Pharmatrope

Computational analysis of ligand recognition sites of homo- and heteropentameric 5-HT(3) receptors.

Eur J Med Chem. 2010 Jul 27;

Authors: Moura Barbosa AJ, De Rienzo F, Ramos MJ, Menziani MC

Inhibition of the 5-hydroxytryptamine receptor (5-HT(3)R), a member of the Cys-loop superfamily of Ligand-Gated Ion Channels (LGICs), has been recognized to have important antiemetic effects. With respect to the many other drugs already in use, such as the first generation 5-HT(3)R antagonist granisetron, palonosetron, a second generation antagonist, clearly demonstrates superior inhibition potency towards the 5-HT(3)Rs. Five different receptor monomers, the 5-HT(3)R A-E, have been identified although the A and B subunits are the only known to build functional receptors, the homopentameric 5-HT(3A)R and the heteropentameric 5-HT(3B-A)R (with BBABA subunit arrangement). At present, however, no three-dimensional structure has been reported for any of the 5-HT(3)R subunits. To understand the binding properties of agonists and antagonists, models of the extracellular portion of the 5-HT(3)R A and B subunits are built and assembled into the receptor (homo- and hetero-) pentameric structure on the basis of the known three-dimensional structure of the nicotinic-acetylcholine receptor (nACh-R). The results of docking studies of the natural agonist serotonin and the antagonists palonosetron and granisetron into the modelled homomeric and heteromeric 5-HT(3)R binding interfaces, provide a possible rationalization both of the higher potency of palonosetron with respect to other antagonists, and of its previously reported allosteric binding and positive cooperativity properties.

PMID: 20724042 [PubMed - as supplied by publisher]

Molecular docking and 3D-QSAR studies on beta-phenylalanine derivatives as dipeptidyl peptidase IV inhibitors.

J Mol Model. 2010 Jul;16(7):1239-49

Authors: Jiang YK

Three-dimensional quantitative structure-activity relationship (3D-QSAR) and molecular docking studies were carried out to explore the binding of 73 inhibitors to dipeptidyl peptidase IV (DPP-IV), and to construct highly predictive 3D-QSAR models using comparative molecular field analysis (CoMFA) and comparative molecular similarity indices analysis (CoMSIA). The negative logarithm of IC(50) (pIC(50)) was used as the biological activity in the 3D-QSAR study. The CoMFA model was developed by steric and electrostatic field methods, and leave-one-out cross-validated partial least squares analysis yielded a cross-validated value (r(2)(cv)) of 0.759. Three CoMSIA models developed by different combinations of steric, electrostatic, hydrophobic and hydrogen-bond fields yielded significant r(2)(cv) values of 0.750, 0.708 and 0.694, respectively. The CoMFA and CoMSIA models were validated by a structurally diversified test set of 18 compounds. All of the test compounds were predicted accurately using these models. The mean and standard deviation of prediction errors were within 0.33 and 0.26 for all models. Analysis of CoMFA and CoMSIA contour maps helped identify the structural requirements of inhibitors, with implications for the design of the next generation of DPP-IV inhibitors for the treatment of type 2 diabetes.

PMID: 20069322 [PubMed - indexed for MEDLINE]

Improving performance of docking-based virtual screening by structural filtration.

J Mol Model. 2010 Jul;16(7):1223-30

Authors: Novikov FN, Stroylov VS, Stroganov OV, Chilov GG

In the current study an innovative method of structural filtration of docked ligand poses is introduced and applied to improve the virtual screening results. The structural filter is defined by a protein-specific set of interactions that are a) structurally conserved in available structures of a particular protein with its bound ligands, and b) that can be viewed as playing the crucial role in protein-ligand binding. The concept was evaluated on a set of 10 diverse proteins, for which the corresponding structural filters were developed and applied to the results of virtual screening obtained with the Lead Finder software. The application of structural filtration resulted in a considerable improvement of the enrichment factor ranging from several folds to hundreds folds depending on the protein target. It appeared that the structural filtration had effectively repaired the deficiencies of the scoring functions that used to overestimate decoy binding, resulting into a considerably lower false positive rate. In addition, the structural filters were also effective in dealing with some deficiencies of the protein structure models that would lead to false negative predictions otherwise. The ability of structural filtration to recover relatively small but specifically bound molecules creates promises for the application of this technology in the fragment-based drug discovery.

PMID: 20041273 [PubMed - indexed for MEDLINE]

Addressing limitations with the MM-GB/SA scoring procedure using the WaterMap method and free energy perturbation calculations.

J Chem Inf Model. 2010 Apr 26;50(4):547-59

Authors: Guimarães CR, Mathiowetz AM

The MM-GB/SA scoring technique has become an important computational approach in drug design. We, and others, have demonstrated that for congeneric molecules the correlation with experimental data obtained with the physics-based scoring is usually superior to scoring functions from typical docking algorithms. Despite showing good accuracy when applied within a series, much work is necessary to improve the MM-GB/SA method in order to gain greater efficiency in drug design. Here, we investigate the poor estimation of protein desolvation provided by the GB/SA solvation model and the large dynamic range observed in the MM-GB/SA scoring compared to that of the experimental data. In the former, replacing the GB/SA protein desolvation in the MM-GB/SA method by the free energy associated with displacing binding site waters upon ligand binding estimated by WaterMap provides the best results when ranking congeneric series of factor Xa and cyclin-dependent kinase 2 (CDK2) inhibitors. However, the improvement is modest over results obtained with the MM-GB/SA and WaterMap methods individually, apparently due to the high correlation between the free energy liberation of the displaced solvent and the protein-ligand van der Waals interactions, which in turn may be interpretable as estimates of the hydrophobic effect and hydrophobic-like interactions, respectively. As for the large dynamic range, comparisons between MM-GB/SA and FEP calculations indicate that for the factor Xa test set this problem has its origin in the lack of shielding effects of protein--ligand electrostatic interactions; that overly favors ligands that engage in hydrogen bonds with the protein.

PMID: 20235592 [PubMed - indexed for MEDLINE]

Computational Modeling Toward Understanding Agonist Binding on Dopamine 3.

J Chem Inf Model. 2010 Aug 9;

Authors: Zhao Y, Lu X, Yang CY, Huang Z, Fu W, Hou T, Zhang J

The dopamine 3 (D3) receptor is a promising therapeutic target for the treatment of nervous system disorders, such as Parkinson's disease, and current research interests primarily focus on the discovery/design of potent D3 agonists. Herein, a well-designed computational protocol, which combines pharmacophore identification, homology modeling, molecular docking, and molecular dynamics (MD) simulations, was employed to understand the agonist binding on D3 aiming to provide insights into the development of novel potent D3 agonists. We (1) identified the chemical features required in effective D3 agonists by pharmacophore modeling based upon 18 known diverse D3 agonists; (2) constructed the three-dimensional (3D) structure of D3 based on homology modeling and the pharmacophore hypothesis; (3) identified the binding modes of the agonists to D3 by the correlation between the predicted binding free energies and the experimental values; and (4) investigated the induced fit of D3 upon agonist binding through MD simulations. The pharmacophore models of the D3 agonists and the 3D structure of D3 can be used for either ligand- or receptor-based drug design. Furthermore, the MD simulations further give the insight that the long and flexible EL2 acts as a "door" for agonist binding, and the "ionic lock" at the bottom of TM3 and TM6 is essential to transduce the activation signal.

PMID: 20695484 [PubMed - as supplied by publisher]

Endocannabinoid binding to the cannabinoid receptors: what is known and what remains unknown.

Curr Med Chem. 2010;17(14):1468-86

Authors: Reggio PH

The cannabinoid CB1 and CB2 receptors are Class A G protein-coupled receptors (GPCRs). While many Class A GPCRs have endogenous ligands that are hydrophilic cations (e.g., the serotonin and dopamine receptors), the cannabinoid receptors have neutral, highly lipophilic ligands derived from the fatty acid, arachidonic acid. The most well-studied of these are N-arachidonoylethanolamine (anandamide, AEA) and sn-2-arachidonoylglycerol (2-AG). This review focuses on the experimental and computational studies that have been used to probe the nature of endocannabinoid interaction with the cannabinoid receptors. These studies include mutation, SAR and NMR studies, as well as, QSAR, docking and molecular dynamics simulations. Gaps in our knowledge are identified. The review begins more generally, however, by discussing the entire endocannabinoid system, of which the cannabinoid receptors are part. For in order to understand endocannabinoid action, one needs an appreciation for the environments for which these ligands have been designed and the conformational changes these ligands must undergo in order to act on the cannabinoid receptors.

PMID: 20166921 [PubMed - indexed for MEDLINE]

A computational study of the binding of 3-(arylidene) anabaseines to two major brain nicotinic acetylcholine receptors and to the acetylcholine binding protein.

Eur J Med Chem. 2010 Jun;45(6):2433-46

Authors: Slavov SH, Radzvilovits M, LeFrancois S, Stoyanova-Slavova IB, Soti F, Kem WR, Katritzky AR

Nicotinic acetylcholine receptors (nAChRs) have become targets for drug development in recent years. 3-(2,4-dimethoxybenzylidene)-anabaseine (DMXBA), which selectively stimulates the alpha7 nAChR, has been shown to alleviate some cognitive deficits associated with schizophrenia. In this paper we report an analysis of the interactions between 47 arylidene-anabaseines (including 45 benzylidene-anabaseines) and rat brain alpha7 and alpha4beta2 nicotinic acetylcholine receptors, using three different modeling techniques, namely 2D-QSAR, 3D-QSAR and molecular docking to the Aplysia californica acetylcholine binding protein (AChBP), a water soluble, homomeric nAChR surrogate receptor with a known crystal structure. Our investigation indicates the importance of: (1) the nitrogen atom of the tetrahydropyridyl (THP) ring for hydrogen bond formation; (2) pi-pi interactions between the aromatic rings of the ligands and the nAChBP binding site; (3) molecular surface recognition expressed in terms of steric complimentarity. On the basis of the 3D-QSAR results, bulky substituents at positions 2 (and due to the rotational freedom also at position 6) and 4 of the benzylidene moiety, with highly electronegative atoms projecting approximately 3-3.5A away from the benzylidene ring at position 4 seem optimal for enhancing binding affinity to the alpha7 nAChR.

PMID: 20236734 [PubMed - indexed for MEDLINE]

Computational Methodologies for Compound Database Searching that Utilize Experimental Protein-Ligand Interaction Information.

Chem Biol Drug Des. 2010 Jul 15;

Authors: Tan L, Batista J, Bajorath J

Ligand- and target structure-based methods are widely used in virtual screening, but there is currently no methodology available that fully integrates these different approaches. Herein, we provide an overview of various attempts that have been made to combine ligand- and structure-based computational screening methods. We then review different types of approaches that utilize protein-ligand interaction information for database screening and filtering. Interaction-based approaches make use of a variety of methodological concepts including pharmacophore modeling and direct or indirect encoding of protein-ligand interactions in fingerprint formats. These interaction-based methods have been successfully applied to tackle different tasks related to virtual screening including postprocessing of docking poses, prioritization of binding modes, selectivity analysis, or similarity searching. Furthermore, we discuss the recently developed interacting fragment approach that indirectly incorporates 3D interaction information into 2D similarity searching and bridges between ligand- and structure-based methods.

PMID: 20636330 [PubMed - as supplied by publisher]

A computational study on cannabinoid receptors and potent bioactive cannabinoid ligands: homology modeling, docking, de novo drug design and molecular dynamics analysis.

Mol Divers. 2010 May;14(2):257-76

Authors: Durdagi S, Papadopoulos MG, Zoumpoulakis PG, Koukoulitsa C, Mavromoustakos T

When X-ray structure of a ligand-bound receptor is not available, homology models of the protein of interest can be used to obtain the ligand-binding cavities. The steroelectronic properties of these cavities are directly related to the performed molecular model coordinates. Thus, the use of different template structures for homology may result in variation of ligand-binding modes. We have recently reported the MD simulations of a potent CB ligand at bovine rhodopsin-based CB1 and CB2 receptors (Durdagi et al., Bioorg Med Chem 16:7377-7387, 2008). In this present study, a homology modeling study based on the beta2-adrenergic receptor for both CB1 and CB2 receptors was performed, and the results were compared with rhodopsin-based models. In addition, the role of membrane bilayers to the adopted conformations of potent AMG3 CB ligand has been analyzed for receptor-free and membrane-associated receptor systems. The performed MD trajectory analysis results have shown that gauche conformations at the terminal segment of the alkyl side chain of AMG3 are not favored in solution. Different adopting dihedral angles defined between aromatic and dithiolane rings at the active sites of the CB1 and CB2 receptors, which are adapted lead to different alkyl side chain orientations and thus, may give clues to the medicinal chemists to synthesize more selective CB ligands. The binding sites of receptors derived by rhodopsin-based models have been regenerated using the beta2-adrenergic based template receptors. The re-obtained models confirmed the ligand-binding pockets that were derived based on rhodopsin.

PMID: 19536636 [PubMed - indexed for MEDLINE]

Computational analysis of the binding ability of heterocyclic and conformationally constrained epibatidine analogs in the neuronal nicotinic acetylcholine receptor.

Mol Divers. 2010 May;14(2):201-11

Authors: Soriano E, Marco-Contelles J, Colmena I, Gandía L

One of the most critical issues on the study of ligand-receptor interactions in drug design is the knowledge of the bioactive conformation of the ligand. In this study, we describe a computational approach aimed at estimating the binding ability of epibatidine analogs to interact with the neuronal nicotinic acetylcholine receptor (nAChR) and get insights into the bioactive conformation. The protocol followed consists of a docking analysis and evaluation of pharmacophore parameters of the docked structures. On the basis of the biological data, the results have revealed that the docking analysis is able to predict active ligands, whereas further efforts are needed to develop a suitable and solid pharmacophore model.

PMID: 19479336 [PubMed - indexed for MEDLINE]

Synthesis and pharmacological characterization of a new series of 5,7-disubstituted-[1,2,4]triazolo[1,5-a][1,3,5]triazine derivatives as adenosine receptor antagonists: A preliminary inspection of ligand-receptor recognition process.

Bioorg Med Chem. 2010 Apr 1;18(7):2524-36

Authors: Pastorin G, Federico S, Paoletta S, Corradino M, Cateni F, Cacciari B, Klotz KN, Gao ZG, Jacobson KA, Spalluto G, Moro S

A new series of triazolotriazines variously substituted at the C5 and N7 (5-25) positions was synthesized and fully characterized at the four adenosine receptor (AR) subtypes. In particular, arylacetyl or arylcarbamoyl moieties were introduced at the N7 position, which enhanced affinity at the hA(2B) and hA(3) ARs, respectively, when utilized on the pyrazolo-triazolopyrimidine nucleus as we reported in the past. In general, compounds with a free amino group at the 7 position (5, 6), showed good affinity at the rat (r) A(2A) AR (range 18.3-96.5nM), while the introduction of a phenylcarbamoyl moiety at the N7 position (12, 19, 24) slightly increased the affinity at the hA(3) AR (range 311-633nM) with respect to the unsubstituted derivatives. The binding profiles of the synthesized analogues seemed to correlate with the substitutions at the C5 and N7 positions. At the hA(2B) AR, derivative 5, which contained a free amino group at the 7 position, was the most potent (EC(50) 3.42microM) and could represent a starting point for searching new non-xanthine hA(2B) AR antagonists. Molecular models of the rA(2A) and hA(3) ARs were constructed by homology to the recently reported crystallographic structure of the hA(2A) AR. A preliminary receptor-driven structure-activity relationship (SAR) based on the analysis of antagonist docking has been provided.

PMID: 20304654 [PubMed - indexed for MEDLINE]

Receptor- and ligand-based study on novel 2,2'-bithienyl derivatives as non-peptidic AANAT inhibitors.

J Chem Inf Model. 2010 Mar 22;50(3):446-60

Authors: Lepailleur A, Lemaître S, Feng X, Sopkova-de Oliveira Santos J, Delagrange P, Boutin J, Renard P, Bureau R, Rault S

Arylalkylamine N-acetyl transferase (serotonin N-acetyl transferase, AANAT) is a critical enzyme in the light-mediated regulation of melatonin production and circadian rythm. With the objective of discovering new chemical entities with inhibitory potencies against AANAT, a medium-throughput screening campaign was performed on a chemolibrary. We found a class of molecules based on a 2,2'-bithienyl scaffold, and compound 1 emerged as a first hit. Herein, we describe our progress from hit discovery and to optimization of this new class of compounds. To complete the study, computational approaches were carried out: a docking study which provided insights into the plausible binding modes of these new AANAT inhibitors and a three-dimensional quantitative structure-activity relationship study that applied comparative molecular field analysis (CoMFA) methodology. Several CoMFA models were developed (variable alignments and options), and the best predictive one yields good statistical results (q(2) = 0.744, r(2) = 0.891, and s = 0.273). The resulting CoMFA contour maps were used to illustrate the pharmacomodulations relevant to the biological activities in this series of analogs and to design new active inhibitors. This novel series of 2,2'-bithienyl derivatives gives new insights into the design of AANAT inhibitors.

PMID: 20196559 [PubMed - indexed for MEDLINE]

Thermodynamic analysis of protein kinase A Ialpha activation.

Biochemistry (Mosc). 2010 Feb;75(2):233-41

Authors: Rogacheva ON, Popov AV, Savvateeva-Popova EV, Stefanov VE, Shchegolev BF

Thermodynamic analysis of protein kinase A (PKA) Ialpha activation was performed using Quantum 3.3.0 docking software and a Gaussian 03W quantum mechanical computational package. Expected stacking interactions between adenine of 3':5'-AMP and aromatic moieties of amino acids were taken into account by means of MP2/6-31G(d) IPCM (isodensity polarizable continuum model) computations (epsilon = 4.0). It is demonstrated that thermodynamically favorable agonist-induced PKA Ialpha activation is mediated by two processes. First, 3':5'-AMP binding is accompanied by structural changes leading to a thermodynamically favorable regulatory subunit conformation, which is hardly realized in the absence of the ligand (DeltaG degrees (R) = -23.9 +/- 8.2 kJ/mol). Second, 3':5'-AMP affinity to the regulatory subunit conformation observed after agonist-induced PKA Ialpha activation is higher than that to inactive holoenzyme complex (DeltaG degrees (3':5'-AMP) = -28.1 +/- 9.7 kJ/mol). ATP is capable of docking into the 3':5'-AMP-binding site B of the regulatory subunit complexed with the catalytic one, resulting in inhibition of kinase activation. True constants of 3':5'-AMP binding to PKA Ialpha holoenzyme were found to be 60 and 57 microM for the regulatory subunit domains A and B, respectively. These constants, unlike the binding equilibrium constant determined using established experimental techniques and ranging from 15 nM to 2.9 microM, are proved to be direct measures of 3':5'-AMP-PKA Ialpha binding affinity. Their values are in a reasonable agreement with the changes in 3':5'-AMP concentration in the cell (2-55 microM) and account for PKA Ialpha activation in response to adequate stimuli.

PMID: 20367611 [PubMed - indexed for MEDLINE]

AutoDock Vina: improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading.

J Comput Chem. 2010 Jan 30;31(2):455-61

Authors: Trott O, Olson AJ

AutoDock Vina, a new program for molecular docking and virtual screening, is presented. AutoDock Vina achieves an approximately two orders of magnitude speed-up compared with the molecular docking software previously developed in our lab (AutoDock 4), while also significantly improving the accuracy of the binding mode predictions, judging by our tests on the training set used in AutoDock 4 development. Further speed-up is achieved from parallelism, by using multithreading on multicore machines. AutoDock Vina automatically calculates the grid maps and clusters the results in a way transparent to the user.

PMID: 19499576 [PubMed - indexed for MEDLINE]

Design of new secreted phospholipase A2 inhibitors based on docking calculations by modifying the pharmacophore segments of the FPL67047XX inhibitor.

J Comput Aided Mol Des. 2010 Feb;24(2):107-15

Authors: Mouchlis VD, Mavromoustakos TM, Kokotos G

Docking calculations that allow the estimation of the binding energy of small ligands in the GIIA sPLA(2) active site were used in a structure-based design protocol. Four GIIA sPLA(2) inhibitors co-crystallised with the enzyme, were used for examining the enzyme active site and for testing the FlexX in SYBYL 6.8 molecular docking program to reproduce the crystallographic experimental data. The FPL67047XX inhibitor was chosen as a prototype structure for applying free energy perturbation (FEP) studies. Structural modifications of the initial structure of the FPL67047XX inhibitor (IC(50) 0.013 microM) were performed in an effort to optimise the interactions in the GIIA sPLA(2) active site. The structural modifications were based on: (1) the exploration of absolute configuration (i.e. comparison of the binding score of (R)- and (S)-enantiomers); (2) bioisosterism (i.e. replacement of the carboxylate group with the bioisosteric sulphonate and phosphonate groups); (3) insertion of substituents that fit better in the active site. The generated new structures exhibited higher binding energy. Such structures may spark off the interest of medicinal chemists for synthesizing potentially more active GIIA sPLA(2) inhibitors.

PMID: 20130961 [PubMed - indexed for MEDLINE]

Anti-metatype peptides, a molecular tool with high sensitivity and specificity to monitor small ligands.

Anal Biochem. 2009 May 1;388(1):63-70

Authors: Inaba J, Nakamura S, Shimizu K, Asami T, Suzuki Y

To develop a new immunological detection system of gibberellins (GAs), a class of phytohormones, peptides that interact with an antibody against GA4 in a GA4-dependent manner, were screened from phage display random peptide libraries. The biopanning procedure yielded peptides designated as anti-metatype peptides (AM-peps), which showed specific binding to the complex of the antibody and its ligand GA4; that is, the antibody could not be replaced with the other anti-GA4 antibody, and GA4 could not be replaced with GA1, another ligand of the antibody. Together with computational analyses such as analysis of structural propensity of the AM-peps and docking simulation of the AM-peps and the 8/E9-GA4 complex, it was suggested that AM-peps formed a helix in their central region and interacted with a part of the 8/E9-GA4 complex located in close proximity to the GA4 molecule. Based on the property of AM-peps to make a ternary complex with antibody and its ligand, a noncompetitive enzyme-linked immunosorbent assay (ELISA) system corresponding to sandwich ELISA was developed to detect GA4. GA4 as low as 30 pg, which could not be achieved by conventional competitive ELISA, could be detected by the new system, demonstrating the feasibility of this system.

PMID: 19454218 [PubMed - indexed for MEDLINE]

Computational docking of biomolecular complexes with AutoDock.

Cold Spring Harb Protoc. 2009 May;2009(5):pdb.prot5200

Authors: Goodsell DS

PMID: 20147154 [PubMed - indexed for MEDLINE]

[Computer-aided molecular modeling and activity estimation for ligand screening with specific phage clone as the target]

Nan Fang Yi Ke Da Xue Xue Bao. 2007 Aug;27(8):1127-31

Authors: Luo HB, Hu YD, Liu BY, Li S, Fu N

OBJECTIVE: To investigate the interaction between tumor necrosis factor alpha (TNF alpha) mimotopes and TNF alpha-binding peptides screened from random phage display peptide library with TNF alpha mimotopes displayed on phage clone as the target, the computational docking program AutoDock (with confirmation calculations using Discover) was used to predict and analyze the binding modes of LLT-18 (TNF alpha binding peptide, sequence EHMALTYPFRPP) with TNF alpha, after which LCS-7 (TNF alpha mimic phage clone, displayed positive sequence c-RRPAQSG-c) was docked to LLT-18 manually. The binding between LLT-18 and TNF alpha or LCS-7 was stabilized predominantly through electrostatic interaction and H-bond formation. The Arg residues in TNF alpha or LCS-7 were important for their interaction with LLT-18. For LLT-18, the key amino acid residues were Glu1, His2, Met3 and Tyr7. These results suggest the feasibility of screening ligand to single epitope with specific phage clone as the target, and of predicting the interaction between small peptides by computer-aided molecular modeling.

PMID: 17715007 [PubMed - indexed for MEDLINE]

Concentration dependent effects of commonly used pesticides on activation versus inhibition of the quince (Cydonia Oblonga) polyphenol oxidase.

Food Chem Toxicol. 2010 Mar;48(3):957-63

Authors: Fattouch S, Raboudi-Fattouch F, Ponce JV, Forment JV, Lukovic D, Marzouki N, Vidal DR

Polyphenol oxidase (PPO) catalyzes the oxidation of o-diphenols to their respective quinones which undergo autopolymerization and form dark pigments. The interaction of PPO with various substrates and effectors remains the focus of intensive investigations due to the enzyme's key role in pigments biosynthesis including animal melanogenesis and fruit/fungi enzymatic browning. In this study, the effect of a range of commonly used pesticides on the enzyme activity has been evaluated using the purified quince (Cydonia oblonga Miller) PPO. The biochemical analysis showed that, in the presence of high pesticide concentrations, the enzyme was competitively inhibited, particularly with benomyl, carbaryl, deltamethrine and parathion methyl for which inhibition constants (K(i)) were 8.3, 5.7, 12 and 4 microM, respectively. At lower pesticide concentrations (2-10 microM), however, the catecholase activity was significantly activated (p<0.01), suggesting a homotropic behavior of these chemical compounds. Furthermore, the use of in silico structure-based analyses, known as computational docking, highlighted the nature of the PPO-pesticides interactions and confirmed the in vitro observations. Catechol substrate and parathion methyl inhibitor showed lower total energy scores of -120.06 and -117.4 3 kcal mol(-1), indicating that these ligands had higher PPO-binding affinities. The obtained data bring to light new pesticide functional features of great interest in the medicinal, agro-chemical and environmental circles.

PMID: 20060877 [PubMed - indexed for MEDLINE]

Mapping of ligand-binding cavities in proteins.

Proteins. 2010 May 1;78(6):1408-22

Authors: Andersson CD, Chen BY, Linusson A

The complex interactions between proteins and small organic molecules (ligands) are intensively studied because they play key roles in biological processes and drug activities. Here, we present a novel approach to characterize and map the ligand-binding cavities of proteins without direct geometric comparison of structures, based on Principal Component Analysis of cavity properties (related mainly to size, polarity, and charge). This approach can provide valuable information on the similarities and dissimilarities, of binding cavities due to mutations, between-species differences and flexibility upon ligand-binding. The presented results show that information on ligand-binding cavity variations can complement information on protein similarity obtained from sequence comparisons. The predictive aspect of the method is exemplified by successful predictions of serine proteases that were not included in the model construction. The presented strategy to compare ligand-binding cavities of related and unrelated proteins has many potential applications within protein and medicinal chemistry, for example in the characterization and mapping of "orphan structures", selection of protein structures for docking studies in structure-based design, and identification of proteins for selectivity screens in drug design programs.

PMID: 20034113 [PubMed - indexed for MEDLINE]