Computer-aided drug design of novel PLA2 inhibitor candidates for treatment of snakebite.

Abstract:

:Phospholipases A(2) (PLA(2)) are enzymes commonly found in snake venoms from Viperidae and Elaphidae families, which are major components thereof. Many plants are used in traditional medicine as active agents against various effects induced by snakebite. This article presents the PLA(2) BthTX-I structure prediction based on homology modeling. In addition, we have performed virtual screening in a large database yielding a set of potential bioactive inhibitors. A flexible docking program was used to investigate the interactions between the receptor and the new ligands. We have performed molecular interaction fields (MIFs) calculations with the phospholipase model. Results confirm the important role of Lys49 for binding ligands and suggest three additional residues as well. We have proposed a theoretically nontoxic, drug-like, and potential novel BthTX-I inhibitor. These calculations have been used to guide the design of novel phospholipase inhibitors as potential lead compounds that may be optimized for future treatment of snakebite victims as well as other human diseases in which PLA(2) enzymes are involved.

journal_name

J Biomol Struct Dyn

authors

Hage-Melim LI,da Silva CH,Semighini EP,Taft CA,Sampaio SV

doi

10.1080/07391102.2009.10507293

subject

Has Abstract

pub_date

2009-08-01 00:00:00

pages

27-36

issue

1

eissn

0739-1102

issn

1538-0254

pii

d=3035&c=4288&p=17548&do=detail

journal_volume

27

pub_type

杂志文章
  • Molecular dynamics simulations reveal structural differences among wild-type NPC1 protein and its mutant forms.

    abstract::NPC1 is a 25-exon gene located on the long arm of chromosome 18q11.2 and encodes NPC1, a transmembrane protein comprising 1278 amino acid residues. Mutations in the NPC1 gene can cause Niemann-Pick disease type C (NP-C), a rare autosomal-recessive neurovisceral disease. We assessed mutant protein folding using compute...

    journal_title:Journal of biomolecular structure & dynamics

    pub_type: 杂志文章

    doi:10.1080/07391102.2019.1664324

    authors: Martínez-Archundia M,Hernández Mojica TG,Correa-Basurto J,Montaño S,Camacho-Molina A

    更新日期:2020-08-01 00:00:00

  • DNA sequences at and between the GC and TATA boxes: potential DNA looping and spatial juxtapositioning of the protein factors.

    abstract::Regulation of gene expression in eukaryotes involves a complex assembly of DNA recognition sequence elements and their respective protein factors. The upstream promoter/enhancer sequences are position and orientation independent. Despite their variable distances from the TATA box and transcription start site, interact...

    journal_title:Journal of biomolecular structure & dynamics

    pub_type: 杂志文章

    doi:10.1080/07391102.1992.10507988

    authors: Nussinov R

    更新日期:1992-06-01 00:00:00

  • Evidence for double helical kappa-carrageenan in aqueous LiI-solution and model for iodide binding.

    abstract::NMR experiments with a 21412 Redfield observation pulse were carried out on a kappa-carrageenan aqueous solution containing 0.5M LiI. A detected hydrogen-bonded proton resonance at approximately 17.6 ppm, is in accordance with an ordered carrageenan structure in the solution similar to the double, parallel-stranded he...

    journal_title:Journal of biomolecular structure & dynamics

    pub_type: 杂志文章

    doi:10.1080/07391102.1993.10508676

    authors: Nerdal W,Haugen F,Knutsen S,Grasdalen H

    更新日期:1993-04-01 00:00:00

  • Prediction of potential inhibitors against SARS-CoV-2 endoribonuclease: RNA immunity sensing.

    abstract::The World Health Organization has classified the COVID-19 outbreak a pandemic which is caused by severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2) and declared it a global health emergency. Repurposing drugs with minimum side effects are one approach to quickly respond in attempt to prevent the spread of CO...

    journal_title:Journal of biomolecular structure & dynamics

    pub_type: 杂志文章

    doi:10.1080/07391102.2020.1863265

    authors: Al-Rashedi NAM,Munahi MG,Ah ALObaidi L

    更新日期:2020-12-27 00:00:00

  • An insight to conserved water molecular dynamics of catalytic and structural Zn(+2) ions in matrix metalloproteinase 13 of human.

    abstract::Matrix Metalloproteinase (MMP)--13 or Collagenase--3 plays a significant role in the formation and remodeling of bone, tumor invasion and causes osteoarthritis. Water molecular dynamic studies of the five (1XUC, 1XUD, 1XUR, 456C, 830C) PDB and solvated structures of MMP-13 in human have been carried out upto 5 ns on a...

    journal_title:Journal of biomolecular structure & dynamics

    pub_type: 杂志文章

    doi:10.1080/07391102.2011.10508591

    authors: Chakrabarti B,Bairagya HR,Mallik P,Mukhopadhyay BP,Bera A

    更新日期:2011-02-01 00:00:00

  • Experimental and computational interaction studies of terbium (III) and lanthanide (III) complexes containing 2,2'-bipyridine with bovine serum albumin and their in vitro anticancer and antimicrobial activities.

    abstract::To investigate the chemotherapeutic and pharmacokinetic aspects of two lanthanide complexes (Tb(III) and La(III) containing 2,2'-bipyridine ligand), in vitro binding studies were carried out with BSA by employing multiple biophysical methods and molecular modeling study. There are different techniques containing fluor...

    journal_title:Journal of biomolecular structure & dynamics

    pub_type: 杂志文章

    doi:10.1080/07391102.2020.1792988

    authors: Aramesh-Boroujeni Z,Aramesh N,Jahani S,Khorasani-Motlagh M,Kerman K,Noroozifar M

    更新日期:2020-07-16 00:00:00

  • Moroccan Medicinal plants as inhibitors against SARS-CoV-2 main protease: Computational investigations.

    abstract::The new Corona-virus, recently called the severe acute respiratory syndrome Coronavirus (SARS-CoV-2) appears for the first time in China and more precisely in Wuhan (December 2019). This disease can be fatal. Seniors, and people with other medical conditions (diabetes, heart disease…), may be more vulnerable and becom...

    journal_title:Journal of biomolecular structure & dynamics

    pub_type: 杂志文章

    doi:10.1080/07391102.2020.1758790

    authors: Aanouz I,Belhassan A,El-Khatabi K,Lakhlifi T,El-Ldrissi M,Bouachrine M

    更新日期:2020-05-06 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

  • Structural analysis, molecular docking and molecular dynamics simulations of G-protein-coupled receptor (kisspeptin) in fish.

    abstract::Kisspeptins are neuropeptide that has emerged as an essential gatekeeper for reproduction and onset of puberty in higher vertebrates including fish. In present study, structural analysis, molecular docking and molecular dynamics simulations of kisspeptin receptor (kiss2r) were carried out, which is a G-protein-coupled...

    journal_title:Journal of biomolecular structure & dynamics

    pub_type: 杂志文章

    doi:10.1080/07391102.2019.1633407

    authors: Rather MA,Dutta S,Guttula PK,Dhandare BC,Yusufzai SI,Zafar MI

    更新日期:2020-05-01 00:00:00

  • Three-dimensional folding of Tetrahymena thermophila rRNA IVS sequence: a proposal.

    abstract::We studied the Tetrahymena thermophila rRNA IVS sequence with the aim of obtaining a model of the structure characterized by the bases proximity of the self-reactions sites. The considered sequence kept up those fragments essential for its catalytic activity as demonstrated by deletion mutants. The first step was the ...

    journal_title:Journal of biomolecular structure & dynamics

    pub_type: 杂志文章

    doi:10.1080/07391102.1991.10507864

    authors: Benedetti G,Morosetti S

    更新日期:1991-04-01 00:00:00

  • Influence of divalent magnesium ion on DNA: molecular dynamics simulation studies.

    abstract::A large amount of experimental evidence is available on the effect of magnesium ions on the structure and stability of DNA double helix. Less is known, however, on how these ions affect the stability and dynamics of the molecule. The static time average pictures from X-ray structures or the quantum chemical energy min...

    journal_title:Journal of biomolecular structure & dynamics

    pub_type: 杂志文章

    doi:10.1080/07391102.2012.713780

    authors: Mukherjee S,Bhattacharyya D

    更新日期:2013-01-01 00:00:00

  • SARS-CoV-2 mutations and where to find them: an in silico perspective of structural changes and antigenicity of the spike protein.

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

    journal_title:Journal of biomolecular structure & dynamics

    pub_type: 信件

    doi:10.1080/07391102.2020.1844052

    authors: Gonçalves RL,Leite TCR,Dias BP,Caetano CCDS,de Souza ACG,Batista UDS,Barbosa CC,Reyes-Sandoval A,Coelho LFL,Silva BM

    更新日期:2020-11-06 00:00:00

  • The comparative analysis of the properties and structures of purine nucleoside phosphorylases from thermophilic bacterium Thermus thermophilus HB27.

    abstract::Two recombinant purine nucleoside phosphorylases from thermophilic bacterium Thermus thermophilus HB27 encoded by genes TT_C1070 (TthPNPI) and TT_C0194 (TthPNPII) were purified and characterized. The comparative analysis of their sequences, molecular weight, enzymes specificity and kinetics of the catalyzed reaction w...

    journal_title:Journal of biomolecular structure & dynamics

    pub_type: 杂志文章

    doi:10.1080/07391102.2020.1848628

    authors: Timofeev VI,Fateev IV,Kostromina MA,Abramchik YA,Konstantinova ID,Volkov VV,Lykoshin DD,Mikheeva OO,Muravieva TI,Esipov RS,Kuranova IP

    更新日期:2020-11-23 00:00:00

  • Disorderness in Escherichia coli proteome: perception of folding fidelity and protein-protein interactions.

    abstract::Traditionally biased usage of synonymous codons renders selective advantage to proteins expressed at high levels with a few exceptions like in Escherichia coli. Proteome-wide characteristics indicative of trends in highly expressed proteins of E. coli is analyzed in this communication. Implications for the nature of i...

    journal_title:Journal of biomolecular structure & dynamics

    pub_type: 杂志文章

    doi:10.1080/07391102.2012.706071

    authors: Kahali B,Ghosh TC

    更新日期:2013-01-01 00:00:00

  • Conformations of complexes derived from the interactions of two stereoisomeric bay-region 5-methylchrysene diol epoxides with DNA.

    abstract::The reaction mechanisms of two isomeric bay-region diol epoxides of 5-methylchrysene (trans-1,2-dihydroxy-anti-3,4-epoxy-1,2,3,4-tetrahydro-5-methylchrysene (DE-I) and trans-7,8-dihydroxy-anti-9,10-epoxy-7,8,9,10-tetrahydro-5-methylchrysene (DE-II) with double-stranded DNA in aqueous solutions were studied utilizing k...

    journal_title:Journal of biomolecular structure & dynamics

    pub_type: 杂志文章

    doi:10.1080/07391102.1986.10508476

    authors: Kim MH,Roche CJ,Geacintov NE,Pope M,Pataki J,Harvey RG

    更新日期:1986-04-01 00:00:00

  • Structural clones of UAG decoding RNA.

    abstract::Functions of non-coding RNAs are related in part to their secondary structures. We investigate the uniqueness of the secondary structure of a non-coding RNA (ncRNA) decoding UAG to read pyrrolysine (pyl). Nineteen archaeal methanogens are searched with our tRNA-pyl-tracker, TPYLT, perl-script downloadable from www.gya...

    journal_title:Journal of biomolecular structure & dynamics

    pub_type: 杂志文章

    doi:10.1080/07391102.2009.10507324

    authors: Das S,Mukherjee R,Sahoo S,Thakkar R,Chakrabarti J

    更新日期:2009-12-01 00:00:00

  • Molecular dynamics simulation of a 13-mer duplex DNA: a PvuII substrate.

    abstract::Parallel version of AMBER 4.1 was ported and optimised on the Indian parallel supercomputer PARAM OpenFrame built around Sun Ultra Sparc processors. This version of AMBER program was then used to carry out molecular dynamics (MD) simulations on 5'-TGACCAGCTGGTC-3', a substrate for PvuII enzyme. MD simulations in water...

    journal_title:Journal of biomolecular structure & dynamics

    pub_type: 杂志文章

    doi:10.1080/07391102.1998.10509009

    authors: Kolaskar AS,Joshi RR

    更新日期:1998-06-01 00:00:00

  • A note on crystal packing and global helix structure in short A-DNA duplexes.

    abstract::A simple relation exists between the packing density in crystals of short A-DNA duplexes and their global double-helical structure. The volume per nucleotide pair shows a linear inverse correlation with the mean displacement of base pairs from the best straight helix axis. The mean displacement is a measure of major g...

    journal_title:Journal of biomolecular structure & dynamics

    pub_type: 杂志文章

    doi:10.1080/07391102.1991.10507846

    authors: Heinemann U

    更新日期:1991-02-01 00:00:00

  • Calculating degree based multiplicative topological indices of Hyaluronic Acid-Paclitaxel conjugates' molecular structure in cancer treatment.

    abstract::A large number of medical experiments have confirmed that the features of drugs have a close correlation with their molecular structure. Drug properties can be obtained by studying the molecular structure of corresponding drugs. The calculation of the topological index of a drug structure enables scientists to have a ...

    journal_title:Journal of biomolecular structure & dynamics

    pub_type: 杂志文章

    doi:10.1080/07391102.2020.1800512

    authors: Jahanbani A,Shao Z,Sheikholeslami SM

    更新日期:2020-07-30 00:00:00

  • 2-aminopurine fluorescence: discrimination between specific and unspecific ligand binding to the kissing-loop dimer of the HIV-1 RNA.

    abstract::The fluorescent 2-aminopurine probe (2-AP) incorporated into the loop of 23-mer RNA hairpin of HIV-1 genome dimerization initiation site (DIS) was used for discrimination of specific and unspecific binding of paromomycin and spermine to the kissing loop dimer (KD) formed in solution. While both ligands stabilized the ...

    journal_title:Journal of biomolecular structure & dynamics

    pub_type: 杂志文章

    doi:10.1080/07391102.2008.10507213

    authors: Kaluzhny DN,Beniaminov AD,Minyat EE

    更新日期:2008-06-01 00:00:00

  • Transmembrane helix 6 observed at the interface of β2AR homodimers in blind docking studies.

    abstract::Peptide- and protein-protein dockings were carried out on β2-adrenergic receptor (β2AR) to confirm the presence of transmembrane helix 6 (TM6) at the interface region between two β2AR monomers, thereby its possible role in dimerization as suggested in numerous experimental and computational studies. Initially, a porti...

    journal_title:Journal of biomolecular structure & dynamics

    pub_type: 杂志文章

    doi:10.1080/07391102.2014.962094

    authors: Koroglu A,Akten ED

    更新日期:2015-01-01 00:00:00

  • A preliminary structure for the DNA binding protein from bacteriophage IKe.

    abstract::A modelling procedure has been utilized to obtain a preliminary three-dimensional structural model for the bacteriophage IKe DNA binding protein (IKe-DBP) based on the known high resolution X-ray diffraction structure of a functionally related protein (G5BP) from bacteriophage fd. The degree of structural homology obs...

    journal_title:Journal of biomolecular structure & dynamics

    pub_type: 杂志文章

    doi:10.1080/07391102.1987.10507683

    authors: Brayer GD

    更新日期:1987-04-01 00:00:00

  • A new bithiazole derivative with intercalative properties.

    abstract::In the course of studies related to new molecules with intercalative properties, we have been led to design and synthesize a bithiazole derivative, namely the 2-phenyl-6-[2'-(4'-(ethoxy-carbonyl)thiazolyl)]thiazolo[3,2- b][1,2,4]triazole (PETT). Its interaction with calf thymus DNA was studied using thermal denaturati...

    journal_title:Journal of biomolecular structure & dynamics

    pub_type: 杂志文章

    doi:10.1080/07391102.1986.10506341

    authors: Houssin R,Helbecque N,Bernier JL,Henichart JP

    更新日期:1986-10-01 00:00:00

  • Probing the effect of a plus 1bp frameshift mutation in protein-DNA interface of domestication gene, NAMB1, in wheat.

    abstract::Transcription factor NAM-B1 has a major role in the process of senescence, which results in higher Fe and Zn concentrations in grains of wild wheat (T. durum; Td). The absence of the wild type NAMB1 in T. aestivum (Ta), one of the cardinal crops essential for more than 1/3rd of the global population, affects Fe and Zn...

    journal_title:Journal of biomolecular structure & dynamics

    pub_type: 杂志文章

    doi:10.1080/07391102.2019.1680435

    authors: Kaul T,Eswaran M,Ahmad S,Thangaraj A,Jain R,Kaul R,Raman NM,Bharti J

    更新日期:2020-08-01 00:00:00

  • Investigation of flap flexibility of β-secretase using molecular dynamic simulations.

    abstract::Flap motif and its dynamics were extensively reported in aspartate proteases, e.g. HIV proteases and plasmepsins. Herein, we report the first account of flap dynamics amongst different conformations of β-secretase using molecular dynamics simulation. Various parameters were proposed and a selected few were picked whic...

    journal_title:Journal of biomolecular structure & dynamics

    pub_type: 杂志文章

    doi:10.1080/07391102.2015.1064831

    authors: Kumalo HM,Bhakat S,Soliman ME

    更新日期:2016-05-01 00:00:00

  • Stereochemistry of 2',5' nucleic acids and their constituents.

    abstract::Shape and dimension of the preferred nucleotide repeats in nucleic acids are found to depend on whether the sugar-phosphate linkage is of 2',5' or 3',5' type. It is shown that a nucleotide which is "compact" in 3',5' nucleic acids is rendered "extended" and vice versa for a given sugar pucker. It is interesting that t...

    journal_title:Journal of biomolecular structure & dynamics

    pub_type: 杂志文章

    doi:10.1080/07391102.1998.10508249

    authors: Premraj BJ,Yathindra N

    更新日期:1998-10-01 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

  • Heterodimerization of the Entamoeba histolytica EhCPADH virulence complex through molecular dynamics and protein-protein docking.

    abstract::EhCPADH is a protein complex involved in the virulence of Entamoeba histolytica, the protozoan responsible for human amebiasis. It is formed by the EhCP112 cysteine protease and the EhADH adhesin. To explore the molecular basis of the complex formation, three-dimensional models were built for both proteins and molecul...

    journal_title:Journal of biomolecular structure & dynamics

    pub_type: 杂志文章

    doi:10.1080/07391102.2016.1151831

    authors: Montaño S,Orozco E,Correa-Basurto J,Bello M,Chávez-Munguía B,Betanzos A

    更新日期:2017-02-01 00:00:00

  • Exploring the effect of D61G mutation on SHP2 cause gain of function activity by a molecular dynamics study.

    abstract::Noonan syndrome (NS) is a common autosomal dominant congenital disorder which could cause the congenital cardiopathy and cancer predisposition. Previous studies reported that the knock-in mouse models of the mutant D61G of SHP2 exhibited the major features of NS, which demonstrated that the mutation D61G of SHP2 could...

    journal_title:Journal of biomolecular structure & dynamics

    pub_type: 杂志文章

    doi:10.1080/07391102.2017.1402709

    authors: Li HL,Ma Y,Zheng CJ,Jin WY,Liu WS,Wang RL

    更新日期:2018-11-01 00:00:00

  • Dynamical study, hydrogen bond analysis, and constant pH simulations of the beta carbonic anhydrase of Methanobacterium thermoautotrophicum.

    abstract::Within the five classes (α, β, γ, δ, and ζ) of carbonic anhydrases (CAs) the first two, containing mammal and plant representatives, are the most studied among all CAs. In this study, we have focused our investigation on the beta-class carbonic anhydrase of Methanobacterium thermoautotrophicum. We investigated both th...

    journal_title:Journal of biomolecular structure & dynamics

    pub_type: 杂志文章

    doi:10.1080/07391102.2015.1025100

    authors: Bracht F,de Alencastro RB

    更新日期:2016-01-01 00:00:00