Advances in applications of molecular dynamics simulation techniques to the research of self-assembled nano-drug delivery systems / 药学学报

Molecular dynamics simulation technology relies on Newtonian mechanics to simulate the motion of molecular system of the real system by computer simulation. It has been used in the research of self-assembly processes illustration and macroscopic performance prediction of self-assembly nano-drug delivery systems (NDDS) in recent years, which contributes to the facilitation and accurate design of preparations. In this review, the definitions, catalogues, and the modules of molecular dynamics simulation techniques are introduced, and the current status of their applications are summarized in the acquisition and analysis of microscale information, such as particle size, morphology, the formation of microdomains, and molecule distribution of the self-assembly NDDS and the prediction of their macroscale performances, including stability, drug loading capacity, drug release kinetics and transmembrane properties. Moreover, the existing applications of the molecular dynamic simulation technology in the formulation prediction of self-assembled NDDS were also summarized. It is expected that the new strategies will promote the prediction of NDDS formulation and lay a theoretical foundation for an appropriate approach in NDDS studies and a reference for the wider application of molecular dynamics simulation technology in pharmaceutics.

Fosfatase Cdc25B: Interações transientes intramoleculares e complexação com pequenos ligantes / Cdc25B phosphatase: Transient intramolecular interactions and small molecules complexation

Proteínas tirosina-fosfatase (PTPs) possuem papel fundamental na regulação da transdução de sinais e estão envolvidas em diversos processos fundamentais do ciclo celular. As Cdc25 (Cell Division Cycle 25) são fosfatases duais encontradas em todos os organismos eucarióticos e atuam em checkpoints do ciclo celular, permitindo ou inibindo o prosseguimento deste. Este grupo de proteínas pertence à classe de PTPs com atividade baseada em cisteína, apresenta domínio catalítico altamente conservado assim como o motivo catalítico, P-loop. Devido sua função, as Cdc25 são consideradas possíveis alvos terapêuticos para tratamento de câncer e sua interação com pequenas moléculas e inibidores tem sido investigada de forma que análises estruturais e de ligação das Cdc25 com inibidores podem elucidar aspectos importantes do mecanismo de ação destes além de direcionar para o desenho racional de fármacos. Interações cátion-π são interações intra ou intermoleculares não-covalentes que ocorrem entre uma espécie química catiônica, como o grupo guanidino de argininas, e uma das faces de um sistema π rico em elétrons, como dos anéis indólicos de triptofanos. Apesar de pouco discutidas na literatura, quando em comparação às interações não-covalentes mais convencionais, do ponto de vista energético as interações cátion-π são tão importantes na estruturação de proteínas quanto às ligações de hidrogênio ou pontes salinas. De fato estas interações são observadas com frequência em estruturas proteicas resolvidas. O domínio catalítico da Cdc25B possui diversas argininas expostas em sua superfície e um único resíduo de triptofano localizado na região C-terminal flexível, muito próximo do sítio catalítico da proteína. A flexibilidade de proteínas ou de regiões proteicas apresenta importante papel no reconhecimento entre biomoléculas participantes de vias de sinalização e tem sido muito estudada atualmente. Aqui, simulações de dinâmica molecular, experimentos de 1H-15N HSQC RMN, ensaios de cinética de inibição e de ancoragem molecular, evidenciam a existência de contatos cátion-π transientes na superfície de um importante membro da família das Cdc25, a Cdc25B, e de sítios de interação entre inibidores testados e a proteína com destaque a sítios na proximidades do P-loop, região próxima ao C-terminal desordenado, onde se demonstra estabilidade da interação com os pequenos ligantes

Protein tyrosine phosphatase (PTPs) play a fundamental role in the regulation of signal transduction and are involved in several fundamental processes of the cell cycle. Cdc25 (Cell Division Cycle 25) are dual phosphatases found in all eukaryotic organisms and act at checkpoints of the cell cycle, allowing or inhibiting its progression. This group of proteins belongs to the class of PTPs with cysteine-based activity, presenting a highly conserved catalytic domain as well as the catalytic motif, P-loop. Due to their function, Cdc25 are considered possible therapeutic targets for cancer treatment and their interaction with small molecules and inhibitors has been investigated so that structural and binding analyzes of Cdc25 with inhibitors can elucidate important aspects of their mechanism of action besides directing to rational drug design. Cation-π interactions are non-covalent intra- or intermolecular interactions that occur between a cationic chemical species, such as the guanidino group of arginines, and one of the faces of an electron-rich system, such as the indole rings of tryptophans. Although little discussed in the literature, when compared to more conventional non-covalent interactions, from the energetic point of view, cation-π interactions are as important in the structuring of proteins as hydrogen bonds or salt bridges. In fact, these interactions are frequently observed in solved protein structures. The catalytic domain of Cdc25B has several arginines exposed on its surface and a single tryptophan residue located in the flexible C-terminal region, very close to the catalytic site of the protein. The flexibility of proteins or protein regions plays an important role in the recognition between biomolecules participating in signaling pathways and has been extensively studied today. Here, molecular dynamics simulations, 1H-15N HSQC NMR experiments, inhibition kinetics and molecular anchoring assays, evidence the existence of transient cation-π contacts on the surface of an important member of the Cdc25 family, Cdc25B, and of sites of interaction between tested inhibitors and the protein, with emphasis on sites in the vicinity of the P-loop, a region close to the disordered C-terminus, where stability of the interaction with the small ligands is demonstrated

Mechanical properties and immunotherapeutic effects of dissolving microneedles with different drug loadings based on hyaluronic acid

Abstract Improving vaccine immunity and reducing antigen usage are major challenges in the clinical application of vaccines. Microneedles have been proven to be painless, minimally invasive, highly efficient, and have good patient compliance. Compared with traditional transdermal drug delivery, it can effectively deliver a large-molecular-weight drug into the skin, resulting in a corresponding immune response. However, few studies have examined the relationship between microneedle loading dose and immune effects. In this study, the hyaluronic acid (HA) conical and pyramidal dissolving microneedles were prepared by the two-step vacuum drying method, respectively. The model drug ovalbumin (OVA) was added to HA to prepare dissolving microneedles with different loading amounts. The mass ratios of HA to OVA were 5:1, 5:3, and 5:5. The mechanical properties of the dissolving microneedles were characterized using nanoindentation and in vitro puncture studies. The immune effects of the matrix and drug content were studied in Sprague-Dawley (SD) rats. Finally, the diffusion behavior of OVA and the binding mode of HA and OVA in the microneedles were simulated using Materials Studio and Autodocking software. The experimental results showed that the conical microneedles exhibited better mechanical properties. When the mass ratio of HA to OVA was 5:3, the immune effect can be improved by 37.01% compared to subcutaneous injection, and achieved a better immune effect with relatively fewer drugs. This conclusion is consistent with molecular simulations. This study provides theoretical and experimental support for the drug loading and efficacy of microneedles with different drug loadings

Improving the thermal stability of Proteus mirabilis lipase based on multiple computational design strategies / 生物工程学报

Proteus mirabilis lipase (PML) features tolerance to organic solvents and great potential for biodiesel synthesis. However, the thermal stability of the enzyme needs to be improved before it can be used industrially. Various computational design strategies are emerging methods for the modification of enzyme thermal stability. In this paper, the complementary algorithm-based ABACUS, PROSS, and FoldX were employed for positive selection of PML mutations, and their pairwise intersections were further subjected to negative selection by PSSM and GREMLIN to narrow the mutation library. Thereby, 18 potential single-point mutants were screened out. According to experimental verification, 7 mutants had melting temperature (Tm) improved, and the ΔTm of K208G and G206D was the highest, which was 3.75 ℃ and 3.21 ℃, respectively. Five mutants with activity higher than the wild type (WT) were selected for combination by greedy accumulation. Finally, the Tm of the five-point combination mutant M10 increased by 10.63 ℃, and the relative activity was 140% that of the WT. K208G and G206D exhibited certain epistasis during the combination, which made a major contribution to the improvement of the thermal stability of M10. Molecular dynamics simulation indicated that new forces were generated at and around the mutation sites, and the rearrangement of forces near G206D/K208G might stabilize the Ca2+ binding site which played a key role in the stabilization of PML. This study provides an efficient and user-friendly computational design scheme for the thermal stability modification of natural enzymes and lays a foundation for the modification of PML and the expansion of its industrial applications.

Mechanism of Astragaloside Ⅳ on HepG2 Cells Based on Molecular Dynamics Simulation and Experimental Evaluation / 肿瘤防治研究

Objective To reveal the mechanism of action of AS-Ⅳ on HepG2 cells based on molecular dynamics simulation and experimental evaluation. Methods We constructed a "drug-disease" network pharmacological map, analyzed the core genes of astragaloside Ⅳ (AS-Ⅳ) in HCC, screened key signaling pathways, and established a "drug-target" molecular dynamics model. In vitro assay was used to detect migration, proliferation and invasion abilities. Flow cytometry and qRT-PCR were used to detect the effect of AS-Ⅳ on the cell cycle and apoptosis, and the expression of core gene of HepG2. Results The core target of AS-Ⅳ acting on HCC was VEGFA. Compared with the control group, the high concentration of AS-Ⅳ significantly inhibited the migration, invasion and proliferation of HepG2 cells, blocked the metastasis of HepG2 cells from G1 to G2 phase, promoted their apoptosis, down-regulated VEGFA expression and up-regulated TGF-β1 expression. Conclusion AS-Ⅳ may inhibit the proliferation of hepatocellular carcinoma cells through multi-target and multi-pathway.

Structure-based optimization and design of CRISPR protein xCas9 / 生物工程学报

Streptococcus pyogenes Cas9 (SpCas9) has become a powerful genome editing tool, but has a limited range of recognizable protospacer adjacent motifs (PAMs) and shows off-target effects. To address these issues, we present a rational approach to optimize the xCas9 mutant derived from SpCas9 by directed evolution. Firstly, energy minimization with the Rosetta program was applied to optimize the three-dimensional structure of Cas9 to obtain the lowest energy conformation. Subsequently, combinatorial mutations were designed based on the mutations sites of xCas9 acquired during the directed evolution. Finally, optimal mutants were selected from the designed mutants by free energy ranking and subjected to experimental verification. A new mutant yCas9 (262A/324R/409N/480K/543D/694L/1219T) with multiple PAM recognition ability and low off-target effects was obtained and verified by DNA cleavage experiments. This mutant recognizes the NG, GAA and GAT PAMs and shows low off-target DNA cleavage activity guided by mismatched sgRNA, thus provides a gene editing tool with potential applications in biomedical field. Furthermore, we performed molecular dynamics simulations on the structures of SpCas9, xCas9 and yCas9 to reveal the mechanisms of their PAM recognition and off-target effects. These may provide theoretical guidance for further optimization and modification of CRISPR/Cas9 proteins.

Effect of graphene oxide on the function of erythrocytes / 生物工程学报

The biocompatibility of nanomaterials has attracted much attention. Graphene oxide (GO) is a nanomaterial widely used in biomedicine, but its toxicity can not be ignored. In this study, the effect of GO on the blood system (the hemolysis rate, the fragility of erythrocyte, and acetylcholinesterase activity) was systematically investigated. The results showed that the hemolysis rate of erythrocytes was lower than 8% when the GO concentration was below 100 μg/mL (P5 μm (LGO) increased the activity of acetylcholinesterase by 42.67% (P<0.05). Then molecular dynamics simulation was used to study how GO interacted with acetylcholinesterase and increased its activity. The results showed that GO was attached to the cell membrane, thus may provide an electronegative environment that helps the hydrolysate to detach from the active sites more quickly so as to enhance the activity of acetylcholinesterase.

Computational study of the potential molecular target for antibreast cancer activity of limonoid derivatives from chisocheton sp

Limonoid is a class of natural compounds that are originated from lemon and other citrus fruits. However, derivativesof limonoids are also produced in other plants, such as Chisocheton sp. Limonoids from Chisocheton sp. showedvarious biological activities, including anticancer. Nevertheless, the molecular target for anticancer activity of thesecompounds is still unclear. Many studies suggested nuclear receptors (NR) as the protein target for limonoids. In thisstudy, we investigated the possible NR as a molecular target for limonoids from Chisocheton sp. using moleculardocking and molecular dynamics (MD) simulation. The docking study was done on AutoDock Vina. Two out of 11NR expressed in breast tissue, i.e., progesterone receptor (PR) and glucocorticoid receptor, was used as the mostpotential target for limonoids. The docking pose was further observed by MD simulation. Both receptors showedstable molecular interactions with limonoids, indicated with a low deviation of binding site residues. Interestingly,simulations of PR showed the alteration of Helix-12, which is one of the key factors to the antagonist action of theligand. It is hoped that the findings could shed insight into the further molecular assay development of anticanceragents based on limonoids.

Structural basis of SARS-CoV-23CLpro and anti-COVID-19 drug discovery from medicinal plants / 药物分析学报

The recent pandemic of coronavirus disease 2019 (COVID-19) caused by SARS-CoV-2 has raised global health concerns. The viral 3-chymotrypsin-like cysteine protease (3CLpro) enzyme controls coronavirus replication and is essential for its life cycle. 3CLpro is a proven drug discovery target in the case of severe acute respiratory syndrome coronavirus (SARS-CoV) and Middle East respiratory syndrome coronavirus (MERS-CoV). Recent studies revealed that the genome sequence of SARS-CoV-2 is very similar to that of SARS-CoV. Therefore, herein, we analysed the 3CLpro sequence, constructed its 3D homology model, and screened it against a medicinal plant library containing 32,297 potential anti-viral phytochemicals/traditional Chinese medicinal compounds. Our analyses revealed that the top nine hits might serve as potential anti- SARS-CoV-2 lead molecules for further optimisation and drug development process to combat COVID-19.

Molecular Dynamics Study on Docking of A3/A1 and Interdomain Interactions / 医用生物力学

Objective To investigate the interaction between von Willebrand factor (vWF) A1 and A3 domain, and type 2 M mutant W1745C-A3 effect on thermal stability and mechanical stability of A3/A1. Methods The crystal structures of A1 and A3 were downloaded from Protein Data Base (PDB). The wild-type (WT) A3/A1 structure was obtained by using SwarmDock Server, then W1745C-A3/A1 mutant was constructed by replacing the Trp1745 with Cys1745 in A3/A1. Through steered molecular dynamics simulation, formation and evolution of hydrogen bond and salt bridge between A1 and A3 interfaces were observed, and the differences in conformation, disrupted force and dissociation time between WT-A3/A1 and W1745C-A3/A1 were compared. Results There were 5 pairs of hydrogen bonds with survival rate > 0-2 and 1 pair of salt bridge with survival rate > 0-5 between A1 and A2. The W1745C-A3/A1 complex could withstand greater disrupted force and longer dissociation time compared with WT-A3/A1, by improving the stability of hydrogen bonds and increasing 1 pair of stable salt bridge. Conclusions The interaction between A1 and A3 would hinder the binding sites of A1 to GPIbα, and the W1745C-A3 mutation would further reduce the affinity of A1 to platelets. These results provide references for revealing the molecular mechanism of von Willebrand diseases in the clinic and developing the corresponding drugs targeted to hemostasis disorders.

Screening of type II 5α-reductase inhibitors from traditional Chinese medicine based on molecular docking and molecular dynamics simulation technology / 中草药

Objective: To screen the potential type II 5α-reductase inhibitors from active ingredients of traditional Chinese medicine (TCM) based on molecular docking and molecular dynamics (MD) simulation technology. Methods: The molecular docking was used to screen 26 monomer compositions from TCM. Based on the docking results, MD was performed to evaluate the binding strength of compounds with protein. The binding free energy of the system was calculated using the MM/PBSA method. The in vitro micro-reaction system was used to investigate biological activity. Results: The binding energies of 26 monomer compositions from TCM to type II 5-alpha Reductase were different. Among them, ligustroflavone, safflower yellow and hinokiflavone have low binding energies to type II 5-alpha reductase, and their binding abilities were strong. The molecular dynamics simulation results are consistent with the docking results (binding capacity: ligustroflavone-protein > safflower yellow-protein > hinokiflavone-protein). The three components ligustroflavone, safflower yellow and hinokiflavone have a certain inhibitory activity on type II 5α-reductase with the IC50 value of (42.12 ± 3.83), (69.06 ± 6.35), and (191.28 ± 5.90) μmol/L, respectively. Conclusion: Among the screened 26 monomer compositions, ligustroflavone, safflower yellow and hinokiflavone have the potential to be used in the study of treatment and prevention of androgen-dependent diseases, which provides a reference for further exploration and discovery of type II 5α-reductase inhibitors.

Exploring potential affected site for the inhibition of Aβ42 polymerization based on Asn27 deamidation modification / 药学学报

One of pathological features of Alzheimer's disease (AD) is extracelluar aggregation of amyloid-β protein (Aβ) forming senile plaques. Investigation on inhibition of Aβ aggregation can be crucial for designing effective drugs against AD. Previous studies have demonstrated that the deamidation at Asn27, a type of post translation modification, significantly prevented the polymerization of Aβ monomers. But the underlying mechanism is still unclear. Therefore, we investigated the possible effect of Asn27 deamidation on structure and aggregation of Aβ42 monomer using molecular dynamics simulation. The results showed that the deamidation of Asn27 can directly disrupt the salt bridge formed between D23 and K28, and effectively decrease the content of β-sheet that is important for aggregation of Aβ. Moreover, the inability at C-terminal region (CTR) and N-terminal region (NTR) to form antiparallel β-sheets further weakens the intra-peptide interaction of Aβ42 monomer. These changes caused by Asn27 deamidation lead to the decline of the aggregated trend of Aβ42 monomer, which is consistent with the experimental observation. According to these results, the salt bridge formed between D23 and K28 plays an important role in promoting the polymerization process between Aβ42 monomers, and disrupting this interaction may be a potential direction for further designing drugs to inhibit aggregation of Aβ42. In summary, this study shows a potential affected site that can efficiently inhibit aggregation of Aβ42.

Identification of polyketide synthase 13 inhibitor: Pharmacophore-based virtual screening and molecular dynamics simulation

Polyketide synthase 13 (Pks13) is one of prominent targets to treat Mycobacterium tuberculosis (Mtb). In the presentstudy, pharmacophore features for Pks13, including two hydrogen bond donors, one hydrogen bond acceptor, and onehydrophobic feature, were built using a novel Pks13 inhibitor, TAM16. The pharmacophore features were then usedto perform virtual screening on ZINC database to identify small molecules of Pks13 inhibitors. The obtained virtualhits of 107 small molecules were subjected to molecular docking studies employing iDock software to reveal theirbinding orientation to Pks13. Furthermore, four best hits, each bound to Pks13, were submitted to 40-ns moleculardynamics simulation to explore their conformational changes throughout simulation. The result showed that all hitcompounds, i.e., Lig79/ZINC09281113, Lig94/ZINC09584070, Lig95/ZINC09209668, and Lig97/ZINC09216165,have better stabilities than that of TAM16 as indicated by their lower values of root-mean-square-deviation and rootmean-square-fluctuation. In a similar way, prediction of binding free energy using molecular mechanics Poisson–Boltzmann Surface Area method showed that all hit compounds have lower binding free energies than that of TAM16,indicating their potential as novel compounds of Pks13 inhibitors.

Molecular dynamics simulation of collagen molecular mechanics under different conditions / 医疗卫生装备

Objective To study the mechanical properties of collagen molecules by molecular dynamics simulation,and to determine the relationship between the mechanical properties of the microstructure of cartilage and the macroscopic mechanical properties. Methods Obtaining the collagen molecular model from the protein database and using GROMACS molecular dynamics simulation software,an analog box was built with a size of 24 nm× 3.2 nm × 3.2 nm. The simulation system contained 6 719 water molecules, 20 sodium ions and 20 chloride ions. This solution was equivalent to a saline environment. The uniaxial tensile simulation of collagen molecules was executed under the conditions of different temperature,different tensile rates and different pressures in this environment.Results When the temperature was constant, the tensile rate and the elastic modulus of collagen increased; when the tensile rate was certain, the temperature of the simulation system rose while the modulus of elasticity decreased;under the conditions of certain temperature and tensile rate, the pressure of the system gradually increased,and its modulus of elasticity decreased gradually. Conclusion Through the uniaxial tensile simulation of collagen molecules under different conditions,the mechanical laws of collagen molecules are obtained.There is a certain correlation between the elastic modulus and the tensile strain during the stretching process,and a way of thinking is provided on the study of the correlation of cartilage rate from the microscopic aspect.

Effects of Calcium on the Stability of VWF-A2 Domain by Molecular Dynamics Simulation / 医用生物力学

Objective To investigate the effect of calcium on the stability of VWF-A2 domain. Methods The crystal structures of A2 (not containing calcium) and A2/Ca2+ (with calcium bound) were downloaded from protein data bank. For A2 domain, the conformational changes, unfolding pathway differences and the exposure degree variance of cleavage sites caused by calcium binding were observed and analyzed by steered Molecular Dynamics simulations under constant force. Results The unfolding pathway of A2 domain and exposure process of cleavage sites were force-dependent. Calcium binding did not affect the unfolding process of A2 in the early stage. As the conformational rearrangement of α3β4-loop reduced its localized dynamic properties, the movement among β1-β4-β5 strands was restrained, which suppressed its further unfolding to stay in the intermediate steady state and delayed the cleavage-site exposure. Conclusions Stretch force could induce β5 strand of A2 unfolding and the cleavage-site exposure, while calcium binding inhibited ADAMTS13 proteolysis efficiency through stabilizing A2 hydrophobic core and covering its cleavage sites. These results way help to understand how ADAMTS13 cleavages the VWF-A2 domain and regulates the hemostatic potential of VWF, and further provide useful guidance on the design of related anti-thrombus drugs.

Improving the thermostability of α-amylase from Rhizopus oryzae by rational design / 生物工程学报

Fungal α-amylases are widely used in the production of maltose syrup, while additional production costs may be required in the syrup production process due to the loss of enzyme activity, because of the poor thermostability exhibited in this type of enzyme. After deeply studying the importance of thermostability of fungal α-amylases applied in industrial production, with attempt to improve the thermostability of Rhizopus oryzae α-amylase (ROAmy), single-point mutations and combined mutations that based on analysis of B-factor values and molecular dynamics simulations were carried out for amino acid residues G128, K269 and G393 of ROAmy by overlapping PCR. The results showed that all the 7 mutants obtained presented better thermostability than the wild-type enzyme, and the best mutant was G128L/K269L/G393P which showed a 5.63-fold increase in half-life at 55 ℃ compared with the wild-type enzyme. Meanwhile, its optimum temperature increased from 50 ℃ to 65 ℃, the maximum reaction rate (Vmax) and catalytic efficiency (kcat/Km) increased by 65.38% and 99.86%. By comparing and analyzing the protein structure and function between the mutants and the wild-type enzyme, it was found that the increase of the number of hydrogen bonds or the introduction of proline in special position may be the main reasons for the improved thermostability that found in the mutants.

Molecular dynamics simulation and analysis of BAFF which is incorporated with p-nitro-L-phenylalanine / 中国药科大学学报

In order to study the structure-function relationship in the protein which is incorporated with p-nitro-L-phenylalanine,the method of MD(Molecular Dynamics) simulation was established and successfully used in the analysis of protein which contains p-nitro-L-phenylalanine.The force field of CHARMM can only stimulate protein with natural amino acid in NAMD.Compared with phenylalanine,p-nitro-L-phenylalanine just has one more group of nitro.If the parameter of group of nitro was defined,the protein containing p-nitro-L-phenylalanine can be simulated.CGenFF-paramchem was used to calculate the energy and topological structure of p-nitro-L-phenylalanine' s new bonds (r),angles (θ),dihendrals (φ) and improper angle (ψ).And then the new defined parameter and topology information was input into the related parameter files and topology files in CHARMM.On the basis of correct parameter,NAMD can successfully simulate the modified BAFF(B lymphocyte stimulator) which contains p-nitro-L-phenylalanine.The changes in structure indicated that there might be new B cell epitopes.The temperature distribution of each frame in the process of dynamics stimulation was in accord with normal distribution,which proved the defined force field parameters was feasible.The RMSD of whole protein solution systemis 2.5.Calculate each resides' RMSF in BAFF,the RMSF of p-nitro-L-phenylalanine's residue is 3.7,which is obviously higher than that of the other residues in β-pleated sheet,and close to the loop rings,indicate that there might be variation in the area of p-nitro-L-phenylalanine residue and might produce new comformational epitopes.The results of MD stimulation will guide the immunogenicity experiments of p-nitro-L-phenylalanine modified proteins.

New perspectives on the computational characterization of the kinetics of binding-unbinding in drug design: implications for novel therapies / Nuevas perspectivas sobre la caracterización computacional de la cinética de unión-desunión en el diseño de fármacos: implicaciones para terapias de vanguardia

Abstract: The efficiency and the propensity of a drug to be bound to its target protein have been inseparable concepts for decades now. The correlation between the pharmacological activity and the binding affinity has been the first rule to design and optimize a new drug rationally. However, this argument does not prove to be infallible when the results of in vivo assays have to be confronted. Only recently, we understand that other magnitudes as the kinetic rates of binding and unbinding, or the mean residence time of the complex drug-protein, are equally relevant to draw a more accurate model of the mechanism of action of a drug. It is in this scenario where new computational techniques to simulate the all-atom dynamics of the biomolecular system find its valuable place on the challenge of designing new molecules for more effective and less toxic therapies.

Resumen: La eficiencia de un fármaco se ha relacionado habitualmente con su constante de afinidad, magnitud que puede ser medida experimentalmente in vitro y que cuantifica la propensión mostrada por la molécula ligando para interaccionar con su proteína diana. Este modo de entender el mecanismo de acción ha guiado durante años el desarrollo de nuevas moléculas con potencial farmacológico. Sin embargo, dicho modelo o criterio no es infalible cuando se confronta con los resultados de ensayos in vivo. Otras magnitudes, como las constantes cinéticas de asociación o disociación o el tiempo de residencia del ligando acoplado a su proteína diana, demuestran ser igualmente necesarias para comprender y predecir la capacidad farmacológica del compuesto químico. En este nuevo escenario, con ayuda de las técnicas computacionales de simulación molecular, la correcta caracterización del proceso dinámico de unión y desunión del ligando y receptor resulta imprescindible para poder diseñar racionalmente nuevas moléculas que permitan terapias más eficaces y menos tóxicas.

Quercetin Directly Interacts with Vitamin D Receptor (VDR): Structural Implication of VDR Activation by Quercetin

The vitamin D receptor (VDR) is a member of the nuclear receptor (NR) superfamily. The VDR binds to active vitamin D3 metabolites, which stimulates downstream transduction signaling involved in various physiological activities such as calcium homeostasis, bone mineralization, and cell differentiation. Quercetin is a widely distributed flavonoid in nature that is known to enhance transactivation of VDR target genes. However, the detailed molecular mechanism underlying VDR activation by quercetin is not well understood. We first demonstrated the interaction between quercetin and the VDR at the molecular level by using fluorescence quenching and saturation transfer difference (STD) NMR experiments. The dissociation constant (K(d)) of quercetin and the VDR was 21.15 ± 4.31 µM, and the mapping of quercetin subsites for VDR binding was performed using STD-NMR. The binding mode of quercetin was investigated by a docking study combined with molecular dynamics (MD) simulation. Quercetin might serve as a scaffold for the development of VDR modulators with selective biological activities.

Molecular simulation study on the recognition between hydroxy isoindolin ketone derivatives and HIV-1 integrase / 中国药科大学学报

@#To discuss the conformational change and the recognition mechanism of hydroxy isoindol ketone derivatives with HIV-1 integrase, fifty-eight hydroxy isoindol ketone derivatives were docked to the integrase using AutoDock program. Molecular dynamics simulation with 16 ns was carried out for the two complex modes, respectively, in which the corresponding small molecules exhibited strong inhibition ability. Main force acting on the association of small molecules with integrase was explored based on the docking complex model. After analyzing the hydrogen-bond and conformational changes, it was found that the hydrogen-bond between N155 and D64 was the key factor maintaining the DDE motif stability. Furthermore, the hydrophobic interactions between the loop region where Y143 located and the hydroxy isoindol ketone derivatives were found to play an important role for their recognition.