Molecular Docking Strategies Research Articles

Role of Thermolysin in Catalytic-Controlled Self-Assembly of Fmoc-Dipeptides

In recent years, short peptide self-assembled materials, prepared under the control of the thermolysin catalyst, have been investigated extensively and shown to acquire various morphologies and fun...

Mechanisms of Spica Prunellae against thyroid-associated Ophthalmopathy based on network pharmacology and molecular docking

BackgroundThyroid-associated ophthalmopathy (TAO) is an autoimmune inflammatory disorder, which lacks effective treatment currently. Spica Prunellae (SP) is popularly used for its anti-inflammatory and immune-regulating properties, indicating SP may have potential therapeutic value in TAO. Therefore, the purpose of this study is to identify the efficiency and potential mechanism of SP in treating TAO.MethodsA network pharmacology integrated molecular docking strategy was used to predict the underlying molecular mechanism of treating TAO. Firstly, the active compounds of SP were obtained from TCMSP database and literature research. Then we collected the putative targets of SP and TAO based on multi-sources databases to generate networks. Network topology analysis, GO and KEGG pathway enrichment analysis were performed to screen the key targets and mechanism. Furthermore, molecular docking simulation provided an assessment tool for verifying drug and target binding.ResultsOur results showed that 8 targets (PTGS2, MAPK3, AKT1, TNF, MAPK1, CASP3, IL6, MMP9) were recognized as key therapeutic targets with excellent binding affinity after network analysis and molecular docking-based virtual screening. The results of enrichment analysis suggested that the underlying mechanism was mainly focused on the biological processes and pathways associated with immune inflammation, proliferation, and apoptosis. Notably, the key pathway was considered as the PI3K-AKT signaling pathway.ConclusionIn summary, the present study elucidates that SP may suppress inflammation and proliferation and promote apoptosis through the PI3K-AKT pathway, which makes SP a potential treatment against TAO. And this study offers new reference points for future experimental research and provides a scientific basis for more widespread clinical application.

Pharmacophore-enabled virtual screening, molecular docking and molecular dynamics studies for identification of potent and selective histone deacetylase 8 inhibitors

Histone deacetylases (HDACs) play important roles in various biological processes, but are also notorious for their over-expression in numerous cancers and neurological disorders. Therefore, the development of isoform selective HDAC inhibitors is crucial in order to prevent any side effects of pan inhibition. This work focuses on identifying novel inhibitors for the selective inhibition of HDAC8, an isoform implicated in fatal diseases like T-cell lymphoma, colon cancer and childhood neuroblastoma. Virtual screening of the ‘In-trials’ subset of ZINC database has been carried out with the help of two pharmacophore models signifying potent and selective HDAC8 inhibition. A detailed molecular docking strategy, followed by molecular dynamics simulations and post-scoring with MM-GBSA calculations, has led to the identification of six promising molecules that have excellent binding with the HDAC8 active site. In order to establish the selectivity profile of these molecules, their binding to off-target HDAC isoforms has also been evaluated. Substitution analyses of the proposed inhibitors suggest that aromatic substituents that access the adjacent hydrophobic pocket of the HDAC8 active site have the potential to further enhance the HDAC8 selectivity.

Revealing the synergistic mechanism of Shenfu Decoction for anti-heart failure through network pharmacology strategy.

The present study was designed to investigate the targets and synergistic mechanism of Shenfu Decoction (SFD) in the treatment of heart failure. A heart failure animal models was established to evaluate the pharmacological effects of SFD for anti-heart failure, then constructed ingredient-target interaction network by developing ingredient and target databases, the Discovery sdudio software was used for molecular docking. In addition, we validated the predicted protein targets of active ingredients in SFD by using surface plasmon resonance (SPR) technology. Our results demonstrated that SFD could enhance ejection fraction, alleviate myocardial histopathological characteristics, and reduce the level of angiotensin converting enzyme (ACE), aldosterone (ALD), atrial natriuretic polypeptide (ANP) and Renin (REN) in heart failure rat model. In addition, the ingredient database including 349 constituents and target database including 236 proteins were established, and 75 proteins were screened and identified by molecular docking strategy. 22 core target proteins were identified through network pharmacology, and the component-core target network was constructed. Finally, the affinity between the compounds and targets were verified by the SPR analysis method. The present study suggested that SFD may act on ACE 2, REN, ACE, ICAM-1, EGF, HTR2B, PARP1, NPPB and other proteins through AC, BAC, ACN, Re, Rg1, Rb1 to exert synergistic effects against heart failure.

In Silico Modelling in the Development of Novel Radiolabelled Peptide Probes.

This review describes the usefulness of in silico design approaches in the design of new radiopharmaceuticals, especially peptide-based radiotracers (including peptidomimetics). Although not part of the standard arsenal utilized during radiopharmaceutical design, the use of in silico strategies is steadily increasing in the field of radiochemistry as it contributes to a more rational and scientific approach. The development of new peptide-based radiopharmaceuticals as well as a short introduction to suitable computational approaches are provided in this review. The first section comprises a concise overview of the three most useful computeraided drug design strategies used, namely i) a Ligand-based Approach (LBDD) using pharmacophore modelling, ii) a Structure-based Design Approach (SBDD) using molecular docking strategies and iii) Absorption-Distribution-Metabolism-Excretion-Toxicity (ADMET) predictions. The second section summarizes the challenges connected to these computer-aided techniques and discusses successful applications of in silico radiopharmaceutical design in peptide-based radiopharmaceutical development, thereby improving the clinical procedure in Nuclear Medicine. Finally, the advances and future potential of in silico modelling as a design strategy is highlighted.

Molecular docking and network connections of active compounds from the classical herbal formula Ding Chuan Tang.

BackgroundDing Chuan Tang (DCT), a traditional Chinese herbal formula, has been consistently prescribed for the therapeutic management of wheezing and asthma-related indications since the Song Dynasty (960–1279 AD). This study aimed to identify molecular network pharmacology connections to understand the biological asthma-linked mechanisms of action of DCT and potentially identify novel avenues for asthma drug development.MethodsEmploying molecular docking (AutoDock Vina) and computational analysis (Cytoscape 3.6.0) strategies for DCT compounds permitted examination of docking connections for proteins that were targets of DCT compounds and asthma genes. These identified protein targets were further analyzed to establish and interpret network connections associated with asthma disease pathways.ResultsA total of 396 DCT compounds and 234 asthma genes were identified through database search. Computational molecular docking of DCT compounds identified five proteins (ESR1, KDR, LTA4H, PDE4D and PPARG) mutually targeted by asthma genes and DCT compounds and 155 docking connections associated with cellular pathways involved in the biological mechanisms of asthma.ConclusionsDCT compounds directly target biological pathways connected with the pathogenesis of asthma including inflammatory and metabolic signaling pathways.

Anti-proliferation and anti-migration effects of an aqueous extract of Cinnamomi ramulus on MH7A rheumatoid arthritis-derived fibroblast-like synoviocytes through induction of apoptosis, cell arrest and suppression of matrix metalloproteinase

Context Cinnamomi ramulus, the dry twig of Cinnamomum cassia Presl. (Lauraceae), has been reported to exert several activities such as antitumor, anti-inflammatory, and analgesic effects. Objective This study investigates the effects of an aqueous extract of Cinnamomi ramulus (ACR) on rheumatoid arthritis (RA). Materials and methods TNF-α-induced RA-derived fibroblast-like synoviocyte MH7A cells were incubated with ACR (0.1–2 mg/mL) for 24 h. The proliferation was tested using CCK-8 and colony formation assays. The migration and invasion abilities were measured using transwell tests and wound healing assays. Apoptosis and cell cycle were examined by flow cytometry. The potential mechanisms were determined by western blotting and quantitative real-time PCR. UPLC-QE-MS/MS was used for chromatographic analysis of ACR and its compounds were identified. Molecular docking strategy was used to screen the potential anti-RA active compounds of ACR. Results We found that ACR induced apoptosis in MH7A cells at concentrations of 0.4, 0.8, and 1.2 mg/mL. The proliferation of MH7A cells was reduced and the cell cycle was blocked in the G2/M phase at concentrations of 0.2, 0.4, 0.6 mg/mL. Migration and invasion of MH7A cells were reduced through inhibiting the expression of MMP-1, MMP-2, and MMP-3. The molecular docking strategy results showed that 9 compounds in ACR have good affinity with protein crystal, and benzyl cinnamate (10–100 µg/mL) could inhibit cell migration and induce apoptosis. Conclusions The anti-RA effect of ACR may be attributed to its anti-proliferative and anti-migration effects on synovial fibroblasts. These data suggest that Cinnamomi ramulus may have therapeutic value for the treatment of RA.

Molecular Docking in Formulation and Development.

In pharmaceutical research drug discovery and development process is timeconsuming and expensive. In many cases, it produces incompetent results due to the failure of in vitro and in vivo conventional approaches. Before any new drug is placed in the market it must undergo rigorous testing to get FDA approval. Due to the several limitations imposed by the drug discovery process, in recent times in silico approaches are widely applied in this field. The purpose of this review is to highlight the current molecular docking strategies used in drug discovery and to explore various advances in the field. In this review we have compiled database after an extensive literature search on docking studies which has found its applications relevant to the field of formulation and development. The papers retrieved were further screened to appraise the quality of work. In depth strategic analysis was carried out to confirm the credibility of the findings. The papers included in this review highlight the promising role of docking studies to overcome the challenges in formulation and development by emphasizing it's applications to predict drug excipient interactions which in turn assist to increase protein stability; to determine enzyme peptide interactions which maybe further used in drug development studies; to determine the most stable drug inclusion complex; to analyze structure at molecular level that ascertain an increase in solubility, dissolution and in turn the bioavailability of the drug; to design a dosage form that amplify the drug discovery and development process. This review summarizes recent findings of critical role played by molecular docking in the process of drug discovery and development. The application of docking approach will assist to design a dosage form in the most cost effective and time saving manner.

Role of Conserved Histidine and Serine in the HCXXXXXRS Motif of Human Dual-Specificity Phosphatase 5.

The mitogen-activated protein kinase (MAPK) pathway is functionally generic and critical in maintaining physiological homeostasis and normal tissue development. This pathway is under tight regulation, which is in part mediated by dual-specific phosphatases (DUSPs), which dephosphorylate serine, threonine, and tyrosine residues of the ERK family of proteins. DUSP5 is of high clinical interest because of mutations we identified in this protein in patients with vascular anomalies. Unlike other DUSPs, DUSP5 has unique specificity toward substrate pERK1/2. Using molecular docking and simulation strategies, we previously showed that DUSP5 has two pockets, which are utilized in a specific fashion to facilitate specificity toward catalysis of its substrate pERK1/2. Remarkably, most DUSPs share high similarity in their catalytic sites. Studying the catalytic domain of DUSP5 and identifying amino acid residues that are important for dephosphorylating pERK1/2 could be critical in developing small molecules for therapies targeting DUSP5. In this study, we utilized computational modeling to identify and predict the importance of two conserved amino acid residues, H262 and S270, in the DUSP5 catalytic site. Modeling studies predicted that catalytic activity of DUSP5 would be altered if these critical conserved residues were mutated. We next generated independent Glutathione-S-Transferase (GST)-tagged full-length DUSP5 mutant proteins carrying specific mutations H262F and S270A in the phosphatase domain. Biochemical analysis was performed on these purified proteins, and consistent with our computational prediction, we observed altered enzyme activity kinetic profiles for both mutants with a synthetic small molecule substrate (pNPP) and the physiological relevant substrate (pERK) when compared to wild type GST-DUSP5 protein. Our molecular modeling and biochemical studies combined demonstrate that enzymatic activity of phosphatases can be manipulated by mutating specific conserved amino acid residues in the catalytic site (phosphatase domain). This strategy could facilitate generation of small molecules that will serve as agonists/antagonists of DUSP5 activity.

Molecular docking, dynamics, and pharmacology studies on bexarotene as an agonist of ligand-activated transcription factors, retinoid X receptors.

Retinoid X receptors (RXRs) belong to the nuclear receptor superfamily, and upon ligand activation, these receptors control gene transcription via either homodimerization with themselves or heterodimerization with the partner-nuclear receptor. The protective effects of RXRs and RXR agonists have been reported in several neurodegenerative diseases, including in the retina. This study was aimed to prioritize compounds from natural and synthetic origin retinoids as potential RXR agonists by molecular docking and molecular dynamic simulation strategies. The docking studies indicated bexarotene as a lead compound that can activate various RXR receptor isoforms (α, β, and γ) and has a strong binding affinity to the receptor protein than retinoic acid, which is known as a natural endogenous RXR agonist. Dynamic simulation studies confirmed that the hydrogen bonding and hydrophobic interactions were highly stable in all the three isoforms of the RXR-bexarotene complex. To further validate the significance of the RXR receptor in neurons, in vitro pharmacological treatment of neuronal SH-SY5Y cells with bexarotene was performed. In vitro data from SH-SY5Y cells confirmed that bexarotene activated RXR-simulated neurite outgrowth significantly. We conclude that bexarotene could be potentially used as an exogenous activator of RXRs and emerge as a good drug target for several neurodegenerative disorders.

Pharmacophore-guided discovery of CDC25 inhibitors causing cell cycle arrest and tumor regression

CDC25 phosphatases play a key role in cell cycle transitions and are important targets for cancer therapy. Here, we set out to discover novel CDC25 inhibitors. Using a combination of computational methods, we defined a minimal common pharmacophore in established CDC25 inhibitors and performed virtual screening of a proprietary library. Based on the availability of crystal structures for CDC25A and CDC25B, we implemented a molecular docking strategy and carried out hit expansion/optimization. Enzymatic assays revealed that naphthoquinone scaffolds were the most promising CDC25 inhibitors among selected hits. At the molecular level, the compounds acted through a mixed-type mechanism of inhibition of phosphatase activity, involving reversible oxidation of cysteine residues. In 2D cell cultures, the compounds caused arrest of the cell cycle at the G1/S or at the G2/M transition. Mitotic markers analysis and time-lapse microscopy confirmed that CDK1 activity was impaired and that mitotic arrest was followed by death. Finally, the compounds induced differentiation, accompanied by decreased stemness properties, in intestinal crypt stem cell-derived Apc/K-Ras-mutant mouse organoids, and led to tumor regression and reduction of metastatic potential in zebrafish embryo xenografts used as in vivo model.

2D QSAR, Admet prediction and multiple receptor molecular docking strategy in bioactive compounds of Gracilaria corticata against Plasmodium falciparum (contractile Protein)

Abstract Background Delivering a safer drug is a challenge for medicinal chemistry. In this study, bioactive compounds of Gracilaria corticata were screened by predicting their drug-like properties such as solubility, permeability, efficacy, metabolic stability, and toxicity. The potential drug optimization against virulent enzymes was calculated by docking algorithm using AutoDock 4.2.3. Molecular docking analysis reveals that the compounds are insoluble and impermeable, with better potential inhibition against virulent enzymes. Materials and methods The bioactive compounds of Gracilaria corticata were screened for drug likeliness using the Lipinski rule of five and ADMET prediction. The structurally based docking analysis was done between organic compounds of plants against virulent proteins that are mainly responsible for causing disease. The interaction of rigid structure docked compounds was visualized using Discovery Studio. The QSAR studies of the compounds that have high binding energy against virulent enzymes were studied. Results The structurally based drug screening of bioactive compounds resulted in better drug properties with controlled lipophilicity level, without causing toxicity that harms the natural habitat of humans. The compound Mono (2-Ethylhexyl) phthalate has the highest binding energy of −8.73 kcal/mol followed by 2-ethylhexyl isohexyl ester −7.73 kcal/mol against virulent enzymes. The QSAR studies of Mono (2-Ethylhexyl) phthalate were done to show the relationship between the set of atoms with correlative factors. Hence, molecular docking and in silico ADMET studies play a major role in improving prediction of drug compounds, and these compounds are able to act as potential inhibitors against contractile proteins of Plasmodium falciparum.

Probing of Phytofungal Proteins for Fungicidal Activity by Molecular Docking

Background: Plant fungal diseases are the primary causes of foliage and crop loss eventually affecting the overall economic outcome and yield quality. Hence, various chemical compounds are employed to eradicate the fungi in agriculture. Methods: Virtual screening and molecular docking strategies provide themselves as great alternatives to find lead compounds. Lead compounds for each fungal infection was docked to target protein sequence and assessed for the strongest interaction. Findings: Various molecules were taken under the study, for being the target ligands to bring about a fungicidal reaction in the plant pathogen system. The screening of molecules was done thoroughly to produce the results. Ligands identified through this study allow us to make plant host fight against the fungal pathogen and prevent the occurrence of the disease. The interactions have been thoroughly studied with various softwares like SPDBV and PyMol and through various online databases like STRING, GenePept, PDB, UniProt, PatchDock, Protein structure prediction server -2 and others for the overall evaluation of the drug molecule designed and to study its overall effects for the overall higher efficacy and to prevent the occurrence of the fungal disease and management of the fungal pathogens in agriculture against various economically valuable plants. The lead compounds revealed several hydrophobic and polar contacts were demonstrated by comparing interactions. Applications: The molecular affinity of the fungicidal compound has been tested against the target pathogen as well as the host system components to understand the interaction and to draw out the functioning and the analysis. The compatibility between the molecule and the protein has been studied to decipher the effectiveness of the molecule and its effects in the system. The present results let us establish lead compounds that can be used for the development of antifungal drugs although structural activity relationship studies have to be undertaken.

Inhibition of C298S mutant of human aldose reductase for antidiabetic applications: Evidence from in silico elementary mode analysis of biological network model.

Human aldose reductase (hAR) is the key enzyme in sorbitol pathway of glucose utilization and is implicated in the etiology of secondary complications of diabetes, such as, cardiovascular complications, neuropathy, nephropathy, retinopathy, and cataract genesis. It reduces glucose to sorbitol in the presence of NADPH and the major cause of diabetes complications could be the change in the osmotic pressure due to the accumulation of sorbitol. An activated form of hAR (activated hAR or ahAR) poses a potential obstacle in the development of diabetes drugs as hAR-inhibitors are ineffective against ahAR. The therapeutic efficacy of such drugs is compromised when a large fraction of the enzyme (hAR) undergoes conversion to the activated ahAR form as has been observed in the diabetic tissues. In the present study, attempts have been made to employ systems biology strategies to identify the elementary nodes of human polyol metabolic pathway, responsible for normal metabolic states, followed by the identification of natural potent inhibitors of the activated form of hAR represented by the mutant C298S for possible antidiabetic applications. Quantum Mechanical Molecular Mechanical docking strategy was used to determine the probable inhibitors of ahAR. Rosmarinic acid was found as the most potent natural ahAR inhibitor and warrants for experimental validation in the near future.

Synergistic Promotion on Tyrosinase Inhibition by Antioxidants.

When exposed to ultraviolet radiation, the human skin produces profuse reactive oxygen species (ROS), which in turn activate a variety of biological responses. Mounting ROS levels activate tyrosinase by mobilizing α-melanocyte-stimulating hormone in the epidermis and finally stimulates the melanocytes to produce melanin. Meanwhile, the Keap1-Nrf2/ARE pathway, which removes ROS, is activated at increased ROS levels, and antioxidant compounds facilitates the dissociation of Nrf2. In this study, we explored the possible suppressing effects of antioxidant compounds and tyrosine inhibitors on melanin formation and the promotory effects of these compounds on ROS scavenging. The antioxidant activity of glabridin (GLA), resveratrol (RES), oxyresveratrol (OXYR), and phenylethylresorcinol (PR) were investigated via the stable free radical 2,2-diphenyl-1-picrylhydrazyl method. The inhibitory effects of the four compounds and their mixtures on tyrosinase were evaluated. l-Tyrosine or 3-(3,4-dihydroxyphenyl)-l-alanine (l-DOPA) was used as a substrate. The results showed that all mixtures did not exhibit synergistic effects with the l-tyrosine as a substrate, suggesting that l-tyrosine is not suitable as a substrate. However, the mixtures of “GLA:RES,” “GLA:OXYR,” “OXYR:RES,” and “PR:RES” demonstrated synergistic effects (CI < 0.9, p < 0.05), whereas “GLA:RES” and “PR:OXYR” indicated an additive effect (0.9 ditive1, p < 0.05). Furthermore, we used a molecular docking strategy to study the interactions of the four compounds with tyrosinase and l-DOPA. The molecular docking result is consistent with that of the experiment. Finally, we selected RES + OXYR and used PIG1 cells to verify whether OXYR synergistically promotes RES activity on tyrosinase. The two agents had a synergistic inhibitory effect on tyrosinase activity. These results provided a novel synergistic strategy for antioxidants and tyrosinase inhibitors, and this strategy is useful in skin injury treatment.

Identifying potential liver toxicants using in vitro and in silico methods in a weight-of-evidence based approach

BJcuL is a snake venom galactoside-binding lectin (SVgalL) isolated from Bothrops jararacussu and is involved in a wide variety of biological activities including triggering of pro-inflammatory response, disruption of microbial biofilm structure and induction of apoptosis. In the present work, we determined the crystallographic structure of BJcuL, the first holo structure of a SVgalL, and introduced the fluorescence-based thermal stability assay (Thermofluor) as a tool for screening and characterization of the binding mechanism of SVgalL ligands. BJcuL structure revealed the existence of a porous and flexible decameric arrangement composed of disulfide-linked dimers related by a five-fold symmetry. Each monomer contains the canonical carbohydrate recognition domain, a calcium ion required for BJcuL lectinic activity and a sodium ion required for protein stabilization. BJcuL thermostability was found to be induced by calcium ion and galactoside sugars which exhibit hyperbolic saturation profiles dependent on ligand concentration. Serendipitously, the gentamicin group of aminoglycoside antibiotics (gAGAs) was also identified as BJcuL ligands. On contrast, gAGAs exhibited a sigmoidal saturation profile compatible with a cooperative mechanism of binding. Thermofluor, hemagglutination inhibition assay and molecular docking strategies were used to identify a distinct binding site in BJcuL localized at the dimeric interface near the fully conserved intermolecular Cys86-Cys86 disulfide bond. The hybrid approach used in the present work provided novel insights into structural behavior and functional diversification of SVgaLs.

Statistical molecular identification of kinase inhibitors to disrupt c‐Jun N‐terminal protein kinase involved in paraquat‐mediated toxicological effects

Paraquat is a toxic chemical that is widely used as an herbicide (plant killer), primarily for weed and grass control. Recently, kinase inhibitors have shown great potential against paraquat‐mediated toxicological effects and, specifically, the c‐Jun N‐terminal protein kinase (JNK) was found as a new and promising target for relieving the paraquat toxicity. Here, we developed a statistical molecular identification protocol that systematically profiles a variety of existing kinase inhibitors against JNK. A consensus molecular docking strategy was developed to examine the binding behavior of inhibitor candidates, from which top‐8 hit compounds were selected and tested; several compounds were found to show high or moderate inhibitory potency against JNK with IC50 values at nanomolar level, which are comparable to the sophisticated JNK inhibitor SP600125. We also performed atomistic molecular dynamics simulations and post binding free energy analyses to dissect the structural basis, energetic property, and biological implication underlying the intermolecular interaction of JNK kinase domain with these promising compounds, highlighting the complicated interaction pattern between the kinase and potent hit compounds.

Molecular Docking toward Panchromatic Dye Sensitizers for Solar Cells Based upon Tetraazulenylporphyrin and Tetraanthracenylporphyrin.

Novel dye sensitizers are highly expected in the development of dye-sensitized solar cells (DSSCs) because dye sensitizers can significantly affect the power conversion efficiency (PCE). Here, the molecular docking strategy is applied to design panchromatic dye sensitizers for DSSCs to improve light-harvesting efficiency covering the full solar spectrum. Considering the broad absorption bands of tetraanthracenylporphyrins (TAnPs) and tetraazuleneporphyrins (TAzPs), based upon porphyrin dye sensitizer YD2-o-C8, the panchromatic dye sensitizers coded as H2(TAnP)-α, H2(TAzP)-γ, H2(TAzP)-ε, and H2(TAzP)-δ are designed by the substitution of the porphyrin-ring in YD2-o-C8 with TAnPs and TAzPs moieties at different positions. The geometries, electronic structures, and excitation properties of the designed dye sensitizers are investigated using density functional theory (DFT) and time-dependent DFT methods. The analysis of geometries, conjugation lengths, electronic structures, absorption spectra, transition configurations, exciton binding energies, and free energy variations for electron injection and dye regeneration supports that the designed molecules are effective to be applied as potential candidates of dye sensitizers for DSSCs. Among the designed dye sensitizers, H2(TAzP)-γ and H2(TAnP)-α must have the better performance in DSSCs.

Structural and binding studies of a C-type galactose-binding lectin from Bothrops jararacussu snake venom

BJcuL is a snake venom galactoside-binding lectin (SVgalL) isolated from Bothrops jararacussu and is involved in a wide variety of biological activities including triggering of pro-inflammatory response, disruption of microbial biofilm structure and induction of apoptosis. In the present work, we determined the crystallographic structure of BJcuL, the first holo structure of a SVgalL, and introduced the fluorescence-based thermal stability assay (Thermofluor) as a tool for screening and characterization of the binding mechanism of SVgalL ligands. BJcuL structure revealed the existence of a porous and flexible decameric arrangement composed of disulfide-linked dimers related by a five-fold symmetry. Each monomer contains the canonical carbohydrate recognition domain, a calcium ion required for BJcuL lectinic activity and a sodium ion required for protein stabilization. BJcuL thermostability was found to be induced by calcium ion and galactoside sugars which exhibit hyperbolic saturation profiles dependent on ligand concentration. Serendipitously, the gentamicin group of aminoglycoside antibiotics (gAGAs) was also identified as BJcuL ligands. On contrast, gAGAs exhibited a sigmoidal saturation profile compatible with a cooperative mechanism of binding. Thermofluor, hemagglutination inhibition assay and molecular docking strategies were used to identify a distinct binding site in BJcuL localized at the dimeric interface near the fully conserved intermolecular Cys86-Cys86 disulfide bond. The hybrid approach used in the present work provided novel insights into structural behavior and functional diversification of SVgaLs.

Anti-amyloidogenic behavior and interaction of Diallylsulfide with Human Serum Albumin

In this work, binding of garlic component-Diallysulfide (DAS) with major human blood transport protein, Human Serum Albumin (HSA) and its anti- amyloidogenic behavior has been studied by utilizing various spectroscopic and molecular docking strategies. The HSA exhibit significant reduction in fluorescence intensity upon interaction with DAS. DAS quenches the fluorescence of HSA in concentration dependent manner with binding affinity of 1.14ÿ103M⿿1. UV⿿visible spectroscopy results confirm the formation of DAS-HSA complex and secondary structure of HSA get stabilized upon complexation with DAS as observed by far UV CD spectroscopy and Differential Scanning Calorimetry. The topology of HSA in absence and presence of DAS was monitored through Dynamic Light Scattering (DLS) technique, inferred that protein becomes more compact in presence of DAS. Further, molecular docking study shows that DAS bind to the nearby site II in subdomain III of HSA. Moreover, effect of DAS was studied on HSA fibrillation process. ThT binding, ANS fluorescence assay, CD measurement, DLS and Transmission Electron Microscopy (TEM) results altogether confirm the anti-amyloidogenic property of DAS. This work will provide biophysical insight into the interaction of DAS with HSA and will help in designing more potential therapeutic strategies against protein aggregation by exploiting other related compounds.