Calculating Electrochemical Activity of Regular-Structure Porous Electrodes with an Immobilized Enzyme

A porous electrode of regular structure with an immobilized enzyme is studied. The electrode carcass, which consists of substrate particles, is a system of two sets of mutually perpendicular planes crossing one another (cellular structure). A monomolecular layer of enzyme molecules is deployed on the inner surface of such a porous substrate. In the center of each cell of the substrate gas pores, which are cylinders of porous grains of a hydrophobizing agent one grain thick, are situated. The rest of the cell space is filled by a solid polymer electrolyte. The ultimate goal of calculations is to estimate the electrochemical activity of such an electrode. The estimation is done for an oxygen electrode with an enzyme whose characteristics are close to those of laccase. The calculation assumes that active centers of enzyme molecules undergo a direct, i.e. without participation of mediators, reduction. It is shown that at an overvoltage of 30 mV, it would be possible to obtain a current density of 0.44 A cm^–2 in an electrode 16 m thick.     

A Bait-and-Switch Method for the Construction of Artificial Esterases for Substrate-Selective Hydrolysis

Outcomes of chemical reactions are generally dominated by the intrinsic reactivities of reaction partners, but enzymes frequently override such constraints to transform less reactive molecules in the presence of more reactive ones. Despite the attractiveness of such catalysis, it is difficult to build synthetic catalysts with these features. Micellar imprinting is a powerful method to create template-complementary binding sites inside protein-sized water-soluble nanoparticles. When a photocleavable functional monomer was used to bind two phosphonate/phosphate templates as transition-state analogues, active sites with predetermined size and shape were formed inside doubly cross-linked micelles through molecular imprinting. Postmodification replaced the binding group with a catalytic pyridyl group, forming highly selective artificial esterases. The catalysts displayed enzyme-like kinetics and turnover numbers that were in the hundreds. The selectivity of the catalysts, derived from the substrate-complementary imprinted active sites, enabled transformation of less reactive esters in the presence of more reactive ones.     

基于环糊精和冠醚偶联体系的新型超分子主体模型

超分子化学是当今化学界的前沿学科之一,超分子主体化合物的选择性合成是其一个重要的方面。环糊精与冠醚同为超分子化学中应用广泛的主体分子,各有自己独特的特点及不足,而将二者偶联起来,可得到拥有两个甚至多个识别位点的化合物,通过协同作用可在分子识别、模拟酶、色谱等方面的应用范围,并有较好的的效果。本文综述了近年来环糊精与冠醚偶联体系的研究进展：首先介绍了不同种类的环糊精与冠醚偶联体系的合成,包括合成思路、步骤以及方法;然后着重叙述了此体系的应用研究进展,包括其在分子识别、模拟酶、异构体分离以及光能量传导等领域;最后指出目前研究工作仍然存在的不足,并对其前景进行了展望。     

蛋白质功能的扩展与人工金属结合位点的理性设计

生物体系中金属离子在调节金属蛋白的结构和功能中发挥着至关重要的作用。本文综述了利用人工金属结合位点的理性设计来扩展蛋白质功能范围的研究进展,包括在蛋白分子内部通过探索潜在的结合金属位点、重新设计已有的金属结合位点、以及设计全新的金属结合位点的方法来设计人工金属结合位点,和在蛋白分子表面进行设计,来获得结构及功能的转化、研究与纳米材料间的相互作用、以及进行蛋白质分子的自组装。这些研究进展极大地丰富了我们对金属蛋白结构与功能关系的认识。同时,也赋予了我们控制及利用感兴趣蛋白的能力。     

A Computational Study of the Molecular Recognition of Nucleic Acid Bases by Poly(vinyldiaminotriazine)

Summary: The enthalpic gain upon formation of the complexes of the poly(vinyldiaminotriazine) model with purine, uracil and xanthine has been assessed by means of the RI-MP2 interaction energy calculations. Based on the underlying RI-DFT-D geometrical optimizations, the molecular-level insight into the recognition processes has been proposed.     

Computational Insights into the Allosteric Effect and Dynamic Structural Features of the SARS-COV-2 Spike Protein

COVID-19 caused by SARS-COV-2 is continuing to surge globally. The spike (S) protein is the key protein of SARS-COV-2 that recognizes and binds to the host target ACE2. In this study, molecular dynamics simulation was used to elucidate the allosteric effect of the S protein. Binding of ACE2 caused a centripetal movement of the receptor-binding domain of the S protein. The dihedral changes in Phe329 and Phe515 played a key role in this process. Two potential cleavage sites S1/S2 and S2′ were exposed on the surface after the binding of ACE2. The binding affinity of SARS-COV-2 S protein and ACE2 was higher than that of SARS-COV. This was mainly due to the mutation of Asp480 in SARS-COV to Ser494 in SARS-COV-2, which greatly weakened the electrostatic repulsion. The result provides a theoretical basis for the SARS-COV-2 infection and aids the development of biosensors and detection reagents.     

Study on the Model for Regulation of the Allosteric Enzyme Activity

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Design,Synthesis, Molecular Modeling and Antitumor Evaluation of Novel Indolyl-Pyrimidine Derivatives with EGFR Inhibitory Activity

Scaffolds hybridization is a well-known drug design strategy for antitumor agents. Herein, series of novel indolyl-pyrimidine hybrids were synthesized and evaluated in vitro and in vivo for their antitumor activity. The in vitro antiproliferative activity of all compounds was obtained against MCF-7, HepG2, and HCT-116 cancer cell lines, as well as against WI38 normal cells using the resazurin assay. Compounds 1–4 showed broad spectrum cytotoxic activity against all these cancer cell lines compared to normal cells. Compound 4g showed potent antiproliferative activity against these cell lines (IC₅₀ = 5.1, 5.02, and 6.6 μM, respectively) comparable to the standard treatment (5-FU and erlotinib). In addition, the most promising group of compounds was further evaluated for their in vivo antitumor efficacy against EAC tumor bearing mice. Notably, compound 4g showed the most potent in vivo antitumor activity. The most active compounds were evaluated for their EGFR inhibitory (range 53–79%) activity. Compound 4g was found to be the most active compound against EGFR (IC₅₀ = 0.25 µM) showing equipotency as the reference treatment (erlotinib). Molecular modeling study was performed on compound 4g revealed a proper binding of this compound inside the EGFR active site comparable to erlotinib. The data suggest that compound 4g could be used as a potential anticancer agent.     

新型希夫碱型钳形人工受体的微波合成及其对中性分子的识别性能

以对苯二甲酸为起始原料,设计并合成了8个新型的芳环钳形人工受体(3a～3h),其结构经1H NMR,IR,ESI-MS和元素分析表征。利用UV-Vis滴定法初步考察了3a～3h对中性分子(邻苯二胺,间苯二胺,对苯二胺和二苯甲酮)的识别性能,结果表明3a～3h对其具有良好的识别性能。     

Freezing the Dynamic Gap for Selectivity: Motion‐Based Design of Inhibitors of the Shikimate Kinase Enzyme

Shikimate kinase (SK), the fifth enzyme of the aromatic amino acid biosynthesis, is a recognized target for antibiotic drug discovery. The potential of the distinct dynamic apolar gap, which isolates the natural substrate from the solvent environment for catalysis, and the motion of Mycobacterium tuberculosis and Helicobacter pylori SK enzymes, which was observed by molecular dynamics simulations, was explored for inhibition selectivity. The results of the biochemical and computational studies reveal that the incorporation of bulky groups at position C5 of 5‐aminoshikimic acid and the natural substrate enhances the selectivity for the H. pylori enzyme due to key motion differences in the shikimic acid binding domain (mainly helix α5). These studies show that the less‐exploited motion‐based design approach not only is an alternative strategy for the development of competitive inhibitors, but could also be a way to achieve selectivity against a particular enzyme among its homologues.     

A Dual Enzyme Microgel with High Antioxidant Ability Based on Engineered Seleno‐Ferritin and Artificial Superoxide Dismutase

An antioxidant microgel with both glutathione peroxidase (GPx) and superoxide dismutase (SOD) activities is reported. Using computational design and genetic engineering methods, the main catalytic components of GPx are fabricated onto the surface of ferritin. The resulting seleno‐ferritin (Se‐Fn) monomers can self‐assemble into nanocomposites that exhibit remarkable GPx activity due to the well organized multi‐GPx catalytic centers. Subsequently, a porphyrin derivative is synthesized as an SOD mimic, and is employed to construct a synergistic dual enzyme system by crosslinking Se‐Fn nanocomposites into a microgel. Significantly, this dual enzyme microgel is demonstrated to display better antioxidant ability than single GPx or SOD mimics in protecting cells from oxidative damage.

     

Design of SARS-CoV-2 Main Protease Inhibitors Using Artificial Intelligence and Molecular Dynamic Simulations

Drug design is a time-consuming and cumbersome process due to the vast search space of drug-like molecules and the difficulty of investigating atomic and electronic interactions. The present paper proposes a computational drug design workflow that combines artificial intelligence (AI) methods, i.e., an evolutionary algorithm and artificial neural network model, and molecular dynamics (MD) simulations to design and evaluate potential drug candidates. For the purpose of illustration, the proposed workflow was applied to design drug candidates against the main protease of severe acute respiratory syndrome coronavirus 2. From the ∼140,000 molecules designed using AI methods, MD analysis identified two molecules as potential drug candidates.     

Precisely Designed Isopeptide Bridge‐Crosslinking Endows Artificial Hydrolases with High Stability and Catalytic Activity under Extreme Denaturing Conditions

Enzymes normally lose their activities under extreme conditions due to the dissociation of their active tertiary structure. If an enzyme could maintain its catalytic activity under non‐physiological or denaturing conditions, it might be used in more applications in the pharmaceutical and chemical industries. Recently, we reported a coiled‐coil six‐helical bundle (6HB) structure as a scaffold for designing artificial hydrolytic enzymes. Here, intermolecular isopeptide bonds were incorporated to enhance the stability and activity of such biomolecules under denaturing conditions. These isopeptide bridge‐tethered 6HB enzymes showed exceptional stability against unfolding and retained or even had increased catalytic activity for a model hydrolysis reaction under thermal and chemical denaturing conditions. Thus, isopeptide bond‐tethering represents an efficient route to construct ultrastable artificial hydrolases, with promising potential to maintain biocatalysis under extreme conditions.     

Insights into the Allosteric Effect of SENP1 Q597A Mutation on the Hydrolytic Reaction of SUMO1 via an Integrated Computational Study

Small ubiquitin-related modifier (SUMO)-specific protease 1 (SENP1) is a cysteine protease that catalyzes the cleavage of the C-terminus of SUMO1 for the processing of SUMO precursors and deSUMOylation of target proteins. SENP1 is considered to be a promising target for the treatment of hepatocellular carcinoma (HCC) and prostate cancer. SENP1 Gln597 is located at the unstructured loop connecting the helices α4 to α5. The Q597A mutation of SENP1 allosterically disrupts the hydrolytic reaction of SUMO1 through an unknown mechanism. Here, extensive multiple replicates of microsecond molecular dynamics (MD) simulations, coupled with principal component analysis, dynamic cross-correlation analysis, community network analysis, and binding free energy calculations, were performed to elucidate the detailed mechanism. Our MD simulations showed that the Q597A mutation induced marked dynamic conformational changes in SENP1, especially in the unstructured loop connecting the helices α4 to α5 which the mutation site occupies. Moreover, the Q597A mutation caused conformational changes to catalytic Cys603 and His533 at the active site, which might impair the catalytic activity of SENP1 in processing SUMO1. Moreover, binding free energy calculations revealed that the Q597A mutation had a minor effect on the binding affinity of SUMO1 to SENP1. Together, these results may broaden our understanding of the allosteric modulation of the SENP1−SUMO1 complex.     

Structural Basis for Expansion of the Genetic Alphabet with an Artificial Nucleobase Pair

Hydrophobic artificial nucleobase pairs without the ability to pair through hydrogen bonds are promising candidates to expand the genetic alphabet. The most successful nucleobase surrogates show little similarity to each other and their natural counterparts. It is thus puzzling how these unnatural molecules are processed by DNA polymerases that have evolved to efficiently work with the natural building blocks. Here, we report structural insight into the insertion of one of the most promising hydrophobic unnatural base pairs, the dDs–dPx pair, into a DNA strand by a DNA polymerase. We solved a crystal structure of KlenTaq DNA polymerase with a modified template/primer duplex bound to the unnatural triphosphate. The ternary complex shows that the artificial pair adopts a planar structure just like a natural nucleobase pair, and identifies features that might hint at the mechanisms accounting for the lower incorporation efficiency observed when processing the unnatural substrates.     

Design of Enzyme Micelles with Controllable Concavo‐Convex Micromorphologies for Highly Enhanced Stability and Catalytical Activity

Concavo‐convex micelles with controllable sizes and nanostructures are prepared via self‐assembling polymer–enzyme (e.g., shellac enzyme) conjugates with heterogeneous polymer chains, which exhibit higher enzyme stability (300%) and bioactivity (760%) comparing with the well‐defined ones. The applied amphiphilic and negatively charged copolymer, poly (methyl methacrylate)‐block‐poly (sodium p‐styrene sulfonate), is synthesized via reversible addition–fragmentation chain transfer polymerization to modify shellac enzyme and immobilize the enzyme bioactivity inducer by covalent conjugation and electrostatic attraction, respectively. The degradation test of catechol confirms the application potential of as‐prepared micelles as an efficient and economical decontaminant.     

The Influence of Chemical Change on Protein Dynamics: A Case Study with Pyruvate Formate-Lyase

Pyruvate formate-lyase (PFL) catalyzes the reversible conversion of pyruvate and coenzyme A (CoA) into formate and acetyl-CoA in two half-reactions. For the second half-reaction to take place, the S−H group of CoA must enter the active site of the enzyme to retrieve a protein-bound acetyl group. However, CoA is bound at the protein surface, whereas the active site is buried in the protein interior, some 20–30 Å away. The PFL system was therefore subjected to a series of extensive molecular dynamics simulations (in the μs range) and a host of advanced analysis procedures. Models representing PFL before and after the first half-reaction were used to examine the possible effect of enzyme acetylation. All simulated structures were found to be relatively stable compared to the initial crystal structure. Although the adenine portion of CoA remained predominantly bound at the protein surface, the binding of the S−H group was significantly more labile. A potential entry channel for CoA, which would allow the S−H group to reach the active site, was identified and characterized. The channel was found to be associated with accentuated fluctuations and a higher probability of being in an open state in acetylated systems. This result suggests that the acetylation of the enzyme assumes a prominent functional role, whereby the formation of the acyl intermediate serves to initiate a subtle signaling cascade that influences the protein dynamics and facilitates the entry of the second substrate.     

Novel Design of RNA Aptamers as Cancer Inhibitors and Diagnosis Targeting the Tyrosine Kinase Domain of the NT-3 Growth Factor Receptor Using a Computational Sequence-Based Approach

Aptamers, the nucleic acid analogs of antibodies, bind to their target molecules with remarkable specificity and sensitivity, making them promising diagnostic and therapeutic tools. The systematic evolution of ligands by exponential enrichment (SELEX) is time-consuming and expensive. However, regardless of those issues, it is the most used in vitro method for selecting aptamers. Therefore, recent studies have used computational approaches to reduce the time and cost associated with the synthesis and selection of aptamers. In an effort to present the potential of computational techniques in aptamer selection, a simple sequence-based method was used to design a 69-nucleotide long aptamer (mod_09) with a relatively stable structure (with a minimum free energy of −32.2 kcal/mol) and investigate its binding properties to the tyrosine kinase domain of the NT-3 growth factor receptor, for the first time, by employing computational modeling and docking tools.