scholarly journals The impact of crystallization conditions on structure-based drug design: A case study on the methylene blue/acetylcholinesterase complex

2016 ◽  
Vol 25 (6) ◽  
pp. 1096-1114 ◽  
Author(s):  
Orly Dym ◽  
Wanling Song ◽  
Clifford Felder ◽  
Esther Roth ◽  
Valery Shnyrov ◽  
...  
Keyword(s):  
Methylene Blue ◽  
Drug Design ◽  
Structure Based Drug Design ◽  
Crystallization Conditions ◽  
The Impact

scholarly journals The critical role of QM/MM X-ray refinement and accurate tautomer/protomer determination in structure-based drug design

2020 ◽  
Author(s):  
Oleg Y. Borbulevych ◽  
Roger I. Martin ◽  
Lance M. Westerhoff
Keyword(s):  
Drug Design ◽  
Critical Role ◽  
Pharmaceutical Research ◽  
Energy Functional ◽  
Structural Refinement ◽  
Structure Based Drug Design ◽  
X Ray ◽  
X Ray Crystallography ◽  
Refinement Method ◽  
The Impact

Abstract Conventional protein:ligand crystallographic refinement uses stereochemistry restraints coupled with a rudimentary energy functional to ensure the correct geometry of the model of the macromolecule—along with any bound ligand(s)—within the context of the experimental, X-ray density. These methods generally lack explicit terms for electrostatics, polarization, dispersion, hydrogen bonds, and other key interactions, and instead they use pre-determined parameters (e.g. bond lengths, angles, and torsions) to drive structural refinement. In order to address this deficiency and obtain a more complete and ultimately more accurate structure, we have developed an automated approach for macromolecular refinement based on a two layer, QM/MM (ONIOM) scheme as implemented within our DivCon Discovery Suite and "plugged in" to two mainstream crystallographic packages: PHENIX and BUSTER. This implementation is able to use one or more region layer(s), which is(are) characterized using linear-scaling, semi-empirical quantum mechanics, followed by a system layer which includes the balance of the model and which is described using a molecular mechanics functional. In this work, we applied our Phenix/DivCon refinement method—coupled with our XModeScore method for experimental tautomer/protomer state determination—to the characterization of structure sets relevant to structure-based drug design (SBDD). We then use these newly refined structures to show the impact of QM/MM X-ray refined structure on our understanding of function by exploring the influence of these improved structures on protein:ligand binding affinity prediction (and we likewise show how we use post-refinement scoring outliers to inform subsequent X-ray crystallographic efforts). Through this endeavor, we demonstrate a computational chemistry ↔ structural biology (X-ray crystallography) "feedback loop" which has utility in industrial and academic pharmaceutical research as well as other allied fields.

scholarly journals An Overview of Computational Approaches in Structure Based Drug Design

1970 ◽  
Vol 2 (1) ◽  
pp. 53-61 ◽  
Author(s):  
Dipali Singh ◽  
Anushree Tripathi ◽  
Gautam Kumar
Keyword(s):  
Drug Design ◽  
Computer Aided Drug Design ◽  
Structure Based Drug Design ◽  
Computational Approaches ◽  
Ras Protein ◽  
Design Structure ◽  
Drug Lead ◽  
Computer Aided ◽  
Drug Designing

Drug design is a costly and difficult process. Drug must fulfill several criteria of being active, nontoxic and bioavailable. The conventional way of synthesizing drugs is a monotonous process. But computer aided drug design is a proficient way to overcome the tedious process of conventional method. Drugs can be designed computationally by structure or target based drug designing (SBDD). This review summarizes the methods of structure based drug design, usage of related softwares and a case study that explores to find a suitable drug (lead) molecule for the mutated state of H-Ras protein in order to prevent complex formation with Raf protein.Keywords: computer aided drug design; structure based drug design; Ras-proteinDOI: http://dx.doi.org/10.3126/njb.v2i1.5680Nepal Journal of Biotechnology Jan.2012, Vol.2(1): 53-61

Stabilised G protein-coupled receptors in structure-based drug design: a case study with adenosine A2A receptor

MedChemComm ◽  
2013 ◽  
Vol 4 (1) ◽  
pp. 52-67 ◽  
Author(s):  
Stephen P. Andrews ◽  
Benjamin Tehan
Keyword(s):  
Parkinson’S Disease ◽  
Drug Design ◽  
G Protein ◽  
G Protein Coupled Receptors ◽  
Adenosine A2a Receptor ◽  
Structure Based Drug Design ◽  
A2a Receptor ◽  
Adenosine A2a ◽  
G Protein Coupled

The first example of structure-based drug design with stabilised GPCRs has enabled the identification of a preclinical candidate for the treatment of Parkinson's disease.

scholarly journals Rational mutagenesis to support structure-based drug design: MAPKAP kinase 2 as a case study

2009 ◽  
Vol 9 (1) ◽  
pp. 16 ◽  
Author(s):  
Maria A Argiriadi ◽  
Silvino Sousa ◽  
David Banach ◽  
Douglas Marcotte ◽  
Tao Xiang ◽  
...  
Keyword(s):  
Drug Design ◽  
Support Structure ◽  
Structure Based Drug Design ◽  
Rational Mutagenesis

scholarly journals Drug design and repurposing with DockThor-VS web server focusing on SARS-CoV-2 therapeutic targets and their non-synonym variants

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Isabella A. Guedes ◽  
Leon S. C. Costa ◽  
Karina B. dos Santos ◽  
Ana L. M. Karl ◽  
Gregório K. Rocha ◽  
...  
Keyword(s):  
Drug Design ◽  
Therapeutic Targets ◽  
Web Server ◽  
Drug Repurposing ◽  
World Health ◽  
Design Strategies ◽  
Structure Based Drug Design ◽  
N Protein ◽  
The Impact ◽  
The Web

AbstractThe COVID-19 caused by the SARS-CoV-2 virus was declared a pandemic disease in March 2020 by the World Health Organization (WHO). Structure-Based Drug Design strategies based on docking methodologies have been widely used for both new drug development and drug repurposing to find effective treatments against this disease. In this work, we present the developments implemented in the DockThor-VS web server to provide a virtual screening (VS) platform with curated structures of potential therapeutic targets from SARS-CoV-2 incorporating genetic information regarding relevant non-synonymous variations. The web server facilitates repurposing VS experiments providing curated libraries of currently available drugs on the market. At present, DockThor-VS provides ready-for-docking 3D structures for wild type and selected mutations for Nsp3 (papain-like, PLpro domain), Nsp5 (Mpro, 3CLpro), Nsp12 (RdRp), Nsp15 (NendoU), N protein, and Spike. We performed VS experiments of FDA-approved drugs considering the therapeutic targets available at the web server to assess the impact of considering different structures and mutations to identify possible new treatments of SARS-CoV-2 infections. The DockThor-VS is freely available at www.dockthor.lncc.br.

scholarly journals Drug Design and Repurposing with DockThor-VS Web Server: Virtual Screening focusing on SARS-CoV-2 Therapeutic Targets and their Non-Synonym Variants

2020 ◽  
Author(s):  
Isabella A. Guedes ◽  
Leon S. C. Costa ◽  
Karina B. dos Santos ◽  
Ana L. M. Karl ◽  
Gregório K. Rocha ◽  
...  
Keyword(s):  
Virtual Screening ◽  
Drug Design ◽  
Therapeutic Targets ◽  
Web Server ◽  
Drug Repurposing ◽  
World Health ◽  
Design Strategies ◽  
Structure Based Drug Design ◽  
The Impact ◽  
The Web

Abstract The COVID-19 caused by the SARS-CoV-2 virus was declared as a pandemic disease in March 2020 by the World Health Organization (WHO). Structure-Based Drug Design strategies based on docking methodologies have been widely used for both new drug development and drug repurposing to find effective treatments against this disease. In this work, we present the developments implemented in the DockThor-VS web server to provide a virtual screening (VS) platform with curated structures of potential therapeutic targets from SARS-CoV-2 incorporating genetic information regarding relevant non-synonymous variations. The web server facilitates repurposing VS experiments providing curated libraries of currently available drugs on the market. Currently, DockThor-VS provides ready-for-docking 3D structures for wild type and selected mutations for Nsp3 (papain-like, PLpro domain), Nsp5 (Mpro, 3CLpro), Nsp12 (RdRp), Nsp15 (NendoU), N protein and Spike. We performed VS experiments of FDA-approved drugs considering the therapeutic targets available at the web server to assess the impact of considering different structures and mutations in the identification of possible new treatments of SARS-CoV-2 infections. The DockThor-VS is freely available at www.dockthor.lncc.br.

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