共查询到20条相似文献,搜索用时 31 毫秒
1.
Boosting Affinity by Correct Ligand Preorganization for the S2 Pocket of Thrombin: A Study by Isothermal Titration Calorimetry,Molecular Dynamics,and High‐Resolution Crystal Structures 下载免费PDF全文
Dr. Eggert H. Rühmann Melinda Rupp Dr. Michael Betz Prof. Dr. Andreas Heine Prof. Dr. Gerhard Klebe 《ChemMedChem》2016,11(3):309-319
Structural preorganization to fix bioactive conformations at protein binding sites is a popular strategy to enhance binding affinity during late‐stage optimization. The rationale for this enhancement relates to entropic advantages assigned to rigidified versus flexible ligands. We analyzed a narrow series of peptidomimetics binding to thrombin. The individual ligands exhibit at P2 a conformationally flexible glycine, more restricted alanine, N‐methylglycine, N‐methylhomoalanine, and largely rigidified proline moiety. Overall, affinity was found to increase by a factor of 1000, explained partly by an entropic advantage. All ligands adopt the same binding mode with small deviations. The residual mobility of the bound ligands is decreased across the series, and a protein side chain differs in its order/disorder behavior along with changes in the surface‐water network pattern established across the newly generated protein–ligand surfaces. The enthalpy/entropy inventory displays a rather complex picture and emphasizes that thermodynamics can only be compared in terms of relative differences within a structurally similar ligand series. 相似文献
2.
Standard docking approaches used for the prediction of protein–ligand complexes in the drug development process have problems identifying the correct binding mode of large flexible ligands. Herein we show how additional experimental data from NMR experiments can be used to predict the binding mode of a mucin 1 (MUC‐1) pentapeptide recognized by the breast‐cancer‐selective monoclonal antibody SM3. Distance constraints derived from trNOE and saturation transfer difference NMR experiments are combined with the docking approach PLANTS. The resulting complex structures show excellent agreement with the NMR data and with a published X‐ray crystal structure. The method was then further tested on two complexes in order to demonstrate its more general applicability: T‐antigen disaccharide bound to Maclura pomifera agglutinin, and the inhibitor SBi279 bound to S100B protein. Our new approach has the advantages of being fully automatic, rapid, and unbiased; moreover, it is based on relatively easily obtainable experimental data and can greatly increase the reliability of the generated structures. 相似文献
3.
Dr. Barbara Wienen‐Schmidt Tobias Wulsdorf Dr. Hendrik R. A. Jonker Dr. Krishna Saxena Dr. Denis Kudlinzki Verena Linhard Dr. Sridhar Sreeramulu Prof. Dr. Andreas Heine Prof. Dr. Harald Schwalbe Prof. Dr. Gerhard Klebe 《ChemMedChem》2018,13(18):1988-1996
A ligand‐binding study is presented focusing on thermodynamics of fragment expansion. The binding of four compounds with increasing molecular weight to protein kinase A (PKA) was analyzed. The ligands display affinities between low‐micromolar to nanomolar potency despite their low molecular weight. Binding free energies were measured by isothermal titration calorimetry, revealing a trend toward more entropic and less enthalpic binding with increase in molecular weight. All protein–ligand complexes were analyzed by crystallography and solution NMR spectroscopy. Crystal structures and solution NMR data are highly consistent, and no major differences in complex dynamics across the series are observed that would explain the differences in the thermodynamic profiles. Instead, the thermodynamic trends result either from differences in the solvation patterns of the conformationally more flexible ligand in aqueous solution prior to protein binding as molecular dynamics simulations suggest, or from local shifts of the water structure in the ligand‐bound state. Our data thus provide evidence that changes in the solvation pattern constitute an important parameter for the understanding of thermodynamic data in protein–ligand complex formation. 相似文献
4.
Christian Scheibe Dr. Stefanie Wedepohl Sebastian B. Riese Dr. Jens Dernedde Prof. Dr. Oliver Seitz 《Chembiochem : a European journal of chemical biology》2013,14(2):236-250
Nucleic acid architectures offer intriguing opportunities for the interrogation of structural properties of protein receptors. In this study, we performed a DNA‐programmed spatial screening to characterize two functionally distinct receptor systems: 1) structurally well‐defined Ricinus communis agglutinin (RCA120), and 2) rather ill‐defined assemblies of L‐selectin on nanoparticles and leukocytes. A robust synthesis route that allowed the attachment both of carbohydrate ligands—such as N‐acetyllactosamine (LacNAc), sialyl‐Lewis‐X (sLeX), and mannose—and of a DNA aptamer to PNAs was developed. A systematically assembled series of different PNA–DNA complexes served as multivalent scaffolds to control the spatial alignments of appended lectin ligands. The spatial screening of the binding sites of RCA120 was in agreement with the crystal structure analysis. The study revealed that two appropriately presented LacNAc ligands suffice to provide unprecedented RCA120 affinity (KD=4 μM ). In addition, a potential secondary binding site was identified. Less dramatic binding enhancements were obtained when the more flexible L‐selectin assemblies were probed. This study involved the bivalent display both of the weak‐affinity sLeX ligand and of a high‐affinity DNA aptamer. Bivalent presentation led to rather modest (sixfold or less) enhancements of binding when the self‐assemblies were targeted against L‐selectin on gold nanoparticles. Spatial screening of L‐selectin on the surfaces of leukocytes showed higher affinity enhancements (25‐fold). This and the distance–activity relationships indicated that leukocytes permit dense clustering of L‐selectin. 相似文献
5.
Roberto Buratto Aurélien Bornet Jonas Milani Daniele Mammoli Basile Vuichoud Dr. Nicola Salvi Maninder Singh Aurélien Laguerre Dr. Solène Passemard Dr. Sandrine Gerber‐Lemaire Dr. Sami Jannin Prof. Geoffrey Bodenhausen 《ChemMedChem》2014,9(11):2509-2515
Transverse and longitudinal relaxation times (T1ρ and T1) have been widely exploited in NMR to probe the binding of ligands and putative drugs to target proteins. We have shown recently that long‐lived states (LLS) can be more sensitive to ligand binding. LLS can be excited if the ligand comprises at least two coupled spins. Herein we broaden the scope of ligand screening by LLS to arbitrary ligands by covalent attachment of a functional group, which comprises a pair of coupled protons that are isolated from neighboring magnetic nuclei. The resulting functionalized ligands have longitudinal relaxation times T1(1H) that are sufficiently long to allow the powerful combination of LLS with dissolution dynamic nuclear polarization (D‐DNP). Hyperpolarized weak “spy ligands” can be displaced by high‐affinity competitors. Hyperpolarized LLS allow one to decrease both protein and ligand concentrations to micromolar levels and to significantly increase sample throughput. 相似文献
6.
Matthew D. Disney Prof. Melissa M. Lee Alexei Pushechnikov Dr. Jessica L. Childs‐Disney Prof. Dr. 《Chembiochem : a European journal of chemical biology》2010,11(3):375-382
Modularly assembled ligands were designed to target the RNAs that cause two currently untreatable neuromuscular disorders, myotonic dystrophy types 1 (DM1) and 2 (DM2). DM1 is caused by an expanded repeating sequence of CUG, and DM2 is caused by expanded CCUG repeats. Both are present in noncoding regions and fold into hairpins with either repeating 1×1 nucleotide UU (DM1) or 2×2 nucleotide 5′‐CU/3′‐UC (DM2) internal loops separated by two GC pairs. The repeats are toxic because they sequester the RNA splicing regulator muscleblind‐like 1 protein (MBNL1). Rational design of ligands targeting these RNAs was enabled by a database of RNA motif–ligand partners compiled by using two‐dimensional combinatorial screening (2DCS). One 2DCS study found that the 6′′‐azido‐kanamycin A module binds internal loops similar to those found in DM1 and DM2. In order to further enhance affinity and specificity, the ligand was assembled on a peptoid backbone to precisely control valency and the distance between ligand modules. Designed compounds are more potent and specific binders to the toxic RNAs than MBNL1 and inhibit the formation of the RNA–protein complexes with nanomolar IC50 values. This study shows that three important factors govern potent inhibition: 1) the surface area sequestered by the assembled ligands; 2) the spacing between ligand modules since a longer distance is required to target DM2 RNAs than DM1 RNAs; and 3) flexibility in the modular assembly scaffold used to display the RNA‐binding module. These results have impacts on the general design of assembled ligands targeting RNAs present in genomic sequence. 相似文献
7.
Rational structure-based drug design relies on a detailed, atomic-level understanding of protein–ligand interactions. The chiral nature of drug binding sites in proteins has led to the discovery of predominantly chiral drugs. A mechanistic understanding of stereoselectivity (which governs how one stereoisomer of a drug might bind stronger than the others to a protein) depends on the topology of stereocenters in the chiral molecule. Chiral graphs and reduced chiral graphs, introduced here, are new topological representations of chiral ligands using graph theory, to facilitate a detailed understanding of chiral recognition of ligands/drugs by proteins. These representations are demonstrated by application to all ≈14 000+ chiral ligands in the Protein Data Bank (PDB), which will facilitate an understanding of protein–ligand stereoselectivity mechanisms. Ligand modifications during drug development can be easily incorporated into these chiral graphs. In addition, these chiral graphs present an efficient tool for a deep dive into the enormous chemical structure space to enable sampling of unexplored structural scaffolds. 相似文献
8.
Hardegger LA Kuhn B Spinnler B Anselm L Ecabert R Stihle M Gsell B Thoma R Diez J Benz J Plancher JM Hartmann G Isshiki Y Morikami K Shimma N Haap W Banner DW Diederich F 《ChemMedChem》2011,6(11):2048-2054
In two series of small‐molecule ligands, one inhibiting human cathepsin L (hcatL) and the other MEK1 kinase, biological affinities were found to strongly increase when an aryl ring of the inhibitors is substituted with the larger halogens Cl, Br, and I, but to decrease upon F substitution. X‐ray co‐crystal structure analyses revealed that the higher halides engage in halogen bonding (XB) with a backbone C?O in the S3 pocket of hcatL and in a back pocket of MEK1. While the S3 pocket is located at the surface of the enzyme, which provides a polar environment, the back pocket in MEK1 is deeply buried in the protein and is of pronounced apolar character. This study analyzes environmental effects on XB in protein–ligand complexes. It is hypothesized that energetic gains by XB are predominantly not due to water replacements but originate from direct interactions between the XB donor (Caryl? X) and the XB acceptor (C?O) in the correct geometry. New X‐ray co‐crystal structures in the same crystal form (space group P212121) were obtained for aryl chloride, bromide, and iodide ligands bound to hcatL. These high‐resolution structures reveal that the backbone C?O group of Gly61 in most hcatL co‐crystal structures maintains water solvation while engaging in XB. An aryl? CF3‐substituted ligand of hcatL with an unexpectedly high affinity was found to adopt the same binding geometry as the aryl halides, with the CF3 group pointing to the C?O group of Gly61 in the S3 pocket. In this case, a repulsive F2C? F???O?C contact apparently is energetically overcompensated by other favorable protein–ligand contacts established by the CF3 group. 相似文献
9.
Sarah A. Allman Henrik H. Jensen Drs. Balakumar Vijayakrishnan James A. Garnett Ester Leon Yan Liu Dr. Daniel C. Anthony Dr. Nicola R. Sibson Dr. Ten Feizi Prof. Stephen Matthews Prof. Benjamin G. Davis Prof. 《Chembiochem : a European journal of chemical biology》2009,10(15):2522-2529
Unnatural, NMR‐ and MRI‐active fluorinated sugar probes, designed and synthesised to bind to the pathogenic protein TgMIC1 from Toxoplasma gondii, were found to display binding potency equal to and above that of the natural ligand. Dissection of the binding mechanism and modes, including the first X‐ray crystal structures of a fluoro‐oligosaccharide bound to a lectin, demonstrate that it is possible to create effective fluorinated probe ligands for the study of, and perhaps intervention in, sugar–protein binding events. 相似文献
10.
Methyl,Ethyl, Propyl,Butyl: Futile But Not for Water,as the Correlation of Structure and Thermodynamic Signature Shows in a Congeneric Series of Thermolysin Inhibitors 下载免费PDF全文
Stefan G. Krimmer Michael Betz Prof. Dr. Andreas Heine Prof. Dr. Gerhard Klebe 《ChemMedChem》2014,9(4):833-846
Water is ubiquitously present in any biological system and has therefore to be regarded as an additional binding partner in the protein–ligand binding process. Upon complex formation, a new solvent‐exposed surface is generated and water molecules from the first solvation layer will arrange around this newly formed surface. So far, the influence of such water arrangements on the ligand binding properties is unknown. In this study, the binding modes of nine congeneric phosphonamidate‐type inhibitors with systematically varied, size‐increasing hydrophobic P2′ substituents (from methyl to phenylethyl) addressing the hydrophobic, solvent‐exposed S2′ pocket of thermolysin were analyzed by high‐resolution crystal structures and correlated with their thermodynamic binding profiles as measured by isothermal titration calorimetry. Overall, ΔΔG spreads over 7.0 kJ mol?1, ΔΔH varies by 15.8 kJ mol?1, and ?TΔΔS by 12.1 kJ mol?1. Throughout the series, these changes correlate remarkably well with the geometric differences of water molecules arranged adjacent to the P2′ substituents. Ligands with medium‐sized P2′ substituents exhibit highest affinities, presumably because of their optimal solvation patterns around these complexes. The addition, removal, or rearrangement of even a single methyl group can result in a strong modulation of the adjacent water network pattern shifting from enthalpy to entropy‐driven binding. In conclusion, the quality of a water network assembled around a protein–ligand complex influences the enthalpy/entropy signature and can even modulate affinity to a surprising extent. 相似文献
11.
Dr. Nadja Bertleff‐Zieschang Julian Bechold Dr. Clemens Grimm Dr. Michael Reutlinger Dr. Petra Schneider Prof. Dr. Gisbert Schneider Prof. Dr. Jürgen Seibel 《Chembiochem : a European journal of chemical biology》2017,18(15):1477-1481
Galectin‐1 is a tumor‐associated protein recognizing the Galβ1‐4GlcNAc motif of cell‐surface glycoconjugates. Herein, we report the stepwise expansion of a multifunctional natural scaffold based on N‐acetyllactosamine (LacNAc). We obtained a LacNAc mimetic equipped with an alkynyl function on the 3′‐hydroxy group of the disaccharide facing towards a binding pocket adjacent to the carbohydrate‐recognition domain. It served as an anchor motif for further expansion by the Sharpless–Huisgen–Meldal reaction, which resulted in ligands with a binding mode almost identical to that of the natural carbohydrate template. X‐ray crystallography provided a structural understanding of the galectin‐1–ligand interactions. The results of this study enable the development of bespoke ligands for members of the galectin target family. 相似文献
12.
Knowledge about the orientation of ligands or inhibitors bound to a protein is vital for the development of new drugs. It was recently shown that solvent accessibility epitopes for protein ligands can be mapped by transferring magnetization from water molecules to the ligand to derive the ligand orientation. This is based on the fact that NMR signals of ligands arising from magnetization transferred from solvent molecules via the protein have a different sign from those arising from direct magnetization transfer from bulk water. Herein we critically evaluate the applicability of solvent accessibility mapping to derive binding orientations for ligands of two dehydrogenases (AKR1C3 and HSD17beta1) with very different binding pockets, including complexes in which the ligand is buried more deeply inside the protein. We also evaluate the possibility of using co-solvents, such as DMSO, for magnetization transfer. 相似文献
13.
Jason England CatherineR. Davies Maria Banaru Andrew J.P. White George J.P. Britovsek 《Advanced Synthesis \u0026amp; Catalysis》2008,350(6):883-897
A series of iron(II) bis(triflate) complexes [Fe(L)(OTf)2] containing linear tetradentate bis(pyridylmethyl)diamine ligands with a range of ligand backbones has been prepared. The backbone of the ligand series has been varied from a two‐carbon linkage [ethylene ( 1 ), 4,5‐dichlorophenylene ( 2 ) and cyclohexyl ( 3 )] to a three‐carbon [propyl ( 4 )) and a four‐carbon linkage (butyl ( 5 )]. The coordination geometries of these complexes have been investigated in the solid state by X‐ray crystallography and in solution by 1H and 19F NMR spectroscopy. Due to the labile nature of high‐spin iron(II) complexes in solution, dynamic equilibria of complexes with different coordination geometries (cis‐α, cis‐β and trans) are observed with ligands 2 – 5 . In these cases, the geometry observed in the solid state does not necessarily represent the only or even the major geometry present in solution. The ligand field strength in the various complexes has been investigated by variable temperature magnetic moment measurements and UV‐vis spectroscopy. The strongest ligand field is observed with the most rigid ligands 1 and 2 , which generate complexes [Fe(L)(OTf)2] with a cis‐α coordination geometry and the corresponding complexes [Fe(L)(CH3CN)2]2+ display spin crossover behaviour. The catalytic properties of the complexes for the oxidation of cyclohexane, using hydrogen peroxide as the oxidant, have been investigated. An increased flexibility in the ligand results in a weaker ligand field, which increases the lability of the complexes. The activity and selectivity of the catalysts appear to be related to the strength of the ligand field and the stability of the catalyst in the oxidising environment. 相似文献
14.
15.
Kalina Atkovska Sergey A. Samsonov Maciej Paszkowski-Rogacz M. Teresa Pisabarro 《International journal of molecular sciences》2014,15(2):2622-2645
Molecular docking has been extensively applied in virtual screening of small molecule libraries for lead identification and optimization. A necessary prerequisite for successful differentiation between active and non-active ligands is the accurate prediction of their binding affinities in the complex by use of docking scoring functions. However, many studies have shown rather poor correlations between docking scores and experimental binding affinities. Our work aimed to improve this correlation by implementing a multipose binding concept in the docking scoring scheme. Multipose binding, i.e., the property of certain protein-ligand complexes to exhibit different ligand binding modes, has been shown to occur in nature for a variety of molecules. We conducted a high-throughput docking study and implemented multipose binding in the scoring procedure by considering multiple docking solutions in binding affinity prediction. In general, improvement of the agreement between docking scores and experimental data was observed, and this was most pronounced in complexes with large and flexible ligands and high binding affinities. Further developments of the selection criteria for docking solutions for each individual complex are still necessary for a general utilization of the multipose binding concept for accurate binding affinity prediction by molecular docking. 相似文献
16.
Victoria A. Roberts Pnina Dauber-Osguthorpe David J. Osguthorpe Eugene Levin Arnold T. Hagler 《Israel journal of chemistry》1986,27(2):198-210
In this paper, we report on studies of ligand binding to the enzyme dihydrofolate reductase (DHFR). Energy minimizations of four complexes of DHFR with the inhibitor trimethoprim, an antibiotic, and the cofactor NADPH have been carried out in order to investigate the energetics responsible for the 100,000-fold increase in binding affinity of trimethoprim to E. coli DHFR compared with chicken liver DHFR. Several factors suggested to be responsible for the enhanced binding in bacterial DHFR's were investigated in terms of intermolecular and intramolecular energetics. The strain energies of trimethoprim in the four complexes were calculated and found to be about 6 kcal mol−1 in all complexes of the two species. In the binary complex of chicken liver DHFR, where the largest variation was observed, 2 kcal mol−1 higher than in the other complexes, it was found that this increase was compensated for by the slightly more favorable intermolecular interaction of the trimethoxyphenyl moiety with the protein. Comparison of the minimized binary and ternary complexes of E. coli allowed us to investigate the cooperativity in the binding of trimethoprim and NADPH in the bacterial enzyme in terms of the underlying intermolecular forces. This cooperativity was found to be due to a direct trimethoprim - NADPH interaction in the E. coli enzyme rather than enhanced protein-inhibitor interactions induced upon binding of the cofactor. These interactions are not as favorable in the vertebrate enzyme, consistent with the significantly diminished cooperativity observed in this enzyme. 相似文献
17.
Douglas A. Kuntz Dr. Wei Zhong Dr. Jun Guo Dr. David R. Rose Dr. Geert‐Jan Boons Dr. 《Chembiochem : a European journal of chemical biology》2009,10(2):268-277
Mannostatin A is a potent inhibitor of the mannose‐trimming enzyme, Golgi α‐mannosidase II (GMII), which acts late in the N‐glycan processing pathway. Inhibition of this enzyme provides a route to blocking the transformation‐associated changes in cancer cell surface oligosaccharide structures. Here, we report on the synthesis of new Mannostatin derivatives and analyze their binding in the active site of Drosophila GMII by X‐ray crystallography. The results indicate that the interaction with the backbone carbonyl of Arg876 is crucial to the high potency of the inhibitor—an effect enhanced by the hydrophobic interaction between the thiomethyl group and an aromatic pocket vicinal to the cleavage site. The various structures indicate that differences in the hydration of protein–ligand complexes are also important determinants of plasticity as well as selectivity of inhibitor binding. 相似文献
18.
《分离科学与技术》2012,47(12):1957-1965
The adsorption behaviors of hydrophobic charge induction chromatography (HCIC) adsorbents with different functional ligands were investigated with immunoglobulin of egg yolk (IgY) as a model antibody. The adsorption isotherm and retention behavior in the column were studied, and the influences of the ligand structure and the pH on the adsorption were discussed. The results indicated that the pI of the target protein and pKa of HCIC ligand are the important parameter to determine the maximum adsorption pH of HCIC adsorbent, and high adsorption of IgY was found at pH 5 for all five adsorbents tested. Some differences could be found for different HCIC adsorbents, and the ligand structure influenced pH effect on the binding/elution of target protein. 2-mercapto-1-methyl-imidazole (MMI) ligand with a sulfone group showed a high adsorption capacity and strong pH-sensitivity, which would be more suitable for antibody purification. Moreover, the retention experiments indicated that IgY could be efficiently eluted from the adsorbents with 4-mercapto-ethyl-pyridine (MEP) or MMI as the ligand at acid conditions, while 2-mercapto-benzimidazole (MBI) ligand showed some difficulties on the elution. The retention study would help in defining not only the effective pH of elution for a given protein but also the elution efficiency of a given adsorbent. 相似文献
19.
Erika F. Dudás Dr. Gyula Pálfy Dr. Dóra K. Menyhárd Fanni Sebák Dr. Péter Ecsédi Dr. László Nyitray Dr. Andrea Bodor 《Chembiochem : a European journal of chemical biology》2020,21(21):3087-3095
Conformationally flexible protein complexes represent a major challenge for structural and dynamical studies. We present herein a method based on a hybrid NMR/MD approach to characterize the complex formed between the disordered p53TAD1–60 and the metastasis-associated S100A4. Disorder-to-order transitions of both TAD1 and TAD2 subdomains upon interaction is detected. Still, p53TAD1–60 remains highly flexible in the bound form, with residues L26, M40, and W53 being anchored to identical hydrophobic pockets of the S100A4 monomer chains. In the resulting “fuzzy” complex, the clamp-like binding of p53TAD1–60 relies on specific hydrophobic anchors and on the existence of extended flexible segments. Our results demonstrate that structural and dynamical NMR parameters (cumulative Δδ, SSP, temperature coefficients, relaxation time, hetNOE) combined with MD simulations can be used to build a structural model even if, due to high flexibility, the classical solution structure calculation is not possible. 相似文献
20.
Small highly soluble probe molecules such as aniline, urea, N‐methylurea, 2‐bromoacetate, 1,2‐propanediol, nitrous oxide, benzamidine, and phenol were soaked into crystals of various proteins to map their binding pockets and to detect hot spots of binding with respect to hydrophobic and hydrophilic properties. The selected probe molecules were first tested at the zinc protease thermolysin. They were then applied to a wider range of proteins such as protein kinase A, D ‐xylose isomerase, 4‐diphosphocytidyl‐2C‐methyl‐D ‐erythritol synthase, endothiapepsin, and secreted aspartic protease 2. The crystal structures obtained clearly show that the probe molecules populate the protein binding pockets in an ordered fashion. The thus characterized, experimentally observed hot spots of binding were subjected to computational active site mapping using HotspotsX. This approach uses knowledge‐based pair potentials to detect favorable binding positions for various atom types. Good agreement between the in silico hot spot predictions and the experimentally observed positions of the polar hydrogen bond forming functional groups and hydrophobic portions was obtained. Finally, we compared the observed poses of the small‐molecule probes with those of much larger structurally related ligands. They coincide remarkably well with the larger ligands, considering their spatial orientation and the experienced interaction patterns. This observation confirms the fundamental hypothesis of fragment‐based lead discovery: that binding poses, even of very small molecular probes, do not significantly deviate or move once a ligand is grown further into the binding site. This underscores the fact that these probes populate given hot spots and can be regarded as relevant seeds for further design. 相似文献