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Showing 1 - 41 of 41 Journals sorted alphabetically
ACS Omega     Open Access   (Followers: 2)
Advances in Image and Video Processing     Open Access   (Followers: 18)
Advances in Physical Organic Chemistry     Full-text available via subscription   (Followers: 4)
Advances in Redox Research     Open Access   (Followers: 4)
American Journal of Organic Chemistry     Open Access   (Followers: 15)
Asian Journal of Organic Chemistry     Hybrid Journal   (Followers: 4)
Beilstein Journal of Organic Chemistry     Open Access   (Followers: 13)
Biochemia Medica     Open Access  
Current Organic Chemistry     Hybrid Journal   (Followers: 14)
Current Organic Synthesis     Hybrid Journal   (Followers: 12)
European Journal of Organic Chemistry     Hybrid Journal   (Followers: 59)
Herbal Medicine: Open Access     Open Access  
International Journal of Organic Chemistry     Open Access   (Followers: 9)
International Journal of Polymeric Materials     Hybrid Journal   (Followers: 6)
Journal of Bioactive and Compatible Polymers     Hybrid Journal   (Followers: 2)
Journal of Biomaterials Science, Polymer Edition     Hybrid Journal   (Followers: 9)
Journal of Organic Semiconductors     Open Access   (Followers: 6)
Journal of Peptide Science     Hybrid Journal   (Followers: 14)
Journal of Physical Organic Chemistry     Hybrid Journal   (Followers: 8)
Journal of Physiology and Biochemistry     Hybrid Journal   (Followers: 3)
Journal of Progressive Research in Chemistry     Open Access  
Journal of Proteins and Proteomics     Open Access   (Followers: 2)
Mini-Reviews in Organic Chemistry     Hybrid Journal   (Followers: 10)
Nigerian Journal of Chemical Research     Full-text available via subscription   (Followers: 1)
Open Journal of Organic Polymer Materials     Open Access   (Followers: 1)
Organic & Biomolecular Chemistry     Hybrid Journal   (Followers: 56)
Organic and Medicinal Chemistry Letters     Open Access   (Followers: 5)
Organic Chemistry : Current Research     Open Access   (Followers: 12)
Organic Chemistry Frontiers     Hybrid Journal   (Followers: 9)
Organic Chemistry International     Open Access   (Followers: 7)
Organic Geochemistry     Hybrid Journal   (Followers: 3)
Organic Letters     Hybrid Journal   (Followers: 92)
Organic Preparations and Procedures International: The New Journal for Organic Synthesis     Hybrid Journal   (Followers: 3)
Organic Process Research & Development     Hybrid Journal   (Followers: 32)
Progress in Organic Coatings     Hybrid Journal   (Followers: 7)
Reports in Organic Chemistry     Open Access   (Followers: 7)
Russian Journal of Organic Chemistry     Hybrid Journal   (Followers: 3)
Synthetic Communications: An International Journal for Rapid Communication of Synthetic Organic Chemistry     Hybrid Journal   (Followers: 31)
The Journal of Organic Chemistry     Hybrid Journal   (Followers: 135)
Vibrational Spectroscopy     Hybrid Journal   (Followers: 11)
World Journal of Organic Chemistry     Open Access   (Followers: 5)
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Journal Cover
Journal of Proteins and Proteomics
Number of Followers: 2  

  This is an Open Access Journal Open Access journal
ISSN (Print) 0975-8151 - ISSN (Online) 2524-4663
Published by Springer-Verlag Homepage  [2537 journals]
  • Analyzing the effect of deleterious non-synonymous SNPs causing CHARGE
           syndrome associated with the CHD7 protein using computational approaches

    • Abstract: The chromodomain helicase DNA-binding protein 7 (CHD7) is also known as ATP-dependent helicase CHD7. In humans, the CHD7 gene encodes it. Heterozygous mutations in this protein cause aggregation and have been linked to the development of the CHARGE syndrome. CHD7 is known to be a subcategory of CHD proteins identified only in metazoans containing the BRK domain. Numerous studies suggest that the protein’s functional activity is affected by non-synonymous single nucleotide polymorphisms (nsSNPs). Using computational methods, this study predicted and analyzed the most deleterious nsSNPs for their functional effect on the CHD7 protein. Eight computational tools: PhD-SNP, Polyphen-1, Polyphen-2, SIFT, SNAP, I-Mutant, MUpro, and iStable were used to predict the deleterious and unstable nsSNPs. Based on the structure availability (2V0F with the mutational position 2631–2715) and the study reported by Bartels et al., two highly deleterious nsSNPs (P2683S and R2702C) were selected, which were predicted to be deleterious and unstable from pathogenicity analysis and stability analysis. The nsSNPs (P2683S and R2702C) were determined to fall under the conserved region of the protein using the ConSurf server. The Swiss PDB viewer and PyMOL software version 2.0 were used to conduct the structural analysis of the proteins. GROMACS was used for molecular dynamics simulation to understand the stability of wild and mutant structures. In silico study indicated that P2683S will be more deleterious among the two widely studied nsSNPs. In this current study, docking analysis was performed to determine drug activity against hypogonadotropic hypogonadism associated with CHARGE syndrome. Finally, molecular docking was performed for the wild and the mutant structure P2683S to study the binding efficacy of the existing drugs Methyltestosterone and Estradiol, resulting in a similar score with a minimal difference between each other. Detailed studies about the disease, the effect of nsSNPs, and the response of the drug towards the mutation are the critical factors to launch a new personalized medicine. Experimental biologists will use the findings of our investigation to understand the variations in the CDH7 protein better.
      PubDate: 2022-01-15
  • The prediction of specific oil palm extracellular signal peptides using
           plant secretomics approach

    • Abstract: Signal peptide is an essential part during protein translocation for extracellular expression in the plants. A secretomics approach was performed to identify secretory proteins from oil palm and predict the presence of the signal peptide in each protein. The transcriptome and secretome profiles were generated from oil palm ramets. A combination of bioinformatics tools including SignalP, TargetP, TMHMM, and SecretomeP was used to predict both classical and leaderless secretory proteins. The secretome analysis from transcriptome data revealed 2259 genes that encoded secretory proteins. The proteome analysis identified a total of 37 proteins from which 10 classical secretory proteins can be distinguished. It was important to note that oil palm ramet’s secretome was dominated by stress or defence related proteins which may act as protection during certain plant developmental stages. We also found that some proteins can be both intracellular and extracellular protein. Among 10 identified classical secretory proteins, the signal peptides of oil palm beta-1,3-glucanase and putative class III chitinase were interesting for further study due to their high cleavage site scores. Overall, this study provided broader view of oil palm secretomes and specific signal peptides for extracellular expression.
      PubDate: 2021-11-16
  • Proteomic analysis of serum protein during early pregnancy

    • Abstract: An early and accurate pregnancy diagnosis is a prime tool for the efficient breeding management. During maternal recognition of pregnancy, there is a release of various proteins in the circulation. These proteins may be helpful in diagnosing early pregnancy in animals. Therefore, a study was conducted on the protein profiling in serum of Sahiwal cattle. Blood samples were collected from 30 Sahiwal cows on day 0, 12, 16, 19 and 22 post-breeding. Serum was separated and subjected to 1D SDS PAGE which revealed specific protein band of molecular weight between 33 and 43 kDa and over expression of 66.0 kDa band in pregnant animals from day 16 to 22. Day 19 serum was then subjected to nano-LC–MS/MS. Total 4406 peptide mass spectra were generated leading to identification of 1,416 peptides finally mapping to give 248 proteins. Out of 248 proteins, 127 were upregulated and 54 were downregulated. 17 proteins were highly upregulated having fold change more than 30. There were total 19 proteins in LC–MS which corresponded to the specific bands in 1D SDS PAGE. Gene ontology using PANTHER 15.0 revealed majority of the proteins are having binding property which is necessary during maternal recognition of pregnancy and implantation. Proteins like lactotransferrin, Golgin A4, MYRIP, PKD1 and PWWP domain containing protein MUM1 have the potential to be the biomarker for pregnancy diagnosis and may be used in developing pregnancy diagnostic kit in future.
      PubDate: 2021-11-10
  • Quantitative proteomic analysis reveals differential modulation of crucial
           stage specific proteins during promastigote to amastigote differentiation
           in Leishmania donovani

    • Abstract: Leishmaniasis is a neglected tropical disease (NTD) caused by the protozoan parasite Leishmania. The disease has several clinical manifestations with visceral leishmaniasis (VL) being the most fatal. The apicomplexan protozoan has a digenetic life cycle between the sandfly vectors (promastigote stage) and the mammalian hosts (amastigote stage). Promastigote to amastigote differentiation is crucial for intracellular survival and for successful establishment of infection. However, the underlying molecular mechanisms still remain elusive. We investigated the proteome changes during the early differentiation stages of Leishmania donovani clinical isolate from an Amphotericin B (AmB) relapse patient. Sequential Window Acquisition of All Theoretical Mass Spectra (SWATH-MS) based quantitative proteomics revealed 814 and 921 differentially modulated proteins after 24 h and 48 h of promastigote to amastigote differentiation. We identified several key proteins like Tb-292-membrane-associated-protein-like-protein, Glycoprotein 96–92, p22 proteins, Maoc family dehydratase-like protein, KH domain-containing putative protein, Apolipoprotein-A1/A4/E-domain-containing-protein, Mkiaa0324 protein-like protein and Protein YIPF not reported hitherto. Several key metabolic proteins, proteases and proteins involved in post-translational modifications (PTM) were also differentially modulated between the amastigote and promastigote stages. Bioinformatics analyses of the proteomics data revealed several metabolic pathways viz., glycolysis, oxidative stress, fatty acid metabolism, asparagine/glutamine biosynthesis and purine/pyrimidine biosynthesis to be differentially regulated between the digenetic stages. Further studies to investigate the role of these proteins would allow better understanding of Leishmania pathogenesis and identification of targets for therapeutic intervention and biomarker studies. Graphic abstract
      PubDate: 2021-11-08
  • Unravelling the natural dual-target inhibiting potential of cucurbit
           bioactive compounds for the management of cucumber mosaic virus (CMV)
           through computational approaches

    • Abstract: Cucumber mosaic virus (CMV), one of the top ten most devastating plant pathogenic viruses infects nearly 1300 crop species causing huge economic losses. It is transmitted by more than 80 aphid species (Insecta: Hemiptera: Aphidoidea) including Myzus persicae and Aphis gossypii in a non-persistent, stylet-borne manner. The coat protein (CP) of the virus is identified as the primary determinant for aphid transmission, and a stylet-borne M. persicae Cuticle Protein (MPCP4) RR1 is crucial for the CMV acquisition. All the conventional management strategies rely on heavy use of eco-unfriendly agrochemicals, leading to the development of multi-drug insect resistance. Though, cucurbits lack completely resistant varieties for CMV, have a powerhouse of several endogenous bioactive compounds. In the present study, molecular docking was performed with 61 selected cucurbit bioactive compounds against two target proteins; the CMV–CP and RR1 protein for their binding energies, molecular interactions, and inhibition constant. The prime MM–GBSA approach was further used for calculating the change in Gibb’s free energy of binding (ΔG) and the per residue contribution of the selected top-scored ligand molecules. Our docking results showed that two phenolic compounds topped the list viz., amentoflavone and quercetin with higher binding affinities towards both the targets by which these compounds exhibit the anti-viral and insecticidal effect. Furthermore, the lead molecule amentoflavone had energetically more favorable ΔG value for the CP and cucurbitacin D for RR1 protein, respectively. These compounds also had lower toxicity and better agrochemical-like properties than synthetic pesticides. Based on these results, it would be interesting to determine their dual inhibiting potential and field applicability as a safe sustainable approach for CMV disease management.
      PubDate: 2021-09-30
      DOI: 10.1007/s42485-021-00079-6
  • Purification and partial characterization of acid phosphatase from rice
           bean (Vigna umbellata Thunb.)

    • Abstract: Acid phosphatase from rice bean (Vigna umbellata Thunb.) got isolated with 740-fold purification and specific activity 80 U/mg protein. In the native PAGE, a single protein band got observed upon silver staining. The activity staining revealed that the band corresponded to acid phosphatase. The molecular mass of the native acid phosphatase was 80 kDa. The SDS-PAGE exhibited a single protein band of molecular mass 40–41 kDa. Acid phosphatase is colorless and exhibited maximum absorbance at 278 nm but no absorption maximum at 550 nm. The enzyme retained 91.8% activity after 120 days when stored at 4 °C and improved further in the presence of polyethylene glycol (95.6%) and bovine serum albumin (97.0%) under similar storage conditions. The enzyme functioned optimally at pH 5.5 and 60 °C. The energy of activation was 32.6 kJ/mol. The values of Km and Vmax determined by the Lineweaver–Burk plot were 0.108 mM (p-nitrophenylphosphate) and 90.09 μmol/min/mg, respectively. The value of kcat and kcat/Km were 120.12 s−1 and 1.11 × 106 M−1 s−1, respectively.
      PubDate: 2021-09-20
      DOI: 10.1007/s42485-021-00076-9
  • Metagenomic sequencing reveals altered gut microbiota of sojourners at
           high altitude: a longitudinal study

    • Abstract: Human microbial alterations are associated with environmental stress, nutrition, genetic, and triggering de-novo variations. Nevertheless, the human gut microbiome at extreme altitude (> 5800 m) remains unexplored. We aimed to demonstrate the microbial predominance in individuals with the same ethnicity and dietary pattern at extreme altitude with unique challenges like cold, hypoxia, radiation, etc. Different analysis pipelines were used for fecal whole genome sequencing at 210 m, 3500 m, 4420 m and 5805 m, and 16S rRNA V3-V4 regions amplification sequencing of 19 individuals belonging to the same ethnicity and dietary pattern for the presence of taxonomy and functional potential and confirming the prediction up to the strain level within the same cohort. Principal component analysis revealed distinct microbiome changes at different altitudes, with varied and higher Bacteroides and Prevotella ratio. There was a predominance of genus Prevotella at altitudes 4420 m and 5805 m than at 210 m and 3500 m. The appearance of species Prevotella copri strain 61,740 increased significantly at extreme altitude, whereas co-occurrence of other bacterial strains had a different pattern than Prevotella. The extensive strain-level analysis indicated alteration in the metabolic pathways. This study under the stressful and hypoxic environment of extreme altitudes, associated microbial variation with altered metabolic pathways, reveals the influence of extreme environment on human gut microbiota with the predominance of Prevotella.
      PubDate: 2021-09-20
      DOI: 10.1007/s42485-021-00077-8
  • Therapeutically effective covalent spike protein inhibitors in treatment
           of SARS-CoV-2

    • Abstract: COVID-19 [coronavirus disease 2019] has resulted in over 204,644,849 confirmed cases and over 4,323,139 deaths throughout the world as of 12 August 2021, a total of 4,428,168,759 vaccine doses have been administered. The lack of potentially effective drugs against the virus is making the situation worse and dangerous. Numerous forces are working on finding an effective treatment against the virus but it is believed that a de novo drug would take several months even if huge financial support is provided. The only solution left with is drug repurposing that would not only provide effective therapy with the already used clinical drugs, but also save time and cost of the de novo drug discovery. The initiation of the COVID-19 infection starts with the attachment of spike glycoprotein of SARS-CoV-2 to the host receptor. Hence, the inhibition of the binding of the virus to the host membrane and the entry of the viral particle into the host cell are one of the main therapeutic targets. This paper not only summarizes the structure and the mechanism of spike protein, but the main focus is on the potential covalent spike protein inhibitors.
      PubDate: 2021-09-15
      DOI: 10.1007/s42485-021-00074-x
  • Role of ORF4 in Hepatitis E virus regulation: analysis of intrinsically
           disordered regions

    • Abstract: Hepatitis E virus (HEV) is one of the causative agents of liver infections. The essential open reading frame 4 (ORF4) encoded protein role in HEV regulation remains undetermined. Intrinsically disordered protein regions (IDPRs)/intrinsically disordered protein (IDPs) in viral proteomes are linked with virus’s pathogenicity and infectivity. Therefore, in the present study, we have examined the unstructured/disordered regions of ORF4 proteins by analyzing the prevalence of intrinsic disorder. The intrinsic disorder propensity analysis of ORF4 proteins revealed JN167538 (Rat) as a structured protein, LC057248 (HEV) and LC177791 (Ferret) as moderately disordered proteins and KU168733 (Human) as a highly disordered protein, categorizing them as ORDP, IDPRs and IDR, respectively. All the ORF4 proteins consisted of molecular recognition features (MoRFs), i.e., intrinsic disorder-based protein–protein interaction (PPI) sites used by proteins to interact with specific partners, in addition to several nucleotide-binding sites. As IDPR and IDP, in conjunction with molecular recognition (PPI, RNA binding and DNA binding), our results signified the ORF4 protein’s interactions with the host membranes and further viral infection. In particular, as IDP, the ORF4 protein (Human) could possibly contribute to viral replication through PPIs. The presence of various disordered-based phosphorylation sites further signified the role of ORF4 proteins in various biological processes, such as post-translational modifications (/PTMs). Furthermore, structure-based analyses of ORF4 proteins revealed it as a multifunctional-associated protein, due to its involvement in various binding and catalytic activities. Collectively, data from this comprehensive investigation suggested ORF4 protein’s role in regulation and pathogenesis of HEV.
      PubDate: 2021-09-15
      DOI: 10.1007/s42485-021-00075-w
  • Proteomics: an emerging tool for the discovery of bone mineral density
           molecular pathways

    • Abstract: Osteoporosis is a polygenic disease associated with low bone mineral density and deterioration of bone miniscule architecture and increased chance of bone fractures. However, several signaling pathways regulate bone mineral density including parathyroid hormone (PTH), Core-binding factor α-1 (CBFA1), Wnt/β-catenin, the receptor activator of the nuclear factor kappa-B (NF-κB) ligand (RANKL), myostatin, estrogen, and osteogenic exercise signaling pathways. These signaling pathways occur at protein level that depends not only on messenger RNA transcriptional regulation but also on a number of translational and posttranslational controls. Moreover, proteomic alterations in bone tissue due to a disease may occur in several ways that are unpredictable from either genome or transcriptome analysis. Decades of genome and transcriptome analyses have identified few causative genes; nonetheless, the majority of osteoporosis susceptibility genes remain unknown. It appears that a deeper view of bone proteome alterations will influence bone health and disease. This article highlights the efficacy of proteomics as an emerging tool for the discovery of bone mineral density molecular pathways.
      PubDate: 2021-09-11
      DOI: 10.1007/s42485-021-00071-0
  • Prioritization of potential drug targets and antigenic vaccine candidates
           against Klebsiella aerogenes using the computational subtractive
           proteome-driven approach

    • Abstract: Klebsiella aerogenes is a multidrug-resistant Gram-negative bacterium that causes nosocomial infections. The organism showed resistance to most of the conventional antibiotics available. Because of the high resistance of the species, the treatment of K. aerogenes is difficult. These species are resistant to third-generation cephalosporins due to the production of chromosomal beta-lactams with cephalosporin activity. The lack of better treatment and the development of therapeutic resistance in hospitals hinders better/new broad-spectrum-based treatment against this pathogen. This study identifies potential drug targets/vaccine candidates through a computational subtractive proteome-driven approach. This method is used to predict proteins that are not homologous to humans and human symbiotic intestinal flora. The resultant proteome of K. aerogenes was further searched for proteins, which are essential, virulent, and determinants of antibiotic/drug resistance. Subsequently, their druggability properties were also studied. The data set was reduced based on its presence in the pathogen-specific metabolic pathways. The subtractive proteome analysis predicted 13 proteins as potential drug targets for K. aerogenes. Furthermore, these target proteins were annotated based on their spectrum of activity, cellular localization, and antigenicity properties, which ensured that they are potent candidates for broad-spectrum antibiotic and vaccine design. The results open up new opportunities for designing and manufacturing powerful antigenic vaccines against K. aerogenes and the detection and release of new and active drugs against K. aerogenes without altering the gut microbiome.
      PubDate: 2021-09-01
      DOI: 10.1007/s42485-021-00068-9
  • Digging deeper into the immunopeptidome: characterization of
           post-translationally modified peptides presented by MHC I

    • Abstract: Peptides presented by MHC molecules on the cell surface, or the immunopeptidome, play an important role in the adaptive arm of the immune response. Antigen processing for MHC class I molecules is a ubiquitous pathway present in all nucleated cells which generates and presents peptides of both self and non-self-origin. Peptides with post-translational modifications represent one category of peptides presented by MHC class I molecules. However, owing to the complexity of self-peptides presented by cells, the diversity of peptides with post-translational modifications is not well-studied. In this study, we carried out MHC Class I immunopeptidomics analysis of Loucy T-cell leukemia and A375 malignant melanoma cell line to characterize the diversity of post-translational modifications of MHC class I-bound peptides. Using high resolution mass spectrometry, we identified 25,761 MHC-bound peptides across both cell lines using Bolt and Sequest search engines. The enrichment method was highly specific as ~ 90% of the peptides were of typical length (8–12 amino acids long) and the motifs were expected based on previously reported motifs for MHC I alleles. Among the MHC-bound peptides, we identified phosphorylation as a major post-translational modification followed by deamidation. We observed site-specific localization of these post-translational modifications, at position P4 for phosphorylated peptides and position P3 for deamidated peptides. We identified a smaller number of peptides with acetylated and methylated lysine, possibly due to very low stoichiometric levels of these PTMs compared to phosphorylation and deamidation. Using PEAKS de novo sequencing algorithm, we identified spliced peptides that accounted for ~ 5–7% of MHC-bound peptides that were otherwise similar in their features as normal MHC-bound peptides. We validated the identity of several post-translationally modified peptides and spliced peptides through mass spectrometric analysis of synthetic peptides. Our study confirms post-translationally modified peptides to be present at low stoichiometric levels along with unusual spliced peptides through unbiased identification using high resolution mass spectrometry.
      PubDate: 2021-09-01
      DOI: 10.1007/s42485-021-00066-x
  • Comprehensive characterization of Allium cepa leaf lectin (ACAL1) for its
           potential use against sap-sucking plant pests: in silico study

    • Abstract: Monocot mannose-binding lectins (MMBLs) play crucial role in plant protection against sap-sucking insects. In current investigation, onion leaf lectin gene ACAL1 (Allium cepa L. leaf agglutinin) was cloned, sequenced and characterized on bioinformatics grounds to predict its physio-chemical properties as well as its evolutionary relation with previously cloned monocot mannose-binding lectins. Sequence analysis revealed 336 bp open reading frame (ORF) including C-terminal stop codon, encoding a putative polypeptide of 111 amino acids in ACAL1. Multiple sequence alignments of amino acid with those of 21 other MMBLs revealed a distinct degree of similarity. Three highly conserved domains indicated that cloned genes belong to a member of the MMBL super family. The amino acid sequence alignment of ACAL1 with previously reported sequence (AY376826.1), showed certain variations, but these variations are predicted to be neutral to its function. Phylogenetic analysis revealed that after AAP divergent event, ACAL1 showed distinct degree of evolution that played a fundamental role in its function. Protein analysis revealed that ACAL1 belonged to the family B_Lectin and showed specificity towards D-mannose. The predicted molecular weight of ACAL1 proteins was 12.5 kD. Subcellular localization of the protein revealed that it is secretary in nature, and its 3D modeled oligomeric structure revealed that it has typical β prism type-2 structure, a characteristic feature of most of the MMBLs. The molecular cloning and characterization of onion leaf lectin gene enabled us to understand its physio-chemical properties, evolutionary nature and its potential to be used in plant genetic transformation for the development of plant varieties with desired insect resistance.
      PubDate: 2021-09-01
      DOI: 10.1007/s42485-021-00073-y
  • Identification of effective and specific serotonin1B receptor ligands by
           structure-based virtual screening and molecular dynamics

    • Abstract: The serotonergic systems are the most important therapeutic targets for neurological disorders. Many serotonergic drugs have been used to treat neurological disorders, which are well known for their adverse side effects because of the off-target interactions. Development of selective ligands for a specific target is the suitable approach to minimize the off-target interactions and side effects. To identify selective ligands for serotonin 1B receptor (5-HT1BR), the structural analogs of inverse agonist methiothepin (MT) and natural products were screened against 5-HT1BR and other 5-HTR subtypes (5-HT2AR, 5-HT2BR, and 5-HT2CR). In the present study, five compounds were selected out of 9963 screened compounds having higher binding affinity with 5-HT1BR over other 5-HTRs. Amongst them, ZINC31166967 and ZINC31162553 exhibited relatively higher binding affinity towards 5-HT1BR with the binding energy of − 10.1 and − 9.1 kcal/mol, respectively. The pharmacokinetic assessments considered them safe and non-toxic. Molecular dynamics (MD) simulation revealed the stability of these compounds within the active site of the receptor. The overall analysis suggested that ZINC31166967 and ZINC31162553 may be considered as the selective ligands for 5-HT1BR. However, detailed experimental investigations will be required to substantiate the findings.
      PubDate: 2021-09-01
      DOI: 10.1007/s42485-021-00069-8
  • Screening of FDA-approved compound library identifies potential
           small-molecule inhibitors of SARS-CoV-2 non-structural proteins NSP1,
           NSP4, NSP6 and NSP13: molecular modeling and molecular dynamics studies

    • Abstract: COVID-19, the current global pandemic has caused immense damage to human lives and the global economy. It is instigated by the SARS-CoV-2 virus and there is an immediate need for the identification of effective drugs against this deadly virus. SARS-CoV-2 genome codes for four structural proteins, sixteen non-structural proteins (NSPs) and several accessory proteins for its survival inside the host cells. In the present study, through in silico approaches, we aim to identify compounds that are effective against the four NSPs namely, NSP1, NSP4, NSP6 and NSP13 of SARS-CoV-2. The selection criteria of these four NSP proteins are they are least explored and potential targets. First, we have modeled the 3D structures of these proteins using homology modeling methods. Further, through molecular docking studies, we have screened the FDA-approved compounds against these modeled proteins and reported their docking scores. To gain dynamic insights, molecular dynamics studies have also been carried out for the best scored ligand against the NSPs. This study can further pave way for exposing more number of compounds against these proteins and enhance COVID-19 treatment.
      PubDate: 2021-09-01
      DOI: 10.1007/s42485-021-00067-w
  • In silico molecular docking of SARS-CoV-2 surface proteins with microbial
           non-ribosomal peptides: identification of potential drugs

    • Abstract: Outbreak of COVID-19 by SARS-CoV-2 infection caused severe acute respiratory syndrome that has been declared a public health emergency of international concern. To control infections, there is urgent need to develop an effective therapeutic strategy. COVID-19 viral spike glycoprotein and proteases play major role in viral entry and mediating virus replication and spread and thus can serve as potential antiviral drug target. Being highly specific, efficacious and safe, peptides hold their place in therapeutics. In present study, molecular docking of 21 pharmacologically active non ribosomal peptides (NRPs) from marine microbes with SARS-CoV-2 spike glycoprotein and papain such as protease was done. Dactinomycin, Tyrocidine A and Gramicidin S showed highest binding interaction with target proteins. The binding affinity of Dactinomycin and Gramicidin S docked with SARS-CoV-2 spike glycoprotein was − 12.4 kcal/mol and − 11.4 kcal/mol, respectively. This suggested their potential to destabilize SARS spike protein binding with human host ACE2 receptor and thus hindering viral entry to the cells. Binding affinity of Tyrocidine A and Gramicidin S with SARS-CoV-2 papain-like protease was − 13.1 kcal/mol and − 11.4 kcal/mol, respectively which might be inhibited COVID-19 by acting on the protease. Gramicidin S showed same binding affinity for both target proteins and thus expected to be most potent. Based on the binding energy score, it was suggested that these pharmacologically active NRPs are potential molecules to be tested against SARS-CoV-2 and used to develop effective antiviral drugs.
      PubDate: 2021-09-01
      DOI: 10.1007/s42485-021-00072-z
  • Harnessing the potential of omics for prevention and management of the
           complex crop plant’s diseases

    • Abstract: Crop plants are hosting a variety of microorganisms in their surroundings, some are beneficial, but others are causing diseases that account for huge financial losses to the farmers. To prevent these, we need to understand molecular machinay of plant–pathogen interactions and genes/proteins involved in concerned biochemical pathways. Omics has provided us various approaches to unveil the different key components responsible for disease resistance/susceptibility. In this article, we are highlighting the existing omics techniques, i.e., genomics, transcriptomics, proteomics, metabolomics and phenomics which yield valuable data, along with bioinformatics, networks and system biology which aid in analyzing this enormous data for novel discovery. We are also highlighting the application of omics in the prevention and management of crop plant diseases, which include designing and development of markers, immunodiagnostic kits, defence inducers, agrochemicals and disease resistant transgenic plants. Thus, concluding that omics is a solution for safe, fast and efficient way to prevent and manage complex and recalcitrant diseases in crop plants.
      PubDate: 2021-09-01
      DOI: 10.1007/s42485-021-00070-1
  • Structure-based inhibitor screening of natural products against NSP15 of
           SARS-CoV-2 revealed thymopentin and oleuropein as potent inhibitors

    • Abstract: Coronaviruses are enveloped, non-segmented positive-sense RNA viruses with the largest genome among RNA viruses. Their genome contains a large replicase ORF which encodes nonstructural proteins (NSPs), structural, and accessory genes. NSP15 is a nidoviral RNA uridylate-specific endoribonuclease (NendoU) with C-terminal catalytic domain. The endoribonuclease activity of NSP15 interferes with the innate immune response of the host. Here, we screened Selleckchem Natural product database of the compounds against NSP15, and we found that thymopentin and oleuropein displayed highest binding energies. The binding of these molecules was further validated by molecular dynamic simulations that revealed them as very stable complexes. These drugs might serve as effective counter molecules in the reduction of virulence of this virus; may be more effective if treated in combination with replicase inhibitors. Future validation of both these inhibitors is worth the consideration for patients being treated for COVID-19.
      PubDate: 2021-06-01
      DOI: 10.1007/s42485-021-00059-w
  • Thermal and chemical inactivation of phytase from rice bean (Vigna
           umbellata Thunb.)

    • Abstract: This study aimed to evaluate the results of the thermal (50 °C) and the chemical inactivation kinetics (urea 0.1 M) of the rice bean phytase along with spectral analysis at elevated temperature (80 °C, 1 h) and in the presence of urea (8 M, 1 h). Thermal inactivation of the phytase from rice bean (Vigna umbellata), exhibited a biphasic kinetic pattern with a distinct fast and a slow phase in the loss of the activity. Bovine serum albumin showed a little protection. The ultraviolet spectrum of the heat-inactivated phytase exhibited a higher absorbance at all wavelengths in comparison to the native enzyme. The emission maxima of the native and heat-inactivated phytase were at 330 and 340 nm, respectively in the fluorescence spectrum. The intensity in the heat-treated enzyme was lower in comparison to the native enzyme. A biphasic curve was also obtained in the chemical inactivation of the phytase. The fluorescence spectrum exhibited a lower emission intensity in comparison to the native enzyme. The emission maximum of the inactivated phytase was at 335 nm. The result indicates that in the presence of urea, more tertiary structure is retained in comparison to the heat-inactivated phytase.
      PubDate: 2021-06-01
      DOI: 10.1007/s42485-021-00061-2
  • Evidence of new calcium-dependent cysteine protease of Melia dubia latex
           with fibrinolytic potential

    • Abstract: Melia dubia of the Meliaceae family is one of the latex-bearing plants which has been topically used for various skin diseases and to heal wounds. The present work reports the presence of protease in the latex of Melia dubia and evaluation of the fibrinolytic activity of protease. Latex protease was partially purified by ammonium sulphate precipitation and subjected to dialysis. The partially purified extract exhibited proteolytic activity which was confirmed by caseinolytic assay and zymography. The sample was named Melia dubia latex protease (MDLP). Furthermore, MDLP activity was determined under varying conditions of pH, incubation temperature, different substrates, incubation time, and presence of metal ions. The optimum pH and temperature for MDLP activity were recorded as 7.5 and 37 °C, respectively. MDLP was more specific to casein as a substrate over gelatin and bovine serum albumin (BSA). It was also identified that the protease activity is calcium dependent and inhibited by zinc ions. MDLP has been distinguished to be a cysteine protease as indicated by its inhibition with IAA. It is noteworthy that the cysteine protease of Melia dubia showed plasmin-like activity. To evaluate this ability, MDLP was investigated for its effect on plasma clot and blood clot, in a concentration-dependent manner. MDLP induced degradation of clot suggesting plasmin-like activity as it hydrolyses fibrin clot efficiently compared to trypsin. MDLP hydrolyzed blood clots, α-chains and β-chains of partially cross-linked fibrin clot which implies that it has fibrinolytic activity with potentials as thrombolytic agents. This research work is the primary report on identifying a protease from latex of Melia dubia which possesses ethnopharmacological importance in clot hydrolysis and wound healing. Furthermore, purification and characterization are in progress.
      PubDate: 2021-06-01
      DOI: 10.1007/s42485-021-00064-z
School of Mathematical and Computer Sciences
Heriot-Watt University
Edinburgh, EH14 4AS, UK
Tel: +00 44 (0)131 4513762

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