Predicting liposome formulations by the integrated machine learning and molecular modeling approaches

Liposome is one of the most widely used carriers for drug delivery because of the great biocompatibility and biodegradability.Due to the complex formulation components and preparation process,formulation screening mostly relies on trial-and-error process with low efficiency.Here liposome formulation prediction models have been built by machine learning(ML)approaches.The important parameters of liposomes,including size,polydispersity index(PDI),zeta potential and encapsulation,are predicted individually by optimal ML algorithm,while the formulation features are also ranked to provide important guidance for formulation design.The analysis of key parameter reveals that drug molecules with logS[-3,-6],molecular complexity[500,1000]and XLogP3(≥2)are priority for preparing liposome with higher encapsulation.In addition,naproxen(NAP)and palmatine HCl(PAL)represented the insoluble and water-soluble molecules are prepared as liposome formulations to validate prediction ability.The consistency between predicted and experimental value verifies the satisfied accuracy of ML models.As the drug properties are critical for liposome particles,the molecular interactions and dynamics of NAP and PAL liposome are further investigated by coarse-grained molecular dynamics simulations.The modeling structure reveals that NAP molecules could distribute into lipid layer,while most PAL molecules aggregate in the inner aqueous phase of liposome.The completely different physical state of NAP and PAL confirms the importance of drug properties for liposome formulations.In summary,the general prediction models are built to predict liposome formulations,and the impacts of key factors are analyzed by combing ML with molecular modeling.The availability and rationality of these intelligent prediction systems have been proved in this study,which could be applied for liposome formulation development in the future.

A SARS-CoV-2 neutralizing antibody discovery by single cell sequencing and molecular modeling

Although vaccines have been developed,mutations of SARS-CoV-2,especially the dominant B.1.617.2(delta)and B.1.529(omicron)strains with more than 30 mutations on their spike protein,have caused a significant decline in prophylaxis,calling for the need for drug improvement.Antibodies are drugs preferentially used in infectious diseases and are easy to get from immunized organisms.The current study combined molecular modeling and single memory B cell sequencing to assess candidate sequences before experiments,providing a strategy for the fabrication of SARS-CoV-2 neutralizing antibodies.A total of 128 sequences were obtained after sequencing 196 memory B cells,and 42 sequences were left after merging extremely similar ones and discarding incomplete ones,followed by homology modeling of the antibody variable region.Thirteen candidate sequences were expressed,of which three were tested positive for receptor binding domain recognition but only one was confirmed as having broad neutralization against several SARS-CoV-2 variants.The current study successfully obtained a SARS-CoV-2 antibody with broad neutralizing abilities and provided a strategy for antibody development in emerging infectious diseases using single memory B cell BCR sequencing and computer assistance in antibody fabrication.

Synthesis, Spectroscopic, Molecular Modeling and Anti-Fungal Studies of Some Divalent Metal Complexes of 4-Hydroxyacetophenone Isonicotinoyl Hydrazone

A novel ligand N-4-hydroxyacetophenone isonicotinoyl hydrazone and its manganese(II) and nickel(II) metal complexes have been synthesized. The synthesized Schiff base and its metal complexes have been characterized by physical state determination, melting point and solubility measurements in different solvents, infrared, proton nuclear magnetic resonance, mass spectrometric and powder X-ray spectroscopic techniques. The thermal properties of the prepared compounds were obtained from TG/DTG measurements. On the basis of the analytical techniques, the ligand was found to be bidentate in nature coordinating to the metal ions through the azomethine nitrogen and carbonyl oxygen atoms leading to distorted octahedral geometries of the metal complexes which were modeled using MM2 force field. The ligand and its metal(II) complexes were evaluated for antifungal activity against Aspergillus fumigatus, Aspergillus niger, Candida albicans and Rhizopus stolonifera. The antifungal evaluation results revealed an enhanced activity upon coordination of the ligand with the metal(II) ions. The activity of the metal complex to the tested fungal strains was in the order Ni(II) > Mn(II).

Study of the Influence of Nanoparticles on the Molecular Model of an Ideal Fluid

In the article a molecular model of oil with nanoparticles on the basis of the model of ideal fluid is considered. It is assumed that the molecular model of the oil can be represented as a homogenous distribution of identical molecules in space. It is assumed that the central interaction between the oil molecules and nanoparticles, results in a change of the model parameters. It is shown that for an ideal fluid the effect of nanoparticles is reduced to a change of the coefficient at the pressure.

Molecular Modeling and Synthesis of Ethyl Benzyl Carbamates as Possible Ixodicide Activity

Carbamates are molecules that have different types of biological activities and provide a particular chemical control against ticks. The new structures of the proposed compounds were optimized and synthetized respectively, through a molecular model using the methods:PM3, HF and DFT applying the B3LYP functional, with the basis 6-31+G(d) and 6-311+G(d,p), BVP86 and PBEPBE with 6-31+G(d) and the vibrational frequencies computed. These calculated frequencies were compared with the experimental ones to determine the most accurate level of theory for the prediction of vibrational frequencies of the compounds. The best results were obtained through HF/631+G(d). Additionally, we report a modification to obtain this type of compounds, and based on the amino-dehalogenation of ethyl chloroformate, different benzyl ethyl carbamates were synthesized modifying the base molecule. The performances obtained were compared to others already reported. The methodology used allowed us to synthesize new carbamates using benzylamine derivatives through a modification on the basic catalysis of the addition-elimination reaction.

Thermal,infrared spectroscopy and molecular modeling characterization of bone:An insight in the apatite-collagen type I interaction

An insight into the interaction of collagen type I with apatite in bone tissue was performed by using differential scanning calorimetry, Fourier transform infrared spectroscopy, and molecular modeling. Scanning electron microscopy shows that bone organic content incinerate gradually through the different temperatures studied. We suggest that the amide regions of the type I collagen molecule (mainly C=O groups of the peptide bonds) will be important in the control of the interactions with the apatite from bone. The amide I infrared bands of the collagen type I change when interacting to apatite, what might confirm our assumption. Bone tissue results in a loss of thermal stability compared to the collagen studied apart, as a consequence of the degradation and further combustion of the collagen in contact with the apatite microcrystals in bone. The thermal behavior of bone is very distinctive. Its main typical combustion temperature is at 360°C with a shoulder at 550°C compared to the thermal behavior of collagen, with the mean combustion peak at ca. 500°C. Our studies with molecular mechanics (MM+ force field) showed different interaction energies of the collagen-like molecule and different models of the apatite crystal planes. We used models of the apatite (100) and (001) planes;additional two planes (001) were explored with phosphate-rich and calcium-rich faces;an energetic preference was found in the latter case. We preliminary conclude that the peptide bond of collagen type I is modified when the molecule interacts with the apatite, producing a decrease in the main peak from ca. 500°C in collagen, up to 350°C in bone. The combustion might be related to collagen type I, as the ΔH energies present only small variations between mineralized and non-mineralized samples. The data obtained here give a molecular perspective into the structural properties of bone and the change in collagen properties caused by the interaction with the apatite. Our study can be useful to understand the biological synthesis of minerals as well as the organic-inorganic interaction and the synthesis of apatite implant materials.

Inclusion complexes of cefuroxime axetil with β-cyclodextrin:Physicochemical characterization, molecular modeling and effect of Larginine on complexation

The inclusion complexes of poorly water-soluble cephalosporin, cefuroxime axetil(CFA), were prepared with β-cyclodextrin(βCD) with or without addition of L-arginine(ARG) to improve its physicochemical properties. We also investigated the effect of ARG on complexation efficiency(CE) of βCD towards CFA in an aqueous medium through phase solubility behaviour according to Higuchi and Connors. Although phase solubility studies showed AL(linear) type of solubility curve in presence and absence of ARG, the CE and association constant(Ks) of βCD towards CFA were significantly promoted in presence of ARG,justifying its use as a ternary component. The solid systems of CFA with βCD were obtained by spray drying technique with or without incorporation of ARG and characterized by differential scanning calorimetry(DSC), X-ray powder diffractometry(XRPD), scanning electron microscopy(SEM), and saturation solubility and dissolution studies. The molecular modeling studies provided a better insight into geometry and inclusion mode of CFA inside βCD cavity. The solubility and dissolution rate of CFA were significantly improved upon complexation with βCD as compared to CFA alone. However, ternary system incorporated with ARG performed better than binary system in physicochemical evaluation. In conclusion, ARG could be exploited as a ternary component to improve the physicochemical properties of CFA via βCD complexation.

Characterization of Gallic Acid Interaction with Human Serum Albumin by Spectral and Molecular Modeling Methods

The binding of drugs with human serum albumin(HSA) is a crucial factor influencing the distribution and bioactivity of drugs in the body.To understand the action mechanisms between gallic acid(GA,3,4,5-trihydroxybenzoic acid) and HSA,the binding of GA with HSA was investigated by a combined experimental and computational approach.The fluorescence properties of HSA and the binding parameters of GA collectively indicate that the binding is characterized by static quenching mechanism at one high affinity binding site.According to the estimated molecular distance between the donor(HSA) and the acceptor(GA),the binding is related to the fluorescence resonance energy transfer.As indicated by the thermodynamic parameters,hydrophobic interaction plays a major role in the GA-HSA complex.Further,the experimental results reveal that GA is bound in the large hydrophobic cavity of subdomain IIA in the site I of HSA,which is well approved by molecular docking.

Investigation of molecular aggregation mechanism of glipizide/cyclodextrin complexation by combined experimental and molecular modeling approaches

Cyclodextrin complexation is a wise strategy to enhance aqueous solubility of waterinsoluble drugs.However,the aggregation mechanism of drug-cyclodextrin complexes is still unclear.This research aimed to investigate the molecular aggregation mechanism of glipizide/cyclodextrin complexation by the combination of experimental and modeling methods.Binding free energies between glipizide and cyclodextrins from modeling calculations were higher than those by the phase solubility diagram method.Both experimental and modeling results showed that methylated-β-cyclodextrin exhibited the best solubilizing capability to glipizide.Size-measurement results confirmed the aggregation between glipizide and all four cyclodextrins in high concentrations.Glipizide/γ-cyclodextrin and glipizide/β-cyclodextrin complexes showed stronger aggregation trend than HP-β-cyclodextrin and methylated-β-cyclodextrin.The substituted groups in the rim of HP-β-cyclodextrin and methylated-β-cyclodextrin lead to weak aggregation.This research provided us a clear molecular mechanism of glipizide/cyclodextrin complexation and aggregation.This research will also benefit the formulation development of cyclodextrin solubilization.

MOLECULAR MODEL AND FLOW CALCULATION:Ⅰ.THE NUMERICAL SOLUTIONS TO MULTIBEAD-ROD MODELS INHOMOGENEOUS FLOWS

The Galerkin method is used to solve the diffusion equation of the distribution function inconfigurational space for a multibead-rod model,and the dimensionless components of the extra stresstensor are then calculated by means of the expression of ensemble average.The material functionsfor steady-state shear flow and uniaxial flow and the mechanical properties of rigid-rodlike molecule suspen-sions in superposed flows are obtained numerically.The results indicate that it is promising to employ themu ltibead-rod models without the constitutive equation in numerical simulations of flows of suspensions.

MOLECULAR MODELS AND FLOW CALCULATIONS Ⅱ.SIMULATION OF STEADY PLANAR FLOW

A multibead-rod model is used to replace the constitutive equation of continuum me-chanics in solving flow problems of steady-state planar flows of rigid-rodlike molecular suspensions.Thegoverning equations then constitute a set of differential equations of the elliptic type,which is more ame-nable to numerical treatment than those of the mixed type.The conservation equations of the flowfields are solved by the boundary element method with linear boundary elements in physical space and thediffusion equation of the distribution function is solved separately by the Galerkin method in phase space.The solution to the flow problem is obtained when the convergence of the iteration procedure betweenthe two spaces has been reached.Several numerical examples are shown and the interesting features ofthe present method are discussed in this paper.

Host-guest interaction of β-cyclodextrin with isomeric ursolic acid and oleanolic acid:physicochemical characterization and molecular modeling study

Ursolic acid(UA) and oleanolic acid(OA) are insoluble drugs. The objective of this study was to encapsulate them into β-cyclodextrin(β-CD) and compare the solubility and intermolecular force of β-CD with the two isomeric triterpenic acids. The host-guest interaction was explored in liquid and solid state by ultraviolet-visible absorption,~1H NMR, phase solubility analysis, and differential scanning calorimetry, X-ray powder diffractometry, and molecular modeling studies. Both experimental and theoretical studies revealed that β-CD formed 1: 1 water soluble inclusion complexes and the complexation process was naturally favorable. In addition, the overall results suggested that ring E with a carboxyl group of the drug was encapsulated into the hydrophobic CD nanocavity. Therefore, a clear different inclusion behavior was observed, and UA exhibited better affinity to β-CD compared with OA in various media due to little steric interference, which was beneficial to form stable inclusion complex with β-CD and increase its water solubility effectively.

Expression,purification and molecular modeling of iron-containing superoxide dismutase from Acidithiobacillus ferrooxidans

从 Acidithiobacillus ferrooxidans 的 superoxide dismutase (草皮) 可以在它的忍耐起一个重要作用到 bioleaching 的极其有毒、氧化的环境。这基因在 Escherichia 被克隆然后成功地表示了 coli。表示蛋白质被一步舞亲密关系层析最后净化到同质并且观察了根据 SDS 页和 MALDI-TOF-MS 更暗淡。金属内容决心和 recombinant 蛋白质的光系列结果证实蛋白质是包含铁的 superoxide dismutase。为蛋白质的分子的建模表明铁原子被 His26， His75， Asp158 和 His162 绑扎。

The LBFGS quasi-Newtonian method for molecular modeling prion AGAAAAGA amyloid fibrils

Experimental X-ray crystallography, NMR (Nuclear Magnetic Resonance) spectroscopy, dual polarization interferometry, etc. are indeed very powerful tools to determine the 3-Dimensional structure of a protein (including the membrane protein);theoretical mathematical and physical computational approaches can also allow us to obtain a description of the protein 3D structure at a submicroscopic level for some unstable, noncrystalline and insoluble proteins. X-ray crystallography finds the X-ray final structure of a protein, which usually need refinements using theoretical protocols in order to produce a better structure. This means theoretical methods are also important in determinations of protein structures. Optimization is always needed in the computer-aided drug design, structure-based drug design, molecular dynamics, and quantum and molecular mechanics. This paper introduces some optimization algorithms used in these research fields and presents a new theoretical computational method—an improved LBFGS Quasi-Newtonian mathematical optimization method—to produce 3D structures of prion AGAAAAGA amyloid fibrils (which are unstable, noncrystalline and insoluble), from the potential energy minimization point of view. Because the NMR or X-ray structure of the hydrophobic region AGAAAAGA of prion proteins has not yet been determined, the model constructed by this paper can be used as a reference for experimental studies on this region, and may be useful in furthering the goals of medicinal chemistry in this field.

Inclusion Property and Molecular Modeling of Calix[4]arene Derivatives

The inclusion properties of two calix[4]arene derivatives 5,11,17,23 tetra tert butyl 25, 27 bis (isopropyl carbamoyl methoxy) 26,28 diundecenyloxy calix[4]arene (C[4]A) and 25,27 dibutoxy 5,11,17,23 tetra tert butyl 26,28 diundecenyloxy calix[4]arene (C[4]B) were studied by gas chromatographic method. It was found that C[4]A could form inclusion complexes with benzene, toluene, methanol and ethanol while C[4]B could only form inclusion complex with methanol, which might be due to the different conformations of C[4]A and C[4]B. Molecular modeling showed that CH/π and OH/π interactions played important roles in the forming of inclusion complexes.

Prediction of antigenic determinants of trichosanthin by molecular modeling

The antigenic determinants of trichosanthin were predicted by molecular modeling. First, the threedimensional structure model of the antigen-binding fragment of anti-trichosanthin immunoglobulin E was built on the basis of its amino-acid sequence and the known three-dimensional structure of an antibody with similar sequence. Secondly, the preferable antigen-antibody interactions were obtained based on the known three-dimensional structure of trichosanthin and of the hypervariable regions of anti-trichosanthin immunoglobulin E. Two regions in the molecular surface of trichosanthin were found to form extensive interactions with the hypervariable regions of the antibody and have been predicted to be the possible antigenic determinants: one is composed of two polypeptide segments, Ile201-Glu210 and Ile225-Asp229, which are close to each other in the three-dimensional structure; and the other is the segment Lys173-Thr178. The former region seems to be the more reasonable antigenic determinant than the latter one.

Structural analysis and molecular modeling of twoantitrichosanthin IgE clones from phage antibody library

Recently we constructed a murine IgE phage surfacedisplay library and screened out two IgE (Fab) cloneswith specific binding activity to Trichosanthin (TCS). Inthis work, the Vε and Vκ genes of the two clones weresequenced and their putative germline gene usages werestudied. On the basis of the known 3D structure of Trichosanthin and antibody, molecular modeling was carriedout to study the antigen-antibody interaction. The possible antigenic determinant sites on the surface of TCSrecognized by both the clones were analyzed, and the reaction forces between TCS and two Fab fragments werealso analyzed respectively.

Efficient molecular model for squeeze-film damping in rarefied air

Based on the energy transfer model(ETM) proposed by Bao et al.and the Monte Carlo(MC) model proposed by Hutcherson and Ye, this paper proposes an efficient molecular model(MC-S) for squeeze-film damping(SQFD) in rarefied air by releasing the assumption of constant molecular velocity in the gap.Compared with the experiment data, the MC-S model is more efficient than the MC model and more accurate than ETM.Besides, by using the MC-S model, the feasibility of the empirical model proposed by Sumali for SQFD of different plate sizes is discussed.It is proved that, for various plate sizes, the accuracy of the empirical model is relatively high.At last, the SQFD of various vibration frequencies is discussed, and it shows that, for low vibration frequency, the MC-S model is reduced to ETM.

Molecular modeling study of the effect of base methylation on internal interactions and motions in DNA and implication to B-Z conformation change

Methylation in the bases of DNA is known to induce B-Z conformation change. In this work, molecular mechanics and normal mode analysis are used to probe how certain methylation affects the internal interactions and thermodynamic motions in the DNA double helixes in both B and Z conformations, and its implication to B-Z conformation change. By molecular modeling with Insight II, two cases involving cytosine C5 and guanine C8 methylation on both B and Z-form DNA duplex d(CGCGCG)2 are studied in comparison with the corresponding unmethylated duplexes. The internal interaction energies computed based on a molecular mechanics force field and the entropies due to internal motions computed according to a normal mode analysis are in fare agreement with respective observed thermodynamic quantities. The analysis on the computed individual energy terms suggests that the observed B-Z conformation change induced by methylation is primarily driven by enthalpic factors. A combination of changes in Van der Waals interaction, electrostatic interaction and hydrogen bonding likely contributes to the change of enthalpy that favors Z-conformation in the methylated states.

Molecular Modeling and Synthesis of New Heterocyclic Compounds Containing Pyrazole as Anticancer Drugs

Several modifications in CA-4 were reported in literature for the development of various tubulin inhibitors. In our study, twenty-two newly synthesized heterocyclic derivatives of Combretastatin A-4 (CA-4) have been tested for their cytotoxic effect on four different types of cells with malignant behavior using CA-4 as a positive control. Compounds 5b, 15 and 16 showed the foremost potent antiproliferative activities as compared to CA-4 with IC50 starting from 6.9 to 13.7 μM. Molecular docking was performed with the crystal structure of tubulin employing a potent tubulin inhibitor CA-4 as a parent molecule. Molecular study advised that 5b, 15, 16 and 17 are promising tubulin inhibitors.