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In Silico Pharmacology

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https://read.qxmd.com/read/30607325/design-of-novel-amyloid-%C3%AE-aggregation-inhibitors-using-qsar-pharmacophore-modeling-molecular-docking-and-adme-prediction
#1
Lilly Aswathy, Radhakrishnan S Jisha, Vijay H Masand, Jayant M Gajbhiye, Indira G Shibi
The inhibition of abnormal amyloid β (Aβ) aggregation has been regarded as a good target to control Alzheimer's disease. The present study adopted 2D-QSAR, HQSAR and 3D QSAR (CoMFA & CoMSIA) modeling approaches to identify the structural and physicochemical requirements for the potential Aβ aggregation inhibition. A structure-based molecular docking technique is utilized to approve the features that are obtained from the ligand-based techniques on 30 curcumin derivatives. The combined outputs were then used to screen the modified 10 compounds...
2018: In Silico Pharmacology
https://read.qxmd.com/read/30607324/identification-of-potential-drug-targets-and-inhibitor-of-the-pathogenic-bacteria-shigella-flexneri-2a-through-the-subtractive-genomic-approach
#2
Arafat Rahman Oany, Mamun Mia, Tahmina Pervin, Md Nazmul Hasan, Akinori Hirashima
Shigella flexneri 2a is one of the most pathogenic bacteria among the Shigella spp., which is responsible for dysentery and causes masses of deaths throughout the world per year. A proper identification of the potential drug targets and inhibitors is crucial for the treatment of the shigellosis due to their emerging multidrug resistance (MDR) patterns. In this study, a systematic subtractive approach was implemented for the identification of novel therapeutic targets of S. flexneri 2a (301) through genome-wide metabolic pathway analysis of the essential genes and proteins...
2018: In Silico Pharmacology
https://read.qxmd.com/read/30607323/frangulosid-as-a-novel-hepatitis-b-virus-dna-polymerase-inhibitor-a-virtual-screening-study
#3
Mokhtar Nosrati, Zahra Shakeran, Zainab Shakeran
Hepatitis B virus (HBV) infects more than 400 million humans Worldwide. Currently, development of new anti-HBV agents is focused on inhibiting of HBV DNA polymerase activity. The natural components of medicinal plant have a broad spectrum of biological activities with therapeutic properties which can be exploited in various steps of drug discovery. Currently, in silico analyses have been introduced as alternative or supplements methods for drug discovery. This study was planned to in silico screening novel HBV DNA polymerase inhibitor(s) from R...
2018: In Silico Pharmacology
https://read.qxmd.com/read/30607322/high-throughput-screening-against-pantothenate-synthetase-identifies-amide-inhibitors-against-mycobacterium-tuberculosis-and-staphylococcus-aureus
#4
Sayantan Pradhan, Chittaranjan Sinha
Pantothenate is a crucial enzyme for the synthesis of coenzyme A and acyl carrier protein in Mycobacterium tuberculosis and Staphylococcus aureus . It is indispensable for the growth and survival of these bacteria. Amides analogs are designed and have been used as inhibitors of pantothenate synthetase. Molecular docking approach has been used to design and predict the drug activity of molecule to the specific disease. In this work, more than hundred amides have been screened by Discovery Studio molecular docking programme to search best suitable molecule for the treatment of Mycobacterium tuberculosis ...
2018: In Silico Pharmacology
https://read.qxmd.com/read/30607321/taxifolin-as-dual-inhibitor-of-mtb-dna-gyrase-and-isoleucyl-trna-synthetase-in-silico-molecular-docking-dynamics-simulation-and-in-vitro-assays
#5
Charles Kozhikkadan Davis, K Nasla, A K Anjana, G K Rajanikant
DNA gyrase and aminoacyl-tRNA synthetases are two essential bacterial enzymes involved in DNA replication, transcription and translation. Flavonoids are plant secondary metabolites with variable phenolic structures. In this study, eight flavonoids structurally similar to quercetin were selected and their ADMET properties were evaluated. Molecular docking and free energy calculations were carried out to examine the binding of these flavonoids to the ATP-binding site and editing domain of DNA gyrase and Isoleucyl-tRNA synthetase, respectively...
2018: In Silico Pharmacology
https://read.qxmd.com/read/30607320/lncrna-based-study-of-epigenetic-regulations-in-diabetic-peripheral-neuropathy
#6
Muhamad Fachrul, Didik H Utomo, Arli A Parikesit
Diabetes remains one of the most prevalent non-communicable diseases in the world, affecting over 400 million of people worldwide, causing serious complications leading to amputations and even death. Over the years, researchers have found that, in addition to genomic mutations, epigenetic mechanisms also play a role in the development of diabetes-specifically type-2 diabetes. Long noncoding RNAs (lncRNAs) have been linked to mediate epigenetic mechanisms, including those in late-stage diabetes. This study attempts to assess the unexplored topic of how lncRNAs could be used to assess the epigenetic mechanisms present in diabetic peripheral neuropathy (DPN); a serious complication of the disease often leading to amputation...
2018: In Silico Pharmacology
https://read.qxmd.com/read/30607319/molecular-docking-and-dynamics-of-nickel-schiff-base-complexes-for-inhibiting-%C3%AE-lactamase-of-mycobacterium-tuberculosis
#7
Md Junaid, Md Jahangir Alam, Md Kamal Hossain, Mohammad A Halim, M Obayed Ullah
In recent years, multidrug-resistance has become a primary concern in the treatment and management of tuberculosis, an infectious disease caused by Mycobacterium tuberculosis . In this context, searching new anti-tuberculosis agents particularly targeting the β-lactamase (BlaC) is reported to be promising as this enzyme is one of the key player in the development of multidrug resistance. This study reports the design of some Nickel (Ni) based tetradentate N2 O2 Schiff bases, employing density functional theory...
2018: In Silico Pharmacology
https://read.qxmd.com/read/30607318/computer-aided-drug-design-based-on-3d-qsar-and-molecular-docking-studies-of-5-1h-indol-5-yl-1-3-4-thiadiazol-2-amine-derivatives-as-pim2-inhibitors-a-proposal-to-chemists
#8
Adnane Aouidate, Adib Ghaleb, Mounir Ghamali, Samir Chtita, Abdellah Ousaa, M'barek Choukrad, Abdelouahid Sbai, Mohammed Bouachrine, Tahar Lakhlifi
PIM2 kinase plays a crucial role in the cell cycle events including survival, proliferation, and differentiation in normal and neoplastic neuronal cells. Thus, it is regarded as an essential target for cancer pharmaceutical. Design of novel 5-(1H-indol-5-yl)-1,3,4-thiadiazol-2-amine derivatives with enhanced PIM2 inhibitory activity. A series of twenty-five PIM2 inhibitors reported in the literature containing 5-(1H-indol-5-yl)-1,3,4-thiadiazol-2-amines scaffold was studied by using two computational techniques, namely, three-dimensional quantitative structure activity relationship (3D-QSAR) and molecular docking...
2018: In Silico Pharmacology
https://read.qxmd.com/read/30607317/sulfonamide-derivatives-as-mycobacterium-tuberculosis-inhibitors-in-silico-approach
#9
Sayantan Pradhan, Chittaranjan Sinha
Both DHPS (dihydropteroate synthase) and DHFR (dihydrofolate reductase) play important physiological roles in the survivability of Mycobacterium tuberculosis (MTB). Sulfonamides are the potent drugs to monitor growth and proliferation of MTBs by inhibiting the activity of DHPS and DHFR which could explain the mechanism of action of these molecules. In this work, 102 heterocyclic sulfonamides (HSF) have been screened by discovery studio molecular docking programme to search the best suitable molecule for the treatment of MTBs...
2018: In Silico Pharmacology
https://read.qxmd.com/read/30607316/molecular-docking-and-adme-properties-of-bioactive-molecules-against-human-acid-beta-glucosidase-enzyme-cause-of-gaucher-s-disease
#10
Vijayakumar Subramaniyan, Sathiya Mathiyalagan, Arulmozhi Praveenkumar, Prabhu Srinivasan, Manogar Palani, Vinothkannan Ravichandran, Parameswari Nallasamy
Gaucher disease is one of the common lysosomal storage diseases widespread all over the world. It is divided into three types such as type 1 (non-neuropathic), type 2 (acute infantile neuropathic) and type 3 (chronic neuropathic). This is caused by the deficiency of glucocerebrosidases from the midpoint nervous system. Recent years, computational tools are very important and play a vital role in identifying new leads for disease treatment. This study was performed to screen the effective bioactive molecules against glucocerebrosidases...
2018: In Silico Pharmacology
https://read.qxmd.com/read/30607315/molecular-modeling-of-inhibitors-against-fructose-bisphosphate-aldolase-from-candida-albicans
#11
Andréia Lima de Amorim, Alan Vitor Morais de Lima, Ana Carolina de Almeida do Rosário, Érica Tailana Dos Santos Souza, Jaderson Vieira Ferreira, Lorane Izabel da Silva Hage-Melim
Candida albicans is an opportunistic pathogen that causes from vulvovaginal and oropharyngeal candidiasis to systemic infections. The enzyme 1,6-fructose bisphosphate aldolase class II (FBA II), is a macromolecule existing only in lower organisms, being essential for the survival of the pathogen due to its function of maintaining the glycolysis process. The aim of this paper was to evaluate the inhibitors of FBA II regarding their physicochemical, pharmacokinetic and toxicological properties and apply concepts of rational drug development to propose new compounds for the treatment of fungal infections of C...
2018: In Silico Pharmacology
https://read.qxmd.com/read/30607314/in-silico-quest-of-selective-naphthyl-based-crebbp-bromodomain-inhibitor
#12
Raju Dash, Sarmistha Mitra, Md Arifuzzaman, S M Zahid Hosen
The reader proteins like bromodomains have recently gained increased attentions in the area of epigenetic drug discovery, as they are the potent regulators in gene transcription process. Among the other bromodomains, cAMP response element-binding protein (CREB) binding protein or CREBBP bomodomain involved in various cancer progressions and therefore, efforts to develop specific inhibitors of CREBBP bomodomain are of clinical value. In this study, we tried to identify selective CREBBP bromodomain inhibitor, which was accomplished by using molecular docking, free energy calculation and molecular dynamics (MD) simulation studies, considering a series of naphthyl based compounds...
2018: In Silico Pharmacology
https://read.qxmd.com/read/29308353/molecular-docking-of-selected-phytoconstituents-with-signaling-molecules-of-ultraviolet-b-induced-oxidative-damage
#13
Umar Muzaffer, V I Paul, N Rajendra Prasad
The signaling molecules TNF-α, AP-1, and NF-κB act to integrate multiple stress signals into a series of diverse antiproliferative responses. Disruption of these processes can promote tumor progression and chemoresistance. Naturally occurring plant derived compounds are considered as attractive candidates for cancer treatment and prevention. Phytoconstituents can control and modify various biological activities by interacting with molecules involved in concerned signaling pathways. The aim of this study was to find binding conformations between phytoconstituents and these signaling molecules responsible for multiple stress signals of UVB induced photodamage...
2017: In Silico Pharmacology
https://read.qxmd.com/read/29308352/impact-of-protein-ligand-solvation-and-desolvation-on-transition-state-thermodynamic-properties-of-adenosine-a-2a-ligand-binding-kinetics
#14
Giuseppe Deganutti, Andrei Zhukov, Francesca Deflorian, Stephanie Federico, Giampiero Spalluto, Robert M Cooke, Stefano Moro, Jonathan S Mason, Andrea Bortolato
Ligand-protein binding kinetic rates are growing in importance as parameters to consider in drug discovery and lead optimization. In this study we analysed using surface plasmon resonance (SPR) the transition state (TS) properties of a set of six adenosine A2A receptor inhibitors, belonging to both the xanthine and the triazolo-triazine scaffolds. SPR highlighted interesting differences among the ligands in the enthalpic and entropic components of the TS energy barriers for the binding and unbinding events...
2017: In Silico Pharmacology
https://read.qxmd.com/read/29308351/molecular-docking-analysis-of-curcumin-analogues-against-kinase-domain-of-alk5
#15
Shivananda Kandagalla, B S Sharath, Basavapattana Rudresh Bharath, Umme Hani, Hanumanthappa Manjunatha
During metastasis, cancer cells transcend from primary site to normal cells area upon attaining epithelial to mesenchymal transition (EMT) causing malignant cancer disease. Increased expression of TGF-β and its receptor ALK5 is an important hallmark of malignant cancer. In the present study, efficacy of curcumin and its analogues as inhibitors of ALK5 (TGFβR-I) receptor was evaluated using in silico approaches. A total of 142 curcumin analogues and curcumin were retrieved from peer reviewed literature and constructed a combinatorial library...
2017: In Silico Pharmacology
https://read.qxmd.com/read/29308350/computational-chemistry-study-of-toxicity-of-some-m-tolyl-acetate-derivatives-insecticides-and-molecular-design-of-structurally-related-products
#16
Nnabuk Okon Eddy, Nsikak Bassey Essien
Molecular descriptors (including quantum chemical, topological and physicochemical descriptors) were calculated for five m -tolyl derivatives insecticides [namely, carbosulfan (CBS), carbofuran (CBF), isoprocab (IFP), methiocarb (MTC) and isocarbophos (ICP)]. Calculated quantum chemical parameters included the total energy, the electronic energy, the binding energy, the core-core repulsion energy, the heat of formation, the dipole moment and the frontier molecular orbital energies. All the calculated quantum chemical parameters (except dipole moment) exhibited strong correlation with the experimental LD50 values of the studied insecticides (at various Hamiltonians)...
2017: In Silico Pharmacology
https://read.qxmd.com/read/29098139/in-silico-screening-for-identification-of-pyrrolidine-derivatives-dipeptidyl-peptidase-iv-inhibitors-using-comfa-comsia-hqsar-and-docking-studies
#17
M C Sharma, S Jain, R Sharma
To explore the relationship between the structures of substituted pyrrolidine derivatives and their inhibition of dipeptidyl peptidase IV inhibitors. The QSAR, including CoMFA, CoMSIA and HQSAR, were applied to identify the key structures impacting their inhibitory potencies. The CoMFA, CoMSIA and HQSAR with cross-validated correlation coefficient (q2 ) value of 0.727, 0.870 and 0.939 and r2 value of 0.973, 0.981 and 0.949. Based on the structure-activity relationship revealed by the present study, we have designed a set of novel dipeptidyl peptidase IV inhibitors that showed excellent potencies in the developed models...
2017: In Silico Pharmacology
https://read.qxmd.com/read/29098138/antiquorum-sensing-activity-of-silver-nanoparticles-in-p-aeruginosa-an-in-silico-study
#18
Syed Ghazanfar Ali, Mohammad Azam Ansari, Qazi Mohd Sajid Jamal, Haris M Khan, Mohammad Jalal, Hilal Ahmad, Abbas Ali Mahdi
Pseudomonas aeruginosa an opportunistic pathogen regulates its virulence through Quorum sensing (QS) mechanism comprising of Las and Rhl system. Targeting of QS mechanism could be an ideal strategy to combat infection caused by P . aeruginosa . Silver nanoparticles (AgNPs) have been broadly applied as antimicrobial agents against a number of pathogenic bacterial and fungal strains, but have not been reported as an anti-QS agent. Therefore, the aim of present work was to show the computational analysis for the interaction of AgNPs with the QS system using an In silico approach...
2017: In Silico Pharmacology
https://read.qxmd.com/read/29085768/molecular-interactions-with-redox-sites-and-salt-bridges-modulate-the-anti-aggregatory-effect-of-flavonoid-tannin-and-cardenolide-moieties-against-amyloid-beta-1-42-in-silico
#19
Rafael Vincent M Manalo
In this study, the interactions of flavonoid, tannin and cardenolide moieties as well as their known metabolites were docked against the apolar NMR structure of the aggregatory amyloid-beta fragment (Aβ1-42 ). Results showed that the catechin moiety favorably bound Aβ1-42 peptide at Asp23, Asn27, Ser26 and Glu22 residues, with chalcone similarly binding the middle region of the peptide. Remarkably, hippuric and ferulic acids exhibited hydrophobic interactions with Aβ1-42 at the latter portion of the peptide, possibly blocking the salt bridges formed by Glu22-Lys28 which stabilizes Phe19-Gly25, as well as the β-sheet Leu34-Gly38 that are known to exist in peptide aggregation...
2017: In Silico Pharmacology
https://read.qxmd.com/read/29085767/novel-dihydropyrimidine-derivatives-as-potential-hdac-inhibitors-in-silico-study
#20
Ganapathi Thipparapu, Rajanna Ajumeera, Vijayalakshmi Venkatesan
Dihydropyrimidine derivatives possess many biological activities due to presence of pyrimidine ring structure in various nucleic acids, vitamins, coenzymes, uric acid and their derivatives. They have possessed broad spectrum actions like antibacterial, antifungal, antiviral, anticancer and antihypertensive etc. Before synthesis of compounds, it is good to predict biological activity using in silico methods. Here, we have selected some of N ( 3a - f ) and O ( 4a - f ) mannich bases of dihydro pyrimidine derivatives emphasized on histone deacetylase 4 (HDAC-4) inhibitions activity...
2017: In Silico Pharmacology
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