Showing papers in "Chemical Biology & Drug Design in 2010"
TL;DR: Detailed all‐atom molecular dynamics simulations are used to study a series of stapled α‐helical peptides and find significant variation in local structural flexibility of the peptides with the position of the linker, which appears to be more closely related to the observed differences in activity than the absolute α‐ Helical stability.
Abstract: Reactivation of the p53 cell apoptosis pathway through inhibition of the p53-hDM2 interaction is a viable approach to suppress tumor growth in many human cancers and stabilization of the helical structure of synthetic p53 analogs via a hydrocarbon cross-link (staple) has been found to lead to increased potency and inhibition of protein-protein binding (J. Am. Chem. Soc. 129: 5298). However, details of the structure and dynamic stability of the stapled peptides are not well understood. Here, we use extensive all-atom molecular dynamics simulations to study a series of stapled alpha-helical peptides over a range of temperatures in solution. The peptides are found to exhibit substantial variations in predicted alpha-helical propensities that are in good agreement with the experimental observations. In addition, we find significant variation in local structural flexibility of the peptides with the position of the linker, which appears to be more closely related to the observed differences in activity than the absolute alpha-helical stability. These simulations provide new insights into the design of alpha-helical stapled peptides and the development of potent inhibitors of alpha-helical protein-protein interfaces.
376 citations
TL;DR: The phenolic acids investigated here showed interesting hCA I and hCA II inhibitory effects and might be used as leads for generating enzyme inhibitors possibly targeting other CA isoforms which have not been yet assayed for their interactions with such agents.
Abstract: The inhibitory effects of some phenolic acids on the cytosolic human carbonic anhydrase (hCA, EC 4.2.1.1) isozymes hCA I and hCA II were investigated. Ellagic acid, gallic acid, ferulic acid, caffeic acid, quercetin, p-coumaric acid, p-hydroxybenzoic acid, and syringic acid showed K(I) values in the range of 99-1061 microm for hCA I and of 105-758 microm against hCA II, respectively. Quercetin (for hCA I), p-coumaric acid (for hCA II), and gallic acid (for hCA II) exhibited competitive inhibitory effects with 4-nitrophenyl acetate as substrate. All of the other phenolic acids were found as non-competitive inhibitors with 4-nitrophenylacetate as substrate for hCA I and hCA II. The phenolic acids investigated here showed thus interesting hCA I and hCA II inhibitory effects and might be used as leads for generating enzyme inhibitors possibly targeting other CA isoforms which have not been yet assayed for their interactions with such agents.
139 citations
TL;DR: This study reviews important progress in drug metabolism and common in silico techniques adopted to predict drug regioselectivity, stereoselectivities, reactive metabolites, induction, inhibition and mechanism‐based inactivation, as well as their implementation in hit‐to‐lead drug discovery.
Abstract: Significant progress has been made in structure-based drug design by pharmaceutical companies at different stages of drug discovery such as identifying new hits, enhancing molecule binding affinity in hit-to-lead, and reducing toxicities in lead optimization. Drug metabolism is a major consideration for modifying drug clearance and also a primary source for drug metabolite-induced toxicity. With major cytochrome P450 structures identified and characterized recently, structure-based drug metabolism prediction becomes increasingly attractive. In silico methods based on molecular and quantum mechanics such as docking, molecular dynamics and ab initio chemical reactivity calculations bring us closer to understand drug metabolism and predict drug–drug interactions. In this study, we review important progress in drug metabolism and common in silico techniques adopted to predict drug regioselectivity, stereoselectivity, reactive metabolites, induction, inhibition and mechanism-based inactivation, as well as their implementation in hit-to-lead drug discovery.
128 citations
TL;DR: This work maps the surfaces of the β1 (β1AR) and β2 (β2AR) adrenergic receptor structures to detect a series of five potentially druggable allosteric sites and uses the FTMAP algorithm to identify ‘hot spots’ with affinity for a variety of organic probe molecules corresponding to drug fragments.
Abstract: To address the problem of specificity in G-protein coupled receptor (GPCR) drug discovery, there has been tremendous recent interest in allosteric drugs that bind at sites topographically distinct from the orthosteric site. Unfortunately, structure-based drug design of allosteric GPCR ligands has been frustrated by the paucity of structural data for allosteric binding sites, making a strong case for predictive computational methods. In this work, we map the surfaces of the beta1 (beta1AR) and beta2 (beta2AR) adrenergic receptor structures to detect a series of five potentially druggable allosteric sites. We employ the FTMAP algorithm to identify 'hot spots' with affinity for a variety of organic probe molecules corresponding to drug fragments. Our work is distinguished by an ensemble-based approach, whereby we map diverse receptor conformations taken from molecular dynamics (MD) simulations totaling approximately 0.5 micros. Our results reveal distinct pockets formed at both solvent-exposed and lipid-exposed cavities, which we interpret in light of experimental data and which may constitute novel targets for GPCR drug discovery. This mapping data can now serve to drive a combination of fragment-based and virtual screening approaches for the discovery of small molecules that bind at these sites and which may offer highly selective therapies.
106 citations
TL;DR: The solid phase synthesis, characterization, microbiological and toxicological evaluation of a library of ultrashort cationic antimicrobial lipopeptides based on the previously described tetrapeptide amides conjugated with saturated fatty acids which have inherent antimicrobial activity are described.
Abstract: The increasing emergence of multidrug-resistant micro-organisms presents one of the greatest challenges in the clinical management of infectious diseases. Therefore, novel antimicrobial agents are urgently required to address this issue. In this report, we describe the solid phase synthesis, characterization, microbiological and toxicological evaluation of a library of ultrashort cationic antimicrobial lipopeptides based on the previously described tetrapeptide amide H-Orn-Orn-Trp-Trp-NH2 conjugated with saturated fatty acids which have inherent antimicrobial activity. The microbiological activity of these ultrashort cationic lipopeptides, which exhibit excellent, broad-spectrum antimicrobial activity against a number of clinically important pathogenic bacteria and fungi, including multidrug resistant micro-organisms in both planktonic and sessile (biofilm) cultures is reported.
96 citations
TL;DR: Tools like alternative substrates, testing the enzyme reaction in the reverse direction and monitoring inhibition time dependence can be applied to enable distinction between ‘badly behaving’ active site binders and true exosite inhibitors.
Abstract: Classical enzymology has been used for generations to understand the interactions of inhibitors with their enzyme targets. Enzymology tools enabled prediction of the biological impact of inhibitors as well as the development of novel, more potent, ones. Experiments designed to examine the competition between the tested inhibitor and the enzyme substrate(s) are the tool of choice to identify inhibitors that bind in the active site. Competition between an inhibitor and a substrate is considered a strong evidence for binding of the inhibitor in the active site, while the lack of competition suggests binding to an alternative site. Nevertheless, exceptions to this notion do exist. Active site-binding inhibitors can display non-competitive inhibition patterns. This unusual behavior has been observed with enzymes utilizing an exosite for substrate binding, isomechanism enzymes, enzymes with multiple substrates and/or products and two-step binding inhibitors. In many of these cases, the mechanisms underlying the lack of competition between the substrate and the inhibitor are well understood. Tools like alternative substrates, testing the enzyme reaction in the reverse direction and monitoring inhibition time dependence can be applied to enable distinction between 'badly behaving' active site binders and true exosite inhibitors.
80 citations
TL;DR: Novel sixteen chalcones and thirteen 1,3,5‐triphenyl‐2‐pyrazolines were synthesized and characterized andHydrophilic/lipophilic balance of the compounds plays a major role in their antibacterial activity.
Abstract: Novel sixteen chalcones and thirteen 1,3,5-triphenyl-2-pyrazolines were synthesized and characterized using FT-IR, HR-Mass, NMR (¹H-NMR, ¹³C-NMR, 135 DEPT, ¹H-¹H CoSY and ¹H and ¹³C CoSY) and XRD. These compounds were evaluated for their antibacterial activity against six micro-organisms, namely Bacillus subtilis NCIM 2718, Staphylococcus aureus NCIM 5021, Salmonella typhi NCIM 2501, Enterobacter aerogenes NCIM 5139, Pseudomonas aeruginosa NCIM 5029, and Proteus vulgaris NCIM 2813 by twofold dilution method using resazurin as the indicator dye. In the case of chalcones, compounds with hydroxyl and bromo substitutions in the B-ring favor activity and benzyloxy substitution irrespective of its position in the A-ring. In the case of 1,3,5-triphenyl-2-pyrazolines, chloro substitution in the A-ring favors activity. Hydrophilic/lipophilic balance of the compounds plays a major role in their antibacterial activity.
79 citations
TL;DR: The utility of alkyne‐containing isoprenoid analogs for chemical proteomics experiments is investigated by showing that these compounds readily penetrate mammalian cells in culture and become incorporated into proteins that are normally prenylated.
Abstract: Protein prenyltransferases catalyze the attachment of C15 (farnesyl) and C20 (geranylgeranyl) groups to proteins at specific sequences localized at or near the C-termini of specific proteins. Determination of the specific protein prenyltransferase substrates affected by the inhibition of these enzymes is critical for enhancing knowledge of the mechanism of such potential drugs. Here, we investigate the utility of alkyne-containing isoprenoid analogs for chemical proteomics experiments by showing that these compounds readily penetrate mammalian cells in culture and become incorporated into proteins that are normally prenylated. Derivatization via Cu(I) catalyzed click reaction with a fluorescent azide reagent allows the proteins to be visualized and their relative levels to be analyzed. Simultaneous treatment of cells with these probes and inhibitors of prenylation reveals decreases in the levels of some but not all of the labeled proteins. Two-dimensional electrophoretic separation of these labeled proteins followed by mass spectrometric analysis allowed several labeled proteins to be unambiguously identified. Docking experiments and density functional theory calculations suggest that the substrate specificity of protein farnesyl transferase may vary depending on whether azide- or alkyne-based isoprenoid analogs is employed. These results demonstrate the utility of alkyne-containing analogs for chemical proteomic applications.
79 citations
TL;DR: Evidence is provided that novel synthetic methods can be applied to develop small molecules with antiretroviral activity that target host factors important for HIV‐1 replication.
Abstract: Targeting host factors is a complementary strategy for the development of new antiviral drugs. We screened a library of isoxazolidine and isoxazole sulfonamides and found four compounds that inhibited HIV-1 infection in human CD4+ lymphocytic T cells with no toxicity at IC90 concentrations. Structure-activity relationship showed that benzyl sulfonamides and a halo-substituted aromatic ring on the heterocycle scaffold were critical for antiretroviral activity. The size and position of the incorporated halogen had a marked effect on the antiretroviral activity. The sulfonamide derivatives had no significant effect on HIV-1 entry, reverse transcription and integration but impaired a step necessary for activation of viral gene expression. This step was Tat-independent, strongly suggesting that the target is a cell factor. A virus partially resistant to the least potent compounds could be selected but could not be propagated in the long term, consistent with the possibility that HIV-1 may be less likely to develop resistance against drugs targeting some host factors. Here, we provide evidence that novel synthetic methods can be applied to develop small molecules with antiretroviral activity that target host factors important for HIV-1 replication.
76 citations
TL;DR: This study is the first fragment‐based crystallographic screen against HIV PR, and the first time that fragments were screened against an inhibitor‐bound drug target to search for compounds that both bind to novel sites and stabilize the inhibited conformation of the target.
Abstract: We have employed a fragment-based screen against wild-type (NL4-3) HIV protease (PR) using the Active Sight fragment library and X-ray crystallography. The experiments reveal two new binding sites for small molecules. PR was co-crystallized with fragments, or crystals were soaked in fragment solutions, using five crystal forms, and 378 data sets were collected to 2.3-1.3 A resolution. Fragment binding induces a distinct conformation and specific crystal form of TL-3 inhibited PR during co-crystallization. One fragment, 2-methylcyclohexanol, binds in the 'exo site' adjacent to the Gly(16)Gly(17)Gln(18)loop where the amide of Gly(17)is a specific hydrogen bond donor, and hydrophobic contacts occur with the side chains of Lys(14)and Leu(63). Another fragment, indole-6-carboxylic acid, binds on the 'outside/top of the flap' via hydrophobic contacts with Trp(42), Pro(44), Met(46), and Lys(55), a hydrogen bond with Val(56), and a salt-bridge with Arg(57). 2-acetyl-benzothiophene also binds at this site. This study is the first fragment-based crystallographic screen against HIV PR, and the first time that fragments were screened against an inhibitor-bound drug target to search for compounds that both bind to novel sites and stabilize the inhibited conformation of the target.
65 citations
TL;DR: Results from in vitro biological assays indicated that chloro‐substituted 1‐(6‐methoxy‐2H‐chromen‐3‐yl)‐3-phenylpropen‐1‐ones exhibited excellent activity against Leishmania major at non‐cytotoxic concentrations.
Abstract: Two types of regioisomeric chromene-based chalcones namely, 1-(6-methoxy-2H-chromen-3-yl)-3-phenylpropen-1-ones and 3-(6-methoxy-2H-chromen-3-yl)-1-phenylpropen-1-ones were prepared and investigated for their antileishmanial activity against promastigotes form of Leishmania major. The obtained results from in vitro biological assays indicated that chloro-substituted 1-(6-methoxy-2H-chromen-3-yl)-3-phenylpropen-1-ones exhibited excellent activity against Leishmania major at non-cytotoxic concentrations.
TL;DR: A series of cycloadducts‐‐pyrazoles via 1,3‐dipolar cycloaddition reactions of generated nitrilimines with N‐(4‐chloro‐2‐fluorophenyl)maleimide were described, showing significant fungicidal activities against Corynespora cassiicola.
Abstract: A series of cycloadducts--pyrazoles via 1,3-dipolar cycloaddition reactions of generated nitrilimines with N-(4-chloro-2-fluorophenyl)maleimide were described. The novel compounds synthesized were characterized by (1)H NMR, MS, and elemental analysis. The fungicidal tests showed that most of the title compounds exhibit significant fungicidal activities against Corynespora cassiicola.
TL;DR: 1,4‐Thienodiazepine‐2,5‐diones have been synthesized via the Ugi‐Deprotection‐Cyclization (UDC) approach starting from Gewald 2‐aminothiophenes in a convergent and versatile manner and some compounds exhibited promising antagonistic activity.
Abstract: 1,4-Thienodiazepine-2,5-diones have been synthesized via the Ugi-Deprotection-Cyclization (UDC) approach starting from Gewald 2-aminothiophenes in a convergent and versatile manner. The resulting scaffold is unprecedented, cyclic, and peptidomimetic with four points of diversity introduced from readily available starting materials. In addition to eighteen synthesized and characterized compounds, a virtual compound library was generated and evaluated for chemical space distribution and drug-like properties. A small focused compound library of 1,4-thienodiazepine-2,5-diones has been screened for the activity against p53-Mdm2 interaction. Biological evaluations demonstrated that some compounds exhibited promising antagonistic activity.
TL;DR: A prototype antimicrobial peptide capable of achieving high activity exclusively at low environmental pH to target bacterial species like Streptococcus mutans that produce acid and thrive under the low pH conditions detrimental for tooth integrity is developed.
Abstract: Dental caries is a microbial biofilm infection in which the metabolic activities of plaque bacteria result in a dramatic pH decrease and shift the demineralization/remineralization equilibrium on the tooth surface towards demineralization. In addition to causing a net loss in tooth minerals, creation of an acidic environment favors growth of acid-enduring and acid-generating species, which causes further reduction in the plaque pH. In this study, we developed a prototype antimicrobial peptide capable of achieving high activity exclusively at low environmental pH to target bacterial species like Streptococcus mutans that produce acid and thrive under the low pH conditions detrimental for tooth integrity. The features of clavanin A, a naturally occurring peptide rich in histidine and phenylalanine residues with pH-dependent antimicrobial activity, served as a design basis for these prototype ‘acid-activated peptides’ (AAPs). Employing the major cariogenic species S. mutans as a model system, the two AAPs characterized in this study exhibited a striking pH-dependent antimicrobial activity, which correlated well with the calculated charge distribution. This type of peptide represents a potential new way to combat dental caries.
TL;DR: A compendium of chemical modulators of riboflavin biosynthesis and regulatory networks is listed and demonstrates the promise of riboswitch regulatory mechanisms as potential therapeutic targets for novel antibiotic drug discovery.
Abstract: Riboflavin (vitamin B2) is the direct precursor of redox enzyme cofactors flavin mononucleotide (FMN) and flavin adenine dinucleotide (FAD), which are essential for multiple cell physiology. The riboflavin biosynthetic pathway is regarded as a rich resource for therapeutic targets for broad spectrum antibiotics. Enzymatic pathways, regulatory factors of the riboflavin biosynthesis, and relevant drug discovery are summarized in this review. The novel riboswitch regulatory mechanism of riboflavin metabolism is also described. A compendium of chemical modulators of riboflavin biosynthesis and regulatory networks is listed and such demonstrates the promise of riboflavin biosynthesis and regulatory mechanisms as potential therapeutic targets for novel antibiotic drug discovery.
TL;DR: Detailed models are developed for modeling and predicting both MEK inhibitory activity and oral bioavailability of novel isothiazole‐4‐carboxamidines and serve as a first guideline for the design of novel and potent MEK inhibitors with desired ADME properties.
Abstract: In this study, quantitative structure-activity/property models are developed for modeling and predicting both MEK inhibitory activity and oral bioavailability of novel isothiazole-4-carboxamidines. The models developed are thoroughly discussed to identify the key components that influence the inhibitory activity and oral bioavailability of the selected compounds. These selected descriptors serve as a first guideline for the design of novel and potent MEK inhibitors with desired ADME properties.
TL;DR: The thermodynamic consequences of filling a binding cavity with functionalities of increasing van der Waals radii that improve the geometric fit without participating in hydrogen bonding or other specific interactions are evaluated.
Abstract: Binding affinity optimization is critical during drug development. Here, we evaluate the thermodynamic consequences of filling a binding cavity with functionalities of increasing van der Waals radii (–H, –F, –Cl, and CH3) that improve the geometric fit without participating in hydrogen bonding or other specific interactions. We observe a binding affinity increase of two orders of magnitude. There appears to be three phases in the process. The first phase is associated with the formation of stable van der Waals interactions. This phase is characterized by a gain in binding enthalpy and a loss in binding entropy, attributed to a loss of conformational degrees of freedom. For the specific case presented in this article, the enthalpy gain amounts to −1.5 kcal/mol while the entropic losses amount to +0.9 kcal/mol resulting in a net 3.5-fold affinity gain. The second phase is characterized by simultaneous enthalpic and entropic gains. This phase improves the binding affinity 25-fold. The third phase represents the collapse of the trend and is triggered by the introduction of chemical functionalities larger than the binding cavity itself [CH(CH3)2]. It is characterized by large enthalpy and affinity losses. The thermodynamic signatures associated with each phase provide guidelines for lead optimization.
TL;DR: The pyranoxanthone 5 was verified as a new scaffold that may guide the design of small molecules with better affinity profile for Bcl‐xL and may block the binding of anti‐apoptotic BclxL to pro‐APoptotic Bad and Bim.
Abstract: Naturally occurring xanthones have been documented as having antitumor properties, with some of them presently undergoing clinical trials. In an attempt to improve the biological activities of dihydroxyxanthones, prenylation and other molecular modifications were performed. All the compounds reduced viable cell number in a leukemia cell line K-562, with the fused xanthone 3,4-dihydro-12-hydroxy-2,2-dimethyl-2H,6H-pyrano[3,2-b]xanthen-6-one (5) being the most potent. The pyranoxanthone 5 was particularly effective in additional leukemia cell lines (HL-60 and BV-173). Furthermore, the pyranoxanthone 5 decreased cellular proliferation and induced an S-phase cell cycle arrest. In vitro, the pyranoxanthone 5 increased the percentage of apoptotic cells which was confirmed by an appropriate response at the protein level (e.g., PARP cleavage). Using a computer screening strategy based on the structure of several anti- and pro-apoptotic proteins, it was verified that the pyranoxanthone 5 may block the binding of anti-apoptotic Bcl-xL to pro-apoptotic Bad and Bim. The structure-based screening revealed the pyranoxanthone 5 as a new scaffold that may guide the design of small molecules with better affinity profile for Bcl-xL.
TL;DR: Effect on electron transport and respiration was demonstrated by butyrate plumbagin inhibiting oxygen consumption in M. smegmatis and M. tuberculosis H37Rv.
Abstract: Electron transport and respiratory pathways are active in both latent and rapidly growing mycobacteria and remain conserved in all mycobacterial species. In mycobacteria, menaquinone is the sole electron carrier responsible for electron transport. Menaquinone biosynthesis pathway is found to be essential for the growth of mycobacteria. Structural analogs of the substrate or product of this
pathway are found to be inhibitory for the growth of Mycobacterium,smegmatis and M. tuberculosis. Several plumbagin [5-hydroxy-2-methyl-1, 4-naphthaquinone] derivatives have been analyzed for their inhibitory effects of which butyrate plumbagin was found to be most effective on M. smegmatis mc2155, whereas crotonate plumbagin showed greater activity on M. tuberculosis H37Rv. Effect on electron transport and respiration was demonstrated by butyrate plumbagin inhibiting oxygen consumption in M. smegmatis. Structural modifications of these molecules can further be improved upon to generate new molecules against mycobacteria.
TL;DR: A novel purification technique is reported for paraoxonase 1, which may be useful for other enzymes such as those related to acetylcholinesterase, and demonstrates the off‐target activity of sulfonamides.
Abstract: Paraoxonase 1 (PON1), a high-density lipoprotein (HDL)-associated esterase, is known to mediate antioxidant and antiatherogenic properties. Purification of PON1 has been challenging for a long time. Here, we report a novel purification technique for this enzyme, which allowed us to obtain human serum paraoxonase 1 (hPON1) using straightforward chromatographic methods, such as Diethylaminoethyl-Sephadex anion exchange chromatography and Sepharose 4B–4-phenylazo-2-naphthaleneamine hydrophobic interaction chromatography. We purified the enzyme 302-fold with a final specific activity of 4775 U/mg and a yield of 32%. Furthermore, we examined the in vitro effects of some sulfonamide derivatives, such as sulfacetamide, homosulfanilamide (mafenide), sulfosalazine, furosemide, acetazolamide, and 1,3,4-thiadiazole-2-sulfonamide on the enzyme activity to better understand the inhibitory properties of the molecules. The six sulfonamides dose-dependently decreased the activity of hPON1 with inhibition constants in the millimolar – micromolar range. This study provides an efficient method, which may be useful for other enzymes such as those related to acetylcholinesterase. It also demonstrates the off-target activity of sulfonamides.
TL;DR: The results of quantitative structure–activity relationship (QSAR) studies of tyrosinase inhibitory activity are shown, by using the bond‐based quadratic indices as molecular descriptors and linear discriminant analysis (LDA) to generate discriminant functions to predict the anti‐tyrosinases activity.
Abstract: In this report, we show the results of quantitative structure–activity relationship (QSAR) studies of tyrosinase inhibitory activity, by using the bond-based quadratic indices as molecular descriptors (MDs) and linear discriminant analysis (LDA), to generate discriminant functions to predict the anti-tyrosinase activity. The best two models [Eqs (6) and (12)] out of the total 12 QSAR models developed here show accuracies of 93.51% and 91.21%, as well as high Matthews correlation coefficients (C) of 0.86 and 0.82, respectively, in the training set. The validation external series depicts values of 90.00% and 89.44% for these best two equations (6) and (12), respectively. Afterwards, a second external prediction data are used to perform a virtual screening of compounds reported in the literature as active (tyrosinase inhibitors). In a final step, a series of lignans is analysed using the in silico-developed models, and in vitro corroboration of the activity is carried out. An issue of great importance to remark here is that all compounds present greater inhibition values than Kojic Acid (standard tyrosinase inhibitor: IC50 = 16.67 μm). The current obtained results could be used as a framework to increase the speed, in the biosilico discovery of leads for the treatment of skin disorders.
TL;DR: The results show that there exist different interaction modes between RT and ligands and different specific interactions with some residues, and the higher binding affinity of the most potent inhibitor in the series of molecules under study is favoured by electrostatic interactions and solvation contribution.
Abstract: Molecular dynamics (MD) simulations in water environment were carried out on the HIV-1 reverse transcriptase (RT), and its complexes with one representative of each of three series of inhibitors: 2-amino-6-arylsulphonylbenzonitriles and their thio and sulphinyl congeners. Molecular Mechanics Generalized Born Surface Area (MM-GBSA) was used to calculate the binding free energy based on the obtained MD trajectories. Calculated energies are correlated to activity. A comparison of interaction modes, binding free energy, contributions of the residues to the binding free energy and H-bonds was carried out with the average structures. The results show that there exist different interaction modes between RT and ligands and different specific interactions with some residues. The higher binding affinity of the most potent inhibitor in the series of molecules under study is favoured by electrostatic interactions and solvation contribution.
TL;DR: Successful targeting of tumor necrosis factor alpha converting enzyme may result in multifunctional therapy and this approach may become a novel therapy for treatment of rheumatoid arthritis and other inflammatory disorders.
Abstract: Tumor necrosis factor alpha is one of the most common pro-inflammatory cytokines responsible for various inflammatory disorders It plays an important role in the origin and progression of rheumatoid arthritis and also in other autoimmune disease conditions Some anti-tumor necrosis factor alpha antibodies like Enbrel®, Humira® and Remicade® have been successfully used in these disease conditions as antagonists of tumor necrosis factor alpha Inhibition of generation of active form of tumor necrosis factor alpha is a promising therapy for various inflammatory disorders Therefore, the inhibition of an enzyme (tumor necrosis factor alpha converting enzyme), which is responsible for processing inactive form of tumor necrosis factor alpha into its active soluble form, is an encouraging target Many tumor necrosis factor alpha converting enzyme inhibitors have been the candidates of clinical trials but none of them have reached in to the market because of their broad spectrum inhibitory activity for other matrix metalloproteases Selectivity of tumor necrosis factor alpha converting enzyme inhibition over matrix metalloproteases is of utmost importance If selectivity is achieved successfully, side-effects can be over-ruled and this approach may become a novel therapy for treatment of rheumatoid arthritis and other inflammatory disorders This cytokine not only plays a pivotal role in inflammatory conditions but also in some cancerous conditions Thus, successful targeting of tumor necrosis factor alpha converting enzyme may result in multifunctional therapy
TL;DR: In this article, the authors used density functional theory (DFT) and ab initio calculation results for the proton transfer reaction in Kirby's enzyme models 1-6 reveal that the reaction rate is largely dependent on the existence of a hydrogen bonding net in the reactants and the corresponding transition states.
Abstract: Density Functional Theory (DFT) and ab initio calculation results for the proton transfer reaction in Kirby's enzyme models 1-6 reveal that the reaction rate is largely dependent on the existence of a hydrogen bonding net in the reactants and the corresponding transition states. Further, the distance between the two reacting centers and the angle of the hydrogen bonding formed along the reaction path has profound effects on the rate. Hence, the study on the systems reported herein could provide a good basis for designing antimalarial (atovaquone) pro-drug systems that can be used to release the parent drug in a controlled manner. For example, based on the calculated log EM, the cleavage process for pro-drug 1Pro may be predicted to be about 10¹¹ times faster than that for a pro-drug 4Pro and about 10⁴ times faster than pro-drug 2Pro: rate (1Pro) > rate (2Pro > rate (4Pro). Thus, the rate by which the pro-drug releases the antimalarial drug can be determined according to the nature of the linker (Kirby's enzyme model 1-6).
TL;DR: The observed BMS‐509744 binding mode allows rationalization of structure–activity relationships reported for this inhibitor class and facilitates further structure‐based drug design, and sequence‐based analysis of this binding mode provides guidance for the rational design of inhibitor selectivity.
Abstract: IL-2-inducible T cell kinase plays an essential role in T cell receptor signaling and is considered a drug target for the treatment of Th2-mediated inflammatory diseases. By applying high-throughput protein engineering and crystallization, we have determined the X-ray crystal structures of IL-2-inducible T cell kinase in complex with its selective inhibitor BMS-509744 and the broad-spectrum kinase inhibitors sunitinib and RO5191614. Sunitinib uniquely stabilizes IL-2-inducible T cell kinase in the helix C-in conformation by inducing side chain conformational changes in the ATP-binding site. This preference of sunitinib to bind to an active kinase conformation is reflective of its broad-spectrum kinase activity. BMS-509744 uniquely stabilizes the activation loop in a substrate-blocking inactive conformation, indicating that structural changes described for Src family kinases are also involved in the regulation of IL-2-inducible T cell kinase activity. The observed BMS-509744 binding mode allows rationalization of structure–activity relationships reported for this inhibitor class and facilitates further structure-based drug design. Sequence-based analysis of this binding mode provides guidance for the rational design of inhibitor selectivity.
TL;DR: The results revealed that introduction of electron‐donating groups at 2nd position decreased the antioxidant activities of 8‐hydroxyquinoline derivatives, and compound 4, the structure of which is similar to melatonin, exhibited superior antioxidant activities in scavenging DPPH freeradical, ˙O2 free radical, and anti‐LPO activities.
Abstract: Novel 2-vinyl-8-hydroxyquinoline derivatives as potential antioxidants and regulators of H2O2-induced oxidative stress in rat bone marrow mesenchymal stem cells (MSCs) are first reported. The antiradical properties and the reducing power of these compounds were assessed using 2, 2-diphenyl-1-picrylhydrazyl (DPPH) and auto-oxidation of pyrogallol method, respectively. The activity against lipid peroxidation was determined using ammonium thiocyanate method. The results revealed that introduction of electron-donating groups at 2nd position decreased the antioxidant activities of 8-hydroxyquinoline derivatives. In addition, compound 4, the structure of which is similar to melatonin, exhibited superior antioxidant activities in scavenging DPPH free radical, ˙O2 free radical, and anti-LPO activities. Except for compounds 7, 12, and 15, the other compounds exhibited a stimulatory effect on MSCs growth. Using hydrogen peroxide (H2O2), we also investigated the protective efficacy of 2-vinyl-8-hydroxyquinoline derivatives against oxidative stress-induced cell death of MSCs. Cell viability assayed by MTT method indicated that exposure of MSCs cultures to hydrogen peroxide resulted in a concentration-dependent decrease in cell viability, and compounds 4 and 5 at given concentration (2.62 × 10−3 m) could protect MSCs against H2O2-induced oxidative stress in bone mesenchymal stem cell (BMSCs).
TL;DR: A small library of 50 analogues of 4‐(arylamino)coumarins with various aromatic amines at the C4‐ position of the coumarin scaffold is synthesized, finding compound 9 was found to be most potent with a minimum inhibitory concentration >6.25 μg/mL for 100% inhibition.
Abstract: The resurgence of tuberculosis and the emergence of multidrug-resistant strains of Mycobacteria necessitate the search for new classes of antimycobacterial agents. We have synthesized a small library of 50 analogues of 4-(arylamino)coumarins with various aromatic amines at the C4- position of the coumarin scaffold. The compounds were evaluated for antimycobacterial activity against Mycobacterium tuberculosis H37Rv with rifampicin as the standard. Of the molecules synthesized, compound 9 was found to be most potent with a minimum inhibitory concentration >6.25 μg/mL for 100% inhibition. In an effort to develop new and more effective molecules in this series, the relationship between structure and activity was investigated by comparative molecular field analysis. Various models were generated using comparative molecular field analysis alone and comparative molecular field analysis plus a hydropathy field (HINT). In all, eight models were generated with atom-fit and field-fit alignment strategies. The comparative molecular field analysis models (Models 3a and 4a) based on field-fit alignment were the best with statistically good correlation coefficients (r2) and cross-validated q2. The values of r2pred for the validation set were 0.469 and 0.516. Based on the comparative molecular field analysis contours, some insights into the structure–activity relationship of the compounds could be gained.
TL;DR: The goal of this study was to identify some pair‐wise receptor–ligand atomic contacts that confer selective PERK inhibition and to understand these structure–activity relationships may accelerate rational PERK inhibitor design.
Abstract: The unfolded protein response (UPR) is a coordinated program that promotes cell survival under conditions of endoplasmic reticulum stress and is required in tumor progression as well. To date, no specific small molecule inhibitor targeting this pathway has been identified. Pancreatic endoplasmic reticulum kinase (PERK), one of the UPR transducers, is an eIF2α kinase. Compromising PERK function inhibits tumor growth in mice, suggesting that PERK may be a cancer drug target, but identifying a specific inhibitor of any kinase is challenging. The goal of this study was to identify some pair-wise receptor-ligand atomic contacts that confer selective PERK inhibition. Compounds selectively inhibiting PERK-mediated phosphorylation in vitro were identified using an initial virtual library screen, followed by structure-activity hypothesis testing. The most potent PERK selective inhibitors utilize three specific kinase active site contacts that, when absent from chemically similar compounds, abrogates the inhibition: (i) a strong van der Waals contact with PERK residue Met7, (ii) interactions with the N-terminal portion of the activation loop, and (iii) groups providing electrostatic complementarity to Asp144. Interestingly, the activation loop contact is required for PERK selectivity to emerge. Understanding these structure-activity relationships may accelerate rational PERK inhibitor design.
TL;DR: The replacement of imidazole by other azoles led to the discovery of novel 1H‐1,2,4‐triazole‐ and1H‐tetrazole‐based inhibitors equipotent to a leadImidazoles‐based inhibitor, which proved to be detrimental to the inhibition of HO, with a few exceptions.
Abstract: A series of 1-azolyl-4-phenyl-2-butanones was designed and synthesized for the inhibition of heme oxygenases (heme oxygenase-1 and heme oxygenase-2). The replacement of imidazole by other azoles led to the discovery of novel 1H-1,2,4-triazole- and 1H-tetrazole-based inhibitors equipotent to a lead imidazole-based inhibitor. The inhibitors featuring 2H-tetrazole or 1H-1,2,3-triazole as the pharmacophore were less potent. Monosubstitution at position 2 or 4(5), or identical disubstitution at positions 4 and 5 of imidazole by a variety of electron-withdrawing or electron-donating, small or bulky groups, as well as the replacement of the traditional imidazole pharmacophore by an array of 3- or 5-substituted triazoles, identically 3,5-disubstituted triazoles, 5-substituted-1H- and 5-substituted-2H-tetrazoles proved to be detrimental to the inhibition of HO, with a few exceptions. The azole-dioxolanes and the azole-alcohols derived from the active azole-ketones were synthesized also, but these inhibitors were less active than the corresponding imidazole-based analogs. The first reported X-ray crystal structure of human heme oxygenase-1 in complex with a 1,2,4-triazole-based inhibitor, namely 4-phenyl-1-(1H-1,2,4-triazol-1-yl)-2-butanone, was also determined. The inhibitor binds to the human heme oxygenase-1 distal pocket through the coordination of heme iron by the N 4 in the triazole moiety, whereas the phenyl group is stabilized by hydrophobic interactions from residues within the binding pocket.
TL;DR: A series of potent bis‐azaindole inhibitors of IGF1‐R have been synthesized using rational drug design and SAR based on a in silico binding mode hypothesis, but the model was not validated by the co‐crystallization experiments with IGF 1‐R.
Abstract: From an azaindole lead, identified in high throughput screen, a series of potent bis-azaindole inhibitors of IGF1-R have been synthesized using rational drug design and SAR based on a in silico binding mode hypothesis. Although the resulting compounds produced the expected improved potency, the model was not validated by the co-crystallization experiments with IGF1-R.