Free energy simulation of helical transitions

An umbrella sampling method for the calculation of free energies for helical transitions is presented. The method biases structures toward helices of a desired radius and pitch. Although computationally complex, the method has negligible overhead in actual applications. To illustrate the method, calculations of the helical free energy landscape of several peptides are presented for both the CHARMM and the AMBER force fields. © 2012 Wiley Periodicals, Inc.     

联合UV及SDS-PAGE监测并优化碳二亚胺偶联法制备多肽免疫原

建立了一种多肽免疫抗原偶联的双监测法,获得一种操作简便、成功率高、适用范围广的碳二亚胺偶联法,并应用于多种肿瘤相关多肽标志物的免疫抗原制备。以合成多肽SP0104为标准品,牛血清白蛋白(BSA)为载体蛋白,碳二亚胺(EDC)为偶联剂,对加样顺序、投料比、偶联时间等关键条件进行考察,采用UV和SDS-PAGE对反应产物进行联合监测,以偶联比和偶联率联合评价反应条件。加样顺序为多肽和载体蛋白先混合再加到碳二亚胺中,三者质量比为1∶1∶1,偶联时间为12 h,偶联比在4∶1～12∶1之间,偶联率在9%～20%之间,所得SP0104多抗效价达到1∶80 000,MALDI-TOF质谱分析证实该抗体准确捕获目标抗原。用优化的偶联方法制备多肽SPC09、SPC15、SPG01、SPG03、SPG04的免疫抗原,所得免疫血清效价均在1∶1万以上,最高可达1∶51.2万。所建碳二亚胺多肽偶联联合监测法简便实用,可提高多肽抗体制备的成功率。     

基于多肽与金属离子作用的一种高选择性Cd2+荧光比率传感器

利用固相多肽合成法合成了一种新的多肽,将该多肽与荧光基团Dansyl偶联制备了一种新的荧光化学比率传感器:Dansyl-Cys-Pro-Pro-Cys-Trp-NH₂。利用荧光光谱研究了它与金属离子的相互作用。结果表明,与其它13种金属离子相比该多肽对金属Cd²⁺有很好的选择性。它能特异性识别Cd²⁺,具有水溶性好,响应时间快等优点。该肽对Cd²⁺具有很强的键合作用,其结合常数为3.0×10¹¹L²·mol^-2,检出限为11.5nmol·L^-1。     

An improved sample preparation method for the sensitive detection of peptides by MALDI‐MS

We describe here an optimization study of the sample preparation conditions for sensitive detection of peptides by matrix‐assisted laser desorption/ionization mass spectrometry (MALDI‐MS). Among many factors in the conditions, we varied the percent acetonitrile in the peptide solution, the percent acetonitrile in the matrix solution and the α‐cyano‐4‐hydroxycinnamic acid (CHCA) concentration in the matrix solution. CHCA was chosen because it is the most frequently used matrix for analyzing peptides. The well‐established dried‐droplet method was employed for sample deposition. The examined range of the concentration of CHCA was from 0.01 to 10 mg/ml, and the MeCN content of the solvent for matrix/analyte was 10% to 50%. The indicator for the detection sensitivity was the S/N ratio of the peaks of peptides used. Highly increased sensitivity (100‐ to 1000‐fold) was observed for the optimal CHCA concentration of 0.1 mg/ml in 20% MeCN/0.1% aq. trifluoroacetic acid (TFA), as compared with the conventional concentration (10 mg/ml) in 50% MeCN/0.1% aq. TFA. For example, the limit of detection of human ACTH 18–39 was 10 amol/well for the optimal condition but 10 fmol/well for the conventional condition. The optimal condition (0.1 mg/ml CHCA in 20% MeCN/0.1% aq. TFA) was verified with five model peptides and provided significant improvement in sensitivity (by two to three orders of magnitude) compared with the conventional conditions. Optimizing the CHCA concentration and solvent composition significantly improved the detection sensitivity in the analysis of peptides by MALDI‐MS. Copyright © 2013 John Wiley & Sons, Ltd.     

Bringing the Science of Proteins into the Realm of Organic Chemistry: Total Chemical Synthesis of SEP (Synthetic Erythropoiesis Protein)

Erythropoietin, commonly known as EPO, is a glycoprotein hormone that stimulates the production of red blood cells. Recombinant EPO has been described as “arguably the most successful drug spawned by the revolution in recombinant DNA technology”. Recently, the EPO glycoprotein molecule has re‐emerged as a major target of synthetic organic chemistry. In this article I will give an account of an important body of earlier work on the chemical synthesis of a designed EPO analogue that had full biological activity and improved pharmacokinetic properties. The design and synthesis of this “synthetic erythropoiesis protein” was ahead of its time, but has gained new relevance in recent months. Here I will document the story of one of the major accomplishments of synthetic chemistry in a more complete way than is possible in the primary literature, and put the work in its contemporaneous context.     

Cysteine/Penicillamine Ligation Independent of Terminal Steric Demands for Chemical Protein Synthesis

The chemical ligation of two unprotected peptides to generate a natural peptidic linkage specifically at the C‐ and N‐termini is a desirable goal in chemical protein synthesis but is challenging because it demands high reactivity and selectivity (chemo‐, regio‐, and stereoselectivity). We report an operationally simple and highly effective chemical peptide ligation involving the ligation of peptides with C‐terminal salicylaldehyde esters to peptides with N‐terminal cysteine/penicillamine. The notable features of this method include its tolerance of steric hinderance from the side groups on either ligating terminus, thereby allowing flexible disconnection at sites that are otherwise difficult to functionalize. In addition, this method can be expanded to selective desulfurization and one‐pot ligation‐desulfurization reactions. The effectiveness of this method was demonstrated by the synthesis of VISTA (216‐311), PD‐1 (192‐288) and Eglin C.     

A Novel d‐Peptide Identified by Mirror‐Image Phage Display Blocks TIGIT/PVR for Cancer Immunotherapy

The low response rate and adaptive resistance of PD‐1/PD‐L1 blockade demands the studies on novel therapeutic targets for cancer immunotherapy. We discovered that a novel immune checkpoint TIGIT expressed higher than PD‐1 in many tumors especially anti‐PD‐1 resistant tumors. Here, mirror‐image phage display bio‐panning was performed using the d ‐enantiomer of TIGIT synthesized by hydrazide‐based native chemical ligation. d ‐peptide ^DTBP‐3 was identified, which could occupy the binding interface and effectively block the interaction of TIGIT with its ligand PVR. ^DTBP‐3 showed proteolytic resistance, tumor tissue penetrating ability, and significant tumor suppressing effects in a CD8⁺ T cell dependent manner. More importantly, ^DTBP‐3 could inhibit tumor growth and metastasis in anti‐PD‐1 resistant tumor model. This is the first d ‐peptide targeting TIGIT, which could serve as a potential candidate for cancer immunotherapy.     

Design,identification, antifungal evaluation and molecular modeling of chlorotetaine derivatives as new anti-fungal agents

Abstract

It is feasible to rationally modify existing bioactive components for new drug development, achieving molecules with improved biological activities. In this study, rational modification of chlorotetaine was carried out following in silico molecular modelling to enhance interactions between the fungal oligopeptide transmembrane transporter PTR22 and the ligand. The peptide obtained with the lowest docking energy, Lys-chlorotetaine (LC), displayed an improved antifungal effect compared with chlorotetaine. The lowest minimum inhibitory concentration observed against a tested pathogen was 1.47?µg/mL (Candida krusei CBS573), which was satisfactory. To thoroughly explore the detailed interactions between the transporter and LC, molecular dynamics simulation was also performed, which revealed that LC could bind to the transporter via different intermolecular interactions from chlorotetaine, and predicted electrostatic interactions (salt-bridges) would enable the more efficient release of LC. This study provides a simple and reliable method for the rational modification of oligopeptide antibiotics.