Outcome of the First wwPDB/CCDC/D3R Ligand Validation Workshop.

Crystallographic studies of ligands bound to biological macromolecules (proteins and nucleic acids) represent an important source of information concerning drug-target interactions, providing atomic level insights into the physical chemistry of complex formation between macromolecules and ligands. Of the more than 115,000 entries extant in the Protein Data Bank (PDB) archive, ∼75% include at least one non-polymeric ligand. Ligand geometrical and stereochemical quality, the suitability of ligand models for in silico drug discovery and design, and the goodness-of-fit of ligand models to electron-density maps vary widely across the archive. We describe the proceedings and conclusions from the first Worldwide PDB/Cambridge Crystallographic Data Center/Drug Design Data Resource (wwPDB/CCDC/D3R) Ligand Validation Workshop held at the Research Collaboratory for Structural Bioinformatics at Rutgers University on July 30-31, 2015. Experts in protein crystallography from academe and industry came together with non-profit and for-profit software providers for crystallography and with experts in computational chemistry and data archiving to discuss and make recommendations on best practices, as framed by a series of questions central to structural studies of macromolecule-ligand complexes. What data concerning bound ligands should be archived in the PDB? How should the ligands be best represented? How should structural models of macromolecule-ligand complexes be validated? What supplementary information should accompany publications of structural studies of biological macromolecules? Consensus recommendations on best practices developed in response to each of these questions are provided, together with some details regarding implementation. Important issues addressed but not resolved at the workshop are also enumerated.

Molecular dynamics of a DNA Holliday junction: the inverted repeat sequence d(CCGGTACCGG)4.

All-atom molecular dynamics (MD) computer simulations have been applied successfully to duplex DNA structures in solution for some years and found to give close accord with observed results. However, the MD force fields have generally not been parameterized against unusual DNA structures, and their use to obtain dynamical models for this class of systems needs to be independently validated. The four-way junction (4WJ), or Holliday junction, is a dynamic DNA structure involved in central cellular processes of homologous replication and double strand break repair. Two conformations are observed in solution: a planar open-X form (OPN) with a mobile center and four duplex arms, and an immobile stacked-X (STX) form with two continuous strands and two crossover strands, stabilized by high salt conditions. To characterize the accuracy of MD modeling on 4WJ, we report a set of explicit solvent MD simulations of ∼100 ns on the repeat sequence d(CCGGTACCGG)(4) starting from the STX structure (PDB code 1dcw), and an OPN structure built for the same sequence. All 4WJ MD simulations converged to a stable STX structure in close accord with the crystal structure. Our MD beginning in the OPN form converts to the STX form spontaneously at both high and low salt conditions, providing a model for the conformational transition. Thus, these simulations provide a successful account of the dynamical structure of the STX form of d(CCGGTACCGG)(4) in solution, and provide new, to our knowledge, information on the conformational stability of the junction and distribution of counterions in the junction interior.

Dynamical allosterism in the mechanism of action of DNA mismatch repair protein MutS.

The multidomain protein Thermus aquaticus MutS and its prokaryotic and eukaryotic homologs recognize DNA replication errors and initiate mismatch repair. MutS actions are fueled by ATP binding and hydrolysis, which modulate its interactions with DNA and other proteins in the mismatch-repair pathway. The DNA binding and ATPase activities are allosterically coupled over a distance of ∼70 Å, and the molecular mechanism of coupling has not been clarified. To address this problem, all-atom molecular dynamics simulations of ∼150 ns including explicit solvent were performed on two key complexes--ATP-bound and ATP-free MutS⋅DNA(+T bulge). We used principal component analysis in fluctuation space to assess ATP ligand-induced changes in MutS structure and dynamics. The molecular dynamics-calculated ensembles of thermally accessible structures showed markedly small differences between the two complexes. However, analysis of the covariance of dynamical fluctuations revealed a number of potentially significant interresidue and interdomain couplings. Moreover, principal component analysis revealed clusters of correlated atomic fluctuations linking the DNA and nucleotide binding sites, especially in the ATP-bound MutS⋅DNA(+T) complex. These results support the idea that allosterism between the nucleotide and DNA binding sites in MutS can occur via ligand-induced changes in motion, i.e., dynamical allosterism.

U1A protein-stem loop 2 RNA recognition: prediction of structural differences from protein mutations.

Molecular dynamics (MD) simulations were carried out to compare the free and bound structures of wild type U1A protein with several Phe56 mutant U1A proteins that bind the target stem loop 2 (SL2) RNA with a range of affinities. The simulations indicate the free U1A protein is more flexible than the U1A-RNA complex for both wild type and Phe56 mutant systems. A complete analysis of the hydrogen-bonding (HB) and non-bonded (VDW) interactions over the course of the MD simulations suggested that changes in the interactions in the free U1A protein caused by the Phe56Ala and Phe56Leu mutations may stabilize the helical character in loop 3, and contribute to the weak binding of these proteins to SL2 RNA. Compared with wild type, changes in HB and VDW interactions in Phe56 mutants of the free U1A protein are global, and include differences in ß-sheet, loop 1 and loop 3 interactions. In the U1A-RNA complex, the Phe56Ala mutation leads to a series of differences in interactions that resonate through the complex, while the Phe56Leu and Phe56Trp mutations cause local differences around the site of mutation. The long-range networks of interactions identified in the simulations suggest that direct interactions and dynamic processes in both the free and bound forms contribute to complex stability.

Accurate reaction enthalpies and sources of error in DFT thermochemistry for aldol, Mannich, and alpha-aminoxylation reactions.

Enthalpies for bond-forming reactions that are subject to organocatalysis have been predicted using the high-accuracy CBS-QB3 model chemistry and six DFT functionals. Reaction enthalpies were decomposed into contributions from changes in bonding and other intramolecular effects via the hierarchy of homodesmotic reactions. The order of the reaction exothermicities (aldol < Mannich approximately alpha-aminoxylation) arises primarily from changes in formal bond types mediated by contributions from secondary intramolecular interactions. In each of these reaction types, methyl substitution at the beta- and gamma-positions stabilizes the products relative to the unsubstituted case. The performance of six DFT functionals (B3LYP, B3PW91, B1B95, MPW1PW91, PBE1PBE, and M06-2X), MP2, and SCS-MP2 has been assessed for the prediction of these reaction enthalpies. Even though the PBE1PBE and M06-2X functionals perform well for the aldol and Mannich reactions, errors roughly double when these functionals are applied to the alpha-aminoxylation reactions. B3PW91 and B1B95, which offer modest accuracy for the aldol and Mannich reactions, yield reliable predictions for the two alpha-aminoxylation reactions. The excellent performance of the M06-2X and PBE1PBE functionals for aldol and Mannich reactions stems from the cancellation of sizable errors arising from inadequate descriptions of the underlying bond transformations and intramolecular interactions. SCS-MP2/cc-pVTZ performs most consistently across these three classes of reactions, although the reaction exothermicities are systematically underestimated by 1-3 kcal mol(-1). Conventional MP2, when paired with the cc-pVTZ basis set, performs somewhat better than SCS-MP2 for some of these reactions, particularly the alpha-aminoxylations. Finally, the merits of benchmarking DFT functionals for the set of simple chemically meaningful transformations underlying all bond-forming reactions are discussed.

Acid-catalyzed aza-Diels-Alder reactions for the total synthesis of (+/-)-lapatin B.

A 5-step total synthesis of microfungal alkaloid (+/-)-lapatin B has been accomplished via a key 2-aza-Diels-Alder reaction. Brønsted acids catalyze the cycloaddition step and provide improved exo selectivity. This synthetic route has been applied to the construction of related spiro-quinazoline structures.

Halo substituent effects on intramolecular cycloadditions involving furanyl amides.

Intramolecular Diels-Alder reactions involving a series of N-alkenyl-substituted furanyl amides were investigated. Stable functionalized oxanorbornenes were formed in high yield upon heating at 80-110 degrees C. The cycloaddition reactions include several bromo-substituted furanyl amides, and these systems were found to proceed at a much faster rate and in higher yield than without substitution. This effect was observed by incorporating a halogen in the 3- or 5-position of the furan ring and appears to be general. The origin of increased cycloaddition rates for halo-substituted furans has been investigated with quantum mechanical calculations. The success of these reactions is attributed to increases in reaction exothermicities; this both decreases activation enthalpies and increases barriers to retrocycloadditions. Halogen substitution on furan increases reactant energy and stabilizes the product, which is attributed to the preference of electronegative halogens to be attached to a more highly alkylated and therefore more electropositive framework.

Synthesis of stable derivatives of c(62): the first nonclassical fullerene incorporating a four-membered ring.

A rational synthetic approach to the first four-membered ring-containing derivatives of C(62) is reported. They were synthesized by an inverse electron demand Diels-Alder reaction of 3,6-diaryl-1,2,4,5-tetrazines with C(60) in o-dichlorobenzene, followed by visible light irradiation at reflux. The structure of these nonclassical fullerenes derivatives was determined by X-ray single-crystal diffraction.