ForceGen 3D structure and conformer generation: from small lead-like molecules to macrocyclic drugs

We introduce the ForceGen method for 3D structure generation and conformer elaboration of drug-like small molecules. ForceGen is novel, avoiding use of distance geometry, molecular templates, or simulation-oriented stochastic sampling. The method is primarily driven by the molecular force field, implemented using an extension of MMFF94s and a partial charge estimator based on electronegativity-equalization. The force field is coupled to algorithms for direct sampling of realistic physical movements made by small molecules. Results are presented on a standard benchmark from the Cambridge Crystallographic Database of 480 drug-like small molecules, including full structure generation from SMILES strings. Reproduction of protein-bound crystallographic ligand poses is demonstrated on four carefully curated data sets: the ConfGen Set (667 ligands), the PINC cross-docking benchmark (1062 ligands), a large set of macrocyclic ligands (182 total with typical ring sizes of 12–23 atoms), and a commonly used benchmark for evaluating macrocycle conformer generation (30 ligands total). Results compare favorably to alternative methods, and performance on macrocyclic compounds approaches that observed on non-macrocycles while yielding a roughly 100-fold speed improvement over alternative MD-based methods with comparable performance.     

Heptametallic bowl-shaped complexes derived from conjugated Schiff-base macrocycles: synthesis, characterization, and X-ray crystal structures

The reaction of chelating conjugated macrocycles 1a-c with Zn(OAc)2 gives bowl-shaped heptanuclear Zn complexes featuring Zn in tetrahedral, octahedral, and square-pyramidal geometries. Crystallographic and NMR results indicate that vacant Zn coordination sites within the bowl may be accessed, suggesting that these coordination complexes may be used as mimics for Zn fingers and carbonic anhydrase.     

Isomer generation: semantic rules for detection of isomorphism

The problem of exhaustive generation of a nonredundant set of structural formulas (graphs) of acyclic alkanes was considered. A technique based on the compressed adjacency matrix (CAM) was proposed. The algorithm generates CAMs, which encode trees numbered according to the Morgan naming algorithm. Out of this set of CAMs those corresponding to the maximal Morgan codes--which in fact are the CAMs of canonically numbered isomers--must be found. CAMs are conceived as "sentences" of a primitive language. Sentences violating the syntactic and semantic rules of this language have to be discarded. In this paper three semantic rules have been proposed. The algorithm devised is efficient, and the decision to retain or to reject the actual structure does not involve any comparison with other structures. It was proved that several subsets of CAMs will not contain any maximal CAM and therefore it is not necessary to generate them. The whole procedure was illustrated by generating CAMs of all acyclic graphs containing nine vertices.     

Chi1 torsion angle dynamics in proteins from dipolar couplings.

Experiments are presented for the measurement of one-bond carbon-proton dipolar coupling values at CH and CH2 ositions in 13C-labeled, approximately 50% fractionally deuterated proteins. 13Cbeta-1Hbeta dipolar couplings have been measured for 38 of 49 possible residues in the 63-amino-acid B1 domain of peptostreptococcal protein L in two aligning media and interpreted in the context of side-chain chi1 torsion angle dynamics. The beta protons for 18 of the 25 beta-methylene-containing amino acids for which dipolar data are available can be unambiguously stereoassigned, and for those residues which are best fit to a single rotamer model the chi(1) angles obtained deviate from crystal structure values by only 5.2 degrees (rmsd). The results for 11 other residues are significantly better fit by a model that assumes jumps between the three canonical (chi1 approximately -60 degrees, 60 degrees, 180 degrees ) rotamers. Relative populations of the rotamers are determined to within +/-6% uncertainty on average and correlate with dihedral angles observed for the three molecules in the crystal asymmetric unit. Entropic penalties for quenching chi1 jumps are considered for six mobile residues thought to be involved in binding to human immunoglobulins. This study demonstrates that dipolar couplings may be used to characterize both the conformation of static residues and side-chain motion with high precision.     

New generation ionic liquids: cations derived from amino acids

Two families of a new generation of ionic liquids, in which the chiral cations are directly derived from naturally occurring alpha-amino acids and alpha-amino acid ester salts, have been obtained via very simple preparations.     

Small angle X-ray scattering from amorphous polymers arising from heterogeneities

Summary The small angle X-ray scattering of glassy polymers (PET, PC, PVC, PMMA) and of polymer melts (PE) was studied. The dependence of the intensity scattered at small angles on the sample treatment suggests that neither the inherent structure of the pure polymer phase nor microholes are the origin of the scattering. In agreement with all experimental facts the scattering can be attributed to foreign particles such as for instance stabilizers in the polymer matrix. The consequence of this result is discussed with respect to the nodular structure of the amorphous phase and with respect to structural models of the amorphous phase. The nodular structure is not related to regions of different densities within the pure amorphous phase.The small angle X-ray scattering can be used to characterize the microscopic and macroscopic distribution of additives in polymer samples.

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Zusammenfassung Es wurden Röntgenkleinwinkeluntersuchungen an glasig erstarrten Polymeren (PÄT, PC, PVC, PMMA) und an Polymerschmelzen vorgenommen (PÄ). Die Abhängigkeit der bei kleinen Winkeln beobachteten Streuung von der Probenbehandlung weist darauf hin, daß weder die innere Struktur der amorphen Phase noch Mikrolöcher die Ursache für die Streuung sein können. In Übereinstimmung mit allen Ergebnissen wird die Streuung Fremdpartikeln wie z. B. Stabilisatoren in der Polymermatrix zugeschrieben. Die Folgerungen, die sich hieraus ergeben, werden hinsichtlich der Körnerstruktur der amorphen Phase und der Strukturmodelle diskutiert. Die Körnerstruktur kann nicht durch Bereiche unterschiedlicher Dichte in der amorphen Phase erklärt werden.Die Röntgenkleinwinkelstreuung kann zur Charakterisierung der makroskopischen und der mikroskopischen Verteilung der Zusätze im Polymeren herangezogen werden.

     

Metal transition complexes of tridentate Schiff base ligands derived from 2-hydrazinopyridine: synthesis,spectroscopic characterization and X-ray structures

Transition Metal Chemistry - Mononuclear complexes of 1-(pyridin-2-ylmethylidene)-2-(pyridin-2-yl)hydrazine (HL1) and 1-(pyridin-2-yl)-2-(1-(pyridin-2-yl)ethylidene)hydrazine (HL2),...     

Chiral ferrocene amines derived from amino acids and peptides: synthesis, solution and X-ray crystal structures and electrochemical investigations

For the recognition of all but the simplest naturally occurring molecules, electrochemical sensors based on ferrocene will certainly require chiral centers. To advance the necessary chemistry, this work describes the synthesis and properties of ferrocene derivatives of enantiomerically pure amino acids, peptides, and other chiral amines. Ferrocene aldehyde is condensed with amino acid esters to yield the corresponding Schiff bases 2, which are reduced by NaBH4 in methanol to the ferrocene methyl amino acids 3. An X-ray single-crystal analysis was carried out on the phenylalanine derivative 3a (monoclinic space group P2(1), a = 10.301(1) A, b = 9.647(1) A, c = 18.479(2) A, beta = 102.98(2) degrees, Z = 4). Further peptide chemistry at the C terminus proceeds smoothly as demonstrated by the synthesis of the ferrocene labeled dipeptide Fc-CH2-Phe-Gly-OCH3 5 (Fc = ferrocenyl ((eta-C5H4)Fe(eta-C5H5))). We also report the synthesis of the C,N-bis-ferrocene labeled tripeptide Phe-Ala-Leu and its electrochemical characterization. Starting from the enantiomerically pure ferrocene derivative 9, which was synthesized from ferrocene aldehyde and L-1-amino-ethylbenzene, two diastereomers 10 were obtained by peptide coupling with N-Boc protected D- and L-alanine. There was, however, only very little diastereomeric induction if 0.5 equiv of a racemic mixture of alanine were used. This suggests that amino acid activation rather than coupling is the rate-determining step. A combination of NOESY (nuclear Overhauser effect spectroscopy) spectra and molecular modeling furnished detailed insights into the solution structures of 3, 9, and 10 and was used to rationalize their different reactivity.     

X-ray crystal structures and conformational analysis of cyclic acetals derived from tartaric acid and rigid spacer units

Three tartaric ester and tartaric acid derivatives (1?C3) with the hydroxy groups being linked via cyclic acetal (1,3-dioxolane) formation to a rigid core, containing phenyl and ethynyl units, have been synthesized. Their crystal structures are reported, emphasizing the molecular geometry, intermolecular interactions, and the resulting packing motifs. All dioxolane rings present in the crystal structures of 1?C3 are analyzed and compared with regard to their conformational behavior. In spite of similar substitution patterns, the dioxolane units adopt different conformations including twist and varying envelope isomers. The crystal structures are dominated by C?CH···O (esters 1 and 2) and O?CH···O (acid 3) hydrogen bonds, leading to different types of packing motifs being characteristic of strand and layer formation.     

Relations between 77Se NMR chemical shifts of (phenylseleno)-benzenes and their molecular structures derived from nine X-ray crystal structures

An extensive library of 77Se chemical shifts have been generated from the NMR measurements on substituted (phenylseleno)benzenes, including 33 new compounds. The variation in chemical shifts cover 265 ppm ranging from 446 to 181 ppm. Crystal structures have been determined for nine selected representatives of the substituted (phenylseleno)-benzenes. The analysis of the crystal structures supported that through-space interactions between selenium and the ortho-substituent observed in the crystal structures also are likely to be present in solution. The variation in the 77Se NMR chemical shifts can be rationalised from the intramolecular interactions with the substituent in the ortho-position. Furthermore it appears that these ortho-effects are roughly additive, and that it is the actual interactions and not the resulting conformational constraints that are responsible for the variations in the 77Se NMR chemical shifts.     

New boryl radicals derived from N-heteroaryl boranes: generation and reactivity

Recently, boryl radicals have been the subject of revived interest. These structures were generated by hydrogen-abstraction reactions from the corresponding boranes (i.e., from amine or phosphine boranes). However, the classical issue remains their high B--H bond-dissociation energy (BDE), thereby preventing a very efficient hydrogen-abstraction process. In the present paper, new N-heteroaryl boranes that exhibiting low B--H BDE are presented; excellent hydrogen-transfer properties have been found. Both the generation and the reactivity of the associated boryl radicals have been investigated through their direct observation in laser flash photolysis. The boryl radical interactions with double bonds, oxygen, oxidizing agent, and alkyl halides have been studied. Some selected applications of N-heteroaryl boryl radicals as new polymerization-initiating structures are proposed to evidence their high intrinsic reactivity.     

Bengamides revisited: new structures and antitumor studies

The structural chemistry and biological activity of the bengamide class of compounds have been further characterized. Extracts prepared from recollected Jaspis cf. coriacea from five sites in Fiji were pooled. Six new bengamides, M (7b), N (8a), O (8b), P (9a), Q (9b), and R (10), were identified, accompanied by the known bengamides A (1a), B (1b), E (3a), F (3b), Y (5), Z (6), L (7a), G (11a), H (11b), and I (12). The structures of the new compounds were determined from spectroscopic data, and some were additionally confirmed by semisynthesis. Cytotoxicity screening data were obtained from the NCI-DTP 60 cell screen for bengamides A, B, and P. Bengamides A and B were more potent than bengamide P, with average IC(50) values of 0.046, 0.011, and 2.70 FM, respectively. The in vitro antitumor activity against MDA-MB-435 human mammary carcinoma was also determined for natural bengamides A, B, E, F, P, M, O, and Z and for synthetic samples of B and O. The best activity was observed for the natural bengamides A (IC(50) = 1 nM) and O (IC(50) = 0.3 nM).     

Identification of biomolecular conformations from incomplete torsion angle observations by hidden Markov models

We present a novel method for the identification of the most important conformations of a biomolecular system from molecular dynamics or Metropolis Monte Carlo time series by means of Hidden Markov Models (HMMs). We show that identification is possible based on the observation sequences of some essential torsion or backbone angles. In particular, the method still provides good results even if the conformations do have a strong overlap in these angles. To apply HMMs to angular data, we use von Mises output distributions. The performance of the resulting method is illustrated by numerical tests and by application to a hybrid Monte Carlo time series of trialanine and to MD simulation results of a DNA-oligomer.     

Crystal structures of aroylhydrazones derived from 5-methoxysalicylaldehyde

Two new aroylhydrazones 3-bromo-N′-(2-hydroxy-5-methoxybenzylidene)benzohydrazide (1) and 4-hydroxy-3-methoxy-N′-(2-hydroxy-5-methoxybenzylidene)benzohydrazide (2), derived from 5-methoxysalicylaldehyde, are prepared and determined by means of infrared and ¹H NMR spectroscopy and single crystal X-ray diffraction. Compound 1 crystallizes in the monoclinic space group P2₁/n with a = 5.9406(7) Å, b = 31.833(3) Å, c = 7.6460(8) Å, β = 94.522(4)°, V = 1441.4(3) ų, Z = 4. Compound 2 crystallizes in the monoclinic space group P2₁/c with a = 14.3471(9) Å, b = 11.3893(7) Å, c = 9.6853(6) Å, β = 94.063(2)°, V = 1578.6(2) ų, Z = 4. Both molecules have very similar bond lengths and angles. The crystal structures of both compounds are stabilized by N-H...O and O-H...O hydrogen bonds as well as π...π interactions.     

Application of torsion angle molecular dynamics for efficient sampling of protein conformations

We investigate the application of torsion angle molecular dynamics (TAMD) to augment conformational sampling of peptides and proteins. Interesting conformational changes in proteins mainly involve torsional degrees of freedom. Carrying out molecular dynamics in torsion space does not only explicitly sample the most relevant degrees of freedom, but also allows larger integration time steps with elimination of the bond and angle degrees of freedom. However, the covalent geometry needs to be fixed during internal coordinate dynamics, which can introduce severe distortions to the underlying potential surface in the extensively parameterized modern Cartesian-based protein force fields. A "projection" approach (Katritch et al. J Comput Chem 2003, 24, 254-265) is extended to construct an accurate internal coordinate force field (ICFF) from a source Cartesian force field. Torsion crossterm corrections constructed from local molecular fragments, together with softened van der Waals and electrostatic interactions, are used to recover the potential surface and incorporate implicit bond and angle flexibility. MD simulations of dipeptide models demonstrate that full flexibility in both the backbone phi/psi and side chain chi1 angles are virtually restored. The efficacy of TAMD in enhancing conformational sampling is then further examined by folding simulations of small peptides and refinement experiments of protein NMR structures. The results show that an increase of several fold in conformational sampling efficiency can be reliably achieved. The current study also reveals some complicated intrinsic properties of internal coordinate dynamics, beyond energy conservation, that can limit the maximum size of the integration time step and thus the achievable gain in sampling efficiency.     

Atomic tungsten for ultrafast hard X-ray generation

High-resolution X-ray absorption measurements (with an accuracy of +/-0.3 eV) of ZnSO(4) (aq) were performed with ultrafast selected energy X-ray absorption spectroscopy (USEXAS) using a laser-driven tungsten target X-ray source. The results were used to determine the absolute spectral positions of characteristic emission lines. By comparing these positions to those predicted for the line emission from tungsten of different oxidation states using the Dirac-Fock formula, the tungsten species responsible for ultrafast hard X-ray generation were found to be tungsten atoms. This finding provides the first direct evidence to support the mechanism of X-ray generation via high-energy electrons interacting with tungsten atoms in the solid target.     

CAESAR: a new conformer generation algorithm based on recursive buildup and local rotational symmetry consideration

A highly efficient conformer search algorithm based on a divide-and-conquer and recursive conformer build-up approach is presented in this paper. This approach is combined with consideration of local rotational symmetry so that conformer duplicates due to topological symmetry in the systematic search can be efficiently eliminated. This new algorithm, termed CAESAR (Conformer Algorithm based on Energy Screening and Recursive Buildup), has been implemented in Discovery Studio 1.7 as part of the Catalyst Component Collection. CAESAR has been validated by comparing the conformer models generated by the new method and Catalyst/FAST. CAESAR is consistently 5-20 times faster than Catalyst/FAST for all data sets investigated. The speedup is even more dramatic for molecules with high topological symmetry or for molecules that require a large number of conformers to be sampled. The quality of the conformer models generated by CAESAR has been validated by assessing the ability to reproduce the receptor-bound X-ray conformation of ligands extracted for the Protein Data Bank (PDB) and assessing the ability to adequately cover the pharmacophore space. It is shown that CAESAR is able to reproduce the receptor-bound conformation slightly better than the Catalyst/FAST method for a data set of 918 ligands retrieved from the PDB. In addition, it is shown that CEASAR covers the pharmacophore space as well or better than Catalyst/FAST.     

Computer generation of chemical structures from known fragments

The interactive generation of chemical structures from given fragments is described and discussed. It is implemented as a part of our expert system CARBON, based on C-13 NMR spectra. As it is designed, this program can also be a useful tool in the structure elucidation process when information on parts of the structure is obtained by other means (IR, mass and other spectrometries, chemical analysis, other relevant information). The topological characteristics of candidate fragments are first chosen interactively and then the elements are connected in all topologically possible ways. In the following step, the topological building blocks are substituted by chemical structural fragments resulting in a set of all chemical structures consistent with the input information.