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Current Computer-aided Drug Design

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https://www.readbyqxmd.com/read/28294050/an-integrated-multi-qsar-modeling-approach-for-designing-knoevenagel-type-indoles-with-enhancing-cytotoxic-profiles
#1
Sk Abdul Amin, Nilanjan Adhikari, Tarun Jha, Shovanlal Gayen
BACKGROUND: Unconventional Knoevenagel-type indoles have been the topic of interest of many synthetic chemists because of its promising efficacy in different diseases including in cancer. OBJECTIVE: To explore the structural requirements of Knoevenagel-type cytotoxic indoles for higher efficacy. METHODS: Multi-QSAR modeling (MLR, ANN, SVM, Bayesian classification, HQSAR and Topomer CoMFA) was performed on these analogs. RESULTS: All these modeling techniques were validated individually and interpreted with the experimental SAR observations...
March 9, 2017: Current Computer-aided Drug Design
https://www.readbyqxmd.com/read/28294049/in-silico-analysis-of-amp-activated-protein-kinase-and-ligand-based-virtual-screening-for-identification-of-novel-ampk-activators
#2
Ammarah Ghaffar, Sidra Batool, Gohar Mushtaq, Muhammad Amjad Kamal
BACKGROUND: Adenosine-Monophosphate-Activated protein kinase (AMPK) is a conserved kinase that plays an important role in maintaining the homeostasis of cells. AMPK activation has a positive impact on treatment of diseases such as diabetes, obesity and cancer as well. This observation led to the development of AMPK activators. Certain naturally occurring compounds have also been known to activate AMPK. METHOD: In this study, we retrieved the AMPK activators that includes chemical drugs, xenobiotics and natural compounds and analyzed their interactions with AMPK via docking studies...
March 9, 2017: Current Computer-aided Drug Design
https://www.readbyqxmd.com/read/28294048/computer-aided-structure-based-drug-design-approaches-for-the-discovery-of-new-anti-chikv-agents
#3
Surender Singh Jadav, Barij Nayan Sinha, Rolf Hilgenfeld, Venkatesan Jayaprakash
BACKGROUND: Chikungunya is a viral infection caused by Chikungunya virus (CHIKV), an arbovirus transmitted through mosquito (Aedes aegypti and Aedes albopictus) bite. The virus from sylvatic cycle in Africa mutated to new vector adaptation and became one of the major emerging and re-emerging viral infections in the past decade, affecting more than 40 countries. Efforts are being made by many researches to develop means to prevent and control the infection through vaccines and vector control strategy...
March 9, 2017: Current Computer-aided Drug Design
https://www.readbyqxmd.com/read/28260510/prediction-of-activities-of-braf-v600e-inhibitors-by-sw-mlr-and-ga-mlr-methods
#4
Parinaz Pargolghasemi, Mir Saleh Hoseininezhad-Namin, Aiyoub Parchehbaf Jadid
BACKGROUND: quantitative structure-activity relationship(QSAR) models couldprovide both statistical significanceand useful chemical insights for drug design. The QSARmethod has found applications for predicting diverse properties of organic compounds, including antiviral activities, toxicities and biological activities. In this work, a quantitative structure-activity relationship was utilized for prediction of allosteric BRAF (V600E) inhibitory activities. METHODS: A data set which contains 54 molecules was classified to training and test sets...
March 3, 2017: Current Computer-aided Drug Design
https://www.readbyqxmd.com/read/28260509/adsorption-of-antifungal-drugs-inside-pristine-and-functionalized-fullerenes-and-nanotubes-dft-investigation
#5
Tomasz Pieńko, Monika Grudzień, Przemysław Paweł Taciak, Aleksander Paweł Mazurek
BACKGROUND: Econazole, sulconazole and tioconazole usage as antifungal agents is limited due to poor pharmacokinetic properties. Pristine and hydroxylated structures of the C240 fullerene and single walled carbon nanotube (SWCNT) were proposed as transporters of these imidazoles potentially enhancing their pharmacokinetics. METHODS: To assess possibility of creation of the endohedral complexes of the azoles and carbon nanostructures, their adsorption and interaction energies were calculated with the hybrid exchange-correlation density functional B97-1 and 6-31(d,p) basis set...
March 3, 2017: Current Computer-aided Drug Design
https://www.readbyqxmd.com/read/28260518/molecular-dynamics-simulations-of-novel-potential-inhibitors-for-penicillin-binding-protein-2b-of-the-resistant-5204-strain-of-streptococcus-pneumoniae
#6
Suvaiyarasan Suvaithenamudhan, Subbiah Parthasarathy
BACKGROUND: Top five best hit compounds (ZINC59376795, ZINC60175365, ZINC36922620, ZINC39550705 and ZINC36953975) were obtained through our high throughput virtual screening (HTVS) analysis with resistant 5204-PBP2B (5204 Penicillin Binding Protein 2B) and sensitive R6-PBP2B (R6 Penicillin Binding Protein 2B) proteins of Streptococcus pneumoniae. OBJECTIVE: To gain insight in molecular docking and dynamics simulations of these top five best hit compounds with both resistant 5204-PBP2B and sensitive R6-PBP2B targets...
March 1, 2017: Current Computer-aided Drug Design
https://www.readbyqxmd.com/read/28260517/capi-computational-model-for-apicoplast-inhibitors-prediction-against-plasmodium-parasite
#7
Surabhi Dixit, Deepak Singla
Background Discovery of apicoplast as a drug target offers a new direction in the development of novel anti-malarial compounds, especially against the drug-resistant strains. Drugs such as azithromycin were reported to block the apicoplast development that leads to unusual phenotypes affecting the parasite. This phenomenon suggeststhat identification of new apicoplast inhibitors will aid in the anti-malarial drug discovery. Therefore, in this study, we developed a computational model to predict apicoplast inhibitors by applying state-of-the-art machine learning techniques...
March 1, 2017: Current Computer-aided Drug Design
https://www.readbyqxmd.com/read/28120705/investigation-of-isoindolo-2-1-a-quinoxaline-6-imines-as-topoisomerase-i-inhibitors-with-molecular-modeling-methods
#8
Balazs Balogh, Anna Carbone, Virginia Spanò, Alessandra Montalbano, Paola Barraja, Stella Cascioferro, Patrizia Diana, Barbara Parrino
BACKGROUND: Isoindolo[2,1-a]quinoxalines constitute an important class of compounds which demonstrated potent antiproliferative activity against different human tumor cell lines and topoisomerase I inhibition. In particular, their water soluble imine or iminium salts recently synthesized, showed potent growth inhibitory effect on NCI-60 tumor cell line panel and biological studies performed on the most active compounds demonstrated that they cause DNA damage via topoisomerase I poisoning...
January 23, 2017: Current Computer-aided Drug Design
https://www.readbyqxmd.com/read/28120704/qsar-modeling-of-the-arylthioindole-class-of-colchicine-polymerization-inhibitors-as-anticancer-agents
#9
Elnaz Habibpour, Shahin Ahmadi
BACKGROUND: The health and life of humans have been seriously threatened by cancer for a long period and cancer has become the leading disease-related cause of deaths of human population. Natural products such as colchicine and vinblastine inhibit microtubule assembly by preventing tubulin polymerization. GA-MLR is a powerful search technique based on the evolution of biological systems for QSAR modeling. In this paper, we studied QSAR modeling of some arylthioindole class of colchicine polymerization inhibitors as anticancer agents using GA-MLR and stepwise-MLR...
January 23, 2017: Current Computer-aided Drug Design
https://www.readbyqxmd.com/read/28103771/structure-based-study-of-natural-products-with-anti-schistosoma-activity
#10
Ibezim Akachukwu, Olujide Oludayo Olubiyi, Ata Kosisochukwu, Mbah Chika John, Nwodo Ngozi Justina
Background Schistosomiasis is a parasitic protozoal disease caused by flatworms of the genus Schistosoma. Although the disease threatens millions of lives, it is still at the top list of neglected tropical diseases and praziquantel, the only common schistosocidal drug in use, has records of decreasing efficiency and cases of resistance. Also, reports revealed that people in the rural areas, who are most affected, rely mostly on traditional herbal medicines because of limited access to modern healthcare. The use of computers in drug development has become a routine practice because they are cost and time effective...
January 19, 2017: Current Computer-aided Drug Design
https://www.readbyqxmd.com/read/28103770/integrating-multiple-receptor-conformation-docking-and-multi-dimensional-qsar-for-enhancing-accuracy-of-binding-affinity-prediction
#11
Vangala Radhika, Hassan Araimsh Jaraf, Sivan Sree Kanth, Manga Vijjulatha
BACKGROUND: The accuracy of molecular conformation for Quantitative Structure Activity Relationship (QSAR) studies is an important criteria, and the most favourable bioactive conformer selection is a tough task. Correct ligand alignment as input for 3D-QSAR is an important step that is prone to human biases. Multiple-dimensional QSAR (mQSAR) approach provides a promising alternative to classic 3D-QSAR for drug discovery purposes. OBJECTIVE: Obtaining ligand conformations from multiple receptor conformation docking (MRCD) will reduce the margin of error by incorporating the receptor based alignment of ligand conformations...
January 19, 2017: Current Computer-aided Drug Design
https://www.readbyqxmd.com/read/28222673/editorial-descriptor-spaces-for-qsar-delving-into-the-history-of-the-expanding-frontier
#12
EDITORIAL
Subhash C Basak, Rama K Mishra
No abstract text is available yet for this article.
2017: Current Computer-aided Drug Design
https://www.readbyqxmd.com/read/27897106/predicting-isoform-specific-binding-selectivities-of-benzensulfonamides-using-qsar-and-3d-qsar
#13
Vytautas Raskevicius, Visvaldas Kairys
BACKGROUND: Design of isoform-specific inhibitors is a major challenge in the new therapeutic agents development. METHODS: The article describes the development of a robust selectivity for CA XII QSAR and 3DQSAR models of 40 benzenesulfonamide derivatives bearing pyrimidine moieties using PHASE module of Schrödinger for 3D-QSAR or E-DRAGON and R software for 2D-QSAR. Two QSAR protocols were explored: traditional (affinity) and selectivity (affinity ratio) based...
2017: Current Computer-aided Drug Design
https://www.readbyqxmd.com/read/27748170/screening-of-potential-lead-molecule-as-novel-mure-inhibitor-virtual-screening-molecular-dynamics-and-in-vitro-studies
#14
Kunal Zaveri, Patnala Kiranmayi
BACKGROUND: The prevalence of multi-drug resistance S. aureus is one of the most challenging tasks for the treatment of nosocomial infections. Proteins and enzymes of peptidoglycan biosynthesis pathway are one among the well-studied targets, but many of the enzymes are unexplored as targets. MurE is one such enzyme featured to be a promising target. As MurE plays an important role in ligating the L-lys to stem peptide at third position that is crucial for peptidoglycan synthesis. OBJECTIVE: To screen the potential MurE inhibitor by in silico approach and evaluate the best potential lead molecule by in vitro methods...
2017: Current Computer-aided Drug Design
https://www.readbyqxmd.com/read/27719631/understanding-the-action-of-indolizines-as-biologically-active-moieties-a-molecular-dynamics-study
#15
Beata Szefler, Przemyslaw Czelen, Mircea V Diudea
BACKGROUND: Indolizines represent a class of heteroaromatic compounds, of pharmacological importance, containing two condensed 5- and 6-memebered rings bridged by a nitrogen atom. Despite indolizine is an important medicinal moiety, a detailed view on the mechanism of action of biologically active indolizines is unavailable. OBJECTIVE: The study of ligand-enzyme affinity is of high interest; description of characteristics (energetic and geometric ones) of ligand binding to the active sites of an enzyme could be useful in understanding the action mechanism of a given ligand on the concerned enzyme...
2017: Current Computer-aided Drug Design
https://www.readbyqxmd.com/read/27632988/computational-analysis-of-physicochemical-factors-driving-cyp2d6-ligand-interaction
#16
Olujide O Olubiyi, Maryam O Olagunju, Abiola O Obisesan
BACKGROUND: The metabolic action of CYP2D6 remains a crucial factor influencing the therapeutic outcomes for many drug molecules while others are either only slightly affected or not affected altogether. OBJECTIVE: This study seeks to understand, atomistic resolution, the structural and physicochemical factors influencing CYP2D6 metabolic discrimination. METHOD: Explicit solvent molecular dynamics simulations in GROMACS were employed to probe the conformational dynamics of CYP2D6 following which the most populated structures were employed for ligand interaction docking studies with AutoDock Vina using selected CYP2D6 drug substrates...
2017: Current Computer-aided Drug Design
https://www.readbyqxmd.com/read/27632987/molecular-modeling-investigation-of-some-new-2-mercaptoimidazoles
#17
Nidhi Rani, Randhir Singh
BACKGROUND: Docking study has become an important and interesting tool for the investigation of drug- receptor interaction. Computational methodologies have become a crucial component in the drug discovery programs which involves identification of target and lead along with their ADME and pharmacokinetic studies so as to obtain a potent lead. OBJECTIVE: Synthesis and Molecular modeling investigation of some new 2-mercaptoimidazoles. METHOD: New 2- mercaptoimidazoles were synthesized via solid phase synthesis and were characterized by spectral studies i...
2017: Current Computer-aided Drug Design
https://www.readbyqxmd.com/read/27457083/nerve-conduction-through-dendrites-via-proton-hopping
#18
Lemont B Kier
BACKGROUND: In our previous studies of nerve conduction conducted by proton hopping, we have considered the axon, soma, synapse and the nodes of Ranvier. The role of proton hopping described the passage of information through each of these units of a typical nerve system. The synapse projects information from the axon to the dendrite and their associated spines. METHODS: We have invoked the passage of protons via a hopping mechanism to illustrate the continuum of the impulse through the system, via the soma following the dendrites...
2017: Current Computer-aided Drug Design
https://www.readbyqxmd.com/read/28019636/in-silico-design-synthesis-and-bioactivity-of-n-2-4-dinitrophenyl-3-oxo-3-phenyl-n-aryl-phenyl-propanamide-derivatives-as-breast-cancer-inhibitors
#19
Mucheli Ramana, Rama Lokhande, Shanta Bhar, Prasanna Ranade, Ankita Mehta, Gayatri Gadre
BACKGROUND: Breast cancer is a systemic disease which has challenged physicians worldwide as it is the most predominant cancer in women often leading to fatality. One of the types of treatment is chemotherapy which includes targeted oral or intravenous cancer-killing drugs. Treatment options are often limited to surgery and/or chemotherapy. OBJECTIVE: The discovery and design of new small molecule estrogen inhibitors is necessitated in order to circumvent the problem of drug-induced resistance in chemotherapy resulting in disease relapse...
December 23, 2016: Current Computer-aided Drug Design
https://www.readbyqxmd.com/read/27981900/pharmacophore-and-docking-guided-virtual-screening-study-for-discovery-of-type-i-inhibitors-of-vegfr-2-kinase
#20
Heena R Bhojwani, Urmila J Joshi
BACKGROUND: Kinase domain of VEGFR-2 displays conformational flexibility which leads to existence of two kinds of inhibitors viz. type I and type II inhibitors. They exhibit different binding modes and this necessitates the development of separate pharmacophore models for them. METHODS: The virtual screening study for discovery of type I inhibitors of VEGFR-2 kinase was done by using combined pharmacophore (generated using PHASE and validated by 3D-QSAR) and docking (Glide) based approach...
December 14, 2016: Current Computer-aided Drug Design
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