SARS-CoV-2 variants are constantly emerging,hampering public health measures in controlling the number of infections.While it is well established that mutations in spike proteins observed for the different variants di...SARS-CoV-2 variants are constantly emerging,hampering public health measures in controlling the number of infections.While it is well established that mutations in spike proteins observed for the different variants directly affect virus entry into host cells,there remains a need for further expansion of systematic and multifaceted comparisons.Here,we comprehensively studied the effect of spike protein mutations on spike expression and proteolytic activation,binding affinity,viral entry efficiency and host cell tropism of eight variants of concern(VOC)and variants of interest(VOI).We found that both the full-length spike and its receptor-binding domain(RBD)of Omicron bind to hACE2 with an affinity similar to that of the wild-type.In addition,Alpha,Beta,Delta and Lambda pseudoviruses gained significantly enhanced cell entry ability compared to the wild-type,while the Omicron pseudoviruses showed a slightly increased cell entry,suggesting the vastly increased rate of transmission observed for Omicron variant is not associated with its affinity to hACE2.We also found that the spikes of Omicron and Mu showed lower S1/S2 cleavage efficiency and inefficiently utilized TMPRSS2 to enter host cells than others,suggesting that they prefer the endocytosis pathway to enter host cells.Furthermore,all variants'pseudoviruses we tested gained the ability to enter the animal ACE2-expressing cells.Especially the infection potential of rats and mice showed significantly increased,strongly suggesting that rodents possibly become a reservoir for viral evolution.The insights gained from this study provide valuable guidance for a targeted approach to epidemic control,and contribute to a better understanding of SARS-CoV-2 evolution.展开更多
Direct separation of high purity ethylene(C_(2)H_(4))from an ethane(C_(2)H_(6))/ethylene mixture is a critical and challenging task owing to the very similar molecular size and physical properties of the two component...Direct separation of high purity ethylene(C_(2)H_(4))from an ethane(C_(2)H_(6))/ethylene mixture is a critical and challenging task owing to the very similar molecular size and physical properties of the two components.While some studies have attempted this separation,there is a lack of excellent porous materials with strong binding affinity for C_(2)H_(6)-selective adsorption via an energy-efficient adsorptive separation process.Herein,we report a titanium metal-organic framework with strong binding affinity and excellent stability for the highly efficient removal of C_(2)H_(6) from C_(2)H_(6)/C_(2)H_(4) mixtures.Single component adsorption isotherms demonstrated a larger amount of adsorbed ethane(1.16 mmol·g^(-1) under 1 kPa)and high C_(2)H_(6)/C_(2)H_(4) selectivity(2.7)for equimolar C_(2)H_(6)/C_(2)H_(4) mixtures,especially in the low-pressure range,which is further confirmed by the results of grand canonical Monte Carlo simulations for C_(2)H_(6) adsorption in this framework.The experimental breakthrough curves showed that C_(2)H_(4) with a high purity was collected directly from both 1:9 and 1:15 C_(2)H_(6)/C_(2)H_(4)(volume ratio)mixtures at 298 K and 100 kPa.Moreover,the unchanged adsorption and separation performance after cycling experiments confirmed the promising applicability of this material in future.展开更多
Drug target relationship(DTR)prediction is a rapidly evolving area of research in com-putational drug discovery.Despite recent advances in computational solutions that have overcome the challenges of in vitro and in v...Drug target relationship(DTR)prediction is a rapidly evolving area of research in com-putational drug discovery.Despite recent advances in computational solutions that have overcome the challenges of in vitro and in vivo experiments,most computational methods still focus on binary classification.They ignore the importance of binding affinity,which correctly distinguishes between on-targets and off-targets.In this study,we propose a deep learning model based on the microstruc-ture of compounds and proteins to predict drug-target binding affinity(DTA),which utilizes topo-logical structure information of drug molecules and sequence semantic information of proteins.In this model,graph attention network(GAT)is used to capture the deep features of the compound molecular graph,and bidirectional long short-term memory(BiLSTM)network is used to extract the protein sequence features,and the pharmacological context of DTA is obtained by combining the two.The results show that the proposed model has achieved superior performance in both cor-rectly predicting the value of interaction strength and correctly discriminating the ranking of bind-ing strength compared to the state-of-the-art baselines.A case study experiment on COVID-19 con-firms that the proposed DTA model can be used as an effective pre-screening tool in drug discovery.展开更多
Environmental control of the alcohol dehydrogenase(Adh)and other stress response genes in plants is in part brought about by transcriptional regulation involving the G-box cis-acting DNA element and bZIP G-box Binding...Environmental control of the alcohol dehydrogenase(Adh)and other stress response genes in plants is in part brought about by transcriptional regulation involving the G-box cis-acting DNA element and bZIP G-box Binding Factors(GBFs).The mechanisms of GBF regulation and requirements for additional factors in this control process are not well understood.In an effort to identify potential GBF binding and control partners,maize GBF1 was used as bait in a yeast two-hybrid screen of an A.thaliana cDNA library.GBF Interacting Protein 1(GIP1)arose from the screen as a 496 amino acid protein with a predicted molecular weight of 53,748 kDa that strongly interacts with GBFs.Northern analysis of A.thaliana tissue suggests a 1.8-1.9 kb GIP1 transcript,predominantly in roots.Immunolocalization studies indicate that GIP1 protein is mainly localized to the nucleus.In vitro electrophoretic mobility shift assays using an Adh G-box DNA probe and recombinant A.thaliana GBF3 or maize GBF1,showed that the presence of GIP1 resulted in a tenfold increase in GBF DNA binding activity without altering the migration,suggesting a transient association between GIP1 and GBF.Addition of GIP1 to intentionally aggregated GBF converted GBF to lower molecular weight macromolecular complexes and GIP1 also refolded denatured rhodanese in the absence of ATP.These data suggest GIP1 functions to enhance GBF DNA binding activity by acting as a potent nuclear chaperone or crowbar,and potentially regulates the multimeric state of GBFs,thereby contributing to bZIP-mediated gene regulation.展开更多
Integrins are heterodimers that mediate cell adhesion and transduce signals bidirectionally across the cell membrane.Integrins often exist in low affinity(or inactive) states for
The cellular functions of proteins are maintained by forming diverse complexes.The stability of these com-plexes is quantified by the measurement of binding affinity,and mutations that alter the binding affinity can c...The cellular functions of proteins are maintained by forming diverse complexes.The stability of these com-plexes is quantified by the measurement of binding affinity,and mutations that alter the binding affinity can cause various diseases such as cancer and diabetes.As a result,accurate estimation of the binding stability and the effects of mutations on changes of binding affinity is a crucial step to understanding the biological functions of proteins and their dysfunctional consequences.It has been hypothesized that the stability of a protein complex is dependent not only on the residues at its binding interface by pairwise interactions but also on all other remaining residues that do not appear at the binding interface.Here,we computationally reconstruct the binding affinity by decomposing it into the contributions of interfacial residues and other non-interfacial residues in a protein complex.We further assume that the contributions of both interfacial and non-interfacial residues to the binding affinity depend on their local structural environments such as solvent-accessible surfaces and secondary structural types.The weights of all corresponding parameters are optimized by Monte-Carlo simulations.After cross-validation against a large-scale dataset,we show that the model not only shows a strong correlation between the absolute values of the experimental and calculated binding affinities,but can also be an effective approach to predict the relative changes of binding affinity from mutations.Moreover,we have found that the optimized weights of many parameters can capture the first-principle chemical and physical features of molecular recognition,therefore re-versely engineering the energetics of protein complexes.These results suggest that our method can serve as a useful addition to current computational approaches for predicting binding affinity and understanding the molecular mechanism of protein–protein interactions.展开更多
Many efforts have been exerted toward screening potential drugs for targets,and conducting wet experiments remains a laborious and time-consuming approach.Artificial intelligence methods,such as Convolutional Neural N...Many efforts have been exerted toward screening potential drugs for targets,and conducting wet experiments remains a laborious and time-consuming approach.Artificial intelligence methods,such as Convolutional Neural Network(CNN),are widely used to facilitate new drug discovery.Owing to the structural limitations of CNN,features extracted from this method are local patterns that lack global information.However,global information extracted from the whole sequence and local patterns extracted from the special domain can influence the drugtarget affinity.A fusion of global information and local patterns can construct neural network calculations closer to actual biological processes.This paper proposes a Fingerprint-embedding framework for Drug-Target binding Affinity prediction(FingerDTA),which uses CNN to extract local patterns and utilize fingerprints to characterize global information.These fingerprints are generated on the basis of the whole sequence of drugs or targets.Furthermore,FingerDTA achieves comparable performance on Davis and KIBA data sets.In the case study of screening potential drugs for the spike protein of the coronavirus disease 2019(COVID-19),7 of the top 10 drugs have been confirmed potential by literature.Ultimately,the docking experiment demonstrates that FingerDTA can find novel drug candidates for targets.All codes are available at http://lanproxy.biodwhu.cn:9099/mszjaas/FingerDTA.git.展开更多
Pre-formed V7-type short amylose(SA)could interact with curcumin to form inclusion complex(IC)thereby to improve the stability of curcumin.However,the complexation mechanism of V7-type SA and curcumin is not clear,whi...Pre-formed V7-type short amylose(SA)could interact with curcumin to form inclusion complex(IC)thereby to improve the stability of curcumin.However,the complexation mechanism of V7-type SA and curcumin is not clear,which limit the improvement of inclusion efficiency.To obtain a starch nanocarrier with high loading capacity,the encapsulation process and interaction parameters of V7-type SA-curcumin IC was studied.The analysis results demonstrated that stoichiometric ratio value of the SA-curcumin complex was around 1.V7-type SA performed excellently in the delivery of curcumin attributing to their high loading capacity(over 20%).It was found that curcumin could enter into the pre-formed helical cavity of SA to form an IC.The conformation change of SA caused the reduction in the interaction ratio in the last 20 ns of simulation.However,SA and curcumin always remained complexation status during the simulation.Hydrogen bonds(H-bonds)and hydrophobic interaction were the most critical acting forces involved in the formation and stability of V7-type SA-curcumin complex.Molecular docking presented that H-bonds interaction between curcumin ligand and V7-type SA chain(O3 at the 25th glucose unit,and O6 at the 17th and 20th glucose units)were found.Furthermore,the hydrophobic interactions were discovered between curcumin ligand and SA chain(18th,19th,21st,22nd and 23rd glucose units).展开更多
G protein coupled receptor kinase 2 (GRK2) is a kinase that regulates cardiac signaling activity. Inhibiting GRK2 is a promising mechanism for the treatment of heart failure (HF). Further development and optimization ...G protein coupled receptor kinase 2 (GRK2) is a kinase that regulates cardiac signaling activity. Inhibiting GRK2 is a promising mechanism for the treatment of heart failure (HF). Further development and optimization of inhibitors targeting GRK2 are highly meaningful. Therefore, in order to design GRK2 inhibitors with better performance, the most active molecule was selected as a reference compound from a data set containing 4-pyridylhydrazone derivatives and triazole derivatives, and its scaffold was extracted as the initial scaffold. Then, a powerful optimization-based framework for de novo drug design, guided by binding affinity, was used to generate a virtual molecular library targeting GRK2. The binding affinity of each virtual compound in this dataset was predicted by our developed deep learning model, and the designed potential compound with high binding affinity was selected for molecular docking and molecular dynamics simulation. It was found that the designed potential molecule binds to the ATP site of GRK2, which consists of key amino acids including Arg199, Gly200, Phe202, Val205, Lys220, Met274 and Asp335. The scaffold of the molecule is stabilized mainly by H-bonding and hydrophobic contacts. Concurrently, the reference compound in the dataset was also simulated by docking. It was found that this molecule also binds to the ATP site of GRK2. In addition, its scaffold is stabilized mainly by H-bonding and π-cation stacking interactions with Lys220, as well as hydrophobic contacts. The above results show that the designed potential molecule has similar binding modes to the reference compound, supporting the effectiveness of our framework for activity-focused molecular design. Finally, we summarized the interaction characteristics of general GRK2 inhibitors and gained insight into their molecule-target binding mechanisms, thereby facilitating the expansion of lead to hit compound.展开更多
Excessive Fe^(3+) ion concentrations in wastewater pose a long-standing threat to human health.Achieving low-cost,high-efficiency quantification of Fe^(3+) ion concentration in unknown solutions can guide environmenta...Excessive Fe^(3+) ion concentrations in wastewater pose a long-standing threat to human health.Achieving low-cost,high-efficiency quantification of Fe^(3+) ion concentration in unknown solutions can guide environmental management decisions and optimize water treatment processes.In this study,by leveraging the rapid,real-time detection capabilities of nanopores and the specific chemical binding affinity of tannic acid to Fe^(3+),a linear relationship between the ion current and Fe^(3+) ion concentration was established.Utilizing this linear relationship,quantification of Fe^(3+) ion concentration in unknown solutions was achieved.Furthermore,ethylenediaminetetraacetic acid disodium salt was employed to displace Fe^(3+) from the nanopores,allowing them to be restored to their initial conditions and reused for Fe^(3+) ion quantification.The reusable bioinspired nanopores remain functional over 330 days of storage.This recycling capability and the long-term stability of the nanopores contribute to a significant reduction in costs.This study provides a strategy for the quantification of unknown Fe^(3+) concentration using nanopores,with potential applications in environmental assessment,health monitoring,and so forth.展开更多
The clustered regularly interspaced short palindromic repeats(CRISPR)/CRISPR-associated protein 9(Cas9)is widely used for targeted genomic and epigenomic modifications and imaging in cells and organisms,and holds trem...The clustered regularly interspaced short palindromic repeats(CRISPR)/CRISPR-associated protein 9(Cas9)is widely used for targeted genomic and epigenomic modifications and imaging in cells and organisms,and holds tremendous promise in clinical applications.The efficiency and accuracy of the technology are partly determined by the target binding affinity and residence time of Cas9-single-guide RNA(sgRNA)at a given site.However,little attention has been paid to the effect of target binding affinity and residence duration on the repair of Cas9-induced DNA double-strand breaks(DSBs).We propose that the choice of DSB repair pathway may be altered by variation in the binding affinity and residence duration of Cas9-sgRNA at the cleaved target,contributing to significantly heterogeneous mutations in CRISPR/Cas9 genome editing.Here,we discuss the effect of Cas9-sgRNA target binding and residence on the choice of DSB repair pathway in CRISPR/Cas9 genome editing,and the opportunity this presents to optimize Cas9-based technology.展开更多
The Bacillus thuringiensis vegetative insecticidal protein, Vip3 A, represents a new family of Bt toxin and is currently applied to commercial transgenic cotton. To determine whether the Cry1Ac-resistant Helicoverpa a...The Bacillus thuringiensis vegetative insecticidal protein, Vip3 A, represents a new family of Bt toxin and is currently applied to commercial transgenic cotton. To determine whether the Cry1Ac-resistant Helicoverpa armigera is cross-resistant to Vip3 Aa protein, insecticidal activities, proteolytic activations and binding properties of Vip3 Aa toxin were investigated using Cry1Ac-susceptible（96S） and Cry1Ac-resistant H. armigera strain（Cry1Ac-R）. The toxicity of Vip3 Aa in Cry1Ac-R slightly reduced compared with 96 S, the resistance ratio was only 1.7-fold. The digestion rate of full-length Vip3 Aa by gut juice extracts from 96 S was little faster than that from Cry1Ac-R. Surface plasmon resonance（SPR） showed there was no significant difference between the binding affinity of Vip3 Aa and BBMVs between 96 S and Cry1Ac-R strains, and there was no significant competitive binding between Vip3 Aa and Cry1 Ac in susceptible or resistant strains. So there had little cross-resistance between Vip3 Aa and Cry1 Ac,Vip3A＋Cry proteins maybe the suitable pyramid strategy to control H. armigera in China in the future.展开更多
Small-molecule drugs are essential for maintaining human health. The objective of this study is to identify a molecule that can inhibit the Factor Xa protein and be easily procured. An optimization-based de novo drug ...Small-molecule drugs are essential for maintaining human health. The objective of this study is to identify a molecule that can inhibit the Factor Xa protein and be easily procured. An optimization-based de novo drug design framework, Drug CAMD, that integrates a deep learning model with a mixed-integer nonlinear programming model is used for designing drug candidates. Within this framework, a virtual chemical library is specifically tailored to inhibit Factor Xa. To further filter and narrow down the lead compounds from the designed compounds, comprehensive approaches involving molecular docking,binding pose metadynamics(BPMD), binding free energy calculations, and enzyme activity inhibition analysis are utilized. To maximize efficiency in terms of time and resources, molecules for in vitro activity testing are initially selected from commercially available portions of customized virtual chemical libraries. In vitro studies assessing inhibitor activities have confirmed that the compound EN300-331859shows potential Factor Xa inhibition, with an IC_(50)value of 34.57 μmol·L^(-1). Through in silico molecular docking and BPMD, the most plausible binding pose for the EN300-331859-Factor Xa complex are identified. The estimated binding free energy values correlate well with the results obtained from biological assays. Consequently, EN300-331859 is identified as a novel and effective sub-micromolar inhibitor of Factor Xa.展开更多
Human immunodeficiency virus-1(HIV-1)exploits the viral gp120 protein and host CD4/CCR5 receptors for the pandemic infection to humans.The host co-receptors of not only humans but also several primates and HIV-model m...Human immunodeficiency virus-1(HIV-1)exploits the viral gp120 protein and host CD4/CCR5 receptors for the pandemic infection to humans.The host co-receptors of not only humans but also several primates and HIV-model mice can interact with the HIV receptor.However,the molecular mechanisms of these interactions remain unclear.Using Shaik et al.(2019)'s gp120/CD4/CCR5 structure of HIV-1B and human,here,we investigate the molecular dynamics between HIV sub-lineages(B,C,N,and O)and potential hosts in Euarchontoglires(primates and rodents).Although both host genes show similar protein structures conserved in all animals,CD4 gene demonstrates significantly stronger binding affinities in Catarrhini(apes and Old-World monkeys).Its known candidate residues interacted with gp120 fail to explain these affinity variations.Therefore,we identified novel candidate sites under positive selection on the Catarrhini lineage.Among four positively selected sites,residue R58 in humans is located within an antigen-antibody binding domain,exhibiting apomorphic amino acid substitutions as Arginine(R)in Catarrhini,which are mutually exclusive to the other animals where Lysine(K)is prevalent.Applying for artificial mutation test,we validated that K to R substitutions can lead stronger binding affinities of Catarrhini.Ecologically,these dynamics may relate to shared equatorial habitats in Africa and Asia.Our findings suggest a new candidate site R58 driven by the lineage-specific evolution as a molecular foundation on HIV infection.展开更多
Bisphenol A(BPA)is one of the environmental endocrine disruptors(EDCs),and BPA contamination in environment can cause high risks to human health.Rapid determination of BPA on sites is in high demand in environmental a...Bisphenol A(BPA)is one of the environmental endocrine disruptors(EDCs),and BPA contamination in environment can cause high risks to human health.Rapid determination of BPA on sites is in high demand in environmental analysis.Taking advantage of aptamers as affinity ligands and fluorescence anisotropy(FA)analysis,we developed a simple and rapid FA assay for BPA by employing a single tetramethylrhodamine(TMR)labeled short 35-mer DNA aptamer against BPA.The assay is based on the BPA-binding induced conformation change of TMR-labeled aptamer and alteration of interaction between TMR and guanine bases,resulting in change of FA signals.We screened the FA change of aptamer probes having TMR label on a specific site of the aptamer upon BPA addition.The aptamer with a TMR label on the 22nd T base showed large FA-decreasing response to BPA and maintained good binding affinity to BPA.By using this TMR-labeled aptamer,we achieved FA detection of BPA with a detection limit of 0.5μmol/L under the optimized conditions.This assay was selective towards BPA and enabled the detection of BPA spiked in tap water sample,showing the potential applications on water samples.展开更多
Odorant binding proteins （OBPs） in insects are postulated to solubilize and transport the hydrophobic odorants across the hydrophilic antennal lymph to the olfactory receptors （ORs） located on the dendrite membran...Odorant binding proteins （OBPs） in insects are postulated to solubilize and transport the hydrophobic odorants across the hydrophilic antennal lymph to the olfactory receptors （ORs） located on the dendrite membrane of the sensory neurons. OBPs in adult insects have been intensively reported, but those in larvae are rarely addressed. In our study, a full-length OBP cDNA, namely SexiOBP13, was cloned by RT-PCR and RACE strategy from the heads of Spodoptera exigua larvae. The quantitative real-time PCR （qPCR） measurement indicated that SexiOBP13 was highly expressed in larval head, but very low in other parts of larva and was not detected in any tissues of adult. The binding affinities of SexiOBP13 to plant volatiles and female sex pheromone components were measured by competitive binding assays. Interestingly, SexiOBP13 displayed a high binding affinity （Ki=3.82 IJmol L-1） to Z9,E12-14：Ac, the major sex pheromone component of S. exigua, while low affinities to the tested host plant volatiles （Ki〉27 μmol L-l）. The behavioral tests further confirmed that Z9,E12-14：Ac was indeed active to elicit the behavioral activity of the third instar larvae of S. exigua. Taken together, our results suggest that SexiOBP13 may play a role in reception of female sex pheromone in S. exigua larvae. The ecological significance of the larvae preference to the adult female sex pheromone was discussed.展开更多
In this study, phosphorus(P) sorption of thirteen light-weight aggregates(LWAs) from USA was compared during batch equilibrium experiments in order to identify those materials which had the highest P sorption capacity...In this study, phosphorus(P) sorption of thirteen light-weight aggregates(LWAs) from USA was compared during batch equilibrium experiments in order to identify those materials which had the highest P sorption capacity for further study. Seven different levels of sorption activity were observed, which were broadly grouped into three categories—high performing, middle performing, and low performing aggregates. Chemical analysis of Ca, Al, Fe, and Mg was used to describe the differences between LWAs. There was a significant correlation between cation(especially Al, Ca, Fe, and Mg) content and P sorbed. Langmuir isotherms were used to describe P sorption maximum and binding affinity for four of the top five performing LWAs, Universal, Stalite "D", Stalite "Mix", and TXI.The fifth aggregate, Lehigh, exhibited more complex sorption, and was better described by the Freundlich isotherm. Universal had a mean P sorption at the highest concentration of 824 mg kg-1, well above its calculated sorption maximum(702 mg kg-1), and also had the highest binding affinity(1.1 L mg-1). This experiment suggests that the top performing LWA(Universal) may perform poorly in column and field studies due to observed precipitates, which could degrade constructed wetland performance. Other LWAs may exhibit superior field performance due to their high calculated sorption maxima. In general, these results highlight the importance of batch experiments as a first step in identifying materials suitable for column and field experiments.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
Kirsten rat sarcoma viral oncogene homolog(KRAS)-phosphodiesterase-delta(PDEδ)is a promising target for antitumor drug discovery.Herein,highly efficient and environmentally sensitive fluorescent probes of PDEδ(DS-Pr...Kirsten rat sarcoma viral oncogene homolog(KRAS)-phosphodiesterase-delta(PDEδ)is a promising target for antitumor drug discovery.Herein,highly efficient and environmentally sensitive fluorescent probes of PDEδ(DS-Probes)were rationally designed.As compared with the reported PDEδprobes,DS-Probes showed higher binding affinity and selectivity,which were able to conveniently and efficiently label PDEδin live cells as well as tumor tissues.Therefore,these fluorescent probes are expected to facilitate PDEδ-based mechanism elucidation,drug discovery and pathologic diagnosis.展开更多
The BH3 mimetics targeting the interaction between the BH3-only proteins and their prosurvival Bcl-2family proteins have shown enormous potential as cancer therapeutics. Herein, seven analogues targeting anti-apoptoti...The BH3 mimetics targeting the interaction between the BH3-only proteins and their prosurvival Bcl-2family proteins have shown enormous potential as cancer therapeutics. Herein, seven analogues targeting anti-apoptotic Bcl-2 proteins derived from the Bim BH3 domain via sequence simplification and/or modification are described. The in vitro binding affinity on anti-apoptotic Bcl-2 proteins and cell killing activity were evaluated. The results showed that analogues could significantly bind to target proteins and exhibited anti-cancer effect against three cancer cell lines. Of particular interest were the analogue SM-5（KD= 9.48 nmol/L for Bcl-2） and SM-6（KD= 0.08 nmol/L for Bcl-xL）, which exhibited improved binding affinity compared with the lead Bim（KD= 16.90 nmol/L for Bcl-2 and 22.2 nmol/L for Bcl-xL, respectively）. These results indicated that the peptide sequence containing the four hydrophobic side chains occupying pockets within the BH3-recognition cleft of anti-apoptotic Bcl-2 proteins might be the minimum sequence required for the bioactivity and the active core region of Bim. Promising inhibitors of anti-apoptotic Bcl-2 proteins with high bioactivity might be designed based on the active core.展开更多
基金supported by the Strategic Priority Research Program of the Chinese Academy of Sciences (Grant No.XDB29050100)the National Key Research and Development Program of China (Grant No.2022YFC0869900,2022YFC2303501,2020YFC0861100)the Program of the Chinese Academy of Sciences (Grant No.2020YJFK-Z-0150).
文摘SARS-CoV-2 variants are constantly emerging,hampering public health measures in controlling the number of infections.While it is well established that mutations in spike proteins observed for the different variants directly affect virus entry into host cells,there remains a need for further expansion of systematic and multifaceted comparisons.Here,we comprehensively studied the effect of spike protein mutations on spike expression and proteolytic activation,binding affinity,viral entry efficiency and host cell tropism of eight variants of concern(VOC)and variants of interest(VOI).We found that both the full-length spike and its receptor-binding domain(RBD)of Omicron bind to hACE2 with an affinity similar to that of the wild-type.In addition,Alpha,Beta,Delta and Lambda pseudoviruses gained significantly enhanced cell entry ability compared to the wild-type,while the Omicron pseudoviruses showed a slightly increased cell entry,suggesting the vastly increased rate of transmission observed for Omicron variant is not associated with its affinity to hACE2.We also found that the spikes of Omicron and Mu showed lower S1/S2 cleavage efficiency and inefficiently utilized TMPRSS2 to enter host cells than others,suggesting that they prefer the endocytosis pathway to enter host cells.Furthermore,all variants'pseudoviruses we tested gained the ability to enter the animal ACE2-expressing cells.Especially the infection potential of rats and mice showed significantly increased,strongly suggesting that rodents possibly become a reservoir for viral evolution.The insights gained from this study provide valuable guidance for a targeted approach to epidemic control,and contribute to a better understanding of SARS-CoV-2 evolution.
基金the financial support from the National Natural Science Foundation of China (21922810, 21908153, 21908155)program of Innovative Talents of Higher Education Institutions of Shanxithe supported by Cultivate Scientific Research Excellence Programs of Higher Education Institutions in Shanxi (CSREP)
文摘Direct separation of high purity ethylene(C_(2)H_(4))from an ethane(C_(2)H_(6))/ethylene mixture is a critical and challenging task owing to the very similar molecular size and physical properties of the two components.While some studies have attempted this separation,there is a lack of excellent porous materials with strong binding affinity for C_(2)H_(6)-selective adsorption via an energy-efficient adsorptive separation process.Herein,we report a titanium metal-organic framework with strong binding affinity and excellent stability for the highly efficient removal of C_(2)H_(6) from C_(2)H_(6)/C_(2)H_(4) mixtures.Single component adsorption isotherms demonstrated a larger amount of adsorbed ethane(1.16 mmol·g^(-1) under 1 kPa)and high C_(2)H_(6)/C_(2)H_(4) selectivity(2.7)for equimolar C_(2)H_(6)/C_(2)H_(4) mixtures,especially in the low-pressure range,which is further confirmed by the results of grand canonical Monte Carlo simulations for C_(2)H_(6) adsorption in this framework.The experimental breakthrough curves showed that C_(2)H_(4) with a high purity was collected directly from both 1:9 and 1:15 C_(2)H_(6)/C_(2)H_(4)(volume ratio)mixtures at 298 K and 100 kPa.Moreover,the unchanged adsorption and separation performance after cycling experiments confirmed the promising applicability of this material in future.
文摘Drug target relationship(DTR)prediction is a rapidly evolving area of research in com-putational drug discovery.Despite recent advances in computational solutions that have overcome the challenges of in vitro and in vivo experiments,most computational methods still focus on binary classification.They ignore the importance of binding affinity,which correctly distinguishes between on-targets and off-targets.In this study,we propose a deep learning model based on the microstruc-ture of compounds and proteins to predict drug-target binding affinity(DTA),which utilizes topo-logical structure information of drug molecules and sequence semantic information of proteins.In this model,graph attention network(GAT)is used to capture the deep features of the compound molecular graph,and bidirectional long short-term memory(BiLSTM)network is used to extract the protein sequence features,and the pharmacological context of DTA is obtained by combining the two.The results show that the proposed model has achieved superior performance in both cor-rectly predicting the value of interaction strength and correctly discriminating the ranking of bind-ing strength compared to the state-of-the-art baselines.A case study experiment on COVID-19 con-firms that the proposed DTA model can be used as an effective pre-screening tool in drug discovery.
基金This research was supported by the U S Department of Agriculture Grants 00-35304-96Ol and 98-35301-6083.
文摘Environmental control of the alcohol dehydrogenase(Adh)and other stress response genes in plants is in part brought about by transcriptional regulation involving the G-box cis-acting DNA element and bZIP G-box Binding Factors(GBFs).The mechanisms of GBF regulation and requirements for additional factors in this control process are not well understood.In an effort to identify potential GBF binding and control partners,maize GBF1 was used as bait in a yeast two-hybrid screen of an A.thaliana cDNA library.GBF Interacting Protein 1(GIP1)arose from the screen as a 496 amino acid protein with a predicted molecular weight of 53,748 kDa that strongly interacts with GBFs.Northern analysis of A.thaliana tissue suggests a 1.8-1.9 kb GIP1 transcript,predominantly in roots.Immunolocalization studies indicate that GIP1 protein is mainly localized to the nucleus.In vitro electrophoretic mobility shift assays using an Adh G-box DNA probe and recombinant A.thaliana GBF3 or maize GBF1,showed that the presence of GIP1 resulted in a tenfold increase in GBF DNA binding activity without altering the migration,suggesting a transient association between GIP1 and GBF.Addition of GIP1 to intentionally aggregated GBF converted GBF to lower molecular weight macromolecular complexes and GIP1 also refolded denatured rhodanese in the absence of ATP.These data suggest GIP1 functions to enhance GBF DNA binding activity by acting as a potent nuclear chaperone or crowbar,and potentially regulates the multimeric state of GBFs,thereby contributing to bZIP-mediated gene regulation.
文摘Integrins are heterodimers that mediate cell adhesion and transduce signals bidirectionally across the cell membrane.Integrins often exist in low affinity(or inactive) states for
基金supported by the National Institutes of Health (Grant Nos. R01GM120238 and R01GM122804)partially supported by a start-up grant from Albert Einstein College of Medicine
文摘The cellular functions of proteins are maintained by forming diverse complexes.The stability of these com-plexes is quantified by the measurement of binding affinity,and mutations that alter the binding affinity can cause various diseases such as cancer and diabetes.As a result,accurate estimation of the binding stability and the effects of mutations on changes of binding affinity is a crucial step to understanding the biological functions of proteins and their dysfunctional consequences.It has been hypothesized that the stability of a protein complex is dependent not only on the residues at its binding interface by pairwise interactions but also on all other remaining residues that do not appear at the binding interface.Here,we computationally reconstruct the binding affinity by decomposing it into the contributions of interfacial residues and other non-interfacial residues in a protein complex.We further assume that the contributions of both interfacial and non-interfacial residues to the binding affinity depend on their local structural environments such as solvent-accessible surfaces and secondary structural types.The weights of all corresponding parameters are optimized by Monte-Carlo simulations.After cross-validation against a large-scale dataset,we show that the model not only shows a strong correlation between the absolute values of the experimental and calculated binding affinities,but can also be an effective approach to predict the relative changes of binding affinity from mutations.Moreover,we have found that the optimized weights of many parameters can capture the first-principle chemical and physical features of molecular recognition,therefore re-versely engineering the energetics of protein complexes.These results suggest that our method can serve as a useful addition to current computational approaches for predicting binding affinity and understanding the molecular mechanism of protein–protein interactions.
基金funded by the China National Key Research and Development Program(No.2019YFA0904300).
文摘Many efforts have been exerted toward screening potential drugs for targets,and conducting wet experiments remains a laborious and time-consuming approach.Artificial intelligence methods,such as Convolutional Neural Network(CNN),are widely used to facilitate new drug discovery.Owing to the structural limitations of CNN,features extracted from this method are local patterns that lack global information.However,global information extracted from the whole sequence and local patterns extracted from the special domain can influence the drugtarget affinity.A fusion of global information and local patterns can construct neural network calculations closer to actual biological processes.This paper proposes a Fingerprint-embedding framework for Drug-Target binding Affinity prediction(FingerDTA),which uses CNN to extract local patterns and utilize fingerprints to characterize global information.These fingerprints are generated on the basis of the whole sequence of drugs or targets.Furthermore,FingerDTA achieves comparable performance on Davis and KIBA data sets.In the case study of screening potential drugs for the spike protein of the coronavirus disease 2019(COVID-19),7 of the top 10 drugs have been confirmed potential by literature.Ultimately,the docking experiment demonstrates that FingerDTA can find novel drug candidates for targets.All codes are available at http://lanproxy.biodwhu.cn:9099/mszjaas/FingerDTA.git.
基金supported by the Natural Science Foundation of Jiangsu Province (BK20220416)University Science Research Project of Jiangsu Province (22KJB550009)the National Key Research and Development Program of China (2023YFD2201300).
文摘Pre-formed V7-type short amylose(SA)could interact with curcumin to form inclusion complex(IC)thereby to improve the stability of curcumin.However,the complexation mechanism of V7-type SA and curcumin is not clear,which limit the improvement of inclusion efficiency.To obtain a starch nanocarrier with high loading capacity,the encapsulation process and interaction parameters of V7-type SA-curcumin IC was studied.The analysis results demonstrated that stoichiometric ratio value of the SA-curcumin complex was around 1.V7-type SA performed excellently in the delivery of curcumin attributing to their high loading capacity(over 20%).It was found that curcumin could enter into the pre-formed helical cavity of SA to form an IC.The conformation change of SA caused the reduction in the interaction ratio in the last 20 ns of simulation.However,SA and curcumin always remained complexation status during the simulation.Hydrogen bonds(H-bonds)and hydrophobic interaction were the most critical acting forces involved in the formation and stability of V7-type SA-curcumin complex.Molecular docking presented that H-bonds interaction between curcumin ligand and V7-type SA chain(O3 at the 25th glucose unit,and O6 at the 17th and 20th glucose units)were found.Furthermore,the hydrophobic interactions were discovered between curcumin ligand and SA chain(18th,19th,21st,22nd and 23rd glucose units).
基金supported by the National Natural Science Foundation of China Excellent Young Scientist Fund(22422801)the National Natural Science Foundation of China General Project(22278053)+1 种基金the National Natural Science Foundation of China General Project(22078041)Dalian High-level Talents Innovation Support Program(2023RQ059).
文摘G protein coupled receptor kinase 2 (GRK2) is a kinase that regulates cardiac signaling activity. Inhibiting GRK2 is a promising mechanism for the treatment of heart failure (HF). Further development and optimization of inhibitors targeting GRK2 are highly meaningful. Therefore, in order to design GRK2 inhibitors with better performance, the most active molecule was selected as a reference compound from a data set containing 4-pyridylhydrazone derivatives and triazole derivatives, and its scaffold was extracted as the initial scaffold. Then, a powerful optimization-based framework for de novo drug design, guided by binding affinity, was used to generate a virtual molecular library targeting GRK2. The binding affinity of each virtual compound in this dataset was predicted by our developed deep learning model, and the designed potential compound with high binding affinity was selected for molecular docking and molecular dynamics simulation. It was found that the designed potential molecule binds to the ATP site of GRK2, which consists of key amino acids including Arg199, Gly200, Phe202, Val205, Lys220, Met274 and Asp335. The scaffold of the molecule is stabilized mainly by H-bonding and hydrophobic contacts. Concurrently, the reference compound in the dataset was also simulated by docking. It was found that this molecule also binds to the ATP site of GRK2. In addition, its scaffold is stabilized mainly by H-bonding and π-cation stacking interactions with Lys220, as well as hydrophobic contacts. The above results show that the designed potential molecule has similar binding modes to the reference compound, supporting the effectiveness of our framework for activity-focused molecular design. Finally, we summarized the interaction characteristics of general GRK2 inhibitors and gained insight into their molecule-target binding mechanisms, thereby facilitating the expansion of lead to hit compound.
基金supported by the National Natural Science Foundation of China(Nos.52303380,52025132,52273305,22205185,21621091,22021001,and 22121001)Fundamental Research Funds for the Central Universities(No.20720240041)+3 种基金the 111 Project(Nos.B17027 and B16029)the National Science Foundation of Fujian Province of China(No.2022J02059)the Science and Technology Projects of Innovation Laboratory for Sciences and Technologies of Energy Materials of Fujian Province(No.RD2022070601)the New Cornerstone Science Foundation through the XPLORER PRIZE。
文摘Excessive Fe^(3+) ion concentrations in wastewater pose a long-standing threat to human health.Achieving low-cost,high-efficiency quantification of Fe^(3+) ion concentration in unknown solutions can guide environmental management decisions and optimize water treatment processes.In this study,by leveraging the rapid,real-time detection capabilities of nanopores and the specific chemical binding affinity of tannic acid to Fe^(3+),a linear relationship between the ion current and Fe^(3+) ion concentration was established.Utilizing this linear relationship,quantification of Fe^(3+) ion concentration in unknown solutions was achieved.Furthermore,ethylenediaminetetraacetic acid disodium salt was employed to displace Fe^(3+) from the nanopores,allowing them to be restored to their initial conditions and reused for Fe^(3+) ion quantification.The reusable bioinspired nanopores remain functional over 330 days of storage.This recycling capability and the long-term stability of the nanopores contribute to a significant reduction in costs.This study provides a strategy for the quantification of unknown Fe^(3+) concentration using nanopores,with potential applications in environmental assessment,health monitoring,and so forth.
基金supported by the National Natural Science Foundation of China(Nos.31671385 and 31870806)the Zhejiang Provincial Natural Science Foundation of China(Nos.LY18C050001 and LQ20C050004)the Fundamental Research Funds for the Central Universities in China(No.2019QNA7031)。
文摘The clustered regularly interspaced short palindromic repeats(CRISPR)/CRISPR-associated protein 9(Cas9)is widely used for targeted genomic and epigenomic modifications and imaging in cells and organisms,and holds tremendous promise in clinical applications.The efficiency and accuracy of the technology are partly determined by the target binding affinity and residence time of Cas9-single-guide RNA(sgRNA)at a given site.However,little attention has been paid to the effect of target binding affinity and residence duration on the repair of Cas9-induced DNA double-strand breaks(DSBs).We propose that the choice of DSB repair pathway may be altered by variation in the binding affinity and residence duration of Cas9-sgRNA at the cleaved target,contributing to significantly heterogeneous mutations in CRISPR/Cas9 genome editing.Here,we discuss the effect of Cas9-sgRNA target binding and residence on the choice of DSB repair pathway in CRISPR/Cas9 genome editing,and the opportunity this presents to optimize Cas9-based technology.
基金supported by the Key Project for Breeding Genetically Modified Organisms,China (2014ZX08011-002)the National Natural Science Foundation of China (30971921, 31321004)
文摘The Bacillus thuringiensis vegetative insecticidal protein, Vip3 A, represents a new family of Bt toxin and is currently applied to commercial transgenic cotton. To determine whether the Cry1Ac-resistant Helicoverpa armigera is cross-resistant to Vip3 Aa protein, insecticidal activities, proteolytic activations and binding properties of Vip3 Aa toxin were investigated using Cry1Ac-susceptible（96S） and Cry1Ac-resistant H. armigera strain（Cry1Ac-R）. The toxicity of Vip3 Aa in Cry1Ac-R slightly reduced compared with 96 S, the resistance ratio was only 1.7-fold. The digestion rate of full-length Vip3 Aa by gut juice extracts from 96 S was little faster than that from Cry1Ac-R. Surface plasmon resonance（SPR） showed there was no significant difference between the binding affinity of Vip3 Aa and BBMVs between 96 S and Cry1Ac-R strains, and there was no significant competitive binding between Vip3 Aa and Cry1 Ac in susceptible or resistant strains. So there had little cross-resistance between Vip3 Aa and Cry1 Ac,Vip3A＋Cry proteins maybe the suitable pyramid strategy to control H. armigera in China in the future.
基金financial supports of the National Natural Science Foundation of China (22078041, 22278053,22208042)Dalian High-level Talents Innovation Support Program (2023RQ059)“the Fundamental Research Funds for the Central Universities (DUT20JC41, DUT22YG218)”。
文摘Small-molecule drugs are essential for maintaining human health. The objective of this study is to identify a molecule that can inhibit the Factor Xa protein and be easily procured. An optimization-based de novo drug design framework, Drug CAMD, that integrates a deep learning model with a mixed-integer nonlinear programming model is used for designing drug candidates. Within this framework, a virtual chemical library is specifically tailored to inhibit Factor Xa. To further filter and narrow down the lead compounds from the designed compounds, comprehensive approaches involving molecular docking,binding pose metadynamics(BPMD), binding free energy calculations, and enzyme activity inhibition analysis are utilized. To maximize efficiency in terms of time and resources, molecules for in vitro activity testing are initially selected from commercially available portions of customized virtual chemical libraries. In vitro studies assessing inhibitor activities have confirmed that the compound EN300-331859shows potential Factor Xa inhibition, with an IC_(50)value of 34.57 μmol·L^(-1). Through in silico molecular docking and BPMD, the most plausible binding pose for the EN300-331859-Factor Xa complex are identified. The estimated binding free energy values correlate well with the results obtained from biological assays. Consequently, EN300-331859 is identified as a novel and effective sub-micromolar inhibitor of Factor Xa.
基金supported by the BK21 FOUR Program of the Department of Agricultural Biotechnology,Seoul National University,Seoul,South Korea and was supported by HHMI,USA。
文摘Human immunodeficiency virus-1(HIV-1)exploits the viral gp120 protein and host CD4/CCR5 receptors for the pandemic infection to humans.The host co-receptors of not only humans but also several primates and HIV-model mice can interact with the HIV receptor.However,the molecular mechanisms of these interactions remain unclear.Using Shaik et al.(2019)'s gp120/CD4/CCR5 structure of HIV-1B and human,here,we investigate the molecular dynamics between HIV sub-lineages(B,C,N,and O)and potential hosts in Euarchontoglires(primates and rodents).Although both host genes show similar protein structures conserved in all animals,CD4 gene demonstrates significantly stronger binding affinities in Catarrhini(apes and Old-World monkeys).Its known candidate residues interacted with gp120 fail to explain these affinity variations.Therefore,we identified novel candidate sites under positive selection on the Catarrhini lineage.Among four positively selected sites,residue R58 in humans is located within an antigen-antibody binding domain,exhibiting apomorphic amino acid substitutions as Arginine(R)in Catarrhini,which are mutually exclusive to the other animals where Lysine(K)is prevalent.Applying for artificial mutation test,we validated that K to R substitutions can lead stronger binding affinities of Catarrhini.Ecologically,these dynamics may relate to shared equatorial habitats in Africa and Asia.Our findings suggest a new candidate site R58 driven by the lineage-specific evolution as a molecular foundation on HIV infection.
基金supported by the National Natural Science Foundation of China(Nos.21874146,21575153,21435008)。
文摘Bisphenol A(BPA)is one of the environmental endocrine disruptors(EDCs),and BPA contamination in environment can cause high risks to human health.Rapid determination of BPA on sites is in high demand in environmental analysis.Taking advantage of aptamers as affinity ligands and fluorescence anisotropy(FA)analysis,we developed a simple and rapid FA assay for BPA by employing a single tetramethylrhodamine(TMR)labeled short 35-mer DNA aptamer against BPA.The assay is based on the BPA-binding induced conformation change of TMR-labeled aptamer and alteration of interaction between TMR and guanine bases,resulting in change of FA signals.We screened the FA change of aptamer probes having TMR label on a specific site of the aptamer upon BPA addition.The aptamer with a TMR label on the 22nd T base showed large FA-decreasing response to BPA and maintained good binding affinity to BPA.By using this TMR-labeled aptamer,we achieved FA detection of BPA with a detection limit of 0.5μmol/L under the optimized conditions.This assay was selective towards BPA and enabled the detection of BPA spiked in tap water sample,showing the potential applications on water samples.
基金supported by a grant from the National Natural Science Foundation of China (31372264)the Special Fund for Agro-Scientific Research in the Public Interest,China (201203036)
文摘Odorant binding proteins （OBPs） in insects are postulated to solubilize and transport the hydrophobic odorants across the hydrophilic antennal lymph to the olfactory receptors （ORs） located on the dendrite membrane of the sensory neurons. OBPs in adult insects have been intensively reported, but those in larvae are rarely addressed. In our study, a full-length OBP cDNA, namely SexiOBP13, was cloned by RT-PCR and RACE strategy from the heads of Spodoptera exigua larvae. The quantitative real-time PCR （qPCR） measurement indicated that SexiOBP13 was highly expressed in larval head, but very low in other parts of larva and was not detected in any tissues of adult. The binding affinities of SexiOBP13 to plant volatiles and female sex pheromone components were measured by competitive binding assays. Interestingly, SexiOBP13 displayed a high binding affinity （Ki=3.82 IJmol L-1） to Z9,E12-14：Ac, the major sex pheromone component of S. exigua, while low affinities to the tested host plant volatiles （Ki〉27 μmol L-l）. The behavioral tests further confirmed that Z9,E12-14：Ac was indeed active to elicit the behavioral activity of the third instar larvae of S. exigua. Taken together, our results suggest that SexiOBP13 may play a role in reception of female sex pheromone in S. exigua larvae. The ecological significance of the larvae preference to the adult female sex pheromone was discussed.
基金Supported by the Soil Characterization Laboratory,University of Masachusetts,Amherst,MA,USA
文摘In this study, phosphorus(P) sorption of thirteen light-weight aggregates(LWAs) from USA was compared during batch equilibrium experiments in order to identify those materials which had the highest P sorption capacity for further study. Seven different levels of sorption activity were observed, which were broadly grouped into three categories—high performing, middle performing, and low performing aggregates. Chemical analysis of Ca, Al, Fe, and Mg was used to describe the differences between LWAs. There was a significant correlation between cation(especially Al, Ca, Fe, and Mg) content and P sorbed. Langmuir isotherms were used to describe P sorption maximum and binding affinity for four of the top five performing LWAs, Universal, Stalite "D", Stalite "Mix", and TXI.The fifth aggregate, Lehigh, exhibited more complex sorption, and was better described by the Freundlich isotherm. Universal had a mean P sorption at the highest concentration of 824 mg kg-1, well above its calculated sorption maximum(702 mg kg-1), and also had the highest binding affinity(1.1 L mg-1). This experiment suggests that the top performing LWA(Universal) may perform poorly in column and field studies due to observed precipitates, which could degrade constructed wetland performance. Other LWAs may exhibit superior field performance due to their high calculated sorption maxima. In general, these results highlight the importance of batch experiments as a first step in identifying materials suitable for column and field experiments.
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supported by the National Key Research and Development Program of China(No.2020YFA0509200 to C.Sheng)National Natural Science Foundation of China(Nos.81903436 to Y.Li,82204211 to W.Wang and 22077138 to S.Wu)Shanghai Rising-Star Program(No.22QA1411300 to S.Wu).
文摘Kirsten rat sarcoma viral oncogene homolog(KRAS)-phosphodiesterase-delta(PDEδ)is a promising target for antitumor drug discovery.Herein,highly efficient and environmentally sensitive fluorescent probes of PDEδ(DS-Probes)were rationally designed.As compared with the reported PDEδprobes,DS-Probes showed higher binding affinity and selectivity,which were able to conveniently and efficiently label PDEδin live cells as well as tumor tissues.Therefore,these fluorescent probes are expected to facilitate PDEδ-based mechanism elucidation,drug discovery and pathologic diagnosis.
基金financially supported by Postdoctoral Applied Research Project of Qingdao(No.861605040085,to CZ,SW)Grant of Innovation Plan in Biomedical Research of Qingdao City(No.15-10-3-15-(28)-zch,to SW)
文摘The BH3 mimetics targeting the interaction between the BH3-only proteins and their prosurvival Bcl-2family proteins have shown enormous potential as cancer therapeutics. Herein, seven analogues targeting anti-apoptotic Bcl-2 proteins derived from the Bim BH3 domain via sequence simplification and/or modification are described. The in vitro binding affinity on anti-apoptotic Bcl-2 proteins and cell killing activity were evaluated. The results showed that analogues could significantly bind to target proteins and exhibited anti-cancer effect against three cancer cell lines. Of particular interest were the analogue SM-5（KD= 9.48 nmol/L for Bcl-2） and SM-6（KD= 0.08 nmol/L for Bcl-xL）, which exhibited improved binding affinity compared with the lead Bim（KD= 16.90 nmol/L for Bcl-2 and 22.2 nmol/L for Bcl-xL, respectively）. These results indicated that the peptide sequence containing the four hydrophobic side chains occupying pockets within the BH3-recognition cleft of anti-apoptotic Bcl-2 proteins might be the minimum sequence required for the bioactivity and the active core region of Bim. Promising inhibitors of anti-apoptotic Bcl-2 proteins with high bioactivity might be designed based on the active core.
