The potential role of procyanidin as a therapeutic agent against SARS-CoV-2: a text mining, molecular docking and molecular dynamics simulation approach.

A novel coronavirus (SARS-CoV-2) has caused a major outbreak in human all over the world. There are several proteins interplay during the entry and replication of this virus in human. Here, we have used text mining and named entity recognition method to identify co-occurrence of the important COVID 19 genes/proteins in the interaction network based on the frequency of the interaction. Network analysis revealed a set of genes/proteins, highly dense genes/protein clusters and sub-networks of Angiotensin-converting enzyme 2 (ACE2), Helicase, spike (S) protein (trimeric), membrane (M) protein, envelop (E) protein, and the nucleocapsid (N) protein. The isolated proteins are screened against procyanidin-a flavonoid from plants using molecular docking. Further, molecular dynamics simulation of critical proteins such as ACE2, Mpro and spike proteins are performed to elucidate the inhibition mechanism. The strong network of hydrogen bonds and hydrophobic interactions along with van der Waals interactions inhibit receptors, which are essential to the entry and replication of the SARS-CoV-2. The binding energy which largely arises from van der Waals interactions is calculated (ACE2=-50.21 ± 6.3, Mpro=-89.50 ± 6.32 and spike=-23.06 ± 4.39) through molecular mechanics Poisson-Boltzmann surface area also confirm the affinity of procyanidin towards the critical receptors. Communicated by Ramaswamy H. Sarma.

Mitochondria-targeted dual-channel colorimetric and fluorescence chemosensor for detection of Sn2+ ions in aqueous solution based on aggregation-induced emission and its bioimaging applications.

Several fluorescence and colorimetric chemosensory for Sn2+ detection in an aqueous media have been reported, but applications remain limited for discriminative Sn2+ detection in live human cells and zebrafish larvae. Herein, a mitochondria-targeted Sn2+ "turn-on" colorimetric and fluorescence chemosensor, 2CTA, with an aggregation-induced emission (AIE) response was developed. The sensing of Sn2+ was enabled by a reduction-enabled binding pathway, with the conversion of -CË­O groups to -C-OH groups at the naphthoquinone moiety. The color changed from light maroon to milky white in a buffered aqueous solution. The chemosensor 2CTA possessed the excellent characteristics of good water solubility, fast response (less than 10 s), and high sensitivity (79 nM) and selectivity for Sn2+ over other metal ions, amino acids, and peptides. The proposed binding mechanism was experimentally verified by means of FT-IR and NMR studies. The chemosensor 2CTA was successfully employed to recognize Sn2+ in live human cells and in zebrafish larvae. In addition, a colocalization study proved that the chemosensor had the ability to target mitochondria and overlapped almost completely with MitoTracker Red. Furthermore, a bioimaging study of live cells demonstrated the discriminative detection of Sn2+ in human cancer cells and the practical applications of 2CTA in biological systems.

Tunable Anticancer Activity of Furoylthiourea-Based RuII -Arene Complexes and Their Mechanism of Action.

Fourteen new RuII -arene (p-cymene/benzene) complexes (C1-C14) have been synthesized by varying the N-terminal substituent in the furoylthiourea ligand and satisfactorily characterized by using analytical and spectroscopic techniques. Electrostatic potential maps predicted that the electronic effect of the substituents was mostly localized, with some influence seen on the labile chloride ligands. The structure-activity relationships of the Ru-p-cymene and Ru-benzene complexes showed opposite trends. All the complexes were found to be highly toxic towards IMR-32 cancer cells, with C5 (Ru-p-cymene complex containing C6 H2 (CH3 )3 as N-terminal substituent) and C13 (Ru-benzene complex containing C6 H4 (CF3 ) as N-terminal substituent) showing the highest activity among each set of complexes, and hence they were chosen for further study. These complexes showed different behavior in aqueous solutions, and were also found to catalytically oxidize glutathione. They also promoted cell death by apoptosis and cell cycle arrest. Furthermore, the complexes showed good binding ability with the receptors Pim-1 kinase and vascular endothelial growth factor receptor 2, commonly overexpressed in cancer cells.

Novel 2019 coronavirus structure, mechanism of action, antiviral drug promises and rule out against its treatment.

In the past two decades, the world has faced several infectious disease outbreaks. Ebola, Influenza A (H1N1), SARS, MERS, and Zika virus have had a massive global impact in terms of economic disruption, the strain on local and global public health. Most recently, the global outbreak of novel coronavirus 2019 (SARS-CoV-2) that causes COVID-19 is a newly discovered virus from the coronavirus family in Wuhan city, China, known to be a great threat to the public health systems. As of 15 April 2020, The Johns Hopkins University estimated that the COVID-19 affected more than two million people, resulting in a death toll above 130,000 around the world. Infected people in Europe and America correspond about 40% and 30% of the total reported cases respectively. At this moment only few Asian countries have controlled the disease, but a second wave of new infections is expected. Predicting inhibitor and target to the COVID-19 is an urgent need to protect human from the disease. Therefore, a protocol to identify anti-COVID-19 candidate based on computer-aided drug design is urgently needed. Thousands of compounds including approved drugs and drugs in the clinical trial are available in the literature. In practice, experimental techniques can measure the time and space average properties but they cannot be captured the structural variation of the COVID-19 during the interaction of inhibitor. Computer simulation is particularly suitable to complement experiments to elucidate conformational changes at the molecular level which are related to inhibition process of the COVID-19. Therefore, computational simulation is essential tool to elucidate the phenomenon. The structure-based virtual screening computational approach will be used to filter the best drugs from the literature, the investigate the structural variation of COVID-19 with the interaction of the best inhibitor is a fundamental step to design new drugs and vaccines which can combat the coronavirus. This mini-review will address novel coronavirus structure, mechanism of action, and trial test of antiviral drugs in the lab and patients with COVID-19.

Application of real sample analysis and biosensing: Synthesis of new naphthyl derived chemosensor for detection of Al3+ ions.

A new chemosensor (NANH) based on naphthyl moiety was synthesized with good selectivity and sensitivity towards Al3+ ions via the inhibition by operating through dual mechanisms like photo-induced electron transfer (PET) and excited-state intramolecular proton transfer (ESIPT). The synthesized NANH was validated by various techniques such as 1H, 13C NMR and mass spectrum. While prominent fluorescent enhancement was observed from the NANH upon binding with Al3+ ions, however, other metal ions have not responded in the emission spectrum. Detection limit and association constant of NANH for Al3+ were calculated as 1.2 × 10-7 M and 4.09 × 104 M-1 by using fluorescence titration method. Binding ratio (1:1) of NANH with Al3+ ions were proved by Job's plot and DFT studies. Furthermore, aluminium in variety of water samples was determined, and NANH could be used for biosensing of Al3+ in living cells.

Insight into the photophysics of strong dual emission (blue & green) producing graphene quantum dot clusters and their application towards selective and sensitive detection of trace level Fe3+ and Cr6+ ions.

Graphene-nanostructured systems, such as graphene quantum dots (GQDs), are well known for their interesting light-emitting characteristics and are being applied to a variety of luminescence-based applications. The emission properties of GQDs are complex. Therefore, understanding the science of the photophysics of coupled quantum systems (like quantum clusters) is still challenging. In this regard, we have successfully prepared two different types of GQD clusters, and explored their photophysical properties in detail. By co-relating the structure and photophysics, it was possible to understand the emission behavior of the cluster in detail. This gave new insight into understanding the clustering effect on the emission behaviour. The results clearly indicated that although GQDs are well connected, the local discontinuity in the structure prohibits the dynamics of photoexcited charge carriers going from one domain to another. Therefore, an excitation-sensitive dual emission was possible. Emission yield values of about 18% each were recorded at the blue and green emission wavelengths at a particular excitation energy. This meant that the choice of emission color was decided by the excitation energy. Through systematic analysis, it was found that both intrinsic and extrinsic effects contributed to the blue emission, whereas only the intrinsic effect contributed to the green emission. These excitation-sensitive dual emissive GQD clusters were then used to sense Fe3+ and Cr6+ ions in the nanomolar range. While the Cr6+ ions were able to quench both blue and green emissions, the Fe3+ ions quenched blue emission only. The insensitivity of the Fe3+ ions in the quenching of the green emission was also understood through quantum chemical calculations.

Comparative study of stability and transport of molecules through cyclic peptide nanotube and aquaporin: a molecular dynamics simulation approach.

The structural stability and transport properties of the cyclic peptide nanotube (CPN) 8 × [Cys-Gly-Met-Gly]2 in different phospholipid bilayers such as POPA (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphatidic acid), POPE (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoethanolamine), POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine), POPG (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoglycerol) and POPS (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoserine) with water have been investigated using molecular dynamics (MD) simulation. The hydrogen bonds and non-bonded interaction energies were calculated to study the stability in different bilayers. One µs MD simulation in POPA lipid membrane reveals the stability of the cyclic peptide nanotube, and the simulations at various temperatures manifest the higher stability of 8 × [Cys-Gly-Met-Gly]2. We demonstrated that the presence of sulphur-containing amino acids in CPN enhances the stability through disulphide bonds between the adjacent rings. Further, the water permeation coefficient of the CPN is calculated and compared with human aquaporin-2 (AQP2) channel protein. It is found that the coefficients are highly comparable to the AQP2 channel though the mechanism of water transport is not similar to AQP 2; the flow of water in the CPN is taking place as a two-line 1-2-1-2 file fashion. In addition to that, the transport behavior of Na+ and K+ ions, single water molecule, urea and anti-cancer drug fluorouracil were investigated using pulling simulation and potential of mean force calculation. The above transport behavior shows that Na+ is trapped in CPN for a longer time than other molecules. Also, the interactions of the ions and molecules in Cα and mid-Cα plane were studied to understand the transport behavior of the CPN. AbbreviationsAQP2Aquaporin-2CPNCyclic peptide nanotubeMDMolecular dynamicsPOPA1-Palmitoyl-2-oleoyl-sn-glycero-3-phosphatidic acidPOPE1-Palmitoyl-2-oleoyl-sn-glycero-3-phosphoethanolaminePOPG1-Palmitoyl-2-oleoyl-sn-glycero-3-phosphoglycerolPOPS1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoserineCommunicated by Ramaswamy H. Sarma.

Molecular Mechanism of T-2 Toxin-Induced Cerebral Edema by Aquaporin-4 Blocking and Permeation.

The present study aimed to reveal the molecular mechanism of T-2 toxin-induced cerebral edema by aquaporin-4 (AQP4) blocking and permeation. AQP4 is a class of aquaporin channels that is mainly expressed in the brain, and its structural changes lead to life-threatening complications such as cardio-respiratory arrest, nephritis, and irreversible brain damage. We employed molecular dynamics simulation, text mining, and in vitro and in vivo analysis to study the structural and functional changes induced by the T-2 toxin on AQP4. The action of the toxin leads to disrupted permeation of water and permeation coefficients are found to be affected, from the native (2.49 ± 0.02 × 10-14 cm3/s) to toxin-treated AQP4 (7.68 ± 0.15 × 10-14 cm3/s) channels. Furthermore, the T-2 toxin forms strong electrostatic interactions at the binding site and pushes the key residues (Ala210, Phe77, Arg216, and His201) outward at the selectivity filter. Also, the role of a histidine residue in the AQP4 channel was identified by alchemical transformation and umbrella sampling methods. Alchemical free-energy perturbation energy for H201A ↔ A201H, which was found to be 3.07 ± 0.18 kJ/mol, indicates the structural importance of the histidine residue at 201. In addition, histopathology and expression of AQP4 in the Mus musculus brain tissues show the damaged and altered expression of the protein. Text mining reveals the co-occurrence of genes/proteins associated with the AQP4 expression and T-2 toxin-induced cell apoptosis, which leads to cerebral edema.

Combined Inhibitory Effects of Citrinin, Ochratoxin-A, and T-2 Toxin on Aquaporin-2.

Aquaporins form a large family of transmembrane protein channel that facilitates selective and fast water transport across the cell membrane. The inhibition of aquaporin channels leads to many water-related diseases such as nephrogenic diabetes insipidus, edema, cardiac arrest, and stroke. Herein, we report the molecular mechanism of mycotoxins (citrinin, ochratoxin-A, and T-2 mycotoxin) inhibition of aquaporin-2 (AQP2) and arginine vasopressin receptor 2. Molecular docking, molecular dynamics simulations, quantum chemical calculations, residue conservation-coupling analysis, sequence alignment, and in vivo studies were utilized to explore the binding interactions between the mycotoxins and aquaporin-2. Theoretical studies revealed that the electrostatic interactions induced by the toxins pulled the key residues (187Arg, 48Phe, 172His, and 181Cys) inward, hence reduced the pore diameter and water permeation. The permeability coefficient of the channel was reduced from native ((3.32 ± 0.75) × 10-14 cm3/s) to toxin-treated AQP2 ((1.08 ± 0.03) × 10-14 cm3/s). The hydrogen bonds interruption and formation of more hydrogen bonds with toxins also led to the reduced number of water permeation. Further, in vivo studies showed renal damages and altered level of aquaporin expression in mycotoxin-treated Mus musculus. Furthermore, the multiple sequence alignments among the model organism along with evolutionary coupling analysis provided the information about the interdependences of the residues in the channel.

A theoretical study on the stability of CNT encased cyclic peptide beyond hydrogen bond cut-off.

The Carbon nanotubes (CNT) are potential candidate for many biomedical applications especially in targeted drug delivery for cancer diseases. However, the use of CNT has limitations due to its insolubility in aqueous media. The self-assembly of cyclic peptide encased on the CNT has enhanced its dispersion in aqueous medium which extend their applications as antibacterial and drug delivery agents. To understand this process, an attempt has been made to investigate the dynamics and stability of trimer cyclic peptide encasing with CNT using classical molecular dynamics. The model cyclic peptide monomer constitutes 14 series of amino acids viz.; (cyclo-[(D-ARG-L-VAL-D-ARG-L-THR-D-AGR-L-LYS-D-GLY-L-ARG-D-ARG-L-ILE-D-ARG-L-ILE-D-PRO-L-PRO)]). Each cyclic peptide in the assembly stacking far apart at approximately 15 Å each other beyond hydrogen bond cut-off distance. The trimer was observed to be stable only over 10 ns of entire MD trajectory. But when there is electrostatic interaction between cyclic peptides at 6.5 Å distance then assembly is stable for entire 50 ns. Our result reveals that for a stable assembly, beyond the hydrogen bond cut-off distance, the electrostatic interaction plays significant role.

Effect of mutation on Aß1-42-Heme complex in aggregation mechanism: Alzheimer's disease.

Amyloid ß (Aß) peptide aggregation is one of the root causes for Alzheimer's disease. Recently, experimental studies show that three active binding sites (His6, His13 and His14) of Aß peptides were bound with heme to form Aß-Heme complex, which leads to inhibit the aggregation process. We apply molecular dynamic simulation to investigate the aggregation pathways of Aß-Heme peptides. The above three binding sites were mutated by Glycine residue individually and generate three complex systems such as Aß(His6Gly)-Heme, Aß(His13Gly)-Heme and Aß(His14Gly)-Heme. These complexes were simulated in explicit water using gromos53a6 force field for 200ns. We found that the His13Gly mutation increase the ß-sheet contents (75%) in Aß peptide. On the other hand, heme binds with His13 residue of native peptide plays an important role to reduce the formation ß-sheet content (50%) in Aß peptide. This finding is in agreement with experimental study, which showed that the effect of mutation on His6 is not directly involved in ß-sheet formation, but the effect of mutation in His13 and His14 has involved in ß-sheet formation [J. Neurochem. (2009), 110, 1784-1795]. So, our results may be useful to understand the pathway mechanism of aggregation of Aß peptides.

Understanding the potency of fatty acids with the amino acid side chains of bovine ß lactoglobulin-A quantum chemical approach.

The present study aims to spotlight on the strength of interaction between different fatty acids with the Bovine-lactoglobulin (LGB) protein side chains along with the crystal water molecules at M062X/def2-QZVP level of theory. To analyse the role of carboxylic acid and its interaction with side chains and to reveal the significance of carboxylic acid, it was replaced by Acyl chloride (COCl), Acyl Bromide (COBr) and Acyl-Fluorine (COF) group and COS group. The ligands are linear with a straight and branched chain of carbon atoms, but extended methyl group make the ligand bend resulting in non-planar geometry. The least and highest band gap energy reveals the conductivity properties of ligands. 3UEW, the Palmitic acid is well-built owing to the interaction with the amino acid side chains Lys 69 and Glu 62 resulting in interaction energy of -124.98kcal/mol. 3D-NCIplot isosurface map and 2D-NCIplot graph plays a key role to confirm and analyse the occurrence of various non covalent interactions. The overall analysis of the fatty acids implies the fact that depending on the aliphatic chain length, the carboxyl group was capable of positioning favourable binding site.

Fe(2+) binding on amyloid ß-peptide promotes aggregation.

The metal ions Zn(2+) , Cu(2+) , and Fe(2+) play a significant role in the aggregation mechanism of Aß peptides. However, the nature of binding between metal and peptide has remained elusive; the detailed information on this from the experimental study is very difficult. Density functional theory (dft) (M06-2X/6-311++G (2df,2pd) +LANL2DZ) has employed to determine the force field resulting due to metal and histidine interaction. We performed 200 ns molecular dynamics (MD) simulation on Aß1-42 -Zn(2+) , Aß1-42 -Cu(2+) , and Aß1-42 -Fe(2+) systems in explicit water with different combination of coordinating residues including the three Histidine residues in the N-terminal. The present investigation, the Aß1-42 -Zn(2+) system possess three turn conformations separated by coil structure. Zn(2+) binding caused the loss of the helical structure of N-terminal residues which transformed into the S-shaped conformation. Zn(2+) has reduced the coil and increases the turn content of the peptide compared with experimental study. On the other hand, the Cu(2+) binds with peptide, ß sheet formation is observed at the N-terminal residues of the peptide. Fe(2+) binding is to promote the formation of Glu22-Lys28 salt-bridge which stabilized the turn conformation in the Phe19-Gly25 residues, subsequently ß sheets were observed at His13-Lys18 and Gly29-Gly37 residues. The turn conformation facilitates the ß sheets are arranged in parallel by enhancing the hydrophobic contact between Gly25 and Met35, Lys16 and Met35, Leu17 and Leu34, Val18 and Leu34 residues. The Fe(2+) binding reduced the helix structure and increases the ß sheet content in the peptide, which suggested, Fe(2+) promotes the oligomerization by enhancing the peptide-peptide interaction. Proteins 2016; 84:1257-1274. © 2016 Wiley Periodicals, Inc.

Study on the inter- and intra-peptide salt-bridge mechanism of Aß23-28 oligomer interaction with small molecules: QM/MM method.

Amyloid ß (Aß) peptides have long been known to be a potential candidate for the onset of Alzheimer's disease (AD). The biophysical properties of Aß42 peptide aggregates are of significant importance for the amyloid cascade mechanism of AD. It is necessary to design an inhibitor using small molecules to reduce the aggregation process in Aß42 peptides. Attention has been given to use the natural products as anti-aggregation compounds, directly targeting Aß peptides. Polyphenols have been extensively studied as a class of amyloid inhibitors. 9,10-Anthraquinone (AQ) is present in abundance in medicinal plants (rhubarb), the Trp-Pro-Tyr (TPT) peptide has been found in the venom of the black mamba snake, and the morin molecule is naturally present in wine and green tea; several other polyphenol derivatives are under clinical trials to develop anti-neurodegenerative drugs. In vitro and in vivo results strongly suggest that AQ and morin molecules are potential inhibitors of Aß aggregation; however, the detailed understanding of the inhibition mechanism remains largely unknown. The formation of Aß fibrils and oligomers requires a conformational change from α-helix to ß-sheet, which occurs due to the formation of a salt-bridge between Asp(23) and Lys(28) residues. The present study focused on investigating the salt-bridge mechanism in the monomer, dimer and oligomer of the Aß23-28 peptide during the interaction with TPT, morin and AQ molecules. Interaction energy and natural bond orbital analyses have been carried out using the ONIOM(M05-2X/6-31++G(d,p):UFF) method. The QM/MM studies have been performed to study the mechanism of salt-bridge formation during the inhibition process of amyloid ß protein aggregation. The TPT molecule, which binds with the Asp(23) and Lys(28) residues of Aß, prevents the salt-bridge formation between Asp(23) and Lys(28) residues and consequently the probability of the formation of Aß fibrils is reduced.

Targeted studies on the interaction of nicotine and morin molecules with amyloid ß-protein.

Alzheimer's disease (AD) is a neurodegenerative disorder that occurs due to progressive deposition of amyloid ß-protein (Aß) in the brain. Stable conformations of solvated Aß1₋42 protein were predicted by molecular dynamics (MD) simulation using the OPLSAA force field. The seven residue peptide (Lys-Leu-Val-Phe-Phe-Ala-Glu) Aß16₋22 associated with AD was studied and reported in this paper. Since effective therapeutic agents have not yet been studied in detail, attention has focused on the use of natural products as effective anti-aggregation compounds, targeting the Aß1₋42 protein directly. Experimental and theoretical investigation suggests that some compounds extracted from natural products might be useful, but detailed insights into the mechanism by which they might act remains elusive. The molecules nicotine and morin are found in cigarettes and beverages. Here, we report the results of interaction studies of these compounds at each hydrophobic residue of Aß16₋22 peptide using the hybrid ONIOM (B3LYP/6-31G**:UFF) method. It was found that interaction with nicotine produced higher deformation in the Aß16₋22 peptide than interaction with morin. MD simulation studies revealed that interaction of the nicotine molecule with the ß-sheet of Aß16₋22 peptide transforms the ß-sheet to an α-helical structure, which helps prohibit the aggregation of Aß-protein.

Density functional theory investigation of cocaine water complexes.

Twenty cocaine-water complexes were studied using density functional theory (DFT) B3LYP/6-311++G** level to understand their geometries, energies, vibrational frequencies, charge transfer and topological parameters. Among the 20 complexes, 12 are neutral and eight are protonated in the cocaine-water complexes. Based on the interaction energy, the protonated complexes are more stable than the neutral complexes. In both complexes, the most stable structure involves the hydrogen bond with water at nitrogen atom in the tropane ring and C=O groups in methyl ester. Carbonyl groups in benzoyl and methyl ester is the most reactive site in both forms and it is responsible for the stability order. The calculated topological results show that the interactions involved in the hydrogen bond are electrostatic dominant. Natural bond orbital (NBO) analysis confirms the presence of hydrogen bond and it supports the stability order. Atoms in molecules (AIM) and NBO analysis confirms the C-H···O hydrogen bonds formed between the cocaine-water complexes are blue shifted in nature.

Molecular dynamics simulations and density functional theory studies of NALMA and NAGMA dipeptides.

Classical molecular dynamics (MD) simulations using fixed charged force field (AMBER ff03) and density functional theory method using the M05-2X/6-31G** level of theory have been used to investigate the plasticity of the hydrogen bond formed between dipeptides of N-Acetyl-Leucine-MethylAmide (NALMA), N-Acetyl-Glycine-MethylAmide (NAGMA), and vicinity of water molecules at temperature of 300 K. We have noticed that 2-3 water molecules contribute to change in the conformations of dipeptides NAGMA and NALMA. The self-assembly of 11 water molecules leads to the formation of water bridge at vicinity of the dipeptides and it constrain the conformations of dipeptides. We have found that the energy balance between breaking of the C = O…H-N H bonds and the formation of the C = O…H-O (wat) H bonds may be one of the determining factors to control the dynamics of the folding process of protein molecules.

Microsolvation and hydrogen bond interactions in Glycine Dipeptide: molecular dynamics and density functional theory studies.

Molecular dynamics (MD) simulations were carried out to study the conformational characteristics of Glycine Dipeptide (GD) in the presence of explicit water molecules for over 10 ns with a MD time step of 2 fs. The density functional theory (DFT) methods with 6-311G** basis set have been employed to study the effects of microsolvation on the conformations of GD with 5-10 water molecules. The interaction energy with BSSE corrections and the strength of the intermolecular hydrogen bond interactions have been analyzed. The Bader's Atoms in Molecules (AIM) theory has been employed to investigate H-bonding patterns in water interacting complexes. The natural bond orbital (NBO) analysis has been carried out to analyze the charge transfer between proton acceptor to the antibonding orbital of the XH bond in the hydrated complexes. NMR calculations have been carried out at B3LYP/6-311G (2d, 2p) level of theory to analyse the changes in structure and hydrogen bonding environment that occur upon solvation.

Effect of piratoxin II and acutohaemolysin phospholipase (PLA2) proteins on myristic fatty acid--an ONIOM and DFT study.

A theoretical investigation on the interaction of myristic fatty acid (M) with Acutohaemolysin and Piratoxin-II of PLA2 family is performed using two layered ONIOM (B3LYP/6-31G*: UFF) method. The results predict that though proteins show revulsion to incoming fatty acid, the interaction of the phenyl ring of Phenylalanine restricts the passage of M through the channel. To unveil the nature of interaction of M, quantum chemical studies are carried out on the palindromic tripeptides Alanine-Phenylalanine-Alanine (AFA) and Alanine-Valine-Alanine (AVA) present in Acutohaemolysin and Piratoxin-II at B3LYP/6-311G** level of theory. The mode of interaction of the fatty acid with protein is electrostatic, confirmed further through molecular electrostatic potential (MEP) maps. The AFA shows stronger interaction than AVA, validating the impact of mutation on catalytic activity. Further such strong interaction and hence the higher probability of prohibition for catalytic activity exists only when the fatty acid interacts at the center of phenyl ring than at its edges. The preferred secondary structural configuration and conformational properties of AVA and AFA also validate the strong interaction of fatty acid with Phenylalanine. In general, this theoretical investigation shows that the loss of catalytic activity would take place only when fatty acid interacts at the center of phenyl ring.

Metal ion binding of the alpha-gamma hybrid cyclic peptide nanotubes--a theoretical study based on the ONIOM method.

The quantum mechanics/molecular mechanics ONIOM calculations have been performed to study the structure and metal-ion binding properties of all-trans cyclo[1R-3S-gamma-Acc-Gly]3 hexapeptide nanotube (TAG)3PNT. The intersubunit distances and tube angle of (TAG)3PNT exhibited the sturdy nature of (TAG)3 stacks upon Li+ , K+ , Mg2+, and Zn2+ enclosure.The calculated dimer binding energies of (TAG)3PNT and its ionic complexes confirm that the building blocks are bound by C=O...H-N hydrogen bond interactions. The binding energy of (TAG)3PNT with ions interacting at the surface cavity exhibit the affinity of ions at the entrance of the channel and the many-body analysis for the ion interacting at the central region substantiates the major contribution of two-body interactions to the total binding energy. In general, the binding energies of (TAG)3PNT metal ion interacting complexes with well-maintained channel shows alpha-gamma hybrid cyclic peptides as the promising peptidic nanochannels of biological interests.