Binding Ensembles of p53-MDM2 Peptide Inhibitors by Combining Bayesian Inference and Atomistic Simulations

Designing peptide inhibitors of the p53-MDM2 interaction against cancer is of wide interest. Computational modeling and virtual screening are a well established step in the rational design of small molecules. But they face challenges for binding flexible peptide molecules that fold upon binding. We look at the ability of five different peptides, three of which are intrinsically disordered, to bind to MDM2 with a new Bayesian inference approach (MELD × MD). The method is able to capture the folding upon binding mechanism and differentiate binding preferences between the five peptides. Processing the ensembles with statistical mechanics tools depicts the most likely bound conformations and hints at differences in the binding mechanism. Finally, the study shows the importance of capturing two driving forces to binding in this system: the ability of peptides to adopt bound conformations (ΔGconformation) and the interaction between interface residues (ΔGinteraction).     

Rate-equilibrium relationships in hydride transfer reactions: the role of intrinsic barriers

A literature survey on the kinetics of hydride abstractions from CH-groups by carbocations reveals a general phenomenon: Variation of the hydride acceptor affects the rates of hydride transfer to a considerably greater extent than an equal change of the thermodynamic driving force caused by variation of the hydride donor. The origin of this relationship was investigated by quantum chemical calculations on various levels of ab initio and DFT theory for the transfer of an allylic hydrogen from 1-mono- and 1,1-disubstituted propenes (XYC=CH-CH(3)) to the 3-position of 1-mono- and 1,1-disubstituted allyl cations (XYC=CH-CH(2)(+)). The discussion is based on the results of the MP2/6-31+G(d,p)//RHF/6-31+G(d,p) calculations. Electron-releasing substituents X and Y in the hydride donors increase the exothermicity of the reaction, while electron-releasing substituents in the hydride acceptors decrease exothermicity. In line with Hammond's postulate, increasing exothermicity shifts the transition states on the reaction coordinate toward reactants, as revealed by the geometry parameters and the charge distribution in the activated complexes. Independent of the location of the transition state on the reaction coordinate, a value of 0.72 is found for Hammond-Leffler's alpha = deltaDeltaG/deltaDelta(r)G degrees when the hydride acceptor is varied, while alpha = 0.28 when the hydride donor is varied. The value of alpha thus cannot be related with the position of the transition state. Investigation of the degenerate reactions XYC=CH-CH(3) + XYC=CH-CH(2)(+) indicates that the migrating hydrogen carries a partial positive charge in the transition state and that the intrinsic barriers increase with increasing electron-releasing abilities of X and Y. Substituent variation in the donor thus influences reaction enthalpy and intrinsic barriers in the opposite sense, while substituent variation in the acceptor affects both terms in the same sense, in accord with the experimental findings. Marcus theory is employed to treat these effects quantitatively.     

Studies on solid state reactions of coordination compounds. LXIII. Solid state synthesis of a series of tetranuclear Mo(W)—Ag mixed-metal clusters. Crystal structures of [(n-Bu)4N]3[MoOS3Ag3Br4] and [(n-Bu)4N]3[WS4Ag3Cl4]

A series of tetranuclear Mo(W)-Ag mixed-metal clusters have been synthesized by making use of the solid state reactions of [NH₄]₂[MYS₃](M= Mo, W; Y= O, S), AgX(X= Cl, Br, I) and (n-Bu)₄NX' (X' =Cl, Br), two of which [(n-Bu)₄N]₃[MoOS₃Ag₃Br₄] (1) and [(n-Bu)₄N]₃[WS₄Ag₃Cl₄] ( 2 ) have been structurally characterized by X-ray analysis. The crystal data: 1 , cubic, P4 3m, αequals;12.093(4) Å, Z=1, R =0.076; 2 , cubic, P4 3m, αequals;12.059(2) Å, Z =1, R =0.075. The cluster anion core [Ag₃MS₃X'] of the two compounds can be viewed as a cube in which the four metal atoms and the four non-metal atoms are statistically distributed, respectively. Substitution reaction with PPh₃ ligand is also discussed for this type of tetranuclear clusters.     

Solid state synthesis of copper(I) thiotungstate cluster compounds at low heating temperatures. Crystal structures of [(n-Bu)4N]3-[WS4Cu3Cl3Br] and [Et4N]4[WS4Cu4I6]

Summary Reaction of [NH₄]₂[WS₄] with CuX (X = Cl or I) and R₄NX (R = Et or n-Bu) in the solid state gave two new bimetallic compounds with W:Cu compositions from 1:3 to 1:4. Compound (1), [(n-Bu)₄N]₃[WS₄Cu₃Cl₃Br], crystallizes in the hexagonal space group R3c with a = 17.051(5), c = 38.372(5) Å, V = 9661.8 ų, Z = 6. The cluster anion of (1) comprises a cubane-like cluster core [WS₃Cu₃Br] of C₃ symmetry with a Cl atom attached to each of the three Cu atoms and one terminal sulphido ligand attached to the W atom. Compound (2), [Et₄N]₄[WS₄Cu₄I₆], crystallizes in the monoclinic space group C2/m with a = 29.702(6), b = 12.7887(5), c = 15.327(3)Å, = 99.69(2), V = 5738.1 ų, Z = 4. In the cluster anion of (2), four edges of the WS₄ core are coordinated by four Cu atoms, giving a WS₄Cu₄ aggregate of approximate C_2V symmetry.     

Isolierung und Eigenschaften der sauren Phosphatase aus Ananas comosus

Zusammenfassung Im Bromelin, einer Protease aus Ananas comosus Var. Cayenne, sind einige Fremdaktivitäten enthalten. Durch Gel-Chromatographie an Sephadex G-75 läßt sich die saure Phosphatase und eine Esterase, die N-Acetyl-l-tyrosinäthylester spaltet, von der Protease abtrennen. Durch Blektrofokussierung konnte die saure Phosphatase in mindestens zwei Isoenzyme vom isoelektrischen Punkt 4, 3 bzw. 6,1 aufgetrennt werden.Die Michaelis-Konstante der sauren Phosphatase gegenüber p-Nitrophenylphosphat beträgt 0,76 · 10^–3 M (nach Lineweaver-Burk) bzw. 0,73 · 10^–3 (nach Eadie). Das pH-Optimum in Citratpuffer liegt bei pH 5,5. Es bestehen Anzeichen dafür, daß neben der höhermolekularen Phosphatase (Mol.-Gew. > 100000) auch eine niedermolekulare saure Phosphatase in den Stengeln der Ananas comosus vorkommt.In den Strünken der Ananas lassen sich erhebliche Mengen einer pflanzlichen Ribonuclease nachweisen. Dieses Enzym läßt sich durch Ionenaustausch-Chromatographie an DEAE-Cellulose von den anderen Begleitenzymen abtrennen.Eine weitere Varietät von Ananas comosus, die in Brasilien vorkommt, enthält ebenfalls große Aktivitäten an saurer Phosphatase sowie Ribonuclease, jedoch wenig Protease und keine Aktivität gegenüber N-Acetyl-l-tyrosinäthylester.

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Isolation and properties of the acid phosphatase from ananas comosus

Bromelin, a protease from pineapple (ananas comosus var. Cayenne), contains several foreign activities. Acid phosphatase and an esterase splitting N-acetyl-l-tyrosineethyl ester can be separated from the protease by gel chromatography on Sephadex G-75. The acid phosphatase can be separated into at least two isoenzymes with isoelectric points of 4.3 and 6.1, resp., by means of electrofocusing.The Michaelis constant of acid phosphatase for p-nitrophenylphosphate is 0.76×10^–3 M (according to Lineweaver-Burk) and 0.73×10^–3M (according to Eadie). The optimum pH value in citrate buffer is about 5.5. Besides the higher-molecular phosphatase (mol.-weight > 100000) also a lower-molecular acid phosphatase seems to occur in the stems of ananas comosus.Considerable amounts of a vegetable ribonuclease can be detected in the stalks of ananas. This enzym can be separated from other accompanying enzymes by ionexchange chromatography on DEAE-cellulose. Another variety of ananas comosus, occurring in Brazil, also contains high activities of acid phosphatase and ribonuclease, but only small amounts of protease and no activity towards N-acetyl-l-tyrosineethyl ester.

     

Acetic acid induced self-assembly of supramolecular compounds [Et4N]3[(WS4Cu2)2(mu-CN)3].2MeCN and [PPh4][WS4Cu3(mu-CN)2].MeCN from preformed clusters [A]2[WS4(CuCN)2] (A = Et4N, PPh4)

Reactions of two preformed trinuclear W/Cu/S clusters, [A](2)[WS(4)(CuCN)(2)] (1: A = Et(4)N; 2: A = PPh(4)), with different concentrations of acetic acid in MeCN generate two interesting 2D polymeric clusters [Et(4)N](3)[(WS(4)Cu(2))(2)(mu-CN)(3)].2MeCN (3), and [PPh(4)][WS(4)Cu(3)(mu-CN)(2)].MeCN (4), respectively. Compound 4 can also be readily obtained in a high yield from the reaction of 2 with equimolar [Cu(MeCN)(4)]PF(6) in MeCN. These compounds have been characterized by elemental analysis, IR spectra, thermal analysis, and single-crystal X-ray diffraction. An X-ray analysis reveals that compound 3 retains the WS(4)Cu(2) cluster core, which serves as a 3-connecting node to link equivalent nodes via single cyanide bridges, forming an anionic 2D (6,3) net. Compound 4 consists of a T-shaped WS(4)Cu(3) core, which also acts as a 3-connecting node, with links to 3 equivalent clusters either through single or double cyanide bridges, affording a different anionic 2D (6,3) network. The acetic acid induced aggregation of 3 and 4 from the two cluster precursors 1 and 2 suggests that this simple synthetic strategy is likely to be applicable to many related systems.     

一步室温固相化学反应合成纳米氨基酸杂多电荷转移配合物(HPhe)3PMo12O40·2H2O

以Keggin结构的钼磷酸(H3PMo12O40·13H2O)与苯丙氨酸(Phe)为原料,利用一步固相化学反应于室温合成了纳米氨基酸杂多电荷转移配合物(HPhe)3PMo12O40·2H2O,采用元素分析,IR,XRD,TEM,UV和循环伏安法等手段对其进行了结构表征及性质研究.结果表明,标题化合物纳米粒子为均匀的球状,粒径约为30～40nm.该化合物中杂多阴离子部分仍保持Keggin结构,但在钼磷酸与苯丙氨酸之间发生了显著的电荷转移.     

Carbonyl‐Komplexe von Chrom,Molybdän und Wolfram mit Isocyanacetat. Reaktionen am koordinierten Isocyanacetat. Stabilisierung von Isocyanessigsäure und Isocyanacetylchlorid am Metall. Isocyanopeptide [1]

Carbonyl Complexes of Chromium, Molybdenum and Tungsten with Isocyano Acetate. Reactions of Coordinated Isocyanoacetate. Stabilization of Isocyanoacetic Acid and Isocyanoacetyl Chloride at the Metal Atom. Isocyanopeptides The reactions of [(OC)₅MCNCH₂CO₂Et] (M = Cr, W) with Na[N(SiMe₃)₂] or with KOH afford the isocyanoacetate complexes [(OC)₅MCNCH₂CO₂]^? ( 1,2 ). Similarly, the complex [(OC)₃Mo(CNCH₂CO₂^?Li⁺)₃] ( 4 ) was obtained from [(OC)₃Mo(CNCH₂CO₂Et)₃] ( 3 ) and LiOH. Protonation of 1 and 2 affords the sublimable isocyanoacetic acid complexes [(OC)₅MCNCH₂CO₂H] ( 5 , 6 ; M = Cr, W) in which the functional isocyanide is stabilized at the metal atom. Reactions of [(OC)₅WCNCH₂CO₂^?K⁺] and of [(OC)₃Mo(CNCH₂CO₂^?Li⁺)₃] with oxalyl dichloride give the isocyanoacetyl chloride compounds [(OC)₅WCNCH₂COCl] ( 9 ) (sublimable) and [(OC)₃Mo(CNCH₂COCl)₃] ( 10 ); the latter ( 10 ) was not isolated. Complexes 9 and 10 were reacted in situ with β‐alanine, glycine, phenylalanine and methionine esters as well as the peptide esters GlyGlyOEt, PhePheOMe, Phe‐β‐AlaOMe, and GlyGlyGlyOMe to form the isocyanoacetyl amino acid esters ( 11 ‐ 14 ) and the isocyanoacetyl peptide esters ( 15 ‐ 18 ) which are stabilized at the molybdenum atom.