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Computational drug design

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https://www.readbyqxmd.com/read/28095555/megasessions-for-robotic-hair-restoration
#1
Joa O Carlos Pereira, Joa O Carlos Pereira Filho, Joa O Pedro Cabrera Pereira
A robotic system can select and remove individual hair follicles from the donor area with great precision and without fatigue. This report describes the use of the robotic system in a megasession for hair restoration. Patients were instructed to cut their hair to 1.0 to 1.2 mm before surgery. The robot selected and removed 600 to 800 grafts per hour so the follicular units (FU)s could be transplanted manually to recipient sites. The robot arm consists of a sharp inner punch and a blunt outer punch which together separate FUs from the sur- rounding tissue...
November 1, 2016: Journal of Drugs in Dermatology: JDD
https://www.readbyqxmd.com/read/28087697/development-of-high-affinity-and-high-specificity-inhibitors-of-metalloproteinase-14-through-computational-design-and-directed-evolution
#2
Valeria Arkadash, Gal Yosef, Jason Shirian, Itay Cohen, Yuval Horev, Moran Grossman, Irit Sagi, Evette S Radisky, Julia M Shifman, Niv Papo
Degradation of the extracellular matrices in the human body is controlled by matrix metalloproteinases (MMPs), a family of more than 20 homologous enzymes. Imbalance in MMP activity can result in many diseases, such as arthritis, cardiovascular diseases, neurological disorders, fibrosis, and cancers. Thus, MMPs present attractive targets for drug design and have been a focus for inhibitor design for as long as three decades. Yet, to date, all MMP inhibitors have failed in clinical trials because of their broad activity against numerous MMP family members and the serious side effects of the proposed treatment...
January 13, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/28076845/molecular-dynamics-simulation-reveals-how-phosphorylation-of-tyrosine-26-of-phosphoglycerate-mutase-1-upregulates-glycolysis-and-promotes-tumor-growth
#3
Yan Wang, Wen-Sheng Cai, Luonan Chen, Guanyu Wang
Phosphoglycerate mutase 1 (PGAM1) catalyzes the eighth step of glycolysis and is often found upregulated in cancer cells. To test the hypothesis that the phosphorylation of tyrosine 26 residue of PGAM1 greatly enhances its activity, we performed both conventional and steered molecular dynamics simulations on the binding and unbinding of PGAM1 to its substrates, with tyrosine 26 either phosphorylated or not. We analyzed the simulated data in terms of structural stability, hydrogen bond formation, binding free energy, etc...
January 5, 2017: Oncotarget
https://www.readbyqxmd.com/read/28074360/exploring-the-stability-of-ligand-binding-modes-to-proteins-by-molecular-dynamics-simulations
#4
Kai Liu, Etsurou Watanabe, Hironori Kokubo
The binding mode prediction is of great importance to structure-based drug design. The discrimination of various binding poses of ligand generated by docking is a great challenge not only to docking score functions but also to the relatively expensive free energy calculation methods. Here we systematically analyzed the stability of various ligand poses under molecular dynamics (MD) simulation. First, a data set of 120 complexes was built based on the typical physicochemical properties of drug-like ligands. Three potential binding poses (one correct pose and two decoys) were selected for each ligand from self-docking in addition to the experimental pose...
January 10, 2017: Journal of Computer-aided Molecular Design
https://www.readbyqxmd.com/read/28072512/a-high-performance-hybrid-bismuth-carbon-nanotube-based-contrast-agent-for-x-ray-ct-imaging
#5
Mayra Hernández-Rivera, Ish Kumar, Stephen Y Cho, Benjamin Y Cheong, Merlyn X Pulikkathara, Sakineh E Moghaddam, Kenton Herbert Whitmire, Lon J Wilson
Carbon nanotubes (CNTs) have been used for a plethora of biomedical applications including their use as delivery vehi-cles for drugs, imaging agents, proteins, DNA, and other materials. Here we describe the synthesis and characterization of a new CNT-based contrast agent (CA) for X-ray computed tomography (CT) imaging. The CA is a hybrid material derived from ultra-short single-walled carbon nanotubes (20-80 nm long, US-tubes) and Bi(III) oxo-salicylate clusters with four Bi(III) ions per cluster (Bi4C). The element bismuth was chosen over iodine, which is the conventional element used for CT CAs in the clinic today, due to its high X-ray attenuation capability and its low toxicity, which make bismuth a more promising element for new CT CA design...
January 10, 2017: ACS Applied Materials & Interfaces
https://www.readbyqxmd.com/read/28070730/cadd-medicine-design-is-the-potion-that-can-cure-my-disease
#6
Eric S Manas, Darren V S Green
The acronym "CADD" is often used interchangeably to refer to "Computer Aided Drug Discovery" and "Computer Aided Drug Design". While the former definition implies the use of a computer to impact one or more aspects of discovering a drug, in this paper we contend that computational chemists are most effective when they enable teams to apply true design principles as they strive to create medicines to treat human disease. We argue that teams must bring to bear multiple sub-disciplines of computational chemistry in an integrated manner in order to utilize these principles to address the multi-objective nature of the drug discovery problem...
January 9, 2017: Journal of Computer-aided Molecular Design
https://www.readbyqxmd.com/read/28070197/a-survey-on-the-prevalence-of-depression-in-blood-donors-with-hepatitis-c-in-shiraz
#7
Leila Kasraian, Neda Negarestani, Mohammad Hossein Karimi, Sahar Dehbidi
BACKGROUND: Depression is the most common psychiatric disorder associated with hepatitis C. OBJECTIVES: This study aimed to survey the prevalence rate of depression in patients with Hepatitis C Virus (HCV) before they were aware of their HCV test result. METHODS: This cross-sectional study was conducted on all blood donors with confirmed positive HCV test results who donated blood between March 21, 2012 to March 21, 2013 at Fars blood transfusion center in Iran as case group and age- and sex-matched blood donors with negative screening test results as control group...
November 2016: Hepatitis Monthly
https://www.readbyqxmd.com/read/28069634/a-review-of-connectivity-map-and-computational-approaches-in-pharmacogenomics
#8
Aliyu Musa, Laleh Soltan Ghoraie, Shu-Dong Zhang, Galina Galzko, Olli Yli-Harja, Matthias Dehmer, Benjamin Haibe-Kains, Frank Emmert-Streib
Large-scale perturbation databases, such as Connectivity Map (CMap) or Library of Integrated Network-based Cellular Signatures (LINCS), provide enormous opportunities for computational pharmacogenomics and drug design. A reason for this is that in contrast to classical pharmacology focusing at one target at a time, the transcriptomics profiles provided by CMap and LINCS open the door for systems biology approaches on the pathway and network level. In this article, we provide a review of recent developments in computational pharmacogenomics with respect to CMap and LINCS and related applications...
January 9, 2017: Briefings in Bioinformatics
https://www.readbyqxmd.com/read/28069262/advanced-modeling-reconciles-counterintuitive-decisions-in-lead-optimization
#9
REVIEW
Ariel Fernández, L Ridgway Scott
Lead optimization (LO) is essential to fulfill the efficacy and safety requirements of drug-based targeted therapy. The ease with which water may be locally removed from around the target protein crucially influences LO decisions. However, inferred binding sites often defy intuition and the resulting LO decisions are often counterintuitive, with nonpolar groups in the drug placed next to polar groups in the target. We first introduce biophysical advances to reconcile these apparent mismatches. We incorporate three-body energy terms that account for the net stabilization of preformed target structures upon removal of interfacial water concurrent with drug binding...
January 6, 2017: Trends in Biotechnology
https://www.readbyqxmd.com/read/28065712/experimentally-reducing-corticosterone-mitigates-rapid-captivity-effects-on-behavior-but-not-body-composition-in-a-wild-bird
#10
Christine R Lattin, Anita V Pechenenko, Richard E Carson
Wild animals and captives display physiological and behavioral differences, and it has been hypothesized, but rarely tested, that these differences are caused by sustained elevation of the hormone corticosterone. We used repeated computed tomography (CT) imaging to examine body composition changes in breeding male and female wild house sparrows (Passer domesticus; n=20) in response to two weeks of captivity, and assessed behavioral changes using video recordings. Half of the birds received the drug mitotane, which significantly decreased stress-induced corticosterone titers compared to controls...
January 5, 2017: Hormones and Behavior
https://www.readbyqxmd.com/read/28059445/computational-de-novo-design-of-antibodies-binding-to-a-peptide-with-high-affinity
#11
Venkata Giridhar Poosarla, Tong Li, Boon Chong Goh, Klaus Schulten, Thomas K Wood, Costas D Maranas
Antibody drugs play a critical role in infectious diseases, cancer, autoimmune diseases, and inflammation. However, experimental methods for the generation of therapeutic antibodies such as using immunized mice or directed evolution remain time consuming and cannot target a specific antigen epitope. Here, we describe the application of a computational framework called OptMAVEn combined with molecular dynamics to de novo design antibodies. Our reference system is antibody 2D10, a single-chain antibody (scFv) that recognizes the dodecapeptide DVFYPYPYASGS, a peptide mimic of mannose-containing carbohydrates...
January 6, 2017: Biotechnology and Bioengineering
https://www.readbyqxmd.com/read/28059043/natural-products-as-anticancerous-therapeutic-molecules-with-special-reference-to-enzymatic-targets-topoisomerase-cox-lox-and-aromatase
#12
Swati Singh, Manika Awasthi, Veda P Pandey, Upendra Dwivedi
Cancer, characterized by uncontrolled growth and proliferation of cells, is affecting millions of people every year and estimated as the second leading cause of death. Its successful treatment yet remains a challenge due to the lack of selectivity, toxicity and the development of multi-drug resistant cells to the currently available drugs. Plant derived natural products hold great promise for discovery and development of new pharmaceuticals against cancer as evident by the fact that out of 121 drugs prescribed for cancer treatment till date, 90 are derived from plant sources...
January 5, 2017: Current Protein & Peptide Science
https://www.readbyqxmd.com/read/28058254/special-issue-novel-antifungal-drug-discovery
#13
Maurizio Del Poeta
This Special Issue is designed to highlight the latest research and development on new antifungal compounds with mechanisms of action different from the ones of polyenes, azoles, and echinocandins. The papers presented here highlight new pathways and targets that could be exploited for the future development of new antifungal agents to be used alone or in combination with existing antifungals. A computational model for better predicting antifungal drug resistance is also presented.
December 2016: Journal of Fungi (Basel, Switzerland)
https://www.readbyqxmd.com/read/28057408/dithiocarbamates-effectively-inhibit-the-%C3%AE-carbonic-anhydrase-from-the-dandruff-producing-fungus-malassezia-globosa
#14
Daniela Vullo, Sonia Del Prete, Alessio Nocentini, Sameh M Osman, Zeid AlOthman, Clemente Capasso, Murat Bozdag, Fabrizio Carta, Paola Gratteri, Claudiu T Supuran
A series of dithiocarbamates (DTCs) was investigated for the inhibition of the β-class carbonic anhydrase (CAs, EC 4.2.1.1) from the fungal parasite Malassezia globosa, MgCA, a validated anti-dandruff drug target. These DTCs incorporate various scaffold, among which those of N,N-dimethylaminoethylenediamine, the aminoalcohols with 3-5 carbon atoms in their molecule, 3-amino-quinuclidine, piperidine, morpholine and piperazine derivatives, as well as phenethylamine and its 4-sulfamoylated derivative. Several DTCs resulted more effective in inhibiting MgCA compared to the standard sulfonamide drug acetazolamide (KI of 74μM), with KIs ranging between 383 and 6235nM...
December 27, 2016: Bioorganic & Medicinal Chemistry
https://www.readbyqxmd.com/read/28054952/computer-aided-drug-design-using-sesquiterpene-lactones-as-sources-of-new-structures-with-potential-activity-against-infectious-neglected-diseases
#15
REVIEW
Chonny Herrera Acevedo, Luciana Scotti, Mateus Feitosa Alves, Margareth De Fátima Formiga Melo Diniz, Marcus Tullius Scotti
This review presents an survey to the biological importance of sesquiterpene lactones (SLs) in the fight against four infectious neglected tropical diseases (NTDs)-leishmaniasis, schistosomiasis, Chagas disease, and sleeping sickness-as alternatives to the current chemotherapies that display several problems such as low effectiveness, resistance, and high toxicity. Several studies have demonstrated the great potential of some SLs as therapeutic agents for these NTDs and the relationship between the protozoal activities with their chemical structure...
January 3, 2017: Molecules: a Journal of Synthetic Chemistry and Natural Product Chemistry
https://www.readbyqxmd.com/read/28045654/information-systems-in-clinical-pharmacy-applied-to-parenteral-nutrition-management-and-traceability-a-systematic-review
#16
Josefa Martínez Gabarrón, Javier Sanz-Valero, Carmina Wanden-Berghe
OBJECTIVE: To review the scientific literature on clinical pharmacy information systems applied to parenteral nutrition (PN) management and traceability. METHOD: A systematic review of the documents retrieved from the MEDLINE (PubMed), Web of Science, Scopus, Cochrane Library, International Pharmaceutical Abstracts (IPA) and Google Scholar databases up to May, 2016. The terms used, as descriptors and free text, were: "Parenteral Nutrition" and "Drug Information Services"...
January 1, 2017: Farmacia Hospitalaria
https://www.readbyqxmd.com/read/28045544/chembench-a-publicly-accessible-integrated-cheminformatics-portal
#17
Stephen Joseph Capuzzi, Ian Sang-June Kim, Wai In Lam, Thomas E Thornton, Eugene N Muratov, Diane Pozefsky, Alexander Tropsha
The enormous increase in the amount of publicly available chemical genomics data and the growing emphasis on data sharing and open science mandates that cheminformaticians make their models publicly available for broad use by the scientific community. Chembench is one of the first publicly-accessible, integrated cheminformatics Web portals. It has been extensively used by researchers from different fields for curation, visualization, analysis, and modeling of chemogenomics data. Since its launch in 2008, Chembench has been accessed more than 1 million times by more than 5K users from a total of 98 countries...
January 3, 2017: Journal of Chemical Information and Modeling
https://www.readbyqxmd.com/read/28043134/factorial-design-based-multivariate-modeling-and-optimization-of-tunable-bioresponsive-arginine-grafted-poly-cystaminebis-acrylamide-diaminohexane-polymeric-matrix-based-nanocarriers
#18
Rongbing Yang, Kihoon Nam, Sung Wan Kim, James Turkson, Ye Zou, Yi Y Zuo, Rahul V Haware, Mahavir B Chougule
Desired characteristics of nanocarriers are crucial to explore its therapeutic potential. This investigation aimed to develop tunable bioresponsive newly synthesized unique arginine grafted poly(cystaminebis(acrylamide)-diaminohexane) [ABP] polymeric matrix based nanocarriers by using L9 Taguchi factorial design, desirability function, and multivariate method. The selected formulation and process parameters were ABP concentration, acetone concentration, the volume ratio of acetone to ABP solution, and drug concentration...
January 3, 2017: Molecular Pharmaceutics
https://www.readbyqxmd.com/read/28042165/coupled-gel-spreading-and-diffusive-transport-models-describing-microbicidal-drug-delivery
#19
Claire Funke, Kelsey MacMillan, Anthony Ham, Andrew J Szeri, David F Katz
Gels are a drug delivery platform that is being evaluated for application of active pharmaceutical ingredients, termed microbicides, that act topically against vaginal and rectal mucosal infection by sexually transmitted HIV. Despite success in one Phase IIb trial of a vaginal gel delivering tenofovir, problems of user adherence to designed gel application scheduling have compromised results in two other trials. The microbicides field is responding to this dilemma by expanding behavioral analysis of the determinants of adherence while simultaneously improving the pharmacological, biochemical, and biophysical analyses of the determinants of microbicide drug delivery...
October 2, 2016: Chemical Engineering Science
https://www.readbyqxmd.com/read/28041833/x-ray-structure-based-evaluation-of-analogs-of-citalopram-compounds-with-increased-affinity-and-selectivity-compared-with-r-citalopram-for-the-allosteric-site-s2-on-hsert
#20
Sid Topiol, Benny Bang-Andersen, Connie Sanchez, Per Plenge, Claus J Loland, Karsten Juhl, Krestian Larsen, Peter Bregnedal, Klaus P Bøgesø
The recent publication of X-ray structures of SERT includes structures with the potent antidepressant S-Citalopram (S-Cit). Earlier predictions of ligand binding at both a primary (S1) and an allosteric modulator site (S2), were confirmed. We provide herein examples of a series of Citalopram analogs, showing distinct structure-activity relationship (SAR) at both sites that is independent of the SAR at the other site. Analogs with a higher affinity and selectivity than benchmark R-Citalopram (R-Cit) for the S2 versus the S1 site were identified...
December 21, 2016: Bioorganic & Medicinal Chemistry Letters
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