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Hematopoietic prostaglandin D synthase (HPGDS) is primarly expressed in mast cells, antigen-presenting cells, and Th-2 cells. HPGDS converts PGH2 into PGD2, a mediator thought to play a pivotal role in airway allergy and inflammatory processes. In this letter, we report the discovery of an orally potent and selective inhibitor of HPGDS that reduces the antigen-induced response in allergic sheep.

In the past few years, a significant effort has been devoted by Pharmacia toward the discovery of novel antibiotics. We have recently described the identification of an anthranilic acid lead 1 and the optimization resulting in the advanced lead 2. In this report, we describe the preparation of several selected amide bioisosteres connecting the A- and the B-rings. The E-alkene provided a rigid analog with equal potency to the corresponding amide. This indicates that the amide is not a recognition element rather acts as an appropriate spatial linker of the two important aryl A and B rings. The work here clearly demonstrates that the amide linker can be replaced with several functionalities without significant deterioration in the MIC activity.

Discovery of novel antibacterial agents is a significant challenge. We have recently reported on our discovery of novel antibacterial agents in which we have rapidly optimized potency utilizing a parallel chemistry approach. These advanced leads suffer from high affinity for human serum albumin (HSA). In an effort to decrease the affinity for HSA we have prepared a series of heterocyclic analogs, which retained antibacterial activity and demonstrated reduced affinity for HSA.

There have recently been developments in the methods used to access the accuracy of the prediction and applicability domain of absorption, distribution, metabolism, excretion and toxicity models, and also in the methods used to predict the physicochemical properties of compounds in the early stages of drug development. The methods are classified into two main groups: those based on the analysis of similarity of molecules, and those based on the analysis of calculated properties. An analysis of octanol-water distribution coefficients is used to exemplify the consistency of estimated and calculated accuracy of the ALOGPS program (http://www.vcclab.org) to predict in-house and publicly available datasets.

Peptidyl deformylase (PDF) is a metallo protease that catalyzes the removal of a formyl group from the N-termini of prokaryotic prepared polypeptides, an essential step in bacterial protein synthesis. Screening of our compound collection using Staphylococcus aureus PDF afforded a very potent inhibitor with an IC 50 in the low nanomolar range. Unfortunately, the compound that contains a hydroxamic acid did not exhibit antibacterial activity (MIC). In order to address the lack of activity in the MIC assay and to determine what portion of the molecule was responsible for binding to PDF, we prepared several analogues. This paper describes our findings that the hydroxamic acid functionality found in 1 is mainly responsible for the high affinity to PDF. In addition, we identified an alternative class of PDF inhibitors, the N- hydroxy urea 18 , which has both PDF and antibacterial activity.

An analysis of the relationship among alignment solutions obtained from field-based matching of a representative set of rigid conformers of three non-nucleoside HIV-1 reverse transcriptase inhibitors and solutions obtained from flexible matching of the same conformers is presented. In some cases, different alignment solutions obtained from rigid matching converge to the same solution when conformational rigidity is relaxed, indicating that a reduced set of conformers per molecule may be sufficient in many field-based similarity studies. Furthermore, the results also indicate the importance of going beyond the pairwise similarity level to obtain consistent solutions in flexible-matching studies. In this respect, the best conformationally flexible multi-molecule alignment obtained is found to be in good agreement with the relative binding geometry and orientation found experimentally from protein-ligand crystal structures. The rms separation between corresponding atoms in computed and `experimental' sets of three inhibitor structures is 0.94 A.

This article describes a molecular-field-based similarity method for aligning molecules by matching their steric and electrostatic fields and an application of the method to the alignment of three structurally diverse non-nucleoside HIV-1 reverse transcriptase inhibitors. A brief description of the method, as implemented in the program MIMIC, is presented, including a discussion of pairwise and multi-molecule similarity-based matching. The application provides an example that illustrates how relative binding orientations of molecules can be determined in the absence of detailed structural information on their target protein. In the particular system studied here, availability of the X-ray crystal structures of the respective ligand–protein complexes provides a means for constructing an 'experimental model' of the relative binding orientations of the three inhibitors. The experimental model is derived by using MIMIC to align the steric fields of the three protein P66 subunit main chains, producing an overlay with a 1.41 A average rms distance between the corresponding Cα's in the three chains. The inter-chain residue similarities for the backbone structures show that the main-chain conformations are conserved in the region of the inhibitor-binding site, with the major deviations located primarily in the 'finger' and RNase H regions. The resulting inhibitor structure overlay provides an experimental-based model that can be used to evaluate the quality of the direct a priori inhibitor alignment obtained using MIMIC. It is found that the 'best' pairwise alignments do not always correspond to the experimental model alignments. Therefore, simply combining the best pairwise alignments will not necessarily produce the optimal multi-molecule alignment. However, the best simultaneous three-molecule alignment was found to reproduce the experimental inhibitor alignment model. A pairwise consistency index has been derived which gauges the quality of combining the pairwise alignments and aids in efficiently forming the optimal multi-molecule alignment analysis. Two post-alignment procedures are described that provide information on feature-based and field-based pharmacophoric patterns. The former corresponds to traditional pharmacophore models and is derived from the contribution of individual atoms to the total similarity. The latter is based on molecular regions rather than atoms and is constructed by computing the percent contribution to the similarity of individual points in a regular lattice surrounding the molecules, which when contoured and colored visually depict regions of highly conserved similarity. A discussion of how the information provided by each of the procedures is useful in drug design is also presented.

The design and synthesis of a novel conformationally constrained spiro analog of the BHAP class of HIV-1 reverse transcriptase inhibitors, based on the molecular modeling and the X-ray crystal structure of the clinical candidate atevirdine, is described.

The discovery and initial optimization of a novel anthranilic acid derived class of antibacterial agents has been described in a recent series of papers. This paper describes the discovery of 1-acylindazol-3-ols as a novel bioisostere of an anthranilic acid. The synthesis and structure-activity relationships of the indazol bioisosteres are described herein.

We report a new class of non-nucleoside antivirals, the 7-oxo-4,7-dihydrothieno[3,2-b]pyridine-6-carboxamides, some of which possess remarkable potency versus a broad spectrum of herpesvirus DNA polymerases and excellent selectivity compared to human DNA polymerases. A critical factor in the level of activity is hypothesized to be conformational restriction of the key 2-aryl-2-hydroxyethylamine sidechain by an adjacent methyl group.

During the 1980s, modern drug discovery was dominated by the idea of “structure-based drug design.” The promise was, given an x-ray structure of the protein target, one could design the ideal protein ligand in a small number of iterations. If our computational methods could predict accurately which ligands would bind a protein best, this approach would be wildly successful; however, our methods are not that accurate, and in the end many experimental iterations have been required (for a review, see [1]). It was during this era that a small number of groups began experimenting with novel approaches to discovering leads in silico, now generically called “3D database searching.” Here, either a pharmacophore or a protein pocket was used to sift through a database of conformers of molecules, and those molecules which met the criteria were submitted to a biological assay (for a review, see [2]).

The number of protein structures available in the PDB1 (7415 in July 22, 1998) is constantly growing and it is expected to increase even more rapidly in coming years.2 This tremendous body of information is certainly having an impact in ligand design and modelling where the knowledge of the crystal structure of the target protein, or a closely related protein, makes a significant difference in the process of ligand optimization.3 When a crystal structure of the target protein is unavailable, ligand optimization must rely on indirect approaches based on the similarity between the structures of the ligands themselves.4 However, if a three-dimensional structure of the target protein is available docking methods can be applied,5 which have the potential of providing important information on the interaction between the ligand and the residues of the given receptor site.

A new field-based similarity forcing procedure for matching conformationally-flexible molecules is presented. The method extends earlier work on similarity matching of molecules based upon the program MIMIC, by directly coupling a similarity function to a molecular mechanics force field. In this way conformational energetics are fully accounted for in the similarity matching process. Simultaneous similarity/conformational searches can then be undertaken within a Monte Carlo or molecular dynamics framework. Here, a Monte Carlo approach is used to provide a simple example of two HIV-1 reverse transcriptase inhibitors, nevirapine and alpha APA, that illustrates the basic characteristics of the method and suggests areas for further investigation.

The use of molecular field-based similarity approaches for obtaining quality molecular alignments and for identifying field-based patterns in bioactive molecules is described. In addition to pairwise similarities, computation of multimolecule similarities affords a means for determining consensus multimolecule alignments. These multimolecule alignments constitute the basis for developing models for the relative binding of bioactive molecules to common protein-binding sites and for the graphical portrayal of molecular field similarity surface plots that identify, visually, molecular regions possessing similar molecular field characteristics. The latter information can then be exploited in the design of molecules that mimic appropriate characteristics of these highly similar steric and electrostatic domains. Regions with low steric and electrostatic similarity in suitably aligned sets of bioactive molecules represent tolerant domains where new structural motifs can be incorporated without significant reductions in activity. To illustrate the potential applicability of the actual molecular field-based similarity approaches to the design of bioactive molecules, a study on a set of HIV-1 protease inhibitors is presented.

Medicinal Chemistry 7254-209-615, Pharmacia, Kalamazoo, MI 49001-0199, USA Protein Science, Pharmacia, Kalamazoo, MI 49001-0199, USA Computer Aided Drug Discovery Research, Pharmacia, Kalamazoo, MI 49001-0199, USA Discovery Technologies, Pharmacia, Kalamazoo, MI 49001-0199, USA Biology I, Pharmacia, Kalamazoo, MI 49001-0199, USA Structural, Analytical & Medicinal Chemistry Research, Pharmacia, Kalamazoo, MI 49001-0199, USA

This study describes a new method for comparing three-dimensional protein structures based on an optimal alignment of their steric fields. The method is based upon the use of spherical Gaussian functions located on individual atoms. This representation generates a flexible description of the underlying fold geometry of proteins that can be adjusted by changing the ‘width’ of the Gaussians. Reducing the width sharpens the representation and leads to a more ‘atomlike’ description; increasing the width creates a fuzzier representation that preserves the general shape features of the chain fold but with a consequent loss in atomic resolution. The width used in this study is based upon the features of individual atoms and provides a representation that is quite robust with respect to the variety of geometric features typically encountered in the alignment process. In addition, a post-alignment analysis is performed that generates sequence alignments from the corresponding structure alignments. An example, based on five mammalian and fungal matrix metalloproteinase crystal structures (human fibroblast collagenase, neutrophil collagenase, stromelysin, astacin, and adamalysin), illustrates a number of features of the Gaussian-based approach. © 2001 by Elsevier Science Inc.

Grignard addition of phenylmagnesium bromide to 3,5-O-benzylidene-1-deoxy-D-erythro-2-pentulose (1) affords C-phenyl branched-chain pentitols having exclusively either the D-arabino (2) or D-ribo (5) stereochemistry according to the mode of substitution of 1. In order to determine the chirality of these products conclusively, the crystal and molecular structure of the unsubstituted pentitol 6 (from 2) has been determined. Crystals of 1-deoxy-2-C-phenyl-D-arabinitol (6; C11H16O4) are orthorhombic, space group P212121, with cell dimensions a = 8.9420(6), b = 18.910(1), c = 6.4263(6) Å, and Z = 4. The structure was solved by multi-solution direct methods and refined to a final discrepancy index of 5.6%. The molecule has an extended, planar zigzag conformation with the phenyl ring nearly perpendicular to this plane. Compound 6 forms one intramolecular (between 2-OH and O-4) and three intermolecular hydrogen bonds. Palladium-catalyzed hydrogenolysis of the 2-phenylcarbamate of 2 results in deoxygenation of the benzylic center with complete-inversion of configuration, as established by crystal-structure determination of the product 7. Crystals of 2(S)-4-O-acetyl-3,5-O-benzylidene-1,2-dideoxy-2-C-phenyl-D-erytro-pentitol (7; C20H22O4) are monoclinic, space group C2, with cell dimensions a = 19.102(1), b = 6.1925(5), c = 16.098(1) Å, β = 108.325(9)°, and Z = 4. The structure was solved by multi-solution direct methods and refined to a final discrepancy index of 5.9%. The molecule has an almost ideal planar, zigzag backbone conformation which incorporates the 1,3-dioxane ring. Comparison of the conformation observed in the crystal with that calculated from proton–proton coupling constants shows good agreement

The crystal and molecular structure of 3-methoxy-9 (10 → 19) abeo -1, 3, 5 (10)-estratrien-17-one has been determined by X-ray analysis in order to ascertain the configuration at C (9). The seven-membered B-ring has a chair conformation and this causes the molecule to bow towards the α-face rather than towards the β-face as in estradiol.

Earlier studies have shown that the β-D-digitoxose (2,6-dideoxy-β-D-mannopyranose) directly attached to the cardiac glycoside steroid C3 has the greatest effect on biological activity. This report describes the synthesis of eight digitoxosides (2a-9a), with widely varying cyclic and acyclic C17β-side groups, and the corresponding C3',C4'-acetonides (2b-9b). NMR analysis of conformational strain introduced by the acetonide groups is supported by crystallographic analysis of the sugars' torsion angles.

Previous models of digitalis genin interaction with the (Na+,K+)-ATPase system (the putative receptor for such drugs) were deficient in explaining the (Na+,K+)-ATPase inhibitory activity of a number of digitalis genin analogues. With rat brain (Na+,K+)-ATPase we observed that the C-17 side chain carbonyl (C = O) oxygen distance of a given genin in relation to its position in the reference compound digitoxigenin was the primary determinant of its biological activity. With a number of genin analogues, we observed a strict correlation of this structural parameter with its binding site compatibility as well as inhibitory potency with respect to the (Na+,K+)-ATPase. In every case the correlation to inhibition data was obtained using a minimum energy conformation for the genin structure. The general applicability of that model is now proposed based on the following observations. The carbonyl oxygen position versus the biological activity relationship fully holds with (Na+,K+)-ATPase preparations from other tissues and species and also when different binding conditions are used for the enzyme genin interaction. The relationship is equally valid for the K+-p-nitrophenyl phosphatase activity. Correlations of the data obtained under these various conditions provide further support for this relationship and for the concept that altered affinities of the enzyme for a given genin under different binding conditions reflect conformational variations of a single binding site.

Cystallographic data on over 400 steroids collected in the Atlas of Steroid Structure provide information concerning preferred conformations, relative stabilities and substituent influence of the interactive potential of steroid hormones. Analysis of these data indicates that observed conformational details are intramolecularly controlled and that the influence of crystal packing forces is negligible. Crystallographic data on the orientation of the progesterone side chain contradict published force-field calculations. In 84 of 88 structures having a 20-one substituent, the C(16)-C(17)-C(20)-O(20) torsion angle is between 0 degrees and -46 degrees. The 4 torsion angles that lie outside this range do so because of a 16 beta-substituent and not because of crystal packing forces. Not one of the 88 structures is found to have a conformation in which the C(16)-C(17)-C(20)-O(20) torsion angle is within +/- 15 degrees of the most commonly calculated minimum energy value. The narrow range of side chain conformations seen in very different crystalline environments in the 88 crystal structure determinations and the predictable substituent influence apparent in the data strongly suggest that crystallographically observed conformers seldom deviate from minimum energy positions, regardless of hypothetical broad energy minima, metastable states and small barriers to rotation. The 96 crystallographically independent determinations of the cholestane 17-side chain show that the chain has 4 principal conformations (A:B:C:D), occurring in the ratio 69:8:8:11. Although the fully extended side chain is clearly the energetically most favored one, in 16 observations of cholesterol itself only 6 are in the extended conformation. Some of the correlated conformational changes in the chains can be rationalized on the basis of model studies, but others apparently result from subtle intramolecular forces. The unsaturated B ring provides another element of flexibility in the structure of cholesterol. The 5-ene B ring is normally observed in an 8 beta, 9 alpha-half-chair conformation. However, in structures containing more than one molecular in the crystallographic asymmetric unit, at least one of the 2 molecules is found to differ significantly from this form. It may be that this inherent flexibility is responsible for the presence of conformationally distnct molecules in the same crystal. The intermolecular interaction observed in the crystal structure of cholesterol and its fatty acid derivatives illustrate the type of interaction between the steroid ring system and hydrocarbon chains that can be expected in membrane bilayers.

Cs 2 TiCl 5 .4H 2 O cristallise dans P2 1 /c avec a=9,565, b=9,3077 et c=2813 A, β=116,44°, Z=2; affinement jusqu'a R=0,048. Les cristaux contiennent des ions trans-[TiCl 2 (H 2 O) 4 ] + qui reposent sur des centres cristallographiques de symetrie. Antiprisme carre deforme autour de Cs + a coordination 8. Discussion des spectres optiques

22-Methylene-3beta-hydroxy-5beta,20(S)-card-14-enolide (11) and 22-methylene-3beta-hydroxy-5beta,20(R)-card-14-enolide (12) were synthesized from digitoxin (1). Attempts to prepare the 14beta-hydroxy-22-methylene analogues were unsuccessful. The 20(R) isomer (12) was found in Na+, K+-ATPase inhibition studies to be twice as active as 14-dehydrogitoxigenin (17). The 20(S) isomer (11) was significantly less active than 17. The hydrolysis of steroid 3beta-tert-butyldimethysilyl ethers was also found to be much more difficult than with nonsteroids.

The crystal and molecular structure of 1,2-seco-A-bisnor-5α-androstan-17β-ol acetate has been determined to evaluate the conformational importance of the intact steroid nucleus. The resulting tricyclic compound retains nearly the same steric profile for the remainder of the molecule when compared to the structures of dihydrotestosterone derivatives with intact A-rings. This may help to explain why these types of molecules retain a significant level of androgenic activity.

Le compose C 12 O 2 Cl 2 cristallise dans le systeme triclinique, groupe P1 et sa structure est affinee jusqu'a R=0,047. Le cycle phenoxy est plan tandis que le cycle cyclohexenone possede une conformation enveloppe. Spectre RMN- 13 C