks), followed by a 2-fold increase in NR4A2 at the late disease stage (19 weeks). NR4A2 and RelA proteins were overexpressed in inflamed synovium prior to symptoms of arthritis, suggesting that gene expression changes documented in whole paws were largely driven by elevated expression in diseased synovium. Broader screening of RA-related genes by RT-qPCR identified several differentially expressed genes in hTNF-α joints including those encoding inflammatory cytokines and chemokines, matrix-degrading enzymes and inhibitors, cell surface receptors, intracellular signaling proteins and transcription factors. Consensus binding sites for NR4A receptors and NF-κB1 were enriched in the promoters of differentially expressed genes suggesting central roles for these transcription factors in this model. This study is the first comprehensive analysis of NR4A2 in an animal model of RA and validates the hTNF-α model for testing of small molecules and genetic strategies targeting this transcription factor.

Axial chirality and affinity at the GABAA receptor of triazolobenzodiazepines

Triazolobenzodiazepines substituted with a methyl group at the C1- and C10-positions and chloro group at C2′ of pendant-phenyl were prepared and their physicochemical properties were investigated. The atropisomers of 1,10-disubstituted triazolobenzodiazepines, 1d and 1f, were isolated as (a1R, a2S) and (a1S, a2R) isomers. Their absolute configurations were determined on the basis of CD spectra in comparison with those of stereochemically defined 9-methyl-1,4-benzodiazepin-2-ones. Examination of the affinity at the human GABAA receptors revealed that each (a1R, a2S) isomer of 1d and 1f possessed higher activity than its antipode (a1S, a2R) isomer. It was also found that 1a, which behaves achirally due to the rapid conformational change, had the highest GABAA affinity, equal to that of triazolam. Considering that each eutomer of 1d and 1f is (a1R, a2S), the conformation of 1a at the binding site of the GABAA receptor is expected to be (a1R, a2S).

New Mutants of Epsilon Toxin from Clostridium perfringens with an Altered Receptor-Binding Site and Cell-Type Specificity.

Epsilon toxin (Etx) from Clostridium perfringens is the third most potent toxin after the botulinum and tetanus toxins. Etx is the main agent of enterotoxemia in ruminants and is produced by Clostridium perfringens toxinotypes B and D, causing great economic losses. Etx selectively binds to target cells, oligomerizes and inserts into the plasma membrane, and forms pores. A series of mutants have been previously generated to understand the cellular and molecular mechanisms of the toxin and to obtain valid molecular tools for effective vaccination protocols. Here, two new non-toxic Etx mutants were generated by selective deletions in the binding (Etx-ΔS188-F196) or insertion (Etx-ΔV108-F135) domains of the toxin. As expected, our results showed that Etx-ΔS188-F196 did not exhibit the usual Etx binding pattern but surprisingly recognized specifically an O-glycoprotein present in the proximal tubules of the kidneys in a wide range of animals, including ruminants. Although diminished, Etx-ΔV108-F135 maintained the capacity for binding and even oligomerization, indicating that the mutation particularly affected the pore-forming ability of the toxin.

Vaccine based on folded receptor binding domain-PreS fusion protein with potential to induce sterilizing immunity to SARS-CoV-2 variants.

BackgroundSevere acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) is responsible for the ongoing global COVID‐19 pandemic. One possibility to control the pandemic is to induce sterilizing immunity through the induction and maintenance of neutralizing antibodies preventing SARS‐CoV‐2 from entering human cells to replicate in.MethodsWe report the construction and in vitro and in vivo characterization of a SARS‐CoV‐2 subunit vaccine (PreS‐RBD) based on a structurally folded recombinant fusion protein consisting of two SARS‐CoV‐2 Spike protein receptor‐binding domains (RBD) fused to the N‐ and C‐terminus of hepatitis B virus (HBV) surface antigen PreS to enable the two unrelated proteins serving as immunologic carriers for each other.ResultsPreS‐RBD, but not RBD alone, induced a robust and uniform RBD‐specific IgG response in rabbits. Currently available genetic SARS‐CoV‐2 vaccines induce mainly transient IgG1 responses in vaccinated subjects whereas the PreS‐RBD vaccine induced RBD‐specific IgG antibodies consisting of an early IgG1 and sustained IgG4 antibody response in a SARS‐CoV‐2 naive subject. PreS‐RBD‐specific IgG antibodies were detected in serum and mucosal secretions, reacted with SARS‐CoV‐2 variants, including the omicron variant of concern and the HBV receptor‐binding sites on PreS of currently known HBV genotypes. PreS‐RBD‐specific antibodies of the immunized subject more potently inhibited the interaction of RBD with its human receptor ACE2 and their virus‐neutralizing titers (VNTs) were higher than median VNTs in a random sample of healthy subjects fully immunized with registered SARS‐CoV‐2 vaccines or in COVID‐19 convalescent subjects.ConclusionThe PreS‐RBD vaccine has the potential to serve as a combination vaccine for inducing sterilizing immunity against SARS‐CoV‐2 and HBV by stopping viral replication through the inhibition of cellular virus entry.

Multivalent designed proteins neutralize SARS-CoV-2 variants of concern and confer protection against infection in mice.

New variants of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) continue to arise and prolong the coronavirus disease 2019 (COVID-19) pandemic. Here we used a cell-free expression workflow to rapidly screen and optimize constructs containing multiple computationally designed miniprotein inhibitors of SARS-CoV-2. We found the broadest efficacy with a homo-trimeric version of the 75-residue angiotensin converting enzyme 2 (ACE2) mimic AHB2 (TRI2–2) designed to geometrically match the trimeric spike architecture. In the cryo-electron microscopy structure, TRI2 formed a tripod on top of the spike protein which engaged all three receptor binding domains (RBDs) simultaneously as in the design model. TRI2–2 neutralized Omicron (B.1.1.529), Delta (B.1.617.2), and all other variants tested with greater potency than that of monoclonal antibodies used clinically for the treatment of COVID-19. TRI2–2 also conferred prophylactic and therapeutic protection against SARS-CoV-2 challenge when administered intranasally in mice. Designed miniprotein receptor mimics geometrically arrayed to match pathogen receptor binding sites could be a widely applicable antiviral therapeutic strategy with advantages over antibodies and native receptor traps. By comparison, the designed proteins have resistance to viral escape and antigenic drift by construction, precisely tuned avidity, and greatly reduced chance of autoimmune responses.

Annotating Spike Protein Polymorphic Amino Acids of Variants of SARS-CoV-2, Including Omicron.

The prolonged global spread and community transmission of severe acute respiratory syndrome virus 2 (SARS-CoV-2) has led to the emergence of variants and brought questions regarding disease severity and vaccine effectiveness. We conducted simple bioinformatics on the spike gene of a representative of each variant. The data show that a number of polymorphic amino acids are located mostly on the amino-terminal side of the S1/S2 cleavage site. The Omicron variant diverges from the others, with the highest number of amino acid substitutions, including the receptor-binding site (RBS), epitopes, S1/S2 cleavage site, fusion peptide, and heptad repeat 1. The current sharp global increase in the frequency of the Omicron genome constitutes evidence of its high community transmissibility. In conclusion, the proposed guideline could give an immediate insight of the probable biological nature of any variant of SARS-Cov-2. As the Omicron diverged the farthest from the original pandemic strain, Wuhan-Hu-1, we expect different epidemiological and clinical patterns of Omicron cases. On vaccine efficacy, slight changes in some epitopes while others are conserved should not lead to a significant reduction in the effectiveness of an approved vaccine.

Second Receptor-Binding Site of Influenza a Virus Neuraminidase: A Key Factor for Virus Host range?

Second Receptor-Binding Site of Influenza a Virus Neuraminidase: A Key Factor for Virus Host range?

Dihydromyricetin Protects Against Ethanol-Induced Toxicity in SH-SY5Y Cell Line: Role of GABAA Receptor.

Toxicity induced by binge alcohol drinking, particularly in adolescent and young adults, is of major medical and social consequence. Recently, we reported that butyrate, a short chain fatty acid, can protect against ethanol (ETOH)-induced toxicity in an in vitro model. In this study, we sought to evaluate the potential effectiveness of dihydromyricetin (DHM), a natural bioactive flavonoid, alone or in combination with butyrate in the same model. Exposure of SH-SY5Y cells for 24h to 500mM ETOH resulted in approximately 40% reduction in cell viability, which was completely prevented by 0.1 μM DHM. Combinations of DHM and butyrate provided synergistic protection against alcohol toxicity. Whereas butyrate effect was shown to be mediated primarily through fatty acid receptor 3 activation, DHM protection appears to be mediated primarily via benzodiazepine receptor site of GABAA receptor. This is based on the finding that DHM's effect could be completely prevented by pretreatment with flumazenil, a selective antagonist at this site, but not by bicuculline, a selective antagonist at the actual GABAA receptor binding site. These findings suggest potential utility of DHM alone or in combination with butyrate against ETOH-induced toxicity.

Identification of potent aldose reductase inhibitors as antidiabetic (Anti-hyperglycemic) agents using QSAR based virtual Screening, molecular Docking, MD simulation and MMGBSA approaches

The aldose reductase (AR) enzyme is an important target enzyme in the development of therapeutics against hyperglycaemia induced health complications such as retinopathy, etc. In the present study, a quantitative structure activity relationship (QSAR) evaluation of a dataset of 226 reported AR inhibitor (ARi) molecules is performed using a genetic algorithm – multi linear regression (GA-MLR) technique. Multi-criteria decision making (MCDM) analysis furnished two five variables based QSAR models with acceptably high performance reflected in various statistical parameters such as, R2 = 0.79–0.80, Q2LOO = 0.78–0.79, Q2LMO = 0.78–0.79. The QSAR model analysis revealed some of the molecular features that play crucial role in deciding inhibitory potency of the molecule against AR such as; hydrophobic Nitrogen within 2 Å of the center of mass of the molecule, non-ring Carbon separated by three and four bonds from hydrogen bond donor atoms, number of sp2 hybridized Oxygen separated by four bonds from sp2 hybridized Carbon atoms, etc. 14 in silico generated hits, using a compound 18 (a most potent ARi from present dataset with pIC50 = 8.04 M) as a template, on QSAR based virtual screening (QSAR-VS) furnished a scaffold 5 with better ARi activity (pIC50 = 8.05 M) than template compound 18. Furthermore, molecular docking of compound 18 (Docking Score = –7.91 kcal/mol) and scaffold 5 (Docking Score = –8.08 kcal/mol) against AR, divulged that they both occupy the specific pocket(s) in AR receptor binding sites through hydrogen bonding and hydrophobic interactions. Molecular dynamic simulation (MDS) and MMGBSA studies right back the docking results by revealing the fact that binding site residues interact with scaffold 5 and compound 18 to produce a stable complex similar to co-crystallized ligand's conformation. The QSAR analysis, molecular docking, and MDS results are all in agreement and complementary. QSAR-VS successfully identified a more potent novel ARi and can be used in the development of therapeutic agents to treat diabetes.

In Silico Personalized Study for Zolpidem Based on Sex Difference

Zolpidem is a non-benzodiazepine agonist at the benzodiazepine binding site in GABAA receptors. It is a hypnotic agent which has been shown to be effective in inducing and maintaining sleep in adults and is one of the most frequently prescribed hypnotics in the world. This study aimed to perform an in silico study to assess both EMA and FDA positions on the dose adjustment of Zolpidem based on sex. Both agencies based their position on clinical studies but endorsed different approaches to the need for dose adjustments between men and females. Clinical studies of Zolpidem tablets in single-and multiple-dose regimens were gathered and digitized from the literature. The collected profiles were used for model building, evaluation, and simulation. A 2-compartment model with first-order absorption, lag-time, and linear elimination best described the data. To minimize bias, the distribution of data on females and males were balanced, comprising, respectively, four and eight patients. Simulation of dose regimen comparing the efficacy and safety of 10 and 12.5 mg zolpidem tablets showed that with the 10 mg tablets there was a 69% chance of being more efficient for an individual of the population simulated, for the selected dose of regimen, while the 12.5 mg tablet there was only a 42% chance of being more efficient. Moreover, the safety target for 12.5 mg was very low, with only a 14% of chance of being a safe treatment for an individual of this population. Based on these differences, this study compared the results gathered in simulations with the rationale behind EMA and FDA positions. It is very important that all health care professionals and patients have access to the same and most up-to-date safety and efficacy information, especially in this situation where the discussion focuses on the same active substance, same formulations, same treatment indications, and same target populations.

Unraveling the molecular determinants of the anti-phagocytic protein cloak of plague bacteria.

The pathogenic bacterium Yersina pestis is protected from macrophage engulfment by a capsule like antigen, F1, formed of long polymers of the monomer protein, Caf1. However, despite the importance of this pathogen, the mechanism of protection was not understood. Here we demonstrate how F1 protects the bacteria from phagocytosis. First, we show that Escherichia coli expressing F1 showed greatly reduced adherence to macrophages. Furthermore, the few cells that did adhere remained on the macrophage surface and were not engulfed. We then inserted, by mutation, an “RGDS” integrin binding motif into Caf1. This did not change the number of cells adhering to macrophages but increased the fraction of adherent cells that were engulfed. Therefore, F1 protects in two separate ways, reducing cell adhesion, possibly by acting as a polymer brush, and hiding innate receptor binding sites needed for engulfment. F1 is very robust and we show that E. coli expressing weakened mutant polymers are engulfed like the RGDS mutant. This suggests that innate attachment sites on the native cell surface are exposed if F1 is weakened. Single-molecule force spectroscopy (SMFS) experiments revealed that wild-type F1 displays a very high mechanical stability of 400 pN. However, the mechanical resistance of the destabilised mutants, that were fully engulfed, was only 20% weaker. By only marginally exceeding the mechanical force applied to the Caf1 polymer during phagocytosis it may be that the exceptional tensile strength evolved to resist the forces applied at this stage of engulfment.

Design, Synthesis and Molecular Docking Study of N-Heterocyclic Chalcone Derivatives as an Anti-cancer Agents

The Claisen-Schmidt condensation of 4-(aryl)-aminobenzaldehyde and 2-hydroxyacetophenone resulted in a new series of heterocyclic chalcone (4a-4g) derivatives. Nucleophilic aromatic substitution (SNAr) of 4-fluorobenzaldehyde with heterocycle amines by ultrasonication in the presence of a base and polar aprotic solvent yielde 4-(aryl)-aminobenzaldehydes. Spectral investigations were used to establish the structures of synthesized compounds. The in vitro anti-cancer activity of the synthesized derivative was evaluated against MCF-7 (breast cancer) cells by SRB assay. Compounds 4c, 4b, and 4c have a high affinity for the ER receptor binding site, whereas compounds 4c and 4g have a moderate affinity for the VEGER-2 receptor. The GI50 value of 4c ((E)-1-(2-hydroxyphenyl)-3-(4-(4-methylpiperazin-1-yl)-phenyl) prop-2-en-1-one) was 44.6 uM, while the GI50 value of all other derivatives was greater than 80 uM. These findings lay the groundwork for additional research into the combination's potential uses in cancer therapy.

Challenges of the Omicron (B.1.1.529) Variant and Its Lineages: A Global Perspective.

The SARS‐CoV‐2 virus has shown increased ability to mutate over the past two years, especially in the regions of the spike protein and receptor binding sites. Omicron (B.1.1.529) is the fifth variant of concern (VOC) after the emergence of the Alpha, Beta, Gamma, and Delta VOCs of SARS‐CoV‐2. This new variant has now circulated in 128 countries and according to the Global Initiative on Sharing All Influenza Data (GISAID), these 128 countries have shared 650,657 Omicron genome sequences as of 26 January, 2022. In this article, we highlight the real challenges of Omicron and its different lineages.

A formalization of one of the main claims of “Overlap of vitamin A and vitamin D target genes with CAKUT-related processes” by Ozisik et al. 20211

In a previous paper that we co-authored (Ozisik et al. 2021) we showed that in some cases Vitamin A and Vitamin D receptor binding sites are present in genes associated with Congenital Anomalies of the Kidney and Urinary Tract (CAKUT). From that finding we derived the statement that sometimes Vitamin A targets are the same as genes associated with CAKUT. We present here a formalization of that claim, stating that all things of class “genes associated with CAKUT” sometimes have a relation of type “is same as” to a thing of class “targets of vitamin A”.

Inhibition of avian influenza virus H9N2 infection by antiviral hexapeptides that target viral attachment to epithelial cells

The H9N2 subtype of influenza A virus circulates frequently among poultry in Asian and North African countries causing economic loss in the poultry sector. The antigenic variations of the H9N2 virus were at the origin of its genetic evolution through the emergence of viral strains transmissible to humans and resistant to chemical antivirals, which require a strengthening of the fight means against this virus. In this study, we used a random linear hexapeptide library fused to the gene III protein of M13 filamentous bacteriophage to select new antiviral peptides that inhibit the infectivity of H9N2 virus. After three rounds of stringent selection and amplification, polyclonal phage-peptides directed against H9N2 virus were assessed by ELISA, and the optimal phage-peptides were grown individually and characterized for binding to H9N2 virus by monoclonal phage ELISA. The DNA of 27 phage-peptides clones was amplified by PCR, sequenced, and their amino acid sequences were deduced. Sixteen different phage-peptides were able to bind specifically the H9N2 virus, among them, 13 phage-peptides interacted with the hemagglutinin H9. Two selected peptides, P1 (LSRMPK) and P2 (FAPRWR) have shown antiviral activity in ovo and P1 was more protective in vivo then P2 when co-administered with the H9N2 virus. Mechanistically, these peptides prevent infection by inhibiting the attachment of the H9N2 virus to the cellular receptor. Molecular docking revealed that the peptides LSRMPK and FAPRWR bind to hemagglutinin protein H9, but interact differently with the receptor binding site (RBS). The present study demonstrated that the peptide P1 (LSRMPK) could be used as a new inhibitory molecule directed against the H9N2 virus.

In Silico Screening for Pesticide Candidates against the Desert Locust Schistocerca gregaria.

Adipokinetic hormone (AKH) is one of the most important metabolic neuropeptides in insects, with actions similar to glucagon in vertebrates. AKH regulates carbohydrate and fat metabolism by mobilizing trehalose and diacylglycerol into circulation from glycogen and triacylglycerol stores, respectively, in the fat body. The short peptide (8 to 10 amino acids long) exerts its function by binding to a rhodopsin-like G protein-coupled receptor located in the cell membrane of the fat body. The AKH receptor (AKHR) is, thus, a potential target for the development of novel specific (peptide) mimetics to control pest insects, such as locusts, which are feared for their prolific breeding, swarm-forming behavior and voracious appetite. Previously, we proposed a model of the interaction between the three endogenous AKHs of the desert locust, Schistocerca gregaria, and the cognate AKHR (Jackson et al., Peer J. 7, e7514, 2019). In the current study we have performed in silico screening of two databases (NCI Open 2012 library and Zinc20) to identify compounds which may fit the endogenous Schgr-AKH-II binding site on the AKHR of S. gregaria. In all, 354 compounds were found to fit the binding site with glide scores < −8. Using the glide scores and binding energies, 7 docked compounds were selected for molecular dynamic simulation in a phosphatidylcholine membrane. Of these 7 compounds, 4 had binding energies which would allow them to compete with Schgr-AKH-II for the receptor binding site and so are proposed as agonistic ligand candidates. One of the ligands, ZINC000257251537, was tested in a homospecific in vivo biological assay and found to have significant antagonistic activity.

Robust and predictive QSAR models for predicting the D2, 5-HT1A, and 5-HT2A inhibition activities of fused tricyclic heterocycle piperazine (piperidine) derivatives as atypical antipsychotic drugs

In this research, QSAR models were developed for predicting the inhibition activities of tricyclic heterocycle piperazine (piperidine) derivatives against the D2, 5-HT1A, and 5-HT2A receptors. These develop 2D and 3D-QSAR models were use for determining chemical structural features that improve the activities of molecules. For the D2 inhibition activities of molecules, reliable MLR and CoMFA models and for their 5-HT2A inhibition activities, reliable MLR and ε-SVR were developed. For the 5-HT1A inhibition activities of molecules, three QSAR models (based on the application of CoMFA, MLR, and ε-SVR) were developed. For all models, the applicability domain of created models was investigated by calculating leverage. Residual plots show that there is no systematic error in creating all models and all QSAR models were validated by calculating several statistical parameters for both train and test sets. Based on the interpretation of developed QSAR models, new molecules with high activityis against all three receptors were designed. Finally, three molecules, including m5, m20, and m36, were docked to the binding site of the D2 receptor to investigate their binding pose and interaction with this binding site. The docking results show that m36 has the most negative binding energy, and molecular dynamics simulations results show that the binding of m36 to the D2 makes the receptor more stable with respect to risperidone.