Chemical Probing of the Human Sirtuin 5 Active Site Reveals Its Substrate Acyl Specificity and Peptide‐Based Inhibitors

Sirtuins are NAD⁺‐dependent deacetylases acting as sensors in metabolic pathways and stress response. In mammals there are seven isoforms. The mitochondrial sirtuin 5 is a weak deacetylase but a very efficient demalonylase and desuccinylase; however, its substrate acyl specificity has not been systematically analyzed. Herein, we investigated a carbamoyl phosphate synthetase 1 derived peptide substrate and modified the lysine side chain systematically to determine the acyl specificity of Sirt5. From that point we designed six potent peptide‐based inhibitors that interact with the NAD⁺ binding pocket. To characterize the interaction details causing the different substrate and inhibition properties we report several X‐ray crystal structures of Sirt5 complexed with these peptides. Our results reveal the Sirt5 acyl selectivity and its molecular basis and enable the design of inhibitors for Sirt5.     

Peptide-Hypervalent Iodine Reagent Chimeras: Enabling Peptide Functionalization and Macrocyclization**

Herein, we report a novel strategy for the modification of peptides based on the introduction of highly reactive hypervalent iodine reagents—ethynylbenziodoxolones (EBXs)—onto peptides. These peptide-EBXs can be readily accessed, by both solution- and solid-phase peptide synthesis (SPPS). They can be used to couple the peptide to other peptides or a protein through reaction with Cys, leading to thioalkynes in organic solvents and hypervalent iodine adducts in water buffer. Furthermore, a photocatalytic decarboxylative coupling to the C-terminus of peptides was developed using an organic dye and was also successful in an intramolecular fashion, leading to macrocyclic peptides with unprecedented crosslinking. A rigid linear aryl alkyne linker was essential to achieve high affinity for Keap1 at the Nrf2 binding site with potential protein-protein interaction inhibition.     

Synthesis,Biochemical Characterization,and Genetic Encoding of a 1,2,4-Triazole Amino Acid as an Acetyllysine Mimic for Bromodomains of the BET Family

Lysine acetylation is a charge-neutralizing post-translational modification of proteins bound by bromodomains (Brds). A 1,2,4-triazole amino acid (ApmTri) was established as acetyllysine (Kac) mimic recruiting Brds of the BET family in contrast to glutamine commonly used for simulating this modification. Optimization of triazole substituents and side chain spacing allowed BET Brd recruitment to ApmTri-containing peptides with affinities similar to native substrates. Crystal structures of ApmTri-containing peptides in complex with two BET Brds revealed the binding mode which mirrored that of Kac ligands. ApmTri was genetically encoded and recombinant ApmTri-containing proteins co-enriched BRD3(2) from cellular lysates. This interaction was blocked by BET inhibitor JQ1. With genetically encoded ApmTri, biochemistry is now provided with a stable Kac mimic reflecting charge neutralization and Brd recruitment, allowing new investigations into BET proteins in vitro and in vivo.     

硅烷化和多聚赖氨酸化衬底结合容量的比较

微流控芯片和生物芯片因其筛选高通量、体积微型化和便携化、功能集成化、分析快速等特点,在生物学研究中得到广泛的应用,促进了基因组学[1]和蛋白质组学[2]的研究。衬底的修饰是生物芯片制备工序中一道重要的环节,对保持生物样品的活性、提高生物样品的有效结合率起着非常重要     

两类手性PNA单体及其对映异构体的合成

分别以保护的Ｌ－和Ｄ－赖氨酸作为起始原料合成了两种类型的ＰＮＡ单体。在类型Ｉ中，碱基通过－ＣＨ２Ｃ（Ｏ）－间隔臂与赖氨酸的α－ＮＨ相连，而类型Ⅱ中，－Ｃ（Ｏ）－用作连接臂。     

A Macrocyclic Peptide Library with a Structurally Constrained Cyclopropane‐containing Building Block Leads to Thiol‐independent Inhibitors of Phosphoglycerate Mutase

Here we report the construction of an mRNA‐encoded library of thioether‐closed macrocyclic peptides by using an N‐chloroacetyl‐cyclopropane‐containing exotic initiator whose structure is more constrained than the ordinary N‐chloroacetyl‐α‐amino acid initiators. The use of such an initiator has led to a macrocycle library with significantly suppressed population of lariat‐shaped species compared with the conventional libraries. We previously used a conventional library and identified a small lariat thioether‐macrocycle with a tail peptide with a C‐terminal free Cys whose sidechain plays an essential role in potent inhibitory activity against a parasitic model enzyme, phosphoglycerate mutase. On the other hand, the cyclopropane‐containing macrocycle library has yielded a larger thioether‐macrocycle lacking a free Cys residue, which exhibits potent inhibitory activity to the same enzyme with a different mode of action. This result indicates that such a cyclopropane‐containing macrocycle library would allow us to access mechanistically distinct macrocycles.     

Detection and Verification of a Key Intermediate in an Enantioselective Peptide Catalyzed Acylation Reaction

Until now, the intermediate responsible for the acyl transfer of a highly enantioselective tetrapeptide organocatalyst for the kinetic resolution of trans-cycloalkane-1,2-diols has never been directly observed. It was proposed computationally that a π-methylhistidine moiety is acylated as an intermediate step in the catalytic cycle. In this study we set out to investigate whether we can detect and characterize this key intermediate using NMR-spectroscopy and mass spectrometry. Different mass spectrometric experiments using a nano-ElectroSpray Ionization (ESI) source and tandem MS-techniques allowed the identification of tetrapeptide acylium ions using different acylation reagents. The complexes of trans-cyclohexane-1,2-diols with the tetrapeptide were also detected. Additionally, we were able to detect acylated tetrapeptides in solution using NMR-spectroscopy and monitor the acetylation reaction of a trans-cyclohexane-1,2-diol. These findings are important steps towards the understanding of this highly enantioselective organocatalyst.     

多肽抑制剂抑制淀粉质多肽42构象转换的分子动力学模拟和结合自由能计算

应用分子动力学模拟和结合自由能计算方法研究了多肽抑制剂KLVFF、VVIA和LPFFD抑制淀粉质多肽42 (Aβ42)构象转换的分子机理. 结果表明, 三种多肽抑制剂均能够有效抑制Aβ42的二级结构由α-螺旋向β-折叠的构象转换. 另外, 多肽抑制剂降低了Aβ42分子内的疏水相互作用, 减少了多肽分子内远距离的接触, 有效抑制了Aβ42的疏水塌缩, 从而起到稳定其初始构象的作用. 这些抑制剂与Aβ42之间的疏水和静电相互作用(包括氢键)均有利于它们抑制Aβ42的构象转换. 此外, 抑制剂中的带电氨基酸残基可以增强其和Aβ42之间的静电相互作用(包括氢键), 并降低抑制剂之间的聚集, 从而大大增强对Aβ42构象转换的抑制能力. 但脯氨酸的引入会破坏多肽的线性结构, 从而大大降低其与Aβ42 之间的作用力. 上述分子模拟的结果揭示了多肽抑制剂KLVFF、VVIA和LPFFD抑制Aβ42构象转换的分子机理, 对于进一步合理设计Aβ的高效短肽抑制剂具有非常重要的理论指导意义.     

Engineering Peptide Inhibitors of the HFE–Transferrin Receptor 1 Complex

The protein HFE (homeostatic iron regulator) is a key regulator of iron metabolism, and mutations in HFE underlie the most frequent form of hereditary haemochromatosis (HH-type I). Studies have shown that HFE interacts with transferrin receptor 1 (TFR1), a homodimeric type II transmembrane glycoprotein that is responsible for the cellular uptake of iron via iron-loaded transferrin (holo-transferrin) binding. It has been hypothesised that the HFE/TFR1 interaction serves as a sensor to the level of iron-loaded transferrin in circulation by means of a competition mechanism between HFE and iron-loaded transferrin association with TFR1. To investigate this, a series of peptides based on the helical binding interface between HFE and TFR1 were generated and shown to significantly interfere with the HFE/TFR1 interaction in an in vitro proximity ligation assay. The helical conformation of one of these peptides, corresponding to the α1 and α2 helices of HFE, was stabilised by the introduction of sidechain lactam “staples”, but this did not result in an increase in the ability of the peptide to disrupt the HFE/TFR1 interaction. These peptides inhibitors of the protein–protein interaction between HFE and TFR1 are potentially useful tools for the analysis of the functional role of HFE in the regulation of hepcidin expression.     

Synthesis of 6- and 7-acyl-4H-benzothiazin-3-ones

Synthesis of 6- and 7-substituted benzoxazin-3-ones was already described in the literature by acylation of the corresponding benzoxazin-3-ones or cyclization of the corresponding 4- or 5-acyl-2-aminophenols. This paper describes original synthetic pathways to afford the 6- and 7-acyl products in the benzothiazin-3-one series, respectively, via Stille coupling reaction and by acylation.     

Photomodulation of the Conformation of Cyclic Peptides with Azobenzene Moieties in the Peptide Backbone

The cis ⇌ trans photoisomerization of the azobenzene building block 4-(4-aminophenylazo)benzoic acid incorporated in a cyclic peptide (see scheme) facilitated a two-state transition of the peptide chain from a rigid constrained conformation in the trans isomer into the largely free conformational space of the cis isomer.     

人类丝氨酸消旋酶的同源模建及其与多肽类抑制剂的分子对接

利用同源模建和分子动力学模拟方法构建了人类丝氨酸消旋酶(hSR)的三维结构, 并利用profile-3D和procheck方法评估了模型的可靠性. 在此基础上用分子对接程序(affinity)将多肽类抑制剂A和B分别与hSR进行对接, 获得了其复合物结构的理论模型. 通过配体与受体之间相互作用能和结构分析给出了此类抑制剂与hSR的具体结合方式, 明确了hSR与此类抑制剂结合时起重要作用的氨基酸残基, 为基于人类丝氨酸消旋酶三维结构的药物设计提供重要的参考信息.     

Synthesis,Biological Evaluation and Molecular Modeling of Cyclic Tetrapeptide Based Inhibitors HDAC

Histone deacetylases(HDACs) are considered to be among the most promising targets for the development of anti-cancer drugs, and HDAC inhibitors(HDACIs) have become a promising class of anti-cancer drugs. To explore whether thioacetyl group as the zinc binding group(ZBG) and a slight change in the hydrophobicity of the recognition domain of HDACIs could alter their activities, we synthesized a series of cyclo[-L-Am7(SAc)-Aib-L-Phe(n-Cl)-D-Pro-] and evaluated their HDAC-inhibitory and antiproliferative activities. The results show that these peptides could inhibit HDAC at 10^-9 mol/L level, and could selectively inhibit the proliferation of three human cancer cell lines with IC₅₀ at 10^-6 mol/L level. Docking study was conducted to examine the mechanisms by which these peptides interact with HDAC2. It appeared that a zinc ion in the active site of HDAC was coordinated by the carbonyl oxygen atom of the ZBG in the inhibitor. Both the ZBG domain of all the peptides and the surface recognition domain of cyclo[-L-Am7(SAc)-Aib-L-Phe(o-Cl)-D-Pro-] and that of cyclo[-L-Am7(SAc)-Aib-L-Phe(m-Cl)-D-Pro-] interacted with HDAC2 via hydrogen bonding. Hydrophobic interaction has been considered to provide favorable contributions to stabilizing the complexes, and the introduction of a chlorine atom at the aromatic ring on the L-Phe position of these peptides affected the interaction between each of these inhibitors and the enzyme, resulting in slight change in the structure of the surface recognition domain of the peptides.     

Mechanism‐Based Inhibitors of the Human Sirtuin 5 Deacylase: Structure–Activity Relationship,Biostructural, and Kinetic Insight

The sirtuin enzymes are important regulatory deacylases in a variety of biochemical contexts and may therefore be potential therapeutic targets through either activation or inhibition by small molecules. Here, we describe the discovery of the most potent inhibitor of sirtuin 5 (SIRT5) reported to date. We provide rationalization of the mode of binding by solving co‐crystal structures of selected inhibitors in complex with both human and zebrafish SIRT5, which provide insight for future optimization of inhibitors with more “drug‐like” properties. Importantly, enzyme kinetic evaluation revealed a slow, tight‐binding mechanism of inhibition, which is unprecedented for SIRT5. This is important information when applying inhibitors to probe mechanisms in biology.     

Mechanism‐Based Inhibitors of the Human Sirtuin 5 Deacylase: Structure–Activity Relationship,Biostructural, and Kinetic Insight

The sirtuin enzymes are important regulatory deacylases in a variety of biochemical contexts and may therefore be potential therapeutic targets through either activation or inhibition by small molecules. Here, we describe the discovery of the most potent inhibitor of sirtuin 5 (SIRT5) reported to date. We provide rationalization of the mode of binding by solving co‐crystal structures of selected inhibitors in complex with both human and zebrafish SIRT5, which provide insight for future optimization of inhibitors with more “drug‐like” properties. Importantly, enzyme kinetic evaluation revealed a slow, tight‐binding mechanism of inhibition, which is unprecedented for SIRT5. This is important information when applying inhibitors to probe mechanisms in biology.     

Mutual Effects of Substrates and Inhibitors in Reactions Catalyzed by the Nitrogenase Iron–Molybdenum Cofactor outside the Enzyme

The inhibiting effects of CO and N₂ on the ability of the nitrogenase iron–molybdenum cofactor (FeMoco) to catalyze acetylene reduction outside the protein were studied to obtain data on the mechanism of substrate reduction at the active center of the enzyme nitrogenase. It was found that CO and N₂ reacted with FeMoco that was separated from the enzyme and reduced by zinc amalgam (E = –0.84 V with reference to a normal hydrogen electrode (NHE)) (I) or europium amalgam (E = –1.4 V with reference to NHE) (II). In system I, CO reversibly inhibited the reaction of acetylene reduction to ethylene with K _i = 0.05 atm CO. In system II, CO inhibited the formation of the two products of C₂H₂ reduction in different manners: the mixed-type or competitive inhibition of ethylene formation with K _i = 0.003 atm CO and the incomplete competitive inhibition of ethane formation with K _i = 0.006 atm CO. The fraction of C₂H₆ in the reaction products was higher than 50% at a CO pressure of 0.05 atm because of the stronger inhibiting effect of CO on the formation of C₂H₄. A change in the product specificity of acetylene-reduction centers under exposure to CO was explained by some stabilization of the intermediate complex [FeMoco · C₂H₂] upon the simultaneous coordination of CO to the catalytic cluster. Because of this, the fraction of the many-electron reduction product (ethane) increased. The experimental results suggest that several active sites in the FeMoco cluster reduced outside the protein can be simultaneously occupied by substrates and (or) inhibitors. The inhibition of both ethane and ethylene formation by molecular nitrogen in system II is competitive with K _i = 0.5 atm N₂ for either product. That is, N₂ and C₂H₂ as ligands compete for the same coordination site in the reduced FeMoco cluster. The inhibiting effects of CO and N₂ on the catalytic behaviors of FeMoco outside the protein and as an enzyme constituent were compared.     

Preparation and Application of a Chemical Probe for Identifying the Targets of the Marine Cyclic Peptide Kapakahine A

Marine organisms are a rich source of bioactive secondary metabolites. Although many marine natural products with bioactivities have been isolated, successful elucidation of their mechanisms of action remains limited. In this study, we prepared a probe molecule based on the marine cyclic peptide kapakahine A (1) by introducing a linker with an azide terminal group, which enables the introduction of fluorescent groups for the effective monitoring of subcellular localization, or coupling to affinity beads for the pull-down of target proteins. The results of LC/MS/MS measurements, ProteinPilot analysis, and Western blotting suggest that kapakahine A interacts with the mitochondrial inner membrane proteins PHB1, PHB2, and ANT2, which is consistent with the results of the subcellular localization analysis using a fluorescent probe.