Laccase belongs to the family of blue multi-copper oxidases and are capable of oxidizing a wide range of aromatic compounds. Laccases have industrial applications in paper pulping or bleaching and hydrocarbon bioremediation as a biocatalyst. We describe the design of a laccase with broader substrate spectrum in bioremediation. The application of evolutionary trace (ET) analysis of laccase at the ligand binding site for optimal design of the enzyme is described. In this attempt, class specific sites from ET analysis were mapped onto known crystal structure of laccase. The analysis revealed 162PHE as a critical residue in structure function relationship studies.
Recent studies show that some metal ions, injure microbial cells in various ways due to membrane breakdown, protein malfunction, and oxidative stress. Metal complexes are suited for creating novel antibacterial medications due to their distinct mechanisms of action and the variety of three-dimensional geometries they can acquire. In this Perspective, the present study focused on new antibacterial strategies based on metal oleoyl amide complexes. Thus, oleoyl amides ligand (fatty hydroxamic acid and fatty hydrazide hydrate) with the transition metal ions named Ag (I), Co (II), Cu (II), Ni (II) and Sn (II) complexes were successfully synthesized in this study. The metals- oleoyl amide were characterized using elemental analysis, and fourier transforms infrared (FTIR) spectroscopy. The antibacterial effect of metals- oleoyl amide complexes was investigated for Gram-negative bacteria (Escherichia coli) and Gram-positive bacteria (Staphylococcus aureus) by analysing minimum inhibitory concentration (MIC), minimal bactericidal concentration (MBC), and scanning electron microscopy (SEM). The results showed that metal-oleoyl amide complexes have high antibacterial activity at low concentrations. This study inferred that metal oleoyl amide complexes could be utilised as a promising therapeutic antibacterial agent.
Fabry disease (FD) is caused by a defective α-galactosidase A (α-GAL A) enzyme responsible for breaking down globotriaosylceramide (Gb3). To develop affordable therapeutics, more effort is needed to obtain insights into the underlying mechanism of FD and understanding human α-GAL A structure and function in related animal models. We adopted C. elegans as a model to elucidate the sequence and 3D structure of its GANA-1 enzyme and compared it to human α-GAL A. We constructed GANA-1 3D structure by homology modelling and validated the quality of the predicted GANA-1 structure, followed by computational docking of human ligands. The GANA-1 protein shared sequence similarities up to 42.1% with the human α-GAL A in silico and had dual active sites. GANA-1 homology modelling showed that 11 out of 13 amino acids in the first active site of GANA-1 protein overlapped with the human α-GAL A active site, indicating the prospect for substrate cross-reaction. Computational molecular docking using human ligands like Gb3 (first pocket), 4-nitrophenyl-α-D-galactopyranoside (second pocket), α-galactose (second pocket), and N-acetyl-D-galactosamine (second pocket) showed negative binding energy. This revealed that the ligands were able to bind within both GANA-1 active sites, mimicking the human α-GAL A and α-NAGA enzymes. We identified human compounds with adequate docking scores, predicting robust interactions with the GANA-1 active site. Our data suggested that the C. elegans GANA-1 enzyme may possess structural and functional similarities to human α-GAL A, including an intrinsic capability to metabolize Gb3 deposits.Communicated by Ramaswamy H. Sarma.
The asymmetric unit of the title complex, [Pd(C15H13FNO)2], contains one half of the mol-ecule with the Pd(II) cation lying on an inversion centre and is coordinated by the bidentate Schiff base anion. The geometry around the cationic Pd(II) centre is distorted square planar, chelated by the imine N- and phenolate O-donor atoms of the two Schiff base ligands. The N- and O-donor atoms of the two ligands are mutually trans, with Pd-N and Pd-O bond lengths of 2.028 (2) and 1.9770 (18) Å, respectively. The fluoro-phenyl ring is tilted away from the coordination plane and makes a dihedral angle of 66.2 (2)° with the phenolate ring. In the crystal, mol-ecules are linked into chains along the [101] direction by weak C-H⋯O hydrogen bonds. Weak π-π inter-actions with centroid-centroid distances of 4.079 (2) Å stack the mol-ecules along c.
In the asymmetric unit of the title complex, [Ni(C16H14N3OS)2], the nickel ion is tetra-coordinated in a distorted square-planar geometry by two independent mol-ecules of the ligand which act as mononegative bidentate N,S-donors and form two five-membered chelate rings. The ligands are in trans (E) conformations with respect to the C=N bonds. The close approach of hydrogen atoms to the Ni(2+) atom suggests anagostic inter-actions (Ni⋯H-C) are present. The crystal structure is built up by a network of two C-H⋯O inter-actions. One of the inter-actions forms inversion dimers and the other links the mol-ecules into infinite chains parallel to [100]. In addition, a weak C-H⋯π inter-action is also present.
Cathine is the stable form of cathinone, the major active compound found in khat (Catha edulis Forsk) plant. Khat was found to inhibit major phase I drug metabolizing cytochrome P450 (CYP) enzyme activities in vitro and in vivo. With the upsurge of khat consumption and the potential use of cathine to combat obesity, efforts should be channelled into understanding potential cathine-drug interactions, which have been rather limited. The present study aimed to assess CYPs activity and inhibition by cathine in a high-throughput in vitro fluorescence-based enzyme assay and molecular docking analysis to identify how cathine interacts within various CYPs' active sites. The half maximal inhibitory concentration (IC50) values of cathine determined for CYP2A6 and CYP3A4 were 80 and 90 μM, while CYP1A2, CYP2B6, CYP2C8, CYP2C9, CYP2C19, CYP2D6, CYP2E1, CYP2J2 and CYP3A5 showed no significant inhibition. Furthermore, in Ki analysis, the Lineweaver-Burk plots depicted non-competitive mixed inhibition of cathine on both CYP2A6 and CYP3A4 with Ki value of 63 and 100 μM, respectively. Cathine showed negligible time-dependent inhibition on CYPs. Further, molecular docking studies showed that cathine was bound to CYP2A6 via hydrophobic, hydrogen and π-stacking interactions and formed hydrophobic and hydrogen bonds with active site residues in CYP3A4. Both molecular docking prediction and in vitro outcome are in agreement, granting more detailed insights for predicting CYPs metabolism besides the possible cathine-drug interactions. Cathine-drug interactions may occur with concomitant consumption of khat or cathine-containing products with medications metabolized by CYP2A6 and CYP3A4.
The performance of lysozyme adsorption by the aminated nanofiber membrane immobilized with Reactive Green 19 (RG19) dyes was evaluated in batch and flow systems. The physicochemical properties of the dye-immobilized nanofiber membrane were characterized. The parameters of batch-mode adsorption of lysozyme (e.g., pH, initial dye concentration, and lysozyme concentration) were optimized using the Taguchi method. In a flow process, the factors influencing the dynamic binding performance for lysozyme adsorption in the chicken egg white (CEW) solution include immobilized dye concentration, adsorption pH value, feed flow rate, and feed CEW concentration. The impact of these operating conditions on the lysozyme purification process was investigated. Under optimal conditions, the recovery yield and purification factor of lysozyme achieved from the one-step adsorption process were 98.52% and 143 folds, respectively. The dye-affinity nanofiber membrane also did not exhibit any significant loss in its binding capacity and purification performance after five consecutive uses.
An anti-biofilm that can inhibit the matrix of biofilm formation is necessary to prevent recurrent and chronic Pseudomonas aeruginosa infection. This study aimed to design compounds with a new mechanism through competitive inhibitory activity against phosphomannomutase/phosphoglucomutase (PMM/PGM), using in vitro assessment and a computational (in silico) approach. The active site of PMM/PGM was assessed through molecular redocking using L-tartaric acid as the native ligand and other small molecules, such as glucaric acid, D-sorbitol, and ascorbic acid. The docking program set the small molecules to the active site, showing a stable complex formation. Analysis of structural similarity, bioavailability, absorption, distribution, metabolism, excretion, and toxicity properties proved the potential application of ligands as an anti-biofilm. In vitro assessment with crystal violet showed that the ligands could reach up to 95.87% inhibition at different concentrations. The nitrocellulose membrane and scanning electron microscopic visualization showed that the untreated P. aeruginosa biofilm was denser than the ligand-treated biofilm.
Information technology has become an integral aspect of the drug development process. The virtual screening process (VS) is a computational technique for screening chemical compounds in a reasonable amount of time and cost. The similarity search is one of the primary tasks in VS that estimates a molecule's similarity. It is predicated on the idea that molecules with similar structures may also have similar activities. Many techniques for comparing the biological similarity between a target compound and each compound in the database have been established. Although the approaches have a strong performance, particularly when dealing with molecules with homogenous active structural, they are not enough good when dealing with structurally heterogeneous compounds. The previous works examined many deep learning methods in the enhanced Siamese similarity model and demonstrated that the Enhanced Siamese Multi-Layer Perceptron similarity model (SMLP) and the Siamese Convolutional Neural Network-one dimension similarity model (SCNN1D) have good outcomes when dealing with structurally heterogeneous molecules. To further improve the retrieval effectiveness of the similarity model, we incorporate the best two models in one hybrid model. The reason is that each method gives good results in some classes, so combining them in one hybrid model may improve the retrieval recall. Many designs of the hybrid models will be tested in this study. Several experiments on real-world data sets were conducted, and the findings demonstrated that the new approaches outperformed the previous method.
Targeting vascular endothelial growth factor receptor (VEFGR) and its co-receptor neuropilin-1 (NRP-1) is an interesting vascular strategy. tLyp-1 is a tumor-homing and penetrating peptide of 7 amino acids (CGNKRTR). It is a truncated form of Lyp-1 (CGNKRTRGC), which is known to target NRP-1 receptor, with high affinity and specificity. It is mediated by endocytosis via C-end rule (CendR) internalization pathway. The aim of this study is to evaluate the importance of each amino acid in the tLyp-1 sequence through alanine-scanning (Ala-scan) technique, during which each of the amino acid in the sequence was systematically replaced by alanine to produce 7 different analogues. In silico approach through molecular docking and molecular dynamics are employed to understand the interaction between the peptide and its analogues with the NRP-1 receptor, followed by in vitro ligand binding assay study. The C-terminal Arg is crucial in the interaction of tLyp-1 with NRP-1 receptor. Substituting this residue dramatically reduces the affinity of this peptide which is clearly seen in this study. Lys-4 is also important in the interaction, which is confirmed via the in vitro study and the MM-PBSA analysis. The finding in this study supports the CendR, in which the presence of R/K-XX-R/K motif is essential in the binding of a ligand with NRP-1 receptor. This presented work will serve as a guide in the future work pertaining the development of active targeting agent towards NRP-1 receptor.
Aptamers are single-stranded oligonucleotide molecules that bind with high affinity and specificity to a wide range of target molecules. The method of systematic evolution of ligands by exponential enrichment (SELEX) plays an essential role in the isolation of aptamers from a randomized oligonucleotide library. To date, significant modifications and improvements of the SELEX process have been achieved, engendering various forms of SELEX from conventional SELEX to microfluidics-based full-chip SELEX. While full-chip SELEX is generally considered advantageous over conventional SELEX, there has not yet been a conclusive comparison between the methods. Herein, we present a comparative study of three SELEX strategies for aptamer isolation, including those using conventional agarose bead-based partitioning, microfluidic affinity selection, and fully integrated microfluidic affinity selection and PCR amplification. Using immunoglobulin E (IgE) as a model target molecule, we compare these strategies in terms of the time and cost for each step of the SELEX process including affinity selection, amplification, and oligonucleotide conditioning. Target-binding oligonucleotides in the enriched pools are sequenced and compared to assess the relative efficacy of the SELEX strategies. We show that the microfluidic strategies are more time- and cost-efficient than conventional SELEX.
CNS disorders are indications with a very high unmet medical needs, relatively smaller number of available drugs, and a subpar satisfaction level among patients and caregiver. Discovery of CNS drugs is extremely expensive affair with its own unique challenges leading to extremely high attrition rates and low efficiency. With explosion of data in information age, there is hardly any aspect of life that has not been touched by data driven technologies such as artificial intelligence (AI) and machine learning (ML). Drug discovery is no exception, emergence of big data via genomic, proteomic, biological, and chemical technologies has driven pharmaceutical giants to collaborate with AI oriented companies to revolutionise drug discovery, with the goal of increasing the efficiency of the process. In recent years many examples of innovative applications of AI and ML techniques in CNS drug discovery has been reported. Research on therapeutics for diseases such as schizophrenia, Alzheimer's and Parkinsonism has been provided with a new direction and thrust from these developments. AI and ML has been applied to both ligand-based and structure-based drug discovery and design of CNS therapeutics. In this review, we have summarised the general aspects of AI and ML from the perspective of drug discovery followed by a comprehensive coverage of the recent developments in the applications of AI/ML techniques in CNS drug discovery.
Nanotechnology science has been diverged its application in several fields with the advantages to operate with nanometric range of objects. Emerging field of nanotechnology has been also being approached and applied in medical biology for improved efficacy and safety. Increased success in therapeutic field has focused several approaches in the treatment of the common metabolic disorder, diabetes. The development of nanocarriers for improved delivery of different oral hypoglycemic agents compared to conventional therapies includes nanoparticles (NPs), liposomes, dendrimer, niosomes and micelles, which produces great control over the increased blood glucose level and thus becoming an eye catching and most promising technology now-a-days. Besides, embellishment of nanocarriers with several ligands makes it more targeted delivery with the protection of entrapped hypoglycaemic agents against degradation, thereby optimizing prolonged blood glucose lowering effect. Thus, nanocarriers of hypoglycemic agents provide the aim towards improved diabetes management with minimized risk of acute and chronic complications. In this review, we provide an overview on distinctive features of each nano-based drug delivery system for diabetic treatment and current NPs applications in diabetes management.
Blood as connective tissue potentially contains evidence of all processes occurring within the organism, at least in trace amounts (Petricoin et al., 2006) [1]. Because of their small size, peptides penetrate cell membranes and epithelial barriers more freely than proteins. Among the peptides found in blood, there are both fragments of proteins secreted by various tissues and performing their function in plasma and receptor ligands: hormones, cytokines and mediators of cellular response (Anderson et al., 2002) [2]. In addition, in minor amounts, there are peptide disease markers (for example, oncomarkers) and even foreign peptides related to pathogenic organisms and infection agents. To propose an approach for detailed peptidome characterization, we carried out an LC-MS/MS analysis of blood serum and plasma samples taken from 20 healthy donors on a TripleTOF 5600+ mass-spectrometer. We prepared samples based on our previously developed method of peptide desorption from the surface of abundant blood plasma proteins followed by standard chromatographic steps (Ziganshin et al., 2011) [3]. The mass-spectrometry peptidomics data presented in this article have been deposited to the ProteomeXchange Consortium (Deutsch et al., 2017) [4] via the PRIDE partner repository with the dataset identifier PXD008141 and 10.6019/PXD008141.
A mononuclear and new tetranuclear metal complexes of Zn(II) with Schiff base ligands L1 and L2 respectively, were synthesised. L1 was obtained through the condensation of salicylaldehyde with ortho-phenylenediamine while L2 was the product of reaction between of ortho-vanillin with 2,4,6-trimethyl-m-phenylenediamine. The ligands and complexes were characterised via elemental analysis, melting point, IR and NMR spectroscopy. The shifting of v(C=N), v(C-OH) and v(O-CH3) infrared peaks upon coordination with Zn(II) indicated that these three moieties play a significant role in the complexation. It was found that L1 acted as tetradentate ligand, coordinating with Zn(II) centres through phenolic oxygen and imine nitrogen. The ligand L2 acted as a hexadentate ligand, bonded to metal via phenolic oxygen, imine nitrogen and methoxy oxygen, where four Zn(II) centres formed bridges to connect two ligands.
Present work aimed to synthesize some unique bi-heterocyclic benzamides as lead compounds for the in vitro inhibition of urease enzyme, followed by in silico studies. These targeted benzamides were synthesized in good yields through a multi-step protocol and their structures were confirmed by IR, 1H NMR, 13C NMR, EI-MS and elemental analysis. The in vitro screening results showed that most of the ligands exhibited good inhibitory potentials against the urease. Chemo-informatics analysis envisaged that all these compounds obeyed the Lipinski's rule. Molecular docking results showed that 7h exhibited good binding energy value (-8.40 kcal/mol) and was bound within the active region of urease enzyme. From the present investigation, it was inferred that some of these potent urease inhibitors might serve as novel templates in drug designing.
Proteins of the DUF866 superfamily are exclusively found in eukaryotic cells. A member of the DUF866 superfamily, C1ORF123, is a human protein found in the open reading frame 123 of chromosome 1. The physiological role of C1ORF123 is yet to be determined. The only available protein structure of the DUF866 family shares just 26% sequence similarity and does not contain a zinc binding motif. Here, we present the crystal structure of the recombinant human C1ORF123 protein (rC1ORF123). The structure has a 2-fold internal symmetry dividing the monomeric protein into two mirrored halves that comprise of distinct electrostatic potential. The N-terminal half of rC1ORF123 includes a zinc-binding domain interacting with a zinc ion near to a potential ligand binding cavity. Functional studies of human C1ORF123 and its homologue in the fission yeast Schizosaccharomyces pombe (SpEss1) point to a role of DUF866 protein in mitochondrial oxidative phosphorylation.
Glioblastoma multiforme (GBM) is a high-grade brain tumor of which the survival patients remain poor.
Tousled-like kinase 1 (TLK1), a serine-threonine kinase, was identified to be overexpressed in cancers such
as GBM. TLK1 plays an important role in controlling survival pathways. To date, there is no structure
available for TLK1 as well as its inhibitors. We aimed to create a homology model of TLK1 and to identify
suitable molecular inhibitors that are likely to bind and inhibit TLK1 activity via in silico high-throughput
virtual screening (HTVS) protein-ligand docking. The 3D homology models of TLK1 were derived from
various servers. All models were evaluated using Swiss Model QMEAN server. Validation was performed
using multiple tools. Energy minimization was performed using YASARA. Subsequently, HTVS was
performed using Molegro Virtual Docker 6.0 and ligands derived from ligand.info database. Drug-like
molecules were filtered using ADME-Tox filtering program. Best homology model was obtained from the
Aurora B kinase (PDB ID:4B8M) derived from Xenopus levias structure that share sequence similarity with
human TLK1. Two compounds were identified from HTVS to be the potential inhibitors as it did not violate
the Lipinski rule of five and the CNS-based filter as a potential drug-like molecule for GBM
The food and health applications of bioactive peptides have grown remarkably in the past few decades. Current elucidations have shown that bioactive peptides have unique structural arrangement of amino acids, conferring distinct functionalities, and molecular affinity characteristics. However, whereas interest in the biological potency of bioactive peptides has grown, cost-effective techniques for monitoring the structural changes in these peptides and how these changes affect the biological properties have not grown at the same rate. Due to the high binding affinity of aptamers for other biomolecules, they have a huge potential for use in tracking the structural, conformational, and compositional changes in bioactive peptides. This review provides an overview of bioactive peptides and their essential structure-activity relationship. The review further highlights on the types and methods of synthesis of aptamers before the discussion of the prospects, merits, and challenges in the use of aptamers for bioaffinity interactions with bioactive peptides.
Organostannum(IV) complexes derived from dicarboxylic acids have been successfully synthesised from triphenylstannum(IV) hydroxide (Ph3SnOH). The complexes were obtained by refluxing Ph3SnOH and the respective dicarboxylic acids (malonic, succinic, glutaric and adipic acids) using a Dean and Stark apparatus in the appropriate solvent. The free ligands and complexes were characterised by C, Hand Sn elemental analysis and spectroscopic methods such as infrared and nuclear magnetic resonance (1H, 13C NMR). Structure determination of triphenylstannum(IV) succinate, 2, showed that each dicarboxylate anion was bonded monodentatically to two triphenylstannum(IV) moieties. The geometry surrounding each stannum atom is close to a tetrahedron. Spectroscopic data obtained for all complexes were found to be similar and thus it may be concluded that all complexes have the same structure as 2.