Computer-aided drug discovery research at a global contract research organization

Computer-aided drug discovery started at Albany Molecular Research, Inc in 1997. Over nearly 20 years the role of cheminformatics and computational chemistry has grown throughout the pharmaceutical industry and at AMRI. This paper will describe the infrastructure and roles of CADD throughout drug discovery and some of the lessons learned regarding the success of several methods. Various contributions provided by computational chemistry and cheminformatics in chemical library design, hit triage, hit-to-lead and lead optimization are discussed. Some frequently used computational chemistry techniques are described. The ways in which they may contribute to discovery projects are presented based on a few examples from recent publications.     

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.     

Unexpected Self‐Sorting Self‐Assembly Formation of a [4:4] Sulfate:Ligand Cage from a Preorganized Tripodal Urea Ligand

The design and synthesis of tripodal ligands 1 – 3 based upon the N‐methyl‐1,3,5‐benzenetricarboxamide platform appended with three aryl urea arms is reported. This ligand platform gives rise to highly preorganized structures and is ideally suited for binding SO₄^2? and H₂PO₄^? ions through multiple hydrogen‐bonding interactions. The solid‐state crystal structures of 1 – 3 with SO₄^2? show the encapsulation of a single anion within a cage structure, whereas the crystal structure of 1 with H₂PO₄^? showed that two anions are encapsulated. We further demonstrate that ligand 4 , based on the same platform but consisting of two bis‐urea moieties and a single ammonium moiety, also recognizes SO₄^2? to form a self‐assembled capsule with [4:4] SO₄^2?: 4 stoichiometry in which the anions are clustered within a cavity formed by the four ligands. This is the first example of a self‐sorting self‐assembled capsule where four tetrahedrally arranged SO₄^2? ions are embedded within a hydrophobic cavity.     

Computational models to predict blood–brain barrier permeation and CNS activity

The blood-brain permeation of a structurally diverse set of 281 compounds was modeled using linear regression and a multivariate genetic partial least squares (G/PLS) approach. Key structural features affecting the logarithm of blood-brain partitioning (logBB) were captured through statistically significant quantitative structure-activity relationship (QSAR) models. These relationships reveal the importance of logP, polar surface area, and a variety of electrotopological indices for accurate predictions of logBB. The best models reveal an excellent correlation (r > 0.9) for a training set of 58 compounds. Likewise, the comparison of the average logBB values obtained from an ensemble of QSAR models with experimental values also verifies the statistical quality of the models (r > 0.9). The models provide good agreement (r approximately 0.7) between the predicted logBB values for 34 molecules in the external validation set and the experimental values. To further validate the models for use during the drug discovery process, a prediction set of 181 drugs with reported CNS penetration data was used. A >70% success rate is obtained by using any of the QSAR models in the qualitative prediction for CNS permeable (active) drugs. A lower success rate (approximately 60%) was obtained for the best model for CNS impermeable (inactive) drugs. Combining the predictions obtained from all the models (consensus) did not significantly improve the discrimination of CNS active and CNS inactive molecules. Finally, using the therapeutic classification as a guiding tool, the CNS penetration capability of over 2000 compounds in the Synthline database was estimated. The results were very similar to the smaller set of 181 compounds.     

Color Tunable Emission and Oxygen Sensing from a Discrete Europium−Pyrene Assembly

We report the synthesis of a new pyrene, dipicolinic acid-based ligand ( L₁H ) and its corresponding multi-emissive and multifunctional europium complex [Eu( L₁ )₃] that is capable of single component color switchable emission from red to blue and also white. At high concentration (10 mM) the single component system results in near pure white emission (CIE coordinates x,y=0.329, 0.324). Furthermore, the system showed ratiometric oxygen sensing with oxygen significantly quenching the pyrene centered emission but not the Eu³⁺ emission, resulting in an overall emission color change from blue to red on increasing oxygen content.     

High and low spin mononuclear and dinuclear iron(II) complexes of 4-amino and 4-pyrrolyl-3,5-di(2-pyridyl)-4H-1,2,4-triazoles

The first dinuclear iron(II) complexes of any 4-substituted 3,5-di(2-pyridyl)-4H-1,2,4-triazole ligands, [Fe(II)2(adpt)2(H2O)1.5(CH3CN)2.5](BF4)4 and [Fe(II)2(pldpt)2(H2O)2(CH3CN)2](BF4)4, are presented [where adpt is 4-amino-3,5-di(2-pyridyl)-4H-1,2,4-triazole and pldpt is 4-pyrrolyl-3,5-di(2-pyridyl)-4H-1,2,4-triazole]. Both dinuclear complexes feature doubly triazole bridged iron(II) centers that are found to be [high spin-high spin] at all temperatures, 4-300 K, and to exhibit weak antiferromagnetic coupling. In the analogous monometallic complexes, [Fe(II)(Rdpt)2(X)2](n+), the spin state of the iron(II) center was controlled by appropriate selection of the axial ligands X. Specifically, both of the chloride complexes, [Fe(II)(adpt)2(Cl)2] x 2 MeOH and [Fe(II)(pldpt)2(Cl)2] x 2 MeOH x H2O, were found to be high spin whereas the pyridine adduct [Fe(II)(adpt)2(py)2](BF4)2 was low spin. Attempts to prepare [Fe(II)(pldpt)2(py)2](BF4)2 and the dinuclear analogues [Fe(II)2(Rdpt)2(py)4](BF4)4 failed, illustrating the significant challenges faced in attempts to develop control over the nature of the product obtained from reactions of iron(II) and these bis-bidentate ligands.     

Production of monodisperse cerium oxide microspheres with diameters near 100 µm by internal-gelation sol–gel methods

Internal-gelation sol–gel methods have used a variety of sphere-forming methods in the past to produce metal oxide microspheres, but typically with poor control over the size uniformity at diameters near 100?µm. This work describes efforts to make and measure internal-gelation, sol–gel microspheres with very uniform diameters in the 100–200-µm size range using a two-fluid nozzle. A custom apparatus was used to form aqueous droplets of sol–gel feed solutions in silicone oil and heat them to cause gelation of the spheres. Gelled spheres were washed, dried, and sintered prior to mounting them on glass slides for optical imaging and analysis. Microsphere diameters and shape factors were determined as a function of silicone oil flow rate in a two-fluid nozzle and the size of a needle dispensing the aqueous sol–gel solution. Nine batches of microspheres were analyzed and had diameters ranging from 65.5?±?2.4?µm for the smallest needle and the fastest silicone oil flow rate to 211?±?4.7?µm for the largest needle and the slowest silicone oil flow rate. Standard deviations for measured diameters were less than 8% for all samples and most of them were less than 4%. Microspheres had excellent circularity with measured shape factors of 0.9–1. However, processing of optical images was complicated by shadow effects in the photoresist layer on glass slides and by overlapping microspheres. Based on the calculated flow parameters, microspheres were produced in a simple dripping mode in the two-fluid nozzle. Using flow rates consistent with a simple dripping mode in a two-fluid nozzle configuration allows for very uniform oxide microspheres to be produced using the internal-gelation sol–gel method.

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Introduction of the Impulse Response Function in Common-Path Interferometers with Fourier Plane Filters

In the present paper it will be shown how the introduction of a Fourier plane filter can create various types of common-path interferometers for measuring changes in surface tilt or curvature of an object surface. This is obtained by placing a holographic optical element in the Fourier plane of a 4-f optical system. The interferometers are analysed by using the paraxial approximation of the Huygens-Fresnel integral formalism, and the interferometer functions are given by a novel formalism using impulse response functions. Based on this technique, an interferometer for measuring dedicated changes in surface deflection is presented. This interferometer is insensitive to rigid surface rotations and displacements. The interferometer can be embedded in systems based on single point measurement of a time dependent deflection, i.e. vibrometers, as well as in full-field measurements such as electronic speckle interferometers.This paper was originally presented at the 2001 International Conference (2nd Joint OSJ-SPIE Conference) on Optical Engineering for Sensing and Nanotechnology, ICOSN 2001 which was held June 6-8, 2001 at the Pacifico-Yokohama Conference Center, Yokohama, Japan.