scholarly journals PoreMatMod.jl: Julia Package for in Silico Postsynthetic Modification of Crystal Structure Models

2022 ◽  
Author(s):  
E. Adrian Henle ◽  
Nickolas Gantzler ◽  
Praveen K. Thallapally ◽  
Xiaoli Z. Fern ◽  
Cory M. Simon
Keyword(s):  
Crystal Structure ◽  
In Silico ◽  
Postsynthetic Modification

scholarly journals Identification of novel α7 nicotinic receptor ligands by in silico screening against the crystal structure of a chimeric α7 receptor ligand binding domain

2012 ◽  
Vol 20 (19) ◽  
pp. 5992-6002 ◽  
Author(s):  
Atilla Akdemir ◽  
Ewald Edink ◽  
Andrew J. Thompson ◽  
Sarah C.R. Lummis ◽  
Albert J. Kooistra ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Ligand Binding ◽  
In Silico ◽  
Nicotinic Receptor ◽  
Binding Domain ◽  
Ligand Binding Domain ◽  
Receptor Ligands ◽  
In Silico Screening ◽  
Receptor Ligand

scholarly journals Antiangiogenic Activity and in Silico Cereblon Binding Analysis of Novel Thalidomide Analogs

Molecules ◽  
2020 ◽  
Vol 25 (23) ◽  
pp. 5683
Author(s):  
Megan L. Peach ◽  
Shaunna L. Beedie ◽  
Cindy H. Chau ◽  
Matthew K. Collins ◽  
Suzana Markolovic ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Molecular Docking ◽  
In Silico ◽  
Ex Vivo ◽  
Rat Aorta ◽  
Mechanisms Of Action ◽  
Immunomodulatory Activity ◽  
Antiangiogenic Activity ◽  
Aorta Ring ◽  
Clinical Interest

Due to its antiangiogenic and anti-immunomodulatory activity, thalidomide continues to be of clinical interest despite its teratogenic actions, and efforts to synthesize safer, clinically active thalidomide analogs are continually underway. In this study, a cohort of 27 chemically diverse thalidomide analogs was evaluated for antiangiogenic activity in an ex vivo rat aorta ring assay. The protein cereblon has been identified as the target for thalidomide, and in silico pharmacophore analysis and molecular docking with a crystal structure of human cereblon were used to investigate the cereblon binding abilities of the thalidomide analogs. The results suggest that not all antiangiogenic thalidomide analogs can bind cereblon, and multiple targets and mechanisms of action may be involved.

scholarly journals NUOVI APPROCCI TEORICI E SPERIMENTALI ALLA SCOPERTA DI FARMACI

2012 ◽  
Author(s):  
Martino Bolognesi
Keyword(s):  
Crystal Structure ◽  
Drug Discovery ◽  
In Silico ◽  
Active Sites ◽  
Yellow Fever Virus ◽  
Enzyme Inhibitor ◽  
Therapeutic Interventions ◽  
Research Activity ◽  
In Silico Docking ◽  
Structural And Functional Properties

New theoretic and experimental approaches to drug discovery. Environmental, demographic and ecological reasons suggest that either novel or known viruses will continue to emerge worldwide, posing new threats to the human population. Additionally, therapeutic interventions present different outcomes; for example, vaccination campaigns in the Third World often encounter local distribution problems and reach an insufficient fraction of the population. For many viruses no vaccine is available, such that the toll death is high, particularly in tropical countries and among infants. On the other hand, resistance of bacteria to know antibiotics is increasingly a serious threat, often associated to nosocomial infections. As a result, new ideas and approaches to the discovery or design of new effective drugs are a high priority in all civilized countries, to prevent and be ready to face potential pandemics. In this context, our group at the University of Milano, in collaboration with several European and extra- European labs, has been exploring the structural and functional properties of enzymes involved in the replication of (+)stranded RNA viruses as targets for the design of antiviral drugs. The rationale behind the choice of specific target viral is the idea that these are structurally and functionally sufficiently different from their human counterparts; thus, blocking the virus enzyme with a new drug should not be reflected by adverse reactions in the human host. The discovery approach applied in our laboratory has been based on a series of specific experimental steps: i) the analysis of crystal structure of the free enzymes, through X-ray crystallography; ii) in silico (computational) preliminary screening of selected enzyme regions towards which the drug search is targeted (e.g. mostly the enzyme active sites); iii) biochemical and biophysical tests of enzyme inhibition; iv) crystal structure analyses of enzyme/inhibitor complexes; v) in cell/in vivo testing; vi) inference for drug-lead optimization. This research method proved effective in discovering low molecular weight inhibitors of two key enzymes from Yellow fever virus (and partly for Dengue virus), and for Norovirus. Specifically, we targeted Norovirus studying the long known drug Suramin (used in the therapy of ‘sleeping sickness’), which was selected through the procedure described above through our in silico docking screenings. Our crystallographic and inhibition assays allowed to highlight the inhibitor binding mode and satisfactory functional inhibitory parameters. Subsequently, in the context of an international collaboration, we could test a series of Suramin molecular fragments, in search of new active compounds endowed with suitable pharmacological parameters. The described research activity, which is based on new conceptual and multidisciplinary approaches to drug discovery, has led to the production of several small molecules that will be further developed into antiviral compounds.

Synthesis, Crystal Structure, Solution Study and In Silico ADME Profiling of Various Asymmetric Functionalized Triazenes

2015 ◽  
Vol 25 (4) ◽  
pp. 892-905 ◽  
Author(s):  
Jafar Attar Gharamaleki ◽  
Atousa Goodarzi ◽  
Houra Sadat Bolouhari ◽  
Shabnam Hooshmand ◽  
Mohammad Kazem Rofouei ◽  
...  
Keyword(s):  
Crystal Structure ◽  
In Silico ◽  
Solution Study ◽  
Structure Solution

scholarly journals Crystal structure of calcium bound outer membrane phospholipase A (OmpLA) from Salmonella typhi and in silico anti-microbial screening

2020 ◽  
Author(s):  
Perumal Perumal ◽  
Rahul Raina ◽  
Sundara Baalaji Narayanan ◽  
Arulandu Arockiasamy
Keyword(s):  
Crystal Structure ◽  
Outer Membrane ◽  
In Silico ◽  
Membrane Integrity ◽  
Acid Tolerance ◽  
Salmonella Typhi ◽  
Phospholipase A ◽  
Gram Negative ◽  
Activated State ◽  
Outer Membrane Phospholipase A

AbstractAntimicrobial resistance is widespread in Salmonella infections that affect millions worldwide. Salmonella typhi and other Gram-negative bacterial pathogens encode an outer membrane phospholipase A (OmpLA), crucial for their membrane integrity. Further, OmpLA is implicated in pathogen internalization, haemolysis, acid tolerance, virulence and sustained infection in human hosts. OmpLA is an attractive drug target for developing novel anti-microbials that attenuate virulence, as the abrogation of OmpLA encoding pldA gene causes loss of virulence. Here, we present the crystal structure of Salmonella typhi OmpLA in dimeric calcium bound activated state at 2.95 Å. Structure analysis suggests that OmpLA is a potential druggable target. Further, we have identified and shortlisted small molecules that bind at the dimer interface using structure based in silico screening, docking and molecular dynamics. While it requires further experimental validation, anti-microbial discovery targeting OmpLA from gram-negative pathogens offers an advantage as OmpLA is required for virulence.

scholarly journals Correction: Synthesis, crystal structure, and optical properties of fluorinated poly(pyrazole) ligands and in silico assessment of their affinity for volatile organic compounds

2020 ◽  
Vol 44 (30) ◽  
pp. 13216-13216
Author(s):  
Alessandro Pedrini ◽  
Angelo Maspero ◽  
Silvia Bracco ◽  
Angiolina Comotti ◽  
Simona Galli ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Optical Properties ◽  
Volatile Organic Compounds ◽  
Organic Compounds ◽  
In Silico ◽  
Volatile Organic ◽  
Pyrazole Ligands

Correction for ‘Synthesis, crystal structure, and optical properties of fluorinated poly(pyrazole) ligands and in silico assessment of their affinity for volatile organic compounds’ by Alessandro Pedrini et al., New J. Chem., 2020, 44, 6443–6455, DOI: 10.1039/D0NJ00259C.

Supramolecular architectures in dihydropyridones: Synthesis, crystal structure, Hirshfeld analysis, cytotoxicity and in silico studies

2022 ◽  
Vol 1250 ◽  
pp. 131671
Author(s):  
Lalhruaizela ◽  
Devanshi Patel ◽  
Brilliant N. Marak ◽  
Jayanta Dowarah ◽  
Balkaran Singh Sran ◽  
...  
Keyword(s):  
Crystal Structure ◽  
In Silico ◽  
Supramolecular Architectures ◽  
In Silico Studies ◽  
Hirshfeld Analysis
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