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Computational drug design

Abdulkadir Kocak, Ismail Erol, Muslum Yildiz, Hatice Can
Developing small compound based drugs targeting the β-secretase (BACE) enzyme is one of the most promising strategies in treatment of the Alzheimer's disease. As the enzyme shows the activity based on the acid-base reaction at a very narrow pH range, the protonation state of aspartic acids with the residue number 32 and 228 (Asp32 and Asp228), which forms the active site dyad, along with the protonation state of the ligand (substrate or inhibitor) play very critical role in interactions between the ligand and enzyme...
October 17, 2016: Journal of Molecular Graphics & Modelling
Arathi Kizhedath, Simon Wilkinson, Jarka Glassey
Biopharmaceuticals, monoclonal antibody (mAb)-based therapeutics in particular, have positively impacted millions of lives. MAbs and related therapeutics are highly desirable from a biopharmaceutical perspective as they are highly target specific and well tolerated within the human system. Nevertheless, several mAbs have been discontinued or withdrawn based either on their inability to demonstrate efficacy and/or due to adverse effects. Approved monoclonal antibodies and derived therapeutics have been associated with adverse effects such as immunogenicity, cytokine release syndrome, progressive multifocal leukoencephalopathy, intravascular haemolysis, cardiac arrhythmias, abnormal liver function, gastrointestinal perforation, bronchospasm, intraocular inflammation, urticaria, nephritis, neuropathy, birth defects, fever and cough to name a few...
October 20, 2016: Archives of Toxicology
David A Winkler
Nanoparticles are finding many applications in medicine and other field like photonics. Magnetic nanoparticles have additional advantages in medicine over non-magnetic hard nanoparticles, as their magnetic properties make them ideal for hyperthermic applications in therapy and for sensitive diagnostic imaging applications. I review the literature on computational models of the magnetic properties of nanoparticles specifically. Such models have the potential to accelerate the design of magnetic nanoparticles for medical applications...
October 18, 2016: Current Medicinal Chemistry
Lee N Newcomer, Richard Weininger, Robert W Carlson
PURPOSE: To evaluate a computer-based prior authorization system that was designed to include and test two new concepts for physician review: (1) the tool would minimize denials by providing real-time decision support with alternative options if the original request was noncompliant, and (2) the tool would collect sufficient information to create a patient registry. METHODS: A new prior authorization tool incorporating real-time decision support was tested with a large national payer...
October 18, 2016: Journal of Oncology Practice
Sanjay Kumar Dey, Pankaj Prabhakar, Manisha Saini, Toyanji Joseph, B K Thelma, Subir K Maulik, Suman Kundu
OBJECTIVE: To identify novel inhibitors of dopamine beta hydroxylase (DBH) and evaluate their antihypertensive properties in L-NAME induced hypertensive rat model. DESIGN AND METHOD: An experimentally validated computational model for hDBH, built in our lab, was used for structure-based, rational drug-design. The three-dimensional model was used for virtual-screening against small molecule databases from NCI, USA and elsewhere. Identified top hits were then tested in vitro against DBH with known inhibitors nepicastat and disulfiram as controls...
September 2016: Journal of Hypertension
Fatiha Benmansour, Iuni Trist, Bruno Coutard, Etienne Decroly, Gilles Querat, Andrea Brancale, Karine Barral
With the aim to help drug discovery against dengue virus (DENV), a fragment-based drug design approach was applied to identify ligands targeting a main component of DENV replication complex: the NS5 AdoMet-dependent mRNA methyltransferase (MTase) domain, playing an essential role in the RNA capping process. Herein, we describe the identification of new inhibitors developed using fragment-based, structure-guided linking and optimization techniques. Thermal-shift assay followed by a fragment-based X-ray crystallographic screening lead to the identification of three fragment hits binding DENV MTase...
October 5, 2016: European Journal of Medicinal Chemistry
Ren-Yu Qu, Jing-Fang Yang, Yu-Chao Liu, Qiong Chen, Ge-Fei Hao, Cong-Wei Niu, Zhen Xi, Guang-Fu Yang
BACKGOUND: Acetohydroxyacid synthase (AHAS; EC is the first common enzyme in the biosynthetic pathway leading to the branched-chain amino acids in plants and a wide range of microorganisms. With the long-term and wide application of AHAS inhibitors, weed resistance is becoming a global problem, which leads to an urgent demand for novel inhibitors to antagonize both wild-type and resistant AHAS. RESULTS: Pyrimidinyl-Salicylic acid derivatives, as one of the main classes of commercial AHAS herbicides, show potential anti-resistant bioactivity to wild-type and P197L mutant...
October 17, 2016: Pest Management Science
Jenny M Pedersen, Yoo-Sik Shim, Vaibhav Hans, Martin B Phillips, Jeffrey M Macdonald, Glenn Walker, Melvin E Andersen, Harvey J Clewell, Miyoung Yoon
Accurate prediction of metabolism is a significant outstanding challenge in toxicology. The best predictions are based on experimental data from in vitro systems using primary hepatocytes. The predictivity of the primary hepatocyte-based culture systems, however, is still limited due to well-known phenotypic instability and rapid decline of metabolic competence within a few hours. Dynamic flow bioreactors for three-dimensional cell cultures are thought to be better at recapitulating tissue microenvironments and show potential to improve in vivo extrapolations of chemical or drug toxicity based on in vitro test results...
2016: Frontiers in Bioengineering and Biotechnology
Sean Ekins, John Liebler, Bruno J Neves, Warren G Lewis, Megan Coffee, Rachelle Bienstock, Christopher Southan, Carolina H Andrade
The Zika virus (ZIKV) is a flavivirus of the family Flaviviridae, which is similar to dengue virus, yellow fever and West Nile virus. Recent outbreaks in South America, Latin America, the Caribbean and in particular Brazil have led to concern for the spread of the disease and potential to cause Guillain-Barré syndrome and microcephaly. Although ZIKV has been known of for over 60 years there is very little in the way of knowledge of the virus with few publications and no crystal structures. No antivirals have been tested against it either in vitro or in vivo...
2016: F1000Research
P Sneha, C George Priya Doss
The pace of anti-diabetic drug discovery is very slow in spite of increasing rate of prevalence of Type 2 Diabetes which remains a major public health concern. Though extensive research steps are taken in the past decade, yet craves for better of new treatment strategies to overcome the current scenario. One such general finding is the evolution of gliptins which discriminately inhibits DPP4 (Dipeptidyl peptidase-4) enzyme. Although the mechanism of action of gliptin is highly target oriented and accurate, still its long-term use stands unknown...
October 12, 2016: Life Sciences
Shashikant Srivastava, Devyani Deshpande, Jotam G Pasipanodya, Tania Thomas, Soumya Swaminathan, Eric Nuermberger, Tawanda Gumbo
Children with tuberculosis are treated with drug regimens copied from adults despite significant differences in antibiotic pharmacokinetics, pathology, and the microbial burden between childhood and adult tuberculosis. We sought to develop a new and effective oral treatment regimen specific to children of different ages. We investigated and validated the concept that target drug concentrations associated with therapy failure and death in children are different from those of adults. On that basis, we proposed a 4-step program to rapidly develop treatment regimens for children...
November 1, 2016: Clinical Infectious Diseases: An Official Publication of the Infectious Diseases Society of America
Arup K Ghose, Gregory R Ott, Robert L Hudkins
At the drug discovery stage, it is important to understand the design concepts of a CNS drug compared to a non-CNS drug. Previously we published on ideal CNS drug space and defined in detail the physicochemical property space distribution of CNS and non-CNS oral drugs, the application of radar charting (a graphical representation of multiple physicochemical properties used during CNS lead optimization) and a recursive partition classification tree to differentiate between CNS and non-CNS drugs. The objective of the present study was to further the understanding of differentiations between CNS and non-CNS oral drugs into the development and application of an effective CNS algorithm TEMPO (Technically Extended Multiparameter Optimization)...
October 14, 2016: ACS Chemical Neuroscience
Nan Gao, Tao Liang, Yuan Yuan, Xiuchan Xiao, Yihuan Zhao, Yanzhi Guo, Menglong Li, Xuemei Pu
G-protein-coupled receptors (GPCRs) are important drug targets and generally activated by ligands. However, some experiments found that GPCRs also give rise to constitutive activity through some mutations (viz., CAM), which are usually associated with different kinds of diseases. However, the mechanisms of CAMs and their roles in interactions with drug-ligands are unclear in experiments. Herein, we used microsecond molecular dynamics simulations to study the effect of one important F282L mutation on β2AR in order to address the questions above...
October 13, 2016: Physical Chemistry Chemical Physics: PCCP
Qin Wang, Simone Sciabola, Gabriela Barreiro, Xinjun Hou, Guoyun Bai, Michael J Shapiro, Frank E Koehn, Anabella Villalobos, Matthew P Jacobson
Macrocycles pose challenges for computer-aided drug design due to their conformational complexity. One fundamental challenge is identifying all low-energy conformations of the macrocyclic ring, which is important for modeling target binding, passive membrane permeation, and other conformation-dependent properties. Macrocyclic polyketides are medically and biologically important natural products characterized by structural and functional diversity. Advances in synthetic biology and semi-synthetic methods may enable creation of an even more diverse set of non-natural product polyketides for drug discovery and other applications...
October 12, 2016: Journal of Chemical Information and Modeling
Saghi Sepehri, Lotfollah Saghaie, Afshin Fassihi
The fusion of viral and host cell membranes is mediated using gp41 subunit of the human immunodeficiency virus type 1 (HIV-1) envelope glycoprotein. As the HIV-1 enters the host cells, the two helical regions (HR1 and HR2) in the ectodomain of gp41 form a six-helix bundle, which carries the target and viral cell membranes to close proximity. Steps of this process serve as attractive targets for developing HIV-1 fusion inhibitors. Identification of some novel HIV fusion inhibitors with the goal of blocking the formation of the six-helix bundle was accomplished by computer-aided drug design techniques...
October 12, 2016: Molecular Informatics
Bo Lin, Shihua Xiang, Mengsen Li
Nicotinic acetylcholine receptors (nAChRs) are targets for developing new drugs to treat severe pain, nicotine addiction, Alzheimer disease, epilepsy, etc. α-Conotoxins are biologically and chemically diverse. With 12-19 residues and two disulfides, they can be specifically selected for different nAChRs. Acetylcholine-binding proteins from Aplysia californica (Ac-AChBP) are homologous to the ligand-binding domains of nAChRs and pharmacologically similar. X-ray structures of the α-conotoxin in complex with Ac-AChBP in addition to computer modeling have helped to determine the binding site of the important residues of α-conotoxin and its affinity for nAChR subtypes...
October 11, 2016: Marine Drugs
Jamil Al-Asri, Gyöngyi Gyémánt, Erika Fazekas, Gábor Lehoczki, Matthias F Melzig, Gerhard Wolber, Jérémie Mortier
Better control of postprandial hyperglycemia can be achieved by delaying the absorption of glucose resulting from carbohydrate digestion. Because α-amylase initiates the hydrolysis of polysaccharides, the design of α-amylase inhibitors can lead to the development of new treatments for metabolic disorders such as type II diabetes and obesity. In this study, a rational computer-aided approach was developed to identify novel α-amylase inhibitors. Three-dimensional pharmacophores were developed based on the binding mode analysis of six different families of compounds that bind to this enzyme...
October 11, 2016: ChemMedChem
Stephan Jan Bachmann, Jurij Kotar, Lucia Parolini, Anđela Šarić, Pietro Cicuta, Lorenzo Di Michele, Bortolo Matteo Mognetti
We study phase behaviour of lipid-bilayer vesicles functionalised by ligand-receptor complexes made of synthetic DNA by introducing a modelling framework and a dedicated experimental platform. In particular, we perform Monte Carlo simulations that combine a coarse grained description of the lipid bilayer with state of art analytical models for multivalent ligand-receptor interactions. Using density of state calculations, we derive the partition function in pairs of vesicles and compute the number of ligand-receptor bonds as a function of temperature...
September 20, 2016: Soft Matter
Gennady M Verkhivker
Protein kinases are versatile molecule switches that govern functional processes in signal transduction networks and regulate fundamental biological processes of cell cycle and organism development. The continuous growth of biological information and a remarkable breath of structural, genetic, and pharmacological studies on protein kinase genes have significantly advanced our knowledge of the kinase activation, drug binding and allosteric mechanisms underlying kinase regulation and interactions in signaling cascades...
October 6, 2016: Current Medicinal Chemistry
Jinyan Li, Simon Fong, Shirley Siu, Sabah Mohammed, Jinan Fiaidhi, Kelvin K L Wong
Drug design involves classification of protein binding which is usually done in a computer simulation prior to extensive actual tests. Accurate classification of protein binding is essential but it is obstructed with a very challenging task of feature selection (FS) because there are too many potential features. Dorothea as a case of virtual screening in drug design, has 100,000 features that inflate to a very huge (of size 2(100,000) possible candidate feature subsets to be selected) but very sparse search space...
September 30, 2016: Computerized Medical Imaging and Graphics: the Official Journal of the Computerized Medical Imaging Society
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