The role of molecular modeling in the design of analogues of the fungicidal natural products crocacins A and D.

Abstract:

:Extensive molecular modeling based on crystallographic data was used to aid the design of synthetic analogues of the fungicidal naturally occurring respiration inhibitors crocacins A and D, and an inhibitor binding model to the mammalian cytochrome bc(1) complex was constructed. Simplified analogues were made which showed high activity in a mitochondrial beef heart respiration assay, and which were also active against certain plant pathogens in glasshouse tests. A crystal structure was obtained of an analogue of crocacin D bound to the chicken heart cytochrome bc(1) complex, which validated the binding model and which confirmed that the crocacins are a new class of inhibitor of the cytochrome bc(1) complex.

journal_name

Bioorg Med Chem

authors

Crowley PJ,Berry EA,Cromartie T,Daldal F,Godfrey CR,Lee DW,Phillips JE,Taylor A,Viner R

doi

10.1016/j.bmc.2008.10.030

subject

Has Abstract

pub_date

2008-12-15 00:00:00

pages

10345-55

issue

24

eissn

0968-0896

issn

1464-3391

pii

S0968-0896(08)00982-6

journal_volume

16

pub_type

杂志文章
  • A-ring and E-ring modifications of the cytotoxic alkaloid Luotonin A: Synthesis, computational and biological studies.

    abstract::A series of new Luotonin A derivatives with substituents at rings A and E was synthesized, together with some E-ring-unsubstituted derivatives. Subsequently, the compound library was examined in silico for their binding into a previously proposed site in the DNA/topoisomerase I binary complex. Whereas no convincing co...

    journal_title:Bioorganic & medicinal chemistry

    pub_type: 杂志文章

    doi:10.1016/j.bmc.2020.115443

    authors: Ibric A,Battisti V,Deckardt S,Haller AV,Lee C,Prötsch C,Langer T,Heffeter P,Schueffl HH,Marian B,Haider N

    更新日期:2020-05-01 00:00:00

  • Quinazolindione derivatives as potent 5-HT3A receptor antagonists.

    abstract::5-HT(3A) receptor antagonists have been used mainly for the treatment of nausea and vomiting. These days, the antagonists are of special interest due to their therapeutic potential to treat other diseases such as depression, psychotic disorder, drug abuse, and irritable bowel syndrome. To discover novel 5-HT(3A) recep...

    journal_title:Bioorganic & medicinal chemistry

    pub_type: 杂志文章

    doi:10.1016/j.bmc.2009.04.029

    authors: Lee BH,Choi MJ,Jo MN,Seo HJ,Nah SY,Cho YS,Nam G,Pae AN,Rhim H,Choo H

    更新日期:2009-07-01 00:00:00

  • Synthesis, evaluation and structural studies of antiproliferative tubulin-targeting azetidin-2-ones.

    abstract::A series of azetidin-2-ones substituted at positions 1, 3 and 4 of the azetidinone ring scaffold were synthesised and evaluated for antiproliferative, cytotoxic and tubulin-binding activity. In these compounds, the cis double bond of the vascular targeting agent combretastatin A-4 is replaced with the azetidinone ring...

    journal_title:Bioorganic & medicinal chemistry

    pub_type: 杂志文章

    doi:10.1016/j.bmc.2011.02.022

    authors: O'Boyle NM,Greene LM,Bergin O,Fichet JB,McCabe T,Lloyd DG,Zisterer DM,Meegan MJ

    更新日期:2011-04-01 00:00:00

  • Synthesis of brequinar analogue inhibitors of malaria parasite dihydroorotate dehydrogenase.

    abstract::A series of 2-phenyl quinoline-4-carboxylic acid derivatives related to brequinar, an inhibitor of human dihydroorotate dehydrogenase (DHODH), has been prepared and evaluated as inhibitors of DHODH from the malaria parasite Plasmodium falciparum. Brequinar was essentially inactive against PfDHODH (IC(50) 880 microM) w...

    journal_title:Bioorganic & medicinal chemistry

    pub_type: 杂志文章

    doi:10.1016/j.bmc.2005.01.017

    authors: Boa AN,Canavan SP,Hirst PR,Ramsey C,Stead AM,McConkey GA

    更新日期:2005-03-15 00:00:00

  • Synthesis, biological evaluation, and metabolic stability of acrylamide derivatives as novel CCR3 antagonists.

    abstract::Our laboratory has identified several acrylamide derivatives with potent CCR3 inhibitory activity. In the present study, we evaluated the in vitro metabolic stability (CL(int); mL/min/kg) of these compounds in human liver microsomes (HLMs), and assessed the relationship between their structures and CL(int) values. Amo...

    journal_title:Bioorganic & medicinal chemistry

    pub_type: 杂志文章

    doi:10.1016/j.bmc.2009.06.066

    authors: Sato I,Morihira K,Inami H,Kubota H,Morokata T,Suzuki K,Ohno K,Iura Y,Nitta A,Imaoka T,Takahashi T,Takeuchi M,Ohta M,Tsukamoto S

    更新日期:2009-08-15 00:00:00

  • Design, synthesis and biological evaluation of succinimide derivatives as potential mechanism-based inhibitors of human leukocyte elastase, cathepsin G and proteinase 3.

    abstract::Structure-activity relationship study and in vitro biochemical studies with human leukocyte elastase, cathepsin G and proteinase 3 were conducted using a series of succinimide derivatives. ...

    journal_title:Bioorganic & medicinal chemistry

    pub_type: 杂志文章

    doi:10.1016/0968-0896(95)00024-b

    authors: Groutas WC,Brubaker MJ,Chong LS,Venkataraman R,Huang H,Epp JB,Kuang R,Hoidal JR

    更新日期:1995-04-01 00:00:00

  • Molecular docking identifies the binding of 3-chloropyridine moieties specifically to the S1 pocket of SARS-CoV Mpro.

    abstract::The 3C-like main proteinase of the severe acute respiratory syndrome (SARS) coronavirus, SARS-CoV M(pro), is widely considered to be a major drug target for the development of anti-SARS treatment. Based on the chemical structure of a lead compound from a previous screening, we have designed and synthesized a number of...

    journal_title:Bioorganic & medicinal chemistry

    pub_type: 杂志文章

    doi:10.1016/j.bmc.2007.09.034

    authors: Niu C,Yin J,Zhang J,Vederas JC,James MN

    更新日期:2008-01-01 00:00:00

  • On the topological evidences for modelling lipophilicity.

    abstract::Topological evidences for modelling lipophilicity of a large series of diversed compounds have been provided on the basis of distance-based topological indices. A pool of topological indices along with indicator parameters related to the type of the compounds present in the set of 140 compounds were used for this purp...

    journal_title:Bioorganic & medicinal chemistry

    pub_type: 杂志文章

    doi:10.1016/s0968-0896(02)00299-7

    authors: Agrawal VK,Singh J,Khadikar PV

    更新日期:2002-12-01 00:00:00

  • Synthesis and anti-HIV-1 evaluation of phosphonates which mimic the 5'-monophosphate of 4'-branched 2',3'-didehydro-2',3'-dideoxy nucleosides.

    abstract::Synthesis of the 4'-ethynyl and 4'-cyano phosphonates 8-11, which mimic the 5'-monophosphate of 4'-branched 2',3'-didehydro-2',3'-dideoxy nucleosides, was investigated by employing the 3',4'-unsaturated nucleosides (13 and 28) as the starting material. The synthesis was initiated by the electrophilic addition of NIS/(...

    journal_title:Bioorganic & medicinal chemistry

    pub_type: 杂志文章

    doi:10.1016/j.bmc.2010.08.037

    authors: Kubota Y,Ishizaki N,Haraguchi K,Hamasaki T,Baba M,Tanaka H

    更新日期:2010-10-15 00:00:00

  • C-nucleoside analogues of furanfurin as ligands to A1 adenosine receptors.

    abstract::Furanfurin (2-beta-D-ribofuranosylfuran-4-carboxamide) derivatives and analogues were synthesized and their affinity for adenosine receptors was determined. The agonistic behavior of furanfurin against A1 receptors is preserved only when the furan ring is substituted with isosteric pentatomic ring systems such as oxaz...

    journal_title:Bioorganic & medicinal chemistry

    pub_type: 杂志文章

    doi:10.1016/s0968-0896(00)00167-x

    authors: Franchetti P,Cappellacci L,Marchetti S,Martini C,Costa B,Varani K,Borea PA,Grifantini M

    更新日期:2000-09-01 00:00:00

  • Synthesis of 6-N-(benzothiazol-2-yl)deoxyadenosine and its exciton-coupled circular dichroism.

    abstract::6-N-(Benzothiazol-2-yl)deoxyadenosine (A(BT)) was synthesized and incorporated into DNAs. Although, the multipoint benzothiazole (BT) modification of oligodeoxynucleotides reduced the stability of duplexes with their complementary strands, it induced the strong exciton coupling between BT moieties. The circular dichro...

    journal_title:Bioorganic & medicinal chemistry

    pub_type: 杂志文章

    doi:10.1016/j.bmc.2009.12.009

    authors: Masaki Y,Ohkubo A,Seio K,Sekine M

    更新日期:2010-01-15 00:00:00

  • Synthesis of (+)-crocacin D and simplified bioactive analogues.

    abstract::The total synthesis of (+)-crocacin D has been achieved in 15 steps (9 isolated intermediates) and 14% overall yield from commercially available starting materials and using (+)-crocacin C as a key intermediate. A number of simplified analogues and their biological activities are also reported. ...

    journal_title:Bioorganic & medicinal chemistry

    pub_type: 杂志文章

    doi:10.1016/j.bmc.2015.01.008

    authors: Pasqua AE,Ferrari FD,Crawford JJ,Whittingham WG,Marquez R

    更新日期:2015-03-01 00:00:00

  • Enhanced RNA binding of dimerized aminoglycosides.

    abstract::Aminoglycoside antibiotics have recently emerged as an intriguing family of RNA binding molecules and they became leading structures for the design of novel RNA ligands. The demystification of the aminoglycoside-RNA recognition phenomenon is required for the development of superior binders. To explore the existence of...

    journal_title:Bioorganic & medicinal chemistry

    pub_type: 杂志文章

    doi:10.1016/s0968-0896(99)00071-1

    authors: Michael K,Wang H,Tor Y

    更新日期:1999-07-01 00:00:00

  • A new dihydroxanthenone from a plant-associated strain of the fungus Chaetomium globosum demonstrates anticancer activity.

    abstract::Bioassay-guided fractionation of a cytotoxic EtOAc extract of the fungal strain, Chaetomium globosum, inhabiting the rhizosphere of the Christmas cactus, Opuntia leptocaulis, of the Sonoran desert afforded a new dihydroxanthenone, globosuxanthone A (1), a new tetrahydroxanthenone, globosuxanthone B (2), two new xantho...

    journal_title:Bioorganic & medicinal chemistry

    pub_type: 杂志文章

    doi:10.1016/j.bmc.2006.07.048

    authors: Wijeratne EM,Turbyville TJ,Fritz A,Whitesell L,Gunatilaka AA

    更新日期:2006-12-01 00:00:00

  • Tryptophan-based fluorophores for studying protein conformational changes.

    abstract::With the continuing interest in deciphering the interplay between protein function and conformational changes, small fluorescence probes will be especially useful for tracking changes in the crowded protein interior space. Presently, we describe the potential utility of six unnatural amino acid fluorescence donors str...

    journal_title:Bioorganic & medicinal chemistry

    pub_type: 杂志文章

    doi:10.1016/j.bmc.2014.09.015

    authors: Talukder P,Chen S,Liu CT,Baldwin EA,Benkovic SJ,Hecht SM

    更新日期:2014-11-01 00:00:00

  • Design, synthesis, biological evaluation and docking studies of pterostilbene analogs inside PPARalpha.

    abstract::Pterostilbene, a naturally occurring analog of resveratrol, has previously shown PPARalpha activation in H4IIEC3 cells and was found to decrease cholesterol levels in animals. In this study, analogs of pterostilbene were synthesized and their ability to activate PPARalpha was investigated. Among analogs that was synth...

    journal_title:Bioorganic & medicinal chemistry

    pub_type: 杂志文章

    doi:10.1016/j.bmc.2008.01.051

    authors: Mizuno CS,Ma G,Khan S,Patny A,Avery MA,Rimando AM

    更新日期:2008-04-01 00:00:00

  • Synthesis of lipid A monosaccharide analogues containing acidic amino acid: exploring the structural basis for the endotoxic and antagonistic activities.

    abstract::For elucidation of the structural and conformational requirements on the endotoxic and antagonistic activity of lipid A derivatives, we designed and synthesized lipid A analogues containing acidic amino acid residues in place of the non-reducing end phosphorylated glucosamine. Definite switching of the endotoxic or an...

    journal_title:Bioorganic & medicinal chemistry

    pub_type: 杂志文章

    doi:10.1016/j.bmc.2006.05.051

    authors: Akamatsu M,Fujimoto Y,Kataoka M,Suda Y,Kusumoto S,Fukase K

    更新日期:2006-10-01 00:00:00

  • Towards the first inhibitors of trihydroxynaphthalene reductase from Curvularia lunata: synthesis of artificial substrate, homology modelling and initial screening.

    abstract::Trihydroxynaphthalene reductase (3HNR) is an essential enzyme in the biosynthesis of fungal melanin and it represents an emerging target for the development of new fungicides and antimicotics. To promote the discovery of new inhibitors, an improved chemical synthesis of the artificial substrate 2,3-dihydro-2,5-dihydro...

    journal_title:Bioorganic & medicinal chemistry

    pub_type: 杂志文章

    doi:10.1016/j.bmc.2008.04.066

    authors: Brunskole M,Stefane B,Zorko K,Anderluh M,Stojan J,Lanisnik Rizner T,Gobec S

    更新日期:2008-06-01 00:00:00

  • Toward protein-cleaving catalytic drugs: artificial protease selective for myoglobin.

    abstract::A protein-cleaving catalyst highly selective for a disease-related protein can be used as a catalytic drug. As the first protein-cleaving catalyst selective for a protein substrate, a catalyst for myoglobin (Mb) was designed by attaching the Cu(II) or Co(III) complex of cyclen to a binding site searched by a combinato...

    journal_title:Bioorganic & medicinal chemistry

    pub_type: 杂志文章

    doi:10.1016/s0968-0896(03)00216-5

    authors: Jeon JW,Son SJ,Yoo CE,Hong IS,Suh J

    更新日期:2003-07-03 00:00:00

  • Stereoselective synthesis and anti-inflammatory activities of 6- and 7-membered dioxacycloalkanes.

    abstract::A class of 5-trifluoroacetylamino-1,3-dioxacycloalkanes, 5-benzoylamino-1,3-dioxacycloalkanes, and 5-amino-1,3-dioxacycloalkane compounds were stereoselectively synthesized as potential anti-inflammatory drug candidates. The anti-inflammatory activities of these compounds were tested using the xylene-induced mouse ear...

    journal_title:Bioorganic & medicinal chemistry

    pub_type: 杂志文章

    doi:10.1016/j.bmc.2005.09.068

    authors: Gu K,Bi L,Zhao M,Wang C,Dolan C,Kao MC,Tok JB,Peng S

    更新日期:2006-03-01 00:00:00

  • Pyrazolo[1',5':1,6]pyrimido[4,5-d]pyridazin-4(3H)-ones as selective human A(1) adenosine receptor ligands.

    abstract::A series of pyrazolo[1',5':1,6]pyrimido[4,5-d]pyridazin-4(3H)-ones was synthesized and tested in radioligand binding assays to determine their affinities for the human adenosine A(1), A(2A), A(2B) and A(3) receptors. Results indicated that this scaffold is appropriate for adenosine receptor subtype A(1) ligands and th...

    journal_title:Bioorganic & medicinal chemistry

    pub_type: 杂志文章

    doi:10.1016/j.bmc.2010.09.043

    authors: Giovannoni MP,Vergelli C,Cilibrizzi A,Crocetti L,Biancalani C,Graziano A,Dal Piaz V,Loza MI,Cadavid MI,Díaz JL,Gavaldà A

    更新日期:2010-11-15 00:00:00

  • Synthesis, biological evaluation and molecular modelling of diversely functionalized heterocyclic derivatives as inhibitors of acetylcholinesterase/butyrylcholinesterase and modulators of Ca2+ channels and nicotinic receptors.

    abstract::The synthesis and the biological activity of compounds 5-40 as inhibitors of acetylcholinesterase (AChE) and butyrylcholinesterase (BuChE), as well as modulators of voltage-dependent Ca(2+) channels and nicotinic receptors, are described. These molecules are tacrine analogues, which have been prepared from polyfunctio...

    journal_title:Bioorganic & medicinal chemistry

    pub_type: 杂志文章

    doi:10.1016/j.bmc.2004.02.017

    authors: Marco JL,de los Ríos C,García AG,Villarroya M,Carreiras MC,Martins C,Eleutério A,Morreale A,Orozco M,Luque FJ

    更新日期:2004-05-01 00:00:00

  • Discovery of novel 4-anilinoquinazoline derivatives as potent inhibitors of epidermal growth factor receptor with antitumor activity.

    abstract::Two new series of new compounds containing a 6-amino-substituted group or 6-acrylamide-substituted group linked to a 4-anilinoquinazoline nucleus have been discovered as potential EGFR inhibitors. These compounds proved efficient effects on antiproliferative activity and EGFR-TK inhibitory activity. Especially, N(6)-(...

    journal_title:Bioorganic & medicinal chemistry

    pub_type: 杂志文章

    doi:10.1016/j.bmc.2013.06.070

    authors: Xu YY,Li SN,Yu GJ,Hu QH,Li HQ

    更新日期:2013-10-01 00:00:00

  • Design, synthesis, and structure-activity relationships of potent GPIIb/IIIa antagonists: discovery of FK419.

    abstract::The discovery of the non-peptide antiplatelet injectable agent FK419 is reported. Based on the beta-turn structure of RGD peptide sequences in the alpha chain of fibrinogen, which binds the glycoprotein IIb/IIIa (GPIIb/IIIa) on the surface of platelets to induce platelet aggregation, the prototype 2 was designed. Afte...

    journal_title:Bioorganic & medicinal chemistry

    pub_type: 杂志文章

    doi:10.1016/j.bmc.2005.03.056

    authors: Yamanaka T,Ohkubo M,Kuroda S,Nakamura H,Takahashi F,Aoki T,Mihara K,Seki J,Kato M

    更新日期:2005-07-01 00:00:00

  • Thionation of segetalins A and B, cyclic peptides with estrogen-like activity from seeds of Vaccaria segetalis.

    abstract::Thionation of estrogen-like active cyclic peptides, segetalins A (1) and B (2), with Lawesson's reagent provided each two thiosegetalins; thiosegetalin A1 [Gly-1-psi(CS-NH)-Val-2; Trp-5-psi (CS-NH)-Ala-6]segetalin A, thiosegetalin A2 [Gly-1-psi(CS-NH)-Val-2; Ala-6-psi(CS-NH)-Gly-1]segetalin A, thiosegetalin B1 [Gly-1-...

    journal_title:Bioorganic & medicinal chemistry

    pub_type: 杂志文章

    doi:10.1016/s0968-0896(97)00001-1

    authors: Morita H,Yun YS,Takeya K,Itokawa H,Shirota O

    更新日期:1997-03-01 00:00:00

  • Thiopyrano[2,3-e]indol-2-ones: angelicin heteroanalogues with potent photoantiproliferative activity.

    abstract::A new class of compounds, the thiopyrano[2,3-e]indol-2-ones, bioisosters of the angular furocoumarin angelicin, was synthesized with the aim of obtaining new photochemotherapeutic agents. In particular 7,8-dimethyl-thiopyranoindolone 6c s showed a remarkable phototoxicity and a great dose UVA dependence reaching IC(50...

    journal_title:Bioorganic & medicinal chemistry

    pub_type: 杂志文章

    doi:10.1016/j.bmc.2008.10.002

    authors: Barraja P,Diana P,Montalbano A,Carbone A,Cirrincione G,Viola G,Salvador A,Vedaldi D,Dall'acqua F

    更新日期:2008-11-15 00:00:00

  • Probing the human estrogen receptor-α binding requirements for phenolic mono- and di-hydroxyl compounds: a combined synthesis, binding and docking study.

    abstract::Various estrogen analogs were synthesized and tested for binding to human ERα using a fluorescence polarization displacement assay. Binding affinity and orientation were also predicted using docking calculations. Docking was able to accurately predict relative binding affinity and orientation for estradiol, but only i...

    journal_title:Bioorganic & medicinal chemistry

    pub_type: 杂志文章

    doi:10.1016/j.bmc.2013.11.024

    authors: McCullough C,Neumann TS,Gone JR,He Z,Herrild C,Wondergem Nee Lukesh J,Pandey RK,Donaldson WA,Sem DS

    更新日期:2014-01-01 00:00:00

  • Synthesis of racemic 6,10,14-trimethylpentadecan-2-ol, a pheromone of rice moth and 5,9,13-trimethyltetradecanoic acid, a component of marine sponge from a common intermediate.

    abstract::A facile synthesis of dl-6,10,14-trimethylpentadecan-2-ol (1) a pheromone component of rice moth, Corcyra cephalonica Stainton and 5,9,13-trimethyltetradecanoic acid (2) a component of marine sponge, Cinachyrella alloclada Uliczka, using a common, intermediate, hexahydrofarnesol is accomplished. The salient features f...

    journal_title:Bioorganic & medicinal chemistry

    pub_type: 杂志文章

    doi:10.1016/s0968-0896(00)82149-5

    authors: Rane SS,Chadha MS,Mamdapur VR

    更新日期:1993-12-01 00:00:00

  • Synthesis, biological evaluation and molecular docking studies of benzyloxyacetohydroxamic acids as LpxC inhibitors.

    abstract::The inhibition of the UDP-3-O-[(R)-3-hydroxymyristoyl]-N-acetylglucosamine deacetylase (LpxC) represents a promising strategy to combat infections caused by multidrug-resistant Gram-negative bacteria. In order to elucidate the functional groups being important for the inhibition of LpxC, the structure of our previousl...

    journal_title:Bioorganic & medicinal chemistry

    pub_type: 杂志文章

    doi:10.1016/j.bmc.2013.12.057

    authors: Szermerski M,Melesina J,Wichapong K,Löppenberg M,Jose J,Sippl W,Holl R

    更新日期:2014-02-01 00:00:00

  • Discovery and structural characterization of peficitinib (ASP015K) as a novel and potent JAK inhibitor.

    abstract::Janus kinases (JAKs) are considered promising targets for the treatment of autoimmune diseases including rheumatoid arthritis (RA) due to their important role in multiple cytokine receptor signaling pathways. Recently, several JAK inhibitors have been developed for the treatment of RA. Here, we describe the identifica...

    journal_title:Bioorganic & medicinal chemistry

    pub_type: 杂志文章

    doi:10.1016/j.bmc.2018.08.005

    authors: Hamaguchi H,Amano Y,Moritomo A,Shirakami S,Nakajima Y,Nakai K,Nomura N,Ito M,Higashi Y,Inoue T

    更新日期:2018-10-01 00:00:00