Effects of Orientation on the Stability and Affinity of Antibody-GNP Conjugation

In medicine, gold nanoparticles are widely used because of its unique properties. They are usually attached to a monoclonal antibody in treatment and diagnosis. Computational and laboratory work has demonstrated that the structure of the protein can change after interaction with gold nanoparticle and the effect of nanoparticle on the protein is dependent on the type of bond between them. Thus, finding out how nanoparticles affect the protein structure can help us to design the optimal complex of gold nanoparticle-antibody. In the present study, docking and molecular dynamic simulation were performed to obtain an insight at the molecular level in the binding of immunoglobulin G to the Gold nanoparticles, the structure change in immunoglobulin G, and binding energies of Fab and Fc domains of Immunoglobulin G to the GNP. We found the Fab region was more stable than the Fc region when bound to the GNP surface and it also had less structural changes. In neutral pH, Van der Waals interactions contribute more to the Fab-GNP interaction compared to electrostatic interactions; However, in Fc-GNP interaction, the main contributor is the electrostatic energy.

Data related to conformation dependence of tyrosine binding on the surface of graphene: Bent prefers over parallel orientation

In this data article, M06-2X/6-31G(d) level optimized geometries of complexes of tyrosine conformers binding with graphene sheets are shown in top and side views with selected non-bonding distances. The images of frontier molecular orbitals from HOMO-15 to LUMO+15 of the complexes involving graphene with tyrosine conformers are presented and the isovalue is 0.003 au. For some complexes involving small graphene, the orbitals are from HOMO-5 to LUMO+5. The molecular orbitals highlighted with frames show obvious overlaps between the fragments. Total energies of small and large graphene (G _S and G _L ) and selected tyrosine conformers in gas and aqueous phases obtained at M06-2X/6-31G(d) level are given. The data also include total energies of all complexes in the gas phase and the aqueous phase, binding energies, BSSE (basis set superposition error) correction, and BSSE-corrected binding energies in gas phase and solvation effect on the binding energies obtained at M06-2X/6-31G(d) level. Mulliken charges of tyrosine conformers in gas and aqueous phases, and the deformation energy for tyrosine and graphene in the gas phase complexes are provided. The values of the highest occupied molecular orbital (HOMO), the lowest unoccupied molecular orbital (LUMO) and HOMO-LUMO energy gaps for some of graphene-tyrosine complexes that were not reported in the article [1] are given. The data is related to the research article "Conformation dependence of tyrosine binding on the surface of graphene: Bent prefers over parallel orientation" [1].

Theoretical calculation into the effect of molar ratio on the structures, stability, mechanical properties and detonation performance of 1,3,5,7-tetranitro-1,3,5,7-tetrazocane/ 1,3,5-trinitro-1,3,5-triazacyco-hexane cocrystal

Molecular dynamics (MD) simulation was conducted to research the effect of molar ratio on the thermal stability, mechanical properties, and detonation performance of HMX (1,3,5,7-tetranitro-1,3,5,7-tetrazocane)/RDX (1,3,5-trinitro-1,3,5-triazacyco-hexane) cocrystal explosive at ambient condition. The binding energy, mechanical properties, and the detonation parameters of the pure β-HMX, RDX crystal, and the cocrystal models were got and contrasted. The results demonstrate that molar ratio has a great influence on the properties of the cocrystal system. The binding energy of the cocrystals has the maximum values at the 1:1 molar ratio, indicating that the stability of HMX/RDX(1:1) cocrystal is the best and HMX and RDX may prefer to cocrystallizing at 1:1 molar ratio. What's more, the tensile modulus (E) and shear modulus (G) of the HMX/RDX(1:1) cocrystals have the minimum value, while the C₁₂-C₄₄ and K/G have the maximum value, implying that the cocrystal at 1:1 molar ratio has the best mechanical properties. Simultaneously, the E, K, and G of the cocrystals are all smaller than those of β-HMX's and generally larger than those RDX's, while the Cauchy pressure (C₁₂-C₄₄) and K/G ratio were greater, demonstrating that cocrystallizing can improve the brittleness and enhance the ductility. The detonation velocity (D) and detonation pressure (P) decrease with the rising RDX content, while the properties are still superior to the pure RDX crystal; thus, the energy properties of the cocrystal are still excellent. In a word, HMX/RDX cocrystal at 1:1 molar ratio has the best thermal stability, mechanical properties, and the excellent energetic performance.

Antimicrobial peptide ROAD-1 triggers phase change in local membrane environment to execute its activity

Emergence of antibiotic-resistant pathogens has paved way for development of newer class of drugs that would not be susceptible to resistance. Antimicrobial peptides such as defensins that target the microbial membrane are promising candidates. ROAD-1 is an alpha-defensin present in the oral cavity of rhesus macaque and shares very high sequence similarity to human enteric defensin 5. In this study we have performed microsecond long all atom molecular dynamic simulations to understand the mechanism of action of ROAD-1. We find that ROAD-1 is able to adopt an energetically stable conformation predominantly stabilized by electrostatic interactions only in presence of bacterial membranes. In mammalian membrane even though it gets absorbed onto the bilayer, it is unable to adopt an equilibrium conformation. Binding of ROAD-1 to bilayer induces clustering of POPG molecules up to 15 Å around the peptide. POPG molecules show higher order parameters than the neighboring POPE implying coexistence of different phases. Analysis of binding free energy of ROAD-1-membrane complex indicates Arg1, Arg2, Arg7, and Arg25 to play key role in its antimicrobial activity. Unlike its homolog HD5, ROAD-1 is not observed to form a dimer. Our study gives insight into the membrane-bound conformation of ROAD-1 and its mechanism of action that can aid in designing defensin-based therapeutics. Graphical abstract Antimicrobial peptide ROAD-1 adopts a different membrane-bound conformation as compared with HD5 even though they belong to the same family implying a different mechanism of action.

Molecular dynamics simulation of the adsorption behavior of two different drugs on hydroxyapatite and Zn-doped hydroxyapatite

Hydroxyapatite (HAp) is a highly promising material as a drug carrier. The solubility, osteoinductivity, antibacterial properties and drug loading efficiency of HAp can be further enhanced by Zn doping. In this study, we carried out first-principles and molecular dynamics (MD) simulations to investigate the influence of Zn doping on the crystal structure and adsorption capacity of macromolecular drugs on HAp. Our results showed that the binding energy of doxorubicin (DOX) on HAp is significantly increased in consequence of Zn-doping. Moreover, the interaction between surface Ca ions and carbonyl-O mostly contributed to the adsorption. The binding energy of tinidazole on HAp was much lower than that observed for DOX. The number of active "O" atoms in the drug and binding stability were positively correlated. These simulations provide important insight into the understanding of drug adsorption on HAp or ion-doped HAp.

Structure-based screening and validation of potential dengue virus inhibitors through classical and QM/MM affinity estimation

The recurrent outbreaks of dengue virus around the globe represent a huge challenge for governments and public health organizations. With the rapid growth and ease of transportation, dengue disease continues to spread, placing more of the world population under constant threat. Despite decades of research efforts, no effective small molecule antivirals are available against dengue virus. With the efficacy of the recently developed vaccine to be determined, there is an urgent unmet need for small molecule dengue virus treatments. In the current study, we employed state-of-the-art molecular modelling simulations to identify novel inhibitors of the dengue virus envelope protein. The binding modes of all compounds within the conserved β-OctylGlucoside (β-OG) pocket were studied using a combination of docking, molecular dynamics simulations and binding free energy calculations. Here, we describe ten new compounds that significantly reduce production of dengue virus as determined using standard cell-based virological assays. Moreover, we present a comprehensive structural analysis of the identified hits, focusing on their electrostatic and lipophilic binding energy contributions. Finally, we highlight the effect of the desolvation penalty in limiting the activity of some of these compounds. The data presented here paves the way toward rationally designing selective and potent novel inhibitors against dengue virus.

Influence of noise-binding energy interplay on the second and third-order nonlinear optical properties of impurity doped quantum dots

We inspect the role of binding energy (BE) on second-order and third-order nonlinear optical (NLO) properties of doped G a A s quantum dot (QD). In the study ample stress is given on understanding the role of noise on the manifestations of these NLO properties. The profiles of these NLO properties are analyzed mainly on the basis of variation of two important criteria viz. peak-shift and peak-height as a function of BE. Both these features depend on the presence of noise, its pathway (mode) of introduction and sometimes on the identity of the NLO properties. The findings of the study deem significance in realizing the binding energy-dependence of the said NLO properties of low-dimensional semiconductor materials when noise contribution becomes noticeable.

Visualizing protein-ligand binding with chemical energy-wise decomposition (CHEWD): application to ligand binding in the kallikrein-8 S1 Site

Kallikrein-8, a serine protease, is a target for structure-based drug design due to its therapeutic potential in treating Alzheimer's disease and is also useful as a biomarker in ovarian cancer. We present a binding assessment of ligands to kallikrein-8 using a residue-wise decomposition of the binding energy. Binding of four putative inhibitors of kallikrein-8 is investigated through molecular dynamics simulation and ligand binding energy evaluation with two methods (MM/PBSA and WaterSwap). For visualization of the residue-wise decomposition of binding energies, chemical energy-wise decomposition or CHEWD is introduced as a plugin to UCSF Chimera and Pymol. CHEWD allows easy comparison between ligands using individual residue contributions to the binding energy. Molecular dynamics simulations indicate one ligand binds stably to the kallikrein-8 S1 binding site. Comparison with other members of the kallikrein family shows that residues responsible for binding are specific to kallikrein-8. Thus, ZINC02927490 is a promising lead for development of novel kallikrein-8 inhibitors.

Thermodynamic analysis of remote substrate binding energy in 3α-hydroxysteroid dehydrogenase/carbonyl reductase catalysis

The binding energy of enzyme and substrate is used to lower the activation energy for the catalytic reaction. 3α-HSD/CR uses remote binding interactions to accelerate the reaction of androsterone with NAD⁺. Here, we examine the enthalpic and entropic components of the remote binding energy in the 3α-HSD/CR-catalyzed reaction of NAD⁺ with androsterone versus the substrate analogs, 2-decalol and cyclohexanol, by analyzing the temperature-dependent kinetic parameters through steady-state kinetics. The effects of temperature on k_cat/K_m for 3α-HSD/CR acting on androsterone, 2-decalol, and cyclohexanol show the reactions are entropically favorable but enthalpically unfavorable. Thermodynamic analysis from the temperature-dependent values of K_m and k_cat shows the binding of the E-NAD⁺ complex with either 2-decalol or cyclohexanol to form the ternary complex is endothermic and entropy-driven, and the subsequent conversion to the transition state is both enthalpically and entropically unfavorable. Hence, solvation entropy may play an important role in the binding process through both the desolvation of the solute molecules and the release of bound water molecules from the active site into bulk solvent. As compared to the thermodynamic parameters of 3α-HSD/CR acting on cyclohexanol, the hydrophobic interaction of the B-ring of steroids with the active site of 3α-HSD/CR contributes to catalysis by increasing exclusively the entropy of activation (ΔTΔS^‡ = 1.8 kcal/mol), while the BCD-ring of androsterone significantly lowers ΔΔH^‡ by 10.4 kcal/mol with a slight entropic penalty of -1.9 kcal/mol. Therefore, the remote non-reacting sites of androsterone may induce a conformational change of the substrate binding loop with an entropic cost for better interaction with the transition state to decrease the enthalpy of activation, significantly increasing catalytic efficiency.

Theoretical investigations on structures, stability, energetic performance, sensitivity, and mechanical properties of CL-20/TNT/HMX cocrystal explosives by molecular dynamics simulation

In this article, the CL-20, TNT, HMX, CL-20/TNT, CL-20/HMX and different CL-20/TNT/HMX cocrystal models were established. Molecular dynamics method was selected to optimize the structures, predict the stability, sensitivity, energetic performance, and mechanical properties of cocrystal models. The binding energy, trigger bond length, trigger bond energy, cohesive energy density, detonation parameters, and mechanical properties of each crystal model were obtained. The influences of co-crystallization and molar ratios on performances of cocrystal explosives were investigated and evaluated. The results show that the CL-20/TNT/HMX cocrystal explosive with a molar ratio of 3:1:2 or 3:1:3 had larger binding energy and better stability, i.e., CL-20/TNT/HMX cocrystal explosive was more likely to be formed with these molar ratios. The cocrystal explosive had shorter maximal trigger bond length, but larger trigger bond energy and cohesive energy density than CL-20, namely, the cocrystal explosive had lower mechanical sensitivity and better safety than CL-20 and the safety of cocrystal model was effectively improved. The cocrystal model with a molar ratio of 3:1:2 had the best safety. The energetic performance of the cocrystal explosive with a molar ratio of 3:1:1, 3:1:2, or 3:1:3 was the best. These CL-20/TNT/HMX cocrystal models exhibited better and more desirable mechanical properties. In a word, the cocrystal model with molar ratio of 3:1:2 exhibited the most superior properties and was a novel and potential high-energy-density compound. This paper could provide practical helpful guidance and theoretical support to better understand co-crystallization mechanisms and design novel energetic cocrystal explosives.

Resistance determination of the ACCase-inhibiting herbicide of clodinafop propargyl in Avena ludoviciana (Durieu), and study of their interaction using molecular docking and simulation

Structural mutations providing herbicide resistance may cause a modification of the three dimensional structure of a protein which will lead to a decrease in the herbicide efficacy. Wild oat (Avena ludoviciana Durieu.) is an increasingly disruptive weed in areas of intensive cereal production, thus the aim of this research was to identify mutations conferring resistance to ACCase-inhibitor herbicides at greenhouse, laboratory and in silico scales. Among the selected biotypes, No. 3 in the position 1781 (Ile1781-Leu) and No. 14 in the position 2041 (Ile2041-Asn), showed resistance to ACCase-inhibitor. The above mutations were confirmed using the specific primers and PCR-based methods. Analysis of molecular docking indicated that residues of Trp1948 and Pro2001 are important in the binding site and showed remarkable variation in the mutation types. Using molecular dynamic simulation analysis, we demonstrated that mutation types changed the conformation of the enzyme. These changes resulted in compressed conformation in the active site, which limited the availability of binding herbicide-enzyme. In present, no crystallography molecular structure and modeling reported on the ACCase of plants and this study investigated interactions of clodinafop propargyl and ACCase CT domain in A. ludoviciana by modeling, docking and simulations for the first time. Totally, bioinformatics analysis as well as PCR-based method confirmed that herbicide resistance conferred by nucleotide mutations in the gene sequence.

Improvement in hydrogen binding ability of closo-dicarboranes via functionalization and designing of extended frameworks

Neutral closo-dicarboboranes are reported to have very low H₂ binding ability. Herein, we report an improvement in H₂ binding energy (E_b) of C₂B₄H₆ by substituting H atoms with different functional groups like X = F, Cl, Br, and XY = BO, CN and NC via quantum-chemical density functional theory based computations. In going from B₆H₆^2- to C₂B₄H₆, the E_b value is reduced from 14.6 kJ mol^-1 to 2.7 kJ mol^-1. C₂B₄X₆ and C₂B₄(XY)₆ systems, which can bind a total of eight H₂ molecules, with one H₂ molecule occupying at each B-B-C face, possess an E_b value per H₂ in the range of 4.5 kJ mol^-1 for X = F, 3.9 kJ mol^-1 for X = Cl, 5.9 kJ mol^-1 for X = Br, 6.8 kJ mol^-1 for XY = BO, 5.8 kJ mol^-1 for XY = CN and 5.2 kJ mol^-1 for XY = NC. The improvement in E_b value is found to be the highest in case of C₂B₄(BO)₆, which has the ability to bind 6.6 gravimetric wt% of H₂. The situation can be made more favorable by applying an external electric field. Energy decomposition analysis reveals that although the dispersion interaction (ca. 55-65%) has significant role in binding H₂ with such types of molecules, contribution from electrostatic and orbital interaction is also considerable. Further, we modeled an extended system by linking C₂B₄(BO)_n through 'C ≡ C' units for H₂ storage purpose. The energy difference between the highest occupied and the lowest unoccupied molecular orbitals gradually lessens with the increase in molecular length. Therefore, it can be tuned gradually by controlling the chain length, which may further open up their potency in the field of electronics. Graphical abstract C₂B₄X₆ (X = F, Cl, Br) and C₂B₄(XY)₆ (XY = BO, CN, NC) show enhanced H₂ binding ability from C₂B₄H₆. Further, 1D, 2D and 3-D frameworks can be built by joining C₂B₄(BO)_n units via 'C ≡ C' linkage.

Investigation on extracellular polymeric substances, sludge flocs morphology, bound water release and dewatering performance of sewage sludge under pretreatment with modified phosphogypsum

Modified phosphogypsum (MPG) was developed to improve dewaterability of sewage sludge, and dewatering performance, properties of treated sludge, composition and morphology distribution of EPS, dynamic analysis and multiple regression model on bound water release were investigated. The results showed that addition of MPG caused extracellular polymeric substances (EPS) disintegration through charge neutralization. Destruction of EPS promoted the formation of larger sludge flocs and the release of bound water into supernatant. Simultaneously, content of organics with molecular weight between 1000 and 7000 Da in soluble EPS (SB-EPS) increased with increasing of EPS dissolved into the liquid phase. Besides, about 8.8 kg•kg^-1DS of bound water was released after pretreatment with 40%DS MPG dosage. Additionally, a multiple linear regression model for bound water release was established, showing that lower loosely bond EPS (LB-EPS) content and specific resistance of filtration (SRF) may improve dehydration performance, and larger sludge flocs may be beneficial for sludge dewatering.

Pharmacoinformatics analysis of merbarone binding site in human topoisomerase IIα

Merbarone is a derivative of thiobarbituric acid, possessing catalytic inhibitory potential against human topoisomerase IIα (hTopoIIα). Merbarone was reported to inhibit DNA cleavage by hTopoIIα. It is important to understand the molecular mechanism of hTopoIIα inhibition by merbarone, as these details guide the rational design of new ligands. In this work, a systematic pharmacoinformatics analysis has been reported to analyze the merbarone-hTopoIIα interactions and to identify merbarone analogs as potential hTopoIIα inhibitors. The reported crystal structure of hTopoIIα-DNA complex (PDB ID: 4FM9) is not suitable for analyzing the merbarone-binding domain, because it is a biological assembly of hTopoIIα in C-gate open conformation. Therefore, 3D structure of hTopoIIα-DNA complex suitable for molecular modeling analysis at merbarone binding site was first generated. Using this generated complex, molecular docking analysis and molecular dynamics simulations were performed to explore the effect of merbarone on hTopoIIα-DNA complex. The binding energy for the enol form of merbarone with hTopoIIα-DNA was estimated to be -51.28 kcal/mol. The explored binding site and identified molecular recognition interactions were in accordance with the previously reported interference in the DNA-cleavage by merbarone. Virtual screening was performed using drug likeness filters, toxicity filters and ADMET descriptor based filters followed by molecular docking (ZINC database). Sixteen compounds were identified as merbarone-functional analogs suitable for hTopoIIα inhibition. These identified molecules can be considered for further evaluation of their anti-hTopoIIα activity.

Theoretical investigations on the structures and properties of CL-20/TNT cocrystal and its defective models by molecular dynamics simulation

"Perfect" and defective models of CL-20/TNT cocrystal explosive were established. Molecular dynamics methods were introduced to determine the structures and predict the comprehensive performances, including stabilities, sensitivity, energy density and mechanical properties, of the different models. The influences of crystal defects on the properties of these explosives were investigated and evaluated. The results show that, compared with the "perfect" model, the rigidity and toughness of defective models are decreased, while the ductility, tenacity and plastic properties are enhanced. The binding energies, interaction energy of the trigger bond, and the cohesive energy density of defective crystals declined, thus implying that stabilities are weakened, the explosive molecule is activated, trigger bond strength is diminished and safety is worsened. Detonation performance showed that, owing to the influence of crystal defects, the density is lessened, detonation pressure and detonation velocity are also declined, i.e., the power of defective explosive is decreased. In a word, the crystal defects may have a favorable effect on the mechanical properties, but have a disadvantageous influence on sensitivity, stability and energy density of CL-20/TNT cocrystal explosive. The results could provide theoretical guidance and practical instructions to estimate the properties of defective crystal models.

The design of high affinity human PD-1 mutants by using molecular dynamics simulations (MD)

BACKGROUND

Programmed cell death protein 1 (PD-1), a negative co-stimulatory molecule, plays crucial roles in immune escape. Blockade of the interaction between PD-1 and PD-L1 shows exciting clinical responses in a fraction of cancer patients and the success makes PD-1 as a valuable target in immune checkpoint therapy. For the rational design of PD-1 targeting modulators, the ligand binding mechanism of PD-1 should be well understood in prior.

METHODS

In this study, we applied 50 ns molecular dynamics simulations to observe the structural properties of PD-1 molecule in both apo and ligand bound states, and we studied the structural features of PD-1 in human and mouse respectively.

RESULTS

The results showed that the apo hPD-1 was more flexible than that in PD-L1 bound state. We unexpectedly found that K135 was important for binding energy although it was not at the binding interface. Moreover, the residues which stabilized the interactions with PD-L1 were distinguished. Taking the dynamic features of these residues into account, we identified several residual sites where mutations may gain the function of ligand binding. The in vitro binding experiments revealed the mutants M70I, S87 W, A129L, A132L, and K135 M were better in ligand binding than the wild type PD-1.

CONCLUSIONS

The structural information from MD simulation combined with in silico mutagenesis provides guidance to design engineered PD-1 mutants to modulate the PD-1/PD-L1 pathway.

Role of protein structure and the role of individual fingers in zinc finger protein-DNA recognition: a molecular dynamics simulation study and free energy calculations

Molecular dynamics and MM_GBSA energy calculations on various zinc finger proteins containing three and four fingers bound to their target DNA gave insights into the role of each finger in the DNA binding process as part of the protein structure. The wild type Zif 268 (PDB code: 1AAY) gave a ΔG value of - 76.1 (14) kcal/mol. Zinc fingers ZF1, ZF2 and ZF3 were mutated in one experiment and in another experiment one finger was cut and the rest of the protein was studied for binding. The ΔΔG values for the Zinc Finger protein with both ZF1 and ZF2 mutated was + 80 kcal/mol, while mutating only ZF1 the ΔΔG value was + 52 kcal/mol (relative to the wild type). Cutting ZF3 and studying the protein consisting only of ZF1 linked to ZF2 gave a ΔΔG value of + 68 kcal/mol. Upon cutting ZF1, the resulting ZF2 linked to ZF3 protein gave a ΔΔG value of + 41 kcal/mol. The above results shed light on the importance of each finger in the binding process, especially the role of ZF1 as the anchoring finger followed in importance by ZF2 and ZF3. The energy difference between the binding of the wild type protein Zif268 (1AAY) and that for individual finger binding to DNA according to the formula: ΔΔG_{linkers, otherstructuralfactors} = ΔG_zif268 - (ΔG_F1+F2+F3) gave a value = - 44.5 kcal/mol. This stabilization can be attributed to the contribution of linkers and other structural factors in the intact protein in the DNA binding process. DNA binding energies of variant proteins of the wild type Zif268 which differ in their ZF1 amino acid sequence gave evidence of a good relationship between binding energy and recognition and specificity, this finding confirms the reported vital role of ZF1 in the ZF protein scanning and anchoring to the target DNA sequence. The role of hydrogen bonds in both specific and nonspecific amino acid-DNA contacts is discussed in relation to mutations. The binding energies of variant Zinc Finger proteins confirmed the role of ZF1 in the recognition, specificity and anchoring of the zinc finger protein to DNA.

Identification of inhibitor against H. pylori HtrA protease using structure-based virtual screening and molecular dynamics simulations approaches

The HtrA protease of Helicobacter pylori, which efficiently colonizes at the gastric epithelial of host cells, disrupts the mucosal integrity of E-cadherin and spreads inflammatory diseases including gastric cancer by cleaving the cell-cell adhesion of the host. The lack of knowledge on the molecular diversity, structural and functional behavior of HpHtrA necessitated the present study to explore its inhibition mechanism. At first, the similarity of HpHtrA with other gastro-intestinal pathogenic HtrA bacteria and its remote relationship with the Human HtrA homologs were ensured by the phylogenetic analysis and hence was identified as a novel therapeutic target for further design of inhibitors. The three dimensional structure of HpHtrA was modeled and simulated to achieve its stable conformation and was used as a receptor to screen for the possible lead compound through virtual screening (using ∼ 1.3 million compounds). Molecular dynamics simulations followed by the binding energy analysis revealed the affinity of the compound 300040 in forming a stable complex with HpHtrA and thereby revealed its potent role in inhibiting HpHtrA. It is also worthy to mention that, structurally, the ligand binding at the catalytic site of HpHtrA is mainly facilitated by the significant dynamics of L2 loop. Based on the present study, the hydroxyl-piperidine with 4-aminopiperidine scaffold is proposed to be one of the best possible lead compounds for the inhibition of H. pylori.

Theoretical investigation of the structures and properties of CL-20/DNB cocrystal and associated PBXs by molecular dynamics simulation

In this work, a CL-20/DNB cocrystal explosive model was established and six different kinds of fluoropolymers, i.e., PVDF, PCTFE, F₂₃₁₁, F₂₃₁₂, F₂₃₁₃ and F₂₃₁₄ were added into the (1 0 0), (0 1 0), (0 0 1) crystal orientations to obtain the corresponding polymer bonded explosives (PBXs). The influence of fluoropolymers on PBX properties (energetic property, stability and mechanical properties) was investigated and evaluated using molecular dynamics (MD) methods. The results reveal a decrease in engineering moduli, an increase in Cauchy pressure (i.e., rigidity and stiffness is lessened), and an increase in plastic properties and ductility, thus indicating that the fluoropolymers have a beneficial influence on the mechanical properties of PBXs. Of all the PBXs models tested, the mechanical properties of CL-20/DNB/F₂₃₁₁ were the best. Binding energies show that CL-20/DNB/F₂₃₁₁ has the highest intermolecular interaction energy and best compatibility and stability. Therefore, F₂₃₁₁ is the most suitable fluoropolymer for PBXs. The mechanical properties and binding energies of the three crystal orientations vary in the order (0 1 0) > (0 0 1) > (1 0 0), i.e., the mechanical properties of the (0 1 0) crystal orientation are best, and this is the most stable crystal orientation. Detonation performance results show that the density and detonation parameters of PBXs are lower than those of the pure CL-20 and CL-20/DNB cocrystal explosive. The power and energetic performance of PBXs are thus weakened; however, these PBXs still have excellent detonation performance and are very promising. The results and conclusions provide some helpful guidance and novel instructions for the design and manufacture of PBXs.

Ab Initio Computational Study of Chromate Molecular Anion Adsorption on the Surfaces of Pristine and B- or N-Doped Carbon Nanotubes and Graphene

Density functional theory (DFT) computations of the electronic structures of undoped, B- and N-doped CNT(3,3), CNT(5,5) carbon nanotubes, and graphene with adsorbed chromate anions CrO₄^2- were performed within molecular cluster approach. Relaxed geometries, binding energies, charge differences of the adsorbed CrO₄^2- anions, and electronic wave function contour plots were calculated using B3LYP hybrid exchange-correlation functional. Oscillator strengths of electronic transitions of CrO₄^2- anions adsorbed on the surfaces of studied carbon nanostructures were calculated by the TD-DFT method. Calculations reveal covalent bonding between the anion and the adsorbents in all studied adsorption configurations. For all studied types of adsorbent structures, doping with N strengthens chemical bonding with CrO₄^2- anions, providing a ~2-eV increase in binding energies comparatively to adsorption of the anion on undoped adsorbents. Additional electronic transitions of CrO₄^2- anions appear in the orange-green spectral region when the anions are adsorbed on the N-doped low-diameter carbon nanotubes CNT(3,3) and CNT(5,5).

Molecular dynamics calculation on structures, stabilities, mechanical properties, and energy density of CL-20/FOX-7 cocrystal explosives

In this article, different CL-20/FOX-7 cocrystal models were established by the substitution method based on the molar ratios of CL-20:FOX-7. The structures and comprehensive properties, including mechanical properties, stabilities, and energy density, of different cocrystal models were obtained and compared with each other. The main aim was to estimate the influence of molar ratios on properties of cocrystal explosives. The molecular dynamics (MD) simulation results show that the cocrystal model with molar ratio 1:1 has the best mechanical properties and highest binding energy, so the CL-20/FOX-7 cocrystal model is more likely to form in 1:1 M ratio. The detonation parameters show that the cocrystal explosive exhibited preferable energy density and excellent detonation performance. In a word, the 1:1 cocrystal model has the best comprehensive properties, is very promising, and worth more theoretical investigations and experimental tests. This paper gives some original theories to better understand the cocrystal mechanism and provides some helpful guidance and useful instructions to help design CL-20 cocrystal explosives.

A heuristic model for computational prediction of human branch point sequence

BACKGROUND

Pre-mRNA splicing is the removal of introns from precursor mRNAs (pre-mRNAs) and the concurrent ligation of the flanking exons to generate mature mRNA. This process is catalyzed by the spliceosome, where the splicing factor 1 (SF1) specifically recognizes the seven-nucleotide branch point sequence (BPS) and the U2 snRNP later displaces the SF1 and binds to the BPS. In mammals, the degeneracy of BPS motifs together with the lack of a large set of experimentally verified BPSs complicates the task of BPS prediction in silico.

RESULTS

In this paper, we develop a simple and yet efficient heuristic model for human BPS prediction based on a novel scoring scheme, which quantifies the splicing strength of putative BPSs. The candidate BPS is restricted exclusively within a defined BPS search region to avoid the influences of other elements in the intron and therefore the prediction accuracy is improved. Moreover, using two types of relative frequencies for human BPS prediction, we demonstrate our model outperformed other current implementations on experimentally verified human introns.

CONCLUSION

We propose that the binding energy contributes to the molecular recognition involved in human pre-mRNA splicing. In addition, a genome-wide human BPS prediction is carried out. The characteristics of predicted BPSs are in accordance with experimentally verified human BPSs, and branch site positions relative to the 3'ss and the 5'end of the shortened AGEZ are consistent with the results of published papers. Meanwhile, a webserver for BPS predictor is freely available at http://biocomputer.bio.cuhk.edu.hk/BPS .

Comparative studies on structures, mechanical properties, sensitivity, stabilities and detonation performance of CL-20/TNT cocrystal and composite explosives by molecular dynamics simulation

To investigate and compare the differences of structures and properties of CL-20/TNT cocrystal and composite explosives, the CL-20/TNT cocrystal and composite models were established. Molecular dynamics simulations were performed to investigate the structures, mechanical properties, sensitivity, stabilities and detonation performance of cocrystal and composite models with COMPASS force field in NPT ensemble. The lattice parameters, mechanical properties, binding energies, interaction energy of trigger bond, cohesive energy density and detonation parameters were determined and compared. The results show that, compared with pure CL-20, the rigidity and stiffness of cocrystal and composite models decreased, while plastic properties and ductility increased, so mechanical properties can be effectively improved by adding TNT into CL-20 and the cocrystal model has better mechanical properties. The interaction energy of the trigger bond and the cohesive energy density is in the order of CL-20/TNT cocrystal > CL-20/TNT composite > pure CL-20, i.e., cocrystal model is less sensitive than CL-20 and the composite model, and has the best safety parameters. Binding energies show that the cocrystal model has higher intermolecular interaction energy values than the composite model, thus illustrating the better stability of the cocrystal model. Detonation parameters vary as CL-20 > cocrystal > composite, namely, the energy density and power of cocrystal and composite model are weakened; however, the CL-20/TNT cocrystal explosive still has desirable energy density and detonation performance. This results presented in this paper help offer some helpful guidance to better understand the mechanism of CL-20/TNT cocrystal explosives and provide some theoretical assistance for cocrystal explosive design.

Ionization spectroscopies and theoretical calculations of cis and trans 3-fluoro-N-methylaniline-Arn(n=1,2) van der Waals clusters: Structures and binding energies

The ab initio and dispersion-corrected density functional theory (DFT) calculations of the van der Waals (vdW) clusters of cis and trans 3-fluoro-N-methylaniline-Ar_n (3FNMA-Ar_n) (n=1,2) predict that, for cis and trans 3FNMA-Ar₁ clusters, the π-bound geometry with the Ar atom sitting over the ring is the global minimum in both neutral and cationic states, while for cis and trans 3FNMA-Ar₂ clusters, the [π|π]-bound sandwich structure with two Ar ligands occupying nearly equivalent π-bound positions above and below the ring plane is the global minimum. The vibronic spectra of cis and trans 3FNMA-Ar₁ clusters in the S₁ state were recorded by using one-color and two-color resonant two-photon ionization (R2PI) techniques, the comparison of which yields an estimate of the binding energy of cluster in the S₁ state. It is found that the linear correlation between the redshift of the S₁←S₀ electronic transition energy (E₁) of cluster and the E₁ of the monomer also holds for the Ar clusters of hetero-di-substituted aromatics. By recording the photoionization efficiency (PIE) curves and mass-analyzed threshold ionization (MATI) dissociation spectra of cis and trans 3FNMA-Ar₁ clusters, the ionization energies (IE) and binding energies of clusters in the D₀ state are obtained. The MATI spectra of the cis and trans 3FNMA-Ar₁ cations exhibit significant progressions of the vdW bending mode (b_x), indicating the structural changes of the clusters in the bending coordinate upon ionization. The combination of the three kinds of spectroscopic methods provides the binding energies of cis and trans 3FNMA-Ar₁ clusters in the S₀, S₁ and D₀ states with good accuracy, and the values estimated by dispersion-corrected DFT calculations compare well with the experimental results. From our studies, the ωB97X-D and TD-ωB97X-D methods using high quality basis set are recommended for studying the intermolecular interaction of such vdW clusters in the ground and excited states.

Inhibition of Gelatinases (MMP-2 and MMP-9) by Withania somnifera Phytochemicals Confers Neuroprotection in Stroke: An In Silico Analysis

A stroke or cerebrovascular accident is a serious, life-threatening medical condition that occurs when the blood supply to part of the brain is severely reduced or cut off, depriving brain tissue of oxygen and nutrients. Studies suggested that level of gelatinases (MMP-2 and MMP-9) usually increases in the brain after stroke. The elevated activity of gelatinases plays the deleterious role in ischemic stroke, hemorrhagic stroke and perinatal hypoxic-ischemic brain injury. Therefore, matrix metalloproteinase (MMP)-2 and MMP-9 inhibition have therapeutic importance in stroke condition. Present in silico study investigates whether Withania somnifera (WS) phytochemicals inhibit the MMP-2 and MMP-9 by binding to the catalytic domain, as similar to their inhibitor or not. For that, we performed molecular docking study to evaluate the gelatinases-inhibitory potential of 36 WS phytochemicals, which compared with gelatinases inhibitors viz. hydroxamic acid, quercetin, doxycycline, minocycline and reverse hydroxamate. The results suggest that 28 out of 36 WS phytochemicals show higher affinity for MMP-2 owing to bind with active site residues of S1'-pocket with lower binding energy and smaller inhibition constant (Ki) than considered inhibitors. As well as, withanolide G and withafastuosin E show higher affinity for MMP-9 than reverse hydroxamate inhibitor. These phytochemicals have neuroprotective potential as an inherently useful oral drug to combat ischemic and hemorrhagic stroke mediated by gelatinases.

Substituted furans as potent lipoxygenase inhibitors: Synthesis, in vitro and molecular docking studies

A number of 2-methyl-4-(2-oxo-2-phenyl-ethyl)-5-phenyl-furan-3-carboxylic acid alkyl ester derivatives (3a-j) were synthesized and evaluated for their in vitro inhibitory activity on soybean lipoxygenase enzyme. Among the screened compounds, 5-(4-bromo-phenyl)-4-[2-(4-bromo-phenyl)-2-oxo-ethyl]-2-methyl-furan-3-carboxylic acid methyl ester (3g) has been found to exhibit potent inhibitory activity with IC5012.8μM using nordihydroguaiaretic acid (NDGA) as standard. Molecular modeling was employed for better understanding of the binding between compounds and soybean lipoxygenase enzyme. The predicted binding energy values correlated well with the observed in vitro data.

Deciphering molecular properties and docking studies of hepatitis C and non-hepatitis C antiviral inhibitors - A computational approach

BACKGROUND

Hepatitis C is an infectious liver disease with high mortality rate which is caused by Hepatitis C virus. Several treatment methods have been applied to combat this deadly virus including interferons, vaccine and direct acting antivirals (DAAs). However, the later shows promising effects in HCV treatment with lower adverse effect. Specifically, the DAAs target the non-structural proteins (NS3 and NS5B).

PURPOSE

The objective of the present study is to hypothesize an alternative antiviral inhibitor for HCV from the available other antivirals.

METHODS

Computation of 2D molecular descriptors for the selected antiviral inhibitors followed by clustering the descriptor features. The closely clustered compounds were subjected to the interaction studies against the HCV target protein to validate the cluster result.

RESULTS AND DISCUSSION

The clustering result showed that indinavir (HIV inhibitor) and AT130 (HBV inhibitor) molecule are close to the HCV inhibitor. The indinavir complexed with NS3 protein shows -5.33kcal/mol and AT-130 complexed with NS5B protein possess the binding energy of -8.87kcal/mol. The docking interaction study indicated a better binding affinity than other viral inhibitors.

CONCLUSION

From the descriptor based feature similarity analysis and the interaction study, it can be concluded that indinavir and AT-130 could be a potential alternative agent for HCV treatment.

Molecular Docking: From Lock and Key to Combination Lock

Accurate modeling of protein ligand binding is an important step in structure-based drug design, is a useful starting point for finding new lead compounds or drug candidates. The 'Lock and Key' concept of protein-ligand binding has dominated descriptions of these interactions, and has been effectively translated to computational molecular docking approaches. In turn, molecular docking can reveal key elements in protein-ligand interactions-thereby enabling design of potent small molecule inhibitors directed against specific targets. However, accurate predictions of binding pose and energetic remain challenging problems. The last decade has witnessed more sophisticated molecular docking approaches to modeling protein-ligand binding and energetics. However, the complexities that confront accurate modeling of binding phenomena remain formidable. Subtle recognition and discrimination patterns governed by three-dimensional features and microenvironments of the active site play vital roles in consolidating the key intermolecular interactions that mediates ligand binding. Herein, we briefly review contemporary approaches and suggest that future approaches treat protein-ligand docking problems in the context of a 'combination lock' system.

Contribution of remote substrate binding energy to the enzymatic rate acceleration for 3α-hydroxysteroid dehydrogenase/carbonyl reductase

3α-Hydroxysteroid dehydrogenase/carbonyl reductase (3α-HSD/CR) catalyzes the oxidation of androsterone with NAD⁺ to form androstanedione and NADH with the rate limiting step being the release of NADH. In this study, we elucidate the role of remote substrate binding interactions contributing to the rate enhancement by 3α-HSD/CR through steady-state kinetic studies with the truncated substrate analogs. No enzyme activity was detected for methanol, ethanol, and 2-propanol, which lack the steroid scaffold of androsterone, implying that the steroid scaffold plays an important role in enzyme catalytic specificity. As compared to cyclohexanol, the activity for 2-decalol, androstenol, and androsterone increases by 0.9-, 90-, and 200-fold in k_cat, and 37-, 1.9 × 10⁶-, and 1.8 × 10⁶-fold in k_cat/K_B, respectively. The rate limiting step is hydride transfer for 3α-HSD/CR catalyzing the reaction of cyclohexanol with NAD⁺ based on the observed rapid equilibrium ordered mechanism and equal deuterium isotope effects of 3.9 on V and V/K for cyclohexanol. The k_cat/K_B value results in ΔG^‡ of 14.7, 12.6, 6.2, and 6.2 kcal/mol for the 3α-HSD/CR catalyzed reaction of cyclohexanol, 2-decalol, androstenol, and androsterone, respectively. Thus, the uniform binding energy from the B-ring of steroids with the active site of 3α-HSD/CR equally contributes 2.1 kcal/mol to stabilize both the transition state and ground state of the ternary complex, leading to the similarity in k_cat for 2-decalol and cyclohexanol. Differential binding interactions of the remote BCD-ring and CD-ring of androsterone with the active site of 3α-HSD/CR contribute 8.5 and 6.4 kcal/mol to the stabilization of the transition state, respectively. The removal of the carbonyl group at C17 of androsterone has small effects on catalysis. Both uniform and differential binding energies from the remote sites of androsterone compared to cyclohexanol contribute to the 3α-HSD/CR catalysis, resulting in the increases in k_cat and k_cat/K_B.

Theoretical insights into the effects of molar ratios on stabilities, mechanical properties, and detonation performance of CL-20/HMX cocrystal explosives by molecular dynamics simulation

To research and estimate the effects of molar ratios on structures, stabilities, mechanical properties, and detonation properties of CL-20/HMX cocrystal explosive, the CL-20/HMX cocrystal explosive models with different molar ratios were established in Materials Studio (MS). The crystal parameters, structures, stabilities, mechanical properties, and some detonation parameters of different cocrystal explosives were obtained and compared. The molecular dynamics (MD) simulation results illustrate that the molar ratios of CL-20/HMX have a direct influence on the comprehensive performance of cocrystal explosive. The hardness and rigidity of the 1:1 cocrystal explosive was the poorest, while the plastic property and ductibility were the best, thus implying that the explosive has the best mechanical properties. Besides, it has the highest binding energy, so the stability and compatibility is the best. The cocrystal explosive has better detonation performance than HMX. In a word, the 1:1 cocrystal explosive is worth more attention and further research. This paper could offer some theoretical instructions and technological support, which could help in the design of the CL-20 cocrystal explosive.

In Silico Molecular Modeling and Docking Studies on Novel Mutants (E229V, H225P and D230C) of the Nucleotide-Binding Domain of Homo sapiens Hsp70

In this study, we explored the possibility of determining the synergistic interactions between nucleotide-binding domain (NBD) of Homo sapiens heat-shock 70 kDa protein (Hsp70) and E1A 32 kDa of adenovirus serotype 5 motif (PNLVP) in the efficiency of killing of tumor cells in cancer treatment. At present, the protein interaction between NBD and PNLVP motif is still unknown, but believed to enhance the rate of virus replication in tumor cells. Three mutant models (E229V, H225P and D230C) were built and simulated, and their interactions with PNLVP motif were studied. The PNLVP motif showed the binding energy and intermolecular energy values with the novel E229V mutant at -7.32 and -11.2 kcal/mol. The E229V mutant had the highest number of hydrogen bonds (7). Based on the root mean square deviation, root mean square fluctuation, hydrogen bonds, salt bridge, secondary structure, surface-accessible solvent area, potential energy and distance matrices analyses, it was proved that the E229V had the strongest and most stable interaction with the PNLVP motif among all the four protein-ligand complex structures. The knowledge of this protein-ligand complex model would help in designing Hsp70 structure-based drug for cancer therapy.

Method for measuring the unbinding energy of strongly-bound membrane-associated proteins

We describe a new method to measure the activation energy for unbinding (enthalpy ΔH*_u and free energy ΔG*_u) of a strongly-bound membrane-associated protein from a lipid membrane. It is based on measuring the rate of release of a liposome-bound protein during centrifugation on a sucrose gradient as a function of time and temperature. The method is used to determine ΔH*_u and ΔG*_u for the soluble dengue virus envelope protein (sE) strongly bound to 80:20 POPC:POPG liposomes at pH5.5. ΔH*_u is determined from the Arrhenius equation whereas ΔG*_u is determined by fitting the data to a model based on mean first passage time for escape from a potential well. The binding free energy ΔG_b of sE was also measured at the same pH for the initial, predominantly reversible, phase of binding to a 70:30 PC:PG lipid bilayer. The unbinding free energy (20±3kcal/mol, 20% PG) was found to be roughly three times the binding energy per monomer, (7.8±0.3kcal/mol for 30% PG, or est. 7.0kcal/mol for 20% PG). This is consistent with data showing that free sE is a monomer at pH5.5, but assembles into trimers after associating with membranes. This new method to determine unbinding energies should be useful to understand better the complex interactions of integral monotopic proteins and strongly-bound peripheral membrane proteins with lipid membranes.

The use of chlorogenic acid and its analogues as inhibitors: an investigation of the inhibition of sortase A of Staphylococcus aureus using molecular docking and dynamic simulation

OBJECTIVES

To use molecular docking and dynamic simulation to investigate the inhibitory action of chlorogenic acid (CHA) and its analogues against sortase A of Staphylococcus aureus.

RESULTS

Five novel, natural inhibitors with different activities were discovered for sortase A (SrtA). The inhibition mechanism of the novel inhibitors was consistent with the mechanism of CHA, which was reported previously by Wang et al. (Front Microbiol 6:1031, 2015). Based on structure-activity relationship analysis, the hydroxyl moiety (C1) of the inhibitors is critical in the catalytic region of SrtA, which could be confirmed by the calculation of the binding free energy between SrtA and the inhibitors.

CONCLUSIONS

The mechanism obtained by molecular dynamics simulation is thus useful for the development of novel, selective SrtA inhibitors.

Non-covalent carriage of anticancer agents by humanized antibody trastuzumab

This article explores the internalization and non-covalent carriage of small molecule anticancer agents like vinca alkaloids by humanized monoclonal antibody trastuzumab. Such carriage is marked by significant reduction in side effects and increased therapeutic value of these anticancer agents. This study is coherent with few clinical observations of enhanced efficiency of these anticancer agents when co-administered with therapeutic antibodies. This study will also serve as the foundation for screening a database of anticancer agents for possible compounds that may be co-delivered alongwith the antibody. Based on this study vincristine conformation inside antibody and its charge environment may be used as descriptors for screening purposes.

Structural Interactions of Curcumin Biotransformed Molecules with the N-Terminal Residues of Cytotoxic-Associated Gene A Protein Provide Insights into Suppression of Oncogenic Activities

Curcumin as a natural product has drawn considerable attention in recent years for its multiple pharmacological activities against various diseases, but more studies are required to understand the curcumin pharmacological action considering its low bioavailability. Though numerous reasons contribute to the low bioavailability of curcumin, one of the important reasons is associated with biotransformation of curcumin through either conjugation or reduction depending on curcumin administration route. The orally administered curcumin (CUR) is metabolised into curcumin glucuronidase (CUR-GLR) and curcumin sulphate by conjugation, whereas dihydroxycurcumin, tetrahydrocurcumin, and hexahydrocurcumin (HHC) are formed by reduction after intraperitoneal administration of curcumin. The main aim of the current study was to investigate the pharmacological properties of curcumin and its biotransformed molecules and its inhibitory potential against CagA (cytotoxic-associated gene A) oncoprotein of Helicobacter pylori. All lead molecules followed the Lipinski's five rules for biological activities, except CUR-GLR, whereas druglikeness scores were obtained for all molecules. Subsequently, molecular docking was employed to analyse the binding affinity of molecules with CagA. The docking studies revealed that CUR-GLR has highest binding affinity with CagA, whereas less interactive affinity was observed in HHC. From the virtual screening and docking studies, the current study suggests that the biotransformation of curcumin through conjugation has more potential for inhibition of oncogenic activities of CagA+ H. pylori than reduction.

Thermodynamics-based models of transcriptional regulation with gene sequence

Quantitative models of gene regulatory activity have the potential to improve our mechanistic understanding of transcriptional regulation. However, the few models available today have been based on simplistic assumptions about the sequences being modeled or heuristic approximations of the underlying regulatory mechanisms. In this work, we have developed a thermodynamics-based model to predict gene expression driven by any DNA sequence. The proposed model relies on a continuous time, differential equation description of transcriptional dynamics. The sequence features of the promoter are exploited to derive the binding affinity which is derived based on statistical molecular thermodynamics. Experimental results show that the proposed model can effectively identify the activity levels of transcription factors and the regulatory parameters. Comparing with the previous models, the proposed model can reveal more biological sense.

Novel integrated approach of adsorption and photo-oxidation using Ag-TiO2/PU for bioaerosol removal under visible light

We investigated a novel approach by synthesizing an integrated material, which could act as both adsorbent and photocatalytic material, for bioaerosol purification under visible light conditions. Ag was used as a dopant agent to enhance photocatalytic activity of TiO₂, leading to high photocatalytic activity of the doped TiO₂ even under visible light. Under visible light, the doped TiO₂ photocatalyst could produce oxy radicals, oxidative agents, that participate in oxidation reactions to decompose important organic components of bacteria, leading to death or removal of bacteria from an aerosol. Adsorption property was integrated into the enhanced TiO₂ photocatalyst by using polyurethane (PU), a honeycomb structure material, as a substrate for coating process of the doped TiO₂. Three materials including pristine PU, TiO₂ coating on PU (TiO₂/PU), and Ag-doped TiO₂ coating on PU (Ag-TiO₂/PU) were used to remove Escherichia coli in an aerosol under visible light. Under dark conditions, the removal capacities of E. coli in the aerosol by PU, TiO₂/PU, and Ag-TiO₂/PU were 1.2 × 10⁵, 2.7 × 10⁵, and 6.2 × 10⁵ (CFU/cm³), respectively. Under visible light irradiation, the removal capacities of E. coli in an aerosol by PU, TiO₂/PU, and Ag-TiO₂/PU were 1.2 × 10⁵, 2.7 × 10⁵, and 1.8 × 10⁶ (CFU/cm³), respectively. The improvement of the removal capacity by TiO₂/PU and Ag-TiO₂/PU, versus PU, is due to adsorption alone and the combination of adsorption plus photocatalytic activity, respectively.

Molecular design and synthesis of certain new quinoline derivatives having potential anticancer activity

EGFR, which plays a vital role as a regulator of cell growth, is one of the intensely studied TK targets of anticancer inhibitors. The most two common anticancer inhibitors are anilinoquiazolines and anilinoquinolines that inhibit EGFR kinase intracellularly. The present investigation dealt with design (pharmacophore, docking and binding energy) and synthesis of a new series of 4-anilinoquinoline-3-carboxamide derivatives as potential anticancer agents targeting EGFR. All the newly synthesized compounds were screened for their anticancer activity against MCF-7 and compounds 4f, 7a and 7b showed significant activity with IC50 values 13.96 μM, 2.16 μM and 3.46 μM, respectively. Most of the synthesized compounds were subjected to enzyme assay (EGFR TK) for measuring their inhibitory activity with the determination of IC50 values and the preliminary results revealed that compound 7b, which had potent inhibitory activity in tumor growth and had potent activity on the EGFR TK enzyme with 67% inhibition compared to ATP would be a potential anticancer agent.

Tissue mechanics and adhesion during embryo development

During development cells interact mechanically with their microenvironment through cell-cell and cell-matrix adhesions. Many proteins involved in these adhesions serve both mechanical and signaling roles. In this review we will focus on the mechanical roles of these proteins and their complexes in transmitting force or stress from cell to cell or from cell to the extracellular matrix. As forces operate against tissues they establish tissue architecture, extracellular matrix assembly, and pattern cell shapes. As tissues become more established, adhesions play a major role integrating cells with the mechanics of their local environment. Adhesions may serve as both a molecular-specific glue, holding defined populations of cells together, and as a lubricant, allowing tissues to slide past one another. We review the biophysical principles and experimental tools used to study adhesion so that we may aid efforts to understand how adhesions guide these movements and integrate their signaling functions with mechanical function. As we conclude we review efforts to develop predictive models of adhesion that can be used to interpret experiments and guide future efforts to control and direct the process of tissue self-assembly during development.

Vibrational spectra, electronic absorption, nonlinear optical properties, evaluation of bonding, chemical reactivity and thermodynamic properties of ethyl 4-(1-(2-(hydrazinecarbonothioyl)hydrazono)ethyl)-3,5-dimethyl-1H-pyrrole-2-carboxylate molecule by ab initio HF and density functional methods

In this work, detailed vibrational spectral analysis of ethyl 4-(1-(2-(hydrazinecarbonothioyl)hydrazono)ethyl)-3,5-dimethyl-1H-pyrrole-2-carboxylate (EHCHEDPC) molecule has been carried out using FT-IR spectroscopy and potential energy distribution (PED). Theoretical calculations were performed by ab initio RHF and density functional theory (DFT) method, using 6-31G(d,p) and 6-311+G(d,p) basis sets. The other carried outwork cover: structural, thermodynamic properties, electronic transitions, bonding, multiple interaction, chemical reactivity and hyperpolarizability analysis. The results of the calculation were applied to the simulated spectra of (EHCHEDPC), which show excellent agreement with observed spectra. The vibrational analysis shows red shift in both group, the proton donor (pyrrole N-H) and proton acceptor (C=O of ester) indicating the presence of intermolecular hydrogen bonding. Time dependent density functional theory (TD-DFT) has been used to find electronic excitations and their nature. The results of natural bond orbital (NBOs) analysis show the charges transfer and delocalization in various intra- and intermolecular interactions. The binding energy of intermolecular multiple interactions is calculated to be 12.54 kcal mol(-1) using QTAIM calculation. The electronic descriptors analyses reveal the investigated molecule used as precursor for heterocyclic derivatives synthesis. First hyperpolarizability (β0) has been computed to evaluate non-linear optical (NLO) response.

Design, synthesis and molecular docking of substituted 3-hydrazinyl-3-oxo-propanamides as anti-tubercular agents

Based on the anti-mycobacterial activity of various acid hydrazides, a series of substituted 3-hydrazinyl-3-oxo-propanamides has been designed. The target compounds have been synthesized from diethylmalonate using substituted amines and hydrazine hydrate in ethanol. Computational studies and anti-tubercular activity screenings were undertaken to test their inhibitory effect on protein kinase PknB from Mycobacterium tuberculosis. Binding poses of the compounds were energetically favorable and showed good interactions with active site residues. Designed molecules obey the Lipinski's rule of 5 and gave moderate to good drug likeness score. Among the sixteen compounds (1-16) taken for in silico and in vitro studies, 3 compounds (11, 12 and 15) have shown good binding energies along with exhibiting good anti-tubercular activity and thus may be considered as a good inhibitors of PknB.

Effect of electric and magnetic fields on impurity binding energy in zinc-blend symmetric InGaN/GaN multiple quantum dots

The binding energy of ground state for hydrogenic impurity in multiple quantum dots is calculated in the framework of effective-mass approximation and using a variational method. It is shown that the binding energy is a function of the size of dots, impurity position and external fields strength. The binding energy has a maximum value when the impurity is located on the center of dots and decreases for other impurity positions. The external electric and magnetic fields change the magnitude and the position of peaks. PACS Codes 73.20.D; 71.21.La; 71.55.Eq.

Structural and dynamic investigation of bovine folate receptor alpha (FOLR1), and role of ultra-high temperature processing on conformational and thermodynamic characteristics of FOLR1-folate complex

The folate receptor alpha (FOLR1) present in milk has widely been studied to investigate the effects of pasteurization, ultra-high temperature (UHT) processing and fermentation on net folate concentration. However, the folate binding mechanism with FOLR1, and effect of temperature on FOLR1-folate complex is poorly explored till now in bovine milk which is a chief resource of folate. Despite of enormous importance of folic acid and the routine intake of bovine milk, folic acid deficiency diseases are common in human race. To understand the folate deficiency in milk after processing, in absence of experimental structure, 3D model of bovine FOLR1 (bvFOLR1) was built followed by 40ns molecular dynamics (MD) simulation. The folate and its derivatives binding sites in bvFOLR1 were anticipated by molecular docking using AutoDock 4.2. Essential MD studies suggested the presence of a longer signal peptide (22 residues) and a short propeptide (7 residues) at the C-terminus that may cleaved during post-translational modification. MD analysis of bvFOLR1-folate complex at 298, 323, 353, 373 and 408K followed by binding energy (BE) calculation showed maximum binding affinity at ∼353K. However, at 373K and UHT (408K), the folate BE is significantly decreased with substantial conformational alteration. Heating at UHT followed by cooling within 298-408K range demoed no structural reformation with temperature reduction, and the folate was displaced from the active site. This study presented the disintegration of folate from bvFOLR1 during high temperature processing and revealed a lower folate concentration in UHT milk and dairy products.

Molecular modeling studies and comparative analysis on structurally similar HTLV and HIV protease using HIV-PR inhibitors

Retroviruses are most perilous viral family, which cause much damage to the Homo sapiens. HTLV-1 mechanism found to more similar with HIV-1 and both retroviruses are causative agents of severe and fatal diseases including adult T-cell leukemia (ATL) and the acquired immune deficiency syndrome (AIDS). Both viruses code for a protease (PR) that is essential for replication and therefore represents a key target for drugs interfering with viral infection. In this work, the comparative study of HIV-1 and HTLV-1 PR enzymes through sequence and structural analysis is reported along with approved drugs of HIV-PR. Conformation of each HIV PR drugs have been examined with different parameters of interactions and energy scorings parameters. MD simulations with respect to timescale event of 20 ns favors that, few HIV-PR inhibitors can be more active inside the HTLV-1 PR binding pocket. Overall results suggest that, some of HIV inhibitors like Tipranavir, Indinavir, Darunavir and Amprenavir are having good energy levels with HTLV-1. Due to absence of interactions with MET37, here we report that derivatives of these compounds can be much better inhibitors for targeting HTLV-1 proteolytic activity.

Structures and Stabilities of the Metal Doped Gold Nano-Clusters: M@Au10 (M = W, Mo, Ru, Co)

The structures and stabilities of a series of endohedral gold clusters containing ten gold atoms M@Au₁₀ (M = W, Mo, Ru, Co) have been determined using density functional theory. The gradient-corrected functional BP86, the Tao-Perdew-Staroverov-Scuseria TPSS meta-GGA functional, and the hybrid density functionals B3LYP and PBE1PBE were employed to calculate the structures, binding energies, adiabatic ionization potentials, and adiabatic electron affinities for these clusters. The LanL2DZ effective core potentials and the corresponding valence basis sets were employed. The M@Au₁₀ (M = W, Mo, Ru, Co) clusters have higher binding energies than an empty Au₁₀ cluster. In addition, the large HOMO-LUMO gaps suggest that the M@Au₁₀ (M = W, Mo, Ru, Co) clusters are all likely to be stable chemically. The ionization potentials and electron affinities for these clusters are very high, and the W@Au₁₀ and Mo@Au₁₀ clusters have electron affinities similar to the super-halogen Al₁₃.

Virtual Screening Analysis and In-vitro Xanthine Oxidase Inhibitory Activity of Some Commercially Available Flavonoids

Allopurinol, the xanthine oxidase inhibitor, is the only drug available for the treatment of gout. We examined the xanthine oxidase inhibitory activity of some commercially available flavonoids such asepigallocatechin, acacatechin, myricetin, naringenin, daidzein and glycitein by virtual screening and in-vitro studies. The interacting residues within the complex model and their contact types were identified. The virtual screening analysis were carried out using AutoDock 4.2 and in-vitro xanthine oxidase inhibitory activity was carried out using xanthine as the substrate. In addition, enzyme kinetics was performed using LineweaverBurkplot analysis. Allopurinol, a known xanthine oxidase inhibitor was used as the standard. The docking energy ofglycitein was found to be -8.49 kcal/mol which was less than that of the standard (-4.47 kcal/ mol). All the selected flavonoids were found to exhibit lower binding energy (-8.08 to -6.03 kcal/ mol) than allopurinol. The docking results confirm that flavonoids showed greater inhibition of xanthine oxidase due to their active binding sites and lesser binding energies compared to allopurinol. This may be attributed to the presence of benzopyran ring in the flavonoids. In the xanthine oxidase assay, IC50 value of glycitein was found to be 12±0.86 μg/mL, whereas that of allopurinol was 24±0.28 μg/mL. All the remaining compounds exhibited IC50 values ranging between 22±0.64 to 62±1.18 μg/mL. In the enzyme kinetic studies, flavonoids showed competitive type of enzyme inhibition. It can be concluded that flavonoids could be a promising remedy for the treatment of gout and related inflammatory disorders. Further in-vivo studies are required to develop potential compounds with lesser side effects.

Protein-ligand interaction studies of retinol-binding protein 3 with herbal molecules using AutoDock for the management of Eales' disease

Eales' disease is an idiopathic retinal vasculitis of the eye. The disease is predominantly characterized by recurrent vitreous hemorrhage. Interphotoreceptor retinol-binding protein 3 plays a significant role in the etiopathogenesis of this condition. It transports retinoids between the retinal pigment epithelium and the photoreceptors; hence, this protein is a potential target for docking studies. In silico data reveal that herbal molecules interact with regulatory domains of interphotoreceptor retinol-binding protein 3 (IRBP-3), resulting into significant docking score and also forms H-bond and several hydrophobic interactions between active residues of IRBP-3. These interactions between the active residues may lead to significant conformational change in that particular portion of the protein. This efficacy and suitability of ligand was determined on the basis of binding energy calculations. Ginkgolide showed minimum binding energy calculations among selected 10 other natural ligands. This fact of virtual screening for potential ligand can give new insights toward the therapeutic intonations and alterations toward the advances in treatment for Eales' disease.