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https://www.readbyqxmd.com/read/28330175/exploration-of-the-binding-modes-of-l-asparaginase-complexed-with-its-amino-acid-substrates-by-molecular-docking-dynamics-and-simulation
#1
Erva Rajeswara Reddy, Rajulapati Satish Babu, Potla Durthi Chandrasai, Pola Madhuri
Acute lymphocytic leukemia (ALL) is an outrageous disease worldwide. L-Asparagine (L-Asn) and L-glutamine (L-Gln) deamination plays crucial role in ALL treatment. Role of Erwinaze(®) (L-asparaginase from Erwinia chrysanthemi) in regulation of L-Asn and L-Gln has been confirmed by the experimental studies. Therapeutic research against ALL remained elusive with the lack of structural information on Erwinaze(®) enzyme. In this present study, homology model of the Erwinaze(®) was developed using MODELLER and the same was validated by various quality indexing tools...
June 2016: 3 Biotech
https://www.readbyqxmd.com/read/28330159/in-silico-characterization-and-differential-expression-pattern-analysis-of-conserved-hmg-coa-reductase-domain-isolated-from-aconitum-balfourii-stapf
#2
Eti Sharma, Saurabh Pandey, A K Gaur
The 3-hydroxy-3-methyl glutaryl CoA reductase (HMGR) is the key enzyme of mevalonate pathway in plants. A partial genomic DNA fragment encoding HMGR conserved domain (denoted as AbHMGR) is isolated from Aconitum balfourii Stapf. It comprises 871 bp encoding 290 amino acids. In silico analysis reveals that it had extensive similarities to other plant HMGR gene. Domain analysis of AbHMGR showed two highly conserved NADPH and HMG CoA domains. Docking study predicted inhibitor, substrate and cofactor binding sites in the protein...
June 2016: 3 Biotech
https://www.readbyqxmd.com/read/28330095/potential-mosquito-repellent-compounds-of-ocimum-species-against-3n7h-and-3q8i-of-anopheles-gambiae
#3
Venugopal Gaddaguti, Talluri Venkateswara Rao, Allu Prasada Rao
Mosquitoes are exceptionally efficient in detecting their hosts for blood meal using odorant binding proteins, viz. 3N7H and 3Q8I and spread several dreadful diseases. DEET is a synthetic mosquito repellent widely used all over world for protection against mosquito bite. Reports reveal that, synthetic mosquito repellents may pose health problems in considerably large population. In view of the above fact, we made an attempt to discover efficient and novel natural mosquito repellent compounds with least impact on human health...
June 2016: 3 Biotech
https://www.readbyqxmd.com/read/28330089/discovery-of-potential-alk-inhibitors-by-virtual-screening-approach
#4
Anish Kumar, V Shanthi, K Ramanathan
Crizotinib is an anticancer drug used for the treatment of non-small cell lung cancer. Evidences available suggest that there is a development of an acquired resistance against crizotinib action due to the emergence of several mutations in the ALK gene. It is therefore necessary to develop potent anti-cancer drugs for the treatment of crizotinib resistance non-small cell lung cancer types. In the present study, a novel class of lead molecule was identified using virtual screening, molecular docking and molecular dynamic approach...
June 2016: 3 Biotech
https://www.readbyqxmd.com/read/28330072/molecular-dynamic-simulations-of-escherichia-coli-l-asparaginase-to-illuminate-its-role-in-deamination-of-asparagine-and-glutamine-residues
#5
Rajeswara Reddy Erva, Satish Babu Rajulapati, Chandrasai Potla Durthi, Mayuri Bhatia, Madhuri Pola
Acute lymphocytic leukemia (ALL) is an outrageous disease worldwide. L-Asparagine (L-Asn) and L-Glutamine (L-Gln) deamination play a crucial role in ALL treatment. Role of Elspar(®) (L-asparaginase from Escherichia coli) in regulation of L-Asn and L-Gln has been confirmed by the other researchers through experimental studies. Therapeutic research against ALL remained elusive with the lack of information on molecular interactions of Elspar(®) with amino acid substrates. In the present study, using different docking tools binding cavities, key residues in binding and ligand binding mechanisms were identified...
June 2016: 3 Biotech
https://www.readbyqxmd.com/read/28329447/formation-of-a-multi-ligand-complex-of-bovine-serum-albumin-with-retinol-resveratrol-and-epigallocatechin-3-gallate-for-the-protection-of-bioactive-components
#6
Yi Wu, Hao Cheng, Yantao Chen, Lingyun Chen, Zheng Fang, Li Liang
Clarification of the interaction mechanisms between proteins and bioactive components is important to develop effective carriers for encapsulation and protection of bioactive components. Bovine serum albumin (BSA), a globular protein in serum and milk, contains multiple sites to bind a variety of low-molecular-weight molecules, forming protein-mono-ligand complexes. In this study, the interactions of BSA with retinol, resveratrol and/or (-)-epigallocatechin-3-gallate (EGCG) were investigated by using fluorescence, circular dichroism and molecular docking techniques...
March 22, 2017: Journal of Agricultural and Food Chemistry
https://www.readbyqxmd.com/read/28328173/design-synthesis-biological-evaluation-and-molecular-docking-of-novel-flavones-as-h3-r-inhibitors
#7
Gang Wen, Qian Liu, Huabin Hu, Dongmei Wang, Song Wu
A series of novel flavone derivatives were designed, synthesized, and evaluated for their H3 R inhibitory activity. The results showed that four compounds exhibited significant anti-H3 R activity. Molecular docking experiments indicated that a salt bridge, hydrogen-bonding, and hydrophobic interactions all contributed to interactions between inhibitors and H3 R. This article is protected by copyright. All rights reserved.
March 22, 2017: Chemical Biology & Drug Design
https://www.readbyqxmd.com/read/28327793/insights-into-cytochrome-bc1-complex-binding-mode-of-antimalarial-2-hydroxy-1-4-naphthoquinones-through-molecular-modelling
#8
Ana Carolina Rennó Sodero, Bárbara Abrahim-Vieira, Pedro Henrique Monteiro Torres, Pedro Geraldo Pascutti, Célia Rs Garcia, Vitor Francisco Ferreira, David Rodrigues da Rocha, Sabrina Baptista Ferreira, Floriano Paes Silva
BACKGROUND: Malaria persists as a major public health problem. Atovaquone is a drug that inhibits the respiratory chain of Plasmodium falciparum, but with serious limitations like known resistance, low bioavailability and high plasma protein binding. OBJECTIVES: The aim of this work was to perform molecular modelling studies of 2-hydroxy-1,4-naphthoquinones analogues of atovaquone on the Qo site of P. falciparum cytochrome bc1 complex (Pfbc1) to suggest structural modifications that could improve their antimalarial activity...
April 2017: Memórias do Instituto Oswaldo Cruz
https://www.readbyqxmd.com/read/28327441/structure-based-design-synthesis-and-biological-evaluation-of-amino-phosphonate-derivatives-as-human-glucokinase-activators
#9
Nanda Kumar Yellapu, Ravendra Babu Kilaru, Nagaraju Chamarthi, Sarma Pvgk, Bhaskar Matcha
Glucokinase (GK) is a potential therapeutic target of type 2 diabetes and GK activators (GKAs) represent a promising class of small organic molecules which enhance GK activity. Based on the configuration and conformation of the allosteric site of GK, we have designed a novel class of amino phosphonate derivatives in order to develop potent GKAs. The QSAR model developed using numerous descriptors revealed its potential with the best effective statistical values of RMSE=1.52 and r(2)=0.30. Moreover, application of this model on the present test set GKAs proved to be worthy to predict their activities as a better linear relationship was observed with RMSE=0...
March 2, 2017: Computational Biology and Chemistry
https://www.readbyqxmd.com/read/28327439/an-in-silico-functional-annotation-and-screening-of-potential-drug-targets-derived-from-leishmania-spp-hypothetical-proteins-identified-by-immunoproteomics
#10
Miguel A Chávez-Fumagalli, Mônica S Schneider, Daniela P Lage, Ricardo A Machado-de-Ávila, Eduardo A F Coelho
Leishmaniasis is a parasitic disease caused by the protozoan of the Leishmania genus. While no human vaccine is available, drugs such as pentavalent antimonials, pentamidine and amphotericin B are used for treat the patients. However, the high toxicity of these pharmaceutics, the emergence of parasite resistance and/or their high cost have showed to the urgent need of identify new targets to be employed in the improvement of the treatment against leishmaniasis. In a recent immunoproteomics approach performed in the Leishmania infantum species, 104 antigenic proteins were recognized by antibodies in sera of visceral leishmaniasis (VL) dogs...
March 19, 2017: Experimental Parasitology
https://www.readbyqxmd.com/read/28327436/investigating-the-affinity-of-bde154-and-3oh-bde154-with-hsa-experimental-and-simulation-validation
#11
Wu Yang, Lulu Yang, Zhongsheng Yi, Zhiwei Wu, Jinfang Nie, Aiqian Zhang
The physicochemical properties of polybrominated diphenyl ethers are important for modeling their transport, but these data are often missing. Here, satisfactory bioactivity results were obtained using human serum albumin as the carrier, 2,2',4,4',5,6'-hexabromodiphenyl ether (BDE154) and 3-hydroxy-2,2',4,4', 5,6'-hexabromodiphenyl ether (3OH-BDE154) as the ligands, using UV-visible absorbance, fluorescence, circular dichroism, molecular docking, and molecular dynamics methods. The interactions between human serum albumin and BDE154 or 3OH-BDE154 were verified, consistent with the static quenching procedure...
March 6, 2017: Environmental Toxicology and Pharmacology
https://www.readbyqxmd.com/read/28327306/design-synthesis-antibacterial-activity-and-docking-study-of-some-new-trimethoprim-derivatives
#12
Umer Rashid, Waqas Ahmad, Syed Fahad Hassan, Naveeda Akhtar Qureshi, Basit Niaz, Bakhtiar Muhammad, Sameera Imdad, Muhammad Sajid
In present study, nineteen novel trimethoprim (TMP) derivatives were designed, synthesized and evaluated for their antibacterial potential. Hydroxy trimethoprim 2 (HTMP) was synthesized by following the demethylation of 4-methoxy group at trimethoxy benzyl ring of TMP. Structure-activity relationship (SAR) studies were explored on HTMP by incorporating various substituents leading to the identification of some new compounds with improved antibacterial activities. The results revealed that the introduction of benzyloxy (4a-e) and phenyl ethanone (5a-e) group at 4-position of dimethoxy benzyl ring leads to overall increase in the antibacterial activity...
December 1, 2016: Bioorganic & Medicinal Chemistry Letters
https://www.readbyqxmd.com/read/28325932/a-stochastic-model-of-active-zone-material-mediated-synaptic-vesicle-docking-and-priming-at-resting-active-zones
#13
Jae Hoon Jung, Sebatian Doniach
Synaptic vesicles (SVs) fuse with the presynaptic membrane (PM) at specialized regions called active zones for synaptic transmission. SVs are associated with dense aggregates of macromolecules called active zone material (AZM) that has been thought to be involved in SV release. However, its role has recently begun to be elucidated. Several morphological studies proposed distinctively different AZM mediated SV docking and priming models: sequential and concurrent SV docking/priming. To explore ways to reconcile the contradictory models we develop a stochastic AZM mediated SV docking and priming model...
March 21, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28325601/design-and-synthesis-of-novel-6-aryl-substituted-4-anilinequinazoline-derivatives-as-potential-pi3k%C3%AE-inhibitors
#14
Minhang Xin, Yuan-Yuan Hei, Hao Zhang, Ying Shen, San-Qi Zhang
In this study, a series of new 6-aryl substituted 4-anilinequinazolines was designed and synthesized as PI3Kδ inhibitors based on our reported chemical structures. The preliminary structure-activity relationship (SAR) was established, and compounds 13h and 13k displayed most potent PI3Kδ inhibitory activities with the IC50 values of 9.3nM and 9.7nM, respectively. Compound 13h demonstrated similar anti-proliferative profiles to idelalisib against three human B cell lines. Three key hydrogen bonding interactions were found in the docking of 13h with PI3Kδ enzyme...
March 11, 2017: Bioorganic & Medicinal Chemistry Letters
https://www.readbyqxmd.com/read/28325152/synthesis-computational-and-pharmacological-evaluation-of-n-2-benzoyl-4-chlorophenyl-2-4-substituted-phenyl-piperazin-1-yl-acetamides-as-cns-agents
#15
Shweta Verma, Surendra Kumar, Sushil Kumar
A series of new N-(2-benzoyl-4-chlorophenyl)-2-(4-(substituted phenyl) piperazin-1-yl) acetamides (3a-j) have been synthesized by the chloroacetylation of 2-amino-5-chlorbenzophenone which was further reacted with substituted phenylpiperazine. The chemical structures of the compounds were confirmed on the basis of their TLC, IR, 1HNMR, 13CNMR and by elemental analysis. The physicochemical similarity of the target compounds with respect to standard drug diazepam was assessed by calculating from a set of physicochemical properties using software programs...
March 21, 2017: Central Nervous System Agents in Medicinal Chemistry
https://www.readbyqxmd.com/read/28323889/towards-a-critical-evaluation-of-an-empirical-and-volume-based-solvation-function-for-ligand-docking
#16
Heloisa S Muniz, Alessandro S Nascimento
Molecular docking is an important tool for the discovery of new biologically active molecules given that the receptor structure is known. An excellent environment for the development of new methods and improvement of the current methods is being provided by the rapid growth in the number of proteins with known structure. The evaluation of the solvation energies outstands among the challenges for the modeling of the receptor-ligand interactions, especially in the context of molecular docking where a fast, though accurate, evaluation is ought to be achieved...
2017: PloS One
https://www.readbyqxmd.com/read/28323850/ligand-guided-homology-modelling-of-the-gabab2-subunit-of-the-gabab-receptor
#17
Thibaud Freyd, Dawid Warszycki, Stefan Mordalski, Andrzej J Bojarski, Ingebrigt Sylte, Mari Gabrielsen
γ-aminobutyric acid (GABA) is the main inhibitory neurotransmitter in the central nervous system, and disturbances in the GABAergic system have been implicated in numerous neurological and neuropsychiatric diseases. The GABAB receptor is a heterodimeric class C G protein-coupled receptor (GPCR) consisting of GABAB1a/b and GABAB2 subunits. Two GABAB receptor ligand binding sites have been described, namely the orthosteric GABA binding site located in the extracellular GABAB1 Venus fly trap domain and the allosteric binding site found in the GABAB2 transmembrane domain...
2017: PloS One
https://www.readbyqxmd.com/read/28323527/design-synthesis-and-anticancer-evaluation-of-novel-pyrazole-pyrazolo-3-4-d-pyrimidine-and-their-glycoside-derivatives
#18
Ibrahim F Nassar, Ahmed F El Farargy, Fathy M Abdelrazek, Nasser S M Ismail
The chalcone derivatives 3a,b were cyclized upon reaction with thiourea to give the pyrazolo[3,4-d]pyrimidine derivatives 5a,b. Condensation of 5a,b and their hydrazide derivatives 8a,b with cyclic and acyclic glucose gave the condensed S- and N-glycosides 7a,b and 9a,b, respectively. Reaction of 3b with ethyl cyanoacetate followed by reaction with cyclic glucose afforded a mixture of the O- and/or N-glycoside isomers 12 and 13, respectively. The pyrazolo[3,4-c]pyrazole derivative 14 was also obtained from the reaction of 3b with hydrazine hydrate...
March 21, 2017: Nucleosides, Nucleotides & Nucleic Acids
https://www.readbyqxmd.com/read/28323400/stepwise-loop-insertion-strategy-for-active-site-remodeling-to-generate-novel-enzyme-functions
#19
Md Anarul Hoque, Yong Zhang, Liuqing Chen, Guang-Yu Yang, Mst Afroza Khatun, Hai-Feng Chen, Liu Hao, Yan Feng
The remodeling of active sites to generate novel biocatalysts is an attractive and challenging task. We developed a stepwise loop insertion strategy (StLois), in which randomized residue pairs are inserted into active site loops. The phosphotriesterase-like lactonase from Geobacillus kaustophilus (GkaP-PLL) was used to investigate StLois's potential for changing enzyme function. By inserting 6 residues into active site loop7, the best variant ML7-B6 demonstrated a 16 fold further increase in catalytic efficiency toward ethyl-paraoxon compared with its initial template, that is a 609-fold higher, >107 fold substrate specificity shift relative to that of wild-type lactonase...
March 21, 2017: ACS Chemical Biology
https://www.readbyqxmd.com/read/28322965/inhibitory-effect-of-hesperetin-on-%C3%AE-glucosidase-molecular-dynamics-simulation-integrating-inhibition-kinetics
#20
Yan Gong, Xiu-Yuan Qin, Yuan-Yuan Zhai, Hao Hao, Jinhyuk Lee, Yong-Doo Park
The α-glucosidase inhibitor is of interest to researchers due to its association with type-2 diabetes treatment. Hesperetin is a flavonoid with natural antioxidant properties. This paper presents an evaluation on the effects of hesperetin on α-glucosidase via inhibitory kinetics using a Molecular Dynamics (MD) simulation integration method. Due to the antioxidant properties of hesperetin, it reversibly inhibits α-glucosidase in a slope-parabolic mixed-type manner (IC50=0.38±0.05mM; Kslope=0.23±0.01mM), accompanied by tertiary structural changes...
March 17, 2017: International Journal of Biological Macromolecules
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