Structure-based design of parasitic protease inhibitors

Li, Rongshi; Chen, Xiaowu; Bi, Gong; Selzer, Paul M.; Li, Zhe; Davidson, Eugene A.; Kurzban, Gary P.; Miller, Robert E.; Nuzum, Edwin O.; McKerrow, James H.; Fletterick, Robert J.; Gillmor, S.A.; Craik, Charles S.; Kuntz, Irwin D.; Cohen, Fred E.; Kenyon, George L.

doi:10.1016/0968-0896(96)00136-8

Cited by 119 publications

(68 citation statements)

References 23 publications

Supporting

Mentioning

Contrasting

Unclassified

Order By: Relevance

“…The resistance indexes are defined as ratios of the IC 50 of a drug against W2 to the IC 50 of the same drug against D6 (18). The calculated indexes for 72 h experiments using combined MSF and [ 3 H]hypoxanthine data are shown in Table 3.…”

Section: Resultsmentioning

confidence: 99%

Assessment and Continued Validation of the Malaria SYBR Green I-Based Fluorescence Assay for Use in Malaria Drug Screening

Johnson

Dennull

Gerena

et al. 2007

Antimicrob Agents Chemother

296

289

View full text Add to dashboard Cite

Several new fluorescence malaria in vitro drug susceptibility microtiter plate assays that detect the presence of malarial DNA in infected erythrocytes have recently been reported, in contrast to traditional isotopic screens that involve radioactive substrate incorporation to measure in vitro malaria growth inhibition. We have assessed and further characterized the malaria SYBR Green I-based fluorescence (MSF) assay for its ability to monitor drug resistance. In order to use the MSF assay as a drug screen, all assay conditions must be thoroughly examined. In this study we expanded upon the capabilities of this assay by including antibiotics and antifolates in the drug panel and testing folic acid-free growth conditions. To do this, we evaluated a more expansive panel of antimalarials in combination with various drug assay culture conditions commonly used in drug sensitivity screening for their activity against Plasmodium falciparum strains D6 and W2. The detection and quantitation limits of the MSF assay were 0.04 to 0.08% and ϳ0.5% parasitemia, respectively. The MSF assay quality was significantly robust, displaying a Z range of 0.73 to 0.95. The 50% inhibitory concentrations for each drug and culture condition combination were determined by using the MSF assay. Compared to the standard [ 3 H]hypoxanthine assay, the MSF assay displayed the expected parasite drug resistance patterns with a high degree of global and phenotypic correlation (r 2 > 0.9238), regardless of which culture condition combination was used. In conclusion, the MSF assay allows for reliable one-plate high-throughput, automated malaria in vitro susceptibility testing without the expense, time consumption, and hazard of other screening assays.

show abstract

Section: Resultsmentioning

confidence: 99%

Assessment and Continued Validation of the Malaria SYBR Green I-Based Fluorescence Assay for Use in Malaria Drug Screening

Johnson

Dennull

Gerena

et al. 2007

Antimicrob Agents Chemother

296

289

View full text Add to dashboard Cite

show abstract

“…Chalcones 1, 2, 4, 5, 8-12, 14, 17, 19, 21, 23-26, 28, 31-33 were previously described in the literature, 18 while compounds 3, 6, 7, 13, 15, 16, 18, 20, 22, 27, 29 and 30 are novel compounds which have not been reported. The chalcones (3)(4)(5)(6) showed yields in the range of 40-50% due the presence of the bromine atom in the starting material acetophenone, which stabilizes the enolate intermediate of the reaction making it less reactive. This effect was not observed for the chalcones (7)(8)(9)(10)(11)(12)(13)(14)(15)(16)(17)(18)(19)(20), which showed yields in the range of 70-98%.…”

Section: Physicochemical Data Of the Synthesized Compoundsmentioning

confidence: 99%

“…5 To the best of our knowledge, only two chalcones were reported as inhibitors of T. cruzi cruzain. 6 In that respect, there is a justifiable interest in developing structure-activity relationships (SAR) for this class of compounds. On the other hand, acylhydrazides (a class of compounds structurally related to chalcones) have been successfully investigated against T. cruzi cruzain.…”

Section: Introductionmentioning

confidence: 99%

Biochemical evaluation of a series of synthetic chalcone and hydrazide derivatives as novel inhibitors of cruzain from Trypanosoma cruzi

Borchhardt¹,

Mascarello²,

Chiaradia³

et al. 2010

J. Braz. Chem. Soc.

View full text Add to dashboard Cite

A doença de Chagas, uma infecção parasitária amplamente distribuída na América Latina, é um problema grave de saúde pública com conseqüências devastadoras em termos de morbidade e mortalidade humana. A enzima cruzaína é a principal cisteíno protease do Trypanosoma cruzi, agente etiológico da tripanossomíase Americana ou doença de Chagas, e foi selecionada como alvo atrativo para o desenvolvimento de novos fármacos tripanocidas. No presente trabalho, a síntese e os efeitos inibitórios de uma série de trinta e três chalconas e sete hidrazidas são descritos contra a enzima cruzaína de T.cruzi. A maioria dos compostos mostraram inibição promissora in vitro (valores de IC 50 na faixa de 20-60 μM), o que sugere o potencial desses compostos como candidatos a líderes para contínuo desenvolvimento. Doze compostos são inéditos, sendo que quatro destes (7, 13, 16 e 18) estão entre os inibidores mais potentes da série.Chagas' disease, a parasitic infection widely distributed throughout Latin America, is a major public health problem with devastating consequences in terms of human morbidity and mortality. The enzyme cruzain is the major cysteine protease from Trypanosoma cruzi, the etiologic agent of American trypanosomiasis or Chagas' disease, and has been selected as an attractive target for the development of novel trypanocidal drugs. In the present work, we describe the synthesis and inhibitory effects of a series of thirty-three chalcone and seven hydrazide derivatives against the enzyme cruzain from T. cruzi. Most of the compounds showed promising in vitro inhibition (IC 50 values in the range of 20-60 μM), which suggest the potential of these compounds as lead candidates for further development. Twelve compounds have not been reported before, and four of them (7, 13, 16 e 18) are among the most potent inhibitors of the series.

show abstract

“…For example, comparative models can be helpful in designing mutants to test hypotheses about the protein's function (Wu et al, 1999;Vernal et al, 2002); in identifying active and binding sites (Sheng et al, 1996); in searching for, designing, and improving ligand binding strength for a given binding site (Ring et al, 1993;Li et al, 1996;Selzer et al, 1997;Enyedy et al, 2001;Que et al, 2002); modeling substrate specificity (Xu et al, 1996); in predicting antigenic epitopes ; in simulating protein-protein docking (Vakser, 1995); in inferring function from calculated electrostatic potential around the protein (Matsumoto et al, 1995); in facilitating molecular replacement in X-ray structure determination (Howell et al, 1992); in refining models based on NMR constraints (Modi et al, 1996); in testing and improving a sequence-structure alignment (Wolf et al, 1998); in annotating single nucleotide polymorphisms (Mirkovic et al, 2004;Karchin et al, 2005); in structural characterization of large complexes by docking to low-resolution cryo-electron density maps (Spahn et al, 2001;Gao et al, 2003); and in rationalizing known experimental observations.…”

Section: Evaluations Of Self-consistencymentioning

confidence: 99%

Comparative Protein Structure Modeling Using Modeller

Eswar

Webb

Martí‐Renom

et al. 2006

CP in Bioinformatics

3,406

2,083

View full text Add to dashboard Cite

Supplemental methods Homology ModellingThe homology model of the NatA WT complex was built with Modeller version 9.8 (1) using the NatA complex of S. pombe as a template. The sequence identity between the target and the template is around 67% and 37% for the subunits Naa10 and Naa15, respectively (Figure S1). The sequence alignments were obtained using ClustalW. Thirty models were generated and evaluated using the Discrete Optimized Protein Energy potential (DOPE score). The models with the lowest overall DOPE score were selected. The S37P NatA complex was designed from the human WT NatA complex using SCWRL instead of Modeller, in order to have starting structures as similar as possible as to avoid bias in the comparison between the wild type and mutant NatA complex. System PreparationPROPKA (2) was used to determine the protonation state of histidines. All other titratable groups were modelled in their standard protonation states. Hydrogen atoms were constructed using the HBUILD module of the CHARMM program (3). The complexes were solvated in cubic boxes of TIP3P water (4) with 120 Å-long edges. Water molecules overlapping the proteins, determined by a cut-off of 2.8Å, were removed. Molecular dynamicsMolecular dynamics (MD) simulations were used to explore the conformational space. As the aim was to uncover differences between the two systems, we ran long simulations (100 ns) in order to allow the systems to rearrange. These simulations were performed at a temperature of 300K using the NAMD program (5) and the CHARMM27 force field (4). The SHAKE algorithm was used to constrain all bonds between hydrogen and heavy atoms. Non-bonded interactions were truncated at a cut-off of 14Å, using a switch function for both the van der Waals, and electrostatic interactions (6). The particle-mesh Ewald algorithm (7) was used to evaluate the long range electrostatic interactions. The system was subjected to an energy minimization of 1000 steps using the conjugated gradient algorithm, followed by a gradual heating consisting of four successive simulations at temperatures of 10K, 100K, 200K and 300K. This was followed by a 1 ns equilibration phase during which velocities were reassigned every picosecond. The production phase consisted of a 100 ns simulation in the NPT ensemble, with a time step of 1fs. Two simulations (replicas) using a different set of

show abstract

Structure-based design of parasitic protease inhibitors

Cited by 119 publications

References 23 publications

Assessment and Continued Validation of the Malaria SYBR Green I-Based Fluorescence Assay for Use in Malaria Drug Screening

Assessment and Continued Validation of the Malaria SYBR Green I-Based Fluorescence Assay for Use in Malaria Drug Screening

Biochemical evaluation of a series of synthetic chalcone and hydrazide derivatives as novel inhibitors of cruzain from Trypanosoma cruzi

Comparative Protein Structure Modeling Using Modeller

Contact Info

Product

Resources

About