Dissecting cellular processes using small molecules: identification of colchicine-like, taxol-like and other small molecules that perturb mitosis

BACKGROUND: Understanding the molecular mechanisms of complex cellular processes requires unbiased means to identify and to alter conditionally gene products that function in a pathway of interest. Although random mutagenesis and screening (forward genetics) provide a useful means to this end, the complexity of the genome, long generation time and redundancy of gene function have limited their use with mammalian systems. We sought to develop an analogous process using small molecules to modulate conditionally the function of proteins. We hoped to identify simultaneously small molecules that may serve as leads for the development of therapeutically useful agents. RESULTS: We report the results of a high-throughput, phenotype-based screen for identifying cell-permeable small molecules that affect mitosis of mammalian cells. The predominant class of compounds that emerged directly alters the stability of microtubules in the mitotic spindle. Although many of these compounds show the colchicine-like property of destabilizing microtubules, one member shows the taxol-like property of stabilizing microtubules. Another class of compounds alters chromosome segregation by novel mechanisms that do not involve direct interactions with microtubules. CONCLUSIONS: The identification of structurally diverse small molecules that affect the mammalian mitotic machinery from a large library of synthetic compounds illustrates the use of chemical genetics in dissecting an essential cellular pathway. This screen identified five compounds that affect mitosis without directly targeting microtubules. Understanding the mechanism of action of these compounds, along with future screening efforts, promises to help elucidate the molecular mechanisms involved in chromosome segregation during mitosis.     

Uranium-mediated activation of small molecules

Molecular complexes of uranium are capable of activating a range of industrially and economically important small molecules such as CO, CO(2), and N(2); new and often unexpected reactions provide insight into an element that needs to be well-understood if future clean-energy solutions are to involve nuclear power.     

Bacteriophage that display small molecules

Technology has been developed to display small molecules on phage particles. This innovation enables the generation of libraries of phage-tagged compounds with novel properties that are well suited for in vivo assays.     

How metallylenes activate small molecules

We have studied the activation of dihydrogen by metallylenes using relativistic density functional theory (DFT). Our detailed activation strain and Kohn–Sham molecular orbital analyses have quantified the physical factors behind the decreased reactivity of the metallylene on going down Group 14, from carbenes to stannylenes. Along this series, the reactivity decreases due to a worsening of the back-donation interaction between the filled lone-pair orbital of the metallylene and the σ*-orbital of H₂, which, therefore, reduces the metallylene–substrate interaction and increases the reaction barrier. As the metallylene ligand is varied from nitrogen to phosphorus to arsenic a significant rate enhancement is observed for the activation of H₂ due to (i) a reduced steric (Pauli) repulsion between the metallylene and the substrate; and (ii) less activation strain, as the metallylene becomes increasingly more predistorted. Using a rationally designed metallylene with an optimal Group 14 atom and ligand combination, we show that a number of small molecules (i.e. HCN, CO₂, H₂, NH₃) may also be readily activated. For the first time, we show the ability of our H₂ activated designer metallylenes to hydrogenate unsaturated hydrocarbons. The results presented herein will serve as a guide for the rational design of metallylenes toward the activation of small molecules and subsequent reactions.

Quantum chemical analyses reveal how model metallylene catalysts activate H₂. This is the first step towards the rational design of metallylenes for the activation of small molecules and subsequent reactions.     

Transport and separation of small organic molecules through nanotubules.

An electroless plating method was applied to deposit Au onto the surfaces and the walls of pores of polycarbonate membranes to prepare gold nanotubules. The nanotubules were modified with cysteine (Cys) or with carbamidine thiocyante (Gua). The effects of modifiers and of the fine structure of organic molecules on the transport properties of those molecules through the gold nanotubules were investigated. Studies show that the hydrophilicity of modifiers and the planar structure of permeating molecules clearly affect the transport of small organic molecules in gold nanotubules. Tryptophan (Try) and vitamin B(2) (VB(2)) was cleanly separated at pH 6.8.     

MolAlign: an algorithm for aligning multiple small molecules

In small molecule drug discovery projects, the receptor structure is not always available. In such cases it is enormously useful to be able to align known ligands in the way they bind in the receptor. Here we shall present an algorithm for the alignment of multiple small molecule ligands. This algorithm takes pre-generated conformers as input, and proposes aligned assemblies of the ligands. The algorithm consists of two stages: the first stage is to perform alignments for each pair of ligands, the second stage makes use of the results from the first stage to build up multiple ligand alignment assemblies using a novel iterative procedure. The scoring functions are improved versions of the one mentioned in our previous work. We have compared our results with some recent publications. While an exact comparison is impossible, it is clear that our algorithm is fast and produces very competitive results.     

Hexabromo‐ and hexaiododisilane: small and simple molecules showing completely different crystal structures

The title compounds were prepared through dephenylation of hexaphenyldisilane with acetyl bromide or acetyl iodide in the presence of the corresponding aluminium halide. Both substances were purified via sublimation and, for the first time, single crystals of hexabromodisilane, Si₂Br₆, and a new polymorph of hexaiododisilane, Si₂I₆, could be isolated. Molecules of Si₂Br₆ are located on a special position of site symmetry 2/m with a quarter of a molecule in the asymmetric unit. Molecules of Si₂I₆ are located on a special position of site symmetry with a sixth of a molecule in the asymmetric unit. The bond lengths of Si₂Br₆ and Si₂I₆ are in the usual ranges and both molecules adopt a staggered conformation. It is interesting to note that Si₂Br₆ and Si₂I₆ do not form isomorphous structures. Moreover, an orthorhombic polymorph of the present structure of Si₂I₆ is already known [Jansen & Friede (1996). Acta Cryst. C 52 , 1333–1334]. Although the title compounds feature such small and simple molecules they show completely different crystal structures.     

Self‐diffusion of small molecules into rubbery polymers: A lattice free‐volume theory

In the framework of the free‐volume (FV) theory, a new equation was derived for the evaluation of self‐diffusion coefficients of small molecules in polymers above the mixture glass transition temperature. The derivation of the equation turned out to be straightforward once the equivalence between the free volume and the unoccupied volume given by thermodynamic lattice theories is assumed. A parameter evaluation scheme is proposed, which is substantially simpler compared with the conventional Vrentas–Duda approach, even without losing generality. The key assumption is discussed, and its consistency is verified from a numerical viewpoint. A comparison with experimental solvent self‐diffusion coefficients for several solvent/polymer binary systems confirmed that the proposed theory presents good correlative ability over wide temperature and composition ranges. Moreover, the introduced thermodynamic foundation allows one to easily include the pressure effect too. In the frame of the proposed lattice free volume theory, the sizes of the polymer jumping units decrease with temperature and increase with pressure. Such behavior converges with theoretical expectations and opens the way for a predictive FV theory. © 2010 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 48: 529–540, 2010     

‘Catch and release’ cascades: a resin-mediated three-component cascade approach to small molecules

The application of a ‘catch and release’ approach to palladium-catalysed multi-component cascade reactions leads to diverse libraries of pharmacologically interesting small molecules in high yield and with excellent purity.     

Conformational searching methods for small molecules. II. Genetic algorithm approach

We demonstrate the use of a genetic algorithm (GA) search procedure for finding low-energy conformations of small to medium organic molecules (1–12 rotatable bonds). GAS are in a class of biologically motivated optimization methods that evolve a population of individuals where individuals who are more “fit” have a higher probability of surviving into subsequent generations. Here, an individual is a conformation of a given molecule and the fitness is the molecule's conformational energy. In the course of a simulated evolution, the population produces conformations having increasingly lower energy. We test the GA method on a suite of 72 molecules and compare the performance against the CSEARCH algorithm in Sybyl. For molecules with more than eight rotatable bonds, the GA method is more efficient computationally and as the number of rotatable bonds increases the relative efficiency of the GA method grows. The GA method also found energies equal to or lower than the energy of the relaxed crystal structure in the large majority of cases. © John Wiley & Sons, Inc.     

Automatic assignment of 1H‐NMR spectra of small molecules

A novel data‐evaluation procedure for the automatic atom to peak or multiplet assignment of ¹H‐NMR spectra of small molecules has been developed using a fast and robust expert system. The applicability and reliability of the method are demonstrated by comparison of a manually assigned database of ¹H‐NMR spectra with the assignments produced by the automatic procedure. The results of this analysis show an excellent success ratio, indicating that this new algorithm can have a major impact as a time saving tool for the organic chemist. A new graphical feature used to illustrate both the stability and quality of the elementary assignments is also introduced. Copyright © 2013 John Wiley & Sons, Ltd.     

Dissecting RNA-interference pathway with small molecules

RNA interference (RNAi) is a process whereby short-interfering RNAs (siRNA) silence gene expression in a sequence-specific manner. We have screened a chemical library of substituted dihydropteridinones and identified a nontoxic, cell permeable, and reversible inhibitor of the RNAi pathway in human cells. Biochemical and fluorescence resonance-energy transfer experiments demonstrated that one of the compounds, named ATPA-18, inhibited siRNA unwinding that occurred within 6 hr of siRNA transfection. Extracts prepared from ATPA-18-treated cells also exhibited a decrease in target RNA cleavage by activated RNA-induced silencing complex (RISC*). Interestingly, when activated RISC*, which harbors unwound antisense siRNA, was treated with ATPA-18 in vitro, target RNA cleavage was not affected, indicating that this compound inhibited siRNA unwinding or steps upstream of unwinding in the RNAi pathway. Our results also establish the timing of siRNA unwinding and show that siRNA helicase activity is required for RNAi. ATPA-18 analogs will therefore provide a new class of small molecules for studying RNAi mechanisms in a variety of model organisms and deciphering in vivo genetic functions through reverse genetics.     

Revisiting small clusters of water molecules

The geometries and relative energies of small clusters of water molecules, (H₂O)_n with 4 ⩽ n ⩽ 8, are reported. For each value of n we have considered the conformations corresponding to the lowest-energy minimum and those in nearby relative minima. Thus we report on six tetramers, four pentamers, six hexanlers, four heptamers, and eigth octamers. The geometrical conformations have been obtained using the Metropolis Monte Carlo method as a minimization technique, where the interaction energy is computed with the MCY potential plus three- and four-body corrections previously discussed. All the reported structures for a given cluster size are found to be close in energy. For the lowest conformation the geometry was optimized with ab initio SCF computations using energy gradients. Our results are compared with previous theoretical studies. We discuss the convergence of the interaction potential for liquid water when expressed in terms of a many-body series expansion.     

Infrared multiphoton excitation of small molecules

The collisionless infrared excitation by short CO₂ laser pulses of the molecules SO₂, OCS, NO₂, NH₃ and DN₃ is compared with that of larger molecules. The average number of photons absorbed per molecule and the fraction of molecules dissociated depends predominantly on the laser intensity, while for larger molecules with higher densities of vibrational states the excitation is primarily determined by the laser fluence.     

The Gaussian Generalized Born model: application to small molecules

This work presents a Generalized Born model for the computation of the electrostatic component of solvation energies which is based on volume integration. An analytic masking function is introduced to remove Coulombic singularities. This approach leads to analytic formulae for the computation of Born radii, which are differentiable to arbitrary order, and computationally straightforward to implement.     

Anticalins versus antibodies: made-to-order binding proteins for small molecules

Engineering proteins to bind small molecules presents a challenge as daunting as drug discovery, for both hinge upon our understanding of receptor-ligand molecular recognition. However, powerful techniques from combinatorial molecular biology can be used to rapidly select artificial receptors. While traditionally researchers have relied upon antibody technologies as a source of new binding proteins, the lipocalin scaffold has recently emerged as an adaptable receptor for small molecule binding. 'Anticalins', engineered lipocalin variants, offer some advantages over traditional antibody technology and illuminate features of molecular recognition between receptors and small molecule ligands.