With the continuous progress on affinity peptide research, it has become more and more popular in pharmacology and medicine. lt is promising to study these viruses affinity peptide to treat infectious diseases. And th...With the continuous progress on affinity peptide research, it has become more and more popular in pharmacology and medicine. lt is promising to study these viruses affinity peptide to treat infectious diseases. And the analysis on the virus affinity peptide with high selectivity and high sensitivity could provide valuable means for disease detection, treatment as wel as the study on the molecular mechanism of virus affinity peptide. Therefore, we reviewed the bioinformatics pre-diction technologies of computer simulation, molecular docking and homology model-ing, as wel as the research method on analyzing and screening virus affinity pep-tide, such as Phage display technology.展开更多
Objective: To provide essential information for peptide inhibitor design, the interactions of Eps15 homology domain of Eps15 homology domain-containing protein 1 (EHD1 EH domain) with three peptides containing NPF ...Objective: To provide essential information for peptide inhibitor design, the interactions of Eps15 homology domain of Eps15 homology domain-containing protein 1 (EHD1 EH domain) with three peptides containing NPF (asparagine-proline-phenylalanine), DPF (aspartic acid-proline-phenylalanine), and GPF (glycine-proline-phenylalanine) motifs were deciphered at the atomic level. The binding affinities and the underlying structure basis were investigated. Methods: Molecular dynamics (MD) simulations were performed on EHD1 EH domain/peptide complexes for 60 ns using the GROMACS package. The binding free energies were calculated and decomposed by molecular mechanics/ generalized Born surface area (MM/GBSA) method using the AMBER package. The alanine scanning was performed to evaluate the binding hot spot residues using FoldX software. Results: The different binding affinities for the three peptides were affected dominantly by van der Waals interactions. Intermolecular hydrogen bonds provide the struc- tural basis of contributions of van der Waals interactions of the flanking residues to the binding. Conclusions: van der Waals interactions should be the main consideration when we design peptide inhibitors of EHD1 EH domain with high affinities. The ability to form intermolecular hydrogen bonds with protein residues can be used as the factor for choosing the flanking residues.展开更多
The concept of“pharmacophylogeny”was proposed by Peigen Xiao in the 1980s based on long-term studies of Chinese researchers since ancient times and especially the 1950s.The complicated relationships and connectivity...The concept of“pharmacophylogeny”was proposed by Peigen Xiao in the 1980s based on long-term studies of Chinese researchers since ancient times and especially the 1950s.The complicated relationships and connectivity between kinship of medicinal plants,their chemical profiles and therapeutic utilities are consistent goals of pharmacophylogeny studies,which benefit innovative drug R&D.In the present work,we reviewed the origin and a brief history of research in this field,as well as the status quo and recent progress of pharmacophylogeny.The concept“pharmacophylogenomics”is put forward to represent the expanding utility of pharmacophylogeny in botanical drug R&D.Pharmacophylogeny and pharmacophylogenomics are the synthesis of multiple disciplines,such as chemotaxonomy,plant morphology,plant biochemistry/molecular biology and omics,etc.Medicinal plants within the same phylogenetic groups may have the same or similar therapeutic compounds/effects,thus forming the core of pharmacophylogeny,which is the scientific law summed up from practice and applied to practice after refining and sublimation.In the past,pharmacophylogeny plays a big role in looking for alternative resources of imported drugs in China.At present,it continues to play an active role in expanding medicinal plant resources,quality control/identification of herbal medicines,as well as predicting the chemical constituents or active ingredients of herbal medicine and the identification and determination of chemical constituents.In the ongoing future,it will play a bigger role in the search for new drugs,sorting out,summarizing,and improving herbal medicine experiences,thus boosting the sustainable conservation and utilization of traditional/natural medicinal resources.展开更多
基金Supported by the Key Science and Technology Program of Henan Province(162102110136)the Science and Technology Fund for Outstanding Young People of Henan Academy of Agricultural Sciences(2016YQ28)~~
文摘With the continuous progress on affinity peptide research, it has become more and more popular in pharmacology and medicine. lt is promising to study these viruses affinity peptide to treat infectious diseases. And the analysis on the virus affinity peptide with high selectivity and high sensitivity could provide valuable means for disease detection, treatment as wel as the study on the molecular mechanism of virus affinity peptide. Therefore, we reviewed the bioinformatics pre-diction technologies of computer simulation, molecular docking and homology model-ing, as wel as the research method on analyzing and screening virus affinity pep-tide, such as Phage display technology.
基金supported by the National Natural Science Foundation of China(Nos.11172259 and 31471807)the Special Fund for Agro-scientific Research in the Public Interest(No.201403030),China
文摘Objective: To provide essential information for peptide inhibitor design, the interactions of Eps15 homology domain of Eps15 homology domain-containing protein 1 (EHD1 EH domain) with three peptides containing NPF (asparagine-proline-phenylalanine), DPF (aspartic acid-proline-phenylalanine), and GPF (glycine-proline-phenylalanine) motifs were deciphered at the atomic level. The binding affinities and the underlying structure basis were investigated. Methods: Molecular dynamics (MD) simulations were performed on EHD1 EH domain/peptide complexes for 60 ns using the GROMACS package. The binding free energies were calculated and decomposed by molecular mechanics/ generalized Born surface area (MM/GBSA) method using the AMBER package. The alanine scanning was performed to evaluate the binding hot spot residues using FoldX software. Results: The different binding affinities for the three peptides were affected dominantly by van der Waals interactions. Intermolecular hydrogen bonds provide the struc- tural basis of contributions of van der Waals interactions of the flanking residues to the binding. Conclusions: van der Waals interactions should be the main consideration when we design peptide inhibitors of EHD1 EH domain with high affinities. The ability to form intermolecular hydrogen bonds with protein residues can be used as the factor for choosing the flanking residues.
基金National Natural Science Foundation of China(Grant No.41977048)Natural Science Fund of Liaoning Province(Grant No.20180550190)the Scientific Research Funds Project of Liaoning Education Department(Grant No.JDL2019012)。
文摘The concept of“pharmacophylogeny”was proposed by Peigen Xiao in the 1980s based on long-term studies of Chinese researchers since ancient times and especially the 1950s.The complicated relationships and connectivity between kinship of medicinal plants,their chemical profiles and therapeutic utilities are consistent goals of pharmacophylogeny studies,which benefit innovative drug R&D.In the present work,we reviewed the origin and a brief history of research in this field,as well as the status quo and recent progress of pharmacophylogeny.The concept“pharmacophylogenomics”is put forward to represent the expanding utility of pharmacophylogeny in botanical drug R&D.Pharmacophylogeny and pharmacophylogenomics are the synthesis of multiple disciplines,such as chemotaxonomy,plant morphology,plant biochemistry/molecular biology and omics,etc.Medicinal plants within the same phylogenetic groups may have the same or similar therapeutic compounds/effects,thus forming the core of pharmacophylogeny,which is the scientific law summed up from practice and applied to practice after refining and sublimation.In the past,pharmacophylogeny plays a big role in looking for alternative resources of imported drugs in China.At present,it continues to play an active role in expanding medicinal plant resources,quality control/identification of herbal medicines,as well as predicting the chemical constituents or active ingredients of herbal medicine and the identification and determination of chemical constituents.In the ongoing future,it will play a bigger role in the search for new drugs,sorting out,summarizing,and improving herbal medicine experiences,thus boosting the sustainable conservation and utilization of traditional/natural medicinal resources.