MTiOpenScreen: a web server for structure-based virtual screening

Labbé, Céline M.; Rey, Julien; Lagorce, David; Vavruša, Marek; Becot, Jérôme; Spérandio, Olivier; Villoutreix, Bruno O.; Tufféry, Pierre; Miteva, Maria A.

doi:10.1093/nar/gkv306

Cited by 175 publications

(143 citation statements)

References 34 publications

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“…Furthermore, as shown in section 2.2., it was possible to observe a spatial repositioning of the ligands during molecular dynamics simulations due to rearrangements in segments of the main chain around the NAT1 recognition site. Vina [33] implemented in the MTiOpenSreen [28] web server. Each compound is identified according to the registration number in the ZINC15 [27] database.…”

Section: Virtual Screening and Docking Resultsmentioning

confidence: 99%

“…There is currently a wide range of free resources [23][24][25][26][27][28] and free software packages [29][30][31][32][33][34][35] dedicated to drug discovery and design. The availability of free resources and tools allows scientists from all over the world, independent of the financial support, to plan and test hypotheses through in silico experiments.…”

Section: Introductionmentioning

confidence: 99%

“…Since of none of the ten best ligands found for NAT1 presented better binding score when compared to NAT2 (Table S1 in Supplementary Materials), the selection criterion was based on the best binding score with TBNAT and worse binding score with NAT2. Thus, only the ten best compounds for TBNAT were locally re-evaluated for the purpose of verifying the results generated by the virtual screening with AutoDock Vina [33] (Vina) software implemented in the MTiOpenScreen [28] web server (Table 1). with ID codes 2IJA [41], which refers to the structure of the mutant NAT1 F125S, and 2PQT, which refers to a structure with the cysteine residue at position 68 substituted by a non-standard S-(2-anilino-2-oxoethyl)-l-cysteine (Tyx68) residue.…”

Section: Introductionmentioning

confidence: 99%

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<em>In Silico</em> Screening and Analysis of Potential Inhibitors of Arylamine N-Acetyltransferases (NATs) from the Traditional Chinese Medicine: A Study Using Free Available Tools

Azevedo¹,

Richardt²,

Oliveira³

et al. 2017

Preprint

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Arylamine N-acetyltransferases (NATs) are cytosolic enzymes, highly polymorphic, present in both eukaryotes and prokaryotes. These enzymes play an important role in the detoxification and activation of xenobiotics as well as in the synthesis of endogenous compounds. Specific NATs have been pointed out in the literature as possible therapeutic targets. In particular, the human NAT1, for the treatment of certain cancers, and the NAT from M. tuberculosis (TBNAT), for the treatment of tuberculosis. This paper describes an in silico approach to prospect and select potentially inhibitors of NAT1 and TBNAT from the Traditional Chinese Medicine (TCM) using free available tools. A library with ligands from TCM was previously screened in order to select only compounds with optimal pharmacological properties. The affinity of the selected ligands with respect to NAT enzymes was then evaluated by virtual screening (VS). Subsequently, the complexes with the best ligands were submitted to molecular dynamics (MD) simulations aiming to obtain better quality information on affinity and selectivity. The results for one specific ligand, ZINC14690579, indicated its potential for affinity and selectivity. ZINC14690579 structure may represent the discovery of a new scaffold for future development of NAT inhibitors.

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Section: Virtual Screening and Docking Resultsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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<em>In Silico</em> Screening and Analysis of Potential Inhibitors of Arylamine N-Acetyltransferases (NATs) from the Traditional Chinese Medicine: A Study Using Free Available Tools

Azevedo¹,

Richardt²,

Oliveira³

et al. 2017

Preprint

View full text Add to dashboard Cite

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“…UCSF Chimera package was implemented for analyzing the hydrophobicity molecular surface [25]. AutoDock 4.2, InterProSurf, MGLTools, and MTiAutoDock were utilized for the molecular docking analysis of thrombin-like serine protease obtained from the snake venom of sharp-nosed pit viper with the natural compound hesperetin [26][27][28][29][30].…”

Section: Methodsmentioning

confidence: 99%

Molecular Docking Studies of Snake Venom Serine Protease of Sharp-Nosed Pit Viper With Hesperetin

Panda¹,

Ehsan

2018

Asian J Pharm Clin Res

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Objective: The management of snake bite envenomation is a global challenge affecting millions of people. Immunotherapy is still regarded as the treatment of choice; however, their subsequent adverse effects restrict their potential use for therapy against snake venom poisoning. In recent years, more attention has been given to the exploration of indigenous medicinal plants for their outstanding benefits for the treatment of several diseases and disorders, including snake venom poisoning. Hesperetin is a naturally occurring compound derived from a flavanone glycoside, hesperidin and is obtained from various citrus fruits. It is known to possess significant inhibitory activity against snake venom serine proteases. The aim of our present study was to investigate the significant inhibitory action of hesperetin on thrombin-like serine protease from sharp-nosed pit viper (Deinagkistrodon acutus) snake venom. Methods:We have employed molecular docking analysis by implementing the state-of-the-art docking program to validate the hypothesis of the prospective inhibitory properties of hesperetin on thrombin-like serine proteases of snake venom. AutoDock 4.2, InterProSurf, MGLTools, and MTiAutoDock were utilized for the molecular docking analysis of thrombin-like serine protease obtained from the snake venom of sharp-nosed pit viper with the natural compound hesperetin. Results:The results generated from in silico based approach reveals the significant inhibitory role of hesperetin against thrombin-like snake venom proteases, which might lead to the drug designing of the inhibitors of snake venom serine proteases. Conclusion:The implementation of molecular docking analysis by the employment of state-of-the-art docking program supports the potential of inhibitory activity of naturally obtained hesperetin compound on thrombin-like serine proteases of snake venom. The generated in silico results suggests that the novel structure hesperetin -flavanone might act as a potent inhibitor of thrombin-like snake venom proteases, and unlocks the possibilities for designing drugs of the inhibitors of snake venom serine proteases. Moreover, the investigation of the novel compound obtained from natural sources for their inhibitory activity against snake venom serine proteases would lead to the discovery of newer inhibitory compound from a highly uninvestigated research arena.

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“…It is pivotal for complete comprehension of the molecular mechanisms of biological frameworks [1]. Five selected TCM compounds (eriodictyol 7-O-glucuronide, luteolin 8-C-beta-glucopyranoside, (-)-epicatechin-3-O-gallate, 6-O-trans-p-coumaroylgeniposide and luteolin-7-O-glucoside) were docked again into the receptor structure to form complex structures using MTiAutoDock server [14]. The molecular docking results showed that all the selected inhibitors showed good binding affinity with DENV NS3pro.…”

Section: Molecular Interaction Studies Of Selected Compoundsmentioning

confidence: 99%

Identification of new potent inhibitors of dengue virus NS3 protease from traditional Chinese medicine database

et al. 2016

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Dengue virus (DENV) has emerged as an increasing fitness problem in the world for which no specialized drug is available. The non-structural protein NS3 protease of DENV has already been recognized as a potential therapeutic target for the discovery and development of novel antiviral agents against DENV infections. In this study, we employed the virtual screening technique to explore the potent inhibitors of DENV NS2B/NS3pro from Traditional Chinese Medicine (TCM) database. Total 200 inhibitors from TCM against DENV NS3pro were screened and only five TCM compounds like eriodictyol 7-O-glucuronide, luteolin 8-C-beta-glucopyranoside, (-)-epicatechin-3-O-gallate, 6-O-trans-p-coumaroylgeniposide and luteolin-7-O-glucoside were selected for further analysis which showed binding energies, -7.000, -7.380, -7.380, -7.440 and -7.440 kcal/mol, respectively. The findings of this study suggest that these five TCM compounds can be considered as potent inhibitors for DENV NS2B/NS3pro for the development of anti-dengue drugs.

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MTiOpenScreen: a web server for structure-based virtual screening

Cited by 175 publications

References 34 publications

<em>In Silico</em> Screening and Analysis of Potential Inhibitors of Arylamine N-Acetyltransferases (NATs) from the Traditional Chinese Medicine: A Study Using Free Available Tools

<em>In Silico</em> Screening and Analysis of Potential Inhibitors of Arylamine N-Acetyltransferases (NATs) from the Traditional Chinese Medicine: A Study Using Free Available Tools

Molecular Docking Studies of Snake Venom Serine Protease of Sharp-Nosed Pit Viper With Hesperetin

Identification of new potent inhibitors of dengue virus NS3 protease from traditional Chinese medicine database

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