Identification of novel antiplasmodial compound by hierarquical virtual screening and in vitro assays.

Abstract:

:Malaria is an infectious disease caused by protozoa of the genus Plasmodium spp. with approximately 219 million cases in 2017. P. falciparum is main responsible for the most severe form of the disease, cerebral malaria. Despite of public health impacts, chemotherapy against malaria is still limited due to the emergence of drug resistance cases used in monotherapy and combination therapies. Thus, the development of new antimalarial drugs becomes emergency. One way of achieve this goal is to explore essential and/or unique therapeutic targets of the parasite, or at least sufficiently different to ensure selective inhibition. Enoil-ACP reductase (ENR) is a NADH-dependent enzyme responsible for the limiting step of the type II fatty acid biosynthetic pathway (FAS II). Thus, pharmacophore and docking based virtual screening were applied to prioritize molecules for in vitro assays against P. falciparum W2 strain. The application of successive filters at OOCC database (n = 618) resulted in the identification of one molecule (13) (EC50 = 0.098 ± 0.021 μM) with similar biological activity to artemether. The molecule 13 is a typical drug repurposing case due to previous other approved therapeutic uses on Chinese medicine as a non-specific cholinergic antagonist, thus it could be accelerated the drug development process. Additionally, molecular dynamics studies were used to confirm stability of the molecular interactions identified by molecular docking. Thus, representative structures of P. falciparum ENR can be used in a study to propose new derivatives for evaluation of biological activity in vitro and in vivo. Communicated by Ramaswamy H. Sarma.

journal_name

J Biomol Struct Dyn

authors

Costa Júnior DB,Araújo JSC,de Mattos Oliveira L,Neri FSM,Moreira POL,Taranto AG,Fonseca AL,de Pilla Varotti F,Leite FHA

doi

10.1080/07391102.2020.1763837

subject

Has Abstract

pub_date

2020-05-13 00:00:00

pages

1-9

eissn

0739-1102

issn

1538-0254

pub_type

杂志文章
  • Studies on adaptability of binding residues and flap region of TMC-114 resistance HIV-1 protease mutants.

    abstract::Drug resistant mutations have severely restricted the success of HIV therapy. These mutations frequently involve the aspartic protease encoded by the virus. Knowledge of the molecular mechanisms underlying the conformational changes of HIV-1 protease mutants may be useful in developing more effective and longer lastin...

    journal_title:Journal of biomolecular structure & dynamics

    pub_type: 杂志文章

    doi:10.1080/07391102.2011.10507379

    authors: Purohit R,Rajendran V,Sethumadhavan R

    更新日期:2011-08-01 00:00:00

  • Elucidation of molecular mechanism of stability of the heme-regulated eIF2α kinase upon binding of its ligand, hemin in its catalytic kinase domain.

    abstract::The eIF2α kinase activity of the heme-regulated inhibitor (HRI) is regulated by heme which makes it a unique member of the family of eIF2α kinases. Since heme concentrations create an equilibrium for the kinase to be active/inactive, it becomes important to study the heme binding effects upon the kinase and understand...

    journal_title:Journal of biomolecular structure & dynamics

    pub_type: 杂志文章

    doi:10.1080/07391102.2017.1368417

    authors: Bhavnani V,Kaviraj S,Panigrahi P,Suresh CG,Yapara S,Pal J

    更新日期:2018-08-01 00:00:00

  • Unusual stability exhibited by (AT)XN12(AT)Y motif associated with high fetal hemoglobin levels.

    abstract::Quasi-palindromic sequences (AT) X N12(AT) Y present in HS2 (hypersensitive site 2) of the human β-globin locus are known to be significantly associated with increased fetal hemoglobin (HbF) levels. High HbF levels in some adults ...

    journal_title:Journal of biomolecular structure & dynamics

    pub_type: 杂志文章

    doi:10.1080/07391102.2018.1532320

    authors: Roy K,Mahendru S,Kukreti R,Kukreti S

    更新日期:2019-09-01 00:00:00

  • Cyclic peptide engineered from phytocystatin inhibitory hairpin loop as an effective modulator of falcipains and potent antimalarial.

    abstract::Cystatins are classical competitive inhibitors of C1 family cysteine proteases (papain family). Phytocystatin superfamily shares high sequence homology and typical tertiary structure with conserved glutamine-valine-glycine (Q-X-V-X-G) loop blocking the active site of C1 proteases. Here, we develop a cysteine-bounded c...

    journal_title:Journal of biomolecular structure & dynamics

    pub_type: 杂志文章

    doi:10.1080/07391102.2020.1848629

    authors: Mishra M,Singh V,Tellis MB,Joshi RS,Pandey KC,Singh S

    更新日期:2020-12-09 00:00:00

  • Modeling the correlation functions of conformational motions in proteins.

    abstract::A first principles calculation of the correlation function for conformational motion (CM) in proteins is carried out within the framework of a microscopic model of a protein as a heterogeneous system. The fragments of the protein are assumed to be identical hard spheres undergoing the CM within their conformational po...

    journal_title:Journal of biomolecular structure & dynamics

    pub_type: 杂志文章

    doi:10.1080/07391102.2000.10506563

    authors: Sitnitsky AE

    更新日期:2000-02-01 00:00:00

  • Quantum-chemical analysis of C-H...O and C-H...N interactions in RNA base pairs--H-bond versus anti-H-bond pattern.

    abstract::Geometries and interaction energies of unusual UU and AA base pairs with one standard hydrogen bond (H-bond) and additional C-H...O or C-H...N contacts have been determined by quantum-chemical methods taking into account electron correlation. Whereas the C-H bond length in the UU C-H...O contact increases upon complex...

    journal_title:Journal of biomolecular structure & dynamics

    pub_type: 杂志文章

    doi:10.1080/07391102.2001.10506687

    authors: Brandl M,Meyer M,Sühnel J

    更新日期:2001-02-01 00:00:00

  • DNA-drug interaction measurements using surface plasmon resonance.

    abstract::The interactions of the drugs 2,7-bis[(diethylamino)-ethoxy]-fluoren-9-one dihydrochloride (Tilorone), 2,7-bis[(dipropylamino)-acetamido]-fluoren-9-one dihydrochloride (FA-2), 2'-(4-hydroxyphenyl)-5-(4-methyl-1-piperazinyl)-2,5'-bi-1H-benzimidazole trihydrochloride (Hoechst 33258), and hematoporphyrin IX derivative (H...

    journal_title:Journal of biomolecular structure & dynamics

    pub_type: 杂志文章

    doi:10.1080/07391102.1998.10508239

    authors: Bischoff G,Bischoff R,Birch-Hirschfeld E,Gromann U,Lindau S,Meister WV,de A Bambirra S,Bohley C,Hoffmann S

    更新日期:1998-10-01 00:00:00

  • Exploration of good and bad structural fingerprints for inhibition of indoleamine-2,3-dioxygenase enzyme in cancer immunotherapy using Monte Carlo optimization and Bayesian classification QSAR modeling.

    abstract::Indoleamine-2,3-dioxygenase 1 (IDO1) is an extrahepatic, heme-containing and tryptophan-catalyzing enzyme responsible for causing blockade of T-cell proliferation and differentiation by depleting tryptophan level in cancerous cells. Therefore, inhibition of IDO1 may be a useful strategy for immunotherapy against cance...

    journal_title:Journal of biomolecular structure & dynamics

    pub_type: 杂志文章

    doi:10.1080/07391102.2019.1615000

    authors: Jain S,Bhardwaj B,Amin SA,Adhikari N,Jha T,Gayen S

    更新日期:2020-04-01 00:00:00

  • New small-size peptides modulators of the exosite of BACE1 obtained from a structure-based design.

    abstract::We report here two new small-size peptides acting as modulators of the β-site APP cleaving enzyme 1 (BACE1) exosite. Ac-YPYFDPL-NH2 and Ac-YPYDIPL-NH2 displayed a moderate but significant inhibitory effect on BACE1. These peptides were obtained from a molecular modeling study. By combining MD simulations with ab initi...

    journal_title:Journal of biomolecular structure & dynamics

    pub_type: 杂志文章

    doi:10.1080/07391102.2016.1145143

    authors: Gutierrez LJ,Angelina E,Gyebrovszki A,Fülöp L,Peruchena N,Baldoni HA,Penke B,Enriz RD

    更新日期:2017-02-01 00:00:00

  • Study on the interaction of taiwaniaquinoids with FTO by spectroscopy and molecular modeling.

    abstract::In this work, an attempt has been made to study the interaction of four taiwaniaquinoids with fat mass and obesity-associated protein (FTO) by UV-vis absorption, fluorescence spectroscopy, and molecular docking techniques. The results indicated that taiwaniaquinoids effectively quenched the intrinsic fluorescence of F...

    journal_title:Journal of biomolecular structure & dynamics

    pub_type: 杂志文章

    doi:10.1080/07391102.2016.1249957

    authors: Ren T,Zhang L,Wang J,Song C,Wang R,Chang J

    更新日期:2017-11-01 00:00:00

  • Three-quasiperiodicity, mutual correlations, ordering and long-range modulations in genomic nucleotide sequences for viruses.

    abstract::Using Fourier transform, we investigate the structural characteristics of genomes for several viruses. The mutual correlations and ordering of the different nucleotides in genomes are compared versus their counterparts from the random sequences with the same nucleotide composition. In order to assess the stastical sig...

    journal_title:Journal of biomolecular structure & dynamics

    pub_type: 杂志文章

    doi:10.1080/07391102.1994.10508741

    authors: Chechetkin VR,Knizhnikova LA,Turygin AYu

    更新日期:1994-10-01 00:00:00

  • Spectroscopic and molecular modeling approaches to investigate the binding of proton pump inhibitors to human serum albumin.

    abstract::The interaction between two proton pump inhibitors viz., omeprazole (OME) and esomeprazole (EPZ) with human serum albumin (HSA) was studied by fluorescence, absorption, circular dichroism (CD), Fourier transform infrared spectroscopy (FT-IR), voltammetry, and molecular modeling approaches. The Stern-Volmer quenching c...

    journal_title:Journal of biomolecular structure & dynamics

    pub_type: 杂志文章

    doi:10.1080/07391102.2016.1251337

    authors: Pawar SK,Punith R,Naik RS,Seetharamappa J

    更新日期:2017-11-01 00:00:00

  • Docking and DFT studies on ligand binding to Quercetin 2,3-dioxygenase.

    abstract::Simple molecular docking calculations on quercetin, kojic acid and diethylcarbamatodithoic acid using the software package MOE are shown to be close to the geometries reported in the X-ray crystal structures of the protein co-crystallized with the respective ligands. Furthermore, DFT optimization of the docked conform...

    journal_title:Journal of biomolecular structure & dynamics

    pub_type: 杂志文章

    doi:10.1080/07391102.2015.1123190

    authors: Malkhasian AY,Howlin BJ

    更新日期:2016-11-01 00:00:00

  • An insight into selective and potent inhibition of histone deacetylase 8 through induced-fit docking, pharmacophore modeling and QSAR studies.

    abstract::Histone deacetylase 8 (HDAC8) has emerged as an important therapeutic target due to its involvement in various cancerous and neurodegenerative disease states. Since pan HDAC inhibition has been linked to various side effects, the need of the hour is to develop inhibitors truly selective for one isoform. This work atte...

    journal_title:Journal of biomolecular structure & dynamics

    pub_type: 杂志文章

    doi:10.1080/07391102.2019.1567388

    authors: Kashyap K,Kakkar R

    更新日期:2020-01-01 00:00:00

  • Biophysical studies of mutated K562 DNA (erythroleukemic cells) binding to adriamycin and daunomycin reveal that mutations induce structural changes influencing binding behavior.

    abstract::K562 cells are erythroleukemic cells derived from a chronic myeloid leukemia patient in blast crisis. Comparison of the genome from K562 cells and normal human genome has been very useful strategy, in uncovering eight genes, implicated in acute myeloid leukemia (AML). These genes carry mutations in K562 genome and the...

    journal_title:Journal of biomolecular structure & dynamics

    pub_type: 杂志文章

    doi:10.1080/07391102.2012.698190

    authors: Ghosh D,Saha C,Hossain M,Dey SK,Kumar GS

    更新日期:2013-03-01 00:00:00

  • Flexibility of DNA and RNA upon binding to different metal cations. An investigation of the B to A to Z conformational transition by Fourier transform infrared spectroscopy.

    abstract::The interaction of DNA and RNA with Cu(II), Mg(II), [Co(NH3)6]3+ [Co(NH3)5Cl]2+ chlorides and, cis- and trans-Pt(NH3)2Cl2 (CIS-DDP, trans-DDP) has been studied by Fourier Transform Infrared (FT-IR) spectroscopy and a correlation between metal-base binding and conformational transitions in the sugar pucker has been est...

    journal_title:Journal of biomolecular structure & dynamics

    pub_type: 杂志文章

    doi:10.1080/07391102.1985.10507615

    authors: Theophanides T,Tajmir-Riahi HA

    更新日期:1985-02-01 00:00:00

  • Exploration of the effects of sequence variations between HIV-1 and HIV-2 proteases on their three-dimensional structures.

    abstract::HIV protease inhibitors (PIs) approved by the FDA (US Food and Drug Administration) are a major class of antiretroviral. HIV-2 protease (PR2) is naturally resistant to most of them as PIs were designed for HIV-1 protease (PR1). In this study, we explored the impact of amino-acid substitutions between PR1 and PR2 on th...

    journal_title:Journal of biomolecular structure & dynamics

    pub_type: 杂志文章

    doi:10.1080/07391102.2019.1704877

    authors: Triki D,Kermarrec M,Visseaux B,Descamps D,Flatters D,Camproux AC,Regad L

    更新日期:2020-10-01 00:00:00

  • Handedness of structural units depends on their mutual arrangement in protein structure.

    abstract::Communicated by Ramaswamy H. Sarma. ...

    journal_title:Journal of biomolecular structure & dynamics

    pub_type: 信件

    doi:10.1080/07391102.2019.1580220

    authors: Efimov AV

    更新日期:2020-02-01 00:00:00

  • In search of AKT kinase inhibitors as anticancer agents: structure-based design, docking, and molecular dynamics studies of 2,4,6-trisubstituted pyridines.

    abstract::The AKT isoforms are a group of key kinases that play a critical role in tumorigenesis. These enzymes are overexpressed in different types of cancers, such as breast, colon, prostate, ovarian, and lung. Because of its relevance the AKT isoforms are attractive targets for the design of anticancer molecules. However, it...

    journal_title:Journal of biomolecular structure & dynamics

    pub_type: 杂志文章

    doi:10.1080/07391102.2017.1285724

    authors: Trejo-Soto PJ,Hernández-Campos A,Romo-Mancillas A,Medina-Franco JL,Castillo R

    更新日期:2018-02-01 00:00:00

  • Monte-Carlo simulation of DNA duplex hydration. B and B' conformations of poly(dA).poly(dT) have different hydration shells.

    abstract::Monte-Carlo simulation of poly(dA).poly(dT) hydration by 30 water molecules per nucleotide pair has been performed. Two B-family conformations, both with a 36 degrees helical twist but with different minor groove widths, were considered. One conformation is Arnott's standard B form, the other one is specific for poly(...

    journal_title:Journal of biomolecular structure & dynamics

    pub_type: 杂志文章

    doi:10.1080/07391102.1988.10506508

    authors: Poltev VI,Teplukhin AV,Chuprina VP

    更新日期:1988-12-01 00:00:00

  • Effect of seven Indian plant extracts on Fenton reaction-mediated damage to DNA constituents.

    abstract::The influences of substoichiometric amounts of seven plant extracts in the Fenton reaction-mediated damage to deoxynucleosides, deoxynucleoside monophosphates, deoxynucleoside triphosphates, and supercoiled plasmid DNA were studied to rationalize anticancer properties reported in some of these extracts. Extracts from ...

    journal_title:Journal of biomolecular structure & dynamics

    pub_type: 杂志文章

    doi:10.1080/07391102.2016.1244493

    authors: Kar I,Chattopadhyaya R

    更新日期:2017-11-01 00:00:00

  • Computational investigation of potential inhibitors of novel coronavirus 2019 through structure-based virtual screening, molecular dynamics and density functional theory studies.

    abstract::Despite the intensive research efforts towards antiviral drug against COVID-19, no potential drug or vaccines has not yet discovered. Initially, the binding site of COVID-19 main protease was predicted which located between regions 2 and 3. Structure-based virtual screening was performed through a hierarchal mode of e...

    journal_title:Journal of biomolecular structure & dynamics

    pub_type: 杂志文章

    doi:10.1080/07391102.2020.1791957

    authors: Mishra SS,Ranjan S,Sharma CS,Singh HP,Kalra S,Kumar N

    更新日期:2020-07-15 00:00:00

  • A novel method to analyze the similarity of biological sequences.

    abstract::In this paper, we propose a new method based on the 2-D graphical representation to analyze the similarity of biological sequences and classify the protein secondary structure sequences. Instead of computing some characteristics from the distance matrix, the average area surrounded by the curve and X axis is computed ...

    journal_title:Journal of biomolecular structure & dynamics

    pub_type: 杂志文章

    doi:10.1080/07391102.2009.10507275

    authors: Huang W,Guo Y,Zhang J

    更新日期:2009-04-01 00:00:00

  • Left-handed βαβ-units: frequency of occurrence and arrangement in protein structure.

    abstract::Communicated by Ramaswamy H. Sarma. ...

    journal_title:Journal of biomolecular structure & dynamics

    pub_type: 信件

    doi:10.1080/07391102.2019.1591306

    authors: Kargatov AM,Efimov AV

    更新日期:2020-03-01 00:00:00

  • Structure of the nucleosome core particle at 8 A resolution.

    abstract::The x-ray crystallographic structure of the nucleosome core particle has been determined using 8 A resolution diffraction data. The particle has a mean diameter of 106 A and a maximum thickness of 65 A in the superhelical axis direction. The longest chord through the histone core measures 85 A and is in a non-axial di...

    journal_title:Journal of biomolecular structure & dynamics

    pub_type: 杂志文章,评审

    doi:10.1080/07391102.1989.10507747

    authors: Uberbacher EC,Bunick GJ

    更新日期:1989-08-01 00:00:00

  • An in-silico analysis of ivermectin interaction with potential SARS-CoV-2 targets and host nuclear importin α.

    abstract::Ivermectin (IVM) is a broad-spectrum antiparasitic agent, having inhibitory potential against wide range of viral infections. It has also been found to hamper SARS-CoV-2 replication in vitro, and its precise mechanism of action against SARS-CoV-2 is yet to be understood. IVM is known to interact with host importin (IM...

    journal_title:Journal of biomolecular structure & dynamics

    pub_type: 杂志文章

    doi:10.1080/07391102.2020.1841028

    authors: Azam F,Taban IM,Eid EEM,Iqbal M,Alam O,Khan S,Mahmood D,Anwar MJ,Khalilullah H,Khan MU

    更新日期:2020-11-02 00:00:00

  • Cyanobacterial metabolites as promising drug leads against the Mpro and PLpro of SARS-CoV-2: an in silico analysis.

    abstract::A novel severe acute respiratory syndrome coronavirus (SARS-CoV-2) has emerged as the causative agent behind the coronavirus disease 2019 (COVID-19) pandemic. Treatment efforts have been severely impeded due to the lack of specific effective antiviral drugs for the treatment of COVID-associated pathologies. In the pre...

    journal_title:Journal of biomolecular structure & dynamics

    pub_type: 杂志文章

    doi:10.1080/07391102.2020.1794972

    authors: Naidoo D,Roy A,Kar P,Mutanda T,Anandraj A

    更新日期:2020-07-21 00:00:00

  • Sequence selectivity, a test of the nature of the covalent adduct formed between benzo[a]pyrene and DNA.

    abstract::A theoretical study is presented of the energetic and structural properties of covalent adducts of benzo[a]pyrene and a DNA fragment. Energy optimisation is performed with the use of minimiser with constraints and an advanced semiempirical energy formula. Three types of adducts are studied: an external complex with th...

    journal_title:Journal of biomolecular structure & dynamics

    pub_type: 杂志文章

    doi:10.1080/07391102.1987.10507682

    authors: Zakrzewska K,Pullman B

    更新日期:1987-04-01 00:00:00

  • Novel oseltamivir-resistant mutations distant from the active site of influenza B neuraminidase.

    abstract::We performed a neuraminidase sequence analysis of thirty-two pediatric patients with influenza B who visited Teikyo University Hospital from January 2016 to March 2017, and found oseltamivir-resistant samples belonging to the Yamagata and Victoria lineages. Comparison with the neuraminidase sequence of oseltamivir-sus...

    journal_title:Journal of biomolecular structure & dynamics

    pub_type: 杂志文章

    doi:10.1080/07391102.2020.1765872

    authors: Kato Y,Takahashi K,Ito F,Suzuki S,Fukui K,Mimaki M,Suzuki K

    更新日期:2020-05-25 00:00:00

  • Using recurrence quantification analysis descriptors for protein sequence classification with support vector machines.

    abstract::In this work, we integrate a non-linear signal analysis method, recurrence quantification analysis (RQA), with the well-known machine-learning algorithm, support vector machines for the binary classification of protein sequences. Two different classification problems were selected, discriminating between aggregating a...

    journal_title:Journal of biomolecular structure & dynamics

    pub_type: 杂志文章

    doi:10.1080/07391102.2007.10507177

    authors: Mitra J,Mundra P,Kulkarni BD,Jayaraman VK

    更新日期:2007-12-01 00:00:00