Binding of an RNA pol II Ligand to the WW Domain of Pin1 Using Molecular Dynamics Docking Simulations

A novel docking protocol using a long, all atom molecular dynamics (MD) simulation, in an explicit solvent medium, without using any distance constraints is presented. This MD docking protocol is able to dock ligands, based on the C-terminal domain (CTD) of RNA polymerase II, into the tryptophan-tryptophan (WW) domain of Pin1. In this docking process, a significant loop-bending event occurs in order to encircle the ligand into its solvent exposed binding site, which cannot be simulated using current protocols. The simulations were validated structurally and energetically against an X-ray structure to confirm correct sampling of conformational space. Based on these simulations, and justification of the starting structure as a valid intermediate structure, a potential molecular basis for binding was predicted as well as confirming the key residues involved in the formation of the final strong and stable Pin1 WW domain-ligand complex.

Design, synthesis, and DNA sequence selectivity of formaldehyde-mediated DNA-adducts of the novel N-(4-aminobutyl) acridine-4-carboxamide

A novel derivative of the anti-tumor agent N-[2-(dimethylamino)ethyl]acridine-4-carboxamide (DACA) was prepared by reduction of 9-oxoacridan-4-carboxylic acid to acridine-4-carboxylic acid with subsequent conversion to N-(4-aminobutyl)acridine-4-carboxamide (C4-DACA). Molecular modeling studies suggested that a DACA analogue comprising a side chain length of four carbons was optimal to form formaldehyde-mediated drug-DNA adducts via the minor groove. An in vitro transcription assay revealed that formaldehyde-mediated C4-DACA-DNA adducts selectively formed at CpG and CpA dinucleotide sequences, which is strikingly similar to that of formaldehyde-activated anthracenediones such as pixantrone.

Effect of structural stress on the flexibility and adaptability of HIV-1 protease

Resistance remains a major issue with regards to HIV-1 protease, despite the availability of numerous HIV-1 protease inhibitors and copious amounts of structural and binding data. In an effort to improve our understanding of how HIV-1 protease is able to "outsmart" new drugs, we have investigated the flexibility of HIV-1 protease and in particular how it adapts to different structural stresses. Our analysis has highlighted the effects of space group on the variability between structures of HIV-1 protease and suggests that consideration of multiple structures and appropriate consideration of different conformations of the Ile50 residue is necessary in any structural analysis. Calculation of the root-mean-square deviation on a per-residue basis has been used to identify 'natural variation', while mutational and ligand analyses have been carried out to identify the effect on structure as a result of specific stresses. It was observed that mutations readily cause changes to occur at sites both close to and distant from a mutation site, with changes more likely to occur at residues that are sites of other major mutations. It is also revealed that HIV-1 protease adaption is dependent on the type and the structure of any bound ligand. Identification of the specific changes that occur due to these stresses will aid in the understanding of resistance and also aid in the design of new drugs.

Structural characterisation of PinA WW domain and a comparison with other group IV WW domains, Pin1 and Ess1

The NMR solution structure of the PinA WW domain from Aspergillus nidulans is presented. The backbone of the PinA WW domain is composed of a triple-stranded anti-parallel beta-sheet and an alpha-helix similar to Ess1 and Pin1 without the alpha-helix linker. Large RMS deviations in Loop I were observed both from the NMR structures and molecular dynamics simulation suggest that the Loop I of PinA WW domain is flexible and solvent accessible, thus enabling it to bind the pS/pT-P motif. The WW domain in this structure are stabilised by a hydrophobic core. It is shown that the linker flexibility of PinA is restricted because of an alpha-helical structure in the linker region. The combination of NMR structural data and detailed Molecular Dynamics simulations enables a comprehensive structural and dynamic understanding of this protein.

Solution-Phase Peptide Synthesis; Synthesis of 'North-Western' and 'South-Eastern' Fragments of the Antifungal Cyclodepsipeptide Petriellin A

The solution-phase synthesis of two highly modified peptides, a hexamer and a heptamer, that constitute the two halves of the antifungal cyclic depsipeptide, Petriellin A, is reported.

PinA from Aspergillus nidulans binds to pS/pT-P motifs using the same Loop I and XP groove as mammalian Pin1

Binding of the Cdc25c-T48 ligand to PinA from Aspergillus nidulans has been characterised by the identification of 15N and 1H resonances from 1H-15N HSQC NMR titration experiments using previous backbone assignments. It is shown that the binding site for the Cdc25c-T48 ligand with PinA is the same as in the mammalian protein Pin1, although with a reduced binding affinity. It had previously been proposed that the arginine residue (R17) in the loop I region of the Pin1 WW domain is essential for binding to the pSer/pThr-Pro motifs of phosphorylated ligands such as Cdc25c. In PinA, a fungal homologue of Pin1, the arginine residue (R17) is replaced with an asparagine residue (N17). The effect of substitution of R17 by N17 in Pin1 has been investigated via a computational study, which predicted that changing R17 to N17 in Pin1 lowers the ligand binding affinity as a result of reduced hydrogen bonding between the protein and the phosphate group of the ligand.

An FcgammaRIIa-binding peptide that mimics the interaction between FcgammaRIIa and IgG

A disulphide-constrained peptide that binds to the low affinity Fc receptor, FcgammaRIIa (CD32) has been identified and its structure solved by NMR. Linear (7-mer and 12-mer) and disulphide-constrained (7-mer) phage display peptide libraries were panned on recombinant soluble FcgammaRIIa genetically fused to HSA (HSA-FcgammaRIIa). Peptides were isolated only from the constrained peptide library and these contained the consensus sequence, CWPGWxxC. Phage clones displaying variants of the peptide consensus sequence bound to FcgammaRIIa and the strongest binding clone C7C1 (CWPGWDLNC) competed with IgG for binding to FcgammaRIIa and was inhibited from binding to FcgammaRIIa by the FcgammaRIIa-blocking antibody, IV.3, suggesting that C7C1 and IgG share related binding sites on FcgammaRIIa. A synthetic disulphide-constrained peptide, pep-C7C1 bound to FcgammaRIIa by biosensor analysis, albeit with low affinity (KD approximately 100microM). It was significant that the FcgammaRIIa consensus peptide sequence contained a Proline (Pro3), which when substituted with alanine abrogated FcgammaRIIa binding, consistent with Pro3 contributing to receptor binding. Upon binding of IgG and IgE to their respective Fc receptors (FcgammaRs and FcepsilonRI) Pro329 in the Fc makes a critical interaction with two highly conserved Trp residues (Trp90 and Trp113) of the FcRs. The NMR structure of pep-C7C1 revealed a stabilizing type II beta-turn between Trp2 and Trp5, with Pro3 solvent exposed. Modelling of the pep-C7C1 structure in complex with FcgammaRIIa suggests that Pro3 of C7C1 binds to FcgammaRIIa by inserting between Trp90 and Trp113 of FcgammaRIIa thereby mimicking the molecular interaction made between FcgammaRIIa and IgG.

Characterisation of the extracellular polysaccharides produced by isolates of the fungus Acremonium

Solid state (13)C NMR studies of the extracellular glucans from the fungi Acremonium persicinum C38 (QM107a) and Acremonium sp. strain C106 indicated a backbone of (1-->3)-beta-linked glucosyl residues with single (1-->6)-beta-linked glucosyl side branches for both glucans. Analyses of enzymatic digestion products suggested that the average branching frequency for the A. persicinum glucan (66.7% branched) was much higher than that of the Acremonium sp. strain C106 glucan (28.6% branched). The solid state (13)C NMR spectra also indicated that both glucans are amorphous polymers with no crystalline regions, and the individual chains are probably arranged as triple helices.

The conformation of acetylated virginiamycin M1 and virginiamycin M1 in explicit solvents

The three-dimensional structure of acetylated virginiamycin M(1) (acetylated VM1) in chloroform and in a water/acetonitrile mixture (83:17 v/v) have been established through 2D high resolution NMR experiments and molecular dynamics modeling and the results compared with the conformation of the antibiotic VM1 in the same and other solvents. The results indicated that acetylation of the C-14 OH group of VM1 caused it to rotate about 90 degrees from the position it assumed in non-acetylated VM1. The conformation of both VM1 and acetylated VM1 appear to flatten in moving from a nonpolar to polar solvent. However, the acetylated form has a more hydrophobic nature. The acetylated VM1 in chloroform and in water/acetonitrile solution had a similar configuration to that of VM1 bound to 50S ribosomes and to the Vat(D) active sites as previously determined by X-ray crystallography. Docking studies of VM1 to the 50S ribosomal binding site and the Vat(D) gave conformations very similar to those derived from X-ray crystallographic studies. The docking studies with acetylated VM1 suggested the possibility of a hydrogen bond from the acetyl carbonyl group oxygen of acetylated VM1 to the 2' hydroxyl group of ribose of adenosine 2538 at the ribosomal VM1 binding site. No hydrogen bonds between acetylated VM1 and the Vat(D) active sites were found; the loss of this binding interaction partly accounts for the release of the product from the active site.

A convenient gram-scale synthesis of uridine diphospho(13C6)glucose

A simple gram-scale synthesis of uridine diphospho(13C6)glucose is presented from D-(13C6)glucose. The critical step uses a 1H-tetrazole-catalyzed coupling of 2,3,4,6-tetra-O-acetyl-alpha-D-glucopyranosyl-1-phosphate and UMP-morpholidate. The uridine diphospho(13C6)glucose was used in the structural identification of (1-->3)-beta-D-glucan from Lolium multiflorum.

Structure and assembly of epiglucan, the extracellular (1→3;1→6)-β-glucan produced by the fungus Epicoccum nigrum strain F19

In a previous article [Carbohydr. Res.2001, 331, 163-171] two different structures for the possible modular repeating unit of the extracellular beta-glucan, epiglucan produced by the fungus Epicoccum nigrum strain F19 were proposed. Clarifying which was the more likely one was considered essential before attempts were made to understand how epiglucan was assembled by this fungus. Data from Smith degradation analyses of epiglucan were consistent with the repeating unit of structure I, where single glucosyl residues are attached by (1-->6)-beta-linkages to two out of every three glucosyl residues in the (1-->3)-beta-linked glucan backbone. Repeated Smith degradations of 14C-glucose labelled epiglucan showed that chain elongation occurred from its non-reducing end. Side chain insertion into the growing glucan was followed by analysis of real time incorporation of 13C-glucose into epiglucan by 13C NMR, and 14C-glucose by enzymic digestion of the synthesised 14C-epiglucan. All data obtained were consistent with the view that single (1-->6)-beta-linked glucosyl side residues are inserted simultaneously as the glucan backbone elongates.

Solution structures by NMR of a novel antifungal drug: Petriellin A

Petriellin A is a novel cyclic depsipeptide antifungal compound consisting of nine l-configured residues, one d-phenyllactic acid (PhLac) and three unknown chiral centres: two N-methyl-threonines (MeThr1 & MeThr2) and one N-methyl-isoleucine (MeIle). NMR experiments including 2D ROESY, NOESY along with structural and energy calculations predicted that the unknown chiral centres were all l-configured, which was later verified chemically. Simulated annealing, dynamics calculations and minimisation processes showed Petriellin A to have a folded "C-shaped" structure.

Determination of the Complete Absolute Configuration of Petriellin A

We report the full structural determination of the depsipeptide petriellin A. The absolute configuration of the amino acid residues, N-methyl isoleucine and N-methyl threonine, have been determined by a combination of HPLC and TLC comparison of synthetic Marfey’s derivatives and Marfey’s derivatives of the natural product hydrolysate. The configuration of the chiral centres in these two N-methylated residues was found to be the same as those of the common unmethylated l-amino acids.

The conformational flexibility of the antibiotic virginiamycin M(1)

The antibiotic virginiamycin is a combination of two molecules, virginiamycin M(1) (VM1) and virginiamycin S(1) (VS1) or analogues, which function synergistically by binding to bacterial ribosomes and inhibiting bacterial protein synthesis. Both VM1 and VS1 dissolve poorly in water and are soluble in more hydrophobic solvents. We have recently reported that the 3D conformation of VM1 in CDCl(3) solution differs markedly from the conformation bound to a VM1 binding enzyme and to 50S ribosomes as found by X-ray crystallographic studies. We now report the results of further NMR studies and subsequent molecular modeling of VM1 dissolved in CD(3)CN/H(2)O and compare the structure with that in CD(3)OD and CDCl(3). The conformations of VM1 in CD(3)CN/H(2)O, CD(3)OD and CDCl(3) differ substantially from one another and from the bound form, with the aqueous form most like the bound structure. We propose that the flexibility of the VM1 molecule in response to environmental conditions contributes to its effectiveness as an antibiotic.

Solvent affects the conformation of virginiamycin M1 (pristinamycin IIA, streptogramin A)

The streptogramins are antibiotics which act by binding two different components at separate nearby sites on the bacterial 50S ribosome, inhibiting protein synthesis. The first component, a macrolactone, is common to many of the streptogramin antibiotics and, thus, is referred to by many names including virginiamycin M1(VM1), pristinamycin IIA, ostreogrycin A and streptogramin A. X-Ray crystallographic studies of VM1 bound to ribosomes and to a deactivating enzyme show a different conformation to that of VM1 in chloroform solution. We now report the results of high resolution 2D NMR experiments that show that the conformation of VM1 in dimethyl sulfoxide and methanol differs from both that in chloroform solution and in the bound form. The 3D structure and the 1H NMR and 13C NMR chemical shifts of VM1 in dimethyl sulfoxide and methanol are described.

Difference in Conformation of Virginiamycin M1 in Chloroform and Bound Form in the 50S Ribosome or Streptogramin Acetyltransferase

The conformation of virginiamycin M1 (VM1) in chloroform, determined by high-resolution NMR experiments, differs significantly from that of the X-ray crystal structure of VM1 bound to the 50S ribosome and to the active site of a streptogramin acetyltransferase enzyme. This implies that the binding process to these entities causes a major change in VM1 conformation.

An efficient synthesis of N-methyl amino acids by way of intermediate 5-oxazolidinones

N-Methyl amino acids occur in many natural products. Experimental strategies are presented for a unified approach to the synthesis of N-methyl derivatives through 5-oxazolidinones of the 20 common l-amino acids. The amino acids with reactive side chains that required protecting groups or devoted syntheses for side chain construction for N-methylation to proceed included serine, threonine, tyrosine, cysteine, methionine, tryptophan, asparagine, histidine, and arginine. The studies have provided improved methods for the preparation of N-methyl serine, threonine, and tyrosine. All 20 of the common l-amino acids are now available in suitable forms for solid or solution-phase peptide synthesis.

A novel synthesis of N-methyl asparagine, arginine, histidine, and tryptophan

[reaction: see text] N-Methyl amino acid residues in peptides modify several pharmacologically useful parameters, but synthesis of alkylated peptides is hampered by unavailability of N-methylated monomers. The syntheses of four N-methyl amino acids with basic side chains are presented. The side chains of these basic amino acids needed to be specially protected or constructed. This completes the set of 20 common L-amino acid N-methyl derivatives prepared via 5-oxazolidinone intermediates by our group.

The Facile Production of N-Methyl Amino Acids via Oxazolidinones

A range of oxazolidinones derived from N-carbamoyl α-amino acids were prepared by an efficient method as key intermediates in the synthesis of N-methyl amino acids and peptides. The method was readily applied to most α-amino acids except those with basic side chains. The oxazolidinones were converted by reductive cleavage into N-methyl α-amino acids.

Tris(N,N-dialkyldithiocarbamato-S,S')thiotungsten(VI) Complexes and the X-Ray Crystal Structure of [WS(S2CNEt2)3]BF4

The orange, diamagnetic compounds [WS(S2CNR2)3]X(R = Me, X- = BF4-, BPh4-;R = Et, X- =BF4-) were prepared by reacting WSCl4 and Me3SiS2CNR2 in dichloromethane, followed by metathesis with NaX in methanol. The compounds were characterized by elemental analysis, infrared and variable-temperature 1H n.m.r. spectroscopy and X-ray crystallography. Crystals of [WS(S2CNEt2)3] BF4 were monoclinic, space group P21/a with a 12.293(1), b 17.229(5), c 14.257(2) Ǻ,β 113.69(1)°, V 2765(2) Ǻ3 and Dc = 1.796 g cm-3 for Z = 4. The structure was solved by the Patterson method and refined by a full-matrix least-squares procedure, 3961data being used, to a conventional R value of 0.039 ( Rw = 0.040). The seven-coordinate cation possesses a pentagonal-bipyramidal geometry; the terminal thio ligand [W=S 2.127(2)Ǻ] occupies an axial position, a unique dithiocarbamate ligand spans the other axial position and an equatorial position while the two other dithiocarbamate ligands occupy the four remaining equatorial sites.

Cupric Ion Chelation Assisted Synthesis of N(α)-Protected N(ω)-Acridin-9-yl α,ω-Diamino Carboxylic Acids

The synthesis of Nα-protected Nω-acridin-9-yl derivatives of the α,w-diamino carboxylic acids ornithine and lysine is reported. Direct introduction of the acridin-9-yl moiety to the amino side chain of the free amino acid was achieved in methanol through temporary copper(II) chelation protection of the α-amino and carboxy groups. Nα-Fmoc protection was introduced by using N-(fluoren-9-ylmethoxycarbonyloxy)succinimide in aqueous dioxan.

Applications of 95Mo N.M.R. Spectroscopy. XVIII. Relaxation Times, Quadrupole Coupling Constants and Partial Field Gradients in [Mo(CO)5L] Complexes

A study of ,95Mo spin-lattice relaxation times (T1) and linewidths of [Mo(CO)5L] complexes, where L = PPh3, AsPh3, SbPh3, pyridine and Cl-, has shown that the relaxation times are due entirely to the quadrupolar mechanism, with no scalar coupling contribution to linewidth where molybdenum is bonded to a quadrupolar nucleus. Based on the literature value of the quadrupole coupling constant obtained by n.q.r . for the PPh3 complex (1.972 MHz), the quadrupole coupling constants of the arsine and stibine complexes are determined to be 3.36 and 3.75 MHz respectively. These values, and that of the pyridine complex (2.80 MHz), are found to correlate with ligand partial field gradient parameters obtained from Mossbauer spectra of FeII complexes, and are rationalized in terms of metal- ligand bonding interactions. For Et4N [Mo(CO)5Cl], the correlation is very poor; this result is attributed to the effects of ion in solution.

Applications of 95Mo N.M.R-Spectroscopy. XVI. Structure and Bonding in [Mo(Co)3(η6-Arene)] Complexes From 95Mo,13C and 17O Relaxation-Times

Spin-lattice relaxation times (T1) have been measured for the 95Mo, 17O and methine and carbonyl 13C nuclei for a series of [Mo(CO)3(η6-C6H6- nMen)] complexes. In addition to the expected decrease in T1 with increasing molecular volume, the 95Mo and methine 13C data are interpreted in terms of variations in arene -molybdenum bonding. The methine 13C T1 values decrease in the order o- xylene > toluene > p- xylene > m- xylene > mesitylene . The methyl substitution pattern determines the distribution of electron-rich sites on the arene ligand , affecting the molybdenum- arene bond strength and the barrier to arene rotation. These observations support an earlier proposal that downfield 95Mo chemical shifts are associated with increased molybdenum- arene bond strength. 95Mo T1 values are unaffected by the rotational barriers, since they depend only on molecular tumbling perpendicular to the pseudo C3v symmetry axis. While these T1 values decrease as the number of methyl groups increases, an effect due to increasing molecular volume, the order of 95Mo T1 for the xylene complexes is opposite to that of the 13C T1, due to a reduction in the electric field gradient at the 95Mo nucleus. 95Mo quadrupole coupling constants for the series are 1.2�0.2 MHz. The 17O T1 values have also been measured for this series. They are considerably longer, and quadrupole coupling constants smaller (0.87�0.07 MHz), than those of other metallocarbonyls , indicating a significant increase in metal- ligand dπ-pπ - back bonding in the present system. A correlation between carbonyl force constants and 17O quadrupole coupling constants is presented.

N.M.R. Spectra of the Β-Methylcinnamic Acids and their Methyl Esters

The configurations of the (E)- and (Z)-β- methylcinnamic acids and their methyl esters have been confirmed by 1H and 13C n.m.r . spectroscopy.

Applications of molybdenum-95 N.M.R. spectroscopy. X. Polyoxomolybdates

An initial survey of the 95Mo n.m.r. properties of a range of 12 polyoxomolybdates is presented. The species resonate in the range - 18 to + 140 ppm. The observed line widths generally exceed 100 Hz for six-coordinate molybdenum sites of low symmetry, but can be narrow (< 20 Hz at 20�) for four-coordinate sites. Aqueous solutions of [Mo7O24]6- at pH 6.1 exhibit exchange between Mo- and Mo7-based species. Solutions of α-[Mo8O26]4- in MeCN feature a single narrow resonance (δ16, Wh/2 23 Hz at 20�) assigned to the tetrahedral capping sites, while two broad resonances (δ19, Wh/2 240 Hz; δ109, Wh/2 C. 270 HZ) are seen in equivalent solutions of β-[Mo8O26]4-. In the cases cited above, 17O n.m.r. is used to confirm the integrity of sample solutions and assists in correction of the 95Mo n.m.r. properties of β-[Mo8O26]4 reported in a previous communication.

Conformational analysis of picrotoxinin by N.M.R., X-ray crystallography, and molecular orbital and classical potential-energy calculations

The conformation of the potent convulsant drug picrotoxinin has been studied by proton n.m.r., X-ray crystallography, molecular orbital calculations and classical calculations. The calculations reveal two alternative low-energy conformations, either of which is consistent with the n.m.r. data, and one of which is also observed crystallographically. The energy difference is sufficiently small to suggest that either conformation may be the biologically active form.

Applications of molybdenum-95 N.M.R. spectroscopy. VI. 95Mo and 13C N.M.R. of certain cis-dioxomolybdenum(VI) compounds and related species. The crystal and molecular structure of Bis(N,N-diethylhydroxylamido(l -)-O,N)- disulfidomolybdenum(VI) hemibenzene

The 95MO n.m.r. spectra of a series of compounds containing the fac-[MoVIO3] and cis-[ MoVIO2] units are reported, together with those for the series [MoX2(R2NO)2] (X = O or S; R = Et, PhCH2). Trends in the data are discussed. The stereochemistry in solution of certain of the cis-dioxo species is assigned by means of 13C n.m.r. spectroscopy. The crystal and molecular structure of [MoS2(Et2NO)2],0.5C6H6 has been determined by X-ray crystallography. The steric and electronic requirements of the terminal sulfide ligands significantly affect the detailed coordination geometry relative to that observed for the dioxo analogue [MoO2(Et2NO)2]. Crystal data: a 10.162(2), b 11.836(2), c 14.437(2) �, β 106.12(2)� P21/a; Z 4.