Application of descriptors based on Lipinski's rules in the QSPR study of aqueous solubilities.

Abstract:

:We complement new physically interpretable descriptors inspired by the Lipinski's rules of drug bioavailability with others obtained from the Dragon 3.0 software, in order to find the best QSPR relationship for aqueous solubilities of 100 structurally heterogeneous organic, drug-like compounds. The simultaneous linear regression analyses of 1367 variables lead to a six-parameter model containing two of the new proposed descriptors and which also possess good predictive ability given by R=0.8798 and cross-validated R(1-10%-o)=0.8199. We further validate the model found with an external test set composed of 48 compounds.

journal_name

Bioorg Med Chem

authors

Duchowicz PR,Talevi A,Bellera C,Bruno-Blanch LE,Castro EA

doi

10.1016/j.bmc.2007.03.044

subject

Has Abstract

pub_date

2007-06-01 00:00:00

pages

3711-9

issue

11

eissn

0968-0896

issn

1464-3391

pii

S0968-0896(07)00242-8

journal_volume

15

pub_type

杂志文章
  • Bis-pyrene-labeled molecular beacon: a monomer-excimer switching probe for the detection of DNA base alteration.

    abstract::A new bis-pyrene-labeled oligonucleotide probe (BP-probe) has been designed for the detection of a single base mismatch in single strand (ss) DNA as a target. The sequence of BP-probe was chosen to form stem-loop structure similar to a molecular beacon (MB-probe), yielding bis-pyrene-labeled molecular beacon (BP-MB-pr...

    journal_title:Bioorganic & medicinal chemistry

    pub_type: 杂志文章

    doi:10.1016/j.bmc.2007.04.053

    authors: Yamana K,Ohshita Y,Fukunaga Y,Nakamura M,Maruyama A

    更新日期:2008-01-01 00:00:00

  • d(G3T4G4) forms unusual dimeric G-quadruplex structure with the same general fold in the presence of K+, Na+ or NH4+ ions.

    abstract::We have recently communicated that DNA oligonucleotide d(G(3)T(4)G(4)) forms a dimeric G-quadruplex in the presence of K(+) ions [J. Am. Chem. Soc.2003, 125, 7866-7871]. The high-resolution NMR structure of d(G(3)T(4)G(4))(2) G-quadruplex exhibits G-quadruplex core consisting of three stacked G-quartets. The two overh...

    journal_title:Bioorganic & medicinal chemistry

    pub_type: 杂志文章

    doi:10.1016/j.bmc.2004.08.009

    authors: Sket P,Crnugelj M,Plavec J

    更新日期:2004-11-15 00:00:00

  • Drug design and synthesis of epsilon opioid receptor agonist: 17-(cyclopropylmethyl)-4,5alpha-epoxy-3,6beta-dihydroxy-6,14-endoethenomorphinan-7alpha-(N-methyl-N-phenethyl)carboxamide (TAN-821) inducing antinociception mediated by putative epsilon opioid

    abstract::Here we report the new drug design and synthesis of a series of 6,14-endoethenomorphinan-7-carboxamide derivatives as a putative epsilon opioid receptor agonist. One of these compounds, 17-(cyclopropylmethyl)-4,5alpha-epoxy-3,6beta-dihydroxy-6,14-endoethenomorphinan-7alpha-(N-methyl-N-phenethyl)carboxamide (TAN-821), ...

    journal_title:Bioorganic & medicinal chemistry

    pub_type: 杂志文章

    doi:10.1016/j.bmc.2004.05.024

    authors: Fujii H,Narita M,Mizoguchi H,Murachi M,Tanaka T,Kawai K,Tseng LF,Nagase H

    更新日期:2004-08-01 00:00:00

  • Carbonic anhydrase inhibitors. Inhibition of Plasmodium falciparum carbonic anhydrase with aromatic sulfonamides: towards antimalarials with a novel mechanism of action?

    abstract::The malarial parasite Plasmodium falciparum encodes for an alpha-carbonic anhydrase (CA) enzyme possessing catalytic properties distinct of that of the human host, which was only recently purified. A series of aromatic sulfonamides, most of which were Schiff's bases derived from sulfanilamide/homosulfanilamide/4-amino...

    journal_title:Bioorganic & medicinal chemistry

    pub_type: 杂志文章

    doi:10.1016/j.bmc.2004.10.015

    authors: Krungkrai J,Scozzafava A,Reungprapavut S,Krungkrai SR,Rattanajak R,Kamchonwongpaisan S,Supuran CT

    更新日期:2005-01-17 00:00:00

  • Identification of 2-mercaptohexanoic acids as dual inhibitors of 5-lipoxygenase and microsomal prostaglandin E₂ synthase-1.

    abstract::5-Lipoxygenase (5-LO) and microsomal prostaglandin E₂ synthase (mPGES)-1 are key enzymes in the biosynthesis of leukotrienes and prostaglandin (PG)E₂, respectively, and are considered as valuable targets for the treatment of inflammatory diseases. Here, we present the identification of 2-mercaptohexanoic acid derivati...

    journal_title:Bioorganic & medicinal chemistry

    pub_type: 杂志文章

    doi:10.1016/j.bmc.2011.04.034

    authors: Greiner C,Zettl H,Koeberle A,Pergola C,Northoff H,Schubert-Zsilavecz M,Werz O

    更新日期:2011-06-01 00:00:00

  • Synthesis and evaluation of verticipyrone analogues as mitochondrial complex I inhibitors.

    abstract::Verticipyrone has recently been isolated from the culture broth of Verticillium sp. and shown to inhibit NADH fumarate reductase, as well as NADH oxidoreductase (complex I) of the mitochondrial electron transport chain. In order to assess the structural elements in verticipyrone essential for complex I inhibitor, 15 s...

    journal_title:Bioorganic & medicinal chemistry

    pub_type: 杂志文章

    doi:10.1016/j.bmc.2010.03.070

    authors: Leiris SJ,Khdour OM,Segerman ZJ,Tsosie KS,Chapuis JC,Hecht SM

    更新日期:2010-05-15 00:00:00

  • Mutation of active site residues Asn67 to Ile, Gln92 to Val and Leu204 to Ser in human carbonic anhydrase II: influences on the catalytic activity and affinity for inhibitors.

    abstract::Site-directed mutagenesis has been used to change three amino acid residues involved in the binding of inhibitors (Asn67Ile; Gln92Val and Leu204Ser) within the active site of human carbonic anhydrase (CA, EC 4.2.1.1) II (hCA II). Residues 67, 92 and 204 were changed from hydrophobic to hydrophilic ones, and vice versa...

    journal_title:Bioorganic & medicinal chemistry

    pub_type: 杂志文章

    doi:10.1016/j.bmc.2012.02.029

    authors: Turkoglu S,Maresca A,Alper M,Kockar F,Işık S,Sinan S,Ozensoy O,Arslan O,Supuran CT

    更新日期:2012-04-01 00:00:00

  • Synthesis of 4-substituted nipecotic acid derivatives and their evaluation as potential GABA uptake inhibitors.

    abstract::In this study, we disclose the design and synthesis of novel 4-susbtituted nipecotic acid derivatives as inhibitors of the GABA transporter mGAT1. Based on molecular modeling studies the compounds are assumed to adopt a binding pose similar to that of the potent mGAT1 inhibitor nipecotic acid. As substitution in 4-pos...

    journal_title:Bioorganic & medicinal chemistry

    pub_type: 杂志文章

    doi:10.1016/j.bmc.2016.03.038

    authors: Hellenbrand T,Höfner G,Wein T,Wanner KT

    更新日期:2016-05-01 00:00:00

  • Synthesis and pharmacological evaluation of pentacyclic 6a,7-dihydrodiindole and 2,3-dihydrodiindole derivatives as novel melatoninergic ligands.

    abstract::The synthesis of novel melatonin analogues 3a and 4a-c designed as melatonin receptor ligands is described. Among the newly synthesized ligands, 2-((S)-2-hydroxymethylindolin-1-ylmethyl)-melatonin 4b displayed the highest affinity for MT(1) receptors (K(i)=9.8 nM) and for MT(2) subtype (K(i)=7.8 nM), whereas the rigid...

    journal_title:Bioorganic & medicinal chemistry

    pub_type: 杂志文章

    doi:10.1016/j.bmc.2008.07.012

    authors: Attia MI,Witt-Enderby PA,Julius J

    更新日期:2008-08-15 00:00:00

  • Biodistribution of (125)I-labeled polymeric vaccine carriers after subcutaneous injection.

    abstract::Polymeric nanoparticles (NPs) comprised of hydrophilic poly(γ-glutamic acid) in the main chain and hydrophobic phenylalanine in the side chain (γ-PGA-Phe) are a promising vaccine carrier for various kinds of diseases. However, little is known about the fate of subcutaneously administered γ-PGA-Phe NPs. Therefore, we n...

    journal_title:Bioorganic & medicinal chemistry

    pub_type: 杂志文章

    doi:10.1016/j.bmc.2013.06.021

    authors: Toita R,Kanai Y,Watabe H,Nakao K,Yamamoto S,Hatazawa J,Akashi M

    更新日期:2013-09-01 00:00:00

  • Cell surface biotinylation by azaelectrocyclization: easy-handling and versatile approach for living cell labeling.

    abstract::Versatile method for living cell labeling has been established. Cell surfaces are initially biotinylated by azaelectrocyclization, and then treated with the fluorescence-labeled avidin or the anti-biotin antibody. ...

    journal_title:Bioorganic & medicinal chemistry

    pub_type: 杂志文章

    doi:10.1016/j.bmc.2011.12.043

    authors: Tanaka K,Yokoi S,Morimoto K,Iwata T,Nakamoto Y,Nakayama K,Koyama K,Fujiwara T,Fukase K

    更新日期:2012-03-15 00:00:00

  • The hemA gene encoding glutamyl-tRNA reductase from the archaeon Methanobacterium thermoautotrophicum strain Marburg.

    abstract::In archaea the first general tetrapyrrole precursor 5-aminolevulinic acid (ALA) is formed via the tRNA-dependent five-carbon pathway from glutamate. We have cloned the hemA gene encoding the central enzyme of the pathway glutamyl-tRNA reductase from the methanogenic archaeon Methanobacterium thermoautotrophicum by com...

    journal_title:Bioorganic & medicinal chemistry

    pub_type: 杂志文章

    doi:10.1016/0968-0896(96)00098-3

    authors: Hungerer C,Weiss DS,Thauer RK,Jahn D

    更新日期:1996-07-01 00:00:00

  • Three-dimensional quantitative structure-activity relationship (3D-QSAR) of 3-aryloxazolidin-2-one antibacterials.

    abstract::Three-dimensional quantitative structure-activity relationship (3D-QSAR) studies for 3-aryloxazolidin-2-one antibacterials were performed using the genetic function approximation algorithm. This study was performed using 60 compounds, in which the QSAR models were developed using a training set of 50 compounds. The in...

    journal_title:Bioorganic & medicinal chemistry

    pub_type: 杂志文章

    doi:10.1016/s0968-0896(01)00186-9

    authors: Karki RG,Kulkarni VM

    更新日期:2001-12-01 00:00:00

  • Preparation and biological properties of biotinylated PhTX derivatives.

    abstract::We report the synthesis of several highly functionalized biotinylated philanthotoxin (PhTX) analogues (7, 8, 10, 13-16) designed on the basis of earlier structure-activity relationship studies. Despite the extensive modifications, the binding to nicotinic acetylcholine receptor (nAChR) is in the low micromolar range a...

    journal_title:Bioorganic & medicinal chemistry

    pub_type: 杂志文章

    doi:10.1016/s0968-0896(99)00054-1

    authors: Hashimoto M,Liu Y,Fang K,Li HY,Campiani G,Nakanishi K

    更新日期:1999-06-01 00:00:00

  • Study on synthesis, characterization and biological activity of some new nitrogen heterocycle porphyrins.

    abstract::Seven new nitrogen heterocycle porphyrins, 5,10,15,20-tetra[4-(N-pyrrolidinyl)phenyl]porphine (TBPPH(2)), 5,10,15,20-tetra[4-(4'-ethylpiperazinyl)phenyl]porphine (TEPPH(2)), 5,10,15,20-tetra [4-(4'-butylpiperazinyl)phenyl]porphine (TUPPH(2)), 5,10,15,20-tetra[4-(4'-heptylpiperazinyl) phenyl]porphine (THPPH(2)), 5-[4-(...

    journal_title:Bioorganic & medicinal chemistry

    pub_type: 杂志文章

    doi:10.1016/s0968-0896(03)00027-0

    authors: Guo CC,Li HP,Zhang XB

    更新日期:2003-04-17 00:00:00

  • 2-Methylene 19-nor-25-dehydro-1alpha-hydroxyvitamin D3 26,23-lactones: synthesis, biological activities and molecular basis of passive antagonism.

    abstract::To investigate the molecular mechanism of vitamin D receptor (VDR) antagonists having no structurally bulky group interfering with helix 12 of the ligand-binding domain of the VDR, we have synthesized four diastereomers at C(20) and C(23) of 19-nor-1alpha-hydroxyvitamin D(3) 25-methylene-26,23-lactone bearing a 2MD-ty...

    journal_title:Bioorganic & medicinal chemistry

    pub_type: 杂志文章

    doi:10.1016/j.bmc.2007.09.017

    authors: Yoshimoto N,Inaba Y,Yamada S,Makishima M,Shimizu M,Yamamoto K

    更新日期:2008-01-01 00:00:00

  • Allosteric kidney-type glutaminase (GLS) inhibitors with a mercaptoethyl linker.

    abstract::A series of allosteric kidney-type glutaminase (GLS) inhibitors possessing a mercaptoethyl (SCH2CH2) linker were synthesized in an effort to further expand the structural diversity of chemotypes derived from bis-2-(5-phenylacetamido-1,3,4-thiadiazol-2-yl)ethyl sulfide (BPTES), a prototype allosteric inhibitor of GLS. ...

    journal_title:Bioorganic & medicinal chemistry

    pub_type: 杂志文章

    doi:10.1016/j.bmc.2020.115698

    authors: Duvall B,Zimmermann SC,Gao RD,Thomas AG,Kalčic F,Veeravalli V,Elgogary A,Rais R,Rojas C,Le A,Slusher BS,Tsukamoto T

    更新日期:2020-10-15 00:00:00

  • Synthesis, structure, molecular docking, and structure-activity relationship analysis of enamines: 3-aryl-4-alkylaminofuran-2(5H)-ones as potential antibacterials.

    abstract::Thirty-one 3-aryl-4-alkylaminofuran-2(5H)-ones were designed, prepared and tested for their antibacterial activity. Some of them showed significant antibacterial activity against Gram-positive organisms, especially against Staphylococcus aureus ATCC 25923, but all were inactive against Gram-negative organisms. Out of ...

    journal_title:Bioorganic & medicinal chemistry

    pub_type: 杂志文章

    doi:10.1016/j.bmc.2011.01.051

    authors: Xiao ZP,He XB,Peng ZY,Xiong TJ,Peng J,Chen LH,Zhu HL

    更新日期:2011-03-01 00:00:00

  • Substituted thiophene-anthranilamides as potent inhibitors of human factor Xa.

    abstract::A series of thiophene-containing non-amidine factor Xa inhibitors is described. Simple methyl-substituted thiophene analogs were relatively weak inhibitors. However, introduction of hydrophilic substituents at C-4 or C-5 of the thiophene afforded inhibitors with low nanomolar potency. Optimization of the thiophene sub...

    journal_title:Bioorganic & medicinal chemistry

    pub_type: 杂志文章

    doi:10.1016/j.bmc.2006.12.019

    authors: Kochanny MJ,Adler M,Ewing J,Griedel BD,Ho E,Karanjawala R,Lee W,Lentz D,Liang AM,Morrissey MM,Phillips GB,Post J,Sacchi KL,Sakata ST,Subramanyam B,Vergona R,Walters J,White KA,Whitlow M,Ye B,Zhao Z,Shaw KJ

    更新日期:2007-03-01 00:00:00

  • Preparation and antioxidant activity of alpha-pyridoin and its derivatives.

    abstract::Focusing on alpha-pyridoin (1, 1,2-di(2-pyridyl)-1,2-ethenediol) as the lead compound of the novel antioxidative enediol, we synthesized 5,5'- or 6,6'-bis-substituted derivatives of 1 from disubstituted pyridines. The antioxidant activity of 1 and its synthetic derivatives 2-7 was evaluated by DPPH (1,1-diphenyl-2-pic...

    journal_title:Bioorganic & medicinal chemistry

    pub_type: 杂志文章

    doi:10.1016/j.bmc.2005.07.065

    authors: Hatanaka M,Takahashi K,Nakamura S,Mashino T

    更新日期:2005-12-15 00:00:00

  • Kinetic controlled affinity labeling of target enzyme with thioester chemistry.

    abstract::High specificity has been an important feature in affinity labeling for target profiling. Especially, to label targets via rapidly progressing reactions with consumption of ligand (probe), high specificity of reaction with common functional groups of target protein should be achieved without reactions with similar gro...

    journal_title:Bioorganic & medicinal chemistry

    pub_type: 杂志文章

    doi:10.1016/j.bmc.2016.05.059

    authors: Tomohiro T,Nakabayashi M,Sugita Y,Morimoto S

    更新日期:2016-08-01 00:00:00

  • Tools and methodologies capable of isolating and identifying a target molecule for a bioactive compound.

    abstract::Elucidating the mechanism of action of bioactive compounds, such as commonly used pharmaceutical drugs and biologically active natural products, in the cells and the living body is important in drug discovery research. To this end, isolation and identification of target protein(s) for the bioactive compound are essent...

    journal_title:Bioorganic & medicinal chemistry

    pub_type: 杂志文章

    doi:10.1016/j.bmc.2011.12.022

    authors: Sakamoto S,Hatakeyama M,Ito T,Handa H

    更新日期:2012-03-15 00:00:00

  • Peptide T-araC conjugates: solid-phase synthesis and biological activity of N4-(acylpeptidyl)-araC.

    abstract::Due to the capability of peptidyl derivatives of araC to behave as prodrugs of this antimetabolite, and because of the well known biological properties of peptide T and its analogues (in particular that of targeting CD4+ cells), new peptide T-araC conjugates were prepared and tested in vitro for antiproliferative acti...

    journal_title:Bioorganic & medicinal chemistry

    pub_type: 杂志文章

    doi:10.1016/s0968-0896(99)00317-x

    authors: Manfredini S,Marastoni-M,Tomatis R,Durini E,Spisani S,Pani A,Marceddu T,Musiu C,Marongiu ME,La Colla P

    更新日期:2000-03-01 00:00:00

  • Design, synthesis and molecular docking of α,β-unsaturated cyclohexanone analogous of curcumin as potent EGFR inhibitors with antiproliferative activity.

    abstract::A type of novel α,β-unsaturated cyclohexanone analogous, which designed based on the curcumin core structure, have been discovered as potential EGFR inhibitors. These compounds exhibit potent antiproliferative activity in two human tumor cell lines (Hep G2 and B16-F10). Among them, compounds I(3) and I(12) displayed t...

    journal_title:Bioorganic & medicinal chemistry

    pub_type: 杂志文章

    doi:10.1016/j.bmc.2012.11.031

    authors: Xu YY,Cao Y,Ma H,Li HQ,Ao GZ

    更新日期:2013-01-15 00:00:00

  • Novel 2,5-disubtituted-1,3,4-oxadiazoles with benzimidazole backbone: a new class of β-glucuronidase inhibitors and in silico studies.

    abstract::A library of novel 2,5-disubtituted-1,3,4-oxadiazoles with benzimidazole backbone (3a-3r) was synthesized and evaluated for their potential as β-glucuronidase inhibitors. Several compounds such as 3a-3d, 3e-3j, 3l-3o, 3q and 3r showed excellent inhibitory potentials much better than the standard (IC50=48.4±1.25μM: d-s...

    journal_title:Bioorganic & medicinal chemistry

    pub_type: 杂志文章

    doi:10.1016/j.bmc.2015.04.081

    authors: Zawawi NK,Taha M,Ahmat N,Wadood A,Ismail NH,Rahim F,Ali M,Abdullah N,Khan KM

    更新日期:2015-07-01 00:00:00

  • Myxobacteria versus sponge-derived alkaloids: the bengamide family identified as potent immune modulating agents by scrutiny of LC-MS/ELSD libraries.

    abstract::A nuclear factor-κB (NF-κB) luciferase assay has been employed to identify the bengamides, previously known for their anti-tumor activity, as a new class of immune modulators. A unique element of this study was that the bengamide analogs were isolated from two disparate sources, Myxococcus virescens (bacterium) and Ja...

    journal_title:Bioorganic & medicinal chemistry

    pub_type: 杂志文章

    doi:10.1016/j.bmc.2012.05.043

    authors: Johnson TA,Sohn J,Vaske YM,White KN,Cohen TL,Vervoort HC,Tenney K,Valeriote FA,Bjeldanes LF,Crews P

    更新日期:2012-07-15 00:00:00

  • High-throughput evaluation of relative cell permeability between peptoids and peptides.

    abstract::Peptides are limited in their use as drugs due to low cell permeability and vulnerability to proteases. In contrast, peptoids are immune to enzymatic degradation and some peptoids have been shown to be relatively cell permeable. In order to facilitate future design of peptoid libraries for screening experiments, it wo...

    journal_title:Bioorganic & medicinal chemistry

    pub_type: 杂志文章

    doi:10.1016/j.bmc.2008.04.074

    authors: Tan NC,Yu P,Kwon YU,Kodadek T

    更新日期:2008-06-01 00:00:00

  • Allosteric inhibitors of hepatitis C virus NS5B polymerase thumb domain site II: structure-based design and synthesis of new templates.

    abstract::Chronic hepatitis C virus (HCV) infections are a significant medical problem worldwide. The NS5B Polymerase of HCV plays a central role in virus replication and is a prime target for the discovery of new treatment options. We recently disclosed 1H-benzo[de]isoquinoline-1,3(2H)-diones as allosteric inhibitors of NS5B P...

    journal_title:Bioorganic & medicinal chemistry

    pub_type: 杂志文章

    doi:10.1016/j.bmc.2010.03.024

    authors: Malancona S,Donghi M,Ferrara M,Martin Hernando JI,Pompei M,Pesci S,Ontoria JM,Koch U,Rowley M,Summa V

    更新日期:2010-04-15 00:00:00

  • Pharmacophore-based discovery of FXR-agonists. Part II: identification of bioactive triterpenes from Ganoderma lucidum.

    abstract::The farnesoid X receptor (FXR) belonging to the metabolic subfamily of nuclear receptors is a ligand-induced transcriptional activator. Its central function is the physiological maintenance of bile acid homeostasis including the regulation of glucose and lipid metabolism. Accessible structural information about its li...

    journal_title:Bioorganic & medicinal chemistry

    pub_type: 杂志文章

    doi:10.1016/j.bmc.2011.09.039

    authors: Grienke U,Mihály-Bison J,Schuster D,Afonyushkin T,Binder M,Guan SH,Cheng CR,Wolber G,Stuppner H,Guo DA,Bochkov VN,Rollinger JM

    更新日期:2011-11-15 00:00:00

  • Design, synthesis and evaluation of novel quinazoline-2,4-dione derivatives as chitin synthase inhibitors and antifungal agents.

    abstract::A series of novel 1-methyl-3-substituted quinazoline-2,4-dione derivatives were designed, synthesized, and characterized by (1)H NMR, (13)C NMR and MS spectral data. Their inhibition against chitin synthase (CHS) and antifungal activities were evaluated in vitro. Results showed compounds 5b, 5c, 5e, 5f, 5j, 5k, 5l, an...

    journal_title:Bioorganic & medicinal chemistry

    pub_type: 杂志文章

    doi:10.1016/j.bmc.2014.04.042

    authors: Ji Q,Yang D,Wang X,Chen C,Deng Q,Ge Z,Yuan L,Yang X,Liao F

    更新日期:2014-07-01 00:00:00