Polyamines and its analogue modulates amyloid fibrillation in lysozyme: A comparative investigation.

BACKGROUND: Polyamines can induce protein aggregation that can be related to the physiology of the cellular function. Polyamines have been implicated in protein aggregation which may lead to neuropathic and non neuropathic amyloidosis. SCOPE OF REVIEW: Change in the level of polyamine concentration has been associated with ageing and neurodegeneration such as Parkinson's disease, Alzheimer's disease. Lysozyme aggregation in the presence of polyamines leads to non neuropathic amyloidosis. Polyamine analogues can suppress or inhibit protein aggregation suggesting their efficacy against amyloidogenic protein aggregates. MAJOR CONCLUSIONS: In this study we report the comparative interactions of lysozyme with the polyamine analogue, 1-naphthyl acetyl spermine in comparison with the biogenic polyamines through spectroscopy, calorimetry, imaging and docking techniques. The findings revealed that the affinity of binding varied as spermidine > 1-naphthyl acetyl spermine > spermine. The biogenic polyamines accelerated the rate of fibrillation significantly, whereas the analogue inhibited the rate of fibrillation to a considerable extent. The polyamines bind near the catalytic diad residues viz. Glu35 and Asp52, and in close proximity of Trp62 residue. However, the analogue showed dual nature of interaction where its alkyl amine region bind in same way as the biogenic polyamines bind to the catalytic site, while the naphthyl group makes hydrophobic contacts with Trp62 and Trp63, thereby suggesting its direct influence on fibrillation. GENERAL SIGNIFICANCE: This study, thus, potentiates, the development of a polyamine analogue that can perform as an effective inhibitor targeted towards aggregation of amyloidogenic proteins.

Use of Molecular Dynamics Simulations in Structure-Based Drug Discovery.

BACKGROUND: Traditional drug discovery is a lengthy process which involves a huge amount of resources. Modern-day drug discovers various multidisciplinary approaches amongst which, computational ligand and structure-based drug designing methods contribute significantly. Structure-based drug designing techniques require the knowledge of structural information of drug target and drug-target complexes. Proper understanding of drug-target binding requires the flexibility of both ligand and receptor to be incorporated. Molecular docking refers to the static picture of the drug-target complex(es). Molecular dynamics, on the other hand, introduces flexibility to understand the drug binding process. OBJECTIVE: The aim of the present study is to provide a systematic review on the usage of molecular dynamics simulations to aid the process of structure-based drug design. METHOD: This review discussed findings from various research articles and review papers on the use of molecular dynamics in drug discovery. All efforts highlight the practical grounds for which molecular dynamics simulations are used in drug designing program. In summary, various aspects of the use of molecular dynamics simulations that underline the basis of studying drug-target complexes were thoroughly explained. RESULTS: This review is the result of reviewing more than a hundred papers. It summarizes various problems that use molecular dynamics simulations. CONCLUSION: The findings of this review highlight how molecular dynamics simulations have been successfully implemented to study the structure-function details of specific drug-target complexes. It also identifies the key areas such as stability of drug-target complexes, ligand binding kinetics and identification of allosteric sites which have been elucidated using molecular dynamics simulations.

Cross-talk between allosteric and orthosteric binding sites of γ-amino butyric acid type A receptors (GABAA-Rs): A computational study revealing the structural basis of selectivity.

The γ-amino butyric acid type A receptors (GABAA-Rs) are GABA-gated chloride ion channels that mediate fast inhibitory neurotransmissions. Due to their essential role in normal brain function, neuromodulatory therapies are targeted at them for restoring GABA-mediated inhibition. The receptor modulation by benzodiazepine (BZD) shows therapeutically useful actions. The mechanisms, by which BZD-site performs selective transduction while modulating GABAA-Rs, and its correlation with the occurrence of sedation is not fully known. In pursuance, we performed a computational study starting from modeling of α2-subtype GABAA-R, docking of α1/2-selective ligands followed by molecular dynamics simulations of the obtained complexes. The results show that during early stages of activation, a) allosteric binding initiate structural changes through BZD-site for GABA-elicited activation; b) selective BZD-binders positively modulate orthosteric GABA-bound site with fin-like C- and F-loop movements, which supports twisting of inner and outer ß-barrel; c) modulation by α1/2-selective ligands was only evident at site 1, mimicking mandatory doubly bound state; d) strength of allosteric communication was prominent for α2-modulators, however, the basic nature of allosteric-orthosteric site cross-talk remains same for both α1/2-modulators; and e) ratio of hydrophobic:hydrophilic ligand contact surface decides α2-selectivity, less value of ratio favors it. These insights would enable us to design better α2-selective modulator/s. Altogether our computational study reveals early stages of allosteric modulation, highlighting subtype selective activation and pathways recommending GABA binding sites during selective modulation. Communicated by Ramaswamy H. Sarma.

Localization of MIF-II on mammalian spermatozoa: A study revealing its structure, function and motility inhibitory pathway.

Motility of spermatozoa is a crucial factor for determining semen quality. Here we report motility inhibitory factor (MIF-II) from goat epididymal plasma, revealing its structure, function, localization and motility inhibitory pathway. Structural characterization with MALDI revealed novelty of this protein while circular dichroism data confirmed its alpha helical nature. Higher dilutions of MIF-II antibody increased cauda sperm motility and induced immature/immotile caput sperm motility as tested microscopically. Higher number of sperm cells and lower dilutions of antibody induced agglutination in cauda sperm showing surface localization. Indirect immuno-fluorescence showed MIF-II localization throughout the caput sperm surface which relocated more towards acrosomal region with maturation. ELISA assay revealed gradual increase and decrease in concentration of MIF-II in epididymal plasma and plasma membrane respectively from caput to cauda. Signaling cascade that leads to sperm motility inhibition elevates nitric oxide levels through cAMP dependent pathway. MIF-II treatment doesn't alter sperm surface morphology. Expression pattern of MIF-II during epididymal maturation goes hand-in-hand with gaining motility potential as well as dormancy of spermatozoa before ejaculation. Both MIF-II and its antibody inhibit fertilization in-vitro thus expected to open new gateway for future male infertility and contraceptive development research.

Identification of novel hits as highly prospective dual agonists for mu and kappa opioid receptors: an integrated in silico approach.

Opioid agonists are used clinically for the treatment of acute and chronic pain, however, their clinical use is limited due to the presence of undesired side effects. Dual agonists, simultaneously targeting mu and kappa opioid receptors, show fewer side effects than that of selective agonists. In the present work, 2D- and 3D- Quantitative Structure Activity Relationship studies were performed on a series of aminomorphinan derivatives as dual agonists, using a wide range of descriptors. The aim of the study was to identify the structural requirements for the activity of these compounds towards mu and kappa opioid receptors and using the models, with best external predictability, for predicting the activities of new hits obtained from shape based virtual screening of drug like compounds from ZINC database. Genetic algorithm-based GFA and G/PLS techniques were used to derive the 2D-QSAR models. Common feature-based pharmacophore was used for aligning the compounds for 3D-QSAR. All the models were validated both internally and externally using statistical metrics. The coverage estimation of the models was carried out with applicability domain calculation. Six enriched hits were identified as novel prospective dual agonist based on good Blood Brain Barrier permeability and their activities towards mu and kappa opioid receptors, predicted by the best QSAR models. The known potent dual agonist, cyclorphan, and two highly prospective dual agonists were docked to both the receptors and binding free energies were calculated using MMGBSA. Molecular dynamics studies were performed on the docked complexes with both the receptors to establish stability of the complexes.

Structural and thermodynamic analysis of the binding of tRNA(phe) by the putative anticancer alkaloid chelerythrine: Spectroscopy, calorimetry and molecular docking studies.

The interaction of the putative anticancer alkaloid chelerythrine with tRNA(phe) was characterized by spectroscopy, calorimetry and molecular docking studies. The charged iminium form of chelerythrine binds with tRNA(phe) in a cooperative mode with a binding affinity value of (4.06±0.01)×10(5)M(-1). The neutral alkanolamine form does not bind to tRNA(phe) but in the presence of high concentration of tRNA(phe) this form gets converted to the iminium form and then binds with tRNA(phe). The partial intercalative mode of binding of chelerythrine to the tRNA(phe) was characterized from the steady state anisotropy, iodide ion-induced fluorescence quenching and viscosity measurements. Chelerythrine binding induced conformational perturbations in tRNA(phe) as observed from the circular dichroism spectroscopy. The strong binding was also supported by the ethidium bromide displacement assay. The binding was favoured by both enthalpy and entropy contributions. Although the binding was dependent on the [Na(+)], non-electrostatic forces contributed predominantly to the Gibbs energy change. The negative value of the heat capacity change proposed the involvement of hydrophobic forces in the binding. Molecular docking study was carried out to decipher the details of the recognition of tRNA(phe) by chelerythrine. The study provided insights about the chelerythrine binding pockets on tRNA(phe) and marked the necessary interactions for binding of chelerythrine molecule. Partially intercalative mode of the alkaloid binding was supported by docking studies. In total, docking studies corroborated well with our experiential observations. The structural and thermodynamic results of chelerythrine binding to tRNA(phe) may be helpful to develop new RNA therapeutic agents.

Structure-based designing of sordarin derivative as potential fungicide with pan-fungal activity.

Fungal infections have become a significant problem for immunosuppressed patients. Sordarin, a promising fungicidal agent, inhibits fungal protein synthesis by impairing elongation factor-2 (eEF2) function. Intriguingly, despite high sequence similarity among eEF2s from different species, sordarin has been shown to inhibit translation specifically in certain fungi while unable to do so in some other fungal species (e.g. Candida parapsilosis and Candida lusitaniae). The sordarin binding site on eEF2 as well as its mechanism of action is known. In a previous study, we have detailed the interactions between sordarin and eEF2 cavities from different fungal species at the molecular level and predicted the probable cause of sordarin sensitivity. Guided by our previous analysis, we aimed for computer-aided designing of sordarin derivatives as potential fungicidal agents that still remain ineffective against human eEF2. We have performed structural knowledge-based designing of several sordarin derivatives and evaluated predicted interactions of those derivatives with the sordarin-binding cavities of different eEF2s, against which sordarin shows no inhibitory action. Our analyses identify an amino-pyrrole derivative as a good template for further designing of promising broad-spectrum antifungal agents. The drug likeness and ADMET prediction on this derivative also supports its suitability as a drug candidate.

Capturing state-dependent dynamic events of GABAA-receptors: a microscopic look into the structural and functional insights.

The γ-amino butyric acid type A receptors (GABAA-Rs) are the key players in the mammalian brain that meditate fast inhibitory neurotransmission events. The structural integrity of these ligand-gated ion channel controls chloride ion permeability, which in turn monitors important pharmacological functions. Despite ample studies on GABAA-Rs, there was a need for a study on full-length receptor structures, devoted to track structure-function correlations based on their dynamic behavior consideration. We have employed molecular dynamics simulations accompanied by other biophysical methods to shed light on sequential and unaddressed questions like How GABAA-R structure facilitates the entry of GABA molecules at its two orthosteric binding sites? After entry, what structural features and changes monitor site-wise GABA binding differences? In the same context, what are the roles and responsibilities of loops such as C and F? On physiologically relevant time scales, how open to close state transition occurs? How salt bridges such as E155-R207 and E153-R207 maintain state-dependent C-loop structures? In an attempt, our simulation study unravels the complete course of GABA binding-unbinding pathway. This provides us with the relevant understanding of state-dependent dynamic events of GABAA-Rs.

Evaluation of anti-diabetic and alpha glucosidase inhibitory action of anthraquinones from Rheum emodi.

Rheum emodi is used as a culinary plant across the world and finds an eminent role in the Ayurvedic and traditional Chinese systems of medicine. The plant is known to principally contain 1,8-dihydroxyanthraquinones (DHAQs) like rhein, aloe emodin, emodin, chrysophanol and physcion that possess diverse pharmacological and therapeutic actions. The present work deals with developing a platform technology for isolation of these DHAQs and evaluating their anti-diabetic potential. Herein, we report the anti-hyperglycemic activity and alpha glucosidase (AG) inhibitory actions of five isolated DHAQs from R. emodi. All the five isolated DHAQs showed good anti-hyperglycemic activity with aloe emodin exhibiting maximum lowering of blood glucose in an oral glucose tolerance test. However, on evaluation of the AG inhibitory potential of the DHAQs only emodin exhibited potent intestinal AG inhibition (93 ± 2.16%) with an IC50 notably lower than acarbose. Subsequent kinetic studies indicated a mixed type of inhibition for emodin. In vivo studies using oral maltose load showed almost total inhibition for emodin when compared to acarbose. Molecular docking studies revealed the presence of an allosteric topographically distinct 'quinone binding site' and showed that interaction with Ser 74 occurs exclusively with emodin, which is vital for AG inhibition. The net benefit from the glucose lowering effect and mixed type inhibition by emodin would enable the administration of a small dosage that is safe and non-toxic in the case of prolonged use in treating diabetes.

Chelerythrine-lysozyme interaction: spectroscopic studies, thermodynamics and molecular modeling exploration.

The binding of the iminium and alkanolamine forms of chelerythrine to lysozyme (Lyz) was investigated by spectroscopy and docking studies. The thermodynamics of the binding was studied by calorimetry. Spectroscopic evidence suggested that Trp-62 and Trp-63 in the ß-domain of the protein are closer to the binding site; moreover, the binding site was at a distance of 2.27 and 2.00 nm from the iminium and alkanolamine forms, respectively, according to the Forster theory of non-radiation energy transfer. The equilibrium binding constants for the iminium and alkanolamine forms at 298 K were evaluated to be 1.29 × 10(5) and 7.79 × 10(5) M(-1), respectively. The binding resulted in an alteration of the secondary structure of the protein with a distinct reduction of the helical organization. The binding of iminium was endothermic, involving electrostatic and hydrophobic interactions, while that of alkanolamine form was exothermic and dominated by hydrogen bonding interactions. Docking studies provided the atomistic details pertaining to the binding of both forms of chelerythrine and supported the higher binding in favour of the alkanolamine over the iminium. Furthermore, molecular dynamics study provided accurate insights regarding the binding of both chelerythrine forms in accordance with the experimental results obtained. Chelerythrine binding pocket involves the catalytic region and aggregation prone K-peptide region, which are sandwiched between one another. Overall, these results suggest that both the forms of the alkaloid bind to the protein but the neutral form has higher affinity than the cationic form.

Binding of the iminium and alkanolamine forms of sanguinarine to lysozyme: spectroscopic analysis, thermodynamics, and molecular modeling studies.

Sanguinarine (SGR) exists in charged iminium (SGRI) and neutral alkanolamine (SGRA) forms. The binding of these two forms to the protein lysozyme (Lyz) was investigated by fluorescence, UV-vis absorbance and circular dichroism spectroscopy, and in silico molecular docking approaches. Binding thermodynamics were studied by microcalorimetry. Both forms of sanguinarine quenched the intrinsic fluorescence of Lyz, but the quenching efficiencies varied on the basis of binding that was derived after correction for an inner-filter effect. The equilibrium binding constants at 25 ± 1.0 °C for the iminium and alkanolamine forms were 1.17 × 10(5) and 3.32 × 10(5) M(-1), respectively, with approximately one binding site for both forms of the protein. Conformational changes of the protein in the presence of SGR were confirmed by absorbance, circular dichroism, three-dimensional fluorescence, and synchronous fluorescence spectroscopy. Microcalorimetry data revealed that SGRI binding is endothermic and predominantly involves electrostatic and hydrophobic interactions, whereas SGRA binding is exothermic and dominated by hydrogen-bonding interactions. The molecular distances (r) of 3.27 and 3.04 nm between the donor (Lyz) and the SGRI and SGRA acceptors, respectively, were calculated according to Förster's theory. These data suggested that both forms were bound near the Trp-62/63 residues of Lyz. Stronger binding of SGRA than SGRI was apparent from the results of both structural and thermodynamic experiments. Molecular docking studies revealed that the putative binding site for the SGR analogues resides at the catalytic site. The docking results are in accordance with the spectroscopic and thermodynamic data, further validating the stronger binding of SGRA over SGRI to Lyz. The binding site is situated near a deep crevice on the protein surface and is close to several crucial amino acid residues, including Asp-52, Glu-35, Trp-62, and Trp-63. This study advances our knowledge of the structural nature and thermodynamic aspects of binding between the putative anticancer alkaloid sanguinarine and lysozyme.

Modeling the closed and open state conformations of the GABA(A) ion channel--plausible structural insights for channel gating.

Recent disclosure of high resolution crystal structures of Gloeobacter violaceus (GLIC) in open state and Erwinia chrysanthemii (ELIC) in closed state provides newer avenues to advance our knowledge and understanding of the physiologically and pharmacologically important ionotropic GABA(A) ion channel. The present modeling study envisions understanding the complex molecular transitions involved in ionic conductance, which were not evident in earlier disclosed homology models. In particular, emphasis was put on understanding the structural basis of gating, gating transition from the closed to the open state on an atomic scale. Homology modeling of two different physiological states of GABA(A) was carried out using their respective templates. The ability of induced fit docking in breaking the critical inter residue salt bridge (Glu155ß(2) and Arg207ß(2)) upon endogenous GABA docking reflects the perceived side chain rearrangements that occur at the orthosteric site and consolidate the quality of the model. Biophysical calculations like electrostatic mapping, pore radius calculation, ion solvation profile, and normal-mode analysis (NMA) were undertaken to address pertinent questions like the following: How the change in state of the ion channel alters the electrostatic environment across the lumen; How accessible is the Cl(-) ion in the open state and closed state; What structural changes regulate channel gating. A "Twist to Turn" global motion evinced at the quaternary level accompanied by tilting and rotation of the M2 helices along the membrane normal rationalizes the structural transition involved in gating. This perceived global motion hints toward a conserved gating mechanism among pLGIC. To paraphrase, this modeling study proves to be a reliable framework for understanding the structure function relationship of the hitherto unresolved GABA(A) ion channel. The modeled structures presented herein not only reveal the structurally distinct conformational states of the GABA(A) ion channel but also explain the biophysical difference between the respective states.