Docking of Noncompetitive Inhibitors into Dengue Virus Type 2 Protease: Understanding the Interactions with Allosteric Binding Sites

Othman, Rozana; Kiat, Tan Siew; Khalid, Norzulaani; Yusof, Rohana; Newhouse, E. Irene; Newhouse, James S.; Alam, Masqudul; Rahman, Noorsaadah Abdul

doi:10.1021/ci700388k

Cited by 56 publications

(66 citation statements)

References 36 publications

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“…Binding of ligands at the same pocket with different conformation may be due to changes of receptor specific conformation as explained by [35].…”

Section: Molecular Docking Studiesmentioning

confidence: 99%

Molecular Docking and ADMET Study of Emodin Derivatives as Anticancer Inhibitors of NAT2, COX2 and TOP1 Enzymes

Shadrack¹,

Ndesendo²

2017

CMB

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Over the past years natural products and/or their derivatives have continued to provide cancer chemotherapeutics. Glycosides derivatives of emodin are known to possess anticancer activities. An in silico study was carried out to evaluate emodin derivatives as inhibitors of Arylamine N-Acetyltransferase 2, Cyclooxygenase 2 and Topoisomerase 1 enzymes, predict their pharmacokinetics and explore their bonding modes. Molecular docking study suggested that D2, D5, D6 and D9 to be potent inhibitors of NAT2, while D8 was suggested to be a potent inhibitor of TOP1. Derivatives D2, D5, D6 and D9 bind to the same pocket with different binding conformation. Pharmacokinetic study suggested that selected emodin derivatives can be potential cancer chemotherapeutic agent. Physicochemical parameters such density, balaban index, surface tension, logP and molar reflectance correlated to compounds activity. These finding provides a potential strategy towards developing NAT2 and TOP1 inhibitors.

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“…Binding of ligands at the same pocket with different conformation may be due to changes of receptor specific conformation as explained by [35].…”

Section: Molecular Docking Studiesmentioning

confidence: 99%

Molecular Docking and ADMET Study of Emodin Derivatives as Anticancer Inhibitors of NAT2, COX2 and TOP1 Enzymes

Shadrack¹,

Ndesendo²

2017

CMB

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“…Notably, DG is produced on-the-fly by a scoring function during the docking procedure. Besides the location of the pocket of primary ligands, numerous studies [11][12][13][14][15] have shown that the BD approach is useful in the solution of delicate problems such as the detection of subsidiary binding pockets containing e.g. exosites or allosteric binding sites.…”

Section: Introductionmentioning

confidence: 99%

Toward prediction of functional protein pockets using blind docking and pocket search algorithms

Hetényi

Spoel

2011

Protein Science

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Location of functional binding pockets of bioactive ligands on protein molecules is essential in structural genomics and drug design projects. If the experimental determination of ligand-protein complex structures is complicated, blind docking (BD) and pocket search (PS) calculations can help in the prediction of atomic resolution binding mode and the location of the pocket of a ligand on the entire protein surface. Whereas the number of successful predictions by these methods is increasing even for the complicated cases of exosites or allosteric binding sites, their reliability has not been fully established. For a critical assessment of reliability, we use a set of ligand-protein complexes, which were found to be problematic in previous studies. The robustness of BD and PS methods is addressed in terms of success of the selection of truly functional pockets from among the many putative ones identified on the surfaces of ligand-bound and ligand-free (holo and apo) protein forms. Issues related to BD such as effect of hydration, existence of multiple pockets, and competition of subsidiary ligands are considered. Practical cases of PS are discussed, categorized and strategies are recommended for handling the different situations. PS can be used in conjunction with BD, as we find that a consensus approach combining the techniques improves predictive power.

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“…Theoretical simulations about how cardamonin interacts with DV2 protease can also be found in literature. 90 …”

Section: Anti-infectious Activitymentioning

confidence: 99%

An Overview on Cardamonin

Gonçalves

Valente

Rodrigues

2014

Journal of Medicinal Food

103

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Cardamonin, as shown by the increasing number of publications, has received growing attention from the scientific community due to the expectations toward its benefits to human health. In this study, research on cardamonin is reviewed, including its natural sources, health promoting aspects, and analytical methods for its determination. Therefore, this article hopes to aid current and future researchers on the search for reliable answers concerning cardamonin's value in medicine.

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Docking of Noncompetitive Inhibitors into Dengue Virus Type 2 Protease: Understanding the Interactions with Allosteric Binding Sites

Cited by 56 publications

References 36 publications

Molecular Docking and ADMET Study of Emodin Derivatives as Anticancer Inhibitors of NAT2, COX2 and TOP1 Enzymes

Molecular Docking and ADMET Study of Emodin Derivatives as Anticancer Inhibitors of NAT2, COX2 and TOP1 Enzymes

Toward prediction of functional protein pockets using blind docking and pocket search algorithms

An Overview on Cardamonin

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