Lipinski’s “Rule of Five” was introduced for predicting oral bioavailability to describe drug-like molecules. For the purpose of this research the rules were used to separate potential inhibitors of HIV-1 integrase...Lipinski’s “Rule of Five” was introduced for predicting oral bioavailability to describe drug-like molecules. For the purpose of this research the rules were used to separate potential inhibitors of HIV-1 integrase (1BIS.pdb) into two groups: drug-like and nondrug-like. If one of Lipinski’s “Rule of Five” was not followed the potential inhibitor was classified as nondrug-like. Thirty molecules were identified from the literature, twenty-four drug-like and six nondrug-like, that were docked into the active site of 1BIS.pdb (considered the non-mutated protein) and two mutant models, Y143R and N155H. These are two of the mutations that have led to increased resistance to HIV-1 integrase drugs such as raltegravir and elvitegravir. The computational software, ICM-Pro (Molsoft L.L.C.), was used to determine the estimated binding energy (EBE) of the drug/protein complex. It was found that the nondrug-like molecules generally had a more negative EBE, that is, tighter binding with 1BIS. pdb, though there were several exceptions in the drug-like group. With the protein mutant model Y143R, the majority of drug-like (58%) and nondrug-like molecules (67%) had tighter binding. However, for the mutant model N155H, there was the same percent (46%) of drug-like molecules with tighter binding with the mutant model as with 1BIS.pdb. The drug-like molecules were used when there was a ≥1 kcal/mole difference between 1BIS.pdb and either of the two mutant models to suggest a pharmacophore with structural characteristics for an HIV-1 integrase inhibitor.展开更多
Abstract Conotoxins belong to the large families of disulfide-rich peptide toxins from cone snail venom, and can act on a broad spectrum of ion channels and receptors. They are classified into different subtypes based...Abstract Conotoxins belong to the large families of disulfide-rich peptide toxins from cone snail venom, and can act on a broad spectrum of ion channels and receptors. They are classified into different subtypes based on their targets. The a-conotoxins selectively inhibit the current of the nicotinic acetylcholine receptors. Because of their unique selectivity towards distinct nAChR subtypes, a-conotoxins become valuable tools in nAChR study. In addition to the X-ray structures of a-conotoxins in complex with acetyleholine-binding protein, a homolog of the nAChR ligand-binding domain, the high-resolution crystal structures of the extracellular domain of the al and a9 subunits are also obtained. Such structures not only revealed the details of the configuration of nAChR, but also provided higher sequence identity templates for modeling the binding modes of a-conotoxins to nAChR. This mini-review summarizes recent modeling studies for the determination of the binding modes of a-conotoxins to nAChR. As there are not crystal structures of the nAChR in complex with conotoxins, computational modeling in combination of mutagenesis data is expected to reveal the molecular recognition mechanisms that govern the interactions between a-conotoxins and nAChR at molecular level. An accurate determination of the binding modes of a-conotoxins on AChRs allows rational design of a-conotoxin analogues with improved potency or selectivity to nAChRs.展开更多
Influenza A(A/H_(x)N_(y))is a significant public health concern due to its high infectiousness and mortality.Neuraminidase,which interacts with sialic acid(SIA)in host cells,has become an essential target since its hi...Influenza A(A/H_(x)N_(y))is a significant public health concern due to its high infectiousness and mortality.Neuraminidase,which interacts with sialic acid(SIA)in host cells,has become an essential target since its highly conserved catalytic center structure,while resistance mutations have already generated.Here,a detailed investigation of the drug resistance mechanism caused by mutations was performed for subtype N9(A/H7N9).Molecular dynamics simulation and alanine-scanning-interaction-entropy method(ASIE)were used to explore the critical differences between N9 and Zanamivir(ZMR)before and after R294K mutation.The results showed that the mutation caused the hydrogen bond between Arg294 and ZMR to break,then the hydrogen bonding network was disrupted,leading to weakened binding ability and resistance.While in wild type(A/H7N9^(WT)),this hydrogen bond was initially stable.Meanwhile,N9 derived from A/H11N9 was obtained as an R292K mutation.Then the relative binding free energy of N9 with five inhibitors(SIA,DAN,ZMR,G28,and G39)was predicted,basically consistent with experimental values,indicating that the calculated results were reliable by ASIE.In addition,Arg292 and Tyr406 were hot spots in the A/H11N9^(WT)-drugs.However,Lys292 was not observed as a favorable contributing residue in A/H11N9^(R292K),which may promote resistance.In comparison,Tyr406 remained the hotspot feature when SIA,ZMR,and G28 binding to A/H11N9^(R292K).Combining the two groups,we speculate that the resistance was mainly caused by the disruption of the hydrogen bonding network and the transformation of hotspots.This study could guide novel drug delivery of drug-resistant mutations in the treatment of A/H_(x)N9.展开更多
As a general mechanism for governing the bioactivity of membrane receptors,allosteric modulation is critical in cell signaling and cell communication but remains difficult to measure in situ.Herein,we introduce a data...As a general mechanism for governing the bioactivity of membrane receptors,allosteric modulation is critical in cell signaling and cell communication but remains difficult to measure in situ.Herein,we introduce a data mining-integrated tracking microscopy(DMITM)to investigate allosteric modulation of membrane receptors in the native state in live cells.Using Kmeans clustering-based hidden Markov modeling to uncover the ligand binding and unbinding events with diffusivity variations of ligand-conjugated nanoprobes as observations.展开更多
Molecular dynamics(MD)simulation is a computational technique that analyzes the movement of a system of particles over a given period.MD can provide detailed information about the fluctuations and conformational chang...Molecular dynamics(MD)simulation is a computational technique that analyzes the movement of a system of particles over a given period.MD can provide detailed information about the fluctuations and conformational changes of biomolecules at the atomic level over time.In recent years,MD has been widely applied to the discovery of peptides and peptide-like molecules that may serve as severe acute respiratory syndrome coronavirus 2(SARS-CoV-2)inhibitors.This review summarizes recent advances in such explorations,focusing on four protein targets:angiotensin-converting enzyme 2(ACE2),spike protein(S protein),main protease(M^(pro)),and papain-like protease(PL^(pro)).These four proteins are important druggable targets of SARS-CoV-2 because of their roles in viral entry,maturation,and infectivity of the virus.A review of the literature revealed that ACE2,S protein,and M^(pro) have received more attention in MD research than PL^(pro).Inhibitors of the four targets identified by MD simulations included peptides derived from food and other bioresources,peptides designed using the targets as templates,and peptide-like molecules retrieved from databases.Many of the inhibitors have yet to be validated in experimental assays for potency.Nevertheless,the role of MD simulation as an efficient tool in the early stages of anti-SARS-CoV-2 drug discovery agents has been demonstrated.展开更多
Recent studies have revealed that bile acids(BAs)are not only facilitators of dietary lipid absorption but also important signaling molecules exerting multiple physiological functions.Some major signaling pathways inv...Recent studies have revealed that bile acids(BAs)are not only facilitators of dietary lipid absorption but also important signaling molecules exerting multiple physiological functions.Some major signaling pathways involving the nuclear BAs receptor farnesoid X receptor and the G protein-coupled BAs receptor TGR5/M-BAR have been identified to be the targets of BAs.BAs regulate their own homeostasis via signaling pathways.BAs also affect diverse metabolic pathways including glucose metabolism,lipid metabolism and energy expenditure.This paper suggests the mechanism of controlling metabolism via BA signaling and demonstrates that BA signaling is an attractive therapeutic target of the metabolic syndrome.展开更多
传统的观点认为G蛋白偶联受体(G protein coupled receptor,GPCR)主要以单体形式存在,其作用是线性的,即配体结合到正位作用位点来引起信号下游传导。但大量事实证明,GPCR也能以同源或异源二聚体的形式存在。在二聚体中,由于配体结合到...传统的观点认为G蛋白偶联受体(G protein coupled receptor,GPCR)主要以单体形式存在,其作用是线性的,即配体结合到正位作用位点来引起信号下游传导。但大量事实证明,GPCR也能以同源或异源二聚体的形式存在。在二聚体中,由于配体结合到二聚体中的一个单体而引起对另一个单体的别构调节,从而形成别构位点,使受体的信号途径发生改变,引起一系列功能变化。别构调节剂与传统的激动剂相比有许多优点,因此是重要的GPCR靶标的候选药物。本文就GPCR二聚体的别构调节对受体功能的影响,以及筛选GPCR二聚体别构药物的技术做一简要综述,从而有助于GPCR药物的开发和利用。展开更多
文摘Lipinski’s “Rule of Five” was introduced for predicting oral bioavailability to describe drug-like molecules. For the purpose of this research the rules were used to separate potential inhibitors of HIV-1 integrase (1BIS.pdb) into two groups: drug-like and nondrug-like. If one of Lipinski’s “Rule of Five” was not followed the potential inhibitor was classified as nondrug-like. Thirty molecules were identified from the literature, twenty-four drug-like and six nondrug-like, that were docked into the active site of 1BIS.pdb (considered the non-mutated protein) and two mutant models, Y143R and N155H. These are two of the mutations that have led to increased resistance to HIV-1 integrase drugs such as raltegravir and elvitegravir. The computational software, ICM-Pro (Molsoft L.L.C.), was used to determine the estimated binding energy (EBE) of the drug/protein complex. It was found that the nondrug-like molecules generally had a more negative EBE, that is, tighter binding with 1BIS. pdb, though there were several exceptions in the drug-like group. With the protein mutant model Y143R, the majority of drug-like (58%) and nondrug-like molecules (67%) had tighter binding. However, for the mutant model N155H, there was the same percent (46%) of drug-like molecules with tighter binding with the mutant model as with 1BIS.pdb. The drug-like molecules were used when there was a ≥1 kcal/mole difference between 1BIS.pdb and either of the two mutant models to suggest a pharmacophore with structural characteristics for an HIV-1 integrase inhibitor.
基金supported by the National Natural Science Foundation of China (81502977 to Dr. Yu R. and 81373322 to Dr. Jiang T.)China Postdoctoral Science Foundation funded project (No.861505020050 for Dr. Yu R.)+1 种基金Special Foundation for Qingdao Basic Research Program (15-9-1-85-jch)Fundamental Research Funds for the Central Universities (No.841512007 for Dr. Yu R.)
文摘Abstract Conotoxins belong to the large families of disulfide-rich peptide toxins from cone snail venom, and can act on a broad spectrum of ion channels and receptors. They are classified into different subtypes based on their targets. The a-conotoxins selectively inhibit the current of the nicotinic acetylcholine receptors. Because of their unique selectivity towards distinct nAChR subtypes, a-conotoxins become valuable tools in nAChR study. In addition to the X-ray structures of a-conotoxins in complex with acetyleholine-binding protein, a homolog of the nAChR ligand-binding domain, the high-resolution crystal structures of the extracellular domain of the al and a9 subunits are also obtained. Such structures not only revealed the details of the configuration of nAChR, but also provided higher sequence identity templates for modeling the binding modes of a-conotoxins to nAChR. This mini-review summarizes recent modeling studies for the determination of the binding modes of a-conotoxins to nAChR. As there are not crystal structures of the nAChR in complex with conotoxins, computational modeling in combination of mutagenesis data is expected to reveal the molecular recognition mechanisms that govern the interactions between a-conotoxins and nAChR at molecular level. An accurate determination of the binding modes of a-conotoxins on AChRs allows rational design of a-conotoxin analogues with improved potency or selectivity to nAChRs.
基金supported by the National Natural Science Foundation of China(No.11774207)。
文摘Influenza A(A/H_(x)N_(y))is a significant public health concern due to its high infectiousness and mortality.Neuraminidase,which interacts with sialic acid(SIA)in host cells,has become an essential target since its highly conserved catalytic center structure,while resistance mutations have already generated.Here,a detailed investigation of the drug resistance mechanism caused by mutations was performed for subtype N9(A/H7N9).Molecular dynamics simulation and alanine-scanning-interaction-entropy method(ASIE)were used to explore the critical differences between N9 and Zanamivir(ZMR)before and after R294K mutation.The results showed that the mutation caused the hydrogen bond between Arg294 and ZMR to break,then the hydrogen bonding network was disrupted,leading to weakened binding ability and resistance.While in wild type(A/H7N9^(WT)),this hydrogen bond was initially stable.Meanwhile,N9 derived from A/H11N9 was obtained as an R292K mutation.Then the relative binding free energy of N9 with five inhibitors(SIA,DAN,ZMR,G28,and G39)was predicted,basically consistent with experimental values,indicating that the calculated results were reliable by ASIE.In addition,Arg292 and Tyr406 were hot spots in the A/H11N9^(WT)-drugs.However,Lys292 was not observed as a favorable contributing residue in A/H11N9^(R292K),which may promote resistance.In comparison,Tyr406 remained the hotspot feature when SIA,ZMR,and G28 binding to A/H11N9^(R292K).Combining the two groups,we speculate that the resistance was mainly caused by the disruption of the hydrogen bonding network and the transformation of hotspots.This study could guide novel drug delivery of drug-resistant mutations in the treatment of A/H_(x)N9.
基金supported by theNationalNatural Science Foundation of China(grant nos.21874039,21605045,21890744,and 21521063)Fundamental Research Funds for Central Universities at Hunan University。
文摘As a general mechanism for governing the bioactivity of membrane receptors,allosteric modulation is critical in cell signaling and cell communication but remains difficult to measure in situ.Herein,we introduce a data mining-integrated tracking microscopy(DMITM)to investigate allosteric modulation of membrane receptors in the native state in live cells.Using Kmeans clustering-based hidden Markov modeling to uncover the ligand binding and unbinding events with diffusivity variations of ligand-conjugated nanoprobes as observations.
文摘Molecular dynamics(MD)simulation is a computational technique that analyzes the movement of a system of particles over a given period.MD can provide detailed information about the fluctuations and conformational changes of biomolecules at the atomic level over time.In recent years,MD has been widely applied to the discovery of peptides and peptide-like molecules that may serve as severe acute respiratory syndrome coronavirus 2(SARS-CoV-2)inhibitors.This review summarizes recent advances in such explorations,focusing on four protein targets:angiotensin-converting enzyme 2(ACE2),spike protein(S protein),main protease(M^(pro)),and papain-like protease(PL^(pro)).These four proteins are important druggable targets of SARS-CoV-2 because of their roles in viral entry,maturation,and infectivity of the virus.A review of the literature revealed that ACE2,S protein,and M^(pro) have received more attention in MD research than PL^(pro).Inhibitors of the four targets identified by MD simulations included peptides derived from food and other bioresources,peptides designed using the targets as templates,and peptide-like molecules retrieved from databases.Many of the inhibitors have yet to be validated in experimental assays for potency.Nevertheless,the role of MD simulation as an efficient tool in the early stages of anti-SARS-CoV-2 drug discovery agents has been demonstrated.
文摘Recent studies have revealed that bile acids(BAs)are not only facilitators of dietary lipid absorption but also important signaling molecules exerting multiple physiological functions.Some major signaling pathways involving the nuclear BAs receptor farnesoid X receptor and the G protein-coupled BAs receptor TGR5/M-BAR have been identified to be the targets of BAs.BAs regulate their own homeostasis via signaling pathways.BAs also affect diverse metabolic pathways including glucose metabolism,lipid metabolism and energy expenditure.This paper suggests the mechanism of controlling metabolism via BA signaling and demonstrates that BA signaling is an attractive therapeutic target of the metabolic syndrome.
文摘传统的观点认为G蛋白偶联受体(G protein coupled receptor,GPCR)主要以单体形式存在,其作用是线性的,即配体结合到正位作用位点来引起信号下游传导。但大量事实证明,GPCR也能以同源或异源二聚体的形式存在。在二聚体中,由于配体结合到二聚体中的一个单体而引起对另一个单体的别构调节,从而形成别构位点,使受体的信号途径发生改变,引起一系列功能变化。别构调节剂与传统的激动剂相比有许多优点,因此是重要的GPCR靶标的候选药物。本文就GPCR二聚体的别构调节对受体功能的影响,以及筛选GPCR二聚体别构药物的技术做一简要综述,从而有助于GPCR药物的开发和利用。
