An informatic pipeline for managing high-throughput screening experiments and analyzing data from stereochemically diverse libraries

Integration of flexible data-analysis tools with cheminformatics methods is a prerequisite for successful identification and validation of “hits” in high-throughput screening (HTS) campaigns. We have designed, developed, and implemented a suite of robust yet flexible cheminformatics tools to support HTS activities at the Broad Institute, three of which are described herein. The “hit-calling” tool allows a researcher to set a hit threshold that can be varied during downstream analysis. The results from the hit-calling exercise are reported to a database for record keeping and further data analysis. The “cherry-picking” tool enables creation of an optimized list of hits for confirmatory and follow-up assays from an HTS hit list. This tool allows filtering by computed chemical property and by substructure. In addition, similarity searches can be performed on hits of interest and sets of related compounds can be selected. The third tool, an “S/SAR viewer,” has been designed specifically for the Broad Institute’s diversity-oriented synthesis (DOS) collection. The compounds in this collection are rich in chiral centers and the full complement of all possible stereoisomers of a given compound are present in the collection. The S/SAR viewer allows rapid identification of both structure/activity relationships and stereo-structure/activity relationships present in HTS data from the DOS collection. Together, these tools enable the prioritization and analysis of hits from diverse compound collections, and enable informed decisions for follow-up biology and chemistry efforts.     

Assessment of conformational ensemble sizes necessary for specific resolutions of coverage of conformational space

The size of conformational ensembles required for regular coverage of the conformational space of druglike molecules was examined. Using the conformer generation program Omega, the number of regularly distributed conformers (NRC) of flexible compounds was determined as a function of the root-mean-square deviation (RMSD) resolution of coverage. A regression equation was developed predicting the NRC of a molecule as a function of RMSD. The model yielded R(2) of 0.91 for both training and test sets, which consisted of 3414 and 3352 compounds, respectively. Utilizing 14 504 ligands from the Protein Data Bank with experimentally determined 3-D conformations, the regression equation was applied to the estimation of the NRC and the success rate of reproduction of experimental conformations from a theoretical conformation ensemble as a function of RMSD and flexibility was explored.     

Efficient implementation of constant pH molecular dynamics on modern graphics processors

The treatment of pH sensitive ionization states for titratable residues in proteins is often omitted from molecular dynamics (MD) simulations. While static charge models can answer many questions regarding protein conformational equilibrium and protein–ligand interactions, pH‐sensitive phenomena such as acid‐activated chaperones and amyloidogenic protein aggregation are inaccessible to such models. Constant pH molecular dynamics (CPHMD) coupled with the Generalized Born with a Simple sWitching function (GBSW) implicit solvent model provide an accurate framework for simulating pH sensitive processes in biological systems. Although this combination has demonstrated success in predicting pK_a values of protein structures, and in exploring dynamics of ionizable side‐chains, its speed has been an impediment to routine application. The recent availability of low‐cost graphics processing unit (GPU) chipsets with thousands of processing cores, together with the implementation of the accurate GBSW implicit solvent model on those chipsets (Arthur and Brooks, J. Comput. Chem. 2016, 37, 927), provide an opportunity to improve the speed of CPHMD and ionization modeling greatly. Here, we present a first implementation of GPU‐enabled CPHMD within the CHARMM‐OpenMM simulation package interface. Depending on the system size and nonbonded force cutoff parameters, we find speed increases of between one and three orders of magnitude. Additionally, the algorithm scales better with system size than the CPU‐based algorithm, thus allowing for larger systems to be modeled in a cost effective manner. We anticipate that the improved performance of this methodology will open the door for broad‐spread application of CPHMD in its modeling pH‐mediated biological processes. © 2016 Wiley Periodicals, Inc.     

Interpolation on Symmetric Spaces Via the Generalized Polar Decomposition

We construct interpolation operators for functions taking values in a symmetric space—a smooth manifold with an inversion symmetry about every point. Key to our construction is the observation that every symmetric space can be realized as a homogeneous space whose cosets have canonical representatives by virtue of the generalized polar decomposition—a generalization of the well-known factorization of a real nonsingular matrix into the product of a symmetric positive-definite matrix times an orthogonal matrix. By interpolating these canonical coset representatives, we derive a family of structure-preserving interpolation operators for symmetric space-valued functions. As applications, we construct interpolation operators for the space of Lorentzian metrics, the space of symmetric positive-definite matrices, and the Grassmannian. In the case of Lorentzian metrics, our interpolation operators provide a family of finite elements for numerical relativity that are frame-invariant and have signature which is guaranteed to be Lorentzian pointwise. We illustrate their potential utility by interpolating the Schwarzschild metric numerically.     

A Dinitrogen Dicopper(I) Complex via a Mixed‐Valence Dicopper Hydride

Low‐temperature reaction of the tris(pyrazolyl)borate copper(II) hydroxide [^iPr2TpCu]₂(μ‐OH)₂ with triphenylsilane under a dinitrogen atmosphere gives the bridging dinitrogen complex [^iPr2TpCu]₂(μ‐1,2‐N₂) ( 3 ). X‐ray crystallography reveals an only slightly activated N₂ ligand (N‐N: 1.111(6) Å) that bridges between two monovalent ^iPr2TpCu fragments. While DFT studies of mono‐ and dinuclear copper dinitrogen complexes suggest weak π‐backbonding between the d¹⁰ Cu^I centers and the N₂ ligand, they reveal a degree of cooperativity in the dinuclear Cu‐N₂‐Cu interaction. Addition of MeCN, CNAr^2,6‐Me, or O₂ to 3 releases N₂ with formation of ^iPr2TpCu(L) (L=NCMe, CNAr^2,6‐Me2) or [^iPr2TpCu]₂(μ‐η²:η²‐O₂) ( 1 ). Addition of triphenylsilane to [^iPr2TpCu]₂(μ‐OH)₂ in pentane allows isolation of a key intermediate [^iPr2TpCu]₂(μ‐H) ( 5 ). Although 5 thermally decays under N₂ to give 3 , it reduces unsaturated substrates, such as CO and HC≡CPh to HC(O)H and H₂C=CHPh, respectively.     

Catalytically active mu-Oxodiiron(IV) oxidants from Iron(III) and dioxygen

The reaction between an Fe(III) complex and O(2) to afford a stable catalytically active diiron(IV)-mu-oxo compound is described. Phosphonium salts of orange five-coordinated Fe(III)-TAML complexes with an axial aqua ligand ([PPh(4)]1-H(2)O, tetraamidato macrocyclic Fe(III) species derived from 3,3,6,6,9,9-hexamethyl-3,4,8,9-tetrahydro-1H-1,4,8,11-benzotetraazacyclotridecine-2,5,7,10(6H,11H)-tetraone) react rapidly with O(2) in CH(2)Cl(2) or other weakly coordinating solvents to produce black mu-oxo-bridged diiron(IV) complexes, 2, in high yields. Complexes 2 have been characterized by X-ray crystallography (2 cases), microanalytical data, mass spectrometry, UV/Vis, Mossbauer, and (1)H NMR spectroscopies. Mossbauer data show that the diamagnetic Fe-O-Fe unit contains antiferromagnetically coupled S = 1 Fe(IV) sites; diamagnetic (1)H NMR spectra are observed. The oxidation of PPh(3) to OPPh(3) by 2 was confirmed by UV/Vis and GC-MS. Labeling experiments with (18)O(2) and H(2)(18)O established that the bridging oxygen atom of 2 derives from O(2). Complexes 2 catalyze the selective oxidation of benzylic alcohols into the corresponding aldehydes and bleach rapidly organic dyes, such as Orange II in MeCN-H(2)O mixtures; reactivity evidence suggests that free radical autoxidation is not involved. This work highlights a promising development for the advancement of green oxidation technology, as O(2) is an abundant, clean, and inexpensive oxidizing agent.     

The reaction of fluoroxysulfate,sof-. liith aromatic compounds: catalysis by acids

The effects of the acid catalysts HF, H₂S0₄, BF₃, CF₃S0₃H, FSO₃H, and SbF₅.FS0₃H on the reactions of CsSO₄F with toluene, nitrobenzene and naphthalene in CH₃CN have been studied. The catalys general accelerate reaction and enhance yields of ring-fluorinated products. Efficacity roughly parallels H₀ of the acids, though H₂S0₄ is more effective than stronger acids for the fluorination of naphthalene. Combined room temperature yields of fluorine-substituted products are as much as 45-50% for toluene and naphthalene and up to 30% for nitrobenzene. The predominant products are o-fluorotoluene, 1- fluoronaphthalene, and m-fluoronitrobenzene. With naphthalene the isomer selectivity is considerably less than in the absence of catalyst. Low yields (10%) of monomeric oxygenated products are obtained, along with considerable oxygen- and fluorine-containing dimers and higher polymers. The results are interpreted in terms of acid-catalyzed electrophilic fluorination or oxygenation, followed by further fluorination and/or free-radical-induced oxidative coupling of the oxygenated products.     

Phosphine triggered [3+2] allenoate-acrylate annulation: a mechanistic enlightenment

A mechanistic study of phosphine-mediated [3+2] annulation of allenoate and acrylate is presented. The insight gained has identified that (1) [3+2] cycloaddition proceeds through a stepwise mechanism and (2) the involvement of a molecule of water, which services as a proton-shuttle, is essential for annulated product formation.     

Energy-dependent Electrospray Ionisation Mass Spectrometry of Carbonyl Clusters

The electrospray ionisation mass spectra (EDESI-MS) of Ru₆C(CO)₁₆(PPh₃) and Ir₄(CO)₁₁(PR₃) (PR₃=PPh₃, P(p-C₆H₄OMe)₃, P(p-C₆H₄NMe₂)₃, P(p-C₆H₄Cl)₃, P(OPh)₃, P(OMe)₃, PO₃C₅H₉) are described and the relative importance of carbonyl loss versus phosphine loss as a fragmentation pathway is assessed. Qualitatively, the phosphine ligands bind more strongly to Ir₄(CO)₁₁ clusters than to Ru₆C(CO)₁₆. The influence on the collision cell pressure on MS/MS spectra of transition metal carbonyl cluster anions is also explored showing that a greater, simultaneous, distribution of fragment ions is produced as the collision cell pressure is increased.Dedicated to Prof. Brian F. G. Johnson on the occasion of his retirement.