The Search for the Spatial and Electronic Requirements of a Drug

A new program called GAMMA (genetic algorithm for multiple molecule alignment) has been developed for the superimposition of several three-dimensional chemical structures. Superimposition of molecules and evaluation of structural similarity is an important task in drug design and pharmaceutical research. Similarities of compounds are determined by this program either based on their structural or their physicochemical properties by defining different matching criteria. These matching criteria are atomic properties such as atomic number or partial atomic charges. The program is based on a combination of a genetic algorithm with a numerical optimization process. A major goal of this hybrid procedure is to address the conformational flexibility of ligand molecules adequately. Thus, only one conformation per structure is necessary and the program can work even when only one conformation of a compound is stored in a database. The genetic algorithm optimizes in a nondeterministic process the size and the geometric fit of the overlay. The geometric fit of the conformations is further improved by changing torsional angles combining the genetic algorithm and the directed tweak method. The determination of the fitness of a superimposition is based on the Pareto optimization. As an application the superimposition of a set of Cytochrome P450c17 enzyme inhibitors has been performed.Electronic Supplementary Material available.     

On the properties of aqueous amide solutions through classical molecular dynamics simulations

The structure and dynamics of infinitely diluted aqueous amide solutions is studied for 13 compounds in the NVT ensemble using classical molecular dynamics simulations. The aim of this work is to provide valuable insights into the effect of amides on liquid water properties in order to understand the amides role in the kinetic inhibition of clathrate hydrate formation in natural gas mixtures. The OPLS-AA forcefield is used to describe the amides, with parameters obtained through fitting of computed B3LYP/6-311++g^{* *} data when not available in the literature, and the SPC-E model is applied for water molecules. Structural properties of the solutions are analyzed via calculated radial distribution functions and dynamic properties are studied with the computed mean square displacements and velocity autocorrelation functions. Most of the studied compounds show a remarkable structuring effect on the surrounding water with strong interactions resulting from hydrogen bonding between solute and solvent molecules. Hydrophobic and hydrophilic synergistic effects influence the amide–water interaction and the properties of the water solvation shells around amides.     

A quantitative structure–activity relationship study on some aromatic/heterocyclic sulfonamides and their charged derivatives acting as carbonic anhydrase inhibitors

A quantitative structure–activity relationship (QSAR) study is made on a series of aromatic/heterocyclic sulfonamides and their charged derivatives acting as carbonic anhydrase (CA) inhibitors. These compounds were studied by Scozzafava et al. (J. Med. Chem. 2000; 43: 292) for the selective inhibition of CAs—sulfonamides generally do not discriminate between different CA isozymes and hence exhibit many undesirable side effects when used as drugs against a particular disease. In this communication, an attempt has been made to investigate the physicochemical and structural properties that can make them selective for a given CA isozyme. Based on in vitro data reported by Scozzafava et al. against two cytosolic isozymes and one membrane-bound isozyme, the QSAR study has shown that uncharged compounds cannot be made selective for cytosolic or membrane-bound isozyme since in both the cases the compounds appear to follow the same mechanism of inhibition. However, for the charged compounds the polarizability of the molecule seems to greatly favor the inhibition of the membrane-bound enzyme, and hence they can be made selective for this enzyme by enhancing their polarizability, which is found to play no role in the inhibition of cytosolic enzymes.     

About factors providing the fast protein-protein recognition in processes of complex formation

A package of programs for the examination of areas of subunit contacts (interface) in protein-protein (PP) complexes has been created and used for a detailed study of amino acid (AA) composition and interface structure in a large number of PP complexes from Brookhaven database (PBD). It appeared that in about 75% of the complexes, the AA composition of the subunit surface is not important. This suggests that, along with the surface AA composition, interactions between AA from the inner parts of protein globules may play a significant role in PP recognition. Such interactions between relatively distant AA residues can only be of electrostatic nature and contribute to the total electric field of the protein molecule. The configuration of the electric field itself appears to determine the PP recognition. The total electric field created by protein molecules can be calculated as a result of superimposition of the fields created by the protein multipole (i.e. by the totality of partial electric charges assigned to each atom of the molecule). We performed preliminary calculations for the distant electrostatic interaction of ribonuclease subunits in a vacuum. The results reveal that the effect of the electric fields of the protein multipole is strong enough to orient protein molecules prior to their Brown collision.     

Scoring ligand similarity in structure‐based virtual screening

Scoring to identify high‐affinity compounds remains a challenge in virtual screening. On one hand, protein–ligand scoring focuses on weighting favorable and unfavorable interactions between the two molecules. Ligand‐based scoring, on the other hand, focuses on how well the shape and chemistry of each ligand candidate overlay on a three‐dimensional reference ligand. Our hypothesis is that a hybrid approach, using ligand‐based scoring to rank dockings selected by protein–ligand scoring, can ensure that high‐ranking molecules mimic the shape and chemistry of a known ligand while also complementing the binding site. Results from applying this approach to screen nearly 70 000 National Cancer Institute (NCI) compounds for thrombin inhibitors tend to support the hypothesis. EON ligand‐based ranking of docked molecules yielded the majority (4/5) of newly discovered, low to mid‐micromolar inhibitors from a panel of 27 assayed compounds, whereas ranking docked compounds by protein–ligand scoring alone resulted in one new inhibitor. Since the results depend on the choice of scoring function, an analysis of properties was performed on the top‐scoring docked compounds according to five different protein–ligand scoring functions, plus EON scoring using three different reference compounds. The results indicate that the choice of scoring function, even among scoring functions measuring the same types of interactions, can have an unexpectedly large effect on which compounds are chosen from screening. Furthermore, there was almost no overlap between the top‐scoring compounds from protein–ligand versus ligand‐based scoring, indicating the two approaches provide complementary information. Matchprint analysis, a new addition to the SLIDE (Screening Ligands by Induced‐fit Docking, Efficiently) screening toolset, facilitated comparison of docked molecules' interactions with those of known inhibitors. The majority of interactions conserved among top‐scoring compounds for a given scoring function, and from the different scoring functions, proved to be conserved interactions in known inhibitors. This was particularly true in the S1 pocket, which was occupied by all the docked compounds. Copyright © 2009 John Wiley & Sons, Ltd.     

Classification of proteins based on the properties of the ligand-binding site: the case of adenine-binding proteins

Comparative analysis of protein binding sites for similar ligands yields information about conserved interactions, relevant for ligand affinity, and variable interactions, which are important for specificity. The pattern of variability can indicate new targets for a pharmacologically validated class of compounds binding to a similar site. A particularly vast group of therapeutically interesting proteins using the same or similar substrates are those that bind adenine-containing ligands. Drug development is focusing on compounds occupying the adenine-binding site and their specificity is an issue of paramount importance. We use a simple scheme to characterize and classify the adenine-binding sites in terms of their intermolecular interactions, and show that this classification does not necessarily correspond to protein classifications based on either sequence or structural similarity. We find that only a limited number of the different hydrogen bond patterns possible for adenine-binding is used, which can be utilized as an effective classification scheme. Closely related protein families usually share similar hydrogen patterns, whereas non-polar interactions are less well conserved. Our classification scheme can be used to select groups of proteins with a similar ligand-binding site, thus facilitating the definition of the properties that can be exploited to design specific inhibitors.     

A high-throughput assay for assessing the cell permeability of combinatorial libraries

There is great interest in the identification of synthetic molecules that are capable of manipulating protein-protein interactions in living cells. Peptides, unlike other classes of small molecules, have binding properties appropriate for this application, but most are poorly cell permeable and sensitive to proteases. Therefore, considerable effort has been expended in the development of libraries of oligomeric peptide-like molecules. However, there are no clear-cut rules to guide the design of libraries rich in cell permeable compounds. Furthermore, currently available empirical methods to assess permeability may not accurately reflect true permeability and/or are capable of only modest throughput. We describe here an assay for assessing the relative cell permeability of synthetic molecules in the context of steroid fusions that is capable of high throughput and can be used in any transfectable cell line.     

Assay Optimization and Screening of RNA-Protein Interactions by AlphaScreen

The lack of lead compounds that specifically recognize and manipulate the function of RNA molecules limits our ability to consider RNA targets valid for drug discovery. Herein is reported a high-throughput biochemical screen for inhibitors of RNA-protein interactions based on AlphaScreen technology that incorporates several layers of specificity measurements into the primary screen. This screen was used to analyze approximately 5500 compounds from a collection of bioactive small molecules to detect inhibitors of the HIV-1 Rev-RRE and BIV Tat-TAR interactions. This proof-of-concept screen validates the assay as one that accurately identifies hit molecules and determines the selectivity of those hits.     

发现靶向蛋白质间相互作用的小分子药物研究进展

蛋白质-蛋白质相互作用在多种细胞功能中具有重要的作用。靶向蛋白质-蛋白质相互作用已经成为新药发现的重要策略,但发现能阻断蛋白质-蛋白质相互作用的小分子药物是一个巨大的挑战。尽管如此,近年来人们还是发现了许多能调控蛋白质-蛋白质相互作用的小分子。该文主要总结了在病毒进入、细胞凋亡通路和神经退行性疾病等方面的蛋白质-蛋白质相互作用小分子抑制剂的研究进展。     

Comparison of anti-inflammatory compounds in the carrageenan induced paw edema model and the reversed passive Arthus model utilizing the same animal

In order to better define antiinflammatory activity in new agents, a test was devised utilizing both carrageenan induced paw edema and the reversed passive Arthus reaction in the same animal. The model of carrageenan induced rat paw edema is a standard laboratory assay used to predict classical "aspirin-like" antiinflammatory molecules. The reversed passive cutaneous Arthus reaction involves precipitating antigen-antibody complexes, complement and infiltrating polymorphonuclear leukocytes (PMN's) and can be used to identify agents that affect one or more of these factors specifically. Antiinflammatory compounds were given orally one hour prior to the administration of carrageenan and goat anti-rat serum. Comparisons were made between several non-steroidal compounds and the steroid hydrocortisone. All of the compounds tested gave good carrageenan activity, but only hydrocortisone produced significant Arthus lesion inhibition in this assay.     

On the role of chirality in structure-odor relationships

The influence of chirality on odors was studied on 16 enantiomericpairs according to the dispersion/hydrogen bonding theory ofreceptor-odorant interaction. Comparisons of molecular structures were made by superimpositionof optimized conformations, using the Alchemy II package. Thequality of fit was assessed using the RMS parameter includedin Alchemy II and a new index for hydrogen bonding: the anglebetween H-bonds in the two molecules. In the case of camphoraceous odorants where an interaction modelwas already known superimposition according to the model ledto correct predictions of the high similarity of odors observedin enantiomeric pairs. For several urinous odorants comparisons were made using d-androstenoneas a reference compound for the urinous odor. Correct predictionswere obtained for l-androstenone, both enantiomers of androsta-4,16-dienone, and (+)-2-methyl-4-(5,5,6-exo-trimethy1-2-exonorbornyl)-cyclobexane.The (–) enantiomer of the latter compound was correctlypredicted only if it was assumed that its weak intensity isdue to a partial interaction with the hydrophobic zone of thereceptor. For ambergris odorants which have a complex odor (–)-Ambroxwas selected as the reference compound. The odors of (+)-Ambroxand enantiomers of four other compounds (ambergris or woody)were correctly predicted by superimposition. For nootkatone and three derivatives which have a grapefruitnote for one enantiomer and a woody note for the other no modelsor reference compounds were available. The superimpositionswere made between grapefruit enantiomers, on the one hand, andwoody enantiomers on the other hand. Woody and grapefruit characterswere correctly predicted in all cases. The limits of this approach based on molecular modelling arediscussed.     

Pharmacophore feature prediction and molecular docking approach to identify novel anti‐HCV protease inhibitors

Discovering a potential drug for HCV treatment is a challenging task in the field of drug research. This study initiates with computational screening and modeling of promising ligand molecules. The foremost modeling method involves the identification of novel compound and its molecular interaction based on pharmacophore features. A total of 197 HCV compounds for NS3/4A protein target were screened for our study. The pharmacophore models were generated using PHASE module implemented in Schrodinger suite. The pharmacophore features include one hydrogen bond acceptor, one hydrogen bond donor, and three hydrophobic sites. As a result, based on mentioned hypothesis the model ADHHH.159 corresponds to the CID 59533233. Furthermore, docking was performed using maestro for all the 197 compounds. Among these, the CID 59533313 and 59533233 possess the best binding energy of ?11.75 and ?10.40 kcal/mol, respectively. The interactions studies indicated that the CID complexed with the NS3/4A protein possess better binding affinity with the other compounds. Further the compounds were subjected to calculate the ADME properties. Therefore, it can be concluded that these two compounds could be a potential alternative drug for the development of HCV.     

Solubility enhancement of cox-2 inhibitors using various solvent systems

This study examined the solubility enhancement of 4 cox-2 inhibitors, celecoxib, rofecoxib, meloxicam, and nimesulide, using a series of pure solvents and solvent mixtures. Water, alcohols, glycols, glycerol, and polyethylene glycol 400 (PEG 400) were used as solvents and water-ethanol, glycerol-ethanol, and polyethylene glycol-ethanol were used as mixed-solvent systems. A pH-solubility profile of drugs was obtained in the pH range 7.0 to 10.9 using 0.05M glycine-sodium hydroxide buffer solutions. Lower alcohols, higher glycols, and PEG 400 were found to be good solvents for these drugs. The aqueous solubility of celecoxib, rofecoxib, and nimesulide could be enhanced significantly by using ethanol as the second solvent. Among the mixed-solvent systems, PEG 400-ethanol system had highest solubilization potential. In the case of meloxicam and nimesulide, solubility increased significantly with increase in pH value. Physico-chemical properties of the solvent such as polarity, intermolecular interactions, and the ability of the solvent to form a hydrogen bond with the drug molecules were found to be the major factors involved in the dissolution of drugs by pure solvents. The greater the difference in the polarity of the 2 solvents in a given mixed solvent, the greater was the solubilization power. However, in a given mixed-solvent system, the solubilization power could not be related to the polarity of the drugs. Significance of the solubility data in relation to the development of formulations has also been discussed in this study.     

New photocrosslinkable polymers for second-order nonlinear optics

Among all the strategies developed by chemists to stabilize NLO properties of poled amorphous polymeric films, one of the most efficient is the formation of a network into which NLO moieties are covalently bound by both ends after their alignment under a DC electric field. For that purpose, complementary chemical groups can be used, reacting either thermally or photochemically. In our work, the use of photocrosslinkable groups (cinnamate and furylacrylate) has been investigated. In that case, photocrosslinking reactions occur between the photocrosslinkable groups functionalized into NLO molecules and the same photocrosslinkable groups appended via an alkyl spacer group into a polymer acting as the matrix. After synthesis of the different compounds and film realization, the photocrosslinking process was characterized by UV-visible spectroscopy, thus giving evidence of the higher efficiency of the furylacrylate-based system with respect to the cinnamate-based one. The alkyl spacer group was recognized as playing a crucial role in furthering the dimerization reactions between the polymer and the NLO moieties. Evolution of the maximal absorption band corresponding to the NLO moiety itself (around 500 nm) was interpreted through UV-visible spectroscopic studies using different model compounds. This was not due to NLO moiety damage, as first feared, but only to a modification in the surrounding polarity during the crosslinking process. The furylacrylate-based system was then poled and photocrosslinked in the poled state, yielding a material with excellent optical quality and very stable optical nonlinearity.     

Porphyrins and metalloporphyrins: versatile circular dichroic reporter groups for structural studies

During the last few years, porphyrins and metalloporphyrins have attracted widespread attention as chromophores for studies in circular dichroism (CD), an indispensable chiroptical tool for monitoring chiral interactions. This review summarizes the multifaceted properties of porphyrins and metalloporphyrins, powerful CD chromophores that are characterized by their intense and red-shifted Soret band, propensity to undergo pi-pi stacking, facile incorporation of metals, and ease in varying solubility. Such attributes make porphyrins one of the most attractive and sensitive chromophores used in CD studies. They offer possibilities for studying the stereochemistry of chiral porphyrin assemblies, large organic molecules, biopolymers, and compounds available in miniscule quantities. The tendency of porphyrins to undergo pi-pi stacking and zinc porphyrins to coordinate with amines enable the CD exciton chirality method to be extended to configurational assignments of flexible compounds containing only one stereogenic center. Various artificial porphyrin receptors have been synthesized for the recognition of biologically important chiral guests such as carbohydrates, amino acids, and their derivatives. The induced CD of the host porphyrin Soret band reflects the identity of guests and binding modes of host/guest complexation with high sensitivity.     

Molecular modeling study on chemically diverse series of cyclooxygenase-2 selective inhibitors: generation of predictive pharmacophore model using Catalyst

Cyclooxygenase (COX) enzymes catalyse the biosynthesis of prostaglandins and thromboxane from arachidonic acid (AA). We summarize in this paper, the development of pharmacophores of a dataset of inhibitors for COX-2 by using the Catalyst/Hypogen module using six chemically diverse series of compounds. Training set consisting of 24 compounds was carefully selected. The activity spread of the training set molecules was from 0.1 to 10000 nM. The most predictive pharmacophore model (hypothesis 1), consisting of four features, namely, one hydrogen bond donor, one hydrogen bond acceptor, one hydrophobic aliphatic and one ring aromatic feature, had a correlation (r) of 0.954 and a root mean square deviation of 0.894. The entropy (configuration cost) value of the hypotheses was 16.79, within the allowed range. The difference between the null hypothesis and the fixed cost and between the null hypothesis and the total cost of the best hypothesis (hypothesis 1) was 88.37 and 78.51, respectively. The model was validated on a test set consisting of six different series of structurally diverse 22 compounds and performed well in classifying active and inactive molecules correctly. This validation approach provides confidence in the utility of the predictive pharmacophore model developed in this work as a 3D query tool in the virtual screening of drug like molecules to retrieve new chemical entities as potent COX-2 inhibitors. The model can also be used to predict the biological activities of compounds prior to their costly and time-consuming synthesis. Figure 3D Pharmacophore model generated using structurally diverse COX-2 inhibitors     

Differential interactions of beta particles with liquid enantiomers and internal timing of chiral molecules

The Cerenkov and liquid scintillation technique was applied to detect differential interactions between beta particles and chiral molecules. The highly helical beta emitting 32P and the barely helical beta emitting 3H were dissolved in the liquid enantiomers of 2-phenylbutyric acid. The interactions of the beta particles with the enantiomers were compared. Differential interactions were observed in case of 32P. The stopping power of R enantiomers was greater than that of the S enantiomer. The apparent decay of 32P was faster in the S enantiomer than in the R enantiomer. It is not clear whether this is due to some mistake in measurement or reflects the postulated difference of internal timing of the two enantiomers. Since, in spite of all efforts, contamination could not totally be excluded and data are significant only to one sigma, results must be considered preliminary. The method, however, seems to be more sensitive than all previously used methods. The differential effect was always in the same direction in at least 5 replicas.     

Synthesis, molecular modeling and QSAR studies in chiral 2,3-disubstituted-1,2,3,4-tetrahydro-9H-pyrido(3,4-b)indoles as potential modulators of opioid antinociception.

In view of coexistence of opioid and cholecystokinin (CCK) in the brain areas concerned with pain processing, some semirigid racemic and chiral analogues of a potent CCK receptor antagonist (benzotript) have been synthesized and tested for their modulatory role on opioid antinociception, which may be mediated by CCK-B receptor. Some of these compounds, 3e, 3g, 3h, 4a, 4b and 4h, exhibited antinociceptive potentiation comparable to benzotript and proglumide. In order to identify the essential chemical structural features important for this potentiation, molecular modeling and quantitative structure activity relationship (QSAR) studies have been carried out in the S and R enantiomers of some of these semi-rigid compounds. The 3D-biophore models, common to all molecules of the training set have been derived. These models with superimposition (match value >0.25) depicted three biophoric sites one each for, pi/hydrophobic interactions, hydrogen bonding and ionic interactions among the phenyl/pyrrole ring, indole nitrogen, amidic oxygen, pyridyl nitrogen and lone pair of amidic oxygen. The total hydrophobicity and S absolute stereochemistry are found to positively contribute to potentiation of antinociception induced by morphine and the resulting quantitative pharmacophoric model with good correlation is found to well describe the observed activity.