High throughput virtual screening based discovery of dengue protease inhibitor (original) (raw)
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Frontiers in Molecular Biosciences
The viral disease dengue is transmitted by the Aedes mosquito and is commonly seen to occur in the tropical and subtropical regions of the world. It is a growing public health concern. To date, other than supportive treatments, there are no specific antiviral treatments to combat the infection. Therefore, finding potential compounds that have antiviral activity against the dengue virus is essential. The NS2B-NS3 dengue protease plays a vital role in the replication and viral assembly. If the functioning of this protease were to be obstructed then viral replication would be halted. As a result, this NS2B-NS3 proves to be a promising target in the process of anti-viral drug design. Through this study, we aim to provide suggestions for compounds that may serve as potent inhibitors of the dengue NS2B-NS3 protein. Here, a ligand-based pharmacophore model was generated and the ZINC database was screened through ZINCPharmer to identify molecules with similar features. 2D QSAR model was dev...
Scientia Pharmaceutica, 2019
Dengue infection is caused by a mosquito-borne virus, particularly in children, which may even cause death. No effective prevention or therapeutic agents to cure this disease are available up to now. The dengue viral envelope (E) protein was discovered to be a promising target for inhibition in several steps of viral infection. Structure-based virtual screening has become an important technique to identify first hits in a drug screening process, as it is possible to reduce the number of compounds to be assayed, allowing to save resources. In the present study, pharmacophore models were generated using the common hits approach (CHA), starting from trajectories obtained from molecular dynamics (MD) simulations of the E protein complexed with the active inhibitor, flavanone (FN5Y). Subsequently, compounds presented in various drug databases were screened using the LigandScout 4.2 program. The obtained hits were analyzed in more detail by molecular docking, followed by extensive MD simu...
Computational screening of potent anti-dengue inhibitors against dengue NS2B/NS3 protease
2021
Worldwide, the Dengue Virus (DENV) contamination has become a significant undermining medical problem. The World Health Organization (WHO) has announced 390 million individuals are getting influenced with DENV consistently. Despite the fact that there are some enemy of viral accessible in the market to diminish the seriousness of the illness, Still there is a need of medication to totally obstruct the infection replication and fixes the sickness. Consequently, it is of most extreme direness to receive imaginative methods to propel the medication disclosure measure. In our investigation, we zeroed in on the distinguishing proof of inhibitors against DENV NS2B/NS3 protease complex. NS2B/NS3 protease goes about as a remedial objective in computational enemy of viral medication revelation. In view of the medication repurposing contemplates, a few enemy of viral were drilled down from the past investigations. Out of which, Bromocriptine was chosen as a source of perspective ligand, pharm...
Ligand based drug discovery of novel dengue-2 NS2B-NS3 protease inhibitors
2016
The reported dengue cases are increasing yearly, yet no anti-dengue agent is available in the market. Therefore, the search for anti-dengue is critical. In Malaysia, Dengue-2 (DEN-2) is the most prevalent serotype. NS2B-NS3 protease is the enzyme for the cleavage of polyprotein precursor, which is crucial for the flavivirus replications. This makes it a potential target for the development of therapeutics against the dengue virus. In this study, ligand-based approach was implemented in searching for the new potential DEN-2 NS2B-NS3 protease inhibitors. Pharmacophore models were developed from diverse reported structures of DEN-2 NS2B-NS3 protease inhibitors, comprising peptide and non-peptide molecules. The selected pharmacophore models were employed to screen the US National Cancer Institute (NCI) list of compounds to search for new DEN-2 NS2B-NS3 protease inhibitors. The list of natural products in Natural Product Discovery System (NADI) database was also screened and the structur...
Structure-guided fragment-based in silico drug design of dengue protease inhibitors
Journal of Computer-Aided Molecular Design, 2011
An in silico fragment-based drug design approach was devised and applied towards the identification of small molecule inhibitors of the dengue virus (DENV) NS2B-NS3 protease. Currently, no DENV protease co-crystal structure with bound inhibitor and fully formed substrate binding site is available. Therefore a homology model of DENV NS2B-NS3 protease was generated employing a multiple template spatial restraints method and used for structure-based design. A library of molecular fragments was derived from the ZINC screening database with help of the retrosynthetic combinatorial analysis procedure (RECAP). 150,000 molecular fragments were docked to the DENV protease homology model and the docking poses were rescored using a target-specific scoring function. High scoring fragments were assembled to small molecule candidates by an implicit linking cascade. The cascade included substructure searching and structural filters focusing on interactions with the S1 and S2 pockets of the protease. The chemical space adjacent to the promising candidates was further explored by neighborhood searching. A total of 23 compounds were tested experimentally and two compounds were discovered to inhibit dengue protease (IC 50 = 7.7 lM and 37.9 lM, respectively) and the related West Nile virus protease (IC 50 = 6.3 lM and 39.0 lM, respectively). This study demonstrates the successful application of a structure-guided fragment-based in silico drug design approach for dengue protease inhibitors providing straightforward hit generation using a combination of homology modeling, fragment docking, chemical similarity and structural filters.
Journal of Computer-Aided Molecular Design, 2010
Serine protease activity of the NS3 protein of Dengue virus is an important target of antiviral agents that interfere with the viral polyprotein precursor processing catalyzed by the NS3 protease (NS3pro), which is important for the viral replication and maturation. Recent studies showed that substrate-based peptidomimetics carrying an electrophilic warhead inhibit the NS2B-NS3pro cofactorprotease complex with inhibition constants in the low micromolar concentration range when basic amino acid residues occupy P 1 and P 2 positions of the inhibitor, and an aldehyde warhead is attached to the P 1 . We have used computer-assisted combinatorial techniques to design, focus using the NS2B-NS3pro receptor 3D structure, and in silico screen a virtual library of more than 9,200 peptidomimetic analogs targeted around the template inhibitor Bz-Nle-Lys-Arg-Arg-H (Bz-benzoyl) that are composed mainly of unusual amino acid residues in all positions P 1 -P 4 . The most promising virtual hits were analyzed in terms of computed enzyme-inhibitor interactions and Adsorption, Distribution, Metabolism and Excretion (ADME) related physico-chemical properties. Our study can direct the interest of medicinal chemists working on a next generation of antiviral chemotherapeutics against the Dengue Fever towards the explored subset of the chemical space that is predicted to contain peptide aldehydes with NS3pro inhibition potencies in nanomolar range which display ADME-related properties comparable to the training set inhibitors.
Dengue virus is a major issue of tropical and subtropical regions. Dengue virus has been the cause behind the major alarming epidemics in the history with mass causalities from the decades. Unavailability of on-shelf drugs for the prevention of further proliferation of virus inside the human body results in immense number of deaths each year. This issue necessitates the design of novel anti-dengue drug. The protease enzyme pathway is the critical target for drug design due to its significance in the replication, survival and other cellular activities of dengue virus. Therefore, approximately eighteen million compounds from the ZINC database have been virtually screened against nonstructural protein 3 (NS3). The incremental construction algorithm of Glide docking program has been used with its features high throughput virtual screening (HTVS), standard precision (SP), extra precision (XP) and in combination of Prime module, induced fit docking (IFD) approach has also been applied. Five top-ranked compounds were then selected from the IFD results with better predicted binding energies with the catalytic triad residues (His51, Asp75, and Ser135) that may act as potential inhibitors for the underlying target protease enzyme. The top-ranked compounds ZINC95518765, ZINC44921800, ZINC71917414, ZINC39500661, ZINC36681949 have shown the predicted binding energies of −7.55, −7.36, −8.04, −8.41, −9.18 kcal/mol, respectively, forming binding interactions with three catalytically important amino acids. Top-docking poses of compounds are then used in molecular dynamics (MD) simulations. In computational studies, our proposed compounds confirm promising results against all the four serotypes of dengue virus, strengthening the opportunity of these compounds to work as potential on-shelf drugs against dengue virus. Further experimentation on the proposed compounds can result in development of strong inhibitors.
Design of New Competitive Dengue Ns2b/Ns3 Protease InhibitorsA Computational Approach
International Journal of …, 2011
Dengue is a serious disease which has become a global health burden in the last decade. Currently, there are no approved vaccines or antiviral therapies to combat the disease. The increasing spread and severity of the dengue virus infection emphasizes the importance of drug discovery strategies that could efficiently and cost-effectively identify antiviral drug leads for development into potent drugs. To this effect, several computational approaches were applied in this work. Initially molecular docking studies of reference ligands to the DEN2 NS2B/NS3 serine protease were carried out. These reference ligands consist of reported competitive inhibitors extracted from Boesenbergia rotunda (i.e., 4-hydroxypanduratin A and panduratin A) and three other synthesized panduratin A derivative compounds (i.e., 246DA, 2446DA and 20H46DA). The design of new lead inhibitors was carried out in two stages. In the first stage, the enzyme complexed to the reference ligands was minimized and their complexation energies (i.e., sum of interaction energy and binding energy) were computed. New compounds as potential dengue inhibitors were then designed by putting various substituents successively on the benzyl ring A of the reference molecule. These substituted benzyl compounds were then computed for their enzyme-ligand complexation energies. New enzyme-ligand complexes, exhibiting the lowest complexation energies and closest to the computed energy for the reference compounds, were then chosen for the next stage manipulation and design, which involved substituting positions 4 and 5 of the benzyl ring A (positions 3 and 4 for 2446DA) with various substituents.
Identification of covalent active site inhibitors of dengue virus protease
Drug Design, Development and Therapy, 2015
Dengue virus (DENV) protease is an attractive target for drug development; however, no compounds have reached clinical development to date. In this study, we utilized a potent West Nile virus protease inhibitor of the pyrazole ester derivative class as a chemical starting point for DENV protease drug development. Compound potency and selectivity for DENV protease were improved through structure-guided small molecule optimization, and proteaseinhibitor binding interactions were validated biophysically using nuclear magnetic resonance. Our work strongly suggests that this class of compounds inhibits flavivirus protease through targeted covalent modification of active site serine, contrary to an allosteric binding mechanism as previously described.
IN SILICO DRUG DESIGNING STUDIES ON DENGUE VIRUS NS2B/NS3 PROTEASE
Indo American Journal of Pharmaceutical Sciences, 2018
The seven key proteins are involved in causing dengue, which are considered as major therapeutic targets for dengue drug development. Recent studies have reported positively for dengue virus NS2B/NS3 protease in dysregulation of causing dengue process in humans. Dragon fruit seed phytochemicals are reported to have antioxidant and antiviral properties. In the present study we studied binding efficiency of 11 compounds that are present in the dragon fruit seeds with NS2B/NS3 protease through Insilico methods. By our virtual screening and docking result, we found that the Compound J and Compound K have highest binding affinity with the NS2B/NS3 protease and also we predicted the binding site amino acid residues and the nature of hydrogen bonding. However more invivo experimental validation of our results with animal models will enlighten the development of more potent drugs from these compounds for treatment of dengue.