Insights into Protein-Ligand Noncovalent Interaction Networks: A Database Survey and Quantum Chemistry Calculation Study
文献类型：期刊论文
| 作者 | Luo, Ruitong1,5,6; Han, Zijian1,5,6; Li, Jintian1,5,6; Chen, Yuanjie5,6,7; Peng, Ziyu4,5,6; Zhang, Qian3; Zhu, Weiliang1,4,5,6; Xu, Zhijian1,2,4,5,6,7 |
| 刊名 | JOURNAL OF MEDICINAL CHEMISTRY
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| 出版日期 | 2026-02-16 |
| 页码 | 11 |
| ISSN号 | 0022-2623 |
| DOI | 10.1021/acs.jmedchem.5c03216 |
| 英文摘要 | Protein-ligand binding is largely determined by multiple noncovalent interactions (NCIs), which may exhibit synergistic or antagonistic effects. Here, we applied an approach combining PDB statistics with QM/MM calculations to quantify relationships among five major NCIs: halogen bonds (XB), hydrogen bonds (HB), cation-pi interactions (CP), pi-pi interactions (PP), and salt bridges (SB). Statistical analysis showed that 69.28% of the ligands with SB acceptors interact with protein residues, followed by HB acceptors (65.21%) and XB donors (62.76%). Energy analysis revealed the strongest antagonism between the CP acceptor and SB acceptor (median Delta E-Syn = 1.31 kcal/mol) and the strongest synergy between the HB donor and acceptor (-0.73 kcal/mol). The effects are enhanced when their interaction distances are <7.5 & Aring;. For three-NCI systems, overall energies were well approximated by the sum of the two-NCI systems (R-2 = 0.980). These results reveal a complicated NCI network, which provides guidance for rational ligand design. |
| WOS关键词 | MOLECULAR-ORBITAL METHODS ; AUGMENTED BASIS-SETS ; 3RD-ROW ATOMS ; HALOGEN BOND ; ELEMENTS ; COOPERATIVITY ; POLARIZATION ; EXTENSION ; HYDROGEN ; DESIGN |
| 资助项目 | Shanghai Municipal Education Commission[2024AI02010] ; National Natural Science Foundation of China[82273851] ; National Key Research and Development Program of China[2022YFA1004304] |
| WOS研究方向 | Pharmacology & Pharmacy |
| 语种 | 英语 |
| WOS记录号 | WOS:001693028000001 |
| 出版者 | AMER CHEMICAL SOC |
| 源URL | [http://119.78.100.183/handle/2S10ELR8/323047]  |
| 专题 | 国家级研究中心_原创新药研究全国重点实验室 |
| 通讯作者 | Zhu, Weiliang; Xu, Zhijian |
| 作者单位 | 1.Univ Chinese Acad Sci, Sch Pharm, Beijing 100049, Peoples R China 2.East China Univ Sci & Technol, Shanghai Frontiers Sci Ctr Optogenet Tech Cell Met, Shanghai Key Lab New Drug Design, State Key Lab Bioreactor Engn,Sch Pharm, Shanghai 200237, Peoples R China 3.East China Normal Univ, Shanghai Frontiers Sci Ctr Mol Intelligent Synth, Sch Comp Sci & Technol, Shanghai 200241, Peoples R China 4.Nanjing Univ Chinese Med, Sch Chinese Mat Med, Nanjing 210046, Peoples R China 5.Chinese Acad Sci, State Key Lab Drug Res, Shanghai 201203, Peoples R China 6.Chinese Acad Sci, Shanghai Inst Mat Med, Drug Discovery & Design Ctr, Shanghai 201203, Peoples R China 7.Henan Univ, Sch Pharm, Kaifeng 475004, Peoples R China |
| 推荐引用方式 GB/T 7714 | Luo, Ruitong,Han, Zijian,Li, Jintian,et al. Insights into Protein-Ligand Noncovalent Interaction Networks: A Database Survey and Quantum Chemistry Calculation Study[J]. JOURNAL OF MEDICINAL CHEMISTRY,2026:11. |
| APA | Luo, Ruitong.,Han, Zijian.,Li, Jintian.,Chen, Yuanjie.,Peng, Ziyu.,...&Xu, Zhijian.(2026).Insights into Protein-Ligand Noncovalent Interaction Networks: A Database Survey and Quantum Chemistry Calculation Study.JOURNAL OF MEDICINAL CHEMISTRY,11. |
| MLA | Luo, Ruitong,et al."Insights into Protein-Ligand Noncovalent Interaction Networks: A Database Survey and Quantum Chemistry Calculation Study".JOURNAL OF MEDICINAL CHEMISTRY (2026):11. |
入库方式： OAI收割
来源：上海药物研究所
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