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In Silico Pharmacology

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https://www.readbyqxmd.com/read/28726171/qsar-modeling-docking-and-admet-studies-for-exploration-of-potential-anti-malarial-compounds-against-plasmodium-falciparum
#1
Tabish Qidwai
Development of resistance in the Plasmodium falciparum to Artemisinin, the most effective anti-malarial compound, threatens malaria elimination tactics. To gain more efficacious Artemisinin derivatives, QSAR modeling and docking was performed. In the present study, 2D-QSAR model and molecular docking were used to evaluate the Artemisinin compounds and to reveal their binding modes and structural basis of inhibitory activity. Moreover, ADMET-related descriptors have been calculated to predict the pharmacokinetic properties of the effective compounds...
December 2016: In Silico Pharmacology
https://www.readbyqxmd.com/read/28721542/molecular-characterization-modeling-in-silico-analysis-of-equine-pituitary-gonadotropin-alpha-subunit-and-docking-interaction-studies-with-ganirelix
#2
Anuradha Bhardwaj, Varij Nayan, Parvati Sharma, Sanjay Kumar, Yash Pal, Jitender Singh
Equine pituitary gonadotropins (eLH, eFSH, eCG) are heterodimeric glycoprotein hormones with alpha (α) and beta (β) subunits. It is responsible for maintenance of pregnancy in mares during early gestation and fairly valuable for inducing superovulation in animals other than equines. The alpha subunit is common, while beta subunit is species-specific in all glycoprotein hormones. In the present investigation, molecular cloning and in silico characterization including homology modeling and molecular docking analysis of the equine chorionic gonadotropin (eCG) alpha subunit was carried out for gaining structural and functional insights into the eCG alpha subunit and its possible interaction with ganirelix, a gonadotropin-releasing hormone (GnRH) antagonist...
December 2016: In Silico Pharmacology
https://www.readbyqxmd.com/read/28667488/molecular-docking-studies-on-thirteen-fluoroquinolines-with-human-topoisomerase-ii-a-and-b
#3
Ashwini Khanderao Jadhav, Sankunny Mohan Karuppayil
DNA relaxation is an important step in DNA replication. DNA topoisomerases play a major role in DNA relaxation. Hence these enzymes are important targets for cancer drugs. DNA topoisomerase inhibitors bind to the transient enzyme-DNA complex and inhibit DNA replication. Various inhibitors of topoisomerase I and II are prescribed as drugs. Topoisomerase II is considered as an important target for the development of anticancer drugs. In this study we have demonstrated molecular docking of thirteen fluoroquinolines with human DNA topoisomerase II alpha (a) and beta (b)...
December 2016: In Silico Pharmacology
https://www.readbyqxmd.com/read/28653156/revealing-the-potency-of-annona-muricata-leaves-extract-as-foxo1-inhibitor-for-diabetes-mellitus-treatment-through-computational-study
#4
Dini Sri Damayanti, Didik Huswo Utomo, Chandra Kusuma
FOXO1 protein inactivation in the nucleus is one of targets for the treatment of diabetes mellitus. Annona muricata leaves contain flavonoid and phenolic compound alkaloids that were known to be able to increase pancreatic β cell proliferation in animal experiment. This research aimed to predict the active compound ability of the Annona muricata leaves to bind and inhibit FOXO1 protein through in silico study. Analysis of molecular docking was performed by using Autodock Vina PyRx. this research proved that anonaine, rutin, muricatocin a, isolaureline, xylopine, and kaempferol 3-O-rutinoside had an equal or smaller free binding energy compared to the control compound...
December 2016: In Silico Pharmacology
https://www.readbyqxmd.com/read/28534196/in-silico-analysis-of-shiga-toxins-stxs-to-identify-new-potential-vaccine-targets-for-shiga-toxin-producing-escherichia-coli
#5
Maryam Golshani, Mana Oloomi, Saeid Bouzari
Shiga toxins belong to a family of structurally and functionally related toxins serving as the main virulence factors for pathogenicity of the Shiga toxin-producing Escherichia coli (STEC) associating with Hemolytic uremic syndrome (HUS). At present, there is no effective treatment or prevention for HUS. The aim of the present study was to find conserved regions within the amino acid sequences of Stx1, Stx2 (Shiga toxin) and their variants. In this regard, In-silico identification of conformational continuous B cell and T-cell epitopes was performed in order to introduce new potential vaccine candidates...
December 2016: In Silico Pharmacology
https://www.readbyqxmd.com/read/28401513/study-of-intra-inter-species-protein-protein-interactions-for-potential-drug-targets-identification-and-subsequent-drug-design-for-escherichia-coli-o104-h4-c277-11
#6
Shakhinur Islam Mondal, Zabed Mahmud, Montasir Elahi, Arzuba Akter, Nurnabi Azad Jewel, Md Muzahidul Islam, Sabiha Ferdous, Taisei Kikuchi
Protein-protein interaction (PPI) and host-pathogen interactions (HPI) proteomic analysis has been successfully practiced for potential drug target identification in pathogenic infections. In this research, we attempted to identify new drug target based on PPI and HPI computation approaches and subsequently design new drug against devastating enterohemorrhagic Escherichia coli O104:H4 C277-11 (Broad), which causes life-threatening food borne disease outbreak in Germany and other countries in Europe in 2011...
December 2016: In Silico Pharmacology
https://www.readbyqxmd.com/read/27388622/classification-model-of-amino-acid-sequences-prone-to-aggregation-of-therapeutic-proteins
#7
Monika Marczak, Krystyna Okoniewska, Tomasz Grabowski
BACKGROUND: Total body clearance of biological drugs is for the most part dependent on the receptor mechanisms (receptor mediated clearance) and the concentration of antibodies aimed at administered drug - anti-drug-antibodies (ADA). One of the significant factors that induces the increase of ADA level after drug administration could be the aggregates present in the finished product or formed in the organism. Numerous attempts have been made to identify the sequence fragments that could be responsible for forming the aggregates - aggregate prone regions (APR)...
December 2016: In Silico Pharmacology
https://www.readbyqxmd.com/read/27376537/in-silico-proposition-to-predict-cluster-of-b-and-t-cell-epitopes-for-the-usefulness-of-vaccine-design-from-invasive-virulent-and-membrane-associated-proteins-of-c-jejuni
#8
Tahirah Yasmin, Salma Akter, Mouly Debnath, Akio Ebihara, Tsutomu Nakagawa, A H M Nurun Nabi
PURPOSE: Campylobacter jejuni is the one of the leading causes of bacterial diarrheal illness worldwide. This study aims to design specific epitopes for the utility of designing peptide vaccine(s) against C. jejuni by targeting invasive, virulent and membrane associated proteins like FlaA, Cia, CadF, PEB1, PEB3 and MOMP. METHODS: In the present study, various immunoinformatics approaches have been applied to design a potential epitope based vaccine against C. jejuni...
December 2016: In Silico Pharmacology
https://www.readbyqxmd.com/read/26979449/a-momentary-biomarker-for-depressive-mood
#9
REVIEW
Jinhyuk Kim, Toru Nakamura, Yoshiharu Yamamoto
Many biomarkers from genetic, neuroimaging, and biological/biochemical measures have been recently developed in order to make a shift toward the objective evaluation of psychiatric disorders. However, they have so far been less successful in capturing dynamical changes or transitions in pathological states, such as those occurring during the course of clinical treatments or pathogenic processes of disorders. A momentary biomarker is now required for objective monitoring of such dynamical changes. The development of ecological momentary assessment (EMA) allows the assessment of dynamical aspects of diurnal/daily clinical conditions and subjective symptoms...
December 2016: In Silico Pharmacology
https://www.readbyqxmd.com/read/26932471/population-physiologically-based-pharmacokinetic-model-incorporating-lymphatic-uptake-for-a-subcutaneously-administered-pegylated-peptide
#10
Elliot Offman, Colin Phipps, Andrea N Edginton
PURPOSE: Physiologically-based pharmacokinetic (PBPK) models provide a rational mechanistic approach for predicting the time course of macromolecules in plasma. Population PBPK models for large molecules necessitate incorporation of lymphatic circulation to mechanistically account for biodistribution. Moreover, characterization of subcutaneous absorption requires consideration of the microvascular transit from the injection site to the systemic circulation. A PBPK model for a pegylated peptide conjugate, previously developed for primates, was modified to describe the lymphatic uptake in a population of humans by incorporation of interindividual variability in the lymphatic circulation and a unique lymphatic drainage compartment (LDC)...
December 2016: In Silico Pharmacology
https://www.readbyqxmd.com/read/26894412/functioning-of-drug-metabolizing-microsomal-cytochrome-p450s-in-silico-probing-of-proteins-suggests-that-the-distal-heme-active-site-pocket-plays-a-relatively-passive-role-in-some-enzyme-substrate-interactions
#11
Avanthika Venkatachalam, Abhinav Parashar, Kelath Murali Manoj
PURPOSE: The currently held mechanistic understanding of microsomal cytochrome P450s (CYPs) seeks that diverse drug molecules bind within the deep-seated distal heme pocket and subsequently react at the heme centre. To explain a bevy of experimental observations and meta-analyses, we indulge a hypothesis that involves a "diffusible radical mediated" mechanism. This new hypothesis posits that many substrates could also bind at alternate loci on/within the enzyme and be reacted without the pertinent moiety accessing a bonding proximity to the purported catalytic Fe-O enzyme intermediate...
December 2016: In Silico Pharmacology
https://www.readbyqxmd.com/read/26831872/determining-optimal-diagnostic-criteria-through-chronicity-and-comorbidity
#12
Douglas Steinley, Sean P Lane, Kenneth J Sher
PURPOSE: Contemporary approaches to clinical diagnosis have not adequately exploited state-of-the-art empirical techniques in deriving diagnostic criterion sets that are statistically optimal based on 1) relevant external indicators and 2) replicability across data sets. We provide a proof of concept that optimal criterion sets can be derived with respect to alcohol use disorder (AUD) diagnosis that are both more efficient and precise than current systems. METHODS: Using data from the National Epidemiologic Survey on Alcohol and Related Conditions we selected chronicity (i...
December 2016: In Silico Pharmacology
https://www.readbyqxmd.com/read/26820895/molecular-docking-studies-on-inha-maba-and-pank-enzymes-from-mycobacterium-tuberculosis-of-ellagic-acid-derivatives-from-ludwigia-adscendens-and-trewia-nudiflora
#13
Jamil A Shilpi, Mohammad Tuhin Ali, Sanjib Saha, Shihab Hasan, Alexander I Gray, Véronique Seidel
PURPOSE: There is an urgent need to discover and develop new drugs to combat Mycobacterium tuberculosis, the causative agent of tuberculosis (TB) in humans. In recent years, there has been a renewed interest in the discovery of new anti-TB agents from natural sources. In the present investigation, molecular docking studies were carried out on two ellagic acid derivatives, namely pteleoellagic acid (1) isolated from Ludwigia adscendens, and 3,3'-di-O-methyl ellagic acid 4-O-α-rhamnopyranoside (2) isolated from Trewia nudiflora, to investigate their binding to two enzymes involved in M...
December 2015: In Silico Pharmacology
https://www.readbyqxmd.com/read/26820894/in-vitro-cytotoxic-and-in-silico-activity-of-piperine-isolated-from-piper-nigrum-fruits-linn
#14
Padmaa M Paarakh, Dileep Chandra Sreeram, Shruthi S D, Sujan P S Ganapathy
BACKGROUND: Piper nigrum [Piperaceae], commonly known as black pepper is used as medicine fairly throughout the greater part of India and as a spice globally. PURPOSE: To isolate piperine and evaluate in vitro cytotoxic [antiproliferative] activity and in silico method. METHODS: Piperine was isolated from the fruits of P.nigrum. Piperine was characterized by UV,IR, (1)H-NMR, (13)C-NMR and Mass spectrum. Standardization of piperine was done also by HPTLC fingerprinting...
December 2015: In Silico Pharmacology
https://www.readbyqxmd.com/read/26820893/computational-modeling-to-predict-the-functions-and-impact-of-drug-transporters
#15
Pär Matsson, Christel A S Bergström
Transport proteins are important mediators of cellular drug influx and efflux and play crucial roles in drug distribution, disposition and clearance. Drug-drug interactions have increasingly been found to occur at the transporter level and, hence, computational tools for studying drug-transporter interactions have gained in interest. In this short review, we present the most important transport proteins for drug influx and efflux. Computational tools for predicting and understanding the substrate and inhibitor interactions with these membrane-bound proteins are discussed...
December 2015: In Silico Pharmacology
https://www.readbyqxmd.com/read/26820892/highly-conserved-regions-in-ebola-virus-rna-dependent-rna-polymerase-may-be-act-as-a-universal-novel-peptide-vaccine-target-a-computational-approach
#16
Arafat Rahman Oany, Tahmina Sharmin, Afrin Sultana Chowdhury, Tahmina Pervin Jyoti, Md Anayet Hasan
PURPOSE: Ebola virus (EBOV) is such kind of virus which is responsible for 23,825 cases and 9675 deaths worldwide only in 2014 and with an average diseases fatality rate between 25 % and 90 %. Although, medical technology has tried to handle the problems, there is no Food and Drug Administration (FDA)-approved therapeutics or vaccines available for the prevention, post exposure, or treatment of Ebola virus disease (EVD). METHODS: In the present study, we used the immunoinformatics approach to design a potential epitope-based vaccine against the RNA-dependent RNA polymerase-L of EBOV...
December 2015: In Silico Pharmacology
https://www.readbyqxmd.com/read/26820891/use-of-in-silico-assays-to-characterize-the-admet-profile-and-identify-potential-therapeutic-targets-of-fusarochromanone-a-novel-anti-cancer-agent
#17
Madison Wynne El-Saadi, Tara Williams-Hart, Brian A Salvatore, Elahe Mahdavian
PURPOSE: For 30 years nature has provided a plethora of natural products with potential meaningful anti-cancer activity. Fusarochromanone (FC101a) is a small molecule fungal metabolite exhibiting potent in-vitro growth inhibitory effects and is capable of inducing apoptosis, suppressing angiogenesis and tumorigenesis, and inhibiting endothelial cell growth in multiple cancer cell lines. Despite all we know regarding FC101a, the mechanism of action and molecular target(s) of this compound have remained an enigma...
December 2015: In Silico Pharmacology
https://www.readbyqxmd.com/read/26820890/permeation-thresholds-for-hydrophilic-small-biomolecules-across-microvascular-and-epithelial-barriers-are-predictable-on-basis-of-conserved-biophysical-properties
#18
Hemant Sarin
PURPOSE: Neutral small hydrophiles are permeable to varying degrees, across the aqueous pores of phospholipid bilayer protein channels, with their potential for permeation into cells being predictable, on the basis of hydrophilicity and size. Here, it is hypothesized that permeation thresholds for small hydrophiles, across capillary zona occludens tight junction and inter-epithelial junction pore complexes are predictable, on the basis of predicted hydrophilicity in context of predicted molecular size and charge distribution, as are those of cations and anions, on the basis of predicted ionization in context of predicted atomic size...
December 2015: In Silico Pharmacology
https://www.readbyqxmd.com/read/25878948/a-molecular-docking-study-of-phytochemical-estrogen-mimics-from-dietary-herbal-supplements
#19
Chelsea N Powers, William N Setzer
PURPOSE: The purpose of this study is to use a molecular docking approach to identify potential estrogen mimics or anti-estrogens in phytochemicals found in popular dietary herbal supplements. METHODS: In this study, 568 phytochemicals found in 17 of the most popular herbal supplements sold in the United States were built and docked with two isoforms of the estrogen receptor, ERα and ERβ (a total of 27 different protein crystal structures). RESULTS: The docking results revealed six strongly docking compounds in Echinacea, three from milk thistle (Silybum marianum), three from Gingko biloba, one from Sambucus nigra, none from maca (Lepidium meyenii), five from chaste tree (Vitex agnus-castus), two from fenugreek (Trigonella foenum-graecum), and two from Rhodiola rosea...
2015: In Silico Pharmacology
https://www.readbyqxmd.com/read/25717426/high-throughput-molecular-dynamics-for-drug-discovery
#20
Nathaniel Stanley, Gianni De Fabritiis
Molecular dynamics simulations hold the promise to be an important tool for biological research and drug discovery. Historically, however, there were several obstacles for it to become a practical research tool. Limitations in computer hardware had previously made it difficult to simulate for long enough to see interesting biological processes. Recent improvements in hardware and algorithms have largely removed this issue, leaving data analysis as the main obstacle. Advances in Markov state modeling appear to be on the way to remove this obstacle...
2015: In Silico Pharmacology
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