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関連する概念動画

Peptide Bonds02:43

Peptide Bonds

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A peptide bond covalently attaches amino acids through a dehydration reaction. One amino acid's carboxyl group and another amino acid's amino group combine, releasing a water molecule. The resulting bond is the peptide bond. The products that such linkages form are peptides. As more amino acids join this growing chain, the resulting chain is a polypeptide. Each polypeptide has a free amino group at one end. This end has the N-terminal, or the amino-terminal, and the other end has a free...
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Protein and Protein Structure02:15

Protein and Protein Structure

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Proteins are one of the most abundant organic molecules in living systems and have the most diverse range of functions of all macromolecules. Proteins may be structural, regulatory, contractile, or protective. They may serve in transport, storage, or membranes; or they may be toxins or enzymes. Their structures, like their functions, vary greatly. They are all, however, amino acid polymers arranged in a linear sequence.
A protein's shape is critical to its function. For example, an enzyme...
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Covalently Linked Protein Regulators02:04

Covalently Linked Protein Regulators

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Proteins can undergo many types of post-translational modifications, often in response to changes in their environment. These modifications play an important role in the function and stability of these proteins. Covalently linked molecules include functional groups, such as methyl, acetyl, and phosphate groups, and also small proteins, such as ubiquitin. There are around 200 different types of covalent regulators that have been identified.
These groups modify specific amino acids in a protein....
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VSEPR Theory for Determination of Electron Pair Geometries
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In most mammalian species, females have two X sex chromosomes and males have an X and Y. As a result, mutations on the X chromosome in females may be masked by the presence of a normal allele on the second X. In contrast, a mutation on the X chromosome in males more often causes observable biological defects, as there is no normal X to compensate. Trait variations arising from mutations on the X chromosome are called “X-linked”.
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Stereoisomerism of Cyclic Compounds02:33

Stereoisomerism of Cyclic Compounds

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In this lesson, we delve into the role of ring conformation and its stability, which determines the spatial arrangement and, consequently, the molecular symmetry and stereoisomerism of cyclic compounds. 1,2-Dimethylcyclohexane is used as a case study to evaluate the possible number of stereoisomers. Here, given the multiple (n = 2) chiral centers, there are 2n = 4 possible configurations that lack a plane of symmetry, as the ring skeleton exists in a non-planar chair conformation. In addition,...
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Constructing Thioether/Vinyl Sulfide-tethered Helical Peptides Via Photo-induced Thiol-ene/yne Hydrothiolation
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StrEAMM-Thioether：チオエーテル結合環状ペプチドの効率的な構造予測

Minh Ngoc Ho1, Jiayuan Miao1, Yi Shan2

  • 1Department of Chemistry, School of Arts and Sciences, Tufts University, Medford, Massachusetts 02155, United States.

The journal of physical chemistry. B
|February 6, 2026
PubMed
まとめ
この要約は機械生成です。

環状ペプチド構造を予測する機械学習法を開発し、創薬を改善した。この計算ツールは、チオエーテル結合環状ペプチドを正確にモデル化し、新規治療薬のデザインを支援する。

キーワード:
環状ペプチドチオエーテル構造予測創薬計算化学機械学習

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Constructing Cyclic Peptides Using an On-Tether Sulfonium Center
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科学分野:

  • 計算化学
  • 生物物理学
  • 医薬品化学

背景:

  • 環状ペプチドは、タンパク質間相互作用や細胞膜を標的とする有望な治療薬である。
  • 環状ペプチドの構造アンサンブルの予測は、合理的な創薬デザインに不可欠であるが、実験的には困難である。
  • 分子動力学（MD）などの既存の計算方法は計算負荷が高い。

研究 の 目的:

  • StrEAMM（Structural Ensembles Achieved by Molecular Dynamics and Machine Learning）プラットフォームをチオエーテル結合環状ペプチドに拡張する。
  • チオエーテル結合環状ペプチドの構造アンサンブルを予測するための高速かつ正確な計算方法を開発する。
  • mRNAディスプレイ（display）スクリーニングと互換性のある環状ペプチド治療薬のデザインと発見を容易にする。

主な方法:

  • StrEAMMフレームワーク内でグラフニューラルネットワークモデルを開発およびトレーニングした。
  • モデルを適用して、チオエーテル結合環状ペプチドの構造アンサンブルを予測した。
  • 予測された環状ペプチドを実験的に合成し、溶液核磁気共鳴（NMR）を用いて特性評価した。

主要な成果:

  • StrEAMM-チオエーテルモデルは、チオエーテル結合環状ペプチドの構造アンサンブルを正確に予測する。
  • モデル予測に基づいて、構造的に良好な4つのチオエーテル結合環状ペンタペプチドが同定された。
  • 実験的なNMR特性評価は、計算によって予測された構造と一般的に一致した。

結論:

  • StrEAMM-チオエーテルモデルは、環状ペプチド構造アンサンブルを予測するための高速かつ信頼性の高い方法を提供する。
  • このアプローチは、環状ペプチド治療薬のデザインと発見を合理化する。
  • モデルは、効率的な創薬のためにmRNAディスプレイプラットフォームと統合できる。