Cargando…

A multi-reference poly-conformational method for in silico design, optimization, and repositioning of pharmaceutical compounds illustrated for selected SARS-CoV-2 ligands

BACKGROUND: This work presents a novel computational multi-reference poly-conformational algorithm for design, optimization, and repositioning of pharmaceutical compounds. METHODS: The algorithm searches for candidates by comparing similarities between conformers of the same compound and identifies...

Descripción completa

Detalles Bibliográficos
Autores principales:	Alexandrov, Vadim, Kirpich, Alexander, Kantidze, Omar, Gankin, Yuriy
Formato:	Online Artículo Texto
Lenguaje:	English
Publicado:	PeerJ Inc. 2022
Materias:	Biochemistry
Acceso en línea:	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9701500/ https://www.ncbi.nlm.nih.gov/pubmed/36447514 http://dx.doi.org/10.7717/peerj.14252

Ejemplares similares

Novel Efficient Multistage Lead Optimization Pipeline Experimentally Validated for DYRK1B Selective Inhibitors
por: Alexandrov, Vadim, et al.
Publicado: (2022)

VEGFR-2 conformational switch in response to ligand binding
por: Sarabipour, Sarvenaz, et al.
Publicado: (2016)

Excess mortality in Belarus during the COVID-19 pandemic as the case study of a country with limited non-pharmaceutical interventions and limited reporting
por: Kirpich, Alexander, et al.
Publicado: (2022)

Development of an interactive, agent-based local stochastic model of COVID-19 transmission and evaluation of mitigation strategies illustrated for the state of Massachusetts, USA
por: Kirpich, Alexander, et al.
Publicado: (2021)

Ligand-induced shifts in conformational ensembles that describe transcriptional activation
por: Khan, Sabab Hasan, et al.
Publicado: (2022)

Phosphorylation-mediated PTEN conformational closure and deactivation revealed with protein semisynthesis
por: Bolduc, David, et al.
Publicado: (2013)

Structure and conformational states of the bovine mitochondrial ATP synthase by cryo-EM
por: Zhou, Anna, et al.
Publicado: (2015)

Measuring ligand efficacy at the mu-opioid receptor using a conformational biosensor
por: Livingston, Kathryn E, et al.
Publicado: (2018)

Mapping transiently formed and sparsely populated conformations on a complex energy landscape
por: Wang, Yong, et al.
Publicado: (2016)

Rapid restructurization of conformationally-distinct alpha-synuclein amyloid fibrils at an elevated temperature
por: Ziaunys, Mantas, et al.
Publicado: (2022)

Steroidal glycoalkaloids from Solanum nigrum target cytoskeletal proteins: an in silico analysis
por: Ahmad, Rumana
Publicado: (2019)

Discrete analysis of camelid variable domains: sequences, structures, and in-silico structure prediction
por: Melarkode Vattekatte, Akhila, et al.
Publicado: (2020)

Relief of autoinhibition by conformational switch explains enzyme activation by a catalytically dead paralog
por: Volkov, Oleg A, et al.
Publicado: (2016)

Conformational dynamics of the nucleotide binding domains and the power stroke of a heterodimeric ABC transporter
por: Mishra, Smriti, et al.
Publicado: (2014)

Differential Scanning Calorimetry — A Method for Assessing the Thermal Stability and Conformation of Protein Antigen
por: Durowoju, Ibrahim B., et al.
Publicado: (2017)

Conformational heterogeneity of Savinase from NMR, HDX-MS and X-ray diffraction analysis
por: Wu, Shanshan, et al.
Publicado: (2020)

In silico screening of 393 mutants facilitates enzyme engineering of amidase activity in CalB
por: Hediger, Martin R., et al.
Publicado: (2013)

TRIP13 is a protein-remodeling AAA+ ATPase that catalyzes MAD2 conformation switching
por: Ye, Qiaozhen, et al.
Publicado: (2015)

Ligand-binding characteristics of feline insulin-binding immunoglobulin G
por: SUZUKI, Takafumi, et al.
Publicado: (2015)

In silico structural homology modeling and characterization of multiple N-terminal domains of selected bacterial Tcps
por: Alaidarous, Mohammed
Publicado: (2020)

Resolving dual binding conformations of cellulosome cohesin-dockerin complexes using single-molecule force spectroscopy
por: Jobst, Markus A, et al.
Publicado: (2015)

ProminTools: shedding light on proteins of unknown function in biomineralization with user friendly tools illustrated using mollusc shell matrix protein sequences
por: Skeffington, Alastair W., et al.
Publicado: (2020)

Proteomic identification of galectin-11 and 14 ligands from Haemonchus contortus
por: Sakthivel, Dhanasekaran, et al.
Publicado: (2018)

Extensive translation of small Open Reading Frames revealed by Poly-Ribo-Seq
por: Aspden, Julie L, et al.
Publicado: (2014)

The C-terminal region of the motor protein MCAK controls its structure and activity through a conformational switch
por: Talapatra, Sandeep K, et al.
Publicado: (2015)

Cofilin-induced unidirectional cooperative conformational changes in actin filaments revealed by high-speed atomic force microscopy
por: Ngo, Kien Xuan, et al.
Publicado: (2015)

Differential TAM receptor–ligand–phospholipid interactions delimit differential TAM bioactivities
por: Lew, Erin D, et al.
Publicado: (2014)

Ligand determinants of fatty acid activation of the pronociceptive ion channel TRPA1
por: Redmond, William John, et al.
Publicado: (2014)

Poly(A) tail length regulates PABPC1 expression to tune translation in the heart
por: Chorghade, Sandip, et al.
Publicado: (2017)

Translation repression via modulation of the cytoplasmic poly(A)-binding protein in the inflammatory response
por: Zhang, Xu, et al.
Publicado: (2017)

Hybridization of green synthesized silver nanoparticles with poly(ethylene glycol) methacrylate and their biomedical applications
por: Anwar, Natasha, et al.
Publicado: (2022)

Bordetella adenylate cyclase toxin is a unique ligand of the integrin complement receptor 3
por: Osicka, Radim, et al.
Publicado: (2015)

Investigating the first stage of the COVID-19 pandemic in Ukraine using epidemiological and genomic data
por: Gankin, Yuriy, et al.
Publicado: (2021)

Investigating the first stage of the COVID-19 pandemic in Ukraine using epidemiological and genomic data
por: Gankin, Yuriy, et al.
Publicado: (2021)

Automatic scoring of COVID-19 severity in X-ray imaging based on a novel deep learning workflow
por: Danilov, Viacheslav V., et al.
Publicado: (2022)

Control of the structural landscape and neuronal proteotoxicity of mutant Huntingtin by domains flanking the polyQ tract
por: Shen, Koning, et al.
Publicado: (2016)

Computer modelling reveals new conformers of the ATP binding loop of Na(+)/K(+)-ATPase involved in the transphosphorylation process of the sodium pump
por: Tejral, Gracian, et al.
Publicado: (2017)

Classification of RNA backbone conformations into rotamers using (13)C′ chemical shifts: exploring how far we can go
por: Icazatti, Alejandro A., et al.
Publicado: (2019)

Comparison of reference gene expression stability in mouse skeletal muscle via five algorithms
por: Ma, Jianfeng, et al.
Publicado: (2022)

Inhibition by small-molecule ligands of formation of amyloid fibrils of an immunoglobulin light chain variable domain
por: Brumshtein, Boris, et al.
Publicado: (2015)

Cannot write session to /tmp/vufind_sessions/sess_5v0md6ge9gddvh35kl750kq2mr